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Genomic and Functional Characterization of Heat Shock Protein Families in Jujube Genome (Ziziphus jujuba) by in silico Methods

Yıl 2021, Cilt: 21 Sayı: 3, 277 - 294, 31.12.2021

Yusuf Ceylan , Kevser Betül Ceylan Yasemin Çelik Altunoğlu Mehmet Cengiz Baloğlu

https://doi.org/10.17475/kastorman.1049963
Cited By: 1

Öz

Aim of study: It was aimed to identify and characterize Hsp genes in jujube genome using genomics methods.
Material and method: Protein sequences of jujube Hsp genes were obtained from NCBI databases. GSDS program was used to detect of exon-intron sites. To define the conserved motifs and estimated 3D-structures, Hsp proteins were used in the MEME-SUITE and PHYRE2 program, respectively. miRNAs targeting ZjuHsp transcripts were identified using the psRNATarget Server database. The gene annotations of Hsp proteins were presented by Blast2GO program. Sequence alignment was performed with ClustalW software, and then the phylogenetic tree was drawn using MEGAX program.
Main results: A total of 474 genes were defined in the jujube genome. The amino acid length of the Hsp proteins changes from 75 aa to 2577 aa. The estimated 3-D structure of the ZjuHsp proteins revealed the dominance of the α-helix structure. Phylogenetic tree was constructed to detect evolutionary relationships revealed the eight major groups of the ZjuHsp100 and ZjuHsp60. ZjuHsp proteins could be mainly found in cell parts, membranes, and organelles. It was determined that the ZjuHsp100 genes was targeted by 313 miRNAs.
Highlights: This study helps the researchers who would like to comparative and functional genomic studies.

Anahtar Kelimeler

Heat Shock Proteins (Hsp) Ziziphus jujuba Genome Wide Identification Gene Ontology Analysis Phylogenetic Tree

Kaynakça

  • Altunoglu, Y. C., Baloglu, P., Yer, E. N., Pekol, S., & Baloglu, M. C. (2016). Identification and expression analysis of LEA gene family members in cucumber genome. Plant Growth Regulation, 80(2), 225-241. doi: 10.1007/s10725-016-0160-4.
  • Altunoğlu, Y. Ç., Keleş, M., Can, T. H., & Baloğlu, M. C. (2019). Identification of watermelon heat shock protein members and tissue-specific gene expression analysis under combined drought and heat stresses. Turkish Journal of Biology, 43(6), 404-419.
  • Bailey, T. L., & Elkan, C. (1994). Fitting a mixture model by expectation maximization to discover motifs in bipolymers. International Conference on Intelligent Systems for Molecular Biology, 28-36.
  • Baloglu, M. C., Eldem, V., Hajyzadeh, M., & Unver, T. (2014). Genome-wide analysis of the bZIP transcription factors in cucumber. PloS One, 9(4), e96014. doi: 10.1371/journal.pone.0096014.
  • Cagliari, T. C., Tiroli, A. O., Borges, J. C., & Ramos, C. H. (2005). Identification and in silico expression pattern analysis of Eucalyptus expressed sequencing tags (ESTs) encoding molecular chaperones. Genetics and Molecular Biology, 28, 520-528. doi: 10.1590/s1415-47572005000400006.
  • Çelik Altunoğlu, Y. (2016). Isı Şoku Protein Ailesinden Hsp70 Genlerinin Okaliptüs Genomunda Saptanması ve Karakterizasyonu. Kastamonu Üniversitesi Orman Fakültesi Dergisi, 16(2), 497-509. doi: 10.17475/kastorman.289759.
  • Ceylan, K. B., Ceylan, Y., Ustaoğlu, B., Baloğlu, M. C., & Altunoğlu, Y. Ç. (2019). Molecular Identification and Characterization of LEA Proteins in Jujube Genome. Kastamonu University Journal of Engineering and Sciences, 5(2), 101-146.
  • Chen, J., Gao, T., Wan, S., Zhang, Y., Yang, J., Yu, Y., & Wang, W. (2018). Genome-wide identification, classification and expression analysis of the HSP gene superfamily in tea plant (Camellia sinensis). International Journal of Molecular Sciences, 19(9), 2633. doi: 10.3390/ijms19092633.
  • Cho, E. K., & Choi, Y. J. (2009). A nuclear-localized HSP70 confers thermoprotective activity and drought-stress tolerance on plants. Biotechnology Letters, 31(4), 597-606. doi: 10.1007/s10529-008-9880-5.
  • Conesa, A., & Götz, S. (2008). Blast2GO: a comprehensive suite for functional analysis in plant genomics. International Journal of Plant Genomics, doi: 10.1155/2008/619832.
  • Dai, X., & Zhao, P. X. (2011). psRNATarget: a plant small RNA target analysis server. Nucleic Acids Research, 39(suppl_2), W155-W159. doi: 10.1093/nar/gkr319.
  • Deocaris, C. C., Kaul, S. C., & Wadhwa, R. (2006). On the brotherhood of the mitochondrial chaperones mortalin and heat shock protein 60. Cell Stress & Chaperones, 11(2), 116.
  • Devi, U., & Bora, D. (2017). Growth inhibitory effect of phenolic extracts of Ziziphus jujuba Mill. in dengue vector Aedes aegypti (L) in parent and F1 generation. Asian Pacific Journal of Tropical Medicine, 10(8), 787-791. doi: 10.1016/j.apjtm.2017.08.003.
  • Ding, X., Ruan, H., Yu, L., Li, Q., Song, Q., Yang, S., & Gai, J. (2020). miR156b from soybean CMS line modulates floral organ development. Journal of Plant Biology, 63(2), 141-153. doi: 10.1007/s12374-020-09237-7.
  • Frydman, J. (2001). Folding of newly translated proteins in vivo: the role of molecular chaperones. Annual Review of Biochemistry, 70(1), 603-647.
  • Gasteiger, E., Gattiker, A., Hoogland, C., Ivanyi, I., Appel, R. D., & Bairoch, A. (2003). ExPASy: the proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Research, 31(13), 3784-3788. doi: 10.1093/nar/gkg563.
  • Goodstein, D. M., Shu, S., Howson, R., Neupane, R., Hayes, R. D., Fazo, J. & Rokhsar, D. S. (2012). Phytozome: a comparative platform for green plant genomics. Nucleic Acids Research, 40(D1), D1178-D1186. doi: 10.1093/nar/gkr944.
  • Gün, S. (2017). Hünnap meyvesinin (Ziziphus jujuba Mill.) soğukta muhafaza performansı üzerine farklı olgunluk safhası ve modifiye atmosfer paketlemenin (MAP) etkisi (Master's thesis, Fen Bilimleri Enstitüsü).
  • Gupta, O. P., Meena, N. L., Sharma, I., & Sharma, P. (2014). Differential regulation of microRNAs in response to osmotic, salt and cold stresses in wheat. Molecular Biology Reports, 41(7), 4623-4629. doi: 10.1007/s11033-014-3333-0.
  • Hu, B., Jin, J., Guo, A. Y., Zhang, H., Luo, J., & Gao, G. (2015). GSDS 2.0: an upgraded gene feature visualization server. Bioinformatics, 31(8), 1296-1297. doi: 10.1093/bioinformatics/btu817.
  • Huen, A., Bally, J., & Smith, P. (2018). Identification and characterisation of microRNAs and their target genes in phosphate-starved Nicotiana benthamiana by small RNA deep sequencing and 5’RACE analysis. BMC Genomics, 19(1), 1-18. doi: 10.1186/s12864-018-5258-9.
  • Chen, J., Liu, X., Li, Z., Qi, A., Yao, P., Zhou, Z., ... & Tsim, K. W. (2017). A review of dietary Ziziphus jujuba fruit (Jujube): Developing health food supplements for brain protection. Evidence-Based Complementary and Alternative Medicine, doi: https://doi.org/10.1155/2017/3019568.
  • Karıncalı, M. (2003). Zizyphus jujuba mill.(hünnap) bitkisinin morfolojik, anatomik, ekolojik ve polen özelliklerinin araştırılması (Doctoral dissertation, Pamukkale Üniversitesi).
  • Kelley, L. A., & Sternberg, M. J. (2009). Protein structure prediction on the Web: a case study using the Phyre server. Nature Protocols, 4(3), 363-371. doi: 10.1038/nprot.2009.2.
  • Khan, S., Jabeen, R., Deeba, F., Waheed, U., Khanum, P., & Iqbal, N. (2021). Heat Shock Proteins: Classification, Functions and Expressions in Plants during Environmental Stresses. Journal of Bioresource Management, 8(2), 9. https://doi.org/10.35691/jbm.1202.0183.
  • Krishna, P., & Gloor, G. (2001). The Hsp90 family of proteins in Arabidopsis thaliana. Cell Stress & Chaperones, 6(3), 238. doi: 10.1379/1466-1268(2001)006<0238:thfopi>2.0.co;2.
  • Kumar, A., Sharma, S., Chunduri, V., Kaur, A., Kaur, S., Malhotra, N., ... & Garg, M. (2020). Genome-wide Identification and Characterization of Heat Shock Protein Family Reveals Role in Development and Stress Conditions in Triticum aestivum L. Scientific Reports, 10(1), 1-12. doi: 10.1038/s41598-020-64746-2.
  • Kumar, G. P., Sekhar, Y. C., Ashok, G., Anand, K., & Anilakumar, K. R. (2018). Functional benefits of Ziziphus jujuba fruits: anti-fatigue activity and antioxidant enzyme activities in experimental animal models. EC Nutrition, 13(5), 288-298.
  • Kumar NS, N., SP, A., Sinha, D., Veedin Rajan, V. B., Esthaki, V. K., & D’Silva, P. (2012). HSPIR: a manually annotated heat shock protein information resource. Bioinformatics, 28(21), 2853-2855.
  • Letunic, I., & Bork, P. (2016). Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Research, 44(W1), W242-W245. doi: 10.1093/nar/gkw290.
  • Letunic, I., Doerks, T., & Bork, P. (2012). SMART 7: recent updates to the protein domain annotation resource. Nucleic Acids Research, 40(D1), D302-D305. doi: 10.1093/nar/gkr931.
  • Li, J. W., Ding, S. D., & Ding, X. L. (2005). Comparison of antioxidant capacities of extracts from five cultivars of Chinese jujube. Process Biochemistry, 40(11), 3607-3613. doi: 10.1016/j.procbio.2005.03.005.
  • Li, Y., Li, W., & JIN, Y. X. (2005). Computational identification of novel family members of microRNA genes in Arabidopsis thaliana and Oryza sativa. Acta biochimica et Biophysica Sinica, 37(2), 75-87. doi: 10.1111/j.1745-7270.2005.00012.x.
  • Lindquist, S. (1986). The heat-shock response. Annual Review of Biochemistry, 55(1), 1151-1191.
  • Lu, Y., Liu, L., Wang, X., Han, Z., Ouyang, B., Zhang, J., & Li, H. (2016). Genome-wide identification and expression analysis of the expansin gene family in tomato. Molecular Genetics and Genomics, 291(2), 597-608. doi: 10.1007/s00438-015-1133-4.
  • Lynch, M., & Conery, J. S. (2000). The evolutionary fate and consequences of duplicate genes. Science, 290(5494), 1151-1155. doi: 10.1126/science.290.5494.1151.
  • Nagaraju, M., Kumar, S. A., Reddy, P. S., Kumar, A., Rao, D. M., & Kavi Kishor, P. B. (2019). Genome-scale identification, classification, and tissue specific expression analysis of late embryogenesis abundant (LEA) genes under abiotic stress conditions in Sorghum bicolor L. PloS One, 14(1), e0209980. doi: 10.1371/journal.pone.0209980.
  • Nollen, E. A., Brunsting, J. F., Roelofsen, H., Weber, L. A., & Kampinga, H. H. (1999). In vivo chaperone activity of heat shock protein 70 and thermotolerance. Molecular and Cellular Biology, 19(3), 2069-2079. doi: 10.1128/mcb.19.3.2069.
  • Pandey, A., Singh, R., Radhamani, J., & Bhandari, D. C. (2010). Exploring the potential of Ziziphus nummularia (Burm. f.) Wight et Arn. from drier regions of India. Genetic Resources and Crop Evolution, 57(6), 929-936. doi: 10.1007/s10722-010-9566-4.
  • Panzade, K. P., Kale, S. S., Chavan, N. R., & Hatzade, B. (2021). Genome-wide analysis of Hsp70 and Hsp100 gene families in Ziziphus jujuba. Cell Stress and Chaperones, 26(2), 341-353. doi: 10.1007/s12192-020-01179-w.
  • Pelham, H. R. (1986). Speculations on the functions of the major heat shock and glucose-regulated proteins. Cell, 46(7), 959-961.
  • Sabehat, A., Lurie, S., & Weiss, D. (1998). Expression of small heat-shock proteins at low temperatures: a possible role in protecting against chilling injuries. Plant Physiology, 117(2), 651-658. https://doi.org/10.1104/pp.117.2.651.
  • Shen, J., Zeng, Y., Zhuang, X., Sun, L., Yao, X., Pimpl, P., & Jiang, L. (2013). Organelle pH in the Arabidopsis endomembrane system. Molecular Plant, 6(5), 1419-1437. https://doi.org/10.1093/mp/sst079.
  • Shukla, P. S., Borza, T., Critchley, A. T., Hiltz, D., Norrie, J., & Prithiviraj, B. (2018). Ascophyllum nodosum extract mitigates salinity stress in Arabidopsis thaliana by modulating the expression of miRNA involved in stress tolerance and nutrient acquisition. PLoS One, 13(10), e0206221. https://doi.org/10.1371/journal.pone.0206221.
  • Singh, R. K., Jaishankar, J., Muthamilarasan, M., Shweta, S., Dangi, A., & Prasad, M. (2016). Genome-wide analysis of heat shock proteins in C 4 model, foxtail millet identifies potential candidates for crop improvement under abiotic stress. Scientific Reports, 6(1), 1-14. https://doi.org/10.1038/srep32641.
  • Srivastava, S., Srivastava, A. K., Suprasanna, P., & D’souza, S. F. (2013). Identification and profiling of arsenic stress-induced microRNAs in Brassica juncea. Journal of Experimental Botany, 64(1), 303-315. https://doi.org/10.1093/jxb/ers333.
  • Suyama, M., Torrents, D., & Bork, P. (2006). PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Research, 34(suppl_2), W609-W612. https://doi.org/10.1093/nar/gkl315.
  • Swindell, W. R., Huebner, M., & Weber, A. P. (2007). Transcriptional profiling of Arabidopsis heat shock proteins and transcription factors reveals extensive overlap between heat and non-heat stress response pathways. BMC Genomics, 8(1), 1-15. https://doi.org/10.1186/1471-2164-8-125.
  • Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., & Kumar, S. (2011). MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution, 28(10), 2731-2739. https://doi.org/10.1093/molbev/msr121
  • Thompson, J. (1997). The CLUSTAL X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucl. Acids Res., 24, 4876-4882. https://doi.org/10.1093/nar/25.24.4876
  • Wang, B., Huang, Q., Venkitasamy, C., Chai, H., Gao, H., Cheng, N., ... & Pan, Z. (2016). Changes in phenolic compounds and their antioxidant capacities in jujube (Ziziphus jujuba Miller) during three edible maturity stages. LWT-Food Science and Technology, 66, 56-62. https://doi.org/10.1016/j.lwt.2015.10.005.
  • Wang, C., Wang, Q., Zhu, X., Cui, M., Jia, H., Zhang, W., ... & Shen, W. (2019). Characterization on the conservation and diversification of miRNA156 gene family from lower to higher plant species based on phylogenetic analysis at the whole genomic level. Functional & Integrative Genomics, 19(6), 933-952. https://doi.org/10.1007/s10142-019-00679-y.
  • Wang, W., Vinocur, B., Shoseyov, O., & Altman, A. (2004). Role of plant heat-shock proteins and molecular chaperones in the abiotic stress response. Trends in Plant Science, 9(5), 244-252. https://doi.org/10.1016/j.tplants.2004.03.006.
  • Waters, E. R., Lee, G. J., & Vierling, E. (1996). Evolution, structure and function of the small heat shock proteins in plants. Journal of Experimental Botany, 47(3), 325-338. https://doi.org/10.1093/jxb/47.3.325.
  • Xu, G., Guo, C., Shan, H., & Kong, H. (2012). Divergence of duplicate genes in exon–intron structure. Proceedings of the National Academy of Sciences, 109(4), 1187-1192. https://doi.org/10.1073/pnas.1109047109.
  • Xu, J., Zheng, Y., Pu, S., Zhang, X., Li, Z., & Chen, J. (2020). Third-generation sequencing found LncRNA associated with heat shock protein response to heat stress in Populus qiongdaoensis seedlings. BMC Genomics, 21(1), 1-14. https://doi.org/10.1186/s12864-020-06979-z.
  • Xu, M. Y., Zhang, L., Li, W. W., Hu, X. L., Wang, M. B., Fan, Y. L., ... & Wang, L. (2014). Stress-induced early flowering is mediated by miR169 in Arabidopsis thaliana. Journal of Experimental Botany, 65(1), 89-101. https://doi.org/10.1093/jxb/ert353.
  • Yer, E. N., Baloglu, M. C., & Ayan, S. (2018). Identification and expression profiling of all Hsp family member genes under salinity stress in different poplar clones. Gene, 678, 324-336. https://doi.org/10.1016/j.gene.2018.08.049
  • Young, J. C., Moarefi, I., & Hartl, F. U. (2001). Hsp90: a specialized but essential protein-folding tool. The Journal of Cell Biology, 154(2), 267. https://doi.org/10.1083/jcb.200104079.
  • Yu, N., Niu, Q. W., Ng, K. H., & Chua, N. H. (2015). The role of miR156/SPL s modules in Arabidopsis lateral root development. The Plant Journal, 83(4), 673-685. https://doi.org/10.1111/tpj.12919.
  • Yu, Y., Ni, Z., Wang, Y., Wan, H., Hu, Z., Jiang, Q., ... & Zhang, H. (2019). Overexpression of soybean miR169c confers increased drought stress sensitivity in transgenic Arabidopsis thaliana. Plant Science, 285, 68-78. https://doi.org/10.1016/j.plantsci.2019.05.003.
  • Zhang, Y. (2005). miRU: an automated plant miRNA target prediction server. Nucleic Acids Research, 33(suppl_2), W701-W704. https://doi.org/10.1093/nar/gki383.
  • Zhao, Q., Wang, J., Levichkin, I. V., Stasinopoulos, S., Ryan, M. T., & Hoogenraad, N. J. (2002). A mitochondrial specific stress response in mammalian cells. The EMBO Journal, 21(17), 4411-4419. https://doi.org/10.1093/emboj/cdf445.
  • Zhou, L., Liu, Y., Liu, Z., Kong, D., Duan, M., & Luo, L. (2010). Genome-wide identification and analysis of drought-responsive microRNAs in Oryza sativa. Journal of Experimental Botany, 61(15), 4157-4168. https://doi.org/10.1093/jxb/erq237.
  • Zou, J., Liu, C., Liu, A., Zou, D., & Chen, X. (2012). Overexpression of OsHsp17. 0 and OsHsp23. 7 enhances drought and salt tolerance in rice. Journal of Plant Physiology, 169(6), 628-635. https://doi.org/10.1016/j.jplph.2011.12.014
  • Zou, Y., Wang, Y., Wang, L., Yang, L., Wang, R., & Li, X. (2013). miR172b controls the transition to autotrophic development inhibited by ABA in Arabidopsis. PloS One, 8(5), e64770. https://doi.org/10.1371/journal.pone.0064770.

Hünnap Genomunda (Ziziphus jujuba) Isı Şoku Protein Ailelerinin in silico Yöntemler ile Genomik ve Fonksiyonel Karakterizasyonu

Yıl 2021, Cilt: 21 Sayı: 3, 277 - 294, 31.12.2021

Yusuf Ceylan , Kevser Betül Ceylan Yasemin Çelik Altunoğlu Mehmet Cengiz Baloğlu

https://doi.org/10.17475/kastorman.1049963
Cited By: 1

Öz

Çalışmanın amacı : Bu çalıĢmada, genomic yöntemler kullanarak hünnap genomunda yer alan Hsp genlerini tanımlamak ve karakterize etmek amaçlanmıĢtır.
Materyal ve yöntem : NCBI veritabanı kullanılarak Hsp genlerinin protein dizileri elde edilmiĢtir. Genlerin ekzon-intron bölgelerinin tespiti, GSDS program ile yapılmıĢtır. Hsp proteinlerinin korunmuĢ motiflerini ve tahmini üç boyutlu yapılarını tanımlamak için sırasıyla MEME-SUITE ve PHYRE2 programı kullanılmıĢtır. Hsp transkriptlerini hedefleyen miRNA'lar, psRNATarget Server veritabanı kullanılarak tanımlanmıĢtır. Hsp proteinlerinin moleküler fonksiyonu, hücresel bileĢeni ve biyolojik fonksiyonları Blast2GO program ile sunulmuĢtur. Hsp proteinlerinin evrimsel iliĢkilerini belirlemek amacı ile ClustalW yazılımı ile dizi hizalaması yapılmıĢ ve ardından MEGAX program ile filogenetik ağaç çizilmiĢtir.
Temel sonuçlar: Hünnap genomunda toplam 474 gen tanımlanmıĢ ve genler çoğunlukla 1. ve 2. kromozomda dağılım göstermiĢtir. Hsp proteinlerinin amino asit uzunluğu 75 aa (ZjuHsp100-117) ile 2577 aa (ZjuHsp40-104 ve ZjuHsp40-157) arasında değiĢim göstermiĢtir. ZjuHsp proteinlerinin tahmini üç boyutlu yapısında α-sarmal yapısının baskın olduğu görülmüĢtür. Proteinlerin evrimsel iliĢkilerini saptamak için oluĢturulan filogenetik ağaçta, ZjuHsp100 ve ZjuHsp60 grup proteinlerin sekiz ana gruba ayrıldığı gözlenmiĢtir. ZjuHsp proteinlerinin esas olarak hücre kısımlarında, zarlarda, ve organellerde bulunduğu tespit edilmiĢtir. ZjuHsp transkriptlerini hedef alan miRNA'lardan 313'ünün ZjuHsp100 genlerini hedeflediği bulunmuĢtur.
Araştırma vurguları : Bu çalıĢma, karĢılaĢtırmalı ve fonksiyonel genomic çalıĢmalar yapmak isteyen araĢtırmacılara yardımcı olmaktadır.
Anahtar Kelimeler: Isı şoku Proteinleri (Hsp), Ziziphus jujuba, Genom Analizi, Gen Ontoloji Analizi, Filogenetik Ağaç

Anahtar Kelimeler

Ziziphus jujuba Genom Analizi Gen Ontoloji Analizi Filogenetik Ağaç Isı şoku Proteinleri (Hsp) Ziziphus jujuba Genom Analizi Gen Ontoloji Analizi Filogenetik Ağaç

Kaynakça

  • Altunoglu, Y. C., Baloglu, P., Yer, E. N., Pekol, S., & Baloglu, M. C. (2016). Identification and expression analysis of LEA gene family members in cucumber genome. Plant Growth Regulation, 80(2), 225-241. doi: 10.1007/s10725-016-0160-4.
  • Altunoğlu, Y. Ç., Keleş, M., Can, T. H., & Baloğlu, M. C. (2019). Identification of watermelon heat shock protein members and tissue-specific gene expression analysis under combined drought and heat stresses. Turkish Journal of Biology, 43(6), 404-419.
  • Bailey, T. L., & Elkan, C. (1994). Fitting a mixture model by expectation maximization to discover motifs in bipolymers. International Conference on Intelligent Systems for Molecular Biology, 28-36.
  • Baloglu, M. C., Eldem, V., Hajyzadeh, M., & Unver, T. (2014). Genome-wide analysis of the bZIP transcription factors in cucumber. PloS One, 9(4), e96014. doi: 10.1371/journal.pone.0096014.
  • Cagliari, T. C., Tiroli, A. O., Borges, J. C., & Ramos, C. H. (2005). Identification and in silico expression pattern analysis of Eucalyptus expressed sequencing tags (ESTs) encoding molecular chaperones. Genetics and Molecular Biology, 28, 520-528. doi: 10.1590/s1415-47572005000400006.
  • Çelik Altunoğlu, Y. (2016). Isı Şoku Protein Ailesinden Hsp70 Genlerinin Okaliptüs Genomunda Saptanması ve Karakterizasyonu. Kastamonu Üniversitesi Orman Fakültesi Dergisi, 16(2), 497-509. doi: 10.17475/kastorman.289759.
  • Ceylan, K. B., Ceylan, Y., Ustaoğlu, B., Baloğlu, M. C., & Altunoğlu, Y. Ç. (2019). Molecular Identification and Characterization of LEA Proteins in Jujube Genome. Kastamonu University Journal of Engineering and Sciences, 5(2), 101-146.
  • Chen, J., Gao, T., Wan, S., Zhang, Y., Yang, J., Yu, Y., & Wang, W. (2018). Genome-wide identification, classification and expression analysis of the HSP gene superfamily in tea plant (Camellia sinensis). International Journal of Molecular Sciences, 19(9), 2633. doi: 10.3390/ijms19092633.
  • Cho, E. K., & Choi, Y. J. (2009). A nuclear-localized HSP70 confers thermoprotective activity and drought-stress tolerance on plants. Biotechnology Letters, 31(4), 597-606. doi: 10.1007/s10529-008-9880-5.
  • Conesa, A., & Götz, S. (2008). Blast2GO: a comprehensive suite for functional analysis in plant genomics. International Journal of Plant Genomics, doi: 10.1155/2008/619832.
  • Dai, X., & Zhao, P. X. (2011). psRNATarget: a plant small RNA target analysis server. Nucleic Acids Research, 39(suppl_2), W155-W159. doi: 10.1093/nar/gkr319.
  • Deocaris, C. C., Kaul, S. C., & Wadhwa, R. (2006). On the brotherhood of the mitochondrial chaperones mortalin and heat shock protein 60. Cell Stress & Chaperones, 11(2), 116.
  • Devi, U., & Bora, D. (2017). Growth inhibitory effect of phenolic extracts of Ziziphus jujuba Mill. in dengue vector Aedes aegypti (L) in parent and F1 generation. Asian Pacific Journal of Tropical Medicine, 10(8), 787-791. doi: 10.1016/j.apjtm.2017.08.003.
  • Ding, X., Ruan, H., Yu, L., Li, Q., Song, Q., Yang, S., & Gai, J. (2020). miR156b from soybean CMS line modulates floral organ development. Journal of Plant Biology, 63(2), 141-153. doi: 10.1007/s12374-020-09237-7.
  • Frydman, J. (2001). Folding of newly translated proteins in vivo: the role of molecular chaperones. Annual Review of Biochemistry, 70(1), 603-647.
  • Gasteiger, E., Gattiker, A., Hoogland, C., Ivanyi, I., Appel, R. D., & Bairoch, A. (2003). ExPASy: the proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Research, 31(13), 3784-3788. doi: 10.1093/nar/gkg563.
  • Goodstein, D. M., Shu, S., Howson, R., Neupane, R., Hayes, R. D., Fazo, J. & Rokhsar, D. S. (2012). Phytozome: a comparative platform for green plant genomics. Nucleic Acids Research, 40(D1), D1178-D1186. doi: 10.1093/nar/gkr944.
  • Gün, S. (2017). Hünnap meyvesinin (Ziziphus jujuba Mill.) soğukta muhafaza performansı üzerine farklı olgunluk safhası ve modifiye atmosfer paketlemenin (MAP) etkisi (Master's thesis, Fen Bilimleri Enstitüsü).
  • Gupta, O. P., Meena, N. L., Sharma, I., & Sharma, P. (2014). Differential regulation of microRNAs in response to osmotic, salt and cold stresses in wheat. Molecular Biology Reports, 41(7), 4623-4629. doi: 10.1007/s11033-014-3333-0.
  • Hu, B., Jin, J., Guo, A. Y., Zhang, H., Luo, J., & Gao, G. (2015). GSDS 2.0: an upgraded gene feature visualization server. Bioinformatics, 31(8), 1296-1297. doi: 10.1093/bioinformatics/btu817.
  • Huen, A., Bally, J., & Smith, P. (2018). Identification and characterisation of microRNAs and their target genes in phosphate-starved Nicotiana benthamiana by small RNA deep sequencing and 5’RACE analysis. BMC Genomics, 19(1), 1-18. doi: 10.1186/s12864-018-5258-9.
  • Chen, J., Liu, X., Li, Z., Qi, A., Yao, P., Zhou, Z., ... & Tsim, K. W. (2017). A review of dietary Ziziphus jujuba fruit (Jujube): Developing health food supplements for brain protection. Evidence-Based Complementary and Alternative Medicine, doi: https://doi.org/10.1155/2017/3019568.
  • Karıncalı, M. (2003). Zizyphus jujuba mill.(hünnap) bitkisinin morfolojik, anatomik, ekolojik ve polen özelliklerinin araştırılması (Doctoral dissertation, Pamukkale Üniversitesi).
  • Kelley, L. A., & Sternberg, M. J. (2009). Protein structure prediction on the Web: a case study using the Phyre server. Nature Protocols, 4(3), 363-371. doi: 10.1038/nprot.2009.2.
  • Khan, S., Jabeen, R., Deeba, F., Waheed, U., Khanum, P., & Iqbal, N. (2021). Heat Shock Proteins: Classification, Functions and Expressions in Plants during Environmental Stresses. Journal of Bioresource Management, 8(2), 9. https://doi.org/10.35691/jbm.1202.0183.
  • Krishna, P., & Gloor, G. (2001). The Hsp90 family of proteins in Arabidopsis thaliana. Cell Stress & Chaperones, 6(3), 238. doi: 10.1379/1466-1268(2001)006<0238:thfopi>2.0.co;2.
  • Kumar, A., Sharma, S., Chunduri, V., Kaur, A., Kaur, S., Malhotra, N., ... & Garg, M. (2020). Genome-wide Identification and Characterization of Heat Shock Protein Family Reveals Role in Development and Stress Conditions in Triticum aestivum L. Scientific Reports, 10(1), 1-12. doi: 10.1038/s41598-020-64746-2.
  • Kumar, G. P., Sekhar, Y. C., Ashok, G., Anand, K., & Anilakumar, K. R. (2018). Functional benefits of Ziziphus jujuba fruits: anti-fatigue activity and antioxidant enzyme activities in experimental animal models. EC Nutrition, 13(5), 288-298.
  • Kumar NS, N., SP, A., Sinha, D., Veedin Rajan, V. B., Esthaki, V. K., & D’Silva, P. (2012). HSPIR: a manually annotated heat shock protein information resource. Bioinformatics, 28(21), 2853-2855.
  • Letunic, I., & Bork, P. (2016). Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Research, 44(W1), W242-W245. doi: 10.1093/nar/gkw290.
  • Letunic, I., Doerks, T., & Bork, P. (2012). SMART 7: recent updates to the protein domain annotation resource. Nucleic Acids Research, 40(D1), D302-D305. doi: 10.1093/nar/gkr931.
  • Li, J. W., Ding, S. D., & Ding, X. L. (2005). Comparison of antioxidant capacities of extracts from five cultivars of Chinese jujube. Process Biochemistry, 40(11), 3607-3613. doi: 10.1016/j.procbio.2005.03.005.
  • Li, Y., Li, W., & JIN, Y. X. (2005). Computational identification of novel family members of microRNA genes in Arabidopsis thaliana and Oryza sativa. Acta biochimica et Biophysica Sinica, 37(2), 75-87. doi: 10.1111/j.1745-7270.2005.00012.x.
  • Lindquist, S. (1986). The heat-shock response. Annual Review of Biochemistry, 55(1), 1151-1191.
  • Lu, Y., Liu, L., Wang, X., Han, Z., Ouyang, B., Zhang, J., & Li, H. (2016). Genome-wide identification and expression analysis of the expansin gene family in tomato. Molecular Genetics and Genomics, 291(2), 597-608. doi: 10.1007/s00438-015-1133-4.
  • Lynch, M., & Conery, J. S. (2000). The evolutionary fate and consequences of duplicate genes. Science, 290(5494), 1151-1155. doi: 10.1126/science.290.5494.1151.
  • Nagaraju, M., Kumar, S. A., Reddy, P. S., Kumar, A., Rao, D. M., & Kavi Kishor, P. B. (2019). Genome-scale identification, classification, and tissue specific expression analysis of late embryogenesis abundant (LEA) genes under abiotic stress conditions in Sorghum bicolor L. PloS One, 14(1), e0209980. doi: 10.1371/journal.pone.0209980.
  • Nollen, E. A., Brunsting, J. F., Roelofsen, H., Weber, L. A., & Kampinga, H. H. (1999). In vivo chaperone activity of heat shock protein 70 and thermotolerance. Molecular and Cellular Biology, 19(3), 2069-2079. doi: 10.1128/mcb.19.3.2069.
  • Pandey, A., Singh, R., Radhamani, J., & Bhandari, D. C. (2010). Exploring the potential of Ziziphus nummularia (Burm. f.) Wight et Arn. from drier regions of India. Genetic Resources and Crop Evolution, 57(6), 929-936. doi: 10.1007/s10722-010-9566-4.
  • Panzade, K. P., Kale, S. S., Chavan, N. R., & Hatzade, B. (2021). Genome-wide analysis of Hsp70 and Hsp100 gene families in Ziziphus jujuba. Cell Stress and Chaperones, 26(2), 341-353. doi: 10.1007/s12192-020-01179-w.
  • Pelham, H. R. (1986). Speculations on the functions of the major heat shock and glucose-regulated proteins. Cell, 46(7), 959-961.
  • Sabehat, A., Lurie, S., & Weiss, D. (1998). Expression of small heat-shock proteins at low temperatures: a possible role in protecting against chilling injuries. Plant Physiology, 117(2), 651-658. https://doi.org/10.1104/pp.117.2.651.
  • Shen, J., Zeng, Y., Zhuang, X., Sun, L., Yao, X., Pimpl, P., & Jiang, L. (2013). Organelle pH in the Arabidopsis endomembrane system. Molecular Plant, 6(5), 1419-1437. https://doi.org/10.1093/mp/sst079.
  • Shukla, P. S., Borza, T., Critchley, A. T., Hiltz, D., Norrie, J., & Prithiviraj, B. (2018). Ascophyllum nodosum extract mitigates salinity stress in Arabidopsis thaliana by modulating the expression of miRNA involved in stress tolerance and nutrient acquisition. PLoS One, 13(10), e0206221. https://doi.org/10.1371/journal.pone.0206221.
  • Singh, R. K., Jaishankar, J., Muthamilarasan, M., Shweta, S., Dangi, A., & Prasad, M. (2016). Genome-wide analysis of heat shock proteins in C 4 model, foxtail millet identifies potential candidates for crop improvement under abiotic stress. Scientific Reports, 6(1), 1-14. https://doi.org/10.1038/srep32641.
  • Srivastava, S., Srivastava, A. K., Suprasanna, P., & D’souza, S. F. (2013). Identification and profiling of arsenic stress-induced microRNAs in Brassica juncea. Journal of Experimental Botany, 64(1), 303-315. https://doi.org/10.1093/jxb/ers333.
  • Suyama, M., Torrents, D., & Bork, P. (2006). PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Research, 34(suppl_2), W609-W612. https://doi.org/10.1093/nar/gkl315.
  • Swindell, W. R., Huebner, M., & Weber, A. P. (2007). Transcriptional profiling of Arabidopsis heat shock proteins and transcription factors reveals extensive overlap between heat and non-heat stress response pathways. BMC Genomics, 8(1), 1-15. https://doi.org/10.1186/1471-2164-8-125.
  • Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., & Kumar, S. (2011). MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution, 28(10), 2731-2739. https://doi.org/10.1093/molbev/msr121
  • Thompson, J. (1997). The CLUSTAL X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucl. Acids Res., 24, 4876-4882. https://doi.org/10.1093/nar/25.24.4876
  • Wang, B., Huang, Q., Venkitasamy, C., Chai, H., Gao, H., Cheng, N., ... & Pan, Z. (2016). Changes in phenolic compounds and their antioxidant capacities in jujube (Ziziphus jujuba Miller) during three edible maturity stages. LWT-Food Science and Technology, 66, 56-62. https://doi.org/10.1016/j.lwt.2015.10.005.
  • Wang, C., Wang, Q., Zhu, X., Cui, M., Jia, H., Zhang, W., ... & Shen, W. (2019). Characterization on the conservation and diversification of miRNA156 gene family from lower to higher plant species based on phylogenetic analysis at the whole genomic level. Functional & Integrative Genomics, 19(6), 933-952. https://doi.org/10.1007/s10142-019-00679-y.
  • Wang, W., Vinocur, B., Shoseyov, O., & Altman, A. (2004). Role of plant heat-shock proteins and molecular chaperones in the abiotic stress response. Trends in Plant Science, 9(5), 244-252. https://doi.org/10.1016/j.tplants.2004.03.006.
  • Waters, E. R., Lee, G. J., & Vierling, E. (1996). Evolution, structure and function of the small heat shock proteins in plants. Journal of Experimental Botany, 47(3), 325-338. https://doi.org/10.1093/jxb/47.3.325.
  • Xu, G., Guo, C., Shan, H., & Kong, H. (2012). Divergence of duplicate genes in exon–intron structure. Proceedings of the National Academy of Sciences, 109(4), 1187-1192. https://doi.org/10.1073/pnas.1109047109.
  • Xu, J., Zheng, Y., Pu, S., Zhang, X., Li, Z., & Chen, J. (2020). Third-generation sequencing found LncRNA associated with heat shock protein response to heat stress in Populus qiongdaoensis seedlings. BMC Genomics, 21(1), 1-14. https://doi.org/10.1186/s12864-020-06979-z.
  • Xu, M. Y., Zhang, L., Li, W. W., Hu, X. L., Wang, M. B., Fan, Y. L., ... & Wang, L. (2014). Stress-induced early flowering is mediated by miR169 in Arabidopsis thaliana. Journal of Experimental Botany, 65(1), 89-101. https://doi.org/10.1093/jxb/ert353.
  • Yer, E. N., Baloglu, M. C., & Ayan, S. (2018). Identification and expression profiling of all Hsp family member genes under salinity stress in different poplar clones. Gene, 678, 324-336. https://doi.org/10.1016/j.gene.2018.08.049
  • Young, J. C., Moarefi, I., & Hartl, F. U. (2001). Hsp90: a specialized but essential protein-folding tool. The Journal of Cell Biology, 154(2), 267. https://doi.org/10.1083/jcb.200104079.
  • Yu, N., Niu, Q. W., Ng, K. H., & Chua, N. H. (2015). The role of miR156/SPL s modules in Arabidopsis lateral root development. The Plant Journal, 83(4), 673-685. https://doi.org/10.1111/tpj.12919.
  • Yu, Y., Ni, Z., Wang, Y., Wan, H., Hu, Z., Jiang, Q., ... & Zhang, H. (2019). Overexpression of soybean miR169c confers increased drought stress sensitivity in transgenic Arabidopsis thaliana. Plant Science, 285, 68-78. https://doi.org/10.1016/j.plantsci.2019.05.003.
  • Zhang, Y. (2005). miRU: an automated plant miRNA target prediction server. Nucleic Acids Research, 33(suppl_2), W701-W704. https://doi.org/10.1093/nar/gki383.
  • Zhao, Q., Wang, J., Levichkin, I. V., Stasinopoulos, S., Ryan, M. T., & Hoogenraad, N. J. (2002). A mitochondrial specific stress response in mammalian cells. The EMBO Journal, 21(17), 4411-4419. https://doi.org/10.1093/emboj/cdf445.
  • Zhou, L., Liu, Y., Liu, Z., Kong, D., Duan, M., & Luo, L. (2010). Genome-wide identification and analysis of drought-responsive microRNAs in Oryza sativa. Journal of Experimental Botany, 61(15), 4157-4168. https://doi.org/10.1093/jxb/erq237.
  • Zou, J., Liu, C., Liu, A., Zou, D., & Chen, X. (2012). Overexpression of OsHsp17. 0 and OsHsp23. 7 enhances drought and salt tolerance in rice. Journal of Plant Physiology, 169(6), 628-635. https://doi.org/10.1016/j.jplph.2011.12.014
  • Zou, Y., Wang, Y., Wang, L., Yang, L., Wang, R., & Li, X. (2013). miR172b controls the transition to autotrophic development inhibited by ABA in Arabidopsis. PloS One, 8(5), e64770. https://doi.org/10.1371/journal.pone.0064770.
Toplam 66 adet kaynakça vardır.

Ayrıntılar

Birincil Dil İngilizce
Bölüm Makaleler
Yazarlar

Yusuf Ceylan

Kevser Betül Ceylan Bu kişi benim

Yasemin Çelik Altunoğlu Bu kişi benim

Mehmet Cengiz Baloğlu Bu kişi benim

Yayımlanma Tarihi 31 Aralık 2021
Yayımlandığı Sayı Yıl 2021 Cilt: 21 Sayı: 3

Kaynak Göster

APA Ceylan, Y., Ceylan, K. B., Çelik Altunoğlu, Y., Baloğlu, M. C. (2021). Genomic and Functional Characterization of Heat Shock Protein Families in Jujube Genome (Ziziphus jujuba) by in silico Methods. Kastamonu University Journal of Forestry Faculty, 21(3), 277-294. https://doi.org/10.17475/kastorman.1049963
AMA Ceylan Y, Ceylan KB, Çelik Altunoğlu Y, Baloğlu MC. Genomic and Functional Characterization of Heat Shock Protein Families in Jujube Genome (Ziziphus jujuba) by in silico Methods. Kastamonu University Journal of Forestry Faculty. Aralık 2021;21(3):277-294. doi:10.17475/kastorman.1049963
Chicago Ceylan, Yusuf, Kevser Betül Ceylan, Yasemin Çelik Altunoğlu, ve Mehmet Cengiz Baloğlu. “Genomic and Functional Characterization of Heat Shock Protein Families in Jujube Genome (Ziziphus Jujuba) by in Silico Methods”. Kastamonu University Journal of Forestry Faculty 21, sy. 3 (Aralık 2021): 277-94. https://doi.org/10.17475/kastorman.1049963.
EndNote Ceylan Y, Ceylan KB, Çelik Altunoğlu Y, Baloğlu MC (01 Aralık 2021) Genomic and Functional Characterization of Heat Shock Protein Families in Jujube Genome (Ziziphus jujuba) by in silico Methods. Kastamonu University Journal of Forestry Faculty 21 3 277–294.
IEEE Y. Ceylan, K. B. Ceylan, Y. Çelik Altunoğlu, ve M. C. Baloğlu, “Genomic and Functional Characterization of Heat Shock Protein Families in Jujube Genome (Ziziphus jujuba) by in silico Methods”, Kastamonu University Journal of Forestry Faculty, c. 21, sy. 3, ss. 277–294, 2021, doi: 10.17475/kastorman.1049963.
ISNAD Ceylan, Yusuf vd. “Genomic and Functional Characterization of Heat Shock Protein Families in Jujube Genome (Ziziphus Jujuba) by in Silico Methods”. Kastamonu University Journal of Forestry Faculty 21/3 (Aralık 2021), 277-294. https://doi.org/10.17475/kastorman.1049963.
JAMA Ceylan Y, Ceylan KB, Çelik Altunoğlu Y, Baloğlu MC. Genomic and Functional Characterization of Heat Shock Protein Families in Jujube Genome (Ziziphus jujuba) by in silico Methods. Kastamonu University Journal of Forestry Faculty. 2021;21:277–294.
MLA Ceylan, Yusuf vd. “Genomic and Functional Characterization of Heat Shock Protein Families in Jujube Genome (Ziziphus Jujuba) by in Silico Methods”. Kastamonu University Journal of Forestry Faculty, c. 21, sy. 3, 2021, ss. 277-94, doi:10.17475/kastorman.1049963.
Vancouver Ceylan Y, Ceylan KB, Çelik Altunoğlu Y, Baloğlu MC. Genomic and Functional Characterization of Heat Shock Protein Families in Jujube Genome (Ziziphus jujuba) by in silico Methods. Kastamonu University Journal of Forestry Faculty. 2021;21(3):277-94.

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