Разработка векторов для молекулярного клонирования с позитивной селекцией, основанных на использовании летального эффекта гена барназы
Диссертация
Впервые разработана высокоэффективная векторная система для молекулярного клонирования с позитивной селекцией, использующая в качестве селективного маркера ген рибонуклеазы. Получены векторные плазмиды, содержащие в кодирующей части гена рибонуклеазы из Bacillus amyloliquefaciens — барназы участки узнавания 2 (рМТ438) и 10 (рМТ440) наиболее употребительных рестрикционных эндонуклеаз. Разработана… Читать ещё >
Содержание
- Список использованных сокращений
- ГЛАВА 1. Литературный обзор
- 1. 1. Вектора с позитивной селекцией
- 1. 2. РНКаза барназа как фактор летальности
- 1. 2. 1. Характеристика фермента
- 1. 2. 2. Внутриклеточный ингибитор барназы — барстар
- 3. 1. Разработка на основе гена барназы вектора рМТ440 с позитивной селекцией
- 3. 1. 1. Изучение влияния уровня индукции tac—промотора на выживаемость различных штаммов E. coli, трансформированных плазмидой рМТ
- 3. 1. 2. Клонирование с помощью плазмиды рМТ416 ПЦР— продукта, кодирующего вариабельные регионы легкой цепи антитела к белку р24 вируса HIV
- 3. 1. 3. Введение полилинкера в ген барназы и конструкция векторов рМТ438, рМТ438а и рМТ
- 3. 1. 4. Использование вектора рМТ440 с позитивной селекцией для клонирования фрагментов чужеродной ДНК
- 3. 2. Конструирование вектора рВа —7 с позитивной селекцией.70 3.2.1. Конструирование плазмид рВа —2, рВа — 3s и рВа
- 3. 2. 2. Сайт — специфический мутагенез для удаления. повторяющихся сайтов рестрикции и конструкция вектора рВа
- 3. 2. 3. Использование вектора рВа —7 для клонирования фрагментов чужеродной ДНК
- 3. 2. 4. Использование вектора рВа — 7 для клонирования генов иммуноглобулинов мыши
- 3. 3. Исследование с помощью иммуноблотинга рекомбинантной барназы и ее мутантов, продуцируемых с помощью плазмид рМТ440 и рВа
- 3. 4. Характеристика вклада ряда мутаций в ферментативную активность модифицированной барназы
Список литературы
- Bernard Р, New ccdB positive — selection cloning vectors with kanamycin or chloramphenicol selectable markers. Gene 162(1): 159 — 60, 1995.
- Yazynin SA, Deyev SM, Jucovic M and Hartley RW, A plasmid vector with positive selection and directional cloning based on a conditionally lethal gene. Gene 159(1): 131−2, 1996.
- Deyev SM, Yazynin SA, Kuznetsov DA, Jukovich M and Hartley RW, Ribonuclease — charged vector for facile direct cloning with positive selection. Mol Gen Genet 259(4): 379−82, 1998.
- Vieira J and Messing J, The pUC plasmids, an M13mp7 —derived system for insertion mutagenesis and sequencing with synthetic universal primers. Gene 19(3): 259−68, 1982.
- Henrich В and Schmidtberger B, Positive — selection vector with enhanced lytic potential based on a variant of phi X174 phage gene E. Gene 154(1): 51−4, 1995.
- Henrich В and Plapp R, Use of the lysis gene of bacteriophage phi XI74 for the construction of a positive selection vector. Gene 42(3): 345 — 9, 1986.
- Ozaki LS, Maeda S, Shimada К and Takagi Y, A novel ColEl: Tn3 plasmid vector that allows direct selection of hybrid clones in E. coli. Gene 8(3): 301−14, 1980.
- Vernet T, Lau PC, Narang SA and Visentin LP, A direct — selection vector derived from pColE3 — CA38 and adapted for foreign gene expression. Gene 34(1): 87−93, 1985.
- Sambrook J, Fritsch EF and Maniatis T, Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y., 1989.
- Ullmann A, Complementation in beta — galactosidase: from protein structure to genetic engineering. Bioessays 14(3): 201 — 5, 1992.
- Testori A, Listowsky I and Sollitti P, Direct cloning of unmodified PCR products by exploiting an engineered restriction site. Gene 143(1): 151 — 2, 1994.
- Shuman S and Prescott J, Specific DNA cleavage and binding by vaccinia virus DNA topoisomerase I. J Biol Chem 265(29): 17 826−36, 1990.
- Shuman S, Novel approach to molecular cloning and polynucleotide synthesis using vaccinia DNA topoisomerase. J Biol Chem 269(51): 32 678 — 84, 1994.
- Gabant P, Dreze PL, Van Reeth T, Szpirer J and Szpirer C, Bifunctional lacZ alpha —ccdB genes for selective cloning of PCR products. Biotechniques 23(5): 938−41, 1997.
- Hengen PN, Methods and reagents. Reducing background colonies with positive selection vectors. Trends Biochem Sci 22(3): 105 — 6, 1997.
- Miki T, Yoshioka K and Horiuchi T, Control of cell division by sex factor F in Escherichia coli. I. The 42.84 — 43.6 F segment couples cell division of the host bacteria with replication of plasmid DNA. J Mol Biol 174(4): 605 — 25, 1984.
- Miki T, Chang ZT and Horiuchi T, Control of cell division by sex factor F in Escherichia coli. II. Identification of genes for inhibitor protein and trigger protein on the 42.84−43.6 F segment. J Mol Biol 174(4): 627−46, 1984.
- Karoui H, Bex F, Dreze P and Couturier M, Ham22, a mini —F mutation which is lethal to host cell and promotes recA— dependent induction of lambdoid prophage. Embo J 2(11): 1863−8, 1983.
- Ogura T and Hiraga S, Mini —F plasmid genes that couple host cell division to plasmid proliferation. Proc Natl Acad Sci USA 80(15): 4784 — 8, 1983.
- Jaffe A, Ogura T and Hiraga S, Effects of the ccd function of the F plasmid on bacterial growth. J Bacteriol 163(3): 841−9, 1985.
- Bernard P and Couturier M, Cell killing by the F plasmid CcdB protein involves poisoning of DNA— topoisomerase II complexes. J Mol Biol 226(3): 735−45, 1992.
- Bernard P, Kezdy KE, Van Melderen L, Steyaert J, Wyns L, Pato ML, Higgins PN and Couturier M, The F plasmid CcdB protein induces efficient ATP-dependent DNA cleavage by gyrase. J Mol Biol 234(3): 534−41, 1993.
- Van Melderen L, Bernard P and Couturier M, Lon — dependent proteolysis of CcdA is the key control for activation of CcdB in plasmid — free segregant bacteria. Mol Microbiol 11(6): 1151 — 7, 1994.
- Van Melderen L, Thi MHD, Lecchi P, Gottesman S, Couturier M and Maurizi MR, ATP — dependent degradation of CcdA by Lon protease. Effects of secondary structure and heterologous subunit interactions. J Biol Chem 271(44): 27 730−8, 1996.
- Bernard P, Gabant P, Bahassi EM and Couturier M, Positive — selection vectors using the F plasmid ccdB killer gene. Gene 148(1): 71 — 4, 1994.
- Kolb A, Busby S, Buc H, Garges S and Adhya S, Transcriptional regulation by cAMP and its receptor protein. Annu Rev Biochem 62: 749 — 95, 1993.
- Stryer L, Biochemie. Spektrum, Heidelberg, 836−7, 1990 .
- Lopata M, Schlieper D, von Wilcken — Bergmann B and Muller —Hill B, A lethal mutant of the catabolite gene activator protein CAP of Escherichia coli. Biol Chem 378(10): 1153−62, 1997.
- Schultz SC, Shields GC and Steitz TA, Crystal structure of a CAP-DNA complex: the DNA is bent by 90 degrees. Science 253(5023): 1001−7, 1991.
- Parkinson G, Wilson C, Gunasekera A, Ebright YW, Ebright RE and Berman HM, Structure of the CAP —DNA complex at 2.5 angstroms resolution: a complete picture of the protein —DNA interface. J Mol Biol 260(3): 395−408, 1996.
- Pevny L, Simon MC, Robertson E, Klein WH, Tsai SF, D’Agati V, Orkin SH and Costantini F, Erythroid differentiation in chimaeric mice blocked by a targeted mutation in the gene for transcription factor GATA— 1. Nature 349(6306): 257−60, 1991.
- Trudel P, Provost S, Massie B, Chartrand P and Wall L, pGATA: a positive selection vector based on the toxicity of the transcription factor GATA — 1 to bacteria. Biotechniques 20(4): 684−93, 1996.
- Ko U and Engel JD, DNA-binding specificities of the GATA transcription factor family. Mol Cell Biol 13(7): 4011−22, 1993.
- Merika M and Orkin SH, DNA—binding specificity of GATA family transcription factors. Mol Cell Biol 13(7): 3999−4010, 1993.
- Smith DB and Johnson KS, Single —step purification of polypeptides expressed in Escherichia coli as fusions with glutathione S — transferase. Gene 67(1): 31−40, 1988.
- Chan RY, Palfree RG, Congote LF and Solomon S, Development of a novel type of cloning vector for suicide selection of recombinants. DNA Cell Biol 13(3): 311−9, 1994.
- Zhu QZ, Hu J, Mulay S, Esch F, Shimasaki S and Solomon S, Isolation and structure of corticostatin peptides from rabbit fetal and adult lung. Proc Natl Acad Sci USA 85(2): 592−6, 1988.
- Selsted ME, Harwig SS, Ganz T, Schilling JW and Lehrer RI, Primary structures of three human neutrophil defensins. J Clin Invest 76(4): 1436 — 9,1985.
- Mongkolsuk S, Rabibhadana S, Vattanaviboon P and Loprasert S, Generalized and mobilizable positive — selection cloning vectors. Gene 143(1): 145−6, 1994.
- Marsh JL, Erfle M and Wykes EJ, The pIC plasmid and phage vectors with versatile cloning sites for recombinant selection by insertional inactivation. Gene 32(3): 481−5, 1984.
- Kast P, pKSS--a second — generation general purpose cloning vectorfor efficient positive selection of recombinant clones. Gene 138(1 — 2): 109— 14, 1994.
- Kuhn I, Stephenson FH, Boyer HW and Greene PJ, Positive — selection vectors utilizing lethality of the EcoRI endonuclease. Gene 42(3): 253 — 63,1986.
- Arakawa Y, Wacharotayankun R, Ohta M, Shoji K, Watahiki M, Horii T and Kato N, Construction of a novel suicide vector: selection for Escherichia coli HB101 recombinants carrying the DNA insert. Gene 104(1): 81−4, 1991.
- Stevis PE and Ho NW, A novel xylB—based positive selection vector. Plasmid 20(1): 92−5, 1988.
- Noyer—Weidner M and Reiners — Schramm L, Highly efficient positive selection of recombinant plasmids using a novel rglB—based Escherichia coli K- 12 vector system. Gene 66(2): 269−78, 1988.
- Barros EV, Bataus LA, Valencia FF, Maranhao AQ and Astolfi Filho S, A novel cloning system for direct screening using a suicidal strategy. Gene 179(2): 287−9, 1996.
- Burns DM and Beacham IR, Positive selection vectors: a small plasmid vector useful for the direct selection of Sau3A—generated overlapping DNA fragments. Gene 27(3): 323−5, 1984.
- Collins FS, Patrinos A, Jordan E, Chakravarti A, Gesteland R and Walters L, New goals for the U.S. Human Genome Project: 1998−2003. Science 282(5389): 682−9, 1998.
- Lennon G, Auffray C, Polymeropoulos M and Soares MB, The I.M.A.G.E. Consortium: an integrated molecular analysis of genomes and their expression. Genomics 33(1): 151 — 2, 1996.
- Lelias JM, de Leon L, Jerpseth B and Soares S, Human universal cDNA Library Array I. Strategies Newsletter 11(2): 29−32, 1998.
- Paddon CJ and Hartley RW, Cloning, sequencing and transcription of an inactivated copy of Bacillus amyloliquefaciens extracellular ribonuclease (barnase). Gene 40(2−3): 231−9, 1985.
- Paddon CJ and Hartley RW, Expression of Bacillus amyloliquefaciens extracellular ribonuclease (barnase) in Escherichia coli following an inactivating mutation. Gene 53(1): 11 — 9, 1987.
- Hartley RW and Paddon CJ, Use of plasmid pTVl in transposon mutagenesis and gene cloning in Bacillus amyloliquefaciens. Plasmid 16(1): 45−51, 1986.
- Hartley RW, Barnase and barstar. Expression of its cloned inhibitor permits expression of a cloned ribonuclease. J Mol Biol 202(4): 913 — 5, 1988.
- Hartley RW, Barnase and barstar: two small proteins to fold and fit together. Trends Biochem Sci 14(11): 450−4, 1989.
- Nambiar KP, Stackhouse J, Presnell SR and Benner SA, Expression of bovine pancreatic ribonuclease A in Escherichia coli published erratum appears in Eur J Biochem 1987 May 4−164(3):713. Eur J Biochem 163(1): 6771, 1987.
- Tarragona —Fiol A, Taylorson CJ, Ward JM and Rabin BR, Production of mature bovine pancreatic ribonuclease in Escherichia coli. Gene 118(2): 239−45, 1992.
- Mossakowska DE, Nyberg K and Fersht AR, Kinetic characterization of the recombinant ribonuclease from Bacillus amyloliquefaciens (barnase) andinvestigation of key residues in catalysis by site — directed mutagenesis. Biochemistry 28(9): 3843−50, 1989.
- Meiering EM, Bycroft M and Fersht AR, Characterization of phosphate binding in the active site of barnase by site — directed mutagenesis and NMR. Biochemistry 30(47): 11 348−56, 1991.
- Meiering EM, Serrano L and Fersht AR, Effect of active site residues in barnase on activity and stability. J Mol Biol 225(3): 585−9, 1992.
- Bastyns K, Froeyer M, Volckaert G and Engelborghs Y, The role of Glu —60 in the specificity of the recombinant ribonuclease from Bacillus amyloliquefaciens (barnase) towards dinucleotides, poly (A) and RNA. Biochem J300(Pt 3): 737−42, 1994.
- Day AG, Parsonage D, Ebel S, Brown T and Fersht AR, Barnase has subsites that give rise to large rate enhancements. Biochemistry 31(28): 6390 — 5, 1992.
- Buckle AM, Schreiber G and Fersht AR, Protein — protein recognition: crystal structural analysis of a barnase— barstar complex at 2.0 —A resolution. Biochemistry 33(30): 8878−89, 1994.
- Baudet S and Janin J, Crystal structure of a barnase —d (GpC) complex at 1.9 A resolution. J Mol Biol 219(1): 123−32, 1991.
- Sancho J and Fersht AR, Dissection of an enzyme by protein engineering. The N and C — terminal fragments of barnase form a native — like complex with restored enzymic activity. J Mol Biol 224(3): 741 — 7, 1992.
- Hartley RW, Rogerson DL, Jr. and Smeaton JR, Production and purification of the extracellular ribonuclease of Bacillus amyloliguefaciens (barnase) and its intracellular inhibitor (barstar). II. Barstar. Prep Biochem 2(3): 243−50, 1972.
- Hartley RW and Smeaton JR, On the reaction between the extracellular ribonuclease of Bacillus amyloliquefaciens (barnase) and its intracellular inhibitor (barstar). J Biol Chem 248(16): 5624−6, 1973.
- Hartley RW, A reversible thermal transition of the extracellular ribonuclease of Bacillus amyloliquefaciens. Biochemistry 7(6): 2401 — 8, 1968.
- Hartley RW, A two —state conformational transition of the extracellular ribonuclease of Bacillus amyloliquefaciens (barnase) induced by sodium dodecyl sulfate. Biochemistry 14(11): 2367−70, 1975.
- Guillet V, Lapthorn A, Fourniat J, Benoit JP, Hartley RW and Mauguen Y, Crystallization and preliminary X —ray investigation of barstar, the intracellular inhibitor of barnase. Proteins 17(3): 325 — 8, 1993.
- Lubienski MJ, Bycroft M, Freund SM and Fersht AR, Three-dimensional solution structure and 13C assignments of barstar using nuclear magnetic resonance spectroscopy. Biochemistry 33(30): 8866 — 77, 1994.
- Schreiber G and Fersht AR, Interaction of barnase with its polypeptide inhibitor barstar studied by protein engineering. Biochemistry 32(19): 5145 — 50, 1993.
- Jones DN, Bycroft M, Lubienski MJ and Fersht AR, Identification of the barstar binding site of barnase by NMR spectroscopy and hydrogen — deuterium exchange. FEBS Lett 331(1−2): 165−72, 1993.
- Fasman GD and Chemical Rubber Company., Handbook of biochemistry and molecular biology. CRC Press, Cleveland, 1975.
- Maniatis T, Fritsch EF and Sambrook J, Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y., 1982.
- Mullis KB and Faloona FA, Specific synthesis of DNA in vitro via a polymerase — catalyzed chain reaction. Methods Enzymol 155: 335 — 50, 1987.
- Lange H, Solterbeck M, Berek C and Lemke H, Correlation between immune maturation and idiotypic network recognition. Eur J Immunol 26(9): 2234−42, 1996.
- Hanahan D, Studies on transformation of Escherichia coli with plasmids. J Mol Biol 166(4): 557−80, 1983.
- Perrin S and Gilliland G, Site — specific mutagenesis using asymmetric polymerase chain reaction and a single mutant primer. Nucleic Acids Res 18(24): 7433−8, 1990.
- Lee LG, Spurgeon SL, Heiner CR, Benson SC, Rosenblum BB, Menchen SM, Graham RJ, Constantinescu A, Upadhya KG and Cassel JM, New energy transfer dyes for DNA sequencing. Nucleic Acids Res 25(14): 2816−22, 1997.
- Chomczynski P and Sacchi N, Single —step method of RNA isolation by acid guanidinium thiocyanate— phenol — chloroform extraction. Anal Biochem 162(1): 156−9, 1987.
- Laemmli UK, Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227(259): 680−5, 1970.
- Kabat EA, National Institutes of Health (U.S.) and Columbia University., Sequences of proteins of immunological interest. U.S. Dept. of Health and Human Services, Bethesda, 1991.
- Yanisch — Perron C, Vieira J and Messing J, Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mpl8 and pUC 19 vectors. Gene 33(1): 103−19, 1985.
- Abagyan R and Totrov M, Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins. J Mol Biol 235(3): 983- 1002, 1994.
- Wu E, Croucher PI and McKie N, Expression of members of the novel membrane linked metalloproteinase family ADAM in cells derived from a range of haematological malignancies. Biochem Biophys Res Commun 235(2): 437−42, 1997.
- Jucovic M and Hartley RW, In vivo system for the detection of low level activity barnase mutants. Protein Eng 8(5): 497 — 9, 1995.
- Нуркиянова K.M., Шульга А. А., Захарьев B.M., Кирпичников М. П., Скрябин К. Г., Баев А. А. Клонирование и определение нуклеотидной последовательности гена РНКазы Bacillus intermedius, Докл. Академии наук СССР, т. 309. с. 1476- 1479, 1989.
- Курбанов Ф.Т. Структурно — функциональное картирование молекул барназы и биназы методом гибридных генов. Диссертация на соискание ученой степени кандидата биологических наук, Москва, 1996.
- Афанасенко Г. А., Дудкин С. М., Каминир A.B. Первичная структура РНКазы Bacillus intermedius. Биоорганическая химия., т. 5., с. 187 — 202, 1979
- Shiyanov P.A., Bespalov I.A., Terletskaya H.N. and Deyev S.M. X78108 GenBank report. M. musculus (BALB/c) mRNA for immunoglobulin kappa light chain variable region, 1994.
- Shiyanov P.A., Bespalov I.A., Terletskaya H.N. and Deyev S.M. X78107 GenBank report. M. musculus (BALB/c) mRNA for immunoglobulin gamma 1 chain heavy chain variable region, 1994.