Genomic and proteomic analysis of lignin degrading and polyhydroxyalkanoate accumulating β-proteobacterium Pandoraea sp. ISTKB

Genomic and proteomic analysis of lignin degrading and polyhydroxyalkanoate accumulating... Background: Lignin is a major component of plant biomass and is recalcitrant to degradation due to its complex and heterogeneous aromatic structure. The biomass-based research mainly focuses on polysaccharides component of biomass and lignin is discarded as waste with very limited usage. The sustainability and success of plant polysac- charide-based biorefinery can be possible if lignin is utilized in improved ways and with minimal waste generation. Discovering new microbial strains and understanding their enzyme system for lignin degradation are necessary for its conversion into fuel and chemicals. The Pandoraea sp. ISTKB was previously characterized for lignin degradation and successfully applied for pretreatment of sugarcane bagasse and polyhydroxyalkanoate (PHA) production. In this study, genomic analysis and proteomics on aromatic polymer kraft lignin and vanillic acid are performed to find the impor - tant enzymes for polymer utilization. Results: Genomic analysis of Pandoraea sp. ISTKB revealed the presence of strong lignin degradation machinery and identified various candidate genes responsible for lignin degradation and PHA production. We also applied label-free quantitative proteomic approach to identify the expression profile on monoaromatic compound vanillic acid ( VA) and polyaromatic kraft lignin (KL). Genomic and proteomic analysis simultaneously discovered Dyp-type peroxidase, peroxidases, glycolate oxidase, aldehyde oxidase, GMC oxidoreductase, laccases, quinone oxidoreductase, dioxyge- nases, monooxygenases, glutathione-dependent etherases, dehydrogenases, reductases, and methyltransferases and various other recently reported enzyme systems such as superoxide dismutases or catalase–peroxidase for lignin degradation. A strong stress response and detoxification mechanism was discovered. The two important gene clus- ters for lignin degradation and three PHA polymerase spanning gene clusters were identified and all the clusters were functionally active on KL–VA. Conclusions: The unusual aerobic ‘-CoA’-mediated degradation pathway of phenylacetate and benzoate (reported only in 16 and 4–5% of total sequenced bacterial genomes), peroxidase-accessory enzyme system, and fenton chem- istry based are the major pathways observed for lignin degradation. Both ortho and meta ring cleavage pathways for aromatic compound degradation were observed in expression profile. Genomic and proteomic approaches provided *Correspondence: pkv@nipgr.ac.in; isthakur@hotmail.com; isthakur@mail.jnu.ac.in School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, 110067, India National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India Full list of author information is available at the end of the article © The Author(s) 2018. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creat iveco mmons .org/licen ses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creat iveco mmons .org/ publi cdoma in/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Kumar et al. Biotechnol Biofuels (2018) 11:154 Page 2 of 23 validation to this strain’s robust machinery for the metabolism of recalcitrant compounds and PHA production and provide an opportunity to target important enzymes for lignin valorization in future. Keywords: Genomics, Lignin, Polyhydroxyalkanoate, Gene cluster, Label-free quantification, Vanillic acid Background industry [6, 9–11]. The application of advanced ‘omics’ The genus Pandoraea is a very recently classified genus approach such as genomics, transcriptomics, and pro- proposed in the year 2000. Bacteria belonging to genus teomics to individual microbial strains or microbial Pandoraea are Gram-negative, non-sporulating, and community will help in identification and functional motile bacteria with single polar flagellum [1]. The characterization of novel ligninolytic enzymes in the genus belongs to Burkholderiaceae family and class near future [12–14]. With the increase in genomic data β-proteobacteria. The Pandoraea genus was earlier misi - of bacteria and fungi, the biomass degrading potential dentified and grouped together with Burkholderia or across different taxa can be identified that will further Ralstonia [1] This genus contains five species (Pandoraea enhance our understanding related to lignin degra- pnomenusa, Pandoraea sputorum, Pandoraea norimber- dation [12, 13]. The lignin degrading bacterial isolate gensis, Pandoraea apista, and Pandoraea pulmonicola) belongs to actinobacteria, alpha proteobacteria, beta and four genomospecies of thiosulfate-oxidizing (Pan- proteobacteria, gamma proteobacteria, delta proteobac- doraea thiooxydans) and oxalate-oxidizing species as teria, bacteroides, and archaea [7]. The novel bacterial Pandoraea vervacti, Pandoraea faecigallinarum, and enzymes responsible for lignin degradation and their Pandoraea oxalativorans. Pandoraea is a taxonomically mechanism of action have also been described [15]. In distinct genus having close similarity with Burkholderia recent years, LC–MS-based proteomics studies have and Ralstonia. Pandoraea has been isolated from various been widely performed. Quantitative LC–MS-based environments such as soil, landfill site, sediments, clinical proteomics such as label free and ITRAQ labeling-based samples (only P. apista, P. pnomenusa, and P. sputorum quantification methods are generally used to identify isolated until date), and water [1–4]. The Burkholderia the novel enzymes and their level of expression in a par- and Ralstonia are very much explored and established ticular process [16–18]. genera with their promising potential environmental We have earlier sequenced the genome of Pando- and industrial applications. Pandoraea is a relatively new raea sp. ISTKB and the sequence has been submitted to genus, so there are very few findings available about their NCBI with accession number MAOS00000000.1 which biotechnological potential. The species from this genus is openly available [19]. In the present study, we describe have been documented for utilization of polychlorinated the comprehensive analysis of the Pandoraea sp. ISTKB biphenyl, dichloromethane, dyes, lignin, oxalate, thiosul- genome. The bioinformatics analysis was performed fate, and quorum sensing [3–6]. At present, the genomic to identify a large set of genes and pathways putatively insights for Pandoraea are limiting and such studies responsible for lignin degradation and PHA production. would eventually help to widen the biotechnological pro- The important gene clusters responsible for lignin degra - spective of this genus. dation and PHA production were also highlighted. This Lignin is a complex aromatic heteropolymer and it strain has already been shown to utilize monoaromatic is the most abundant aromatic polymer available on lignin derivatives with great ease compared to polymeric earth. In nature, lignin is degraded mainly by bacte- kraft lignin for PHA production [20]. Therefore, the pro - ria and fungi. Fungi have been studied extensively for teomic study of Pandoraea sp. ISTKB was performed lignin degradation and only a few bacterial species have for identification of set of a proteins expressed during its been reported for lignin degradation [7, 8]. Compared growth on monoaromatic vanillic acid (VA) and aromatic to fungi, bacteria offer advantage as its genome size is polymer lignin, i.e., kraft lignin (KL) that can be overex- small, genetic manipulations, and large-scale recom- pressed for enhanced KL utilization. VA was selected, binant expression of important enzymes can be per- because most of the lignin linkages proceed through gen- formed with a greater ease. Therefore, the focus again eration of vanillin or VA as nodal point during the course shifted to bacteria for the identification of novel strains of degradation [21]. Proteomic studies provide insight and enzymes for lignin degradation. The discovery of into the protein profile and also complement the genom - novel ligninolytic microbes, enzymes, and their bio- ics analysis. Genomic and proteomic analyses would chemical characterization will help in deconstruction of enable us to understand the novel enzymes and pathways biomass for their application in biofuel and bioproduct responsible for lignin degradation and biovalorization. Kumar et al. Biotechnol Biofuels (2018) 11:154 Page 3 of 23 oxidoreductase activity. Abundance of ion binding and Results small molecule-binding proteins indicates their role in Salient features of Pandoraea sp. ISTKB genome transcriptional regulation and transportation of mol- The Pandoraea sp. ISTKB was previously character- ecules across cell membrane. Representation of trans- ized for lignin degradation and successfully applied for ferase and hydrolase in good proportion indicates their pretreatment of sugarcane bagasse and polyhydroxyal- assistance during metabolism of organic compounds. kanoate (PHA) production [6, 20, 22]. The genome size of Pandoraea sp. ISTKB is 6.37 Mb with 65× coverage hav- Metabolism, respiratory mechanism, transporters, ing GC content of 62.05%, 5356 predicted protein-coding and transcriptional factors in Pandoraea sp. ISTKB genome genes [prokaryotic genome annotation pipeline (PGAP) Pandoraea sp. ISTKB can metabolize diverse substrates; and Pfam annotation] and the other general genome which includes five and six carbon sugar molecules. This features has also been reported earlier [19]. Among the bacterium can utilize monosaccharide (galactose, man- predicted proteins, 1740 proteins were categorized as nose, and fructose), disaccharides (sucrose), polysaccha- hypothetical proteins. Out of total predicted proteins, rides (starch), glucuronate, ascorbate, aldarate, amino 456 proteins were identified having signal sequences. Cir - sugar and nucleotide sugar, propionate, and butanoate cular map displaying genomic features provides a space metabolism. This strain can also utilize pentoses (xylose, efficient and clear representation of gene arrangement on xylulose), C5-branched dibasic acid, and other glyoxy- the genome, as shown in Fig. 1. The annotation of impor - late, dicarboxylate and pyruvate as predicted by KEGG. tant genes and pathways related to lignin or aromatic The growth of this strain was observed to be poor on compound degradation has also been represented in the glucose and the KEGG pathway analysis of carbohydrate circular plot. KEGG–KAAS pathway analysis of protein- metabolism also supported this observation. Analysis of coding genes from Pandoraea sp. ISTKB categorized respiratory mechanism showed various terminal elec- 2590 genes in 22 different functional KAAS pathway tron acceptor, electron donors, and also other relevant (Additional file  1: Table  S1). The KEGG predicted 148 genes related to respiration. The abundance of formate proteins responsible for degradation and metabolism of dehydrogenase, quinone oxidoreductase family proteins, aromatic and xenobiotic compound. The annotation and oxidoreductases, ubiquinol oxidase, soluble cytochrome, analysis by RAST predicted 5658 coding genes and 48% and other related electron carriers highlights their impor- of coding genes have been classified into 26 subsystems tance and assistance in metabolism of various recalci- features. The percent contribution of genes present in trant compounds (Additional file  1: Figure S1). There different functional groups in subsystem features is rep - were 346 transcriptional factors identified in the genome, resented in Fig.  2. The subsystem features count showed and among these regulators, LysR family was found to be dominance of general process related to carbohydrate, dominant. Transcriptional regulator families related to amino acids, cell wall components, prosthetics, cofactors, metabolism of aromatic compound such as GntR, MarR, proteins, and lipid metabolism. After normal cellular IclR, XRE, aromatic hydrocarbon utilization, anaerobic processes, the subsystem feature count is dominated by benzoate metabolism, and organic hydroperoxide regu- membrane transport, aromatic compound metabolism, lators are also present in this strain (Additional file  1: respiration stress response regulation, and cell signaling. Figure S2). There are 587 transporters identified in the Gene ontology (GO) analysis was performed to gain genome, and among these, there were 279 ABC family functional information about predicted proteins in the transporters present. This family represents almost half genome. The analysis provided information about dis - of the total transporters present in the genome and was tribution of genes among various metabolic processes, found to be dominant followed by two-component sys- cellular functions, and molecular components in the tem and MFS transporters (Additional file 1: Figure S3). genome of Pandoraea sp. ISTKB (Fig.  3). In the biologi- cal processes, the organic substance metabolic process Metabolism of aromatic compounds was found to be the dominant process. Molecular func- The annotation of Pandoraea sp. ISTKB genes and their tions analysis revealed the major distribution of proteins classification into pathways involved in lignin or aro - into three important functions, i.e., organic cyclic com- matic compounds degradation have been identified by pound binding, heterocyclic compound binding, and (See figure on next page.) Fig. 1 Circos plot of genes compared with the genome for Pandoraea sp. ISTKB. Circles from outside to inside represent; a scaffold arrangement, b gene position on the scaffolds, c GC skew, and d GC content. Syntenic representation of genes associated with the pathways and Pandoraea sp. ISTKB. Different genes associated with the selected pathways with different colors and shapes Kumar et al. Biotechnol Biofuels (2018) 11:154 Page 4 of 23 Kumar et al. Biotechnol Biofuels (2018) 11:154 Page 5 of 23 Fig. 2 Classification of proteins in subsystem features and their abundance in different functional groups shown in Pandoraea sp. ISTKB KEGG pathway analysis, blast search against ‘nr’ data- thioesterases, transferases, and hydrolases has also been base, and subsystem feature of RAST. There were 42 observed. dioxygenase, 25 monooxygenase, 17 peroxidase (includ- The pathway analysis revealed genes responsible for ing one DyP-type peroxidase), and 2 laccases discovered lignin degradation and diverse aromatic compound in genome (Additional file  1: Figure S4; Tables S2, S3, and metabolism (Fig.  4). Genes responsible for funneling of S4). The presence of various oxidoreductase [grouped lignin or aromatic components’ degradation through into FAD, NAD(P)H, SDR, GMC, YggW, quinone, pyri- peripheral degradation pathways have been observed. dine nucleotide–disulfide, flavin, Fe–S, and unclassified Genes related to pathways for degradation of vanillin, oxidoreductases), reductases, dedydrogenases, esterases, ferulate, biphenyl, phenylpropanoic acid, benzoyl-CoA mediated, phenylacetate, and phenol were observed and Kumar et al. Biotechnol Biofuels (2018) 11:154 Page 6 of 23 Fig. 3 GO analysis of Pandoraea sp. ISTKB genome and classification of genes into biological processes, cellular components, and molecular functions their abundance is depicted in Fig. 4 and Additional file  1: N-heterocyclic aromatic compound, and meta cleavage Table  S5. Subsystem feature analysis identified genes as pathways were also identified. ‘lignin degradation fragments’ responsible for lignin metabolism and this is discussed as cluster later section. Identification of stress response genes, secondary The KEGG analysis indicates that this strain can utilize metabolites, and genomic islands various xenobiotic compounds such as benzoate deriva- Lignin or aromatic compound degradation requires tives (amino, ethyl, p-hydroxy, and fluoro), BTX, salicy - concerted action of various oxidoreductases. The degra - late esters, quinate, pesticides, PAHs, synthetic aromatic dation process generates free radicals and reactive inter- monomer, furfural, and steroids. The degradation of mediates and their removal or transformation into stable lignin and xenobiotic aromatic compounds results into and less toxic component is essential for cell survival. generation of some restricted common central inter- Genome analysis identified various proteins related to mediates (catechol, protocatechuate, and gentisate) that stress response and detoxification mechanisms (Addi - are further metabolized by beta-ketoadipate and aro- tional file  1: Figure S5 and Table  S7). The presence of matic ring cleaving pathways. The genes responsible for superoxide dismutase, catalases, glutathione, thiore- degradation of central intermediates were identified in doxin, peroxiredoxins, glyoxylases, rubrerythrin, glutar- abundance (Fig.  4 and Additional file  1: Table  S6). The edoxins, aldo/keto reductase, and alkyl hydroperoxidase genes observed in central intermediate pathways can highlights this strain’s arsenal against oxidative stress, metabolize common aromatic intermediates through protection from reactive species and detoxification of both ortho and meta cleavage pathways [23]. The genes toxic components during aromatic metabolism [24, 25]. responsible for metabolism of central intermediates such There are nine gene clusters identified in the genome as catechol, protocatechuate, salicylate, homogentisate, of Pandoraea sp. ISTKB that has been represented with their contigs and position marked in Additional file  1: Kumar et al. Biotechnol Biofuels (2018) 11:154 Page 7 of 23 Fig. 4 Predicted lignin and aromatic compounds degradation genes and their number responsible for funneling into peripheral pathways and central intermediate metabolism Table S8. Secondary metabolite cluster analysis identified file  2: Table  S9). The other proteins present were related some novel metabolites that are specific to Pandoraea to DNA replication, cell division and partitioning, trans- sp. ISTKB. These clusters included genes responsible position, recombination, phage-mediated integration, for the synthesis of terpenes, nonribosomal peptides, repair, and DNA-binding response regulators. There are thailanstatin/mangotoxin, arylpropane, 2 homoserine various proteins identified in the island that plays impor - lactone, phosphonate–terpene, bacteriocin, and lasso- tant role in stress response, detoxification mechanism peptide. The cluster 9 (lassopeptide), cluster 2 (Nrps), and their regulation, electron carrier, antibiotic resist- and cluster 4 (arylpropane) were found to be unique to ance, metal resistance, and transportation of molecules this strain, since cluster 9 did not show any match with across cell membrane. The proteins related to phosphate Pandoraea genus or Burkholderia genus. However, clus- and sulfur metabolism and few for aromatic compound ters 2 and 4 showed only one match with Burkholderia. degradation were also observed. Clusters 1 (terpenes), 3 (thailanstatin/mangotoxin), and 5 (homoserine lactone) are distributed among Pandoraea Identification of gene clusters for the degradation lignin and Burkholderia genus. Moreover, clusters 6 (phospho- derivatives and PHA production nate–terpene), 7 (bacteriocin), and 8 (homoserine lac- The two gene clusters responsible for degradation of tone) are highly represented in Pandoraea genus. The lignin derivatives have been identified and the order of novel clusters such as cluster 9 (lassopeptide), 2 (Nrps), gene arrangement on the cluster is shown in Fig.  5a, b. and 4 (arylpropane) can prove to be significant as these The first cluster ‘lignin degradation fragment’ predicted are unique to this strain. by RAST contains genes responsible for protocatechuate There were 12 genomic islands identified in the meta cleavage-mediated degradation of lignin deriva- genome that are mainly dominated by the hypotheti- tives. The presence of LysR family transcriptional regu - cal proteins (Additional file  1: Figure S6 and Additional lator for aromatics can be observed in the cluster. ABC Kumar et al. Biotechnol Biofuels (2018) 11:154 Page 8 of 23 Fig. 5 Gene clusters with contig number 40.1 and 13.1 identified in Pandoraea genome responsible for lignin degradation represented as a and b. The size of DNA fragment selected for cluster analysis is between 12 and 17 Kb transporters and MFS transporter were also present in this cluster. The β-ketothiolase was present in multiple this cluster that might be regulating the movement of copies in the genome. This cluster is dominated by stress aromatic compounds across the cell. The benzoyl for - responsive proteins primarily related to heavy metal or mate decarboxylase present in the cluster is known for multidrug efflux system. The third cluster contains only the degradation of benzene, xylene, and toluene. The PHA synthetase and presence of genes predominantly second cluster contains genes mainly responsible for the related to oxidative stress as thiol-disulfide interchange degradation of vanillic acid. The presence of ABC trans - protein, protein disulfide reductase, thioredoxin, two- porters for regulating movement of molecules can also component system response regulator protein, sensory be observed in this cluster. This cluster also contains glu - proteins, secretory proteins, and ABC-type multidrug tathione peroxidase, dehydrogenases, and glyoxylase that permeases was present around polymerase in the cluster. play important role in protection from oxidative damage by detoxifying reactive intermediates such as methylgly- Proteomics analysis on kraft lignin and vanillic acid oxal and other aldehydes formed during metabolism of Proteomic analysis was performed to identify the genes aromatic compounds [25]. expressed on monoaromatic compound vanillic acid and PHA is carbon and energy reserve accumulated by polyaromatic compound kraft lignin. The identification microbes under nutrient imbalance condition [26]. We of important proteins responsible for polymeric lignin have earlier characterized PHA production by strain degradation and their overexpression will provide oppor- ISTKB while growing on lignin and its derivatives (as sole tunity for lignin valorization. There were total 2484 pro - carbon source) and the genes responsible for PHA syn- teins detected during LC–MS analysis covering almost thesis have been identified in the genome [20]. Here, the 44.61% of the total protein-coding genes present in the arrangement of PHA biosynthetic genes on cluster was genome. There were 2318 proteins common in both KL analyzed in detail (Fig. 6a–c). The clusters were identified and VA and 166 proteins were found to be expressed spanning PHA synthase or polymerase gene that is anno- either on KL or on VA. Among 166 expressed proteins, tated in the genome. The first cluster revealed the pres - 74 were expressed on VA and 78 proteins on KL, as ence of complete set of genes (acetoacetyl-CoA reductase, shown in Fig.  7a, b. GO analysis was performed on the β-ketothiolase, PHA polymerase, and regulatory protein) protein expressed on KL and VA to obtain the overview responsible for short-chain PHA production. In case of of functional information about the proteins involved in second cluster, PHA polymerase was followed by acetoa- various biological processes, cellular components, and cetyl-CoA reductase but β-ketothiolase was missing from molecular functions. Kumar et al. Biotechnol Biofuels (2018) 11:154 Page 9 of 23 Fig. 6 Gene clusters with contig numbers 23.1, 34.1, and 48.1 identified in Pandoraea genome responsible for PHA production represented as a–c. The size of DNA fragment selected for cluster analysis is between 12 and 17 Kb The GO analysis of genomics was supported by prot - Expressed proteins involved in lignin or aromatic eomics (especially biological processes and molecular compound degradation functions) on KL and VA (Fig.  8). The molecular func - Proteomic profile of Pandoraea sp. ISTKB revealed the tions category indicates an abundance of protein in cata- presence of relevant proteins expressed only on KL or lytic activity, heterocyclic compound binding, organic VA (Table  1) and KL–VA, as represented in Tables  2, 3, compound binding, and transcription factor activity on and 4. There are 17, 29, and 394 uncharacterized pro - KL and absent on VA. Single organism process was found teins observed in the KL, VA, and KL–VA, respectively. to be dominant in KL and VA (after normal cellular and The various functionally active oxidoreductases, meth - metabolic processes) indicates this strain specific pro - yltransferases, hydrolases, isomerases, dehydrogenases, cess. The proteins involved in localization process on VA reductases, transferases, esterases, transporters, tran- were almost double compared to KL. The membrane pro - scriptional factors, stress response, and detoxification- tein was present in KL and VA, but their representation related proteins were observed that could play important on VA was found to be more than double as compared to role in degradation of lignin or aromatic compounds. KL and the transporters were also expressed more in VA. (See figure on next page.) Fig. 7 a Venn diagram showing total number of proteins expressed on kraft lignin and vanillic acid and their distribution among KL and VA. b Heat map showing differential expression of relevant proteins on kraft lignin–vanillic acid that are responsible for lignin degradation Kumar et al. Biotechnol Biofuels (2018) 11:154 Page 10 of 23 Kumar et al. Biotechnol Biofuels (2018) 11:154 Page 11 of 23 Fig. 8 GO analysis of protein expressed by Pandoraea sp. ISTKB while growing on KL and VA. The expressed proteins were classified into biological processes, cellular components, and molecular functions Kumar et al. Biotechnol Biofuels (2018) 11:154 Page 12 of 23 Table 1 Identification of relevant proteins expressed only on kraft lignin (KL) or vanillic acid (VL) that can assist in lignin degradation Uniprot entry Gene locus tag Protein names LFQ Razor + unique Sequence Mol. weight Intensity intensity KL peptides KL coverage (%) (kDa) Relevant protein expressed only on kraft lignin (KL) A0A1E3LHD6 A9762_20370 Tryptophan 2,3-dioxygenase 22.9781 2 12.3 36.655 0.00043 A0A1E3LB56 A9762_07750 Benzoyl-CoA oxygenase subunit B 28.4307 15 41.7 54.265 2.06E−87 A0A1E3LET3 A9762_23815 Acriflavine resistance protein 22.5124 1 1.2 112.36 0.00162 A0A1E3LL12 A9762_14780 Glycine betaine ABC transporter 23.8554 2 6.2 36.204 0.00036 substrate-binding protein A0A1E3LI04 A9762_22630 Enoyl-CoA hydratase 23.5827 2 13.3 28.399 1.38E−14 A0A1E3LPU3 A9762_13345 Pyruvate ferredoxin oxidoreductase 17.3225 3 4 129.05 0.00016 A0A1E3LLU4 A9762_13050 Carboxyvinyl-carboxyphosphonate 24.4057 2 14.3 31.557 0.00039 phosphorylmutase A0A1E3LBB9 A9762_07755 Benzoyl-CoA oxygenase/reductase, 23.9233 2 5 45.826 5.25E−07 BoxA protein A0A1E3LGI4 A9762_03990 SAM-dependent methyltransferase 24.6086 2 9.6 31.525 1.73E−06 A0A1E3LDW7 A9762_25245 (2Fe–2S)-binding protein 24.4339 2 24.5 20.242 2.06E−06 A0A1E3LNU5 A9762_10215 LysR family transcriptional regulator 23.5144 2 8.4 33.65 4.15E−07 A0A1E3LEP7 A9762_23880 Phenylacetic acid degradation protein 24.5346 3 12.4 39.494 4.34E−14 A0A1E3LJ38 A9762_17050 ABC transporter 26.2152 5 18.3 32.972 3.46E−34 A0A1E3LB77 A9762_07880 ABC transporter ATP-binding protein 24.5787 2 9.7 25.723 2.69E−12 A0A1E3LF42 A9762_23860 1,2-Phenylacetyl-CoA epoxidase subu- 25.5084 4 14 37.739 4.64E−20 nit A (monooxygenase) A0A1E3LGK2 A9762_23865 1,2-Phenylacetyl-CoA epoxidase subu- 24.5067 2 20.4 11.224 6.77E−06 nit B (monooxygenase) A0A1E3LHG4 A9762_23220 Formyl-CoA:oxalate CoA transferase 26.7341 5 17.8 45.737 4.76E−34 A0A1E3LNE1 A9762_10935 Salicylate hydroxylase 22.5412 1 3.1 41.287 0.00183 A0A1E3LF93 A9762_23590 Ligand-gated channel protein 24.4315 2 3.4 81.344 8.95E−05 A0A1E3LHJ6 A9762_19845 NADPH:quinone reductase 23.3346 1 3.1 31.317 0.00029 A0A1E3LIQ8 A9762_17970 Glycolate oxidase subunit GlcE 24.8966 2 7.3 40.542 3.71E−10 A0A1E3LEZ8 A9762_23215 2-Hydroxyhepta-2,4-diene-1,7-dioate 24.1273 2 14.8 27.8 1.39E−06 isomerase Relevant protein expressed only on vanillic acid ( VA) A0A1E3LRS2 A9762_00545 Alkene reductase 26.4047 7 29.1 39.612 3.91E−37 A0A1E3LLI9 A9762_02605 Alpha/beta hydrolase 25.8742 4 23.2 30.983 3.92E−11 A0A1E3LLX9 A9762_03340 Tol-pal system-associated acyl-CoA 24.2249 2 14.4 17.548 2.38E−05 thioesterase A0A1E3LDT8 A9762_25265 Acetyltransferase 24.2249 2 14.4 17.548 2.38E−05 A0A1E3LPL0 A9762_01420 Glutathione S-transferase 24.4839 2 15.3 24.629 2.35E−07 A0A1E3LCR5 A9762_26030 Aminomethyltransferase 25.197 2 11 34.276 8.63E−05 A0A1E3LPI9 A9762_13065 Methyltransferase 22.991 2 7.7 29.85 1.53E−06 A0A1E3LEN5 A9762_06460 Rieske (2Fe–2S) protein 25.0064 1 6.5 43.065 1.25E−08 A0A1E3LHR2 A9762_19260 Glycine/betaine ABC transporter 24.0824 1 4.9 25.659 0.0001153 permease Important proteins expressed either on kraft lignin benzoyl-CoA oxygenase, enoyl-CoA hydratase, trypto- or on vanillic acid phan 2,3-dioxygenase, and salicylate hydroxylase were The analysis of expression profile on KL revealed the also active on KL. Proteins for methyl group transfer presence of 1,2-phenylacetyl-CoA epoxidase (monooxy- and decarboxylation such as SAM-dependent methyl- genase), phenylacetic acid degradation protein, and transferase, pyruvate ferredoxin oxidoreductase, and 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase enzymes (2Fe–2S)-binding protein were also observed. Genera- for the degradation of phenylacetate. Proteins such as tion of reactive intermediates and their detoxification Kumar et al. Biotechnol Biofuels (2018) 11:154 Page 13 of 23 by oxidative stress-resistance protein glycolate oxidase The expression of antioxidant and stress response pro - and NADPH:quinone reductase was present. Glycine teins glutathione peroxidase, glutathione-disulfide reduc - betaine ABC transporter substrate-binding protein and tase, catalase, glyoxylase, thioredoxin, peroxiredoxin, formyl-CoA:oxalate CoA-transferase (FCOCT) proteins alkyl hydroperoxide reductase, aldo/keto reductase, and for osmoprotection and acid response regulator were glutathione S-transferases was upregulated in case of present to maintain the smooth functioning of intracellu- KL. Superoxide dismutase was downregulated in case of lar environment. There were six LysR family, two unclas - KL and catalases were downregulated on VA. The pro - sified and one each of GntR family, AsnC family, Cd(II)/ teins formyl-coA transferase, formate dehydrogenase Pb(II)-responsive, Crp/Fnr family, MarR, and MerR tran- for oxalate, and formate metabolism were also found to scriptional regulator found on KL. The VA was mainly be upregulated on KL. Various other dehydrogenases, dominated by transporters and stress response proteins reductases, and transferases such as hydroxypyruvate [glutathione S-transferase, Rieske (2Fe–2S) protein, thi- reductase, NAD dehydrogenase, alcohol dehydrogenase, oesterase, glycine betaine permease, and alkene reduc- aldehyde dehydrogenase, ferredoxin reductase, ferre- tase]. One methyltransferases, aminomethyltransferase, doxin, acyl-CoA dehydrogenase, acetyltransferases, and and LysR family transcriptional regulator were also enoyl-CoA hydratase, were upregulated on KL. observed. The expression of vanillate O-demethylase oxidore - ductase, chloroperoxidase, hydroglutathione hydro- Proteins differentially expressed on kraft lignin and vanillic lase, protocatechuate 3,4-dioxygenase, protocatechuate acid 4,5-dioxygenase, 2OG-Fe(II) oxygenase, antibiotic There were 1979 proteins obtained on KL–VA after nor - synthesis monooxygenase, 2-hydroxyl acid oxidase, malization, and among these, 1110 proteins upregulated cytochrome c oxidase, NADH quinone oxidoreductase, and 869 downregulated on kraft lignin. There are 164 glutathione peroxidase, and other oxidoreductases was transporters detected out of which 127 are ABC, 5 RND, upregulated in case of VA. The expression of protocate - and 4 MFS. There are 163 transcription factors identified chuate 4,5-dioxygenase was more than double compared comparising 34 LysR family, 21 GntR family, 17 tetR fam- to protocatechuate 3,4-dioxygenase on VA. Compared ily, 12 each MarR, and IcIR family. We are discussing here to KL, the expression of oxidases enzymes was very less important proteins that can perform lignin degradation on VA. The expression of laccase, FAD-dependent oxi - and transformation. Some of the differentially expressed doreductase, phytanoyl-CoA dioxygenase, YggW fam- proteins that may involve in prospective lignin degrada- ily oxidoreductase, ubiquinol oxidase, one glutathione tion are shown in Fig.  7b. The presence of various oxi - S-transferase, and NADH quinone oxidoreductase, was doreductases, dehydrogenase, reductases, transferases, almost same in both KL and VA. There were several PHA biosynthetic proteins, and several stress response NADH:quinone oxidoreductases observed in KL–VA and detoxification proteins was detected in the expres - and some are upregulated in KL other in VA. Short- sion profile. The phenylacetic acid degradation protein chain dehydrogenase, acyl-CoA dehydrogenase, alcohol and ‘CoA’-mediated degradation of phenylacetate, phe- dehydrogenase, acyltransferase, alkene reductase, FMN nylpropionate, and benzoate proteins were found to be reductase, NADH:quinone reductase, and acetyl-CoA upregulated on kraft lignin. The DyP-type peroxidase, acetyl transferase was found to be upregulated on VA. peroxidase-like proteins, and various accessory enzymes The clusters predicted for lignin degradation and PHA such as aldehyde oxidase, glycolate oxidase, cytochrome production were found to functionally active and the C oxidase, oxidase, NADH:quinone oxidoreductase, genes for degradation of lignin derivatives as well as all FAD-linked oxidase, and GMC family oxidoreductase the three PHA polymerase were present in the expression were found to be upregulated on KL. GMC family oxi- profile (Additional file  3: Table  S10, also contains other doreductase or aryl alcohol oxidase is also known as dehydrogenase, reductases, transferases, esterases, thi- auxiliary enzymes in case of fungi and their role is estab- oesterases, hydrolases not discussed here but expressed lished in lignin degradation [27]. The homogentisate on KL–VA). The PHA production was induced on both 1,2-dioxygenase, quercetin 2,3-dioxygenase, 4-hydroxy- the substrate, i.e., kraft lignin and vanillic acid. The acti - phenylpyruvate dioxygenase, dioxygenase, and nitropro- vation of PHA biosynthetic genes on lignin was also pane dioxygenase were found to be upregulated on KL. recently reported [17]. There were six SAM-dependent methyltransferase and one methyltransferase identified on KL–VA. Four SAM- Discussion dependent methyl transferase and methyltransferase was The detail of genomic and proteomic studies of lignin upregulated on KL and two SAM-dependent methyl- degrading bacterium is limited, so we tried to provide the transferase was upregulated on VA. comprehensive genomic and proteomic analysis of lignin Kumar et al. Biotechnol Biofuels (2018) 11:154 Page 14 of 23 Table 2 Differentially expressed proteins for phenylacetic acid, benzene degradation, and various oxidoreductases on kraft lignin Uniprot IDs Locus tag Name Log2 fold Unique Sequence Mol. weight Intensity change peptides coverage (%) (kDa) Phenylacetic acid degradation protein A0A1E3LF26 A9762_23720 Phenylacetic acid degradation protein PaaD 0.529261 3 27.3 15.022 8.65E−26 A0A1E3LF48 A9762_23735 Phenylacetic acid degradation protein PaaN 0.244067 18 58.3 60.008 1.24E−140 A0A1E3LFB3 A9762_23725 2-(1,2-Epoxy-1,2-dihydrophenyl)acetyl-CoA 0.724358 9 56.1 27.854 1.32E−76 isomerase A0A1E3LFJ2 A9762_22495 Phenylacetic acid degradation protein 0.790541 4 36.3 15.888 3.07E−15 A0A1E3LHE3 A9762_23715 Phenylacetate–coenzyme A 0.514503 14 57.5 47.386 1.43E−109 A0A1E3LQE8 A9762_10500 Phenylacetic acid degradation protein 1.426558 5 44.4 14.521 5.16E−22 Peroxidases A0A1E3LDX8 A9762_24250 Dyp-type peroxidase 1.43239 15 72 40.756 1.29E−104 A0A1E3LHN8 A9762_20355 Peroxidase − 1.69967 18 90.6 23.753 0 A0A1E3LPA6 A9762_00985 Chloroperoxidase − 1.927944 16 84.7 30.075 8.73E−175 A0A1E3LF97 A9762_25345 Peroxidase-like protein 1.353771 7 59 18.981 4.85E−31 A0A1E3LNE3 A9762_13620 Laccase − 0.13346 10 57.5 28.644 5.45E−43 Oxidases A0A1E3LC86 A9762_26490 Glycolate oxidase subunit GlcE 1.96696 9 38.1 38.774 4.18E−40 A0A1E3LDU3 A9762_25250 Aldehyde oxidase 1.94888 25 43.2 106.43 3.40E−153 A0A1E3LG04 A9762_25240 Cytochrome C oxidase Cbb3 1.88749 12 44.8 44.919 5.64E−68 A0A1E3LL61 A9762_17965 Glycolate oxidase iron–sulfur subunit 1.88269 5 14.3 46.4 1.56E−20 A0A1E3LCC6 A9762_07195 Oxidase 1.12594 23 67.7 43.498 4.04E−279 A0A1E3LQ45 A9762_00290 FAD-linked oxidase 0.7576 46 47.6 148.68 8.22E−260 A0A1E3LDS7 A9762_25555 Ubiquinol oxidase subunit 2 − 0.72481 3 21.5 35.767 2.50E−21 A0A1E3LLY2 A9762_16250 l -Aspartate oxidase − 1.51593 5 14.2 58.534 1.25E−24 A0A1E3LRG9 A9762_02095 Cytochrome c oxidase assembly protein − 1.76256 6 49.8 22.192 2.52E−27 A0A1E3LCR8 A9762_26505 2-Hydroxy-acid oxidase − 1.92172 13 43.3 51.242 1.38E−99 Oxidoreductases A0A1E3L9T7 A9762_09290 NADH–quinone oxidoreductase subunit I 1.983 13 54.6 18.63 1.26E−66 A0A1E3LC99 A9762_26255 Oxidoreductase 1.46342 9 62.5 26.21 1.99E−100 A0A1E3LAC9 A9762_09275 NADH oxidoreductase (quinone) subunit F 0.86275 19 70.7 47.093 5.72E−135 A0A1E3LMK8 A9762_03120 NADP oxidoreductase 0.82498 10 55.5 32.458 3.02E−38 A0A1E3LHK5 A9762_23470 FAD-dependent oxidoreductase 0.33833 3 14.7 38.458 4.28E−15 A0A1E3LLW4 A9762_03220 GMC family oxidoreductase 0.24372 23 54.8 64.908 3.74E−163 A0A1E3LFG3 A9762_22500 NADP-dependent oxidoreductase 0.05857 13 63.4 35.64 5.98E−106 A0A1E3LKB2 A9762_03335 Oxidoreductase − 0.24038 18 82.3 31.785 3.07E−157 A0A1E3LGB9 A9762_21450 YggW family oxidoreductase − 0.68269 3 10.3 45.723 1.71E−14 A0A1E3LC87 A9762_26930 Fe–S oxidoreductase − 1.47441 6 49.8 26.119 2.01E−34 A0A1E3LG91 A9762_21265 Vanillate O-demethylase ferredoxin subunit − 1.5017 15 57.9 33.723 1.13E−114 A0A1E3LG83 A9762_21255 Vanillate O-demethylase oxidoreductase 0.298001 15 48.1 50.745 1.80E−76 A0A1E3LFZ4 A9762_25310 FAD-dependent oxidoreductase − 1.67016 5 17.9 54.42 2.53E−15 A0A1E3LA58 A9762_09270 NADH-quinone oxidoreductase subunit E − 1.69506 9 80.1 18.129 9.41E−90 A0A1E3LFR2 A9762_22175 Oxidoreductase − 1.8627 9 61.8 30.679 4.89E−178 A0A1E3LCB2 A9762_09255 NADH-quinone oxidoreductase subunit B − 1.96385 10 72.3 17.519 1.56E−64 A0A1E3LEJ8 A9762_05735 Oxidoreductase − 1.97509 18 85.7 26.372 6.17E−220 A0A1E3LKX1 A9762_15740 Quinone oxidoreductase − 1.99406 18 90.7 34.556 1.06E−219 Oxygenases A0A1E3LHN5 A9762_23090 2-Nitropropane dioxygenase 1.84558 3 15.1 38.789 7.50E−15 A0A1E3LFU3 A9762_22350 Quercetin 2,3-dioxygenase 1.82796 7 51.5 26.31 4.21E−24 A0A1E3LFX1 A9762_21815 Homogentisate 1,2-dioxygenase 1.51818 13 56.9 48.611 5.10E−81 Kumar et al. Biotechnol Biofuels (2018) 11:154 Page 15 of 23 Table 2 (continued) Uniprot IDs Locus tag Name Log2 fold Unique Sequence Mol. weight Intensity change peptides coverage (%) (kDa) A0A1E3LPA9 A9762_00970 4-Hydroxyphenylpyruvate dioxygenase 1.43964 2 5.9 40.191 3.14E−09 A0A1E3LFB4 A9762_23095 2-Nitropropane dioxygenase 1.31977 9 45.1 39.332 6.27E−61 A0A1E3LDU6 A9762_24595 Phytanoyl-CoA dioxygenase − 0.60384 6 38.3 27.846 2.72E−52 A0A1E3LF51 A9762_25450 Putative dioxygenase − 0.666263 9 88.7 15.676 1.86E−122 A0A1E3LIM3 A9762_17955 Dioxygenase − 0.91661 8 52 29.958 6.54E−31 A0A1E3LI70 A9762_22255 2-Nitropropane dioxygenase − 1.45193 12 64.4 33.509 1.71E−146 A0A1E3LIR0 A9762_17450 Protocatechuate 3,4-dioxygenase subunit − 1.63442 13 83.4 21.895 2.50E−246 alpha A0A1E3LJ07 A9762_17445 Protocatechuate 3,4-dioxygenase subunit − 1.71052 16 78.4 26.513 2.43E−152 beta A0A1E3LG93 A9762_21285 Protocatechuate 4,5-dioxygenase subunit − 1.83931 6 80.7 13.769 6.11E−47 alpha A0A1E3LG93 A9762_21285 Protocatechuate 4,5-dioxygenase subunit − 1.83931 6 80.7 13.769 6.11E−47 beta A0A1E3LEL8 A9762_04935 Antibiotic biosynthesis monooxygenase − 1.86712 6 81.8 11.026 1.02E−172 A0A1E3LBV9 A9762_07570 2OG-Fe(II) oxygenase − 1.682965 7 50.7 30.695 9.21E−31 A0A1E3LL67 A9762_14910 2OG-Fe(II) oxygenase − 0.037474 8 43 37.152 3.47E−45 Benzoate degradation A0A1E3LBS0 A9762_08405 2-Aminobenzoate–CoA ligase 1.569646 5 15.2 59.58 4.06E−18 A0A1E3LF67 A9762_23480 3-Octaprenyl-4-hydroxybenzoate carboxy- − 1.471879 4 32.4 15.528 1.01E−27 lyase (Fragment) A0A1E3LLJ4 A9762_17745 3-Octaprenyl-4-hydroxybenzoate carboxy- 1.567849 11 32.8 57.345 1.54E−68 lyase A0A1E3LM76 A9762_12465 2-Nonaprenyl-3-methyl-6-methoxy-1,4-ben- − 1.895105 5 47.4 23.511 1.50E−34 zoquinol hydroxylase A0A1E3LDW9 A9762_24905 Carboxymethylenebutenolidase − 1.707803 8 49 27.008 1.57E−119 A0A1E3LDA6 A9762_06440 Carboxymethylenebutenolidase − 1.951469 18 77 31.135 1.41E−118 degrading bacterium Pandoraea sp. ISTKB. The genome VA as compared to KL can be explained that these pro- size of this genus available in NCBI varies between 4.4 teins might be localized near the membrane and actively and 6.5  Mb and this strain’s genome is one of the larg- involved in transportation and metabolism of VA into est genome sequences available until date from Pando- the cell. The absence of proteins in VA for organic cyclic raea genus. The degradation of aromatic compounds by compound binding, heterocyclic compound binding, bacteria is mostly aerobic and is tightly regulated process. iron–sulfur cluster binding, receptor activity, ion bind- Their degradation by oxidoreductases generates reactive ing, cofactor binding, small molecule binding, and their intermediates, so a robust stress response and detoxifi - presence in KL suggests that these are the important cation mechanism is required for survival of microbes. molecular functions’ category proteins that would have The dominance of these subsystem features such as res - facilitated the depolymerization and utilization of poly- piration, aromatic metabolism, and stress response (after mer KL by this strain. normal cellular processes) and their complementation The analysis of expression profile on KL indicates the highlights the ability of Pandoraea sp. ISTKB to survive presence of metacleavage and unusual pathways, i.e., and metabolize lignin or aromatic compound. ‘-CoA’-mediated degradation of lignin derivatives in The GO analysis especially biological process and aerobic microorganisms. The presence of 2-hydroxy - molecular functions indeed supported this strain’s hepta-2,4-diene-1,7-dioate isomerase in the expression robust genomic machinery for the utilization of organic profile of KL possibly indicated 4-hydroxyphenylac - substance, organic cyclic compounds, heterocyclic etate degradation through meta cleavage pathways [28]. compound binding, solute binding, ion binding, and oxi- Benzoyl-CoA oxygenase-mediated degradation of aro- doreductase activity. The abundance of localization pro - matic compound is completely different mechanisms cess proteins, membrane proteins, and transporters in and observed in 4–5% of sequenced bacterial genomes. Kumar et al. Biotechnol Biofuels (2018) 11:154 Page 16 of 23 Table 3 Differentially expressed antioxidant and stress response proteins on kraft lignin Uniprot IDs Locus tag Name Log2 fold Unique Sequence Mol. Intensity change peptides coverage (%) weight (kDa) Glutathione enzymes A0A1E3LF33 A9762_23395 Glutathione ABC transporter substrate-binding 1.80871 29 77.1 57.261 0 protein A0A1E3LKY8 A9762_17040 Glutathione S-transferase 1.18746 8 41.1 24.027 3.57E−36 A0A1E3LF68 A9762_25435 Glutathione S-transferase 0.61286 8 65.2 22.821 1.27E−72 A0A1E3LBR6 A9762_09395 Glutathione S-transferase 0.55477 4 25.7 24.666 5.23E−14 A0A1E3LQD9 A9762_10375 Glutathione S-transferase 0.51263 5 37.8 27.794 1.84E−17 A0A1E3LFJ0 A9762_24585 Glutathione-disulfide reductase 0.35879 22 63.6 48.837 7.37E−222 A0A1E3LI91 A9762_18915 Glutathione S-transferase 0.05437 5 39 25.252 2.31E − 26 A0A1E3LP56 A9762_00695 Glutathione S-transferase − 0.96784 8 53.6 23.768 4.31E−48 A0A1E3LI39 A9762_18265 Glutathione S-transferase − 1.44982 18 82.3 23.728 3.01E−285 A0A1E3LAC5 A9762_09365 Glutathione S-transferase − 1.70035 15 72.6 26.078 1.22E−149 A0A1E3LPY3 A9762_02245 Glutathione synthetase − 1.79520 21 82.4 34.566 2.19E−195 A0A1E3LL68 A9762_15125 Glutathione S-transferase − 1.85572 4 21 23.996 5.81E−18 A0A1E3LI75 A9762_04000 Lactoylglutathione lyase − 1.97244 4 64.5 14.032 1.22E−30 A0A1E3LBC2 A9762_08325 Hydroxyacylglutathione hydrolase − 1.98082 10 57.5 29.087 5.85E−75 A0A1E3LC63 A9762_26475 Glutathione peroxidase 1.59171 9 82.6 18.506 1.18E−57 A0A1E3LN82 A9762_11030 Glutathione peroxidase − 1.47148 10 55.2 19.852 3.04E−128 A0A1E3LL32 A9762_17770 S-(Hydroxymethyl)glutathione dehydrogenase − 1.97881 22 83.7 39.609 5.20E−235 A0A1E3LCG8 A9762_26430 S-Formylglutathione hydrolase − 1.5565 9 49.6 31.49 2.83E−45 Catalases A0A1E3LJG2 A9762_17205 Catalase − 1.90503 31 69.7 55.065 0 A0A1E3LHV5 A9762_19890 Catalase 1.96803 20 58.3 54.314 2.70E−159 A0A1E3LL41 A9762_15065 Catalase 1.96803 20 58.3 54.314 2.70E−159 Superoxide dismutase A0A1E3LHJ2 A9762_20590 Superoxide dismutase − 1.97424 2 12.2 22.201 8.04E−07 A0A1E3LJK7 A9762_16420 Superoxide dismutase − 1.6319 16 93.2 21.3 0 Thioredoxin A0A1E3LA95 A9762_09775 Thioredoxin 1.50102 6 68.5 11.693 1.86E−50 A0A1E3LIM9 A9762_21500 Thioredoxin 0.26594 13 64 30.297 2.12E−120 A0A1E3LMC9 A9762_12720 Probable thiol peroxidase − 1.29118 15 95.8 17.552 1.19E−229 A0A1E3LK52 A9762_19935 Thioredoxin reductase − 0.42918 12 71.1 33.796 6.61E−169 Peroxiredoxin A0A1E3LFM2 A9762_22670 Peroxiredoxin 0.06241 4 27.7 19.976 2.59E−09 A0A1E3LG33 A9762_25080 Peroxiredoxin − 0.7565 5 51.9 17.411 3.34E−34 A0A1E3LIX5 A9762_17525 Peroxiredoxin 1.63617 11 84.5 20.829 4.52E−87 A0A1E3LNW8 A9762_00130 Peroxiredoxin − 1.41372 5 35 14.926 1.51E−22 Glyoxylase A0A1E3LJS5 A9762_02855 Glyoxalase 1.90407 4 26.4 24.933 1.26E−10 A0A1E3LML8 A9762_12845 Glyoxalase − 1.55877 4 40.7 15.609 4.05E−12 Glutaredoxin A0A1E3LF15 A9762_23485 Glutaredoxin − 0.65795 4 51.9 11.612 1.33E−69 A0A1E3LQ32 A9762_02205 Glutaredoxin 3 1.02376 8 79.1 9.8904 4.95E−60 Alkylperoxide reductase A0A1E3LAL5 A9762_08705 Alkyl hydroperoxide reductase − 1.92917 10 79.1 16.924 2.59E−121 A0A1E3LDK0 A9762_25350 Alkyl hydroperoxide reductase AhpD 1.76395 5 40.7 22.242 5.04E−30 A0A1E3LCA5 A9762_26215 Alkyl hydroperoxide reductase AhpD − 1.58398 5 49.5 19.7 1.06E−56 A0A1E3LGT9 A9762_04630 Alkyl hydroperoxide reductase AhpD − 0.87073 6 67.7 14.207 2.45E−17 Kumar et al. Biotechnol Biofuels (2018) 11:154 Page 17 of 23 Table 3 (continued) Uniprot IDs Locus tag Name Log2 fold Unique Sequence Mol. Intensity change peptides coverage (%) weight (kDa) A0A1E3LKG5 A9762_16100 Alkyl hydroperoxide reductase AhpD − 1.52586 9 64.9 21.888 2.68E−61 A0A1E3LLQ8 A9762_13730 Alkyl hydroperoxide reductase AhpD − 0.29909 10 77.7 18.588 4.23E−101 A0A1E3LLX0 A9762_13735 Alkyl hydroperoxide reductase − 0.30453 16 85.7 20.001 0 This mechanism helps to overcome the high resonance compounds [15, 36, 37]. Laccases can degrade lignin in stabilization of aromatic ring by forming epoxide. Ben- the presence of mediators and there are several natural zoyl-CoA oxygenase leads to formation of 2,3-epoxide mediators observed during lignin degradation [38, 39]. followed by enoyl-CoA hydratase (also expressed on KL) Two laccase genes were discovered in the genome and and NADP -dependent aldehyde dehydrogenase (upreg- found to be functionally active in this strain. Laccases ulated on KL)-mediated degradation resulting into for- are reported for ether linkage (aryl β-O-4) and β-1 bond mic acid, acetyl-CoA, and succinyl-CoA formation [29]. cleavage on lignin model dimers. The degradation of 1,2-phenylacetyl-CoA epoxidase-mediated degradation phenolic as well as non-phenolic substrate in the pres- of phenylacetic acid occurs via 1,2-epoxide intermedi- ence of mediators by laccases has also been reported [40, ate and this pathway is found functional in only 16% of 41]. Formate dehydrogenase coverts formate into carbon all bacteria genome reported also observed in Escherichia dioxide and these formate radicals induce MnP activ- coli and Pseudomonas putida [30]. The upregulation of ity, as they can use formate as peroxide in the absence Salicylate hydroxylase on lignin was also observed in the of H O [31]. Formyl transferase is reported for oxalate 2 2 3+ case of Pseudomonas A514 strain [17]. degradation and oxalate forms complex with Mn (MnP 2+ 3+ The expression of glycolate oxidase, oxidase, oxidase, oxidizes Mn –Mn ) and the complex acts as diffusible aldehyde oxidase, and GMC family oxidoreductase (aryl redox mediator for the degradation of phenolics in lignin alcohol oxidase) was observed on KL–VA and these acts [31]. The expression of quinone oxidoreductase, acetyl- as an accessory enzyme and the peroxides produced by CoA acetyltransferase, enoyl-CoA hydratase, dehydro- them is utilized by peroxidases for lignin degradation [27, genase (responsible for cleavage of ether linkage), and 31]. Expression of these oxidases has also been reported cytochrome peroxidase was expressed on lignin, but recently in Pseudomonas A514 and Pantoea ananatis other known bacterial lignin degrader was not observed Sd-1 [17, 27]. The detection of NADPH:quinone oxi - in Bacillus ligniniphilus L1 expression profile [33]. The doreductase in Pandoraea strain ISTKB indicates lignin catalase/hydroperoxidase, multicopper oxidase, GMC degradation by Fenton reaction. NADPH:quinone oxi- oxidoreductase, glutathione S-transferase, and quinone doreductase overexpression on lignin and rice straw oxidoreductases were observed in the secretome of P. was also reported recently [17, 27, 32, 33]. Quinone oxi- ananatis Sd-1 on rice straw [27]. In addition to these pro- doreductase system is of special interest in case of lignin teins, various other proteins were also expressed in Pan- degradation as fungi especially brown rot used fenton doraea sp. strain ISTKB that are responsible for lignin chemistry for lignin degradation with the help of quinone degradation. oxidoreductase [9, 31]. The role of NADPH: quinone The presence of demethylases, methyltransferases, and oxidoreductase in degradation and depolymerization of SAM-dependent methyltransferase indicated demethyla- lignin is well established and reported for Phanerochaete tion or rearrangement of methyl group during lignin deg- chrysosporium and Trametes versicolor [34, 35]. radation [42]. Demethylation is an important process in Dyp-type peroxidases are fungal counterparts of per- conversion of lignin-derived aromatic intermediates into oxidase (LiP or MnP) present in bacteria for lignin deg- common central intermediates such as catechol, pro- radation. The peroxidases such as DyP-type peroxidase, tocatechuate, or gallate that further undergo ring cleav- peroxidase, chloroperoxidase, and peroxidase-like pro- age. Demethylation system removes methyl group from tein were detected in Pandoraea sp. ISTKB genome methoxy-substituted lignin-derived aromatic compounds and in proteome. Some DyPs are secreted through such as syringate, vanillate, or guaiacol in the pres- TAT pathway and their encapsulation has been shown ence of cofactors. The demethylases include Rieske type to increase the enzyme’s activity [36]. There are vari - ([2Fe–2S] cluster) and reductase (a flavin and a [2Fe–2S]) ous functions reported recently for bacterial DyPs such redox center. The demethylases or methyltransferases as depolymerization, dimer formation, and degrada- were also reported and functionally validated in Pseu- tion of aryl ether bonds in lignin and lignin containing domonas and Acinetobacter [9, 42, 43]. Several acyl-CoA Kumar et al. Biotechnol Biofuels (2018) 11:154 Page 18 of 23 Table 4 Differentially expressed reductase, dehydrogenase, transferase, and hydratase proteins on kraft lignin Uniprot IDs Locus tag Name Log2 fold Unique Sequence Mol. Intensity change peptides coverage (%) weight (kDa) Reductases A0A1E3LM36 A9762_03695 Aldo/keto reductase − 1.446536 54 95.1 38.448 0 A0A1E3LPJ8 A9762_01385 Aldo/keto reductase − 1.811371 8 43.3 37.797 1.87E−50 A0A1E3LS07 A9762_01040 Aldo/keto reductase 0.040585 20 73.6 30.685 1.63E−183 A0A1E3LG16 A9762_22220 Glyoxylate/hydroxypyruvate reductase 1.99991 14 69.4 33.941 4.47E−124 A0A1E3LQJ8 A9762_00050 Bifunctional glyoxylate/hydroxypyru- − 0.601011 20 82.2 34.525 1.34E−204 vate reductase B A0A1E3LI17 A9762_19295 Alkene reductase − 0.075801 28 92 40.61 0 A0A1E3LIA9 A9762_18295 2-Alkenal reductase 0.117504 12 46.4 42.805 2.10E−74 A0A1E3LDX7 A9762_24675 Ferredoxin–NADP(+) reductase 1.250238 18 77 29.272 3.54E−106 A0A1E3LFT3 A9762_21855 NADPH-dependent FMN reductase − 0.973988 9 69.1 19.818 1.98E−77 A0A1E3LAB2 A9762_08440 NADPH:quinone reductase − 1.850827 14 71.9 36.075 3.86E−109 A0A1E3LQJ8 A9762_00050 Hydroxypyruvate reductase B − 0.601011 20 82.2 34.525 1.34E−204 A0A1E3LLZ7 A9762_13130 Fumarate reductase 1.805886 2 7.4 52.225 7.89E−05 Dehydrogenases A0A1E3LDJ7 A9762_25850 Formate dehydrogenase subunit beta 1.664541 6 23.2 34.213 1.25E−22 A0A1E3LDC4 A9762_25845 Formate dehydrogenase-N subunit 1.414862 16 34.2 90.668 3.91E−102 alpha A0A1E3LDS6 A9762_24610 Formate dehydrogenase 0.761355 2 57.1 8.7799 3.84E−22 A0A1E3LE53 A9762_24625 Formate dehydrogenase 1.257519 9 30 56.957 3.45E−62 A0A1E3LG97; A9762_24620 Formate dehydrogenase subunit alpha 1.020855 21 34 104.98 1.29E−121 A0A1E3LF08 A0A1E3LL63 A9762_15395 NADH dehydrogenase 0.064345 9 60.8 21.897 5.70E−49 A0A1E3LPJ3 A9762_01450 Aldehyde dehydrogenase 1.745055 17 54.5 52.735 1.72E−105 A0A1E3LJ61 A9762_20360 Acyl-CoA dehydrogenase 0.210716 11 46.1 43.33 1.22E−90 A0A1E3LH50 A9762_22885 Alcohol dehydrogenase 0.448181 14 55.4 40.556 1.68E−67 A0A1E3LGE7 A9762_21150 Aldehyde dehydrogenase 0.513856 4 14.4 51.073 1.64E−12 A0A1E3LFY2 A9762_21880 NAD(FAD)-utilizing dehydrogenase 1.806462 3 12.9 42.366 7.90E−09 A0A1E3LF76 A9762_23430 Acyl-CoA dehydrogenase 0.067218 9 31.6 40.901 1.33E−56 A0A1E3LKN0 A9762_15340 Acyl-CoA dehydrogenase − 1.0527852 7 24.4 41.792 1.04E−41 A0A1E3LP12 A9762_00210 Acyl-CoA dehydrogenase − 0.467758 37 72.4 65.029 0 A0A1E3LKM0 A9762_16035 NAD(P)H dehydrogenase (quinone) − 1.786348 11 55.7 22.107 2.74E−162 A0A1E3LKB6 A9762_03215 Alcohol dehydrogenase − 1.58185 16 63.3 44.426 1.36E−99 A0A1E3LJV2 A9762_02775 Putative NADH dehydrogenase − 0.256436 15 86.3 21.594 1.71E−184 A0A1E3LIB8 A9762_18460 Short-chain dehydrogenase − 1.862879 2 13.3 26.395 8.23E−08 A0A1E3LI49 A9762_22120 Short-chain dehydrogenase − 1.335172 6 29.3 24.127 2.78E−23 A0A1E3LI38 A9762_22070 Short-chain dehydrogenase − 1.826239 3 15.2 29.599 1.04E−17 A0A1E3LHQ0 A9762_20005 Dehydrogenase − 0.022626 13 53.6 38.384 2.57E−91 A0A1E3LHP2 A9762_20015 Aldehyde dehydrogenase − 0.39059 15 63.3 51.925 2.00E−131 A0A1E3LHJ3 A9762_19710 Short-chain dehydrogenase − 0.299807 5 32.7 26.91 1.68E−19 A0A1E3LLS1 A9762_17065 Short-chain dehydrogenase − 1.1228889 10 50.4 29.165 2.51E−85 A0A1E3LFZ7 A9762_24160 Acyl-CoA dehydrogenase − 1.977129 8 13.2 90.723 3.27E−24 A0A1E3LFV1 A9762_21935 Alcohol dehydrogenase − 0.223075 15 71.1 36.536 2.10E−159 A0A1E3LF72 A9762_23085 NADPH:quinone dehydrogenase − 1.970038 12 66.5 34.703 2.88E−132 A0A1E3LE86 A9762_05015 Short-chain dehydrogenase − 0.122157 19 90.8 26.28 1.25E−173 A0A1E3LE78 A9762_24110 Short-chain dehydrogenase − 1.0213605 8 59.1 24.582 6.63E−39 A0A1E3LE10 A9762_24765 Aldehyde dehydrogenase − 0.713344 26 69.6 50.552 2.84E−236 A0A1E3LDF9 A9762_25465 Short-chain dehydrogenase − 1.0369092 18 82.1 26.766 0 Kumar et al. Biotechnol Biofuels (2018) 11:154 Page 19 of 23 Table 4 (continued) Uniprot IDs Locus tag Name Log2 fold Unique Sequence Mol. Intensity change peptides coverage (%) weight (kDa) A0A1E3LCV6 A9762_26070 Acyl-CoA dehydrogenase − 0.559374 33 78.2 63.6 0 A0A1E3LCK3 A9762_26745 Aldehyde dehydrogenase − 1.998458 41 82.4 55.098 0 A0A1E3LCD2 A9762_09370 Acyl-CoA dehydrogenase − 0.349182 10 31.9 45.179 6.63E−43 Transferase and hydratase A0A1E3LDE2 A9762_25255 Acetyltransferase 1.1424203 5 42.2 19.294 9.45E−19 A0A1E3LEG1 A9762_24350 Acyl-CoA transferase − 1.894681 5 23.8 49.528 1.44E−09 A0A1E3LE25 A9762_26525 Acyltransferase − 0.658173 11 53.7 31.029 2.25E−127 A0A1E3LCY1 A9762_06345 CoA transferase − 1.644591 5 19.7 43.746 5.43E−17 A0A1E3LAQ8 A9762_09850 Formyl-CoA transferase 1.63564 16 57 43.01 7.70E−140 A0A1E3LEY2 A9762_23230 Formyl-CoA:oxalate CoA transferase 1.480644 23 65.9 45.431 4.87E−142 A0A1E3LF20 A9762_25975 N-Hydroxyarylamine O-acetyltrans- − 0.812216 13 68.8 31.71 1.16E−71 ferase A0A1E3LB74 A9762_08395 Enoyl-CoA hydratase 0.844962 4 17.4 30.92 1.3832E−11 A0A1E3LG06 A9762_22140 Enoyl-CoA hydratase − 0.845624 7 39.9 28.125 5.7526E−122 A0A1E3LD66 A9762_27340 Enoyl-CoA hydratase 1.887871 9 53.1 29.49 1.5759E−26 A0A1E3LNX6 A9762_00200 Acetyl-CoA acetyltransferase − 0.329002 26 92.5 41.664 0 A0A1E3LED2 A9762_24145 Acetyl-CoA acetyltransferase − 0.647329 11 34.2 46.667 5.8563E−44 A0A1E3LFL9 A9762_22115 Acetyl-CoA acetyltransferase − 1.992637 21 75.9 40.895 0 A0A1E3LLK2 A9762_13635 Acetyl-CoA acetyltransferase − 1.672549 24 85 40.687 0 A0A1E3LLN7 A9762_13660 Acetyl-CoA acetyltransferase − 1.969308 20 70.5 41.273 0 A0A1E3LFA3 A9762_23740 Enoyl-CoA hydratase − 1.935441 19 86.8 28.063 8.927E−161 A0A1E3LNG2 A9762_11320 Enoyl-CoA hydratase 0.497127 6 36.4 27.805 7.4808E−33 A0A1E3LNH0 A9762_11445 Enoyl-CoA hydratase − 1.83413 8 45.4 29.067 2.3968E−55 A0A1E3LNY9 A9762_00195 Enoyl-CoA hydratase − 0.4152 17 84.7 27.622 1.6359E−146 synthetases, acyl-CoA hydratases/lyases, acyl-CoA been known for detoxification mechanism and stress- transferase, acetyl-CoA-acetyl transferases, and decar- related response. However, glutathione-dependent cleav- boxylases have been discovered in Pandoraea sp. ISTKB age of β-aryl ether linkages (most dominant linkage in genome and in expression profile. These enzymes help in lignin) by β-etherase has also been described in Novo- activation and decarboxylation of aromatic compounds sphingobium, Sphingobium SYK-6, Novosphingobium sp. (hydroxycinnamates, carboxyvanillin) and play an impor- PP1Y, and io Th bacillus denitrificans ATC 25259 [15, 45, tant role in diversion of substrate towards central degra- 46]. Therefore, the presence of glutathione enzymes can dation [42–44]. The expression of both protocatechuate help in lignin degradation in this strain. Superoxide dis- 3,4-dioxygenase and protocatechuate 4,5-dioxygenase mutase and catalase–peroxidases were recently reported on both KL–VA indicated that this strain has both func- for lignin or lignin model compound in Sphingobacte- tional ortho and meta cleavage pathway for degradation rium sp. T2 and Amycolatopsis sp. 75iv2, respectively, of lignin and its derivatives. The expression of metacleav - and these were also observed on KL–VA in this strain age outperformed ortho pathway on vanillic acid. The [47, 48]. presence of both ortho and meta cleavage pathways in Dehydrogenase acts on toxic aldehydes and converts single strain is rare phenomenon and the ortho cleavage them into their less toxic intermediates inside cells and pathway was found to be dominant among lignin degrad- also reported for cleavage of ether bond [43, 44]. There ing bacteria [9, 23]. The expression of both ortho and are various dehydrogenases observed in this strain and meta cleavage pathways in this strain illustrates its robust these might play important role in ether linkage degrada- metabolic machinery for the degradation of aromatic tion. The dehydrogenase-mediated degradation of ether compounds. linkage in lignin model compounds by SG61-1L and There are various glutathione-dependent enzymes Lig DEG enzyme system in Sphingobium sp. SYK6 has identified in Pandoraea sp. ISTKB and glutathione has been well documented [42, 49]. The combined action of Kumar et al. Biotechnol Biofuels (2018) 11:154 Page 20 of 23 alcohol dehydrogenase from short-chain dehydrogenase/ Methods reductase family and glutathione S-transferases has been The draft genome of Pandoraea sp. ISTKB was sequenced show to degrade ether linkage (most prominent linkage using the Illumina MiSeq platform, and the raw data in lignin 50–70%) in lignin model compounds [50]. The processing, quality reads, assembly, scaffold generation, pathway for cleavage of β-aryl ether linkage in lignin by and genes prediction were carried out as described ear- NAD-dependent dehydrogenases (LigD, LigO, and LigL) lier [19]. Arrangement of genes of Pandoraea sp. strain and the glutathione-dependent lyase (LigG) was struc- ISTKB with respect to its genome was performed using turally and biochemically characterized [51]. There are clicO FS, i.e., circular layout interactive converter free glutathione enzymes, superoxide dismutase, catalases, services [55]. The proteins having signal sequence were alkyl hydroperoxidase, thioredoxin, glyoxylase, aldo/keto identified using the SignalP 3.0 software [56]. The anno - reductase, and peroxiredoxin identified in Pandoraea tation and analysis of Pandoraea sp. ISTKB genome were sp. ISTKB. The presence of theses stress response and also performed by Rapid Annotations using Subsystems detoxification proteins has also been reported in genome technology (RAST). The RAST subsystem classification sequence of Pseudomonas fluorescens Pf-5 [52]. The followed by pathway analysis was performed [57, 58]. specificity of aldo/keto reductase against various lignin- GO analysis was performed and the genes predicted in derived phenolics, aldehyde, and fermentable inhibi- genome have been classified into major biological pro - tors was demonstrated and was also shown to produce cesses, cellular component, and molecular functions ROS and initiate fenton reaction [53]. Alky hydroperox- using Blast2GO [59]. To identify the potential involve- ide reductase has greater catalytic efficiency under low ment of the genes of Pandoraea sp. ISTKB in biological H O concentration and is responsible for the detoxi- pathways, genes were mapped to reference canonical 2 2 fication of organic hydroperoxides, as catalases cannot pathways in Kyoto encyclopedia of genes’ and genomes’ degrade organic hydroperoxides [54]. The analysis of (KEGG) database. The output of KEGG analysis includes such a diverse set of proteins and their level of expression KEGG orthology (KO) assignments and corresponding helped us to identify the important enzymes responsible enzyme commission (EC) numbers and metabolic path- for lignin or aromatic compound degradation that will ways of genes using KEGG automated annotation server further provide opportunity for lignocellulosic biomass KAAS (http://www.genom e.jp/kaas-bin/kaasm ain) [60]. valorization. A total of 5568 genes for Pandoraea sp. ISTKB were provided as input to KEGG–KAAS and genes involved Conclusion in different pathways were further classified into 22 The genomic and proteomic analysis of Pandoraea sp. functional pathways. The antimicrobial and secondary ISTKB revealed the presence of various candidate genes metabolite clusters were predicted by antiSMASH 3.0 responsible for lignin degradation and PHA production. and genomic islands were predicted using islandviewer4 GO analysis of genomic and proteomic data also sup- [61, 62]. ported the findings. The peroxidase-accessory enzyme system, fenton reaction, and ‘CoA’-mediated degradation Culture conditions and sample preparation for proteomic of phenylacetate and benzoate are the major pathways analysis observed for lignin degradation. The gene cluster respon - Pandoraea sp. ISTKB was grown in mineral medium sible for lignin degradation and PHA production was (MM) containing vanillic acid and kraft lignin as sole found to be functionally active. The functional analysis carbon source. The composition of MM was the same supported genomic findings and a strong antioxidant and as described earlier [6]. A single colony was transferred stress responsive machinery for the survival and metab- from LB plate to broth and incubated overnight at olism of lignin or aromatic compounds was observed. 30  °C and 165  rpm. One milliliter of overnight culture Some secondary metabolites such as lassopeptide unique was transferred to fresh 100  ml LB media and allowed to this strain were also predicted that needs to be vali- to grow until OD reached around 0.5. The cells were dated. The study indicated the pathways and enzymes pelleted, washed twice with phosphate-buffered saline important for metabolism of lignin or aromatic com- (PBS), and inoculated in flask containing VA and KL pounds that can be applied in the future for value addi- having initial OD of around 0.06. Bacteria were grown tion to lignocellulosics. at 30 °C, 165 rpm and the OD was monitored at regular Kumar et al. Biotechnol Biofuels (2018) 11:154 Page 21 of 23 interval. The culture was harvested during exponential Additional files growth phase for proteomics study. Cells were pelleted by cold centrifugation at 10,000  rpm for 15  min washed Additional file 1: Figure S1. Representation of various proteins responsi- with PBS and then resuspended in lysis buffer followed ble for respiratory machinery of Pandoraea sp. ISTKB. Figure S2. Transcrip- tional regulators identified in the genome of Pandoraea sp. ISTKB. Figure by sonication as described earlier [6]. Total protein con- S3. Representation of various transporters present in the genome of centration was estimated by Bradford method, and then, Pandoraea sp. ISTKB. Figure S4. Representation of major oxidoreductases digestion was performed taking equal volume of proteins responsible for lignin and aromatic compound degradation. Figure S5. Representation of proteins into various groups involved in stress regula- from both KL and VA. tion mechanism. Figure S6. Representation of genomic islands predicted by Islandviewer 4 in the Pandoraea sp. ISTKB genome. Table S1. KEGG Digestion of proteins, LC–MS/MS analyses, and data Pathway classification of Pandoraea sp. ISTKB. Table S2. Annotation of Monooxygenase genes identified in the genome of Pandoraea sp. ISTKB. analysis Table S3. Annotation of Dioxygenase genes identified in the genome of The protein concentration of 25 µg from both KL and VA Pandoraeasp. ISTKB. Table S4. Annotation of Peroxidase genes identified was reduced with 5 mM concentration TCEP for 10 min in the genome of Pandoraea sp. ISTKB. Table S5. Peripheral pathways for catabolism of aromatic compounds. Table S6. Annotation of genes at room temperature and further alkylated with 15  mM responsible for metabolism of central aromatic intermediates. Table S7. iodoacetamide in dark at room temperature for 30  min. Annotation of genes related to Glutathione metabolism and stress The sample was diluted to 0.6  M final Gn-HCl concen - response. Table S8. Represents secondary metabolite clusters identified in Pandoraea sp. ISTKB genome. tration with 25  mM ammonium bicarbonate buffer. For Additional file 2: Table S9. Detail of genomic islands identified in Pando - digestion of protein, trypsin was added in a trypsin-to- raea sp. ISTKB genome. lysate ratio of 1:50 after and incubation was performed Additional file 3: Table S10. Other differentially expressed proteins overnight at 37  °C. The supernatant was vacuum dried (related to PHA metabolism, dehydrogenase, reductases, transferases, and the peptides were reconstituted in 5% formic acid esterases and hydrolases) on kraft lignin. followed by purification using C18 silica cartridge and dried using speed vac. The dried pellets were resus - Authors’ contributions pended in buffer-A (5% acetonitrile/0.15 formic acid). MK, IST, PKV, and AP designed the study and experiments. MK, SV, RKG, and The peptides were analyzed using EASY-nLC 1000 MK performed the experiments, bioinformatics, and data analysis. MK and SV wrote the manuscript. AP, IST, and PKV supervised the research work. All system (Thermo Fisher Scientific) coupled to QEx - authors read and approved the final manuscript. tractive mass spectrometer (Thermo Fisher Scientific) equipped with nanoelectrospray ion source. 1  µg of Author details School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, peptide mixture was loaded on precolumn and resolved 110067, India. National Institute of Plant Genome Research, Aruna Asaf Ali using 15  cm Pico Frit filled with 1.8 um C18-resin 3 Marg, New Delhi 110067, India. CSIR-Indian Institute of Toxicology Research, (Dr. Maeisch). The sample was run for 90  min and the 31 MG Marg, Lucknow 226 001, India. peptides were eluted with a 0–40% gradient of buffer Acknowledgements B (95% acetonitrile/0.1% formic acid) at a flow rate of Madan Kumar thanks Council of Scientific and Industrial Research (CSIR), New 300  nl/min. the QExtractive was operated using the Delhi, India for providing Senior Research Fellowship. P.K.V. thanks the National Institute of Plant Genome Research, New Delhi, for financial support. We thank Top10 HCD data-dependent acquisition mode with a Shashi Shekhar Singh and Gagandeep Jhingan for their support in proteom- full-scan resolution of 70,000 at m/z 400. The MS/MS ics work. We are grateful to Jawaharlal Nehru University, New Delhi, India, for scans were acquired at a resolution of 17500 at m/z providing financial support. 400. Lock mass option was enabled for polydimethyl- Competing interests cyclosiloxane (PCM) ions (m/z = 445.120025) for inter- The authors declare that they have no competing interests. nal recalibration during the run. MS identification of Q Ethics approval and consent to participate extractive files was analyzed by the MaxQuant software Not applicable. and searched against databases at a false-discovery rate (FDR) of 1%. A total of protein groups were identified Publisher’s Note and were further filtered according to the label-free Springer Nature remains neutral with regard to jurisdictional claims in pub- quantitation (LFQ) intensity values and their respec- lished maps and institutional affiliations. tive fold change values were calculated. Heat map and Received: 30 December 2017 Accepted: 17 May 2018 profile plots were against the protein groups filtered based on the normalized LFQ intensity values using the Perseus software. 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Genomic and proteomic analysis of lignin degrading and polyhydroxyalkanoate accumulating β-proteobacterium Pandoraea sp. ISTKB

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Chemistry; Biotechnology; Plant Breeding/Biotechnology; Environmental Engineering/Biotechnology; Renewable and Green Energy; Renewable and Green Energy; Microbiology
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Abstract

Background: Lignin is a major component of plant biomass and is recalcitrant to degradation due to its complex and heterogeneous aromatic structure. The biomass-based research mainly focuses on polysaccharides component of biomass and lignin is discarded as waste with very limited usage. The sustainability and success of plant polysac- charide-based biorefinery can be possible if lignin is utilized in improved ways and with minimal waste generation. Discovering new microbial strains and understanding their enzyme system for lignin degradation are necessary for its conversion into fuel and chemicals. The Pandoraea sp. ISTKB was previously characterized for lignin degradation and successfully applied for pretreatment of sugarcane bagasse and polyhydroxyalkanoate (PHA) production. In this study, genomic analysis and proteomics on aromatic polymer kraft lignin and vanillic acid are performed to find the impor - tant enzymes for polymer utilization. Results: Genomic analysis of Pandoraea sp. ISTKB revealed the presence of strong lignin degradation machinery and identified various candidate genes responsible for lignin degradation and PHA production. We also applied label-free quantitative proteomic approach to identify the expression profile on monoaromatic compound vanillic acid ( VA) and polyaromatic kraft lignin (KL). Genomic and proteomic analysis simultaneously discovered Dyp-type peroxidase, peroxidases, glycolate oxidase, aldehyde oxidase, GMC oxidoreductase, laccases, quinone oxidoreductase, dioxyge- nases, monooxygenases, glutathione-dependent etherases, dehydrogenases, reductases, and methyltransferases and various other recently reported enzyme systems such as superoxide dismutases or catalase–peroxidase for lignin degradation. A strong stress response and detoxification mechanism was discovered. The two important gene clus- ters for lignin degradation and three PHA polymerase spanning gene clusters were identified and all the clusters were functionally active on KL–VA. Conclusions: The unusual aerobic ‘-CoA’-mediated degradation pathway of phenylacetate and benzoate (reported only in 16 and 4–5% of total sequenced bacterial genomes), peroxidase-accessory enzyme system, and fenton chem- istry based are the major pathways observed for lignin degradation. Both ortho and meta ring cleavage pathways for aromatic compound degradation were observed in expression profile. Genomic and proteomic approaches provided *Correspondence: pkv@nipgr.ac.in; isthakur@hotmail.com; isthakur@mail.jnu.ac.in School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, 110067, India National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India Full list of author information is available at the end of the article © The Author(s) 2018. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creat iveco mmons .org/licen ses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creat iveco mmons .org/ publi cdoma in/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Kumar et al. Biotechnol Biofuels (2018) 11:154 Page 2 of 23 validation to this strain’s robust machinery for the metabolism of recalcitrant compounds and PHA production and provide an opportunity to target important enzymes for lignin valorization in future. Keywords: Genomics, Lignin, Polyhydroxyalkanoate, Gene cluster, Label-free quantification, Vanillic acid Background industry [6, 9–11]. The application of advanced ‘omics’ The genus Pandoraea is a very recently classified genus approach such as genomics, transcriptomics, and pro- proposed in the year 2000. Bacteria belonging to genus teomics to individual microbial strains or microbial Pandoraea are Gram-negative, non-sporulating, and community will help in identification and functional motile bacteria with single polar flagellum [1]. The characterization of novel ligninolytic enzymes in the genus belongs to Burkholderiaceae family and class near future [12–14]. With the increase in genomic data β-proteobacteria. The Pandoraea genus was earlier misi - of bacteria and fungi, the biomass degrading potential dentified and grouped together with Burkholderia or across different taxa can be identified that will further Ralstonia [1] This genus contains five species (Pandoraea enhance our understanding related to lignin degra- pnomenusa, Pandoraea sputorum, Pandoraea norimber- dation [12, 13]. The lignin degrading bacterial isolate gensis, Pandoraea apista, and Pandoraea pulmonicola) belongs to actinobacteria, alpha proteobacteria, beta and four genomospecies of thiosulfate-oxidizing (Pan- proteobacteria, gamma proteobacteria, delta proteobac- doraea thiooxydans) and oxalate-oxidizing species as teria, bacteroides, and archaea [7]. The novel bacterial Pandoraea vervacti, Pandoraea faecigallinarum, and enzymes responsible for lignin degradation and their Pandoraea oxalativorans. Pandoraea is a taxonomically mechanism of action have also been described [15]. In distinct genus having close similarity with Burkholderia recent years, LC–MS-based proteomics studies have and Ralstonia. Pandoraea has been isolated from various been widely performed. Quantitative LC–MS-based environments such as soil, landfill site, sediments, clinical proteomics such as label free and ITRAQ labeling-based samples (only P. apista, P. pnomenusa, and P. sputorum quantification methods are generally used to identify isolated until date), and water [1–4]. The Burkholderia the novel enzymes and their level of expression in a par- and Ralstonia are very much explored and established ticular process [16–18]. genera with their promising potential environmental We have earlier sequenced the genome of Pando- and industrial applications. Pandoraea is a relatively new raea sp. ISTKB and the sequence has been submitted to genus, so there are very few findings available about their NCBI with accession number MAOS00000000.1 which biotechnological potential. The species from this genus is openly available [19]. In the present study, we describe have been documented for utilization of polychlorinated the comprehensive analysis of the Pandoraea sp. ISTKB biphenyl, dichloromethane, dyes, lignin, oxalate, thiosul- genome. The bioinformatics analysis was performed fate, and quorum sensing [3–6]. At present, the genomic to identify a large set of genes and pathways putatively insights for Pandoraea are limiting and such studies responsible for lignin degradation and PHA production. would eventually help to widen the biotechnological pro- The important gene clusters responsible for lignin degra - spective of this genus. dation and PHA production were also highlighted. This Lignin is a complex aromatic heteropolymer and it strain has already been shown to utilize monoaromatic is the most abundant aromatic polymer available on lignin derivatives with great ease compared to polymeric earth. In nature, lignin is degraded mainly by bacte- kraft lignin for PHA production [20]. Therefore, the pro - ria and fungi. Fungi have been studied extensively for teomic study of Pandoraea sp. ISTKB was performed lignin degradation and only a few bacterial species have for identification of set of a proteins expressed during its been reported for lignin degradation [7, 8]. Compared growth on monoaromatic vanillic acid (VA) and aromatic to fungi, bacteria offer advantage as its genome size is polymer lignin, i.e., kraft lignin (KL) that can be overex- small, genetic manipulations, and large-scale recom- pressed for enhanced KL utilization. VA was selected, binant expression of important enzymes can be per- because most of the lignin linkages proceed through gen- formed with a greater ease. Therefore, the focus again eration of vanillin or VA as nodal point during the course shifted to bacteria for the identification of novel strains of degradation [21]. Proteomic studies provide insight and enzymes for lignin degradation. The discovery of into the protein profile and also complement the genom - novel ligninolytic microbes, enzymes, and their bio- ics analysis. Genomic and proteomic analyses would chemical characterization will help in deconstruction of enable us to understand the novel enzymes and pathways biomass for their application in biofuel and bioproduct responsible for lignin degradation and biovalorization. Kumar et al. Biotechnol Biofuels (2018) 11:154 Page 3 of 23 oxidoreductase activity. Abundance of ion binding and Results small molecule-binding proteins indicates their role in Salient features of Pandoraea sp. ISTKB genome transcriptional regulation and transportation of mol- The Pandoraea sp. ISTKB was previously character- ecules across cell membrane. Representation of trans- ized for lignin degradation and successfully applied for ferase and hydrolase in good proportion indicates their pretreatment of sugarcane bagasse and polyhydroxyal- assistance during metabolism of organic compounds. kanoate (PHA) production [6, 20, 22]. The genome size of Pandoraea sp. ISTKB is 6.37 Mb with 65× coverage hav- Metabolism, respiratory mechanism, transporters, ing GC content of 62.05%, 5356 predicted protein-coding and transcriptional factors in Pandoraea sp. ISTKB genome genes [prokaryotic genome annotation pipeline (PGAP) Pandoraea sp. ISTKB can metabolize diverse substrates; and Pfam annotation] and the other general genome which includes five and six carbon sugar molecules. This features has also been reported earlier [19]. Among the bacterium can utilize monosaccharide (galactose, man- predicted proteins, 1740 proteins were categorized as nose, and fructose), disaccharides (sucrose), polysaccha- hypothetical proteins. Out of total predicted proteins, rides (starch), glucuronate, ascorbate, aldarate, amino 456 proteins were identified having signal sequences. Cir - sugar and nucleotide sugar, propionate, and butanoate cular map displaying genomic features provides a space metabolism. This strain can also utilize pentoses (xylose, efficient and clear representation of gene arrangement on xylulose), C5-branched dibasic acid, and other glyoxy- the genome, as shown in Fig. 1. The annotation of impor - late, dicarboxylate and pyruvate as predicted by KEGG. tant genes and pathways related to lignin or aromatic The growth of this strain was observed to be poor on compound degradation has also been represented in the glucose and the KEGG pathway analysis of carbohydrate circular plot. KEGG–KAAS pathway analysis of protein- metabolism also supported this observation. Analysis of coding genes from Pandoraea sp. ISTKB categorized respiratory mechanism showed various terminal elec- 2590 genes in 22 different functional KAAS pathway tron acceptor, electron donors, and also other relevant (Additional file  1: Table  S1). The KEGG predicted 148 genes related to respiration. The abundance of formate proteins responsible for degradation and metabolism of dehydrogenase, quinone oxidoreductase family proteins, aromatic and xenobiotic compound. The annotation and oxidoreductases, ubiquinol oxidase, soluble cytochrome, analysis by RAST predicted 5658 coding genes and 48% and other related electron carriers highlights their impor- of coding genes have been classified into 26 subsystems tance and assistance in metabolism of various recalci- features. The percent contribution of genes present in trant compounds (Additional file  1: Figure S1). There different functional groups in subsystem features is rep - were 346 transcriptional factors identified in the genome, resented in Fig.  2. The subsystem features count showed and among these regulators, LysR family was found to be dominance of general process related to carbohydrate, dominant. Transcriptional regulator families related to amino acids, cell wall components, prosthetics, cofactors, metabolism of aromatic compound such as GntR, MarR, proteins, and lipid metabolism. After normal cellular IclR, XRE, aromatic hydrocarbon utilization, anaerobic processes, the subsystem feature count is dominated by benzoate metabolism, and organic hydroperoxide regu- membrane transport, aromatic compound metabolism, lators are also present in this strain (Additional file  1: respiration stress response regulation, and cell signaling. Figure S2). There are 587 transporters identified in the Gene ontology (GO) analysis was performed to gain genome, and among these, there were 279 ABC family functional information about predicted proteins in the transporters present. This family represents almost half genome. The analysis provided information about dis - of the total transporters present in the genome and was tribution of genes among various metabolic processes, found to be dominant followed by two-component sys- cellular functions, and molecular components in the tem and MFS transporters (Additional file 1: Figure S3). genome of Pandoraea sp. ISTKB (Fig.  3). In the biologi- cal processes, the organic substance metabolic process Metabolism of aromatic compounds was found to be the dominant process. Molecular func- The annotation of Pandoraea sp. ISTKB genes and their tions analysis revealed the major distribution of proteins classification into pathways involved in lignin or aro - into three important functions, i.e., organic cyclic com- matic compounds degradation have been identified by pound binding, heterocyclic compound binding, and (See figure on next page.) Fig. 1 Circos plot of genes compared with the genome for Pandoraea sp. ISTKB. Circles from outside to inside represent; a scaffold arrangement, b gene position on the scaffolds, c GC skew, and d GC content. Syntenic representation of genes associated with the pathways and Pandoraea sp. ISTKB. Different genes associated with the selected pathways with different colors and shapes Kumar et al. Biotechnol Biofuels (2018) 11:154 Page 4 of 23 Kumar et al. Biotechnol Biofuels (2018) 11:154 Page 5 of 23 Fig. 2 Classification of proteins in subsystem features and their abundance in different functional groups shown in Pandoraea sp. ISTKB KEGG pathway analysis, blast search against ‘nr’ data- thioesterases, transferases, and hydrolases has also been base, and subsystem feature of RAST. There were 42 observed. dioxygenase, 25 monooxygenase, 17 peroxidase (includ- The pathway analysis revealed genes responsible for ing one DyP-type peroxidase), and 2 laccases discovered lignin degradation and diverse aromatic compound in genome (Additional file  1: Figure S4; Tables S2, S3, and metabolism (Fig.  4). Genes responsible for funneling of S4). The presence of various oxidoreductase [grouped lignin or aromatic components’ degradation through into FAD, NAD(P)H, SDR, GMC, YggW, quinone, pyri- peripheral degradation pathways have been observed. dine nucleotide–disulfide, flavin, Fe–S, and unclassified Genes related to pathways for degradation of vanillin, oxidoreductases), reductases, dedydrogenases, esterases, ferulate, biphenyl, phenylpropanoic acid, benzoyl-CoA mediated, phenylacetate, and phenol were observed and Kumar et al. Biotechnol Biofuels (2018) 11:154 Page 6 of 23 Fig. 3 GO analysis of Pandoraea sp. ISTKB genome and classification of genes into biological processes, cellular components, and molecular functions their abundance is depicted in Fig. 4 and Additional file  1: N-heterocyclic aromatic compound, and meta cleavage Table  S5. Subsystem feature analysis identified genes as pathways were also identified. ‘lignin degradation fragments’ responsible for lignin metabolism and this is discussed as cluster later section. Identification of stress response genes, secondary The KEGG analysis indicates that this strain can utilize metabolites, and genomic islands various xenobiotic compounds such as benzoate deriva- Lignin or aromatic compound degradation requires tives (amino, ethyl, p-hydroxy, and fluoro), BTX, salicy - concerted action of various oxidoreductases. The degra - late esters, quinate, pesticides, PAHs, synthetic aromatic dation process generates free radicals and reactive inter- monomer, furfural, and steroids. The degradation of mediates and their removal or transformation into stable lignin and xenobiotic aromatic compounds results into and less toxic component is essential for cell survival. generation of some restricted common central inter- Genome analysis identified various proteins related to mediates (catechol, protocatechuate, and gentisate) that stress response and detoxification mechanisms (Addi - are further metabolized by beta-ketoadipate and aro- tional file  1: Figure S5 and Table  S7). The presence of matic ring cleaving pathways. The genes responsible for superoxide dismutase, catalases, glutathione, thiore- degradation of central intermediates were identified in doxin, peroxiredoxins, glyoxylases, rubrerythrin, glutar- abundance (Fig.  4 and Additional file  1: Table  S6). The edoxins, aldo/keto reductase, and alkyl hydroperoxidase genes observed in central intermediate pathways can highlights this strain’s arsenal against oxidative stress, metabolize common aromatic intermediates through protection from reactive species and detoxification of both ortho and meta cleavage pathways [23]. The genes toxic components during aromatic metabolism [24, 25]. responsible for metabolism of central intermediates such There are nine gene clusters identified in the genome as catechol, protocatechuate, salicylate, homogentisate, of Pandoraea sp. ISTKB that has been represented with their contigs and position marked in Additional file  1: Kumar et al. Biotechnol Biofuels (2018) 11:154 Page 7 of 23 Fig. 4 Predicted lignin and aromatic compounds degradation genes and their number responsible for funneling into peripheral pathways and central intermediate metabolism Table S8. Secondary metabolite cluster analysis identified file  2: Table  S9). The other proteins present were related some novel metabolites that are specific to Pandoraea to DNA replication, cell division and partitioning, trans- sp. ISTKB. These clusters included genes responsible position, recombination, phage-mediated integration, for the synthesis of terpenes, nonribosomal peptides, repair, and DNA-binding response regulators. There are thailanstatin/mangotoxin, arylpropane, 2 homoserine various proteins identified in the island that plays impor - lactone, phosphonate–terpene, bacteriocin, and lasso- tant role in stress response, detoxification mechanism peptide. The cluster 9 (lassopeptide), cluster 2 (Nrps), and their regulation, electron carrier, antibiotic resist- and cluster 4 (arylpropane) were found to be unique to ance, metal resistance, and transportation of molecules this strain, since cluster 9 did not show any match with across cell membrane. The proteins related to phosphate Pandoraea genus or Burkholderia genus. However, clus- and sulfur metabolism and few for aromatic compound ters 2 and 4 showed only one match with Burkholderia. degradation were also observed. Clusters 1 (terpenes), 3 (thailanstatin/mangotoxin), and 5 (homoserine lactone) are distributed among Pandoraea Identification of gene clusters for the degradation lignin and Burkholderia genus. Moreover, clusters 6 (phospho- derivatives and PHA production nate–terpene), 7 (bacteriocin), and 8 (homoserine lac- The two gene clusters responsible for degradation of tone) are highly represented in Pandoraea genus. The lignin derivatives have been identified and the order of novel clusters such as cluster 9 (lassopeptide), 2 (Nrps), gene arrangement on the cluster is shown in Fig.  5a, b. and 4 (arylpropane) can prove to be significant as these The first cluster ‘lignin degradation fragment’ predicted are unique to this strain. by RAST contains genes responsible for protocatechuate There were 12 genomic islands identified in the meta cleavage-mediated degradation of lignin deriva- genome that are mainly dominated by the hypotheti- tives. The presence of LysR family transcriptional regu - cal proteins (Additional file  1: Figure S6 and Additional lator for aromatics can be observed in the cluster. ABC Kumar et al. Biotechnol Biofuels (2018) 11:154 Page 8 of 23 Fig. 5 Gene clusters with contig number 40.1 and 13.1 identified in Pandoraea genome responsible for lignin degradation represented as a and b. The size of DNA fragment selected for cluster analysis is between 12 and 17 Kb transporters and MFS transporter were also present in this cluster. The β-ketothiolase was present in multiple this cluster that might be regulating the movement of copies in the genome. This cluster is dominated by stress aromatic compounds across the cell. The benzoyl for - responsive proteins primarily related to heavy metal or mate decarboxylase present in the cluster is known for multidrug efflux system. The third cluster contains only the degradation of benzene, xylene, and toluene. The PHA synthetase and presence of genes predominantly second cluster contains genes mainly responsible for the related to oxidative stress as thiol-disulfide interchange degradation of vanillic acid. The presence of ABC trans - protein, protein disulfide reductase, thioredoxin, two- porters for regulating movement of molecules can also component system response regulator protein, sensory be observed in this cluster. This cluster also contains glu - proteins, secretory proteins, and ABC-type multidrug tathione peroxidase, dehydrogenases, and glyoxylase that permeases was present around polymerase in the cluster. play important role in protection from oxidative damage by detoxifying reactive intermediates such as methylgly- Proteomics analysis on kraft lignin and vanillic acid oxal and other aldehydes formed during metabolism of Proteomic analysis was performed to identify the genes aromatic compounds [25]. expressed on monoaromatic compound vanillic acid and PHA is carbon and energy reserve accumulated by polyaromatic compound kraft lignin. The identification microbes under nutrient imbalance condition [26]. We of important proteins responsible for polymeric lignin have earlier characterized PHA production by strain degradation and their overexpression will provide oppor- ISTKB while growing on lignin and its derivatives (as sole tunity for lignin valorization. There were total 2484 pro - carbon source) and the genes responsible for PHA syn- teins detected during LC–MS analysis covering almost thesis have been identified in the genome [20]. Here, the 44.61% of the total protein-coding genes present in the arrangement of PHA biosynthetic genes on cluster was genome. There were 2318 proteins common in both KL analyzed in detail (Fig. 6a–c). The clusters were identified and VA and 166 proteins were found to be expressed spanning PHA synthase or polymerase gene that is anno- either on KL or on VA. Among 166 expressed proteins, tated in the genome. The first cluster revealed the pres - 74 were expressed on VA and 78 proteins on KL, as ence of complete set of genes (acetoacetyl-CoA reductase, shown in Fig.  7a, b. GO analysis was performed on the β-ketothiolase, PHA polymerase, and regulatory protein) protein expressed on KL and VA to obtain the overview responsible for short-chain PHA production. In case of of functional information about the proteins involved in second cluster, PHA polymerase was followed by acetoa- various biological processes, cellular components, and cetyl-CoA reductase but β-ketothiolase was missing from molecular functions. Kumar et al. Biotechnol Biofuels (2018) 11:154 Page 9 of 23 Fig. 6 Gene clusters with contig numbers 23.1, 34.1, and 48.1 identified in Pandoraea genome responsible for PHA production represented as a–c. The size of DNA fragment selected for cluster analysis is between 12 and 17 Kb The GO analysis of genomics was supported by prot - Expressed proteins involved in lignin or aromatic eomics (especially biological processes and molecular compound degradation functions) on KL and VA (Fig.  8). The molecular func - Proteomic profile of Pandoraea sp. ISTKB revealed the tions category indicates an abundance of protein in cata- presence of relevant proteins expressed only on KL or lytic activity, heterocyclic compound binding, organic VA (Table  1) and KL–VA, as represented in Tables  2, 3, compound binding, and transcription factor activity on and 4. There are 17, 29, and 394 uncharacterized pro - KL and absent on VA. Single organism process was found teins observed in the KL, VA, and KL–VA, respectively. to be dominant in KL and VA (after normal cellular and The various functionally active oxidoreductases, meth - metabolic processes) indicates this strain specific pro - yltransferases, hydrolases, isomerases, dehydrogenases, cess. The proteins involved in localization process on VA reductases, transferases, esterases, transporters, tran- were almost double compared to KL. The membrane pro - scriptional factors, stress response, and detoxification- tein was present in KL and VA, but their representation related proteins were observed that could play important on VA was found to be more than double as compared to role in degradation of lignin or aromatic compounds. KL and the transporters were also expressed more in VA. (See figure on next page.) Fig. 7 a Venn diagram showing total number of proteins expressed on kraft lignin and vanillic acid and their distribution among KL and VA. b Heat map showing differential expression of relevant proteins on kraft lignin–vanillic acid that are responsible for lignin degradation Kumar et al. Biotechnol Biofuels (2018) 11:154 Page 10 of 23 Kumar et al. Biotechnol Biofuels (2018) 11:154 Page 11 of 23 Fig. 8 GO analysis of protein expressed by Pandoraea sp. ISTKB while growing on KL and VA. The expressed proteins were classified into biological processes, cellular components, and molecular functions Kumar et al. Biotechnol Biofuels (2018) 11:154 Page 12 of 23 Table 1 Identification of relevant proteins expressed only on kraft lignin (KL) or vanillic acid (VL) that can assist in lignin degradation Uniprot entry Gene locus tag Protein names LFQ Razor + unique Sequence Mol. weight Intensity intensity KL peptides KL coverage (%) (kDa) Relevant protein expressed only on kraft lignin (KL) A0A1E3LHD6 A9762_20370 Tryptophan 2,3-dioxygenase 22.9781 2 12.3 36.655 0.00043 A0A1E3LB56 A9762_07750 Benzoyl-CoA oxygenase subunit B 28.4307 15 41.7 54.265 2.06E−87 A0A1E3LET3 A9762_23815 Acriflavine resistance protein 22.5124 1 1.2 112.36 0.00162 A0A1E3LL12 A9762_14780 Glycine betaine ABC transporter 23.8554 2 6.2 36.204 0.00036 substrate-binding protein A0A1E3LI04 A9762_22630 Enoyl-CoA hydratase 23.5827 2 13.3 28.399 1.38E−14 A0A1E3LPU3 A9762_13345 Pyruvate ferredoxin oxidoreductase 17.3225 3 4 129.05 0.00016 A0A1E3LLU4 A9762_13050 Carboxyvinyl-carboxyphosphonate 24.4057 2 14.3 31.557 0.00039 phosphorylmutase A0A1E3LBB9 A9762_07755 Benzoyl-CoA oxygenase/reductase, 23.9233 2 5 45.826 5.25E−07 BoxA protein A0A1E3LGI4 A9762_03990 SAM-dependent methyltransferase 24.6086 2 9.6 31.525 1.73E−06 A0A1E3LDW7 A9762_25245 (2Fe–2S)-binding protein 24.4339 2 24.5 20.242 2.06E−06 A0A1E3LNU5 A9762_10215 LysR family transcriptional regulator 23.5144 2 8.4 33.65 4.15E−07 A0A1E3LEP7 A9762_23880 Phenylacetic acid degradation protein 24.5346 3 12.4 39.494 4.34E−14 A0A1E3LJ38 A9762_17050 ABC transporter 26.2152 5 18.3 32.972 3.46E−34 A0A1E3LB77 A9762_07880 ABC transporter ATP-binding protein 24.5787 2 9.7 25.723 2.69E−12 A0A1E3LF42 A9762_23860 1,2-Phenylacetyl-CoA epoxidase subu- 25.5084 4 14 37.739 4.64E−20 nit A (monooxygenase) A0A1E3LGK2 A9762_23865 1,2-Phenylacetyl-CoA epoxidase subu- 24.5067 2 20.4 11.224 6.77E−06 nit B (monooxygenase) A0A1E3LHG4 A9762_23220 Formyl-CoA:oxalate CoA transferase 26.7341 5 17.8 45.737 4.76E−34 A0A1E3LNE1 A9762_10935 Salicylate hydroxylase 22.5412 1 3.1 41.287 0.00183 A0A1E3LF93 A9762_23590 Ligand-gated channel protein 24.4315 2 3.4 81.344 8.95E−05 A0A1E3LHJ6 A9762_19845 NADPH:quinone reductase 23.3346 1 3.1 31.317 0.00029 A0A1E3LIQ8 A9762_17970 Glycolate oxidase subunit GlcE 24.8966 2 7.3 40.542 3.71E−10 A0A1E3LEZ8 A9762_23215 2-Hydroxyhepta-2,4-diene-1,7-dioate 24.1273 2 14.8 27.8 1.39E−06 isomerase Relevant protein expressed only on vanillic acid ( VA) A0A1E3LRS2 A9762_00545 Alkene reductase 26.4047 7 29.1 39.612 3.91E−37 A0A1E3LLI9 A9762_02605 Alpha/beta hydrolase 25.8742 4 23.2 30.983 3.92E−11 A0A1E3LLX9 A9762_03340 Tol-pal system-associated acyl-CoA 24.2249 2 14.4 17.548 2.38E−05 thioesterase A0A1E3LDT8 A9762_25265 Acetyltransferase 24.2249 2 14.4 17.548 2.38E−05 A0A1E3LPL0 A9762_01420 Glutathione S-transferase 24.4839 2 15.3 24.629 2.35E−07 A0A1E3LCR5 A9762_26030 Aminomethyltransferase 25.197 2 11 34.276 8.63E−05 A0A1E3LPI9 A9762_13065 Methyltransferase 22.991 2 7.7 29.85 1.53E−06 A0A1E3LEN5 A9762_06460 Rieske (2Fe–2S) protein 25.0064 1 6.5 43.065 1.25E−08 A0A1E3LHR2 A9762_19260 Glycine/betaine ABC transporter 24.0824 1 4.9 25.659 0.0001153 permease Important proteins expressed either on kraft lignin benzoyl-CoA oxygenase, enoyl-CoA hydratase, trypto- or on vanillic acid phan 2,3-dioxygenase, and salicylate hydroxylase were The analysis of expression profile on KL revealed the also active on KL. Proteins for methyl group transfer presence of 1,2-phenylacetyl-CoA epoxidase (monooxy- and decarboxylation such as SAM-dependent methyl- genase), phenylacetic acid degradation protein, and transferase, pyruvate ferredoxin oxidoreductase, and 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase enzymes (2Fe–2S)-binding protein were also observed. Genera- for the degradation of phenylacetate. Proteins such as tion of reactive intermediates and their detoxification Kumar et al. Biotechnol Biofuels (2018) 11:154 Page 13 of 23 by oxidative stress-resistance protein glycolate oxidase The expression of antioxidant and stress response pro - and NADPH:quinone reductase was present. Glycine teins glutathione peroxidase, glutathione-disulfide reduc - betaine ABC transporter substrate-binding protein and tase, catalase, glyoxylase, thioredoxin, peroxiredoxin, formyl-CoA:oxalate CoA-transferase (FCOCT) proteins alkyl hydroperoxide reductase, aldo/keto reductase, and for osmoprotection and acid response regulator were glutathione S-transferases was upregulated in case of present to maintain the smooth functioning of intracellu- KL. Superoxide dismutase was downregulated in case of lar environment. There were six LysR family, two unclas - KL and catalases were downregulated on VA. The pro - sified and one each of GntR family, AsnC family, Cd(II)/ teins formyl-coA transferase, formate dehydrogenase Pb(II)-responsive, Crp/Fnr family, MarR, and MerR tran- for oxalate, and formate metabolism were also found to scriptional regulator found on KL. The VA was mainly be upregulated on KL. Various other dehydrogenases, dominated by transporters and stress response proteins reductases, and transferases such as hydroxypyruvate [glutathione S-transferase, Rieske (2Fe–2S) protein, thi- reductase, NAD dehydrogenase, alcohol dehydrogenase, oesterase, glycine betaine permease, and alkene reduc- aldehyde dehydrogenase, ferredoxin reductase, ferre- tase]. One methyltransferases, aminomethyltransferase, doxin, acyl-CoA dehydrogenase, acetyltransferases, and and LysR family transcriptional regulator were also enoyl-CoA hydratase, were upregulated on KL. observed. The expression of vanillate O-demethylase oxidore - ductase, chloroperoxidase, hydroglutathione hydro- Proteins differentially expressed on kraft lignin and vanillic lase, protocatechuate 3,4-dioxygenase, protocatechuate acid 4,5-dioxygenase, 2OG-Fe(II) oxygenase, antibiotic There were 1979 proteins obtained on KL–VA after nor - synthesis monooxygenase, 2-hydroxyl acid oxidase, malization, and among these, 1110 proteins upregulated cytochrome c oxidase, NADH quinone oxidoreductase, and 869 downregulated on kraft lignin. There are 164 glutathione peroxidase, and other oxidoreductases was transporters detected out of which 127 are ABC, 5 RND, upregulated in case of VA. The expression of protocate - and 4 MFS. There are 163 transcription factors identified chuate 4,5-dioxygenase was more than double compared comparising 34 LysR family, 21 GntR family, 17 tetR fam- to protocatechuate 3,4-dioxygenase on VA. Compared ily, 12 each MarR, and IcIR family. We are discussing here to KL, the expression of oxidases enzymes was very less important proteins that can perform lignin degradation on VA. The expression of laccase, FAD-dependent oxi - and transformation. Some of the differentially expressed doreductase, phytanoyl-CoA dioxygenase, YggW fam- proteins that may involve in prospective lignin degrada- ily oxidoreductase, ubiquinol oxidase, one glutathione tion are shown in Fig.  7b. The presence of various oxi - S-transferase, and NADH quinone oxidoreductase, was doreductases, dehydrogenase, reductases, transferases, almost same in both KL and VA. There were several PHA biosynthetic proteins, and several stress response NADH:quinone oxidoreductases observed in KL–VA and detoxification proteins was detected in the expres - and some are upregulated in KL other in VA. Short- sion profile. The phenylacetic acid degradation protein chain dehydrogenase, acyl-CoA dehydrogenase, alcohol and ‘CoA’-mediated degradation of phenylacetate, phe- dehydrogenase, acyltransferase, alkene reductase, FMN nylpropionate, and benzoate proteins were found to be reductase, NADH:quinone reductase, and acetyl-CoA upregulated on kraft lignin. The DyP-type peroxidase, acetyl transferase was found to be upregulated on VA. peroxidase-like proteins, and various accessory enzymes The clusters predicted for lignin degradation and PHA such as aldehyde oxidase, glycolate oxidase, cytochrome production were found to functionally active and the C oxidase, oxidase, NADH:quinone oxidoreductase, genes for degradation of lignin derivatives as well as all FAD-linked oxidase, and GMC family oxidoreductase the three PHA polymerase were present in the expression were found to be upregulated on KL. GMC family oxi- profile (Additional file  3: Table  S10, also contains other doreductase or aryl alcohol oxidase is also known as dehydrogenase, reductases, transferases, esterases, thi- auxiliary enzymes in case of fungi and their role is estab- oesterases, hydrolases not discussed here but expressed lished in lignin degradation [27]. The homogentisate on KL–VA). The PHA production was induced on both 1,2-dioxygenase, quercetin 2,3-dioxygenase, 4-hydroxy- the substrate, i.e., kraft lignin and vanillic acid. The acti - phenylpyruvate dioxygenase, dioxygenase, and nitropro- vation of PHA biosynthetic genes on lignin was also pane dioxygenase were found to be upregulated on KL. recently reported [17]. There were six SAM-dependent methyltransferase and one methyltransferase identified on KL–VA. Four SAM- Discussion dependent methyl transferase and methyltransferase was The detail of genomic and proteomic studies of lignin upregulated on KL and two SAM-dependent methyl- degrading bacterium is limited, so we tried to provide the transferase was upregulated on VA. comprehensive genomic and proteomic analysis of lignin Kumar et al. Biotechnol Biofuels (2018) 11:154 Page 14 of 23 Table 2 Differentially expressed proteins for phenylacetic acid, benzene degradation, and various oxidoreductases on kraft lignin Uniprot IDs Locus tag Name Log2 fold Unique Sequence Mol. weight Intensity change peptides coverage (%) (kDa) Phenylacetic acid degradation protein A0A1E3LF26 A9762_23720 Phenylacetic acid degradation protein PaaD 0.529261 3 27.3 15.022 8.65E−26 A0A1E3LF48 A9762_23735 Phenylacetic acid degradation protein PaaN 0.244067 18 58.3 60.008 1.24E−140 A0A1E3LFB3 A9762_23725 2-(1,2-Epoxy-1,2-dihydrophenyl)acetyl-CoA 0.724358 9 56.1 27.854 1.32E−76 isomerase A0A1E3LFJ2 A9762_22495 Phenylacetic acid degradation protein 0.790541 4 36.3 15.888 3.07E−15 A0A1E3LHE3 A9762_23715 Phenylacetate–coenzyme A 0.514503 14 57.5 47.386 1.43E−109 A0A1E3LQE8 A9762_10500 Phenylacetic acid degradation protein 1.426558 5 44.4 14.521 5.16E−22 Peroxidases A0A1E3LDX8 A9762_24250 Dyp-type peroxidase 1.43239 15 72 40.756 1.29E−104 A0A1E3LHN8 A9762_20355 Peroxidase − 1.69967 18 90.6 23.753 0 A0A1E3LPA6 A9762_00985 Chloroperoxidase − 1.927944 16 84.7 30.075 8.73E−175 A0A1E3LF97 A9762_25345 Peroxidase-like protein 1.353771 7 59 18.981 4.85E−31 A0A1E3LNE3 A9762_13620 Laccase − 0.13346 10 57.5 28.644 5.45E−43 Oxidases A0A1E3LC86 A9762_26490 Glycolate oxidase subunit GlcE 1.96696 9 38.1 38.774 4.18E−40 A0A1E3LDU3 A9762_25250 Aldehyde oxidase 1.94888 25 43.2 106.43 3.40E−153 A0A1E3LG04 A9762_25240 Cytochrome C oxidase Cbb3 1.88749 12 44.8 44.919 5.64E−68 A0A1E3LL61 A9762_17965 Glycolate oxidase iron–sulfur subunit 1.88269 5 14.3 46.4 1.56E−20 A0A1E3LCC6 A9762_07195 Oxidase 1.12594 23 67.7 43.498 4.04E−279 A0A1E3LQ45 A9762_00290 FAD-linked oxidase 0.7576 46 47.6 148.68 8.22E−260 A0A1E3LDS7 A9762_25555 Ubiquinol oxidase subunit 2 − 0.72481 3 21.5 35.767 2.50E−21 A0A1E3LLY2 A9762_16250 l -Aspartate oxidase − 1.51593 5 14.2 58.534 1.25E−24 A0A1E3LRG9 A9762_02095 Cytochrome c oxidase assembly protein − 1.76256 6 49.8 22.192 2.52E−27 A0A1E3LCR8 A9762_26505 2-Hydroxy-acid oxidase − 1.92172 13 43.3 51.242 1.38E−99 Oxidoreductases A0A1E3L9T7 A9762_09290 NADH–quinone oxidoreductase subunit I 1.983 13 54.6 18.63 1.26E−66 A0A1E3LC99 A9762_26255 Oxidoreductase 1.46342 9 62.5 26.21 1.99E−100 A0A1E3LAC9 A9762_09275 NADH oxidoreductase (quinone) subunit F 0.86275 19 70.7 47.093 5.72E−135 A0A1E3LMK8 A9762_03120 NADP oxidoreductase 0.82498 10 55.5 32.458 3.02E−38 A0A1E3LHK5 A9762_23470 FAD-dependent oxidoreductase 0.33833 3 14.7 38.458 4.28E−15 A0A1E3LLW4 A9762_03220 GMC family oxidoreductase 0.24372 23 54.8 64.908 3.74E−163 A0A1E3LFG3 A9762_22500 NADP-dependent oxidoreductase 0.05857 13 63.4 35.64 5.98E−106 A0A1E3LKB2 A9762_03335 Oxidoreductase − 0.24038 18 82.3 31.785 3.07E−157 A0A1E3LGB9 A9762_21450 YggW family oxidoreductase − 0.68269 3 10.3 45.723 1.71E−14 A0A1E3LC87 A9762_26930 Fe–S oxidoreductase − 1.47441 6 49.8 26.119 2.01E−34 A0A1E3LG91 A9762_21265 Vanillate O-demethylase ferredoxin subunit − 1.5017 15 57.9 33.723 1.13E−114 A0A1E3LG83 A9762_21255 Vanillate O-demethylase oxidoreductase 0.298001 15 48.1 50.745 1.80E−76 A0A1E3LFZ4 A9762_25310 FAD-dependent oxidoreductase − 1.67016 5 17.9 54.42 2.53E−15 A0A1E3LA58 A9762_09270 NADH-quinone oxidoreductase subunit E − 1.69506 9 80.1 18.129 9.41E−90 A0A1E3LFR2 A9762_22175 Oxidoreductase − 1.8627 9 61.8 30.679 4.89E−178 A0A1E3LCB2 A9762_09255 NADH-quinone oxidoreductase subunit B − 1.96385 10 72.3 17.519 1.56E−64 A0A1E3LEJ8 A9762_05735 Oxidoreductase − 1.97509 18 85.7 26.372 6.17E−220 A0A1E3LKX1 A9762_15740 Quinone oxidoreductase − 1.99406 18 90.7 34.556 1.06E−219 Oxygenases A0A1E3LHN5 A9762_23090 2-Nitropropane dioxygenase 1.84558 3 15.1 38.789 7.50E−15 A0A1E3LFU3 A9762_22350 Quercetin 2,3-dioxygenase 1.82796 7 51.5 26.31 4.21E−24 A0A1E3LFX1 A9762_21815 Homogentisate 1,2-dioxygenase 1.51818 13 56.9 48.611 5.10E−81 Kumar et al. Biotechnol Biofuels (2018) 11:154 Page 15 of 23 Table 2 (continued) Uniprot IDs Locus tag Name Log2 fold Unique Sequence Mol. weight Intensity change peptides coverage (%) (kDa) A0A1E3LPA9 A9762_00970 4-Hydroxyphenylpyruvate dioxygenase 1.43964 2 5.9 40.191 3.14E−09 A0A1E3LFB4 A9762_23095 2-Nitropropane dioxygenase 1.31977 9 45.1 39.332 6.27E−61 A0A1E3LDU6 A9762_24595 Phytanoyl-CoA dioxygenase − 0.60384 6 38.3 27.846 2.72E−52 A0A1E3LF51 A9762_25450 Putative dioxygenase − 0.666263 9 88.7 15.676 1.86E−122 A0A1E3LIM3 A9762_17955 Dioxygenase − 0.91661 8 52 29.958 6.54E−31 A0A1E3LI70 A9762_22255 2-Nitropropane dioxygenase − 1.45193 12 64.4 33.509 1.71E−146 A0A1E3LIR0 A9762_17450 Protocatechuate 3,4-dioxygenase subunit − 1.63442 13 83.4 21.895 2.50E−246 alpha A0A1E3LJ07 A9762_17445 Protocatechuate 3,4-dioxygenase subunit − 1.71052 16 78.4 26.513 2.43E−152 beta A0A1E3LG93 A9762_21285 Protocatechuate 4,5-dioxygenase subunit − 1.83931 6 80.7 13.769 6.11E−47 alpha A0A1E3LG93 A9762_21285 Protocatechuate 4,5-dioxygenase subunit − 1.83931 6 80.7 13.769 6.11E−47 beta A0A1E3LEL8 A9762_04935 Antibiotic biosynthesis monooxygenase − 1.86712 6 81.8 11.026 1.02E−172 A0A1E3LBV9 A9762_07570 2OG-Fe(II) oxygenase − 1.682965 7 50.7 30.695 9.21E−31 A0A1E3LL67 A9762_14910 2OG-Fe(II) oxygenase − 0.037474 8 43 37.152 3.47E−45 Benzoate degradation A0A1E3LBS0 A9762_08405 2-Aminobenzoate–CoA ligase 1.569646 5 15.2 59.58 4.06E−18 A0A1E3LF67 A9762_23480 3-Octaprenyl-4-hydroxybenzoate carboxy- − 1.471879 4 32.4 15.528 1.01E−27 lyase (Fragment) A0A1E3LLJ4 A9762_17745 3-Octaprenyl-4-hydroxybenzoate carboxy- 1.567849 11 32.8 57.345 1.54E−68 lyase A0A1E3LM76 A9762_12465 2-Nonaprenyl-3-methyl-6-methoxy-1,4-ben- − 1.895105 5 47.4 23.511 1.50E−34 zoquinol hydroxylase A0A1E3LDW9 A9762_24905 Carboxymethylenebutenolidase − 1.707803 8 49 27.008 1.57E−119 A0A1E3LDA6 A9762_06440 Carboxymethylenebutenolidase − 1.951469 18 77 31.135 1.41E−118 degrading bacterium Pandoraea sp. ISTKB. The genome VA as compared to KL can be explained that these pro- size of this genus available in NCBI varies between 4.4 teins might be localized near the membrane and actively and 6.5  Mb and this strain’s genome is one of the larg- involved in transportation and metabolism of VA into est genome sequences available until date from Pando- the cell. The absence of proteins in VA for organic cyclic raea genus. The degradation of aromatic compounds by compound binding, heterocyclic compound binding, bacteria is mostly aerobic and is tightly regulated process. iron–sulfur cluster binding, receptor activity, ion bind- Their degradation by oxidoreductases generates reactive ing, cofactor binding, small molecule binding, and their intermediates, so a robust stress response and detoxifi - presence in KL suggests that these are the important cation mechanism is required for survival of microbes. molecular functions’ category proteins that would have The dominance of these subsystem features such as res - facilitated the depolymerization and utilization of poly- piration, aromatic metabolism, and stress response (after mer KL by this strain. normal cellular processes) and their complementation The analysis of expression profile on KL indicates the highlights the ability of Pandoraea sp. ISTKB to survive presence of metacleavage and unusual pathways, i.e., and metabolize lignin or aromatic compound. ‘-CoA’-mediated degradation of lignin derivatives in The GO analysis especially biological process and aerobic microorganisms. The presence of 2-hydroxy - molecular functions indeed supported this strain’s hepta-2,4-diene-1,7-dioate isomerase in the expression robust genomic machinery for the utilization of organic profile of KL possibly indicated 4-hydroxyphenylac - substance, organic cyclic compounds, heterocyclic etate degradation through meta cleavage pathways [28]. compound binding, solute binding, ion binding, and oxi- Benzoyl-CoA oxygenase-mediated degradation of aro- doreductase activity. The abundance of localization pro - matic compound is completely different mechanisms cess proteins, membrane proteins, and transporters in and observed in 4–5% of sequenced bacterial genomes. Kumar et al. Biotechnol Biofuels (2018) 11:154 Page 16 of 23 Table 3 Differentially expressed antioxidant and stress response proteins on kraft lignin Uniprot IDs Locus tag Name Log2 fold Unique Sequence Mol. Intensity change peptides coverage (%) weight (kDa) Glutathione enzymes A0A1E3LF33 A9762_23395 Glutathione ABC transporter substrate-binding 1.80871 29 77.1 57.261 0 protein A0A1E3LKY8 A9762_17040 Glutathione S-transferase 1.18746 8 41.1 24.027 3.57E−36 A0A1E3LF68 A9762_25435 Glutathione S-transferase 0.61286 8 65.2 22.821 1.27E−72 A0A1E3LBR6 A9762_09395 Glutathione S-transferase 0.55477 4 25.7 24.666 5.23E−14 A0A1E3LQD9 A9762_10375 Glutathione S-transferase 0.51263 5 37.8 27.794 1.84E−17 A0A1E3LFJ0 A9762_24585 Glutathione-disulfide reductase 0.35879 22 63.6 48.837 7.37E−222 A0A1E3LI91 A9762_18915 Glutathione S-transferase 0.05437 5 39 25.252 2.31E − 26 A0A1E3LP56 A9762_00695 Glutathione S-transferase − 0.96784 8 53.6 23.768 4.31E−48 A0A1E3LI39 A9762_18265 Glutathione S-transferase − 1.44982 18 82.3 23.728 3.01E−285 A0A1E3LAC5 A9762_09365 Glutathione S-transferase − 1.70035 15 72.6 26.078 1.22E−149 A0A1E3LPY3 A9762_02245 Glutathione synthetase − 1.79520 21 82.4 34.566 2.19E−195 A0A1E3LL68 A9762_15125 Glutathione S-transferase − 1.85572 4 21 23.996 5.81E−18 A0A1E3LI75 A9762_04000 Lactoylglutathione lyase − 1.97244 4 64.5 14.032 1.22E−30 A0A1E3LBC2 A9762_08325 Hydroxyacylglutathione hydrolase − 1.98082 10 57.5 29.087 5.85E−75 A0A1E3LC63 A9762_26475 Glutathione peroxidase 1.59171 9 82.6 18.506 1.18E−57 A0A1E3LN82 A9762_11030 Glutathione peroxidase − 1.47148 10 55.2 19.852 3.04E−128 A0A1E3LL32 A9762_17770 S-(Hydroxymethyl)glutathione dehydrogenase − 1.97881 22 83.7 39.609 5.20E−235 A0A1E3LCG8 A9762_26430 S-Formylglutathione hydrolase − 1.5565 9 49.6 31.49 2.83E−45 Catalases A0A1E3LJG2 A9762_17205 Catalase − 1.90503 31 69.7 55.065 0 A0A1E3LHV5 A9762_19890 Catalase 1.96803 20 58.3 54.314 2.70E−159 A0A1E3LL41 A9762_15065 Catalase 1.96803 20 58.3 54.314 2.70E−159 Superoxide dismutase A0A1E3LHJ2 A9762_20590 Superoxide dismutase − 1.97424 2 12.2 22.201 8.04E−07 A0A1E3LJK7 A9762_16420 Superoxide dismutase − 1.6319 16 93.2 21.3 0 Thioredoxin A0A1E3LA95 A9762_09775 Thioredoxin 1.50102 6 68.5 11.693 1.86E−50 A0A1E3LIM9 A9762_21500 Thioredoxin 0.26594 13 64 30.297 2.12E−120 A0A1E3LMC9 A9762_12720 Probable thiol peroxidase − 1.29118 15 95.8 17.552 1.19E−229 A0A1E3LK52 A9762_19935 Thioredoxin reductase − 0.42918 12 71.1 33.796 6.61E−169 Peroxiredoxin A0A1E3LFM2 A9762_22670 Peroxiredoxin 0.06241 4 27.7 19.976 2.59E−09 A0A1E3LG33 A9762_25080 Peroxiredoxin − 0.7565 5 51.9 17.411 3.34E−34 A0A1E3LIX5 A9762_17525 Peroxiredoxin 1.63617 11 84.5 20.829 4.52E−87 A0A1E3LNW8 A9762_00130 Peroxiredoxin − 1.41372 5 35 14.926 1.51E−22 Glyoxylase A0A1E3LJS5 A9762_02855 Glyoxalase 1.90407 4 26.4 24.933 1.26E−10 A0A1E3LML8 A9762_12845 Glyoxalase − 1.55877 4 40.7 15.609 4.05E−12 Glutaredoxin A0A1E3LF15 A9762_23485 Glutaredoxin − 0.65795 4 51.9 11.612 1.33E−69 A0A1E3LQ32 A9762_02205 Glutaredoxin 3 1.02376 8 79.1 9.8904 4.95E−60 Alkylperoxide reductase A0A1E3LAL5 A9762_08705 Alkyl hydroperoxide reductase − 1.92917 10 79.1 16.924 2.59E−121 A0A1E3LDK0 A9762_25350 Alkyl hydroperoxide reductase AhpD 1.76395 5 40.7 22.242 5.04E−30 A0A1E3LCA5 A9762_26215 Alkyl hydroperoxide reductase AhpD − 1.58398 5 49.5 19.7 1.06E−56 A0A1E3LGT9 A9762_04630 Alkyl hydroperoxide reductase AhpD − 0.87073 6 67.7 14.207 2.45E−17 Kumar et al. Biotechnol Biofuels (2018) 11:154 Page 17 of 23 Table 3 (continued) Uniprot IDs Locus tag Name Log2 fold Unique Sequence Mol. Intensity change peptides coverage (%) weight (kDa) A0A1E3LKG5 A9762_16100 Alkyl hydroperoxide reductase AhpD − 1.52586 9 64.9 21.888 2.68E−61 A0A1E3LLQ8 A9762_13730 Alkyl hydroperoxide reductase AhpD − 0.29909 10 77.7 18.588 4.23E−101 A0A1E3LLX0 A9762_13735 Alkyl hydroperoxide reductase − 0.30453 16 85.7 20.001 0 This mechanism helps to overcome the high resonance compounds [15, 36, 37]. Laccases can degrade lignin in stabilization of aromatic ring by forming epoxide. Ben- the presence of mediators and there are several natural zoyl-CoA oxygenase leads to formation of 2,3-epoxide mediators observed during lignin degradation [38, 39]. followed by enoyl-CoA hydratase (also expressed on KL) Two laccase genes were discovered in the genome and and NADP -dependent aldehyde dehydrogenase (upreg- found to be functionally active in this strain. Laccases ulated on KL)-mediated degradation resulting into for- are reported for ether linkage (aryl β-O-4) and β-1 bond mic acid, acetyl-CoA, and succinyl-CoA formation [29]. cleavage on lignin model dimers. The degradation of 1,2-phenylacetyl-CoA epoxidase-mediated degradation phenolic as well as non-phenolic substrate in the pres- of phenylacetic acid occurs via 1,2-epoxide intermedi- ence of mediators by laccases has also been reported [40, ate and this pathway is found functional in only 16% of 41]. Formate dehydrogenase coverts formate into carbon all bacteria genome reported also observed in Escherichia dioxide and these formate radicals induce MnP activ- coli and Pseudomonas putida [30]. The upregulation of ity, as they can use formate as peroxide in the absence Salicylate hydroxylase on lignin was also observed in the of H O [31]. Formyl transferase is reported for oxalate 2 2 3+ case of Pseudomonas A514 strain [17]. degradation and oxalate forms complex with Mn (MnP 2+ 3+ The expression of glycolate oxidase, oxidase, oxidase, oxidizes Mn –Mn ) and the complex acts as diffusible aldehyde oxidase, and GMC family oxidoreductase (aryl redox mediator for the degradation of phenolics in lignin alcohol oxidase) was observed on KL–VA and these acts [31]. The expression of quinone oxidoreductase, acetyl- as an accessory enzyme and the peroxides produced by CoA acetyltransferase, enoyl-CoA hydratase, dehydro- them is utilized by peroxidases for lignin degradation [27, genase (responsible for cleavage of ether linkage), and 31]. Expression of these oxidases has also been reported cytochrome peroxidase was expressed on lignin, but recently in Pseudomonas A514 and Pantoea ananatis other known bacterial lignin degrader was not observed Sd-1 [17, 27]. The detection of NADPH:quinone oxi - in Bacillus ligniniphilus L1 expression profile [33]. The doreductase in Pandoraea strain ISTKB indicates lignin catalase/hydroperoxidase, multicopper oxidase, GMC degradation by Fenton reaction. NADPH:quinone oxi- oxidoreductase, glutathione S-transferase, and quinone doreductase overexpression on lignin and rice straw oxidoreductases were observed in the secretome of P. was also reported recently [17, 27, 32, 33]. Quinone oxi- ananatis Sd-1 on rice straw [27]. In addition to these pro- doreductase system is of special interest in case of lignin teins, various other proteins were also expressed in Pan- degradation as fungi especially brown rot used fenton doraea sp. strain ISTKB that are responsible for lignin chemistry for lignin degradation with the help of quinone degradation. oxidoreductase [9, 31]. The role of NADPH: quinone The presence of demethylases, methyltransferases, and oxidoreductase in degradation and depolymerization of SAM-dependent methyltransferase indicated demethyla- lignin is well established and reported for Phanerochaete tion or rearrangement of methyl group during lignin deg- chrysosporium and Trametes versicolor [34, 35]. radation [42]. Demethylation is an important process in Dyp-type peroxidases are fungal counterparts of per- conversion of lignin-derived aromatic intermediates into oxidase (LiP or MnP) present in bacteria for lignin deg- common central intermediates such as catechol, pro- radation. The peroxidases such as DyP-type peroxidase, tocatechuate, or gallate that further undergo ring cleav- peroxidase, chloroperoxidase, and peroxidase-like pro- age. Demethylation system removes methyl group from tein were detected in Pandoraea sp. ISTKB genome methoxy-substituted lignin-derived aromatic compounds and in proteome. Some DyPs are secreted through such as syringate, vanillate, or guaiacol in the pres- TAT pathway and their encapsulation has been shown ence of cofactors. The demethylases include Rieske type to increase the enzyme’s activity [36]. There are vari - ([2Fe–2S] cluster) and reductase (a flavin and a [2Fe–2S]) ous functions reported recently for bacterial DyPs such redox center. The demethylases or methyltransferases as depolymerization, dimer formation, and degrada- were also reported and functionally validated in Pseu- tion of aryl ether bonds in lignin and lignin containing domonas and Acinetobacter [9, 42, 43]. Several acyl-CoA Kumar et al. Biotechnol Biofuels (2018) 11:154 Page 18 of 23 Table 4 Differentially expressed reductase, dehydrogenase, transferase, and hydratase proteins on kraft lignin Uniprot IDs Locus tag Name Log2 fold Unique Sequence Mol. Intensity change peptides coverage (%) weight (kDa) Reductases A0A1E3LM36 A9762_03695 Aldo/keto reductase − 1.446536 54 95.1 38.448 0 A0A1E3LPJ8 A9762_01385 Aldo/keto reductase − 1.811371 8 43.3 37.797 1.87E−50 A0A1E3LS07 A9762_01040 Aldo/keto reductase 0.040585 20 73.6 30.685 1.63E−183 A0A1E3LG16 A9762_22220 Glyoxylate/hydroxypyruvate reductase 1.99991 14 69.4 33.941 4.47E−124 A0A1E3LQJ8 A9762_00050 Bifunctional glyoxylate/hydroxypyru- − 0.601011 20 82.2 34.525 1.34E−204 vate reductase B A0A1E3LI17 A9762_19295 Alkene reductase − 0.075801 28 92 40.61 0 A0A1E3LIA9 A9762_18295 2-Alkenal reductase 0.117504 12 46.4 42.805 2.10E−74 A0A1E3LDX7 A9762_24675 Ferredoxin–NADP(+) reductase 1.250238 18 77 29.272 3.54E−106 A0A1E3LFT3 A9762_21855 NADPH-dependent FMN reductase − 0.973988 9 69.1 19.818 1.98E−77 A0A1E3LAB2 A9762_08440 NADPH:quinone reductase − 1.850827 14 71.9 36.075 3.86E−109 A0A1E3LQJ8 A9762_00050 Hydroxypyruvate reductase B − 0.601011 20 82.2 34.525 1.34E−204 A0A1E3LLZ7 A9762_13130 Fumarate reductase 1.805886 2 7.4 52.225 7.89E−05 Dehydrogenases A0A1E3LDJ7 A9762_25850 Formate dehydrogenase subunit beta 1.664541 6 23.2 34.213 1.25E−22 A0A1E3LDC4 A9762_25845 Formate dehydrogenase-N subunit 1.414862 16 34.2 90.668 3.91E−102 alpha A0A1E3LDS6 A9762_24610 Formate dehydrogenase 0.761355 2 57.1 8.7799 3.84E−22 A0A1E3LE53 A9762_24625 Formate dehydrogenase 1.257519 9 30 56.957 3.45E−62 A0A1E3LG97; A9762_24620 Formate dehydrogenase subunit alpha 1.020855 21 34 104.98 1.29E−121 A0A1E3LF08 A0A1E3LL63 A9762_15395 NADH dehydrogenase 0.064345 9 60.8 21.897 5.70E−49 A0A1E3LPJ3 A9762_01450 Aldehyde dehydrogenase 1.745055 17 54.5 52.735 1.72E−105 A0A1E3LJ61 A9762_20360 Acyl-CoA dehydrogenase 0.210716 11 46.1 43.33 1.22E−90 A0A1E3LH50 A9762_22885 Alcohol dehydrogenase 0.448181 14 55.4 40.556 1.68E−67 A0A1E3LGE7 A9762_21150 Aldehyde dehydrogenase 0.513856 4 14.4 51.073 1.64E−12 A0A1E3LFY2 A9762_21880 NAD(FAD)-utilizing dehydrogenase 1.806462 3 12.9 42.366 7.90E−09 A0A1E3LF76 A9762_23430 Acyl-CoA dehydrogenase 0.067218 9 31.6 40.901 1.33E−56 A0A1E3LKN0 A9762_15340 Acyl-CoA dehydrogenase − 1.0527852 7 24.4 41.792 1.04E−41 A0A1E3LP12 A9762_00210 Acyl-CoA dehydrogenase − 0.467758 37 72.4 65.029 0 A0A1E3LKM0 A9762_16035 NAD(P)H dehydrogenase (quinone) − 1.786348 11 55.7 22.107 2.74E−162 A0A1E3LKB6 A9762_03215 Alcohol dehydrogenase − 1.58185 16 63.3 44.426 1.36E−99 A0A1E3LJV2 A9762_02775 Putative NADH dehydrogenase − 0.256436 15 86.3 21.594 1.71E−184 A0A1E3LIB8 A9762_18460 Short-chain dehydrogenase − 1.862879 2 13.3 26.395 8.23E−08 A0A1E3LI49 A9762_22120 Short-chain dehydrogenase − 1.335172 6 29.3 24.127 2.78E−23 A0A1E3LI38 A9762_22070 Short-chain dehydrogenase − 1.826239 3 15.2 29.599 1.04E−17 A0A1E3LHQ0 A9762_20005 Dehydrogenase − 0.022626 13 53.6 38.384 2.57E−91 A0A1E3LHP2 A9762_20015 Aldehyde dehydrogenase − 0.39059 15 63.3 51.925 2.00E−131 A0A1E3LHJ3 A9762_19710 Short-chain dehydrogenase − 0.299807 5 32.7 26.91 1.68E−19 A0A1E3LLS1 A9762_17065 Short-chain dehydrogenase − 1.1228889 10 50.4 29.165 2.51E−85 A0A1E3LFZ7 A9762_24160 Acyl-CoA dehydrogenase − 1.977129 8 13.2 90.723 3.27E−24 A0A1E3LFV1 A9762_21935 Alcohol dehydrogenase − 0.223075 15 71.1 36.536 2.10E−159 A0A1E3LF72 A9762_23085 NADPH:quinone dehydrogenase − 1.970038 12 66.5 34.703 2.88E−132 A0A1E3LE86 A9762_05015 Short-chain dehydrogenase − 0.122157 19 90.8 26.28 1.25E−173 A0A1E3LE78 A9762_24110 Short-chain dehydrogenase − 1.0213605 8 59.1 24.582 6.63E−39 A0A1E3LE10 A9762_24765 Aldehyde dehydrogenase − 0.713344 26 69.6 50.552 2.84E−236 A0A1E3LDF9 A9762_25465 Short-chain dehydrogenase − 1.0369092 18 82.1 26.766 0 Kumar et al. Biotechnol Biofuels (2018) 11:154 Page 19 of 23 Table 4 (continued) Uniprot IDs Locus tag Name Log2 fold Unique Sequence Mol. Intensity change peptides coverage (%) weight (kDa) A0A1E3LCV6 A9762_26070 Acyl-CoA dehydrogenase − 0.559374 33 78.2 63.6 0 A0A1E3LCK3 A9762_26745 Aldehyde dehydrogenase − 1.998458 41 82.4 55.098 0 A0A1E3LCD2 A9762_09370 Acyl-CoA dehydrogenase − 0.349182 10 31.9 45.179 6.63E−43 Transferase and hydratase A0A1E3LDE2 A9762_25255 Acetyltransferase 1.1424203 5 42.2 19.294 9.45E−19 A0A1E3LEG1 A9762_24350 Acyl-CoA transferase − 1.894681 5 23.8 49.528 1.44E−09 A0A1E3LE25 A9762_26525 Acyltransferase − 0.658173 11 53.7 31.029 2.25E−127 A0A1E3LCY1 A9762_06345 CoA transferase − 1.644591 5 19.7 43.746 5.43E−17 A0A1E3LAQ8 A9762_09850 Formyl-CoA transferase 1.63564 16 57 43.01 7.70E−140 A0A1E3LEY2 A9762_23230 Formyl-CoA:oxalate CoA transferase 1.480644 23 65.9 45.431 4.87E−142 A0A1E3LF20 A9762_25975 N-Hydroxyarylamine O-acetyltrans- − 0.812216 13 68.8 31.71 1.16E−71 ferase A0A1E3LB74 A9762_08395 Enoyl-CoA hydratase 0.844962 4 17.4 30.92 1.3832E−11 A0A1E3LG06 A9762_22140 Enoyl-CoA hydratase − 0.845624 7 39.9 28.125 5.7526E−122 A0A1E3LD66 A9762_27340 Enoyl-CoA hydratase 1.887871 9 53.1 29.49 1.5759E−26 A0A1E3LNX6 A9762_00200 Acetyl-CoA acetyltransferase − 0.329002 26 92.5 41.664 0 A0A1E3LED2 A9762_24145 Acetyl-CoA acetyltransferase − 0.647329 11 34.2 46.667 5.8563E−44 A0A1E3LFL9 A9762_22115 Acetyl-CoA acetyltransferase − 1.992637 21 75.9 40.895 0 A0A1E3LLK2 A9762_13635 Acetyl-CoA acetyltransferase − 1.672549 24 85 40.687 0 A0A1E3LLN7 A9762_13660 Acetyl-CoA acetyltransferase − 1.969308 20 70.5 41.273 0 A0A1E3LFA3 A9762_23740 Enoyl-CoA hydratase − 1.935441 19 86.8 28.063 8.927E−161 A0A1E3LNG2 A9762_11320 Enoyl-CoA hydratase 0.497127 6 36.4 27.805 7.4808E−33 A0A1E3LNH0 A9762_11445 Enoyl-CoA hydratase − 1.83413 8 45.4 29.067 2.3968E−55 A0A1E3LNY9 A9762_00195 Enoyl-CoA hydratase − 0.4152 17 84.7 27.622 1.6359E−146 synthetases, acyl-CoA hydratases/lyases, acyl-CoA been known for detoxification mechanism and stress- transferase, acetyl-CoA-acetyl transferases, and decar- related response. However, glutathione-dependent cleav- boxylases have been discovered in Pandoraea sp. ISTKB age of β-aryl ether linkages (most dominant linkage in genome and in expression profile. These enzymes help in lignin) by β-etherase has also been described in Novo- activation and decarboxylation of aromatic compounds sphingobium, Sphingobium SYK-6, Novosphingobium sp. (hydroxycinnamates, carboxyvanillin) and play an impor- PP1Y, and io Th bacillus denitrificans ATC 25259 [15, 45, tant role in diversion of substrate towards central degra- 46]. Therefore, the presence of glutathione enzymes can dation [42–44]. The expression of both protocatechuate help in lignin degradation in this strain. Superoxide dis- 3,4-dioxygenase and protocatechuate 4,5-dioxygenase mutase and catalase–peroxidases were recently reported on both KL–VA indicated that this strain has both func- for lignin or lignin model compound in Sphingobacte- tional ortho and meta cleavage pathway for degradation rium sp. T2 and Amycolatopsis sp. 75iv2, respectively, of lignin and its derivatives. The expression of metacleav - and these were also observed on KL–VA in this strain age outperformed ortho pathway on vanillic acid. The [47, 48]. presence of both ortho and meta cleavage pathways in Dehydrogenase acts on toxic aldehydes and converts single strain is rare phenomenon and the ortho cleavage them into their less toxic intermediates inside cells and pathway was found to be dominant among lignin degrad- also reported for cleavage of ether bond [43, 44]. There ing bacteria [9, 23]. The expression of both ortho and are various dehydrogenases observed in this strain and meta cleavage pathways in this strain illustrates its robust these might play important role in ether linkage degrada- metabolic machinery for the degradation of aromatic tion. The dehydrogenase-mediated degradation of ether compounds. linkage in lignin model compounds by SG61-1L and There are various glutathione-dependent enzymes Lig DEG enzyme system in Sphingobium sp. SYK6 has identified in Pandoraea sp. ISTKB and glutathione has been well documented [42, 49]. The combined action of Kumar et al. Biotechnol Biofuels (2018) 11:154 Page 20 of 23 alcohol dehydrogenase from short-chain dehydrogenase/ Methods reductase family and glutathione S-transferases has been The draft genome of Pandoraea sp. ISTKB was sequenced show to degrade ether linkage (most prominent linkage using the Illumina MiSeq platform, and the raw data in lignin 50–70%) in lignin model compounds [50]. The processing, quality reads, assembly, scaffold generation, pathway for cleavage of β-aryl ether linkage in lignin by and genes prediction were carried out as described ear- NAD-dependent dehydrogenases (LigD, LigO, and LigL) lier [19]. Arrangement of genes of Pandoraea sp. strain and the glutathione-dependent lyase (LigG) was struc- ISTKB with respect to its genome was performed using turally and biochemically characterized [51]. There are clicO FS, i.e., circular layout interactive converter free glutathione enzymes, superoxide dismutase, catalases, services [55]. The proteins having signal sequence were alkyl hydroperoxidase, thioredoxin, glyoxylase, aldo/keto identified using the SignalP 3.0 software [56]. The anno - reductase, and peroxiredoxin identified in Pandoraea tation and analysis of Pandoraea sp. ISTKB genome were sp. ISTKB. The presence of theses stress response and also performed by Rapid Annotations using Subsystems detoxification proteins has also been reported in genome technology (RAST). The RAST subsystem classification sequence of Pseudomonas fluorescens Pf-5 [52]. The followed by pathway analysis was performed [57, 58]. specificity of aldo/keto reductase against various lignin- GO analysis was performed and the genes predicted in derived phenolics, aldehyde, and fermentable inhibi- genome have been classified into major biological pro - tors was demonstrated and was also shown to produce cesses, cellular component, and molecular functions ROS and initiate fenton reaction [53]. Alky hydroperox- using Blast2GO [59]. To identify the potential involve- ide reductase has greater catalytic efficiency under low ment of the genes of Pandoraea sp. ISTKB in biological H O concentration and is responsible for the detoxi- pathways, genes were mapped to reference canonical 2 2 fication of organic hydroperoxides, as catalases cannot pathways in Kyoto encyclopedia of genes’ and genomes’ degrade organic hydroperoxides [54]. The analysis of (KEGG) database. The output of KEGG analysis includes such a diverse set of proteins and their level of expression KEGG orthology (KO) assignments and corresponding helped us to identify the important enzymes responsible enzyme commission (EC) numbers and metabolic path- for lignin or aromatic compound degradation that will ways of genes using KEGG automated annotation server further provide opportunity for lignocellulosic biomass KAAS (http://www.genom e.jp/kaas-bin/kaasm ain) [60]. valorization. A total of 5568 genes for Pandoraea sp. ISTKB were provided as input to KEGG–KAAS and genes involved Conclusion in different pathways were further classified into 22 The genomic and proteomic analysis of Pandoraea sp. functional pathways. The antimicrobial and secondary ISTKB revealed the presence of various candidate genes metabolite clusters were predicted by antiSMASH 3.0 responsible for lignin degradation and PHA production. and genomic islands were predicted using islandviewer4 GO analysis of genomic and proteomic data also sup- [61, 62]. ported the findings. The peroxidase-accessory enzyme system, fenton reaction, and ‘CoA’-mediated degradation Culture conditions and sample preparation for proteomic of phenylacetate and benzoate are the major pathways analysis observed for lignin degradation. The gene cluster respon - Pandoraea sp. ISTKB was grown in mineral medium sible for lignin degradation and PHA production was (MM) containing vanillic acid and kraft lignin as sole found to be functionally active. The functional analysis carbon source. The composition of MM was the same supported genomic findings and a strong antioxidant and as described earlier [6]. A single colony was transferred stress responsive machinery for the survival and metab- from LB plate to broth and incubated overnight at olism of lignin or aromatic compounds was observed. 30  °C and 165  rpm. One milliliter of overnight culture Some secondary metabolites such as lassopeptide unique was transferred to fresh 100  ml LB media and allowed to this strain were also predicted that needs to be vali- to grow until OD reached around 0.5. The cells were dated. The study indicated the pathways and enzymes pelleted, washed twice with phosphate-buffered saline important for metabolism of lignin or aromatic com- (PBS), and inoculated in flask containing VA and KL pounds that can be applied in the future for value addi- having initial OD of around 0.06. Bacteria were grown tion to lignocellulosics. at 30 °C, 165 rpm and the OD was monitored at regular Kumar et al. Biotechnol Biofuels (2018) 11:154 Page 21 of 23 interval. The culture was harvested during exponential Additional files growth phase for proteomics study. Cells were pelleted by cold centrifugation at 10,000  rpm for 15  min washed Additional file 1: Figure S1. Representation of various proteins responsi- with PBS and then resuspended in lysis buffer followed ble for respiratory machinery of Pandoraea sp. ISTKB. Figure S2. Transcrip- tional regulators identified in the genome of Pandoraea sp. ISTKB. Figure by sonication as described earlier [6]. Total protein con- S3. Representation of various transporters present in the genome of centration was estimated by Bradford method, and then, Pandoraea sp. ISTKB. Figure S4. Representation of major oxidoreductases digestion was performed taking equal volume of proteins responsible for lignin and aromatic compound degradation. Figure S5. Representation of proteins into various groups involved in stress regula- from both KL and VA. tion mechanism. Figure S6. Representation of genomic islands predicted by Islandviewer 4 in the Pandoraea sp. ISTKB genome. Table S1. KEGG Digestion of proteins, LC–MS/MS analyses, and data Pathway classification of Pandoraea sp. ISTKB. Table S2. Annotation of Monooxygenase genes identified in the genome of Pandoraea sp. ISTKB. analysis Table S3. Annotation of Dioxygenase genes identified in the genome of The protein concentration of 25 µg from both KL and VA Pandoraeasp. ISTKB. Table S4. Annotation of Peroxidase genes identified was reduced with 5 mM concentration TCEP for 10 min in the genome of Pandoraea sp. ISTKB. Table S5. Peripheral pathways for catabolism of aromatic compounds. Table S6. Annotation of genes at room temperature and further alkylated with 15  mM responsible for metabolism of central aromatic intermediates. Table S7. iodoacetamide in dark at room temperature for 30  min. Annotation of genes related to Glutathione metabolism and stress The sample was diluted to 0.6  M final Gn-HCl concen - response. Table S8. Represents secondary metabolite clusters identified in Pandoraea sp. ISTKB genome. tration with 25  mM ammonium bicarbonate buffer. For Additional file 2: Table S9. Detail of genomic islands identified in Pando - digestion of protein, trypsin was added in a trypsin-to- raea sp. ISTKB genome. lysate ratio of 1:50 after and incubation was performed Additional file 3: Table S10. Other differentially expressed proteins overnight at 37  °C. The supernatant was vacuum dried (related to PHA metabolism, dehydrogenase, reductases, transferases, and the peptides were reconstituted in 5% formic acid esterases and hydrolases) on kraft lignin. followed by purification using C18 silica cartridge and dried using speed vac. The dried pellets were resus - Authors’ contributions pended in buffer-A (5% acetonitrile/0.15 formic acid). MK, IST, PKV, and AP designed the study and experiments. MK, SV, RKG, and The peptides were analyzed using EASY-nLC 1000 MK performed the experiments, bioinformatics, and data analysis. MK and SV wrote the manuscript. AP, IST, and PKV supervised the research work. All system (Thermo Fisher Scientific) coupled to QEx - authors read and approved the final manuscript. tractive mass spectrometer (Thermo Fisher Scientific) equipped with nanoelectrospray ion source. 1  µg of Author details School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, peptide mixture was loaded on precolumn and resolved 110067, India. National Institute of Plant Genome Research, Aruna Asaf Ali using 15  cm Pico Frit filled with 1.8 um C18-resin 3 Marg, New Delhi 110067, India. CSIR-Indian Institute of Toxicology Research, (Dr. Maeisch). The sample was run for 90  min and the 31 MG Marg, Lucknow 226 001, India. peptides were eluted with a 0–40% gradient of buffer Acknowledgements B (95% acetonitrile/0.1% formic acid) at a flow rate of Madan Kumar thanks Council of Scientific and Industrial Research (CSIR), New 300  nl/min. the QExtractive was operated using the Delhi, India for providing Senior Research Fellowship. P.K.V. thanks the National Institute of Plant Genome Research, New Delhi, for financial support. We thank Top10 HCD data-dependent acquisition mode with a Shashi Shekhar Singh and Gagandeep Jhingan for their support in proteom- full-scan resolution of 70,000 at m/z 400. The MS/MS ics work. We are grateful to Jawaharlal Nehru University, New Delhi, India, for scans were acquired at a resolution of 17500 at m/z providing financial support. 400. Lock mass option was enabled for polydimethyl- Competing interests cyclosiloxane (PCM) ions (m/z = 445.120025) for inter- The authors declare that they have no competing interests. nal recalibration during the run. MS identification of Q Ethics approval and consent to participate extractive files was analyzed by the MaxQuant software Not applicable. and searched against databases at a false-discovery rate (FDR) of 1%. A total of protein groups were identified Publisher’s Note and were further filtered according to the label-free Springer Nature remains neutral with regard to jurisdictional claims in pub- quantitation (LFQ) intensity values and their respec- lished maps and institutional affiliations. tive fold change values were calculated. Heat map and Received: 30 December 2017 Accepted: 17 May 2018 profile plots were against the protein groups filtered based on the normalized LFQ intensity values using the Perseus software. 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Biotechnology for BiofuelsSpringer Journals

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