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Escherichia coli K-12 substr. MG1655 Enzyme: RNase HI, degrades RNA of DNA-RNA hybrids, participates in DNA replication



Gene: rnhA Accession Numbers: EG10860 (EcoCyc), b0214, ECK0214

Synonyms: cer, sin, dasF, herA, rnh, sdrA

Regulation Summary Diagram: ?

Summary:
RNase H cleaves RNA in RNA-DNA hybrids. Targets for RNase H include RNA primers for DNA synthesis, especially longer primers that are cleaved by RNase H prior to digestion by the exonuclease activity of DNA polymerase I [Ogawa84, Kitani85]. RNase H also acts to block the formation of R-loops and the initiation of DNA replication from sites other than the classical origin of replication, oriC.

RNase H carries out the endonucleolytic cleavage of RNA in RNA-DNA hybrids, cleaving near the 3' terminus of the RNA and then digesting the remainder of the RNA [Miller73, Crooke95a]. Though RNase H only cleaves RNA in hybrid duplexes, it binds DNA-DNA, DNA-RNA, and RNA-RNA duplexes [Oda93]. This binding occurs in the minor groove of the duplex, and may involve hydrogen bonds with 2' oxygens in the RNA [Daniher97, Nakamura91]. A-form (RNA-RNA, RNA-DNA) duplexes are bound 60 times more tightly than B-form (DNA-DNA) duplexes, and 300 times more tightly than single-stranded oligonucleotides [Lima97]. Tests with boranophosphate DNA analogs demonstrate that weaker hybridization yields more rapid RNA degradation [Rait99]. Evaluation of duplexes containing arabinonucleic acids suggests that RNase H may recognize RNA-DNA hybrid duplexes by dint of a minor groove width intermediate between that seen in RNA-RNA and DNA-DNA duplexes [Noronha00, Minasov00]. Steric modification of the minor groove results in a substantial increase in kM, whereas modification of the major groove has no effect and altering the 2'-hydroxyl does not alter binding but lowers the cleavage rate [Uchiyama94]. Damaged DNA can disrupt cleavage of hybridized RNA, directing it to sites adjacent to the damaged nucleotides [Shiels01]. Cleavage can also be slowed by the presence of nearby RNA secondary structure [Lima97a]. However, RNase H appears to be able to induce hybrid formation and cleavage even with complementary DNA that exists in stable stem-loops or duplexes [Li98a].

Mutants lacking RNase H function can undergo "constitutive stable DNA replication" (cSDR), replication in the absence of protein synthesis [Casaregola87]. This replication can also take place without functional DnaA and OriC; rnhA mutation suppresses the negative effects of loss of DnaA function [Kogoma83, Lindahl84]. Though RNase H is not required for initiation of replication, it serves as a specificity factor blocking replication from sites other than OriC [Ogawa84a, Hong93, Kogoma85]. Indeed, replication in an double mutant lacking RnhA and OriC starts from multiple origins [deMassy84]. Though cSDR normally requires RecA, a lexA mutant can suppress this requirement, as long as DNA Pol I polymerase activity is present [Cao93a]. This mutation can also suppress the lethality of an rnhA, polA double mutant [Kogoma97]. Various other genotypes allowing cSDR have been examined [Torrey87]. Double mutants lacking rnhA and the helicase gene recG are inviable; mutants in recG alone also display cSDR and a requirement for DNA Pol I function [Hong95]. Double mutants in rep and rnha are also inviable [Sandler05]. Plasmid ColE1 can also undergo cSDR in the absence of RecA [Naito86]. cSDR requires PriA and PriB, but not PriC [Masai94, Sandler05].

RNase H mutants affect plasmid replication even in the presence of protein synthesis. pBR322 can replicate in the absence of DNA Pol I in an rnhA mutant [Kogoma84]. Both pBR322 and ColE1-type plasmids form concatamers in rnhA mutants [Subia86]. Loss of rnhA allows replication of replication-defective ColE1, even if the entire origin of replication is deleted [Naito84, Ohmori87].

RNase H exerts control over the formation of R-loops (single strands of DNA that loop out when RNA binds to their cognate strand), probably by degrading the RNA that induces looping. In the absence of DNA topoisomerase I, DNA gyrase can induce R-loop formation, impairing rRNA transcript elongation and limiting the induction of heat shock proteins. Overexpressed RNase H blocks these effects [Drolet95, Cheng03b, Hraiky00]. Overexpressed RNase H is detrimental at 21 degrees C, though combined rnhA, nusG double mutants are lethal at this temperature [Masse99, Harinarayanan03]. Overexpression of topoisomerase III blocks both the detrimental effects of a topoisomerase I mutant and those of RNase H overexpression at low temperature [Broccoli00]. RNase H overexpression is also detrimental following UV irradiation, which may explain why its abundance is unaltered even during UV-induced stable DNA replication [Bockrath87, Bialy86].

RNase H has been subject to extensive structural analysis. A crystal structure to 1.8 Å resolution showed that RNase H has two domains, and that its metal binding site is near a cluster of four acidic residues, a feature conserved in homologs in other organisms [Katayanagi90]. Based on a 1.48 Å resolution structure, RNase H comprises a five-stranded beta sheet and five α helices [Katayanagi92]. A subsequent cocrystal with divalent magnesium ion shared a similar backbone conformation with the pure protein with minor differences in the substrate binding region, and a single coordinated magnesium [Katayanagi93]. Crystal structures of several active site mutants reveal only localized conformational change around this magnesium-binding site [Katayanagi93a]. A cocrystal with divalent manganese shows two metal-binding sites, one needed for enzymatic activity, the other possibly involved in inhibition [Goedken01]. Indeed, RNase H is activated by low concentrations and inhibited by high concentrations of manganese ion [Keck98]. Crystal structures have also been determined for RNase H bound to RNA-DNA hybrid substrate [Nowotny05]. Alteration of the coordinating residues Asp10 and Glu48 to arginines yields a protein that is structurally similar to wild type by circular dichroism, binds nucleic acids well but does not complement a mutant lacking RNase H activity [Tsunaka01]. Alterations in a "handle" region from residues 84-99 does alter protein conformation and raises kM 3-5 fold [Kanaya91]. Deletion of the carboxy-terminal E helix does not affect structure but diminishes activity; adding a peptide corresponding to this region stimulates activity in this mutant variant [Goedken97]. Removal of a basic helix/loop region that can render homologous HIV Rnase H partially active also diminishes enzymatic activity [Keck96].

Molecular dynamics modeling of various divalent metal ions in RNase H has been carried out, and the stereochemistry of the RNase H reaction has been described [Babu03, Krakowiak02]. RNase H folding has been studied as an example of general protein folding principles [Spudich04, Cecconi05].

The SOS response is active in rnhA mutants [Kogoma93]. Two isoelectric points were found for this protein, 9.0 and 9.6 [Arendes82].

Citations: [Weatherford72, Kanaya83]

Gene Citations: [Nomura85]

Locations: cytosol

Map Position: [235,535 <- 236,002] (5.08 centisomes)
Length: 468 bp / 155 aa

Molecular Weight of Polypeptide: 17.597 kD (from nucleotide sequence)

pI: 9.0 [Arendes82]

Unification Links: ASAP:ABE-0000717 , CGSC:268 , DIP:DIP-47864N , EchoBASE:EB0853 , EcoGene:EG10860 , EcoliWiki:b0214 , Mint:MINT-1224022 , ModBase:P0A7Y4 , OU-Microarray:b0214 , PortEco:rnhA , PR:PRO_000023795 , Pride:P0A7Y4 , Protein Model Portal:P0A7Y4 , RefSeq:NP_414750 , RegulonDB:EG10860 , SMR:P0A7Y4 , String:511145.b0214 , UniProt:P0A7Y4

Relationship Links: InterPro:IN-FAMILY:IPR002156 , InterPro:IN-FAMILY:IPR012337 , InterPro:IN-FAMILY:IPR022892 , PDB:Structure:1F21 , PDB:Structure:1G15 , PDB:Structure:1GOA , PDB:Structure:1GOB , PDB:Structure:1GOC , PDB:Structure:1JL1 , PDB:Structure:1JL2 , PDB:Structure:1JXB , PDB:Structure:1KVA , PDB:Structure:1KVB , PDB:Structure:1KVC , PDB:Structure:1LAV , PDB:Structure:1LAW , PDB:Structure:1RBR , PDB:Structure:1RBS , PDB:Structure:1RBT , PDB:Structure:1RBU , PDB:Structure:1RBV , PDB:Structure:1RCH , PDB:Structure:1RDA , PDB:Structure:1RDB , PDB:Structure:1RDC , PDB:Structure:1RDD , PDB:Structure:1RNH , PDB:Structure:1WSE , PDB:Structure:1WSF , PDB:Structure:1WSG , PDB:Structure:1WSH , PDB:Structure:1WSI , PDB:Structure:1WSJ , PDB:Structure:2RN2 , PDB:Structure:2YV0 , PDB:Structure:2Z1G , PDB:Structure:2Z1H , PDB:Structure:2Z1I , PDB:Structure:2Z1J , PDB:Structure:3AA2 , PDB:Structure:3AA3 , PDB:Structure:3AA4 , PDB:Structure:3AA5 , PDB:Structure:3HYF , PDB:Structure:3QIN , PDB:Structure:3QIO , Pfam:IN-FAMILY:PF00075 , Prosite:IN-FAMILY:PS50879

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0043137 - DNA replication, removal of RNA primer Inferred from experiment [Ogawa84]
GO:0090305 - nucleic acid phosphodiester bond hydrolysis Inferred by computational analysis Inferred from experiment [Miller73, UniProtGOA11a]
GO:0090502 - RNA phosphodiester bond hydrolysis, endonucleolytic Inferred by computational analysis Inferred from experiment [Miller73, GOA06, GOA01, GOA01a]
GO:0006401 - RNA catabolic process Inferred by computational analysis [GOA06]
Molecular Function: GO:0003676 - nucleic acid binding Inferred from experiment Inferred by computational analysis [GOA01a, Miller73]
GO:0004519 - endonuclease activity Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Miller73]
GO:0004523 - RNA-DNA hybrid ribonuclease activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01, GOA01a, Miller73]
GO:0000287 - magnesium ion binding Inferred by computational analysis [GOA06]
GO:0004518 - nuclease activity Inferred by computational analysis [UniProtGOA11a]
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 by computational analysis [UniProtGOA11, UniProtGOA11a, GOA06]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

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

Essentiality data for rnhA knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 1]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 2]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 1]

Enzymatic reaction of: Rnase (RNase HI, degrades RNA of DNA-RNA hybrids, participates in DNA replication)

EC Number: 3.1.26.4

a RNA-DNA hybrid + n H2O <=> DNA + n a nucleoside 5'-monophosphate

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.

Cofactors or Prosthetic Groups: Mg2+ [Goedken01], Mn2+ [Goedken01]

Inhibitors (Unknown Mechanism): Mn2+ [Goedken01]

Primary Physiological Regulators of Enzyme Activity: Mn2+

T(opt): 45 °C [BRENDA14, Chon06]

pH(opt): 7.5 [BRENDA14, Berkower73], 9.8 [BRENDA14, Ohtani00], 10 [BRENDA14, Chon06]


Sequence Features

Feature Class Location Attached Group Citations Comment
Conserved-Region 1 -> 142  
[UniProt09]
UniProt: RNase H;
Mutagenesis-Variant 10  
[Kanaya90, Kanaya90a, UniProt11]
Alternate sequence: D → N; UniProt: Loss of activity.
Metal-Binding-Site 10  
[UniProt10]
UniProt: Magnesium 1;
Metal-Binding-Site 10, 134 Mn2+
[Goedken01]
Asp-10 and Asp-134 coordinate a divalent manganese ion which, when present may inhibit enzymatic activity.
Metal-Binding-Site 10, 48, 70 Mn2+
[Goedken01, Kanaya90]
Asp-10, Glu-48 and Asp-70 coordinate a divalent manganese ion which is required for catalytic activity.
Metal-Binding-Site 44, 48 Mg2+
[Katayanagi93]
Asn-44 and Glu-48 coordinate magnesium when it is present.
Mutagenesis-Variant 48  
[Kanaya90, Kanaya90a, UniProt11]
Alternate sequence: E → Q; UniProt: Loss of activity.
Metal-Binding-Site 48  
[UniProt10]
UniProt: Magnesium 1;
Mutagenesis-Variant 70  
[Kanaya90, Kanaya90a, UniProt11]
Alternate sequence: D → N; UniProt: Loss of activity.
Metal-Binding-Site 70  
[UniProt10]
UniProt: Magnesium 1;
Mutagenesis-Variant 124  
[Kashiwagi96, Keck98, Kanaya90, Kanaya90a, UniProt11]
Alternate sequence: H → A; UniProt: Reduces activity.
Mutagenesis-Variant 130  
[Kanaya90, Kanaya90a, UniProt11]
Alternate sequence: N → A; UniProt: Reduces activity.
Mutagenesis-Variant 134  
[Kashiwagi96, Keck98, Kanaya90, Kanaya90a, UniProt11]
Alternate sequence: D → N; UniProt: Slight decrease of activity.
Alternate sequence: D → H; UniProt: Slight decrease of activity.
Alternate sequence: D → A; UniProt: Loss of activity.
Metal-Binding-Site 134  
[UniProt10]
UniProt: Magnesium 2;


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
3/2/1998 (pkarp) Merged genes G306/b0214 and EG10860/rnhA
10/20/97 Gene b0214 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10860; confirmed by SwissProt match.


References

Arendes82: Arendes J, Carl PL, Sugino A (1982). "A mutation in the rnh-locus of Escherichia coli affects the structural gene for RNase H. Examination of the mutant and wild type protein." J Biol Chem 257(9);4719-22. PMID: 6279646

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

Babu03: Babu CS, Dudev T, Casareno R, Cowan JA, Lim C (2003). "A combined experimental and theoretical study of divalent metal ion selectivity and function in proteins: application to E. coli ribonuclease H1." J Am Chem Soc 125(31);9318-28. PMID: 12889961

Berkower73: Berkower I, Leis J, Hurwitz J (1973). "Isolation and characterization of an endonuclease from Escherichia coli specific for ribonucleic acid in ribonucleic acid-deoxyribonucleic acid hybrid structures." J Biol Chem 248(17);5914-21. PMID: 4580046

Bialy86: Bialy H, Kogoma T (1986). "RNase H is not involved in the induction of stable DNA replication in Escherichia coli." J Bacteriol 165(1);321-3. PMID: 3001028

Bockrath87: Bockrath R, Wolff L, Farr A, Crouch RJ (1987). "Amplified RNase H activity in Escherichia coli B/r increases sensitivity to ultraviolet radiation." Genetics 115(1);33-40. PMID: 3030882

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014." http://www.brenda-enzymes.org.

Broccoli00: Broccoli S, Phoenix P, Drolet M (2000). "Isolation of the topB gene encoding DNA topoisomerase III as a multicopy suppressor of topA null mutations in Escherichia coli." Mol Microbiol 35(1);58-68. PMID: 10632877

Cao93a: Cao Y, Rowland RR, Kogoma T (1993). "DNA polymerase I and the bypassing of RecA dependence of constitutive stable DNA replication in Escherichia coli rnhA mutants." J Bacteriol 175(22);7247-53. PMID: 8226671

Casaregola87: Casaregola S, Khidhir M, Holland IB (1987). "Effects of modulation of RNase H production on the recovery of DNA synthesis following UV-irradiation in Escherichia coli." Mol Gen Genet 209(3);494-8. PMID: 2828881

Cecconi05: Cecconi C, Shank EA, Bustamante C, Marqusee S (2005). "Direct observation of the three-state folding of a single protein molecule." Science 309(5743);2057-60. PMID: 16179479

Cheng03b: Cheng B, Rui S, Ji C, Gong VW, Van Dyk TK, Drolet M, Tse-Dinh YC (2003). "RNase H overproduction allows the expression of stress-induced genes in the absence of topoisomerase I." FEMS Microbiol Lett 221(2);237-42. PMID: 12725933

Chon06: Chon H, Tadokoro T, Ohtani N, Koga Y, Takano K, Kanaya S (2006). "Identification of RNase HII from psychrotrophic bacterium, Shewanella sp. SIB1 as a high-activity type RNase H." FEBS J 273(10);2264-75. PMID: 16650002

Crooke95a: Crooke ST, Lemonidis KM, Neilson L, Griffey R, Lesnik EA, Monia BP (1995). "Kinetic characteristics of Escherichia coli RNase H1: cleavage of various antisense oligonucleotide-RNA duplexes." Biochem J 312 ( Pt 2);599-608. PMID: 8526876

Daniher97: Daniher AT, Xie J, Mathur S, Bashkin JK (1997). "Modulation of RNase H activity by modified DNA probes: major groove vs minor groove effects." Bioorg Med Chem 5(6);1037-42. PMID: 9222496

deMassy84: de Massy B, Fayet O, Kogoma T (1984). "Multiple origin usage for DNA replication in sdrA(rnh) mutants of Escherichia coli K-12. Initiation in the absence of oriC." J Mol Biol 178(2);227-36. PMID: 6387151

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Drolet95: Drolet M, Phoenix P, Menzel R, Masse E, Liu LF, Crouch RJ (1995). "Overexpression of RNase H partially complements the growth defect of an Escherichia coli delta topA mutant: R-loop formation is a major problem in the absence of DNA topoisomerase I." Proc Natl Acad Sci U S A 92(8);3526-30. PMID: 7536935

GOA01: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

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."

Goedken01: Goedken ER, Marqusee S (2001). "Co-crystal of Escherichia coli RNase HI with Mn2+ ions reveals two divalent metals bound in the active site." J Biol Chem 276(10);7266-71. PMID: 11083878

Goedken97: Goedken ER, Raschke TM, Marqusee S (1997). "Importance of the C-terminal helix to the stability and enzymatic activity of Escherichia coli ribonuclease H." Biochemistry 36(23);7256-63. PMID: 9188727

Harinarayanan03: Harinarayanan R, Gowrishankar J (2003). "Host factor titration by chromosomal R-loops as a mechanism for runaway plasmid replication in transcription termination-defective mutants of Escherichia coli." J Mol Biol 332(1);31-46. PMID: 12946345

Hong93: Hong X, Kogoma T (1993). "Absence of a direct role for RNase HI in initiation of DNA replication at the oriC site on the Escherichia coli chromosome." J Bacteriol 175(20);6731-4. PMID: 8407851

Hong95: Hong X, Cadwell GW, Kogoma T (1995). "Escherichia coli RecG and RecA proteins in R-loop formation." EMBO J 14(10);2385-92. PMID: 7774596

Hraiky00: Hraiky C, Raymond MA, Drolet M (2000). "RNase H overproduction corrects a defect at the level of transcription elongation during rRNA synthesis in the absence of DNA topoisomerase I in Escherichia coli." J Biol Chem 275(15);11257-63. PMID: 10753935

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Kanaya83: Kanaya S, Crouch RJ (1983). "DNA sequence of the gene coding for Escherichia coli ribonuclease H." J Biol Chem 258(2);1276-81. PMID: 6296074

Kanaya90: Kanaya S, Kohara A, Miura Y, Sekiguchi A, Iwai S, Inoue H, Ohtsuka E, Ikehara M (1990). "Identification of the amino acid residues involved in an active site of Escherichia coli ribonuclease H by site-directed mutagenesis." J Biol Chem 265(8);4615-21. PMID: 1689729

Kanaya90a: Kanaya S, Kimura S, Katsuda C, Ikehara M (1990). "Role of cysteine residues in ribonuclease H from Escherichia coli. Site-directed mutagenesis and chemical modification." Biochem J 271(1);59-66. PMID: 2171503

Kanaya91: Kanaya S, Katsuda-Nakai C, Ikehara M (1991). "Importance of the positive charge cluster in Escherichia coli ribonuclease HI for the effective binding of the substrate." J Biol Chem 266(18);11621-7. PMID: 1646812

Kashiwagi96: Kashiwagi T, Jeanteur D, Haruki M, Katayanagi K, Kanaya S, Morikawa K (1996). "Proposal for new catalytic roles for two invariant residues in Escherichia coli ribonuclease HI." Protein Eng 9(10);857-67. PMID: 8931125

Katayanagi90: Katayanagi K, Miyagawa M, Matsushima M, Ishikawa M, Kanaya S, Ikehara M, Matsuzaki T, Morikawa K (1990). "Three-dimensional structure of ribonuclease H from E. coli." Nature 347(6290);306-9. PMID: 1698262

Katayanagi92: Katayanagi K, Miyagawa M, Matsushima M, Ishikawa M, Kanaya S, Nakamura H, Ikehara M, Matsuzaki T, Morikawa K (1992). "Structural details of ribonuclease H from Escherichia coli as refined to an atomic resolution." J Mol Biol 223(4);1029-52. PMID: 1311386

Katayanagi93: Katayanagi K, Okumura M, Morikawa K (1993). "Crystal structure of Escherichia coli RNase HI in complex with Mg2+ at 2.8 A resolution: proof for a single Mg(2+)-binding site." Proteins 17(4);337-46. PMID: 8108376

Katayanagi93a: Katayanagi K, Ishikawa M, Okumura M, Ariyoshi M, Kanaya S, Kawano Y, Suzuki M, Tanaka I, Morikawa K (1993). "Crystal structures of ribonuclease HI active site mutants from Escherichia coli." J Biol Chem 268(29);22092-9. PMID: 8408067

Keck96: Keck JL, Marqusee S (1996). "The putative substrate recognition loop of Escherichia coli ribonuclease H is not essential for activity." J Biol Chem 271(33);19883-7. PMID: 8702700

Keck98: Keck JL, Goedken ER, Marqusee S (1998). "Activation/attenuation model for RNase H. A one-metal mechanism with second-metal inhibition." J Biol Chem 273(51);34128-33. PMID: 9852071

Kitani85: Kitani T, Yoda K, Ogawa T, Okazaki T (1985). "Evidence that discontinuous DNA replication in Escherichia coli is primed by approximately 10 to 12 residues of RNA starting with a purine." J Mol Biol 184(1);45-52. PMID: 2411935

Kogoma83: Kogoma T, von Meyenburg K (1983). "The origin of replication, oriC, and the dnaA protein are dispensable in stable DNA replication (sdrA) mutants of Escherichia coli K-12." EMBO J 2(3);463-8. PMID: 11894964

Kogoma84: Kogoma T (1984). "Absence of RNase H allows replication of pBR322 in Escherichia coli mutants lacking DNA polymerase I." Proc Natl Acad Sci U S A 81(24);7845-9. PMID: 6096862

Kogoma85: Kogoma T, Subia NL, von Meyenburg K (1985). "Function of ribonuclease H in initiation of DNA replication in Escherichia coli K-12." Mol Gen Genet 200(1);103-9. PMID: 2993805

Kogoma93: Kogoma T, Hong X, Cadwell GW, Barnard KG, Asai T (1993). "Requirement of homologous recombination functions for viability of the Escherichia coli cell that lacks RNase HI and exonuclease V activities." Biochimie 75(1-2);89-99. PMID: 8389213

Kogoma97: Kogoma T, Maldonado RR (1997). "DNA polymerase I in constitutive stable DNA replication in Escherichia coli." J Bacteriol 179(7);2109-15. PMID: 9079893

Krakowiak02: Krakowiak A, Owczarek A, Koziolkiewicz M, Stec WJ (2002). "Stereochemical course of Escherichia coli RNase H." Chembiochem 3(12);1242-50. PMID: 12465033

Li98a: Li J, Wartell RM (1998). "RNase H1 can catalyze RNA/DNA hybrid formation and cleavage with stable hairpin or duplex DNA oligomers." Biochemistry 37(15);5154-61. PMID: 9548746

Lima97: Lima WF, Crooke ST (1997). "Binding affinity and specificity of Escherichia coli RNase H1: impact on the kinetics of catalysis of antisense oligonucleotide-RNA hybrids." Biochemistry 36(2);390-8. PMID: 9003192

Lima97a: Lima WF, Mohan V, Crooke ST (1997). "The influence of antisense oligonucleotide-induced RNA structure on Escherichia coli RNase H1 activity." J Biol Chem 272(29);18191-9. PMID: 9218455

Lindahl84: Lindahl G, Lindahl T (1984). "Initiation of DNA replication in Escherichia coli: RNase H-deficient mutants do not require the dnaA function." Mol Gen Genet 196(2);283-9. PMID: 6208456

Masai94: Masai H, Asai T, Kubota Y, Arai K, Kogoma T (1994). "Escherichia coli PriA protein is essential for inducible and constitutive stable DNA replication." EMBO J 13(22);5338-45. PMID: 7525276

Masse99: Masse E, Drolet M (1999). "R-loop-dependent hypernegative supercoiling in Escherichia coli topA mutants preferentially occurs at low temperatures and correlates with growth inhibition." J Mol Biol 294(2);321-32. PMID: 10610761

Miller73: Miller HI, Riggs AD, Gill GN (1973). "Ribonuclease H (hybrid) in Escherichia coli. Identification and characterization." J Biol Chem 248(7);2621-4. PMID: 4572736

Minasov00: Minasov G, Teplova M, Nielsen P, Wengel J, Egli M (2000). "Structural basis of cleavage by RNase H of hybrids of arabinonucleic acids and RNA." Biochemistry 39(13);3525-32. PMID: 10736151

Naito84: Naito S, Kitani T, Ogawa T, Okazaki T, Uchida H (1984). "Escherichia coli mutants suppressing replication-defective mutations of the ColE1 plasmid." Proc Natl Acad Sci U S A 81(2);550-4. PMID: 6320195

Naito86: Naito S, Uchida H (1986). "RNase H and replication of ColE1 DNA in Escherichia coli." J Bacteriol 166(1);143-7. PMID: 2870052

Nakamura91: Nakamura H, Oda Y, Iwai S, Inoue H, Ohtsuka E, Kanaya S, Kimura S, Katsuda C, Katayanagi K, Morikawa K (1991). "How does RNase H recognize a DNA.RNA hybrid?." Proc Natl Acad Sci U S A 88(24);11535-9. PMID: 1662398

Nomura85: Nomura T, Aiba H, Ishihama A (1985). "Transcriptional organization of the convergent overlapping dnaQ-rnh genes of Escherichia coli." J Biol Chem 1985;260(11);7122-5. PMID: 2987244

Noronha00: Noronha AM, Wilds CJ, Lok CN, Viazovkina K, Arion D, Parniak MA, Damha MJ (2000). "Synthesis and biophysical properties of arabinonucleic acids (ANA): circular dichroic spectra, melting temperatures, and ribonuclease H susceptibility of ANA.RNA hybrid duplexes." Biochemistry 39(24);7050-62. PMID: 10852702

Nowotny05: Nowotny M, Gaidamakov SA, Crouch RJ, Yang W (2005). "Crystal structures of RNase H bound to an RNA/DNA hybrid: substrate specificity and metal-dependent catalysis." Cell 121(7);1005-16. PMID: 15989951

Oda93: Oda Y, Iwai S, Ohtsuka E, Ishikawa M, Ikehara M, Nakamura H (1993). "Binding of nucleic acids to E. coli RNase HI observed by NMR and CD spectroscopy." Nucleic Acids Res 21(20);4690-5. PMID: 7694232

Ogawa84: Ogawa T, Okazaki T (1984). "Function of RNase H in DNA replication revealed by RNase H defective mutants of Escherichia coli." Mol Gen Genet 193(2);231-7. PMID: 6319961

Ogawa84a: Ogawa T, Pickett GG, Kogoma T, Kornberg A (1984). "RNase H confers specificity in the dnaA-dependent initiation of replication at the unique origin of the Escherichia coli chromosome in vivo and in vitro." Proc Natl Acad Sci U S A 81(4);1040-4. PMID: 6322184

Ohmori87: Ohmori H, Murakami Y, Nagata T (1987). "Nucleotide sequences required for a ColE1-type plasmid to replicate in Escherichia coli cells with or without RNase H." J Mol Biol 198(2);223-34. PMID: 2828638

Ohtani00: Ohtani N, Haruki M, Muroya A, Morikawa M, Kanaya S (2000). "Characterization of ribonuclease HII from Escherichia coli overproduced in a soluble form." J Biochem (Tokyo) 127(5);895-9. PMID: 10788800

Rait99: Rait VK, Shaw BR (1999). "Boranophosphates support the RNase H cleavage of polyribonucleotides." Antisense Nucleic Acid Drug Dev 9(1);53-60. PMID: 10192289

Sandler05: Sandler SJ (2005). "Requirements for replication restart proteins during constitutive stable DNA replication in Escherichia coli K-12." Genetics 169(4);1799-806. PMID: 15716497

Shiels01: Shiels JC, Jerkovic B, Baranger AM, Bolton PH (2001). "RNA-DNA hybrids containing damaged DNA are substrates for RNase H." Bioorg Med Chem Lett 11(19);2623-6. PMID: 11551764

Spudich04: Spudich GM, Miller EJ, Marqusee S (2004). "Destabilization of the Escherichia coli RNase H kinetic intermediate: switching between a two-state and three-state folding mechanism." J Mol Biol 335(2);609-18. PMID: 14672667

Subia86: Subia NL, Kogoma T (1986). "Concatemer formation of ColE1-type plasmids in mutants of Escherichia coli lacking RNase H activity." J Mol Biol 189(3);389-99. PMID: 3023625

Torrey87: Torrey TA, Kogoma T (1987). "Genetic analysis of constitutive stable DNA replication in rnh mutants of Escherichia coli K12." Mol Gen Genet 208(3);420-7. PMID: 2823060

Tsunaka01: Tsunaka Y, Haruki M, Morikawa M, Kanaya S (2001). "Strong nucleic acid binding to the Escherichia coli RNase HI mutant with two arginine residues at the active site." Biochim Biophys Acta 1547(1);135-42. PMID: 11343799

Uchiyama94: Uchiyama Y, Miura Y, Inoue H, Ohtsuka E, Ueno Y, Ikehara M, Iwai S (1994). "Studies of the interactions between Escherichia coli ribonuclease HI and its substrate." J Mol Biol 243(4);782-91. PMID: 7525971

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

UniProt10: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt11: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 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."

Weatherford72: Weatherford SC, Weisberg LS, Achord DT, Apirion D (1972). "Separation of Escherichia coli ribonucleases on a DNA agarose column and the identification of an RNase H activity." Biochem Biophys Res Commun 49(5);1307-15. PMID: 4566677


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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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