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

Yu Wei Wu, Shih Hung Yang, Myung Hwangbo, Kung Hui Chu

Research output: Contribution to journalArticle

Abstract

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.

Original languageEnglish
Article numbere0222143
JournalPLoS ONE
Volume14
Issue number9
DOIs
Publication statusPublished - Jan 1 2019

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Clustered Regularly Interspaced Short Palindromic Repeats
polyhydroxybutyrate
Multigene Family
multigene family
Glycerol
glycerol
Genes
Genome
genome
Nitrates
genes
Gammaproteobacteria
DNA Viruses
Biofuels
Petroleum
Bacteriophages
Plastics
Antiviral Agents
Zobellella
synthesis

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Cite this

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. / Wu, Yu Wei; Yang, Shih Hung; Hwangbo, Myung; Chu, Kung Hui.

In: PLoS ONE, Vol. 14, No. 9, e0222143, 01.01.2019.

Research output: Contribution to journalArticle

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