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Escherichia coli K-12 substr. MG1655 Polypeptide: GutR DNA-binding transcriptional repressor



Gene: srlR Accession Numbers: EG10974 (EcoCyc), b2707, ECK2702

Synonyms: gutR

Regulation Summary Diagram: ?

Component of: GutR-sorbitol (extended summary available)

Summary:
The "glucitol repressor," GutR, is a DNA-binding transcription factor that represses an operon (gut) involved in transport and utilization of glucitol [Yamada88, Yamada87a]. This regulator is located in the unusual gut operon, which contains two glucitol-specific transcription factors, GutR and GutM, that regulate this operon negatively and positively, respectively; both regulators control transcription of glucitol PTS permease [Yamada88].

Expression of gutR is activated in the presence of glucitol and in the absence of glucose. Although DNA binding by GutM does not depend on the presence of glucitol, this compound appears to be necessary for derepressing gutM, perhaps by interacting with GutR [Yamada88].

In addition, Yamada et al. suggested that these regulators have contrary effects, but in the presence of glucitol, GutR interacts with this carbohydrate to dissociate from DNA, causing increments of GutM in sufficient amounts to increase transcription of the gut operon [Yamada88]. To repress transcription, GutR recognizes DNA-binding sites, but no consensus sequence has been identified. When this protein represses genes involved in glucitol transport and utilization, it appears to bind to their regulatory regions without a coeffector [Yamada88]. This regulator belongs to the DeoR family of repressors. GutR is composed of two domains: the amino-terminal domain, which contains the DNA-binding region, and the carboxy-terminal domain, which is responsible for dimerization and inducer binding [Yamada88].

Gene Citations: [Yamada87, McEntee77]

Locations: cytosol

Map Position: [2,827,069 -> 2,827,842] (60.93 centisomes)
Length: 774 bp / 257 aa

Molecular Weight of Polypeptide: 28.236 kD (from nucleotide sequence)

pI: 5.16

Unification Links: ASAP:ABE-0008900 , CGSC:152 , DIP:DIP-10919N , EchoBASE:EB0967 , EcoGene:EG10974 , EcoliWiki:b2707 , Mint:MINT-1226226 , ModBase:P15082 , OU-Microarray:b2707 , PortEco:srlR , PR:PRO_000023987 , Pride:P15082 , Protein Model Portal:P15082 , RefSeq:NP_417187 , RegulonDB:EG10974 , SMR:P15082 , String:511145.b2707 , UniProt:P15082

Relationship Links: InterPro:IN-FAMILY:IPR001034 , InterPro:IN-FAMILY:IPR011991 , InterPro:IN-FAMILY:IPR014036 , InterPro:IN-FAMILY:IPR018356 , Pfam:IN-FAMILY:PF00455 , Pfam:IN-FAMILY:PF08220 , Prosite:IN-FAMILY:PS00894 , Prosite:IN-FAMILY:PS51000 , Smart:IN-FAMILY:SM00420

In Reactions of unknown directionality:

Not in pathways:
GutR + D-sorbitol = GutR-sorbitol

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0045892 - negative regulation of transcription, DNA-templated Inferred from experiment [Yamada88]
GO:0006351 - transcription, DNA-templated Inferred by computational analysis [UniProtGOA11]
GO:0006355 - regulation of transcription, DNA-templated Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0009401 - phosphoenolpyruvate-dependent sugar phosphotransferase system Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0003677 - DNA binding Inferred by computational analysis [UniProtGOA11]
GO:0003700 - sequence-specific DNA binding transcription factor activity Inferred by computational analysis [GOA01]
Cellular Component: GO:0005622 - intracellular Inferred by computational analysis [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 repressor

Symmetry: Inverted Repeat

Regulated Transcription Units (1 total): ?

Notes:

Essentiality data for srlR 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]

Subunit of: GutR-sorbitol

Synonyms: B2707, GutR, SrlR

Subunit composition of GutR-sorbitol = [SrlR][D-sorbitol]
         GutR DNA-binding transcriptional repressor = SrlR (extended summary available)

Summary:
The "glucitol repressor," GutR, is a DNA-binding transcription factor that represses an operon (gut) involved in transport and utilization of glucitol [Yamada88, Yamada87a]. This regulator is located in the unusual gut operon, which contains two glucitol-specific transcription factors, GutR and GutM, that regulate this operon negatively and positively, respectively; both regulators control transcription of glucitol PTS permease [Yamada88].

Expression of gutR is activated in the presence of glucitol and in the absence of glucose. Although DNA binding by GutM does not depend on the presence of glucitol, this compound appears to be necessary for derepressing gutM, perhaps by interacting with GutR [Yamada88].

In addition, Yamada et al. suggested that these regulators have contrary effects, but in the presence of glucitol, GutR interacts with this carbohydrate to dissociate from DNA, causing increments of GutM in sufficient amounts to increase transcription of the gut operon [Yamada88]. To repress transcription, GutR recognizes DNA-binding sites, but no consensus sequence has been identified. When this protein represses genes involved in glucitol transport and utilization, it appears to bind to their regulatory regions without a coeffector [Yamada88]. This regulator belongs to the DeoR family of repressors. GutR is composed of two domains: the amino-terminal domain, which contains the DNA-binding region, and the carboxy-terminal domain, which is responsible for dimerization and inducer binding [Yamada88].

Sequence Length: 257 AAs

Molecular Weight: 28.236 kD (from nucleotide sequence)

Relationship Links: Pfam:IN-FAMILY:PF00455

In Reactions of unknown directionality:

Not in pathways:
GutR + D-sorbitol = GutR-sorbitol

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


Sequence Features

Feature Class Location Citations Comment
Conserved-Region 3 -> 58
[UniProt09]
UniProt: HTH deoR-type;
DNA-Binding-Region 20 -> 39
[UniProt10]
UniProt: H-T-H motif; Non-Experimental Qualifier: potential;


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b2707 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10974; confirmed by SwissProt match.


References

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

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

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."

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

McEntee77: McEntee K (1977). "Genetic analysis of the Escherichia coli K-12 srl region." J Bacteriol 1977;132(3);904-11. PMID: 336611

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

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

Yamada87: Yamada M, Saier MH (1987). "Glucitol-specific enzymes of the phosphotransferase system in Escherichia coli. Nucleotide sequence of the gut operon." J Biol Chem 1987;262(12);5455-63. PMID: 3553176

Yamada87a: Yamada M, Saier MH (1987). "Physical and genetic characterization of the glucitol operon in Escherichia coli." J Bacteriol 169(7);2990-4. PMID: 3036766

Yamada88: Yamada M, Saier MH (1988). "Positive and negative regulators for glucitol (gut) operon expression in Escherichia coli." J Mol Biol 1988;203(3);569-83. PMID: 3062173

Other References Related to Gene Regulation

Beisel11: Beisel CL, Storz G (2011). "The base-pairing RNA spot 42 participates in a multioutput feedforward loop to help enact catabolite repression in Escherichia coli." Mol Cell 41(3);286-97. PMID: 21292161

WhiteZiegler07: White-Ziegler CA, Malhowski AJ, Young S (2007). "Human body temperature (37degrees C) increases the expression of iron, carbohydrate, and amino acid utilization genes in Escherichia coli K-12." J Bacteriol 189(15);5429-40. PMID: 17526711

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


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 18.5 on Mon Dec 22, 2014, biocyc14.