Skip to main content

Advertisement

SpringerLink
Log in

In silico comparative analysis of promoters derived from plant pararetroviruses

  • Original Article
  • Published:
VirusDisease Aims and scope Submit manuscript

Abstract

Promoters are specific sequence of nucleotides present upstream of gene coding region involved in initiation and regulation of transcription. Multiple cis-acting element forms the architecture of promoter to which trans-acting nucleic binding factors bind and regulates its activity. Since 1980 genome of pararetrovirus, are being exploited for developing efficient promoters. Among all of them Cauliflower mosaic virus is the most widely used promoter for gene expression. The basic rational behind the strength of promoter lies in the sequence of cis elements and the spacer nucleotide elements between them, thereby strength of these promoter fragments can be regulated by altering these nucleotide sequences. In the present study sequence of eight putative promoters of plant pararetrovirus are retrieved from National Centre for Biotechnology Information (NCBI) website. These sequence are subjected to various bioinformatics tools comprises of Clustal W, Plant Care, Mathinspector, ModelInspector for establishing the phylogenetic similarity, to identify the quantity and quality of present cis-elements, to find the various common transcription factors binding sites and to determine the presence of module for various specific functions respectively. A range of 28.80–56.0 percentage identification was observed in phylogenetic analysis, with the greatest similarity in Mirabilis mosaic virus and Dahlia mosaic virus. A broad range of cis-elements (51), transcription factor binding site (512) was obtained and 60% observed module are in combination with DOFF motif which shows a function relevance with abiotic stress inducibility. The present study had revealed the functional significance of these elements in gene regulation of pararetrovirus genome and also gives a overall idea for designing novel synthetic promoter.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3

References

  1. Benfy PN, Ren L, Chua NH. Combinatorial and synergistic properties of CaMV 35S enhancer subdomains. EMBO J. 1990;9:1685–96.

    Google Scholar 

  2. Brunt AA, Kitajima EW. Intracellular location and some properties of Mirabilis mosaic virus, a new member of the Cauliflower mosaic group of viruses. Phytopath Z. 1973;76:265–75.

    Article  Google Scholar 

  3. Calvert L, Ospina M, Shepherd RJ. Characterization of cassava vein mosaic virus: a distinct plant pararetrovirus. J Gen Virol. 1995;76:1271–6.

    Article  CAS  PubMed  Google Scholar 

  4. Cartharius K, Frech K, Grote K, Klocke B, Haltmeier M, Klingenhoff A, Frisch M, Bayerlein M, Werner T. MatInspector and beyond: promoter analysis based on transcription factor binding sites. Bioinformatics. 2005;21(13):2933–42.

    Article  CAS  PubMed  Google Scholar 

  5. Czuee M, Mookherjee S, Rajasekaran G, Bansa M. DNA free energy-based promoter prediction and comparative analysis of arabidopsis and rice genomes. Plant Physiol. 2011;156:1300–11.

    Article  Google Scholar 

  6. Dey N, Maiti LB. Structure and promoter/leader deletion analysis of mirabillis mosaic virus (MMV) full length transcript promoter in transgenic plants. Plant Mol Biol. 1999;40:771–82.

    Article  CAS  PubMed  Google Scholar 

  7. Dutt M, Erpen L, Ananthakrishnan G, Barthe GA, Brlansky RH, Maiti IB, Grosser JW. Comparative expression analysis of five caulimovirus promoters in citrus. Plant Cell Tiss Organ Cult. 2016;126:229–38. https://doi.org/10.1007/s11240-016-0993-6.

    Article  CAS  Google Scholar 

  8. Fang RX, Nagy F, Sivasubramaniam S, Chua NH. Multiple cis regulatory elements for maximal expression of the Cauliflower mosaic virus 35S promoter in transgenic plants. Plant Cell. 1989;1:142–50.

    Article  Google Scholar 

  9. Farnham PJ. Insights from genomic profiling of transcription factors. Nat Rev Genet. 2009;10:605–16.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Frech K, Danescu-Mayer J, Werner T. A novel method to develop highly specific models for regulatory units detects a new LTR in GenBank which contains a functional promoter. J Mol Biol. 1997;270(5):674–87.

    Article  CAS  PubMed  Google Scholar 

  11. Gardner C, Howarth A, Hahn P, Leudi MB, Shepherd RJ, Messing J. The complete nucleotide sequence of an infectious clone of Cauliflower mosaic virus by M13mp7 shortgun sequencing. Nucleic Acids Res. 1981;9:2871–88.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Gilmartin PM, Chua NH. Spacing between GT-1 binding sites within a light responsive element is critical for transcriptional activity. Plant Cell. 1990;2:447–55.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Ilyas M, Muhammad S, Naqvi S, Mahmood T. In silico analysis of transcription factor binding sites in promoters of germin-like protein genes in rice. Arch Biol Sci. 2016;68(4):863–76. https://doi.org/10.2298/ABS151116076I.

    Article  Google Scholar 

  14. Jadhao KR, Samal KC, Pradhan SK, Rout GR. Studies on molecular characterization of DREB gene in indica rice (Oryza sativa L.). Hereditary Genet. 2014;3(1):1000133.

    Google Scholar 

  15. Kibbe WA. OligoCalc: an online oligonucleotide properties calculator. Nucleic Acids Res. 2007;35:W43–6.

    Article  PubMed  PubMed Central  Google Scholar 

  16. Kuluev BR, Knyazev AV, Chemeris AV. Activity of promoters of carnation etched ring virus and dahlia mosaic virus in tobacco protoplasts and transgenic plants. Russ J Plant Physiol. 2008;55(5):687.

    Article  CAS  Google Scholar 

  17. Lam E. Analysis of tissue specific elements in the CaMV35S promoter. In: Nover L, editor. Results and problems in cell differentiation: plant promoter and transcription factors, vol. 20. Berlin: Springer; 1994. p. 181–96.

    Chapter  Google Scholar 

  18. Lescot Magali, Dhais Patrice, Thijs Gert, Marchal Kathleen, Moreau Yves, Van de Peer Yves, Rouz Pierre, Rombauts Stephane. PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Res. 2002;30(1):325–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Lohmann JU, Hong RL, Hobe M, Busch MA, Parcy F, Simon R, Weigel D. A molecular link between stem cell regulation and floral patterning in Arabidopsis. Cell. 2001;105(6):793–803.

    Article  CAS  PubMed  Google Scholar 

  20. Petrzik K, Benes V, Mraz L, Honestslegrova-Franova J, Ansorge W, Spak J. Strawberry vein banding virus- definitive member of the genus Caulimovirus. Virus Genes. 1998;16:303–5.

    Article  CAS  PubMed  Google Scholar 

  21. Porto MS, Pinheiro MPN, Batisy VGL, Santos RCC, Filho PDAM, Lima LMD. Plant promoters: an approach of structure and function. Mol Biotechnol. 2014;56:38–49. https://doi.org/10.1007/s12033-013-9713-1.

    Article  CAS  PubMed  Google Scholar 

  22. Ranjan R, Dey N. Development of vascular tissue and stress inducible hybrid-synthetic promoters through Dof-1 motifs rearrangement. Cell Biochem Biophys. 2012;63:235–45. https://doi.org/10.1007/s12013-012-9359-9.

    Article  CAS  PubMed  Google Scholar 

  23. Ranjan R, Gupta D. Introduction to plant promoter. Saarbrücken: Lambert Academic Publication; 2016. p. 149.

    Google Scholar 

  24. Richins R, Richard D. Organization and expression of the peanut chlorotic streak virus genome. Ph.D. Dissertation, 1993, University of Kentucky, Lexington KY (for the PClSV genomic sequence: DNA EMBL Data Library GenBank Accession Number U13988).

  25. Richins RD. The complete nucleotide sequence of peanut chlorotic streak virus (PClSV) DNA. EMBL Data Library GenBank Accession No. U13988. 1994.

  26. Richins RD, Shepherd RJ. Physical maps of the genome of Dahlia mosaic virus and Mirabilis mosaic virus—two members of the caulimovirus group. Virology. 1983;124:208–14.

    Article  CAS  PubMed  Google Scholar 

  27. Rushton PJ, Anja R, Lipka V, Lippok B, Somssich IE. Synthetic plant promoters containing defined regulatory elements provide novel insights into pathogen- and wound-induced signaling. Plant Cell. 2002;14:749–62.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Russell PJ. iGenetics: a molecular approach. 3rd ed. London: Pearson Education; 2009.

    Google Scholar 

  29. Sriraman V, Bartsch JW, Rittger A, Mulders SM, Richards JS. Regulated expression of ADAM8 (a disintegrin and metalloprotease domain 8) in the mouse ovary: evidence for a regulatory role of luteinizing hormone, progesterone receptor, and epidermal growth factor-like growth factors. Biol Reprod. 2008;78(6):1038–48.

    Article  CAS  PubMed  Google Scholar 

  30. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol. 2013;30(12):2725–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Yin Y, Beachy RN. The regulatory region of the Rice tungro bacilliform virus promoters and interacting nuclear factors in rice (Oryza sativa L.). Plant J. 1996;7(6):969–80.

    Article  Google Scholar 

  32. Zhan X, Haley A, Richardson K, Morris B. Analysis of the potential promoter sequences of African cassava mosaic virus by transient expression of the fl-glucuronidase gene. J Gen Virol. 1991;72:2849–52.

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

We greatly acknowledge DAE-BRNS (Mumbai), India (Project Sanction No. 37(1)/14/40/2014- BRNS/1423) for providing financial assistance.

Author information

Authors and Affiliations

  1. Plant Biotechnology Lab, Department of Botany, Faculty of Science, Dayalbagh Educational Institute (Deemed University), Dayalbagh, Agra, 282005, India

    Dipinte Gupta & Rajiv Ranjan

Authors
  1. Dipinte Gupta
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Rajiv Ranjan
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Rajiv Ranjan.

Electronic supplementary material

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Gupta, D., Ranjan, R. In silico comparative analysis of promoters derived from plant pararetroviruses. VirusDis. 28, 416–421 (2017). https://doi.org/10.1007/s13337-017-0410-8

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s13337-017-0410-8

Keywords

Search

Navigation