Analysis of Zobellella denitrificans ZD1 draft genome: Genes and gene clusters responsible for high polyhydroxybutyrate (PHB) production from glycerol under saline conditions and its CRISPR-Cas system

English version

Autoři: Yu-Wei Wu ^aff001; Shih-Hung Yang ^aff003; Myung Hwangbo ^aff003; Kung-Hui Chu ^aff003
Působiště autorů: Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan ^aff001; Clinical Big Data Research Center, Taipei Medical University Hospital, Taipei, Taiwan ^aff002; Zachry Department of Civil and Environmental Engineering, Texas A&M University, College Station, TX, United States of America ^aff003
Vyšlo v časopise: PLoS ONE 14(9)
Kategorie: Research Article
doi: https://doi.org/10.1371/journal.pone.0222143

Souhrn

Polyhydroxybutyrate (PHB) is biodegradable and renewable and thus considered as a promising alternative to petroleum-based plastics. However, PHB production is costly due to expensive carbon sources for culturing PHB-accumulating microorganisms under sterile conditions. We discovered a hyper PHB-accumulating denitrifying bacterium, Zobellella denitrificans ZD1 (referred as strain ZD1 hereafter) capable of using non-sterile crude glycerol (a waste from biodiesel production) and nitrate to produce high PHB yield under saline conditions. Nevertheless, the underlying genetic mechanisms of PHB production in strain ZD1 have not been elucidated. In this study, we discovered a complete pathway of glycerol conversion to PHB, a novel PHB synthesis gene cluster, a salt-tolerant gene cluster, denitrifying genes, and an assimilatory nitrate reduction gene cluster in the ZD1 genome. Interestingly, the novel PHB synthesis gene cluster was found to be conserved among marine Gammaproteobacteria. Higher levels of PHB accumulation were linked to higher expression levels of the PHB synthesis gene cluster in ZD1 grown with glycerol and nitrate under saline conditions. Additionally, a clustered regularly interspaced short palindromic repeat (CRISPR)-Cas type-I-E antiviral system was found in the ZD1 genome along with a long spacer list, in which most of the spacers belong to either double-stranded DNA viruses or unknown phages. The results of the genome analysis revealed strain ZD1 used the novel PHB gene cluster to produce PHB from non-sterile crude glycerol under saline conditions.

Klíčová slova:

Physical sciences – Chemistry – Chemical compounds – Nitrates – Nitrites – Ammonia – Polymer chemistry – Monomers – Glycerol – Environmental chemistry – Biology and life sciences – Evolutionary biology – Evolutionary systematics – Phylogenetics – Phylogenetic analysis – Taxonomy – Bioengineering – CRISPR – Synthetic biology – Synthetic bioengineering – Genome engineering – Synthetic genome editing – Synthetic genomics – Organisms – Viruses – Bacteriophages – Computer and information sciences – Data management – Engineering and technology – Ecology and environmental sciences – Denitrification

Zdroje

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Analysis of Zobellella denitrificans ZD1 draft genome: Genes and gene clusters responsible for high polyhydroxybutyrate (PHB) production from glycerol under saline conditions and its CRISPR-Cas system

Souhrn

Klíčová slova:

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