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A Machine Learning Approach for Prediction of Domains of DELLA Proteins, a Key Component of Gibberellic Acid Signaling in Plants

Affiliations

  • ICAR-Central Plantation Crops Research Institute, Kasaragod - 671124, Kerala, India
  • AIMIT, St. Aloysius College, Mangalore - 575002, Karnataka
  • ICAR-Central Plantation Crops Research Institute, Kasaragod - 671124, Kerala

Abstract


Background/Objective: For the annotation of large scale proteins, generally computational methods or tools are used. One of the drawbacks of these annotation tools is that they are not specific protein prediction programs. Methods/Analysis: In this study, we implement a machine-learning algorithm for fast and accurate prediction of DELLA proteins. Findings: We developed various modules by using conserved protein domains in DELLA proteins. To evaluate the modules classifiers like sequential minimum optimization, J48 decision tree, AD tree and logistic algorithms were used. By analyzing the results obtained from independent data set and cross-validation tests, maximum accuracy was achieved by logistic algorithm. The developed tool was tested with various inputs and it's showed that the algorithm developed in the study would be helpful in predicting plant DELLA domains. Applications: This tool will significantly contribute to deep level functional genome annotation and development of predictors.

Keywords

Algorithms, Coconut, DELLA, Domains, Machine Learning, Prediction

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References


  • Daviere JM, Achard P. Gibberellin signaling in plants. Development. 2013 Mar; 140(6):1147–51.
  • Hauvermale AL, Ariizumi T, Steber CM. Gibberellin signaling: A theme and variations on DELLA repression. Plant Physiol. 2012 Sep; 160(1):83–92.
  • Silverstone AL, Jung HS, Dill A, Kawaide H, Kamiya Y, Sun TP. Repressing a repressor: Gibberellin-induced rapid reduction of the RGA protein in Arabidopsis. Plant Cell. 2001 Jul; 13(7):1555–65.
  • Dill A, Jung HS, Sun TP. The DELLA motif is essential for gibberellin-induced degradation of RGA. Proc Natl Acad Sci USA. 2001 Nov; 98:14162–7.
  • Sasaki A, Itoh H, Gomi K, Ueguchi-Tanaka M, Ishiyama K, Kobayashi M, Jeong DH, An G, Kitano H, Ashikari M, Matsuoka M. Accumulation of phosphorylated repressor for gibberellin signaling in an F-box mutant. Science. 2003 Mar; 299(5614):1896–8.
  • Gomi K, Sasaki A, Itoh H, Ueguchi-Tanaka M, Ashikari M, Kitano H, Matsuoka M. GID2, an F-box subunit of the SCF E3 complex, specifically interacts with phosphorylated SLR1 protein and regulates the gibberellindependent degradation of SLR1 in rice. Plant J. 2004 Feb; 37(4):626–34.
  • Itoh H, Sasaki A, Ueguchi-Tanaka M, Ishiyama K, Kobayashi M, Hasegawa Y, Minami E, Ashikari M, Matsuoka M. Dissection of the phosphorylation of rice DELLA protein, SLENDER RICE1. Plant Cell Physiol. 2005 Aug; 46(8):1392–9.
  • Shimada A, Ueguchi-Tanaka M, Sakamoto T, Fujioka S, Takatsuto S, Yoshida S, Sazuka T, Ashikari M, Matsuoka M. The rice SPINDLY gene functions as a negative regulator of gibberellin signaling by controlling the suppressive function of the DELLA protein, SLR1, and modulating brassinosteroid synthesis. Plant J. 2006 Nov; 48(3):390–402.
  • Gomi K, Matsuoka M. Gibberellin signalling pathway. Current Opinion in Plant Biology. 2003 Oct; 6(5):489–93.
  • Tanaka MU, Hirano K, Hasegawa Y, Kitano H, Matsuoka M. Release of the repressive activity of rice DELLA protein SLR1 by gibberellin does not require SLR1 degradation in the gid2 Mutant. Plant Cell. 2008 Sep; 20(9):2437–46.
  • Sun T. Gibberellin-GID1-DELLA: A pivotal regulatory module for plant growth and development. Plant Physiol. 2010 Oct; 154(2):567–70.
  • Willige BC, Ghosh S, Nill C, Zourelidou M, Dohmann EMN, Maier A, Schwechheimer C. The DELLA domain of GA INSENSITIVE mediates the interaction with the GA INSENSITIVE DWARF1A gibberellin receptor of Arabidopsis. Plant Cell. 2007 Apr; 19(4):1209–20.
  • Chandler PM, Marion-Poll A, Ellis M, Gubler F. Mutants at the Slender1 locus of barley cv. Himalaya: Molecular and physiological characterization. Plant Physiol. 2002 May; 129(1):181–90.
  • Griffiths J, Murase K, Rieu I, Zentella R, Zhang ZL, Powers SJ, Gong F, Phillips AL, Hedden P, Sun TP, Thomas SG. Genetic characterization and functional analysis of the GID1 gibberellin receptors in Arabidopsis. Plant Cell. 2006 Dec; 18(12):3399–414.
  • Iuchi S, Suzuki H, Kim YC, Iuchi A, Kuromori T, UeguchiTanaka M, Asami T, Yamaguchi I, Matsuoka M, Kobayashi M, Nakajima M. Multiple loss-of-function of Arabidopsis gibberellin receptor AtGID1 completely shuts down a gibberellin signal. Plant J. 2007 Jun; 50(6):958–66.

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