The majority of established model organisms belong to the supergroup Opisthokonta, which includes yeasts and animals. While enlightening, this focus has neglected protists, organisms that represent the bulk of eukaryotic diversity and are often regarded as primitive eukaryotes. One of these is the “supergroup” Excavata, which comprises unicellular flagellates of diverse lifestyles and contains species of medical importance, such as Trichomonas, Giardia, Naegleria, Trypanosoma and Leishmania. Excavata exhibits a continuum in mitochondrial forms, ranging from classical aerobic, cristae-bearing mitochondria to mitochondria-related organelles, such as hydrogenosomes and mitosomes, to the extreme case of a complete absence of the organelle. All forms of mitochondria house a machinery for the assembly of Fe–S clusters, ancient cofactors required in various biochemical activities needed to sustain every extant cell. In this review, we survey what is known about the Fe–S cluster assembly in the supergroup Excavata. We aim to bring attention to the diversity found in this group, ree fl cted in gene losses and gains that have shaped the Fe–S cluster biogenesis pathways. Keywords Fe–S cluster · Mitochondria · Excavata · Evolution Introduction (stramenopiles/alveolates/Rhizaria), photosynthetic algae, and Opisthokonta [1, 5]. Organelles of mitochondrial ori- The intimate relationship between eukaryotic cells and mito- gin, of which MROs form a part, have been classified into chondria, as endosymbiont-derived organelles, has taken bil- five types [ 5]: (1) “classical mitochondrion” with a complete lion of years to establish [1, 2]. It was initially accepted that electron transport chain, which is capable of using oxygen as the basis for the presence of mitochondria in virtually every an electron acceptor, and produces metabolic energy from eukaryotic cell had been the provision of energy from their such machinery; (2 and 3) organelles that bear a functional oxidative phosphorylation machinery, yet several lines of electron transport chain, yet use other electron acceptors evidence have proven otherwise . The description of vari- such as fumarate, and are capable of performing both sub- ous types of mitochondria and mitochondria-related orga- strate-level phosphorylation and may or may not produce H ; nelles (or MRO), many of which are found in a spectrum (4) double membrane-bound MROs called hydrogenosomes of unrelated protist clades, has brought into the spotlight that are capable of ATP production in anaerobic or micro- an enormous organellar diversity, or what is rather a con- aerophilic environments and excrete H as one of the end tinuum, ranging from a minimalistic MRO of Giardia to the products of substrate-level phosphorylation in an organelle highly complex mitochondria of trypanosomes . MROs lacking electron transport chain ; finally, (5) mitosomes have been found in eukaryotic supergroups Excavata, SAR represent a type of MRO incapable of energy production, as they lack the components of an active electron chain and mostly have lost their genome [1, 5]. The original version of this article was revised due to a Remarkably, the Fe–S cluster assembly pathway is the retrospective Open Access order. only known common denominator of this conglomerate of * Priscila Peña-Diaz organelles. Moreover, in one of the best-studied eukary- email@example.com otes, the yeast Saccharomyces cerevisiae, this pathway seems to be the only truly essential component of its mito- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic chondria [3, 7]. In this review, we revise what is known about the Fe–S cluster assembly pathways of the unicellular Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic Vol.:(0123456789) 1 3 522 JBIC Journal of Biological Inorganic Chemistry (2018) 23:521–541 supergroup Excavata and attempt to compare its inventory and NIF systems each bear a functional homolog of this with those described in other eukaryotes, but mostly in enzyme which, however, displays significant differences the Opisthokonta, the by far most studied supergroup that addressed below. (2) Assembly of an Fe–S cluster on a scaf- includes, not surprisingly, humans . fold protein; a Cys in the scaffold protein binds sulfur liber - Fe–S clusters are ancient cofactors found in the whole ated from the previous reaction, which physically interacts spectrum of life. In Archaea, Bacteria and Eukaryota, cells with the CD for the Fe–S assembly to occur. (3) Transfer have evolved different machineries for their Fe–S clusters of the Fe–S cluster from the CD–scaffold complex onto a assembly, namely the methanoarchaeal sulfur mobilization delivery protein, which will subsequently interact with the (SUF) machinery , the nitrogen fixation (NIF) pathway recipient proteins and install the cluster. , the cysteine sulfinate desulfinate (CSD) system [ 11], the iron–sulfur cluster assembly (ISC) pathway [12, 13] The ISC system and cytosolic iron–sulfur protein assembly (CIA) pathway [14–16]. The first one is present throughout bacteria and in The Fe–S cluster assembly by the ISC system involves the the chloroplasts of photosynthesizing organisms , while activity of at least five proteins. A cysteine desulfurase the NIF system was initially discovered in the maturation (IscS) provides the sulfur, while the formation of the cluster of nitrogenase in N -fixing bacteria . The CSD system takes place on the scaffold protein named IscU. Ferredoxin has been described in Escherichia coli as a partial func- (Fdx) likely acts as an electron donor in this reaction [31, tional homolog of the SUF system . The ISC pathway is 32]. Subsequently, IscU requires the assistance of the chap- associated with eubacteria and in eukaryotes located within erones HscA (heat shock cognate 66 kDa or Hsc66) and the mitochondria . Finally, the CIA machinery is found HscB (heat shock cognate 20 kDa or Hsc20). HscA is a in the cytosol of eukaryotes, where it assembles, with the member of the Hsp70/DnaK chaperone family and exhib- assistance of mitochondrial ISC, Fe–S clusters eventually its an intrinsic ATPase activity, while HscB belongs to the incorporated into proteins located in this cellular compart- Hsc20/DnaJ J-type co-chaperone family . The binding ment [14, 20]. It is now widely accepted that the latter path- of the chaperones, which is mediated by an LPPVK motif way was bequeathed from an endosymbiont to an ancestral found in IscU, occurs in an orderly fashion to release the eukaryote, while the plastid-bearing eukaryotes inherited nascent Fe–S cluster onto the delivery system in an ATP- their SUF machinery from an early cyanobacterium [17, dependent manner [34–37]. In this scenario, HscA binds 21, 22]. On the other hand, a lateral gene transfer has been IscU, enhanced by the presence of HscB, which increases the proposed to be behind the emergence of the SUF pathway ATPase activity of the former chaperone by approximately in some unicellular eukaryotes that either retain highly 400-fold [35, 38]. The binding model formulated based on diverged MROs, such as Blastocystis, Stygiella incarcerata the studies of the IscU mutants proposes that the chaperone and Pygsuia biforma, or lost the entire organelle, along with complex stabilizes IscU for the release of the cluster to the the ISC pathway, like in the case of Monocercomonoides receptor protein . IscU has also been observed to interact . In any case, the Fe–S cluster assembly represents a with both [2Fe–2S] and [4Fe–4S] clusters . This was hallmark that is always taken into account when analyzing further analyzed upon the binding of the scaffold protein to the evolution of divergent mitochondria-derived organelles Fdx, which has been proposed to mediate, at least partially [12, 24–28]. and in vitro, the reductive coupling of [2Fe–2S] clusters into [4Fe–4S] clusters . Once the Fe–S cluster has been assembled, it is transferred to the delivery system for further Fe–S cluster machineries: a brief overview insertion into apoproteins, a role carried out by the dedicated protein IscA. The bacterial frataxin, named CyaY, plays an Bacterial systems inhibitory role in the biogenesis of the Fe–S cluster assembly by binding to IscS in an iron-sensing regulatory role . The Fe–S cluster assembly machineries in bacteria can be subdivided into four systems mentioned above, their distri- The SUF system bution being species specific [18, 29, 30]. As an example, E. coli with the best-studied bacterial Fe–S assemblies exhibits The SUF system for the Fe–S cluster assembly is induced the ISC, the SUF and the CSD systems [18, 19]. These dis- by iron-depleted and oxidative stress conditions and mainly tinct systems share the main activities for the formation of involves the activity of two sub-complexes . Proteins a [2Fe–2S] cluster, which may be divided into three main SufE and SufS form the heterodimer SufSE, while a second stages: (1) Pyridoxal 5′-phosphate-dependent cysteine (Cys) sub-complex termed SufBCD is composed of SufB, SufC desulfuration with concomitant production of l -alanine, car- and SufD [43, 44]. SufS, which represents the CD and there- ried out by a cysteine desulfurase (CD). The ISC, SUF, CSD fore is an ortholog of IscS, collaborates with SufE, which 1 3 JBIC Journal of Biological Inorganic Chemistry (2018) 23:521–541 523 increases the desulfurase activity of the CD [43, 45, 46]. pneumoniae . The NIF system comprises a CD termed SufSE transfers the sulfur produced by the CD reaction, fol- NifS and a scaffold protein NifU. NifU is a functional lowing the interaction with the scaffold complex SufBCD, homolog of the scaffold protein IscU, yet it exhibits some which further enhances the desulfurase activity . SufB remarkable differences. On its N-terminus it bears cysteines has been defined as a scaffold, capable of interacting with intended for [2Fe–2S] cluster binding, while other cysteines SufD and the soluble ATPase SufC [45, 48, 49]. Moreover, found in its middle and its C-terminus seem to bind Fe–S this complex uses F ADH as a redox cofactor . SufD clusters in a non-transient manner . NifB is an S-adeno- shares substantial sequence similarity with SufB and has sylmethionine (SAM)-dependent enzyme involved in the for- been hypothesized to confer iron to the reaction [50, 51]. mation of an Fe–S cluster precursor of an iron–molybdenum The stoichiometry plays an important role in the structural cofactor (FeMo-co) required for the reconstitution of active dynamics of the SufBCD complex, with its various oligo- nitrogenase . Other proteins involved in the NIF system nif meric forms being capable of transferring in vitro the cluster are IscA , which likely functions as a scaffold for target to the receptor proteins [49, 50]. For in vitro maturation of apoproteins , and a O-acetylserine synthase denoted as Fdx, the SufBC D, SufB C and SufC D sub-complexes CysE1, whose activity has been proposed to increment the 2 2 2 2 2 interact with SufA, which has been proposed to act as a cysteine pool for the Fe–S assembly of nitrogenase . transfer protein for the nascent Fe–S cluster . However, it has also been established in vitro that the SufBCD complex The CSD system is capable of transferring clusters directly to apoproteins without the assistance of SufA . Once the Fe–S cluster is The CD of the CSD system is encoded by the csdA gene. assembled, it is ready to be targeted to the transfer proteins. It differs from SufA by substrate specificity, although both The SUF system exhibits an A-Type carrier protein termed proteins share substantial sequence similarity. CsdA is capa- SufA. . While SufA belongs to the suf operon and IscA ble of transferring sulfur from l -selenocysteine, l -seleno- to the isc operon, another transfer or carrier protein called cystine, l -cysteine, l -cystine and cysteine sulfinate . ErpA is independent of the Fe–S cluster assembly operons CsdE, a homolog of SufE, catalyzes the release of Se, SO . A-type carrier proteins were initially believed to act and S from l -selenocysteine (the most preferred substrate), as alternative scaffolds , but several lines of evidence l -cysteine sulfinate and l -cysteine (the least preferred sub- argued against this premise. It was observed that deletions strate) [70, 71]. Regardless of the CD activity observed of the type-A carrier produced no phenotypes, probably a in vitro for each pure protein, labeling assays confirmed that reflection of the fact that the nascent cluster can be trans- CsdA and CsdE may enhance each other’s activity twofold ferred directly from the scaffold protein . Moreover, the [11, 72]. In E. coli, the CsdAE complex has been observed in binding capacity of type-A carriers did not allow reversible unison with the SufSE and SufBCD sub-complexes. Under transfer of the Fe–S cluster from the scaffold, and their bind- specific nutritional deficiency stress, the CsdAE complex ing to CD was not as efficient as that of IscU . For these may also recruit CsdL, an E1-like protein found in ubiquitin- reasons, two possible roles in Fe–S assembly were consid- like systems . ered: they could either act as iron donors  or assist the process of transfer to the apoproteins once the Fe–S cluster Eukaryotic systems was assembled . Another protein belonging to the SUF system is the Zn- Eukaryotic cells exhibit the ISC system in the mitochon- dependent SufU , which is absent in the Gram-negative dria and the CIA pathway in the cytosol. The photosynthetic bacteria such as E. coli. SufU, a homolog of IscU, is able eukaryotes also carry the SUF system in their plastids . to complement SufE, as it happens in the case of Bacillus Moreover, the SUF system has been retained even in the subtillis, Enterococcus faecalis, Thermatoga maritima and non-photosynthetic apicoplast of the apicomplexan parasites various mycobacteria [58–61]. [74, 75], as well as in the cytosol of some parasitic and com- mensal amitochondriate protists . Finally, the NIF sys- The NIF system tem is rarely present in the mitochondria and cytosol (e.g., in Entamoeba histolytica and Mastigamoeba balamuthi) [76, The NIF system, initially described in nitrogen-fixing 77], while parts of the CSD system were found scattered in bacterium Azotobacter vinelandii, is a dedicated machin- some parasitic protozoan genomes . ery for the maturation of nitrogenase. Later on, it has also been found co-existing with one or more of the other three The mitochondrial ISC system Fe–S assembly systems in ε-proteobacteria, represented by Helicobacter pylori , as well as in the Gram-negative The best-studied mitochondrial ISC systems are those of γ-proteobacteria Dickeya dadantii [63, 64] and Klebsiella yeast, plants and mammalian cells. In this section, we will 1 3 524 JBIC Journal of Biological Inorganic Chemistry (2018) 23:521–541 base our description on the human model and therefore use NFS1–ISD11–ISCU complex, aided by the chaperone com- the nomenclature for the human ISC Fe–S cluster assembly, plex is capable of transferring Fe–S clusters, although these unless indicated otherwise. The ISC system from bacteria experiments were performed in the absence of GLRX5 . and eukaryotes exhibits the same general functional traits, Another piece of evidence to support this model comes from such as the sulfur acquisition from a donor cysteine and the in vitro experiments where GRX5 is capable of interaction assembly of a nascent Fe–S cluster on a scaffold protein, with transfer proteins ISCA1 and ISC2, and also mobilizes with the subsequent transfer to carrier proteins, which will their [2Fe–2S] clusters . Co-immunoprecipitations of in turn deliver the cluster to apoproteins. However, there GLRX5 in mice N2a and HeLa cells also detected an inter- are some important differences between the prokaryotic action with carrier proteins ISCU2 and IBA57 . Moreo- and eukaryotic ISCs. One of them is the ISD11 protein, ver, deletion of GRLX5 in humans is known to cause severe exclusive for eukaryotes . ISD11 is a small accessory microcytic-hypochromic anemia, related to Fe–S cluster protein that acts in concert with NFS1 [80–83], the scaf- biogenesis defects . Regardless, the model involving fold protein ISU2 and the acyl carrier protein ACP . GLRX5 also correlates with the formation and transfer of Within the NFS1–ISD11–ACP tripartite complex, ISD11 the [4Fe–4S] clusters (discussed in detail below), as the forms a dimeric association at its core, with ACP occupying ISD11–ISC2–HSC20–HSC9 complex may only answer for a hydrophobic pocket in each ISD11 monomer that stabilizes the assembly of [2Fe–2S] clusters into the respiratory com- the complex [85, 86]. The complex also binds to the scaf- plexes I through III . fold protein ISCU2 and to ferredoxin (FDX2) , which The LYR-based transfer model described in human cells acts as an electron donor aided by a ferredoxin reductase differs from the one proposed and demonstrated for yeast (FDXR) [88–90]. ISCU2 is the product of alternative splic- mitochondria . We understand these two models are ing of ISCU which also gives origin to ISCU1, also sug- complementary, but we intentionally describe them sepa- gested to play a role in the repair of the [4Fe–4S] clusters in rately, as they rely on different experimental setups. In yeast the cytosol . In humans, the binding is facilitated by the mitochondria, the chaperone Ssq1 binds to monothiol glu- interaction with a chaperone/co-chaperone complex formed taredoxin Grx5 prior to binding to the scaffold protein Isu1, by HSPA9 (also called GRP75 or PBP74) and HSC20 (or making use of two different binding sites for each protein HSCB) [92, 93], while in yeast this role is performed by . The binding of Ssq1 to Grx5 is ATP independent, mitochondrial Hsp70 protein, ATP-dependent Ssq1 and co- which entails that the ATP-dependent stage of Ssq1 activity chaperone Jac1 [94, 95]. Frataxin (FXN) has been proposed takes place in the reaction upstream, while binding to the 2+ to donate Fe for the reaction and/or act as an allosteric co-chaperone Jac1 (Fig. 1). Jac1 is then released from Ssq1 regulator of NFS1, stimulating its activity [96–98]. Moreo- prior to the binding to Grx5, a step that precedes the binding ver, FXN has also been suggested to bind to the chaper- to Isu1. The result is an efficient transfer of the newly formed one–ISCU2 complex . The binding of ISCU2 to the L(I) cluster from Isu1 to Grx5 . The model also implies the YR motif seems essential for the transfer of the cluster to a release of Grx5 bound to the cluster from the Ssq1–Isc1 specific recipient apoprotein . Studies using succinate complex, with the concerted activity of exchange nucleotide dehydrogenase complex (SDH) subunits in mammalian cells factor Mge1 . The integration of Mge1 into this model demonstrate that the clusters are transferred directly from comes from in vitro experiments, in which Mge1 is capable the chaperone complex to the subunits of SDH, achieving of releasing nucleotides bound to Ssq1 when the chaperone their maturation in this step; a similar result was observed is in contact with Isu1. Therefore, the release of the chap- for respiratory complexes I and III . Also a monothiol erone from the scaffold (though these experiments where glutaredoxin, GLRX5, has been observed to interact with made, in the absence of Grx5 and in presence of Jac1), HSC20, through binding to the same group of cysteines that allows the continuation of a new cycle of assembly . the chaperone uses to bind SDH . Hence, GLRX5 must Mutations in Grx5 in S. cerevisiae trigger a severe pheno- be released from the chaperone complex for it to bind to the type of iron accumulation and subsequent defects in the recipient respiratory complex unit. Consequently, it was pro- Fe–S cluster-bearing proteins . The interaction of Grx5 posed that GLRX5 acts as an alternative scaffold for delivery with the Isa1 and Isa2 proteins has also been documented of the Fe–S clusters to apoproteins . in the fission yeast Schizosaccharomyces pombe [ 105]. A An alternative model for the transfer of the cluster from yeast two-hybrid system provided additional evidence for the NFS1–ISD11–ACP–ISC2–FXN complex involves an the interaction between Grx5 and Isa1 in S. cerevisiae . interaction with GLRX5. This model implies that GLRX5 ISCA1 and ISCA2, along with IBA57, form the so-called requires a chaperone-assisted transfer of the Fe–S cluster ISA complex that has been proposed to act as a scaffold from the scaffold complex, which for most apoproteins involved in the assembly of [4Fe–4S] clusters into a range of cannot be bypassed . Mechanistic data for this model mitochondrial proteins, including lipoic acid synthase [89, have been obtained from the NMR spectra where the 107]. Depletion of ISCA1 and ISCA2 in HeLa cells resulted 1 3 JBIC Journal of Biological Inorganic Chemistry (2018) 23:521–541 525 Fig. 1 Schematic representation of the ISC and CIA pathways in ent proteins are depicted in white for ISC and blue for CIA. The CIA eukaryotic cells. The generic representation displays ISC compo- components reflect the complexes described for the mammalian cell nents (in light green) and CIA components (in dark green). Recipi- model in defects in the mitochondrial cristae formation, ultrastruc- [89, 107]. Interestingly, when ISCU2 alone was silenced, ture alterations and acidification of the growth media, which increased amount of ISCU1 was observed in HeLa cells and associates these proteins with the maturation of respiratory vice versa, which led to the suggestion that these proteins complexes and hence metabolic defects . However, in may have redundant functions . This is in partial agree- mouse cell lines, silencing of these proteins did not cause ment with human cases of leukodystrophy and hypergly- any morphological alterations, yet respiration measure- cemia associated with defects in ISCA2 accompanied by ments corroborated the metabolic defects . Silencing of a reduction in [4Fe–4S] clusters in respiratory complexes IBA57 failed to exert an effect on the activity of the Fe–S II and IV . Alternatively, overexpression of ISC2 in cluster-carrying mitochondrial aconitase, yet it decreased an ISCU1 knock-down background in mouse cells showed in the activity of SDH. Similarly, the depletion of ISCA1, that ISCA1, but not ISCA2, was essential for the [4Fe–4S] ISCA2 and IBA57 significantly lowered the activities of cluster assembly, since ISCU2 could not rescue the [4Fe–4S] pyruvate dehydrogenase, 2-oxoglutarate dehydrogenase, defect caused by silencing of ISCU1 . Regardless, the mitochondrial aconitase, the Rieske protein and other Fe–S two scaffold proteins in mouse and human interact with each cluster-containing mitochondrial proteins. The phenotype other in vitro [89, 109], although only ISCU2 was able to could be reversed by RNAi-resistant ectopic expression of bind IBA57 . the two transfer proteins, proving their involvement in the The counterparts of human ISCU1 and ISCU2 in yeast phenotype . However, [2Fe–2S] ferrochelatase was are Isa1 and Isa2, which also function as scaffold proteins unaffected by silencing of ISCU1 in mouse, and of ISCU1, [110–112]. Experiments replacing Isu1 with bacterial ISCU2 and IBA57 in human cells, corroborating their role A-type proteins in an Isu1 mutant background corroborated only in late-acting stages of the Fe–S cluster assembly that this protein, and not Isu2, is the functional ortholog of 1 3 526 JBIC Journal of Biological Inorganic Chemistry (2018) 23:521–541 the bacterial counterpart . Notably, Isu1 and Isu2 inter- three homologs in humans . Yeast BolA1 and BolA3 act unlike their counterparts in humans . Silencing of localize to the mitochondria, while BolA2 is present in the Isu1, Isu2 and Iba57 disrupts the activities of mitochondrial cytosol . BolA1 and BolA3 were shown to physically aconitase, biotin synthase and lipoic acid synthase, just like interact in vitro with human proteins NFU1 and GLRX5, in human cells [110, 111, 113]. Regardless of whether Isu1, respectively, providing further evidence that these proteins Isu2 and Iba57 are indeed directly involved in the [2Fe–2S] fulfill different functions. Indeed, bola1 and bola3 mutants cluster assembly in both humans and yeast [100, 109, 114], exhibit no growth phenotype, but the double bola1–bola3 there is a consensus that they all are late-acting components mutant displays a mild respiratory defect associated with in the Fe–S assembly, directly involved in [4Fe–4S] cluster decreased activities of enzymes related to the product of formation . lipoic acid synthase, all of which require 4Fe–4S clusters Another protein related to the Fe–S cluster assembly and . Previous findings in yeast regarding BolA2 indicate mitochondrial respiratory complexes is the P-loop ATPase that this cytosolic protein interacts with Grx3/4 as a chap- IND1. Silencing of IND1 caused a severe decrease of the erone . Fe–S cluster-carrying complex I subunits, namely NDUFS1, A very important finding that defined the extent of the NDUFV1, NDUFS3 and NDUFA13, leading to a defect in mitochondrial Fe–S assembly machinery was that of Atm1. the assembly of the peripheral arm of the complex . A mutant strain for a mitochondrial ABC transporter in yeast Depletion of Ind1 in the yeast Yarrowia lipolytica also exhibited iron accumulation in mitochondria, respiration causes a defect in complex I assembly . defects and increased concentrations of glutathione . The transfer of the Fe–S clusters to apoproteins involves Labeled iron assays in a mutant for Atm1 indicated that the mobilization of the recently formed cluster to transfer this protein did not affect the assembly of Fe–S clusters in proteins or assembly factors (called carrier proteins in bac- mitochondria, yet it decreased the levels of the Fe–S cluster teria), which will subsequently pass on the cluster to the protein Leu1 in cytosol . The transporter is located in recipient protein. In bacteria, this process has been defined the inner mitochondrial membrane, with its ABC domains to work in a “one-way” mode, i.e., is irreversible [19, 49]. facing the mitochondrial matrix, which implies an export The transfer protein NFU1 (or Nfu in yeast) is known to activity mode . This transporter likely transfers a sulfur form homodimers and functions in mitochondria, cytosol derivative compound across the mitochondrial membrane, and plastids [118–122], although in vitro experiments of the which is essential in cytosol. bacterial protein in A. vinelandii has been recorded form- ing heteromers . The exact role of NFU1 in humans The CIA pathway remains unclear, although defects in NFU1 have been related to multiple mitochondria dysfunction syndrome [124–126]. Impairment of the mitochondrial Fe–S cluster assembly In this syndrome, the lack of lipoic acid, due to the defective affects maturation of the Fe–S proteins in the cytosol of activity of lipoic synthase, causes the subsequent impair- yeast and humans . Indeed, the mitochondrial machin- ment in lipoid acid-dependent enzymes, such as PDH and ery is involved in the formation of a glutathione-based com- KDH . In vitro assays have determined that the pro- pound that is translocated to the cytosol to be integrated into tein interacts with ISCA1  and BOL3 in humans . the cytosolic Fe–S cluster assembly through the ABC trans- Similar assays performed with yeast Nfu detected associa- porter Atm1 (Fig. 1) [131, 134, 135]. The maturation of the tions with Isa1 and Isa2, as well as with the [4Fe–4S] cluster Fe–S cluster proteins in the cytosol is performed by a differ - proteins, Aco1, Aco2, lipoic synthase, biotin synthase and ent machinery from that of the ISC system that depends on homoaconitase (Lys4) . Yeast cells defective in Nfu substrates that must be exported out of the mitochondrion. displayed a relatively mild respiration impairment . The cytosolic and nuclear de novo formation of [4Fe–4S] Yeast triple mutant bola1–bola3–nfu exhibited an enhanced Fe–S clusters requires the heterodimeric association of pro- phenotype unlike any of the individual mutants. Comple- teins Cfd1 and Nbp35, which share signic fi ant sequence sim - mentation experiments using human NFU1 or BOLA1 ilarity [136–138]. The latter also shares homology with its partially recovered the phenotype of the mutant, but not bacterial and archaeal counterpart ApbC, both being classi- BOLA3, which indicates that a concerted activity of NFU1 fied as P-loop-containing nucleoside triphosphate hydrolases and BOLA3 is necessary to recover the phenotype . . The ApbC/Nbp35 proteins were the first Fe–S cluster Moreover, the overexpression of Nfu in a bola3 mutant assembly proteins described in the Archaea . Nbp35 recovered the respiratory defect phenotype, which indicates exhibits an N-terminal Fdx-like domain, an ATP-binding overlapping functions . motif and C-terminal cysteine residues . The forma- The obvious connection between Nfu and BolA assembly tion of the stable heterodimer depends on a shared [4Fe–4S] factors places them in similar, yet non-overlapping roles. C-terminal cluster, labeled as bridging cluster, while both BolA is a recently described protein of bacterial origin with Nbp35 and Cfd1 each bear another [4Fe–4S] cluster in their 1 3 JBIC Journal of Biological Inorganic Chemistry (2018) 23:521–541 527 N-termini [137, 140] (Fig. 1). Of importance is the fact that cluster of Nbp35, yet has no effect on Cfd1 . In human the N-terminal Fe–S cluster of Nbp35 is oxygen stable, cells, CIAPIN1 has been found to interact with GLRX3, a unlike the bridging cluster [138, 140, 141]. Consequently, cytosolic monothiol glutaredoxin [129, 147, 149] described the N-terminal truncations render the protein unable to bear below. Indeed, in vitro assays captured the transfer of a a cluster . The Cfd1–Nbp35 conformation results in [2Fe–2S] cluster from the N-terminus of GLRX3 to the a heterotetrameric association capable of functioning as a N-terminus of CIAPIN1. This result led to propose that the scaffold for the assembly of an Fe–S cluster . Remarka- glutaredoxin feeds the [2Fe–S] cluster to CIAPIN1 . bly, Cfd1 and Nbp35 are not targets of the de novo assembly However, this observation is in disagreement with the previ- factors of the CIA pathway, despite the fact that they them- ously mentioned results from yeast, where the C-terminus selves carry clusters. Their assembly and insertion depend of Dre2 is key for cluster binding . Another piece of on the early steps of the pathway . Importantly, the evidence postulates that the maturation of the [2Fe–S] clus- Cfd1–Nbp35 heterotetramer formation does not take place ter in CIAPIN1 is not dependent on GLRX3, regardless of in plants and certain anaerobic protists due to the absence their physical interaction . of Cfd1 from their genomes [142, 143]. In humans, abla- The transient assembly of the Fe–S cluster on the tion of NBP35 causes an impairment in the iron-regulatory Cfd1–Nbp35 scaffold is followed by the interaction of the protein IRP1, which in turn affects the levels of ferritin and heterotetrameric complex with the iron-only dehydroge- increases the levels of transferrin uptake by a concomitant nase Nar1, which receives the cluster to further pass it on increase of transferrin receptor levels in the cell. This effect to the targeting complex that will install the cluster into the on iron homeostasis involves the CIA machinery in a regu- apotargets . Nar1 also bears an Fdx-like domain on its lation role in mammals that is not observed in yeast . N-terminus and a cysteine domain on its C-terminus typical The answer to which factors feed the stable Fe–S clusters of iron-only hydrogenases (for binding of the H-cluster). to the scaffold protein Nbp35 came about with the char - Since Nar1 is itself an Fe–S cluster protein, its maturation acterization of Dre2 in yeast . The deletion of Dre2 depends on its association with the Cfd1–Nbp35 complex was lethal when combined with those of the mitochondrial . carrier proteins Mrs3 and Mrs4 under iron-depleted condi- The following proteins constitute the CIA targeting com- tions. The rationale behind this experiment was to identify plex in humans: the WD-40-type protein CIA1 (also called protein(s) that provide a compound(s) for the cytosolic Fe–S CIAO), which functions as a scaffold; MMS19 (Met18 in cluster assembly, and resemble the phenotypes of CIA pro- yeast), CIA2A (or FAM96A) and CIA2B (or FAM96B), tein mutants known at the time . Interestingly, although whose role is targeting recipient apoproteins [15, 150–153]. described as a cytosolic protein, low amount of Dre2 was The cytosolic iron–sulfur protein 1 (CIA1) belongs to also found either in the mitochondria and/or bound to the the family of WD-40 proteins, which are known for their cytosolic side of the outer mitochondrial membrane [145, β-propeller structure repeats . It was initially charac- 146]. Dre2 is the yeast counterpart of anamorsin (or CIA- terized in yeast, where its depletion affected the maturation PIN1, cytokine-induced apoptosis inducer 1) in humans, as of the cytosolic and nuclear Fe–S proteins, yet it had no proven by a complementation assay in yeast with the human impact on the levels of Nbp35. Moreover, Cia1 was found to gene [144, 145, 147]. The protein exhibits an N-terminal interact with Nar1, the iron-only hydrogenase that receives SAM methyltransferase-like domain, and on its C-terminus the clusters from the Cfd1–Nbp35 scaffold. Similarly, Fe two motifs named I and II, which display cysteines required incorporation in the Cia1 mutant affected apoproteins, such to bind the clusters . In vitro experiments with overex- as Leu1 and Rli1, but had no significant impact on Nbp35, pressed protein show that maturation of Dre2, which bears Nar1 and mitochondrial Fe–S proteins . Complementa- a [2Fe–2S] and a [4Fe–4S] cluster, is independent of the tion assays of the Cia1 mutant with the human CIAO protein CIA factors, but requires the presence of Nfs1, positioning it recovered the phenotype, confirming their functional redun- functionally upstream of the Cfd1–Nbp35 scaffold step [144, dancy. Moreover, a structural analysis of Cia1 determined 148]. Further analyses revealed that Dre2 interacts and func- that it exhibits a conserved propeller axis structure . tions in association with a diflavin reductase Tah18, which Hence, it was concluded that in the maturation of cytosolic transfers electrons from NADPH to Dre2 (Fig. 1) . Fe–S cluster proteins, Cia1 performs a role downstream of At the same time, the human homolog of Tah18, NDOR, Nar1 . rescues the phenotype of tah18 yeast mutants and cooper- MMS19 was initially discovered in yeast, in mutants ates with Dre2, which further strengthens the relationship with an increased sensitivity to methyl methasulfonate, between Dre2 and Tah18 . However, in this model as reflected by its name . Fe incorporation in cells Dre2 is incapable of transferring clusters to apoproteins, but depleted for Mms19 affected apoproteins in a fashion similar seems indirectly involved, together with Tah18, in the trans- to that described for the Cia1 mutant . Importantly, the fer of electrons for the formation of the [4Fe–4S] N-terminal downregulation of MMS19 influenced proteins involved in 1 3 528 JBIC Journal of Biological Inorganic Chemistry (2018) 23:521–541 the DNA metabolism, such as Rad3 helicase and XPD. In homeostasis . Yeast mutants Grx3/4 exhibit reduced line with this finding, DNA helicase Dna2 and Rli1 were activities of respiratory complexes II and IV, as well as found interacting with MMS19, and the same applies to those of the mitochondrial ISC assembly scaffold proteins components of the CIA complex, namely CIA1, CIA2A and Aco1, Leu1 and Isu1. Moreover, the mutants display up to CIA2B [151, 152, 156]. Combined, these results provide tenfold decrease of iron incorporation into the CIA com- evidence for the role of MMS19 downstream of CIA1, tar- ponents that themselves carry Fe–S clusters, namely Dre2, geting a specific set of proteins, many of which are involved Nar1 and their target protein Rli1, and the same applies in DNA maintenance [151, 152]. for Isu1, biotin synthase, dihydroxyacid dehydratase and Further characterization of proteins that were found to heme-containing catalase [158, 159]. These results point interact with MMS19 revealed their involvement in the late to an overall effect on iron supply, which was markedly stages of the CIA pathway. Interestingly, CIA2A and CIA2B more severe in the cytosol than in the mitochondria . were found to interact in a mutually exclusive fashion with The regulation of iron concentration in yeast is directed CIA1 . Specific associations of these proteins seem to by the transcription factors Aft1 and Aft2, which manage be necessary for the maturation of certain proteins. CIA2A the transport of iron into the cell . In iron-replete is directly involved in the maturation of IRP1, which plays conditions, Aft1 is a cytosolic protein, yet when iron con- a role in cellular iron homeostasis . CIA2B in associa- centration is low, it is mobilized to the nucleus, where it tion with CIA1 and MMS19 is responsible for the assembly activates the transcription of the iron regulon [160–162]. of the Fe–S cluster of DYPD, an enzyme involved in the It has been suggested that this activation is incited by the detoxification of pyrimidine derivatives . Moreover, for failure of the mitochondrial iron supply directed toward the maturation of GPAT, an enzyme of the purine nucleotide the Fe–S cluster assembly, yet the deletion of components synthesis pathway, and POLD, only CIA1 and CIA2B were of the CIA pathway does not induce the same response required [15, 153]. [163, 164]. Mutants that activate the iron regulon by stim- MMS19 exhibits nine HEAT repeats, known to facilitate ulating the activity of the high-affinity iron transport sys- protein–protein interactions, which are distributed through- tem of multicopper oxidase Fet3 led to the discovery of six out the whole protein . Mutations in the C-terminal proteins involved in this role [160, 165]. These are Nfs1, HEAT repeats of MMS19 prove that they are responsible Isu1, Gsh2 , mitochondrial carrier Mtm1, an interac- for the binding of CIA2B. Moreover, the absence of MMS19 tor of the multiprotein regulator complex (which in turns renders CIA2B subject to proteosomal degradation . regulates RNA polymerase II), Sin4,  and Fra1 (Fe Since the binding of CIA2B to MMS19 was often accom- repressor of activation-1), the yeast homolog of bacterial panied by the presence of CIA1, it was proposed that at least BolA . These findings confirm earlier observations, two distinct types of associations, namely CIA1–CIA2A and in which the deletion of Grx3 and Grx4 induced the iron CIA1–MMS19–CIA2B, perform the maturation of differ - regulon when iron concentrations were normal [161, 162]. ent subsets of proteins (Fig. 1). In this model, CIA1 with Fra1 interacts with Fra2, Grx3 and Grx4, interactions that CIA2A act in an iron-regulation/sensing role, as depicted took place regardless of the iron conditions in which the by their specific interaction with IRP1 and IRP2, whereas cells were maintained . It was also described that CIA1 with MMS19 and CIA2B supply DNA metabolism- Grx3 and Grx4 interact with Aft1 . Deletion of the related proteins . gene fra1 does not specifically activate the iron regulon, while that of fra2 does . Fra2 binds Grx3 through Iron sensing and regulation and the relationship a specific interaction mediated via a histidine residue, with the CIA pathway which is critical for modulation of the iron regulon via Aft1 . Based on this finding, Fra1 and Fra2 seem to Iron sensing as a regulatory mechanism differs between interpret the iron conditions of the Fe–S cluster assembly. mammals and yeast. In mammals, the iron-responsive They are related to mitochondrial Fe–S cluster assembly protein 1 (IRP1) exhibits aconitase activity when bound and the iron regulon is induced when their concentration to Fe–S clusters; once the cluster is lost, IRP binds to decreases . iron-responsive elements on mRNAs that specify proteins In humans, only GLRX3 (also called PICOT) is found known to regulate iron homeostasis . In yeast, aco- in the cytosol where it interacts with the cytosolic form nitase does not exhibit mRNA binding activity. However, of the BOLA family in humans, BOLA2 [129, 169]. This two important players related to the cytosolic Fe–S cluster interaction is iron concentration dependent. Moreover, assembly and iron homeostasis are the Grx3/4 proteins. mutation of the GLRX3 cysteines in the motifs GrxA and They affect CIA proteins, their target apoproteins and GrxB, which are involved in binding of the [2Fe–2S] Fe–S some mitochondrial Fe–S assembly proteins, and there- cluster, almost completely disrupts the interaction with fore their involvement in cytosolic and mitochondrial iron BOLA2 . 1 3 JBIC Journal of Biological Inorganic Chemistry (2018) 23:521–541 529 these parasitic groups exhibit a classical cytosolic Fe–S Fe–S clusters in the supergroup Excavata assembly, from the genomic information available to us we predict that similarly conserved situation occurs in Euglenozoa diplonemids and euglenids (our unpubl. data). The Fe–S cluster assembly was systematically stud- Excavata is a eukaryotic “supergroup” that brings together ied only in the model species Trypanosoma brucei, which a diverse array of protists [8, 170, 171], with just a few expresses all components of the ISC and CIA pathways in its studied so far from the perspective of the Fe–S cluster mitochondrion and cytosol (Fig. 2) [172, 174]. Upon deple- assembly. The best-described one is that of the kineto- tion, most of these proteins are essential for both studied plastid flagellates, which are responsible for a range of life cycle stages, namely the bloodstream stage found in the diseases in humans and other vertebrates . The blood of mammals and the procyclic stage that is confined to only information available for the other two euglenozoan the tsetse fly vector. Moreover, rescues by human homologs clades, the euglenids and diplonemids, can be derived or expression of the T. brucei proteins in the corresponding from their genomes which are, however, not yet publicly yeast mutants confirmed sequence-based homology predic- available. All these protists display a single, usually exten- tions [20, 175–185], Tonini et al., resubmitted]. Only FdxB sively reticulated, cristae-bearing mitochondrion, with an , selenocysteine lyase  and TbCia2A (Tonini et al. active and complex electron transport chain. Kinetoplas- 2018, resubmitted) were found to be dispensable for T. bru- tids that belong to the genera Trypanosoma and Leishma- cei. A homolog of the Grx-interacting protein, BolA, has nia are capable of aerobic fermentation, as they excrete also been detected in the genome of T. brucei, although its metabolites from both glucose and amino acid metabo- role and localization have not been studied yet. lisms, but use O as an electron acceptor . Since both Fig. 2 Distribution of ISC (black letters), CIA (white letters), NIF incarcerata*, Naegleria gruberi**, Spironucleus salmonicida§, (light blue letters), CSD (purple letters) and SUF (in dark blue, gene Monocercomonoides sp., Trichomonas vaginalis and Giardia intesti- fusions in red) components in metazoans and representative species nalis. Data presented here should not be assumed for the whole gen- of Excavata. Representative species denoted in the figure are Stygiella era, but only for representative species 1 3 530 JBIC Journal of Biological Inorganic Chemistry (2018) 23:521–541 A number of gene duplications likely took place, as have been found in a wide range of environmental condi- several components of this pathway are supernumerary. In tions such as extreme heat, cold, high altitudes, extreme pH particular, Nfu is represented by three paralogs, which are and hypersaline concentrations [192–197]. We know most expressed in the mitochondrion and the cytosol in T. bru- about the genus Naegleria, as it includes the brain-infect- cei, while four paralogs are found in the related Leishmania ing amoeba N. fowlerii, and the related Paravahlkampfia spp., although these remain unstudied . Moreover, in T. francinae, also responsible for amoebic meningoencephalitis brucei two ferredoxins (FdxA, FdxB) are present and tran- . Both species possess classical mitochondria. On the scribed , Mms19 is found in two genomic loci and Cia2 other hand, a group of heteloboseids, such as Sawyeria mar- has been duplicated into Cia2A and Cia2B  [Tonini ylandensis [199, 200], Psalteriomonas lanterna [201–203], et al., resubmitted], just like in humans . The presence Monopylocystis visvesvarai  and Creneis carolina of supernumerary components is not unique, since f.e. in the , are found mostly in low oxygen conditions and carry plant Arabidopsis thaliana five Nfu homologs are present in the MROs. Other heteroloboseids including the halophilic various subcellular compartments . In some instances, Pleurostomum flabellatum and Vahlkampfia anaerobica the complexity took the path of alternatively spliced versions have been described to harbor cristae-devoid mitochondria, targeted at different locations, as was described in humans although their genomes and metabolisms have not yet been . The finding that all three Nfu proteins are essential thoroughly studied [193, 205]. for T. brucei suggests that they are likely involved in the Naegleria possesses classical ATP-producing mitochon- maturation of different sets of proteins . dria and displays components of the ISC pathway IscS, IscU Several aspects of the Fe–S cluster assembly and Fe–S and Isd11, as well as two putative Fdxs, Isa, Grx, Atm1 and cluster-carrying proteins have also been studied in the a BolA-like protein (Fig. 2). Moreover, the hydrogenosome trypanosomatid parasite Leishmania spp., which unlike T. of Sawyeria marylandensis contains paralogs of IscS and brucei prefers an intracellular niche that requires a range IscU, as well as Fxn and Fdx . of specific metabolic adaptations . Leishmania seems to use several Fe–S clusters containing proteins for redox Jakobids sensing . Trypanosoma cruzi, T. brucei and Leishmania spp. encode three 1-C-Grx genes in their genomes . Mitochondrial genomes of jakobids belong to the most Monothiol (1-C-Grx) and dithiol (2-C-Grx) glutaredoxins bacterial-like genomes known to date, though this premise exhibit distinct active sites motifs, CxxS and CxxC, respec- has been challenged by the plausibility of extensive lateral tively, which differentiate them . It has been observed gene transfer into the mitochondrial genomes [206–208]. in vitro that in T. brucei three 1-C-Grxs proteins are capa- Regardless, the organelle of jakobids contains the most ble of using glutathione and trypanothione as cofactors in gene-rich mitochondrial genomes, with the most extreme the mitochondrial [2Fe–2S] cluster transfer . This is a case represented by Andalucia godoyi, which displays 66 striking difference from the system described in yeast, where protein-coding genes and 29 tRNA genes . The orga- the glutaredoxin-bearing domain of Grx5 uses glutathione nelle of Stygiella incarcerata, originally considered to be a as a sulfur donor . Even more remarkable is the fact mitochondrion devoid of the cristae, is now known to be a that in T. brucei only 1-C-Grx1, but not 1-C-Grx2 and 3, is DNA-lacking hydrogenosome [207, 210]. capable of partially rescuing the deleterious phenotype of Interestingly, the hydrogenosome of S. incarcerata the Grx5 yeast mutant . All other components of the retains a complete Fe–S cluster assembly machinery, which ISC pathway, as well as most proteins known to participate includes IscS, IscU, Isa1 and Isa2, Fxn, Fdx, Grx5, Ssq1 in the CIA pathway, have also been detected in the Leish- chaperone and Nfu (Fig. 2, Table 1) . The ABC trans- mania genome . porter Atm1 is also expressed, suggesting this organism dis- plays a mitochondrion-dependent, cytosol-localized Fe–S Heteroloboseids cluster assembly. At the same time, a SufCB fusion seems to lack the mitochondrial targeting signal, implying its highly This clade brings together amoebic, amoeboflagellated likely cytosolic localization . However, it has been and cyst-forming protists found in both oxic and anoxic documented in other MRO-bearing organisms such as Blas- (or microaerophilic) environments, most of which remain tocystis, Entamoeba and Trichomonas that the hydrogenoso- understudied . Approximately, 150 species are known mal proteins may not require a dedicated targeting signal to to belong to this clade and, though it is not species rich, this be translocated into the organelle [28, 211–213]. The assem- group gathers a high morphological variability and a broad bly of SufBCD in bacteria studied both in vitro and in vivo ecological distribution. Some of its members may transit demonstrated its role in the maturation of [2Fe–2S] Fdx, through the flagellated and amoeba life stages, while others aided by SufA in the transfer of the cluster [48–50]. The have retained either the former or the latter stage . They SufCB fusion, most likely obtained from bacteria, has been 1 3 JBIC Journal of Biological Inorganic Chemistry (2018) 23:521–541 531 Table 1 Presence/absence of ISC, CIA, SUF, NIF and CSD components in different excavates and breviate Pygsuia a a a a a Organism T. brucei L.donovani Naegleria Sawyeria Stygiella Giardia Spironucleus Trichomonas Monocer- Pygsuia como- noides ISC IscS ✓ ✓ ✓ ✓ ✓ ✓ ✓ ✓ ✓ IscU ✓ ✓ ✓ ✓ ✓ ✓ ✓ ✓ Isd11 ✓ ✓ ✓ ✓ ✓ ✓ Isa1 ✓ ✓ Isa2 ✓ ✓ ✓ Fdx ✓ ✓ ✓ ✓ ✓ ✓ ✓ ✓ Fnx ✓ ✓ ✓ ✓ ✓ ✓ ✓ Nfu ✓ ✓ ✓ ✓ ✓ ✓ ✓ Iba57 ✓ Ind1 ✓ ✓ ✓ Atm1 ✓ ✓ ✓ ✓ ✓ CIA Cfd1 ✓ ✓ ✓ ? ✓ ? ✓ ✓ Nbp35 ✓ ✓ ✓ ? ? ✓ ✓ ✓ ✓ ✓ Dre2 ✓ ✓ ✓ ? ? ? Tah18 ✓ ✓ ✓ ? ? ? Nar1 ✓ ✓ ? ? ✓ ✓ ? ✓ ✓ Cia1 ✓ ✓ ✓ ? ? ✓ ✓ ✓ ✓ ✓ Cia2 ✓ ✓ ✓ ? ? ✓ ✓ ✓ ✓ ✓ Mms19 ✓ ✓ ? ? ? ✓ SUF SufS ✓ SufU SufB ✓ ✓ ✓ SufC ✓ NIF NifS CSD CsdA ✓ The data corresponds to representative species (should not be assumed for the whole genera): Sawyeria marylandensis, Stygiella incarcerata, Giardia intestinalis, Spironucleus salmonicida, Trichomonas vaginalis, Monocercomonoides sp. ✓ indicates presence; ? denotes the gene/protein has not been found, but may be present; blank indicates absence documented only in the cytosol of the anaerobic pathogen Giardia mitosomes lack DNA and are unable to generate Blastocystis , in the MRO lumen of Pygsuia biforma or export ATP into the cytosol . Nevertheless, they pos-  and Stygiella . The other bacterial machinery, the sess classic ISC components, such as IscS, IscU, Isa, Nfu NIF pathway, has been observed replacing the ISC system and Grx [216–221]. Although incomplete, most of the CIA of Entamoeba histolytica  and Mastigamoeba balamuthi pathway of Giardia is localized in the cytosol, with three . homologs of Nbp35 (Nbp35-1, Nbp35-2 and Nbp35-3), while Dre2, Tah18 and Mms19 seem to be absent (Table 1) Metamonada . Moreover, the ortholog of Cia2 exhibits dual locali- zation in the intermembrane space of the mitosome and the This group consists of anaerobic or microaerophilic protists cytosol, while Npb35 seems to be associated with the cyto- and is formed by three main lineages: (1) Fornicata (or the solic side of the outer mitosomal membrane . It was diplomonad/retortemonad/carpediemonad clade), repre- rather unexpected to find the CIA pathway in a cell lacking sented in this review by the mitosome-bearing Giardia intes- Atm1 and its cytosolic interactor, the Tah18/Dre2 complex, tinalis and Spironucleus salmonicida ; (2) Parabasalia, as it is widely accepted that the CIA pathway depends on a with the flag species Trichomonas vaginalis, bearer of the sulfur-containing molecule transported from the mitochon- first-described hydrogenosome ; (3) Preaxostyla, denoted drial matrix into the cytosol via Atm1. Therefore, it has been by Monocercomonoides  and the free-living Paratrimas- hypothesized that the dual localization of Cia2 aids in the tix . In all of Excavata, Metamonada exhibits the great- transport of the sulfur-containing molecule necessary for est functional diversity of MROs . the cytosolic assembly, in the apparent absence of the ABC 1 3 532 JBIC Journal of Biological Inorganic Chemistry (2018) 23:521–541 transporter Atm1 . The conspicuous absence of these while it expresses orthologs of Cfd1, Nbp35, Nar1, Cia1 proteins has also been observed in flagellates where the SUF and Cia2 (Table 1) . or the NIF system has replaced the ISC pathway, such as Various other metamonads, namely Carpediemonas Pygsuia and Blastocystis [13, 22]. membranifera, Chilomastix cuspidata, Dysnectes brevis, Spironucleus salmonicida encodes an unusually high Ergobibamus cyprinoides, Spironucleus vortens and Trepo- number of cysteine-rich proteins and evolved an extended monas PC1, for which no complete genomes but expressed system for counteracting oxygen stress . This diplo- sequence tags are available, bear IscS and IscU . Moreo- monad exhibits a standard hydrogenosome with a classical ver, they all seem to express Nbp35 of the CIA pathway, MRO-type ISC pathway [222, 223]. All of its components, while Cfd1 is mostly absent in this group, with the excep- namely IscS, IscU, Nfu, Fxn, two Fdxs and Jac1, have been tion of C. membranifera and C. cuspidata . Cia1 was localized to the organelle and bear MRO targeting signals found in all these protists, except S. vortens. Like in a range . Moreover, a selenocysteine lyase has been detected of metamonads, the Tah18/Dre2 complex and Mms19 are in this parasite, although neither its expression nor its absent. However, it has been suggested that the remaining localization has been confirmed; still, a sequence of a fused CIA components may be present in the genomes, but missed selenophosphate synthetase–NifS is present in its genome, in the available datasets . similar to the one found in T. brucei [78, 214]. Putative com- Finally, the oxymonad Monocercomonoides, the only ponents of the CIA pathway are also found in the S. salmo- genuine “amitochondriate” known so far, is also the most nicida genome, such as Cfd1, Nbp35, Tah18, Nar1, Cia1, extreme example of the Fe–S cluster machinery reduction Mms19 and Cia2 (Fig. 2, Table 1). . With several CIA pathway components complemented The human parasite T. vaginalis is a microaerophile, by the expression of SufB, SufC and the SufS–U fusion, it which exhibits a very strong iron-regulatable gene expres- is the only known eukaryote that completely lacks the mito- sion that allows it to modulate virulence factors and its abil- chondrial ISC machinery and instead acquired the bacterial- ity to adapt to microenvironments upon infection [224–227]. type SUF components. None of these components seem to Changes in the iron concentrations of its environment result bear a MRO targeting signal, as they translocate neither in fold changes in the expression of Fe–S clusters assembly into the hydrogenosome of T. vaginalis nor the mitochon- components [224, 225]. The DNA-lacking hydrogenosome dria of S. cerevisiae . The CIA pathway components of of T. vaginalis  harbors the ISC-type Fe–S cluster Monocercomonoides identified so far are Nbp35, Nar1, Cia1 assembly and makes use of a supernumerary machinery and Cia2A and Cia2B (Table 1). Its composition implies that of components: IscU, two IscS, Isd11s and Fxns, seven the de novo formation of clusters uses the bacterial SufS–U [2Fe–2S] Fdxs, three Isa2, four Nfus, four Ind1s (Table 1), CD-scaffold on SufB and SufC, and was apparently obtained as well as two homologs of the chaperone Hsc20 [24, 225, by a lateral gene transfer. This event likely took place before 229–231]. Upon iron depletion, most of these components the loss of the mitochondrion in Monocercomonoides, as become upregulated at least twofold. An example of this sit- gathered from its closest relative, Paratrimastix pyriformis, uation is Fdx, which in this flagellate exhibits six orthologs, which also possesses homologs of the SUF machinery and of which half is upregulated and half is down-regulated bears an MRO [23, 235]. during low iron conditions. This led to the assumption that the expression levels would relate them to their putatively different function, namely a role in the Fe–S cluster assem- Presence vs functionality: the requirement bly of the upregulated members, whereas those with low for mechanistic data to complement expression are likely involved in metabolic activities . phylogenomic analyses Trichomonas vaginalis is the only member of Excavata and the only other eukaryote apart from Entamoeba histo- The expansion of genomic analysis tools has given rise to lytica to express a homolog of the bacterial-type iron–sul- a high number of publicly available genomes. Studies of fur flavoprotein (Isf) . This hydrogenosomal protein is the evolution of mitochondria and MROs have unraveled involved in ROS detoxification and protection from the oxy - a wide variety of adaptations in the Fe–S cluster assembly gen-rich environmental changes. Moreover, it seems to be machineries that could provide explanations for the substan- present only in methane-synthesizing archaea and bacteria tial differences observed even among the model organisms [233, 234]. Isf is able to reduce oxygen and has a detoxifying from the supergroup Opisthokonta. The mechanisms behind activity against the drugs metronidazole and chlorampheni- the presence or absence of components of the ISC, SUF and col, used to treat anaerobic infections like those caused by T. CIA pathway in these clades, however, are mostly unknown, vaginalis . Isf is able to receive in vitro electrons from basically due to lack of mechanistic data. Fdx and NADH . Like other metamonads, T. vaginalis One of the prevalent differences observed between the also lacks the Tah18/Dre2 complex, along with Mms19, few above-mentioned species and the Opisthokonta model 1 3 JBIC Journal of Biological Inorganic Chemistry (2018) 23:521–541 533 species is the absence of Isd11 in organisms bearing ISC. systems . Its wide distribution among the aerobic and This feature points out to an acquisition of IscS/IscU from anaerobic organisms led to the proposal that it evolved prior bacterial lineages. Regardless, in Excavata IscS is always to oxygenation of the biosphere and adopted mechanisms accompanied by IscU, which confirms the findings of several for counteracting oxidizing conditions . Though the groups on the requirement of the CD for its specific scaffold SUF and ISC systems coexist in various bacterial lineages, to perform desulfuration of cysteine . The presence of the complementation with SUF components in the absence Isd11 in T. vaginalis has been suggested as a unique acquisi- of specific ISC components has not been possible . It tion, from a endosymbiotic event that gave origin to MROs has been well established that in proteobacteria the Fe–S . However, this hypothesis leaves out the fact that the cluster assembly by the SUF pathway is highly regulated protein is also absent in protists described recently as bear- by protein–protein interactions [55, 236, 243]. A study that ing similar organelles. reported the complementation of the SUF system of E. coli The dispersed distribution of the scaffold-type proteins, with that of E. faecalis also conveyed that the SUF machin- particularly those characterized as the carrier or transfer pro- ery of the Gram-positive bacteria could replace IscS neither teins, is important for the determination of the mechanistic in E. coli nor in A. vinelandii . These features pin- specificity of the Fe–S cluster assembly systems. CsdE is point to a specificity of activities, which may explain why a CD incapable of complementing the assembly of Fe–S in the protist systems with the SUF fusions IscS or IscU are clusters on the IscU scaffold, despite the wide range of sub- absent. The presence of the SUF systems in eukaryotes is strates this CD is able to metabolize [46, 71, 73, 236]. This documented in plastids, which also lack ISC . How- is, however, not exactly the same for the transfer proteins, ever, this system displays functional differences from that which to deliver the clusters also require a physical interac- of bacteria. The observation that SufB in A. thaliana has an tion with their recipient apoproteins. Unlike the CDs with ATPase activity, unlike its counterpart in bacteria, denotes U-type scaffolds, the carrier or transfer proteins seem to that in eukaryotes the SUF system has acquired unique fea- be, to a certain extent, interchangeable in bacteria . For tures [245, 246]. example, the deletion of IscA or SufA in E. coli does not The hypothesis mentioned above gives a mechanistic affect survival; however, this is not true for the absence of answer for the characteristic presence of the SUF system ErpA [237, 238]. A similar situation was observed for S. in protists. However, there is no explanation as to why the cerevisiae . However, in the presence of oxygen, Azo- SUF system, rather than the ISC or the NIF systems, was tobacter vinelandii cannot survive mutation of IscA in the obtained. It has been reported that the relationship between presence of oxygen . The distinct phenotypes following the SUF and ISC systems involves regulation of the com- the deletions or mutations of carrier proteins in bacteria indi- plete pathways based on environmental conditions. Such is cate their functional specificity in vivo [53, 237]. This means the case of the SUF operon in E. coli, which is overexpressed that the recipient proteins that require maturation by specific on low-iron conditions and oxidative stress, at the same time transfer proteins may or may not be structurally recognized that the ISC operon is rendered inactive by transcriptional by a given system component . These cellular require- regulation of IscR. In Pseudomonas aeruginosa, IscR regu- ments cannot be bypassed by the apparent overall functional lates cellular iron homeostasis by sensing Fe–S concentra- redundancy of the Fe–S assembly systems. The case of Pyg- tions . T. vaginalis is an example of adaptation of the suia is a notable exception to these observations. Breviate Fe–S cluster machinery to match specific cellular require- Pygsuia exhibits a SufB–C fusion, yet it also harbors a copy ments. This anaerobic parasite displays supernumerary com- of IscS, with no obvious presence of IscU. Therefore, this ponents of various components of the ISC pathway, which fusion scaffold may be capable of providing the structural are up- or down-regulated in response to the changing iron functionality for IscS. . concentrations in its environment . A scaffold protein that has been conserved throughout Therefore, to characterize the regulatory capacity of a evolution is Nbp35. Although the CIA pathway displays the system, one has to determine the expression of its com- characteristics of a relatively new eukaryotic acquisition, the ponents. However, this type of data may be obtained only almost universal presence of this protein conveys how the by analyzing the Fe–S cluster assembly as a whole, a field Fe–S cluster assembly can repurpose a pre-existing protein where microbiologists take the lead when compared with for a new function. On the other hand, the partner of Nbp35, what is known about eukaryotic systems. This should not Cfd1, has a rather patchy distribution in the protist groups. be confused with analytical methods, which are rich in stud- Originally from Archaea, most ApbC homologs in bacteria ies of the Fe–S cluster assembly in Opisthokonta. Still, the and archaea lack the Fdx motif present in Nbp35 . limited set of model organisms restricts our overall picture. Another interesting finding is the gene fusion of various While it is challenging to establish the methodology for a SUF components present in metamonads and jakobids. The new eukaryotic model organism, this has to be overcome. 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Lill R, Dutkiewicz R, Freibert SA et al (2015) The role of mito- chondria and the CIA machinery in the maturation of cytosolic Acknowledgements We are grateful to Dr. Vladimír Hampl (BIOCEV, and nuclear iron–sulfur proteins. Eur J Cell Biol 94:280–291. Charles University, Prague) for critical reading of the manuscript. We https ://doi.org/10.1016/j.ejcb.2015.05.002 would also like to acknowledge the immense amount of guidance from 15. Stehling O, Mascarenhas J, Vashisht AA et al (2013) Human the reviewers of the final manuscript. Support from the Czech Grant CIA2A-FAM96A and CIA2B-FAM96B integrate iron homeo- Agency 16-18699S, ERC CZ LL1601, and the ERD Funds, Project stasis and maturation of different subsets of cytosolic-nuclear OPVVV 16_019/0000759 to JL are kindly acknowledged. This article iron–sulfur proteins. 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