Subsystem: Glycolate, glyoxylate interconversions

This subsystem's description is:

Some bacteria can utilize glycolate as a carbon and energy source in aerobic conditions. This compound is abundant in nature and especially in algae or plants, where it is an important metabolite of photorespiration, often secreted. For example, in marine environment glycolate is a phytoplankton-specific exudate generated during autotrophic photorespiration (e.g. Fogg, 1983; Edenborn and Litchfield, 1987, Lau et al., 2006). Glycolate can compose a substantial proportion (10–50%) of phytoplankton-excreted dissolved organic carbon (DOC) in marine environments (Edenborn and Litchfield, 1987; Leboulanger et al., 1998).

Internally in microorganisms glycolate is formed (i) from 2-phosphoglycolate, a product of some DNA repair processes (Pellicer et al., 2003), by the action of ubiquitous Phosphoglycolate phosphatase (see SS: “2-phosphoglycolate salvage” for details); (ii) from glycoaldehyde via Glycoaldehyde-DH/Aldehyde-DH; and (iii) in cyanobacteria via the oxygenase activity of RUBISCO.

In bacteria glycolate is oxidized into glyoxylate by the enzyme glycolate oxidase (EC, a membrane-bound dehydrogenase that appears to be coupled to the electron transport chain for energy generation (Lord, 1972; Sallal and Nimer, 1989). More energy is generated when glyoxylate enters the TCA cycle (Ornston and Ornston, 1969; Lord, 1972). E.g. in marine bacteria, glycolate is thought to represent a major energy source that drives uptake of other compounds (Lau et al., 2006). Plants and animals contain a different type of glycogen oxidase - a directly O2-coupled, H2O2-producing enzyme (EC It’s putative homologs are present only in a few prokaryotes (mostly cyanobacteria) with complete genome sequences available to date (Eisenhut et al., 2006).

A hypothetical operon similar to GlcFDE, but containing only 2 out of 3 subunits, has been annotated here as HypFDR. It is not clear, whether or not it encodes glycolate oxidase.

The oxidation of glycolate to glyoxylate is counterbalanced by constitutive glyoxylate reductase activity, converting glyoxylate back into glycolate, catalyzed by Glyoxylate/ Hydroxypuryvate reductases, acting as a mechanism to remove the excess of highly reactive glyoxylate, thus preventing its conversion to oxalate (Rumsby, Cregeen, 1999). The net flux of carbon in either direction depends on the relative rate of the oxidative and the reductive processes in an organism. The presence of more than one enzyme with glyoxylate reductase activity in a given organism occurs frequently. These enzymes are all related to hydroxypyruvate reductases, and they usually act on both glyoxylate and hydroxypyruvate (Nunez et al., 2001). The majority of these enzymes display marked preference for NADPH over NADH cofactor (Nunez et al., 2001; Rumsby, Cregeen, 1999), with a notable exception of strictly NADH-specific archaeal enzymes (Ohshima T, et al., 2001). However, since cofactor specificity has been tested in only a handful of species, all other orthologs were annotated here as potentially NAD(P)H–specific: Glyoxylate reductase (EC / Glyoxylate reductase (EC

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