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Gene Review

rph  -  ribonuclease PH

Escherichia coli O157:H7 str. Sakai

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Disease relevance of rph


High impact information on rph

  • An analysis of its amino acid sequence shows that the protein is composed of two core domains related to RNase PH, two RNA binding domains (KH and S1), and an alpha-helical domain [4].
  • Although both PNPase and RNase PH act in a phosphorolytic manner, they differ substantially in size and substrate specificity [5].
  • OrfE/RNase PH contains helix-turn-helix motifs resembling those in DNA-binding proteins, and it binds nonspecifically to DNA [6].
  • The highly purified protein catalyzes the phosphorolytic cleavage of poly(A) at a rate of 1.6 mumol/min/mg and the formation of CDP from tRNA-CCA-Cn and orthophosphate at a rate equal to 0.14 mumol/min/mg, as characteristic for RNase PH [6].
  • To obtain information about the function of this enzyme in vivo, the Escherichia coli rph gene encoding RNase PH was interrupted with either a kanamycin resistance or a chloramphenicol resistance cassette and transferred to the chromosome of a variety of RNase-resistant strains [7].

Chemical compound and disease context of rph


Biological context of rph

  • The equilibrium constant for RNase PH is near unity, suggesting that at the phosphate concentration present in vivo, the enzyme would participate in RNA degradation [9].
  • Here we show that the RNase PH-negative, PNP-negative double-mutant strain actually displays a reversible cold-sensitive phenotype and that tRNA biosynthesis is normal [10].

Anatomical context of rph

  • These data indicate that RNase PH and PNPase play an essential role that affects ribosome metabolism and that this function cannot be taken over by any of the hydrolytic exoribonucleases present in the cell [10].

Analytical, diagnostic and therapeutic context of rph

  • Higher order multimers of RNase PH could be detected by gel filtration at higher protein concentrations and by protein cross-linking [9].


  1. Running rings around RNA: a superfamily of phosphate-dependent RNases. Symmons, M.F., Williams, M.G., Luisi, B.F., Jones, G.H., Carpousis, A.J. Trends Biochem. Sci. (2002) [Pubmed]
  2. The 3' to 5' degradation of yeast mRNAs is a general mechanism for mRNA turnover that requires the SKI2 DEVH box protein and 3' to 5' exonucleases of the exosome complex. Anderson, J.S., Parker, R.P. EMBO J. (1998) [Pubmed]
  3. Identification of the rph (RNase PH) gene of Bacillus subtilis: evidence for suppression of cold-sensitive mutations in Escherichia coli. Craven, M.G., Henner, D.J., Alessi, D., Schauer, A.T., Ost, K.A., Deutscher, M.P., Friedman, D.I. J. Bacteriol. (1992) [Pubmed]
  4. Domain analysis of the chloroplast polynucleotide phosphorylase reveals discrete functions in RNA degradation, polyadenylation, and sequence homology with exosome proteins. Yehudai-Resheff, S., Portnoy, V., Yogev, S., Adir, N., Schuster, G. Plant Cell (2003) [Pubmed]
  5. RNase PH: an Escherichia coli phosphate-dependent nuclease distinct from polynucleotide phosphorylase. Deutscher, M.P., Marshall, G.T., Cudny, H. Proc. Natl. Acad. Sci. U.S.A. (1988) [Pubmed]
  6. Overexpression and rapid purification of the orfE/rph gene product, RNase PH of Escherichia coli. Jensen, K.F., Andersen, J.T., Poulsen, P. J. Biol. Chem. (1992) [Pubmed]
  7. RNase PH is essential for tRNA processing and viability in RNase-deficient Escherichia coli cells. Kelly, K.O., Reuven, N.B., Li, Z., Deutscher, M.P. J. Biol. Chem. (1992) [Pubmed]
  8. Escherichia coli orfE (upstream of pyrE) encodes RNase PH. Ost, K.A., Deutscher, M.P. J. Bacteriol. (1991) [Pubmed]
  9. Characterization of Escherichia coli RNase PH. Kelly, K.O., Deutscher, M.P. J. Biol. Chem. (1992) [Pubmed]
  10. An essential function for the phosphate-dependent exoribonucleases RNase PH and polynucleotide phosphorylase. Zhou, Z., Deutscher, M.P. J. Bacteriol. (1997) [Pubmed]
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