Molecular dissection of a bifidobacterial replicon

Applied and Environmental Microbiology

Volumn 73, Issue 24, 2007, Pages 7858-7866

  Cronin, Michelle ^a   Knobel, Moritz ^a   O'Connell Motherway, Mary ^a   Fitzgerald, Gerald F ^a   Van Sinderen, Douwe ^a,b  

^a UNIVERSITY COLLEGE CORK   (Ireland)

^b UNIVERSITY COLLEGE CORK   (Ireland)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; ESCHERICHIA COLI; GENE ENCODING; PROTEINS;

BIFIDOBACTERIUM ASTEROIDES; DNA BINDING; MOLECULAR DISSECTION;

BACTERIA;

BACTERIAL PROTEIN; DNA BINDING PROTEIN; HELICASE;

BACTERIUM; DNA; GENE EXPRESSION; MOLECULAR ANALYSIS; PROTEIN;

ARTICLE; BACTERIAL GENE; BIFIDOBACTERIACEAE; BIFIDOBACTERIUM; BIFIDOBACTERIUM ASTEROIDES; CONTROLLED STUDY; ESCHERICHIA COLI; GENE REPLICATION; GENETIC CODE; GENETIC TRANSCRIPTION; MOLECULAR GENETICS; NONHUMAN; NUCLEOTIDE SEQUENCE; PLASMID; PROTEIN FUNCTION; REP GENE; REPLICON; SHUTTLE VECTOR;

BIFIDOBACTERIUM; DNA HELICASES; DNA, BACTERIAL; DNA-BINDING PROTEINS; ESCHERICHIA COLI; GENETIC VECTORS; MOLECULAR SEQUENCE DATA; PLASMIDS; PROTEIN BINDING; REPLICATION ORIGIN; REPLICON; SEQUENCE ANALYSIS, DNA; TRANS-ACTIVATORS; TRANSCRIPTION, GENETIC; TRANSFORMATION, BACTERIAL;

BIFIDOBACTERIUM; BIFIDOBACTERIUM ASTEROIDES; ESCHERICHIA COLI;

EID: 37349034983     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.01630-07     Document Type: Article

References (63)

1. Altschul, S. F., W. Gish, W. Miller, E. W. Myers, and D. J. Lipman. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-410.
2. Alvarez-Martín, P., A. B. Florez, and B. Mayo. 2007. Screening for plasmids among human bifidobacteria species: sequencing and analysis of pBC1 from Bifidobacterium catenulatum L48. Plasmid 57:165-174.
3. Argnani, A., R. J. Leer, N. van Luijk, and P. H. Pouwels. 1996. A convenient and reproducible method to genetically transform bacteria of the genus Bifidobacterium. Microbiology 142:109-114.
4. Bergström, M., M. Hermansson, and C. Dahlberg. 2004. Isolation and sequencing of the replication region of plasmid pBFp1 isolated from marine biofilm. Plasmid 51:179-184.
5. Corneau, N., E. Emond, and G. LaPointe. 2004. Molecular characterization of three plasmids from Bifidobacterium longum. Plasmid 51:87-100.
6. de Man, J. C., M. Rogosa, and M. E. Sharpe. 1960. A medium for the cultivation of lactobacilli. J. Appl. Bacteriol. 23:130-135.
7. Ernstsson, S., S. H. Bjornsdottir, Z. O. Jónsson, S. H. Thorbjarnardottir, G. Eggertsson, and A. Palsdottir. 2003. Identification and nucleotide sequence analysis of a cryptic plasmid, pRM21, from Rhodothermus marinus. Plasmid 49:188-191.
8. Fu, G. F., X. Li, Y. Y. Hou, Y. R. Fan, W. H. Liu, and G. X. Xu. 2005. Bifidobacterium longum as an oral delivery system of endostatin for gene therapy on solid liver cancer. Cancer Gene Ther. 12:133-140.
9. Fueki, T., and K. Yamaguchi. 2001. The structure and function of the replication initiator protein (Rep) of pSC101: an analysis based on a novel positive-selection system for the replication-deficient mutants. J. Biochem. (Tokyo) 130:399-105.
10. Fujimori, M. 2006. Genetically engineered bifidobacterium as a drug delivery system for systemic therapy of metastatic breast cancer patients. Breast Cancer 13:27-31.
11. Gstalder, M., M. Faelen, N. Mine, E. M. Top, M. Mergeay, and M. Couturier. 2003. Replication functions of new broad host range plasmids isolated from polluted soils. Res. Microbiol. 154:499-509.
12. Guglielmetti, S., M. Karp, D. Mora, I. Tamagnini, and C. Parini. 2007. Molecular characterization of Bifidobacterium longum biovar longum NAL8 plasmids and construction of a novel replicon screening system. Appl. Microbiol. Biotechnol. 74:1053-1061.
13. Han, S. O., H. Yukawa, M. Inui, and R. H. Doi. 2005. Molecular cloning and transcriptional analysis of engO, encoding a new noncellulosomal family 9 enzyme, from Clostridium cellulovorans. J. Bacteriol. 187:4884-4889.
14. Hefford, M. A., R. M. Teather, and R. J. Forster. 1993. The complete nucleotide sequence of a small cryptic plasmid from a rumen bacterium of the genus Butyrivibrio. Plasmid 29:63-69.
15. Inui, M., J. H. Roh, K. Zahn, and H. Yukawa. 2000. Sequence analysis of the cryptic plasmid pMG101 from Rhodopseudomonas palustris and construction of stable cloning vectors. Appl. Environ. Microbiol. 66:54-63.
16. Isolauri, M. 2004. Dietary modification of atopic disease: use of probiotics in the prevention of atopic dermatitis. Curr. Allergy Asthma Rep. 4:270-275.
17. Kiewiet, R., S. Bron, K. do Jonge, G. Venema, and J. F. Seegers. 1993. Theta replication of the lactococcal plasmid pWVO2. Mol. Microbiol. 10:319-327.
18. Klijn, A., D. Moine, M. Delley, A. Mercenier, F. Arigoni, and R. D. Pridmore. 2006. Construction of a reporter vector for the analysis of Bifidobacterium longum promoters. Appl. Environ. Microbiol. 72:7401-7405.
19. Kuipers, O. P., P. G. G. A. de Ruyter, M. Kleerebezem, and W. M. de Vos. 1998. Quorum sensing-controlled gene expression in lactic acid bacteria. J. Biotechnol. 64:15-21.
20. Kumar, S., K. Tamura, and M. Nei. 2004. MEGA3: integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Brief. Bioinform. 5:150-163.
21. Lee, J. H., and D. J. O'Sullivan. 2006. Sequence analysis of two cryptic plasmids from Bifidobacterium longum DJO10A and construction of a shuttle cloning vector. Appl. Environ. Microbiol. 72:527-535.
22. Lindner, C., R. Nijland, M. van Hartskamp, S. Bron, L. W. Hamoen, and O. P. Kuipers. 2004. Differential expression of two paralogous genes of Bacillus subtilis encoding single-stranded DNA binding protein. J. Bacteriol. 186:1097-1105.
23. MacConaill, L. E., G. F. Fitzgerald, and D. van Sinderen. 2003. Investigation of protein export in Bifidobacterium breve UCC2003. Appl. Environ. Microbiol. 69:6994-7001.
24. Mattarelli, P., B. Biavati, A. Alessandrini, F. Crociani, and V. Scardovi. 1994. Characterization of the plasmid pVS809 from Bifidobacterium globosum. Microbiology 17:327-331.
25. Mazé, A., M. O'Connell-Motherway, G. F. Fitzgerald, J. Deutscher, and D. van Sinderen. 2007. Identification and characterization of a fructose phosphotransferase system in Bifidobacterium breve UCC2003. Appl. Environ. Microbiol. 73:545-553.
26. McGrath, S., G. F. Fitzgerald, and D. van Sinderen. 2001. Improvement and optimization of two engineered phage resistance mechanisms in Lactococcus lactis. Appl. Environ. Microbiol. 67:608-616.
27. Miller, J. H. 1972. Experiments in molecular genetics, p. 433. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
28. Nakamura, T., T. Sasaki, M. Fujimori, K. Yazawa, Y. Kano, J. Amano, and S. Taniguchi. 2002. Cloned cytosine deaminase gene expression of Bifidobacterium longum and application to enzyme/pro-drug therapy of hypoxic solid tumours. Biosci. Biotechnol. Biochem. 66:2362-2366.
29. Ohkubo, S., and K. Yamaguchi. 1995. Two enhancer elements for DNA replication of pSC101, par and a palindromic binding sequence of the Rep protein. J. Bacteriol. 177:558-565.
30. Okumura, M. S., and C. I. Kado. 1992. The region essential for efficient autonomous replication of pSa in Escherichia coli. Mol. Gen. Genet. 235:55-63.
31. O'Riordan, K., and G. F. Fitzgerald. 1999. Molecular characterisation of a 5.75-kb cryptic plasmid from Bifidobacterium breve NCFB2258 and determination of a mode of replication. FEMS Microbiol. Lett. 174:285-294.
32. Park, M. S., D. W. Shin, K. H. Lee, and G. E. Ji. 1997. Isolation and characterisation of two plasmids from Bifidobacterium longum. Lett. Appl. Microbiol. 25:5-7.
33. Park, M. S., D. W. Shin, K. H. Lee, and G. E. Ji. 1999. Sequence analysis of plasmid pKJ50 from Bifidobacterium longum. Microbiology 145:585-592.
34. Paulsson, J., and D. K. Chattoraj. 2006. Origin inactivation in bacterial DNA replication control. Mol. Microbiol. 61:9-15.
35. Picard, C., J. Fioramonti, A. Francois, T. Robinson, F. Neant, and C. Matuchansky. 2005. Review article: bifidobacteria as probiotic agents - physiological effects and clinical benefits. Aliment. Pharmacol. Ther. 22:495-512.
36. Platteeuw, C., G. Simons, and W. M. de Vos. 1994. Use of the Escherichia coli β-glucuronidase (gusA) gene as a reporter gene for analyzing promoters in lactic acid bacteria. Appl. Environ. Microbiol. 60:587-593.
37. Providenti, M. A., J. M. O'Brien, R. J. Ewing, E. S. Paterson, and M. L. Smith. 2006. The copy-number of plasmids and other genetic elements can be determined by SYBR-Green-based quantitative real-time PCR. J. Microbiol. Methods 65:476-487.
38. Rhim, S. L., M. S. Park, and G. E. Ji. 2005. Expression and secretion of Bifidobacterium adolescentis amylase by Bifidobacterium longum. Biotechnol. Lett. 23:163-168.
39. Rossi, M., P. Brigidi, and D. Matteuzzi. 1997. An efficient transformation system for Bifidobacterium spp. Lett. Appl. Microbiol. 24:33-36.
40. Rossi, M., P. Brigidi, R. A. Gonzalez Vara, and D. Matteuzzi. 1996. Characterisation of the plasmid pMB1 from Bifidobacterium longum and its use for shuttle vector construction. Res. Microbiol. 147:133-143.
41. Ryan, S., G. F. Fitzgerald, and D. van Sinderen. 2006. Screening for and identification of starch-, amylopectin-, and pullulan-degrading activities in bifidobacterial strains. Appl. Environ. Microbiol. 72:5289-5296.
42. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
43. Sangrador-Vegas, A., C. Stanton, D. van Sinderen, G. F. Fitzgerald, and R. P. Ross. 2007. Characterisation of plasmid pASV479 from Bifidobacterium pseudolongum subsp. globosum and its use for expression vector construction. Plasmid 58:140-147.
44. Scardovi, V., B. Sgorbati, and G. Zani. 1971. Starch gel electrophoresis of fructose-6-phosphate phophoketolase in the genus Bifidobacterium. J. Bacteriol. 106:1036-1039.
45. AL, p. 1418-1434. In P. H. A. Sneath, N. S. Mair, M. E. Sharpe, and J. G. Holt (ed.), Bergey's manual of systemic bacteriology, vol. 2. Williams & Wilkins, Baltimore, MD.
46. Schell, M. A., M. Karmirantzou, B. Snel, D. Vilanova, B. Berger, G. Pessi, M. C. Zwahlen, F. Desiere, P. Bork, M. Delley, R. D. Pridmore, and F. Arigoni. 2002. The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract. Proc. Natl. Acad. Sci. USA 99:14422-14427.
47. Schurch, C. 2002. Development of a novel DNA transformation system for bifidobacteria. Ph.D. thesis. Swiss Federal Institute of Technology, Zurich (ETHZ), Switzerland.
48. Sgorbati, B., V. Scardovi, and D. J. LeBlanc. 1982. Plasmids in the genus Bifidobacterium. J. Gen. Microbiol. 128:2121-2131.
49. Sgorbati, B., V. Scardovi, and D. J. LeBlanc. 1986. Related structures in the plasmid profiles of Bifidobacterium asteroides, B. indicum and B. globosum. Microbiology 9:443-456.
50. Sugiura, S., M. Tanaka, Y. Masamune, and K. Yamaguchi. 1990. DNA binding properties of purified replication initiator protein (Rep) encoded by plasmid pSC101. J. Biochem. 107:369-376.
51. Takata, T., T. Shirakawa, Y. Kawasaki, S. Kinoshita, A. Gotoh, Y. Kano, and M. Kawabata. 2006. Genetically engineered Bifidobacterium animalis expressing the Salmonella flagellin gene for the mucosal immunization in a mouse model. J. Gene Med. 8:1341-1346.
52. Tanaka, K., K. Samura, and Y. Kano. 2005. Structural and functional analysis of pTB6 from Bifidobacterium longum. Biosci. Biotechnol. Biochem. 69:422-425.
53. Tannock, G. 1999. The bowel microflora: an important source of urinary tract pathogens. World J. Urol. 17:339-344.
54. Tauch, A., S. Schneiker, W. Selbitschka, A. Puhler, L. S. van Overbeek, K. Smalla, C. M. Thomas, M. J. Bailey, L. J. Forney, A. Weightman, P. Ceglowski, T. Pembroke, E. Tietze, G. Schroder, E. Lanka, and J. D. van Elsas. 2002. The complete nucleotide sequence and environmental distribution of the cryptic, conjugative, broad-host-range plasmid pIPO2 isolated from bacteria of the wheat rhizosphere. Microbiology 148:1637-1653.
55. Tauch, A., A. Puhler, J. Kalinowski, and G. Thierbach. 2003. Plasmids in Corynebacterium glutamicum and their molecular classification by comparative genomics. J. Biotechnol. 104:27-40.
56. Tissier, H. 1906. Traitement des infections intestinales par la méthode de transformations de la flore bactérienne de l'intestin. C. R. Soc. Biol. 60:359-361.
57. Ventura, M., D. van Sinderen, G. F. Fitzgerald, and R. Zink. 2004. Insights into the taxonomy, genetics and physiology of bifidobacteria. Antonie Leeuwenhoek 86:205-223.
58. Ventura, M., C. Canchaya, A. D. Casale, F. Dellaglio, E. Neviani, G. F. Fitzgerald, and D. van Sinderen. 2006. Analysis of bifidobacterial evolution using a multilocus approach. Int. J. Syst. Evol. Microbiol. 56:2783-2792.
59. Ventura, M., C. Canchaya, G. F. Fitzgerald, R. S. Gupta, and D. van Sinderen. 2007. Genomics as a means to understand bacterial phylogeny and ecological adaptation: the case of bifidobacteria. Antonie Leeuwenhoek 91:351-372.
60. Xu, Y. F., L. P. Zhu, B. Hu, G. F. Fu, H. Y. Zhang, J. J. Wang, and G. X. Xu. 2007. A new expression plasmid in Bifidobacterium longum as a delivery system of endostatin for cancer gene therapy. Cancer Gene Ther. 14:151-157.
61. Yazawa, K., M. Fujimori, J. Amano, Y. Kano, and S. Taniguchi. 2000. Bifidobacterium longum as a delivery system for cancer gene therapy: selective localization and growth in hypoxic tumors. Cancer Gene Ther. 7:269-274.
62. Yazawa, K., M. Fujimori, T. Nakamura, T. Sasaki, J. Amano, Y. Kano, and S. Taniguchi. 2001. Bifidobacterium longum as a delivery system for gene therapy of chemically induced rat mammary tumors. Breast Cancer Res. Treat. 66:165-170.
63. Yildirim, Z., D. K. Winters, and M. G. Johnson. 1999. Purification, amino acid sequence and mode of action of bifidocin B produced by Bifidobacterium bifidum NCFB 1454. J. Appl. Microbiol. 86:45-54.