Escherichia coli K-12 substr. MG1655 Protein: conserved DNA-binding protein

Gene: ybaB Accession Numbers: EG11100 (EcoCyc), b0471, ECK0465

Regulation Summary Diagram: ?

Regulation summary diagram for ybaB

Subunit composition of conserved DNA-binding protein = [YbaB]2
         conserved DNA-binding protein = YbaB

YbaB is a widely conserved small protein. Like its ortholog from Borrelia burgdorferi, YbaB binds to DNA derived from the B. burgdorferi erpAB promoter. Binding can not be competed with poly(dI-dC) and is thus sequence- or topology-specific, although YbaB does not appear to bind to the same sequence as the B. burgdorferi protein. The structure of YbaB family of DNA-binding proteins is different from any other known DNA-binding protein [Cooley09].

Expression of the ybaB gene is regulated by σE, suggesting involvement in the extracytoplasmic stress response [Rezuchova03].

A ybaB deletion mutant is more sensitive to kasugamycin than wild type [Skunca13].

Overexpression of ybaB from the ASKA library plasmid allows increased expression of the human G protein-coupled receptor bradykinin receptor 2 (BR2) fused to GFP [Skretas10].

Locations: cytosol, bacterial nucleoid

Map Position: [493,300 -> 493,629] (10.63 centisomes, 38°)
Length: 330 bp / 109 aa

Molecular Weight of Polypeptide: 12.015 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0001636 , DIP:DIP-48059N , EchoBASE:EB1092 , EcoGene:EG11100 , EcoliWiki:b0471 , Mint:MINT-1219994 , ModBase:P0A8B5 , OU-Microarray:b0471 , PortEco:ybaB , Pride:P0A8B5 , Protein Model Portal:P0A8B5 , RefSeq:NP_415004 , RegulonDB:EG11100 , SMR:P0A8B5 , String:511145.b0471 , UniProt:P0A8B5

Relationship Links: InterPro:IN-FAMILY:IPR004401 , PDB:Structure:1PUG , Pfam:IN-FAMILY:PF02575

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0006950 - response to stress Inferred from experiment [Rezuchova03]
Molecular Function: GO:0003677 - DNA binding Inferred from experiment Inferred by computational analysis [UniProtGOA11, GOA06, Cooley09]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11, GOA06]
GO:0009295 - nucleoid Inferred by computational analysis [UniProtGOA11a]
GO:0043590 - bacterial nucleoid Inferred by computational analysis [GOA06]

MultiFun Terms: cell processes adaptations

Essentiality data for ybaB 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]

Created 21-Jul-2009 by Keseler I , SRI International
Last-Curated ? 21-Nov-2013 by Keseler I , SRI International

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


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 ].
10/20/97 Gene b0471 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11100; 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

Cooley09: Cooley AE, Riley SP, Kral K, Miller C, Demoll E, Fried MG, Stevenson B (2009). "DNA-binding by Haemophilus influenzae and Escherichia coli YbaB, members of a widely-distributed bacterial protein family." BMC Microbiol 9(1);137. PMID: 19594923

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

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

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

Rezuchova03: Rezuchova B, Miticka H, Homerova D, Roberts M, Kormanec J (2003). "New members of the Escherichia coli sigmaE regulon identified by a two-plasmid system." FEMS Microbiol Lett 225(1);1-7. PMID: 12900013

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

Skretas10: Skretas G, Georgiou G (2010). "Simple genetic selection protocol for isolation of overexpressed genes that enhance accumulation of membrane-integrated human G protein-coupled receptors in Escherichia coli." Appl Environ Microbiol 76(17);5852-9. PMID: 20639362

Skunca13: Skunca N, Bošnjak M, Kriško A, Panov P, Džeroski S, Smuc T, Supek F (2013). "Phyletic profiling with cliques of orthologs is enhanced by signatures of paralogy relationships." PLoS Comput Biol 9(1);e1002852. PMID: 23308060

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."

Other References Related to Gene Regulation

Rhodius05: Rhodius VA, Suh WC, Nonaka G, West J, Gross CA (2005). "Conserved and variable functions of the sigmaE stress response in related genomes." PLoS Biol 4(1);e2. PMID: 16336047

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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 Tue Oct 13, 2015, BIOCYC14A.