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Escherichia coli K-12 substr. MG1655 Enzyme: CP4-57 prophage; RNase LS, toxin of the RnlAB toxin-antitoxin system

Gene: rnlA Accession Numbers: G7365 (EcoCyc), b2630, ECK2626

Synonyms: yfjN, std

Regulation Summary Diagram: ?

Regulation summary diagram for rnlA

Component of: RnlA-RnlB toxin-antitoxin complex

Subunit composition of CP4-57 prophage; RNase LS, toxin of the RnlAB toxin-antitoxin system = [RnlA]2
         CP4-57 prophage; RNase LS, toxin of the RnlAB toxin-antitoxin system = RnlA

RNase LS (RnlA) is the toxin of a novel toxin-antitoxin system. Overexpression of RnlA in ΔrnlAB cells inhibits cell growth and causes mRNA degradation, while overexpression of RnlB in wild-type cells suppresses the growth defect of the T4 dmd mutant, indicating that RnlB inhibits RnlA activity. RnlA and RnlB interact directly. The RnlA protein is relatively stable compared to RnlB [Koga11].

RnlA was first identified as an endoribonuclease that cleaves bacteriophage T4 late mRNA in T4 dmd mutants [Otsuka03]. RNase HI is required for this RnlA activity; it also enhances RnlA-mediated cell toxicity [Naka13]. Interestingly, the T4 Dmd protein acts as a promiscuous antitoxin in vivo, binding to both RnlA and LsoA, the toxin of a plasmid-derived TA system [Otsuka12]. RnlA also plays a role in cellular mRNA degradation. rnlA mutants display slowed degradation of many mRNAs as well as accumulation of a 307-nucleotide fragment derived from 23S rRNA [Otsuka05]. The cyaA mRNA was shown to be a target of RnlA [Iwamoto08].

A crystal structure of RnlA has been solved. The protein consists of three domains, an N-terminal domain, a central N repeated domain and a C-terminal Dmd-binding domain (DBD); the overall structure is unique. The DBD domain is responsible for dimerization of RnlA, its interaction with the antitoxins RnlB and T4 Dmd, and its toxicity [Wei13].

The cleavage of T4 soc mRNA depends on translation termination [Yamanishi05]. RNase LS activity purifies as a large multi-component complex with the RnlA gene product as a central component [Otsuka07]. RNase HI interacts with RnlA in vivo and enhances the RNA cleavage activity of RnlA in vitro [Naka13].

An rnlA mutant is sensitive to high salt concentrations. The effect is due to stabilization of the cyaA mRNA [Iwamoto08]. rnlA expression is induced 2-fold upon overexpression of rpoH [Nonaka06] and is negatively regulated by IscR [Otsuka10].

RnlA: "RNase LS (Late-gene Silencing in T4)" [Otsuka05]

Review: [Yamaguchi11], Comments: [Short12, Jermy12]

Map Position: [2,763,940 -> 2,765,013] (59.57 centisomes, 214°)
Length: 1074 bp / 357 aa

Molecular Weight of Polypeptide: 40.061 kD (from nucleotide sequence)

Molecular Weight of Multimer: 78.0 kD (experimental) [Wei13]

Unification Links: ASAP:ABE-0008659 , DIP:DIP-12079N , EchoBASE:EB2992 , EcoGene:EG13200 , EcoliWiki:b2630 , Mint:MINT-1290895 , OU-Microarray:b2630 , PortEco:rnlA , Protein Model Portal:P52129 , RefSeq:NP_417119 , RegulonDB:G7365 , SMR:P52129 , String:511145.b2630 , UniProt:P52129

Relationship Links: PDB:Structure:4I8O

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for rnlA

GO Terms:

Biological Process: GO:0006402 - mRNA catabolic process Inferred from experiment [Otsuka05, Iwamoto08]
GO:0090502 - RNA phosphodiester bond hydrolysis, endonucleolytic Inferred from experiment [Otsuka07]
GO:0090305 - nucleic acid phosphodiester bond hydrolysis Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0004521 - endoribonuclease activity Inferred from experiment [Otsuka07]
GO:0005515 - protein binding Inferred from experiment [Naka13, Otsuka12, Koga11]
GO:0042803 - protein homodimerization activity Inferred from experiment [Wei13]
GO:0004518 - nuclease activity Inferred by computational analysis [UniProtGOA11a]
GO:0004519 - endonuclease activity Inferred by computational analysis [UniProtGOA11a]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11a]

MultiFun Terms: extrachromosomal prophage genes and phage related functions
information transfer RNA related RNA degradation
metabolism degradation of macromolecules RNA

Essentiality data for rnlA 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 01-Nov-2013 by Keseler I , SRI International
Last-Curated ? 23-Dec-2013 by Keseler I , SRI International

Enzymatic reaction of: RNase

Synonyms: endoribonuclease

EC Number: 3.1.-.-

an mRNA + H2O <=> a single-stranded RNA + a single-stranded RNA

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

The reaction is physiologically favored in the direction shown.

Subunit of: RnlA-RnlB toxin-antitoxin complex

Subunit composition of RnlA-RnlB toxin-antitoxin complex = [RnlB][RnlA]
         CP4-57 prophage; antitoxin of the RnlA-RnlB toxin-antitoxin system = RnlB (summary available)
         CP4-57 prophage; RNase LS, toxin of the RnlAB toxin-antitoxin system = RnlA

Created 01-Nov-2010 by Keseler I , SRI International

Sequence Features

Protein sequence of CP4-57 prophage; RNase LS, toxin of the RnlAB toxin-antitoxin system with features indicated

Feature Class Location Citations Comment
Mutagenesis-Variant 188 -> 196
[Otsuka05, UniProt13]
UniProt: In rnlA5; strongly reduces RNase LS activity.

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram


Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


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

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

Iwamoto08: Iwamoto A, Lemire S, Yonesaki T (2008). "Post-transcriptional control of Crp-cAMP by RNase LS in Escherichia coli." Mol Microbiol 70(6);1570-8. PMID: 19019153

Jermy12: Jermy A (2012). "Phage biology: T4 to TA, checkmate." Nat Rev Microbiol 10(3);160. PMID: 22307030

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

Koga11: Koga M, Otsuka Y, Lemire S, Yonesaki T (2011). "Escherichia coli rnlA and rnlB compose a novel toxin-antitoxin system." Genetics 187(1);123-30. PMID: 20980243

Naka13: Naka K, Koga M, Yonesaki T, Otsuka Y (2013). "RNase HI stimulates the activity of RnlA toxin in Escherichia coli." Mol Microbiol. PMID: 24308852

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

Otsuka03: Otsuka Y, Ueno H, Yonesaki T (2003). "Escherichia coli endoribonucleases involved in cleavage of bacteriophage T4 mRNAs." J Bacteriol 185(3);983-90. PMID: 12533474

Otsuka05: Otsuka Y, Yonesaki T (2005). "A novel endoribonuclease, RNase LS, in Escherichia coli." Genetics 169(1);13-20. PMID: 15677746

Otsuka07: Otsuka Y, Koga M, Iwamoto A, Yonesaki T (2007). "A role of RnlA in the RNase LS activity from Escherichia coli." Genes Genet Syst 82(4);291-9. PMID: 17895580

Otsuka10: Otsuka Y, Miki K, Koga M, Katayama N, Morimoto W, Takahashi Y, Yonesaki T (2010). "IscR regulates RNase LS activity by repressing rnlA transcription." Genetics 185(3);823-30. PMID: 20421606

Otsuka12: Otsuka Y, Yonesaki T (2012). "Dmd of bacteriophage T4 functions as an antitoxin against Escherichia coli LsoA and RnlA toxins." Mol Microbiol 83(4);669-81. PMID: 22403819

Short12: Short FL, Blower TR, Salmond GP (2012). "A promiscuous antitoxin of bacteriophage T4 ensures successful viral replication." Mol Microbiol 83(4);665-8. PMID: 22283468

UniProt13: UniProt Consortium (2013). "UniProt version 2013-08 released on 2013-08-01 00:00:00." Database.

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

Wei13: Wei Y, Gao ZQ, Otsuka Y, Naka K, Yonesaki T, Zhang H, Dong YH (2013). "Structure-function studies of Escherichia coli RnlA reveal a novel toxin structure involved in bacteriophage resistance." Mol Microbiol 90(5);956-65. PMID: 24112600

Yamaguchi11: Yamaguchi Y, Park JH, Inouye M (2011). "Toxin-antitoxin systems in bacteria and archaea." Annu Rev Genet 45;61-79. PMID: 22060041

Yamanishi05: Yamanishi H, Yonesaki T (2005). "RNA Cleavage Linked with Ribosomal Action." Genetics 171(2):419-25. PMID: 16020788

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 19.0 on Thu Sep 3, 2015, biocyc12.