medigraphic.com
Revista Latinoamericana de Microbiología

2008, Número 1-2

<< Anterior Siguiente >>

Microbiología 2008; 50 (1-2)


Recombinería en bacterias: ingeniería del ADN usando recombinación homóloga

Santoyo G

Idioma: Español
Referencias bibliográficas: 64
Paginas: 38-47
Archivo PDF: 157.25 Kb.


RESUMEN

La recombinería es una poderosa metodología para modificar el ADN bacteriano, ya sea cromosomal o plasmídico. Esta novedosa herramienta utiliza las funciones «Red» del bacteriófago λ para llevar a cabo eventos de recombinación homóloga. Comparado con técnicas clásicas de ingeniería genética, la recombinería no usa enzimas de restricción ni ADN ligasas. Además, el uso de oligonucleótidos sintéticos, así como de productos de PCR con regiones pequeñas de homología (~35-50 pb) en sus extremos, brinda una gran ventaja para generar mutaciones en cualquier zona del genoma de bacterias. Esta revisión describe los mecanismos de la recombinación homóloga en E. coli y las funciones Red del fago λ. También se analizan algunos de los usos y ventajas de la recombinería en bacterias Gram-negativas y Gram-positivas. Sin duda, la recombinería está cambiando la forma de realizar modificaciones genéticas en el ADN de una manera precisa, rápida, eficiente y económica.


REFERENCIAS (EN ESTE ARTÍCULO)

  1. Ayora, S., R. Missich, P. Mesa, R. Lurz, S. Yang, E.H. Egelman & J.C. Alonso. 2002. Homologous-pairing activity of the Bacillus subtilis bacteriophage SPP1 replication protein G35P. J Biol Chem. 277:35969-73599.

  2. Baudin, A., O. Ozier-Kalogeropoulos, A. Denouel, F. Lacroute & C. A. Cullin. 1993. Simple and efficient method for direct gene deletion in Saccharomyces cerevisiae. Nucleic Acids Res. 21:3329-3330.

  3. Blomfield, I. C., V. Vaughn, R. F. Rest & B. I. Eisenstein. 1991. Allelic exchange in Escherichia coli using a Bacillus subtilis sacB gene and a temperature-sensitive pSC101 replicon. Mol Microbiol. 5:1447-1457.

  4. Bolivar, F., R. L. Rodriguez, P. J. Greene, M. C. Betlach, H. L. Heyneker & H.W. Boyer. 1977. Construction and characterization of new cloning vehicles. II. A multipurpose cloning system. Gene. 2:95-113.

  5. Brooks, K. & A. J. Clark. 1967. Behavior of lambda bacteriophage in a recombination deficient strain of Escherichia coli. J Virol. 1:283-293.

  6. Carter, D.M. & C. M. Radding. 1971. The role of exonuclease and Beta protein of phage lambda in genetic recombination. II. Substrate specificity and the mode of action of lambda exonuclease. J Biol Chem. 246:2502-2512.

  7. Chaveroche, M. K., J. M. Ghigo & C. d’Enfert. 2000. A rapid method for efficient gene replacement in the filamentous fungus Aspergillus nidulans. Nucleic Acids Res. 28:E97.

  8. Choi, K. H. & H. P. Schweizer. 2005. An improved method for rapid generation of unmarked Pseudomonas aeruginosa deletion mutants. BMC Microbiol. 5:30.

  9. Clark, A. J. & A. D. Margulies. 1965. Isolation and characterization of recombination-deficient mutants of Escherichia coli K12. Proc Natl Acad Sci USA. 53:451-459.

  10. Clark, A. J. & S. J. Sandler. 1994. Homologous genetic recombination: the pieces begin to fall into place. Crit Rev Microbiol. 20:125-142.

  11. Costantino, N. & D. L. Court. 2003. Enhanced levels of lambda Red-mediated recombinants in mismatch repair mutants. Proc Natl Acad Sci USA. 100:15748-53.

  12. Court, D. L. & J. A. Sawitzke & L. C. Thomason. 2002. Genetic engineering using homologous recombination. Annu Rev Genet. 36:361-388.

  13. Court, R., N. Cook, K. Saikrishnan & D. Wigley. 2007. The crystal structure of lambda-Gam protein suggests a model for RecBCD inhibition. J Mol Biol. 371:25-33.

  14. Cox, M. M. & J. R. Battista. 2005. Deinococcus radiodurans - the consummate survivor. Nat Rev Microbiol. 3:882-892.

  15. Datta, S., N. Costantino & D. L. Court. 2006. A set of recombineering plasmids for gram-negative bacteria. 379:109-115.

  16. Datsenko, K. A. & B. L. Wanner. 2000. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc Natl Acad Sci USA. 97:6640-6645.

  17. Derbise, A., B. Lesic, D. Dacheux, J. M. Ghigo & E. Carniel. 2003. A rapid and simple method for inactivating chromosomal genes in Yersinia. FEMS Immunol Med Microbiol. 38:113-116.

  18. Ellis, H. M., D. Yu, T. DiTizio & D. L. Court. 2001. High efficiency mutagenesis, repair, and engineering of chromosomal DNA using single-stranded oligonucleotides. Proc Natl Acad Sci USA. 98:6742-6746.

  19. Fernandez, S., S. Ayora & J. C. Alonso. 2000. Bacillus subtilis homologous recombination: genes and products. Res Microbiol. 151:481-6.

  20. Hall, S.D., M.F. Kane & R. D. Kolodner. 1993. Identification and characterization of the Escherichia coli RecT protein, a protein encoded by the recE region that promotes renaturation of homologous single-stranded DNA. J Bacteriol. 175:277-287.

  21. Hall, S.D. & R. D. Kolodner. 1994. Homologous pairing and strand exchange promoted by the Escherichia coli RecT protein. Proc Natl Acad Sci U S A. 91:3205-3209.

  22. Hill, F., V. Benes, D. Thomasova D, A. F. Stewart, F. C. Kafatos & W. Ansorge. 2000. BAC trimming: minimizing clone overlaps. Genomics. 64:111-113.

  23. Holliday, R. 1990. The history of the DNA heteroduplex. Bioessays. 12:133-42.

  24. Horii, Z. & A. J. Clarck. 1973. Genetic analysis of the recF pathway to genetic recombination in Escherichia coli K12: isolation and characterization of mutants. J Mol Biol. 80:327-344.

  25. Kowalczykowski, S. C. 2000. Initiation of genetic recombination and recombination-dependent replication. Trends Biochem Sci. 25:156-165.

  26. Kowalczykowski, S. C., D. A. Dixon, A. K. Eggleston, S. D. Lauder & W. M. Rehrauer. 1994. Biochemistry of homologous recombination in Escherichia coli. Microbiol Rev. 58:401-465.

  27. Krogh, B. O. & L. S. Symington. 2004. Recombination proteins in yeast. Annu Rev Genet. 38:233-271.

  28. Kulkarni, S. K. & F. W. Stahl. 1989. Interaction between the sbcC gene of Escherichia coli and the gam gene of phage lambda. Genetics. 123:249-253.

  29. Kuzminov, A. 1995. Collapse and repair of replication forks in Escherichia coli. Mol Microbiol. 16:373-384.

  30. Lambert, J. M., R. S. Bongers & M. Kleerebezem. 2007. Cre-lox-based system for multiple gene deletions and selectable-marker removal in Lactobacillus plantarum. Appl Environ Microbiol. 73:1126-1135.

  31. Li, Z., G. Karakousis, S. K. Chiu, G. Reddy & C. M. Radding. 1998. The Beta protein of phage lambda promotes strand exchange. J Mol Biol. 276:733-744.

  32. Li, X. T., N. Costantino, L. Y.Lu, , D. P. Liu, R. M. Watt, K. S. Cheah, D. L. Court & J. D. Huang. 2003. Identification of factors influencing strand bias in oligonucleotide-mediated recombination in Escherichia coli. Nucleic Acids Res. 31:6674-6687.

  33. Martínez-Jiménez, M. I., J. C. Alonso & S. Ayora. 2005. Bacillus subtilis bacteriophage SPP1-encoded gene 34.1 product is a recombination-dependent DNA replication protein. J Mol Biol. 351:1007-1019.

  34. Matsuura, S., J. Komatsu, K. Hirano, H. Yasuda, K. Takashima, S. Katsura & A. Mizuno. 2001. Real-time observation of a single DNA digestion by lambda exonuclease under a fluorescence microscope field. Nucleic Acids Res. 29:E79.

  35. Muniyappa, K. & C. M. Radding. 1986. The homologous recombination system of phage lambda. Pairing activities of Beta protein. J Biol Chem. 261:7472-7478.

  36. Murphy, K. C. 1991. Lambda Gam protein inhibits the helicase and chi-stimulated recombination activities of Escherichia coli RecBCD enzyme. J Bacteriol. 173:5808-5821.

  37. Murphy, K. C. 2007. The lambda Gam Protein Inhibits RecBCD Binding to dsDNA Ends. J Mol Biol. 371:19-24.

  38. Murphy, K. C. & K. G. Campellone. 2003. Lambda Red-mediated recombinogenic engineering of enterohemorrhagic and enteropathogenic E. coli. BMC Mol. Biol. 4:11.

  39. Muyrers, J. P., Y. Zhang, F. Buchholz & A. F. Stewart. 2000. RecE/RecT and Redalpha/Redbeta initiate double-stranded break repair by specifically interacting with their respective partners. Genes Dev. 14:1971-1982.

  40. Muyrers, J. P., Y. Zhang & A. F. Stewart. 2001. Techniques: Recombinogenic engineering- new options for cloning and manipulating DNA. Trends Biochem Sci. 26:325-231.

  41. Muyrers, J. P., Y. Zhang, G. Testa & A. F. Stewart. 1999. Rapid modification of bacterial artificial chromosomes by ET-recombination. Nucleic Acids Res. 27:1555-1557.

  42. Nathans, D. & H. O. Smith. 1975. Restriction endonucleases in the analysis and restructuring of DNA molecules. Annu Rev Biochem. 44:273-293.

  43. Nishinaka, T., Y. Doi, R. Hara & E. Yashima. 2007. Elastic Behavior of RecA-DNA Helical Filaments. J Mol Biol. 370:837-845.

  44. Oppenheim, A. B., A. J. Rattray, M. Bubunenko, L. C. Thomason & D. L. Court. 2004. In vivo recombineering of bacteriophage lambda by PCR fragments and single-strand oligonucleotides. Virology. 319:185-189.

  45. Perkins, T.T., R. V. Dalal, P. G. Mitsis & S. M. Block. 2003. Sequence-dependent pausing of single lambda exonuclease molecules. Science. 301:1914-8.

  46. Ranallo, R. T., S. Barnoy, S. Thakkar, T. Urick & M. M. Venkatesan. 2006. Developing live Shigella vaccines using lambda Red recombineering. FEMS Immunol Med Microbiol. 47:462-469.

  47. Rafferty, J. B., S. E. Sedelnikova, D. Hargreaves, P. J. Artymiuk, P. J. Baker, G. J. Sharples, A. A. Mahdi, R. G. Lloyd & D. W. Rice. 1996. Crystal structure of DNA recombination protein RuvA and a model for its binding to the Holliday junction. Science. 274:415-421.

  48. Sanchez, H., M. C. Cozar & M. I. Martinez-Jimenez. 2007. Targeting the Bacillus subtilis genome: an efficient and clean method for gene disruption. J Microbiol Methods. 70:389-394.

  49. Sawitzke, J. A., L. C. Thomason, N. Costantino, M. Bubunenko, S. Datta & D. L. Court. 2007. Recombineering: in vivo genetic engineering in E. coli, S. enterica, and beyond. Methods Enzymol. 421:171-199.

  50. Sharples, G. J., S. M. Ingleston & R. G. LloyD. 1999. Holliday junction processing in bacteria: insights from the evolutionary conservation of RuvABC, RecG, and RusA. J Bacteriol. 181:5543-5550.

  51. Shen, P. & H. V. Huang. 1986. Homologous recombination in Escherichia coli: dependence on substrate length and homology. 112:441-457.

  52. Silberstein, Z., Y. Tzfati & A. Cohen. 1995. Primary products of break-induced recombination by Escherichia coli RecE pathway. J Bacteriol. 177:1692-1698.

  53. Subramanian, K., W. Rutvisuttinunt, W. Scott & R. S. Myers. 2003. The enzymatic basis of processivity in lambda exonuclease. Nucleic Acids Res. 31:1585-96.

  54. Szostak, J. W., T. L. Orr-Weaver, R. J. Rothstein & F. W. Stahl. 1983. The double-strand-break repair model for recombination. Cell. 33:25-35.

  55. van Oijen, A. M., P. C. Blainey,D. J. Crampton, C. C. Richardson, T. Ellenberger & X. S. Xie. 2003. Single-molecule kinetics of lambda exonuclease reveal base dependence and dynamic disorder. Science. 301:1235-8

  56. van Kessel, J. C. & G. R. Hatfull. 2007. Recombineering in Mycobacterium tuberculosis. Nat Methods. 4:147-152.

  57. Watt, V. M., C. J. Ingles, M .S. Urdea & W. J. Rutter. 1985. Homology requirements for recombination in Escherichia coli. Proc Natl Acad Sci U S A. 82:4768-4772.

  58. Weiss, B. & C. C. Richardson. 1967. Enzymatic breakage and joining of deoxyribonucleic acid. 3. An enzyme-adenylate intermediate in the polynucleotide ligase reaction. J Biol Chem. 242:4270-4272.

  59. Yu, D., H. M. Ellis, E. C. Lee, N. A. Jenkins, N. G. Copeland & D. L. Court. 2000. An efficient recombination system for chromosome engineering in Escherichia coli. Proc Natl Acad Sci U S A. 97:5978-5983.

  60. Yu, D., J. A. Sawitzke, H. M. Ellis & D. L. Court. 2003. Recombineering with overlapping single-stranded DNA oligonucleotides: testing a recombination intermediate. Proc Natl Acad Sci U S A. 100:7207-7212.

  61. Zahradka, K., S. Simic, M. Buljubasic, M. Petranovic, D. Dermic & D. Zahradka. 2006. sbcB15 and DeltasbcB mutations activate two types of recF recombination pathways in Escherichia coli. J Bacteriol. 188:7562-7.

  62. Zeng, X., L. H. He, Y. Yin, M. J. Zhang & J. Z. Zhang. 2007. Deletion of cagA gene of Helicobacter pylori by PCR products. World J Gastroenterol. 11:3255-3259.

  63. Zhang, Y., F. Buchholz, J. P. Muyrers & A. F. Stewart. 1998. A new logic for DNA engineering using recombination in Escherichia coli. Nat Genet. 20:123-128.

  64. Zhang, Y., J. P. Muyrers, G. Testa & A. F. Stewart. 2000. DNA cloning by homologous recombination in Escherichia coli. Nat Biotechnol. 18:1314-1317.




2020     |     www.medigraphic.com