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Gene Review

RNH1  -  Rnh1p

Saccharomyces cerevisiae S288c

Synonyms: RNase H, Ribonuclease H, YM9959.16, YMR234W
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Disease relevance of RNH1


High impact information on RNH1

  • Interestingly, we find that PRP16 promotes a conformational change in the spliceosome which results in the protection of the 3' splice site against oligo-directed RNase H cleavage [6].
  • Differences in the RNase H sensitivity of pre-mRNA found in the two spliceosome forms indicate an increased association of splicing factors with the 5' splice site during spliceosome assembly [7].
  • A gene designated Cfa RNH1 has been cloned by complementation of an RNase H deficiency in an Escherichia coli rnhA mutant by using a genomic DNA library from the trypanosomatid Crithidia fasciculata [1].
  • RNase H degradation in the presence of oligo(dT) demonstrated that the wild-type and mutant PGK1 mRNAs are deadenylated prior to endonucleolytic cleavage and that the half-life of the poly(A) tail is three- to sixfold lower than that of the remainder of the mRNA [8].
  • We have combined oligonucleotide-directed RNase H degradation and immunoprecipitation in a study of the association of the Saccharomyces cerevisiae PRP4 protein with the U4-U6 complex [9].

Chemical compound and disease context of RNH1

  • Surprisingly, NEM strongly inhibits the same bacterial RNase H in the presence of a recombinant form of HIV RT devoid of nuclease activity [10].

Biological context of RNH1

  • Deletion of the gene (called RNH35) from the yeast genome leads to an about 75% decrease of RNase H activity in preparations from the mutated, still viable cells [11].
  • Crystallographic studies of E. coli RNase H indicate that several amino acids, conserved in both cellular and retroviral RNases H, form an active site for hydrolysis of the RNA of RNA-DNA hybrids [4].
  • The C-terminal portion of Ty3 RT encodes a functional RNase H domain, although the hydrolysis profile suggests an increased spatial separation between the catalytic centers [12].
  • The second 4395-base pair open reading frame, TYB4, encodes a polyprotein that has domains with significant homology to retroviral protease, integrase, reverse transcriptase, and RNase H, structurally arranged in that order [13].
  • Reverse transcriptase and RNase H amino acid sequences from elements in the gypsy group--including the recently described SURL elements, TED, Cft1, and Ulysses,--were aligned and analyzed by using parsimony and bootstrapping methods, with plant caulimoviruses and/or retroviruses as outgroups [14].

Anatomical context of RNH1

  • Most of the uncleaved pre-mRNA remaining after RNase H challenge was found associated with two forms of the yeast spliceosome [7].
  • Ribonuclease H IIb, which seems to play a physiological role during transcription, was purified from calf thymus tissue [15].

Associations of RNH1 with chemical compounds

  • Although all mutations had minimal impact on DNA polymerase function, amidation of Asp-358, Glu-401, and Asp-426 eliminated Mg(2+)- and Mn(2+)-dependent RNase H function [16].
  • Deletion of HBV reverse transcriptase (RT) or RNase H domains resulted in a dramatic drop in histidine prototrophs [17].
  • Replacing His-427 and Tyr-459 with Ala and Asp-469 with Asn resulted in reduced RNase H activity in the presence of Mg(2+), whereas in the presence of Mn(2+) these mutants displayed a lack of turnover [16].
  • Two ribonuclease H activities have been found in yeast RNA polymerase A. The nuclease activities comigrated with subunits A49 (Mr = 49,000) and A40 (Mr = 40,000), after electrophoresis in a sodium dodecyl sulfate polyacrylamide gel containing [32P](rG)n . (dC)n as substrate [18].
  • Despite conservation of catalytically important residues in the RNase H domain, Fe(2+) fails to replace Mg(2+) in the RNase H catalytic center for localized generation of hydroxyl radicals, again suggesting this domain may be structurally distinct from its retroviral counterparts [12].

Other interactions of RNH1

  • Two of these genes have recently been further characterized: ORF YGR255w, renamed RTT102, encodes a regulator of the Ty1-element transposition, whereas ORF YGR276c was found to encode the 70 kDa RNase H activity and was renamed RNH70 (Frank et al., 1999) [19].
  • Several lines of evidence suggest that the chromatin RNase H of 49,000 daltons (RNase H49) is the same protein as subunit A49 [18].
  • All retroelements use an RNase H-resistant oligoribonucleotide spanning a purine-rich sequence (the polypurine tract or PPT) to prime plus-strand DNA synthesis [20].
  • Accumulation of Ty1-integrase and Ty1-reverse transcriptase/ribonuclease H is defective in an hsx1 mutant [21].
  • By probing the precatalytic spliceosome formed in temperature-sensitive prp2 mutant extracts with oligonucleotides complementary to snRNAs, we found that the 5' end of U1 was sensitive to RNase H digestion whereas the 5' splice site-interacting region of U6 became resistant [22].

Analytical, diagnostic and therapeutic context of RNH1

  • Targeting a cellular RNase H to HIV may help define the site(s) of RNA-DNA hybrids that are susceptible to nonretroviral RNase H and may be useful for gene therapy to inhibit retroviral replication [23].
  • The native molecular mass for the enzyme of around 45 kDa, as determined by gel filtration, suggests that calf thymus ribonuclease H IIb is most probably monomeric [15].


  1. Functional complementation of an Escherichia coli ribonuclease H mutation by a cloned genomic fragment from the trypanosomatid Crithidia fasciculata. Campbell, A.G., Ray, D.S. Proc. Natl. Acad. Sci. U.S.A. (1993) [Pubmed]
  2. A common 40 amino acid motif in eukaryotic RNases H1 and caulimovirus ORF VI proteins binds to duplex RNAs. Cerritelli, S.M., Fedoroff, O.Y., Reid, B.R., Crouch, R.J. Nucleic Acids Res. (1998) [Pubmed]
  3. Selective cloning of genes encoding RNase H from Salmonella typhimurium, Saccharomyces cerevisiae and Escherichia coli rnh mutant. Itaya, M., McKelvin, D., Chatterjie, S.K., Crouch, R.J. Mol. Gen. Genet. (1991) [Pubmed]
  4. Ribonuclease H: from discovery to 3D structure. Crouch, R.J. New Biol. (1990) [Pubmed]
  5. Amino acids essential for RNase H activity of hepadnaviruses are also required for efficient elongation of minus-strand viral DNA. Chen, Y., Marion, P.L. J. Virol. (1996) [Pubmed]
  6. A conformational rearrangement in the spliceosome is dependent on PRP16 and ATP hydrolysis. Schwer, B., Guthrie, C. EMBO J. (1992) [Pubmed]
  7. Differential nuclease sensitivity identifies tight contacts between yeast pre-mRNA and spliceosomes. Rymond, B.C., Rosbash, M. EMBO J. (1986) [Pubmed]
  8. The rate-limiting step in yeast PGK1 mRNA degradation is an endonucleolytic cleavage in the 3'-terminal part of the coding region. Vreken, P., Raué, H.A. Mol. Cell. Biol. (1992) [Pubmed]
  9. The PRP4 (RNA4) protein of Saccharomyces cerevisiae is associated with the 5' portion of the U4 small nuclear RNA. Xu, Y., Petersen-Bjørn, S., Friesen, J.D. Mol. Cell. Biol. (1990) [Pubmed]
  10. The ribonuclease H activity of HIV-1 reverse transcriptase: further biochemical characterization and search of inhibitors. Andréola, M.L., Tharaud, D., Litvak, S., Tarrago-Litvak, L. Biochimie (1993) [Pubmed]
  11. Yeast RNase H(35) is the counterpart of the mammalian RNase HI, and is evolutionarily related to prokaryotic RNase HII. Frank, P., Braunshofer-Reiter, C., Wintersberger, U. FEBS Lett. (1998) [Pubmed]
  12. Interaction of p55 reverse transcriptase from the Saccharomyces cerevisiae retrotransposon Ty3 with conformationally distinct nucleic acid duplexes. Rausch, J.W., Grice, M.K., Henrietta, M., Nymark-McMahon, n.u.l.l., Miller, J.T., Le Grice, S.F. J. Biol. Chem. (2000) [Pubmed]
  13. Ty4, a new retrotransposon from Saccharomyces cerevisiae, flanked by tau-elements. Janetzky, B., Lehle, L. J. Biol. Chem. (1992) [Pubmed]
  14. Phylogenetic relationships of reverse transcriptase and RNase H sequences and aspects of genome structure in the gypsy group of retrotransposons. Springer, M.S., Britten, R.J. Mol. Biol. Evol. (1993) [Pubmed]
  15. Serological analysis and characterization of calf thymus ribonuclease H IIb. Vonwirth, H., Frank, P., Büsen, W. Eur. J. Biochem. (1989) [Pubmed]
  16. Mutating conserved residues in the ribonuclease H domain of Ty3 reverse transcriptase affects specialized cleavage events. Lener, D., Budihas, S.R., Le Grice, S.F. J. Biol. Chem. (2002) [Pubmed]
  17. Expression of hepatitis B virus polymerase in Ty1-his3AI retroelement of Saccharomyces cerevisiae. Qadri, I., Siddiqui, A. J. Biol. Chem. (1999) [Pubmed]
  18. Identification of two different RNase H activities associated with yeast RNA polymerase A. Iborra, F., Huet, J., Breant, B., Sentenac, A., Fromageot, P. J. Biol. Chem. (1979) [Pubmed]
  19. Disruption of six novel genes from chromosome VII of Saccharomyces cerevisiae reveals one essential gene and one gene which affects the growth rate. Fiori, A., Bianchi, M.M., Fabiani, L., Falcone, C., Francisci, S., Palleschi, C., Solimando, N., Uccelletti, D., Frontali, L. Yeast (2000) [Pubmed]
  20. A sequence immediately upstream of the plus-strand primer is essential for plus-strand DNA synthesis of the Saccharomyces cerevisiae Ty1 retrotransposon. Wilhelm, M., Heyman, T., Boutabout, M., Wilhelm, F.X. Nucleic Acids Res. (1999) [Pubmed]
  21. A rare tRNA-Arg(CCU) that regulates Ty1 element ribosomal frameshifting is essential for Ty1 retrotransposition in Saccharomyces cerevisiae. Kawakami, K., Pande, S., Faiola, B., Moore, D.P., Boeke, J.D., Farabaugh, P.J., Strathern, J.N., Nakamura, Y., Garfinkel, D.J. Genetics (1993) [Pubmed]
  22. Analysis of small nuclear RNAs in a precatalytic spliceosome. Yean, S.L., Lin, R.J. Gene Expr. (1996) [Pubmed]
  23. Escherichia coli RNase HI inhibits murine leukaemia virus reverse transcription in vitro and yeast retrotransposon Ty1 transposition in vivo. Ma, W.P., Crouch, R.J. Genes Cells (1996) [Pubmed]
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