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Gene Review

rnhA  -  ribonuclease HI, degrades RNA of DNA-RNA...

Escherichia coli str. K-12 substr. MG1655

Synonyms: ECK0214, JW0204, cer, dasF, herA, ...
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Disease relevance of rnhA

  • By screening a library of E. coli DNA for clones that suppressed RNase H deficiency of an E. coli rnh mutant, a clone was obtained that produced a protein with RNase H activity [1].
  • Curing the cells of the lambda rnh prophage left the cell with an inactive rnh gene and resulted in cell death [2].
  • A strain was made with two copies of the rnh gene by lysogenizing an E. coli strain with a lambda phage bearing a copy of the rnh gene [2].
  • Because models predict exonucleolytic processing of the cleaved recipient leading to homologous strand invasion of the donor allele, the assay was performed in wild-type and exonuclease-deficient (rnh or dexA) phage [3].

High impact information on rnhA

  • Xer site-specific recombination at natural plasmid recombination sites (e.g., cer in ColE1) is preferentially intramolecular, converting dimers to monomers [4].
  • We have also coupled our mutations with lesions in dnaA, which is required for cell-cycle-specific DNA replication, and rnh (the gene for RNase H), which is required for specificity in the DNA initiation reaction, and determined the effects of the double and triple mutants under permissive and nonpermissive conditions [5].
  • The Xer site-specific recombination system acts at ColE1 cer and pSC101 psi sites to ensure that these plasmids are in a monomeric state prior to cell division [6].
  • Resolution of ColE1 dimers requires a DNA sequence implicated in the three-dimensional organization of the cer site [7].
  • Plasmid pBR322 was found to replicate in rnh mutants in the absence of DNA polymerase I, the polA gene product, which is normally required for replication of this plasmid [8].

Chemical compound and disease context of rnhA


Biological context of rnhA


Anatomical context of rnhA

  • 30S ribosomal subunits, 70S ribosomes or polysomes from E. coli were subjected to mild ultraviolet irradiation, and the 3'-terminal region of the 16S RNA was excised by 'addressed cleavage' using ribonuclease H in the presence of suitable complementary oligodeoxynucleotides [17].

Associations of rnhA with chemical compounds

  • Stopped-flow experiments at sub-zero temperatures in the presence of 30% ethylene glycol allowed us to monitor the evolution of the scattering pattern, including the characteristic scattering peak in an s (=2 sin theta/lambda) range of 0.01-0.06 A-1 [18].
  • A Gly residue inserted between alpha-helices B and C appears to relieve unfavorable interactions in the transition state and alternate conformer(s) and represents an important adaptation to adjust conformational changes within RNase H for activity at high temperatures [19].
  • RP1-S2 retains carbenicillin and tetracycline resistances as well as loci that cause either the loss of P plasmids (incp) or a locus specifying susceptibility to curing (sinp) in the presence of a P plasmid [20].

Other interactions of rnhA

  • From beta-galactosidase levels it was estimated that the promoter for dnaQ is 5 times more active than that for rnh [21].
  • These strains contained a second unlinked mutation in either mutL or mutS or sin [22].
  • This observation indicated that in B. subtilis both the rnhB and rnhC products are involved in certain essential cellular processes that are different from those suggested by E. coli rnh mutation studies [23].
  • The results indicate that the cer-like site of pHS-2, like the ColE1 cer site, acts as a recA-independent, site-specific recombination site involved in the resolution of multimers, requiring the presence of the host-encoded factors ArgR, PepA, XerC, and XerD [24].

Analytical, diagnostic and therapeutic context of rnhA

  • rnh mutants harboring pBR322 were found to contain several slowly migrating DNA species when examined by agarose gel electrophoresis [25].
  • Sequence analysis of hybrids indicates that recombination involving cer and ckr is site-specific and occurs within a 35 bp region of DNA which contains palindromic symmetry [26].


  1. Isolation and characterization of a second RNase H (RNase HII) of Escherichia coli K-12 encoded by the rnhB gene. Itaya, M. Proc. Natl. Acad. Sci. U.S.A. (1990) [Pubmed]
  2. The rnh gene is essential for growth of Escherichia coli. Kanaya, S., Crouch, R.J. Proc. Natl. Acad. Sci. U.S.A. (1984) [Pubmed]
  3. Intron homing with limited exon homology. Illegitimate double-strand-break repair in intron acquisition by phage t4. Parker, M.M., Belisle, M., Belfort, M. Genetics (1999) [Pubmed]
  4. Determinants of selectivity in Xer site-specific recombination. Blakely, G., Sherratt, D. Genes Dev. (1996) [Pubmed]
  5. On the bacterial cell cycle: Escherichia coli mutants with altered ploidy. Trun, N.J., Gottesman, S. Genes Dev. (1990) [Pubmed]
  6. Xer-mediated site-specific recombination in vitro. Colloms, S.D., McCulloch, R., Grant, K., Neilson, L., Sherratt, D.J. EMBO J. (1996) [Pubmed]
  7. Resolution of ColE1 dimers requires a DNA sequence implicated in the three-dimensional organization of the cer site. Summers, D.K., Sherratt, D.J. EMBO J. (1988) [Pubmed]
  8. Absence of RNase H allows replication of pBR322 in Escherichia coli mutants lacking DNA polymerase I. Kogoma, T. Proc. Natl. Acad. Sci. U.S.A. (1984) [Pubmed]
  9. Role of cysteine residues in ribonuclease H from Escherichia coli. Site-directed mutagenesis and chemical modification. Kanaya, S., Kimura, S., Katsuda, C., Ikehara, M. Biochem. J. (1990) [Pubmed]
  10. DNA binding of Escherichia coli arginine repressor mutants altered in oligomeric state. Chen, S.H., Merican, A.F., Sherratt, D.J. Mol. Microbiol. (1997) [Pubmed]
  11. Construction of stable cloning vectors that do not segregate from a human fecal Escherichia coli strain in the streptomycin-treated mouse large intestine. Burghoff, R.L., Laux, D.C., Cohen, P.S. Infect. Immun. (1990) [Pubmed]
  12. Rearranging the domains of pepsinogen. Lin, X., Koelsch, G., Loy, J.A., Tang, J. Protein Sci. (1995) [Pubmed]
  13. Mode of initiation of constitutive stable DNA replication in RNase H-defective mutants of Escherichia coli K-12. von Meyenburg, K., Boye, E., Skarstad, K., Koppes, L., Kogoma, T. J. Bacteriol. (1987) [Pubmed]
  14. Transcriptional organization of the convergent overlapping dnaQ-rnh genes of Escherichia coli. Nomura, T., Aiba, H., Ishihama, A. J. Biol. Chem. (1985) [Pubmed]
  15. DNA sequence of the gene coding for Escherichia coli ribonuclease H. Kanaya, S., Crouch, R.J. J. Biol. Chem. (1983) [Pubmed]
  16. DNA sequence and coding properties of mutD(dnaQ) a dominant Escherichia coli mutator gene. Cox, E.C., Horner, D.L. J. Mol. Biol. (1986) [Pubmed]
  17. The topography of the 3'-terminal region of Escherichia coli 16S ribosomal RNA; an intra-RNA cross-linking study. Döring, T., Greuer, B., Brimacombe, R. Nucleic Acids Res. (1992) [Pubmed]
  18. Kinetics of the quaternary structure change of aspartate transcarbamylase triggered by succinate, a competitive inhibitor. Tsuruta, H., Vachette, P., Sano, T., Moody, M.F., Amemiya, Y., Wakabayashi, K., Kihara, H. Biochemistry (1994) [Pubmed]
  19. An inserted Gly residue fine tunes dynamics between mesophilic and thermophilic ribonucleases H. Butterwick, J.A., Palmer, A.G. Protein Sci. (2006) [Pubmed]
  20. RP1 properties and fertility inhibition among P, N, W, and X incompatibility group plasmids. Olsen, R.H., Shipley, P.L. J. Bacteriol. (1975) [Pubmed]
  21. Structure and expression of the dnaQ mutator and the RNase H genes of Escherichia coli: overlap of the promoter regions. Maki, H., Horiuchi, T., Sekiguchi, M. Proc. Natl. Acad. Sci. U.S.A. (1983) [Pubmed]
  22. Isolation and characterization of Dam+ revertants and suppressor mutations that modify secondary phenotypes of dam-3 strains of Escherichia coli K-12. McGraw, B.R., Marinus, M.G. Mol. Gen. Genet. (1980) [Pubmed]
  23. Isolation of RNase H genes that are essential for growth of Bacillus subtilis 168. Itaya, M., Omori, A., Kanaya, S., Crouch, R.J., Tanaka, T., Kondo, K. J. Bacteriol. (1999) [Pubmed]
  24. Characterization of the stable maintenance of the Shigella flexneri plasmid pHS-2. Réhel, N., Szatmari, G. Plasmid (1996) [Pubmed]
  25. Concatemer formation of ColE1-type plasmids in mutants of Escherichia coli lacking RNase H activity. Subia, N.L., Kogoma, T. J. Mol. Biol. (1986) [Pubmed]
  26. Multimer resolution systems of ColE1 and ColK: localisation of the crossover site. Summers, D., Yaish, S., Archer, J., Sherratt, D. Mol. Gen. Genet. (1985) [Pubmed]
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