Characterization of the integration and modular excision of the integrative conjugative element PAISt in Streptomyces turgidiscabies Car8

PLoS ONE

Volumn 9, Issue 6, 2014, Pages

  Huguet Tapia, Jose C ^a   Bignell, Dawn R D ^b   Loria, Rosemary ^a  

^a UNIVERSITY OF FLORIDA   (United States)

^b MEMORIAL UNIVERSITY OF NEWFOUNDLAND   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL STRAIN; COMPARATIVE GENE MAPPING; CONTROLLED STUDY; DNA FLANKING REGION; GENE AMPLIFICATION; GENE SEQUENCE; GENE STRUCTURE; GENETIC CONSERVATION; GENOMIC ISLAND; HORIZONTAL GENE TRANSFER; INTEGRATIVE CONJUGATIVE ELEMENT; NONHUMAN; NUCLEOTIDE SEQUENCE; POINT MUTATION; PROTEIN MOTIF; STREPTOMYCES; STREPTOMYCES ACIDISCABIES; STREPTOMYCES COELICOLOR; STREPTOMYCES SCABIES; STREPTOMYCES TURGIDISCABIES; BACTERIAL GENE; CHEMICAL STRUCTURE; CHEMISTRY; GENETICS; INVERTED REPEAT; MOLECULAR EVOLUTION;

BACTERIAL DNA; VIRULENCE FACTOR;

DNA, BACTERIAL; EVOLUTION, MOLECULAR; GENES, BACTERIAL; GENOMIC ISLANDS; INVERTED REPEAT SEQUENCES; MODELS, MOLECULAR; STREPTOMYCES; VIRULENCE FACTORS;

EID: 84903195947     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0099345     Document Type: Article

References (35)

1. Burrus V, Waldor MK (2004) Shaping bacterial genomes with integrative and conjugative elements. Genome plasticity and the evolution of microbial genomes 155: 376-386. doi:10.1016/j.resmic.2004.01.012.
2. Wozniak RAF, Waldor MK (2010) Integrative and conjugative elements: mosaic mobile genetic elements enabling dynamic lateral gene flow. Nature Reviews Microbiology 8: 552-563. doi:10.1038/nrmicro2382.
3. Poele EM, Bolhuis H, Dijkhuizen L (2008) Actinomycete integrative and conjugative elements. Antonie Van Leeuwenhoek 94: 127-143. doi:10.1007/s10482- 008-9255-x.
4. Grohmann E, Muth G, Espinosa M (2003) Conjugative Plasmid Transfer in Gram-Positive Bacteria. Microbiol Mol Biol Rev 67: 277-301. doi:10.1128/MMBR.67. 2.277-301.2003. (Pubitemid 36693475)
5. Loria R, Bukhalid RA, Fry BA, King RR (1997) Plant pathogenicity in the genus Streptomyces. Plant Disease 8: 836-841.
6. Miyajima K, Tanaka F, Takeuchi T, Kuninaga S (1998) Streptomyces turgidiscabies sp. nov. Int J Syst Bacteriol 48 Pt 2: 495-502.
7. Loria R, Kers J, Joshi M (2006) Evolution of plant pathogenicity in Streptomyces. Annu Rev Phytopathol 44: 469-487. doi:10.1146/annurev.phyto.44. 032905.091147. (Pubitemid 44435713)
8. Huguet-Tapia JC, Badger JH, Loria R, Pettis GS (2011) Streptomyces turgidiscabies Car8 contains a modular pathogenicity island that shares virulence genes with other actinobacterial plant pathogens. Plasmid 65: 118-124. doi:10.1016/j.plasmid.2010.11.002.
9. Kers JA, Cameron KD, Joshi MV, Bukhalid RA, Morello JE, et al. (2005) A large, mobile pathogenicity island confers plant pathogenicity on Streptomyces species. Mol Microbiol 55: 1025-1033. doi:10.1111/j.1365-2958.2004.04461.x. (Pubitemid 40299174)
10. Seipke RF, Loria R (2008) Streptomyces scabies 87-22 possesses a functional tomatinase. J Bacteriol 190: 7684-7692. doi:10.1128/JB.01010-08.
11. Bukhalid RA, Chung SY, Loria R (1998) nec1, a gene conferring a necrogenic phenotype, is conserved in plant-pathogenic Streptomyces spp. and linked to a transposase pseudogene. MPMI 11: 960-967. doi:10.1094/MPMI.1998.11. 10.960. (Pubitemid 28456199)
12. Loria R, Bignell DRD, Moll S, Huguet-Tapia JC, Joshi MV, et al. (2008) Thaxtomin biosynthesis: the path to plant pathogenicity in the genus Streptomyces. Antonie Van Leeuwenhoek 94: 3-10. doi:10.1007/s10482-008-9240-4.
13. Joshi MV, Loria R (2007) Streptomyces turgidiscabies possesses a functional cytokinin biosynthetic pathway and produces leafy galls. MPMI 20: 751-758. doi:10.1094/MPMI-20-7-0751. (Pubitemid 46944969)
14. Bibb MJ, Janssen GR, Ward JM (1985) Cloning and analysis of the promoter region of the erythromycin resistance gene (ermE) ofStreptomyces erythraeus. Gene 38: 215-226. doi:10.1016/0378-1119(85)90220-3. (Pubitemid 16169920)
15. Carver T, Berriman M, Tivey A, Patel C, Böhme U, et al. (2008) Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database. Bioinformatics 24: 2672-2676. doi:10.1093/bioinformatics/ btn529. (Pubitemid 352722607)
16. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, et al. (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23: 2947-2948. doi:10.1093/bioinformatics/btm404. (Pubitemid 350162903)
17. Lambert C, Leonard N, De Bolle X, Depiereux E (2002) ESyPred3D: Prediction of proteins 3D structures. Bioinformatics 18: 1250-1256. doi:10.1093/bioinformatics/18.9.1250.
18. Guex N, Peitsch MC (1997) SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling. Electrophoresis 18: 2714-2723. doi:10.1002/elps.1150181505. (Pubitemid 28059943)
19. Esposito D, Scocca JJ (1997) The integrase family of tyrosine recombinases: evolution of a conserved active site domain. Nucleic Acids Res 25: 3605-3614. doi:10.1093/nar/25.18.3605. (Pubitemid 27390178)
20. Lee CA, Auchtung JM, Monson RE, Grossman AD (2007) Identification and characterization of int (integrase), xis (excisionase) and chromosomal attachment sites of the integrative and conjugative element ICEBs1 of Bacillus subtilis. Mol Microbiol 66: 1356-1369. doi:10.1111/j.1365-2958.2007.06000.x. (Pubitemid 350179677)
21. Marra D, Scott JR (1999) Regulation of excision of the conjugative transposon Tn916. Mol Microbiol 31: 609-621. (Pubitemid 29046102)
22. Ghinet MG, Bordeleau E, Beaudin J, Brzezinski R, Roy S, et al. (2011) Uncovering the prevalence and diversity of integrating conjugative elements in actinobacteria. PLoS ONE 6: e27846. doi:10.1371/journal.pone.0027846.
23. Pavlovic G, Burrus V, Gintz B, Decaris B, Guédon G (2004) Evolution of genomic islands by deletion and tandem accretion by site-specific recombination: ICESt1-related elements from Streptococcus thermophilus. Microbiology (Reading, Engl) 150: 759-774.
24. Schubert S, Dufke S, Sorsa J, Heesemann J (2004) A novel integrative and conjugative element (ICE) of Escherichia coli: the putative progenitor of the Yersinia high-pathogenicity island. Mol Microbiol 51: 837-848. (Pubitemid 38233948)
25. Quiroz TS, Nieto PA, Tobar HE, Salazar-Echegarai FJ, Lizana RJ, et al. (2011) Excision of an unstable pathogenicity island in Salmonella enterica serovar Enteritidis is induced during infection of phagocytic cells. PLoS ONE 6: e26031. doi:10.1371/journal.pone.0026031.
26. Hochhut B, Beaber JW, Woodgate R, Waldor MK (2001) Formation of chromosomal tandem arrays of the SXT element and R391, two conjugative chromosomally integrating elements that share an attachment site. J Bacteriol 183: 1124-1132. doi:10.1128/JB.183.4.1124-1132.2001. (Pubitemid 32107707)
27. Hall RM (2012) Integrons and gene cassettes: hotspots of diversity in bacterial genomes. Ann N Y Acad Sci 1267: 71-78. doi:10.1111/j.1749-6632.2012. 06588.x.
28. Mazel D (2006) Integrons: agents of bacterial evolution. Nature Reviews Microbiology 4: 608-620. doi:10.1038/nrmicro1462.
29. Bateman A, Coin L, Durbin R, Finn RD, Hollich V, et al. (2004) The Pfam protein families database. Nucleic Acids Res 32: D138-D141. doi:10.1093/nar/ gkh121. (Pubitemid 38081623)
30. Tatusov RL (2000) The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res 28: 33-36. doi:10.1093/nar/28.1.33.
31. Groth AC, Calos MP (2004) Phage integrases: biology and applications. J Mol Biol 335: 667-678. (Pubitemid 38352810)
32. Du L, Liu R-H, Ying L, Zhao G-R (2012) An Efficient Intergeneric Conjugation of DNA from Escherichia coli to Mycelia of the Lincomycin-Producer Streptomyces lincolnensis. Int J Mol Sci 13: 4797-4806. doi:10.3390/ ijms13044797.
33. Lambert DH, Loria R (1989) Streptomyces scabies sp. nov., nom. rev. Int J Syst Bacteriol 39: 387-392. doi:10.1099/00207713-39-4-387. (Pubitemid 19250501)
34. Lambert DH, Loria R (1989) Streptomyces acidiscabies sp. nov. Int J Syst Bacteriol 39: 393-396. doi:10.1099/00207713-39-4-393.
35. Gregory MA, Till R, Smith M (2003) Integration site for Streptomyces phage phi BT1 and development of site-specific integrating vectors. J Bacteriol 185: 5320-5323. doi:10.1128/JB.185.17.5320-5323.2003. (Pubitemid 37021998)