Abstract
BackgroundRedox enzyme maturation proteins (REMPs) describe a diverse family of prokaryotic chaperones involved in the biogenesis of anaerobic complex iron sulfur molybdoenzyme (CISM) respiratory systems. Many REMP family studies have focused on NarJ subfamily members from Escherichia coli: NarJ, NarW, DmsD, TorD and YcdY. The aim of this bioinformatics study was to expand upon the evolution, distribution and genetic association of these 5 REMP members within 130 genome sequenced taxonomically diverse species representing 324 Prokaryotic sequences. NarJ subfamily member diversity was examined at the phylum-species level and at the amino acid/nucleotide level to determine how close their genetic associations were between their respective CISM systems within phyla.ResultsThis study revealed that NarJ members possessed unique motifs that distinguished Gram-negative from Gram-positive/Archaeal species and identified a strict genetic association with its nitrate reductase complex (narGHI) operon compared to all other members. NarW appears to be found specifically in Gammaproteobacteria. DmsD also showed close associations with the dimethylsulfoxide reductase (dmsABC) operon compared to TorD. Phylogenetic analysis revealed that YcdY has recently evolved from DmsD and that YcdY has likely diverged into 2 subfamilies linked to Zn- dependent alkaline phosphatase (ycdX) operons and a newly identified operon containing part of Zn-metallopeptidase FtsH complex component (hflC) and NADH-quinone dehydrogenase (mdaB). TorD demonstrated the greatest diversity in operon association. TorD was identifed within operons from either trimethylamine-N-oxide reductase (torAC) or formate dehydrogenase (fdhGHI), where each type of TorD had a unique motif. Additionally a subgroup of dmsD and torD members were also linked to operons with biotin sulfoxide (bisC) and polysulfide reductase (nrfD) indicating a potential role in the maturation of diverse CISM.ConclusionExamination of diverse prokaryotic NarJ subfamily members demonstrates that the evolution and genetic association of each member is uniquely biased by its CISM operon association.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-015-0412-3) contains supplementary material, which is available to authorized users.
Highlights
Redox enzyme maturation proteins (REMPs) describe a diverse family of prokaryotic chaperones involved in the biogenesis of anaerobic complex iron sulfur molybdoenzyme (CISM) respiratory systems
Closer inspection of DMSO reductase maturation protein D (DmsD) indicated that one or more copies of dmsD/ynfI were located in a dmsABC/ ynfEFGH operon confirming that dmsD was under-represented based on annotation annotators
Discriminating differences between DmsD/ YnfI and its DmsABC and YnfEFGH were impossible beyond Gammaproteobacteria, since pairwise protein sequence identities between known E. coli components and suspected DMSO/selenate reductase components were low (8–28 %) even within many Gammaproteobacterial species
Summary
Redox enzyme maturation proteins (REMPs) describe a diverse family of prokaryotic chaperones involved in the biogenesis of anaerobic complex iron sulfur molybdoenzyme (CISM) respiratory systems. Well-characterized examples from this superfamily include enzyme subfamilies such as dimethylsulfoxide (DMSO) reductase, trimethylamine N-oxide (TMAO) reductase, formate dehydrogenase (Fdh), and nitrate reductase (Nar) Due to their inherent complexity and cofactor requirements, the biogenesis of any CISM requires the aid of a specialized chaperone known as a redox enzyme maturation protein (REMP). Other distantly related REMP family members that are not considered part of this subgroup include, FdhD and FdhE affecting formate dehydrogenase-N complex activity [12, 13], HyaE for hydrogenase-1 maturation [14], chaperone for the periplasmic nitrate reductase (NapD) [15], and a hydrogenase2-specific chaperone (HybE) [14, 16] This subfamily is known by a variety of names all based on their homology to characterized members such as the DmsD/TorD and/ or TorD subfamily [11, 17] and to NarJ [9]. Since this study will focus on characterized members NarJ/NarW, DmsD, TorD and YcdY, the subfamily will be referred to as the NarJ subfamily based on most recent bioinformatics analyses [9] and findings presented in this study
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