title: Identification and analysis of genomic islands in Burkholderia cenocepacia AU 1054 with emphasis on pathogenicity islands.
abstract: Genomic islands (GIs) are genomic regions that reveal evidence of horizontal DNA transfer. They can code for many functions and may augment a bacterium's adaptation to its host or environment. GIs have been identified in strain J2315 of Burkholderia cenocepacia, whereas in strain AU 1054 there has been no published works on such regions according to our text mining and keyword search in Medline.
  
  
  
  In this study, we identified 21 GIs in AU 1054 by combining two computational tools. Feature analyses suggested that the predictions are highly reliable and hence illustrated the advantage of joint predictions by two independent methods. Based on putative virulence factors, four GIs were further identified as pathogenicity islands (PAIs). Through experiments of gene deletion mutants in live bacteria, two putative PAIs were confirmed, and the virulence factors involved were identified as lipA and copR. The importance of the genes lipA (from PAI 1) and copR (from PAI 2) for bacterial invasion and replication indicates that they are required for the invasive properties of B. cenocepacia and may function as virulence determinants for bacterial pathogenesis and host infection.
  
  
  
  This approach of in silico prediction of GIs and subsequent identification of potential virulence factors in the putative island regions with final validation using wet experiments could be used as an effective strategy to rapidly discover novel virulence factors in other bacterial species and strains.
authors.affiliation: School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China.|Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China.|Key Laboratory for Neuro-information of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu, 610054, China.|Department of Microbiology, The University of Hong Kong, Hong Kong, Special Administrative Region, People's Republic of China.
authors.forename: Feng-Biao
authors.initials: FB
authors.lastname: Guo
authors.affiliation: Department of Microbiology, The University of Hong Kong, Hong Kong, Special Administrative Region, People's Republic of China.
authors.forename: Lifeng
authors.initials: L
authors.lastname: Xiong
authors.affiliation: School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China.|Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China.|Key Laboratory for Neuro-information of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu, 610054, China.
authors.forename: Kai-Yue
authors.initials: KY
authors.lastname: Zhang
authors.affiliation: School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China.|Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China.|Key Laboratory for Neuro-information of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu, 610054, China.
authors.forename: Chuan
authors.initials: C
authors.lastname: Dong
authors.affiliation: School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China.|Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China.|Key Laboratory for Neuro-information of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu, 610054, China.
authors.forename: Fa-Zhan
authors.initials: FZ
authors.lastname: Zhang
authors.affiliation: Department of Microbiology, The University of Hong Kong, Hong Kong, Special Administrative Region, People's Republic of China. pcywoo@hku.hk.
authors.forename: Patrick C Y
authors.initials: PC
authors.lastname: Woo
mesh_terms: D000072283:A549 Cells; D001422:Bacterial Adhesion; D001426:Bacterial Proteins / Q000235:genetics; D001482:Base Composition; D019121:Burkholderia Infections / Q000382:microbiology; D057508:Burkholderia cenocepacia / Q000235:genetics* / Q000254:growth & development / Q000472:pathogenicity; D018929:Cell Culture Techniques; D015169:Colony Count, Microbial; D019295:Computational Biology / Q000379:methods; D004269:DNA, Bacterial; D017353:Gene Deletion; D022761:Gene Transfer, Horizontal; D005798:Genes, Bacterial / Q000235:genetics; D016680:Genome, Bacterial / Q000235:genetics; D044404:Genomic Islands / Q000235:genetics*; D023281:Genomics; D006801:Humans; D037521:Virulence Factors / Q000235:genetics* / Q000302:isolation & purification*
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; C079999:LipA protein, Bacteria; D037521:Virulence Factors
keywords: B. cenocepacia AU1054; Genomic Island; Pathogenicity Island; Virulence factor