1887

Abstract

AR39 contains two different ORFs ( and ) encoding ribonuclease H (RNase H) homologues, Cpn-RNase HII and Cpn-RNase HIII. Sequence alignments show that the two homologues both contain the conserved motifs of type 2 RNase H, and Cpn-RNase HII has the conserved active-site motif (DEDD) of RNase HII. Cpn-RNase HIII also contains a unique active-site motif (DEDE), common to other RNase HIIIs. Complementation assays indicated that Cpn-RNase HII can complement both RNase HII and RNase HI, but Cpn-RNase HIII can only complement the latter. enzyme activity experiments showed that neither Cpn-RNase HII nor Cpn-RNase HIII is thermostable and their optimum pH values were 9.0 and 10.0, respectively. Cpn-RNase HII cleaves a 12 bp RNA–DNA substrate at multiple sites, but Cpn-RNase HIII at only one site. When a 35 bp DNA–RNA–DNA/DNA chimeric substrate was used, cleavage was only observed with Cpn-RNase HII. These results indicate that the RNase H combination of AR39 is not simple substitution of RNase H, perhaps representing a more primordial type. This is believed to be the first functional study of RNase Hs and the results should cntribute to the analysis of RNase Hs of other parasite species.

Loading

Article metrics loading...

/content/journal/micro/10.1099/mic.0.2006/003434-0
2007-03-01
2020-07-04
Loading full text...

Full text loading...

/deliver/fulltext/micro/153/3/787.html?itemId=/content/journal/micro/10.1099/mic.0.2006/003434-0&mimeType=html&fmt=ahah

References

  1. Ariyoshi M., Vassylyev D. G., Iwasaki H., Nakamura H., Shinagawa H., Morikawa K.. 1994; Atomic structure of the RuvC resolvase: a Holliday junction-specific endonuclease from E. coli . Cell78:1063–1072[CrossRef]
    [Google Scholar]
  2. Arudchandran A., Cerritelli S., Narimatsu S., Itaya M., Shin D. Y., Shimada Y., Crouch R. J.. 2000; The absence of ribonuclease H1 or H2 alters the sensitivity of Saccharomyces cerevisiae to hydroxyurea, caffeine and ethyl methanesulphonate: implications for roles of RNases H in DNA replication and repair. Genes Cells5:789–802[CrossRef]
    [Google Scholar]
  3. Birnboim H. C., Doly J.. 1979; A rapid alkaline extraction procedure for screening recombinant plasmid DNA. Nucleic Acids Res7:1513–1523[CrossRef]
    [Google Scholar]
  4. Blaszczyk J., Tropea J. E., Bubunenko M., Routzahn K. M., Waugh D. S., Court D. L., Ji X.. 2001; Crystallographic and modeling studies of RNase III suggest a mechanism for double-stranded RNA cleavage. Structure9:1225–1236[CrossRef]
    [Google Scholar]
  5. Broccoli S., Rallu F., Sanscartier P., Cerritelli S. M., Crouch R. T., Drolet M.. 2004; Effects of RNA polymerase modifications on transcription-induced negative supercoiling and associated R-loop formation. Mol Microbiol52:1769–1779[CrossRef]
    [Google Scholar]
  6. Chon H., Nakano R., Ohtani N., Haruki M., Takano K., Morikawa M., Kanaya S.. 2004; Gene cloning and biochemical characterizations of a thermostable ribonuclease HIII from Bacillus stearothermophilus . Biosci Biotechnol Biochem68:2138–2147[CrossRef]
    [Google Scholar]
  7. Chon H., Matsumura H., Koga Y., Takano K., Kanaya S.. 2006a; Crystal structure and structure-based mutational analyses of RNase HIII from Bacillus stearothermophilus : a new type 2 RNase H with TBP-like substrate-binding domain at the N terminus. J Mol Biol356:165–178[CrossRef]
    [Google Scholar]
  8. Chon H., Tadokoro T., Ohtani N., Koga Y., Takano K., Kanaya S.. 2006b; Identification of RNase HII from psychrotrophic bacterium, Shewanella sp. SIB1 as a high-activity type RNase H. FEBS J273:2264–2275[CrossRef]
    [Google Scholar]
  9. Deckert G., Warren P. V., Gaasterland T., Young W. G., Lenox A. L., Graham D. E., Overbeek R., Snead M. A., Keller M.. other authors 1998; The complete genome of the hyperthermophilic bacterium Aquifex aeolicus . Nature392:353–358[CrossRef]
    [Google Scholar]
  10. Hahn D. L., Azenabor A. A., Beatty W. L., Burne G. I.. 2002; Chlamydia pneumoniae as a respiratory pathogen. Front Biosci7:e66–e76[CrossRef]
    [Google Scholar]
  11. Katayanagi K., Miyagawa M., Matsushima M., Ishikawa M., Kanaya S., Ikehara M., Matsuzaki T., Morikawa K.. 1990; Three-dimensional structure of ribonuclease H from E. coli . Nature347:306–309[CrossRef]
    [Google Scholar]
  12. Kogoma T., Foster P. L.. 1998; Physiological functions of E. coli RNase HI. In Ribonucleases H pp39–66 Edited by Crouch R. J.. Toulme J. J.. Paris: INSERM;
    [Google Scholar]
  13. Kostrewa D., Winkler F. K.. 1995; Mg2+ binding to the active site of Eco RV endonuclease: a crystallographic study of complexes with substrate and product DNA at 2 Å resolution. Biochemistry34:683–696[CrossRef]
    [Google Scholar]
  14. Lai L., Yokota H., Hung L. W., Kim R., Kim S. H.. 2000; Crystal structure of archaeal RNase HII: a homologue of human major RNase H. Structure8:897–904[CrossRef]
    [Google Scholar]
  15. Maignan S., Guilloteau J. P., Zhou-Liu Q., Clement-Mella C., Mikol V.. 1998; Crystal structures of the catalytic domain of HIV-1 integrase free and complexed with its metal cofactor: high level of similarity of the active site with other viral integrases. J Mol Biol282:359–368[CrossRef]
    [Google Scholar]
  16. Misra S., Bennett J., Friew Y. N., Abdulghani J., Irvin-Wilson C. V., Tripathi M. K., Williams S., Chaudhuri M., Chaudhuri G.. 2005; A type II ribonuclease H from Leishmania mitochondria: an enzyme essential for the growth of the parasite. Mol Biochem Parasitol143:135–145[CrossRef]
    [Google Scholar]
  17. Mol C. D., Kuo C. F., Thayer M. M., Cunningham R. P., Tainer J. A.. 1995; Structure and function of the multifunctional DNA-repair enzyme exonuclease III. Nature374:381–386[CrossRef]
    [Google Scholar]
  18. Muroya A., Tsuchiya D., Ishikawa M., Haruki M., Morikawa M., Kanaya S., Morikawa K.. 2001; Catalytic center of an archaeal type 2 ribonuclease H as revealed by X-ray crystallographic and mutational analyses. Protein Sci10:707–714[CrossRef]
    [Google Scholar]
  19. Nishino T., Komori K., Ishino Y., Morikawa K.. 2003; X-ray and biochemical anatomy of an archaeal XPF/Rad1/Mus81 family nuclease: similarity between its endonuclease domain and restriction enzymes. Structure11:445–457[CrossRef]
    [Google Scholar]
  20. Ohtani N., Haruki M., Morikawa M., Kanaya S.. 1999a; Molecular diversities of RNase H. J Biosci Bioeng88:12–19[CrossRef]
    [Google Scholar]
  21. Ohtani N., Haruki M., Morikawa M., Crouch R. J., Itaya M., Kanaya S.. 1999b; Identification of the genes encoding Mn2+-dependent RNase HII and Mg2+-dependent RNase HIII from Bacillus subtilis : classification of RNases H into three families. Biochemistry38:605–618[CrossRef]
    [Google Scholar]
  22. Pei D., Liu J., Liu X., Li S.. 2005; Expression of both Chlamydia pneumoniae RNase HIIs in Escherichia coli . Protein Expr Purif40:101–106[CrossRef]
    [Google Scholar]
  23. Read D., Brunham R. C., Shen C., Gill S. R., Heidelberg J. F., White O., Hickey E. K., Peterson J., Utterback T.. other authors 2000; Genome sequences of Chlamydia trachomatis MoPn and Chlamydia pneumoniae AR 39. Nucleic Acids Res28:1397–1406[CrossRef]
    [Google Scholar]
  24. Rice P., Mizuuchi K.. 1995; Structure of the bacteriophage Mu transposase core: a common structural motif for DNA transposition and retroviral integration. Cell82:209–220[CrossRef]
    [Google Scholar]
  25. Tsutakawa S. E., Jingami H., Morikawa K.. 1999; Recognition of a TG mismatch: the crystal structure of very short patch repair endonuclease in complex with a DNA duplex. Cell99:615–623[CrossRef]
    [Google Scholar]
  26. Yang W., Hendrickson W. A., Crouch R. J., Satow Y.. 1990; Structure of ribonuclease H phased at 2 Å resolution by MAD analysis of the selenomethionyl protein. Science249:1398–1405[CrossRef]
    [Google Scholar]
  27. Yu D., Ellis H. M., Lee E. C., Jenkins N. A., Copeland N. G., Court D. L.. 2000; An efficient recombination system for chromosome engineering in Escherichia coli . Proc Natl Acad Sci U S A97:5978–5983[CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/mic.0.2006/003434-0
Loading
/content/journal/micro/10.1099/mic.0.2006/003434-0
Loading

Data & Media loading...

Most cited this month Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error