Genomic islands from five strains of Burkholderia pseudomallei

Tuanyok, Apichai; Leadem, Benjamin R.; Auerbach, Raymond K.; Beckstrom-Sternberg, Stephen M.; Beckstrom-Sternberg, James S.; Mayo, Mark; Wuthiekanun, Vanaporn; Brettin, Thomas; Nierman, William C.; Peacock, Sharon J.; Currie, Bart J.; Wagner, David M.; Keim, Paul

doi:10.1186/1471-2164-9-566

Cited by 97 publications

(143 citation statements)

References 35 publications

Supporting

Mentioning

137

Contrasting

Unclassified

Order By: Relevance

“…A large amount of GIs are created by a site-specific recombination mechanism, which plays a crucial role and therefore is significantly useful in exploring the formation of GIs. Mediated by transfer RNA (tRNA) and initiated at the 3′ ends of the tRNA genes, this kind of site-specific recombination mechanism creates some short and direct repeats identical or nearly identical to the 3′ ends (Reiter et al, 1989;Cheetham and Katz, 1995;Williams, 2002;Baar et al, 2003;Tuanyok et al, 2008).…”

Section: Introductionmentioning

confidence: 99%

Analysis of the 3′ ends of tRNA as the cause of insertion sites of foreign DNA in Prochlorococcus

Liu

Zhu

2010

J. Zhejiang Univ. Sci. B

View full text Add to dashboard Cite

Abstract:The purpose of this study was to investigate the characteristics of transfer RNA (tRNA) responsible for the association between tRNA genes and genes of apparently foreign origin (genomic islands) in five high-light adapted Prochlorococcus strains. Both bidirectional best BLASTP (basic local alignment search tool for proteins) search and the conservation of gene order against each other were utilized to identify genomic islands, and 7 genomic islands were found to be immediately adjacent to tRNAs in Prochlorococcus marinus AS9601, 11 in P. marinus MIT9515, 8 in P. marinus MED4, 6 in P. marinus MIT9301, and 6 in P. marinus MIT9312. Monte Carlo simulation showed that tRNA genes are hotspots for the integration of genomic islands in Prochlorococcus strains. The tRNA genes associated with genomic islands showed the following characteristics: (1) the association was biased towards a specific subset of all iso-accepting tRNA genes; (2) the codon usages of genes within genomic islands appear to be unrelated to the codons recognized by associated tRNAs; and, (3) the majority of the 3' ends of associated tRNAs lack CCA ends. These findings contradict previous hypotheses concerning the molecular basis for the frequent use of tRNA as the insertion site for foreign genetic materials. The analysis of a genomic island associated with a tRNA-Asn gene in P. marinus MIT9301 suggests that foreign genetic material is inserted into the host genomes by means of site-specific recombination, with the 3' end of the tRNA as the target, and during the process, a direct repeat of the 3' end sequence of a boundary tRNA (namely, a scar from the process of insertion) is formed elsewhere in the genomic island. Through the analysis of the sequences of these targets, it can be concluded that a region characterized by both high GC content and a palindromic structure is the preferred insertion site.

show abstract

Section: Introductionmentioning

confidence: 99%

Analysis of the 3′ ends of tRNA as the cause of insertion sites of foreign DNA in Prochlorococcus

Liu

Zhu

2010

J. Zhejiang Univ. Sci. B

View full text Add to dashboard Cite

show abstract

“…For example, when the complete genome sequences of many strains of Bacillus anthracis are compared there is very little genetic difference in the genome organization and sequence of these genomes. However, Burkholderia pseudomallei strains can have tens to hundreds of thousands of base pairs of sequence difference between individual isolates (Tuyanyok A et al, 2008). This wide latitude in core conserved sequence between different biothreat bacteria necessitates the assembly of a large database of sequence information for each of the bacterial agents.…”

Section: Figure 1 Hierarchy Of Genetic Manipulation Versus Capabilitmentioning

confidence: 99%

Genetic Engineering Workshop Report, 2010

Allen¹,

Slezak²

2010

View full text Add to dashboard Cite

“…As an environmental bacterium adapted to a diverse range of tropical and subtropical habitats globally, B. pseudomallei is known to harbor a vast intraspecies genomic diversity as a result of high recombination frequency (21). It is therefore not surprising that the biochemical database of the Vitek 2 system performs variably based on geographical location.…”

mentioning

confidence: 99%

Reliability of Automated Biochemical Identification of Burkholderia pseudomallei Is Regionally Dependent

et al. 2013

Self Cite

View full text Add to dashboard Cite

Misidentifications of Burkholderia pseudomallei as Burkholderia cepacia by Vitek 2 have occurred. Multidimensional scaling ordination of biochemical profiles of 217 Malaysian and Australian B. pseudomallei isolates found clustering of misidentified B. pseudomallei isolates from Malaysian Borneo. Specificity of B. pseudomallei identification in Vitek 2 and potentially other automated identification systems is regionally dependent.

show abstract

Genomic islands from five strains of Burkholderia pseudomallei

Cited by 97 publications

References 35 publications

Analysis of the 3′ ends of tRNA as the cause of insertion sites of foreign DNA in Prochlorococcus

Analysis of the 3′ ends of tRNA as the cause of insertion sites of foreign DNA in Prochlorococcus

Genetic Engineering Workshop Report, 2010

Reliability of Automated Biochemical Identification of Burkholderia pseudomallei Is Regionally Dependent

Contact Info

Product

Resources

About