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Price, Elliott J.; Drapal, Margit; Perez‐Fons, Laura; Amah, Delphine; Bhattacharjee, Ranjana; Heider, Bettina; Rouard, Mathieu; Swennen, Rony; Becerra Lopez‐Lavalle, Luis Augusto; Fraser, Paul D.
doi: 10.1111/tpj.14649pmid: 31845400
Roots, tubers, and bananas (RTB) are vital staples for food security in the world's poorest nations. A major constraint to current RTB breeding programmes is limited knowledge on the available diversity due to lack of efficient germplasm characterization and structure. In recent years large‐scale efforts have begun to elucidate the genetic and phenotypic diversity of germplasm collections and populations and, yet, biochemical measurements have often been overlooked despite metabolite composition being directly associated with agronomic and consumer traits. Here we present a compound database and concentration range for metabolites detected in the major RTB crops: banana (Musa spp.), cassava (Manihot esculenta), potato (Solanum tuberosum), sweet potato (Ipomoea batatas), and yam (Dioscorea spp.), following metabolomics‐based diversity screening of global collections held within the CGIAR institutes. The dataset including 711 chemical features provides a valuable resource regarding the comparative biochemical composition of each RTB crop and highlights the potential diversity available for incorporation into crop improvement programmes. Particularly, the tropical crops cassava, sweet potato and banana displayed more complex compositional metabolite profiles with representations of up to 22 chemical classes (unknowns excluded) than that of potato, for which only metabolites from 10 chemical classes were detected. Additionally, over 20% of biochemical signatures remained unidentified for every crop analyzed. Integration of metabolomics with the on‐going genomic and phenotypic studies will enhance ’omics‐wide associations of molecular signatures with agronomic and consumer traits via easily quantifiable biochemical markers to aid gene discovery and functional characterization.
Murik, Omer; Chandran, Sam Aldrin; Nevo‐Dinur, Keren; Sultan, Laure D.; Best, Corinne; Stein, Yuval; Hazan, Carina; Ostersetzer‐Biran, Oren
doi: 10.1111/tpj.14589pmid: 31657869
Mitochondria serve as major sites of ATP production and play key roles in many other metabolic processes that are critical to the cell. As relicts of an ancient bacterial endosymbiont, mitochondria contain their own hereditary material (i.e. mtDNA, or mitogenome) and a machinery for protein biosynthesis. The expression of the mtDNA in plants is complex, particularly at the post‐transcriptional level. Following transcription, the polycistronic pre‐RNAs undergo extensive modifications, including trimming, splicing and editing, before being translated by organellar ribosomes. Our study focuses on N6‐methylation of adenosine ribonucleotides (m6A‐RNA) in plant mitochondria. m6A is a prevalent modification in nuclear‐encoded mRNAs. The biological significance of this dynamic modification is under investigation, but it is widely accepted that m6A mediates structural switches that affect RNA stability and/or activity. Using m6A‐pulldown/RNA‐seq (m6A‐RIP‐seq) assays of Arabidopsis and cauliflower mitochondria, we provide information on the m6A‐RNA landscapes in Arabidopsis thaliana and Brassica oleracea mitochondria. The results show that m6A targets different types of mitochondrial transcripts, including known genes, mtORFs, as well as non‐coding (transcribed intergenic) RNA species. While ncRNAs undergo multiple m6A modifications, N6‐methylation of adenosine residues with mRNAs seem preferably positioned near start codons and may modulate their translatability.
Serrano‐Bueno, Gloria; Said, Fatima E.; los Reyes, Pedro; Lucas‐Reina, Eva I.; Ortiz‐Marchena, M. Isabel; Romero, José M.; Valverde, Federico
doi: 10.1111/tpj.14590pmid: 31661582
Flowering time is a key process in plant development. Photoperiodic signals play a crucial role in the floral transition in Arabidopsis thaliana, and the protein CONSTANS (CO) has a central regulatory function that is tightly regulated at the transcriptional and post‐translational levels. The stability of CO protein depends on a light‐driven proteasome process that optimizes its accumulation in the evening to promote the production of the florigen FLOWERING LOCUS T (FT) and induce seasonal flowering. To further investigate the post‐translational regulation of CO protein we have dissected its interactome network employing in vivo and in vitro assays and molecular genetics approaches. The immunophilin FKBP12 has been identified in Arabidopsis as a CO interactor that regulates its accumulation and activity. FKBP12 and CO interact through the CCT domain, affecting the stability and function of CO. fkbp12 insertion mutants show a delay in flowering time, while FKBP12 overexpression accelerates flowering, and these phenotypes can be directly related to a change in accumulation of FT protein. The interaction is conserved between the Chlamydomonas algal orthologs CrCO–CrFKBP12, revealing an ancient regulatory step in photoperiod regulation of plant development.
Potuschak, Thomas; Palatnik, Javier; Schommer, Carla; Sierro, Nicolas; Ivanov, Nikolai V.; Kwon, Yerim; Genschik, Pascal; Davière, Jean‐Michel; Otten, Léon
doi: 10.1111/tpj.14591pmid: 31659801
Agrobacterium T‐DNA‐encoded 6B proteins cause remarkable growth effects in plants. Nicotiana otophora carries two cellular T‐DNAs with three slightly divergent 6b genes (TE‐1‐6b‐L, TE‐1‐6b‐R and TE‐2‐6b) originating from a natural transformation event. In Arabidopsis thaliana, expression of 2×35S:TE‐2‐6b, but not 2×35S:TE‐1‐6b‐L or 2×35S:TE‐1‐6b‐R, led to plants with crinkly leaves, which strongly resembled mutants of the miR319a/TCP module. This module is composed of MIR319A and five CIN‐like TCP (TEOSINTHE BRANCHED1, CYCLOIDEA and PROLIFERATING CELL NUCLEAR ANTIGEN BINDING FACTOR) genes (TCP2, TCP3, TCP4, TCP10 and TCP24) targeted by miR319a. The CIN‐like TCP genes encode transcription factors and are required for cell division arrest at leaf margins during development. MIR319A overexpression causes excessive growth and crinkly leaves. TE‐2‐6b plants did not show increased miR319a levels, but the mRNA levels of the TCP4 target gene LOX2 were decreased, as in jaw‐D plants. Co‐expression of green fluorescent protein (GFP)‐tagged TCPs with native or red fluorescent protein (RFP)‐tagged TE‐6B proteins led to an increase in TCP protein levels and formation of numerous cytoplasmic dots containing 6B and TCP proteins. Yeast double‐hybrid experiments confirmed 6B/TCP binding and showed that TE‐1‐6B‐L and TE‐1‐6B‐R bind a smaller set of TCP proteins than TE‐2‐6B. A single nucleotide mutation in TE‐1‐6B‐R enlarged its TCP‐binding repertoire to that of TE‐2‐6B and caused a crinkly phenotype in Arabidopsis. Deletion analysis showed that TE‐2‐6B targets the TCP4 DNA‐binding domain and directly interferes with transcriptional activation. Taken together, these results provide detailed insights into the mechanism of action of the N. otophora TE‐encoded 6b genes.
Hashida, Yoshikazu; Takechi, Katsuaki; Abiru, Tomomi; Yabe, Noriyuki; Nagase, Hiroaki; Hattori, Koro; Takio, Susumu; Sato, Yoshikatsu; Hasebe, Mitsuyasu; Tsukaya, Hirokazu; Takano, Hiroyoshi
doi: 10.1111/tpj.14592pmid:
Zhu, Mengmeng; Geng, Sisi; Chakravorty, David; Guan, Qijie; Chen, Sixue; Assmann, Sarah M.
doi: 10.1111/tpj.14594pmid: 31677315
Environmental stimuli‐triggered stomatal movement is a key physiological process that regulates CO2 uptake and water loss in plants. Stomata are defined by pairs of guard cells that perceive and transduce external signals, leading to cellular volume changes and consequent stomatal aperture change. Within the visible light spectrum, red light induces stomatal opening in intact leaves. However, there has been debate regarding the extent to which red‐light‐induced stomatal opening arises from direct guard cell sensing of red light versus indirect responses as a result of red light influences on mesophyll photosynthesis. Here we identify conditions that result in red‐light‐stimulated stomatal opening in isolated epidermal peels and enlargement of protoplasts, firmly establishing a direct guard cell response to red light. We then employ metabolomics workflows utilizing gas chromatography mass spectrometry and liquid chromatography mass spectrometry for metabolite profiling and identification of Arabidopsis guard cell metabolic signatures in response to red light in the absence of the mesophyll. We quantified 223 metabolites in Arabidopsis guard cells, with 104 found to be red light responsive. These red‐light‐modulated metabolites participate in the tricarboxylic acid cycle, carbon balance, phytohormone biosynthesis and redox homeostasis. We next analyzed selected Arabidopsis mutants, and discovered that stomatal opening response to red light is correlated with a decrease in guard cell abscisic acid content and an increase in jasmonic acid content. The red‐light‐modulated guard cell metabolome reported here provides fundamental information concerning autonomous red light signaling pathways in guard cells.
Lyall, Rafe; Schlebusch, Stephen A.; Proctor, Jessica; Prag, Mayur; Hussey, Steven G.; Ingle, Robert A.; Illing, Nicola
doi: 10.1111/tpj.14596pmid: 31680354
It has been hypothesised that vegetative desiccation tolerance in resurrection plants evolved via reactivation of the canonical LAFL (i.e. LEC1, ABI3, FUS3 and LEC2) transcription factor (TF) network that activates the expression of genes during the maturation of orthodox seeds leading to desiccation tolerance of the plant embryo in most angiosperms. There is little direct evidence to support this, however, and the transcriptional changes that occur during seed maturation in resurrection plants have not previously been studied. Here we performed de novo transcriptome assembly for Xerophyta humilis, and analysed gene expression during seed maturation and vegetative desiccation. Our results indicate that differential expression of a set of 4205 genes is common to maturing seeds and desiccating leaves. This shared set of genes is enriched for gene ontology terms related to abiotic stress, including water stress and abscisic acid signalling, and includes many genes that are seed‐specific in Arabidopsis thaliana and targets of ABI3. However, while we observed upregulation of orthologues of the canonical LAFL TFs and ABI5 during seed maturation, similar to what is seen in A. thaliana, this did not occur during desiccation of leaf tissue. Thus, reactivation of components of the seed desiccation program in X. humilis vegetative tissues likely involves alternative transcriptional regulators.
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In Arabidopsis thaliana the ANGUSTIFOLIA (AN) gene regulates the width of leaves by controlling the diffuse growth of leaf cells in the medio‐lateral direction. In the genome of the moss Physcomitrella patens, we found two normal ANs (PpAN1‐1 and 1‐2). Both PpAN1 genes complemented the A. thaliana an‐1 mutant phenotypes. An analysis of spatiotemporal promoter activity of each PpAN1 gene, using transgenic lines that contained each PpAN1‐promoter– uidA (GUS) gene, showed that both promoters are mainly active in the stems of haploid gametophores and in the middle to basal region of the young sporophyte that develops into the seta and foot. Analyses of the knockout lines for PpAN1‐1 and PpAN1‐2 genes suggested that these genes have partially redundant functions and regulate gametophore height by controlling diffuse cell growth in gametophore stems. In addition, the seta and foot were shorter and thicker in diploid sporophytes, suggesting that cell elongation was reduced in the longitudinal direction, whereas no defects were detected in tip‐growing protonemata. These results indicate that both PpAN1 genes in P. patens function in diffuse growth of the haploid and diploid generations but not in tip growth. To visualize microtubule distribution in gametophore cells of P. patens, transformed lines expressing P. patens α‐tubulin fused to sGFP were generated. Contrary to expectations, the orientation of microtubules in the tips of gametophores in the PpAN1‐1/1‐2 double‐knockout lines was unchanged. The relationships among diffuse cell growth, cortical microtubules and AN proteins are discussed.