Retrieval of glycoside hydrolase family 9 cellulase genes from environmental DNA by metagenomic gene specific multi-primer PCR

Biotechnology Letters

Volumn 34, Issue 5, 2012, Pages 875-882

  Xiong, Xiaolong ^a   Yin, Xiaopu ^a   Pei, Xiaolin ^a   Jin, Peng ^a   Zhang, Ao ^a   Li, Yan ^b   Gong, Weibo ^b   Wang, Qiuyan ^a  

^a HANGZHOU NORMAL UNIVERSITY   (China)

^b RandD Center   (China)

Author keywords

Metagenomic gene specific PCR; Multiplex PCR; Sequence diversity

Indexed keywords

AGAROSE GEL; CELLULASE GENES; DEGENERATE PRIMERS; GEL ELECTROPHORESIS; GENE-SPECIFIC PRIMERS; GLYCOSIDE HYDROLASES; HOMOLOGOUS GENES; METAGENOMIC DNA; METAGENOMIC GENE SPECIFIC PCR; METAGENOMIC LIBRARIES; MULTIPLE ALIGNMENT; MULTIPLE GENES; MULTIPLEX PCR; SEQUENCE DIVERSITY; SEQUENCE IDENTITY; SOIL DNA;

DNA; ELECTROPHORESIS; GENES; MULTIPLEXING;

POLYMERASE CHAIN REACTION;

CELLULASE; DNA; GLYCOSIDASE; PRIMER DNA;

AMINO ACID SEQUENCE; ARTICLE; CHEMISTRY; DNA SEQUENCE; GENETIC VARIABILITY; GENETICS; ISOLATION AND PURIFICATION; METABOLISM; METAGENOME; METHODOLOGY; MOLECULAR GENETICS; MULTIPLEX POLYMERASE CHAIN REACTION; NUCLEOTIDE SEQUENCE; SEQUENCE ALIGNMENT; SOIL;

AMINO ACID SEQUENCE; CELLULASE; DNA; DNA PRIMERS; GENETIC VARIATION; GLYCOSIDE HYDROLASES; METAGENOME; MOLECULAR SEQUENCE DATA; MULTIPLEX POLYMERASE CHAIN REACTION; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SOIL;

EID: 84862813474     PISSN: 01415492     EISSN: 15736776     Source Type: Journal    
DOI: 10.1007/s10529-012-0855-1     Document Type: Article

References (18)

1. Bell PJL, Sunna A, Gibbs MD, Curach NC, Nevalainen H et al (2002) Prospecting for novel lipase genes using PCR. Microbiology 148: 2283-2291.
2. Boubakri H, Beuf M, Simonet P, Vogel TM (2006) Development of metagenomic DNA shuffling for the construction of a xenobiotic gene. Gene 375: 87-94.
3. Contreras-Moreira B, Sachman-Ruiz B, Figueroa-Palacios I, Vinuesa P (2009) Primers4clades: a web server that uses phylogenetic trees to design lineage-specific PCR primers for metagenomic and diversity studies. Nucleic Acids Res 37: W95-W100.
4. Cowan D, Meyer Q, Stafford W, Muyanga S, Cameron R et al (2005) Metagenomic gene discovery: past, present and future. Trends Biotechnol 23: 321-329.
5. Crooks GE, Hon G, Chandonia JM, Brenner SE (2004) WebLogo: a sequence logo generator. Genome Res 14: 1188-1190.
6. Daniel R (2005) The metagenomics of soil. Nat Rev Microbiol 3: 470-478.
7. Eschenfeldt WH, Stols L, Rosenbaum H, Khambatta ZS, Quaite-Randall E et al (2001) DNA from uncultured organisms as a source of 2, 5-diketo-d-gluconic acid reductases. Appl Environ Microbiol 67: 4206-4214.
8. Khademi S, Guarino LA, Watanabe H, Tokuda G, Meyer EF (2002) Structure of an endoglucanase from termite, Nasutitermes takasagoensis. Acta Crystallogr D Biol Crystallogr 58: 653-659.
9. Kim B, Kim S, Park J, Park W, Hwang K et al (2007) Sequence-based screening for self-sufficient P450 monooxygenase from a metagenome library. J Appl Microbiol 102: 1392-1400.
10. Kotik M (2009) Novel genes retrieved from environmental DNA by polymerase chain reaction: current genome-walking techniques for future metagenome applications. J Biotechnol 144: 75-82.
11. Labes A, Karlsson EN, Fridjonsson OH, Turner P, Hreggvidson GO et al (2008) Novel members of glycoside hydrolase family 13 derived from environmental DNA. Appl Environ Microbiol 74: 1914-1921.
12. Liebeton K, Eck J (2004) Identification and expression in E. coli of novel nitrile hydratases from the metagenome. Eng Life Sci 4: 557-562.
13. Rose TM, Schultz ER, Henikoff JG, Pietrokovski S, McCallum CM et al (1998) Consensus-degenerate hybrid oligonucleotide primers for amplification of distantly related sequences. Nucleic Acids Res 26: 1628-1635.
14. Rose TM, Henikoff JG, Henikoff S (2003) CODEHOP (COnsensus-DEgenerate Hybrid Oligonucleotide Primer) PCR primer design. Nucleic Acids Res 31: 3763-3766.
15. Streit WR, Schmitz RA (2004) Metagenomics-the key to the uncultured microbes. Curr Opin Microbiol 7: 492-498.
16. Teather RM, Wood PJ (1982) Use of Congo red-polysaccharide interactions in enumeration and characterization of cellulolytic bacteria from the bovine rumen. Appl Environ Microbiol 43: 777-780.
17. Tuffin M, Anderson D, Heath C, Cowan DA (2009) Metagenomic gene discovery: How far have we moved into novel sequence space? Biotechnol J 4: 1671-1683.
18. Wang Q, Wu H, Wang A, Du P, Pei X et al (2010) Prospecting metagenomic enzyme subfamily genes for DNA family shuffling by a novel PCR-based approach. J Biol Chem 285: 41509-41516.