Subsystem: Formaldehyde assimilation: Ribulose monophosphate pathway

This subsystem's description is:

The ribulose monophosphate (RuMP) pathway, which was originally found in methylotrophic bacteria, is now recognized as a widespread prokaryotic pathway for formaldehyde fixation and detoxification (4, 7). In this pathway, formaldehyde reacts with ribulose 5-phosphate to form D-arabino-3-hexulose 6-phosphate, which is then isomerized to fructose 6-phosphate. These two reactions are catalyzed by D-arabino-3-hexulose 6-phosphate formaldehyde lyase (HPS) and 6-phospho-3-hexuloisomerase (PHI) respectively. These two key enzymatic reactions constitute Stage 1 one of the RuMP pathway.

Cyclic ribulose monophosphate pathway - assimilatory

During Stages 2 and 3 a series of interconversions occur that regenerate the RuMP acceptor molecule. Several variants of these interconverions are possible. In Stage 2 one of fructose-6-P molecules is split into C3 compounds via one of the two pathways – 2-dehydro-3-deoxyphosphogluconate aldolase (KDPGA) pathway using the enzymes of Entner-Doudoroff pathway (net product in this case is pyruvate), or Fructose-bisphosphate aldolase (FBA) pathway (net product– dihydroxyacetone-P) - see diagram.

Stage 3 is a sugar rearrangement stage, during which RuMP is regenerated from the glyceraldehyde 3-phosphate produced in Stage 2 and two fructose-6-P molecules produced in Stage 1. In some organisms this occurs via enzymes of pentose phosphate pathway (so called Transaldolase pathway), in others – via enzymes of Calvin pathway (Sedoheptulose-1,7-bisP aldolase pathway). Three out of the four possible combinations between stage 2 and stage 3 variants have been described. The use of KDPGA and SBPA pathways in combination has not been yet reported (D. White, 2000). Several key enzymes of stages 2 and 3 have been included in this SS as indicators of potential fate of assimilated formaldehyde in an organism.

Cyclic RuMP pathway - dissimilatory

The cyclic formaldehyde oxidation pathway (via 6-phosphogluconate dehydrogenase, decarboxylating (EC has been shown to play crucial role in C1 metabolism of M. flagellatus KT, most probably as the major energy-generating pathway (Chistoserdova et al., 2000). It is outlined as dissimilatory branch of RuMP in the RuMP_diagram.

Unconventional ribulose monophosphate pathways???

In addition to “classic” RuMP pathway, additional connections of the HSP-PHI shunt to core metabolism emerge via analysis of clustering of the corresponding genes with other genes on the chromosome:

1. In all S. aureus and S. epidermidis genomes the hps-phi gene cluster contains a gene encoding Glucosamine-6-phosphate deaminase (EC This may indicate channeling of the produced fructose-6-P produced into aminosugars (Taylor et al., 2004). However, another possibility is the conversion of glucosamine-6-phosphate into RuMP catalyzed by HSP-PHI enzymatic shunt running in reverse. RuMP may serve as an essential precursor of ribose-5-P, etc. Toxic formaldehyde produced in this scenario can be dissipated, for instance, via pyruvate formate-lyase (EC, present in Staphylococci. Exogenous sources of glucosamine-6-phosphate in a form of mucopolysaccharides, glycosaminoglycans, etc. may be are readily available from the host of S.aureus.

2. Another indirect indication of a potential role of the HSP-PHI shunt as a source of ribulose 5-phosphate is clusterization of the hps-phi genes with histidine biosynthetic operon in Aminomonas aminovorus C2A1 (Taylor et al., 2004) and Methylobacillus flagellatus KT – two very diverse methylotrophs. Two copies of HSP are present in M. flagellatus KT genome with one (fig|265072.1.peg.2071) co-localized as expected with other enzymes of C1 carbon metabolism methenyl-H4MPT cyclohydrolase and TA, while the other (fig|265072.1.peg.2331) is embedded in a histidine biosynthetic operon. Co-localization of the His operon with the genes catalyzing formation of RuMP can be rationalized by the fact that 5-phosphoribosyl 1-pyrophosphate is required for histidine synthesis.

3. Utilization of reversed RuMP pathway as the only ribose biosynthetic pathway in some Archaea was suggested in (Soderberg, 2005). See SS: Pentose phosphate pathway.

For more information, please check out the description and the additional notes tabs, below

Literature ReferencesThe physiological role of the ribulose monophosphate pathway in bacteria and archaea. Kato N Bioscience, biotechnology, and biochemistry 2006 Jan16428816
DiagramFunctional RolesSubsystem SpreadsheetDescriptionAdditional Notes 

Diagram 'd01' is not a new diagram.

Showing colors for genome: Staphylococcus aureus subsp. aureus str. Newman ( 426430.8 ), variant code 1

This diagram is not scaled.

Group Alias
Abbrev.Functional RoleReactionsScenario ReactionsGOLiterature

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