Skip to main content
NCBI home page
Genetics logoLink to Genetics
. 1999 Aug;152(4):1307–1314. doi: 10.1093/genetics/152.4.1307

Molecular analysis of pDL10 from Acidianus ambivalens reveals a family of related plasmids from extremely thermophilic and acidophilic archaea.

A Kletzin 1, A Lieke 1, T Urich 1, R L Charlebois 1, C W Sensen 1
PMCID: PMC1460695  PMID: 10430561

Abstract

The 7598-bp plasmid pDL10 from the extremely thermophilic, acidophilic, and chemolithoautotrophic Archaeon Acidianus ambivalens was sequenced. It contains 10 open reading frames (ORFs) organized in five putative operons. The deduced amino acid sequence of the largest ORF (909 aa) showed similarity to bacterial Rep proteins known from phages and plasmids with rolling-circle (RC) replication. From the comparison of the amino acid sequences, a novel family of RC Rep proteins was defined. The pDL10 Rep protein shared 45-80% identical residues with homologous protein genes encoded by the Sulfolobus islandicus plasmids pRN1 and pRN2. Two DNA regions capable of forming extended stem-loop structures were also conserved in the three plasmids (48-69% sequence identity). In addition, a putative plasmid regulatory protein gene (plrA) was found, which was conserved among the three plasmids and the conjugative Sulfolobus plasmid pNOB8. A homolog of this gene was also found in the chromosome of S. solfataricus. Single-stranded DNA of both pDL10 strands was detected with a mung bean nuclease protection assay using PCR detection of protected fragments, giving additional evidence for an RC mechanism of replication.

Full Text

The Full Text of this article is available as a PDF (305.9 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Aagaard C., Leviev I., Aravalli R. N., Forterre P., Prieur D., Garrett R. A. General vectors for archaeal hyperthermophiles: strategies based on a mobile intron and a plasmid. FEMS Microbiol Rev. 1996 May;18(2-3):93–104. doi: 10.1111/j.1574-6976.1996.tb00229.x. [DOI] [PubMed] [Google Scholar]
  2. Akhmanova A. S., Kagramanova V. K., Mankin A. S. Heterogeneity of small plasmids from halophilic archaea. J Bacteriol. 1993 Feb;175(4):1081–1086. doi: 10.1128/jb.175.4.1081-1086.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Aravalli R. N., Garrett R. A. Shuttle vectors for hyperthermophilic archaea. Extremophiles. 1997 Nov;1(4):183–191. doi: 10.1007/s007920050032. [DOI] [PubMed] [Google Scholar]
  4. Cannio R., Contursi P., Rossi M., Bartolucci S. An autonomously replicating transforming vector for Sulfolobus solfataricus. J Bacteriol. 1998 Jun;180(12):3237–3240. doi: 10.1128/jb.180.12.3237-3240.1998. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Charlebois R. L., She Q., Sprott D. P., Sensen C. W., Garrett R. A. Sulfolobus genome: from genomics to biology. Curr Opin Microbiol. 1998 Oct;1(5):584–588. doi: 10.1016/s1369-5274(98)80093-3. [DOI] [PubMed] [Google Scholar]
  6. Erauso G., Marsin S., Benbouzid-Rollet N., Baucher M. F., Barbeyron T., Zivanovic Y., Prieur D., Forterre P. Sequence of plasmid pGT5 from the archaeon Pyrococcus abyssi: evidence for rolling-circle replication in a hyperthermophile. J Bacteriol. 1996 Jun;178(11):3232–3237. doi: 10.1128/jb.178.11.3232-3237.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Hain J., Reiter W. D., Hüdepohl U., Zillig W. Elements of an archaeal promoter defined by mutational analysis. Nucleic Acids Res. 1992 Oct 25;20(20):5423–5428. doi: 10.1093/nar/20.20.5423. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Ilyina T. V., Koonin E. V. Conserved sequence motifs in the initiator proteins for rolling circle DNA replication encoded by diverse replicons from eubacteria, eucaryotes and archaebacteria. Nucleic Acids Res. 1992 Jul 11;20(13):3279–3285. doi: 10.1093/nar/20.13.3279. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Keeling P. J., Klenk H. P., Singh R. K., Feeley O., Schleper C., Zillig W., Doolittle W. F., Sensen C. W. Complete nucleotide sequence of the Sulfolobus islandicus multicopy plasmid pRN1. Plasmid. 1996 Mar;35(2):141–144. doi: 10.1006/plas.1996.0016. [DOI] [PubMed] [Google Scholar]
  10. Keeling P. J., Klenk H. P., Singh R. K., Schenk M. E., Sensen C. W., Zillig W., Doolittle W. F. Sulfolobus islandicus plasmids pRN1 and pRN2 share distant but common evolutionary ancestry. Extremophiles. 1998 Nov;2(4):391–393. doi: 10.1007/s007920050083. [DOI] [PubMed] [Google Scholar]
  11. Khan S. A. Rolling-circle replication of bacterial plasmids. Microbiol Mol Biol Rev. 1997 Dec;61(4):442–455. doi: 10.1128/mmbr.61.4.442-455.1997. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Kramer M. G., Khan S. A., Espinosa M. Lagging-strand replication from the ssoA origin of plasmid pMV158 in Streptococcus pneumoniae: in vivo and in vitro influences of mutations in two conserved ssoA regions. J Bacteriol. 1998 Jan;180(1):83–89. doi: 10.1128/jb.180.1.83-89.1998. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Marsin S., Forterre P. A rolling circle replication initiator protein with a nucleotidyl-transferase activity encoded by the plasmid pGT5 from the hyperthermophilic archaeon Pyrococcus abyssi. Mol Microbiol. 1998 Mar;27(6):1183–1192. doi: 10.1046/j.1365-2958.1998.00759.x. [DOI] [PubMed] [Google Scholar]
  14. Neumann H., Schwass V., Eckerskorn C., Zillig W. Identification and characterization of the genes encoding three structural proteins of the Thermoproteus tenax virus TTV1. Mol Gen Genet. 1989 May;217(1):105–110. doi: 10.1007/BF00330948. [DOI] [PubMed] [Google Scholar]
  15. Neumann H., Zillig W. Structural variability in the genome of the Thermoproteus tenax virus TTV1. Mol Gen Genet. 1990 Jul;222(2-3):435–437. doi: 10.1007/BF00633851. [DOI] [PubMed] [Google Scholar]
  16. Noll K. M., Vargas M. Recent advances in genetic analyses of hyperthermophilic archaea and bacteria. Arch Microbiol. 1997 Aug;168(2):73–80. doi: 10.1007/s002030050472. [DOI] [PubMed] [Google Scholar]
  17. Rasooly A., Rasooly R. S. How rolling circle plasmids control their copy number. Trends Microbiol. 1997 Nov;5(11):440–446. doi: 10.1016/S0966-842X(97)01143-8. [DOI] [PubMed] [Google Scholar]
  18. Röder R., Pfeifer F. Influence of salt on the transcription of the gas-vesicle genes of Haloferax mediterranei and identification of the endogenous transcriptional activator gene. Microbiology. 1996 Jul;142(Pt 7):1715–1723. doi: 10.1099/13500872-142-7-1715. [DOI] [PubMed] [Google Scholar]
  19. Saraste M., Sibbald P. R., Wittinghofer A. The P-loop--a common motif in ATP- and GTP-binding proteins. Trends Biochem Sci. 1990 Nov;15(11):430–434. doi: 10.1016/0968-0004(90)90281-f. [DOI] [PubMed] [Google Scholar]
  20. Schleper C., Holz I., Janekovic D., Murphy J., Zillig W. A multicopy plasmid of the extremely thermophilic archaeon Sulfolobus effects its transfer to recipients by mating. J Bacteriol. 1995 Aug;177(15):4417–4426. doi: 10.1128/jb.177.15.4417-4426.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Schleper C., Röder R., Singer T., Zillig W. An insertion element of the extremely thermophilic archaeon Sulfolobus solfataricus transposes into the endogenous beta-galactosidase gene. Mol Gen Genet. 1994 Apr;243(1):91–96. doi: 10.1007/BF00283880. [DOI] [PubMed] [Google Scholar]
  22. Sensen C. W., Charlebois R. L., Chow C., Clausen I. G., Curtis B., Doolittle W. F., Duguet M., Erauso G., Gaasterland T., Garrett R. A. Completing the sequence of the Sulfolobus solfataricus P2 genome. Extremophiles. 1998 Aug;2(3):305–312. doi: 10.1007/s007920050073. [DOI] [PubMed] [Google Scholar]
  23. She Q., Phan H., Garrett R. A., Albers S. V., Stedman K. M., Zillig W. Genetic profile of pNOB8 from Sulfolobus: the first conjugative plasmid from an archaeon. Extremophiles. 1998 Nov;2(4):417–425. doi: 10.1007/s007920050087. [DOI] [PubMed] [Google Scholar]
  24. Yu J. S., Noll K. M. Plasmid pRQ7 from the hyperthermophilic bacterium Thermotoga species strain RQ7 replicates by the rolling-circle mechanism. J Bacteriol. 1997 Nov;179(22):7161–7164. doi: 10.1128/jb.179.22.7161-7164.1997. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Zillig W., Arnold H. P., Holz I., Prangishvili D., Schweier A., Stedman K., She Q., Phan H., Garrett R., Kristjansson J. K. Genetic elements in the extremely thermophilic archaeon Sulfolobus. Extremophiles. 1998 Aug;2(3):131–140. doi: 10.1007/s007920050052. [DOI] [PubMed] [Google Scholar]
  26. Zillig W., Prangishvilli D., Schleper C., Elferink M., Holz I., Albers S., Janekovic D., Götz D. Viruses, plasmids and other genetic elements of thermophilic and hyperthermophilic Archaea. FEMS Microbiol Rev. 1996 May;18(2-3):225–236. doi: 10.1111/j.1574-6976.1996.tb00239.x. [DOI] [PubMed] [Google Scholar]
  27. Zillig W., Prangishvilli D., Schleper C., Elferink M., Holz I., Albers S., Janekovic D., Götz D. Viruses, plasmids and other genetic elements of thermophilic and hyperthermophilic Archaea. FEMS Microbiol Rev. 1996 May;18(2-3):225–236. doi: 10.1111/j.1574-6976.1996.tb00239.x. [DOI] [PubMed] [Google Scholar]
  28. Zillig W., Yeats S., Holz I., Böck A., Gropp F., Rettenberger M., Lutz S. Plasmid-related anaerobic autotrophy of the novel archaebacterium Sulfolobus ambivalens. 1985 Feb 28-Mar 6Nature. 313(6005):789–791. doi: 10.1038/313789a0. [DOI] [PubMed] [Google Scholar]

Articles from Genetics are provided here courtesy of Oxford University Press

RESOURCES