NarJ subfamily system specific chaperone diversity and evolution is directed by respiratory enzyme associationsReport as inadecuate




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BMC Evolutionary Biology

, 15:110

First Online: 12 June 2015Received: 20 January 2015Accepted: 04 June 2015DOI: 10.1186-s12862-015-0412-3

Cite this article as: Bay, D.C., Chan, C.S. & Turner, R.J. BMC Evol Biol 2015 15: 110. doi:10.1186-s12862-015-0412-3

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.

KeywordsRedox Enzyme Maturation Protein REMP System specific chaperones NarJ NarW DmsD TorD YcdY Complex iron-sulfur molybdoenzymes Anaerobic respiration Chaperone Twin Arginine Translocase Tat AbbreviationsCISMComplex iron-sulfur molybdoenzyme

DMSODimethylsulfoxide

DmsDimethylsulfoxide reductase

FdhFormate dehydrogenase

NarNitrate reductase

MobisPGDMolybdenum-bis pyranopterin guanine dinucleotide

MSAMultiple sequence alignment

dN-dSNon-synonymous to synonymous substitution rate

REMPRedox enzyme maturation protein

TMAOTrimethylamine-N-oxide

TorTrimethylamine-N-oxide reductase

Denice C. Bay and Catherine S. Chan contributed equally to this work.

Electronic supplementary materialThe online version of this article doi:10.1186-s12862-015-0412-3 contains supplementary material, which is available to authorized users.

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Author: Denice C. Bay - Catherine S. Chan - Raymond J. Turner

Source: https://link.springer.com/



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