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



Gene: rpiR Accession Numbers: G7821 (EcoCyc), b4089, ECK4082

Synonyms: yjcY, alsR

Regulation Summary Diagram: ?

Component of: AlsR-allose

Summary:
"Allose utilization regulator," AlsR, negatively controls the expression of genes involved in transport and catabolism of D-allose and low-affinity transport of D-ribose [Sorensen96, Kim97]. It is negatively autoregulated and coordinately represses transcription of the divergent gene rpiB, encoding an enzyme in the pentose pathway [Sorensen96]. Synthesis of alsR and rpiB genes is induced when Escherichia coli is grown on d-allose in the absence of glucose. Gene induction occurs when the physiological inducer, d-allose, binds to AlsR, liberating the repression effect caused by this protein [Kim97, Poulsen99].

As a member of the RpiR/YebK/YfhH family of transcriptional regulators, AlsR features an N-terminal domain containing a helix-turn-helix motif [Sorensen96]. Currently, no DNA-binding sites for this regulator have been reported in the literature.

Locations: cytosol

Map Position: [4,310,124 <- 4,311,014] (92.9 centisomes)
Length: 891 bp / 296 aa

Molecular Weight of Polypeptide: 32.362 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0013400 , EchoBASE:EB2353 , EcoGene:EG12459 , EcoliWiki:b4089 , ModBase:P0ACS7 , OU-Microarray:b4089 , PortEco:rpiR , PR:PRO_000023808 , Pride:P0ACS7 , Protein Model Portal:P0ACS7 , RefSeq:NP_418513 , RegulonDB:G7821 , SMR:P0ACS7 , String:511145.b4089 , UniProt:P0ACS7

Relationship Links: InterPro:IN-FAMILY:IPR000281 , InterPro:IN-FAMILY:IPR001347 , InterPro:IN-FAMILY:IPR009057 , InterPro:IN-FAMILY:IPR011991 , Pfam:IN-FAMILY:PF01380 , Pfam:IN-FAMILY:PF01418 , Prosite:IN-FAMILY:PS51071 , Prosite:IN-FAMILY:PS51464

In Paralogous Gene Group: 353 (4 members)

In Reactions of unknown directionality:

Not in pathways:
D-allose + AlsR = AlsR-allose

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0045892 - negative regulation of transcription, DNA-templated Inferred from experiment [Kim97]
GO:0005975 - carbohydrate metabolic process Inferred by computational analysis [GOA01]
GO:0006351 - transcription, DNA-templated Inferred by computational analysis [UniProtGOA11a]
GO:0006355 - regulation of transcription, DNA-templated Inferred by computational analysis [UniProtGOA11a, GOA01]
Molecular Function: GO:0003677 - DNA binding Inferred by computational analysis [UniProtGOA11a, GOA01]
GO:0003700 - sequence-specific DNA binding transcription factor activity Inferred by computational analysis [GOA01]
GO:0030246 - carbohydrate binding Inferred by computational analysis [GOA01]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: information transfer RNA related Transcription related
metabolism carbon utilization carbon compounds
metabolism central intermediary metabolism non-oxidative branch, pentose pathway
regulation genetic unit regulated operon
regulation type of regulation transcriptional level repressor

Regulated Transcription Units (3 total): ?

Notes:

Essentiality data for rpiR 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: AlsR-allose

Synonyms: RpiR, YjcY, AlsR

Subunit composition of AlsR-allose = [D-allose][RpiR]
         AlsR DNA-binding transcriptional repressor = RpiR (summary available)

Sequence Length: 296 AAs

Relationship Links: Pfam:IN-FAMILY:PF01418

In Reactions of unknown directionality:

Not in pathways:
D-allose + AlsR = AlsR-allose

GO Terms:

Biological Process: GO:0045892 - negative regulation of transcription, DNA-templated Inferred from experiment [Sorensen96]

MultiFun Terms: information transfer RNA related Transcription related
metabolism carbon utilization carbon compounds
metabolism central intermediary metabolism non-oxidative branch, pentose pathway
regulation genetic unit regulated operon
regulation type of regulation transcriptional level repressor


Sequence Features

Feature Class Location Citations Comment
Conserved-Region 14 -> 90
[UniProt09]
UniProt: HTH rpiR-type;
DNA-Binding-Region 50 -> 69
[UniProt10]
UniProt: H-T-H motif; Non-Experimental Qualifier: potential;
Conserved-Region 134 -> 274
[UniProt10]
UniProt: SIS;


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
Peter D. Karp on Wed Jan 18, 2006:
Gene right-end position adjusted based on analysis performed in the 2005 E. coli annotation update [Riley06 ].
Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


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

Kim97: Kim C, Song S, Park C (1997). "The D-allose operon of Escherichia coli K-12." J Bacteriol 1997;179(24);7631-7. PMID: 9401019

Poulsen99: Poulsen TS, Chang YY, Hove-Jensen B (1999). "D-Allose catabolism of Escherichia coli: involvement of alsI and regulation of als regulon expression by allose and ribose." J Bacteriol 1999;181(22);7126-30. PMID: 10559180

Riley06: Riley M, Abe T, Arnaud MB, Berlyn MK, Blattner FR, Chaudhuri RR, Glasner JD, Horiuchi T, Keseler IM, Kosuge T, Mori H, Perna NT, Plunkett G, Rudd KE, Serres MH, Thomas GH, Thomson NR, Wishart D, Wanner BL (2006). "Escherichia coli K-12: a cooperatively developed annotation snapshot--2005." Nucleic Acids Res 34(1);1-9. PMID: 16397293

Sorensen96: Sorensen KI, Hove-Jensen B (1996). "Ribose catabolism of Escherichia coli: characterization of the rpiB gene encoding ribose phosphate isomerase B and of the rpiR gene, which is involved in regulation of rpiB expression." J Bacteriol 1996;178(4);1003-11. PMID: 8576032

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.

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

Other References Related to Gene Regulation

Bennik00: Bennik MH, Pomposiello PJ, Thorne DF, Demple B (2000). "Defining a rob regulon in Escherichia coli by using transposon mutagenesis." J Bacteriol 182(13);3794-801. PMID: 10850996


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 Nov 24, 2014, BIOCYC13A.