Escherichia coli K-12 substr. MG1655 Protein: RNase adaptor protein

Gene: rapZ Accession Numbers: EG12146 (EcoCyc), b3205, ECK3194

Synonyms: yhbJ

Regulation Summary Diagram: ?

Regulation summary diagram for rapZ

Subunit composition of RNase adaptor protein = [RapZ]3
         RNase adaptor protein = RapZ

RapZ regulates the expression of GlmS by controlling the processing and stability of the small RNA regulator GlmZ [Kalamorz07]. RapZ acts as an adaptor protein that guides processing of GlmZ by RNase E. GlmY binds and sequesters RapZ, thereby inhibiting GlmZ processing [Gopel13].

RapZ binds both GlmY and GlmZ, likely via its C terminus, and interacts with RNase E [Gopel13]. RapZ was earlier shown to bind GTP and ATP and to possess NTPase and pNPPase activities in vitro [Luciano09].

RapZ was purified and crystallized; the protein is trimeric in solution [Resch13].

Deletion of rapZ leads to overproduction of GlmS; the effect requires Hfq and the small RNA GlmZ. In a rapZ mutant, GlmZ is present in the unprocessed from [Kalamorz07]. A mutation in rapZ was one of five mutations found to be responsible for increased butanol tolerance [Atsumi10].

RapZ: "RNase adaptor protein for sRNA GlmZ" [Gopel13]

Review: [Gopel14]

Citations: [Salim12]

Gene Citations: [Rhodius05, Jones94]

Locations: cytosol

Map Position: [3,345,137 -> 3,345,991] (72.1 centisomes, 260°)
Length: 855 bp / 284 aa

Molecular Weight of Polypeptide: 32.492 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0010522 , DIP:DIP-35927N , EchoBASE:EB2066 , EcoGene:EG12146 , EcoliWiki:b3205 , Mint:MINT-1232648 , ModBase:P0A894 , OU-Microarray:b3205 , PortEco:yhbJ , PR:PRO_000025046 , Pride:P0A894 , Protein Model Portal:P0A894 , RefSeq:NP_417672 , RegulonDB:EG12146 , SMR:P0A894 , String:511145.b3205 , UniProt:P0A894

Relationship Links: InterPro:IN-FAMILY:IPR005337 , InterPro:IN-FAMILY:IPR027417 , Pfam:IN-FAMILY:PF03668

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0006396 - RNA processing Inferred from experiment [Kalamorz07]
GO:0048518 - positive regulation of biological process Inferred from experiment [Kalamorz07]
Molecular Function: GO:0003723 - RNA binding Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Gopel13]
GO:0005515 - protein binding Inferred from experiment [Gopel13]
GO:0042802 - identical protein binding Inferred from experiment [Resch13]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11a]
GO:0005524 - ATP binding Inferred by computational analysis [UniProtGOA11a, GOA06, GOA01a]
GO:0005525 - GTP binding Inferred by computational analysis [UniProtGOA11a, GOA06]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: regulation type of regulation posttranscriptional

Essentiality data for rapZ 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 18-Mar-2013 by Keseler I , SRI International
Last-Curated ? 18-Mar-2013 by Keseler I , SRI International

Sequence Features

Protein sequence of RNase adaptor protein with features indicated

Feature Class Location Citations Comment
Nucleotide-Phosphate-Binding-Region 8 -> 15
UniProt: ATP; Non-Experimental Qualifier: potential;
Nucleotide-Phosphate-Binding-Region 56 -> 59
UniProt: GTP; Non-Experimental Qualifier: potential;
N6-acetyllysine-Modification 251
[Zhang09, UniProt15]
UniProt: N6-acetyllysine.
Acetylation-Modification 251
[Zhang09, Zhang09]

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

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 ].
1/26/1998 (pkarp) Merged genes G7666/b3205 and EG12146/yhbJ


Atsumi10: Atsumi S, Wu TY, Machado IM, Huang WC, Chen PY, Pellegrini M, Liao JC (2010). "Evolution, genomic analysis, and reconstruction of isobutanol tolerance in Escherichia coli." Mol Syst Biol 6;449. PMID: 21179021

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

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."

Gopel13: Gopel Y, Papenfort K, Reichenbach B, Vogel J, Gorke B (2013). "Targeted decay of a regulatory small RNA by an adaptor protein for RNase E and counteraction by an anti-adaptor RNA." Genes Dev 27(5);552-64. PMID: 23475961

Gopel14: Gopel Y, Khan MA, Gorke B (2014). "Menage a trois: Post-transcriptional control of the key enzyme for cell envelope synthesis by a base-pairing small RNA, an RNase adaptor protein, and a small RNA mimic." RNA Biol 11(5). PMID: 24667238

Jones94: Jones DH, Franklin FC, Thomas CM (1994). "Molecular analysis of the operon which encodes the RNA polymerase sigma factor sigma 54 of Escherichia coli." Microbiology 1994;140 ( Pt 5);1035-43. PMID: 8025669

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

Kalamorz07: Kalamorz F, Reichenbach B, Marz W, Rak B, Gorke B (2007). "Feedback control of glucosamine-6-phosphate synthase GlmS expression depends on the small RNA GlmZ and involves the novel protein YhbJ in Escherichia coli." Mol Microbiol 65(6);1518-33. PMID: 17824929

Luciano09: Luciano J, Foulquier E, Fantino JR, Galinier A, Pompeo F (2009). "Characterization of YvcJ, a conserved P-loop-containing protein, and its implication in competence in Bacillus subtilis." J Bacteriol 191(5);1556-64. PMID: 19074378

Resch13: Resch M, Gopel Y, Gorke B, Ficner R (2013). "Crystallization and preliminary X-ray diffraction analysis of YhbJ from Escherichia coli, a key protein involved in the GlmYZ sRNA regulatory cascade." Acta Crystallogr Sect F Struct Biol Cryst Commun 69(Pt 2);109-14. PMID: 23385747

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

Salim12: Salim NN, Faner MA, Philip JA, Feig AL (2012). "Requirement of upstream Hfq-binding (ARN)x elements in glmS and the Hfq C-terminal region for GlmS upregulation by sRNAs GlmZ and GlmY." Nucleic Acids Res 40(16);8021-32. PMID: 22661574

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

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

Zhang09: Zhang J, Sprung R, Pei J, Tan X, Kim S, Zhu H, Liu CF, Grishin NV, Zhao Y (2009). "Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli." Mol Cell Proteomics 8(2);215-25. PMID: 18723842

Other References Related to Gene Regulation

Kumar11: Kumar R, Shimizu K (2011). "Transcriptional regulation of main metabolic pathways of cyoA, cydB, fnr, and fur gene knockout Escherichia coli in C-limited and N-limited aerobic continuous cultures." Microb Cell Fact 10;3. PMID: 21272324

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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 Oct 9, 2015, biocyc11.