Functional Characterisation of a Calmodulin-Binding Receptor-Like Cytoplasmic Kinase (GmCBRLCK1) in Glycine max (L.) Merr. using Bioinformatic Tools

  • Enetia Disberia Bobo Department of Biological Sciences, Bindura University of Science Education, Bindura, Zimbabwe
  • Pias Munosiyei Department of Biological Sciences, Bindura University of Science Education, Bindura, Zimbabwe
  • Percy Jinga Department of Biological Sciences, Bindura University of Science Education, Bindura, Zimbabwe
  • Emmanuel Zingoni Department of Biological Sciences, Bindura University of Science Education, Bindura, Zimbabwe

Abstract

An understanding of the function of signaling genes/proteins in soybean is vital for comprehending plant growth and development. The objective of this study was to functionally characterize a calmodulin-binding receptor-like cytoplasmic kinase gene (Glyma.13G161700) from Glycine max. Bioinformatic analyses were performed for the characterization. Expression profile of GmCBRLCK1 gene in soybean tissue was assessed using Genevisible. Functional genomic analysis for gene expression regulation and co-expression analysis was evaluated using micro array data from Affymetrix Soybean Genome Array platform in GENEVESTIGATOR v3. Gene ontology functional predictions were determined through FFPred 2.0. The results showed that the calmodulin-binding receptor-like cytoplasmic kinase gene is predominantly expressed in the pericycle and syncytium in root seedlings and in the palisade cells of the legume. The gene was shown to be highly upregulated in response to root exposure to Phytophthora sojae, Heterodera glycines and aluminium stress. Co-expressed genes during the legume development showed Pearson’s correlation co-efficient of 1 to Glyma.13G161700. Gene ontology predictions confirmed the signaling and metabolic functions of the kinase gene and its primary locations are the membrane and endomembrane system of G. max. The study therefore suggests that Glycine max calmodulin-binding receptor-like cytoplasmic kinase (GmCBRLCK1) is involved in receptor signaling pathways to enhance seedling tolerance to root infection by P. sojae, H. glycines, and to aluminium stress. The kinase gene is also involved in regulation of metabolic processes that aid in growth and development of soybean seedling.

Keywords: Calmodulin-binding receptor-like cytoplasmic kinase, Gene, Glycine max, Kinase, Protein, Signaling, Soybean.

Downloads

Download data is not yet available.

References

[1]       T. Yang, S. Chaudhuri, L. Yang, and C. Y. Poovaiah, “Calcium/Calmodulin up-regulates a cytoplasmic receptor-like kinase in plants,”. J. Biol. Chem., vol. 279, pp. 42552-42559, 2004.


[2]        X. Tang, R. D. Frederick, J. Zhou, D. A. Halterman, Y. Jia, and G. B. Martin, “Initiation of plant disease by physical interaction of AvrPto and Pto kinase,” Science., vol. 274, pp. 2060–2063, 1996.


[3]        M. R. Swiderski, R. W. and Innes, “The Arabidopsis PBS1 resistance gene encodes a member of a novel protein kinase subfamily,” Plant J., vol. 26, no. 1, pp. 101–112, 2001.


[4]        Z. Zhang, Y. Liu, H. Huang, M. Gao, D. Wu, Q, Kong, and Y. Zhnag, “The NLR protein SUMM2 senses the disruption of an immune signaling MAP kinase cascade via CRCK3,” EMBO Rep., vol.18, no. 2, pp. 292-302, 2017.


[5]       T.A. DeFalco, D. Chiasson, K. Munro, B.N. Kaiser, and W. A. Snedden, “Characterisation of GmCaMK1, a member of a soybean calmodulin-binding receptor-like kinase family”, FEBS Lett., vol. 584, no 23, pp. 4717–4724, 2010.


[6]        L. Yang, W. Ji, Y. Zhu. P. Gao, Y. Li, H. Cai, X. Bai, D. Guo, “GsCBRLK, a calcium/calmodulin-binding receptor-like kinase, is a positive regulator of plant tolerance to salt and ABA stress,” J. Exp. Biol., vol. 61, no. 9, pp. 2519-2533, 2010.


[7]       J. Schmutz, S. B. Cannon, J. Schlueter, J. Ma, T. Mitros, W. Nelson, D. L. Hyten, Q. Song, J. J. Thelen, J. Cheng, D. Xu, U. Hellsten, G. D. May, Y. Yu, T. Sakurai, T. Umezawa, M. K. Bhattacharyya, D. Sandhu, B. Valliyodan, E. Lindquist, M. Peto, D. Grant, S. Shu, D. Goodstein, K. Barry, M. Futrell-Griggs, B. Abernathy, J. Du, Z. Tian, L. Zhu, N. Gill, T. Joshi, M. Libault, A. Sethuraman, X. C. Zhang, K. Shinozaki, H. T. Nguyen, R. A. Wing, P. Cregan, J Specht, J Grimwood, D. Rokhsar, G. Stacey, R.C. Shoemaker, and S. A. Jackson, “Genome sequence of the palaeopolyploid soybean,” Nature, vol. 463, pp. 178–183, 2010.


[8]       T. K. Attwood, “The quest to deduce protein function from sequence: the role of pattern databases,” Int. J. Biochem. Cell Biol., vol. 32, no. 2, pp. 139–155, 2000.


[9]        T. R. Hvidsten, J. Komoroski, A. K. Sandvik, and A. Leagreid, “Predicting gene function from gene expressions and ontologies,” Pac. Symp on Biocomp., vol. 2001, pp. 299–310, 2001.


[10]     P. Pavlidis, J. Weston, J, Cai, W. N. Grundy, “Gene functional classification from heterogeneous data,” In Proceedings of the Fifth Annual International Conference on Computational Biology, April 22-25, 2001, S. Montreal, M. Istrail, A. Clark, pp. 249-255, 2001


[11]      A. Clare, and R. D. King, “Predicting gene function in Saccharomyces cerevisiae,” Bioinformatics, vol. 19, no. 2, pp. ii42–ii49, 2003.


[12]      R. King, A. Karwath, A. Clare, and L. Dehaspe, L, “The utility of different representations of protein sequence for predicting functional class,” Bioinformatics, vol. 17, no. 5, pp. 445–454, 2001.


[13]     R. D. King, P. H. Wise, and A Clare, “Confirmation of data mining-based predictions of protein function,” Bioinformatics, vol. 20, no. 7, pp. 1110–1118, 2004.


[14]     T. Hruz, O. Laule, G. Szabo, F. Wessendrop, S. Bleuler, L. Oertle, P. Widmayer. W. Gruissem, and P. Zimmermann, “GENEVESTIGATOR v3: a reference expression database for the meta-analysis of Transcriptomes,” Adv. Bioinform., vol 2008, pp. 1–5, 2008.


[15]      F. Minneci, D. Piovesan, D. Cozzetto, and D. T. Jones, “FFPred 2.0: Improved Homology-Independent Prediction of Gene Ontology Terms for Eukaryotic Protein Sequences,”PLoS ONE, vol. 8, e63754, 2013.


[16]      J. E. Malamy, and P. N. Benfey, “Organization and cell differentiation in lateral roots of Arabidopsis thaliana,” Development, vol. 124, no. 1, pp. 33–44, 1997.


[17]      H. Bohlmann. and M. Sobczak, “The plant cell wall in the feeding sites” Front. Plant Sci., vol. 5, pp. 89, 2014.


[18]      I. Gipson, K. S. Kim, and R. D. Riggs, “An ultrastructural study of syncytium development in soybean roots infected with Heterodera glycines,” Phytopathology, vol. 61, pp. 347-353, 1971.


[19]     V. P. Klink, N. Alkharouf, M. MacDonald, and B. Matthews, “Laser capture microdissection (LCM) and expression analyses of Glycine max (soybean) syncytium containing root regions formed by the plant pathogen Heterodera glycines (soybean cyst nematode),”. Plant Mol. Biol., vol. 59, no. 6, pp. 965-979, 2005.


[20]      G. Gheysen, and C. Fenoll, “Gene expression in nematode feeding sites,” Annu. Rev. Phytopathol., vol. 40, pp. 191–219, 2002.


[21]     D. P. Puthoff, D. Nettleton, S.R. Rodermel, and T. J. Baum, “Arabidopsis gene expression changes during cyst nematode parasitism revealed by statistical analyses of microarray expression profiles,”. Plant J., vol. 33, no. 5, pp. 911–921, 2003.


[22]      D. B. Fisher, “An unusual layer of cells in the mesophyll of the soybean leaf,” Bot. Gaz., vol. 128, pp. 215-218, 1967.


[23]      V. R. Franceschi, and R. T. Giaquinta, “The paraveinal mesophyll of soybean leaves in relation to assimilate transfer and compartmentation. Ultrastructure and histochemistry during vegetative development,” Planta, vol. 157, pp. 411- 421, 1983.


[24]      I. Cakmak, and W.J. Horst, “Effect of aluminium on lipid peroxidation, superoxide dismutase, catalase, and peroxidase activities in root tips of soybean (Glycine max),” Physiol. Plant., vol 83, no. 3, pp. 463-468, 1991.


[25]      E. M. Hrabak, C. W. Chan, M. Gribskov, J. F. Harper, J. H. Choi, N. Halford, J. Kudla, S. Luan, H. G.  Nimmo, M. R. Sussman, M. Thomas, K. Walker-Simmons, J. K.  Zhu, and A. C. Harmon, “The Arabidopsis CDPK-SnRK superfamily of protein kinases,” Plant Physiol., vol. 132, pp. 666–680, 2003.


[26]     S. K. Hanks, and T. Hunter, Protein kinases 6. “The eukaryotic protein kinase superfamily: kinase (catalytic) domain structure and classification,” FASEB J., vol. 9, no. 8, pp. 576–596, 1995.


[27]      J. M. Stone, and J. C. Walker, “Plant protein kinase families and signal transduction,” Plant Physiol., vol. 108, pp. 451–457, 1995.


[28]      D. Francis, “The plant cell cycle: 15 years on,” New Phytol., vol. 174, no. 2, pp. 261–278, 2007.


[29]     M. C. Rodriguez, M. Petersen, and J. Mundy, “Mitogen-activated protein kinase signaling in plants,”. Annu. Rev. Plant Biol., vol. 61 pp. 621–649, 2010.


[30]      L. A Gish, and S. E. Clark, “The RLK/Pelle family of kinases,” Plant J., vol. 66 no. 1 pp. 117–127, 2011.


[31]      Y. Xia, H. Suzuki, J. Borevitz, J. Blount, Z. Guo, K. Patel, R. A. Dixon, and C. Lamb, “An extracellular aspartic protease functions in Arabidopsis disease resistance signaling,” EMBO J., vol. 23 no. 4 pp. 980-988, 2004.


[32]      H. H Breitenbach, M. Wenig, F. Wittek, L. Jorda, A. A. Maldonado-Alconada H. Sarioglu, T. Colby, C. Knappe M. Bichlmeier E. Pbst D. Mackey, J. E. Parker and C. Vlot, “Contrasting roles of the apoplastic aspartyl protease apoplastic, enhanced disease susceptibility1-dependent1 and legume lectin-like protein1 in Arabidopsis systemic acquired resistance,” Plant Physiol., vol. 165 no. 2 pp. 791–809, 2014.


[33]      N. Niu, W. Liang, X. Yang, W. Jin, Z. A.  Wilson, J. Hu, and D. Zhang, “EAT1 promotes tapetal cell death by regulating aspartic proteases during male reproductive development in rice,” Nat. Commun., vol. 4, pp. 1445, 2013.


[34]      A. Ambrosone, A. Costa, A. Leone, and S. Grillo, “Beyond transcription: RNA-binding proteins as emerging regulators of plant response to environmental constraints,” Plant Sci., vol. 182, pp. 12–18, 2012.


[35]      Z. Lorkoviċ, “Role of plant RNA-binding proteins in development, stress response and genome organization” Trends Plant Sci., vol. 4, pp. no. 4, 229-236, 2009.


[36]      S. Raab, T. Zsolt, C. Groot, T. Stamminger, and S. Hoth, “ABA-responsive RNA-binding proteins are involved in chloroplast and stromule function in Arabidopsis seedlings,” Planta, vol. 224, no. 4, pp. 900-914, 2006.


[37]     J. Bertomeu, B, Minana, J. S. Mulet. E. Fernandez, J. Romero, J. M. Kuhn, J. Segura, and R. Ros, “Plastidial glyceraldehyde-3-phosphate dehydrogenase deficiency leads to altered root development and affects the sugar and amino acid balance in ArabidopsisPlant Physiol., vol.151, no. 2, pp. 541-558, 2009.


[38]     F. Marty, “Plant vacuoles,” Plant Cell, vol. 11, pp.587–600, 1999.


[39]     E. Martinoia, M. Maeshima, and H. E. Neuhaus, “Vacuolar transporters and their essential role in plant metabolism,”J Exp Bot., vol. 58, no. 1, pp. 83–102, 2007.


[40]      L. Frigerio, and C. Hawes, “The endomembrane system: a green perspective”. Traffic., vol. 9, pp. 1563, 2008.


[41]      J. B. Dacks, A. A. Peden, and M. C. Field, “Evolution of specificity in the eukaryotic endomembrane system” J Biochem Cell Biol., vol. 41, no. 2, pp. 330–340, 2009.


[42]      M. Surpin, and N. Raikhel, “Traffic jams affect plant development and signal transduction” Nat Rev Mol Cell Biol., vol. 5, no. 2, pp. 100–109, 2004.


[43]      H. Itzhaki, L. Naveh, M. Lindahl, M. Cook, and Z. Adams, “Identification and characterisation of DegP, a serine protease associated with the luminal side of the thylakoid membrane,” J. Biol Chem., vol. 273, no. 12, pp. 7094-7098, 1998.


[44]      B. Lipinska, M. Zylicz, and C. Georgopoulos, “The HtrA (DegP) protein, essential for Escherichia coli survival at high temperatures, is an endopeptidase,” J. Bacteriol., vol. 172, no. 4, pp. 1791–1797, 1990.

Published
2019-05-24
How to Cite
[1]
E. Bobo, P. Munosiyei, P. Jinga, and E. Zingoni, “Functional Characterisation of a Calmodulin-Binding Receptor-Like Cytoplasmic Kinase (GmCBRLCK1) in Glycine max (L.) Merr. using Bioinformatic Tools”, Int. Ann. Sci., vol. 7, no. 1, pp. 38-47, May 2019.
Section
Research Article