Detection and speciation of bacteria through PCR using universal major cold-shock protein primer oligomers

Journal of Industrial Microbiology and Biotechnology

Volumn 19, Issue 4, 1997, Pages 286-293

  Francis, K P ^a   Stewart, G S A B ^a  

^a UNIVERSITY OF NOTTINGHAM   (United Kingdom)

Author keywords

Bacterial detection; Major cold shock protein; PCR; Universal primer oligomers

Indexed keywords

OLIGOMER; PRIMER DNA;

ARTICLE; BACTERIUM DETECTION; BACTERIUM IDENTIFICATION; GENE AMPLIFICATION; GENE SEQUENCE; GRAM NEGATIVE BACTERIUM; GRAM POSITIVE BACTERIUM; NONHUMAN; POLYMERASE CHAIN REACTION; SEQUENCE HOMOLOGY;

AMINO ACID SEQUENCE; BACTERIA; BACTERIAL PROTEINS; BASE SEQUENCE; DNA PRIMERS; MOLECULAR SEQUENCE DATA; POLYMERASE CHAIN REACTION;

AEROMONAS; BACTERIA (MICROORGANISMS); CITROBACTER; ENTEROBACTER; ENTEROCOCCUS; ESCHERICHIA; KLEBSIELLA; LACTOBACILLUS; LACTOCOCCUS; LISTERIA; NEGIBACTERIA; PEDIOCOCCUS; PHOTOBACTERIUM; POSIBACTERIA; SALMONELLA; SHIGELLA; STAPHYLOCOCCUS; STREPTOCOCCUS; YERSINIA;

EID: 0031463654     PISSN: 13675435     EISSN: None     Source Type: Journal    
DOI: 10.1038/sj.jim.2900463     Document Type: Article

References (42)

1. Altschull SF, W Gish, W Miller, EW Myers and DJ Lipman. 1990. Basic local alignment search tool. J Mol Biol 215: 403-410. Program utilized via GenBank at National Center for Biotechnology Information, Bethesda, MD, USA.
2. Ausubel FM, R Brent, RE Kingston, DD Moore, JG Seidman, JA Smith and K Struhl. 1995. Current Protocols in Molecular Biology. Section 1: 1.8.4. Wiley, USA.
3. Av-Gay Y, Y Aharonowitz and G Cohen. 1992. Streptomyces contain a 7.0 kDa cold shock like protein. Nucl Acids Res 20: 5478.
4. Berger F, N Morellet, F Menu and P Potier. 1996. Cold shock and cold acclimation proteins in the psychrotrophic bacterium Arthrobacter globiformis S155. J Bacteriol 178: 2999-3007.
5. Blattner FR, G Plunkett, GF Meyhew, NT Perna and FD Glasner. 1997. E. coli genome project. GenBank/EMBL/DDBJ accession No. AE000252(g1787834).
6. Burd CG and G Dreyfuss 1994 Conserved structures and diversity of functions of RNA-binding proteins. Science 265: 615-621.
7. Devlin K and CM Churcher. 1997. Mycobacterium tuberculosis sequencing project. Gen/Bank/EMBL/DDBJ accession no. Z95436.
8. Didier DK, J Schiffenbauer, SL Woulfe, M Zachris and BD Schwartz. 1988. Characterization of the cDNA encoding a protein binding to the major histocompatibility complex class II Y box. Proc Natl Acad Sci USA 85: 7322-7326.
9. Fleischmann RD, MD Adams, O White, RA Clayton, EF Kirkness, AR Kerlavage, CJ Bult, J-F Tomb, BA Dougherty, JM Merrick, K McKenney, G Sutton, W FitzHugh, C Fields, JD Gocayne, J Scott, R Shirley, L Liu, A Glodek, JM Kelley, JF Weidman, CA Phillips, T Spriggs, E Hedblom, MD Cotton, TR Utterback, MC Hanna, DT Nguyen, DM Saudek, RC Brandon, LD Fine, JL Fritchman, JL Fuhrmann, NSM Geoghagen, CL Gnehm, LA McDonald, KV Small, CM Fraser, HO Smith and JC Venter. 1995. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269: 496-512.
10. Francis KP, CED Rees and GSAB Stewart. 1995. Identification of a major cold-shock protein homologue in Listeria monocytogenes. GenBank/EMBL/DDBJ accession No. X91789.
11. Francis KP and GSAB Stewart. 1997. Gene duplication: a mechanism for the evolution of major cold-shock protein families? GenBank/EMBL/DDBJ accession No. AF003591.
12. Goldenberg D, I Azar and AB Oppenheim. 1996. Different mRNA stability of the cspA gene in the cold-shock response of Escherichia coli. Mol Microbiol 19: 241-248.
13. Goldstein J, NS Pollitt and M Inouye. 1990. Major cold shock protein of Escherichia coli. Proc Natl Acad Sci USA 87: 283-287.
14. Glavac D and M Dean. 1993. Optimization of the single strand-conformational polymorphism (SSCP) technique for detection of point mutations. Hum Mutat 2: 404-414.
15. Graumann P and MA Marahiel. 1994. The major cold shock protein of Bacillus subtilis CspB binds with high affinity to the ATTGG- and CCAAT sequences in single stranded oligonucleotides. FEBS Lett 338: 157-160.
16. Graumann P, K Schroder, R Schmid and MA Marahiel. 1996. Cold shock stress-induced proteins in Bacillus subtilis. J Bacteriol 178: 4611-4619.
17. Hebraud M, E Dubois, P Potier and J Labadie. 1994. Effect of growth temperature on the protein levels in the pychrotrophic bacterium, Pseudomonas fragi. J Bacteriol 176: 4017-4024.
18. Holt JG, NR Krieg, PHA Sneath, JT Staley and ST Williams (eds). 1994. Bergey's Manual of Determinative Bacteriology (9th edn). Williams and Wilkins, Baltimore.
19. Jones PG, RA VanBogelen and FC Neidhardt. 1987. Induction of proteins in response to low temperature in Escherichia coli. J Bacteriol 169: 2092-2095.
20. Jones PG and M Inouye. 1994. The cold-shock response - a hot topic. Mol Microbiol 11: 811-818.
21. Landsman D. 1992. RNP-1, an RNA-binding motif is conserved in the DNA-binding cold shock domain. Nucl Acids Res 20: 2861-2864.
22. Law RM and AK Bej. 1993. Identification and characterization of cspS, a cold shock related gene from Salmonella typhimurium. GenBank/EMBL/DDBJ accession No. L23115.
23. Lee SJ, A Xie, W Jiang, J-P Etchegaray, PG Jones and M Inouye. 1994. Family of the major cold-shock protein, CspA (CS7.4), of Escherichia coli, whose members show a high sequence similarity with the eukaryotic Y-box binding proteins. Mol Microbiol 11: 833-839.
24. Livak KJ, J Marmaro and JA Todd. 1995. Towards fully automated genome-wide polymorphism screening. Nature Genet 9: 341-342.
25. Mayo B, S Derzell, M Fernandez, C Leonard, T Ferain, P Hols, J Suarez and J Delcour. 1996. Cloning and characterization of cspL and cspP, two cold-inducible genes from Lactobacillus plantarum. J Bacteriol 179: 3039-3042.
26. Mayr B, T Kaplan, S Lechner and S Scherer. 1996. Identification and purification of a family of dimeric major cold shock protein homologs from the psychrotrophic Bacillus cereus WSBC 10201. J Bacteriol 178: 2916-2925.
27. Michel V, J Labadie and M Hebraud. 1996. Effect of different temperature upshifts on protein synthesis by the psychrotrophic bacterium Pseudomonas fragi. Curr Microbiol 33: 16-25.
28. Nakashima K, K Kanamaru, T Mizuno and K Horikoshi. 1996. A novel member of the cspA family of genes that is induced by cold shock in Escherichia coli. J Bacteriol 178: 2994-2997.
29. Qian L and M Wilkinson. 1991. DNA fragment purification-removal of agarose 10 minutes after electrophoresis. Biotechniques 10: 736.
30. Ray MK, T Sitaramamma, S Ghandhi and S Shivaji. 1994. Occurrence and expression of cspA, a cold shock gene, in Antarctic psychrotrophic bacteria. FEMS Microbiol Lett 116: 55-60.
31. Schindelin H, MA Marahiel and U Heinemann. 1993. Universal nucleic acid-binding domain revealed by crystal structure of the B. subtilis major cold-shock protein. Nature 364: 164-168.
32. Schnuchel A, R Wiltscheck, M Czisch, M Herrier, G Willimsky, P Graumann, MA Marahiel and TA Holak. 1993. Structure in solution of the major cold-shock protein from Bacillus subtilis. Nature 364: 169-171.
33. Schroder K, P Zuber, G Willimsky, B Wagner and M Marahiel. 1993. Mapping of the Bacillus subtilis cspB gene and cloning of its homologs in thermophilic, mesophilic and psychrotrophic bacilli. Gene 136: 277-280.
34. Schroder K, P Graumann, A Schnuchel, TA Holak and MA Marahiel. 1995. Mutational analysis of the putative nucleic acid-binding surface of the cold-shock domain, CspB, revealed an essential role of aromatic and basic residues in binding of single-stranded DNA containing the Y-box motif. Mol Microbiol 16: 699-708.
35. Smith CM, WH Koch, SB Franklin, PL Foster, TA Cebula and E Eisenstadt. 1990. Sequence analysis and mapping of the Salmonella typhimurium LT2 umuDC operon. J Bacteriol 172: 4964-4978.
36. Stamm I, A Leclerque and W Plaga. 1996. A gene encoding a cold shock-like protein (Csp) from Stigmatella aurantiaca. GenBank/EMBL/DDBJ accession No. U70990.
37. Tafuri SR and AP Wolffe. 1990. Xenopus Y-box transcription factors molecular cloning, functional analysis, and developmental regulation. Proc Natl Acad Sci USA 87: 9028-9032.
38. Verpy E, M Biasotto, T Meo and M Tosi. 1994. Efficient detection of point mutations on color-coded strands of target DNA. Proc Natl Acad Sci USA 91: 1873-1877.
39. Willimsky G, H Bang, G Fischer and MA Marahiel. 1992. Characterization of cspB, a Bacillus subtilis inducible cold shock gene affecting cell viability at low temperatures. J Bacteriol 174: 6326-6335.
40. Wistow G. 1990. Cold shock and DNA binding. Nature 344: 823-824.
41. Witham PK, CT Yamashiro, KJ Livak and CA Batt. 1996. A PCR-based assay for the detection of Escherichia coli shiga-like toxin genes in ground beef. Appl Environ Microbiol 62: 1347-1353.
42. Wolffe AP. 1994. Structural and functional properties of the evolutionarily ancient Y-box family of nucleic acid binding proteins. Bioessays 16: 245-251.