Discovery of a new polyhydroxyalkanoate synthase from limestone soil through metagenomic approach

Journal of Bioscience and Bioengineering

Volumn 121, Issue 4, 2016, Pages 355-364

  Tai, Yen Teng ^a   Foong, Choon Pin ^a   Najimudin, Nazalan ^a   Sudesh, Kumar ^a  

^a SCHOOL OF PHYSICS   (Malaysia)

Author keywords

Genome walking; Limestone; Metagenomic; PHA synthase gene; Polyhydroxyalkanoate; Uncultured bacterium

Indexed keywords

BACTERIA; BIODEGRADABLE POLYMERS; CLONING; ENZYMES; LIMESTONE;

BIODEGRADABLE PLASTICS; CHROMOBACTERIUM VIOLACEUM; GENOME-WALKING; METAGENOMIC; PHA SYNTHASES; PHYLOGENETIC CLASSIFICATIONS; POLY-HYDROXYALKANOATE; POLYHYDROXYALKANOATE SYNTHASE;

GENES;

LIMESTONE; POLYHYDROXYALKANOATE SYNTHASE; POLYHYDROXYALKANOIC ACID; ACYLTRANSFERASE; CALCIUM CARBONATE; POLY(3-HYDROXYALKANOIC ACID) SYNTHASE; PRIMER DNA; SOIL;

ARTICLE; CHROMOBACTERIUM VIOLACEUM; CUPRIAVIDUS NECATOR; ENZYME ACTIVITY; GENE; GENE AMPLIFICATION; GENE CLUSTER; GENE EXPRESSION; GENE ISOLATION; GENE SEQUENCE; METAGENOMICS; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; PHAC GENE; PHYLOGENY; CHEMISTRY; CHROMOBACTERIUM; ENZYMOLOGY; GENETICS; ISOLATION AND PURIFICATION; SOIL;

ACYLTRANSFERASES; CALCIUM CARBONATE; CHROMOBACTERIUM; CLONING, MOLECULAR; CUPRIAVIDUS NECATOR; DNA PRIMERS; METAGENOMICS; PHYLOGENY; SOIL;

EID: 84951837920     PISSN: 13891723     EISSN: 13474421     Source Type: Journal    
DOI: 10.1016/j.jbiosc.2015.08.008     Document Type: Article

References (45)

1. Brems A., Dewil R., Baeyens J., Zhang R. Gasification of plastic waste as waste-to-energy or waste-to-syngas recovery route. Nat. Sci. 2013, 5:695-704.
2. Saeed M.O., Hassan M.N., Mujeebu M.A. Assessment of municipal solid waste generation and recyclable materials potential in Kuala Lumpur, Malaysia. Waste Manag. 2009, 29:2209-2213.
3. Lageveen R.G., Huisman G.W., Preusting H., Ketelaar P., Eggink G., Witholt B. Formation of polyesters by Pseudomonas oleovorans: effect of substrates on formation and composition of poly-(R)-3-hydroxyalkanoates and poly-(R)-3-hydroxyalkenoates. Appl. Environ. Microbiol. 1988, 54:2924-2932.
4. Kahar P., Tsuge T., Taguchi K., Doi Y. High yield production of polyhydroxyalkanoates from soybean oil by Ralstonia eutropha and its recombinant strain. Polym. Degrad. Stab. 2004, 83:79-86.
5. Valappil S.P., Misra S.K., Boccaccini A.R., Keshavarz T., Bucke C., Roy I. Large-scale production and efficient recovery of PHB with desirable material properties, from the newly characterised Bacillus cereus SPV. J. Biotechnol. 2007, 132:251-258.
6. Lau N.S., Chee J.Y., Tsuge T., Sudesh K. Biosynthesis and mobilization of a novel polyhydroxyalkanoate containing 3-hydroxy-4-methylvalerate monomer produced by Burkholderia sp. USM (JCM15050). Bioresour. Technol. 2010, 101:7916-7923.
7. Bhubalan K., Kam Y.C., Yong K.H., Sudesh K. Cloning and expression of the PHA synthase gene from a locally isolated Chromobacterium sp. USM2. Malays. J. Microbiol. 2010, 6:81-90.
8. Doi Y. Microbial polyesters 1990, VCH Publishers, Inc., Tokyo Institute of Technology, Yokohama.
9. Amann R.I., Ludwig W., Schleifer K.-H. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 1995, 59:143-169.
10. Schloss P.D., Handelsman J. Biotechnological prospects from metagenomics. Curr. Opin. Biotechnol. 2003, 14:303-310.
11. Sturgeon A., Stull J.W., Costa M.C., Weese J.S. Metagenomic analysis of the canine oral cavity as revealed by high-throughput pyrosequencing of the 16S rRNA gene. Vet. Microbiol. 2013, 162:891-898.
12. Bibby K., Peccia J. Identification of viral pathogen diversity in sewage sludge by metagenome analysis. Environ. Sci. Technol. 2013, 47:1945-1951.
13. Rashamuse K.J., Visser D.F., Hennessy F., Kemp J., Roux-van der Merwe M.P., Badenhorst J., Ronneburg T., Francis-Pope R., Brady D. Characterisation of two bifunctional cellulase-xylanase enzymes isolated from a bovine rumen metagenome library. Curr. Microbiol. 2013, 66:145-151.
14. Schallmey M., Ly A., Wang C., Meglei G., Voget S., Streit W.R., Driscoll B.T., Charles T.C. Harvesting of novel polyhydroxyalkanaote (PHA) synthase encoding genes froma soil metagenome library using phenotypic screening. FEMS Microbiol. Lett. 2011, 321:150-156.
15. Cheema S., Bassas-Galia M., Sarma P.M., Lal B., Arias S. Exploiting metagenomic diversity for novel polyhydroxyalkanoate synthases: production of a terpolymer poly(3-hydroxybutyrate-co-3-hydroxyhexanoate-co-3-hydroxyoctanoate) with a recombinant Pseudomonas putida strain. Bioresour. Technol. 2012, 103:322-328.
16. Frisli T., Haverkamp T.H.A., Jakobsen K.S., Stenseth N.C., Rudi K. Estimation of metagenome size and structure in an experimental soil microbiota from low coverage next-generation sequence data. J. Appl. Microbiol. 2012, 114:141-151.
17. Cheng G., Hu Y., Lu N., Li J., Wang Z., Chen Q., Zhu B. Identification of a novel fosfomycin-resistant UDP-N-acetylglucosamine enolpyruvyl transferase (MurA) from a soil metagenome. Biotechnol. Lett. 2013, 35:273-278.
18. Carpa R., Butiuc-Keul A., Lupan I., Barbu-Tudoran L., Muntean V., Dobrotă C. Poly-β-hydroxybutyrate accumulation in bacterial consortia from different environments. Can. J. Microbiol. 2012, 58:660-667.
19. Doi Y., Kitamura S., Abe H. Microbial synthesis and characterization of poly(3-hydroxybutyrate-co-3-hydroxyhexanoate). Macromolecules 1995, 28:4822-4828.
20. Kovach M.E., Elzer P.H., Hill D.S., Robertson G.T., Farris M.A., Roop R.M., Peterson K.M. Four new derivatives of the broad-host-range cloning vector pBBR1MCS, carrying different antibiotic-resistance cassettes. Gene 1995, 166:175-176.
21. Zhou J., Bruns M.A., Tiedje J.M. DNA recovery from soils of diverse composition. Appl. Environ. Microbiol. 1996, 62:316-322.
22. Romo D.M.R., Grosso M.V., Solano N.C.M., Castano D.M. A most effective method for selecting a broad range of short and medium-chain-length polyhidroxyalcanoate producing microorganisms. Electron. J. Biotechnol. 2007, 10:348-357.
23. Michinaka A., Arou J., Onuki M., Satoh H., Mino T. Analysis of polyhydroxyalkanoate (PHA) synthase gene in activated sludge that produces PHA containing 3-hydroxy-2-methylvalerate. Biotechnol. Bioeng. 2006, 96:871-880.
24. Foong C.P., Lau N.-S., Deguchi S., Toyofuku T., Taylor T.D., Sudesh K., Matsui M. Whole genome amplification approach reveals novel polyhydroxyalkanoate synthases (PhaCs) from Japan trench and nankai trough seawater. BMC Microbiol. 2014, 14:318.
25. Hall T.A. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. Ser. 1999, 41:95-98.
26. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 2011, 28:2731-2739.
27. Uchiyama T., Watanabe K. Improved inverse PCR scheme for metagenome walking. BioTechniques 2006, 41:183-188.
28. Simon R., Priefer U., Pühler A. A broad host range mobilization system for in vivo genetic engineering: transposon mutagenesis in Gram-negative bacteria. Nat. Biotechnol. 1983, 1:784-791.
29. Wong Y.-M., Brigham C.J., Rha C., Sinskey A.J., Sudesh K. Biosynthesis and characterization of polyhydroxyalkanoate containing high 3-hydroxyhexanoate monomer fraction from crude palm kernel oil by recombinant Cupriavidus necator. Bioresour. Technol. 2012, 121:320-327.
30. Bradford M.M. Rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem. 1976, 72:248-254.
31. de Roo G., Ren Q., Witholt B., Kessler B. Development of an improved in vitro activity assay for medium chain length PHA polymerases based on CoenzymeA release measurements. J. Microbiol. Methods 2000, 41:1-8.
32. Takase K., Matsumoto K., Taguchi S., Doi Y. Alteration of substrate chain-length specificity of type II synthase for polyhydroxyalkanoate biosynthesis by in vitro evolution: in vivo and in vitro enzyme assays. Biomacromolecules 2004, 5:480-485.
33. Gerngross T.U., Snell K.D., Peoples P., Sinskey A.J. Overexpression and purification of the soluble polyhydroxyalkanoate synthase from Alcaligenes eutrophus: evidence for a required posttranslational modification for catalytic activity. Biochemistry 1994, 33:9311-9320.
34. Monroe J.S., Wicander R. The changing earth: exploring geology and evolution 2009, Brooks/Cole, USA.
35. Scoffin T.P. An introduction to carbonate sediments and rocks 1987, Blackie & Son Ltd., USA.
36. Rehm B.H.A. Polyester synthases: natural catalysts for plastics. Biochem. J. 2003, 376:15-33.
37. Gerngross T.U., Martin D.P. Enzyme-catalyzed synthesis of poly[(R)-(-)-3-hydroxybutyrate]: formation of macroscopic granules in vitro. Proc. Natl. Acad. Sci. USA 1995, 92:6279-6283.
38. Bhubalan K., Chuah J.-A., Shozui F., Brigham C.J., Taguchi S., Sinskey A.J., Rha C., Sudesh K. Characterization of the highly active polyhydroxyalkanoate synthase of Chromobacterium sp. strain USM2. Appl. Environ. Microbiol. 2011, 77:2926-2933.
39. Reinecke F., Steinbüchel A. Ralstonia eutropha strain H16 as model organism for PHA metabolism and for biotechnological production of technically interesting biopolymers. J. Mol. Microbiol. Biotechnol. 2009, 16:91-108.
40. Akiyama M., Tsuge T., Doi Y. Environmental life cycle comparison of polyhydroxyalkanoates produced from renewable carbon resources by bacterial fermentation. Polym. Degrad. Stab. 2003, 80:183-194.
41. Schlegel H.G., Lafferty R., Kraus I. The isolation of mutants not accumulating poly-β-hydroxybutyric acid. Arch. Microbiol. 1970, 71:283-294.
42. -4. PLoS One 2014, 9:e95907.
43. Rehm B.H.A., Steinbüchel A. Biochemical and genetic analysis of PHA synthases and other proteins required for PHA synthesis. Int. J. Biol. Macromol. 1999, 25:3-19.
44. Rehm B.H.A., Antonio R.V., Spiekermann P., Amara A.A., Steinbüchel A. Molecular characterization of the poly(3-hydroxybutyrate) (PHB) synthase from Ralstonia eutropha: in vitro evolution, site-specific mutagenesis and development of a PHB synthase protein model. Biochim. Biophys. Acta 2002, 1594:178-190.
45. Chen Y.J., Tsai P.C., Hsu C.H., Lee C.Y. Critical residues of class II PHA synthase for expanding the substrate specificity and enhancing the biosynthesis of polyhydroxyalkanoate. Enzyme Microb. Technol. 2014, 56:60-66.