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Identification and Characterization of High Temperature Stress Responsive Novel miRNAs in French Bean (Phaseolus vulgaris)

Applied Biochemistry and Biotechnology volume 176, pages 835–849 (2015)Cite this article

Abstract

MicroRNAs are important gene regulators controlling almost all biological and metabolic functions. They elicit their regulatory response through modulation of their target gene expression. In this study, we identified eight novel microRNAs (miRNAs) belonging to four miRNA families and one miR* sequence from the French bean genome which responded to high temperature. The precursor miRNAs varied in length and showed conserved signatures of RNA polymerase II transcripts in their upstream regions. Promoter region analysis indicated the prevalence of MYB and WRKY binding sites emphasizing auto-inhibition of miRNA biogenesis. The genomic organization study revealed the presence of 150 putative regulatory motifs of which 41 are unique. Common motifs shared by miRNAs involved in more than one abiotic stresses were also identified. Further, the miRNA validation was carried out by stem-loop real-time PCR, and the results emphasize that the differential expression of miRNAs confers stress tolerance. Functional analysis revealed that most of the targets represent transcription factors. The results obtained would provide new insights to the complex regulatory mechanism employing small non-coding regulatory RNAs toward stress adaptation.

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Abbreviations

GO:

Gene Ontology

miRNA:

MicroRNA

TF:

Transcription factor

TSS:

Transcription start site

TFB:

Transcription factor binding site

UTR:

Untranslated region

LEA:

Late embryogenic abundant proteins

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Acknowledgments

The research work is supported by University Grants Commission [No 40-192/2011 (SR)] and Department of Science and Technology [No SR/FT/LS-10/2012] New Delhi, India.

Conflict of Interest

The authors declare that they have no conflict of interest.

Author information

Affiliations

  1. Post Graduate Department of Biochemistry, Maharani’s Science College for Women, Palace Road, Bangalore, 560001, India

    M. N. Jyothi & R. Nagesh babu

  2. Centre for Bioinformatics, Faculty of Biological Engineering, Shobhit University, Meerut, India

    M. N. Jyothi & D. V. Rai

Authors
  1. M. N. Jyothi
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  2. D. V. Rai
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  3. R. Nagesh babu
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Corresponding author

Correspondence to R. Nagesh babu.

Electronic Supplementary Material

Below is the link to the electronic supplementary material.

Supplementary File 1

List of primers used for small RNA library preparation of novel miRNAs expressed under high temperature stress in French bean (PDF 143 kb)

Supplementary File 2

List of stem-loop real time primers used for validation of novel miRNAs expressed under high temperature stress in French bean (PDF 203 kb)

Supplementary File 3

Secondary structure of novel miRNAs characterized in French bean under High temperature stress (PDF 520 kb)

Supplementary File 4

List of cis-regulatory elements identified in French bean novel miRNA genes (XLSX 24 kb)

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Jyothi, M.N., Rai, D.V. & Nagesh babu, R. Identification and Characterization of High Temperature Stress Responsive Novel miRNAs in French Bean (Phaseolus vulgaris). Appl Biochem Biotechnol 176, 835–849 (2015). https://doi.org/10.1007/s12010-015-1614-2

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  • DOI: https://doi.org/10.1007/s12010-015-1614-2

Keywords

  • Differential expression
  • Heat stress
  • MYB
  • Transcription start site
  • Promoters
  • Regulatory motifs
  • WRKY