Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
twitter

Escherichia coli K-12 substr. MG1655 Enzyme: ribonuclease E



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

Synonyms: smbB, ams, hmp1, RNase E

Regulation Summary Diagram: ?

Component of: degradosome (extended summary available)

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

Summary:
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 [Li99e, 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, Li02a]. RNase E similarly cleaves at the 3' CCA terminus of the ssrA 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].

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 degradeosome 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].

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, Moll03, Folichon03]. Hfq also overlaps cleavage sites in the dsrA and ompA mRNAs [Moll03]. The rpsO-pnp transcript is cleaved near the beginning of the rpsO coding sequence and on both sides of the rspO 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]. 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 [Lee02].

RNase E regulates its own abundance by cleaving within the 5' untranslated region of rne mRNA. As RNase E activity can be titrated by other substrates, this acts to modulate its expression to match cellular needs [Mudd93, Diwa02, Sousa01]. 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 [Kim04c, 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].

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 dispensible 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]. 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].

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, Feng01, Marchand01].

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

Citations: [Cohen97, Kushner02, Kennell02]

Gene Citations: [Ow02a]

Locations: cytosol, inner membrane

Map Position: [1,140,405 <- 1,143,590] (24.58 centisomes)
Length: 3186 bp / 1061 aa

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 , 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

In Paralogous Gene Group: 509 (2 members) , 251 (7 members) , 576 (2 members)

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0000967 - rRNA 5'-end processing Inferred from experiment [Li99e]
GO:0006401 - RNA catabolic process Inferred from experiment [Cormack93]
GO:0006364 - rRNA processing Inferred by computational analysis [UniProtGOA11a, GOA06]
GO:0006396 - RNA processing Inferred by computational analysis [GOA01a]
GO:0006402 - mRNA catabolic process Inferred by computational analysis [GOA06]
GO:0008033 - tRNA processing Inferred by computational analysis [UniProtGOA11a, GOA06]
GO:0090305 - nucleic acid phosphodiester bond hydrolysis Inferred by computational analysis [UniProtGOA11a]
GO:0090501 - RNA phosphodiester bond hydrolysis Inferred by computational analysis [GOA01a]
GO:0090502 - RNA phosphodiester bond hydrolysis, endonucleolytic Inferred by computational analysis [GOA06]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Erce10, AitBara10, Butland05, Regonesi06, Callaghan04]
GO:0000287 - magnesium ion binding Inferred by computational analysis [GOA06]
GO:0003723 - RNA binding Inferred by computational analysis [UniProtGOA11a, GOA06, GOA01a]
GO:0004518 - nuclease activity Inferred by computational analysis [UniProtGOA11a]
GO:0004519 - endonuclease activity Inferred by computational analysis [UniProtGOA11a]
GO:0004521 - endoribonuclease activity Inferred by computational analysis [GOA06]
GO:0004540 - ribonuclease activity Inferred by computational analysis [GOA01a]
GO:0008270 - zinc ion binding Inferred by computational analysis [GOA06]
GO:0008995 - ribonuclease E activity Inferred by computational analysis [GOA01a]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005737 - cytoplasm Inferred from experiment Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, GOA06, Bessarab98]
GO:0005886 - plasma membrane Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, Miczak91]
GO:0009898 - cytoplasmic side of plasma membrane Inferred by computational analysis [GOA06]
GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11a]

MultiFun Terms: information transfer RNA related RNA degradation
metabolism degradation of macromolecules RNA

Regulated Transcription Units (3 total): ?

Notes:

Essentiality data for rne knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox No 37 Aerobic 7   No [Baba06, Comment 1]

Enzymatic reaction of: ribonuclease

EC Number: 3.1.26.12

9S rRNA + 2 H2O <=> 5S rRNA + 2 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 of enzyme catalysis.

The reaction is irreversible in the direction shown.


Enzymatic reaction of: ribonuclease

EC Number: 3.1.26.12

RNase E mRNA processing substrate + n H2O <=> RNase E processing product mRNA + n 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 of enzyme catalysis.

The reaction is irreversible in the direction shown.


Enzymatic reaction of: ribonuclease

EC Number: 3.1.26.12

a polycistronic tRNA precursor + H2O <=> a tRNA precursor with a 5' extension and a short 3' extension + a partially processed polycistronic tRNA precursor

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

The reaction is physiologically favored in the direction shown.

In Pathways: tRNA processing


Enzymatic reaction of: ribonuclease

EC Number: 3.1.26.12

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

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

The reaction is irreversible in the direction shown.

In Pathways: tRNA processing


Enzymatic reaction of: ribonuclease

EC Number: 3.1.26.12

RNase E degradation substrate mRNA + n H2O <=> n 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 of enzyme catalysis.

The reaction is irreversible in the direction shown.

Citations: [Ghora78]


Subunit of: degradosome

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)

Summary:
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 [Feng01].

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

Locations: inner membrane

GO Terms:

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


Sequence Features

Feature Class Location Citations Comment
Conserved-Region 39 -> 119
[UniProt09]
UniProt: S1 motif;
Mutagenesis-Variant 57
[Callaghan05, UniProt14]
Alternate sequence: F → A; UniProt: Reduces RNA cleavage by over 98%.
Protein-Segment 57 -> 112
[UniProt14]
UniProt: Interaction with RNA; Sequence Annotation Type: region of interest.
Mutagenesis-Variant 66
[Schubert04, UniProt14]
Alternate sequence: G → S; UniProt: Disrupts folding of the S1 motif.
Mutagenesis-Variant 67
[Callaghan05, UniProt14]
Alternate sequence: F → A; UniProt: Reduces RNA cleavage by over 98%. Reduces affinity for RNA.
Mutagenesis-Variant 112
[Callaghan05, UniProt14]
Alternate sequence: K → A; UniProt: Reduces RNA cleavage by 98%. Loss of RNA-binding.
Protein-Segment 169 -> 170
[UniProt14]
UniProt: Interaction with RNA 5'-terminal monophosphate; Sequence Annotation Type: region of interest.
Mutagenesis-Variant 170
[Callaghan05, Kime10, UniProt14]
Alternate sequence: T → V; 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
[Callaghan05, UniProt14]
Alternate sequence: D → N; UniProt: Reduces RNA cleavage by over 96%.
Metal-Binding-Site 303
[UniProt14]
UniProt: Magnesium; catalytic.
Mutagenesis-Variant 305
[Callaghan05, UniProt14]
Alternate sequence: N → L; UniProt: Reduces RNA cleavage by over 96%.
Alternate sequence: N → D; UniProt: Reduces RNA cleavage by over 96%.
Mutagenesis-Variant 346
[Callaghan05, UniProt14]
Alternate sequence: D → N; UniProt: Reduces RNA cleavage by over 96%. Reduces affinity for RNA.
Metal-Binding-Site 346
[UniProt14]
UniProt: Magnesium; catalytic.
Mutagenesis-Variant 373
[Callaghan05, UniProt14]
Alternate sequence: R → D; UniProt: Reduces RNA cleavage by 89%.
Alternate sequence: R → A; UniProt: Reduces RNA cleavage by 89%.
Sequence-Conflict 390
[ClaverieMartin91a, UniProt10a]
Alternate sequence: Q → H; UniProt: (in Ref. 5; AAA23443);
Mutagenesis-Variant 404
[Callaghan05a, UniProt14]
Alternate sequence: C → A; UniProt: Reduces zinc-binding. Abolishes homotetramerization and enzyme activity.
Metal-Binding-Site 404
[UniProt14]
UniProt: Zinc; shared with dimeric partner.
Protein-Segment 404 -> 407
[UniProt14]
UniProt: Required for zinc-mediated homotetramerization and catalytic activity; Sequence Annotation Type: region of interest.
Mutagenesis-Variant 407
[Callaghan05a, UniProt14]
Alternate sequence: C → A; UniProt: Reduces zinc-binding. Abolishes homotetramerization and enzyme activity.
Metal-Binding-Site 407
[UniProt14]
UniProt: Zinc; shared with dimeric partner.
Sequence-Conflict 487
[Casaregola92, ClaverieMartin91a, UniProt10a]
Alternate sequence: L → V; UniProt: (in Ref. 4 and 5);
Sequence-Conflict 564
[Casaregola92, UniProt10a]
Alternate sequence: A → R; UniProt: (in Ref. 4; CAA47818);
Sequence-Conflict 784
[Casaregola92, UniProt10a]
Alternate sequence: N → K; UniProt: (in Ref. 4; CAA47818);
Protein-Segment 833 -> 850
[UniProt14]
UniProt: Interaction with enolase; Sequence Annotation Type: region of interest.
Sequence-Conflict 838
[ClaverieMartin91a, UniProt10a]
Alternate sequence: A → R; UniProt: (in Ref. 5);
Sequence-Conflict 905
[Casaregola92, UniProt10a]
Alternate sequence: P → R; UniProt: (in Ref. 4; CAA47818);
Protein-Segment 1021 -> 1061
[UniProt14]
UniProt: Interaction with PNPase; Sequence Annotation Type: region of interest.
Sequence-Conflict 1048
[Cormack93, UniProt10a]
Alternate sequence: H → R; UniProt: (in Ref. 7; AAA03347);


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b1084 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10859; confirmed by SwissProt match.


References

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

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

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

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

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

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

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

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

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

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

ClaverieMartin91a: 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

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

Feng01: 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

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

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

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

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

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

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

Kim04c: 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

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

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

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

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

Lee02: 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

Li02a: 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

Li99e: 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

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

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

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

Moll03: 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

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

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

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

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

Ow02a: Ow MC, Liu Q, Mohanty BK, Andrew ME, Maples VF, Kushner SR (2002). "RNase E levels in Escherichia coli are controlled by a complex regulatory system that involves transcription of the rne gene from three promoters." Mol Microbiol 43(1);159-71. PMID: 11849544

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

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

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

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

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

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

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

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

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt14: UniProt Consortium (2014). "UniProt version 2014-01 released on 2014-01-01 00:00:00." 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

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

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

Other References Related to Gene Regulation

MendozaVargas09: Mendoza-Vargas A, Olvera L, Olvera M, Grande R, Vega-Alvarado L, Taboada B, Jimenez-Jacinto V, Salgado H, Juarez K, Contreras-Moreira B, Huerta AM, Collado-Vides J, Morett E (2009). "Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli." PLoS One 4(10);e7526. PMID: 19838305

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. PMID: 19320830


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 18.5 on Sat Nov 22, 2014, biocyc14.