Autotrophic carbon fixation in archaea

Berg, Ivan A.; Kockelkorn, Daniel; Ramos‐Vera, W. Hugo; Say, Rafael F.; Zarzycki, Jan; Hügler, Michael; Alber, Birgit E.; Fuchs, Georg

doi:10.1038/nrmicro2365

Cited by 605 publications

(535 citation statements)

References 113 publications

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“…No other obvious modes of CO or CO 2 fixation were noted in replicate NAG1 assemblies, based on genes coding for key marker enzymes of currently recognized autotrophic pathways (Berg et al, 2010). Although NAG1 has a gene coding for a Type II 4-hydroxybutyryl-CoA dehydratase, it is not known whether this protein is involved in CO 2 fixation.…”

Section: Functional Analysis Of Nag1 Genome Sequencementioning

confidence: 99%

“…Biotin is considered an essential vitamin throughout the domains Bacteria and Eukarya as it is utilized as a carboxyl carrier in pathways that mediate fatty acid synthesis, branched-chain amino-acid catabolism and gluconeogenesis. Moreover, the Sulfolobales, some Desulfurococcales and possibly one member of the Thermoproteales (T. pendens) utilize biotindependent carboxylases for the 3-hydroxypropionate/4-hydroxybutyrate CO 2 fixation pathway, but these enzymes are not required for central carbon metabolism and lipid biosynthesis (Berg et al, 2010). Interestingly, genes encoding biotin-dependent enzymes are not found in the genomes of other archaea including the Korarchaeota, Thermoplasmatales and Acidilobus spp.…”

Section: Cofactor Biosynthesismentioning

confidence: 99%

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Geoarchaeota: a new candidate phylum in the Archaea from high-temperature acidic iron mats in Yellowstone National Park

et al. 2012

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Geothermal systems in Yellowstone National Park (YNP) provide an outstanding opportunity to understand the origin and evolution of metabolic processes necessary for life in extreme environments including low pH, high temperature, low oxygen and elevated concentrations of reduced iron. Previous phylogenetic studies of acidic ferric iron mats from YNP have revealed considerable diversity of uncultivated and undescribed archaea. The goal of this study was to obtain replicate de novo genome assemblies for a dominant archaeal population inhabiting acidic ironoxide mats in YNP. Detailed analysis of conserved ribosomal and informational processing genes indicates that the replicate assemblies represent a new candidate phylum within the domain Archaea referred to here as 'Geoarchaeota' or 'novel archaeal group 1 (NAG1)'. The NAG1 organisms contain pathways necessary for the catabolism of peptides and complex carbohydrates as well as a bacterial-like Form I carbon monoxide dehydrogenase complex likely used for energy conservation. Moreover, this novel population contains genes involved in the metabolism of oxygen including a Type A heme copper oxidase, a bd-type terminal oxidase and a putative oxygen-sensing protoglobin. NAG1 has a variety of unique bacterial-like cofactor biosynthesis and transport genes and a Type3-like CRISPR system. Discovery of NAG1 is critical to our understanding of microbial community structure and function in extant thermophilic iron-oxide mats of YNP, and will provide insight regarding the evolution of Archaea in early Earth environments that may have important analogs active in YNP today.

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Section: Functional Analysis Of Nag1 Genome Sequencementioning

confidence: 99%

Section: Cofactor Biosynthesismentioning

confidence: 99%

Geoarchaeota: a new candidate phylum in the Archaea from high-temperature acidic iron mats in Yellowstone National Park

et al. 2012

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“…Our data support that MGI nitrification is linked to autotrophic CO 2 fixation in Bedford Basin. We identified proteins catalyzing three steps of the archaeal 3-hydroxypropionate/4-hydroxybutyrate pathway of CO 2 fixation (Berg et al, 2010), including …”

Section: Archaeal Nitrification and Carbon Fixationmentioning

confidence: 99%

Metaproteomic analysis of a winter to spring succession in coastal northwest Atlantic Ocean microbial plankton

et al. 2014

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In this study, we used comparative metaproteomics to investigate the metabolic activity of microbial plankton inhabiting a seasonally hypoxic basin in the Northwest Atlantic Ocean (Bedford Basin). From winter to spring, we observed a seasonal increase in high-affinity membrane transport proteins involved in scavenging of organic substrates; Rhodobacterales transporters were strongly associated with the spring phytoplankton bloom, whereas SAR11 transporters were abundant in the underlying waters. A diverse array of transporters for organic compounds were similar to the SAR324 clade, revealing an active heterotrophic lifestyle in coastal waters. Proteins involved in methanol oxidation (from the OM43 clade) and carbon monoxide (from a wide variety of bacteria) were identified throughout Bedford Basin. Metabolic niche partitioning between the SUP05 and ARCTIC96BD-19 clades, which together comprise the Gamma-proteobacterial sulfur oxidizers group was apparent. ARCTIC96BD-19 proteins involved in the transport of organic compounds indicated that in productive coastal waters this lineage tends toward a heterotrophic metabolism. In contrast, the identification of sulfur oxidation proteins from SUP05 indicated the use of reduced sulfur as an energy source in hypoxic bottom water. We identified an abundance of Marine Group I Thaumarchaeota proteins in the hypoxic deep layer, including proteins for nitrification and carbon fixation. No transporters for organic compounds were detected among the thaumarchaeal proteins, suggesting a reliance on autotrophic carbon assimilation. In summary, our analyses revealed the spatiotemporal structure of numerous metabolic activities in the coastal ocean that are central to carbon, nitrogen and sulfur cycling in the sea.

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“…Six mechanisms are currently known by which autotrophic organisms can fix the inorganic carbon (Huber et al, 2008;Berg et al, 2010a, b). Because of the general sensitivity of the corresponding enzymes to the oxygen, only two pathways, namely Calvin-Benson-Bassham and 3-hydroxypropionate/4-hydroxybutyrate (3-HP/4-HB) cycles, could occur in oxygenated seawater (Thauer, 2007;Berg et al, 2007Berg et al, , 2010a. Specially designed and previously tested primer pairs (Elsaied and Naganuma, 2001;Yakimov et al, 2007) were used to amplify the fragment of bacterial genes encoding the large subunit of red and green-like form I RuBisCO (CbbL), the key enzyme of Calvin-Benson-Bassham cycle (See Supplementary Table S2).…”

Section: Molecular Signatures Of Autotrophic Pathways In Mediterraneamentioning

confidence: 99%

Contribution of crenarchaeal autotrophic ammonia oxidizers to the dark primary production in Tyrrhenian deep waters (Central Mediterranean Sea)

et al. 2011

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Mesophilic Crenarchaeota have recently been thought to be significant contributors to nitrogen (N) and carbon (C) cycling. In this study, we examined the vertical distribution of ammonia-oxidizing Crenarchaeota at offshore site in Southern Tyrrhenian Sea. The median value of the crenachaeal cell to amoA gene ratio was close to one suggesting that virtually all deep-sea Crenarchaeota possess the capacity to oxidize ammonia. Crenarchaea-specific genes, nirK and ureC, for nitrite reductase and urease were identified and their affiliation demonstrated the presence of 'deep-sea' clades distinct from 'shallow' representatives. Measured deep-sea dark CO 2 fixation estimates were comparable to the median value of photosynthetic biomass production calculated for this area of Tyrrhenian Sea, pointing to the significance of this process in the C cycle of aphotic marine ecosystems. To elucidate the pivotal organisms in this process, we targeted known marine crenarchaeal autotrophy-related genes, coding for acetyl-CoA carboxylase (accA) and 4-hydroxybutyryl-CoA dehydratase (4-hbd). As in case of nirK and ureC, these genes are grouped with deepsea sequences being distantly related to those retrieved from the epipelagic zone. To pair the molecular data with specific functional attributes we performed [ 14 C]HCO 3 incorporation experiments followed by analyses of radiolabeled proteins using shotgun proteomics approach. More than 100 oligopeptides were attributed to 40 marine crenarchaeal-specific proteins that are involved in 10 different metabolic processes, including autotrophy. Obtained results provided a clear proof of chemolithoautotrophic physiology of bathypelagic crenarchaeota and indicated that this numerically predominant group of microorganisms facilitate a hitherto unrecognized sink for inorganic C of a global importance.

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Autotrophic carbon fixation in archaea

Cited by 605 publications

References 113 publications

Geoarchaeota: a new candidate phylum in the Archaea from high-temperature acidic iron mats in Yellowstone National Park

Geoarchaeota: a new candidate phylum in the Archaea from high-temperature acidic iron mats in Yellowstone National Park

Metaproteomic analysis of a winter to spring succession in coastal northwest Atlantic Ocean microbial plankton

Contribution of crenarchaeal autotrophic ammonia oxidizers to the dark primary production in Tyrrhenian deep waters (Central Mediterranean Sea)

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