Genome‑wide identification of CAMTA gene family members in rice (Oryza sativa L.) and in silico study on their versatility in respect to gene expression and promoter structure

Funct Integr Genomics. 2022 Apr;22(2):193-214. doi: 10.1007/s10142-022-00828-w. Epub 2022 Feb 16.

Abstract

The calmodulin-binding transcription activator (CAMTA) is a family of transcriptional factors containing a cluster of calmodulin-binding proteins that can activate gene regulation in response to stresses. The presence of this family of genes has been reported earlier, though, the comprehensive analyses of rice CAMTA (OsCAMTA) genes, their promoter regions, and the proteins were not deliberated till date. The present report revealed the existence of seven CAMTA genes along with their alternate transcripts in five chromosomes of rice (Oryza sativa) genome. Phylogenetic trees classified seven CAMTA genes into three clades indicating the evolutionary conservation in gene structure and their association with other plant species. The in silico study was carried out considering 2 kilobases (kb) promoter regions of seven OsCAMTA genes regarding the distribution of transcription factor binding sites (TFbs) of major and plant-specific transcription factors whereas OsCAMTA7a was identified with highest number of TFbs, while OsCAMTA4 had the lowest. Comparative modelling, i.e., homology modelling, and molecular docking of the CAMTA proteins contributed the thoughtful comprehension of protein 3D structures and protein-protein interaction with probable partners. Gene ontology annotation identified the involvement of the proteins in biological processes, molecular functions, and localization in cellular components. Differential gene expression study gave an insight on functional multiplicity to showcase OsCAMTA3b as most upregulated stress-responsive gene. Summarization of the present findings can be interpreted that OsCAMTA gene duplication, variation in TFbs available in the promoters, and interactions of OsCAMTA proteins with their binding partners might be linked to tolerance against multiple biotic and abiotic cues.

Keywords: CAMTA genes; Oryza sativa; Protein structure; Stress; Transcription factors.

MeSH terms

  • Gene Expression
  • Gene Expression Profiling
  • Gene Expression Regulation, Plant
  • Molecular Docking Simulation
  • Multigene Family
  • Oryza* / genetics
  • Oryza* / metabolism
  • Phylogeny
  • Plant Proteins / genetics
  • Plant Proteins / metabolism
  • Promoter Regions, Genetic
  • Stress, Physiological / genetics

Substances

  • Plant Proteins