Skip Navigation

This Article
Right arrow Full Text Freely available
Right arrow Print PDF (1241K) Freely available
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (38)
Right arrowRequest Permissions
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Williams, K. P.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Williams, K. P.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Nucleic Acids Research, 2002, Vol. 30, No. 4 866-875
© 2002 Oxford University Press

Survey and Summary

Integration sites for genetic elements in prokaryotic tRNA and tmRNA genes: sublocation preference of integrase subfamilies

Kelly P. Williams*

Department of Biology, Indiana University, 1001 East Third Street, Bloomington, IN 47405, USA

Most classical integrases of prokaryotic genetic elements specify integration into tRNA or tmRNA genes. Sequences shared between element and host integration sites suggest that crossover can occur at any of three sublocations within a tRNA gene, two with flanking symmetry (anticodon-loop and T-loop tDNA) and the third at the asymmetric 3' end of the gene. Integrase phylogeny matches this classification: integrase subfamilies use exclusively either the symmetric sublocations or the asymmetric sublocation, although tRNA genes of several different aminoacylation identities may be used within any subfamily. These two familial sublocation preferences imply two modes by which new integration site usage evolves. The tmRNA gene has been adopted as an integration site in both modes, and its distinctive structure imposes some constraints on proposed evolutionary mechanisms.

* Tel: +1 812 856 5697; Fax: +1 812 855 6705; Email: kwilliam{at}bio.indiana.edu


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 J. Bacteriol.Home page
S. E. Battle, F. Meyer, J. Rello, V. L. Kung, and A. R. Hauser
Hybrid Pathogenicity Island PAGI-5 Contributes to the Highly Virulent Phenotype of a Pseudomonas aeruginosa Isolate in Mammals
J. Bacteriol., November 1, 2008; 190(21): 7130 - 7140.
[Abstract] [Full Text] [PDF]

Home page
 MicrobiologyHome page
J. R. van der Ploeg
Characterization of Streptococcus gordonii prophage PH15: complete genome sequence and functional analysis of phage-encoded integrase and endolysin
Microbiology, October 1, 2008; 154(10): 2970 - 2978.
[Abstract] [Full Text] [PDF]

Home page
 Appl. Environ. Microbiol.Home page
E. Durmaz, M. J. Miller, M. A. Azcarate-Peril, S. P. Toon, and T. R. Klaenhammer
Genome Sequence and Characteristics of Lrm1, a Prophage from Industrial Lactobacillus rhamnosus Strain M1
Appl. Envir. Microbiol., August 1, 2008; 74(15): 4601 - 4609.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
R. Balbontin, N. Figueroa-Bossi, J. Casadesus, and L. Bossi
Insertion Hot Spot for Horizontally Acquired DNA within a Bidirectional Small-RNA Locus in Salmonella enterica
J. Bacteriol., June 1, 2008; 190(11): 4075 - 4078.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
A. J. Lloyd, A. M. Gilbey, A. M. Blewett, G. De Pascale, A. El Zoeiby, R. C. Levesque, A. C. Catherwood, A. Tomasz, T. D. H. Bugg, D. I. Roper, et al.
Characterization of tRNA-dependent Peptide Bond Formation by MurM in the Synthesis of Streptococcus pneumoniae Peptidoglycan
J. Biol. Chem., March 7, 2008; 283(10): 6402 - 6417.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
G. S. Vernikos and J. Parkhill
Resolving the structural features of genomic islands: A machine learning approach
Genome Res., February 1, 2008; 18(2): 331 - 342.
[Abstract] [Full Text] [PDF]

Home page
 MicrobiologyHome page
J. R. Zaneveld, D. R. Nemergut, and R. Knight
Are all horizontal gene transfers created equal? Prospects for mechanism-based studies of HGT patterns
Microbiology, January 1, 2008; 154(1): 1 - 15.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
G. Blanc, H. Ogata, C. Robert, S. Audic, J.-M. Claverie, and D. Raoult
Lateral gene transfer between obligate intracellular bacteria: Evidence from the Rickettsia massiliae genome
Genome Res., November 1, 2007; 17(11): 1657 - 1664.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
H.-Y. Ou, X. He, E. M. Harrison, B. R. Kulasekara, A. B. Thani, A. Kadioglu, S. Lory, J. C. D. Hinton, M. R. Barer, Z. Deng, et al.
MobilomeFINDER: web-based tools for in silico and experimental discovery of bacterial genomic islands
Nucleic Acids Res., July 13, 2007; 35(suppl_2): W97 - W104.
[Abstract] [Full Text] [PDF]

Home page
 MicrobiologyHome page
P. Germon, D. Roche, S. Melo, S. Mignon-Grasteau, U. Dobrindt, J. Hacker, C. Schouler, and M. Moulin-Schouleur
tDNA locus polymorphism and ecto-chromosomal DNA insertion hot-spots are related to the phylogenetic group of Escherichia coli strains
Microbiology, March 1, 2007; 153(3): 826 - 837.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
D. E. Fouts
Phage_Finder: Automated identification and classification of prophage regions in complete bacterial genome sequences
Nucleic Acids Res., November 6, 2006; 34(20): 5839 - 5851.
[Abstract] [Full Text] [PDF]

Home page
 MicrobiologyHome page
G. Erauso, K. M. Stedman, H. J. G. van de Werken, W. Zillig, and J. van der Oost
Two novel conjugative plasmids from a single strain of Sulfolobus
Microbiology, July 1, 2006; 152(7): 1951 - 1968.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
Z. Chen and T. D. Schneider
Comparative analysis of tandem T7-like promoter containing regions in enterobacterial genomes reveals a novel group of genetic islands
Nucleic Acids Res., February 21, 2006; 34(4): 1133 - 1147.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
H.-Y. Ou, L.-L. Chen, J. Lonnen, R. R. Chaudhuri, A. B. Thani, R. Smith, N. J. Garton, J. Hinton, M. Pallen, M. R. Barer, et al.
A novel strategy for the identification of genomic islands by comparative analysis of the contents and contexts of tRNA sites in closely related bacteria
Nucleic Acids Res., January 9, 2006; 34(1): e3 - e3.
[Abstract] [Full Text] [PDF]

Home page
 Infect. Immun.Home page
J.-P. Lavigne, A. C. Vergunst, G. Bourg, and D. O'Callaghan
The IncP Island in the Genome of Brucella suis 1330 Was Acquired by Site-Specific Integration
Infect. Immun., November 1, 2005; 73(11): 7779 - 7783.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
Y. Mantri and K. P. Williams
Islander: a database of integrative islands in prokaryotic genomes, the associated integrases and their DNA site specificities
Nucleic Acids Res., January 1, 2004; 32(90001): D55 - 58.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
M. C. Wolfgang, B. R. Kulasekara, X. Liang, D. Boyd, K. Wu, Q. Yang, C. G. Miyada, and S. Lory
Conservation of genome content and virulence determinants among clinical and environmental isolates of Pseudomonas aeruginosa
PNAS, July 8, 2003; 100(14): 8484 - 8489.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
M. A. Van Sluys, M. C. de Oliveira, C. B. Monteiro-Vitorello, C. Y. Miyaki, L. R. Furlan, L. E. A. Camargo, A. C. R. da Silva, D. H. Moon, M. A. Takita, E. G. M. Lemos, et al.
Comparative Analyses of the Complete Genome Sequences of Pierce's Disease and Citrus Variegated Chlorosis Strains of Xylella fastidiosa
J. Bacteriol., February 1, 2003; 185(3): 1018 - 1026.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
K. P. Williams
Traffic at the tmRNA Gene
J. Bacteriol., February 1, 2003; 185(3): 1059 - 1070.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
H. Genka, Y. Nagata, and M. Tsuda
Site-Specific Recombination System Encoded by Toluene Catabolic Transposon Tn4651
J. Bacteriol., September 1, 2002; 184(17): 4757 - 4766.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.