Abstract
BackgroundHalophilic 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.ResultsThe 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.ConclusionsThe accessibility of genome information would facilitate research on the genetic engineering of halophilic bacteria including Halomonas sp. TD01.
Highlights
Halophilic bacteria have shown their significance in industrial production of polyhydroxyalkanoates (PHA) and are gaining more attention for genetic engineering modification
The results provided invaluable clues, to the understanding of the evolution and genes transfer, and to the strategic guidance of the genetic engineering of halophilic Halomonas sp
The detailed studies on the PHA synthases from the halophilic archaea have extended our insights on their classification, providing solid evidences to support the existence of a novel subclass (IIIA) synthases with distinguished features from the subclass (IIIB) isolated from bacteria [15]
Summary
Halophilic bacteria have shown their significance in industrial production of polyhydroxyalkanoates (PHA) and are gaining more attention for genetic engineering modification. Polyhydroxyalkanoates (PHA) were firstly discovered in prokaryotes as carbon and energy storage materials [1] They are one of the most promising members of biodegradable polymers, which are considered as environmentally friendly substitutes of petrochemical-derived plastics [2]. As the market for green plastics has been growing rapidly, demand for a more productive and low cost PHA production process is evident [1] Some microorganisms, such as Ralstonia eutropha and genetically engineered Escherichia coli, were thoroughly investigated as PHA industrial producers with high productivity, the research and development of strains and methods with further reduced cost were still necessary for PHA commercialization [3,4,5,6]
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