Abstract
BackgroundLaribacter 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.ResultsA 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.ConclusionsThe 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.
Highlights
Laribacter hongkongensis is a Gram-negative, sea gull-shaped rod associated with communityacquired gastroenteritis
Bacteria employ different mechanisms for transport of different chemicals and these mechanisms have been classified into seven major categories according to the Transport Protein Database (TCDB): channels and pores, electrochemical potential-driven transporters, primary active transporters, group translocators, transmembrane electron carriers, accessory factors involved in transport, and incompletely characterized transport systems
We have previously found that transport-related proteins, including all seven major categories of transporters, account for about 14.1% of all coding sequences in the L. hongkongensis genome, suggesting that this group of proteins may be important for survival of the bacterium in the various environments and hosts [14]
Summary
Laribacter hongkongensis is a Gram-negative, sea gull-shaped rod associated with communityacquired gastroenteritis. Bacteria possess sophisticated signaling systems to sense and adapt to various substances in the environment. Depending on whether the environmental substances are attractants or repellents, the bacterium may migrate towards or away from the substances, which include certain amino acids, sugars, and metal ions [10,11,12]. This sense-and-swim ability is important for bacteria to be able to find the suitable environment for optimal growth. The chemoreceptors are called methyl-accepting chemotaxis proteins (MCPs), which are reversibly methylated and function as homodimers [11,13]
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