Identification of HSP60 family gene in the soybean genome and their functional analysis in response to abiotic stresses

Abbas, M., Li, Y., Elbaiomy, R. G., Yan, K., Ragauskas, A. J., Yadav, V., Soaud, S. A., Islam, M. M., Saleem, N., & Noor, Z. (2022). Genome-wide analysis and expression profiling of SlHsp70 gene family in Solanum lycopersicum revealed higher expression of SlHsp70-11 in roots under Cd2+ stress. Frontiers in Bioscience-Landmark, 27(6), 186. Azizi, S., & Zare, N. (2022). Genome-wide identification and functional analysis of lipoxygenase (LOX) gene family in some Fabaceae species using bioinformatics methods. Crop Biotechnology, 11(37), 77-97. Bailey, T. L., Boden, M., Buske, F. A., Frith, M., Grant, C. E., Clementi, L., Ren, J., Li, W. W., & Noble, W. S. (2009). MEME SUITE: tools for motif discovery and searching. Nucleic Acids Research, 37, 202-208. Balchin, D., Hayer-Hartl, M., & Hartl, F. U. (2016). In vivo aspects of protein folding and quality control. Science, 353(6294), aac4354. Braig, K., Otwinowski, Z., Hegde, R., Boisvert, D. C., Joachimiak, A., Horwich, A. L., & Sigler, P. B. (1994). The crystal structure of the bacterial chaperonln GroEL at 2.8 Å. Nature, 371(6498), 578-586. Conesa, A., & Götz, S. (2008). Blast2GO: a comprehensive suite for functional analysis in plant genomics. International Journal of Plant Genomics, 2008, 619832. Ditzel, L., Löwe, J., Stock, D., Stetter, K. O., Huber, H., Huber, R., & Steinbacher, S. (1998). Crystal structure of the thermosome, the archaeal chaperonin and homolog of CCT. Cell, 93(1), 125-138. Finn, R. D., Coggill, P., Eberhardt, R. Y., Eddy, S. R., Mistry, J., Mitchell, A. L., Potter, S. C., Punta, M., Qureshi, M., & Sangrador-Vegas, A. (2015). The Pfam protein families database: towards a more sustainable future. Nucleic Acids Research, 44, 279-285. Gasteiger, E., Hoogland, C., Gattiker, A., Wilkins, M. R., Appel, R. D., & Bairoch, A. (2005). Protein identification and analysis tools on the ExPASy server. In J. M. Walker (Ed.), The proteomics protocols handbook (pp. 571-607). New York City, New York, United States: Humana Press. Guo, M., Liu, J. H., Ma, X., Luo, D. X., Gong, Z. H., & Lu, M. H. (2016). The plant heat stress transcription factors (HSFs): structure, regulation, and function in response to abiotic stresses. Frontiers in Plant Science, 7, 114. Gupta, S. C., Sharma, A., Mishra, M., Mishra, R. K., & Chowdhuri, D. K. (2010). Heat shock proteins in toxicology: how close and how far? Life Sciences, 86(11-12), 377-384. Haq, S. u., Khan, A., Ali, M., Gai, W.-X., Zhang, H. X., Yu, Q. H., Yang, S. B., Wei, A. M., & Gong, Z. H. (2019). Knockdown of CaHSP60-6 confers enhanced sensitivity to heat stress in pepper (Capsicum annuum L.). Planta, 250, 2127-2145. Hartl, F. U., Bracher, A., & Hayer-Hartl, M. (2011). Molecular chaperones in protein folding and proteostasis. Nature, 475(7356), 324-332. Hemmingsen, S. M., Woolford, C., van der Vies, S. M., Tilly, K., Dennis, D. T., Georgopoulos, C. P., Hendrix, R. W., & Ellis, R. J. (1988). Homologous plant and bacterial proteins chaperone oligomeric protein assembly. Nature, 333(6171), 330-334. Hill, J. E., & Hemmingsen, S. M. (2001). Arabidopsis thaliana type I and II chaperonins. Cell Stress & Chaperones, 6(3), 190. Horton, P., Park, K. J., Obayashi, T., Fujita, N., Harada, H., Adams-Collier, C., & Nakai, K. (2007). WoLF PSORT: protein localization predictor. Nucleic Acids Research, 35, 585-587. Hsu, Y. W., Juan, C. T., Wang, C. M., & Jauh, G. Y. (2019). Mitochondrial heat shock protein 60s interact with what’s this factor 9 to regulate RNA splicing of ccmFC and rpl2. Plant and Cell Physiology, 60(1), 116-125. 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. Hu, W., Hu, G., & Han, B. (2009). Genome-wide survey and expression profiling of heat shock proteins and heat shock factors revealed overlapped and stress specific response under abiotic stresses in rice. Plant Science, 176(4), 583-590. Jones, P., Binns, D., Chang, H. Y., Fraser, M., Li, W., McAnulla, C., McWilliam, H., Maslen, J., Mitchell, A., & Nuka, G. (2014). InterProScan 5: genome-scale protein function classification. Bioinformatics, 30(9), 1236-1240. Kawahara, Y., de la Bastide, M., Hamilton, J. P., Kanamori, H., McCombie, W. R., Ouyang, S., Schwartz, D. C., Tanaka, T., Wu, J., & Zhou, S. (2013). Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data. Rice, 6(1), 4. Kelley, L. A., Mezulis, S., Yates, C. M., Wass, M. N., & Sternberg, M. J. (2015). The Phyre2 web portal for protein modeling, prediction and analysis. Nature Protocols, 10(6), 845-858. Kim, S.-R., Yang, J.-I., & An, G. (2013). OsCpn60α1, encoding the plastid chaperonin 60α subunit, is essential for folding of rbcL. Molecules and Cells, 35, 402-409. Kim, T., Samraj, S., Jiménez, J., Gómez, C., Liu, T., & Begcy, K. (2021). Genome-wide identification of heat shock factors and heat shock proteins in response to UV and high intensity light stress in lettuce. BMC Plant Biology, 21, 1-20. Kumar, S., Stecher, G., & Tamura, K. (2016). MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution, 33(7), 1870-1874. Lamesch, P., Berardini, T. Z., Li, D., Swarbreck, D., Wilks, C., Sasidharan, R., Muller, R., Dreher, K., Alexander, D. L., & Garcia-Hernandez, M. (2012). The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic Acids Research, 40(D1), D1202-D1210. Lescot, M., Déhais, P., Thijs, G., Marchal, K., Moreau, Y., Van de Peer, Y., Rouzé, P., & Rombauts, S. (2002). PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Research, 30(1), 325-327. Mantri, N., Patade, V., Penna, S., Ford, R., & Pang, E. (2012). Abiotic stress responses in plants: present and future. Abiotic stress responses in plants: metabolism, productivity and sustainability, 1-19. Mao, D., & Chen, C. (2012). Colinearity and similar expression pattern of rice DREB1s reveal their functional conservation in the cold-responsive pathway. PloS One, 7(10), e47275. Martel, R., Cloney, L. P., Pelcher, L. E., & Hemmingsen, S. M. (1990). Unique composition of plastid chaperonin-60: α and β polypeptide-encoding genes are highly divergent. Gene, 94(2), 181-187. Mohammadi, S., Nematzadeh, G., Najafi Zarrini, H., & Hashemi-petroudi, S. (2022). Abiotic stress-related Cis-elements analysis in promoters of Aeluropus littoralis NAC genes. Journal of Plant Research (Iranian Journal of Biology), 35(3), 632-648. Moore, R. C., & Purugganan, M. D. (2003). The early stages of duplicate gene evolution. Proceedings of the National Academy of Sciences, 100(26), 15682-15687. Nagaraju, M., Kumar, A., Jalaja, N., Rao, D. M., & Kishor, P. (2021). Functional exploration of chaperonin (HSP60/10) family genes and their abiotic stress-induced expression patterns in Sorghum bicolor. Current Genomics, 22(2), 137-152. Nishio, K., Hirohashi, T., & Nakai, M. (1999). Chloroplast chaperonins: evidence for heterogeneous assembly of α and β Cpn60 polypeptides into a chaperonin oligomer. Biochemical and Biophysical Research Communications, 266(2), 584-587. Pareek, A., Sopory, S. K., & Bohnert, H. J. (2010). Abiotic stress adaptation in plants (Vol. 10). Berlin: Springer Dordrecht. Peng, L., Fukao, Y., Myouga, F., Motohashi, R., Shinozaki, K., & Shikanai, T. (2011). A chaperonin subunit with unique structures is essential for folding of a specific substrate. PLoS Biology, 9(4), e1001040. Prasad, T. K., Hack, E., & Hallberg, R. L. (1990). Function of the maize mitochondrial chaperonin hsp60: specific association between hsp60 and newly synthesized F1-ATPase alpha subunits. Molecular and Cellular Biology, 10(8):3979-3986. Prasad, T. K., & Stewart, C. R. (1992). cDNA clones encoding Arabidopsis thaliana and Zea mays mitochondrial chaperonin HSP60 and gene expression during seed germination and heat shock. Plant Molecular Biology, 18, 873-885. Rao, P. K., Roxas, B. A., & Li, Q. (2008). Determination of global protein turnover in stressed mycobacterium cells using hybrid-linear ion trap-fourier transform mass spectrometry. Analytical Chemistry, 80(2), 396-406. Ruggero, D., Ciammaruconi, A., & Londei, P. (1998). The chaperonin of the archaeon Sulfolobus solfataricus is an RNA-binding protein that participates in ribosomal RNA processing. The EMBO Journal, 17(12), 3471-3477. Saibil, H. R., Fenton, W. A., Clare, D. K., & Horwich, A. L. (2013). Structure and allostery of the chaperonin GroEL. Journal of Molecular Biology, 425(9), 1476-1487. Saraei, F., Amini, K., Haddadi, A., & Larypoor, M. (2021). In search of Zrt1 gene expression changes in Saccharomyces cerevisiae under different concentrations of zinc in medium. Cellular and Molecular Research (Iranian Journal of Biology), 34(3), 397-411. Scherf, U., Ross, D.T., Waltham, M., Smith, L.H., Lee, J.K., Tanabe, L., Kohn, K.W., Reinhold, W.C., Myers, T.G., & Andrews, D.T. (2000). A gene expression database for the molecular pharmacology of cancer. Nature Genetics, 24(3), 236-244. Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J.T., Ramage, D., Amin, N., Schwikowski, B., & Ideker, T. (2003). Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Research, 13(11), 2498-2504. Singh, R. K., Jaishankar, J., Muthamilarasan, M., Shweta, S., Dangi, A., & Prasad, M. (2016). Genome-wide analysis of heat shock proteins in C4 model, foxtail millet identifies potential candidates for crop improvement under abiotic stress. Scientific Reports, 6(1), 32641. Szklarczyk, D., Gable, A. L., Lyon, D., Junge, A., Wyder, S., Huerta-Cepas, J., Simonovic, M., Doncheva, N. T., Morris, J. H., & Bork, P. (2019). STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Research, 47(D1), D607-D613. Taj, G., Agarwal, P., Grant, M., & Kumar, A. (2010). MAPK machinery in plants: recognition and response to different stresses through multiple signal transduction pathways. Plant Signaling & Behavior, 5(11), 1370-1378. Thompson, J. D., Gibson, T. J., & Higgins, D. G. (2003). Multiple sequence alignment using ClustalW and ClustalX. Current Protocols in Bioinformatics, 1, 2-3. Tran, L.-S. P., Nakashima, K., Sakuma, Y., Simpson, S. D., Fujita, Y., Maruyama, K., Fujita, M., Seki, M., Shinozaki, K., & Yamaguchi-Shinozaki, K. (2004). Isolation and functional analysis of Arabidopsis stress-inducible NAC transcription factors that bind to a drought-responsive cis-element in the early responsive to dehydration stress 1 promoter. The Plant Cell, 16(9), 2481-2498. Turhan, E., Ergin, S., Aydogan, C., & Ozturk, N. (2016). Influence of grafting on heat shock proteins of tomato (Lycopersicon esculentum Mill) plants under heat stress. Journal of Biotechnology(231), S27. Vaughan, M. M., Block, A., Christensen, S. A., Allen, L. H., & Schmelz, E. A. (2018). The effects of climate change associated abiotic stresses on maize phytochemical defenses. Phytochemistry Reviews, 17, 37-49. Vierling, E. (1991). The roles of heat shock proteins in plants. Annual Review of Plant Biology, 42(1), 579-620. Voorrips, R. (2002). MapChart: software for the graphical presentation of linkage maps and QTLs. Journal of Heredity, 93(1), 77-78. 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. Weiss, C., Bonshtien, A., Farchi-Pisanty, O., Vitlin, A., & Azem, A. (2009). Cpn20: siamese twins of the chaperonin world. Plant Molecular Biology, 69, 227-238. Wilson, R. H., & Hayer-Hartl, M. (2018). Complex chaperone dependence of Rubisco biogenesis. Biochemistry, 57(23), 3210-3216. Xu, C., & Huang, B. (2010). Comparative analysis of drought responsive proteins in Kentucky bluegrass cultivars contrasting in drought tolerance. Crop Science, 50(6), 2543-2552. 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. Zhang, J., Liu, B., Li, J., Zhang, L., Wang, Y., Zheng, H., Lu, M., & Chen, J. (2015). Hsf and Hsp gene families in Populus: genome-wide identification, organization and correlated expression during development and in stress responses. BMC Genomics, 16(1), 1-19. Zhang, L., Zhao, H. K., Dong, Q. l., Zhang, Y. Y., Wang, Y. M., Li, H. Y., Xing, G. J., Li, Q. Y., & Dong, Y. S. (2015). Genome-wide analysis and expression profiling under heat and drought treatments of HSP70 gene family in soybean (Glycine max L.). Frontiers in Plant Science, 6, 773.