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

Gene: yiaJ Accession Numbers: EG12278 (EcoCyc), b3574, ECK3563

Regulation Summary Diagram: ?

Regulation summary diagram for yiaJ

YiaJ is a transcriptional repressor that negatively controls the expression of genes involved in the catabolism of the rare pentose l-lyxose [Ibanez00, Badia98, Plantinga05].

YiaJ is negatively autoregulated, and coordinately represses transcription of the divergent yiaK-S operon, related to degradation of l-lyxose [Ibanez00]. Additionally, its operon is activated by insertion of IS1 into the yiaJ gene [Badia98]. Although little is known about the mechanism of regulation of the YiaJ regulator, recently it has been demonstrated to act as a repressor by binding to cis-acting elements that overlap yiaKp [Ibanez00].

YiaJ shows high homology to the IclR family of regulators; it is composed of two domains, an amino-terminal domain that contains a potential helix-turn-helix DNA-binding motif and a carboxy-terminal region featuring a second motif of unknown function [Badia98].

Locations: cytosol

Map Position: [3,739,707 <- 3,740,555] (80.6 centisomes, 290°)
Length: 849 bp / 282 aa

Molecular Weight of Polypeptide: 31.067 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0011677 , DIP:DIP-12404N , EchoBASE:EB2186 , EcoGene:EG12278 , EcoliWiki:b3574 , Mint:MINT-1308441 , ModBase:P37671 , OU-Microarray:b3574 , PortEco:yiaJ , Pride:P37671 , Protein Model Portal:P37671 , RefSeq:NP_418031 , RegulonDB:EG12278 , SMR:P37671 , String:511145.b3574 , Swiss-Model:P37671 , UniProt:P37671

Relationship Links: InterPro:IN-FAMILY:IPR005471 , InterPro:IN-FAMILY:IPR011991 , InterPro:IN-FAMILY:IPR014757 , InterPro:IN-FAMILY:IPR029016 , PDB:Structure:1YSQ , Pfam:IN-FAMILY:PF01614 , Pfam:IN-FAMILY:PF09339 , Prosite:IN-FAMILY:PS51077 , Prosite:IN-FAMILY:PS51078 , Smart:IN-FAMILY:SM00346

Genetic Regulation Schematic: ?

Genetic regulation schematic for yiaJ

GO Terms:

Biological Process: GO:0045892 - negative regulation of transcription, DNA-templated Inferred from experiment [Ibanez00]
GO:0006351 - transcription, DNA-templated Inferred by computational analysis [UniProtGOA11a]
GO:0006355 - regulation of transcription, DNA-templated Inferred by computational analysis [UniProtGOA11a, GOA01a]
Molecular Function: GO:0003677 - DNA binding Inferred from experiment Inferred by computational analysis [UniProtGOA11a, GOA01a, Ibanez00]
GO:0003700 - sequence-specific DNA binding transcription factor activity Inferred by computational analysis [Gaudet10]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

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

DNA binding site length: 21 base-pairs

Symmetry: Inverted Repeat

Consensus DNA Binding Sequence: ATttGAAATCaGATTTCgcAT

Regulated Transcription Units (2 total): ?


Transcription-unit diagram

Transcription-unit diagram

Essentiality data for yiaJ 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]

Last-Curated ? 05-Dec-2007 by Keseler I , SRI International

Sequence Features

Protein sequence of YiaJ DNA-binding transcriptional repressor with features indicated

Feature Class Location Citations Comment
Conserved-Region 23 -> 85
UniProt: HTH iclR-type;
DNA-Binding-Region 45 -> 64
UniProt: H-T-H motif; Non-Experimental Qualifier: potential;
Conserved-Region 100 -> 272
UniProt: IclR-ED;

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram


10/20/97 Gene b3574 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG12278; 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

Badia98: Badia J, Ibanez E, Sabate M, Baldoma L, Aguilar J (1998). "A rare 920-kilobase chromosomal inversion mediated by IS1 transposition causes constitutive expression of the yiaK-S operon for carbohydrate utilization in Escherichia coli." J Biol Chem 273(14);8376-81. PMID: 9525947

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

Gaudet10: Gaudet P, Livstone M, Thomas P (2010). "Annotation inferences using phylogenetic trees." PMID: 19578431

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

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

Ibanez00: Ibanez E, Campos E, Baldoma L, Aguilar J, Badia J (2000). "Regulation of expression of the yiaKLMNOPQRS operon for carbohydrate utilization in Escherichia coli: involvement of the main transcriptional factors." J Bacteriol 182(16);4617-24. PMID: 10913096

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

Plantinga05: Plantinga TH, van der Does C, Tomkiewicz D, van Keulen G, Konings WN, Driessen AJ (2005). "Deletion of the yiaMNO transporter genes affects the growth characteristics of Escherichia coli K-12." Microbiology 151(Pt 5);1683-9. PMID: 15870475

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

UniProt10a: 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

Campos08: Campos E, de la Riva L, Garces F, Gimenez R, Aguilar J, Baldoma L, Badia J (2008). "The yiaKLX1X2PQRS and ulaABCDEFG gene systems are required for the aerobic utilization of L-ascorbate in Klebsiella pneumoniae strain 13882 with L-ascorbate-6-phosphate as the inducer." J Bacteriol 190(20);6615-24. PMID: 18708499

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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 19.0 on Fri Aug 28, 2015, biocyc13.