A novel Sulfolobus non-conjugative extrachromosomal genetic element capable of integration into the host genome and spreading in the presence of a fusellovirus

Virology

Volumn 363, Issue 1, 2007, Pages 124-133

  Wang, Ying ^a   Duan, Zhenhong ^a   Zhu, Haojun ^b   Guo, Xin ^a   Wang, Ziyi ^a   Zhou, Ju ^a   She, Qunxin ^b   Huang, Li ^a  

^a INSTITUTE OF MICROBIOLOGY   (China)

^b UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

Archaea; Integration; pSSVi; pSSVi SSV1 SSV2 interaction; Satellite virus; Sulfolobus

Indexed keywords

DNA PRIMASE; DOUBLE STRANDED DNA; EXTRACHROMOSOMAL DNA; INTEGRASE; INTEGRATION HOST FACTOR; REPLICATION PROTEIN A; TRANSFER RNA;

ANIMAL CELL; ARTICLE; BACTERIOPHAGE; CATALYSIS; CONTROLLED STUDY; COPG GENE; GENE; GENOME ANALYSIS; HORIZONTAL GENE TRANSFER; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PLASMID; PLRA GENE; PRIORITY JOURNAL; SULFOLOBUS SOLFATARICUS; VIRUS PURIFICATION; VIRUS STRAIN;

AMINO ACID SEQUENCE; ATTACHMENT SITES, MICROBIOLOGICAL; BASE SEQUENCE; CATALYTIC DOMAIN; FUSELLOVIRIDAE; GENE TRANSFER, HORIZONTAL; INTEGRASES; MOLECULAR SEQUENCE DATA; OPEN READING FRAMES; RECOMBINATION, GENETIC; SEQUENCE ALIGNMENT; SULFOLOBUS SOLFATARICUS;

FUSELLOVIRUS; SATELLITE VIRUSES; SUGARCANE STREAK VIRUS; SULFOLOBUS; SULFOLOBUS SOLFATARICUS;

EID: 34247565507     PISSN: 00426822     EISSN: 10960341     Source Type: Journal    
DOI: 10.1016/j.virol.2007.01.035     Document Type: Article

References (35)

1. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., and Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25 17 (1997) 3389-3402
2. Argos P., Landy A., Abremski K., Egan J.B., Haggard-Ljungquist E., Hoess R.H., Kahn M.L., Kalionis B., Narayana S.V., Pierson III L.S., et al. The integrase family of site-specific recombinases: regional similarities and global diversity. EMBO J. 5 2 (1986) 433-440
3. Arnold H.P., She Q., Phan H., Stedman K., Prangishvili D., Holz I., Kristjansson J.K., Garrett R., and Zillig W. The genetic element pSSVx of the extremely thermophilic crenarchaeon Sulfolobus is a hybrid between a plasmid and a virus. Mol. Microbiol. 34 2 (1999) 217-226
4. Bell S.D., and Jackson S.P. Mechanism and regulation of transcription in archaea. Curr. Opin. Microbiol. 4 2 (2001) 208-213
5. Birnboim H.C., and Doly J. A rapid alkaline extraction procedure for screening recombinant plasmid DNA. Nucleic Acids Res. 7 6 (1979) 1513-1523
6. Borodovsky M., and McIninch J. GeneMark: parallel gene recognition for both DNA strands. Comput. Chem. 17 (1993) 123-133
7. Contursi P., Jensen S., Aucelli T., Rossi M., Bartolucci S., and She Q. Characterization of the Sulfolobus host-SSV2 virus interaction. Extremophiles 10 6 (2006) 615-627
8. Erauso G., Stedman K.M., van de Werken H.J., Zillig W., and van der Oost J. Two novel conjugative plasmids from a single strain of Sulfolobus. Microbiology 152 Pt. 7 (2006) 1951-1968
9. Greve B., Jensen S., Brugger K., Zillig W., and Garrett R.A. Genomic comparison of archaeal conjugative plasmids from Sulfolobus. Archaea 1 4 (2004) 231-239
10. Greve B., Jensen S., Phan H., Brugger K., Zillig W., She Q., and Garrett R.A. Novel RepA-MCM proteins encoded in plasmids pTAU4, pORA1 and pTIK4 from Sulfolobus neozealandicus. Archaea 1 5 (2005) 319-325
11. Kawarabayasi, Y., Hino, Y., Horikawa, H., Yamazaki, S., Haikawa, Y., Jin-no, K., Takahashi, M., Sekine, M., Baba, S., Ankai, A., Kosugi, H., Hosoyama, A., Fukui, S., Nagai, Y., Nishijima, K., Nakazawa, H., Takamiya, M., Masuda, S., Funahashi, T., Tanaka, T., Kudoh, Y., Yamazaki, J., Kushida, N., Oguchi, A., Kikuchi, H., et al., 1999. Complete genome sequence of an aerobic hyper-thermophilic crenarchaeon, Aeropyrum pernix K1. DNA Res 6 (2), 83-101, 145-152.
12. Kawarabayasi Y., Hino Y., Horikawa H., Jin-no K., Takahashi M., Sekine M., Baba S., Ankai A., Kosugi H., Hosoyama A., Fukui S., Nagai Y., Nishijima K., Otsuka R., Nakazawa H., Takamiya M., Kato Y., Yoshizawa T., Tanaka T., Kudoh Y., Yamazaki J., Kushida N., Oguchi A., Aoki K., Masuda S., Yanagii M., Nishimura M., Yamagishi A., Oshima T., and Kikuchi H. Complete genome sequence of an aerobic thermoacidophilic crenarchaeon, Sulfolobus tokodaii strain7. DNA Res. 8 4 (2001) 123-140
13. Keeling P.J., Klenk H.P., Singh R.K., Feeley O., Schleper C., Zillig W., Doolittle W.F., and Sensen C.W. Complete nucleotide sequence of the Sulfolobus islandicus multicopy plasmid pRN1. Plasmid 35 2 (1996) 141-144
14. Kletzin A., Lieke A., Urich T., Charlebois R.L., and Sensen C.W. Molecular analysis of pDL10 from Acidianus ambivalens reveals a family of related plasmids from extremely thermophilic and acidophilic archaea. Genetics 152 4 (1999) 1307-1314
15. Lipps G., Ibanez P., Stroessenreuther T., Hekimian K., and Krauss G. The protein ORF80 from the acidophilic and thermophilic archaeon Sulfolobus islandicus binds highly site-specifically to double-stranded DNA and represents a novel type of basic leucine zipper protein. Nucleic Acids Res. 29 24 (2001) 4973-4982
16. Lipps G., Stegert M., and Krauss G. Thermostable and site-specific DNA binding of the gene product ORF56 from the Sulfolobus islandicus plasmid pRN1, a putative archaeal plasmid copy control protein. Nucleic Acids Res. 29 4 (2001) 904-913
17. Lipps G., Rother S., Hart C., and Krauss G. A novel type of replicative enzyme harbouring ATPase, primase and DNA polymerase activity. EMBO J. 22 10 (2003) 2516-2525
18. Lipps G., Weinzierl A.O., von Scheven G., Buchen C., and Cramer P. Structure of a bifunctional DNA primase-polymerase. Nat. Struct. Mol. Biol. 11 2 (2004) 157-162
19. Makino S., Amano N., Koike H., and Suzuki M. Prophages inserted in archaebacterial genomes. Proc. Jpn. Acad. Ser. B 75 (1999) 166-171
20. Peng X., Holz I., Zillig W., Garrett R.A., and She Q. Evolution of the family of pRN plasmids and their integrase-mediated insertion into the chromosome of the crenarchaeon Sulfolobus solfataricus. J. Mol. Biol. 303 4 (2000) 449-454
21. Prato S., Cannio R., Klenk H.P., Contursi P., Rossi M., and Bartolucci S. pIT3, a cryptic plasmid isolated from the hyperthermophilic crenarchaeon Sulfolobus solfataricus IT3. Plasmid 56 1 (2006) 35-45
22. Reiter W.D., Palm P., and Zillig W. Analysis of transcription in the archaebacterium Sulfolobus indicates that archaebacterial promoters are homologous to eukaryotic pol II promoters. Nucleic Acids Res. 16 1 (1988) 1-19
23. Sambrook J., Fritsch E.F., and Maniatis T. Molecular cloning: a laboratory manual. 2nd ed. (1989), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
24. Schleper C., Kubo K., and Zillig W. The particle SSV1 from the extremely thermophilic archaeon Sulfolobus is a virus: demonstration of infectivity and of transfection with viral, DNA. Proc. Natl. Acad. Sci. U. S. A. 89 16 (1992) 7645-7649
25. Schleper C., Holz I., Janekovic D., Murphy J., and Zillig W. A multicopy plasmid of the extremely thermophilic archaeon Sulfolobus effects its transfer to recipients by mating. J. Bacteriol. 177 15 (1995) 4417-4426
26. Serre M.C., Letzelter C., Garel J.R., and Duguet M. Cleavage properties of an archaeal site-specific recombinase, the SSV1 integrase. J. Biol. Chem. 277 19 (2002) 16758-16767
27. She Q., Phan H., Garrett R.A., Albers S.V., Stedman K.M., and Zillig W. Genetic profile of pNOB8 from Sulfolobus: the first conjugative plasmid from an archaeon. Extremophiles 2 4 (1998) 417-425
28. She Q., Peng X., Zillig W., and Garrett R.A. Gene capture in archaeal chromosomes. Nature 409 6819 (2001) 478
29. She Q., Singh R.K., Confalonieri F., Zivanovic Y., Allard G., Awayez M.J., Chan-Weiher C.C., Clausen I.G., Curtis B.A., De Moors A., Erauso G., Fletcher C., Gordon P.M., Heikamp-de Jong I., Jeffries A.C., Kozera C.J., Medina N., Peng X., Thi-Ngoc H.P., Redder P., Schenk M.E., Theriault C., Tolstrup N., Charlebois R.L., Doolittle W.F., Duguet M., Gaasterland T., Garrett R.A., Ragan M.A., Sensen C.W., and Van der Oost J. The complete genome of the crenarchaeon Sulfolobus solfataricus P2. Proc. Natl. Acad. Sci. U. S. A. 98 14 (2001) 7835-7840
30. She Q., Brugger K., and Chen L. Archaeal integrative genetic elements and their impact on genome evolution. Res. Microbiol. 153 6 (2002) 325-332
31. She Q., Shen B., and Chen L. Archaeal integrases and mechanisms of gene capture. Biochem. Soc. Trans. 32 Pt. 2 (2004) 222-226
32. Stedman K.M., She Q., Phan H., Holz I., Singh H., Prangishvili D., Garrett R., and Zillig W. pING family of conjugative plasmids from the extremely thermophilic archaeon Sulfolobus islandicus: insights into recombination and conjugation in Crenarchaeota. J. Bacteriol. 182 24 (2000) 7014-7020
33. Tolstrup N., Sensen C.W., Garrett R.A., and Clausen I.G. Two different and highly organized mechanisms of translation initiation in the archaeon Sulfolobus solfataricus. Extremophiles 4 3 (2000) 175-179
34. Xiang X., Chen L., Huang X., Luo Y., She Q., and Huang L. Sulfolobus tengchongensis spindle-shaped virus STSV1: virus-host interactions and genomic features. J. Virol. 79 14 (2005) 8677-8686
35. Zillig W., Kletzin A., Schleper C., Holz I., Janekovic D., Hain J., Lanzendorfer M., and Kristjansson J.K. Screening for Sulfolobales, their plasmids and their viruses in Icelandic solfataras. Syst. Appl. Microbiol. 16 (1994) 609-628