Complete nucleotide sequence of the 27-kilobase virulence related locus (vrl) of Dichelobacter nodosus: Evidence for extrachromosomal origin

Infection and Immunity

Volumn 67, Issue 3, 1999, Pages 1277-1286

  Billington, Stephen J ^a,b   Huggins, Andrea S ^a   Johanesen, Priscilla A ^a   Crellin, Paul K ^a,c   Cheung, Jackie K ^a   Katz, Margaret E ^a,d   Wright, Catherine L ^a,e   Haring, Volker ^a,f   Rood, Julian I ^a  

^a MONASH UNIVERSITY   (Australia)

^b UNIVERSITY OF ARIZONA   (United States)

^c UNIVERSITY OF OXFORD   (United Kingdom)

^d UNIVERSITY OF NEW ENGLAND   (Australia)

^e VIC INSTITUTE OF ANIMAL SCIENCE   (Australia)

^f CSIRO   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL VIRULENCE; DICHELOBACTER NODOSUS; ESCHERICHIA COLI; GENE DELETION; GENE EXPRESSION; GENE LOCUS; IMMUNOBLOTTING; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PRIORITY JOURNAL; PROTEIN ANALYSIS; SEQUENCE ANALYSIS;

DICHELOBACTER NODOSUS;

EID: 0032976364     PISSN: 00199567     EISSN: None     Source Type: Journal    
DOI: 10.1128/iai.67.3.1277-1286.1999     Document Type: Article

References (50)

1. Alonso, J. C., G. Lüder, A. C. Stiege, S. Chai, F. Weise, and T. A. Trautner. 1997. The complete nucleotide sequence and functional organization of Bacillus subtilis bacteriophage SPP1. Gene 204:201-212.
2. Altschul, S. F., T. L. Madden, A. A. Schäffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
3. Bedford, D. J., C. Laity, and M. J. Buttner. 1995. Two genes involved in the phase-variable φC31 resistance mechanism of Streptomyces coelicolor A3(2). J. Bacteriol. 177:4681-4689.
4. Billington, S. J., and J. I. Rood. Unpublished data.
5. Billington, S. J., J. L. Johnston, and J. I. Rood. 1996. Virulence regions and virulence factors of the ovine footrot pathogen. Dichelobacter nodosus. FEMS Microbiol. Lett. 145:147-156.
6. Billington, S. J., M. Sinistaj, B. F. Cheetham, A. Ayres, E. K. Moses, M. E. Katz, and J. I. Rood. 1996. Identification of a native Dichelobacter nodosus plasmid and implications for the evolution nf the vap regions. Gene 172: 111-116.
7. Blaak, H., J. Schnellmann, S. Walter, B. Henrissat, and H. Schrempf. 1993. Characteristics of an exochitinase from Streptomyces olivaceoviridis, its corresponding gene, putative protein domains and relationship to other chitinases. Eur. J. Biochem. 214:659-669.
8. Bloomfield, G. A., G. Whittle, M. B. McDonaugh, M. E. Katz, and B. F. Cheetham. 1997. Analysis of sequences flanking the vap regions of Dichelobacter nodosus: evidence for multiple integration events and a new genetic element. Microbiology 143:553-562.
9. Bork, P., and E. V. Koonin. 1993. An expanding family of helicases within the "DEAD/H" superfamily. Nucleic Acids Res. 21:751-752.
10. Cabot, E. L., and A. T. Beckenbeck. 1989. Simultaneous editing of multiple nucleic acid and protein sequences with ESEE. Comput. Appl. Biosci. 5:233-234.
11. Chandrasegaran, S., K. D. Lunnen, H. O. Smith, and G. G. Wilson. 1988. Cloning and sequencing the HinfI restriction and modification genes. Gene 70:387-392.
12. Cheetham, B. F., D. R. Tattersall, G. A. Bloomfield, J. I. Rood, and M. E. Katz. 1995. Identification of a bacteriophage-related integrase gene in a vap region of the genome of D. nodosus. Gene 162:53-58.
13. de la Campa, A. G., P. Kale, S. S. Sprinhorn, and S. A. Lacks. 1987. Proteins encoded by the DpnII restriction gene cassette. Two methylases and an endonuclease. J. Mol. Biol. 196:457-469.
14. Dutka-Malen, S., P. Mazodier, and B. Badet. 1988. Molecular cloning and overexpression of the glucosamine synthetase gene from Escherichia coli. Biochimie 70:287-290.
15. Fleishmann, R. D., M. D. Adams, O. White, R. A. Clayton, E. F. Kirkness, A. R. Kerlavage, C. J. Bult, J.-F. Tomb, B. A. Dougherty, J. M. Merrick, K. McKenney, G. Sutton, W. FitzHugh, C. Fields, J. C. Gocayne, J. Scott, R. Shirley, L.-L. Liu, A. Glodek, J. M. Kelley, J. F. Weidman, C. A. Phillips, T. Spriggs, E. Hedblom, M. D. Cotton, T. R. Utterback, M. C. Hanna, D. T. Hguyen, D. M. Saudek, R. C. Brandon, L. D. Fine, J. L. Fritchman, J. L. Fuhrmann, N. S. M. Geoghagen, C. L. Gnehm, L. A. McDonald, K. V. Small, C. M. Fraser, H. O. Smith, and J. C. Venter. 1995. Whole-genome random sequencing and assembly of Haemophilus influenzae RD. Science 269:496-512.
16. Foster, S. J. 1993. Molecular analysis of three major wall-associated proteins of Bacillus subtilis 168: evidence for processing of the product of a gene encoding a 258 kDa precursor two-domain ligand-binding protein. Mol. Microbiol. 8:299-310.
17. Gorbalenya, A. E., and E. V. Koonin. 1993. Helicases: amino acid sequence comparisons and structure-function relationships. Curr. Opin. Struct. Biol. 3:419-429.
18. Gorbalenya, A. E., E. V. Koonin, A. P. Donchenko, and V. M. Blinov. 1989. Two related superfamilies of putative helicases involved in replication, recombination, repair and expression of DNA and RNA genomes. Nucleic Acids Res. 17:4713-4730.
19. Hacker, J., G. Blum-Oehler, I. Mühldorfer, and H. Tschäpe. 1997. Pathogenicity islands of virulent bacteria: structure, function and impact on microbial evolution. Mol. Microbiol. 23:1089-1097.
20. Haring, V., S. J. Billington, C. L. Wright, A. S. Huggins, M. E. Katz, and J. I. Rood. 1995. Delineation of the virulence related locus vrl of Dicheiobacter nodosus. Microbiology 141:2081-2091.
21. AL, p. 604-631. In N. R. Krieg and J. G. Holt (ed.), Bergey's manual of systematic bacteriology, vol. 1. The Williams & Wilkins Co., Baltimore, Md.
22. Isupov, M. N., G. Obmolova, S. Butterworth, M.-A. Badet-Denisot, B. Badet, I. Polikarpov, J. A. Littlechild, and A. Teplyakov. 1996. Substrate binding is required for assembly of the active conformation of the catalytic site of Ntn amidotransferases: evidence from the 1.8 Å crystal structure of the glutaminase domain of glucosamine 6-phosphate synthase. Structure 4:801-810.
23. Katz, M. E., P. M. Howarth, W. K. Yong, G. G. Riffkin, L. J. Depiazzi, and J. I. Rood. 1991. Identification of three gene regions associated with virulence in Dichelobacter nodosus, the causative agent of ovine footrot. J. Gen. Microbiol. 137:2117-2124.
24. Koivula, T. T., H. Hemila, R. Pakkanen, M. Sibakov, and I. Palva. 1993. Cloning and sequencing of a gene encoding acidophilic amylase from Bacillus acidocaldarius. J. Gen. Microbiol. 139:2399-2407.
25. Laemmli, U. K. 1970. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227:680-685.
26. La Fontaine, S., and J. I. Rood. 1997. Physical and genetic map of the chromosome of Dichelobacter nodosus strain A198. Gene 184:291-298.
27. Lauster, R., A. Kriebardis, and W. Guschlbauer. 1987. The GATATC-modification enzyme EcoRV is closely related to the GATC-recognizing methyltransferases DpnII and dam from E. coli and phage T4. FEBS Lett. 220:167-176.
28. Lewis, L. K., M. E. Jenkins, and D. W. Mount. 1992. Isolation of DNA damage-inducible promoters in Escherichia coli: regulation of polB (dinA), dinG, and dinH by LexA repressor. J. Bacteriol. 174:3377-3385.
29. Matuschek, M., G. Burchhardt, K. Sahm, and H. Bahl. 1994. Pullulanase of Thermoanaerobacterium thermosulfurigenes EM1 (Clostridium thermosulfurigenes): molecular analysis of the gene, composite structure of the enzyme, and a common model for its attachment to the cell surface. J. Bacteriol. 176:3295-3302.
30. Meinke, A., N. R. Gilkes, D. G. Kilburn, R. C. Miller, Jr., and R. A. Warren. 1993. Cellulose-binding polypeptides from Cellulomonas fimi: endoglucanase D (CenD), a family A beta-1,4-glucanase. J. Bacteriol. 175:1910-1918.
31. Miyashita, K., and T. Fujii. 1993. Nucleotide sequence and analysis of a gene (chiA) for a chitinase from Streptomyces lividans 66. Biosci. Biotechnol. Biochem. 57:1691-1698.
32. Mulligan, M. E., D. K. Hawley, R. Entriken, and W. R. McClure. 1984. Escherichia coli promoter sequences predict in vitro RNA polymerase selectivity. Nucleic Acids Res. 12:789-800.
33. Pearson, W. R., and D. J. Lipman. 1988. Improved tools for biological comparison. Proc. Natl. Acad. Sci. USA 85:2444-2448.
34. Pedre, X., F. Weise, S. Chai, G. Luder, and J. C. Alonso. 1994. Analysis of cis and trans acting elements required for the initiation of DNA replication in the Bacillus subtilis bacteriophage SPP1. J. Mol. Biol. 236:1324-1340.
35. Pongor, S., Z. Hatsagi, K. Degtyarenko, P. Fabian, V. Skerl, H. Hegyi, J. Murvai, and V. Bevilacqua. 1994. The SBASE protein domain library, release 3.0: a collection of annotated protein sequence segments. Nucleic Acids Res. 22:3610-3615.
36. Ramesh, M. V., S. M. Podkovyrov, S. E. Lowe, and J. G. Zeikus. 1994. Cloning and sequencing of the Thermoanaerobacterium saccharolyticum B6A-RI apu gene and purification and characterization of the amylopullulase from Escherichia coli. Appl. Environ. Microbiol. 60:94-101.
37. Roggentin, P., B. Rothe, J. B. Kaper, J. Galen, I. Lawrisuk, E. R. Vimr, and R. Schauer. 1989. Conserved sequences in bacterial and viral sialidases. Glycoconjugate J. 6:349-353.
38. Rood, J. I., P. A. Howarth, V. Haring, S. J. Billington, W. K. Yong, D. Liu, M. A. Palmer, D. A. Pitman, L. Links, D. A. Stewart, and J. A. Vaughan. 1996. Comparison of gene probe and conventional methods for the differentiation of ovine footrot isolates of Dichelobacter nodosus. Vet. Microbiol. 52:127-141.
39. Russel, M., and P. Model. 1984. Replacement of the ftp gene of Escherichia coli by an inactive gene cloned on a plasmid. J. Bacteriol. 159:1034-1039.
40. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
41. Schägger, H., and G. von Jagow. 1987. Tricine-sodium dodecyl sulfate-polyacrylamide gel electrophoresis for the separation of proteins in the range from 1 to 100 kDa. Anal. Biochem. 166:368-379.
42. Surin, B. P., and J. A. Downie. 1988. Characterization of the Rhizobium leguminosarum genes nodLMN involved in efficient host-specific nodulation. Mol. Microbiol. 2:173-183.
43. Tabor, S., and C. C. Richardson. 1985. A bacteriophage T7 RNA polymerase/promoter system for controlled exclusive expression of specific genes. Proc. Natl. Acad. Sci. USA 82:1074-1078.
44. Walker, J. E., N. J. Gay, M. Saraste, and A. N. Eberle. 1984. DNA sequence around the Escherichia coli unc operon. Completion of the sequence of a 17 kilohase segment containing asnA, oriC, unc, glmS and phoS. Biochem. J. 224:799-815.
45. Walker, J. E., M. Saraste, M. J. Runswick, and N. J. Gay. 1982. Distantly related sequences in the α- and β-subunits of the ATP synthase, myosin, kinases and other ATP-requiring enzymes and a common nucleotide binding fold. EMBO J. 1:945-951.
46. Wang, R. F., and S. R. Kushner. 1991. Construction of versatile low-copy-number vectors for cloning, sequencing and gene expression in Escherichia coli. Gene 100:195-199.
47. Widner, W. R., and R. B. Wickner. 1993. Evidence that the SKI antiviral system in Saccharomyces cerevisiae acts by blocking expression of viral mRNA. Mol. Cell. Biol. 13:4331-4341.
48. Willcock, D. F., D. T. F. Dryden, and N. E. Murray. 1994. A mutational analysis of the two motifs common to adenine methyltransferases. EMBO J. 13:3902-3908.
49. Yanisch-Perron, C., J. Vieira, and J. Messing. 1985. Improved M13 phage cloning vectors and host strains: nucleotide sequence of M13mp18 and pUC19 vectors. Gene 33:103-119.
50. Zweiger, G., G. Marczynski, and L. Shapiro. 1994. A Caulobacter DNA methyltransferase that functions only in the predivisional cell. J. Mol. Biol. 235:472-485.