Identification of Conserved Domains and Motifs for GRF Gene Family

Authors: Jafar Ahmadi, Nafiseh Noormohammadi, Sedigheh Fabriki Ourang

Abstract:

GRF, Growth regulating factor, genes encode a novel class of plant-specific transcription factors. The GRF proteins play a role in the regulation of cell numbers in young and growing tissues and may act as transcription activations in growth and development of plants. Identification of GRF genes and their expression are important in plants to performance of the growth and development of various organs. In this study, to better understanding the structural and functional differences of GRFs family, 45 GRF proteins sequences in A. thaliana, Z. mays, O. sativa, B. napus, B. rapa, H. vulgare and S. bicolor, have been collected and analyzed through bioinformatics data mining. As a result, in secondary structure of GRFs, the number of alpha helices was more than beta sheets and in all of them QLQ domains were completely in the biggest alpha helix. In all GRFs, QLQ and WRC domains were completely protected except in AtGRF9. These proteins have no trans-membrane domain and due to have nuclear localization signals act in nuclear and they are component of unstable proteins in the test tube.

Keywords: Domain, Gene Family, GRF, Motif.

Digital Object Identifier (DOI): doi.org/10.5281/zenodo.1097205

References:

[1] J. H. Kim, D. Choi, H. Kende, “The AtGRF family of putative transcription factors is involved in leaf and cotyledon growth in Arabidopsis” Plant Journal. 2003, 36: 94-104.
[2] E. Van der Knaap, J.H. Kim, H. Kende, “A novel gibberellin-induced gene from rice and its potential regulatory role in stem growth” Plant Physiol. 2000, 122: 695–704.
[3] I. Treich, B. R. Cairns, T. delos Santos, E. Brewster, M. Carlson, “SNF11, a new component of the yeast SNF-SWI complex that interacts with a conserved region of SNF2” Mol. Cell. Biol. 1995, 15: 4240– 4248.
[4] W. Zhang, T. Zhang, Y. Wu, J. Jiang, “Genome-wide identification of regulatory DNA elements and protein-binding footprints using signatures of open chromatin in Arabidopsis” Plant Cell. 2012, 15: 2719–2731. doi: 10.1105/tpc.112.098061.
[5] D. Choi, J. H. Kim, H. Kende “Whole genome analysis of the OsGRF gene family encoding plant specific putative transcription activators in rice (Oryza sativa L.)” Plant Cell Physiol. 2004, 45: 897-904.
[6] J. Kyte and R. F. Doolittle “A simple method for displaying the hydropathic character of a protein” Journal Molecular Biology. 1982, 157: 105–132.