title: Whole genome amplification approach reveals novel polyhydroxyalkanoate synthases (PhaCs) from Japan Trench and Nankai Trough seawater.
abstract: BACKGROUND
  Special features of the Japanese ocean include its ranges of latitude and depth. This study is the first to examine the diversity of Class I and II PHA synthases (PhaC) in DNA samples from pelagic seawater taken from the Japan Trench and Nankai Trough from a range of depths from 24 m to 5373 m. PhaC is the key enzyme in microorganisms that determines the types of monomer units that are polymerized into polyhydroxyalkanoate (PHA) and thus affects the physicochemical properties of this thermoplastic polymer. Complete putative PhaC sequences were determined via genome walking, and the activities of newly discovered PhaCs were evaluated in a heterologous host.
  
  
  RESULTS
  A total of 76 putative phaC PCR fragments were amplified from the whole genome amplified seawater DNA. Of these 55 clones contained conserved PhaC domains and were classified into 20 genetic groups depending on their sequence similarity. Eleven genetic groups have undisclosed PhaC activity based on their distinct phylogenetic lineages from known PHA producers. Three complete DNA coding sequences were determined by IAN-PCR, and one PhaC was able to produce poly(3-hydroxybutyrate) in recombinant Cupriavidus necator PHB-4 (PHB-negative mutant).
  
  
  CONCLUSIONS
  A new functional PhaC that has close identity to Marinobacter sp. was discovered in this study. Phylogenetic classification for all the phaC genes isolated from uncultured bacteria has revealed that seawater and other environmental resources harbor a great diversity of PhaCs with activities that have not yet been investigated. Functional evaluation of these in silico-based PhaCs via genome walking has provided new insights into the polymerizing ability of these enzymes.
authors.affiliation: Synthetic Genomics Research Team, Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, Kanagawa, 230-0045, Japan. choonpin10@gmail.com.|Ecobiomaterial Research Laboratory, School of Biological Sciences, Universiti Sains Malaysia, 11800, Gelugor, Penang, Malaysia. choonpin10@gmail.com.
authors.forename: Choon Pin
authors.initials: CP
authors.lastname: Foong
authors.affiliation: Synthetic Genomics Research Team, Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, Kanagawa, 230-0045, Japan. nyoksean86@gmail.com.|Centre for Chemical Biology, Universiti Sains Malaysia, 11800, Gelugor, Penang, Malaysia. nyoksean86@gmail.com.
authors.forename: Nyok-Sean
authors.initials: NS
authors.lastname: Lau
authors.affiliation: R&D Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan. shigeru.deguchi@jamstec.go.jp.
authors.forename: Shigeru
authors.initials: S
authors.lastname: Deguchi
authors.affiliation: R&D Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan. toyofuku@jamstec.go.jp.
authors.forename: Takashi
authors.initials: T
authors.lastname: Toyofuku
authors.affiliation: Laboratory for Integrated Bioinformatics, Core for Precise Measuring and Modeling, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa, 230-0045, Japan. taylor@riken.jp.
authors.forename: Todd D
authors.initials: TD
authors.lastname: Taylor
authors.affiliation: Ecobiomaterial Research Laboratory, School of Biological Sciences, Universiti Sains Malaysia, 11800, Gelugor, Penang, Malaysia. ksudesh@usm.my.|Centre for Chemical Biology, Universiti Sains Malaysia, 11800, Gelugor, Penang, Malaysia. ksudesh@usm.my.
authors.forename: Kumar
authors.initials: K
authors.lastname: Sudesh
authors.affiliation: Synthetic Genomics Research Team, Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, Kanagawa, 230-0045, Japan. minami@riken.jp.
authors.forename: Minami
authors.initials: M
authors.lastname: Matsui
mesh_terms: D000217:Acyltransferases / Q000235:genetics* / Q000302:isolation & purification* / Q000378:metabolism; D003001:Cloning, Molecular; D016000:Cluster Analysis; D020118:Cupriavidus necator / Q000235:genetics / Q000378:metabolism; D015870:Gene Expression; D014644:Genetic Variation; D006885:Hydroxybutyrates / Q000378:metabolism; D007564:Japan; D053520:Marinobacter / Q000235:genetics; D056186:Metagenomics; D008969:Molecular Sequence Data; D010802:Phylogeny; D011091:Polyesters / Q000378:metabolism; D012623:Seawater / Q000382:microbiology*; D017422:Sequence Analysis, DNA; D017385:Sequence Homology; D000094122:Polyhydroxybutyrates
chemical_list: D000217:Acyltransferases; D006885:Hydroxybutyrates; D011091:Polyesters; C003182:poly-beta-hydroxybutyrate; D000094122:Polyhydroxybutyrates; C077225:poly(3-hydroxyalkanoic acid) synthase