title: Comparative genomics study of polyhydroxyalkanoates (PHA) and ectoine relevant genes from Halomonas sp. TD01 revealed extensive horizontal gene transfer events and co-evolutionary relationships.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  The draft genome of moderately halophilic bacterium, Halomonas 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 in silico. 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 phaC1 and PHA granule binding protein phaP was conserved in the strain TD01, which was also observed in some halophiles and non-halophiles exclusively from γ-proteobacteria. In contrast to haloarchaea, the proteome of Halomonas sp. TD01 did not show obvious inclination towards acidity relative to non-halophilic Escherichia coli MG1655, which signified that Halomonas sp. TD01 preferred the accumulation of organic osmolytes to ions in order to balance the intracellular osmotic pressure with the environment.
  
  
  CONCLUSIONS
  The accessibility of genome information would facilitate research on the genetic engineering of halophilic bacteria including Halomonas sp. TD01.
authors: Department of Biological Sciences and Biotechnology, MOE Key Lab, Bioinformatics (& System Biology), Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.
authors: Lei
authors: L
authors: Cai
authors: Dan
authors: D
authors: Tan
authors: Gulsimay
authors: G
authors: Aibaidula
authors: Xin-Ran
authors: XR
authors: Dong
authors: Jin-Chun
authors: JC
authors: Chen
authors: Wei-Dong
authors: WD
authors: Tian
authors: Guo-Qiang
authors: GQ
authors: Chen
mesh_terms: D000595:Amino Acid Sequence; D000599:Amino Acids, Diamino / Q000378:metabolism*; D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D019143:Evolution, Molecular; D022761:Gene Transfer, Horizontal; D023281:Genomics; D020632:Halomonas / Q000737:chemistry / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D008969:Molecular Sequence Data; D010802:Phylogeny; D054813:Polyhydroxyalkanoates / Q000378:metabolism*; D016415:Sequence Alignment
chemical_list: D000599:Amino Acids, Diamino; D001426:Bacterial Proteins; D054813:Polyhydroxyalkanoates; C045628:ectoine