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Identification of drought-induced transcription factors in Sorghum bicolor using GO term semantic similarity

Abstract

Stress tolerance in plants is a coordinated action of multiple stress response genes that also cross talk with other components of the stress signal transduction pathways. The expression and regulation of stress-induced genes are largely regulated by specific transcription factors, families of which have been reported in several plant species, such as Arabidopsis, rice and Populus. In sorghum, the majority of such factors remain unexplored. We used 2DE refined with MALDI-TOF techniques to analyze drought stress-induced proteins in sorghum. A total of 176 transcription factors from the MYB, AUX_ARF, bZIP, AP2 and WRKY families of drought-induced proteins were identified. We developed a method based on semantic similarity of gene ontology terms (GO terms) to identify the transcription factors. A threshold value (≥ 90%) was applied to retrieve total 1,493 transcription factors with high semantic similarity from selected plant species. It could be concluded that the identified transcription factors regulate their target proteins with endogenous signals and environmental cues, such as light, temperature and drought stress. The regulatory network and cis-acting elements of the identified transcription factors in distinct families are involved in responsiveness to auxin, abscisic acid, defense, stress and light. These responses may be highly important in the modulation of plant growth and development.

Abbreviations

BP:

biological process

CC:

cellular component

GO:

gene ontology

MF:

molecular function

SS:

semantic similarity

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Sekhwal, M.K., Swami, A.K., Sharma, V. et al. Identification of drought-induced transcription factors in Sorghum bicolor using GO term semantic similarity. Cell Mol Biol Lett (2014). https://doi.org/10.2478/s11658-014-0223-3

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Keywords

  • 2D Gel electrophoresis
  • Drought-stress
  • Sorghum bicolor
  • Semantic similarity
  • Transcription factor
  • GO terms
  • Clusters
  • MALDI-TOF
  • Functional annotation
  • Regulatory network
  • Gene ontology
  • Protein family