Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
twitter

Escherichia coli K-12 substr. MG1655 Polypeptide: RNA Polymerase (RNAP)-binding ATPase and RNAP recycling factor



Gene: hepA Accession Numbers: EG11083 (EcoCyc), b0059, ECK0060

Synonyms: yabA, rapA

Regulation Summary Diagram: ?

Summary:
HepA causes increased recycling of RNA Polymerase and activates transcription under conditions under which the DNA is expected to be tightly supercoiled [Sukhodolets01]. HepA interacts with RNA polymerase with 1:1 stoichiometry [Sukhodolets98, Muzzin98]. This interaction activates HepA ATPase activity [Sukhodolets98]. The interaction between HepA and RNA polymerase has been characterized in detail [Sukhodolets00].

HepA is a putative helicase of the SNF2 family [Lindback97] with similarity to RecQ and UvrB [Lewis92a].

hepA mutants exhibits a growth defect under high salt conditions [Sukhodolets01] and sensitivity to UV irradiation [Muzzin98]. In a high-throughput experiment, hepA was found to be important for survival under competitive planktonic growth conditions, but not competitive biofilm growth conditions [Junker06]. However, it was subsequently found that the biofilm of a hepA mutant is more sensitive to penicillin G than wild type [Lynch07].

Transcription of hepA is subject to growth control [Cabrera01]. The hepA gene is not part of the LexA regulon [Lewis92a]. [Salmelin02]

RapA: RNA polymerase (RNAP)-associated protein [Sukhodolets98]

Citations: [Rouby02]

Gene Citations: [Nonaka06]

Map Position: [60,358 <- 63,264] (1.3 centisomes)
Length: 2907 bp / 968 aa

Molecular Weight of Polypeptide: 109.77 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0000198 , CGSC:29491 , DIP:DIP-35881N , EchoBASE:EB1075 , EcoGene:EG11083 , EcoliWiki:b0059 , ModBase:P60240 , OU-Microarray:b0059 , PortEco:hepA , PR:PRO_000023677 , Pride:P60240 , Protein Model Portal:P60240 , RefSeq:NP_414601 , RegulonDB:EG11083 , SMR:P60240 , String:511145.b0059 , UniProt:P60240

Relationship Links: InterPro:IN-FAMILY:IPR000330 , InterPro:IN-FAMILY:IPR001650 , InterPro:IN-FAMILY:IPR014001 , InterPro:IN-FAMILY:IPR022737 , InterPro:IN-FAMILY:IPR023949 , InterPro:IN-FAMILY:IPR027417 , PDB:Structure:3DMQ , Pfam:IN-FAMILY:PF00176 , Pfam:IN-FAMILY:PF00271 , Pfam:IN-FAMILY:PF12137 , Prosite:IN-FAMILY:PS00690 , Prosite:IN-FAMILY:PS51192 , Prosite:IN-FAMILY:PS51194 , Smart:IN-FAMILY:SM00487 , Smart:IN-FAMILY:SM00490

In Paralogous Gene Group: 20 (4 members)

GO Terms:

Biological Process: GO:0006200 - ATP catabolic process Inferred from experiment [Sukhodolets98]
GO:0045893 - positive regulation of transcription, DNA-templated Inferred from experiment [Sukhodolets01]
GO:0006351 - transcription, DNA-templated Inferred by computational analysis [UniProtGOA11]
GO:0006355 - regulation of transcription, DNA-templated Inferred by computational analysis [UniProtGOA11, GOA06, GOA01a]
Molecular Function: GO:0003676 - nucleic acid binding Inferred from experiment [Sukhodolets98]
GO:0005515 - protein binding Inferred from experiment [Rajagopala14, Butland05]
GO:0016887 - ATPase activity Inferred from experiment [Sukhodolets98]
GO:0070063 - RNA polymerase binding Inferred from experiment [Sukhodolets98]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11]
GO:0003677 - DNA binding Inferred by computational analysis [UniProtGOA11, GOA01a]
GO:0004386 - helicase activity Inferred by computational analysis [UniProtGOA11, GOA06]
GO:0005524 - ATP binding Inferred by computational analysis [UniProtGOA11, GOA06, GOA01a]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11]
GO:0016817 - hydrolase activity, acting on acid anhydrides Inferred by computational analysis [GOA01a]

MultiFun Terms: cell processes adaptations
cell processes protection radiation
information transfer RNA related Transcription related
regulation type of regulation DNA structure level
regulation type of regulation transcriptional level

Essentiality data for hepA 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]

Sequence Features

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
[Muzzin98, Sukhodolets98, UniProt11]
UniProt: Removed.
Chain 2 -> 968
[UniProt09]
UniProt: RNA polymerase-associated protein rapA;
Sequence-Conflict 11
[Sukhodolets98, UniProt10a]
Alternate sequence: S → V; UniProt: (in Ref. 7; AA sequence);
Conserved-Region 164 -> 334
[UniProt09]
UniProt: Helicase ATP-binding;
Nucleotide-Phosphate-Binding-Region 177 -> 184
[UniProt10]
UniProt: ATP; Non-Experimental Qualifier: by similarity;
Mutagenesis-Variant 183
[Sukhodolets01, UniProt11]
Alternate sequence: K → A; UniProt: Loss of function. Still interacts with RNAP.
Mutagenesis-Variant 280 -> 281
[UniProt10a]
Alternate sequence: DE → AA; UniProt: Loss of function. Still interacts with RNAP;
Protein-Segment 280 -> 283
[UniProt10a]
UniProt: DEAH box; Sequence Annotation Type: short sequence motif;
Conserved-Region 490 -> 662
[UniProt09]
UniProt: Helicase C-terminal;
Sequence-Conflict 510 -> 538
[Lewis92a, UniProt10a]
Alternate sequence: CAKAATALQLEQVLREREGIRAAVFHEGM → RGIRNHGHSCFLCEIVIRSQFHTTYEPEA; UniProt: (in Ref. 4);


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b0059 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11083; confirmed by SwissProt match.


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

Butland05: Butland G, Peregrin-Alvarez JM, Li J, Yang W, Yang X, Canadien V, Starostine A, Richards D, Beattie B, Krogan N, Davey M, Parkinson J, Greenblatt J, Emili A (2005). "Interaction network containing conserved and essential protein complexes in Escherichia coli." Nature 433(7025);531-7. PMID: 15690043

Cabrera01: Cabrera JE, Jin DJ (2001). "Growth phase and growth rate regulation of the rapA gene, encoding the RNA polymerase-associated protein RapA in Escherichia coli." J Bacteriol 183(20);6126-34. PMID: 11567013

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."

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

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

Junker06: Junker LM, Peters JE, Hay AG (2006). "Global analysis of candidate genes important for fitness in a competitive biofilm using DNA-array-based transposon mapping." Microbiology 152(Pt 8);2233-45. PMID: 16849790

Lewis92a: Lewis LK, Jenkins ME, Mount DW (1992). "Isolation of DNA damage-inducible promoters in Escherichia coli: regulation of polB (dinA), dinG, and dinH by LexA repressor." J Bacteriol 174(10);3377-85. PMID: 1577702

Lindback97: Lindback T, Kolsto AB (1997). "A Bacillus cereus member of the SNF2 family." Microbiology 143 ( Pt 1);171-4. PMID: 9025290

Lynch07: Lynch SV, Dixon L, Benoit MR, Brodie EL, Keyhan M, Hu P, Ackerley DF, Andersen GL, Matin A (2007). "Role of the rapA Gene in Controlling Antibiotic Resistance of Escherichia coli Biofilms." Antimicrob Agents Chemother 51(10):3650-8. PMID: 17664315

Muzzin98: Muzzin O, Campbell EA, Xia L, Severinova E, Darst SA, Severinov K (1998). "Disruption of Escherichia coli hepA, an RNA polymerase-associated protein, causes UV sensitivity." J Biol Chem 273(24);15157-61. PMID: 9614128

Nonaka06: Nonaka G, Blankschien M, Herman C, Gross CA, Rhodius VA (2006). "Regulon and promoter analysis of the E. coli heat-shock factor, sigma32, reveals a multifaceted cellular response to heat stress." Genes Dev 20(13);1776-89. PMID: 16818608

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

Rouby02: Rouby J, Pugniere M, Mani JC, Granier C, Monmouton P, Theulier Saint Germain S, Leonetti JP (2002). "Characterization of monoclonal antibodies against Escherichia coli core RNA polymerase." Biochem J 361(Pt 2);347-54. PMID: 11772406

Salmelin02: Salmelin C, Vilpo J (2002). "Chlorambucil-induced high mutation rate and suicidal gene downregulation in a base excision repair-deficient Escherichia coli strain." Mutat Res 500(1-2);125-34. PMID: 11890942

Sukhodolets00: Sukhodolets MV, Jin DJ (2000). "Interaction between RNA polymerase and RapA, a bacterial homolog of the SWI/SNF protein family." J Biol Chem 275(29);22090-7. PMID: 10801781

Sukhodolets01: Sukhodolets MV, Cabrera JE, Zhi H, Jin DJ (2001). "RapA, a bacterial homolog of SWI2/SNF2, stimulates RNA polymerase recycling in transcription." Genes Dev 15(24);3330-41. PMID: 11751638

Sukhodolets98: Sukhodolets MV, Jin DJ (1998). "RapA, a novel RNA polymerase-associated protein, is a bacterial homolog of SWI2/SNF2." J Biol Chem 273(12);7018-23. PMID: 9507009

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.

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

UniProt11: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Other References Related to Gene Regulation

Nizov76: Nizov AA (1976). "[Immunoglobulins of blood serum and bile in chronic diseases of the liver and gallbladder]." Lab Delo NIL(10);597-601. PMID: 63588

ONeill91: O'Neill MC (1991). "Training back-propagation neural networks to define and detect DNA-binding sites." Nucleic Acids Res 19(2);313-8. PMID: 2014171

Wade06: Wade JT, Roa DC, Grainger DC, Hurd D, Busby SJ, Struhl K, Nudler E (2006). "Extensive functional overlap between sigma factors in Escherichia coli." Nat Struct Mol Biol 13(9);806-14. PMID: 16892065


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 Sat Dec 20, 2014, BIOCYC14A.