methylotrophic

Edge evidence

• methylotrophic uses substrate methanol

  Methanol is a representative reduced C1 substrate for methylotrophy.

  • DOI:10.3389/fbioe.2021.787791 methanol utilization in methylotrophy Supports methanol as a methylotrophic substrate; other C1 substrates are not modeled here.
• methanol dehydrogenase oxidizes methanol METPO:2000016

  Methanol dehydrogenase catalyzes the first methanol oxidation step.

  • DOI:10.3389/fbioe.2021.787791 Mdh is a primary enzyme Supports methanol dehydrogenase as the primary methanol-utilization enzyme.
• methanol oxidized to formaldehyde METPO:2007405

  Methanol oxidation produces formaldehyde for assimilation or further oxidation.

  • DOI:10.3389/fbioe.2021.787791 converts methanol to formaldehyde Supports methanol-to-formaldehyde conversion.
• PQQ-dependent methanol dehydrogenase located in periplasmic space biolink:located_in

  PQQ-dependent MDH oxidizes methanol in the periplasm of Gram-negative methylotrophs.

  • DOI:10.3389/fbioe.2021.787791 oxidation of methanol occurs in the periplasmic space Supports periplasmic localization of PQQ-dependent methanol oxidation.
• PQQ-dependent methanol dehydrogenase produces formaldehyde METPO:2000202

  PQQ-dependent methanol dehydrogenase produces formaldehyde from methanol.

  • DOI:10.3389/fbioe.2021.787791 converts methanol to formaldehyde Source supports formaldehyde as the product of methanol oxidation by methanol dehydrogenases.
• formaldehyde assimilated by ribulose monophosphate cycle

  Formaldehyde can enter the RuMP cycle for growth on methanol.

  • DOI:10.3389/fbioe.2021.787791 ribulose monophosphate (RuMP) cycle Supports RuMP as a native formaldehyde assimilation pathway.
• formaldehyde assimilated by serine pathway

  Formaldehyde can enter the serine pathway for growth on methanol.

  • DOI:10.3389/fbioe.2021.787791 serine pathway Supports the serine pathway as a native formaldehyde assimilation route.
• ribulose monophosphate cycle produces biomass precursor METPO:2000202

  RuMP assimilation incorporates C1 carbon into cellular material.

  • DOI:10.3389/fbioe.2021.787791 growth support of microorganisms in methanol Supports assimilation pathways as growth-supporting routes.
• 3-hexulose-6-phosphate synthase (Hps) catalyzes ribulose monophosphate cycle biolink:catalyzes

  Hps drives formaldehyde assimilation in the RuMP cycle.

  • DOI:10.1038/s41467-023-43610-7 The RuMP pathway relies on 3-hexulose 6-phosphate synthase (Hps) and phosphohexose isomerase (Phi) to assimilate formaldehyde.
• serine-glyoxylate aminotransferase (SgaA/SGT) catalyzes serine pathway biolink:catalyzes

  SgaA/SGT is a conserved serine-cycle enzyme.

  • DOI:10.1128/msystems.00248-24 Serine-glyoxylate transaminase (SGT) occurs in all 75 organisms; strong serine-cycle marker.
• hydroxypyruvate reductase (HprA/HPR) catalyzes serine pathway biolink:catalyzes

  HprA/HPR is a ubiquitous serine-cycle enzyme.

  • DOI:10.1128/msystems.00248-24 Hydroxypyruvate reductase (HPR) is ubiquitous (all 75 genomes); strong serine-cycle marker.
• formaldehyde dehydrogenase (Fld/FDH) oxidizes to formate

  Formaldehyde dehydrogenase oxidizes formaldehyde to formate.

  • DOI:10.1128/msystems.00248-24 FDH converts formaldehyde to formate in the dissimilatory oxidation branch.
• formate dehydrogenase (Fdh) oxidizes to carbon dioxide

  Formate dehydrogenase oxidizes formate to CO2 completing C1 dissimilation.

  • DOI:10.1007/s00284-022-03141-8 Oxidation of formaldehyde via H4F/RuMP routes to formate and then to CO2; strong downstream dissimilation edge.
• MxaFI methanol dehydrogenase requires cofactor pyrroloquinoline quinone (PQQ)

  MxaFI methanol dehydrogenase requires the PQQ redox cofactor.

  • DOI:10.1128/msphere.00685-24 Mxa-type MDHs belong to the PQQ-dependent alcohol dehydrogenase family.
• MxaFI methanol dehydrogenase requires cofactor calcium ion (Ca2+)

  MxaFI methanol dehydrogenase requires a calcium ion in its active site.

  • DOI:10.1016/b978-0-443-13307-7.00014-1 MxaF contains a calcium ion in its active site.