Cloning of prokaryotic genes by a universal degenerate primer PCR

FEMS Microbiology Letters

Volumn 287, Issue 2, 2008, Pages 192-198

  Ping, Liyan ^a   Vogel, Heiko ^a   Boland, Wilhelm ^a  

^a MAX PLANCK INSTITUTE FOR CHEMICAL ECOLOGY   (Germany)

Author keywords

Degenerate primer; Gene cloning; PCR; Shine Dalgarno sequence

Indexed keywords

BACTERIAL DNA;

ARTICLE; BACTERIAL GENE; DNA TEMPLATE; GENE SEQUENCE; MELTING POINT; MOLECULAR CLONING; NONHUMAN; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROKARYOTE;

BACTERIA; BACTERIAL PROTEINS; CLONING, MOLECULAR; DNA PRIMERS; POLYMERASE CHAIN REACTION;

PROKARYOTA;

EID: 51349142712     PISSN: 03781097     EISSN: 15746968     Source Type: Journal    
DOI: 10.1111/j.1574-6968.2008.01311.x     Document Type: Article

References (26)

1. Bibb MJ Buttner MJ (2003) The Streptomyces coelicolor developmental transcription factor sigmaBldN is synthesized as a proprotein. J Bacteriol 185 : 2338 2345.
2. Brady SF, Chao CJ Clardy J (2004) Long-chain N-acyltyrosine synthases from environmental DNA. Appl Environ Microbiol 70 : 6865 6870.
3. Carballeira N, Nazabal M, Brito J Garcia O (1990) Purification of a thermostable DNA polymerase from Thermus thermophilus HB8, useful in the polymerase chain reaction. BioTechniques 9 : 276 281.
4. Carvalho WS, de Miranda SS, Costa KM et al 2003) Low-stringency single-specific-primer PCR as a tool for detection of mutations in the rpoB gene of rifampin-resistant Mycobacterium tuberculosis. J Clin Microbiol 41 : 3384 3386.
5. Cheung VG Nelson SF (1996) Whole genome amplification using a degenerate oligonucleotide primer allows hundreds of genotypes to be performed on less than one nanogram of genomic DNA. Proc Natl Acad Sci USA 93 : 14676 14679.
6. Corvey C, Stein T, Duesterhus S, Karas M Entian K-D (2003) Activation of subtilin precursors by Bacillus subtilis extracellular serine proteases subtilisin (AprE), WprA, and Vpr. Biochem Biophys Res Commun 304 : 48 54.
7. Cuny C Witte W (1996) Typing of Staphylococcus aureus by PCR for DNA sequences flanked by transposon Tn916 target region and ribosomal binding site. J Clin Microbiol 34 : 1502 1505.
8. Dale GE, Langen H, Page MGP, Then RL Stüber D (1995) Cloning and characterization of a novel, plasmid-encoded trimethoprim-resistant dihydrofolate reductase from Staphylococcus haemolyticus MUR313. Antimicrob Agents Chemother 39 : 1920 1924.
9. Fleming JT, Yao W-H Sayler GS (1998) Optimization of differential display of prokaryotic mRNA: application to pure culture and soil microcosms. Appl Environ Microbiol 64 : 3698 3706.
10. Gold L, Pribnow D, Schneider T, Shinedling S, Singer BS Stormo G (1981) Translational initiation in prokaryotes. Annu Rev Microbiol 35 : 365 403.
11. Green-Willms NS, Fox TD Costanzo MC (1998) Functional interactions between yeast mitochondrial ribosomes and mRNA 5′ untranslated leaders. Mol Cell Biol 18 : 1826 1834.
12. Hacker J, Hentschel U Dobrindt U (2003) Prokaryotic chromosomes and disease. Science 301 : 790 793.
13. Hamann C, Hegemann J Hildebrandt A (1999) Detection of polycyclic aromatic hydrocarbon degradation genes in different soil bacteria by polymerase chain reaction and DNA hybridization. FEMS Microbiol Lett 173 : 255 263.
14. Hazle T Bonen L (2007) Comparative analysis of sequences preceding protein-coding mitochondrial genes in flowering plants. Mol Biol Evol 24 : 1101 1112.
15. Hirose T Sugiura M (2004) Functional Shine-Dalgarno-like sequences for translational initiation of chloroplast mRNAs. Plant Cell Physiol 45 : 114 117.
16. Koc EC Spremulli LL (2002) Identification of mammalian mitochondrial translational initiation factor 3 and examination of its role in initiation complex formation with natural mRNAs. J Biol Chem 277 : 35541 35549.
17. Lin N-T Tseng Y-H (1997) Sequence and copy number of the Xanthomonas campestris pv. campestris gene encoding 16S rRNA. Biochem Biophys Res Commun 235 : 276 280.
18. Netto dos Santos KR, de Souza Fonseca L, Martins Teixeira L Pinto Gontijo Filho P (2001) Typing of Staphylococcus aureus from surgical site infections: comparison of pulsed-field gel electrophoresis (PFGE) and PCR technique using repetitive extragenic palindromic (rep) and Tn916-Shine-Dalgarno (TnSD) target sequences. Int J Med Microbiol 291 : 231 236.
19. Piel J (2002) A polyketide synthase-peptide synthetase gene cluster from an uncultured bacterial symbiont of Paederus beetles. Proc Natl Acad Sci USA 99 : 14002 14007.
20. Ping L, Buchler R, Mithofer A et al 2007) A novel Dps-type protein from insect gut bacteria catalyses hydrolysis and synthesis of N-acyl amino acids. Environ Microbiol 9 : 1572 1583.
21. Puskas LG Bottka S (1994) Prokaryotic test system for evaluation of oligonucleotide-affected antisense inhibition. Anal Biochem 222 : 305 309.
22. Rosenthal A, MacKinnon RN Jones DS (1991) PCR walking from microdissection clone M54 identifies three exons from the human gene for the neural cell adhesion molecule L1 (CAM-L1). Nucleic Acids Res 19 : 5395 5401.
23. Sazuka T Ohara O (1996) Sequence features surrounding the translation initiation sites assigned on the genome sequence of Synechocystis sp. strain PCC6803 by amino-terminal protein sequencing. DNA Res 3 : 225 232.
24. Shen Z, Liu J, Wells RL Elkind MM (1993) Cycle sequencing using degenerate primers containing inosines. BioTechniques 15 : 82 89.
25. Shine J Dalgarno L (1974) The 3′-terminal sequence of Escherichia coli 16S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites. Proc Natl Acad Sci USA 71 : 1342 1346.
26. Yan Y, An C, Li L et al 2003) T-linker-specific ligation PCR (T-linker PCR): an advanced PCR technique for chromosome walking or for isolation of tagged DNA ends. Nucleic Acids Res 31 : e68.