title: Expansion of the known Klebsiella pneumoniae species gene pool by characterization of novel alien DNA islands integrated into tmRNA gene sites.
abstract: Klebsiella pneumoniae is an important bacterial pathogen of man that is commonly associated with opportunistic and hospital-associated infections. Increasing levels of multiple-antibiotic resistance associated with this species pose a major emerging clinical problem. This organism also occurs naturally in other diverse environments, including the soil. Consistent with its varied lifestyle and membership of the Enterobacteriaceae family, K. pneumoniae genomes exhibit highly plastic architecture comprising a core genome backbone interspersed with numerous and varied alien genomic islands. In this study the size of the presently known K. pneumoniae pan-genome gene pool was estimated through analysis of complete sequences of three chromosomes and 31 plasmids belonging to K. pneumoniae strains. In addition, using a PCR-based strategy the genomic content of eight tRNA/tmRNA gene sites that serve as DNA insertion hotspots were investigated in 28 diverse environmental and clinical strains of K. pneumoniae. Sequencing and characterization of five newly identified horizontally-acquired tmRNA-associated islands further expanded the archived K. pneumoniae gene pool to a total of 7648 unique gene members. Large-scale investigation of the content of tRNA/tmRNA hotspots will be useful to identify and/or survey accessory sequences dispersed amongst hundreds to thousands of members of many key bacterial species.
authors.affiliation: Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin, PR China.
authors.forename: Jie
authors.initials: J
authors.lastname: Zhang
authors.forename: Jon Jurriaan
authors.initials: JJ
authors.lastname: van Aartsen
authors.forename: Xiaofei
authors.initials: X
authors.lastname: Jiang
authors.forename: Yucheng
authors.initials: Y
authors.lastname: Shao
authors.forename: Cui
authors.initials: C
authors.lastname: Tai
authors.forename: Xinyi
authors.initials: X
authors.lastname: He
authors.forename: Zhilei
authors.initials: Z
authors.lastname: Tan
authors.forename: Zixin
authors.initials: Z
authors.lastname: Deng
authors.forename: Shiru
authors.initials: S
authors.lastname: Jia
authors.forename: Kumar
authors.initials: K
authors.lastname: Rajakumar
authors.forename: Hong-Yu
authors.initials: HY
authors.lastname: Ou
mesh_terms: D000818:Animals; D002876:Chromosomes, Bacterial; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004783:Environmental Microbiology; D022761:Gene Transfer, Horizontal; D016680:Genome, Bacterial; D044404:Genomic Islands; D006801:Humans; D007710:Klebsiella Infections / Q000382:microbiology; D007711:Klebsiella pneumoniae / Q000235:genetics* / Q000302:isolation & purification; D008969:Molecular Sequence Data; D016254:Mutagenesis, Insertional; D010957:Plasmids; D016133:Polymerase Chain Reaction; D012329:RNA, Bacterial / Q000235:genetics*; D017422:Sequence Analysis, DNA
chemical_list: D004269:DNA, Bacterial; D012329:RNA, Bacterial; C096222:tmRNA