Разработка и использование методов направленной модификации целевых генетических локусов хромосомы E. coli при конструировании штаммов-продуцентов аминокислот тема диссертации и автореферата по ВАК РФ 03.00.03, кандидат биологических наук Каташкина, Жанна Иосифовна

  • Каташкина, Жанна Иосифовна
  • кандидат биологических науккандидат биологических наук
  • 2003, Москва
  • Специальность ВАК РФ03.00.03
  • Количество страниц 125
Каташкина, Жанна Иосифовна. Разработка и использование методов направленной модификации целевых генетических локусов хромосомы E. coli при конструировании штаммов-продуцентов аминокислот: дис. кандидат биологических наук: 03.00.03 - Молекулярная биология. Москва. 2003. 125 с.

Заключение диссертации по теме «Молекулярная биология», Каташкина, Жанна Иосифовна

выводы

1. На основе специализированного плазмидного вектора создана коллекция прокариотических регуляторных элементов (промоторов и двух р-независимых терминаторов транскрипции), узнаваемых РНК-полимеразой E.coli, и охарактеризована их относительная эффективность.

2. Проведено КОНСТруИрОВаНИе НОВЫХ Промоторов Р<ac-ideal И P(rc-ideal НЭ ОСНОВе Рtac и Рtrc., имеющих более высокий чем их предшественники уровень репрессии Lacl. Сконструирован новый "сильный" гибридный промотор Рь-гас> который репрессируется как Lacl, так и Я,С1.

3. Созданы и изучены свойства новых авторегулируемых генетических элементов на основе промоторно-операторных областей и генов репрессоров лактозного оперона E.coli и бактериофага X - РiacVy5-^lacI и Рi^clts857.

4. Разработан эффективный метод модификации бактериальной хромосомы с последующей эксцизией селективного маркера в результате использования Int/Xis- и Red-зависимых систем рекомбинации бактериофага X. Показано, что с помощью этого метода можно осуществлять как специфические делеции генов, так и более сложные реконструкции хромосомы, в частности, замену регуляторных элементов генов.

5. Разработана процедура оптимизации экспрессии генов, локализованных в хромосоме E.coli. При использовании гена lacZ в качестве репортера показана возможность значительного (не менее двух порядков величины) изменения уровня экспрессии гена путем замены нативной промоторной области на РНеподобные промоторы с вырожденной последовательностью нуклеотидов в области «-35». При этом получена коллекция фрагментов ДНК, содержащих селективный маркер - XattL-Cm^-XattR, соединеный с Р,^-подобными промоторами с известной относительной эффективностью инициации транскрипции.

Список литературы диссертационного исследования кандидат биологических наук Каташкина, Жанна Иосифовна, 2003 год

1. Abo,Т., Inada,T., Ogawa,K., Aiba,H. 2000. SsrA-mediated tagging and proteolysis of Lacl and its role in the regulation of lac operon. EMBO J. 19: 3762-3769.

2. Ayers,D.G., Auble, D.T., deHaseth.P.L. 1989. Promoter recognition by Escherichia coli RNA polymerase. Role of the spacer DNA in functional complex formation. J.Mol.Biol. 207: 749-756.

3. Barker,M.M., Gaal.T., Josaitis.C.A., Gourse.R.L. 2001. Mechanism of regulation of transcription initiation by ppGpp. I.Effects of ppGpp on transcription initiation in vivo and in vitro. J. Mol. Biol. 305: 673-688.

4. Bar-Nahum G, Nudler E. 2001. Isolation and characterization of sigma(70)-retaining transcription elongation complexes from Escherichia coli. Cell 106(4):443-51.

5. Barne,K.A., Bown,J.A., Busby,S.J.W., Minchin,S.D. 1997. Region 2.5 of the Escherichia coli RNA polymerase cr70-subunit is responsible for the recognition of the "extended -10" motif at promoters. EMBO J. 16:4034-4040.

6. Beckwith J., Grodzicker Т., Arditti R.ll J. Mol. Biol.— 1972. — V.69. — P.155— 160.

7. Bell,C.E„ Lewis,M. 2000. A closer view of the conformation of the Lac repressor bound to operator. Nat. Struct. Biol. 7: 209-214.

8. Bell,C.E., Lewis,M. 2001. The Lac repressor: a second generation of structural and functional studies. Curr. Opin. Stuct. Biol. 11:19-25.

9. Bianco PR, Tracy RB, Kowalczykowski SC. 1998. DNA strand exchange proteins: a biochemical and physical comparison. Front Biosci 3:D570-603.

10. Blattner, F.R., Plunkett, G. 3rd, Bloch,C.A., Perna, N.T., Burland, V., Riley,

11. M.,Collado-Vides, J., Glasner, J.D., Rode, C.K., Mayhew, G.F., Gregor, J., Davis, N.W., Kirkpatrick.H.A., Goeden, M.A., Rose, D.J., Май, В., Shao, Y. 1997. The complete genome sequence of Escherichia coli K-12. Science 277: 1453-1474.

12. Bochner.B.R., Huang,H.C., Schieven.G.L., Ames,B.N. 1980. Positive selection for loss of tetracycline resistance.J.Bacteriol. 143: 926-933.

13. BorowiecJ.A., Zhang,L., Sasse-Dwight,S., GrallaJ.D. 1987. DNA supercoiling promotes formation of a bent repression loop in lac DNA. J. Mol. Biol. 5: 101-111.

14. Brooks,K., Clare,A.J. 1967. Behavior of X bacteriophage in a recombination deficient strain of Escherichia coli. J. Virol. 1: 283-293.

15. Brosius J, ErfleM, StorellaJ. 1985. Spacing of the -10 and -35 regions in the tac promoter. Effect on its in vivo activity. J. Biol. Chem. 260: 3539-3541.

16. Burr,Т., Mitchell,J., Kolb.A., Minchin.S., Busby,S. 2000. DNA sequence elements located immediately upstream of the -10 hexamer in Escherichia coli promoters: a systematic study. Nucleic Acids Res.28:1864-1870.

17. Busby,S., Ebright.R.H. 1994. Promoter structure, promoter recognition and transcription activation in prokaryotes. Cell. 79: 743-746.

18. Busby,S., Ebright,R.H. 1999. Transcription activation by catabolite activator protein (CAP). J. Mol. Biol. 293: 199-213.

19. Campbell,A.M. 1962. Episomes. Adv. Genet. 11: 101-145.

20. Caramel,A., Schnetz,K. 1998. Lac and lambda repressors relieve silencing of the Escherichia coli bgl promoter. Activation by alteration of a repressing nucleoprotein complex. J. Mol. Biol. 284: 875-883.

21. Carpousis,A.J., Gralla,J.D. 1980. Cycling of ribonucleic acid polymerase to produce oligonucleotides during initiation in vitro at the lacUV5 promoter. Biochemistry. 19:3245-3253.

22. Carter,D.M., Radding.C.M. 1971. The role of exonuclease and p protein of phage X in genetic recombination. II. Substrate specificity and mode of action of X exonuclease. J. Biol. Chem. 246: 2502-2510.

23. Cassuto.E., Lash, Т., Sriprakash,K.C., Radding.C.M. 1971. Role of exonuclease and P protein of phage X in genetic recombination. V. Recombination of X DNA in vitro. Proc. Natl. Acad. Sci. USA 68: 1639-1643.

24. Cassuto.E., Radding.C.M. 1971. Mechanism for the action of X exonuclease in genetic recombination. Nat. New Biol. 229:13-16.

25. Cherepanov.P.P., Wackernagel.W. 1995. Gene disruption in Escherichia coli: TcR and KmR cassettes with the option of exision of the antibiotic-resistance determinant. Gene 158: 9-14.

26. Clark,A.J. 1973. Recombination deficient mutants of Escherichia coli and other bacteria. Ann. Rev. Genet. 7: 67-86.

27. Clark,A.J., Margulies.A.D. 1965. Isolation and characterization of recombination deficient mutants of Escherichia coli K12. Proc. Natl. Acad. Sci. USA. 53: 451459.

28. Cosloy.S.D., Oishi.M. 1973. Genetic transformation in Escherichia coli K12. Proc.Natl.Acad.Sci. 70: 84-87.

29. Cosloy,S.D., Oishi,M. 1973a. The nature of the transformation process in Escherichia coli K12. Mol. Gen. Genet. 124: 1-10.

30. Coulombe, В., Burton, Z.F. 1999. DNA banding and wrapping around RNA polymerase: a "revolutionary" model describing transcriptional mechanisms. Microbiol.Mol.Biol.Rev. 63:457-478.

31. Czarniecki,D., Noel,R. J., Jr., Reznikoff,S. 1997. The -^45 region of the Escherichia coli lac promoter: CAP-dependent and CAP-independent transcription. J. Bacteriol. 179:423-429.

32. Dabert.P., Smith, G.R. 1997. Gene replacement with linear DNA fragments in wild-type Escherichia coli: enhancement by Chi sites. Genetics. 145: 877-889.

33. Dale EC, Ow DW. 1991. Gene transfer with subsequent removal of the selection gene from the host genome. Proc Natl Acad Sci USA. 88: 10558-62.

34. Darst,S.A., Polyakov,A., Richter,C., Chang,G. 1998. Insights into Escherichia coli RNA polymerase structure from a combination of X-ray and electron crystallography. J. Struct. Biol. 124: 115-122.

35. Deitsch,K.W., Moxon,E.R„ Wellems,T.E. 1997. Shared themes of antigenic variation and virulence in bacterial, protozoal, and fungal infections. Microbiol. Mol. Biol. Rev. 61:281-293.

36. Deuschle.U., Kammerer.W., Gentz,R., Bujard.H. 1986. Promoters of Escherichia coli: a hierarchy of in vivo strength indicates alternate structures. EMBO J. 5:29872994.

37. Dombroski,A.J., Walter,W.A., Record,M.T.,Jr., Siegele.D.A., Gross,C.A. 1992. Polypeptides, containing highly conserved regions of transcription initiation factor a70 exhibit specificity of binding to promoter DNA. Cell 70: 501-512.

38. Donahue,J.P., Turnbough,C.L.Jr. 1990. Characterization of transcription initiation from promoters Pl and P2 of the pyrBI operon of Escherichia coli K12. J. Biol. Chem. 265: 19091-19099.

39. Dong,F„ Spott.S., Zimmermann.O., Kisters-Woike,B., Miiller-Hill,B. 1999. Dimerisation mutant of Lac repressor. I. A monomeric mutant, L251A, that binds lac operator DNA as a dimer. J. Mol. Biol. 290: 653-666

40. Echols,H., Gingery,R. 1968. Mutants of bacteriophage X defective in vegetative recombination. J. Mol. Biol. 34: 239-249.

41. El KarouiM-, Amundsen, S.K., Dabert,P„ Gruss,A. 1999. Gene replacement with linear DNA in electroporated wild-type Escherichia coli. Nucleic Acids Res.27: 1296-1299.

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

43. Enquist,L.W., Skalka,A. 1973. Replication of bacteriophage X DNA dependent on the function of host and viral genes. I. Interaction of red, gam, and rec. J. Mol. Biol. 75: 185-212.

44. Estrem,S.T., Gaal,T., Ross,W., Gourse.R. 1998. Identification of an UP element consensus sequence for bacterial promoters. Proc. Natl. Acad.Sci. 95:9761-9766.

45. Figueroa-Bossi.N., Guerin,M., Rahmouni,R., Leng,M., Bossi,L. 1998. The supercoiling sensitivity of a bacterial tRNA promoter parallels its responsiveness to stringent control. EMBO J. 17: 2359-2367.

46. Flashner,Y., Gralla, J.D. 1988. Dual mechanism of repression at a distance in the lac operon. Proc. Natl. Acad. Sci. 85: 8968-8972.

47. Franklin,N.C. 1967. Deletion and functions of the center of the cp80-A, phage genome. Evidence for a phage function promoting genetic recombination. Genetics. 57: 301-318.

48. Gaal, T.,Bartlett,M.S., Ross,W., Turnbough,C.L.Jr., Gourse.R.L. 1997. NTP concentration as a regulator of transcription initiation: control of rRNA synthesis in bacteria. Science. 278:2092-2097.

49. Gay,P., Le Coq,D., Steinmetz.M., Berkelman,T., Kado, C.I. 1985. Positive selection procedure for entrapment of insertion sequence elements in gram-negative bacteria. J. Bacteriol. 164: 918-21.

50. Gerk,L.P., Leven.O., Miiller-Hill,B. 2000. Strengthening the dimerisation interface of Lac repressor increases its thermostability by 40°C. J. Mol. Biol. 299: 805-812.

51. Giladi.H., Koby, S„ Prag,G., Engelhorn.M., Geiselmann,J., Oppenheim,A.B. 1998. Participation of IHF and a distant UP element in the stimulation of the phage lambda Pl promoter. Mol. Microbiol. 30: 443-451.

52. Giladi,H., Murakami,K., Ishihama.A., Oppenheim.A.B. 1996. Identification of an UP element within the IHF binding site at the PL1-PL2 tandem promoter of bacteriophage k. J. Mol. Biol. 260:484-491.

53. Gilbert, W., Gralla,J., Majors,J., Maxam,A. 1975. Lactose operator sequence and the action of Lac repressor. \\ Protein-ligand interactions. Ed. Sund,H., Blauer, G. Berlin: de Gruyter. 1975: 193-206.

54. Gillen,J.R., Willis,K„ Clark,A.J. 1981. Genetic analysis of the RecE pathway of genetic recombination in Escherichia coli K-12. J. Bacteriol. 145: 521-532.

55. Gottesman,M.M., Gottesman,M.E., Gottesman,S., Gellert,M. 1974. Characterization of bacteriophage к reverse as an Escherichia coli phage carrying a unique set of host-derived recombination functions. J. Mol. Biol. 88: 471-487.

56. Gourse,R.L. 1988. Visualization and quantitative analysis of complex formation between E.coli RNA polymerase and an rRNA promoter in vitro. Nucleic Acids Res. 16:9789-9809.

57. Gralla,J.D., Carpousis, A.J., Stefano,J.E. 1980. Productive and abortive initiation of transcription in vitro at the lacUV5 promoter. Biochemistry. 19:5864-5869.

58. Gross, C.A., Chan, C„ Dombroski,A., Gruber.T., Sharp,M., Тиру,J., Young,B. 1998. The functional and regulatory roles of sigma factors in transcription. Cold Spring Harbor Symph. Quant. Biol. 63: 141-155.

59. Gross,C.A., Lonetto,R., Losick.R. 1992. Bacterial sigma factors.w McRnight,S.L., Yamamoto, K.R. (ed.). Transcriptional regulation. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.: 129-176.

60. Gutterson,N.I., Koshland,D.E. 1983. Replacement and amplification of bacterial genes with sequences altered in vitro. Proc. Natl. Acad. Sci. USA. 80:4894-4898.

61. Hall,S.D., Kane,M.F., Kolodner.R.D. 1993. Identification and characterization of the Escherichia coli RecT protein, a protein encoded by the recE region thatpromotes renaturation of homologous single-stranded DNA. J. Bacteriol. 175: 277287.

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

63. Hamilton,C.M., Aldea,M„ Washburn,B.K.,Babitzke,P., Knshner.S.R■ 1989. New method for generation deletions and gene replacements in Escherichia coli. J. Bacteriol. 171:4617-4622.

64. Hansen, U.,McClure,W.R. 1980. Role of the sigma subunit of Esherichia coli RNA polymerase in initiation. II. Release of sigma from ternary complexes. J.Biol.Chem. 255:9564-9570.

65. Harley,C.B., Reynolds,R.P. 1987. Analysis of E.coli promoter sequences. Nucleic Acids Res. 15:2343-2361.

66. Harley, С.В., Reynolds,R.P. 1987. Analysis of E.coli promoter sequences. Nucleic Acids Res. 15:2343-2361.

67. Hartley,J.L., Temple,G.F., Brasch.M.A. 2000. DNA cloning using in vitro site specific recombination. Genome Res. 10: 1788-1795.

68. Hawley,D., McCluer,W.R. 1983. Compilation and analysis of Escherichia coli promoter DNA sequences. Nucl.Acids Res. 11:2237-2255.

69. Helinski D.R., Toukdarian A.E., Novick А.Р.П Esherichia coli and Salmonella. Cellular and molecular biology. Second edition. / Eds.: F.S.Neidhardt et al. — Washington: ASM press, 1996. — V.2. — P.2295 — 2324.

70. Hill.S.A., StahlMM, Stahl.F.W. 1997. Singl-strand DNA intermediates in phage X's Red recombination pathway. Proc. Natl. Acad. Sci. USA 94: 2951-2956.

71. Howard-Flanders,P., Theriot.L. 1966. Mutants of Escherichia coli K-12 defective in DNA repair and genetic recombination. Genetics 53: 1137-1150.

72. Hsieh,P„ Camerini-Otero,C.S„ Camerini-Otero,R.D. 1992. The synapsis event in the homologous pairing of DNAs: RecA recognizes and pairs less than one helical repeat of DNA. Proc. Natl. Acad. Sci. USA 89: 6492-6496.

73. Hsu L. 2002. Promoter clearance and escape in prokaryotes. Biochim. Biophys. Acta 1577: 191-207.

74. Hsu LM, Vo NV, Chamberlin MJ. 1995. Escherichia coli transcript cleavage factors GreA and GreB stimulate promoter escape and gene expression in vivo and in vitro. Proc Natl Acad Sci USA. 92(25): 11588-92.

75. Igarishi,K., Fujita.N., Ishichama.A. 1991. Bipatite functional map of the E.coli RNA polymerase alpha subunit: involvment of the C-terminal region in transcription activation by camp-CRP. Cell. 65:1015-1022.

76. Jasin,M., Schimmel,P. 1984. Deletion of an essential gene in Escherichia coli by site-specific recombination with linear DNA fragments. J. Bacteriol. 159: 783-786.

77. Jensen,P.R., Hammer,K. 1998. The sequence of spacers between the consensus sequences modulates the strength of prokaryotic promoters. Appl.Env.Microbiol. 64:82-87.

78. Joseph,J.W., Kolodner,R.D. 1983. Exonuclease VIII of Escherichia coli. II. Mechanism of action. J. Biol. Chem. 258: 10418-10424.

79. Kaiser,K., Murray,N.E. 1979. Physical characterization of the "Rac prophage" in E. coli K-12. Mol. Gen. Genet. 175: 159-174.

80. Kammerer,W., Deuschle.U., Gentz,R., Bujard, W. 1986. Functional dissection of Escherichia coli promoters: information in the transcribed region is involved in late steps of the overall process. EMBO J. 5:2995-3000.

81. Kang.H.Y., Dozois,C.M., Tinge,S.A., Lee,Т.Н., Curtiss JII,R. 2002. Trunsduction-mediated transfer of unmarked deletion and point mutations through use of couterselectable suicide vectors. J.Bacteriol. 184: 307-312.

82. Karakousis.G., Ye,N., Li,Z„ Chiu.S.K, Reddy.G., Radding,C.M. 1998. The Beta protein of phage Xbinds preferentially to an intermediate in DNA renaturation. J. Mol. Biol. 276: 721-731.

83. Keilty,S., Rosenberg,M. 1987. Constitutive function of a positively regulated promoter reveals new sequences essential for activity. J.Biol.Chem. 262:6389-6395.

84. Keilty,S., Rosenberg,M. 1987. Constitutive function of a positively regulated promoter reveals new sequences essential for activity. J.Biol.Chem. 262:6389-6395.

85. King,S.R., Richardson,J.P. 1986. Role of homology and pathway specificity for recombination between plasmids and bacteriophage. Mol. Gen. Genet. 204: 141147.

86. Kmiec.E., HollomanW.K. 1981. p protein of bacteriophage X promotes renaturation of DNA. J. Biol. Chem. 256: 12636-12639.

87. Kolb,A., Busby,S„ Buc,H., Garges,S., Adhya.S. 1993. Transcriptional regulation by cAMP and its receptor protein. Annu. Rev. Biochem. 62: 749-795.

88. Konstantinovic,M., Maksimovic,V., Nikcevic,G., Glisin.V. 1991. Hybrid PLtl promoter with dual regulation control. DNA Cell. Biol. 10: 389-395

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

90. Kristensen,C.S., Eberl,L., Sancez-Romero,J.M., Givskov,M., Molin,S., De Lorenzo, V. 1995. Site-specific deletions of chromosomally located DNA segments with the multimer resolution system of broad-host-range plasmid RP4. J. Bacteriol. 177: 52-58.

91. Krummel,B., Chamberlin,M.J. 1989. RNA chain initiation by Esherichia coli RNA polymerase. Structural transitions of the enzyme in early ternary complexes. Biochemistry. 28:7829-7842.

92. Kumar,A., Grimes,В., Fujita,N., Makino,K, Malloch,R.A., Hayward,R.S., Ishihama,A. 1994. Role of the sigma70 subunit of Escherichia coli RNA polymerase in transcription activation. J. Mol. Biol. 235: 405-413.

93. Kuzminov,A. 1999. Recombinational repair of DNA damage in Escherichia coli and bacteriophage X. Microbiol. Mol. Biol. Rev. 63: 751-813.

94. Kuzminov.A. 2001. DNA replication meets genetic exchange: chromosomal damage and its repair by homologous recombination. PNAS, 98: 8461-8468.

95. Laemmli V.K. 1970. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature. 227: 680-685.

96. Lanzer M., Bujard H. 1988. Promoters largely determine the efficiency of repressor action. Proc. Natl. Acad. Sci. USA. 85: 8973-8977.

97. Lederberg,J. 1947. Gene recombination and linked segregations in Escherichia coli. Genetics 32: 505-525.

98. Lee,J., Goldfarb.A. 1991. Lac repressor acts by modifying the initial transcribing complex so that it cannot leave the promoter. Cell. 66: 793-798.

99. Leenhouts,K., Buist,G., Bolhuis,A., tenBerg,A.,Kiel,J., Mierau,I., Dabrowska,M., Venema,G., Кок,J. 1996. A general system for generating unlebelled gene replacements in bacterial chromosomes. Mol. Gen. Genet. 253: 217-224.

100. Lennox, E.S. 1955. Transduction of linked genetic characters of the host by bacteriophage Pl. Virology, 1,190.

101. Lewin B.// "Genes VI". — Oxford, England: University Press, 1997.

102. Lewis,M., Chang,G., Horton,N.C., Kercher,M.A., Pace,H.C., Schumacher,M.A., Brennan.R.G., Lu,P. 1996. Crystall structure of the lactose operon repressor and its complexes with DNA and inducer. Science. 271: 1247-1254;

103. Li,M., Moyle,H., Susskind,M.M. 1994. Target of the transcriptional activation function of phage lambda cl protein. Science. 263:75-77.

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

105. Liang, S., Bipatnath,M., Xu,Y., Chen,S., Dennis,P., Ehrenberg.M., Bremer,H. 1999. Activities of constitutive promoters in Escherichia coli. J. Mol. Biol. 292:1937.

106. LindsleyJ.E., Cox.M.M. 1989. Dissotiation pathway for RecA nucleoprotein filaments formed on linear duplex DNA. J. Mol. Biol. 205: 695-711.

107. Link,A.J., Phillips,D., Church,G.M. 1997. Methods for generating precise deletions and insertions in the genome of wild-type Escherichia coli: application to open reading frame characterization. J Bacteriol. 179:6228-37.

108. Lisser.S., Margalit,H. 1993. Compilation of E.coli mRNA promoter sequences. Nucleic Acids Res. 21:1507-1516.

109. Little, J. W. 1967. An exonuclease induced by bacteriophage X. II. Nature of the enzymatic reaction. J. Biol. Chem. 242: 679-686.

110. Liu,C., Heath,L.S., Turnbough,C.L.Jr. 1994. Regulation of pyrB operon in Escherichia coli by UTP-sensitive reiterative RNA synthesis during transcriptional initiation. Genes Dev. 8:2904-2912.

111. Liu,J., Turnbough.Jr. 1994. Effects of transcriptional start site sequence and position on nucleotide-sensitive selection of alternative start sites at the pyrC promoter in Escherichia coli. J.Bacteriol.176:2938-2945.

112. Liu-Johnson H.-N., Gartenberg M.R., Crothers D.M. 1986. The DNA binding domain and bending angle of E. coli CAP protein. Cell 47: 995-1005.

113. Lloyd,R.G., Low,K.B. 1996. Homologous recombination. In: Escherichia coli and Salmonella: cellular and molecular biology. / F.C.Neidhardt, et al. (ed.), 2nd edition. ASM Press, Washigton, v.l: 2236-2255.

114. Lloyd,R.G., Thomas,A. 1983. On the nature of the RecBC and RecF pathways of conjugal recombination in Escherichia coli. Mol. Gen. Genet. 190: 156-161.

115. Lovett,S.T., Luisi-DeLuca,C., Kolodner,R.D. 1988. The genetic dependence of recombination in recD mutants of Escherichia coli. Genetics. 120: 37-45.

116. Luria, S.E., Adams, J.N., Ting.R.C. 1960. Trunsduction of lactose-utilizing ability among strains of E.coli and S. dysenteriae and the properties of the trunsducing phage particles. Virology, 12, 348.

117. Lusetti,S.L.r Cox,MM. 2002. The bacterial RecA protein and the recombinational DNA repair of stalled replication forks. Annu. Rev. Biochem. 71:71-100.

118. Malan,T.Ph., McClure, W.R. 1984. Dual promoter control of the Escherichia coli lactose operon. Cell. 39: 173-180.

119. Miller J.H.// Experiments in Molecular Genetics, New York: Cold Spring Harbor Laboratory Press, Cold Spring Harbor, 1972.

120. Mizushima-Sugano, J., Kaziro.Y. 1985. Regulation of the expression of the tufB operon: DNA sequences directly involved in the stringent control. EMBO J. 4: 1053-1058.

121. Miiller,J., Oehler,S., Mtiller-Hill,B. 1996. Repression of lac promoter as a function of distance, phase and quality of an auxiliary lac operator. J. Mol. Biol. 257: 21-29.

122. Midler-Hill,В. 1998. The function of auxiliary operators. Mol. Microbiol. 29: 13-18.

123. Mulligan,M.E., Brosius.J., McClure, W.R. 1985. Characterization of the effect of spacer length on the activity of Escherichia coli RNA polymerase at the TAC promoter. J. Biol. Chem. 260:3529-3538.

124. Munijappa, K., Shaner,S.L., Tang,S.S., Radding, CM. 1984. Mechanism of the concerted action of RecA protein and helix destabilizing proteins in homologous recombination. Proc. Natl. Acad. Sci. USA 81: 2757-2761.

125. Muniyappa.K, Radding.C.M. 1986. The homologous recombination system of phage X: pairing activities of p protein. J. Biol. Chem. 261: 7472-7478.

126. Munson.G.P., Holcomb.L.G., Scott,J.R. 2001. Novel group of virulence activators within the AraC family that are not restricted to upstream binding sites. Infect. Immunol. 69:186-193. '

127. Munson.L.M., Reznikoff.W.S. 1981. Abortive initiation and long ribonucleic acid synthesis. Biochemistry. 20:2081-2085.

128. Murphy,К.C. 1998. Use of bacteriophage X recombination functions to promote gene replacement in Escherichia coli. J. Bacteriol. 180: 2063-2071.

129. Murphy,K.C., Campellone,K.G., Poteete,A.R. 2000. PCR-mediated gene replacement in Escherichia coli. Gene 246(l-2):321-330.

130. Muyrers,J.P., Zhang, Y., Stewart,A.F. 2001. Techniques: Recombinogenic engineering—new options for cloning and manipulating DNA.Trends Biochem Sci. 26: 325-331.

131. MuyrersJ.P.P., Zhang,Y., Benes,V., Testa,G., Ansorge,W., Stewart,A.F. 2000. Point mutation of bacterial artificial chromosomes by ET recombination. EMBO Reports 1: 239-243.

132. Neitz,J., Neitz,M„ Jacobs,J.H. 1989. Analisys of fusion gene and encoded photopigment of color-blind humans. Nature, 342:679-682.

133. Newlands,J.T., Gaal,T., Mecsas,J., Gourse,R.L. 1993. Transcription of the Escherichia coli rrnB Pl promoter by the heat shock RNA polymerase (Eg32) in vitro. J.Bacteriology. 175:661-668.

134. Oehler,S., Eismann,E.,R., Kramer,H., Mttller-Hill.B. 1990. EMBO J. 9: 973-979

135. РасеД.С., Kercher,M.A„ Lu,P., Markievicz,P., Miller,J.H., Chang, G. 1997. Lac repressor genetic map in real space. Trends Biochem. Sci. 22:334-339.

136. Pemberton,I.K, Muskhelishvili,G., Travers,A.A., Buckle,M. 2000. The G+C-rich discriminator region of the tyrT promoter antagonizes the formation of stable preinitiation complexes. J. Mol. Biol. 299: 859-864.

137. Peredelchuk MY, Bennett GN. 1997. A method for construction of E. coli strains with multiple DNA insertions in the chromosome. Gene. 187: 231-8.

138. Perez-Rueda,E., Collado-Vides,J. 2000. The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12. Nucleic Acids Res. 28: 18381847.

139. Ponnambalam,S., Webster, C., Bingham,A., Busby,S. 1986. Transcription initiation at the Escherichia coli galactose operon promoters in the absence of the normal -35 region sequences.J.Biol.Chem. 261:16043-16048.

140. Posfai.G., Kolisnychenko,V, Bereczki.Z., Blattner.F.R. 1999. Markerless gene replacement in Escherichia coli stimulated by a double-strand break in chromosome. Nucleic Acids Res. 27: 4409-4415.

141. Posfai,G., Koob,M., Hradecna,Z., Hasan,N., Filutowicz,M., Szybalski,W. 1994. In vivo exision and amplification of large segments of the genome. Nucleic Acids Res. 22: 2392-2398.

142. Poteete,A.R. 2001. What makes the bacteriophage X Red system useful for genetic engineering: molecular mechanism and biological function. FEMS Microbiol. Lett. 201: 9-14.

143. Poteete,A.R„ Fenton,A.C. 1984. Lambda Red-dependent growth and recombination of phage P22. Virology 134: 161-167.

144. Poteete,A.R., Fenton,A.C. 2000. Genetic requirments of phage X Red-mediated gene replacement in Escherichia coli K12. J. Bacteriol. 182: 2336-2340.

145. Qi,F„ Turnbough C.L.Jr. 1995. Regulation of codBA operon expression in Escherichia coli by UTP-dependent reiterative transcription and UTP-sensitive transcriptional start site switching. J.Mol.Biol. 254:552-565.

146. Reynaud,C.A., Bertocci.B., Dahan,A„ Weill, J.C. 1994. Formation of the chicken B-cell repertoire: ontogenesis, regulation of Ig gene rearangment, and diversification by gene conversion. Adv. Immunol. 57:353-378.

147. Rice.K.P., Eggler,A.L., Sung,P., Cox,M. 2001. DNA pairing and strand exchange by the Escherichia coli RecA and yeast Rad51 proteins without ATP hydrolysis. J. Biol. Chem. 276: 38570-38581.

148. Richet,E., Raibaud.O. 1991. Supercoiling is essential for the formation and stability of the initiation complex at the divergent malEp and malKp promoters. J. Mol. Biol. 218:529-542.

149. Roche,E.D., Sauer,R.T. 2001. Identification of endogenous ssrA-tagged proteins reveals tagging at positions corresponding to stop codons. J. Biol. Chem. 276: 28509-28515.

150. Rogo,F. 1999. Repression of transcription initiation in Bacteria. J. Bacteriol. 181:2987-2991.

151. Ross,W., Aiar,S.E., Salomon,J., Gourse,R.L. 1998. Escherichia coli promoters with UP elements of different strengths: modular structure of bacterial promoters. J.Bacteriology. 180:5375-5383.

152. Ross.W., Gosink,K.K., Salomon,J., Igarashi,K., Zou,C.,Ishihama,A., Severinov,K., Gourse.R.L. 1993. A third recognition element in bacterial promoters: DNA binding by the a subunit of RNA polymerase. Science. 262:1407-1413.

153. Russel,C.B., Dahlquist,F.W. 1989. Exchange of chromosomal and plasmid alleles in Escherichia coli by selection for loss of a dominant antibiotic sensitivity marker. J. Bacteriol. 171: 2614-2618.

154. Russell, D.R., Bennett, G.N. 1982. Construction and analysis of in vivo activity of E. coli promoter hybrids and promoter mutants that alter the -35 to -10 spacing. Gene. 20:231-243.

155. Russell, C.B., Thaler,D.S., Dahlquist,F.W. 1989. Chromosomal transformation of Escherichia coli recD strains with linearized plasmids. J. Bacteriol. 171: 2609-2613.

156. Saarilahti,H.T., Palva,E.T. 1985. In vivo transfer of chromosomal mutations onto multicopy plasmids utilizing polA strains: cloning of an ompR2 mutation in Escherichia coli K-12. FEMS Microbiol. Lett. 26: 27-33.

157. Sadler J.R., Sasmor H., Betz J.L. 1983. A perfectly symmetric lac operator binds the lac repressor very tightly. Proc. Natl. Acad. Sci. USA 80: 6785-6789.

158. Sakaki,Y. 1974. Inactivation of the ATP-dependent Dnase of Escherichia coli after infection with double-stranded DNA phages. J. Virol. 14: 1611-1612.

159. SambrookJ., Fritsch E., Maniatis T.I I Molecular Cloning. A Laboratory Manual. New York: Cold Spring Harbor, 1989.

160. Schlax,P.J., Capp,M.W., Record,M.T. Jr. 1995. Inhibition of transcription initiation by lac repressor. J. Mol. Biol. 27: 331-350.

161. Schofield,M.A., Agbanag,R., Miller,J.H. 1992. DNA inversions between short inverted repeats in Escherichia coli. Genetics 138: 11-29.

162. Scholz,P., Haring,V., Wittmann-Liebold.B., Ashman,K., Bagdasarian,M., Scherzinger.E. 1989. Complete nucleotide sequence and gene organization of the broad-host-range plasmid RSF1010. Gene 75:271-288.

163. Schultz.S.C., Shields,G.C., Steitz.T.A. 1991. Crystal structure of a CAP-DNA complex: the DNA is bent by 90 degrees. Science. 253: 1001-1007.

164. Shaner,S.L., Radding.C.M. 1987. Translocation of Escherichia coli RecA protein from a single-stranded tail to contiguous duplex DNA. J. Biol. Chem. 262: 9211-9219.

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

166. Shulman.M.J., Hallick.L.M., Echols,H., Singer,E.R. 1970. Properties of recombination-deficient mutants of bacteriophage X. J. Mol. Biol. 52: 501-520.

167. Singer,E.R., Weil, J. 1968.Recombination in bacteriophage X. I. Mutants deficient in general recombination. J. Mol. Biol. 34: 261-271.

168. Smith GR, Kunes SM, Schultz DW, Taylor A, Triman KL. 1981 Structure of chi hotspots of generalized recombination. Cell 24:429-36.

169. Sorensen,K.I., Baker,K.E.,Kelln,R.A„ Neuhard.J. 1993. Nucleotide pool-sensitive selection of the transcriptional start site in vivo at the Salmonella typhimurium pyrC and pyrD promoters. J.Bacteriol. 175:4137 -4144.

170. Spott.S., Dong,F., Kisters-Woike,B., Mutter-Hill,В. 2000. Dimerisation mutants of Lac repressor. II. A single amino acid substitution, D278L, changes the specificity of dimerisation. J. Mol. Biol. 296. 673-684;

171. Spronk, C.A.E.M., Bonvin, A.M.J.J., Radha,P.K., Melacini,G., Boelencs.R., Kaptein.R. 1999. The solution structure of Lac repressor headpeace 62 complexed to a symmetrical lac operator. Structure. 7: 1483-1492.

172. Straney,S.B„ Crothers.D.M. 1987. Lac repressor is a transient gene-activating protein. Cell. 51:699-707;

173. Swaminathan,S., Ellis,H.M., Waters,L.S., Yu,D., Lee,E-C., Court,D.L., Sharan,S.K. 2001. Rapid engineering of bacterial artificial chromosomes using oligonucleotides. Genesis 29: 14-21.

174. Szoke.P.A., Allen, T.L., deHaseth,P.L. 1987. Promoter recognition by Escherichia coli RNA polymerase: effect of base substitutions in the -10 and -35 regions. Biochemistry. 26:6188-6194.

175. Tang.H., Severinov.K., Goldfarb,A., Fenyo,D., Chait,B„ Ebright,R.H. 1994. Location, structure, and function of the target of a transcriptional activator protein. Genes. Dev. 8: 3058-3067.

176. Thaler,D.S., Sampson,E., Siddiqi,I., Rosenberg, S.M., Thomason,L.C., Stahl,F.W., Stahl,M.M. 1989. Recombination of bacteriophage X in recD mutants of Escherichia coli.Genome. 31: 53-67.

177. Thieffry,D., Huerta,A., Perez-Rueda,E., Collado-Vides,J. 1998. From specific gene regulation to genomic networks: a global analysis of transcriptional regulation in Escherichia coli. Bioessays. 20: 433-440.

178. Wang, P.L. 2000. Creating hybrid genes by homologous recombination. Dis. Markers 16: 3-13.

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

180. Winans, S.C., Elledge,S.J., KruegerJ.H., Walker,G.C. 1985. Site-directed insertion and deletion mutagenesis with cloned fragments in Escherichia coli. J. Bacteriol. 161: 1219-1221.

181. Wu,C. W., Goldthwait,D.A. 1969. Studies of nucleotide binding to the ribonucleic acid polymerase by equilibrium dialysis. Biochemistry. 8:4458-4464.

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

183. Zhang,P., Li,M.Z., Elledge,J. 2002. Towards genetic genome projects: genomic library screening and gene-targeting vector construction in a single step. Nat. genet. 30:31-39.

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

185. Zissler,J., Signer,E., Schaefer,F. 1971. The role of recombination in growth of bacteriophage X. I. The gamma gene, p.455-468. In A.D.Hershey (ed.), The bacteriophage X. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.

186. Машко С.В., Горовиц Р.Л., Трухан М.Э., Демчук Е.Я., Лебедева М.И., Лапидуе А.Л., Подковыров С.М., Козлов Ю.И., Дебабов В.Г. 1986. Изучение относительной эффективности некоторых промоторов Escherichia coli и фага

187. Доклады АН СССР 291: 1510-1513.

188. Машко С.В., Лапидуе А.Л., Трухан М.Э., Стащук Н.А., Дебабов В.Г. 1987. Исследование эффективности трансляционного сопряжения в гибридных оперонах. Молекулярная биология 21: 1310-1321.