If an enzyme name is shown in bold, there is experimental evidence for this enzymatic activity.
Synonyms: aldolase pathway
|Superclasses:||Degradation/Utilization/Assimilation → Carbohydrates Degradation → Sugars Degradation → L-rhamnose Degradation|
Some taxa known to possess this pathway include : Aureobasidium pullulans , Azotobacter vinelandii NBRC 102612 , Burkholderia cenocepacia , Debaryomyces hansenii hansenii CBS767 , Scheffersomyces stipitis CBS 6054
L-rhamnose is a 6-deoxy-aldohexose that occurs in nature. Some fungi and bacteria posess an L-rhamnose degradation pathway that involves non-phosphorylated intermediates (this pathway), analogous to the Entner-Doudoroff pathway II (non-phosphorylative). This pathway is in contrast to the known bacterial L-rhamnose degradation pathway which involves phosphorylated intermediates (see L-rhamnose degradation I). Genes encoding enzymes of this pathway in Scheffersomyces stipitis CBS 6054 (previously known as Pichia stipitis), Debaryomyces hansenii hansenii CBS767 and Azotobacter vinelandii NBRC 102612 have been cloned, expressed and their products functionally characterized. Phylogenetic studies of the fungal and bacterial 2-keto-3-deoxy-L-rhamnoate aldolases (L-KDR aldolases) suggested that they are unrelated evolutionarily. Their respective non-phosphorylative L-rhamnose degradation pathways appear to have evolved independently and are the result of convergent evolution (in [Watanabe08a] and in [Watanabe09]). In Sphingomonas sp. SKA58, a variation of this non-phosphorylative pathway was demonstrated in which 2-dehydro-3-deoxy-L-rhamnonate is oxidized to L-2,4-diketo-3-deoxyrhamnonate, followed by hydrolysis of this compound to pyruvate and (S)-lactate (L-lactate) [Watanabe09] (see pathway L-rhamnose degradation III).
About This Pathway
The first reaction in this pathway shows the spontaneous conversion of the pyranose ring form of L-rhamnose to its furanose ring form L-rhamnofuranose (the α and β anomers of each form are not specified here). This reaction is shown because the reaction that follows is catalyzed by L-rhamnose 1-dehydrogenase (EC 22.214.171.124) which specifies L-rhamnofuranose as a substrate and L-rhamnono-1,4-lactone (L-rhamnono-γ-lactone) as a product. As noted in [Dahms72], a δ-lactone (1,5-lactone) would be produced by a pyranose ring form. Because the pyranose ring appears to be more stable than the furanose ring in aqueous solution (in [Ma98a] and reviewed in [Franks87]) this raises a question as to the actual identity of the lactone (1,4-lactone versus 1,5-lactone) produced in the dehydrogenase reaction. To date it has been identified as the 1,4-lactone [Watanabe08a, Watanabe09, Watanabe08].
The genes encoding enzymes of this pathway in Scheffersomyces stipitis CBS 6054, Debaryomyces hansenii hansenii CBS767, Azotobacter vinelandii NBRC 102612 and Burkholderia cenocepacia have been identified in homologous clusters and designated lra1, lra2, lra3 and lra4. In Scheffersomyces stipitis CBS 6054 (Pichia stipitis), Debaryomyces hansenii hansenii CBS767 and Azotobacter vinelandii NBRC 102612 they were shown to encode L-rhamnose 1-dehydrogenase, L-rhamnono-γ-lactonase, L-rhamnoate dehydratase and 2-keto-3-deoxy-L-rhamnoate aldolase functions, respectively. The products of the pathway are (S)-lactaldehyde and pyruvate [Watanabe08a]. This pathway is the significant physiological origin of (S)-lactaldehyde in fungi. In addition, a L-lactaldehyde dehydrogenase that produces (S)-lactate (L-lactate) was cloned and characterized in Scheffersomyces stipitis CBS 6054 and Azotobacter vinelandii NBRC 102612 ([Watanabe08a, Watanabe09, Watanabe08]).
In Sphingomonas sp. SKA58 the first three enzymatic reactions of this pathway are shared, but the last two reactions of the pathway were shown to be catalyzed by L-2-keto-3-deoxyrhamnoate 4-dehydrogenase and L-2,4-diketo-3-deoxyrhamnoate hydrolase encoded by genes lra5 and lra6, respectively. pyruvate and (S)-lactate are the end products of that pathway variant and (S)-lactaldehyde was not produced [Watanabe09] (see pathway L-rhamnose degradation III).
Watanabe08a: Watanabe S, Saimura M, Makino K (2008). "Eukaryotic and bacterial gene clusters related to an alternative pathway of nonphosphorylated L-rhamnose metabolism." J Biol Chem 283(29);20372-82. PMID: 18505728
Baldoma88: Baldoma L, Aguilar J (1988). "Metabolism of L-fucose and L-rhamnose in Escherichia coli: aerobic-anaerobic regulation of L-lactaldehyde dissimilation." J Bacteriol 170(1);416-21. PMID: 3275622
Caballero83: Caballero E, Baldoma L, Ros J, Boronat A, Aguilar J (1983). "Identification of lactaldehyde dehydrogenase and glycolaldehyde dehydrogenase as functions of the same protein in Escherichia coli." J Biol Chem 1983;258(12);7788-92. PMID: 6345530
Grochowski06: Grochowski LL, Xu H, White RH (2006). "Identification of lactaldehyde dehydrogenase in Methanocaldococcus jannaschii and its involvement in production of lactate for F420 biosynthesis." J Bacteriol 188(8);2836-44. PMID: 16585745
Inoue85: Inoue Y, Watanabe K, Shimosaka M, Saikusa T, Fukuda Y, Murata K, Kimura A (1985). "Metabolism of 2-oxoaldehydes in yeasts. Purification and characterization of lactaldehyde dehydrogenase from Saccharomyces cerevisiae." Eur J Biochem 153(2);243-7. PMID: 3908097
Rakus08: Rakus JF, Fedorov AA, Fedorov EV, Glasner ME, Hubbard BK, Delli JD, Babbitt PC, Almo SC, Gerlt JA (2008). "Evolution of enzymatic activities in the enolase superfamily: L-rhamnonate dehydratase." Biochemistry 47(38);9944-54. PMID: 18754693
Rea08: Rea D, Hovington R, Rakus JF, Gerlt JA, Fulop V, Bugg TD, Roper DI (2008). "Crystal structure and functional assignment of YfaU, a metal ion dependent class II aldolase from Escherichia coli K12." Biochemistry 47(38);9955-65. PMID: 18754683
Rodionova13a: Rodionova IA, Li X, Thiel V, Stolyar S, Stanton K, Fredrickson JK, Bryant DA, Osterman AL, Best AA, Rodionov DA (2013). "Comparative genomics and functional analysis of rhamnose catabolic pathways and regulons in bacteria." Front Microbiol 4;407. PMID: 24391637
Ryu04: Ryu KS, Kim C, Kim I, Yoo S, Choi BS, Park C (2004). "NMR application probes a novel and ubiquitous family of enzymes that alter monosaccharide configuration." J Biol Chem 279(24);25544-8. PMID: 15060078
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