MetaCyc Enzyme: ribonuclease E

Gene: rne Accession Numbers: EG10859 (MetaCyc), b1084, ECK1069

Synonyms: smbB, ams, hmp1, RNase E

Species: Escherichia coli K-12 substr. MG1655

Component of: degradosome (extended summary available)

Subunit composition of ribonuclease E = [Rne]4
         RNase E = Rne

Ribonuclease E (RNase E) is a single-strand-specific endonuclease that is essential for viability. It processes rRNA, tRNA and other RNAs, is involved in plasmid and phage stability and is part of the degradosome, a multienzyme complex involved in mRNA degradation.

RNase E is involved in processing and cleavage of several rRNAs. It processes the 9S rRNA precursor to yield the mature 5S rRNA by cleaving quite near the 5' end and downstream from the 3' end of the final product [Ghora78, Roy83, Apirion78]. RNase E also participates in the 5' maturation of 16S rRNA from its 17S precursor, as well as being able to cleave single-stranded regions within mature 16S and 23S rRNAs [Li99b, Bessarab98].

RNase E initiates the processing of both poly- and monicistronic tRNA transcripts, including those within rRNA transcripts, by cleaving within a few nucleotides of the mature 3' CCA terminus, thus allowing RNase P and other 3' to 5' exonucleases to complete tRNA maturation [Ow02, Li02]. RNase E similarly cleaves at the 3' CCA terminus of the ssrA RNA precursor to yield its final form [LinChao99]. RNase E may also be involved in processing of the 5' leader of precursor tRNAs [Soderbom05].

RNase E carries out the 3' processing of M1 mRNA, which codes for the catalytic subunit of RNase P [Lundberg95, Sim01]. Other mRNA processing substrates include the cell division inhibitor DicF, the RNA polymerase sigma70 activity modulator 6S RNA, the polycistronic histidine operon mRNA and the papAB primary transcript, which is cleaved to yield stable papA and unstable papB mRNA [Faubladier90, Kim04, Alifano94, Nilsson91]. Domains of RNase E have been identified that are important for the degradation of the Rep mRNA of the ColE2 plasmid, versus the antisense RNA that controls its expression [Nishio09].

The stability of plasmids R1 and Colicin E1 is influenced by RNase E. It initiates degradation of CopA, the R1 copy regulator RNA [Soderbom98]. RNase E also cleaves near the 5' end of the sok component of the hok/sok sense/antisense RNA plasmid stabilization mechanism from R1, allowing subsequent degradation by another degradosome component, PNPase [Dam97]. The Colicin E1 DNA synthesis inhibitor RNA, RNAI, is also cleaved at its 5' end by RNase E [Tomcsanyi85, LinChao91]. Finally, RNase E cleaves FinP, which binds to the 5'-untranslated region of the positive F-plasmid transfer regulator traJ [Jerome99].

RNase E processing maintains the balance between phage f1 proteins pII and PX by cleaving the mRNA coding for pII, thus maintaining a normal replication cycle [Kokoska98]. RNase E is required more generally for production of certain phage f1 mRNAs as well [Stump96]. RNase E processes T4 gene 32 mRNA, cleaves T4 soc mRNA and is involved generally in the destabilizing of T4 mRNA [Mudd88, Otsuka03, Mudd90]. Conversely, the T4 Srd protein stimulates RNase E to degrade host mRNAs [Qi15].

A number of cellular mRNAs are degraded by RNase E. mRNA decay slows 2-3 fold in an rne mutant, and RNase E is the rate-limiting enzyme in the degradation of many of its substrates [Babitzke91, Jain02]. RNase E cleaves both sodB mRNA and its antisense RNA RyhB, though cleavage of the latter can be blocked by Hfq binding to the cleavage site [Afonyushkin05, Masse03, Moll03a, Folichon03]. Hfq also overlaps cleavage sites in the dsrA and ompA mRNAs [Moll03a]. The rpsO-pnp transcript is cleaved near the beginning of the rpsO coding sequence and on both sides of the rpsO 3' stem-loop terminator, after which it is rapidly degraded by PNPase [Hajnsdorf99, Regnier91, Braun96, Hajnsdorf94]. Ribosome binding blocks this cleavage [Braun98]. RNase E is responsible for a number of cleavages within the unc transcripts, which code for subunits of the F1/F0-ATPase [Patel92, Patel95]. It destabilizes the secE, nusG, L11-L1, L10 and beta cistrons from transcripts from the secEnusG and rplKAJLrpoBC operons, though this is not reflected in a change in mRNA abundance [Chow94]. Other transcripts that are degraded by RNase E include ftsA-ftsZ, thrS, pstG, pnp and rnb [Cam96, Nogueira01, Kimata01, Hajnsdorf94a, Zilhao95, Tamura06]. RNase E is also involved in limiting the abundance of mRNAs from rspT, dsbC, pth and tetR [Le02, Zhan04, CruzVera02, Baumeister91]. Finally, although overexpressed RNase G can partially complement a lack of RNase E, about a hundred RNAs are only degraded by RNase E, including many mRNAs coding for proteins involved in energy generation and macromolecule synthesis and degradation [Lee02a].

RNase E regulates its own abundance by cleaving within the 5' untranslated region of rne mRNA. Autoregulation occurs via specific binding of the catalytic domain to the hp2 region of its transcript. As RNase E activity can be titrated by other substrates, this acts to modulate its expression to match cellular needs [Mudd93, Diwa02, Sousa01, Schuck09]. Appending the 5' region of rne to heterologous RNA confers RNase E regulation [Jain95].

In a pnp/rnb/rne triple mutant, RNA polyadenylation is longer and more abundant [OHara95]. Conversely, RNase E indirectly increases polyadenylation by generating new 3' ends on which PAP I, which has a binding region for RNase E, can act [Mohanty00, Raynal99]. Increased polyadenylation stabilizes the rne transcript [Mohanty99, Mohanty02].

RNase E cleaves at regions that are single stranded and rich in A/U sequences [Kim04b, Mackie92, Bessarab98, Babitzke91]. Though RNase E has no canonical target sequence, the effects of local sequence on cleavage placement and effectiveness have been thoroughly characterized [Kaberdin03, McDowall94]. Secondary structure in the form of adjacent stem-loops has been shown to be necessary for RNase E cleavage for a number of substrates, and it has been suggested that these structures maintain a stretch of single-stranded RNA for the enzyme to cleave [Ehretsmann92, Cormack92, Diwa00]. In other cases, however, secondary structures play no definite role in susceptibility or actually impede RNase E cleavage [Mackie93, McDowall95, Lopez96].

RNase E binds to the 5'-monophosphate end of its substrate but then cleaves farther in moving 3' to 5', suggesting a scanning mechanism [Feng02]. In the absence of a 5'-monophosphate, cleavage is slowed [Jiang04]. Blocking the 5' end, either by circularizing the RNA or by adding a 5'-triphosphate also inhibits cleavage [Mackie00, Mackie98]. However, evidence and requirements for a 5' end-independent mechanism of mRNA degradation by RNase E has also been presented [Kime10] and the mechanism of tRNA processing in the absence of recognition of a 5'-monophosphorylated end has been studied [Kime14]. Contrary to previous studies, RNA-seq analysis showed that the 5'-monophosphate-independent (direct entry) cleavage of RNA by RNase E appears to be a major RNA degradation pathway in E. coli [Clarke14].

The catalytic parameters of RNase E have been thoroughly evaluated [Redko03].

RNase E's enzymatic and RNA-binding functions are split between its amino-terminal and carboxy-terminal portions, respectively [McDowall96, Taraseviciene95]. The carboxy-terminal section of the protein and its arginine-rich RNA-binding domain (ARRBD) is required for mRNA degradation and enhances RNase E autoregulatory cleavage of rne mRNA, but is dispensable for rRNA processing [Ow00, Lopez99, Jiang00, Kaberdin00]. Contradicting this observation, it has been reported that the RNA-binding domain of RNase E is not required for feedback regulation [Diwa02a]. Mutations within the RNA-binding do lead to defective binding, but have no effect on RNA cleavage activity [Shin08].

RNase E is catalytically active only as a tetramer, with its RNA-binding domains facing outward [Callaghan03]. However, a conserved RNase E peptide lacking the tetramerization domain was shown to retain core catalytic function [Caruthers06]. Crystallographic and NMR analysis of the isolated RNA-binding domain indicates that it forms a homodimer, possibly contributing to overall tetramer formation [Schubert04]. A crystal structure of the amino-terminal catalytic domain to 2.9 Å resolution shows that the tetramer consists of a dimer of dimers and contains divalent magnesium ion [Callaghan05]. The tetrameric structure is maintained by cysteine-zinc-cysteine linkages between adjacent Rne monomers [Callaghan05a]. Additional crystal structures of the RNase E catalytic domain have been presented [Koslover08], as well as structures of a segment of the C-terminal domain of RNase E in complex with E. coli polynucleotide phosphorylase [Nurmohamed09], and with enolase [Nurmohamed10].

Both RrnA and CspE bind and inhibit RNase E, and T7 gene 0.7 protein kinase phosphorylates its carboxy-terminal half, stabilizing T7 mRNAs against RNase E degradation [Lee03d, Feng01a, Marchand01]. Ribosomal protein L4 interacts with the C-terminal region of RNase E inhibiting its activity, which may regulate the production of stress-induced proteins [Singh09]. The ATP-dependent RNA helicase RhlB binds to RNaseE as part of the degradosome, unwinding double stranded RNA for RNase E degradation. The minimal region on RNase E for RhlB recognition was mapped to RNase E residues 698-762. In addition, residues 628-843 and 694-790 stimulate the RhlB unwinding activity [Chandran07]. Co-expression of RNase E residues 696-762 and RhlB using a di-cistronic vector followed by biophysical study of their interaction demonstrated an avid binding between them [Worrall08].

Analysis of intragenic second-site suppressors of temperature-sensitive RNase E mutants demonstrated dissociation of the in vivo activity of RNase E on mRNA versus tRNA and rRNA substrates [Perwez08]. Substrate recognition determinants have been analyzed by site-directed mutagenesis [Garrey09] and the effect of a hyperactive N-terminal Q36R mutant of RNase E on RNA binding was studied [Go11]. Deletion analysis mapped the C-terminal Hfq binding region of RNase E which targets the degradation of mRNAs mediated by Hfq/sRNAs [Ikeda11]. Analysis of mutants in the 5'-phosphate sensor domain of RNase E suggested overlapping mechanisms of substrate recognition and a hierarchy of efficiencies toward target RNAs [Garrey11]. Other mutant studies showed that two RNA binding sites in the N-terminal domain of RNase E modulate its activity [Kim14].

Electron microscopy studies suggest that the degradosome binds to the cytoplasmic membrane via the N-terminal region of RNase E [Liou01]. The binding of the N-terminal catalytic domain of RNase E to the E. coli plasma membrane enhances stability and substrate affinity [Murashko12]. A segment of RNase E comprising residues 568-582 at the start of the C-terminal non-catalytic region has also been identified as being involved in membrane binding [Khemici08]. Evidence has been presented for the subcellular localization of RNase E and other components of the RNA processing and degradation network in extended cytoskeletal-like structures around the periphery of the cell [Taghbalout14, Taghbalout08, Taghbalout07]. However, contradictory work using live cell microscopy showed that RNase E is anchored to the inner cytoplasmic membrane via a membrane targeting sequence, but is not in cytoskeletal-like structures and is mobile on the membrane surface [Strahl15].

RNase E is required for cell division to occur [Goldblum81]. Inviability of rne mutants may be due to reduced levels of the cell-division protein FtsZ [Takada05]. The growth defect associated with RNase E mutants can be complemented by certain single amino acid substitutions in its paralog RNase G, although mRNA and tRNA metabolism is abnormal [Chung10]. The lethality of an RNase E mutant lacking its C-terminal half in combination with an rppH deletion is suppressed by rho or nusG mutants defective in Rho-dependent transcription termination [Anupama11]. Multiple chromosomal second-site suppressor mutations that restore colony forming ability to an RNase E deletion mutant have been identified, such as those in deaD [Tamura12]. RNase E deficiency also has effects on nutrient utilization by E. coli [Tamura13]. RNase E has a role in modulation of the bacterial SOS response that leads to transient arrest of cell division and initiation of DNA repair [Manasherob12].

The previously reported RNase K appears to be a proteolytic fragment of RNase E [Mudd93].

RNase E is of interest as a drug target because homologs are found in many different bacteria but not in humans or animals. Small molecule inhibitors of E. coli and Mycobacterium tuberculosis RNase E and RNase G have been reported [Kime15].

Reviews: [AitBara15, Bandyra13, Morita11, Kaberdin11, Bouvier11, Carpousis09, Carpousis07, Kushner02, Kennell02, Cohen97]

Citations: [Kemmer06, Takada07, Mackie08, Kime08, Stead11, AitBara15a]

Locations: cytosol, inner membrane

Map Position: [1,141,182 <- 1,144,367]

Molecular Weight of Polypeptide: 118.2 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0003668, CGSC:269, DIP:DIP-10727N, DisProt:DP00207, EchoBASE:EB0852, EcoGene:EG10859, EcoliWiki:b1084, Mint:MINT-1220086, ModBase:P21513, OU-Microarray:b1084, PortEco:rne, PR:PRO_000023789, Pride:P21513, Protein Model Portal:P21513, RefSeq:NP_415602, RegulonDB:EG10859, SMR:P21513, String:511145.b1084, UniProt:P21513

Relationship Links: InterPro:IN-FAMILY:IPR003029, InterPro:IN-FAMILY:IPR004659, InterPro:IN-FAMILY:IPR012340, InterPro:IN-FAMILY:IPR019307, InterPro:IN-FAMILY:IPR021968, InterPro:IN-FAMILY:IPR022967, InterPro:IN-FAMILY:IPR028878, PDB:Structure:1SLJ, PDB:Structure:1SMX, PDB:Structure:1SN8, PDB:Structure:2BX2, PDB:Structure:2C0B, PDB:Structure:2C4R, PDB:Structure:2FYM, PDB:Structure:2VMK, PDB:Structure:2VRT, PDB:Structure:3GCM, PDB:Structure:3GME, PDB:Structure:3H1C, PDB:Structure:3H8A, Pfam:IN-FAMILY:PF00575, Pfam:IN-FAMILY:PF10150, Pfam:IN-FAMILY:PF12111, Prosite:IN-FAMILY:PS50126, Smart:IN-FAMILY:SM00316

Gene-Reaction Schematic

Expand/Contract the Schematic connections:

Gene-Reaction Schematic

GO Terms:
Biological Process:
Inferred from experimentGO:0000967 - rRNA 5'-end processing [Li99b]
Inferred from experimentGO:0006401 - RNA catabolic process [Cormack93]
Inferred from experimentInferred by computational analysisGO:0006402 - mRNA catabolic process [Babitzke91, GOA06]
Inferred from experimentInferred by computational analysisGO:0008033 - tRNA processing [Li02, UniProtGOA11a, GOA06]
Inferred from experimentGO:0051289 - protein homotetramerization [Callaghan03]
Inferred by computational analysisGO:0006364 - rRNA processing [UniProtGOA11a, GOA06]
Inferred by computational analysisGO:0006396 - RNA processing [GOA01a]
Inferred by computational analysisGO:0090305 - nucleic acid phosphodiester bond hydrolysis [UniProtGOA11a]
Inferred by computational analysisGO:0090501 - RNA phosphodiester bond hydrolysis [GOA01a, Gaudet10]
Inferred by computational analysisGO:0090502 - RNA phosphodiester bond hydrolysis, endonucleolytic [GOA06]
Molecular Function:
Inferred from experimentInferred by computational analysisGO:0000287 - magnesium ion binding [Callaghan05, GOA06]
Inferred from experimentGO:0005515 - protein binding [Chandran07, Carpousis94, Py96, Erce10, AitBara10, Butland05, Regonesi06, Callaghan04]
Inferred from experimentInferred by computational analysisGO:0008270 - zinc ion binding [Callaghan05a, GOA06]
Inferred from experimentInferred by computational analysisGO:0008995 - ribonuclease E activity [Feng02, GOA01a]
Inferred by computational analysisGO:0003676 - nucleic acid binding [GOA01a]
Inferred by computational analysisGO:0003723 - RNA binding [UniProtGOA11a, GOA06, GOA01a]
Inferred by computational analysisGO:0004518 - nuclease activity [UniProtGOA11a]
Inferred by computational analysisGO:0004519 - endonuclease activity [UniProtGOA11a]
Inferred by computational analysisGO:0004521 - endoribonuclease activity [GOA06]
Inferred by computational analysisGO:0004540 - ribonuclease activity [GOA01a, Gaudet10]
Inferred by computational analysisGO:0016787 - hydrolase activity [UniProtGOA11a]
Inferred by computational analysisGO:0046872 - metal ion binding [UniProtGOA11a]
Cellular Component:
Inferred from experimentInferred by computational analysisGO:0009898 - cytoplasmic side of plasma membrane [Khemici08, Liou01, GOA06]
Inferred by computational analysisGO:0005737 - cytoplasm [UniProtGOA11, UniProtGOA11a, GOA06]
Inferred by computational analysisGO:0005886 - plasma membrane [UniProtGOA11, UniProtGOA11a, Miczak91]
Inferred by computational analysisGO:0016020 - membrane [UniProtGOA11a]

MultiFun Terms: information transferRNA relatedRNA degradation
metabolismdegradation of macromoleculesRNA

Imported from EcoCyc 15-Mar-2016 by Paley S, SRI International

Enzymatic reaction of: ribonuclease

Inferred from experiment

EC Number:

9S rRNA + 2 H2O → 5S rRNA + 2 an rRNA fragment

The direction shown, i.e. which substrates are on the left and right sides, is in accordance with the direction in which it was curated.

The reaction is physiologically favored in the direction shown.

Imported from EcoCyc 15-Mar-2016 by Paley S, SRI International

Enzymatic reaction of: ribonuclease

Inferred from experiment

EC Number:

RNase E mRNA processing substrate + n H2O → RNase E processing product mRNA + n an mRNA fragment

The direction shown, i.e. which substrates are on the left and right sides, is in accordance with the direction in which it was curated.

The reaction is physiologically favored in the direction shown.

Imported from EcoCyc 15-Mar-2016 by Paley S, SRI International

Enzymatic reaction of: ribonuclease

Inferred from experiment

EC Number:

a polycistronic tRNA precursor + H2O → a tRNA precursor with a 5' extension and a short 3' extension + a partially processed polycistronic tRNA precursor

The direction shown, i.e. which substrates are on the left and right sides, is in accordance with the direction in which it was curated.

The reaction is physiologically favored in the direction shown.

In Pathways: tRNA processing

Imported from EcoCyc 15-Mar-2016 by Paley S, SRI International

Enzymatic reaction of: ribonuclease

Inferred from experiment

EC Number:

a polycistronic tRNA precursor + H2O → a tRNA precursor with a 5' extension and a long 3' trailer + a partially processed polycistronic tRNA precursor

The direction shown, i.e. which substrates are on the left and right sides, is in accordance with the direction in which it was curated.

The reaction is physiologically favored in the direction shown.

In Pathways: tRNA processing

Imported from EcoCyc 15-Mar-2016 by Paley S, SRI International

Enzymatic reaction of: ribonuclease

Inferred from experiment

EC Number:

RNase E degradation substrate mRNA + n H2O → n+1 an mRNA fragment

The direction shown, i.e. which substrates are on the left and right sides, is in accordance with the direction in which it was curated.

The reaction is physiologically favored in the direction shown.

Imported from EcoCyc 15-Mar-2016 by Paley S, SRI International

Subunit of: degradosome

Species: Escherichia coli K-12 substr. MG1655

Subunit composition of degradosome = [(Ppk)2][(Rne)4][(RhlB)2][(Pnp)3][(Eno)2]
         polyphosphate kinase = (Ppk)2 (extended summary available)
         ribonuclease E = (Rne)4 (extended summary available)
                 RNase E = Rne
         RhlB, ATP-dependent RNA helicase of the RNA degradosome = (RhlB)2 (extended summary available)
         polynucleotide phosphorylase = (Pnp)3 (extended summary available)
                 polynucleotide phosphorylase monomer = Pnp
         enolase = (Eno)2 (extended summary available)

The degradosome is a large, multiprotein complex involved in RNA degradation. It consists of the RNA degradation enzymes RNase E and PNPase, as well as the ATP-dependent RNA helicase RhlB and the metabolic enzyme enolase [Py94, Carpousis94, Py96]. Polyphosphate kinase and the chaperone protein DnaK are also associated with and may be components of the degradosome [Blum97, Miczak96]. A "minimal" degradosome composed of only RNase E, PNPase and RhlB degrades malEF REP RNA in an ATP-dependent manner in vitro, with activity equivalent to purified whole degradosomes. RNase E enzymatic function is dispensible for this test case, whereas PNPase must be catalytically active and incorporated into the degradosome for degradation to occur [Coburn99]. Based on immunogold labeling studies, RhlB and RNase E are present in equimolar quantities in the degradosome, which is tethered to the cytoplasmic membrane via the amino-terminus of RNase E [Liou01].

RNase E provides the organizational structure for the degradosome. Its carboxy-terminal half binds PNPase, RhlB and enolase, and the loss of this portion of the protein prevents degradation of a number of degradosome substrates, including the ptsG and mukB mRNAs and RNA I [Kido96, Vanzo98, Morita04]. This scaffold region is flexible, with isolated segments of increased structure that may be involved in binding other degradosome constituents [Callaghan04]. RNase E binding to partner proteins can be selectively disrupted. Loss of RhlB and enolase binding results in reduced degradosome activity. Conversely, disrupted PNPase binding yields increased activity. Strains any alteration in RNase E binding do not grow as well as wild type [Leroy02]. The amino-terminal half of RNase E contains sequences involved in oligomerization [Vanzo98].

In vitro purified degradosome generates 147-nucleotide RNase E cleavage intermediates from rpsT mRNA. Continuous cycles of polyadenylation and PNPase cleavage are necessary and sufficient to break down these intermediates, though RNase II can block this second degradation step [Coburn98]. RNAs with 3' REP stabilizers or stem loops must be polyadenylated to allow breakdown by the degradosome [Khemici04, Blum99]. Poly(G) and poly(U) tails do not allow degradation, though addition of a stretch of mixed nucleotides copied from within a coding region has stimulated degradation of a test substrate [Blum99].

The degradosome copurifies with fragments from its RNA substrates, including rRNA fragments derived from cleavage of 16S and 23S rRNA by RNase E, 5S rRNA and ssrA RNA [Bessarab98, LinChao99].

The DEAD-box helicases SrmB, RhlE and CsdA bind RNase E in vitro at a different site than RhlB. RhlE and CsdA can both replace RhlB in promoting PNPase activity in vitro [Khemici04a]. CsdA is induced by cold shock, and following a shift to 15 degrees C it copurifies with the degradosome [PrudhommeGenere04].

At least two poly(A)-binding proteins interact with the degradosome. The cold-shock protein CspE inhibits internal cleavage and breakdown of polyadenylated RNA by RNase E and PNPase by blocking digestion through the poly(A) tail. S1, a component of the 30S ribosome, binds to RNase E and PNPase without apparent effect on their activities [Feng01a].

The global effects of mutations in degradosome constituents on mRNA levels have been evaluated using microarrays [Bernstein04].

The degradosome has been reconstituted from recombinant components RNase E, RhlB, PNPase and enolase, purified and analyzed biochemically and biophysically. When compared with endogenously expressed degradosome extracted from cells using FLAG-tagged RNase E, data suggested that RNA may modulate the interaction of additional proteins with the degradosome [Worrall08a]. The degradosome associates stably with the 70S ribosome and polysomes, which may recruit degradosomes to translation sites [Tsai12]. RNase II is also associated with the degradosome [Lu14b].

Proteomic studies of the response to mutants in degradosome components RhlB, enolase, PNPase, or RNase E revealed the role of the degradosome in modulating the proteomic response to perturbations in this major RNA degradation pathway [Zhou13a].

Fluorescence microscopy imaging and fluorescence energy transfer measurements produced a model for the degradosome in which interactions between its major components are spatially defined [DominguezMalfav13]. Fluorescence microscopy techniques also show that in E. coli cells the degradosome components RNase E, RhlB, PNPase and enolase are organized into helical filaments coiled around the periphery of the cell in a cytoskeletal-like structure ( [Taghbalout07, Taghbalout08, Taghbalout14] and commented in [Hoch14]). However, a subsequent publication using fluorescence microscopy to visualize RhlB and RNase E under live cell conditions demonstrated their membrane association, but no cytoskeletal-like structures were observed [Strahl15].

Review: [Kaberdin11]

Locations: inner membrane

GO Terms:
Cellular Component:
GO:0005886 - plasma membrane [Liou01]

Imported from EcoCyc 15-Mar-2016 by Paley S, SRI International

Sequence Features

Feature Class Location Citations Comment
Conserved-Region 39 -> 119
Inferred by computational analysis[UniProt15]
UniProt: S1 motif.
Mutagenesis-Variant 57
Inferred from experiment[Callaghan05]
UniProt: Reduces RNA cleavage by over 98%.
Protein-Segment 57 -> 112
Author statement[UniProt15]
UniProt: Interaction with RNA; Sequence Annotation Type: region of interest.
Mutagenesis-Variant 66
Inferred from experiment[Schubert04]
UniProt: Disrupts folding of the S1 motif.
Mutagenesis-Variant 67
Inferred from experiment[Callaghan05]
UniProt: Reduces RNA cleavage by over 98%. Reduces affinity for RNA.
Mutagenesis-Variant 112
Inferred from experiment[Callaghan05]
UniProt: Reduces RNA cleavage by 98%. Loss of RNA-binding.
Protein-Segment 169 -> 170
Author statement[UniProt15]
UniProt: Interaction with RNA 5'-terminal monophosphate; Sequence Annotation Type: region of interest.
Mutagenesis-Variant 170
Inferred from experiment[Kime10, Callaghan05]
UniProt: Abolishes enzyme activity toward RNA substrates with a 5' monophosphate (PubMed:16237448). Strongly reduces enzyme activity toward cspA mRNA (PubMed:19889093).
Mutagenesis-Variant 303
Inferred from experiment[Callaghan05]
UniProt: Reduces RNA cleavage by over 96%.
Metal-Binding-Site 303
Author statement[UniProt15]
UniProt: Magnesium; catalytic.
Mutagenesis-Variant 305
Inferred from experiment[Callaghan05]
D or L: Reduces RNA cleavage by over 96%.
Mutagenesis-Variant 346
Inferred from experiment[Callaghan05]
UniProt: Reduces RNA cleavage by over 96%. Reduces affinity for RNA.
Metal-Binding-Site 346
Author statement[UniProt15]
UniProt: Magnesium; catalytic.
Mutagenesis-Variant 373
Inferred from experiment[Callaghan05]
A or D: Reduces RNA cleavage by 89%.
Sequence-Conflict 390
Inferred by curator[ClaverieMartin91, UniProt15]
UniProt: (in Ref. 5; AAA23443).
Mutagenesis-Variant 404
Inferred from experiment[Callaghan05a]
UniProt: Reduces zinc-binding. Abolishes homotetramerization and enzyme activity.
Metal-Binding-Site 404
Author statement[UniProt15]
UniProt: Zinc; shared with dimeric partner.
Protein-Segment 404 -> 407
Author statement[UniProt15]
UniProt: Required for zinc-mediated homotetramerization and catalytic activity; Sequence Annotation Type: region of interest.
Mutagenesis-Variant 407
Inferred from experiment[Callaghan05a]
UniProt: Reduces zinc-binding. Abolishes homotetramerization and enzyme activity.
Metal-Binding-Site 407
Author statement[UniProt15]
UniProt: Zinc; shared with dimeric partner.
Sequence-Conflict 487
Inferred by curator[ClaverieMartin91, Casaregola92, UniProt15]
UniProt: (in Ref. 4; CAA47818 and 5; AAA23443).
Sequence-Conflict 564
Inferred by curator[Casaregola92, UniProt15]
UniProt: (in Ref. 4; CAA47818).
Sequence-Conflict 784
Inferred by curator[Casaregola92, UniProt15]
UniProt: (in Ref. 4; CAA47818).
Protein-Segment 833 -> 850
Author statement[UniProt15]
UniProt: Interaction with enolase; Sequence Annotation Type: region of interest.
Sequence-Conflict 838
Inferred by curator[ClaverieMartin91, UniProt15]
UniProt: (in Ref. 5; AAA23443).
Sequence-Conflict 905
Inferred by curator[Casaregola92, UniProt15]
UniProt: (in Ref. 4; CAA47818).
Protein-Segment 1021 -> 1061
Author statement[UniProt15]
UniProt: Interaction with PNPase; Sequence Annotation Type: region of interest.
Sequence-Conflict 1048
Inferred by curator[Cormack93, UniProt15]
UniProt: (in Ref. 7; AAA03347).

Sequence Pfam Features

Feature Class Location Citations Comment
Pfam PF00575 36 -> 118
Inferred by computational analysis[Finn14]
S1 : S1 RNA binding domain [More...]
Pfam PF10150 121 -> 391
Inferred by computational analysis[Finn14]
RNase_E_G : Ribonuclease E/G family [More...]
Pfam PF12111 1022 -> 1058
Inferred by computational analysis[Finn14]
PNPase_C : Polyribonucleotide phosphorylase C terminal [More...]


Afonyushkin05: Afonyushkin T, Vecerek B, Moll I, Blasi U, Kaberdin VR (2005). "Both RNase E and RNase III control the stability of sodB mRNA upon translational inhibition by the small regulatory RNA RyhB." Nucleic Acids Res 33(5);1678-89. PMID: 15781494

AitBara10: Ait-Bara S, Carpousis AJ (2010). "Characterization of the RNA degradosome of Pseudoalteromonas haloplanktis: conservation of the RNase E-RhlB interaction in the gammaproteobacteria." J Bacteriol 192(20);5413-23. PMID: 20729366

AitBara15: Ait-Bara S, Carpousis AJ (2015). "RNA degradosomes in bacteria and chloroplasts: classification, distribution and evolution of RNase E homologs." Mol Microbiol 97(6);1021-135. PMID: 26096689

AitBara15a: Ait-Bara S, Carpousis AJ, Quentin Y (2015). "RNase E in the γ-Proteobacteria: conservation of intrinsically disordered noncatalytic region and molecular evolution of microdomains." Mol Genet Genomics 290(3);847-62. PMID: 25432321

Alifano94: Alifano P, Rivellini F, Piscitelli C, Arraiano CM, Bruni CB, Carlomagno MS (1994). "Ribonuclease E provides substrates for ribonuclease P-dependent processing of a polycistronic mRNA." Genes Dev 8(24);3021-31. PMID: 8001821

Anupama11: Anupama K, Leela JK, Gowrishankar J (2011). "Two pathways for RNase E action in Escherichia coli in vivo and bypass of its essentiality in mutants defective for Rho-dependent transcription termination." Mol Microbiol 82(6);1330-48. PMID: 22026368

Apirion78: Apirion D (1978). "Isolation, genetic mapping and some characterization of a mutation in Escherichia coli that affects the processing of ribonuleic acid." Genetics 90(4);659-71. PMID: 369943

Babitzke91: Babitzke P, Kushner SR (1991). "The Ams (altered mRNA stability) protein and ribonuclease E are encoded by the same structural gene of Escherichia coli." Proc Natl Acad Sci U S A 88(1);1-5. PMID: 1846032

Bandyra13: Bandyra KJ, Bouvier M, Carpousis AJ, Luisi BF "The social fabric of the RNA degradosome." Biochim Biophys Acta 1829(6-7);514-22. PMID: 23459248

Baumeister91: Baumeister R, Flache P, Melefors O, von Gabain A, Hillen W (1991). "Lack of a 5' non-coding region in Tn1721 encoded tetR mRNA is associated with a low efficiency of translation and a short half-life in Escherichia coli." Nucleic Acids Res 19(17);4595-600. PMID: 1653948

Bernstein04: Bernstein JA, Lin PH, Cohen SN, Lin-Chao S (2004). "Global analysis of Escherichia coli RNA degradosome function using DNA microarrays." Proc Natl Acad Sci U S A 101(9);2758-63. PMID: 14981237

Bessarab98: Bessarab DA, Kaberdin VR, Wei CL, Liou GG, Lin-Chao S (1998). "RNA components of Escherichia coli degradosome: evidence for rRNA decay." Proc Natl Acad Sci U S A 95(6);3157-61. PMID: 9501232

Blum97: Blum E, Py B, Carpousis AJ, Higgins CF (1997). "Polyphosphate kinase is a component of the Escherichia coli RNA degradosome." Mol Microbiol 1997;26(2);387-98. PMID: 9383162

Blum99: Blum E, Carpousis AJ, Higgins CF (1999). "Polyadenylation promotes degradation of 3'-structured RNA by the Escherichia coli mRNA degradosome in vitro." J Biol Chem 274(7);4009-16. PMID: 9933592

Bouvier11: Bouvier M, Carpousis AJ (2011). "A tale of two mRNA degradation pathways mediated by RNase E." Mol Microbiol 82(6);1305-10. PMID: 22074454

Braun96: Braun F, Hajnsdorf E, Regnier P (1996). "Polynucleotide phosphorylase is required for the rapid degradation of the RNase E-processed rpsO mRNA of Escherichia coli devoid of its 3' hairpin." Mol Microbiol 19(5);997-1005. PMID: 8830280

Braun98: Braun F, Le Derout J, Regnier P (1998). "Ribosomes inhibit an RNase E cleavage which induces the decay of the rpsO mRNA of Escherichia coli." EMBO J 17(16);4790-7. PMID: 9707438

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

Callaghan03: Callaghan AJ, Grossmann JG, Redko YU, Ilag LL, Moncrieffe MC, Symmons MF, Robinson CV, McDowall KJ, Luisi BF (2003). "Quaternary structure and catalytic activity of the Escherichia coli ribonuclease E amino-terminal catalytic domain." Biochemistry 42(47);13848-55. PMID: 14636052

Callaghan04: Callaghan AJ, Aurikko JP, Ilag LL, Gunter Grossmann J, Chandran V, Kuhnel K, Poljak L, Carpousis AJ, Robinson CV, Symmons MF, Luisi BF (2004). "Studies of the RNA degradosome-organizing domain of the Escherichia coli ribonuclease RNase E." J Mol Biol 340(5);965-79. PMID: 15236960

Callaghan05: Callaghan AJ, Marcaida MJ, Stead JA, McDowall KJ, Scott WG, Luisi BF (2005). "Structure of Escherichia coli RNase E catalytic domain and implications for RNA turnover." Nature 437(7062);1187-91. PMID: 16237448

Callaghan05a: Callaghan AJ, Redko Y, Murphy LM, Grossmann JG, Yates D, Garman E, Ilag LL, Robinson CV, Symmons MF, McDowall KJ, Luisi BF (2005). ""Zn-link": a metal-sharing interface that organizes the quaternary structure and catalytic site of the endoribonuclease, RNase E." Biochemistry 44(12);4667-75. PMID: 15779893

Cam96: Cam K, Rome G, Krisch HM, Bouche JP (1996). "RNase E processing of essential cell division genes mRNA in Escherichia coli." Nucleic Acids Res 24(15);3065-70. PMID: 8760895

Carpousis07: Carpousis AJ (2007). "The RNA degradosome of Escherichia coli: an mRNA-degrading machine assembled on RNase E." Annu Rev Microbiol 61;71-87. PMID: 17447862

Carpousis09: Carpousis AJ, Luisi BF, McDowall KJ (2009). "Endonucleolytic initiation of mRNA decay in Escherichia coli." Prog Mol Biol Transl Sci 85;91-135. PMID: 19215771

Carpousis94: Carpousis AJ, Van Houwe G, Ehretsmann C, Krisch HM (1994). "Copurification of E. coli RNAase E and PNPase: evidence for a specific association between two enzymes important in RNA processing and degradation." Cell 76(5);889-900. PMID: 7510217

Caruthers06: Caruthers JM, Feng Y, McKay DB, Cohen SN (2006). "Retention of core catalytic functions by a conserved minimal ribonuclease E peptide that lacks the domain required for tetramer formation." J Biol Chem 281(37);27046-51. PMID: 16854990

Casaregola92: Casaregola S, Jacq A, Laoudj D, McGurk G, Margarson S, Tempete M, Norris V, Holland IB (1992). "Cloning and analysis of the entire Escherichia coli ams gene. ams is identical to hmp1 and encodes a 114 kDa protein that migrates as a 180 kDa protein." J Mol Biol 228(1);30-40. PMID: 1447789

Chandran07: Chandran V, Poljak L, Vanzo NF, Leroy A, Miguel RN, Fernandez-Recio J, Parkinson J, Burns C, Carpousis AJ, Luisi BF (2007). "Recognition and cooperation between the ATP-dependent RNA helicase RhlB and ribonuclease RNase E." J Mol Biol 367(1);113-32. PMID: 17234211

Chow94: Chow J, Dennis PP (1994). "Coupling between mRNA synthesis and mRNA stability in Escherichia coli." Mol Microbiol 11(5);919-31. PMID: 7517486

Chung10: Chung DH, Min Z, Wang BC, Kushner SR (2010). "Single amino acid changes in the predicted RNase H domain of Escherichia coli RNase G lead to complementation of RNase E deletion mutants." RNA 16(7);1371-85. PMID: 20507976

Clarke14: Clarke JE, Kime L, Romero A D, McDowall KJ (2014). "Direct entry by RNase E is a major pathway for the degradation and processing of RNA in Escherichia coli." Nucleic Acids Res 42(18);11733-51. PMID: 25237058

ClaverieMartin91: Claverie-Martin F, Diaz-Torres MR, Yancey SD, Kushner SR (1991). "Analysis of the altered mRNA stability (ams) gene from Escherichia coli. Nucleotide sequence, transcriptional analysis, and homology of its product to MRP3, a mitochondrial ribosomal protein from Neurospora crassa." J Biol Chem 266(5);2843-51. PMID: 1704367

Coburn98: Coburn GA, Mackie GA (1998). "Reconstitution of the degradation of the mRNA for ribosomal protein S20 with purified enzymes." J Mol Biol 279(5);1061-74. PMID: 9642084

Coburn99: Coburn GA, Miao X, Briant DJ, Mackie GA (1999). "Reconstitution of a minimal RNA degradosome demonstrates functional coordination between a 3' exonuclease and a DEAD-box RNA helicase." Genes Dev 13(19);2594-603. PMID: 10521403

Cohen97: Cohen SN, McDowall KJ (1997). "RNase E: still a wonderfully mysterious enzyme." Mol Microbiol 23(6);1099-106. PMID: 9106202

Cormack92: Cormack RS, Mackie GA (1992). "Structural requirements for the processing of Escherichia coli 5 S ribosomal RNA by RNase E in vitro." J Mol Biol 228(4);1078-90. PMID: 1474579

Cormack93: Cormack RS, Genereaux JL, Mackie GA (1993). "RNase E activity is conferred by a single polypeptide: overexpression, purification, and properties of the ams/rne/hmp1 gene product." Proc Natl Acad Sci U S A 90(19);9006-10. PMID: 8415644

CruzVera02: Cruz-Vera LR, Galindo JM, Guarneros G (2002). "Transcriptional analysis of the gene encoding peptidyl-tRNA hydrolase in Escherichia coli." Microbiology 148(Pt 11);3457-66. PMID: 12427937

Dam97: Dam Mikkelsen N, Gerdes K (1997). "Sok antisense RNA from plasmid R1 is functionally inactivated by RNase E and polyadenylated by poly(A) polymerase I." Mol Microbiol 26(2);311-20. PMID: 9383156

Diwa00: Diwa A, Bricker AL, Jain C, Belasco JG (2000). "An evolutionarily conserved RNA stem-loop functions as a sensor that directs feedback regulation of RNase E gene expression." Genes Dev 14(10);1249-60. PMID: 10817759

Diwa02: Diwa AA, Belasco JG (2002). "Critical features of a conserved RNA stem-loop important for feedback regulation of RNase E synthesis." J Biol Chem 277(23);20415-22. PMID: 11919204

Diwa02a: Diwa AA, Jiang X, Schapira M, Belasco JG (2002). "Two distinct regions on the surface of an RNA-binding domain are crucial for RNase E function." Mol Microbiol 46(4);959-69. PMID: 12421303

DominguezMalfav13: Dominguez-Malfavon L, Islas LD, Luisi BF, Garcia-Villegas R, Garcia-Mena J (2013). "The assembly and distribution in vivo of the Escherichia coli RNA degradosome." Biochimie 95(11);2034-41. PMID: 23927922

Ehretsmann92: Ehretsmann CP, Carpousis AJ, Krisch HM (1992). "Specificity of Escherichia coli endoribonuclease RNase E: in vivo and in vitro analysis of mutants in a bacteriophage T4 mRNA processing site." Genes Dev 6(1);149-59. PMID: 1730408

Erce10: Erce MA, Low JK, Wilkins MR (2010). "Analysis of the RNA degradosome complex in Vibrio angustum S14." FEBS J 277(24);5161-73. PMID: 21126315

Faubladier90: Faubladier M, Cam K, Bouche JP (1990). "Escherichia coli cell division inhibitor DicF-RNA of the dicB operon. Evidence for its generation in vivo by transcription termination and by RNase III and RNase E-dependent processing." J Mol Biol 212(3);461-71. PMID: 1691299

Feng01a: Feng Y, Huang H, Liao J, Cohen SN (2001). "Escherichia coli poly(A)-binding proteins that interact with components of degradosomes or impede RNA decay mediated by polynucleotide phosphorylase and RNase E." J Biol Chem 276(34);31651-6. PMID: 11390393

Feng02: Feng Y, Vickers TA, Cohen SN (2002). "The catalytic domain of RNase E shows inherent 3' to 5' directionality in cleavage site selection." Proc Natl Acad Sci U S A 99(23);14746-51. PMID: 12417756

Finn14: Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J, Sonnhammer EL, Tate J, Punta M (2014). "Pfam: the protein families database." Nucleic Acids Res 42(Database issue);D222-30. PMID: 24288371

Folichon03: Folichon M, Arluison V, Pellegrini O, Huntzinger E, Regnier P, Hajnsdorf E (2003). "The poly(A) binding protein Hfq protects RNA from RNase E and exoribonucleolytic degradation." Nucleic Acids Res 31(24);7302-10. PMID: 14654705

Garrey09: Garrey SM, Blech M, Riffell JL, Hankins JS, Stickney LM, Diver M, Hsu YH, Kunanithy V, Mackie GA (2009). "Substrate binding and active site residues in RNases E and G: role of the 5'-sensor." J Biol Chem 284(46);31843-50. PMID: 19778900

Garrey11: Garrey SM, Mackie GA (2011). "Roles of the 5'-phosphate sensor domain in RNase E." Mol Microbiol 80(6);1613-24. PMID: 21518390

Gaudet10: Gaudet P, Livstone M, Thomas P (2010). "Annotation inferences using phylogenetic trees." PMID: 19578431

Ghora78: Ghora BK, Apirion D (1978). "Structural analysis and in vitro processing to p5 rRNA of a 9S RNA molecule isolated from an rne mutant of E. coli." Cell 15(3);1055-66. PMID: 365352

Go11: Go H, Moore CJ, Lee M, Shin E, Jeon CO, Cha CJ, Han SH, Kim SJ, Lee SW, Lee Y, Ha NC, Kim YH, Cohen SN, Lee K "Upregulation of RNase E activity by mutation of a site that uncompetitively interferes with RNA binding." RNA Biol 8(6);1022-34. PMID: 22186084

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."

Goldblum81: Goldblum K, Apririon D (1981). "Inactivation of the ribonucleic acid-processing enzyme ribonuclease E blocks cell division." J Bacteriol 146(1);128-32. PMID: 6163761

Hajnsdorf94: Hajnsdorf E, Steier O, Coscoy L, Teysset L, Regnier P (1994). "Roles of RNase E, RNase II and PNPase in the degradation of the rpsO transcripts of Escherichia coli: stabilizing function of RNase II and evidence for efficient degradation in an ams pnp rnb mutant." EMBO J 13(14);3368-77. PMID: 7519147

Hajnsdorf94a: Hajnsdorf E, Carpousis AJ, Regnier P (1994). "Nucleolytic inactivation and degradation of the RNase III processed pnp message encoding polynucleotide phosphorylase of Escherichia coli." J Mol Biol 239(4);439-54. PMID: 7516438

Hajnsdorf99: Hajnsdorf E, Regnier P (1999). "E. coli RpsO mRNA decay: RNase E processing at the beginning of the coding sequence stimulates poly(A)-dependent degradation of the mRNA." J Mol Biol 286(4);1033-43. PMID: 10047480

Hoch14: Hoch PG, Hartmann RK (2014). "Supramolecular membrane-associated assemblies of RNA metabolic proteins in Escherichia coli." Biochem J 458(1);e1-3. PMID: 24438330

Ikeda11: Ikeda Y, Yagi M, Morita T, Aiba H (2011). "Hfq binding at RhlB-recognition region of RNase E is crucial for the rapid degradation of target mRNAs mediated by sRNAs in Escherichia coli." Mol Microbiol 79(2);419-32. PMID: 21219461

Jain02: Jain C, Deana A, Belasco JG (2002). "Consequences of RNase E scarcity in Escherichia coli." Mol Microbiol 43(4);1053-64. PMID: 11929550

Jain95: Jain C, Belasco JG (1995). "Autoregulation of RNase E synthesis in Escherichia coli." Nucleic Acids Symp Ser (33);85-8. PMID: 8643409

Jerome99: Jerome LJ, van Biesen T, Frost LS (1999). "Degradation of FinP antisense RNA from F-like plasmids: the RNA-binding protein, FinO, protects FinP from ribonuclease E." J Mol Biol 285(4);1457-73. PMID: 9917389

Jiang00: Jiang X, Diwa A, Belasco JG (2000). "Regions of RNase E important for 5'-end-dependent RNA cleavage and autoregulated synthesis." J Bacteriol 182(9);2468-75. PMID: 10762247

Jiang04: Jiang X, Belasco JG (2004). "Catalytic activation of multimeric RNase E and RNase G by 5'-monophosphorylated RNA." Proc Natl Acad Sci U S A 101(25);9211-6. PMID: 15197283

Kaberdin00: Kaberdin VR, Walsh AP, Jakobsen T, McDowall KJ, von Gabain A (2000). "Enhanced cleavage of RNA mediated by an interaction between substrates and the arginine-rich domain of E. coli ribonuclease E." J Mol Biol 301(2);257-64. PMID: 10926508

Kaberdin03: Kaberdin VR (2003). "Probing the substrate specificity of Escherichia coli RNase E using a novel oligonucleotide-based assay." Nucleic Acids Res 31(16);4710-6. PMID: 12907711

Kaberdin11: Kaberdin VR, Singh D, Lin-Chao S (2011). "Composition and conservation of the mRNA-degrading machinery in bacteria." J Biomed Sci 18;23. PMID: 21418661

Kemmer06: Kemmer C, Neubauer P (2006). "Antisense RNA based down-regulation of RNaseE in E. coli." Microb Cell Fact 5;38. PMID: 17164000

Kennell02: Kennell D (2002). "Processing endoribonucleases and mRNA degradation in bacteria." J Bacteriol 184(17);4645-57; discussion 4665. PMID: 12169587

Khemici04: Khemici V, Carpousis AJ (2004). "The RNA degradosome and poly(A) polymerase of Escherichia coli are required in vivo for the degradation of small mRNA decay intermediates containing REP-stabilizers." Mol Microbiol 51(3);777-90. PMID: 14731278

Khemici04a: Khemici V, Toesca I, Poljak L, Vanzo NF, Carpousis AJ (2004). "The RNase E of Escherichia coli has at least two binding sites for DEAD-box RNA helicases: functional replacement of RhlB by RhlE." Mol Microbiol 54(5);1422-30. PMID: 15554979

Khemici08: Khemici V, Poljak L, Luisi BF, Carpousis AJ (2008). "The RNase E of Escherichia coli is a membrane-binding protein." Mol Microbiol 70(4);799-813. PMID: 18976283

Kido96: Kido M, Yamanaka K, Mitani T, Niki H, Ogura T, Hiraga S (1996). "RNase E polypeptides lacking a carboxyl-terminal half suppress a mukB mutation in Escherichia coli." J Bacteriol 178(13);3917-25. PMID: 8682798

Kim04: Kim KS, Lee Y (2004). "Regulation of 6S RNA biogenesis by switching utilization of both sigma factors and endoribonucleases." Nucleic Acids Res 32(20);6057-68. PMID: 15550566

Kim04b: Kim KS, Sim S, Ko JH, Cho B, Lee Y (2004). "Kinetic analysis of precursor M1 RNA molecules for exploring substrate specificity of the N-terminal catalytic half of RNase E." J Biochem (Tokyo) 136(5);693-9. PMID: 15632310

Kim14: Kim D, Song S, Lee M, Go H, Shin E, Yeom JH, Ha NC, Lee K, Kim YH (2014). "Modulation of RNase E activity by alternative RNA binding sites." PLoS One 9(3);e90610. PMID: 24598695

Kimata01: Kimata K, Tanaka Y, Inada T, Aiba H (2001). "Expression of the glucose transporter gene, ptsG, is regulated at the mRNA degradation step in response to glycolytic flux in Escherichia coli." EMBO J 20(13);3587-95. PMID: 11432845

Kime08: Kime L, Jourdan SS, McDowall KJ (2008). "Identifying and characterizing substrates of the RNase E/G family of enzymes." Methods Enzymol 447;215-41. PMID: 19161846

Kime10: Kime L, Jourdan SS, Stead JA, Hidalgo-Sastre A, McDowall KJ (2010). "Rapid cleavage of RNA by RNase E in the absence of 5' monophosphate stimulation." Mol Microbiol 76(3);590-604. PMID: 19889093

Kime14: Kime L, Clarke JE, Romero A D, Grasby JA, McDowall KJ (2014). "Adjacent single-stranded regions mediate processing of tRNA precursors by RNase E direct entry." Nucleic Acids Res 42(7);4577-89. PMID: 24452799

Kime15: Kime L, Vincent HA, Gendoo DM, Jourdan SS, Fishwick CW, Callaghan AJ, McDowall KJ (2015). "The first small-molecule inhibitors of members of the ribonuclease E family." Sci Rep 5;8028. PMID: 25619596

Kokoska98: Kokoska RJ, Steege DA (1998). "Appropriate expression of filamentous phage f1 DNA replication genes II and X requires RNase E-dependent processing and separate mRNAs." J Bacteriol 180(12);3245-9. PMID: 9620980

Koslover08: Koslover DJ, Callaghan AJ, Marcaida MJ, Garman EF, Martick M, Scott WG, Luisi BF (2008). "The crystal structure of the Escherichia coli RNase E apoprotein and a mechanism for RNA degradation." Structure 16(8);1238-44. PMID: 18682225

Kushner02: Kushner SR (2002). "mRNA decay in Escherichia coli comes of age." J Bacteriol 184(17);4658-65; discussion 4657. PMID: 12169588

Le02: Le Derout J, Regnier P, Hajnsdorf E (2002). "Both temperature and medium composition regulate RNase E processing efficiency of the rpsO mRNA coding for ribosomal protein S15 of Escherichia coli." J Mol Biol 319(2);341-9. PMID: 12051911

Lee02a: Lee K, Bernstein JA, Cohen SN (2002). "RNase G complementation of rne null mutation identifies functional interrelationships with RNase E in Escherichia coli." Mol Microbiol 43(6);1445-56. PMID: 11952897

Lee03d: Lee K, Zhan X, Gao J, Qiu J, Feng Y, Meganathan R, Cohen SN, Georgiou G (2003). "RraA. a protein inhibitor of RNase E activity that globally modulates RNA abundance in E. coli." Cell 114(5);623-34. PMID: 13678585

Leroy02: Leroy A, Vanzo NF, Sousa S, Dreyfus M, Carpousis AJ (2002). "Function in Escherichia coli of the non-catalytic part of RNase E: role in the degradation of ribosome-free mRNA." Mol Microbiol 45(5);1231-43. PMID: 12207692

Li02: Li Z, Deutscher MP (2002). "RNase E plays an essential role in the maturation of Escherichia coli tRNA precursors." RNA 8(1);97-109. PMID: 11871663

Li99b: Li Z, Pandit S, Deutscher MP (1999). "RNase G (CafA protein) and RNase E are both required for the 5' maturation of 16S ribosomal RNA." EMBO J 18(10);2878-85. PMID: 10329633

LinChao91: Lin-Chao S, Cohen SN (1991). "The rate of processing and degradation of antisense RNAI regulates the replication of ColE1-type plasmids in vivo." Cell 65(7);1233-42. PMID: 1712252

LinChao99: Lin-Chao S, Wei CL, Lin YT (1999). "RNase E is required for the maturation of ssrA RNA and normal ssrA RNA peptide-tagging activity." Proc Natl Acad Sci U S A 96(22);12406-11. PMID: 10535935

Liou01: Liou GG, Jane WN, Cohen SN, Lin NS, Lin-Chao S (2001). "RNA degradosomes exist in vivo in Escherichia coli as multicomponent complexes associated with the cytoplasmic membrane via the N-terminal region of ribonuclease E." Proc Natl Acad Sci U S A 98(1);63-8. PMID: 11134527

Lopez96: Lopez PJ, Dreyfus M (1996). "The lacZ mRNA can be stabilised by the T7 late mRNA leader in E coli." Biochimie 78(6);408-15. PMID: 8915530

Lopez99: Lopez PJ, Marchand I, Joyce SA, Dreyfus M (1999). "The C-terminal half of RNase E, which organizes the Escherichia coli degradosome, participates in mRNA degradation but not rRNA processing in vivo." Mol Microbiol 33(1);188-99. PMID: 10411735

Lu14b: Lu F, Taghbalout A (2014). "The Escherichia coli major exoribonuclease RNase II is a component of the RNA degradosome." Biosci Rep 34(6);e00166. PMID: 25299745

Lundberg95: Lundberg U, Altman S (1995). "Processing of the precursor to the catalytic RNA subunit of RNase P from Escherichia coli." RNA 1(3);327-34. PMID: 7489504

Mackie00: Mackie GA (2000). "Stabilization of circular rpsT mRNA demonstrates the 5'-end dependence of RNase E action in vivo." J Biol Chem 275(33);25069-72. PMID: 10871599

Mackie08: Mackie GA, Coburn GA, Miao X, Briant DJ, Prud'homme-Genereux A, Stickney LM, Hankins JS (2008). "Preparation of the Escherichia coli RNase E protein and reconstitution of the RNA degradosome." Methods Enzymol 447;199-213. PMID: 19161845

Mackie92: Mackie GA (1992). "Secondary structure of the mRNA for ribosomal protein S20. Implications for cleavage by ribonuclease E." J Biol Chem 267(2);1054-61. PMID: 1370457

Mackie93: Mackie GA, Genereaux JL (1993). "The role of RNA structure in determining RNase E-dependent cleavage sites in the mRNA for ribosomal protein S20 in vitro." J Mol Biol 234(4);998-1012. PMID: 7505337

Mackie98: Mackie GA (1998). "Ribonuclease E is a 5'-end-dependent endonuclease." Nature 395(6703);720-3. PMID: 9790196

Manasherob12: Manasherob R, Miller C, Kim KS, Cohen SN (2012). "Ribonuclease E modulation of the bacterial SOS response." PLoS One 7(6);e38426. PMID: 22719885

Marchand01: Marchand I, Nicholson AW, Dreyfus M (2001). "Bacteriophage T7 protein kinase phosphorylates RNase E and stabilizes mRNAs synthesized by T7 RNA polymerase." Mol Microbiol 42(3);767-76. PMID: 11722741

Masse03: Masse E, Escorcia FE, Gottesman S (2003). "Coupled degradation of a small regulatory RNA and its mRNA targets in Escherichia coli." Genes Dev 17(19);2374-83. PMID: 12975324

McDowall94: McDowall KJ, Lin-Chao S, Cohen SN (1994). "A+U content rather than a particular nucleotide order determines the specificity of RNase E cleavage." J Biol Chem 269(14);10790-6. PMID: 7511606

McDowall95: McDowall KJ, Kaberdin VR, Wu SW, Cohen SN, Lin-Chao S (1995). "Site-specific RNase E cleavage of oligonucleotides and inhibition by stem-loops." Nature 374(6519);287-90. PMID: 7533896

McDowall96: McDowall KJ, Cohen SN (1996). "The N-terminal domain of the rne gene product has RNase E activity and is non-overlapping with the arginine-rich RNA-binding site." J Mol Biol 255(3);349-55. PMID: 8568879

Miczak91: Miczak A, Srivastava RA, Apirion D (1991). "Location of the RNA-processing enzymes RNase III, RNase E and RNase P in the Escherichia coli cell." Mol Microbiol 5(7);1801-10. PMID: 1943711

Miczak96: Miczak A, Kaberdin VR, Wei CL, Lin-Chao S (1996). "Proteins associated with RNase E in a multicomponent ribonucleolytic complex." Proc Natl Acad Sci U S A 93(9);3865-9. PMID: 8632981

Mohanty00: Mohanty BK, Kushner SR (2000). "Polynucleotide phosphorylase, RNase II and RNase E play different roles in the in vivo modulation of polyadenylation in Escherichia coli." Mol Microbiol 36(4);982-94. PMID: 10844684

Mohanty02: Mohanty BK, Kushner SR (2002). "Polyadenylation of Escherichia coli transcripts plays an integral role in regulating intracellular levels of polynucleotide phosphorylase and RNase E." Mol Microbiol 45(5);1315-24. PMID: 12207699

Mohanty99: Mohanty BK, Kushner SR (1999). "Analysis of the function of Escherichia coli poly(A) polymerase I in RNA metabolism." Mol Microbiol 34(5);1094-108. PMID: 10594833

Moll03a: Moll I, Afonyushkin T, Vytvytska O, Kaberdin VR, Blasi U (2003). "Coincident Hfq binding and RNase E cleavage sites on mRNA and small regulatory RNAs." RNA 9(11);1308-14. PMID: 14561880

Morita04: Morita T, Kawamoto H, Mizota T, Inada T, Aiba H (2004). "Enolase in the RNA degradosome plays a crucial role in the rapid decay of glucose transporter mRNA in the response to phosphosugar stress in Escherichia coli." Mol Microbiol 54(4);1063-75. PMID: 15522087

Morita11: Morita T, Aiba H (2011). "RNase E action at a distance: degradation of target mRNAs mediated by an Hfq-binding small RNA in bacteria." Genes Dev 25(4);294-8. PMID: 21325130

Mudd88: Mudd EA, Prentki P, Belin D, Krisch HM (1988). "Processing of unstable bacteriophage T4 gene 32 mRNAs into a stable species requires Escherichia coli ribonuclease E." EMBO J 7(11);3601-7. PMID: 3061803

Mudd90: Mudd EA, Carpousis AJ, Krisch HM (1990). "Escherichia coli RNase E has a role in the decay of bacteriophage T4 mRNA." Genes Dev 4(5);873-81. PMID: 2199322

Mudd93: Mudd EA, Higgins CF (1993). "Escherichia coli endoribonuclease RNase E: autoregulation of expression and site-specific cleavage of mRNA." Mol Microbiol 9(3);557-68. PMID: 8412702

Murashko12: Murashko ON, Kaberdin VR, Lin-Chao S (2012). "Membrane binding of Escherichia coli RNase E catalytic domain stabilizes protein structure and increases RNA substrate affinity." Proc Natl Acad Sci U S A 109(18);7019-24. PMID: 22509045

Nilsson91: Nilsson P, Uhlin BE (1991). "Differential decay of a polycistronic Escherichia coli transcript is initiated by RNaseE-dependent endonucleolytic processing." Mol Microbiol 5(7);1791-9. PMID: 1943710

Nishio09: Nishio SY, Itoh T (2009). "Arginine-rich RNA binding domain and protein scaffold domain of RNase E are important for degradation of RNAI but not for that of the Rep mRNA of the ColE2 plasmid." Plasmid 62(2);83-7. PMID: 19426759

Nogueira01: Nogueira T, de Smit M, Graffe M, Springer M (2001). "The relationship between translational control and mRNA degradation for the Escherichia coli threonyl-tRNA synthetase gene." J Mol Biol 310(4);709-22. PMID: 11453682

Nurmohamed09: Nurmohamed S, Vaidialingam B, Callaghan AJ, Luisi BF (2009). "Crystal structure of Escherichia coli polynucleotide phosphorylase core bound to RNase E, RNA and manganese: implications for catalytic mechanism and RNA degradosome assembly." J Mol Biol 389(1);17-33. PMID: 19327365

Nurmohamed10: Nurmohamed S, McKay AR, Robinson CV, Luisi BF (2010). "Molecular recognition between Escherichia coli enolase and ribonuclease E." Acta Crystallogr D Biol Crystallogr 66(Pt 9);1036-40. PMID: 20823555

OHara95: O'Hara EB, Chekanova JA, Ingle CA, Kushner ZR, Peters E, Kushner SR (1995). "Polyadenylylation helps regulate mRNA decay in Escherichia coli." Proc Natl Acad Sci U S A 92(6);1807-11. PMID: 7534403

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

Ow00: Ow MC, Liu Q, Kushner SR (2000). "Analysis of mRNA decay and rRNA processing in Escherichia coli in the absence of RNase E-based degradosome assembly." Mol Microbiol 38(4);854-66. PMID: 11115119

Ow02: Ow MC, Kushner SR (2002). "Initiation of tRNA maturation by RNase E is essential for cell viability in E. coli." Genes Dev 16(9);1102-15. PMID: 12000793

Patel92: Patel AM, Dunn SD (1992). "RNase E-dependent cleavages in the 5' and 3' regions of the Escherichia coli unc mRNA." J Bacteriol 174(11);3541-8. PMID: 1534325

Patel95: Patel AM, Dunn SD (1995). "Degradation of Escherichia coli uncB mRNA by multiple endonucleolytic cleavages." J Bacteriol 177(14);3917-22. PMID: 7608061

Perwez08: Perwez T, Hami D, Maples VF, Min Z, Wang BC, Kushner SR (2008). "Intragenic suppressors of temperature-sensitive rne mutations lead to the dissociation of RNase E activity on mRNA and tRNA substrates in Escherichia coli." Nucleic Acids Res 36(16);5306-18. PMID: 18689439

PrudhommeGenere04: Prud'homme-Genereux A, Beran RK, Iost I, Ramey CS, Mackie GA, Simons RW (2004). "Physical and functional interactions among RNase E, polynucleotide phosphorylase and the cold-shock protein, CsdA: evidence for a 'cold shock degradosome'." Mol Microbiol 54(5);1409-21. PMID: 15554978

Py94: Py B, Causton H, Mudd EA, Higgins CF (1994). "A protein complex mediating mRNA degradation in Escherichia coli." Mol Microbiol 14(4);717-29. PMID: 7891559

Py96: Py B, Higgins CF, Krisch HM, Carpousis AJ (1996). "A DEAD-box RNA helicase in the Escherichia coli RNA degradosome." Nature 381(6578);169-72. PMID: 8610017

Qi15: Qi D, Alawneh AM, Yonesaki T, Otsuka Y (2015). "Rapid Degradation of Host mRNAs by Stimulation of RNase E Activity by Srd of Bacteriophage T4." Genetics 201(3);977-87. PMID: 26323881

Raynal99: Raynal LC, Carpousis AJ (1999). "Poly(A) polymerase I of Escherichia coli: characterization of the catalytic domain, an RNA binding site and regions for the interaction with proteins involved in mRNA degradation." Mol Microbiol 32(4);765-75. PMID: 10361280

Redko03: Redko Y, Tock MR, Adams CJ, Kaberdin VR, Grasby JA, McDowall KJ (2003). "Determination of the catalytic parameters of the N-terminal half of Escherichia coli ribonuclease E and the identification of critical functional groups in RNA substrates." J Biol Chem 278(45);44001-8. PMID: 12947103

Regnier91: Regnier P, Hajnsdorf E (1991). "Decay of mRNA encoding ribosomal protein S15 of Escherichia coli is initiated by an RNase E-dependent endonucleolytic cleavage that removes the 3' stabilizing stem and loop structure." J Mol Biol 217(2);283-92. PMID: 1704067

Regonesi06: Regonesi ME, Del Favero M, Basilico F, Briani F, Benazzi L, Tortora P, Mauri P, Deho G (2006). "Analysis of the Escherichia coli RNA degradosome composition by a proteomic approach." Biochimie 88(2);151-61. PMID: 16139413

Roy83: Roy MK, Singh B, Ray BK, Apirion D (1983). "Maturation of 5-S rRNA: ribonuclease E cleavages and their dependence on precursor sequences." Eur J Biochem 131(1);119-27. PMID: 6339234

Schubert04: Schubert M, Edge RE, Lario P, Cook MA, Strynadka NC, Mackie GA, McIntosh LP (2004). "Structural characterization of the RNase E S1 domain and identification of its oligonucleotide-binding and dimerization interfaces." J Mol Biol 341(1);37-54. PMID: 15312761

Schuck09: Schuck A, Diwa A, Belasco JG (2009). "RNase E autoregulates its synthesis in Escherichia coli by binding directly to a stem-loop in the rne 5' untranslated region." Mol Microbiol 72(2);470-8. PMID: 19320830

Shin08: Shin E, Go H, Yeom JH, Won M, Bae J, Han SH, Han K, Lee Y, Ha NC, Moore CJ, Sohlberg B, Cohen SN, Lee K (2008). "Identification of amino acid residues in the catalytic domain of RNase E essential for survival of Escherichia coli: functional analysis of DNase I subdomain." Genetics 179(4);1871-9. PMID: 18660536

Sim01: Sim S, Kim S, Lee Y (2001). "Role of the sequence of the rne-dependent site in 3' processing of M1 RNA, the catalytic component of Escherichia coli RNase P." FEBS Lett 505(2);291-5. PMID: 11566192

Singh09: Singh D, Chang SJ, Lin PH, Averina OV, Kaberdin VR, Lin-Chao S (2009). "Regulation of ribonuclease E activity by the L4 ribosomal protein of Escherichia coli." Proc Natl Acad Sci U S A 106(3);864-9. PMID: 19144914

Soderbom05: Soderbom F, Svard SG, Kirsebom LA (2005). "RNase E cleavage in the 5' leader of a tRNA precursor." J Mol Biol 352(1);22-7. PMID: 16081101

Soderbom98: Soderbom F, Wagner EG (1998). "Degradation pathway of CopA, the antisense RNA that controls replication of plasmid R1." Microbiology 144 ( Pt 7);1907-17. PMID: 9695924

Sousa01: Sousa S, Marchand I, Dreyfus M (2001). "Autoregulation allows Escherichia coli RNase E to adjust continuously its synthesis to that of its substrates." Mol Microbiol 42(3);867-78. PMID: 11722748

Stead11: Stead MB, Marshburn S, Mohanty BK, Mitra J, Pena Castillo L, Ray D, van Bakel H, Hughes TR, Kushner SR (2011). "Analysis of Escherichia coli RNase E and RNase III activity in vivo using tiling microarrays." Nucleic Acids Res 39(8);3188-203. PMID: 21149258

Strahl15: Strahl H, Turlan C, Khalid S, Bond PJ, Kebalo JM, Peyron P, Poljak L, Bouvier M, Hamoen L, Luisi BF, Carpousis AJ (2015). "Membrane recognition and dynamics of the RNA degradosome." PLoS Genet 11(2);e1004961. PMID: 25647427

Stump96: Stump MD, Steege DA (1996). "Functional analysis of filamentous phage f1 mRNA processing sites." RNA 2(12);1286-94. PMID: 8972776

Taghbalout07: Taghbalout A, Rothfield L (2007). "RNaseE and the other constituents of the RNA degradosome are components of the bacterial cytoskeleton." Proc Natl Acad Sci U S A 104(5);1667-72. PMID: 17242352

Taghbalout08: Taghbalout A, Rothfield L (2008). "RNaseE and RNA helicase B play central roles in the cytoskeletal organization of the RNA degradosome." J Biol Chem 283(20);13850-5. PMID: 18337249

Taghbalout14: Taghbalout A, Yang Q, Arluison V (2014). "The Escherichia coli RNA processing and degradation machinery is compartmentalized within an organized cellular network." Biochem J 458(1);11-22. PMID: 24266791

Takada05: Takada A, Nagai K, Wachi M (2005). "A decreased level of FtsZ is responsible for inviability of RNase E-deficient cells." Genes Cells 10(7);733-41. PMID: 15966903

Takada07: Takada A, Umitsuki G, Nagai K, Wachi M (2007). "RNase E is required for induction of the glutamate-dependent acid resistance system in Escherichia coli." Biosci Biotechnol Biochem 71(1);158-64. PMID: 17213667

Tamura06: Tamura M, Lee K, Miller CA, Moore CJ, Shirako Y, Kobayashi M, Cohen SN (2006). "RNase E maintenance of proper FtsZ/FtsA ratio required for nonfilamentous growth of Escherichia coli cells but not for colony-forming ability." J Bacteriol 188(14);5145-52. PMID: 16816186

Tamura12: Tamura M, Kers JA, Cohen SN (2012). "Second-site suppression of RNase E essentiality by mutation of the deaD RNA helicase in Escherichia coli." J Bacteriol 194(8);1919-26. PMID: 22328678

Tamura13: Tamura M, Moore CJ, Cohen SN (2013). "Nutrient dependence of RNase E essentiality in Escherichia coli." J Bacteriol 195(6);1133-41. PMID: 23275245

Taraseviciene95: Taraseviciene L, Bjork GR, Uhlin BE (1995). "Evidence for an RNA binding region in the Escherichia coli processing endoribonuclease RNase E." J Biol Chem 270(44);26391-8. PMID: 7592853

Tomcsanyi85: Tomcsanyi T, Apirion D (1985). "Processing enzyme ribonuclease E specifically cleaves RNA I. An inhibitor of primer formation in plasmid DNA synthesis." J Mol Biol 185(4);713-20. PMID: 2414455

Tsai12: Tsai YC, Du D, Dominguez-Malfavon L, Dimastrogiovanni D, Cross J, Callaghan AJ, Garcia-Mena J, Luisi BF (2012). "Recognition of the 70S ribosome and polysome by the RNA degradosome in Escherichia coli." Nucleic Acids Res 40(20);10417-31. PMID: 22923520

UniProt15: UniProt Consortium (2015). "UniProt version 2015-08 released on 2015-07-22." Database.

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

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

Vanzo98: Vanzo NF, Li YS, Py B, Blum E, Higgins CF, Raynal LC, Krisch HM, Carpousis AJ (1998). "Ribonuclease E organizes the protein interactions in the Escherichia coli RNA degradosome." Genes Dev 12(17);2770-81. PMID: 9732274

Worrall08: Worrall JA, Howe FS, McKay AR, Robinson CV, Luisi BF (2008). "Allosteric activation of the ATPase activity of the Escherichia coli RhlB RNA helicase." J Biol Chem 283(9);5567-76. PMID: 18165229

Worrall08a: Worrall JA, Gorna M, Crump NT, Phillips LG, Tuck AC, Price AJ, Bavro VN, Luisi BF (2008). "Reconstitution and analysis of the multienzyme Escherichia coli RNA degradosome." J Mol Biol 382(4);870-83. PMID: 18691600

Zhan04: Zhan X, Gao J, Jain C, Cieslewicz MJ, Swartz JR, Georgiou G (2004). "Genetic analysis of disulfide isomerization in Escherichia coli: expression of DsbC is modulated by RNase E-dependent mRNA processing." J Bacteriol 186(3);654-60. PMID: 14729690

Zhou13a: Zhou L, Zhang AB, Wang R, Marcotte EM, Vogel C (2013). "The proteomic response to mutants of the Escherichia coli RNA degradosome." Mol Biosyst 9(4);750-7. PMID: 23403814

Zilhao95: Zilhao R, Regnier P, Arraiano CM (1995). "The role of endonucleases in the expression of ribonuclease II in Escherichia coli." FEMS Microbiol Lett 130(2-3);237-44. PMID: 7649446

Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
Page generated by Pathway Tools version 20.0 (software by SRI International) on Fri May 6, 2016, BIOCYC13A.