autotrophic

Edge evidence

• autotrophic has carbon source carbon dioxide METPO:2007806

  Autotrophs use CO2 as an inorganic carbon source.

  • DOI:10.1038/nrmicro.2016.130 require only CO2 as a carbon source Supports CO2 as the defining autotrophic carbon source.
• bicarbonate alternative inorganic carbon source for autotrophic

  Bicarbonate is another inorganic carbon species available for autotrophic fixation.

  • DOI:10.1128/AEM.02473-10 autotrophic carbon dioxide assimilation pathway Supports inorganic carbon assimilation by autotrophic pathways.
• energy and reductant regulates CO2-fixation pathway RO:0002211

  Autotrophic carbon fixation requires energy and reducing power.

  • DOI:10.1038/nrmicro2365 energy demand of the autotrophic pathways Supports energy requirements of autotrophic carbon fixation pathways.
• carbon dioxide fixed by CO2-fixation pathway METPO:2007404

  CO2 is converted into organic carbon by autotrophic fixation pathways.

  • DOI:10.1128/AEM.02473-10 autotrophic CO2 fixation Supports CO2 fixation as the core autotrophic biosynthetic process.
• Calvin-Benson cycle example of CO2-fixation pathway rdfs:subClassOf

  The Calvin-Benson cycle is a major autotrophic CO2-fixation pathway.

  • DOI:10.1128/AEM.02473-10 Calvin-Benson reductive pentose phosphate cycle Supports the Calvin-Benson cycle as a microbial autotrophic pathway.
• RuBisCO catalyzes Calvin-Benson cycle biolink:catalyzes

  RuBisCO is the key carboxylating enzyme of the Calvin-Benson cycle.

  • DOI:10.1128/AEM.02473-10 ribulose-1,5-bisphosphate carboxylase Supports RuBisCO as the marker enzyme for Calvin-Benson autotrophy.
• CO2-fixation pathway has output precursor metabolites RO:0002234

  Fixed carbon is converted into central biosynthetic precursors.

  • DOI:10.1128/AEM.02473-10 converted to other central intermediates Supports conversion of fixed carbon into central metabolites.
• precursor metabolites incorporated into biomass biolink:part_of

  Fixed-carbon precursors are incorporated into cellular biomass.

  • DOI:10.1038/nrmicro.2016.130 microbial autotrophic production Supports production of biomass and products from autotrophic CO2 fixation.
• environmental pH determines speciation of dissolved inorganic carbon

  pH sets the relative abundance of CO2, bicarbonate, and carbonate available for fixation.

  • DOI:10.1128/aem.01557-23 CO2 predominates below ~pH 6.4, HCO3- at circumneutral pH, and CO32- above ~pH 10.3; DIC form availability constrains the fixation route.
• carbon-concentrating mechanism supplies substrate to CO2-fixation pathway

  CCMs elevate intracellular CO2 to enhance autotrophic carbon fixation.

  • DOI:10.1128/aem.01557-23 Transporters and CO2-active systems generate elevated intracellular HCO3- delivered for carboxysomal CO2 fixation.
• carboxysome contains RuBisCO

  Carboxysomes encapsulate RuBisCO to concentrate CO2 around the carboxylating enzyme.

  • DOI:10.1111/ppl.14140 Carboxysomes are protein shell encapsulated ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO).
• carboxysome contains carbonic anhydrase

  Carboxysomes house carbonic anhydrase alongside RuBisCO.

  • DOI:10.1128/aem.01075-24 Carboxysomes contain two key enzymes: carbonic anhydrase and RuBisCO.
• carbonic anhydrase converts carbon dioxide

  Carbonic anhydrase converts bicarbonate to CO2 for RuBisCO fixation.

  • DOI:10.1128/aem.01075-24 When cytoplasmic HCO3- enters carboxysomes, CA converts it to CO2, which is fixed by RuBisCO.
• Wood-Ljungdahl pathway example of CO2-fixation pathway rdfs:subClassOf

  The Wood-Ljungdahl pathway is an autotrophic CO2-fixation pathway producing acetyl-CoA.

  • DOI:10.1039/D4CB00099D Two CO2 molecules are fixed to acetyl-CoA via the WLP, requiring one ATP and eight electrons.
• Wood-Ljungdahl pathway has output acetyl-CoA RO:0002234

  The Wood-Ljungdahl pathway yields acetyl-CoA from fixed CO2.

  • DOI:10.1039/D4CB00099D Two CO2 molecules to acetyl-CoA via the WLP.
• CO dehydrogenase/acetyl-CoA synthase (CODH/ACS) catalyzes Wood-Ljungdahl pathway biolink:catalyzes

  CODH/ACS catalyzes the terminal acetyl-CoA-forming step of the Wood-Ljungdahl pathway.

  • DOI:10.1039/D4CB00099D CO dehydrogenase/acetyl-CoA synthase (CODH/ACS) produces acetyl-CoA in the WLP.
• molecular hydrogen provides reductant for Wood-Ljungdahl pathway

  H2 supplies reducing equivalents driving CO2 reduction in the Wood-Ljungdahl pathway.

  • DOI:10.1039/D4CB00099D H2 or CO must be utilized as an energy source to provide reducing equivalents for full CO2 reduction.