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Identification and bioinformatics analyzes of heat shock protein 70 genes Hsp 70 in Fagaceae family

Year 2016, Supplement 1, 84 - 91, 15.08.2016

Abstract

Heat shock proteins Hsps are a group of proteins found in all living organisms. They play key roles in regulating the stress response to salinity, drought, and extreme temperature changes in plants. Hsps also act as molecular chaperones that provide favorable conditions for the correct folding of other proteins, thus preventing protein aggregation. Many studies have been performed to identify molecular functions of individual family members. However, there is a limited study on genome-wide identification and characterizations of Hsp70s in Fagaceae family American beech, American chestnut, Chinese chestnut, European chestnut, Japanese chestnut, Oak, Red oak and White oak . In this study, we have identified 13, 17 and 15 Hsp70 genes in beech, oak and chestnut, respectively. Phylogenetic, conserved motifs and 3D protein structure analysis of identified Hsp70 genes were also performed. According to phylogenetic analysis, Hsp70 genes could be classified into different groups. Specific motifs were found in all predicted Hsp70 proteins and were relatively conserved in beech, oak and chestnut genomes. The protein 3D structure of a total of thirteen Hsp70s “ FagHsp70-03 68% / FagHsp70-08 65% / FagHsp70-09 71% / FagHsp7013 80% / QuerHsp70-03 65% / QuerHsp70-04 68% / QuerHsp70-09 71% / QuerHsp70-14 77% / CasHsp7003 65% / CasHsp70-04 67% / CasHsp70-11 65% / CasHsp70-14 65% / CasHsp70-15 61% ” were modelled at > 90% confidence and the percentage residue varied from 65 to 80. These results provide characterization and functional information of Hsp70 proteins for Fagaceae family. This genome-wide identification will enable researcher to open new perspectives for further studies to improve stress tolerant forest trees

References

  • Atalay, İ., 1992. Kayın (Fagus orientalis Lipsky.) Ormanlarının Ekolojisi ve Tohum Transferi Yönünden Bölgelere Ayrılması, Orman Bakanlığı, Orman Ağaçları ve Tohumları Islah Araştırma Müdürlüğü, Yayın No:5, Ankara.
  • Atay, İ., 1982b. Doğal Gençleştirme Yöntemleri I (Doğal Gençleştirmenin Başarısını Etkileyen Önemli Hususlar). İ.Ü. Orman Fakültesi Yayını, No. 2876/306.
  • Bailey, T.L., Elkan, C. 1994. ‘Fitting a Mixture Model by Expectation Maximization to Discover Motifs in Biopolymers’, Proceedings of the ‘Second İnternational Conference on Intelligent Systems for Molecular Biology’, p.28-36.
  • Berman, Westbrook et al. 2000. Nucleic Acids Res. 28, 235-242; http://www.pdb.org/.Benkert, P., Biasini, M., Schwede, T. 2011. Toward the estimation of the absolute quality of individual protein structure models. Bioinformatics, 27, 343-350.
  • Chen, F., Hayes, P.M., Mulrooney, D.M. and Pan, A. 1994. Nucleotide sequence of a cDNA encoding a heat-shock protein (HSP70) from barley (Hordeum vulgare L). Plant Physiol 106 (2): 815.
  • Dhankher, O.P., Drew, J.E., Gatehouse, J.A. 1997. Characterization of a pea Hsp70 gene which is both developmentally and stress-regulated. Plant Mol Biol 34(2):345-52.
  • Delen, N. 1992. Ege Bölgesi’ nde yeni bir hastalık: Kestane Kanseri. Ege Tarımsal Araştırma Enstitüsü Müdürlüğü, TYUAP Ege-Marmara Dilimi, Bahçe Bitkileri Grubu Abav Toplantısı, (3-6 Kasım 1992), Menemen-İzmir.
  • Frydman, J. 2001. Folding of newly translated proteins in vivo: the role of molecular chaperones. Annual Review of Biochemistry 70, 603647.
  • Efe, R., Soykan, A., Curebal, I., Sonmez, S. 2011. Dede Korkut Monument Oak (Quercus infectoria Olivier) (Kadıköy- Edremit–Balıkesir, Turkey) The 2nd International Geography Symposium GEOMED2010, Procedia Social and Behavioral Sciences, (19) 627–636.
  • Hartl, F.U. 1996. Molecular chaperones in cellular protein folding. Nature 381, 571-580.
  • Jung, K.H., Gho, H.J., Nguyen, M.X., Kim, S.R., An, G. 2013. Genome-wide expression analysis of HSP70 family genes in rice and identification of a cytosolic HSP70 gene highly induced under heat stress. Funct Integr Genomics 13(3):391-402. doi: 10.1007/s10142-013-0331-6.
  • Letunic I., Bork, P. 2011. Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy. Nucleic Acids Res 39: W475–8. doi: 10.1093/nar/gkr201.
  • Liberek, K. Lewandowska, A., Zietkiewicz, S. 2008. Chaperones in Control of Protein Disaggregation. The EMBO Journal, Sayı 27, s. 328-335.
  • Lin, B.L., Wang, J.S., Liu, H.C., Chen, R.W., Meyer, Y., Barakat, A., Delseny, M. 2001. Genomic analysis of the Hsp70 superfamily in Arabidopsis thaliana. Cell Stress Chaperones 6 (3):201–208.
  • Morimoto, R.I. 1998. Regulation of the heat shook transcriptional response: Cross talk between a family of heat shock factors, molecular chaperones, and negative regulators. Genes and Development 12, 37883796.
  • Pelham, H.R.B. 1986. Speculations on the functions of major heat shock and glucose regulated proteins. Cell 46, 959- 961.
  • Ritossa, F. 1996. Discovery of the heat shock response . Cell Stress Chaperones 1 (2): 97–8. doi:10.1379/1466- 1268(1996)0012.3.CO;2. PMC 248460. PMID 9222594.
  • Rochester, D.E., Winer, J.A., Shah, D.M. 1986. The structure and expression of maize genes encoding the major heat- shock protein, Hsp70. EMBO J. 5:451–458.
  • Sarkar, N.K., Kundnani, P., Grover, A. 2013. Functional analysis of Hsp70 superfamily proteins of rice (Oryza sativa). Cell Stress Chaperones, 18(4):427–437.
  • Saıtou, N., Nei, M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4~406-425.
  • Sorensen, J.G., Loeschcke, V. 2004. Effects of relative emergence time on heat stress resistance traits, longevity and Hsp70 expression level in Drosophila melanogaster, Journal of Thermal Biology 29(4-5): 195-203.
  • Sung, D.Y., Vierling, E., Guy, C.L. 2001. Comprehensive expression profile analysis of the Arabidopsis Hsp70 gene family. Plant Physiol, 126(2):789–800.
  • Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., et al. 2011. MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739. doi:10.1093/molbev/msr121.
  • Thomas, N. A., Deng, W., Puente, J. L., Frey, E. A., Yip, C. K., Strynadka, N. C. & Finlay, B. B. 2005. CesT is a multi- effector chaperone and recruitment factor required for the efficient type III secretion of both LEE- and non-LEE- encoded effectors of enteropathogenic Escherichia coli. Mol Microbiol 57, 1762–1779.
  • Yer, E.N., Baloglu, M. C., Ziplar, U.T., Ayan, S., Unver, T. 2016. Drought-Responsive Hsp70 Gene Analysis in Populus at Genome-Wide Level. Plant Mol Biol Repor. 34:483–500. doi:10.1007/s11105-015-0933-3.

Fagaceae familyasında ısı şoku protein 70 gen ailesinin Hsp70 tanımlanması ve biyoinformatik analizleri

Year 2016, Supplement 1, 84 - 91, 15.08.2016

Abstract

Isı şoku proteinleri Hsps: Heat Shock Proteins , canlı organizmalarda bulunan bir grup protein ailesidir. Isı şoku protein genleri stres anında örneğin tuzluluk, kuraklık ve ekstrem sıcaklık değişimlerinin düzenlenmesinde anahtar bir rol üstlenmektedirler. Bu proteinler hücresel şaperonlar gibi fonksiyon görürler, protein sentezinde proteinlerin doğru katlanmasında ve taşınmasında rol oynarlar. Hsp70 gen ailesinin moleküler işlevlerine ait bazı çalışmalar yapılmıştır. Fakat Fagaceae familyası Amerikan kayını, Amerikan kestanesi, Çin kestanesi, Avrupa kestanesi, Japon kestanesi, Meşe, Kırmızı meşe ve Ak meşe Hsp70 gen ailesinin genom analizi ve gen karakterizasyonuna ait sınırlı çalışma mevcuttur. Bu çalışmada Tanımlanan Hsp70 gen ailesi dizilerinin genomdaki dağılımları, korunmuş motiflerinin tanımlanması ve tahmini üç boyutlu protein yapılarının belirlenmesi hedeflenmiştir. Hsp70 gen ailesine ait Kayın, Meşe ve Kestane’de sırasıyla 13, 17 ve 15 gen tanımlanmıştır. Filogenetik analiz sonucuna göre Hsp70 genleri 3 farklı grup oluşturmuştur. Yapılan motif analizine göre Hsp70 proteinlerinin genom içerisinde kayın, meşe ve kestanede nispeten korunduğu görülmüştür. Proteinlerin üç boyutlu modellemesi yapıldığında toplam Fagaceae familyasına ait 13 Hsp70 geni >90% güven düzeyinde test edilmiştir. Bu on üç protein “ FagHsp70-03 %68 / FagHsp70-08 %65 / FagHsp70-09 %71 / FagHsp70-13 %80 / QuerHsp70-03 %65 / QuerHsp70-04 %68 / QuerHsp70-09 %71 / QuerHsp70-14 %77 / CasHsp70-03 %65 / CasHsp70-04 %67 / CasHsp70-11 %65 / CasHsp70-14 %65 / CasHsp70-15 %61 ” data bankta bulunan proteinlerle yaklaşık %65-%80 arasında üç boyutlu homoloji modellemesi göstermiştir. Bu sonuçlar Fagaceae familyasında Hsp70 gen ailesinin karakterizasyonu ve fonksiyonel işlevleri hakkında bilgi sağlamaktadır. Bu çalışma ile bitkilerde stres toleransının geliştirilmesine ait birçok araştırma için yeni bir perspektif sağlanacaktır

References

  • Atalay, İ., 1992. Kayın (Fagus orientalis Lipsky.) Ormanlarının Ekolojisi ve Tohum Transferi Yönünden Bölgelere Ayrılması, Orman Bakanlığı, Orman Ağaçları ve Tohumları Islah Araştırma Müdürlüğü, Yayın No:5, Ankara.
  • Atay, İ., 1982b. Doğal Gençleştirme Yöntemleri I (Doğal Gençleştirmenin Başarısını Etkileyen Önemli Hususlar). İ.Ü. Orman Fakültesi Yayını, No. 2876/306.
  • Bailey, T.L., Elkan, C. 1994. ‘Fitting a Mixture Model by Expectation Maximization to Discover Motifs in Biopolymers’, Proceedings of the ‘Second İnternational Conference on Intelligent Systems for Molecular Biology’, p.28-36.
  • Berman, Westbrook et al. 2000. Nucleic Acids Res. 28, 235-242; http://www.pdb.org/.Benkert, P., Biasini, M., Schwede, T. 2011. Toward the estimation of the absolute quality of individual protein structure models. Bioinformatics, 27, 343-350.
  • Chen, F., Hayes, P.M., Mulrooney, D.M. and Pan, A. 1994. Nucleotide sequence of a cDNA encoding a heat-shock protein (HSP70) from barley (Hordeum vulgare L). Plant Physiol 106 (2): 815.
  • Dhankher, O.P., Drew, J.E., Gatehouse, J.A. 1997. Characterization of a pea Hsp70 gene which is both developmentally and stress-regulated. Plant Mol Biol 34(2):345-52.
  • Delen, N. 1992. Ege Bölgesi’ nde yeni bir hastalık: Kestane Kanseri. Ege Tarımsal Araştırma Enstitüsü Müdürlüğü, TYUAP Ege-Marmara Dilimi, Bahçe Bitkileri Grubu Abav Toplantısı, (3-6 Kasım 1992), Menemen-İzmir.
  • Frydman, J. 2001. Folding of newly translated proteins in vivo: the role of molecular chaperones. Annual Review of Biochemistry 70, 603647.
  • Efe, R., Soykan, A., Curebal, I., Sonmez, S. 2011. Dede Korkut Monument Oak (Quercus infectoria Olivier) (Kadıköy- Edremit–Balıkesir, Turkey) The 2nd International Geography Symposium GEOMED2010, Procedia Social and Behavioral Sciences, (19) 627–636.
  • Hartl, F.U. 1996. Molecular chaperones in cellular protein folding. Nature 381, 571-580.
  • Jung, K.H., Gho, H.J., Nguyen, M.X., Kim, S.R., An, G. 2013. Genome-wide expression analysis of HSP70 family genes in rice and identification of a cytosolic HSP70 gene highly induced under heat stress. Funct Integr Genomics 13(3):391-402. doi: 10.1007/s10142-013-0331-6.
  • Letunic I., Bork, P. 2011. Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy. Nucleic Acids Res 39: W475–8. doi: 10.1093/nar/gkr201.
  • Liberek, K. Lewandowska, A., Zietkiewicz, S. 2008. Chaperones in Control of Protein Disaggregation. The EMBO Journal, Sayı 27, s. 328-335.
  • Lin, B.L., Wang, J.S., Liu, H.C., Chen, R.W., Meyer, Y., Barakat, A., Delseny, M. 2001. Genomic analysis of the Hsp70 superfamily in Arabidopsis thaliana. Cell Stress Chaperones 6 (3):201–208.
  • Morimoto, R.I. 1998. Regulation of the heat shook transcriptional response: Cross talk between a family of heat shock factors, molecular chaperones, and negative regulators. Genes and Development 12, 37883796.
  • Pelham, H.R.B. 1986. Speculations on the functions of major heat shock and glucose regulated proteins. Cell 46, 959- 961.
  • Ritossa, F. 1996. Discovery of the heat shock response . Cell Stress Chaperones 1 (2): 97–8. doi:10.1379/1466- 1268(1996)0012.3.CO;2. PMC 248460. PMID 9222594.
  • Rochester, D.E., Winer, J.A., Shah, D.M. 1986. The structure and expression of maize genes encoding the major heat- shock protein, Hsp70. EMBO J. 5:451–458.
  • Sarkar, N.K., Kundnani, P., Grover, A. 2013. Functional analysis of Hsp70 superfamily proteins of rice (Oryza sativa). Cell Stress Chaperones, 18(4):427–437.
  • Saıtou, N., Nei, M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4~406-425.
  • Sorensen, J.G., Loeschcke, V. 2004. Effects of relative emergence time on heat stress resistance traits, longevity and Hsp70 expression level in Drosophila melanogaster, Journal of Thermal Biology 29(4-5): 195-203.
  • Sung, D.Y., Vierling, E., Guy, C.L. 2001. Comprehensive expression profile analysis of the Arabidopsis Hsp70 gene family. Plant Physiol, 126(2):789–800.
  • Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., et al. 2011. MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739. doi:10.1093/molbev/msr121.
  • Thomas, N. A., Deng, W., Puente, J. L., Frey, E. A., Yip, C. K., Strynadka, N. C. & Finlay, B. B. 2005. CesT is a multi- effector chaperone and recruitment factor required for the efficient type III secretion of both LEE- and non-LEE- encoded effectors of enteropathogenic Escherichia coli. Mol Microbiol 57, 1762–1779.
  • Yer, E.N., Baloglu, M. C., Ziplar, U.T., Ayan, S., Unver, T. 2016. Drought-Responsive Hsp70 Gene Analysis in Populus at Genome-Wide Level. Plant Mol Biol Repor. 34:483–500. doi:10.1007/s11105-015-0933-3.
There are 25 citations in total.

Details

Primary Language Turkish
Journal Section Research Article
Authors

Esra Nurten Yer This is me

Mehmet Cengiz Baloğlu This is me

Yasemin Çelik Altunoğlu This is me

Sezgin Ayan This is me

Publication Date August 15, 2016
Published in Issue Year 2016 Supplement 1

Cite

APA Yer, E. N., Baloğlu, M. C., Altunoğlu, Y. Ç., Ayan, S. (2016). Fagaceae familyasında ısı şoku protein 70 gen ailesinin Hsp70 tanımlanması ve biyoinformatik analizleri. Biological Diversity and Conservation, 9(2), 84-91.

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