Enzymes and coenzymes of the carbon monoxide dehydrogenase pathway for autotrophic CO2 fixation in Archaeoglobus lithotrophicus and the lack of carbon monoxide dehydrogenase in the heterotrophic A. profundus

Vorholt, Julia A.; Kunow, Jasper; Stetter, Karl O.; Thauer, Rudolf K.

doi:10.1007/bf00381784

Cited by 50 publications

(42 citation statements)

References 55 publications

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“…All four Hadesarchaeal genome bins lack most of the genes for the forward and reverse tricarboxylic acid (TCA) cycle (or the glycoxylate bypass) for the production of acetyl-CoA. Instead, they contain genes for the C 1 pathway (the carbon monoxide dehydrogenase pathway), which is typically used by methanogens and numerous other anaerobes for CO 2 fixation or production 10 . The YNP genomic bins (YNP_45 and YNP_N21) lack several genes for the CO dehydrogenase pathway, including those encoding formylmethanofuran-tetrahydromethanopterin N-formyltransferase ( ftr), methenyltetrahydromethanopterin cyclohydrolase (mch) and methylenetetrahydromethanopterin dehydrogenase (mtd), while the WOR bin DG-33 encodes all three (Fig.…”

Section: Euryarchaeotamentioning

confidence: 99%

Genomic inference of the metabolism of cosmopolitan subsurface Archaea, Hadesarchaea

Baker¹,

et al. 2016

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The subsurface biosphere is largely unexplored and contains a broad diversity of uncultured microbes1. Despite being one of the few prokaryotic lineages that is cosmopolitan in both the terrestrial and marine subsurface2–4, the physiological and ecological roles of SAGMEG (South-African Gold Mine Miscellaneous Euryarchaeal Group) Archaea are unknown. Here, we report the metabolic capabilities of this enigmatic group as inferred from genomic reconstructions. Four high-quality (63–90% complete) genomes were obtained from White Oak River estuary and Yellowstone National Park hot spring sediment metagenomes. Phylogenomic analyses place SAGMEG Archaea as a deeply rooting sister clade of the Thermococci, leading us to propose the name Hadesarchaea for this new Archaeal class. With an estimated genome size of around 1.5 Mbp, the genomes of Hadesarchaea are distinctly streamlined, yet metabolically versatile. They share several physiological mechanisms with strict anaerobic Euryarchaeota. Several metabolic characteristics make them successful in the subsurface, including genes involved in CO and H2 oxidation (or H2 production), with potential coupling to nitrite reduction to ammonia (DNRA). This first glimpse into the metabolic capabilities of these cosmopolitan Archaea suggests they are mediating key geochemical processes and are specialized for survival in the subsurface biosphere.

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Section: Euryarchaeotamentioning

confidence: 99%

Genomic inference of the metabolism of cosmopolitan subsurface Archaea, Hadesarchaea

Baker¹,

et al. 2016

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“…For instance, within the Euryarchaeota, the same way of CO 2 fixation (reductive acetyl-CoA pathway) has been found in members of different orders, e.g. in sulfate-reducing Archaeoglobales or in different orders of methanogens (Fuchs 1989;, 1994Jones et al 1987;Vorholt et al 1995Vorholt et al , 1997. One might argue that phylogeny is not an important determinant of the distribution of autotrophic pathways.…”

Section: Distribution Of Autotrophic Pathwaysmentioning

confidence: 95%

“…CO 2 fixation pathways have been studied extensively in Euryarchaeota such as the strictly anaerobic methanogens (Fuchs 1989(Fuchs , 1990(Fuchs , 1994Jones et al 1987), sulfate reducers (e.g. Archaeoglobus lithotrophicus) (Vorholt et al 1995), and nitrate reducers (e.g. Ferroglobus placidus) (Vorholt et al 1997).…”

Section: Introductionmentioning

confidence: 99%

Autotrophic CO2 fixation pathways in archaea (Crenarchaeota)

et al. 2003

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Representative autotrophic and thermophilic archaeal species of different families of Crenarchaeota were examined for key enzymes of the known autotrophic CO(2) fixation pathways. Pyrobaculum islandicum ( Thermoproteaceae) contained key enzymes of the reductive citric acid cycle. This finding is consistent with the operation of this pathway in the related Thermoproteus neutrophilus. Pyrodictium abyssi and Pyrodictium occultum ( Pyrodictiaceae) contained ribulose 1,5-bisphosphate carboxylase, which was active in boiling water. Yet, phosphoribulokinase activity was not detectable. Operation of the Calvin cycle remains to be demonstrated. Ignicoccus islandicus and Ignicoccus pacificus ( Desulfurococcaceae) contained pyruvate oxidoreductase as potential carboxylating enzyme, but apparently lacked key enzymes of known pathways; their mode of autotrophic CO(2) fixation is at issue. Metallosphaera sedula, Acidianus ambivalens and Sulfolobus sp. strain VE6 ( Sulfolobaceae) contained key enzymes of a 3-hydroxypropionate cycle. This finding is in line with the demonstration of acetyl-coenzyme A (CoA) and propionyl-CoA carboxylase activities in the related Acidianus brierleyi and Sulfolobus metallicus. Enzymes of central carbon metabolism in Metallosphaera sedula were studied in more detail. Enzyme activities of the 3-hydroxypropionate cycle were strongly up-regulated during autotrophic growth, supporting their role in CO(2) fixation. However, formation of acetyl-CoA from succinyl-CoA could not be demonstrated, suggesting a modified pathway of acetyl-CoA regeneration. We conclude that Crenarchaeota exhibit a mosaic of three or possibly four autotrophic pathways. The distribution of the pathways so far correlates with the 16S-rRNA-based taxa of the Crenarchaeota.

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“…While present in low levels in some methanogens (e.g., Methanosarcinales), it is present at concentrations between 100 to 400 mg per kg in many hydrogenotrophs (15,61,62). F 420 has also been identified in several nonmethanogenic euryarchaeota, including three species of the sulfate-reducing genus Archaeoglobus (19,(133)(134)(135) and seven species of the photosynthetic genera Halobacteria and Halococcus (20,136). The cofactor is also proposed to be central to the metabolism of the various lineages of the anaerobic methanotrophic archaea (ANME) (21,137).…”

Section: Distributionmentioning

confidence: 99%

“…It is well-established that, during the anaerobic oxidation of lactate to CO 2 , F 420 can be reduced by Mtd and Mer (133,200,202). Given that the organism lacks Frh, it remains to be resolved how A. fulgidus generates F 420 H 2 during hydrogenotrophic growth (203); possible routes include electron transfer from reduced ferredoxin (Fd red ) (via a hypothetical complex), quinols (via reverse electron transfer), or NADPH (via Npo) (135,200).…”

Section: Sulfate-reducing Archaeamentioning

confidence: 99%

Physiology, Biochemistry, and Applications of F₄₂₀- and F_o-Dependent Redox Reactions

Greening

Ahmed

Mohamed

et al. 2016

Microbiol Mol Biol Rev

159

208

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SUMMARY5-Deazaflavin cofactors enhance the metabolic flexibility of microorganisms by catalyzing a wide range of challenging enzymatic redox reactions. While structurally similar to riboflavin, 5-deazaflavins have distinctive and biologically useful electrochemical and photochemical properties as a result of the substitution of N-5 of the isoalloxazine ring for a carbon. 8-Hydroxy-5-deazaflavin (Fo) appears to be used for a single function: as a light-harvesting chromophore for DNA photolyases across the three domains of life. In contrast, its oligoglutamyl derivative F420is a taxonomically restricted but functionally versatile cofactor that facilitates many low-potential two-electron redox reactions. It serves as an essential catabolic cofactor in methanogenic, sulfate-reducing, and likely methanotrophic archaea. It also transforms a wide range of exogenous substrates and endogenous metabolites in aerobic actinobacteria, for example mycobacteria and streptomycetes. In this review, we discuss the physiological roles of F420in microorganisms and the biochemistry of the various oxidoreductases that mediate these roles. Particular focus is placed on the central roles of F420in methanogenic archaea in processes such as substrate oxidation, C1pathways, respiration, and oxygen detoxification. We also describe how two F420-dependent oxidoreductase superfamilies mediate many environmentally and medically important reactions in bacteria, including biosynthesis of tetracycline and pyrrolobenzodiazepine antibiotics by streptomycetes, activation of the prodrugs pretomanid and delamanid byMycobacterium tuberculosis, and degradation of environmental contaminants such as picrate, aflatoxin, and malachite green. The biosynthesis pathways of Foand F420are also detailed. We conclude by considering opportunities to exploit deazaflavin-dependent processes in tuberculosis treatment, methane mitigation, bioremediation, and industrial biocatalysis.

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Enzymes and coenzymes of the carbon monoxide dehydrogenase pathway for autotrophic CO2 fixation in Archaeoglobus lithotrophicus and the lack of carbon monoxide dehydrogenase in the heterotrophic A. profundus

Cited by 50 publications

References 55 publications

Genomic inference of the metabolism of cosmopolitan subsurface Archaea, Hadesarchaea

Genomic inference of the metabolism of cosmopolitan subsurface Archaea, Hadesarchaea

Autotrophic CO2 fixation pathways in archaea (Crenarchaeota)

Physiology, Biochemistry, and Applications of F₄₂₀- and F_o-Dependent Redox Reactions

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Enzymes and coenzymes of the carbon monoxide dehydrogenase pathway for autotrophic CO2 fixation in Archaeoglobus lithotrophicus and the lack of carbon monoxide dehydrogenase in the heterotrophic A. profundus

Cited by 50 publications

References 55 publications

Genomic inference of the metabolism of cosmopolitan subsurface Archaea, Hadesarchaea

Genomic inference of the metabolism of cosmopolitan subsurface Archaea, Hadesarchaea

Autotrophic CO2 fixation pathways in archaea (Crenarchaeota)

Physiology, Biochemistry, and Applications of F420- and Fo-Dependent Redox Reactions

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Physiology, Biochemistry, and Applications of F₄₂₀- and F_o-Dependent Redox Reactions