Escherichia coli K-12 substr. MG1655 Polypeptide: RhaR transcriptional activator

Gene: rhaR Accession Numbers: EG10842 (EcoCyc), b3906, ECK3899

Synonyms: rhaC1

Regulation Summary Diagram: ?

Regulation summary diagram for rhaR

Component of: RhaR-L-rhamnose DNA-binding transcriptional activator (extended summary available)

Citations: [Tobin87, Tate92, GarciaMartin92, Plunkett93, Egan93]

Gene Citations: [Egan93, Via96, Tobin87, Maciag11a]

Locations: cytosol

Map Position: [4,096,669 -> 4,097,517] (88.3 centisomes, 318°)
Length: 849 bp / 282 aa

Molecular Weight of Polypeptide: 32.373 kD (from nucleotide sequence)

pI: 6.69

Unification Links: ASAP:ABE-0012747 , CGSC:290 , DIP:DIP-10693N , EchoBASE:EB0835 , EcoGene:EG10842 , EcoliWiki:b3906 , ModBase:P09378 , OU-Microarray:b3906 , PortEco:rhaR , PR:PRO_000023737 , Protein Model Portal:P09378 , RefSeq:NP_418342 , RegulonDB:EG10842 , SMR:P09378 , String:511145.b3906 , UniProt:P09378

Relationship Links: InterPro:IN-FAMILY:IPR003313 , InterPro:IN-FAMILY:IPR009057 , InterPro:IN-FAMILY:IPR011051 , InterPro:IN-FAMILY:IPR018060 , InterPro:IN-FAMILY:IPR018062 , InterPro:IN-FAMILY:IPR020449 , InterPro:IN-FAMILY:IPR023699 , Pfam:IN-FAMILY:PF00165 , Pfam:IN-FAMILY:PF02311 , Prints:IN-FAMILY:PR00032 , Prosite:IN-FAMILY:PS00041 , Prosite:IN-FAMILY:PS01124 , Smart:IN-FAMILY:SM00342

In Paralogous Gene Group: 22 (29 members)

In Reactions of unknown directionality:

Not in pathways:
RhaR + α-L-rhamnopyranose = RhaR-rhamnose

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for rhaR

GO Terms:

Biological Process: GO:0006351 - transcription, DNA-templated Inferred from experiment Inferred by computational analysis [UniProtGOA11, Wickstrum05]
GO:0006355 - regulation of transcription, DNA-templated Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0019299 - rhamnose metabolic process Inferred by computational analysis [UniProtGOA11, GOA06, GOA01]
GO:0045893 - positive regulation of transcription, DNA-templated Inferred by computational analysis [GOA06, GOA01]
Molecular Function: GO:0043565 - sequence-specific DNA binding Inferred from experiment Inferred by computational analysis [GOA01, Wickstrum05]
GO:0003677 - DNA binding Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0003700 - sequence-specific DNA binding transcription factor activity Inferred by computational analysis [GOA06, GOA01]
Cellular Component: GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, GOA06, GOA01]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: information transfer RNA related Transcription related
metabolism carbon utilization carbon compounds
regulation genetic unit regulated operon
regulation type of regulation transcriptional level activator

Essentiality data for rhaR knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]

Revised 23-May-2011 by Brito D

Subunit of: RhaR-L-rhamnose DNA-binding transcriptional activator

Synonyms: B3906, RhaR, RhaR-rhamnose

Subunit composition of RhaR-L-rhamnose DNA-binding transcriptional activator = [RhaR][α-L-rhamnopyranose]
         RhaR transcriptional activator = RhaR

The "Rhamnose regulator," RhaR, is a transcription factor that regulates genes involved in l-rhamnose degradation and coregulates with the global transcriptional regulator CRP. These regulators bind cooperatively to activate transcription of the unusual operon rhaSR, which encodes two transcriptional regulators, RhaS and RhaR (30% identical), both members of the AraC/XylS family of transcriptional regulators and involved in l-rhamnose transport and degradation [Wickstrum05, Holcroft00a]. In vitro transcription assays indicate that the α-CTD of the RNA polymerase is partially dispensable for RhaR activation and is required for CRP activation of the rhaSR operon [Wickstrum05, Holcroft00a].

Apparently, expression of the operons involved in transport and degradation of l-rhamnose first requires expression of RhaR, which induces transcription of the rhaSR operon. In this way, RhaS activates transcription of l-rhamnose gene clusters.

Transcription of the rhaSR operon is induced when E. coli is grown on l-rhamnose in the absence of glucose. Gene induction occurs when the physiological inducer, l-rhamnose, binds to RhaR and when cellular cyclic AMP levels are high [Wickstrum05, Holcroft00a].

This transcription factor is composed of two domains, a C-terminal domain that contains two potential helix-turn-helix DNA-binding motifs and an N-terminal domain involved in l-rhamnose binding and dimerization of the protein [Wickstrum04, Kolin08, Wickstrum07].

In the presence of l-rhamnose, RhaR binds in tandem to two repeat sequences upstream of the rhaS intergenic region to activate transcription by overlapping the -35 box of rhaSp. The binding targets for RhaR consist of 17-nucleotide-long sequences that possess conserved motifs; each monomer binds to one of these conserved sequences located on different faces of the DNA [Wickstrum05].

Sequence Length: 282 AAs

Molecular Weight: 35.667 kD (from nucleotide sequence)

Relationship Links: Pfam:IN-FAMILY:PF02311

In Reactions of unknown directionality:

Not in pathways:
RhaR + α-L-rhamnopyranose = RhaR-rhamnose

MultiFun Terms: information transfer RNA related Transcription related
metabolism carbon utilization carbon compounds
regulation genetic unit regulated operon
regulation type of regulation transcriptional level activator

DNA binding site length: 17 base-pairs

Symmetry: Asymmetric

Consensus DNA Binding Sequence: CGTCGAnnnTTnAAGnT

Regulated Transcription Units (1 total): ?


Transcription-unit diagram

Sequence Features

Protein sequence of RhaR transcriptional activator with features indicated

Feature Class Location Citations Comment
DNA-Binding-Region 195 -> 214
UniProt: H-T-H motif; Non-Experimental Qualifier: by similarity;
DNA-Binding-Region 244 -> 267
UniProt: H-T-H motif; Non-Experimental Qualifier: by similarity;
Amino-Acid-Site 246
UniProt: Interaction with sigma-70; Sequence Annotation Type: site.

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


Ingrid Keseler on Tue Oct 30, 2007:
Gene start position changed based on personal communication by E. Pradel to K. Rudd.
10/20/97 Gene b3906 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10842; confirmed by SwissProt match.


Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Bhende99: Bhende PM, Egan SM (1999). "Amino acid-DNA contacts by RhaS: an AraC family transcription activator." J Bacteriol 181(17);5185-92. PMID: 10464186

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Egan93: Egan SM, Schleif RF (1993). "A regulatory cascade in the induction of rhaBAD." J Mol Biol 1993;234(1);87-98. PMID: 8230210

GarciaMartin92: Garcia-Martin C, Baldoma L, Badia J, Aguilar J (1992). "Nucleotide sequence of the rhaR-sodA interval specifying rhaT in Escherichia coli." J Gen Microbiol 138(6);1109-16. PMID: 1339463

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Holcroft00a: Holcroft CC, Egan SM (2000). "Interdependence of activation at rhaSR by cyclic AMP receptor protein, the RNA polymerase alpha subunit C-terminal domain, and rhaR." J Bacteriol 2000;182(23);6774-82. PMID: 11073923

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Kolin08: Kolin A, Balasubramaniam V, Skredenske JM, Wickstrum JR, Egan SM (2008). "Differences in the mechanism of the allosteric l-rhamnose responses of the AraC/XylS family transcription activators RhaS and RhaR." Mol Microbiol 68(2);448-61. PMID: 18366439

Maciag11a: Maciag A, Peano C, Pietrelli A, Egli T, De Bellis G, Landini P (2011). "In vitro transcription profiling of the {sigma}S subunit of bacterial RNA polymerase: re-definition of the {sigma}S regulon and identification of {sigma}S-specific promoter sequence elements." Nucleic Acids Res 39(13);5338-55. PMID: 21398637

Plunkett93: Plunkett G, Burland V, Daniels DL, Blattner FR (1993). "Analysis of the Escherichia coli genome. III. DNA sequence of the region from 87.2 to 89.2 minutes." Nucleic Acids Res 1993;21(15);3391-8. PMID: 8346018

Tate92: Tate CG, Muiry JA, Henderson PJ (1992). "Mapping, cloning, expression, and sequencing of the rhaT gene, which encodes a novel L-rhamnose-H+ transport protein in Salmonella typhimurium and Escherichia coli." J Biol Chem 1992;267(10);6923-32. PMID: 1551902

Tobin87: Tobin JF, Schleif RF (1987). "Positive regulation of the Escherichia coli L-rhamnose operon is mediated by the products of tandemly repeated regulatory genes." J Mol Biol 1987;196(4);789-99. PMID: 3316663

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt15: UniProt Consortium (2015). "UniProt version 2015-01 released on 2015-01-16 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

Via96: Via P, Badia J, Baldoma L, Obradors N, Aguilar J (1996). "Transcriptional regulation of the Escherichia coli rhaT gene." Microbiology 1996;142 ( Pt 7);1833-40. PMID: 8757746

Wickstrum04: Wickstrum JR, Egan SM (2004). "Amino acid contacts between sigma 70 domain 4 and the transcription activators RhaS and RhaR." J Bacteriol 186(18);6277-85. PMID: 15342598

Wickstrum05: Wickstrum JR, Santangelo TJ, Egan SM (2005). "Cyclic AMP receptor protein and RhaR synergistically activate transcription from the L-rhamnose-responsive rhaSR promoter in Escherichia coli." J Bacteriol 187(19);6708-18. PMID: 16166533

Wickstrum07: Wickstrum JR, Skredenske JM, Kolin A, Jin DJ, Fang J, Egan SM (2007). "Transcription activation by the DNA-binding domain of the AraC family protein RhaS in the absence of its effector-binding domain." J Bacteriol 189(14);4984-93. PMID: 17513476

Other References Related to Gene Regulation

Tobin90: Tobin JF, Schleif RF (1990). "Transcription from the rha operon psr promoter." J Mol Biol 1990;211(1);1-4. PMID: 1688950

Tobin90a: Tobin JF, Schleif RF (1990). "Purification and properties of RhaR, the positive regulator of the L-rhamnose operons of Escherichia coli." J Mol Biol 1990;211(1);75-89. PMID: 2405166

Wickstrum10: Wickstrum JR, Skredenske JM, Balasubramaniam V, Jones K, Egan SM (2010). "The AraC/XylS family activator RhaS negatively autoregulates rhaSR expression by preventing cyclic AMP receptor protein activation." J Bacteriol 192(1);225-32. PMID: 19854903

Zheng04: Zheng D, Constantinidou C, Hobman JL, Minchin SD (2004). "Identification of the CRP regulon using in vitro and in vivo transcriptional profiling." Nucleic Acids Res 32(19);5874-93. PMID: 15520470

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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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