Redox loops in anaerobic respiration - The role of the widespread NrfD protein family and associated dimeric redox module

Duarte, Américo G.; Barbosa, Ana C.C.; Ferreira, Delfim; Manteigas, Gonçalo; Domingos, Renato Mateus; Pereira, Inês

doi:10.1016/j.bbabio.2021.148416

Cited by 18 publications

(36 citation statements)

References 182 publications

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“…Fdn formate dehydrogenase, for example, oxidizes periplasmic formate and uses those electrons for cytoplasmic uptake of protons. Similar separations occur in the homologous b-type domains of Hyd-1 hydrogenase, Nar nitrate reductase, and Phs thiosulfate reductase [32][33][34] . In CbcL, this implies reduction of periplasmic cytochromes is coupled to cytoplasmic release of protons, which would not contribute to any redox loops or proton motive force generation.…”

Section: Discussionmentioning

confidence: 55%

Single amino acid residues control potential-dependent inactivation of an inner membrane bc-cytochrome

Joshi

Levar

Chan

et al. 2022

Preprint

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During extracellular electron transfer, Geobacter sulfurreducens constitutively expresses the bc-cytochrome CbcL, yet cells containing only this menaquinone oxidase fail to respire above -0.1 V vs. SHE. By identifying mutations within cbcL that permit growth at higher potentials, we provide evidence that this cytochrome is regulated by redox potential. Strains expressing CbcL V205A, CbcL V205G, and CbcL F525Y were capable of growth with high potential electron acceptors including Fe(III) citrate, Mn(IV) oxides, and electrodes poised at +0.1 V vs. SHE. Electrochemical characterization of wild type CbcL revealed oxidative inactivation of electron transfer above -0.1 V, while CbcL V205A, CbcL V205G, and CbcL F525Y remained active. Growth yields of CbcL V205A, CbcL V205G, and CbcL F525Y were only 50% of WT, consistent with CbcL dependent electron transfer conserving less energy. These data support the hypothesis that CbcL has evolved to rapidly shut off in response to redox potential to divert electrons to higher yield oxidases that coexist in the Geobacter membrane

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Section: Discussionmentioning

confidence: 55%

Single amino acid residues control potential-dependent inactivation of an inner membrane bc-cytochrome

Joshi

Levar

Chan

et al. 2022

Preprint

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“…Furthermore, in AArc-CO, only the cells grown with CO expressed one of the four copies of the NrfCD/PsrBC-like membrane-bound complex which is supposed to be able to interact with the quinone pool in various respiratory complexes [60], indicating that it might potentially be involved in the electron transfer from CODH as well.…”

Section: Whole Cell Lysate Shotgun Proteomic Analysismentioning

confidence: 99%

“…(3) ferredoxin>NrfC4D4>membrane protein; the membrane protein in all three loci is conserved but its function cannot be predicted, while the ferredoxin seems to belong to the family of ferredoxin-NAD(P) oxidoreductase family. The NrfC and D are homologues of PsrB and C, respectively, and recently this membrane associated quinol-dehydrogenase module was found to be widely present in various anaerobic quinol-interacting respiratory complexes, for example in the Qrc (as QrcCD) and Dsr (as DsrOP) complexes of sulfate-reducing bacteria [60]. The presence of four such modules in AArc-CO genome strongly suggest that they are an important part of the anaerobic respiration in this organism, but, once more, since they are not in a direct association with the loci encoding either CO, H 2 or formate-oxidizing enzymes, their true function can not be predicted for now.…”

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confidence: 99%

Anaerobic carboxydotrophy in sulfur-respiring haloarchaea from hypersaline lakes

Sorokin

Merkel

Messina³

et al. 2022

The ISME Journal

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“…The DsrO protein is an iron-sulphur protein while DsrP is cofactor-less and member of the NrfD/PsrC protein family. Together they are part of a widespread redox-loop module, involved in redox transfers for the quinone pool [ 95 ]. This is also shown by the high number of false positives identified in genomes devoid of DsrAB.…”

Section: Introductionmentioning

confidence: 99%

DiSCo: a sequence-based type-specific predictor of Dsr-dependent dissimilatory sulphur metabolism in microbial data

Neukirchen

Sousa

2021

Microbial Genomics

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Current methods in comparative genomic analyses for metabolic potential prediction of proteins involved in, or associated with the Dsr (dissimilatory sulphite reductase)-dependent dissimilatory sulphur metabolism are both time-intensive and computationally challenging, especially when considering metagenomic data. We developed DiSCo, a Dsr-dependent dissimilatory sulphur metabolism classification tool, which automatically identifies and classifies the protein type from sequence data. It takes user-supplied protein sequences and lists the identified proteins and their classification in terms of protein family and predicted type. It can also extract the sequence data from user-input to serve as basis for additional downstream analyses. DiSCo provides the metabolic functional prediction of proteins involved in Dsr-dependent dissimilatory sulphur metabolism with high levels of accuracy in a fast manner. We ran DiSCo against a dataset composed of over 190 thousand (meta)genomic records and efficiently mapped Dsr-dependent dissimilatory sulphur proteins in 1798 lineages across both prokaryotic domains. This allowed the identification of new micro-organisms belonging to Thaumarchaeota and Spirochaetes lineages with the metabolic potential to use the Dsr-pathway for energy conservation. DiSCo is implemented in Perl 5 and freely available under the GNU GPLv3 at https://github.com/Genome-Evolution-and-Ecology-Group-GEEG/DiSCo.

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Redox loops in anaerobic respiration - The role of the widespread NrfD protein family and associated dimeric redox module

Cited by 18 publications

References 182 publications

Single amino acid residues control potential-dependent inactivation of an inner membrane bc-cytochrome

Single amino acid residues control potential-dependent inactivation of an inner membrane bc-cytochrome

Anaerobic carboxydotrophy in sulfur-respiring haloarchaea from hypersaline lakes

DiSCo: a sequence-based type-specific predictor of Dsr-dependent dissimilatory sulphur metabolism in microbial data

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