title: Transport genes and chemotaxis in Laribacter hongkongensis: a genome-wide analysis.
abstract: BACKGROUND
  Laribacter hongkongensis is a Gram-negative, sea gull-shaped rod associated with community-acquired gastroenteritis. The bacterium has been found in diverse freshwater environments including fish, frogs and drinking water reservoirs. Using the complete genome sequence data of L. hongkongensis, we performed a comprehensive analysis of putative transport-related genes and genes related to chemotaxis, motility and quorum sensing, which may help the bacterium adapt to the changing environments and combat harmful substances.
  
  
  RESULTS
  A genome-wide analysis using Transport Classification Database TCDB, similarity and keyword searches revealed the presence of a large diversity of transporters (n = 457) and genes related to chemotaxis (n = 52) and flagellar biosynthesis (n = 40) in the L. hongkongensis genome. The transporters included those from all seven major transporter categories, which may allow the uptake of essential nutrients or ions, and extrusion of metabolic end products and hazardous substances. L. hongkongensis is unique among closely related members of Neisseriaceae family in possessing higher number of proteins related to transport of ammonium, urea and dicarboxylate, which may reflect the importance of nitrogen and dicarboxylate metabolism in this assacharolytic bacterium. Structural modeling of two C4-dicarboxylate transporters showed that they possessed similar structures to the determined structures of other DctP-TRAP transporters, with one having an unusual disulfide bond. Diverse mechanisms for iron transport, including hemin transporters for iron acquisition from host proteins, were also identified. In addition to the chemotaxis and flagella-related genes, the L. hongkongensis genome also contained two copies of qseB/qseC homologues of the AI-3 quorum sensing system.
  
  
  CONCLUSIONS
  The large number of diverse transporters and genes involved in chemotaxis, motility and quorum sensing suggested that the bacterium may utilize a complex system to adapt to different environments. Structural modeling will provide useful insights on the transporters in L. hongkongensis.
authors.affiliation: State Key Laboratory of Emerging Infectious Diseases, Hong Kong.|Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong.|Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong.|Department of Microbiology, The University of Hong Kong, Hong Kong.
authors.forename: Susanna Kp
authors.initials: SK
authors.lastname: Lau
authors.affiliation: Department of Microbiology, The University of Hong Kong, Hong Kong.
authors.forename: Rachel Yy
authors.initials: RY
authors.lastname: Fan
authors.affiliation: Department of Microbiology, The University of Hong Kong, Hong Kong.
authors.forename: Gilman Km
authors.initials: GK
authors.lastname: Wong
authors.affiliation: Department of Microbiology, The University of Hong Kong, Hong Kong.
authors.forename: Jade Ll
authors.initials: JL
authors.lastname: Teng
authors.affiliation: Department of Chemistry, The University of Hong Kong, Hong Kong.
authors.forename: Kong-Hung
authors.initials: KH
authors.lastname: Sze
authors.affiliation: State Key Laboratory of Emerging Infectious Diseases, Hong Kong.|Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong.|Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong.|Department of Microbiology, The University of Hong Kong, Hong Kong.
authors.forename: Herman
authors.initials: H
authors.lastname: Tse
authors.affiliation: State Key Laboratory of Emerging Infectious Diseases, Hong Kong.|Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong.|Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong.|Department of Microbiology, The University of Hong Kong, Hong Kong.
authors.forename: Kwok-Yung
authors.initials: KY
authors.lastname: Yuen
authors.affiliation: State Key Laboratory of Emerging Infectious Diseases, Hong Kong.|Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong.|Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong.|Department of Microbiology, The University of Hong Kong, Hong Kong.
authors.forename: Patrick Cy
authors.initials: PC
authors.lastname: Woo