Genome Property Definition Page

AccessionGenProp0457
Namerhamnose catabolism
TypeSYSTEM
DescriptionL-rhamnose, (aka 6-deoxy-L-mannose) is a common sugar synthesized and utilized in oligosaccharides and glcyolipids by many bacteria [2]. The monosaccharide is available in various environments and thus regulatory, transport and enzymatic systems have also evolved for its breakdown and use as a carbon source. The system modeled here includes specific transporters, ketose-aldose isomerases, kinases, and aldolases which result in the production of lactaldehyde and glycerone-phosphate. As these genes are generally organized into operons, assignments can be made for regulatory components as well as transport and enzymatic components which, by homology alone, cannot be assigned a specific substrate. Certain of the enzymes in this system are similar enough to cognate enzymes in the fucose catabolism system (GenProp0458) as to have caused gene naming errors in the past (i.e. fuculokinase/rhamnokinase). The system in certain rhizobial species [1] has been reported to vary from the canonical pathway in that the sugar may be phosphorylated prior to isomerization (i.e. the rhamnulokinase may in fact be a rhamnokinase and the rhamnose isomerase may be a rhamnose-1-phosphate isomerase), although this has not yet been independantly verified. In addition to the characterized rhamnose:proton symporter [3], rhamnose catabolism operons contain transporters from the ABC, and major facilitator families. Regulators are generally members of the DeoR and AraC [4] families. The product of both rhamnose and fucose catabolism is lactaldehyde, and subsequently alcohol and aldehyde dehydrogenases are often present in those operons to convert it to either 1,2-propane diol or lactate depending on oxidation conditions [5]. Rhamnose operons also often contain an epimerase (mutarotase) enzyme which has been proposed to be essential unly under limiting L-rhamnose conditions [6]. Partial rhamnose catabolism operons have been detected in Thermotoga species which appear to handle the import and cleavage of rhamnose-containing oligosaccharides.
JCVI RoleSugars
Parent PropertyGenProp0142: catabolism
Literature References
[ 1 ]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
[ 2 ]Tonetti M, Sturla L, Bisso A, Zanardi D, Benatti U, De Flora A  The metabolism of 6-deoxyhexoses in bacterial and animal cells.  Biochimie 1998 Nov;80(11):923-31.  PMID 9893952
[ 3 ]Muiry JA, Gunn TC, McDonald TP, Bradley SA, Tate CG, Henderson PJ  Proton-linked L-rhamnose transport, and its comparison with L-fucose transport in Enterobacteriaceae.  Biochem J 1993 Mar 15;290 ( Pt 3):833-42.  PMID 8384447
[ 4 ]Tobin JF, Schleif RF  Positive regulation of the Escherichia coli L-rhamnose operon is mediated by the products of tandemly repeated regulatory genes.  J Mol Biol 1987 Aug 20;196(4):789-99.  PMID 3316663
[ 5 ]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
[ 6 ]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. Epub 2005 Apr 7.  PMID 15876375
Web ReferencesKEGG:rhamnose catabolism
Gene Ontology TermGO:0015762: rhamnose transport (biological_process)
GO:0019301: rhamnose catabolic process (biological_process)
GO:0019301: rhamnose catabolic process (biological_process)
GO:0019301: rhamnose catabolic process (biological_process)
GO:0043463: regulation of rhamnose catabolic process (biological_process)

Components
Step NameStep NumRequiredEvidence (Method)Evidence Go Terms
clustered alcohol/aldehyde dehydrogenasesADHNOPF00465 (HMM-CLUST): alcohol dehydrogenase, iron-containing
PF00171 (HMM-CLUST): aldehyde dehydrogenase (NAD) family protein
PF00106 (HMM-CLUST): oxidoreductase, short chain dehydrogenase/reductase family
manual (NOCLUST)

TIGR02638 (NOCLUST): lactaldehyde reductase
GO:0019301: rhamnose catabolic process
GO:0019301: rhamnose catabolic process
GO:0019301: rhamnose catabolic process
GO:0019301: rhamnose catabolic process
GO:0019301: rhamnose catabolic process
rhamnulose-1-P aldolase (RhaD)aldolaseYESTIGR02624 (HMM): rhamnulose-1-phosphate aldolase
TIGR02632 (HMM): rhamnulose-1-phosphate aldolase/alcohol dehydrogenase
GO:0019301: rhamnose catabolic process
GO:0019301: rhamnose catabolic process
rhamnose epimeraseepimeraNOPF05336 (HMM-CLUST): PF05336 domain
TIGR02625 (HMM): L-rhamnose mutarotase
GO:0019301: rhamnose catabolic process
GO:0019301: rhamnose catabolic process
L-rhamnose isomerase (RhaA/RhaI)isomerasYESPF06134 (HMM): L-rhamnose isomerase (RhaA)
TIGR01748 (HMM): L-rhamnose isomerase
TIGR02629 (HMM): L-rhamnose catabolism isomerase
TIGR02635 (HMM): L-rhamnose isomerase
GO:0019301: rhamnose catabolic process
GO:0019301: rhamnose catabolic process
GO:0019301: rhamnose catabolic process
GO:0019301: rhamnose catabolic process
rhamnulokinase (RhaB/RhuK)kinaseYESPF00370 (HMM-CLUST): FGGY family of carbohydrate kinases, N-terminal domain
TIGR02627 (HMM): rhamnulokinase
GO:0019301: rhamnose catabolic process
GO:0019301: rhamnose catabolic process
clustered regulatory componentsregulatNOPF00165 (HMM-CLUST): transcriptional regulator, AraC family
PF00455 (HMM-CLUST): DeoR C-terminal sensor domain
PF00532 (HMM-CLUST): periplasmic binding proteins and sugar binding domain of the LacI family
PF01381 (HMM-CLUST): DNA-binding helix-turn-helix protein
PF00356 (HMM-CLUST): transcriptional regulator, LacI family
GO:0043463: regulation of rhamnose catabolic process
GO:0019301: rhamnose catabolic process
GO:0043463: regulation of rhamnose catabolic process
GO:0019301: rhamnose catabolic process
GO:0043463: regulation of rhamnose catabolic process
GO:0019301: rhamnose catabolic process
GO:0043463: regulation of rhamnose catabolic process
GO:0019301: rhamnose catabolic process
GO:0043463: regulation of rhamnose catabolic process
GO:0019301: rhamnose catabolic process
rhamnose transporters (RhaSTPQ)transporYESPF07690 (HMM-CLUST): transporter, major facilitator family
manual (NOCLUST)

PF00083 (HMM-CLUST): transporter, major facilitator superfamily
PF06379 (HMM): L-rhamnose-proton symport protein (RhaT)
TIGR00776 (HMM): RhaT L-rhamnose-proton symporter family protein
PF02653 (HMM-CLUST): branched-chain amino acid ABC transporter, permease protein
PF00005 (HMM-CLUST): ABC transporter, ATP-binding protein
TIGR02637 (HMM): rhamnose ABC transporter, rhamnose-binding protein
GO:0015762: rhamnose transport
GO:0019301: rhamnose catabolic process
GO:0015762: rhamnose transport
GO:0019301: rhamnose catabolic process
GO:0015762: rhamnose transport
GO:0019301: rhamnose catabolic process
GO:0015762: rhamnose transport
GO:0019301: rhamnose catabolic process
GO:0015762: rhamnose transport
GO:0019301: rhamnose catabolic process
GO:0015762: rhamnose transport
GO:0019301: rhamnose catabolic process
GO:0015762: rhamnose transport
GO:0019301: rhamnose catabolic process
GO:0015762: rhamnose transport
GO:0019301: rhamnose catabolic process

Parent Properties
AccessionName
GenProp0142catabolism


Sibling Properties
AccessionName
GenProp0055polyhydroxyalkanoic acids
GenProp0141galactose-6-phosphate degradation via tagatose-6-phosphate
GenProp0156cyanophycin-like storage polymers
GenProp0168glycogen system
GenProp0210phenylacetic acid catabolism
GenProp02314-hydroxyphenylacetate degradation
GenProp0233GABA utilization
GenProp02382-aminoethylphosphonate catabolism to acetaldehyde
GenProp0239propionyl-CoA catabolism
GenProp0241phosphonate catabolism
GenProp0271trehalose utilization
GenProp0272pyruvate fermentation to acetoin
GenProp0273protocatechuate degradation to beta-ketoadipate
GenProp0283beta-ketoadipate degradation to succinyl-CoA and acetyl-CoA
GenProp0294ethanolamine catabolism to acetaldehyde
GenProp0458fucose catabolism
GenProp0461utilization of deoxynucleosides
GenProp0653ectoine catabolism
GenProp0674malonate decarboxylase
GenProp0686allantoin catabolism to glyoxalate and urea
GenProp0687allantoin catabolism to oxamate and carbamoyl-phosphate
GenProp0688urate catabolism to allantoin
GenProp0691glycolysis
GenProp0693fructose utilization as fructose-1,6-bisphosphate
GenProp0694glucose utilization as fructose-1,6-bisphosphate
GenProp0700purine catabolism via urate, xanthine and allantoin
GenProp0702benzoyl-CoA reductase
GenProp07034-hydroxybenzoyl-CoA reductase
GenProp0706cyclohexa-1,5-diene-1-carbonyl-CoA to 3-hydroxypimelyl-CoA, dch/had/oah pathway
GenProp0708catechol meta-cleavage pathway
GenProp0709benzoate catabolism BoxABC pathway
GenProp0711catechol ortho-cleavage upper pathway
GenProp0714galactarate utilization via tartronate semi-aldehyde
GenProp0715galactarate utilization via 2-oxoglutarate semialdehyde
GenProp0716glucarate utilization via tartronate semi-aldehyde
GenProp0717glucarate utilization via 2-oxoglutarate semialdehyde
GenProp0718oxalate degradation
GenProp0734amino acid catabolism
GenProp0749choline sulfate utilization
GenProp0760putrescine degradation to GABA via gamma-glutamylation
GenProp0763nicotinate fermentation to pyruvate and propionate
GenProp0813pyrimidine utilization operon, RutABCDEFGR
GenProp0902quinohemoprotein amine dehydrogenase
GenProp1071myo-inositol catabolism
GenProp1072cyanase system
GenProp1076choline TMA-lyase system