Клонирование и экспрессия генов литических эндопептидаз L1 и L5 Lysobacter sp. XL1
Диссертация
Бактерия Lysobacter sp. XL1 секретерует в окружающую среду целый ряд литических ферментов. Антимикробный препарат лизоамидаза, получаемый на основе культуральной жидкости этой бактерии, активен против грамположительных и грамотрицательных бактерий, дрожжей, препарат препятствует прорастанию бактериальных и грибных спор (Ryazanova et al., 2005; Begunova et al., 2006). Успешные клинические… Читать ещё >
Содержание
- СПИСОК СОКРАЩЕНИЙ
- ГЛАВА 1. ОБЗОР ЛИТЕРАТУРЫ
- 1. 1. Бактериолитические ферменты
- 1. 2. Классификация пептидаз
- 1. 3. Сериновые протеазы
- 1. 4. Структурная организация протеаз
- 1. 5. Литические протеазы Lysobacter enzymogenes
- 1. 6. Структурная организация а-литической протеазы Lysobacter enzymogenes
- 1. 7. Секреция протеаз
- 1. 7. 1. Внеклеточные протеазы микроорганизмов, I (TISS) тип секреции и ABC транспортеры
- 1. 7. 2. ABC транспортеры
- 1. 7. 3. Внеклеточные протеазы микроорганизмов и II (T2SS) тип секреции
- 1. 7. 4. Внеклеточные протеазы микроорганизмов V тип секркции (T5SS)
- 1. 7. 5. Секреция при помощи везикул
- 1. 8. Регуляция экспрессии генов микробных сериновых протеаз
- 1. 9. Системы экспрессии для наработки рекомбинантных белков
- 1. 10. Продукция рекомбинантных белков в бактериях рода Pseudomonas
- 1. 11. Бактерии рода Lysobacter
- 1. 12. «Лизоамидаза» — препарат, получаемый на основе культуральной жидкости бактерии Lysobacter sp. XL
- 1. 13. Эндопептидазы LI и L5 Lysobacter sp. XL
- ГЛАВА 2. МАТЕРИАЛЫ И МЕТОДЫ ИССЛЕДОВАНИЯ
- 2. 1. Материалы
- 2. 1. 1. Штаммы бактерий
- 2. 1. 2. Плазмидные вектора и рекомбинантные плазмиды
- 2. 1. 3. Среды и основные буферы
- 2. 1. 4. Реактивы
- 2. 1. 5. Олигонулеотидные праймеры
- 2. 2. Методы исследования
- 2. 2. 1. Выделение хромосомной ДНК бактерий
- 2. 2. 2. Обработка ДНК эндонуклеазами рестрикции
- 2. 2. 3. ДНК-ДНК гибридизация по Саузерну
- 2. 2. 4. Полимеразная цепная реакция (ПЦР)
- 2. 2. 5. Препаративное выделение фрагментов ДНК из агарозных гелей
- 2. 2. 6. Цитирование фрагментов ДНК
- 2. 2. 7. Определение нуклеотидной последовательности
- 2. 2. 8. Получение компетентных клеток E. coli и трансформация
- 2. 2. 9. Получение электрокомпетентных клеток бактерий рода Pseudomonas и электропорация
- 2. 2. 10. Конъюгативный перенос плазмид
- 2. 2. 11. Выделение плазмидной ДНК
- 2. 2. 12. Анализ рекомбинантных клонов на наличие вставки в плазмиде
- 2. 2. 13. Экспрессия ОРС alpA и alpB в E. coli и анализ литической активности
- 2. 2. 14. Анализ бактериолитической активности рекомбинантных штаммов Pseudomonas на индикаторной среде
- 2. 2. 15. Культивирование Pseudomonas в жидких средах
- 2. 2. 16. Анализ аминокислотных последовательностей
- 2. 2. 17. Выделение РНК из клеток
- 2. 2. 18. Электрофорез РНК в геле, содержащим формальдегид
- 2. 2. 19. РНК-ДНК гибридизация
- 2. 2. 20. Определение стартовых точек транскрипции генов методом 5'-RACE
- 2. 2. 21. Приготовление агарозных блок- вставок с интактной ДНК бактерий
- 2. 2. 22. Обработка блок-вставок с ДНК эндонуклеазами рестрикции
- 2. 2. 23. Электрофорез в пульсирующих полях
- 2. 2. 24. Скрининг плазмид по методу Экхардта
- 2. 2. 25. Электрофорез в полиакриламидном геле
- 2. 2. 26. Иммуноблоттинг
- 2. 2. 27. Измерение бактериолитической активности
- 2. 1. Материалы
- 3. 1. Поиск и определение нуклеотидной последовательности участка ДНК Lysobacter sp. XL1, кодирующего литические эндопептидазы LI и L
- 3. 2. AlpA и AlpB являются секретируемыми литическими протеазами
- 3. 3. Обнаруженные гены alpA и alpB кодируют функционально активные литические ферменты
- 3. 4. ОРС alpA и alpB транскрибируются с собственных промоторов
- 3. 5. Определение стартовых точек транскрипции
- 3. 6. Определение локализации генов alpA и alpB Lysobacter sp. XL
- 3. 6. 1. Детекция плазмид в клетках по модифицированному методу Экхардта
- 3. 6. 2. Анализ генома Lysobacter sp. XL1 при помощи электрофореза в пульсирующих полях
- 3. 7. Продукция рекомбинантных эндопептидаз AlpA и AlpB в клетках бактерий рода Pseudomonas
- 3. 7. 1. Конструирование системы экспрессии
- 3. 7. 2. Отбор штаммов бактерий рода Pseudomonas
- 3. 7. 3. Анализ бактериолитической активности штаммов псевдомонад
- 3. 7. 4. Спектр устойчивости штаммов Pseudomonas к антибиотикам
- 3. 7. 5. Анализ спектра секретируемых белков
- 3. 8. Конструирование рекомбинантных штаммов для экспрессии генов alpA и alpB в Pseudomonas
- 3. 9. Анализ эффективности системы экспрессии
Список литературы
- Abriouel, H., Franz, C.M., Ben Omar, N. and Galvez, A. Diversity and applications of Bacillus bacteriocins. FEMS Microbiol Rev, 2011. 35(1): p. 201−32.
- Ahmed, K., Chohnan, S., Ohashi, H., Hirata, T., Masaki, T. and Sakiyama, F. Purification, bacteriolytic activity, and specificity of beta-lytic protease from Lysobacter sp. IB-9374. J Biosci Bioeng, 2003. 95(1): p. 27−34.
- Anderson, D.E., Peters, R.J., Wilk, B. and Agard, D.A. alpha-lytic protease precursor: characterization of a structured folding intermediate. Biochemistry, 1999. 38(15): p. 4728−35.
- Bae, H.S., Im, W.T. and Lee, S.T. Lysobacter concretionis sp. nov., isolated from anaerobic granules in an upflow anaerobic sludge blanket reactor. Int J Syst Evol Microbiol, 2005. 55(Pt 3): p. 1155−61.
- Baker, D., Silen, J.L. and Agard, D.A. Protease pro region required for folding is a potent inhibitor of the mature enzyme. Proteins, 1992a. 12(4): p. 339−44.
- Baker, D., Sohl, J.L. and Agard, D.A. A protein-folding reaction under kinetic control. Nature, 1992b. 356(6366): p. 263−5.
- Barequet, I.S., Ben Simon, G.J., Safrin, M., Ohman, D.E. and Kessler, E. Pseudomonas aeruginosa LasA protease in treatment of experimental staphylococcal keratitis. Antimicrob Agents Chemother, 2004. 48(5): p. 1681−7.
- Barrett, A.J., Tolle, D.P. and Rawlings, N.D. Managing peptidases in the genomic era. Biol Chem, 2003. 384(6): p. 873−82.
- Begunova, E.A., Stepnaya, O.A., Lysanskaya, V.Y. and Kulaev, I.S. Specificity of the action of lysoamidase on Staphylococcus aureus 209P cell walls. Biochemistry (Mose), 2003. 68(7): p. 735−9.
- Beveridge, T.J. Structures of gram-negative cell walls and their derived membrane vesicles. J Bacteriol, 1999. 181(16): p. 4725−33.
- Binet, R., Letoffe, S., Ghigo, J.M., Delepelaire, P. and Wandersman, C. Protein secretion by Gram-negative bacterial ABC exporters—a review. Gene, 1997. 192(1): p. 7−11.
- Bleves, S., Viarre, V., Salacha, R., Michel, G.P., Filloux, A. and Voulhoux, R. Protein secretion systems in Pseudomonas aeruginosa: A wealth of pathogenic weapons. Int J Med Microbiol, 2010. 300(8): p. 534−43.
- Blow, D.M., Birktoft, J.J. and Hartley, B.S. Role of a buried acid group in the mechanism of action of chymotrypsin. Nature, 1969. 221(5178): p. 337−40.
- Bone, R., Frank, D., Kettner, C.A. and Agard, D.A. Structural analysis of specificity: alpha-lytic protease complexes with analogues of reaction intermediates. Biochemistry, 1989a. 28(19): p. 7600−9.
- Bone, R., Fujishige, A., Kettner, C.A. and Agard, D.A. Structural basis for broad specificity in alpha-lytic protease mutants. Biochemistry, 1991. 30(43): p. 10 388−98.
- Bone, R., Silen, J.L. and Agard, D.A. Structural plasticity broadens the specificity of an engineered protease. Nature, 1989b. 339(6221): p. 191−5.
- Braun, P., Tommassen, J. and Filloux, A. Role of the propeptide in folding and secretion of elastase of Pseudomonas aeruginosa. Mol Microbiol, 1996. 19(2): p. 297−306.
- Brayer, G.D., Delbaere, L.T. and James, M.N. Molecular structure of the alpha-lytic protease from Myxobacter 495 at 2.8 Angstroms resolution. J Mol Biol, 1979. 131(4): p. 743−75.
- Bychkova, V.E. and Ptitsyn, O.B. The state of unfolded globules of protein molecules is more quickly becoming a rule, rather than an exception. Biofizika, 1993. 38(1): p. 58−66.
- Cascales, E., Buchanan, S.K., Duche, D., Kleanthous, C., Lloubes, R., Postle, K., Riley, M., Slatin, S. and Cavard, D. Colicin biology. Microbiol Mol Biol Rev, 2007. 71(1): p. 158−229.
- Chen, R. Bacterial expression systems for recombinant protein production: E. coli and beyond. Biotechnol Adv, 2011. 30(5): p. 1102−7.
- Chohnan, S., Nonaka, J., Teramoto, K., Taniguchi, K., Kameda, Y., Tamura, H., Kurusu, Y., Norioka, S., Masaki, T. and Sakiyama, F. Lysobacter strain with high lysyl endopeptidase production. FEMS Microbiol Lett, 2002. 213(1): p. 13−20.
- Choi, E.Y., Oh, E.A., Kim, J.H., Kang, D.K. and Hong, S.K. Distinct regulation of the sprC gene encoding Streptomyces griseus protease C from other chymotrypsin genes in Streptomyces griseus IF013350. J Microbiol Biotechnol, 2007. 17(1): p. 81−8.
- Choi, J.H. and Lee, S.Y. Secretory and extracellular production of recombinant proteins using Escherichia coli. Appl Microbiol Biotechnol, 2004. 64(5): p. 625−35.
- Christensen, P. and Cook, F.D. Lysobacter, a new genus of nonfruiting, gliding bacteria with a high base ratio. Int J Syst Bacteriol, 1978. 28(p. 367−393.
- Ciofu, O., Beveridge, T.J., Kadurugamuwa, J., Walther-Rasmussen, J. and Hoiby, N. Chromosomal beta-lactamase is packaged into membrane vesicles and secreted from Pseudomonas aeruginosa. J Antimicrob Chemother, 2000. 45(1): p. 9−13.
- Coutte, L., Antoine, R., Drobecq, H., Locht, C. and Jacob-Dubuisson, F. Subtilisin-like autotransporter serves as maturation protease in a bacterial secretion pathway. EMBO J, 2001. 20(18): p. 5040−8.
- Cunningham, E.L., Mau, T., Truhlar, S.M. and Agard, D.A. The pro region N-terminal domain provides specific interactions required for catalysis of alpha-lytic protease folding. Biochemistry, 2002. 41(28): p. 8860−7.
- Damas, J.M., Oliveira, A.S., Baptista, A.M. and Soares, C.M. Structural consequences of ATP hydrolysis on the ABC transporter NBD dimer: molecular dynamics studies of HlyB. Protein Sci, 2011. 20(7): p. 1220−30.
- Dammeyer, T., Steinwand, M., Kruger, S.C., Dubel, S., Hust, M. and Timmis, K.N. Efficient production of soluble recombinant single chain Fv fragments by a Pseudomonas putida strain KT2440 cell factory. Microb Cell Fact, 2011. 10(p. 11.
- Davis, B.D. The Isolation of Biochemically Deficient Mutants of Bacteria by Means of Penicillin. Proc Natl Acad Sci USA, 1949. 35(1): p. 1−10.
- Demain, A.L. and Vaishnav, P. Production of recombinant proteins by microbes and higher organisms. Biotechnol Adv, 2009. 27(3): p. 297−306.
- Eckhardt, T. A rapid method for the identification of plasmid desoxyribonucleic acid in bacteria. Plasmid, 1978. 1(4): p. 584−8.
- Eder, J. and Fersht, A.R. Pro-sequence-assisted protein folding. Mol Microbiol, 1995. 16(4): p. 609−14.
- Ekici, O.D., Paetzel, M. and Dalbey, R.E. Unconventional serine proteases: variations on the catalytic Ser/His/Asp triad configuration. Protein Sci, 2008. 17(12): p. 2023−37.
- Emanuelsson, O., Brunak, S., von Heijne, G. and Nielsen, H. Locating proteins in the cell using TargetP, SignalP and related tools. Nat. Protoc., 2007. 2(4): p. 953−71.
- Epstein, D.M. and Wensink, P.C. The alpha-lytic protease gene of Lysobacter enzymogenes. The nucleotide sequence predicts a large prepro-peptide with homology to propeptides of other chymotrypsin-like enzymes. J Biol Chem, 1988. 263(32): p. 16 586−90.
- Fath, M.J. and Kolter, R. ABC transporters: bacterial exporters. Microbiol Rev, 1993. 57(4): p. 995−1017.
- Fekkes, P. and Driessen, A.J. Protein targeting to the bacterial cytoplasmic membrane. Microbiol Mol Biol Rev, 1999. 63(1): p. 161−73.
- Filloux, A. The underlying mechanisms of type II protein secretion. Biochim Biophys Acta, 2004. 1694(1−3): p. 163−79.
- Fischetti, V.A. Bacteriophage lysins as effective antibacterials. Curr. Opin. Microbiol., 2008. 11(5): p. 393−400.
- Fujishige, A., Smith, K.R., Silen, J.L. and Agard, D.A. Correct folding of alpha-lytic protease is required for its extracellular secretion from Escherichia coli. J Cell Biol, 1992. 118(1): p. 33−42.
- George, A.M. and Jones, P.M. Perspectives on the structure-function of ABC transporters: The Switch and Constant Contact Models. Prog Biophys Mol Biol, 2012. 109(3): p. 95−107.
- Ghuysen, J.M. Use of bacteriolytic enzymes in determination of wall structure and their role in cell metabolism. Bacteriol Rev, 1968. 32(4 Pt 2): p. 425−64.
- Gillespie, D.C. and Cook, F.D. Extracellular Enzymes from Strains of Sorangium. Can J Microbiol, 1965. ll (p. 109−18.
- Gillings, M.R., Holley, M.P., Stokes, H.W. and Holmes, A.J. Integrons in Xanthomonas: a source of species genome diversity. Proc Natl Acad Sci USA, 2005. 102(12): p. 4419−24.
- Gruber, T.M. and Bryant, D.A. Molecular systematic studies of eubacteria, using sigma70-type sigma factors of group 1 and group 2. J. Bacteriol., 1997. 179(5): p. 1734−47.
- Hartley, B.S. Amino-Acid Sequence of Bovine Chymotrypsinogen-A. Nature, 1964. 201(p. 1284−7.
- Hashizume, H., Hattori, S., Igarashi, M. and Akamatsu, Y. Tripropeptin E, a new tripropeptin group antibiotic produced by Lysobacter sp. BMK333−48F3. J Antibiot (Tokyo), 2004a. 57(6): p. 394−9.
- Hashizume, H., Hirosawa, S., Sawa, R., Muraoka, Y., Ikeda, D., Naganawa, H. and Igarashi, M. Tripropeptins, novel antimicrobial agents produced by Lysobacter sp. J Antibiot (Tokyo), 2004b. 57(1): p. 52−8.
- Hashizume, H., Igarashi, M., Hattori, S., Hori, M., Hamada, M. and Takeuchi, T. Tripropeptins, novel antimicrobial agents produced by Lysobacter sp. I. Taxonomy, isolation and biological activities. J Antibiot (Tokyo), 2001. 54(12): p. 1054−9.
- Henderson, G., Krygsman, P., Liu, C.J., Davey, C.C. and Malek, L.T. Characterization and structure of genes for proteases A and B from Streptomyces griseus. J Bacteriol, 1987. 169(8): p. 3778−84.
- Henderson, I.R. and Nataro, J.P. Virulence functions of autotransporter proteins. Infect Immun, 2001. 69(3): p. 1231−43.
- Hoang, T.T., Karkhoff-Schweizer, R.R., Kutchma, A.J. and Schweizer, H.P. A broad-host-range Flp-FRT recombination system for site-specific excision of chromosomally-located
- DNA sequences: application for isolation of unmarked Pseudomonas aeruginosa mutants. Gene, 1998. 212(1): p. 77−86.
- Hoang, T.T., Kutchma, A.J., Becher, A. and Schweizer, H.P. Integration-proficient plasmids for Pseudomonas aeruginosa: site-specific integration and use for engineering of reporter and expression strains. Plasmid, 2000. 43(1): p. 59−72.
- Holland, I.B. and Blight, M.A. ABC-ATPases, adaptable energy generators fuelling transmembrane movement of a variety of molecules in organisms from bacteria to humans. J Mol Biol, 1999. 293(2): p. 381−99.
- Holland, I.B., Schmitt, L. and Young, J. Type 1 protein secretion in bacteria, the ABCtransporter dependent pathway (review). Mol Membr Biol, 2005. 22(1−2): p. 29−39.
- Hollenstein, K., Dawson, R.J. and Locher, K.P. Structure and mechanism of ABC transporter proteins. Curr Opin Struct Biol, 2007. 17(4): p. 412−8.
- Holtje, J.V., Mirelman, D., Sharon, N. and Schwarz, U. Novel type of murein transglycosylase in Escherichia coli. J Bacteriol, 1975. 124(3): p. 1067−76.
- Howell, C.R. and Stipanovic, R.D. Control of Rhizoctonia solani on Cotton Seedlings with Pseudomonas fluorescens and With an Antibiotic Produced by the Bacterium. Phytopathology 1979. 69(p. 480−482.
- Hu, Z., Haghjoo, K. and Jordan, F. Further evidence for the structure of the subtilisin propeptide and for its interactions with mature subtilisin. J Biol Chem, 1996. 271(7): p. 3375−84.
- Hynes, M.F. and McGregor, N.F. Two plasmids other than the nodulation plasmid are necessary for formation of nitrogen-fixing nodules by Rhizobium leguminosarum. Mol Microbiol, 1990. 4(4): p. 567−74.
- Ikemura, H., Takagi, H. and Inouye, M. Requirement of pro-sequence for the production of active subtilisin E in Escherichia coli. J Biol Chem, 1987. 262(16): p. 7859−64.
- Iyer, L.M., Koonin, E.V. and Aravind, L. Evolution of bacterial RNA polymerase: implications for large-scale bacterial phylogeny, domain accretion, and horizontal gene transfer. Gene, 2004. 335(p. 73−88.
- Jones, P.M. and George, A.M. Subunit interactions in ABC transporters: towards a functional architecture. FEMS Microbiol Lett, 1999.179(2): p. 187−202.
- Jurasek, L. and Whitaker, D.R. Amino acid and metal composition of the alpha- and beta-lytic proteases of Sorangium sp. Can J Biochem, 1967. 45(6): p. 917−27.
- Jurkevitch, E. Isolation and classification of bdellovibrio and like organisms. Curr Protoc Microbiol, 2006. Chapter 7(p. Unit 7B 1.
- Kadurugamuwa, J.L. and Beveridge, T.J. Bacteriolytic effect of membrane vesicles from Pseudomonas aeruginosa on other bacteria including pathogens: conceptually new antibiotics. J Bacteriol, 1996. 178(10): p. 2767−74.
- Kashima, A., Inoue, Y., Sugio, S., Maeda, I., Nose, T. and Shimohigashi, Y. X-ray crystal structure of a dipeptide-chymotrypsin complex in an inhibitory interaction. Eur J Biochem, 1998. 255(1): p. 12−23.
- Khan, A.R. and James, M.N. Molecular mechanisms for the conversion of zymogens to active proteolytic enzymes. Protein Sci, 1998. 7(4): p. 815−36.
- Khan, S.R., Mavrodi, D.V., Jog, G.J., Suga, H., Thomashow, L.S. and Farrand, S.K. Activation of the phz operon of Pseudomonas fluorescens 2−79 requires the LuxR homolog
- PhzR, N-(3-OH-Hexanoyl)-L-homoserine lactone produced by the Luxl homolog Phzl, and a cis-acting phz box. J Bacteriol, 2005. 187(18): p. 6517−27.
- Kilic-Ekici, O. and Yuen, G.Y. Induced Resistance as a Mechanism of Biological Control by Lysobacter enzymogenes Strain C3. Phytopathology, 2003. 93(9): p. 1103−10.
- Kim, E.S., Hong, H.J., Choi, C.Y. and Cohen, S.N. Modulation of actinorhodin biosynthesis in Streptomyces lividans by glucose repression of afsR2 gene transcription. J Bacteriol, 2001. 183(7): p. 2198−203.
- Kok, J., Leenhouts, K.J., Haandrikman, A.J., Ledeboer, A.M. and Venema, G. Nucleotide sequence of the cell wall proteinase gene of Streptococcus cremoris Wg2. Appl Environ Microbiol, 1988. 54(1): p. 231−8.
- Kok, J., van Dijl, J.M., van der Vossen, J.M. and Venema, G. Cloning and expression of a Streptococcus cremoris proteinase in Bacillus subtilis and Streptococcus lactis. Appl Environ Microbiol, 1985. 50(1): p. 94−101.
- Kok, J. and Venema, G. Genetics of proteinases of lactic acid bacteria. Biochimie, 1988. 70(4): p. 475−88.
- Konig, C., Eulberg, D., Groning, J., Lakner, S., Seibert, V., Kaschabek, S.R. and Schlomann, M. A linear megaplasmid, pi CP, carrying the genes for chlorocatechol catabolism of Rhodococcus opacus 1CP. Microbiology, 2004. 150(Pt 9): p. 3075−87.
- Kostakioti, M., Newman, C.L., Thanassi, D.G. and Stathopoulos, C. Mechanisms of protein export across the bacterial outer membrane. J Bacteriol, 2005.187(13): p. 4306−14.
- Koster, M., Bitter, W. and Tommassen, J. Protein secretion mechanisms in Gramnegative bacteria. Int J Med Microbiol, 2000. 290(4−5): p. 325−31.
- Krzeslak, J., Braun, P., Voulhoux, R., Cool, R.H. and Quax, W.J. Heterologous production of Escherichia coli penicillin G acylase in Pseudomonas aeruginosa. J Biotechnol, 2009. 142(3−4): p. 250−8.
- Kuehn, M.J. and Kesty, N.C. Bacterial outer membrane vesicles and the host-pathogen interaction. Genes Dev, 2005. 19(22): p. 2645−55.
- Kulaev, I.S., Stepnaya, O.A., Tsfasman, I.M., Tchermenskaja, T.S., Ledova, L.A., Zubrizkaja, L.G. and Akimenko, V.K.: Bacteriolytic complex, method for producing said complex and strain for carrying out said method. (2006).
- Laemmli, U.K. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature, 1970. 227(5259): p. 680−5.
- Lee, J.W., Im, W.T., Kim, M.K. and Yang, D.C. Lysobacter koreensis sp. nov., isolated from a ginseng field. Int J Syst Evol Microbiol, 2006a. 56(Pt 1): p. 231−5.
- Li, S., Norioka, S. and Sakiyama, F. Purification, staphylolytic activity, and cleavage sites of alpha-lytic protease from Achromobacter lyticus. J Biochem, 1997. 122(4): p. 772−8.
- Likhosherstov, L.M., Senchenkova, S.N., Knirel, Y.A., Shashkov, A.S., Shibaev, V.N., Stepnaya, O.A. and Kulaev, I.S. Structure of an acidic polysaccharide present in the bacteriolytic complex lysoamidase. FEBS Lett, 1995. 368(1): p. 113−6.
- Liu, S.L., Hessel, A. and Sanderson, K.E. Genomic mapping with I-Ceu I, an intron-encoded endonuclease specific for genes for ribosomal RNA, in Salmonella spp., Escherichia coli, and other bacteria. Proc Natl Acad Sci USA, 1993. 90(14): p. 6874−8.
- Mace, J.E. and Agard, D.A. Kinetic and structural characterization of mutations of glycine 216 in alpha-lytic protease: a new target for engineering substrate specificity. J. Mol. Biol., 1995. 254(4): p. 720−36.
- Mahillon, J. and Chandler, M. Insertion sequences. Microbiol Mol Biol Rev, 1998. 62(3): p. 725−74.
- Markham, N.R. and Zuker, M. UNAFold: software for nucleic acid folding and hybridization. Methods Mol. Biol., 2008. 453(p. 3−31.
- McBroom, A.J. and Kuehn, M.J. Release of outer membrane vesicles by Gram-negative bacteria is a novel envelope stress response. Mol Microbiol, 2007. 63(2): p. 545−58.
- Mclver, K.S., Kessler, E., Olson, J.C. and Ohman, D.E. The elastase propeptide functions as an intramolecular chaperone required for elastase activity and secretion in Pseudomonas aeruginosa. Mol Microbiol, 1995. 18(5): p. 877−89.
- Mergulhao, F.J., Summers, D.K. and Monteiro, G.A. Recombinant protein secretion in Escherichia coli. Biotechnol Adv, 2005. 23(3): p. 177−202.
- Michel-Briand, Y. and Baysse, C. The pyocins of Pseudomonas aeruginosa. Biochimie, 2002. 84(5−6): p. 499−510.
- Muranova, T.A., Krasovskaya, L.A., Tsfasman, I.M., Stepnaya, O.A. and Kulaev, I.S. Structural investigations and identification of the extracellular bacteriolytic endopeptidase LI from Lysobacter sp. XL1. Biochemistry (Mosc), 2004. 69(5): p. 501−5.
- Neumann, H., Peak-Chew, S.Y. and Chin, J.W. Genetically encoding N (epsilon)-acetyllysine in recombinant proteins. Nat Chem Biol, 2008. 4(4): p. 232−4.
- Newnham, E., Chang, N. and Taylor, D.E. Expanded genomic map of Campylobacter jejuni UA580 and localization of 23S ribosomal rRNA genes by I-Ceul restriction endonuclease digestion. FEMS Microbiol Lett, 1996.142(2−3): p. 223−9.
- Novick, R.P. and Brodsky, R. Studies on plasmid replication. I. Plasmid incompatibility and establishment in Staphylococcus aureus. J. Mol. Biol., 1972. 68(2): p. 285−302.
- Nudler, E. and Gottesman, M.E. Transcription termination and anti-termination in E. coli. Genes Cells, 2002. 7(8): p. 755−68.
- Oldham, M.L., Davidson, A.L. and Chen, J. Structural insights into ABC transporter mechanism. Curr Opin Struct Biol, 2008. 18(6): p. 726−33.
- Olson, M.O., Nagabhushan, N., Dzwiniel, M., Smillie, L.B. and Whitaker, D.R. Priaary structure of alpha-lytic protease: a bacterial homologue of the pancreatic serine proteases. Nature, 1970. 228(5270): p. 438−42.
- Page, M.J. and Di Cera, E. Serine peptidases: classification, structure and function. Cell Mol Life Sci, 2008. 65(7−8): p. 1220−36.
- Paget, M.S. and Helmann, J.D. The sigma70 family of sigma factors. Genome Biol., 2003. 4(1): p. 203.
- Pohlner, J., Halter, R., Beyreuther, K. and Meyer, T.F. Gene structure and extracellular secretion of Neisseria gonorrhoeae IgA protease. Nature, 1987. 325(6103): p. 458−62.
- Polgar, L. The catalytic triad of serine peptidases. Cell Mol Life Sci, 2005. 62(19−20): p. 2161−72.
- Pugsley, A.P. The complete general secretory pathway in gram-negative bacteria. Microbiol Rev, 1993. 57(1): p. 50−108.
- Raaijmakers, J.M. and Weller, D.M. Natural plant protection by 2,4-diacetylphloroglucinol-producing Pseudomonas spp. in take-all decline soils. Mol. Plant-Microbe Interact., 1998. ll (p. 144−152.
- Raaijmakers, J.M., Weller, D.M. and Thomashow, L.S. Frequency of Antibiotic-Producing Pseudomonas spp. in Natural Environments. Appl Environ Microbiol, 1997. 63(3): p. 881−7.
- Rao, M.B., Tanksale, A.M., Ghatge, M.S. and Deshpande, V.V. Molecular and biotechnological aspects of microbial proteases. Microbiol Mol Biol Rev, 1998. 62(3): p. 597 635.
- Rawlings, N.D. and Barrett, A.J. Evolutionary families of peptidases. Biochem J, 1993. 290 (Pt l)(p. 205−18.
- Rawlings, N.D. and Barrett, A.J. Families of serine peptidases. Methods Enzymol., 1994. 244(p. 19−61.
- Rawlings, N.D., Barrett, A.J. and Bateman, A. MEROPS: the peptidase database. Nucleic Acids Res, 2010. 38(Database issue): p. D227−33.
- Rawlings, N.D., Barrett, A.J. and Bateman, A. MEROPS: the database of proteolytic enzymes, their substrates and inhibitors. Nucleic Acids Res, 2012. 40(Database issue): p. D343−50.
- Recsei, P.A., Grass, A.D. and Novick, R.P. Cloning, sequence, and expression of the lysostaphin gene from Staphylococcus simulans. Proc Natl Acad Sci USA, 1987. 84(5): p. 1127−31.
- Retallack, D.M., Jin, H. and Chew, L. Reliable protein production in a Pseudomonas fluorescens expression system. Protein Expr Purif, 2012. 81(2): p. 157−65.
- Retallack, D.M., Schneider, J.C., Mitchell, J., Chew, L. and Liu, H. Transport of heterologous proteins to the periplasmic space of Pseudomonas fluorescens using a variety of native signal sequences. Biotechnol Lett, 2007. 29(10): p. 1483−91.
- Riley, M.A. and Wertz, J.E. Bacteriocin diversity: ecological and evolutionary perspectives. Biochimie, 2002a. 84(5−6): p. 357−64.
- Riley, M.A. and Wertz, J.E. Bacteriocins: evolution, ecology, and application. Annu Rev Microbiol, 2002b. 56(p. 117−37.
- Roberts, J.W., Shankar, S. and Filter, J.J. RNA polymerase elongation factors. Annu. Rev. Microbiol., 2008. 62(p. 211−33.
- Romanenko, L.A., Uchino, M., Tanaka, N., Frolova, G.M. and Mikhailov, V.V. Lysobacter spongiicola sp. nov., isolated from a deep-sea sponge. Int J Syst Evol Microbiol, 2008. 58(Pt 2): p. 370−4.
- Ryazanova, L.P., Stepnaya, O.A., Suzina, N.E. and Kulaev, I.S. Antifungal action of the lytic enzyme complex from Lysobacter sp. XL 1. Proc. Biochem., 2005. 40(p. 557−564.
- Saitou, N. and Nei, M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol, 1987. 4(4): p. 406−25.
- Sambrook, J., Fritch, E.F. and Maniatis, T.: Molecular cloning: a laboratory manual. Cold Spring Harbor Lab. Press., N. Y (1989).
- Sandkvist, M. Biology of type II secretion. Mol Microbiol, 2001. 40(2): p. 271−83.
- Schleifer, K.H. and Kandler, O. Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev, 1972. 36(4): p. 407−77.
- Schwartz, D.C. and Cantor, C.R. Separation of yeast chromosome-sized DNAs by pulsed field gradient gel electrophoresis. Cell, 1984. 37(1): p. 67−75.
- Schweizer, H.P. Allelic exchange in Pseudomonas aeruginosa using novel ColEl-type vectors and a family of cassettes containing a portable oriT and the counter-selectable Bacillus subtilis sacB marker. Mol Microbiol, 1992. 6(9): p. 1195−204.
- Serkina, A.V., Shevelev, A.B. and Chestukhina, G.G. Structure and functions of bacterial proteinase precursors. Bioorg Khim, 2001. 27(5): p. 323−46.
- Severinov, K., Semenova, E., Kazakov, A., Kazakov, T. and Gelfand, M.S. Low-molecular-weight post-translationally modified microcins. Mol Microbiol, 2007. 65(6): p. 138 094.
- Shinde, U.P., Liu, J.J. and Inouye, M. Protein memory through altered folding mediated by intramolecular chaperones. Nature, 1997. 389(6650): p. 520−2.
- Sidhu, S.S., Kalmar, G.B., Willis, L.G. and Borgford, T.J. Streptomyces griseus protease C. A novel enzyme of the chymotrypsin superfamily. J Biol Chem, 1994. 269(31): p. 20 167−71.
- Sidhu, S.S., Kalmar, G.B., Willis, L.G. and Borgford, T.J. Protease evolution in Streptomyces griseus. Discovery of a novel dimeric enzymes. J Biol Chem, 1995. 270(13): p. 7594−600.
- Silen, J.L. and Agard, D.A. The alpha-lytic protease pro-region does not require a physical linkage to activate the protease domain in vivo. Nature, 1989. 341(6241): p. 462−4.
- Silen, J.L., Frank, D., Fujishige, A., Bone, R. and Agard, D.A. Analysis of prepro-alpha-lytic protease expression in Escherichia coli reveals that the pro region is required for activity. J Bacteriol, 1989. 171(3): p. 1320−5.
- Silen, J.L., McGrath, C.N., Smith, K.R. and Agard, D.A. Molecular analysis of the gene encoding alpha-lytic protease: evidence for a preproenzyme. Gene, 1988. 69(2): p. 237−44.
- Simon, R., Priefer, U. and Puhler, A. A broad host range mobilization system for in vivo genetic engineering: transposon mutagenesis in gram-negative bacteria. Biotechnology, 1983. l (p. 784−791.
- Simonen, M. and Palva, I. Protein secretion in Bacillus species. Microbiol Rev, 1993. 57(1): p. 109−37.
- Sinoquet, C., Demey, S. and Braun, F. Large-scale computational and statistical analyses of high transcription potentialities in 32 prokaryotic genomes. Nucleic Acids Res., 2008. 36(10): p. 3332−40.
- Smillie, L.B. and Whitaker, D.R. Amino acid sequence around the histidine residue of the alpha-lytic protease of Sorangium sp., a bacterial homolog of the pancreatic serine proteases. J Am Chem Soc, 1967. 89(13): p. 3350−2.
- Sohl, J.L., Jaswal, S.S. and Agard, D.A. Unfolded conformations of alpha-lytic protease are more stable than its native state. Nature, 1998. 395(6704): p. 817−9.
- Sohl, J.L., Shiau, A.K., Rader, S.D., Wilk, B.J. and Agard, D.A. Inhibition of alpha-lytic protease by pro region C-terminal steric occlusion of the active site. Biochemistry, 1997. 36(13): p. 3894−902.
- Stahl, M.L. and Ferrari, E. Replacement of the Bacillus subtilis subtilisin structural gene with an In vitro-derived deletion mutation. J Bacteriol, 1984. 158(2): p. 411−8.
- Stepnaya, O.A., Begunova, E.A., Tsfasman, I.M. and Kulaev, I.S. Bacteriolytic enzyme lysoamidase preparation: purification and some properties of bacteriolytic peptidase LI. Biochemistry (Mosc), 1996a. 61(p. 477−482.
- Stepnaya, O.A., Kudryavtseva, A.I., Severin, A.I., Krupyanko, V.l., Kozlovsky, A.G. and Kulaev, I.S. Some properties of bacteriolytic protease L2. Prikl. Biokhim. Mikrobiol., 1992. 28(5): p. 666−673
- Stepnaya, O.A., Severin, A.I., Krupyanko, V.l. and Kulaev, I.S. Purification and some properties of neutral phosphatase of the enzyme preparation of lysoamidase isolated from Pseudomonadaceae bacteria. Biokhimiya (Mose) 1986a. 51(4): p. 684−690
- Stepnaya, O.A., Severin, A.I. and Kulaev, I.S. Some physico-chemical properties of lytic proteinase L2 of the enzyme preparation lysoamidase isolated from bacteria of Pseudomonadaceae family. Biokhimiya (Mose), 1986b. 51(p. 909−915
- Stepnaya, O.A., Tsfasman, I.M., Chaika, I.A., Muranova, T.A. and Kulaev, I.S. Extracellular yeast-lytic enzyme of the bacterium Lysobacter sp. XL 1. Biochemistry (Mose), 2008. 73(3): p. 310−4.
- Stepnaya, O.A., Tsfasman, I.M., Logvina, I.A., Ryazanova, L.P., Muranova, T.A. and Kulaev, I.S. Isolation and characterization of a new extracellular bacteriolytic endopeptidase of Lysobacter sp. XL1. Biochemistry (Mose), 2005. 70(9): p. 1031−7.
- Stroud, R.M., Kossiakoff, A.A. and Chambers, J.L. Mechanisms of zymogen activation. Annu Rev Biophys Bioeng, 1977. 6(p. 177−93.
- Studier, F.W. and Moffatt, B.A. Use of bacteriophage T7 RNA polymerase to direct selective high-level expression of cloned genes. J. Mol. Biol., 1986. 189(1): p. 113−30.
- Swartz, J.R. Advances in Escherichia coli production of therapeutic proteins. Curr Opin Biotechnol, 2001. 12(2): p. 195−201.
- Thomashow, L.S. and Weller, D.M. Role of a phenazine antibiotic from Pseudomonas fluorescens in biological control of Gaeumannomyces graminis var. tritici. J Bacteriol, 1988. 170(8): p. 3499−508.
- Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F. and Higgins, D.G. The CLUSTALX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res, 1997. 25(24): p. 4876−82.
- Toda, T. and Itaya, M. I-Ceul recognition sites in the rrn operons of the Bacillus subtilis 168 chromosome: inherent landmarks for genome analysis. Microbiology, 1995. 141 (Pt 8)(p. 1937−45.
- Tsai, C.S., Whitaker, D.R., Jurasek, L. and Gillespie, D.C. Lytic enzymes of Sorangium sp. Action of the alpha- and beta-lytic proteases on two bacterial mucopeptides. Can J Biochem, 1965. 43(12): p. 1971−83.
- Van de Peer, Y. and De Wachter, R. TREECON for Windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment. Comput Appl Biosci, 1994. 10(5): p. 569−70.
- Vasilyeva, N.V., Tsfasman, I.M., Suzina, N.E., Stepnaya, O.A. and Kulaev, I.S. Secretion of bacteriolytic endopeptidase L5 of Lysobacter sp. XL1 into the medium by means of outer membrane vesicles. FEBS J, 2008. 275(15): p. 3827−35.
- Viarre, V., Cascales, E., Ball, G., Michel, G.P., Filloux, A. and Voulhoux, R. HxcQ liposecretin is self-piloted to the outer membrane by its N-terminal lipid anchor. J Biol Chem, 2009. 284(49): p. 33 815−23.
- Vieira, J. and Messing, J. The pUC plasmids, an M13mp7-derived system for insertion mutagenesis and sequencing with synthetic universal primers. Gene, 1982. 19(3): p. 259−68.
- Vincent, M.N., Harrison, L.A., Brackin, J.M., Kovacevich, P.A., Mukerji, P., Weiler, D.M. and Pierson, E.A. Genetic analysis of the antifungal activity of a soilborne Pseudomonas aureofaciens strain. Appl Environ Microbiol, 1991. 57(10): p. 2928−34.
- Vivian, A., Murillo, J. and Jackson, R.W. The roles of plasmids in phytopathogenic bacteria: mobile arsenals? Microbiology, 2001. 147(Pt 4): p. 763−80.
- Volonte, F., Piubelli, L. and Pollegioni, L. Optimizing HIV-1 protease production in Escherichia coli as fusion protein. Microb Cell Fact, 2011. 10(p. 53.
- Walsh, K.A., Kauffman, D.L., Kumar, K.S. and Neurath, H. On the Structure and Function of Bovine Trypsinogen and Trypsin. Proc Natl Acad Sei USA, 1964. 51(p. 301−8.
- Walsh, K.A. and Neurath, H. Trypsinogen and Chymotrypsinogen as Homologous Proteins. Proc Natl Acad Sei USA, 1964. 52(p. 884−9.
- Weller, D.M., Howie, W.J. and Cook, R.J. Relationship between in vitro inhibition of Gauemannomyces graminis var. tritici and suppression of take-all of wheat by fluorescent pseudomonads. Phytopathology 1988. 78(p. 1094−1100.
- Weon, H.Y., Kim, B.Y., Kim, M.K., Yoo, S.H., Kwon, S.W., Go, S.J. and Stackebrandt, E. Lysobacter niabensis sp. nov. and Lysobacter niastensis sp. nov., isolated from greenhouse soils in Korea. Int J Syst Evol Microbiol, 2007. 57(Pt 3): p. 548−51.
- Whitaker, D.R., Cook, F.D. and Gillespie, D.C. Lytic enzymes of Sorangium sp. Some aspects of enzyme production in submerged culture. Can J Biochem, 1965. 43(12): p. 1927−33.
- Wiederanders, B. The function of propeptide domains of cysteine proteinases. Adv Exp Med Biol, 2000. 477(p. 261−70.
- Wong, C.F., Salleh, A.B., Basri, M. and Abd Rahman, R.N. Organic-solvent stability of elastase strain K overexpressed in an Escherichia-Pseudomonas expression system. Biotechnol Appl Biochem, 57(1): p. 1−7.
- Wong, M.S., Wu, S., Causey, T.B., Bennett, G.N. and San, K.Y. Reduction of acetate accumulation in Escherichia coli cultures for increased recombinant protein production. Metab Eng, 2008.10(2): p. 97−108.
- Wong, S.L. and Doi, R.H. Determination of the signal peptidase cleavage site in the preprosubtilisin of Bacillus subtilis. J Biol Chem, 1986. 261(22): p. 10 176−81.
- Wright, C.S., Alden, R.A. and Kraut, J. Structure of subtilisin BPN' at 2.5 angstrom resolution. Nature, 1969. 221(5177): p. 235−42.
- Yanisch-Perron, C., Viera, J. and Messing, J. Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mpl8 and pUC19 vectors. Gene, 1985. 33: p. 103 119.
- Zaitsev, E.N., Zaitseva, E.M., Bakhlanova, I.V., Gorelov, V.N. and Kuz’min, N.P. Cloning and characteristics of recA gene in Pseudomonas aeruginosa. Genetika, 1986. 22(11): p. 2721−7.
- Zhang, X.X., Kosier, B. and Priefer, U.B. Symbiotic plasmid rearrangement in Rhizobium leguminosarum bv. viciae VF39SM. J Bacteriol, 2001. 183(6): p. 2141−4.
- Zhu, X.L., Ohta, Y., Jordan, F. and Inouye, M. Pro-sequence of subtilisin can guide the refolding of denatured subtilisin in an intermolecular process. Nature, 1989. 339(6224): p. 483−4.
- Zuckerkandl, E. and Pauling, L. Molecules as documents of evolutionary history. J Theor Biol, 1965. 8(2): p. 357−66.
- Антонов, B.K., Химия протеолиза. Издательство: Наука, Москва (1991), с. 504.
- Дейвиса, П.р., Анализ генома. Методы. Издательство: Мир, Москва (1990), с. 246.
- Кулаев Бактериолитические ферменты микробного происхождения в биологии и медицине. Соросовский образовательный журнал, 1997. 3.
- Насонова, Е.С. Пульс-электрофорез: теория метода, инструментальный арсенал и области применения. Цитология, 2008. 50(11): р. 927−935.