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.
Microb Cell Fact. 2011 Nov 1;10:88. doi: 10.1186/1475-2859-10-88.
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.
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.
The accessibility of genome information would facilitate research on the genetic engineering of halophilic bacteria including Halomonas sp. TD01.
嗜盐菌在聚羟基烷酸酯（PHA）的工业生产中表现出重要作用，并且在遗传工程改造方面受到越来越多的关注。然而，迄今为止，关于嗜盐菌的基因组学和 PHA 相关基因的信息还很少披露。
通过计算方法分析了具有工业生产短链长聚羟基烷酸酯（PHA）潜力的中度嗜盐菌 Halomonas sp. TD01 的基因组草图，以揭示渗透压调节机制以及与 PHA 和章鱼胺合成相关的酶的进化关系。对参与 PHA 和渗透物代谢的基因进行了注释和计算机研究。尽管 PHA 合酶、解聚酶、调节剂/抑制剂和 phasin 都参与了 PHA 代谢途径，但它们在不同菌株的基因组中表现出不同的水平基因转移（HGT）事件。相比之下，在同一基因组中观察到章鱼胺基因的共发生更为频繁，并且章鱼胺基因比 PHA 相关基因更可能发生偶然的水平基因转移。此外，PHA 合酶 phaC1 和 PHA 颗粒结合蛋白 phaP 的同源物在 TD01 菌株中的相邻组织被保守，这种情况也在一些嗜盐菌和非嗜盐菌中观察到，仅限于γ-变形菌。与盐杆菌不同，Halomonas sp. TD01 的蛋白质组相对于非嗜盐大肠杆菌 MG1655 没有明显的偏向酸性，这表明 Halomonas sp. TD01 更倾向于积累有机渗透物而不是离子，以平衡细胞内渗透压与环境。
基因组信息的可及性将有助于包括 Halomonas sp. TD01 在内的嗜盐菌的遗传工程研究。
