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



Gene: yqjI Accession Numbers: G7594 (EcoCyc), b3071, ECK3061

Regulation Summary Diagram: ?

Component of: YqjI-nickel

Summary:
YqjI is a local transcription regulator that represses expression of the divergent operon, yqjH-yqjI, related to its autorepression and the synthesis of an NADPH-dependent ferric reductase [Wang11c]. This regulator forms a complex with DNA in the absence of nickel, binding to a 20-bp-long sequence with an imperfect palindromic sequence. YqjI is inactivated under conditions of elevated nickel levels, and the presence of this divalent metal prevents its binding to the target gene. Thus, this regulator maintains the iron homeostasis during high levels of nickel [Wang11c]. However, in vitro studies have shown that YqjI can be affected by other divalent metals.

The YqjI regulator is structurally related to the PadR family, which is characterized by a winged helix-turn-helix (WHTH) motif. The amino-terminal region of this protein is similar to the C-terminal SlyD protein and to the N-terminal RcnA protein [Wang11c]. Comparison with the crystal structure of the AphA protein from Vibrio cholerae suggests that the amino terminal of YqjI contains the WHTH motif and that in the C-terminal domain is located the ligand-binding domain for oligomerization [Wang11c]. YqjI has been observed to be a possible hexamer [Wang11c].

Locations: cytosol

Map Position: [3,214,801 -> 3,215,424] (69.29 centisomes)
Length: 624 bp / 207 aa

Molecular Weight of Polypeptide: 23.401 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0010084 , DIP:DIP-48127N , EchoBASE:EB2788 , EcoGene:EG12954 , EcoliWiki:b3071 , Mint:MINT-1269480 , OU-Microarray:b3071 , PortEco:yqjI , Protein Model Portal:P64588 , RefSeq:NP_417542 , RegulonDB:G7594 , SMR:P64588 , String:511145.b3071 , UniProt:P64588

Relationship Links: InterPro:IN-FAMILY:IPR005149 , InterPro:IN-FAMILY:IPR011991 , Pfam:IN-FAMILY:PF03551

In Reactions of unknown directionality:

Not in pathways:
YqjI + Ni2+ = YqjI-nickel

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006974 - cellular response to DNA damage stimulus Inferred from experiment [Khil02]
GO:0006351 - transcription, DNA-templated Inferred by computational analysis [UniProtGOA11a]
GO:0006355 - regulation of transcription, DNA-templated Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0003677 - DNA binding Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]

MultiFun Terms: information transfer RNA related Transcription related
regulation type of regulation transcriptional level

DNA binding site length: 20 base-pairs

Symmetry: Inverted Repeat

Consensus DNA Binding Sequence: TAaTTAGATATATCTaATTA

Regulated Transcription Units (2 total): ?

Notes:

Essentiality data for yqjI 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]

Credits:
Last-Curated ? 08-Apr-2008 by Keseler I , SRI International


Subunit of: YqjI-nickel

Subunit composition of YqjI-nickel = [YqjI][Ni2+]
         YqjI DNA-binding transcriptional repressor = YqjI (extended summary available)

Sequence Length: 207 AAs

In Reactions of unknown directionality:

Not in pathways:
YqjI + Ni2+ = YqjI-nickel

MultiFun Terms: information transfer RNA related Transcription related
regulation type of regulation transcriptional level


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
Peter D. Karp on Thu Jan 16, 2003:
Predicted gene function revised as a result of E. coli genome reannotation by Serres et al. [Serres01 ].
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

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

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

Khil02: Khil PP, Camerini-Otero RD (2002). "Over 1000 genes are involved in the DNA damage response of Escherichia coli." Mol Microbiol 44(1);89-105. PMID: 11967071

Serres01: Serres MH, Gopal S, Nahum LA, Liang P, Gaasterland T, Riley M (2001). "A functional update of the Escherichia coli K-12 genome." Genome Biol 2(9);RESEARCH0035. PMID: 11574054

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

Wang11c: Wang S, Wu Y, Outten FW (2011). "Fur and the novel regulator YqjI control transcription of the ferric reductase gene yqjH in E. coli." J Bacteriol 193(2):563-74. PMID: 21097627

Other References Related to Gene Regulation

Constantinidou06: Constantinidou C, Hobman JL, Griffiths L, Patel MD, Penn CW, Cole JA, Overton TW (2006). "A reassessment of the FNR regulon and transcriptomic analysis of the effects of nitrate, nitrite, NarXL, and NarQP as Escherichia coli K12 adapts from aerobic to anaerobic growth." J Biol Chem 281(8);4802-15. PMID: 16377617

MendozaVargas09: Mendoza-Vargas A, Olvera L, Olvera M, Grande R, Vega-Alvarado L, Taboada B, Jimenez-Jacinto V, Salgado H, Juarez K, Contreras-Moreira B, Huerta AM, Collado-Vides J, Morett E (2009). "Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli." PLoS One 4(10);e7526. PMID: 19838305


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 Thu Nov 27, 2014, biocyc13.