Genetic profile of pNOB8 from Sulfolobus: The first conjugative plasmid from an archaeon

Extremophiles

Volumn 2, Issue 4, 1998, Pages 417-425

  She, Qunxin ^a   Phan, Hien ^a   Garrett, Roger A ^a   Albers, Sonja Verena ^b   Stedman, Kenneth M ^b   Zillig, Wolfram ^b  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

^b MAX PLANCK INSTITUTE OF BIOCHEMISTRY   (Germany)

Author keywords

Archaeon; Conjugation; PNOB8; Sulfolobus; Thermophile

Indexed keywords

GENETIC ANALYSIS; PLASMID;

AMINO ACID SEQUENCE; BASE SEQUENCE; CONJUGATION, GENETIC; DNA TRANSPOSABLE ELEMENTS; DNA, ARCHAEAL; GENE DELETION; MOLECULAR SEQUENCE DATA; OPEN READING FRAMES; PLASMIDS; SEQUENCE HOMOLOGY, AMINO ACID; SULFOLOBUS; VARIATION (GENETICS);

ARCHAEA; BACTERIA (MICROORGANISMS); SULFOLOBUS; SULFOLOBUS SOLFATARICUS; UNIDENTIFIED BACTERIOPHAGE;

EID: 0032213855     PISSN: 14310651     EISSN: None     Source Type: Journal    
DOI: 10.1007/s007920050087     Document Type: Article

References (42)

1. Aboles AL, Friedman SA, Austin SJ (1985) Partition of unit-copy miniplasmids to daughter cells. III. The DNA sequence and functional organization of the P1 partition region. J Mol Biol 185:261-272
2. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman, DJ (1997) Gapped BLAST and PSI-BLAST:a new generation of protein database search programs. Nucleic Acids Res 25:3389-3402
3. Borodovsky M, McIninch J (1993) GeneMark: parallel gene recognition for both DNA strands, Comput Chem 17:123-133
4. Bairoch A (1993) The PROSITE dictionary of sites and patterns in proteins, its current status. Nucleic Acids Res 21:3097-3103
5. Bull CJ, White O, Olsen GJ, Zhou L, Fleischmann RD, Sutton GG. Blake JA, FitzGerald LM, Clayton RA, Gocayne JD, Kerlavage AR, Dougherty BA. Tomb JF, Adams MD, Reich CI, Overbeek R, Kirkness EF, Weinstock KG, Merrick JM, Glodek A, Scott JL. Geoghagen NSM, Venter JC (1996) Complete genome sequence of the methanogenic archaeon. Methanococcus jannaschii. Science 273:1058-1073
6. Burland V, Plunkett G III. Sofia HJ. Daniels DL, Blattner FR (1995) Analysis of the Escherichia colt genome VI: DNA sequence of the region from 92.8 throuah 100 minutes. Nucleic Acids Res 23:21052119
7. Censini S. Lange C, Xiang Z, Crabtree JE, Ghiara P, Borodovsky M, Rappuoli R, Covacci A (1996) Cag, a pathogenicity island of Helicobacter pytori, encodes type I-specific and disease-associated virulence factors. Proc Natl Acad Sci USA 93:14648-14653
8. Clinton M, Frangou-Lazaridis M, Panneerselvam C, Horecker BL (1989) The sequence of human parathymosin deduced from a cloned human kidney cDNA. Biochem Biophys Res Commun 158:855-862
9. Eckner R, Birnstiel ML (1989) Cloning of cDNAs coding for human HMG I and HMG Y proteins: both are capable of binding to the octamer sequence motif. Nucleic Acids Res 17:5947-5959
10. Hanai R, Liu R, Benedetti P, Caron PR, Lynch AS, Wang JC (1996) Molecular dissection of a protein SopB essential for Escherichia coli F plasmid partition. J Biol Chem 271:17469-17475
11. Henikoff S, Henikoff JG (1994) Protein family classification based on searching a database of blocks. Genomics 19:97-107
12. Herman ND. Schneider TD (1992) High information conservation implies that at least three proteins bind independently to F plasmid incD repeats. Bacteriol 174:3558-3560
13. Keeling P, Klenk H-P. Singh RK, Feeley O, Schleper C, Zillig W, Doolittle WF, Sensen C (1996) Complete nucleotide sequence of the Sulfolobus islandicus multicopy plasmid pRN1. Plasmid 35:141144
14. Kuldau GA, De Vos G, Owen J, McCaffrcy G, Zambryski P (1990) The virB operon of Agrobacterium tumefaciens pTiC58 encodes 11 open reading frames. Mol Gen Genet 221:256-266
15. Lessl M, Balzer D, Pansegrau W, Lanka E (1992a) Sequence similarities bmveen the RP4 Tra2 and the Ti VirB region strongly support the conjugation model for T-DNA transfer. J Biol Chem 267:2047120480
16. Lessl M, Pansegrau W, Lanka E (1992h) Relationship of DNA-transfer systems: essential transfer factors of plasmids RP4. Ti and F share common sequences. Nucleic Acids Res 20:6099-6100
17. Lin Z, Mallavia LP (1995) The partition region of plasmid QpH1 is a member of a family of two trans-acting factors as implied by sequence analysis. Gene 160:69-74
18. Lipsick JS (1996) One billion years of Myb. Oncogene 13:223-235
19. Llosa M, Bolland S, de la Cruz F (1994) Genetic organization of the conjugal DNA processing region of the IncW plasmid R3S8. J Mol Biol 235:448-446
20. Marck C (1988) "DNA Strider": a "C" program for the fast analysis of DNA and protein sequences on the Apple Macintosh family of Computers. Nucleic Acids Res 16:1829-1836
21. Mohl DA, Gober JW (1997) Cell cycle-dependent polar localization of chromosome partitioning proteins in Caulobacter crescentus. Cell 88:675-684
22. Mori H, Kondo A, Ohshima A, Ogura T, Hiraga S (1986) Structure and function of the F plasmid genes essential for partitioning. J Mol Biol 192:1-15
23. Motallebi-Veshareh M, Roueh DA, Thomas CM (1990) A family of ATPases involved in active partitioning of diverse bacterial plasmids, Mol Microbiol 4:1455-1463
24. Nunez B, Avila P, de la Cruz F (1997) Genes involved in conjugative DNA processing of plasmid R6K. Mol Microbiol 24:1157-1168
25. Ogasawara N, Yoshikawa H (1992) Genes and their organization in the replication origin region of the bacterial chromosome. Mol Microbiol 6:629-634
26. Pansegrau W, Lanka E (1996) Enzymology of DNA transfer by conjugative mechanisms. Prog Nucleic Acids Res Mol Biol 54:197-251
27. Pearson WR, Lipman DJ (1988) Improved tools for biological sequence comparison. Proc Natl Acad Sci USA 85:2444-2448
28. Pohlman RF, Genetti HD, Winans SC (1994) Common ancestry between IncN conjugal transfer genes and macromolecular export systems of plant and animal pathogens. Mol Microbiol 14:655668
29. Prangishvili D, Albers S, Holz I, Stedman K, Arnold HP, Klein T, Singh H, Hiort J, Schweier A, Kristjansson JU, Zillig W (1998) A family of conjugative plasmids from strains of the archaeon Sulfolobus islandicus. Plasmid, in press
30. Rogowsky PM, Powell BS, Shirasu K, Lin TS, Morel P, Zyprian EM, Steck TR, Kado CI (1990) Molecular characterization of the vir regulon of Agrobacterium tumefaciens: complete nucleotide sequence and gene organization of the 28.63-kbp regulon cloned as a single unit. Plasmid 23:85-106
31. Rost B, Casadio R, Fariselli P, Sander C (1995) Prediction of helical transmembrane segments at 95% accuracy. Protein Sci 4:521-533
32. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual, 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
33. Sander C, Schneider R (1991) Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins 9:56-68
34. Schleper CI, Holz: I, Janekovic D, Murphy J, Zillig W (1995) A multicopy plasmid of the extremely thermophilic archaeon Sulfolobus effects its transfer to recipients by mating. J Bacteriol 177:4417-4426
35. Sensen CW, Klenk HP, Singh RK, Allard G, Chan CC, Liu QY, Penny SL, Young F, Schenk ME, Gaasterland T, Doolittle WF, Ragan MA, Charlebois RL (1996) Organizational characteristics and information content of an archaeal genome: 156kb of sequence from Sulfolobus solfataricus P2. Mol Microbiol 22:175-191
36. Smith CP, Chater KF (1988) Structure and regulation of controlling sequences for the Streptomyces coelicolor glycerol operon. J Mol Biol 204:569-580
37. Solia HJ, Burland V, Daniels DL, Plunkett G III, Blattner FR (1994) Analysis of the Escherichia coli genome. V. DNA sequence of the region from 76.0 to 81.5 minutes. Nucleic Acids Res 22:2576-2586
38. Sunnarborg A, Klumpp D, Chung T, LaPorte DC (1990) Regulation of the glyoxylate bypass operon: cloning and characterization of iclR. J Bacteriol 172:2642-2649
39. Tabata S, Hooykaas PJ, Oka A (1989) Sequence determination and characterization of the replicator region in the tumor-inducing plasmid pTiB6S3. J Bacteriol 171:1665-1672
40. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673-4680
41. Weaver KE, Clewell DB, An F (1993) Identification, characterization, and nucleotide sequence of a region of Enterococcus faecalis pheromone-responsive plasmid pAD1 capable of autonomous replication. J Bacteriol 175:1900-1909
42. Zillig W, Prangishvilli D, Schleper C, Elferink M, Holz I, Albers S. Janekovic D. Golz D (1996) Viruses, plasmids and other genetic elements of thermophilic and hyperthermophilic Archaea. FEMS Microbiol Rev 18:225-236