|Gene:||rnlA||Accession Numbers: G7365 (EcoCyc), b2630, ECK2626|
Synonyms: yfjN, std
Component of: RnlA-RnlB toxin-antitoxin complex
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]
|Map Position: [2,763,940 -> 2,765,013] (59.57 centisomes)||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 , String:511145.b2630 , UniProt:P52129
Relationship Links: PDB:Structure:4I8O
|Biological Process:||GO:0006402 - mRNA catabolic process
GO:0090502 - RNA phosphodiester bond hydrolysis, endonucleolytic [Otsuka07]
GO:0090305 - nucleic acid phosphodiester bond hydrolysis [UniProtGOA11]
|Molecular Function:||GO:0004521 - endoribonuclease activity
GO:0005515 - protein binding [Naka13, Otsuka12, Koga11]
GO:0042803 - protein homodimerization activity [Wei13]
GO:0004518 - nuclease activity [UniProtGOA11]
GO:0004519 - endonuclease activity [UniProtGOA11]
GO:0016787 - hydrolase activity [UniProtGOA11]
|MultiFun Terms:||extrachromosomal → prophage genes and phage related functions|
|information transfer → RNA related → RNA degradation|
|metabolism → degradation of macromolecules → RNA|
|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]|
Enzymatic reaction of: RNase
EC Number: 3.1.-.-
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
|Mutagenesis-Variant||188 -> 196|
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
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
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
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
©2014 SRI International, 333 Ravenswood Avenue, Menlo Park, CA 94025-3493