Single-stranded nucleic acid binding in Arabidopsis thaliana cold shock protein is cold shock domain dependent

References

• Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W., & Lipman, D. J. (1997). Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Research, 25, 3389–3402.10.1093/nar/25.17.3389
   PubMed Web of Science ®Google Scholar
• Chaikam, V., & Karlson, D. (2008). Functional characterization of two cold shock domain proteins from Oryza sativa. Plant, Cell and Environment, 31, 995–1006.10.1111/j.1365-3040.2008.01811.x
   PubMed Web of Science ®Google Scholar
• Dominguez, C., Boelens, R., & Bonvin, A. M. J. J. (2003). HADDOCK: A protein-protein docking approach based on biochemical and/or biophysical information. Journal of American Chemical Society, 125, 1731–1737.10.1021/ja026939x
   PubMed Web of Science ®Google Scholar
• Fusaro, A. F., Bocca, S. N., Ramos, R. L., Barroco, R. M., Magioli, C., Jorge, V. C., … Sachetto-Martins, G. (2007). AtGRP2, a cold-induced nucleo-cytoplasmic RNA-binding protein, has a role in flower and seed development. Planta, 225, 1339–1351.10.1007/s00425-006-0444-4
   PubMed Web of Science ®Google Scholar
• Graumann, P. L., & Marahiel, M. A. (1998). Superfamily of proteins that contain the cold-shock domain. Trends in Biochemical Sciences, 23, 286–290.10.1016/S0968-0004(98)01255-9
   PubMed Web of Science ®Google Scholar
• Karlson, D., & Imai, R. (2003). Conservation of the cold shock domain protein family in plants. Plant Physiology, 131, 12–15.10.1104/pp.014472
   PubMed Web of Science ®Google Scholar
• Karlson, D., Nakaminami, K., Toyomasu, T., & Imai, R. (2002). A cold-regulated nucleic acid-binding protein of winter wheat shares a domain with bacterial cold shock proteins. Journal of Biological Chemistry, 277, 35248–35256.10.1074/jbc.M205774200
   PubMed Web of Science ®Google Scholar
• Kim, J. S., Park, S. J., Kwak, K. J., Kim, Y. O., Kim, J. Y., Song, J., … Kang, H. (2007). Cold shock domain proteins and glycine-rich RNA-binding proteins from Arabidopsis thaliana can promote the cold adaptation process in Escherichia coli. Nucleic Acids Research, 35, 506–516.
   PubMed Web of Science ®Google Scholar
• Kim, M. H., Sasaki, K., & Imai, R. (2009). Cold shock domain protein 3 regulates freezing tolerance in Arabidopsis thaliana. Journal of Biological Chemistry, 284, 23454–23460.10.1074/jbc.M109.025791
   PubMed Web of Science ®Google Scholar
• Kim, M. H., Satoa, S., Sasakia, K., Saburic, W., Matsuic, H., & Imaia, R. (2013). Cold shock domain protein 3 is involved in salt and drought stress tolerance in Arabidopsis. FEBS Open Biology, 3, 438–442.10.1016/j.fob.2013.10.003
   PubMed Web of Science ®Google Scholar
• Kingsley, D. P., & Palis, J. (1994). GRP2 protein contain both CCHC fingers and a cold shock domain. Plant Cell, 6, 1522–1523.
   PubMed Web of Science ®Google Scholar
• Kohno, K., Izumi, H., Uchiumi, T., Ashizuka, M., & Kuwano, M. (2003). The pleiotropic functions of the Y-box-binding protein, YB-1. BioEssays, 25, 691–698.10.1002/(ISSN)1521-1878
   PubMed Web of Science ®Google Scholar
• Larkin, M. A., Blackshieds, G., Brown, N. P., Chenna, R., McGettigan, P. A., McWilliam, H., … Higgins, D. G. (2007). ClustalW and ClustalX version 2. Bioinformatics, 23, 2947–2948.10.1093/bioinformatics/btm404
   PubMed Web of Science ®Google Scholar
• Laskowski, R. A., Macarthur, M. W., Moss, D. S., & Thornton, J. M. (1993). PROCHECK: A program to check the stereochemical quality of protein structures. Journal of Applied Crystallography, 26, 283–291.10.1107/S0021889892009944
   Web of Science ®Google Scholar
• Mani, A., Yadava, P. K., & Gupta, D. K. (2012). Cold shock domain protein from Philosamia ricini prefers single starnded nucleic acid binding. Journal of Biomolecular Structure and Dynamics, 30, 532–541.10.1080/07391102.2012.687519
   PubMed Web of Science ®Google Scholar
• Morgan, H. P., Mcnae, I., Wear, M. A., Gallagher, M., & Walkinshaw, M. D. (2009). Crystallization and X-ray structure of cold-shock protein E from Salmonella typhimurium. Acta Crystallographica Section F Structural Biology and Crystallization Communications, 65, 1240–1245.10.1107/S1744309109033788
   PubMed Web of Science ®Google Scholar
• 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, USA, 103, 10122–10127.10.1073/pnas.0603168103
   PubMed Web of Science ®Google Scholar
• 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 Experimental Botany, 60, 1047–1062.10.1093/jxb/ern351
   PubMed Web of Science ®Google Scholar
• Nam, Y., Chen, C., Greogory, R. I., Chou, J. J., & Sliz, P. (2011). Molecular basis for interaction of Let-7 molecular basis for interaction of let-7 microRNAs with Lin28. Cell, 147, 1080–1091.10.1016/j.cell.2011.10.020
   PubMed Web of Science ®Google Scholar
• Nei, M., & Kumar, S. (2000). Molecular evolution and phylogenetics. New York, NY: Oxford University Press.
   Google Scholar
• Park, S. J., Kwak, K. J., Oh, T. R., Kim, Y. O., & Kang, H. (2009). Cold shock domain proteins affect seed germination and growth of Arabidopsis thaliana under abiotic stress conditions. Plant Cell and Physiology, 50, 869–878.10.1093/pcp/pcp037
   PubMed Web of Science ®Google Scholar
• Šali, A., & Blundell, T. L. (1993). Comparative protein modelling by satisfaction of spatial restraints. Journal of Molecular Biology, 234, 779–815.
   PubMed Web of Science ®Google Scholar
• Sánchez, R., & Šali, A. (2000). Comparative protein structure modeling: Introduction and practical examples with MODELLER. In: D. M. Webster (Ed.), Protein structure prediction: Methods and protocols (pp. 97–129). New Jersey, NJ: Humana Press.
   Google Scholar
• Sasaki, K., Kim, M. H., & Imai, R. (2007). Arabidopsis COLD SHOCK DOMAIN PROTEIN2 is a RNA chaperone that is regulated by cold and developmental signals. Biochemical and Biophysical Research Communications, 364, 633–638.10.1016/j.bbrc.2007.10.059
   PubMed Web of Science ®Google Scholar
• Sommerville, J. (1999). Activities of cold-shock domain proteins in translational control. BioEssays, 21, 319–325.10.1002/(SICI)1521-1878(199904)21:4<>1.0.CO;2-T
   PubMed Web of Science ®Google Scholar
• 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, 2731–2739.10.1093/molbev/msr121
   PubMed Web of Science ®Google Scholar
• de Vries, S. J., van Dijk, A. D. J., Krzeminski, M., van Dijk, M., Thureau, A., Hsu, V., … Bonvin, A. M. J. J. (2007). HADDOCK versus HADDOCK: New features and performance of HADDOCK2.0 on the CAPRI targets. Proteins: Structure, Function & Bioinformatics, 69, 726–733.
   PubMed Web of Science ®Google Scholar
• Wolffe, A. P. (1994). Structural and functional properties of the evolutionarily ancient Y-box family of nucleic acid binding proteins. BioEssays, 16, 245–251.10.1002/(ISSN)1521-1878
   PubMed Web of Science ®Google Scholar
• Wolffe, A. P., Tafuri, S., Ranjan, M., & Familiari, M. (1992). The Y-box factors: A family of nucleic acid binding proteins conserved from Escherichia coli to man. The New Biologist, 4, 290–298.
   PubMedGoogle Scholar
• Yang, Y., & Karlson, D. T. (2011). Over-expression of AtCSP4 affects late stages of embryo development in Arabidopsis. Journal of Experimental Botany, 62, 2079–2091.10.1093/jxb/erq400
   PubMed Web of Science ®Google Scholar
• Yang, Y., & Karlson, D. (2012). Effects of mutations in the Arabidopsis cold shock domain protein 3 (AtCSP3) gene on leaf cell expansion. Journal Experimental Botany, 63, 4861–4873.10.1093/jxb/ers160
   PubMed Web of Science ®Google Scholar