title: Computational Identification and Comparative Analysis of Secreted and Transmembrane Proteins in SixBurkholderiaSpecies.
abstract: As a step towards discovering novel pathogenesis-related proteins, we performed a genome scale computational identification and characterization of secreted and transmembrane (TM) proteins, which are mainly responsible for bacteria-host interactions and interactions with other bacteria, in the genomes of six representativeBurkholderiaspecies. The species comprised plant pathogens (B. glumaeBGR1,B. gladioliBSR3), human pathogens (B. pseudomalleiK96243,B. cepaciaLO6), and plant-growth promoting endophytes (Burkholderiasp. KJ006,B. phytofirmansPsJN). The proportions of putative classically secreted proteins (CSPs) and TM proteins among the species were relatively high, up to approximately 20%. Lower proportions of putative type 3 non-classically secreted proteins (T3NCSPs) (~10%) and unclassified non-classically secreted proteins (NCSPs) (~5%) were observed. The numbers of TM proteins among the three clusters (plant pathogens, human pathogens, and endophytes) were different, while the distribution of these proteins according to the number of TM domains was conserved in which TM proteins possessing 1, 2, 4, or 12 TM domains were the dominant groups in all species. In addition, we observed conservation in the protein size distribution of the secreted protein groups among the species. There were species-specific differences in the functional characteristics of these proteins in the various groups of CSPs, T3NCSPs, and unclassified NCSPs. Furthermore, we assigned the complete sets of the conserved and unique NCSP candidates of the collectedBurkholderiaspecies using sequence similarity searching. This study could provide new insights into the relationship among plant-pathogenic, human-pathogenic, and endophytic bacteria.
authors.affiliation: Department of Microbiology, Pusan National University, Busan 46241, Korea.
authors.forename: Thao Thi
authors.initials: TT
authors.lastname: Nguyen
authors.affiliation: Department of Microbiology, Pusan National University, Busan 46241, Korea.
authors.forename: Hyun-Hee
authors.initials: HH
authors.lastname: Lee
authors.affiliation: Department of Microbiology, Pusan National University, Busan 46241, Korea.
authors.forename: Jungwook
authors.initials: J
authors.lastname: Park
authors.affiliation: Department of Microbiology, Pusan National University, Busan 46241, Korea; Department of Asian Food and Culinary Arts, Youngsan University, Busan 48015, Korea.
authors.forename: Inmyoung
authors.initials: I
authors.lastname: Park
authors.affiliation: Department of Microbiology, Pusan National University, Busan 46241, Korea.
authors.forename: Young-Su
authors.initials: YS
authors.lastname: Seo
keywords: Burkholderia; endophyte; human pathogen; plant pathogen; secreted protein