The role of Rnf in ion gradient formation in<i>Desulfovibrio alaskensis</i>

Wang, Luyao; Bradstock, Peter; Li, Chuang; McInerney, Michael J.; Krumholz, Lee R.

doi:10.7717/peerj.1919

Cited by 12 publications

(12 citation statements)

References 32 publications

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“…The rnf ( B ) CDGEA organization is found in species of Chlorobium , Bacteroides , and Prosthecochloris ( 42 ). The third configuration, rnfCDGEAB , is found in Acetobacterium woodii , Methanosarcina acetivorans , members of the Clostridia genera, and some Desulfovibrio species, among others ( 48 , 107 , 112 , 113 , 114 ). In Clostridium kluyveri , M. acetivorans , and A. woodii , Rnf ( rnfCDGEAB ) is the key complex in the energy conservation pathway during homoacetogenesis ( 31 ).…”

Section: Resultsmentioning

confidence: 99%

Homoacetogenesis in Deep-Sea Chloroflexi , as Inferred by Single-Cell Genomics, Provides a Link to Reductive Dehalogenation in Terrestrial Dehalococcoidetes

Sewell

Kaster

Spormann

2017

mBio

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The deep marine subsurface is one of the largest unexplored biospheres on Earth and is widely inhabited by members of the phylum Chloroflexi. In this report, we investigated genomes of single cells obtained from deep-sea sediments of the Peruvian Margin, which are enriched in such Chloroflexi. 16S rRNA gene sequence analysis placed two of these single-cell-derived genomes (DscP3 and Dsc4) in a clade of subphylum I Chloroflexi which were previously recovered from deep-sea sediment in the Okinawa Trough and a third (DscP2-2) as a member of the previously reported DscP2 population from Peruvian Margin site 1230. The presence of genes encoding enzymes of a complete Wood-Ljungdahl pathway, glycolysis/gluconeogenesis, a Rhodobacter nitrogen fixation (Rnf) complex, glyosyltransferases, and formate dehydrogenases in the single-cell genomes of DscP3 and Dsc4 and the presence of an NADH-dependent reduced ferredoxin:NADP oxidoreductase (Nfn) and Rnf in the genome of DscP2-2 imply a homoacetogenic lifestyle of these abundant marine Chloroflexi. We also report here the first complete pathway for anaerobic benzoate oxidation to acetyl coenzyme A (CoA) in the phylum Chloroflexi (DscP3 and Dsc4), including a class I benzoyl-CoA reductase. Of remarkable evolutionary significance, we discovered a gene encoding a formate dehydrogenase (FdnI) with reciprocal closest identity to the formate dehydrogenase-like protein (complex iron-sulfur molybdoenzyme [CISM], DET0187) of terrestrial Dehalococcoides/Dehalogenimonas spp. This formate dehydrogenase-like protein has been shown to lack formate dehydrogenase activity in Dehalococcoides/Dehalogenimonas spp. and is instead hypothesized to couple HupL hydrogenase to a reductive dehalogenase in the catabolic reductive dehalogenation pathway. This finding of a close functional homologue provides an important missing link for understanding the origin and the metabolic core of terrestrial Dehalococcoides/Dehalogenimonas spp. and of reductive dehalogenation, as well as the biology of abundant deep-sea Chloroflexi.

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Section: Resultsmentioning

confidence: 99%

Homoacetogenesis in Deep-Sea Chloroflexi , as Inferred by Single-Cell Genomics, Provides a Link to Reductive Dehalogenation in Terrestrial Dehalococcoidetes

Sewell

Kaster

Spormann

2017

mBio

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“…A ferredoxin:NAD + oxidoreductase (RNF) complex is present in all members of the Geovibrio clade and probably involved in the regeneration of oxidized ferredoxins via the reduction of NAD. We assume that this complex is proton‐translocating due to a significant similarity to the complex in Desulfovibrio alaskensis , which presumably pumps protons (Wang et al ., 2016). The observed similarity is based on an identical arrangement of genes ( rnfCDGEAB ) and a close phylogenetic relationship of the RnfD subunit with the homologous subunit in sulfate‐reducing deltaproteobacteria.…”

Section: Resultsmentioning

confidence: 99%

New insights into the energy metabolism and taxonomy ofDeferribacteresrevealed by the characterization of a new isolate from a hypersaline microbial mat

Spring

Rohde

Bunk

et al. 2022

Environmental Microbiology

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Summary Strain L21‐Ace‐BEST, isolated from a lithifying cyanobacterial mat, could be assigned to a novel species and genus within the class Deferribacteres. It is an important model organism for the study of anaerobic acetate degradation under hypersaline conditions. The metabolism of strain L21‐Ace‐BEST was characterized by biochemical studies, comparative genome analyses, and the evaluation of gene expression patterns. The central metabolic pathway is the citric acid cycle, which is mainly controlled by the enzyme succinyl‐CoA:acetate‐CoA transferase. The potential use of a reversed oxidative citric acid cycle to fix CO2 has been revealed through genome analysis. However, no autotrophic growth was detected in this strain, whereas sulfide and H2 can be used mixotrophically. Preferred electron acceptors for the anaerobic oxidation of acetate are nitrate, fumarate and dimethyl sulfoxide, while oxygen can be utilized only under microoxic conditions. Aerotolerant growth by fermentation was observed at higher oxygen concentrations. The redox cycling of sulfur/sulfide enables the generation of reducing power for the assimilation of acetate during growth and could prevent the over‐reduction of cells in stationary phase. Extracellular electron transfer appears to be an essential component of the respiratory metabolism in this clade of Deferribacteres and may be involved in the reduction of nitrite to ammonium.

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“…In the Manleluag spring, Rnf complex encoded by 8 out of 13 bacterial MAGs is a machine for energy conservation. Due to the high extracellular pH, the Rnf in this study is predicted to be a Na + pump, rather than an H + pump (Wang et al ., 2016a). V/A‐type ATPase was encoded by 12 of the MAGs, while three MAGs, MSW‐5 ( Tepidimonas ), MSW‐15 (UBA9089) and MSW‐24 ( Methylovolum ), harbour F‐type ATPase coding genes.…”

Section: Resultsmentioning

confidence: 99%

Carbon metabolism and adaptation of hyperalkaliphilic microbes in serpentinizing spring of Manleluag, the Philippines

Wang

Baker

et al. 2022

Environ Microbiol Rep

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Reduced substrates produced by the serpentinization reaction under hydration of olivine may have fuelled biological processes on early Earth. To understand the adaptive strategies and carbon metabolism of the microbes in the serpentinizing ecosystems, we reconstructed 18 draft genomes representing dominant species of Omnitrophicaeota, Gammaproteobacteria and Methanobacteria from the Manleluag serpentinizing spring in Zambales, Philippines (hyperalkaline and rich in methane and hydrogen). Phylogenomics revealed that two genomes were affiliated with a candidate phylum NPL-UPA2 and the references of all our genomes were derived from ground waters, hot springs and the deep biosphere. C1 metabolism appears to be widespread as most of the genomes code for methanogenesis, CO oxidation and CO 2 fixation. However, likely due to the low CO 2 concentration and election acceptors, the biomass in the spring was extremely low (<10 3 cell/ml). Various Na + and K + transporters and Na + -driving ATPases appear to be encoded by these genomes, suggesting that nutrient acquisition, bioenergetics and normal cytoplasmic pH were dependent on Na + and K + pumps. Our results advance our understanding of the metabolic potentials and bioenergetics of serpentinizing springs and provide a framework of the ecology of early Earth.

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The role of Rnf in ion gradient formation inDesulfovibrio alaskensis

Cited by 12 publications

References 32 publications

Homoacetogenesis in Deep-Sea Chloroflexi , as Inferred by Single-Cell Genomics, Provides a Link to Reductive Dehalogenation in Terrestrial Dehalococcoidetes

Homoacetogenesis in Deep-Sea Chloroflexi , as Inferred by Single-Cell Genomics, Provides a Link to Reductive Dehalogenation in Terrestrial Dehalococcoidetes

New insights into the energy metabolism and taxonomy ofDeferribacteresrevealed by the characterization of a new isolate from a hypersaline microbial mat

Carbon metabolism and adaptation of hyperalkaliphilic microbes in serpentinizing spring of Manleluag, the Philippines

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