Выделение и характеристика кДНК гена поли(АДФ-рибоза) полимеразы 2 Arabidopsis thaliana
DOI:
https://doi.org/10.26577/eb-2018-1-1319Аннотация
Поли(АДФ-рибоза) полимераза (PARP) катализирует синтез полимеров АДФ-рибозы, ковалентно-прикрепленные к акцепторным белкам, при этом донором остатков АДФ-рибозы выступает НАД+. Геном Arabidopsis thaliana, широко используемого модельного растительного организма, кодирует по меньшей мере три предполагаемых PARP фермента: АtPARP1 (At4g02390), AtPARP2 (At2g31320) и AtPARP3 (At5g22470). PARP растений являются структурно гомологичными к PARP белкам млекопитающих. Высокая степень консервативности на уровне аминокислотной последовательности между ферментами арабидопсиса и млекопитающих позволяет предположить, что в растениях PARP выполняет аналогичные функции как в животных системах. Однако в отличие от млекопитающих, значительно мало известно о поли-АДФ-рибозилирований в растениях.
Нами был выделен кДНК ген AtPARP2 с применением реакции обратной транскрипции (РОТ) и полимеразной цепной реакции (ПЦР). Осуществлена функциональная экспрессия AtPARP2 гистидиновым концом в E. cоli и очищена никель аффинной хроматографией до гомогенного состояния. С помощью MALDI-TОF масс-спектрометрии установлена принадлежность рекомбинантного белка к семейству поли(АДФ-рибоза)-полимераз. Выявлено, что продуктом экспрессии гена является глобулярный белок массой 72,2 кДа, состоящий из 637 аминокислот (pI 5,92). На основе очищенного рекомбинантного AtPARP2 были получены поликлональные антитела к AtPARP2. AtPARP2 в присутствии олигонуклеотидного дуплекса с разрывом и НАД+ показал авто-поли(АДФ-рибозил)ирующию активность.
Ключевые слова: поли(АДФ-рибоза) полимераза, PARP2, поли-АДФ-рибозилирование, НАД+ радикалы кислорода, Arabidopsis thaliana.
Библиографические ссылки
1 Cadet J., Douki T., Gasparutto D., Ravanat J.L. Oxidative damage to DNA: formation, measurement and biochemical features // Mutat. Res. – 2003. – Vol. 531. – P. 5-23.
2 Foyer C.H., Noctor G. Redox sensing and signalling associated with reactive oxygen in chloroplasts, peroxisomes and mitochondria // Physiol. Plant. - 2003. - Vol. 119. - P.355–364.
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4 Papamichos-Chronakis M., Peterson C.L. Chromatin and the genome integrity network // Nat Rev Genet. - 2013. - Vol. 14. - № 1. - P.62–75.
5 Ermolaeva M.A., Schumacher B. Systemic DNA damage responses: organismal adaptations to genome instability // Trends Genet. - 2014. - Vol. 30. - № 3. - P.95–102.
6 Schreiber V., Dantzer F., Ame J.C., de Murcia G. Poly (ADP-ribose): novel functions for an old molecule // Nat. Rev. Mol. Cell. Biol. - 2006. - Vol 7. - P.517–528.
7 Kim M.Y., Zhang T., Kraus W.L. Poly(ADP-ribosyl)ation by PARP-1: ’PAR-laying’ NAD+ into a nuclear signal // Genes Dev. - 2005. - Vol. 19. - P.1951–1967.
8 Ame´ J-C., Spenlehauer C., de Murcia G. The PARP superfamily // BioEssays. - 2004. - Vol. 26. - P.882–893
9 Woodhouse B.C., Dianov G.L. Poly ADP-ribose polymerase-1: an international molecule of mystery // DNA Repair. - 2008. - Vol. 7. - P.1077–1086.
10 Kraus W.L., Hottiger M.O. PARP-1 and gene regulation: progress and puzzles // Mol. Aspects Med. - 2013. - Vol. 34. - P.1109–1123.
11 Caldecott K.W. Mammalian single-strand break repair: mechanisms and links with chromatin // DNA Repair. - 2007. - Vol. 6. - P.443–453.
12 Shieh W.M., Ame J.C., Wilson M.V., Wang Z.Q., Koh D.W., JacobsonM.K., Jacobson E.L. Poly(ADP-ribose) polymerase null mouse cells synthesize ADP-ribose polymers // J.Biol.Chem. - 1998. - Vol. 273. - P.30069–30072.
13 de Murcia G., Menissier de Murcia J. Poly(ADP-ribose)polymerase: a molecular nick-sensor // Trends Biochem. Sci. - 1994. - Vol. 19. - P.172–176.
14 Tanaka Y., Yoshihara K., Itaya A., Kamiya T., Koide S.S. Mechanism of the inhibition of Ca2+, Mg2+-dependentendonuclease of bull seminal plasma induced by ADP-ribosylation // J.Biol. Chem. - 1984. - Vol. 259. - P.6579–6585.
15 Satoh M.S., Poirier G.G. and Lindahl T. Dual function forpoly(ADP-ribose) synthesis in response to DNA strand breakage // Biochemistry. - 1994. - Vol. 33. - P.7099–7106.
16 Caldecott K.W. Protein ADP-ribosylation and the cellularresponse to DNA strand breaks // DNA Repair. - 2014. - Vol. 19. - P.108–113.
17 Briggs A.G., Bent A.F. Poly(ADP-ribosyl)ation in plants // Trends Plant Sci. - 2011. - Vol. 16. - № 7. - P.372–80.
18 Lamb R.S., Citarelli M., Teotia S. Functions of the poly(ADP-ribose) polymerase superfamily in plants // Cell Mol Life Sci. - 2012. - Vol. 69. - № 2. - P.175–89.
19 Briggs A.G., Bent A.F. Poly(ADP-ribosyl)ation in plants // Trends in Plant Science. - 2011. - Vol. 16. - № 7. - P.360-1385.
20 Laemmli U.K. Cleavage of structural proteins during the assembly of the head of bacteriophage T4 // Nature. – 1970. – Vol. 227. - № 5259. – P. 680-685.
21 Bradford M.M. A Rapid and Sensitive Method for the Quantitation of Microgram Quantities of Protein Utilizing the Principle of Protein-Dye Binding // Anal. Biochem. - 1976. - Vol. 72. – P. 248-302.
22 Vainonen J.P., Shapiguzov A., Vaattovaara A., Kangasjärvi J. Plant PARPs, PARGs and PARP-like Proteins // Current Protein and Peptide Science. – 2016. – Vol. 17. - P.713-723
23 Hinz J.M., Rodriguez Y., Smerdon M.J. Rotational dynamics of DNA on the nucleosome surface markedly impact accessibility to a DNA repair enzyme // Proc. Natl. Acad. Sci. U.S.A. - 2010. - Vol. 107. - P.4646–4651.
24 Odell I.D., Barbour J.E., Murphy D.L., Della-Maria J.A., Sweasy J.B., Tomkinson A.E., Wallace S.S., Pederson D.S. Nucleosome disruption by DNA ligase III-XRCC1 promotes efficient base excision repair // Mol. Cell. Biol. - 2011. - Vol. 31. - P.4623–4632.
25 Zhang F., Wang Y., Wang L., Luo X., Huang K., Wang C., Du M., Liu F., Luo T., Huang D., Huang K. Poly(ADP-ribose) Polymerase 1 Is a Key Regulator of Estrogen Receptor α-dependent Gene Transcription // J. Biol. Chem. – 2013. - Vol. 288. - № 16. – P. 11348–11357.
References
1. Ame´ J-C., Spenlehauer C., de Murcia G. (2004) The PARP superfamily. BioEssays, vol. 26, pp. 882–893.
2. Briggs A.G, Bent A.F. (2011) Poly(ADP-ribosyl)ation in plants. Trends Plant Sci., vol. 16 (7), pp.372–80.
3. Briggs A.G., Bent A.F. (2011) Poly(ADP-ribosyl)ation in plants. Trends in Plant Science., vol. 16 (7), pp.360-1385.
4. Bradford M. M. (1976) A Rapid and Sensitive Method for the Quantitation of Microgram Quantities of Protein Utilizing the Principle of Protein-Dye Binding. Anal. Biochem., vol. 72, pp. 248-54.
5. Cadet J., Douki T., Gasparutto D., Ravanat J.L. (2003) Oxidative damage to DNA: formation, measurement and biochemical features. Mutat. Res., vol. 531, pp. 5-23.
6. Caldecott K.W. (2007) Mammalian single-strand break repair: mechanisms and links with chromatin. DNA Repair., vol. 6, pp.443–453.
7. Caldecott K.W. (2014) Protein ADP-ribosylation and the cellularresponse to DNA strand breaks. DNA Repair, vol. 19, pp.108–113.
8. de Murcia G., Menissier de Murcia J. (1994) Poly(ADP-ribose)polymerase: a molecular nick-sensor. Trends Biochem. Sci., vol. 19, pp.172–176.
9. Ermolaeva M.A., Schumacher B. (2014) Systemic DNA damage responses: organismal adaptations to genome instability. Trends Genet., vol. 30 (3), pp.95–102.
10. Foyer C.H., Noctor G. (2003) Redox sensing and signalling associated with reactive oxygen in chloroplasts, peroxisomes and mitochondria. Physiol. Plant, vol. 119, pp. 355–364.
11. Hinz J.M., Rodriguez Y., Smerdon M.J. (2010) Rotational dynamics of DNA on the nucleosome surface markedly impact accessibility to a DNA repair enzyme. Proc. Natl. Acad. Sci. U.S.A., vol. 107, pp.4646–4651.
12. Kim M.Y., Zhang T., Kraus W.L. (2005) Poly(ADP-ribosyl)ation by PARP-1: ’PAR-laying’ NAD+ into a nuclear signal. Genes Dev., vol. 19, pp.1951–1967.
13. Kraus W.L., Hottiger M.O. (2013) PARP-1 and gene regulation: progress and puzzles. Mol. Aspects Med., vol. 34, pp.1109–1123.
14. Laemmli U.K. (1970) Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature, vol. 227 (5259), pp. 680-685.
15. Lamb R.S., Citarelli M., Teotia S. (2012) Functions of the poly(ADP-ribose) polymerase superfamily in plants. Cell Mol Life Sci., vol. 69 (2). - P.175–89.
16. Odell I.D., Barbour J.E., Murphy D.L., Della-Maria J.A., Sweasy J.B., Tomkinson A.E., Wallace S.S., Pederson D.S. (2011) Nucleosome disruption by DNA ligase III-XRCC1 promotes efficient base excision repair. Mol. Cell. Biol., vol. 31, pp.4623–4632.
17. Papamichos-Chronakis M., Peterson C.L. (2013) Chromatin and the genome integrity network. Nat Rev Genet., vol. 14 (1), pp.62–75.
18. Schreiber V., Dantzer F., Ame J.C., de Murcia,G. (2006) Poly(ADP-ribose): novel functions for an old molecule // Nat. Rev. Mol. Cell. Biol., vol 7, pp.517–528.
19. Shieh W.M., Ame J.C., Wilson M.V., Wang Z.Q., Koh D.W., JacobsonM.K., Jacobson E.L. (1998) Poly(ADP-ribose) polymerase null mouse cells synthesize ADP-ribose polymers. J.Biol.Chem., vol. 273, pp.30069–30072.
20. Satoh,M.S., Poirier,G.G. and Lindahl,T. (1994) Dual function forpoly(ADP-ribose) synthesis in response to DNA strand breakage. Biochemistry, vol. 33, pp.7099–7106.
21. Tanaka Y., Yoshihara K., Itaya A., Kamiya T., Koide S.S. (1984) Mechanism of the inhibition of Ca2+, Mg2+-dependentendonuclease of bull seminal plasma induced by ADP-ribosylation. J.Biol. Chem., vol. 259, pp.6579–6585.
22. Vainonen J.P., Shapiguzov A., Vaattovaara A., Kangasjärvi J. (2016) Plant PARPs, PARGs and PARP-like Proteins. Current Protein and Peptide Science., vol. 17, pp.713-723
23. Weitzman M.D, Weitzman J.B. (2014) What's the damage? The impact of pathogens on pathways that maintain host genome integrity. Cell Host Microbe, vol.15 (3), pp. 283-294.
24. Woodhouse B.C., Dianov G.L. (2008) Poly ADP-ribose polymerase-1: an international molecule of mystery. DNA Repair., vol. 7, pp.1077–1086.
25. Zhang F., Wang Y., Wang L., Luo X., Huang K., Wang C., Du M., Liu F., Luo T., Huang D., Huang K. (2013) Poly(ADP-ribose) Polymerase 1 Is a Key Regulator of Estrogen Receptor α-dependent Gene Transcription. J. Biol. Chem., vol. 288 (16), pp. 11348–11357.
2 Foyer C.H., Noctor G. Redox sensing and signalling associated with reactive oxygen in chloroplasts, peroxisomes and mitochondria // Physiol. Plant. - 2003. - Vol. 119. - P.355–364.
3 Weitzman M.D., Weitzman J.B. What's the damage? The impact of pathogens on pathways that maintain host genome integrity //Cell Host Microbe. -2014. -Vol.15. - №3. -P.283-294.
4 Papamichos-Chronakis M., Peterson C.L. Chromatin and the genome integrity network // Nat Rev Genet. - 2013. - Vol. 14. - № 1. - P.62–75.
5 Ermolaeva M.A., Schumacher B. Systemic DNA damage responses: organismal adaptations to genome instability // Trends Genet. - 2014. - Vol. 30. - № 3. - P.95–102.
6 Schreiber V., Dantzer F., Ame J.C., de Murcia G. Poly (ADP-ribose): novel functions for an old molecule // Nat. Rev. Mol. Cell. Biol. - 2006. - Vol 7. - P.517–528.
7 Kim M.Y., Zhang T., Kraus W.L. Poly(ADP-ribosyl)ation by PARP-1: ’PAR-laying’ NAD+ into a nuclear signal // Genes Dev. - 2005. - Vol. 19. - P.1951–1967.
8 Ame´ J-C., Spenlehauer C., de Murcia G. The PARP superfamily // BioEssays. - 2004. - Vol. 26. - P.882–893
9 Woodhouse B.C., Dianov G.L. Poly ADP-ribose polymerase-1: an international molecule of mystery // DNA Repair. - 2008. - Vol. 7. - P.1077–1086.
10 Kraus W.L., Hottiger M.O. PARP-1 and gene regulation: progress and puzzles // Mol. Aspects Med. - 2013. - Vol. 34. - P.1109–1123.
11 Caldecott K.W. Mammalian single-strand break repair: mechanisms and links with chromatin // DNA Repair. - 2007. - Vol. 6. - P.443–453.
12 Shieh W.M., Ame J.C., Wilson M.V., Wang Z.Q., Koh D.W., JacobsonM.K., Jacobson E.L. Poly(ADP-ribose) polymerase null mouse cells synthesize ADP-ribose polymers // J.Biol.Chem. - 1998. - Vol. 273. - P.30069–30072.
13 de Murcia G., Menissier de Murcia J. Poly(ADP-ribose)polymerase: a molecular nick-sensor // Trends Biochem. Sci. - 1994. - Vol. 19. - P.172–176.
14 Tanaka Y., Yoshihara K., Itaya A., Kamiya T., Koide S.S. Mechanism of the inhibition of Ca2+, Mg2+-dependentendonuclease of bull seminal plasma induced by ADP-ribosylation // J.Biol. Chem. - 1984. - Vol. 259. - P.6579–6585.
15 Satoh M.S., Poirier G.G. and Lindahl T. Dual function forpoly(ADP-ribose) synthesis in response to DNA strand breakage // Biochemistry. - 1994. - Vol. 33. - P.7099–7106.
16 Caldecott K.W. Protein ADP-ribosylation and the cellularresponse to DNA strand breaks // DNA Repair. - 2014. - Vol. 19. - P.108–113.
17 Briggs A.G., Bent A.F. Poly(ADP-ribosyl)ation in plants // Trends Plant Sci. - 2011. - Vol. 16. - № 7. - P.372–80.
18 Lamb R.S., Citarelli M., Teotia S. Functions of the poly(ADP-ribose) polymerase superfamily in plants // Cell Mol Life Sci. - 2012. - Vol. 69. - № 2. - P.175–89.
19 Briggs A.G., Bent A.F. Poly(ADP-ribosyl)ation in plants // Trends in Plant Science. - 2011. - Vol. 16. - № 7. - P.360-1385.
20 Laemmli U.K. Cleavage of structural proteins during the assembly of the head of bacteriophage T4 // Nature. – 1970. – Vol. 227. - № 5259. – P. 680-685.
21 Bradford M.M. A Rapid and Sensitive Method for the Quantitation of Microgram Quantities of Protein Utilizing the Principle of Protein-Dye Binding // Anal. Biochem. - 1976. - Vol. 72. – P. 248-302.
22 Vainonen J.P., Shapiguzov A., Vaattovaara A., Kangasjärvi J. Plant PARPs, PARGs and PARP-like Proteins // Current Protein and Peptide Science. – 2016. – Vol. 17. - P.713-723
23 Hinz J.M., Rodriguez Y., Smerdon M.J. Rotational dynamics of DNA on the nucleosome surface markedly impact accessibility to a DNA repair enzyme // Proc. Natl. Acad. Sci. U.S.A. - 2010. - Vol. 107. - P.4646–4651.
24 Odell I.D., Barbour J.E., Murphy D.L., Della-Maria J.A., Sweasy J.B., Tomkinson A.E., Wallace S.S., Pederson D.S. Nucleosome disruption by DNA ligase III-XRCC1 promotes efficient base excision repair // Mol. Cell. Biol. - 2011. - Vol. 31. - P.4623–4632.
25 Zhang F., Wang Y., Wang L., Luo X., Huang K., Wang C., Du M., Liu F., Luo T., Huang D., Huang K. Poly(ADP-ribose) Polymerase 1 Is a Key Regulator of Estrogen Receptor α-dependent Gene Transcription // J. Biol. Chem. – 2013. - Vol. 288. - № 16. – P. 11348–11357.
References
1. Ame´ J-C., Spenlehauer C., de Murcia G. (2004) The PARP superfamily. BioEssays, vol. 26, pp. 882–893.
2. Briggs A.G, Bent A.F. (2011) Poly(ADP-ribosyl)ation in plants. Trends Plant Sci., vol. 16 (7), pp.372–80.
3. Briggs A.G., Bent A.F. (2011) Poly(ADP-ribosyl)ation in plants. Trends in Plant Science., vol. 16 (7), pp.360-1385.
4. Bradford M. M. (1976) A Rapid and Sensitive Method for the Quantitation of Microgram Quantities of Protein Utilizing the Principle of Protein-Dye Binding. Anal. Biochem., vol. 72, pp. 248-54.
5. Cadet J., Douki T., Gasparutto D., Ravanat J.L. (2003) Oxidative damage to DNA: formation, measurement and biochemical features. Mutat. Res., vol. 531, pp. 5-23.
6. Caldecott K.W. (2007) Mammalian single-strand break repair: mechanisms and links with chromatin. DNA Repair., vol. 6, pp.443–453.
7. Caldecott K.W. (2014) Protein ADP-ribosylation and the cellularresponse to DNA strand breaks. DNA Repair, vol. 19, pp.108–113.
8. de Murcia G., Menissier de Murcia J. (1994) Poly(ADP-ribose)polymerase: a molecular nick-sensor. Trends Biochem. Sci., vol. 19, pp.172–176.
9. Ermolaeva M.A., Schumacher B. (2014) Systemic DNA damage responses: organismal adaptations to genome instability. Trends Genet., vol. 30 (3), pp.95–102.
10. Foyer C.H., Noctor G. (2003) Redox sensing and signalling associated with reactive oxygen in chloroplasts, peroxisomes and mitochondria. Physiol. Plant, vol. 119, pp. 355–364.
11. Hinz J.M., Rodriguez Y., Smerdon M.J. (2010) Rotational dynamics of DNA on the nucleosome surface markedly impact accessibility to a DNA repair enzyme. Proc. Natl. Acad. Sci. U.S.A., vol. 107, pp.4646–4651.
12. Kim M.Y., Zhang T., Kraus W.L. (2005) Poly(ADP-ribosyl)ation by PARP-1: ’PAR-laying’ NAD+ into a nuclear signal. Genes Dev., vol. 19, pp.1951–1967.
13. Kraus W.L., Hottiger M.O. (2013) PARP-1 and gene regulation: progress and puzzles. Mol. Aspects Med., vol. 34, pp.1109–1123.
14. Laemmli U.K. (1970) Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature, vol. 227 (5259), pp. 680-685.
15. Lamb R.S., Citarelli M., Teotia S. (2012) Functions of the poly(ADP-ribose) polymerase superfamily in plants. Cell Mol Life Sci., vol. 69 (2). - P.175–89.
16. Odell I.D., Barbour J.E., Murphy D.L., Della-Maria J.A., Sweasy J.B., Tomkinson A.E., Wallace S.S., Pederson D.S. (2011) Nucleosome disruption by DNA ligase III-XRCC1 promotes efficient base excision repair. Mol. Cell. Biol., vol. 31, pp.4623–4632.
17. Papamichos-Chronakis M., Peterson C.L. (2013) Chromatin and the genome integrity network. Nat Rev Genet., vol. 14 (1), pp.62–75.
18. Schreiber V., Dantzer F., Ame J.C., de Murcia,G. (2006) Poly(ADP-ribose): novel functions for an old molecule // Nat. Rev. Mol. Cell. Biol., vol 7, pp.517–528.
19. Shieh W.M., Ame J.C., Wilson M.V., Wang Z.Q., Koh D.W., JacobsonM.K., Jacobson E.L. (1998) Poly(ADP-ribose) polymerase null mouse cells synthesize ADP-ribose polymers. J.Biol.Chem., vol. 273, pp.30069–30072.
20. Satoh,M.S., Poirier,G.G. and Lindahl,T. (1994) Dual function forpoly(ADP-ribose) synthesis in response to DNA strand breakage. Biochemistry, vol. 33, pp.7099–7106.
21. Tanaka Y., Yoshihara K., Itaya A., Kamiya T., Koide S.S. (1984) Mechanism of the inhibition of Ca2+, Mg2+-dependentendonuclease of bull seminal plasma induced by ADP-ribosylation. J.Biol. Chem., vol. 259, pp.6579–6585.
22. Vainonen J.P., Shapiguzov A., Vaattovaara A., Kangasjärvi J. (2016) Plant PARPs, PARGs and PARP-like Proteins. Current Protein and Peptide Science., vol. 17, pp.713-723
23. Weitzman M.D, Weitzman J.B. (2014) What's the damage? The impact of pathogens on pathways that maintain host genome integrity. Cell Host Microbe, vol.15 (3), pp. 283-294.
24. Woodhouse B.C., Dianov G.L. (2008) Poly ADP-ribose polymerase-1: an international molecule of mystery. DNA Repair., vol. 7, pp.1077–1086.
25. Zhang F., Wang Y., Wang L., Luo X., Huang K., Wang C., Du M., Liu F., Luo T., Huang D., Huang K. (2013) Poly(ADP-ribose) Polymerase 1 Is a Key Regulator of Estrogen Receptor α-dependent Gene Transcription. J. Biol. Chem., vol. 288 (16), pp. 11348–11357.
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Как цитировать
Kuanbay, A. K., Smekenov, I. T., Saparbayev, M. K., Ishchenko А. А., Taipakova, S. M., & Bissenbaev, A. K. (2018). Выделение и характеристика кДНК гена поли(АДФ-рибоза) полимеразы 2 Arabidopsis thaliana. Вестник КазНУ. Серия биологическая, 74(1), 99–111. https://doi.org/10.26577/eb-2018-1-1319
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МОЛЕКУЛЯРНАЯ БИОЛОГИЯ И ГЕНЕТИКА
