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Gene Review

rep  -  RNA replicase, beta subunit

Enterobacteria phage Qbeta

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Disease relevance of MX1p4

  • The genome of the coliphages contains a well-defined high affinity binding site for the coat protein, which serves to suppress replicase translation and also acts as a nucleation point in capsid formation [1].
  • This contrasts with the situation in the distantly related group I RNA phages such as f2 and MS2 where a small lysis polypeptide is coded for by a region overlapping the end of the coat gene and the beginning of the replicase gene [2].
  • Evidence for de novo production of self-replicating and environmentally adapted RNA structures by bacteriophage Qbeta replicase [3].
  • Highly purified coliphage Qbeta replicase when incubated without added template synthesizes self-replicating RNA species in an autocatalytic reaction [3].
  • Each mutant phage was tested for plaque formation in an Escherichia coli (F+) host strain that supplied helper Q beta replicase in trans from a plasmid DNA [4].

High impact information on MX1p4

  • In the RNA coliphage SP, the gene for the maturation protein was found to be the best target for this type of immune system; mRNA-interfering complementary RNAs specific to the genes for coat protein and replicase were less effective in preventing infection [5].
  • It has been proposed that the nucleotide sequences of the 3' terminal extracistronic regions of phage RNA plus and minus strands have been strictly conserved during evolution because they are stringently required for recognition by the viral replicase [6].
  • We show that the NH2-terminal region of S1 is required for S1 subunit interactions in replicase since a trypsin-resistant fragment (denoted S1-F1) lacking the NH2-terminal 31% of S1 is functionally inactive and does not seem to bind to R(-S1) [7].
  • One of the four subunits of bacteriophage Q beta RNA replicase is elongation factor Tu (EF-Tu), the host aminoacyl-tRNA (AA-tRNA) binding protein [8].
  • Here we report that S1 also interacts strongly with a second oligonucleotide in Qbeta RNA, which is derived from the region recognized by replicase just 5' to the Qbeta coat protein cistron [9].

Chemical compound and disease context of MX1p4

  • To investigate the function of this segment, we changed the Gly residue at position 357 in the conserved sequence Tyr-356-Gly-357-Asp-358-Asp-359 of the replicase of RNA coliphage Q beta to Ala, Ser, Pro, Met, or Val and examined the replicase activity in vivo [10].

Biological context of MX1p4

  • We also show that the S and M replicase binding sites of Q beta are strongly conserved in SP [11].
  • In order to identify the structural elements important for the activity of the Q beta minus strand RNA as a template for Q beta replicase, a series of minus strand RNAs with internal or external deletions were prepared by in vitro transcription from suitable expression plasmids [12].
  • Studies in vivo show that co-translational regulation of the viral coat and replicase genes has been uncoupled in viral genomes carrying deletion delta 159 [13].
  • Analysis of 37 different mutant clones indicated that Q beta replicase can accept amino acid substitutions and insertions at several sites at the amino and carboxy termini without abolishing functional activity in vivo or in vitro [14].
  • Here, we report on the existence of a long-range pseudoknot, base-pairing eight nt in the loop of the 3' terminal hairpin to a single-stranded interdomain sequence located about 1200 nt upstream, close to the internal replicase binding site [15].

Anatomical context of MX1p4

  • Full-length, negative-strand Q beta transcripts were infectious when transfected into spheroplasts containing the induced replicase gene [16].

Associations of MX1p4 with chemical compounds

  • Analysis of the two larger complexes formed by cross-linking with a reversible cross-linker (methyl-4-mercaptobutyrimidate) demonstrates that the 215,000 molecular weight complex is composed of one each of the replicase subunits, while the 135,000 molecular weight complex is composed of the two larger subunits [17].
  • In contrast, substitution of the Gly residue at 390 showed only a slight inhibitory effect, although replicase activity was also lost [10].
  • (3) Qbeta replicase lacking subunit alpha (R-alpha) is capable of replicating templates other than (+) strand, such as (--), "6S" RNA, poly(C) etc., in the absence of the host factor [18].

Analytical, diagnostic and therapeutic context of MX1p4

  • Structural analysis by electron microscopy of the genomic RNAs shows that several long range helices at the base of the read-through domain, that suppress translational initiation of the viral replicase gene in the wild-type genome, have been destabilized in delta 159 RNA [13].
  • Fingerprinting and further sequence analysis established that the three main fragments obtained (chain lengths 88, 71 and 27 nucleotides) all consist of sequences extending from the intercistronic region to the beginning of the replicase cistron [19].


  1. Secondary structure model for the last two domains of single-stranded RNA phage Q beta. Beekwilder, M.J., Nieuwenhuizen, R., van Duin, J. J. Mol. Biol. (1995) [Pubmed]
  2. The lysis function of RNA bacteriophage Qbeta is mediated by the maturation (A2) protein. Karnik, S., Billeter, M. EMBO J. (1983) [Pubmed]
  3. Evidence for de novo production of self-replicating and environmentally adapted RNA structures by bacteriophage Qbeta replicase. Sumper, M., Luce, R. Proc. Natl. Acad. Sci. U.S.A. (1975) [Pubmed]
  4. Q beta RNA bacteriophage: mapping cis-acting elements within an RNA genome. Mills, D.R., Priano, C., Merz, P.A., Binderow, B.D. J. Virol. (1990) [Pubmed]
  5. Engineering of the mRNA-interfering complementary RNA immune system against viral infection. Hirashima, A., Sawaki, S., Inokuchi, Y., Inouye, M. Proc. Natl. Acad. Sci. U.S.A. (1986) [Pubmed]
  6. Site-directed mutagenesis: effect of an extracistronic mutation on the in vitro propagation of bacteriophage Qbeta RNA. Flavell, R.A., Sabo, D.L., Bandle, E.F., Weissmann, C. Proc. Natl. Acad. Sci. U.S.A. (1975) [Pubmed]
  7. The activity of discrete fragments of ribosomal protein S1 in Q beta replicase function. Guerrier-Takada, C., Subramanian, A.R., Cole, P.E. J. Biol. Chem. (1983) [Pubmed]
  8. Transfer RNA cross-linked to the elongation factor Tu subunit of Q beta replicase does not inhibit Q beta RNA replication. Guerrier-Takada, C., Johnson, A.E., Miller, D.L., Cole, P.E. J. Biol. Chem. (1981) [Pubmed]
  9. Escherichia coli ribosomal protein S1 recognizes two sites in bacteriophage Qbeta RNA. Goelz, S., Steitz, J.A. J. Biol. Chem. (1977) [Pubmed]
  10. Interference with viral infection by defective RNA replicase. Inokuchi, Y., Hirashima, A. J. Virol. (1987) [Pubmed]
  11. Analysis of the complete nucleotide sequence of the group IV RNA coliphage SP. Inokuchi, Y., Jacobson, A.B., Hirose, T., Inayama, S., Hirashima, A. Nucleic Acids Res. (1988) [Pubmed]
  12. Identification of recognition elements on bacteriophage Q beta minus strand RNA that are essential for template activity with Q beta replicase. Schuppli, D., Barrera, I., Weber, H. J. Mol. Biol. (1994) [Pubmed]
  13. Structural plasticity in RNA and its role in the regulation of protein translation in coliphage Q beta. Jacobson, A.B., Arora, R., Zuker, M., Priano, C., Lin, C.H., Mills, D.R. J. Mol. Biol. (1998) [Pubmed]
  14. Q beta replicase: mapping the functional domains of an RNA-dependent RNA polymerase. Mills, D.R., Priano, C., DiMauro, P., Binderow, B.D. J. Mol. Biol. (1989) [Pubmed]
  15. A long-range pseudoknot in Qbeta RNA is essential for replication. Klovins, J., van Duin, J. J. Mol. Biol. (1999) [Pubmed]
  16. Infectious positive- and negative-strand transcript RNAs from bacteriophage Q beta cDNA clones. Shaklee, P.N., Miglietta, J.J., Palmenberg, A.C., Kaesberg, P. Virology (1988) [Pubmed]
  17. Phage Q-beta ribonucleic acid replicase. Subunit relationships determined by intramolecular cross-linking. Young, R.A., Blumenthal, T. J. Biol. Chem. (1975) [Pubmed]
  18. Structure and function of RNA replicase of bacteriophage Qbeta. Kondo, M. Arch. Int. Physiol. Biochim. (1975) [Pubmed]
  19. The binding site for coat protein on bacteriophage Qbeta RNA. Weber, H. Biochim. Biophys. Acta (1976) [Pubmed]
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