|Gene:||rnc||Accession Numbers: EG10857 (EcoCyc), b2567, ECK2565|
RNase III is an endonuclease that cleaves double-stranded RNA to yield 5'-phosphates and 3'-hydroxyls [Robertson75]. It is required for processing of ribosomal RNA (rRNA) and phage mRNA, for the regulation of a number of genes and for proper function of regulatory antisense RNAs, usually cleaving dsRNA created by the formation of stem structures within single-stranded RNA.
RNase III is a key enzyme in rRNA processing, cleaving 30S precursor rRNA to yield 23S, 17S and 5S rRNA, though it has been suggested based on degradation experiments that the 30S RNA is not actually a precursor to these rRNAs [Ginsburg75, Nikolaev74, Gegenheimer75]. The 23S rRNA sequence is flanked by RNase III cleavage sites and is cleaved at multiple points at its 5' end and one at its 3' end [Bram80, Sirdeshmukh85, Stark85]. Some of the 5' cleavage of 23S rRNA occurs even in the absence of RNase III [Sirdeshmukh85a]. Regions flanking the 16S rRNA are predicted to form a 26-bp double helical stem at the base of a loop containing the 16S rRNA. RNase III cleaves at both sites that combine to form the stem [Young78]. Electron microscopy confirms that both the 16S and 23S rRNA sequences form loops with stems made from flanking regions that coincide with RNase III cleavage sites [Edlind80]. 5S rRNA is seperated from the 30S precursor as a 7S fragment, which is then cleaved at its 3' end by RNase III and finally by RNase E to yield the final 5S rRNA [Szeberenyi84]. In the absence of RNase III activity, mature 16S rRNA can still be found, but no mature 23S rRNA is detectable and unprocessed 23S rRNA with extraneous sequence is incorporated in 50S ribosomes [King84]. This unprocessed 30S rRNA can contribute elements to multiple ribosomes, resulting in pairs or occasionaly trios of 50S ribosomes linked together by unprocessed rRNA [Clark84a].
Many types of phage RNA require RNase III processing. RNase III limits synthesis of the lambda lysogeny protein Int, possibly due to processing at RNase III sites within the int mRNA and in the nearby sib regulatory region [Belfort80, Schindler81, Guarneros82, Plunkett89]. RNase III also cleaves the lambda early N leader RNA, removing the NUTL binding site and thus preventing negative autoregulatory binding of N protein to NUTL, resulting in a 200-fold increase in N translation [Wilson02]. RNase III processes T4 species I RNA and may be required for proper transcriptional termination as well [Paddock76]. RNase III cleaves at multiple sites within the T7 phage genome, including the initiator RNA A3t and gene 1.2, which is subject to 3' processing [Gross87, Saito81]. RNase III cleavage of T7 RNA has been extensively evaluated at the R.1 site [Li93b]. Cleavage at R1.1 depends not on specific sequence information but on the asymmetry of the 4/5 loop at that site [CalinJageman03]. A mutant with a bulge-helix-bulge motif replacing this asymmetric loop is bound but not hydrolyzed by RNase III [CalinJageman03a]. RNase III processes high molecular weight T3 RNA polymerase transcripts into discrete late T3 RNAs [Majumder77]. MS2 phage RNA with an artificially-inserted RNase III stem-loop target undergoes selective pressure from RNase III, evolving variants with base mismatches, bulges and shortened stems, all of which are inviable RNase II targets [Klovins97].
Polynucleotide phosphorylase (PNP) regulation depends on RNase III. The half life of pnp mRNA increases from 1.5 minutes to from 8 to 40 minutes in the absence of RNase III, leading to an up to eleven-fold increase in the amount of pnp mRNA [Takata87, Portier87, Takata89]. Cleavage of the pnp transcript occurs in the 5' leader of the pnp mRNA, cleaving a stem-loop to leave a short 3' overhang [Regnier86, Jarrige01, Portier87, Takata89, RobertLe92]. Following 5' cleavage by RNase III, the remaining mRNA is processed by RNase E [Hajnsdorf94].
RNase III is also involved in processing quite a few other cellular mRNAs. It processes the end of the ribosomal protein-RNA polymerase rplJL-rpoBC operon [Barry80]. Deletions around an RNase III site in between rplL and rpoB in the same operon substantially reduce the translation efficiency of β mRNA, though there is no observable effect of the absence of RNase III [Dennis84]. RNase III cleaves in the leader of the secEnusG transcript and in the L12-β intercistronic region in the rplKAJLrpoBC transcript. Loss of RNase III stabilizes both mRNAs 1-2 fold without changing steady-state level, indicating a compensatory decrease in transcription [Chow94]. Variants of the rpsO mRNA that are destabilized by polyadenylation can be cleaved by RNase III. The RNase III-cleaved mRNA is no longer destabilized by polyadenylation [HaugelNielsen96]. The 10 Sa precursor RNA is processed twice by RNase III before undergoing a final processing step to become the tmRNA that places the SsrA tag on incompletely translated proteins [Srivastava90, Makarov92, Srivastava92]. RNase III cleaves the trp and lac operons and can inactivate lac α-peptide mRNA in vitro [Shen81, Shen82]. Primary transcripts of the metY-nusA-infB, rnc-era-recO and rpsO-pnp operons are all cleaved by RNase III in their 5' noncoding leader regions. All three mRNAs are degraded much more rapidly following processing [Regnier90]. RNase III cleavage of the metY-nusA-infB operon also releases the metY minor initiator tRNA [Regnier89]. RNase III cleaves the 5' untranslated region of both the rnc-era-recO and rnc-era transcripts, reducing their stability [Matsunaga96]. The second stem-loop in the untranslated region is required for this cleavage [Matsunaga96a]. Cleavage of rnc increases its degradation rate ten fold [Matsunaga97]. Three RNase III sites in the sdhCDAB-sucABCD intergenic region contribute to extreme instability of the operon transcript [Cunningham98a]. RNase III cleavage in the 5' untranslated region of the speF-potE transcript increases translational efficiency and thus enhances expression of ornithine decarboxylase [Kashiwagi94]. Translation from the -292 start site of the adhE gene, which is needed for fermentative growth on glucose, requires RNase III. This may be due to a predicted intramolecular base pairing in the 5' untranslated region which would be expected to block ribosome binding [MembrilloHernan99a, Aristarkhov96]. RNase III cleaves DicF RNA to a precursor stage that is then cleaved by RNase E to its final form as a trans-acting cell division inhibitor [Faubladier90]. Finally, bolA RNA is stabilized in the absence of RNase III [Santos97].
Some antisense RNA regulatory systems are RNase III targets. The antisense RNA-OUT, which regulates IS10 transposition by binding the transposase mRNA RNA-IN, folds into a stable stem-loop structure that is RNase III resistant unless certain point mutations are introduced [Case89]. However, RNase III cleavage is required for destabilization of RNA-IN following binding by RNA-OUT [Case90]. Synthesis of the plasmid IncFII replication protein RepA is controlled by binding of the antisense RNA CopA to the leader region of RepA mRNA (CopT). RNase III cleaves the CopA/CopT duplex, limiting RepA expression [Blomberg90]. Unpaired bases within the stem-loop in CopA reduce its suitability as a substrate for RNase III, limiting this regulatory cleavage [Hjalt95]. Unstable antisense RNAs target for RNase III cleavage truncated mRNAs from the Hok/Sok (plasmid R1), SrnB (F plasmid) and Pnd (plasmid R438) plasmid toxicity systems. Absence of the truncated mRNAs leads to rapid degradation of the stable full-length mRNAs that code for toxins [Gerdes92]. Sok antisense RNA forms a three-way junction with hok mRNA (which forms an internal stem-loop). This Sok binding, along with the presence of a transcriptional terminator hairpin within Sok, allows RNase III cleavage to occur [Franch99].
RNAI, required for replication of the plasmid ColE1, is cleaved by RNase III, with polyadenylated RNAI collecting in the absence of RNase III [Binnie99]. The plasmid R1 gene 19 is also controlled by RNase III, which cleaves within the coding region of gene 19 [Koraimann93]. The copy number of miniR6-5 but not miniF plasmids is reduced 2-fold in the absence of RNase III [Ely81].
Though RNase III is dispensible for growth, mutants lacking its activity do not grow at 45° C and are nonmotile [Takiff89, Apirion75, Apirion78a]. Suppressor mutations that cancel this temperature sensitivity have been discovered [Apirion76]. mRNA is broken down equally quickly in cells with or without RNase III, but during carbon starvation RNA decays faster in cells lacking RNase III [Apirion76a, Freire06]. In strains mutated in multiple ribonucleases, lack of RNase III led to more rapid decay of RNA generally [Babitzke93]. In mutants lacking RNase III function, β-galactosidase induction from the lac operon is twice as slow as normal and yield ten times less enzyme. In vitro, β-galactosidase RNA from the mutant is three times less competent for translation initiation [Talkad78]. Mutants in RNase III supress cold sensitive suhB mutants [Inada95].
RNase III is a dimer, though a single functional active site is sufficient for catalytic activity [Dunn76, March90, Conrad02]. The dominant-negative point mutant rnc70, which binds but does not cleave dsRNA, does not necessarily exert its negative effect on wild type through formation of mixed dimers [Dasgupta98].
RNase III has two modules, an amino-terminal 150-residue catalytic domain and a carboxy-terminal 70-residue recognition module that is homologous to other dsRNA binding domains. By NMR, RNase III has an α-β-β-β-α topology, with a three-stranded β sheet packing on two α helices [Kharrat95]. Both domains play a part in substrate specificity and cleavage site selection, though truncated RNase III lacking the RNA binding domain still cleaves small substrates in vitro and is specific for dsRNA [Conrad01, Sun01]. Changing the interdomain spacer from nine to twenty residues has no effect on RNase III activity [Conrad01]. The RNase III catalytic module has one processing center with two mRNA cleavage sites, generating products with two nucleotide 3' overhangs [Zhang04f]. Cleavage involves incorporation of a solvent oxygen atom into the 5'-phosphate of the RNA product, making cleavage irreversible. The catalytic rate depends on the divalent metal ion used in the reaction. A two-step change in fluorescence may indicate conformational change during distinct substrate binding and catalytic steps [Campbell02a]. Experiments suggest that two magnesium ions are involved in catalysis [Sun05].
Though there are no canonical motifs for RNase III cleavage, certain base pairings are unfavorable, disrupting proper RNase III binding and thus preventing subsequent cleavage. Relative to the cleavage site, GC/CG is never seen at -5, is rarely seen at -4 and -6 and is never seen at -12. UA is never seen at -11. Addition of these unfavored base pairs in the stated locations in T7 R1.1 RNA disrupted RNase III binding. The three base-pair antideterminant sequence from tRNASec, which prevents interaction with incorrect aminoacyl-tRNA-synthetases, also disrupts RNase III binding when placed in the critical -5 and -12 positions, but not when placed in the intervening region [Zhang97a]. RNase III cleavage does not depend on tertiary RNA-RNA interactions or a conserved CUU/GAA base pair sequence [Chelladurai91]. RNase III recognizes RNA duplexes longer than eleven base pairs with little specificity [Lamontagne04]. RNase III is still able to cleave at the expected site in R1.1 RNA even when a phosphorothioate internucleotide linkage is present [Nicholson88].
RNase III activity is stimulated four-fold following infection by T7 phage. The T7 protein kinase gp0.7 PK phosphorylates RNase III at a serine, stimulating processing of T7 early and late mRNAs [Mayer83, Robertson94].
Locations: cytosol, inner membrane
|Map Position: [2,701,405 <- 2,702,085] (58.22 centisomes, 210°)||Length: 681 bp / 226 aa|
Molecular Weight of Polypeptide: 25.55 kD (from nucleotide sequence)
pI: 7.3 [Davidov93]
Unification Links: ASAP:ABE-0008448 , CGSC:271 , DIP:DIP-48223N , EchoBASE:EB0850 , EcoGene:EG10857 , EcoliWiki:b2567 , Mint:MINT-1227120 , ModBase:P0A7Y0 , OU-Microarray:b2567 , PortEco:rnc , Pride:P0A7Y0 , Protein Model Portal:P0A7Y0 , RefSeq:NP_417062 , RegulonDB:EG10857 , SMR:P0A7Y0 , String:511145.b2567 , UniProt:P0A7Y0
Relationship Links: InterPro:IN-FAMILY:IPR000999 , InterPro:IN-FAMILY:IPR011907 , InterPro:IN-FAMILY:IPR014720 , Panther:IN-FAMILY:PTHR11207 , Pfam:IN-FAMILY:PF00035 , Pfam:IN-FAMILY:PF14622 , Prosite:IN-FAMILY:PS00517 , Prosite:IN-FAMILY:PS50137 , Prosite:IN-FAMILY:PS50142 , Smart:IN-FAMILY:SM00358 , Smart:IN-FAMILY:SM00535
|Biological Process:||GO:0006396 - RNA processing
GO:0090501 - RNA phosphodiester bond hydrolysis [Robertson75]
GO:0090502 - RNA phosphodiester bond hydrolysis, endonucleolytic [GOA06, GOA01, GOA01a, Robertson75]
GO:0006364 - rRNA processing [UniProtGOA11a, GOA06]
GO:0006397 - mRNA processing [UniProtGOA11a, GOA06]
GO:0008033 - tRNA processing [UniProtGOA11a]
GO:0016075 - rRNA catabolic process [GOA01a]
GO:0090305 - nucleic acid phosphodiester bond hydrolysis [UniProtGOA11a]
|Molecular Function:||GO:0004525 - ribonuclease III activity
[GOA06, GOA01, GOA01a, Robertson75]
GO:0000166 - nucleotide binding [UniProtGOA11a]
GO:0003723 - RNA binding [UniProtGOA11a, GOA06, GOA01a]
GO:0004518 - nuclease activity [UniProtGOA11a]
GO:0004519 - endonuclease activity [UniProtGOA11a]
GO:0005524 - ATP binding [UniProtGOA11a]
GO:0016787 - hydrolase activity [UniProtGOA11a]
GO:0019843 - rRNA binding [UniProtGOA11a]
GO:0046872 - metal ion binding [UniProtGOA11a]
|Cellular Component:||GO:0005829 - cytosol
[DiazMejia09, Ishihama08, LopezCampistrou05]
GO:0005737 - cytoplasm [UniProtGOA11, UniProtGOA11a, GOA06]
GO:0005886 - plasma membrane [Miczak91]
|MultiFun Terms:||information transfer → RNA related → RNA degradation|
|metabolism → degradation of macromolecules → RNA|
|Growth Medium||Growth?||T (°C)||O2||pH||Osm/L||Growth Observations|
|LB Lennox||No||37||Aerobic||7||No [Baba06, Comment 1]|
Revised 25-May-2011 by Brito D
Enzymatic reaction of: ribonuclease (RNase III)
EC Number: 220.127.116.11
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.
The optimum pH range is 6.9-7.4.
|Conserved-Region||6 -> 128|
|Conserved-Region||155 -> 225|
|Sequence-Conflict||168 -> 195|
10/20/97 Gene b2567 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10857; confirmed by SwissProt match.
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