Subsystem: L-rhamnose utilization

This subsystem's description is:

The well studied L-rhamnose utilization pathways in Escherichia coli include L-rhamnose uptake by RhaT permease, isomerization by RhaA isomerase, phosphorylation by the FGGY family kinase RhaB and breakdown by RhaD aldolase to produce glycerone-P and L-lactaldehyde.
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Microorganisms can utilize pentoses and deoxyhexoses as their sole carbon source. There are generally two pathways for the metabolism of these sugars, one with phosphorylated intermediates and the other without such intermediates. The former pathways of bacteria and/or fungi have been studied extensively. Many bacteria, including Escherichia coli, also metabolize l-rhamnose (l-6-deoxymannose) through this type of pathway, using enzymes consisting of l-rhamnose isomerase (EC 5.3.1.14), rhamnulokinase (EC 2.7.1.5), and rhamnulose-1-phosphate aldolase (EC 4.1.2.19). The l-lactaldehyde obtained, together with dihydroxyacetone phosphate, is further converted to l-lactate or 1,2-propanediol by l-lactaldehyde dehydrogenase (EC 1.2.1.22) and lactaldehyde : propanediol oxidoreductase [EC 1.1.1.77(55)] under aerobic and anaerobic conditions, respectively.

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

Literature ReferencesA genetic locus necessary for rhamnose uptake and catabolism in Rhizobium leguminosarum bv. trifolii. Richardson JS Journal of bacteriology 2004 Dec15576793
Eukaryotic and bacterial gene clusters related to an alternative pathway of nonphosphorylated L-rhamnose metabolism. Watanabe S The Journal of biological chemistry 2008 Jul 1818505728
Metabolism of L-fucose and L-rhamnose in Escherichia coli: aerobic-anaerobic regulation of L-lactaldehyde dissimilation. Baldomà L Journal of bacteriology 1988 Jan3275622
Novel modified version of nonphosphorylated sugar metabolism--an alternative L-rhamnose pathway of Sphingomonas sp. Watanabe S The FEBS journal 2009 Mar19187228
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Taxonomy Pattern 
Organism 
Domain
Variant [?] 
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RhaI*RhaB*RhaD*Lctald_util*RhaM*Rha_T*RhaFGHI*Regulator*Rhi_T*Hydrolase*YesQPO*RtpABCD*rtpEFGKLLRA1LRA2LRA3LRA4LRA5LRA6*LDHGusBRhaARhaCTM1061RhaR3
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The well studied L-rhamnose utilization pathways in Escherichia coli include L-rhamnose uptake by RhaT permease, isomerization by RhaA isomerase, phosphorylation by the FGGY family kinase RhaB and breakdown by RhaD aldolase to produce glycerone-P and L-lactaldehyde.
=======================================================
Microorganisms can utilize pentoses and deoxyhexoses as their sole carbon source. There are generally two pathways for the metabolism of these sugars, one with phosphorylated intermediates and the other without such intermediates. The former pathways of bacteria and/or fungi have been studied extensively. Many bacteria, including Escherichia coli, also metabolize l-rhamnose (l-6-deoxymannose) through this type of pathway, using enzymes consisting of l-rhamnose isomerase (EC 5.3.1.14), rhamnulokinase (EC 2.7.1.5), and rhamnulose-1-phosphate aldolase (EC 4.1.2.19). The l-lactaldehyde obtained, together with dihydroxyacetone phosphate, is further converted to l-lactate or 1,2-propanediol by l-lactaldehyde dehydrogenase (EC 1.2.1.22) and lactaldehyde : propanediol oxidoreductase [EC 1.1.1.77(55)] under aerobic and anaerobic conditions, respectively.
THIS SUBSYSTEM WAS started BY MATTC and EXTENded by OlgaZ AND finally adopted by Rodionov.
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In contrast to E.coli, many other species showed the presence of alternative non-orthologous or weakly similar enzymes for isomearse and aldolase roles.

B. subtilis rhamnose operon lack a rhaD ortholog but has a yuxG gene that is predicted to encode two domain protein with novel rhamnulose-6P aldolase attributed to an N-terminal domain and possible lactaldehyde dehydrogenase as an C-terminal domain (this functional role may be involved in utilization of lactaldehyde formed by aldolase). The rhamnose operons in many Actinobacteria, alphaproteobacteria, T. maritima, and Deinococcus also lack RhaD but has this bifunctional yuxG gene.Also we predicted novel lactaldehyde dehydrogenase genes in rhamnose gene clusters in some species (RhaZ and RhaW) that could be involved in conversion of lactaldehyde to L-lactate to finish the rhamnose pathway. The species that lack these novel roles (like E.coli) are most likely use intrinsic aldehyde dehydrogenases (aldA or aldB) to this final step of rhamnose catabolism.
Alternatively lactaldehyde could be converted to L-1,2-propanediol by lactaldehyde reductase FucO (this route of lactaldehyde utilization is used in the L-fucose pathway of E.coli).

Actinobacteria, alphaproteobacteria, T. maritima, and Deinococcus also has xenologous displacement of L-rhamnose isomerase. The predicted in these species L-rhamnose isomerase RhaI - has a very limited similarity to RhaA from E.coli (~20%) and belongs to the same family of sugar isomerases.
An ortholog of this novel isomerase RhaI was recently chracterized in Pseud. stutzeri as a L-rhamnose isomerase (it has 90 % similarity to RhaI from Rhizobium etli):
Leang K, Takada G, Fukai Y, Morimoto K, Granstrom TB, Izumori K. Novel reactions of L-rhamnose isomerase from Pseudomonas stutzeri and its relation with D-xylose isomerase via substrate specificity. Biochim Biophys Acta. 2004 Sep 6;1674(1):68-77.

The downstream gene of the rhamnose operon in E.coli, yiiL, is present in most L-rhamnose operons of bacteria and is predicted to encode L-rhamnose mutarotase. There are recent evidence of this functional role:
Ryu KS, Kim JI, Cho SJ, Park D, Park C, Cheong HK, Lee JO, Choi BS. Structural insights into the monosaccharide specificity of Escherichia coli rhamnose mutarotase. J Mol Biol. 2005 May 27;349(1):153-62. PMID: 15876375
Ryu KS, Kim C, Kim I, Yoo S, Choi BS, Park C. NMR application probes a novel and ubiquitous family of enzymes that alter monosaccharide configuration. J Biol Chem. 2004 Jun 11;279(24):25544-8.

Some species have new predicted rhamnose transporters like RhaY permease and RhaFGHJ ABC system.

RhaS-RhaR rhamnose regulatory system is substituted by predicted rhamnose regulatory systems from other families (DeoR or LacI).

Utilization Rhamnogalacturonides, or L-rhamnose containing oligosaccharides, was experimentally studied in plant pathogen Erwinia chrysanthemi. Hugouvieux-Cotte-Pattat N. The RhaS activator controls the Erwinia chrysanthemi 3937 genes rhiN, rhiT and rhiE involved in rhamnogalacturonan catabolism. Mol Microbiol. 2004 Mar;51(5):1361-74.
Rhamnogalacturonides utilization genes (rhi) are co-regulated with rha genes by RhaS activator.
E. chrysanthemi is able to degrade the main chain of rhamnogalacturonan I which consists of alternating galacturonate and L-rhamnose residues. Unsaturated rhamnogalacturonides are generated by the extracellular enzyme RhiE. They enter the cells, probably using the RhiT tranporter, where they are degraded by the intracellular enzyme RhiN. The lack of commercially available substrates prevented from obtaining more details on the intermediates generated during this catabolism. RhiE is under the control of rhe RhaS regulator involved in rhamnose catabolism. RhiT and RhiN which probably liberates DKI and rhamnose, are submitted to a double control by RhaS and KdgR.

OTHER REFERENCES:

1. Baldoma L, Aguilar J. Metabolism of L-fucose and L-rhamnose in Escherichia coli: aerobic-anaerobic regulation of L-lactaldehyde dissimilation. J Bacteriol. 1988 Jan;170(1):416-21.
PMID: 3275622.

2. Richardson JS, Hynes MF, Oresnik IJ. A genetic locus necessary for rhamnose uptake and catabolism in Rhizobium leguminosarum bv. trifolii. J Bacteriol. 2004 Dec;186(24):8433-42.PMID: 15576793.

-----alternative pathway of L-rhamnose metabolism:-----------------

3.Watanabe S, Makino K. Novel modified version of nonphosphorylated sugar metabolism--an alternative L-rhamnose pathway of Sphingomonas sp. FEBS J. 2009 Mar;276(6):1554-67. PMID: 19187228


4. Watanabe S, Saimura M & Makino K (2008) Eukaryotic and bacterial gene clusters related to an alternative pathway of non-phosphorylated L-rhamnose metabolism. J Biol Chem., 283, 20372-20382.PMID: 18505728

Currently selected organism: Chloroflexus aurantiacus J-10-fl (open scenarios overview page for organism)