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Gene Review

yeaA  -  nuclease

Escherichia coli

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Disease relevance of yeaA

  • RecBCD enzyme is a complex helicase and nuclease, essential for the major pathway of homologous recombination and DNA repair in Escherichia coli [1].
  • Phage T4-induced anticodon nuclease triggers cleavage-ligation of the host tRNA(Lys) [2].
  • A structural comparison between NucA and the closest analog for which structural data exist, the Serratia nuclease, indicates several interesting differences [3].
  • We have delineated the amino acid to nucleotide contacts made by two interacting dimers of the replication terminator protein (RTP) of Bacillus subtilis with a novel naturally occurring bipolar replication terminus by converting RTP to a site-directed chemical nuclease and mapping its cleavage sites on the terminus [4].
  • On the basis of the biophysical studies on the synthetic mutant (Ile-8----Asn) OmpA signal peptide in the preceding paper (Hoyt, D. C., and Gierasch, L.M. (1991) J. Biol. Chem. 266, 14406-14412), the in vivo effects of the same mutation were examined by fusing the mutant OmpA signal sequence to Staphylococcus aureus nuclease or TEM beta-lactamase [5].

Psychiatry related information on yeaA

  • On the other hand, rRNA cleavage induced by the tethered 1,10-phenanthroline-Cu(II) complex appears localized to the proximity of the chemical nuclease under normal conditions, although the production of an unknown diffusible species appears to occur during long reaction times [6].

High impact information on yeaA

  • The tryptophan gene (trp) repressor of Escherichia coli has been converted into a site-specific nuclease by covalently attaching it to the 1,10-phenanthroline-copper complex [7].
  • The active site of MutH is located at an interface between two subdomains that pivot relative to one another, as revealed by comparison of the crystal structures, and this presumably regulates the nuclease activity [8].
  • The basic promoter and iron-regulatory sequences of the U. maydis sid1 gene were defined by fusing restriction and Bal31 nuclease-generated deletion fragments of the promoter region with the Escherichia coli beta-glucuronidase (GUS) reporter gene [9].
  • The natively disordered N-terminal 83-aa translocation (T) domain of E group nuclease colicins recruits OmpF to a colicin-receptor complex in the outer membrane (OM) as well as TolB in the periplasm of Escherichia coli, the latter triggering translocation of the toxin across the OM [10].
  • The 2'-O-aminopropyl (AP)-RNA modification displays the highest nuclease resistance among all phosphodiester-based analogues and its RNA binding affinity surpasses that of phosphorothioate DNA by 1 degrees C per modified residue [11].

Chemical compound and disease context of yeaA


Biological context of yeaA

  • As shown previously, the C-terminal nuclease region of Rrp1 is sufficient to repair oxidative- and alkylation-induced DNA damage in repair-deficient E. coli mutants [17].
  • The nuclease activity of Mre11 is required for meiosis but not for mating type switching, end joining, or telomere maintenance [18].
  • The transcription initiation sites of the valS gene were determined, in vivo and in vitro, by S1 nuclease protection studies, primer-extension analysis and both alpha-32P labeled and gamma-32P-end-labeled in vitro transcription assays [19].
  • This association exists without significant changes (as measured by nuclease protection, topological state of the heteroduplex DNA, and rates of ATP hydrolysis) for at least 30 min after strand exchange is complete [20].
  • Correlating the reported structural effects of the base modifications with their effects on anticodon nuclease activity suggests preference for substrates where the anticodon nucleotides assume a stacked A-RNA conformation and base pairing interactions in the stem are destabilized [21].

Anatomical context of yeaA

  • We found that the major breakpoint region (mbr) contains an S1 nuclease-sensitive site and is the target of an endogenous nuclease present in early B cells [22].
  • The pattern of cleavages in the anticodon loop of mutant tRNAs by S1 nuclease indicate that the G:C base pairs may be involved directly in interactions of the tRNA with components of the P site on the ribosome rather than indirectly by inducing a particular conformation of the anticodon loop critical for function of the tRNA in initiation [23].
  • On the basis of the sequence of Sr-nuclease, a computer search in the sequence database yielded 60% and 48% positional identities with the sequences of Cunninghamella echinulata nuclease C1 and yeast mitochondria nuclease respectively, and very little similarity to those of several known mammalian DNases I [24].
  • Single-stranded pRQ7 DNA accumulates in strain RQ7, as evidenced by the facts that this DNA bound to nitrocellulose membranes under nondenaturing conditions, was sensitive to S1 nuclease digestion, and hybridized to only one of two homologous DNA probes specific for each strand of the plasmid [25].
  • Microtiter plates were coated with the fusion protein as well as with partially purified calf thymus extract (CTE) containing all natural UsnRNP antigens and RNase digested calf thymus extract (CTERNase) in which the natural 70K antigen was destroyed by the nuclease treatment [26].

Associations of yeaA with chemical compounds

  • Phosphodiester contacts were investigated further using DNA substrates carrying unique methylphosphonate substitutions, together with mutations in the 5' nuclease [27].
  • Using cloned (dG-dA)n X (dC-dT)n DNA duplexes [GA)n) as models of homopurine-homopyrimidine S1-hypersensitive sites, we show that cleavage of the alternate (non-B, non-Z) DNA structure by S1 nuclease is length-dependent, in both supercoiled and linear forms, which are similar because of the identity of their nicking profiles [28].
  • The data also reveal that Stp can be replaced as the activator of latent anticodon nuclease by certain pyrimidine nucleotides, the most potent of which is dTTP [29].
  • The structure of wildtype and mutant 5S rRNA was compared by chemical modification of accessible guanosines with kethoxal and limited enzymatic digestion using RNase T1 and nuclease S1 [30].
  • Six of these residues together with four other partially conserved His or Asp residues were changed to alanine by site-directed PCR-mediated mutagenesis using a variant of the nuclease gene in which the coding sequence of the signal peptide was replaced by the coding sequence for an N-terminal affinity tag [Met(His)6GlySer] [31].

Other interactions of yeaA


Analytical, diagnostic and therapeutic context of yeaA

  • By sequence alignment of the extracellular Serratia marcescens nuclease with three related nucleases we have identified seven charged amino acid residues which are conserved in all four sequences [31].
  • We have derived a secondary structure model for 16S ribosomal RNA on the basis of comparative sequence analysis, chemical modification studies and nuclease susceptibility data [34].
  • We have used Northern blots, S1 nuclease protection and primer extension analysis to map 18 endonucleolytic cleavage sites within the pyrF-orfF dicistronic transcript [35].
  • In a continuation of an earlier study [Carra, J., Anderson, E., & Privalov, P. (1994) Biochemistry 33, 10842-10850], we used differential scanning calorimetry to measure the enthalpy and heat capacity changes of denaturation for 11 mutant forms of staphylococcal nuclease, including the triple mutant [V66L+G88V+G79S] [36].
  • The titration curve is best fit by an association constant of (1.80 +/- 0.05) X 10(7) M-1, within the range estimated by a nuclease mapping study of the same system [Wickstrom, E. (1983) Nucleic Acids Res. 11, 2035-2052] [37].


  1. RecBCD enzyme is a DNA helicase with fast and slow motors of opposite polarity. Taylor, A.F., Smith, G.R. Nature (2003) [Pubmed]
  2. HSD restriction-modification proteins partake in latent anticodon nuclease. Amitsur, M., Morad, I., Chapman-Shimshoni, D., Kaufmann, G. EMBO J. (1992) [Pubmed]
  3. Structural insights into the mechanism of nuclease A, a betabeta alpha metal nuclease from Anabaena. Ghosh, M., Meiss, G., Pingoud, A., London, R.E., Pedersen, L.C. J. Biol. Chem. (2005) [Pubmed]
  4. Structural and functional analysis of a bipolar replication terminus. Implications for the origin of polarity of fork arrest. Mohanty, B.K., Bussiere, D.E., Sahoo, T., Pai, K.S., Meijer, W.J., Bron, S., Bastia, D. J. Biol. Chem. (2001) [Pubmed]
  5. In vivo effect of asparagine in the hydrophobic region of the signal sequence. Goldstein, J., Lehnhardt, S., Inouye, M. J. Biol. Chem. (1991) [Pubmed]
  6. Comparison of rRNA cleavage by complementary 1,10-phenanthroline-Cu(II)- and EDTA-Fe(II)-derivatized oligonucleotides. Bowen, W.S., Hill, W.E., Lodmell, J.S. Methods (2001) [Pubmed]
  7. Chemical conversion of a DNA-binding protein into a site-specific nuclease. Chen, C.H., Sigman, D.S. Science (1987) [Pubmed]
  8. Structural basis for MutH activation in E.coli mismatch repair and relationship of MutH to restriction endonucleases. Ban, C., Yang, W. EMBO J. (1998) [Pubmed]
  9. The distal GATA sequences of the sid1 promoter of Ustilago maydis mediate iron repression of siderophore production and interact directly with Urbs1, a GATA family transcription factor. An, Z., Mei, B., Yuan, W.M., Leong, S.A. EMBO J. (1997) [Pubmed]
  10. Competitive recruitment of the periplasmic translocation portal TolB by a natively disordered domain of colicin E9. Loftus, S.R., Walker, D., Maté, M.J., Bonsor, D.A., James, R., Moore, G.R., Kleanthous, C. Proc. Natl. Acad. Sci. U.S.A. (2006) [Pubmed]
  11. Structural origins of the exonuclease resistance of a zwitterionic RNA. Teplova, M., Wallace, S.T., Tereshko, V., Minasov, G., Symons, A.M., Cook, P.D., Manoharan, M., Egli, M. Proc. Natl. Acad. Sci. U.S.A. (1999) [Pubmed]
  12. Escherichia coli nucleoside diphosphate kinase does not act as a uracil-processing DNA repair nuclease. Bennett, S.E., Chen, C.Y., Mosbaugh, D.W. Proc. Natl. Acad. Sci. U.S.A. (2004) [Pubmed]
  13. Single amino acid changes alter the repair specificity of Drosophila Rrp1. Isolation of mutants deficient in repair of oxidative DNA damage. Gu, L., Huang, S.M., Sander, M. J. Biol. Chem. (1994) [Pubmed]
  14. N-hydroxy-4-aminobiphenyl-DNA binding in human p53 gene: sequence preference and the effect of C5 cytosine methylation. Feng, Z., Hu, W., Rom, W.N., Beland, F.A., Tang, M.S. Biochemistry (2002) [Pubmed]
  15. Regulatory roles of spnT, a novel gene located within transposon TnTIR. Wei, J.R., Soo, P.C., Horng, Y.T., Hsieh, S.C., Tsai, Y.H., Swift, S., Withers, H., Williams, P., Lai, H.C. Biochem. Biophys. Res. Commun. (2006) [Pubmed]
  16. A promoter activity in Saccharomyces cerevisiae of the 3'-noncoding region of the basidiomycetous mushroom gene. Yamazaki, T., Yasuda, T., Miyazaki, Y., Okada, K., Kajiwara, S., Shishido, K. J. Gen. Appl. Microbiol. (2002) [Pubmed]
  17. Overexpression of a Rrp1 transgene reduces the somatic mutation and recombination frequency induced by oxidative DNA damage in Drosophila melanogaster. Szakmary, A., Huang, S.M., Chang, D.T., Beachy, P.A., Sander, M. Proc. Natl. Acad. Sci. U.S.A. (1996) [Pubmed]
  18. The nuclease activity of Mre11 is required for meiosis but not for mating type switching, end joining, or telomere maintenance. Moreau, S., Ferguson, J.R., Symington, L.S. Mol. Cell. Biol. (1999) [Pubmed]
  19. Valyl-tRNA synthetase gene of Escherichia coli K12. Molecular genetic characterization. Heck, J.D., Hatfield, G.W. J. Biol. Chem. (1988) [Pubmed]
  20. recA protein binding to the heteroduplex product of DNA strand exchange. Pugh, B.F., Cox, M.M. J. Biol. Chem. (1987) [Pubmed]
  21. Structural features of tRNALys favored by anticodon nuclease as inferred from reactivities of anticodon stem and loop substrate analogs. Jiang, Y., Blanga, S., Amitsur, M., Meidler, R., Krivosheyev, E., Sundaram, M., Bajji, A.C., Davis, D.R., Kaufmann, G. J. Biol. Chem. (2002) [Pubmed]
  22. Mechanism of the chromosomal translocation t(14;18) in lymphoma: detection of a 45-Kd breakpoint binding protein. Jaeger, U., Purtscher, B., Karth, G.D., Knapp, S., Mannhalter, C., Lechner, K. Blood (1993) [Pubmed]
  23. Role of the three consecutive G:C base pairs conserved in the anticodon stem of initiator tRNAs in initiation of protein synthesis in Escherichia coli. Mandal, N., Mangroo, D., Dalluge, J.J., McCloskey, J.A., Rajbhandary, U.L. RNA (1996) [Pubmed]
  24. Protein structure and gene cloning of Syncephalastrum racemosum nuclease. Ho, H.C., Liao, T.H. Biochem. J. (1999) [Pubmed]
  25. Plasmid pRQ7 from the hyperthermophilic bacterium Thermotoga species strain RQ7 replicates by the rolling-circle mechanism. Yu, J.S., Noll, K.M. J. Bacteriol. (1997) [Pubmed]
  26. A recombinant 70K protein ELISA. Screening for antibodies against U1snRNP proteins in human sera. Seelig, H.P., Ehrfeld, H., Schroeter, H., Heim, C., Renz, M. J. Immunol. Methods (1991) [Pubmed]
  27. Contacts between the 5' nuclease of DNA polymerase I and its DNA substrate. Xu, Y., Potapova, O., Leschziner, A.E., Grindley, N.D., Joyce, C.M. J. Biol. Chem. (2001) [Pubmed]
  28. Sequence-dependent S1 nuclease hypersensitivity of a heteronomous DNA duplex. Evans, T., Efstratiadis, A. J. Biol. Chem. (1986) [Pubmed]
  29. Bacteriophage T4-encoded Stp can be replaced as activator of anticodon nuclease by a normal host cell metabolite. Amitsur, M., Benjamin, S., Rosner, R., Chapman-Shimshoni, D., Meidler, R., Blanga, S., Kaufmann, G. Mol. Microbiol. (2003) [Pubmed]
  30. Oligonucleotide directed mutagenesis of Escherichia coli 5S ribosomal RNA: construction of mutant and structural analysis. Göringer, H.U., Wagner, R., Jacob, W.F., Dahlberg, A.E., Zwieb, C. Nucleic Acids Res. (1984) [Pubmed]
  31. Identification of catalytically relevant amino acids of the extracellular Serratia marcescens endonuclease by alignment-guided mutagenesis. Friedhoff, P., Gimadutdinow, O., Pingoud, A. Nucleic Acids Res. (1994) [Pubmed]
  32. Lincomycin increases the half-life of beta-lactamase mRNA. Matsushita, O., Okabe, A., Hayashi, H., Kanemasa, Y. Antimicrob. Agents Chemother. (1989) [Pubmed]
  33. The functional domains of bacteriophage t4 terminase. Kanamaru, S., Kondabagil, K., Rossmann, M.G., Rao, V.B. J. Biol. Chem. (2004) [Pubmed]
  34. Secondary structure model for bacterial 16S ribosomal RNA: phylogenetic, enzymatic and chemical evidence. Woese, C.R., Magrum, L.J., Gupta, R., Siegel, R.B., Stahl, D.A., Kop, J., Crawford, N., Brosius, J., Gutell, R., Hogan, J.J., Noller, H.F. Nucleic Acids Res. (1980) [Pubmed]
  35. Analysis of the in vivo decay of the Escherichia coli dicistronic pyrF-orfF transcript: evidence for multiple degradation pathways. Arraiano, C.M., Cruz, A.A., Kushner, S.R. J. Mol. Biol. (1997) [Pubmed]
  36. Energetics of denaturation and m values of staphylococcal nuclease mutants. Carra, J.H., Privalov, P.L. Biochemistry (1995) [Pubmed]
  37. Circular dichroism and 500-MHz proton magnetic resonance studies of the interaction of Escherichia coli translational initiation factor 3 protein with the 16S ribosomal RNA 3' cloacin fragment. Wickstrom, E., Heus, H.A., Haasnoot, C.A., van Knippenberg, P.H. Biochemistry (1986) [Pubmed]
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