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Escherichia coli K-12 substr. MG1655 Polypeptide: protein possibly involved in ribosome structure or function

Gene: typA Accession Numbers: EG11837 (EcoCyc), b3871, ECK3864

Synonyms: bipA, yihK

Regulation Summary Diagram: ?

Regulation summary diagram for typA

BipA is a member of the ribosome-binding GTPase superfamily. The variety of phenotypes of a bipA deletion, as well as the genetic interaction with the RluC 23S rRNA pseudouridine synthase suggest that BipA plays a role in modulating the structure or function of the ribosome [Krishnan08].

BipA is necessary for growth under low temperature conditions [Pfennig01, Grant01b]. Deletion of rluC suppresses the cold-sensitive phenotype of a bipA mutant [Krishnan08].

A bipA mutation suppresses the defect in lipopolysaccharide core biosynthesis, the SDS sensitivity, and the defect in mouse intestinal colonization of a waaQ mutant [Moller03]. BipA may be involved in positive regulation of colanic acid synthesis [Krishnan08]. A strain containing a transposon insertion in bipA is more sensitive to chloramphenicol than wild-type [Duo08].

Whereas BipA of E. coli K-12 is reported not to be tyrosine phosphorylated [Freestone98, Pfennig01], BipA of enteropathogenic E. coli [Farris98, Freestone98] and wall-less L-form E. coli [Freestone98a] is phosphorylated on tyrosine.

BipA has been characterized in pathogenic bacteria [Qi95, Farris98, Freestone98, Farris98a, Barker00, Rowe00, Grant03a, Scott03a]. Salmonella enterica serovar Typhimurium BipA is a ribosome-associated GTPase [Qi95, deLivron08]. BipA of enteropathogenic E. coli is a regulatory protein [Freestone98, Rowe00, Farris98, Grant03a] involved in pathogenesis [Farris98, Grant03a] and is required for wild-type translation [Freestone98].

bipA shows differential codon adaptation, resulting in differential translation efficiency signatures, in thermophilic microbes. It was therefore predicted to play a role in the heat shock response. A bipA deletion mutant was shown to be more sensitive than wild-type specifically to heat shock, but not other stresses [Krisko14].

BipA: "BPI-inducible protein A" [Qi95]

TypA: "tyrosine phosphoprotein" [Freestone98]

Locations: cytosol

Map Position: [4,056,430 -> 4,058,253] (87.43 centisomes, 315°)
Length: 1824 bp / 607 aa

Molecular Weight of Polypeptide: 67.355 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0012648 , DIP:DIP-11058N , EchoBASE:EB1783 , EcoGene:EG11837 , EcoliWiki:b3871 , ModBase:P32132 , OU-Microarray:b3871 , PortEco:typA , PR:PRO_000024149 , Pride:P32132 , Protein Model Portal:P32132 , RefSeq:YP_026274 , RegulonDB:EG11837 , SMR:P32132 , String:511145.b3871 , UniProt:P32132

Relationship Links: InterPro:IN-FAMILY:IPR000640 , InterPro:IN-FAMILY:IPR000795 , InterPro:IN-FAMILY:IPR004161 , InterPro:IN-FAMILY:IPR005225 , InterPro:IN-FAMILY:IPR006298 , InterPro:IN-FAMILY:IPR009000 , InterPro:IN-FAMILY:IPR009022 , InterPro:IN-FAMILY:IPR027417 , Panther:IN-FAMILY:PTHR23115:SF14 , Pfam:IN-FAMILY:PF00009 , Pfam:IN-FAMILY:PF00679 , Pfam:IN-FAMILY:PF03144 , Prints:IN-FAMILY:PR00315 , Prosite:IN-FAMILY:PS00301 , Prosite:IN-FAMILY:PS51722 , Smart:IN-FAMILY:SM00838

In Paralogous Gene Group: 77 (16 members)

GO Terms:

Biological Process: GO:0006412 - translation Inferred from experiment [Krishnan08]
GO:0009408 - response to heat Inferred from experiment [Krisko14]
GO:0009409 - response to cold Inferred from experiment [Pfennig01]
GO:0008152 - metabolic process Inferred by computational analysis [GOA01a]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Rajagopala14]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11a]
GO:0003924 - GTPase activity Inferred by computational analysis [GOA01a]
GO:0005525 - GTP binding Inferred by computational analysis [UniProtGOA11a, GOA01a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, Zhang07, LopezCampistrou05]

MultiFun Terms: cell processes adaptations temperature extremes
information transfer protein related translation

Essentiality data for typA 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 ? 07-Oct-2008 by Keseler I , SRI International

Sequence Features

Protein sequence of protein possibly involved in ribosome structure or function with features indicated

Feature Class Location Citations Comment
Conserved-Region 3 -> 198
UniProt: tr-type G.
Nucleotide-Phosphate-Binding-Region 12 -> 19
UniProt: GTP; Non-Experimental Qualifier: by similarity;
Nucleotide-Phosphate-Binding-Region 74 -> 78
UniProt: GTP; Non-Experimental Qualifier: by similarity;
Nucleotide-Phosphate-Binding-Region 128 -> 131
UniProt: GTP; Non-Experimental Qualifier: by similarity;
Extrinsic-Sequence-Variant 489
UniProt: In strain: MAR001..
Extrinsic-Sequence-Variant 497
UniProt: In strain: MAR001..
Sequence-Conflict 592 -> 607
[Farris98, Plunkett93, UniProt10a]
UniProt: (in Ref. 1 and 2);

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


Suzanne Paley on Thu Oct 21, 2004:
Position updated based on U00096.2 release of genome
10/20/97 Gene b3871 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11837; 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

Barker00: Barker HC, Kinsella N, Jaspe A, Friedrich T, O'Connor CD (2000). "Formate protects stationary-phase Escherichia coli and Salmonella cells from killing by a cationic antimicrobial peptide." Mol Microbiol 35(6);1518-29. PMID: 10760151

deLivron08: deLivron MA, Robinson VL (2008). "Salmonella enterica serovar Typhimurium BipA exhibits two distinct ribosome binding modes." J Bacteriol 190(17);5944-52. PMID: 18621905

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

Duo08: Duo M, Hou S, Ren D (2008). "Identifying Escherichia coli genes involved in intrinsic multidrug resistance." Appl Microbiol Biotechnol 81(4);731-41. PMID: 18807027

Farris98: Farris M, Grant A, Richardson TB, O'Connor CD (1998). "BipA: a tyrosine-phosphorylated GTPase that mediates interactions between enteropathogenic Escherichia coli (EPEC) and epithelial cells." Mol Microbiol 28(2);265-79. PMID: 9622352

Farris98a: Farris M, Grant A, Jane S, Chad J, O'Connor CD (1998). "BipA affects Ca++ fluxes and phosphorylation of the translocated intimin receptor (Tir/Hp90) in host epithelial cells infected with enteropathogenic E. coli." Biochem Soc Trans 26(3);S225. PMID: 9765944

Freestone98: Freestone P, Trinei M, Clarke SC, Nystrom T, Norris V (1998). "Tyrosine phosphorylation in Escherichia coli." J Mol Biol 279(5);1045-51. PMID: 9642082

Freestone98a: Freestone P, Grant S, Trinei M, Onoda T, Norris V (1998). "Protein phosphorylation in Escherichia coli L. form NC-7." Microbiology 144 ( Pt 12);3289-95. PMID: 9884220

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."

Grant01b: Grant AJ, Haigh R, Williams P, O'Connor CD (2001). "An in vitro transposon system for highly regulated gene expression: construction of Escherichia coli strains with arabinose-dependent growth at low temperatures." Gene 280(1-2);145-51. PMID: 11738827

Grant03a: Grant AJ, Farris M, Alefounder P, Williams PH, Woodward MJ, O'Connor CD (2003). "Co-ordination of pathogenicity island expression by the BipA GTPase in enteropathogenic Escherichia coli (EPEC)." Mol Microbiol 48(2);507-21. PMID: 12675808

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

Krishnan08: Krishnan K, Flower AM (2008). "Suppression of {Delta}bipA Phenotypes in Escherichia coli by Abolishment of Pseudouridylation at Specific Sites on the 23S rRNA." J Bacteriol 190(23):7675-83. PMID: 18820021

Krisko14: Krisko A, Copi T, Gabaldon T, Lehner B, Supek F (2014). "Inferring gene function from evolutionary change in signatures of translation efficiency." Genome Biol 15(3);R44. PMID: 24580753

LopezCampistrou05: Lopez-Campistrous A, Semchuk P, Burke L, Palmer-Stone T, Brokx SJ, Broderick G, Bottorff D, Bolch S, Weiner JH, Ellison MJ (2005). "Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth." Mol Cell Proteomics 4(8);1205-9. PMID: 15911532

Moller03: Moller AK, Leatham MP, Conway T, Nuijten PJ, de Haan LA, Krogfelt KA, Cohen PS (2003). "An Escherichia coli MG1655 lipopolysaccharide deep-rough core mutant grows and survives in mouse cecal mucus but fails to colonize the mouse large intestine." Infect Immun 71(4);2142-52. PMID: 12654836

Pfennig01: Pfennig PL, Flower AM (2001). "BipA is required for growth of Escherichia coi K12 at low temperature." Mol Genet Genomics 266(2);313-7. PMID: 11683274

Plunkett93: Plunkett G, Burland V, Daniels DL, Blattner FR (1993). "Analysis of the Escherichia coli genome. III. DNA sequence of the region from 87.2 to 89.2 minutes." Nucleic Acids Res 1993;21(15);3391-8. PMID: 8346018

Qi95: Qi SY, Li Y, Szyroki A, Giles IG, Moir A, O'Connor CD (1995). "Salmonella typhimurium responses to a bactericidal protein from human neutrophils." Mol Microbiol 17(3);523-31. PMID: 8559071

Rajagopala14: Rajagopala SV, Sikorski P, Kumar A, Mosca R, Vlasblom J, Arnold R, Franca-Koh J, Pakala SB, Phanse S, Ceol A, Hauser R, Siszler G, Wuchty S, Emili A, Babu M, Aloy P, Pieper R, Uetz P (2014). "The binary protein-protein interaction landscape of Escherichia coli." Nat Biotechnol 32(3);285-90. PMID: 24561554

Rowe00: Rowe S, Hodson N, Griffiths G, Roberts IS (2000). "Regulation of the Escherichia coli K5 capsule gene cluster: evidence for the roles of H-NS, BipA, and integration host factor in regulation of group 2 capsule gene clusters in pathogenic E. coli." J Bacteriol 182(10);2741-5. PMID: 10781541

Scott03a: Scott K, Diggle MA, Clarke SC (2003). "TypA is a virulence regulator and is present in many pathogenic bacteria." Br J Biomed Sci 60(3);168-70. PMID: 14560797

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

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt14a: UniProt Consortium (2014). "UniProt version 2014-08 released on 2014-08-01 00:00:00." Database.

UniProt15: UniProt Consortium (2015). "UniProt version 2015-01 released on 2015-01-16 00:00:00." Database.

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

Zhang07: Zhang N, Chen R, Young N, Wishart D, Winter P, Weiner JH, Li L (2007). "Comparison of SDS- and methanol-assisted protein solubilization and digestion methods for Escherichia coli membrane proteome analysis by 2-D LC-MS/MS." Proteomics 7(4);484-93. PMID: 17309111

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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 Sun Aug 30, 2015, biocyc13.