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Research Articles

In silico identification and evaluation of Bacillus subtilis cold shock protein B (cspB)-like plant RNA chaperones

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Pages 841-850 | Received 05 Sep 2019, Accepted 15 Jan 2020, Published online: 12 Feb 2020

References

  • Abraham M. J., Spoel, D. V D., Lindahl, E., Hess, B., & the GROMACS development team. (2014). GROMACS User Manual version 5.0.4. www.gromacs.org.
  • Barthel, D., Hirst, J. D., Błazewicz, J., Burke, E. K., & Krasnogor, N. (2007). ProCKSI: A decision support system for protein (structure) comparison, knowledge, similarity and information. BMC Bioinformatics, 8, 416. doi:10.1186/1471-2105-8-416
  • Berman, H. M. (2000). The protein data bank. Nucleic Acids Research, 28(1), 235–242. doi:10.1093/nar/28.1.235
  • Bhadauriya, P., Yadav, B. S., Singh, S., & Mani, A. (2017). Binding preferential of chickpea cold shock protein during nucleic acid interactions. Journal of Plant Biochemistry and Biotechnology, 26(2), 208–215. doi:10.1007/s13562-016-0383-5
  • Boratyn, G. M., Schäffer, A. A., Agarwala, R., Altschul, S. F., Lipman, D. J., & Madden, T. L. (2012). Domain enhanced lookup time accelerated BLAST. Biology Direct, 7(1), 12. doi:10.1186/1745-6150-7-12
  • Burney, J., & Ramanathan, V. (2014). Recent climate and air pollution impacts on Indian agriculture. Proceedings of the National Academy of Sciences, 111(46), 16319–16324. doi:10.1073/pnas.1317275111
  • Castiglioni, P., Warner, D., Bensen, R. J., Anstrom, D. C., Harrison, J., Stoecker, M., … Heard, J. E. (2008). Bacterial RNA chaperones confer abiotic stress tolerance in plants and improved grain yield in maize under water-limited conditions. Plant Physiology, 147(2), 446–455. doi:10.1104/pp.108.118828
  • Chaikam, V., & Karlson, D. T. (2010). Comparison of structure, function and regulation of plant cold shock domain proteins to bacterial and animal cold shock domain proteins. BMB Reports, 43(1), 1–8. doi:10.5483/BMBRep.2010.43.1.001
  • Crooks, G. E., Hon, G., Chandonia, J. M., & Brenner, S. E. (2004). WebLogo: A sequence logo generator. Genome Research, 14(6), 1188–1190. doi:10.1101/gr.849004
  • de Vries, S. J., Dijk, M. V., & Bonvin, A. M. J. J. (2010). The HADDOCK web server for data-driven biomolecular docking. Nature Protocols, 5(5), 883–897. doi:10.1038/nprot.2010.32
  • FAO, IFAD, UNICEF, WFP & WHO. (2018). The State of Food Security and Nutrition in the World 2018. Building climate resilience for food security and nutrition. Rome: FAO.
  • Graumann, P. L., & Marahiel, M. A. (1998). A superfamily of proteins that contain the cold-shock domain. Trends in Biochemical Sciences, 23(8), 286–290. doi:10.1016/S0968-0004(98)01255-9
  • Hall, T. (2011). BioEdit: An important software for molecular biology software review. GERF Bulletin of Biosciences, 2(1), 60–61.
  • Huang, X., & Zhou, H. X. (2006). Similarity and difference in the unfolding of thermophilic and mesophilic cold shock proteins studied by molecular dynamics simulations. Biophysical Journal, 91(7), 2451–2463. doi:10.1529/biophysj.106.082891
  • Jones, D. T., Taylor, W. R., & Thornton, J. M. (1992). The rapid generation of mutation data matrices from protein sequences. Bioinformatics, 8, 275–282. doi:10.1093/bioinformatics/8.3.275
  • Karlson, D., & Imai, R. (2003). Conservation of the cold shock domain protein family in plants. Plant Physiology, 131(1), 12–15. doi:10.1104/pp.014472
  • Katiyar, A., Smita, S., Muthusamy, S. K., Chinnusamy, V., Pandey, D. M., & Bansal, K. C. (2015). Identification of novel drought-responsive microRNAs and trans-acting SiRNAs from Sorghum Bicolor (L.) Moench by high-throughput sequencing analysis. Frontiers in Plant Science, 6, 506. doi:10.3389/fpls.2015.00506
  • Khush, G. S. (2005). What it will take to feed 5.0 billion rice consumers in 2030. Plant Molecular Biology, 59(1), 1–6. doi:10.1007/s11103-005-2159-5
  • Kim, M.-H., Sato, S., Sasaki, K., Saburi, W., Matsui, H., & Imai, R. (2013). COLD SHOCK DOMAIN PROTEIN 3 is involved in salt and drought stress tolerance in arabidopsis. FEBS Open Bio, 3(1), 438–442. doi:10.1016/j.fob.2013.10.003
  • Kohno, K., Izumi, H., Uchiumi, T., Ashizuka, M., & Kuwano, M. (2003). The pleiotropic functions of the Y-box-binding protein, YB-1. BioEssays, 25(7), 691–698. doi:10.1002/bies.10300
  • Krishna Kumar, K., Rupa Kumar, K., Ashrit, R. G., Deshpande, N. R., & Hansen, J. W. (2004). Climate impacts on Indian agriculture. International Journal of Climatology, 24(11), 1375–1393. doi:10.1002/joc.1081
  • Krzywinski, M., Schein, J., Birol, I., Connors, J., Gascoyne, R., Horsman, D., … Marra, M. A. (2009). Circos: An information aesthetic for comparative genomics. Genome Research, 19(9), 1639–1645. doi:10.1101/gr.092759.109
  • 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. doi:10.1093/molbev/msw054
  • Laskowski, R. A., Jabłońska, J., Pravda, L., Vařeková, R. S., & Thornton, J. M. (2018). PDBsum: structural summaries of PDB entries. Protein Science, 27(1), 129–134. doi:10.1002/pro.3289
  • Leng, G., & Hall, J. (2019). Crop yield sensitivity of global major agricultural countries to droughts and the projected changes in the future. Science of the Total Environment, 654, 811–821. doi:10.1016/j.scitotenv.2018.10.434
  • Lesk, C., Rowhani, P., & Ramankutty, N. (2016). Influence of extreme weather disasters on global crop production. Nature, 529(7584), 84–87. doi:10.1038/nature16467
  • Li, Z., Natarajan, P., Ye, Y., Hrabe, T., & Godzik, A. (2014). POSA: A user-driven, interactive multiple protein structure alignment server. Nucleic Acids Research, 42(W1), W240–W245. doi:10.1093/nar/gku394
  • Lobell, D. B., Schlenker, W., & Costa-Roberts, J. (2011). Climate trends and global crop production since 1980. Science, 333(6042), 616–620. doi:10.1126/science.1204531
  • Lyabin, D. N., Eliseeva, I. A., & Ovchinnikov, L. P. (2014). YB-1 protein: Functions and regulation. Wiley Interdisciplinary Reviews: RNA, 5(1), 95–110. doi:10.1002/wrna.1200
  • Mani, A., & Gupta, D. K. (2015). Single-stranded nucleic acid binding in arabidopsis thaliana cold shock protein is cold shock domain dependent. Journal of Biomolecular Structure and Dynamics, 33(4), 861–868. doi:10.1080/07391102.2014.907747
  • Mani, A., Yadava, P. K., & Gupta, D. K. (2012). Cold shock domain protein from philosamia ricini prefers single-stranded nucleic acids binding. Journal of Biomolecular Structure and Dynamics, 30(5), 532–541. doi:10.1080/07391102.2012.687519
  • Matsumoto, K., Tanaka, K. J., & Tsujimoto, M. (2005). An acidic protein, YBAP1, mediates the release of YB-1 from MRNA and relieves the translational repression activity of YB-1. Molecular and Cellular Biology, 25(5), 1779–1792. doi:10.1128/MCB.25.5.1779-1792.2005
  • Nakaminami, K., Hill, K., Perry, S. E., Sentoku, N., Long, J. A., & Karlson, D. T. (2009). Arabidopsis cold shock domain proteins: Relationships to floral and silique development. Journal of Experimental Botany, 60(3), 1047–1062.
  • Nakaminami, K., Karlson, D. T., & Imai, R. (2006). Functional conservation of cold shock domains in bacteria and higher plants. Proceedings of the National Academy of Sciences of Sciences, 103(26), 10122–10127. doi:10.1073/pnas.0603168103
  • Nakaminami, K., Sasaki, K., Kajita, S., Takeda, H., Karlson, D., Ohgi, K., & Imai, R. (2005). Heat stable SsDNA/RNA-binding activity of a wheat cold shock domain protein. FEBS Letters, 579(21), 4887–4891. doi:10.1016/j.febslet.2005.07.074
  • Pandey, P., Irulappan, V., Bagavathiannan, M. V., & Senthil-Kumar, M. (2017). Impact of combined abiotic and biotic stresses on plant growth and avenues for crop improvement by exploiting physio-morphological traits. Frontiers in Plant Science, 8, 537. doi:10.3389/fpls.2017.00537
  • Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004). UCSF chimera - A visualization system for exploratory research and analysis. Journal of Computational Chemistry, 25(13), 1605–1612. doi:10.1002/jcc.20084
  • Prasanna, V. (2014). Impact of monsoon rainfall on the total foodgrain yield over India. Journal of Earth System Science, 123(5), 1129–1145. doi:10.1007/s12040-014-0444-x
  • Roy, A., Kucukural, A., & Zhang, Y. (2010). I-TASSER: A unified platform for automated protein structure and function prediction. Nature Protocols, 5(4), 725–738. doi:10.1038/nprot.2010.5
  • Sasaki, K., & Imai, R. (2012). Pleiotropic roles of cold shock domain proteins in plants. Frontiers in Plant Science, 2, 116. doi:10.3389/fpls.2011.00116
  • Sasaki, K., Kim, M.-H., Kanno, Y., Seo, M., Kamiya, Y., & Imai, R. (2015). Arabidopsis cold shock domain protein 2 influences ABA accumulation in seed and negatively regulates germination. Biochemical and Biophysical Research Communications, 456(1), 380–384. doi:10.1016/j.bbrc.2014.11.092
  • Schleussner, C.-F., Deryng, D., Müller, C., Elliott, J., Saeed, F., Folberth, C., … Rogelj, J. (2018). Crop productivity changes in 1.5 °C and 2 °C worlds under climate sensitivity uncertainty. Environmental Research Letters, 13(6), 064007. doi:10.1088/1748-9326/aab63b
  • Senapati, N., Stratonovitch, P., Paul, M. J., & Semenov, M. A. (2019). Drought tolerance during reproductive development is important for increasing wheat yield potential under climate change in Europe. Journal of Experimental Botany, 70(9), 2549–2560. doi:10.1093/jxb/ery226
  • Singh, C., Kumar, B., Mehandi, S., & Chandra, K. (2012). Effect of drought stress in rice: A review on morphological and physiological characteristics. Trends in Biosciences, 5, 261–265.
  • Sippl, M. J. (1993). Recognition of errors in three‐dimensional structures of proteins. Proteins: Structure, Function, and Genetics, 17(4), 355–362. doi:10.1002/prot.340170404
  • Smita, S., Katiyar, A., Chinnusamy, V., Pandey, D. M., & Bansal, K. C. (2015). Transcriptional Regulatory network analysis of MYB transcription factor family genes in rice. Frontiers in Plant Science, 6, 1157. doi:10.3389/fpls.2015.01157
  • Sommerville, J., & Ladomery, M. (1996). Transcription and masking of MRNA in germ cells: Involvement of Y-box proteins. Chromosoma, 104(7), 469–478. doi:10.1007/BF00352111
  • Thompson, J. D., Higgins, D. G., & Gibson, T. J. (1994). CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research, 22(22), 4673–4680. doi:10.1093/nar/22.22.4673
  • Van Der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E., & Berendsen, H. J. C. (2005). GROMACS: Fast, flexible, and free. Journal of Computational Chemistry, 26(16), 1701–1718. doi:10.1002/jcc.20291
  • Vikram, P., Swamy, B. P. M., Dixit, S., Singh, R., Singh, B. P., Miro, B., … Kumar, A. (2015). Drought susceptibility of modern rice varieties: An effect of linkage of drought tolerance with undesirable traits. Scientific Reports, 5(1), 14799. doi:10.1038/srep14799
  • Wang, Z., Lin, L., Zhang, X., Zhang, H., Liu, L., & Xu, Y. (2017). Scenario dependence of future changes in climate extremes under 1.5°C and 2°C global warming. Scientific Reports, 7. Retrieved from https://doi.org/10.1038/srep46432.
  • Wheeler, T., & Braun, J. V. (2013). Climate change impacts on global food security. Science , 341(6145), 508–513. doi:10.1126/science.1239402
  • Wiederstein, M., & Sippl, M. J. (2007). ProSA-web: Interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Research, 35(suppl_2), W407–W410. doi:10.1093/nar/gkm290
  • Yang, X. (2019). The different influences of drought stress at the flowering stage on rice physiological traits, grain yield, and quality. Scientific Reports, 9(1), 1–12. doi:10.1038/s41598-019-40161-0
  • Yang, J., Roy, A., & Zhang, Y. (2013a). BioLiP: A semi-manually curated database for biologically relevant ligand-protein interactions. Nucleic Acids Research, 41(D1), D1096–D1103. doi:10.1093/nar/gks966
  • Yang, J., Roy, A., & Zhang, Y. (2013b). Protein-ligand binding site recognition using complementary binding-specific substructure comparison and sequence profile alignment. Bioinformatics, 29(20), 2588–2595.
  • Yang, J., Yan, R., Roy, A., Xu, D., Poisson, J., & Zhang, Y. (2015). The I-TASSER suite: Protein structure and function prediction. Nature Methods, 12(1), 7–8. doi:10.1038/nmeth.3213
  • Yu, T. F. (2017). Improved drought tolerance in wheat plants overexpressing a synthetic bacterial cold shock protein gene SeCspA. Scientific Reports, 7, 44050. doi:10.1038/srep44050
  • Yu, C.-S., Chen, Y.-C., Lu, C.-H., & Hwang, J.-K. (2006). Prediction of protein subcellular localization. Proteins: Structure, Function, and Bioinformatics, 64(3), 643–651. doi:10.1002/prot.21018
  • Yu, J., Jiang, M., & Guo, C. (2019). Crop pollen development under drought: From the phenotype to the mechanism. International Journal of Molecular Sciences, 20(7), 1550. doi:10.3390/ijms20071550
  • Yu, C.-S., Lin, C.-J., & Hwang, J.-K. (2004). Predicting subcellular localization of proteins for gram-negative bacteria by support vector machines based on n -peptide compositions. Protein Science, 13(5), 1402–1406. doi:10.1110/ps.03479604
  • Zhang, Y. (2008). I-TASSER server for protein 3D structure prediction. BMC Bioinformatics, 9(1), 40. doi:10.1186/1471-2105-9-40
  • Zhang, Y., & Skolnick, J. (2005). TM-Align: A protein structure alignment algorithm based on the TM-score. Nucleic Acids Research, 33(7), 2302–2309. doi:10.1093/nar/gki524

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