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 1.1.1.44)) 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 3.5.99.6). 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 2.3.1.54), 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.

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DiagramFunctional RolesSubsystem SpreadsheetDescriptionAdditional Notes 

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