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Structural and functional based identification of the bean (Phaseolus) microRNAs and their targets from expressed sequence tags

  • Muhammad Younas Khan BarozaiEmail author
  • Muhammad Din
  • Iftikhar Ahmed Baloch
Article

Abstract

MicroRNAs (miRNAs) are small, 18–26 nucleotides long, non-coding RNAs that play role in post-transcriptional gene regulation. Many of these are evolutionarily conserved. This suggests a powerful approach to predict new miRNAs in other species. In this research, structural and functional approaches were combined to make computational prediction of potential miRNAs and their targets in Bean (Phaseolus). Total 55 novel miRNAs were detected from 38 miRNAs families in Bean (Phaseolus). These families are; miR156, 160, 164, 168, 170, 171, 172, 319, 393, 396, 397, 398, 408, 414, 438, 444, 535, 1310, 1424, 1426, 1848, 1860, 1863, 2055, 2091, 2093, 2094, 2102, 2103, 2105, 2864, 2866, 2925, 2926, 4221, 4245, 4246 and 4250. In the 55 putative miRNAs; 28 miRNAs belong to Phaseolus acutifolius, 23 to Phaseolus vulgaris, 4 to Phaseolus coccineus. All the mature miRNAs reside in the stem portion of the hairpin structures. Total 146 potential protein targets were predicted for these miRNAs.

Keywords

Phaseolus MicroRNAs Expressed sequence tags (ESTs) 

Abbreviation

Aly

Arabidopsis lyrata

Ath

Arabidopsis thaliana

BLAST

Basic local Alignment Search Tool

ch_ratio

Core Hairpin Ratio

ESTs

Expressed Sequence Tags

mRNA

Messenger RNA

miRNAs

microRNAs

MFE

Minimum Free Energy

Pre-miRNAs

Precursor microRNAs

NCBI

National Center for Biotechnology Information

Osa

Oryza sativa

Pac

Phaseolus acutifolius

Pco

Phaseolus coccineus

Pvu

Phaseolus vulgaris

Ptc

Populus trichocarpa

Pri-miRNAs

Primary Transcripts of Mature miRNAs

Rco

Ricinus communis

RISC

RNA Induced Silencing Complex

Pol II

RNA Polymerase II Enzyme

Tcc

Theobroma cacao

UTRs

Untranslated Regions

Vvi

Vitis vinifera

Supplementary material

10969_2013_9152_MOESM1_ESM.doc (360 kb)
The novel Phaseolus miRNAs secondary structures. The Phaseolus pre-miRNAs secondary structures were developed through Mfold algorithm. These structures clearly showing the mature miRNAs in stem portion of the stem-loop structures, highlighted in green (DOC 360 kb)
10969_2013_9152_MOESM2_ESM.doc (242 kb)
The Phaseolus miRNAs targets. The Phaseolus miRNA families and their putative targets, predicted with the help of Blastn and RNA-hybrid tools are represented. The targeted proteins name, Genbank Acc., RNA-Hybrid results and functions are also provided (DOC 241 kb)

References

  1. 1.
    Carrington J, Ambros V (2003) Role of microRNAs in plant and animal development. Sci 301:336–338CrossRefGoogle Scholar
  2. 2.
    Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116:281–297PubMedCrossRefGoogle Scholar
  3. 3.
    Gao P, Bai X, Yang L, Lv D (2011) Osa-MIR393: a salinity- and alkaline stress-related microRNA gene. Mol Biol Rep 38:237–242PubMedCrossRefGoogle Scholar
  4. 4.
    Barozai MYK, Kakar S, Sarangzai AM (2013) Profiling the Carrot (Daucus carota L.) microRNAs and their targets. Pak J Bot 45(S1):353–358Google Scholar
  5. 5.
    Reinhart BJ, Weinstein EG, Rhoades MW, Bartel B, Bartel DP (2002) MicroRNAs in plants. Genes Dev 16:1616–1626PubMedCrossRefGoogle Scholar
  6. 6.
    Barozai MYK (2012) Insilico identification of microRNAs and their targets in fiber and oil producing plant Flax (Linum usitatissimum L.). Pak J Bot 44(4):1357–1362Google Scholar
  7. 7.
    Wang J, Yang X, Xu H, Chi X, Zhang M, Hou X (2012) Identification and characterization of microRNAs and their target genes in Brassica oleracea. Gene 505(2):300–308PubMedCrossRefGoogle Scholar
  8. 8.
    Barozai MYK, Irfan M, Yousaf R et al (2008) Identification of micro-RNAs in cotton. Plant Physiol Biochem 46(8–9):739–751CrossRefGoogle Scholar
  9. 9.
    Barozai MYK (2012) The novel 172 sheep (Ovis aries) microRNAs and their targets. Mol Biol Rep 39(5):6259–6266. doi: 10.1007/s11033-012-1446-x PubMedCrossRefGoogle Scholar
  10. 10.
    Barozai MYK (2012) The MicroRNAs and their targets in the channel catfish (Ictalurus punctatus). Mol Biol Rep 39(9):8867–8872PubMedCrossRefGoogle Scholar
  11. 11.
    Barozai MYK, Din M, Baloch IA (2011) Identification of microRNAs in ecological model plant Mimulus. J of Biophy Chem 2(3):322–331. doi: 10.4236/jbpc.2011.23037 CrossRefGoogle Scholar
  12. 12.
    Gepts P, Bliss FA (1985) F1 hybrid weakness in the common bean. J Hered 76:447–450Google Scholar
  13. 13.
    Griffiths-Jones S (2004) The microRNA Registry. Nucleic Acids Res 32D:109–111CrossRefGoogle Scholar
  14. 14.
    Barozai MYK (2012) Identification and characterization of the microRNAs and their targets in Salmo salar. Gene 499(1):163–168PubMedCrossRefGoogle Scholar
  15. 15.
    Altschul S, Gish W, Miller W, Myers E, Lipman D (1990) Basic local alignment search tool. J of Molecular Bio 215:403–410Google Scholar
  16. 16.
    Barozai MYK, Baloch IA, Din M (2011) Identification of MicroRNAs and their targets in Helianthus. Mol Biol Rep 39(3):2523–2532. doi: 10.1007/s11033-011-1004-y PubMedCrossRefGoogle Scholar
  17. 17.
    Altschul S, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402PubMedCrossRefGoogle Scholar
  18. 18.
    Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31:3406–3415PubMedCrossRefGoogle Scholar
  19. 19.
    Li SC, Pan CU, Lin WC (2006) Bioinformatic discovery of microRNA precursors from human ESTs and introns. BMC Genet 7:164Google Scholar
  20. 20.
    Crooks GE, Hon G, Chandonia JM, Brenner SE (2004) WebLogo: a sequence logo generator. Genome Res 14:1188–1190PubMedCrossRefGoogle Scholar
  21. 21.
    Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG (2007) ClustalW and ClustalX version 2. Bioinf 23(21):2947–2948CrossRefGoogle Scholar
  22. 22.
    Barozai MYK (2013) Identification of microRNAs and their targets in Artemisia annua L. Pak J Bot 45(2):461–465Google Scholar
  23. 23.
    Kruger J, Rehmsmeier M (2006) RNA hybrid: microRNA target prediction easy, fast and flexible. Nucl Acids Res 34(2):451–454CrossRefGoogle Scholar
  24. 24.
    Barozai MYK, Husnain T (2012) Identification of biotic and abiotic stress up-regulated ESTs in Gossypium arboretum. Mol Bio Rep 39(2):1011–1018. doi: 10.1007/s11033-011-0826-y CrossRefGoogle Scholar
  25. 25.
    Barozai MYK, Kakar AG, Din M (2012) The relationship between codon usage bias and salt resistant genes in Arabidopsis thaliana and Oryza sativa. Pure Appl Bio 1(2):48–51Google Scholar
  26. 26.
    Barozai MYK, Wahid AH (2012) Insilico identification and characterization of cumulative abiotic stress responding genes in Potato (Solanum tuberosum L.). Pak J Bot 44(SI):57–69Google Scholar
  27. 27.
    Ambros V, Bartel B, Bartel DP (2003) A uniform system for microRNA annotation. RNA 9:277–279PubMedCrossRefGoogle Scholar
  28. 28.
    Meyers BC, Axtell MJ, Bartel B et al (2008) Criteria for annotation of plant MicroRNAs. Plant Cell 20:3186–3190PubMedCrossRefGoogle Scholar
  29. 29.
    Barozai MYK, Baloch IA, Din M (2011) Computational identification of MicroRNAs and their targets in two species of evergreen Spruce tree (Picea). PWaset 75:413–418Google Scholar
  30. 30.
    Gao P, Bai X, Liang Y et al (2011) Osa-MIR393: a salinity and alkaline stress-related microRNA gene. Mol Biol Rep 38(1):237–242PubMedCrossRefGoogle Scholar
  31. 31.
    Chen L, Ren Y, Zhang Y, Xu J, Sun F, Zhang Z, Wang Y (2012) Genome-wide identification and expression analysis of heat-responsive and novel microRNAs in Populus tomentosa. Gene 504(2):160–165PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2013

Authors and Affiliations

  • Muhammad Younas Khan Barozai
    • 1
    Email author
  • Muhammad Din
    • 1
  • Iftikhar Ahmed Baloch
    • 1
  1. 1.Department of BotanyUniversity of BalochistanQuettaPakistan

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