Direct and efficient cloning of full-length genes from environmental DNA by RT-qPCR and modified TAIL-PCR

Applied Microbiology and Biotechnology

Volumn 87, Issue 3, 2010, Pages 1141-1149

  Huang, Huoqing ^a   Wang, Guozeng ^a   Zhao, Yanyu ^a   Shi, Pengjun ^a   Luo, Huiying ^a   Yao, Bin ^a  

^a INSTITUTE OF PLANT PROTECTION   (China)

Author keywords

Environmental DNA; Phytase TAIL PCR; RT qPCR; Xylanase

Indexed keywords

AMPLIFICATION; BIOCHEMISTRY; CLONING; DNA; MOLECULAR BIOLOGY; POLYMERASE CHAIN REACTION;

ENVIRONMENTAL DNA; ENVIRONMENTAL SAMPLE; FLANKING REGIONS; FUNCTIONAL GENES; PCR AMPLIFICATION; PHYTASES; REAL-TIME QUANTITATIVE PCR; RT-QPCR; TECHNICAL CHALLENGES; XYLANASES;

GENES;

DNA; ENVIRONMENTAL DNA; GLYCOSIDASE; GLYCOSIDASE 10; PHYTASE; UNCLASSIFIED DRUG; BACTERIAL DNA; ENDO 1,4 BETA XYLANASE; SEWAGE;

DNA; ENZYME ACTIVITY; GENE EXPRESSION; GENETIC ANALYSIS; MOLECULAR ANALYSIS; POLYMERASE CHAIN REACTION; REAL TIME;

ARTICLE; DNA FLANKING REGION; GENE IDENTIFICATION; GENE SEQUENCE; GENE TARGETING; MODIFIED THERMAL ASYMMETRIC INTERLACED POLYMERASE CHAIN REACTION; MOLECULAR BIOLOGY; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; REAL TIME QUANTITATIVE POLYMERASE CHAIN REACTION; ANIMAL; BACTERIA; BOVINAE; ENZYMOLOGY; EVALUATION STUDY; GENETICS; GOAT; MICROBIOLOGY; MOLECULAR GENETICS; PROCEDURES; RUMINANT STOMACH; SEWAGE;

6-PHYTASE; ANIMALS; BACTERIA; CATTLE; CLONING, MOLECULAR; DNA, BACTERIAL; ENDO-1,4-BETA XYLANASES; ENVIRONMENTAL MICROBIOLOGY; GOATS; MOLECULAR SEQUENCE DATA; POLYMERASE CHAIN REACTION; RUMEN; SEWAGE;

EID: 77955629331     PISSN: 01757598     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00253-010-2613-4     Document Type: Article

References (22)

1. Abulencia CB, Wyborski DL, Garcia JA, Podar M, Chen W, Chang SH, Chang HW, Watson D, Brodie EL, Hazen TC, Keller M (2006) Environmental whole-genome amplification to access microbial populations in contaminated sediments. Appl Environ Microbiol 72:3291-3301
2. Amann RI, Ludwig W, Schleifer KH (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59:143-169
3. Brady SF (2007) Construction of soil environmental DNA cosmid libraries and screening for clones that produce biologically active small molecules. Nat Protoc 2:1297-1305
4. Cantera JJ, Stein LY (2007) Molecular diversity of nitrite reductase genes (nirK) in nitrifying bacteria. Environ Microbiol 9:765-776
5. Henne A, Daniel R, Schmitz RA, Gottschalk G (1999) Construction of environmental DNA libraries in Escherichia coli and screening for the presence of genes conferring utilization of 4- hydroxybutyrate. Appl Environ Microbiol 65:3901-3907
6. Henriques I, Moura A, Alves A, Saavedra MJ, Correia A (2006) Analysing diversity among beta-lactamase encoding genes in aquatic environments. FEMS Microbiol Ecol 56:418-429
7. Huang H, Luo H, Yang P, Meng K, Wang Y, Yuan T, Bai Y, Yao B (2006) A novel phytase with preferable characteristics from Yersinia intermedia. Biochem Biophys Res Commun 350:884-889
8. Huang H, Shi P, Wang Y, Luo H, Shao N, Wang G, Yang P, Yao B (2009) Diversity of beta-propeller phytase genes in the intestinal contents of grass carp provides insight into the release of major phosphorus from phytate in nature. Appl Environ Microbiol 75:1508-1516
9. Jeanmougin F, Thompson JD, Gouy M, Higgins DG, Gibson TJ (1998) Multiple sequence alignment with Clustal X. Trends Biochem Sci 23:403-405
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, Kristjansson JK, Holst O, Schönheit P (2008) Novel members of glycoside hydrolase family 13 derived from environmental DNA. Appl Environ Microbiol 74:1914-1921
12. Liu Y, Whittier RF (1995) Thermal asymmetric interlaced PCR: automatable amplification and sequencing of insert end fragments from P1 and YAC clones for chromosome walking. Genomics 25:674-681
13. Miller GL (1959) Use of dinitrosalicylic acid reagent for determination of reducing sugar. Anal Chem 31:426-428
14. Rose TM, Henikoff JG, Henikoff S (2003) CODEHOP (COnsensus-DEgenerate Hybrid Oligonucleotide Primer) PCR primer design. Nucleic Acids Res 31:3763-3766
15. Singer T, Burke E (2003) High-throughput TAIL-PCR as a tool to identify DNA flanking insertions. Methods Mol Biol 236:241-272
16. Singh J, Behal A, Singla N, Joshi A, Birbian N, Singh S, Bali V, Batra N (2009) Metagenomics: concept, methodology, ecological inference and recent advances. Biotechnol J 4:480-494
17. Sunna A, Bergquist PL (2003) A gene encoding a novel extremely thermostable 1, 4-beta-xylanase isolated directly from an environmental DNA sample. Extremophiles 7:63-70
18. Tang K, Utairungsee T, Kanokratana P, Sriprang R, Champreda V, Eurwilaichitr L, Tanapongpipat S (2006) Characterization of a novel cyclomaltodextrinase expressed from environmental DNA isolated from Bor Khleung hot spring in Thailand. FEMS Microbiol Lett 260:91-99
19. Uchiyama T, Watanabe K (2006) Improved inverse PCR scheme for metagenome walking. Biotechniques 41:183-188
20. Uchiyama T, Abe T, Ikemura T, Watanabe K (2005) Substrate-induced gene-expression screening of environmental metagenome libraries for isolation of catabolic genes. Nat Biotechnol 23:88-93
21. Whitman WB, Coleman DC, Wiebe WJ (1998) Prokaryotes: the unseen majority. Proc Natl Acad Sci USA 95:6578-6583
22. Yokouchi H, Fukuoka Y, Mukoyama D, Calugay R, Takeyama H, Matsunaga T (2006) Whole-metagenome amplification of a microbial community associated with scleractinian coral by multiple displacement amplification using phi29 polymerase. Environ Microbiol 8:1155-1163