Novel toxin-antitoxin system composed of serine protease and AAA-ATPase homologues determines the high level of stability and incompatibility of the tumor-inducing plasmid pTiC58

Journal of Bacteriology

Volumn 191, Issue 14, 2009, Pages 4656-4666

  Yamamoto, Shinji ^a   Kiyokawa, Kazuya ^a   Tanaka, Katsuyuki ^a   Moriguchi, Kazuki ^a   Suzuki, Katsunori ^a  

^a HIROSHIMA UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATASE; ANTITOXIN; BACTERIAL PROTEIN; ENZYME; IETA PROTEIN; IETS PROTEIN; KANAMYCIN; LANTIBIOTIC; MESSENGER RNA; NOPALINE; OCTOPINE; REPA PROTEIN; REPB PROTEIN; SERINE PROTEINASE; SUBTILISIN; TOXIN; UNCLASSIFIED DRUG; BACTERIAL TOXIN;

AMINO ACID SUBSTITUTION; ARTICLE; BACTERIAL GENE; BACTERIAL PLANT DISEASE; BACTERIUM CONJUGATION; BACTERIUM CULTURE; BINDING AFFINITY; COLONY FORMING UNIT; CROWN GALL; CULTURE MEDIUM; ESCHERICHIA COLI; GENE LOCUS; GENE MUTATION; GENE SEQUENCE; GENE TRANSFER; HUMAN; IETA GENE; IETS GENE; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PLASMID; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN EXPRESSION; PROTEIN SECONDARY STRUCTURE; RHIZOBIUM RADIOBACTER; SACB GENE; SITE DIRECTED MUTAGENESIS; TUMOR INDUCING PLASMID; AMINO ACID SEQUENCE; GENE ORDER; GENETICS; GENOMIC INSTABILITY; METABOLISM; MICROBIAL VIABILITY; MICROBIOLOGY; MOLECULAR GENETICS; PLANT; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY;

ADENOSINE TRIPHOSPHATASES; AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ANTITOXINS; BACTERIAL TOXINS; GENE ORDER; GENES, BACTERIAL; GENOMIC INSTABILITY; MICROBIAL VIABILITY; MOLECULAR SEQUENCE DATA; MUTAGENESIS, SITE-DIRECTED; OPEN READING FRAMES; PLANTS; PLASMIDS; RHIZOBIUM RADIOBACTER; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID; SERINE ENDOPEPTIDASES;

EID: 67650281478     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.00124-09     Document Type: Article

References (40)

1. Austin, S. J., and K. Nordström. 1990. Partition-mediated incompatibility of bacterial plasmids. Cell 60:351-354.
2. Cevallos, M. A., R. Cervantes-Rivera, and R. M. Gutiérrez- Ríos. 2008. The repABC plasmid family. Plasmid 60:19-37.
3. Chilton, M. D., T. C. Currier, S. K. Farrand, A. J. Bendich, M. P. Gordon, and E. W. Nester. 1974. Agrobacterium tumefaciens DNA and PS8 bacteriophage DNA not detected in crown gall tumors. Proc. Natl. Acad. Sci. USA 71:3672-3676.
4. Fineran, P. C., T. R. Blower, I. J. Foulds, D. P. Humphreys, K. S. Lilley, and G. P. C. Salmond. 2009. The phage abortive infection system, ToxIN, functions as a protein-RNA toxin-antitoxin pair. Proc. Natl. Acad. Sci. USA 106:894-899.
5. Frickey, T., and A. N. Lupas. 2004. Phylogenetic analysis of AAA proteins. J. Struct. Biol. 146:2-10.
6. Gerdes, K., and E. G. Wagner. 2007. RNA antitoxins. Curr. Opin. Microbiol. 10:117-124.
7. Goodner, B., G. Hinkle, S. Gattung, N. Miller, M. Blanchard, B. Qurollo, B. S. Goldman, Y. Cao, M. Askenazi, C. Halling, L. Mullin, K. Houmiel, J. Gordon, M. Vaudin, O. Iartchouk, A. Epp, F. Liu, C. Wollam, M. Allinger, D. Doughty, C. Scott, C. Lappas, B. Markelz, C. Flanagan, C. Crowell, J. Gurson, C. Lomo, C. Sear, G. Strub, C. Cielo, and S. Slater. 2001. Genome sequence of the plant pathogen and biotechnology agent Agrobacterium tumefaciens C58. Science 294:2323-2328.
8. Hattori, Y., M. Uraji, K. Suzuki, N. Ohta, K. Iwata, A. Kato, and K. Yoshida. 2000. Gene list on a plant tumor-inducing plasmid, pTi-SAKURA in Agrobacterium tumefaciens MAFF301001. DNA Res. 7:371-380.
9. Hayes, F. 2003. Toxins-antitoxins: plasmid maintenance, programmed cell death, and cell cycle arrest. Science 301:1496-1499.
10. Ho, S. N., H. D. Hunt, R. M. Horton, J. K. Pullen, and L. R. Pease. 1989. Site-directed mutagenesis by overlap extension using the polymerase chain reaction. Gene 77:51-59.
11. Holsters, M., J. P. Hernalsteens, M. Van Montagu, and J. Schell. 1982. Ti plasmids of Agrobacterium tumefaciens: the nature of the tip, p. 269-298. In G. Kahl, and J. S. Schell (ed.), Molecular biology of plant tumors. Academic Press, New York, NY.
12. Karata, K., T. Inagawa, A. J. Wilkinson, T. Tatsuta, and T. Ogura. 1999. Dissecting the role of a conserved motif (the second region of homology) in the AAA family of ATPases. Site-directed mutagenesis of the ATP-dependent protease FtsH. J. Biol. Chem. 274:26225-26232.
13. Karata, K., C. S. Verma, A. J. Wilkinson, and T. Ogura. 2001. Probing the mechanism of ATP hydrolysis and substrate translocation in the AAA protease FtsH by modelling and mutagenesis. Mol. Microbiol. 39:890-903.
14. Khan, S. R., J. Gaines, R. M. Roop II, and S. K. Farrand. 2008. Broad-hostrange expression vectors with tightly regulated promoters and their use to examine the influence of TraR and TraM expression on Ti plasmid quorum sensing. Appl. Environ. Microbiol. 74:5053-5062.
15. Kobayashi, I. 2004. Genetic addiction: a principle of gene symbiosis in a genome, p. 105-144. In B. E. Funnell and G. J. Phillips (ed.), Plasmid biology. ASM Press, Washington, DC.
16. Li, P., and S. K. Farrand. 2000. The replicator of the nopaline-type Ti plasmid pTiC58 is a member of repABC family and is influenced by the TraR-dependent quorum-sensing regulatory system. J. Bacteriol. 182:179-188.
17. McCullen, C. A., and A. N. Binns. 2006. Agrobacterium tumefaciens and plant cell interactions and activities required for interkingdom macromolecular transfer. Annu. Rev. Cell Dev. Biol. 22:101-127.
18. Meijer, W. J., G. B. Wisman, P. Terpstra, P. B. Thorsted, C. M. Thomas, S. Holsappel, G. Venema, and S. Bron. 1998. Rolling-circle plasmids from Bacillus subtilis: complete nucleotide sequences and analyses of genes of pTA1015, pTA1040, pTA1050 and pTA1060, and comparisons with related plasmids from gram-positive bacteria. FEMS Microbiol. Rev. 21:337-368.
19. Newman, J. R., and C. Fuqua. 1999. Broad-host-range expression vectors that carry the L-arabinose-inducible Escherichia coli araBAD promoter and the araC regulator. Gene 18:197-203.
20. Penfold, R. J., and J. M. Pemberton. 1992. An improved suicide vector for construction of chromosomal insertion mutations in bacteria. Gene 118:145-146.
21. Pogliano, J. 2002. Dynamic cellular location of bacterial plasmids. Curr. Opin. Microbiol. 5:586-590.
22. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual, 2nd ed., Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.
23. Sawada, H., and H. Ieki. 1992. Phenotypic characteristics of the genus Agrobacterium. Ann. Phytopath. Soc. Jpn. 58:37-45.
24. Schäfer, A., A. Tauch, W. Jäger, J. Kalinowski, G. Thierbach, and A. Pühler. 1994. Small mobilizable multi-purpose cloning vectors derived from the Escherichia coli plasmids pK18 and pK19: selection of defined deletions in the chromosome of Corynebacterium glutamicum. Gene 145:69-73.
25. Siezen, R. J., B. Renckens, and J. Boekhorst. 2007. Evolution of prokaryotic subtilases: genome-wide analysis reveals novel subfamilies with different catalytic residues. Proteins 67:681-694.
26. Siezen, R. J., O. P. Kuipers, and W. M. de Vos. 1996. Comparison of lantibiotic gene clusters and encoded proteins. Antonie van Leeuwenhoek 69:171-184.
27. Simon, R., U. Priefer, and A. Pühler. 1983. A broad host range mobilization system for in vivo genetic engineering: transposon mutagenesis in gramnegative bacteria. Bio/Technology 1:784-794.
28. Stein, T., S. Heinzmann, I. Solovieva, and K. D. Entian. 2003. Function of Lactococcus lactis nisin immunity genes nisI and nisFEG after coordinated expression in the surrogate host Bacillus subtilis. J. Biol. Chem. 278:89-94.
29. Summers, D. 1998. Timing, self-control and a sense of direction are the secrets of multicopy plasmid stability. Mol. Microbiol. 29:1137-1145.
30. Suzuki, K., N. Ohta, Y. Hattori, M. Uraji, A. Kato, and K. Yoshida. 1998. Novel structural difference between nopaline- and octopine-type trbJ genes: construction of genetic and physical map and sequencing of trb/traI and rep gene clusters of a new Ti plasmid pTi-SAKURA. Biochim. Biophys. Acta 1396:1-7.
31. Suzuki, K., Y. Hattori, M. Uraji, N. Ohta, K. Iwata, K. Murata, A. Kato, and K. Yoshida. 2000. Complete nucleotide sequence of a plant tumor-inducing Ti plasmid. Gene 242:331-336.
32. Suzuki, K., K. Iwata, and K. Yoshida. 2001. Genome analysis of Agrobacterium tumefaciens: construction of physical maps for linear and circular chromosomal DNAs, determination of copy number ratio and mapping of chromosomal virulence genes. DNA Res. 8:141-152.
33. Suzuki, K., K. Tanaka, S. Yamamoto, K. Kiyokawa, K. Moriguchi, and K. Yoshida. 2009. Ti and Ri plasmids, p. 133-147. In E. Schwartz (ed.), Microbial megaplasmids. Springer Verlag, Heidelberg, Germany.
34. Tabata, S., P. J. J. Hooykaas, and A. Oka. 1989. Sequence determination and characterization of the replicator region in the tumor-inducing plasmid pTiB6S3. J. Bacteriol. 171:1665-1672.
35. Tanaka, K., H. H. Arafat, H. Urbanczyk, S. Yamamoto, K. Moriguchi, H. Sawada, and K. Suzuki. 2009. Ability of Agrobacterium tumefaciens and A. rhizogenes strains, inability of A. vitis and A. rubi strains to adapt to saltinsufficient environment, and taxonomic significance of a simple salt requirement test in the pathogenic Agrobacterium species. J. Gen. Appl. Microbiol. 55:35-41.
36. Uraji, M., K. Suzuki, and K. Yoshida. 2002. A novel plasmid curing method using incompatibility of plant pathogenic Ti plasmids in Agrobacterium tumefaciens. Genes Genet. Syst. 77:1-9.
37. Wang, R. F., E. B. O'Hara, M. Aldea, C. I. Bargmann, H. Gromley, and S. R. Kushner. 1998. Escherichia coli mrsC is an allele of hflB, encoding a membrane-associated ATPase and protease that is required for mRNA decay. J. Bacteriol. 180:1929-1938.
38. Wise, A. A., Z. Liu, and A. N. Binns. 2006. Culture and maintenance of Agrobacterium strains. Methods Mol. Biol. 343:3-13.
39. Yakushiji, Y., S. Nishikori, K. Yamanaka, and T. Ogura. 2006. Mutational analysis of the functional motifs in the ATPase domain of Caenorhabditis elegans fidgetin homologue FIGL-1: firm evidence for an intersubunit catalysis mechanism of ATP hydrolysis by AAA ATPases. J. Struct. Biol. 156:93-100.
40. Yamamoto, S., M. Uraji, K. Tanaka, K. Moriguchi, and K. Suzuki. 2007. Identification of pTi-SAKURA DNA region conferring enhancement of plasmid incompatibility and stability. Genes Genet. Syst. 82:197-206.