Comparative genomics study of polyhydroxyalkanoates (PHA) and ectoine relevant genes from <it>Halomonas </it>sp. TD01 revealed extensive horizontal gene transfer events and co-evolutionary relationships

• Main Authors: Cai Lei, Tan Dan, Aibaidula Gulsimay, Dong Xin-Ran, Chen Jin-Chun, Tian Wei-Dong, Chen Guo-Qiang
• Format: Article
• Language: English
• Published: BMC 2011-11-01
• Series: Microbial Cell Factories
• Subjects: <it>Halomonas </it>spp.; PHB; polyhydroxyalkanoates; osmolytes; genome; PhaC
• Online Access: http://www.microbialcellfactories.com/content/10/1/88

<p>Abstract</p> <p>Background</p> <p>Halophilic bacteria have shown their significance in industrial production of polyhydroxyalkanoates (PHA) and are gaining more attention for genetic engineering modification. Yet, little information on the genomics and PHA related genes from halophilic bacteria have been disclosed so far.</p> <p>Results</p> <p>The draft genome of moderately halophilic bacterium, <it>Halomonas </it>sp. TD01, a strain of great potential for industrial production of short-chain-length polyhydroxyalkanoates (PHA), was analyzed through computational methods to reveal the osmoregulation mechanism and the evolutionary relationship of the enzymes relevant to PHA and ectoine syntheses. Genes involved in the metabolism of PHA and osmolytes were annotated and studied <it>in silico</it>. Although PHA synthase, depolymerase, regulator/repressor and phasin were all involved in PHA metabolic pathways, they demonstrated different horizontal gene transfer (HGT) events between the genomes of different strains. In contrast, co-occurrence of ectoine genes in the same genome was more frequently observed, and ectoine genes were more likely under coincidental horizontal gene transfer than PHA related genes. In addition, the adjacent organization of the homologues of PHA synthase <it>phaC1 </it>and PHA granule binding protein <it>phaP </it>was conserved in the strain TD01, which was also observed in some halophiles and non-halophiles exclusively from <it>γ-proteobacteria</it>. In contrast to haloarchaea, the proteome of <it>Halomonas </it>sp. TD01 did not show obvious inclination towards acidity relative to non-halophilic <it>Escherichia coli </it>MG1655, which signified that <it>Halomonas </it>sp. TD01 preferred the accumulation of organic osmolytes to ions in order to balance the intracellular osmotic pressure with the environment.</p> <p>Conclusions</p> <p>The accessibility of genome information would facilitate research on the genetic engineering of halophilic bacteria including <it>Halomonas </it>sp. TD01.</p>