Skip to main content

Identification of transcription factor binding sites on promoter of RNA dependent RNA polymerases (RDRs) and interacting partners of RDR proteins through in silico analysis

Abstract

RNA silencing phenomenon in plants provides resistance to various pathogens and also, it maintains genome integrity. The process of RNA silencing is regulated by diverse proteins, among which RNA dependent RNA polymerases (RDRs) are very crucial for the amplification of small RNAs (sRNAs). Out of various RDR proteins present in plants, role of RDR1, RDR2 and RDR6 for providing resistance against various biotic stresses have been well documented. In contrast, very few information is available regarding the role of RDR3, RDR4 and RDR5 proteins in plant biology and stress response. Furthermore, the regulation of RDRs is not yet known. Here, we have carried out in silico studies for identification of the transcription factor (TF) binding sites on the promoter of RDR1-6 genes of various plant species. Among the TFs predicted to bind on the promoter of RDRs, MYB44, AS1/AS2, WRKY1 are the major one. Furthermore, putative interacting protein partners of RDRs proteins of tomato and rice were also predicted by STRING database which suggests that DCL (Dicer-like) proteins are strong candidate proteins as the interacting partners of RDRs. The knowledge of regulation of RDRs and its interacting protein partners might help in developing resistant plants to biotic stresses.

This is a preview of subscription content, access via your institution.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8

References

  1. Basu S, Kushwaha NK, Singh AK, Sahu PP, Kumar RV, Chakraborty S (2018) Dynamics of a geminivirus-encoded pre-coat protein and host RNA-dependent RNA polymerase 1 in regulating symptom recovery in tobacco. J Exp Bot 69(8):2085–2102. https://doi.org/10.1093/jxb/ery043

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Butterbach P, Verlaan MG, Dullemans A, Lohuis D, Visser RGF, Bai Y, Kormelink R (2014) Tomato yellow leaf curl virus resistance by Ty-1 involves increased cytosine methylation of viral genomes and is compromised by cucumber mosaic virus infection. Proc Natl Acad Sci USA 111(35):12942–12947. https://doi.org/10.1073/pnas.1400894111

    Article  CAS  PubMed  Google Scholar 

  3. Cao JY, Xu YP, Li W, Li SS, Rahman H, Cai XZ (2016) Genome-wide identification of dicer-like, Argonaute, and RNA-dependent RNA polymerase gene families in Brassica species and functional analyses of their Arabidopsis homologs in resistance to Sclerotinia sclerotiorum. Front Plant Sci 7:1614. https://doi.org/10.3389/fpls.2016.01614

    Article  PubMed  PubMed Central  Google Scholar 

  4. Cartharius K, Frech K, Grote K, Klocke B, Haltmeier M et al (2005) MatInspector and beyond: promoter analysis based on transcription factor binding sites. Bioinformatics 21:2933–2942. https://doi.org/10.1093/bioinformatics/bti473

    Article  CAS  Google Scholar 

  5. Dalmay T, Hamilton A, Rudd S, Angell S, Baulcombe DC (2000) An RNA-dependent RNA polymerase gene in Arabidopsis is required for posttranscriptional gene silencing mediated by a transgene but not by a virus. Cell 101(5):543–553. https://doi.org/10.1016/S0092-8674(00)80864-8

    Article  CAS  PubMed  Google Scholar 

  6. Devert A, Fabre N, Floris M, Canard B, Robaglia C, Crété P (2015) Primer-dependent and primer-independent initiation of double stranded RNA synthesis by purified Arabidopsis RNA-dependent RNA polymerases RDR2 and RDR6. PLoS ONE 10(3):e0120100. https://doi.org/10.1371/journal.pone.0120100

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Dubos C, Stracke R, Grotewold E, Weisshaar B, Martin C, Lepiniec L (2010) MYB transcription factors in Arabidopsis. Trends Plant Sci 15:573–581. https://doi.org/10.1016/j.tplants.2010.06.005

    Article  CAS  Google Scholar 

  8. Guo M, Thomas J, Collins G, Timmermans MC (2008) Direct repression of KNOX loci by the ASYMMETRIC LEAVES1 complex of Arabidopsis. Plant Cell 20:48–58. https://doi.org/10.1105/tpc.107.056127

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Guo H, Wang Y, Wang L, Hu P, Wang Y et al (2017) Expression of the MYB transcription factor gene BplMYB46 affects abiotic stress tolerance and secondary cell wall deposition in Betula platyphylla. Plant Biotechnol J 15:107–121. https://doi.org/10.1111/pbi.12595

    Article  CAS  PubMed  Google Scholar 

  10. Hunter LJR, Westwood JH, Heath G, Macaulay K, Smith AG et al (2013) Regulation of RNA-dependent RNA polymerase 1 and isochorismate synthase gene expression in Arabidopsis. PLoS ONE 8:e66530. https://doi.org/10.1371/journal.pone.0066530

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Iwasaki M, Takahashi H, Iwakawa H, Nakagawa A, Ishikawa T et al (2013) Dual regulation of ETTIN (ARF3) gene expression by AS1-AS2, which maintains the DNA methylation level, is involved in stabilization of leaf adaxial-abaxial partitioning in Arabidopsis. Development 140:1958–1969. https://doi.org/10.1242/dev.085365

    Article  CAS  PubMed  Google Scholar 

  12. Jouannet V, Moreno AB, Elmayan T, Vaucheret H, Crespi MD, Maizel A (2012) Cytoplasmic Arabidopsis AGO7 accumulates in membrane-associated siRNA bodies and is required for ta-siRNA biogenesis. EMBO J 31:1704–1713. https://doi.org/10.1038/emboj.2012.20

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Kumar S, Stecher G, Tamura K (2016) MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874. https://doi.org/10.1093/molbev/msw054

    Article  CAS  Google Scholar 

  14. Lam P, Zhao L, McFarlane HE, Aiga M, Lam V et al (2012) RDR1 and SGS3, components of RNA-mediated gene silencing, are required for the regulation of cuticular wax biosynthesis in developing inflorescence stems of Arabidopsis. Plant Physiol 159:1385. https://doi.org/10.1104/pp.112.199646

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Law JA, Vashisht AA, Wohlschlegel JA, Jacobsen SE (2011) SHH1, a homeodomain protein required for DNA methylation, as well as RDR2, RDM4, and chromatin remodeling factors, associate with RNA polymerase IV. PLoS Genet 7(7):e1002195. https://doi.org/10.1371/journal.pgen.1002195

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Leibman D, Kravchik M, Wolf D, Haviv S, Weissberg M et al (2018) Differential expression of cucumber RNA-dependent RNA polymerase 1 genes during antiviral defence and resistance. Mol Plant Pathol 19(2):300–312. https://doi.org/10.1111/mpp.12518

    Article  CAS  PubMed  Google Scholar 

  17. Li JB, Luan YB, Liu Z (2015a) Overexpression of SpWRKY1 promotes resistance to Phytophthora nicotianae and tolerance to salt and drought stress in transgenic tobacco. Physiol Plant 155:248–266. https://doi.org/10.1111/ppl.12315

    Article  CAS  PubMed  Google Scholar 

  18. Li JB, Luan YB, Liu Z (2015b) SpWRKY1 mediates resistance to Phytophthora infestans and tolerance to salt and drought stress by modulating reactive oxygen species homeostasis and expression of defense-related genes in tomato. Plant Cell Tissue Org Cult 123:67–81. https://doi.org/10.1007/s11240-015-0815-2

    Article  CAS  Google Scholar 

  19. Lodha M, Marco CF, Timmermans MC (2013) The ASYMMETRIC LEAVES complex maintains repression of KNOX homeobox genes via direct recruitment of Polycomb-repressive complex2. Genes Dev 27:596–601. https://doi.org/10.1101/gad.211425.112

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Mao X, Zhang H, Qian X, Li A, Zhao G, Jing R (2012) TaNAC2, a NAC-type wheat transcription factor conferring enhanced multiple abiotic stress tolerances in Arabidopsis. J Exp Bot 63:2933–2946. https://doi.org/10.1093/jxb/err462

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Marchive C, Mzid R, Deluc L, Barrieu F, Pirrello J et al (2007) Isolation and characterization of a Vitis vinifera transcription factor, VvWRKY1, and its effect on responses to fungal pathogens in transgenic tobacco plants. J Exp Bot 58:1999–2010. https://doi.org/10.1093/jxb/erm062

    Article  CAS  PubMed  Google Scholar 

  22. Mare C, Mazzucotelli E, Crosatti C, Francia E, Stanca AM, Cattivelli L (2004) Hv-WRKY38: a new transcription factor involved in cold- and drought-response in barley. Plant Mol Biol 55:399–416. https://doi.org/10.1007/s11103-004-0906-7

    Article  CAS  PubMed  Google Scholar 

  23. Matsushita A, Furumoto T, Ishida S, Takahashi Y (2007) AGF1, an AT-hook protein, is necessary for the negative feedback of AtGA3ox1 encoding GA 3-oxidase. Plant Physiol 143(3):1152–1162. https://doi.org/10.1104/pp.106.093542

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Melnyk CW, Molnar A, Baulcombe DC (2011) Intercellular and systemic movement of RNA silencing signals. EMBO J 30:3553–3563. https://doi.org/10.1038/emboj.2011.274

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Mendes GC, Reis PAB, Calil IP, Carvalho HH, Aragao FJL, Fontes EPB (2013) GmNAC30 and GmNAC81 integrate the endoplasmic reticulum stress- and osmotic stress-induced cell death responses through a vacuolar processing enzyme. Proc Natl Acad Sci USA 110(48):19627–19632. https://doi.org/10.1073/pnas.1311729110

    Article  CAS  PubMed  Google Scholar 

  26. Mourrain P, Beclin C, Elmayan T, Feuerbach F, Godon C et al (2000) Arabidopsis SGS2 and SGS3 genes are required for posttranscriptional gene silencing and natural virus resistance. Cell 101:533–542. https://doi.org/10.1016/S0092-8674(00)80863-6

    Article  CAS  PubMed  Google Scholar 

  27. Mzid R, Marchive C, Blancard D, Deluc L, Barrieu F et al (2007) Overexpression of VvWRKY2 in tobacco enhances broad resistance to necrotrophic fungal pathogens. Physiol Plant 131:434–447. https://doi.org/10.1111/j.1399-3054.2007.00975.x

    Article  CAS  PubMed  Google Scholar 

  28. Nishimura T (2018) Gene body methylation involved in leaf development. Plant Cell Physiol 59:1288–1289. https://doi.org/10.1093/pcp/pcy109

    Article  CAS  PubMed  Google Scholar 

  29. Noguero M, Atif RM, Ochatt S, Thompson RD (2013) The role of the DNA-binding One Zinc Finger (DOF) transcription factor family in plants. Plant Sci 209:32–45. https://doi.org/10.1016/j.plantsci.2013.03.016

    Article  CAS  PubMed  Google Scholar 

  30. Oh SK, Baek KH, Park JM, Yi SY, Yu SH et al (2008) Capsicum annuum WRKY protein CaWRKY1 is a negative regulator of pathogen defense. New Phytol 177:977–989. https://doi.org/10.1111/j.1469-8137.2007.02310.x

    Article  CAS  PubMed  Google Scholar 

  31. Oh JE, Kwon Y, Kim JH, Noh H, Hong SW, Lee H (2011) A dual role for MYB60 in stomatal regulation and root growth of Arabidopsis thaliana under drought stress. Plant Mol Biol 77:91–103. https://doi.org/10.1007/s11103-011-9796-7

    Article  CAS  PubMed  Google Scholar 

  32. Pandey SP, Baldwin IT (2007) RNA-directed RNA polymerase 1 (RdR1) mediates the resistance of Nicotiana attenuata to herbivore attack in nature. Plant J 50:40–53. https://doi.org/10.1111/j.1365-313X.2007.03030.x

    Article  CAS  PubMed  Google Scholar 

  33. Pandey SP, Gaquerel E, Gase K, Baldwin IT (2008a) RNA-directed RNA polymerase 3 from Nicotiana attenuata is required for competitive growth in natural environments. Plant Physiol 147(3):1212–1224. https://doi.org/10.1104/pp.108.121319

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Pandey SP, Shahi P, Gase K, Baldwin IT (2008b) Herbivory-induced changes in the small-RNA transcriptome and phytohormone signaling in Nicotiana attenuata. Proc Natl Acad Sci USA 105(12):4559–4564. https://doi.org/10.1073/pnas.0711363105

    Article  PubMed  Google Scholar 

  35. Phelps-Durr TL, Thomas J, Vahab P, Timmermans MC (2005) Maize rough sheath2 and its Arabidopsis orthologue ASYMMETRIC LEAVES1 interact with HIRA, a predicted histone chaperone, to maintain knox gene silencing and determinacy during organogenesis. Plant Cell 17:2886–2898. https://doi.org/10.1105/tpc.105.03547

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Prakash V, Devendran R, Chakraborty S (2017) Overview of plant RNA dependent RNA polymerases in antiviral defense and gene silencing. Indian J Plant Physiol 22:493–505. https://doi.org/10.1007/s40502-017-0339-3

    Article  CAS  Google Scholar 

  37. Qi X, Zhang Y, Chai T (2007) characterization of a novel plant promoter specifically induced by heavy metal and identification of the promoter regions conferring heavy metal responsiveness. Plant Physiol 143:50. https://doi.org/10.1104/pp.106.080283

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Qiao Z, Li CL, Zhang W (2016) WRKY1 regulates stomatal movement in drought stressed Arabidopsis thaliana. Plant Mol Biol 91:53–65. https://doi.org/10.1007/s11103-016-0441-3

    Article  CAS  PubMed  Google Scholar 

  39. Qu F, Ye X, Hou G, Sato S, Clemente TE, Morris TJ (2005) RDR6 has a broad-spectrum but temperature-dependent antiviral defense role in Nicotiana benthamiana. J Virol 79:15209–15217. https://doi.org/10.1128/JVI.79.24.15209-15217.2005

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Raja P, Sanville BC, Buchmann RC, Bisaro DM (2008) Viral genome methylation as an epigenetic defense against geminiviruses. J Virol 82(18):8997–9007. https://doi.org/10.1128/JVI.00719-08

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Rakhshandehroo F, Takeshita M, Squires J, Palukaitis P (2009) The influence of RNA-dependent RNA polymerase 1 on potato virus Y infection and on other antiviral response genes. Mol Plant Microbe Interact 22:1312–1318. https://doi.org/10.1094/MPMI-22-10-1312

    Article  CAS  PubMed  Google Scholar 

  42. Schwach F, Vaistij FE, Jones L, Baulcombe DC (2005) An RNA-dependent RNA polymerase prevents meristem invasion by potato virus X and is required for the activity but not the production of a systemic silencing signal. Plant Physiol 138:1842. https://doi.org/10.1104/pp.105.063537

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Seki M, Kamei A, Yamaguchi-Shinozaki K, Shinozaki K (2003) Molecular responses to drought, salinity and frost: common and different paths for plant protection. Curr Opin Biotechnol 14:194–199. https://doi.org/10.1105/tpc.006130

    Article  CAS  PubMed  Google Scholar 

  44. Seo PJ, Park CM (2010) MYB96-mediated abscisic acid signals induce pathogen resistance response by promoting salicylic acid biosynthesis in Arabidopsis. New Phytol 186:471–483. https://doi.org/10.1111/j.1469-8137.2010.03183.x

    Article  CAS  PubMed  Google Scholar 

  45. Shao F, Lu S (2014) Identification, molecular cloning and expression analysis of five RNA-dependent RNA polymerase genes in Salvia miltiorrhiza. PLoS ONE 9(4):e95117. https://doi.org/10.1371/journal.pone.0095117

    Article  PubMed  PubMed Central  Google Scholar 

  46. Shim JS, Jung C, Lee S, Min K, Lee Y, Choi Y, Lee JS, Song JT, Kim J, Choi YD (2013) AtMYB44 regulates WRKY70 expression and modulates antagonistic interaction between salicylic acid and jasmonic acid signaling. Plant J 73:483–495. https://doi.org/10.1111/tpj.12051

    Article  CAS  PubMed  Google Scholar 

  47. Simon SA, Meyers BC (2011) Small RNA-mediated epigenetic modifications in plants. Curr Opin Plant Biol 14:148–155. https://doi.org/10.1016/j.pbi.2010.11.007

    Article  CAS  PubMed  Google Scholar 

  48. Szklarczyk D, Franceschini A, Wyder S, Forslund K, Heller D et al (2015) STRING v10: protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Res 43:D447–D452. https://doi.org/10.1093/nar/gku1003

    Article  CAS  PubMed  Google Scholar 

  49. Vaucheret H (2006) Post-transcriptional small RNA pathways in plants: mechanisms and regulations. Genes Dev 20:759–771. https://doi.org/10.1101/gad.1410506

    Article  CAS  PubMed  Google Scholar 

  50. Verlaan MG, Hutton SF, Ibrahem RM, Kormelink R, Visser RGF, Scott JW et al (2013) The tomato yellow leaf curl virus resistance genes Ty-1 and Ty-3 are allelic and code for DFDGD-class RNA–dependent RNA polymerases. PLoS Genet 9(3):e1003399. https://doi.org/10.1371/journal.pgen.1003399

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Vrbsky J, Akimcheva S, Watson JM, Turner TL, Daxinger L, Vyskot B et al (2010) siRNA–mediated methylation of Arabidopsis telomeres. PLoS Genet 6(6):e1000986. https://doi.org/10.1371/journal.pgen.1000986

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Wang L, Xu Y, Zhang C, Ma Q, Joo SH, Kim SK et al (2008) OsLIC, a novel CCCH-type zinc finger protein with transcription activation, mediates rice architecture via brassinosteroids signaling. PLoS ONE 3(10):e3521. https://doi.org/10.1371/journal.pone.0003521

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Wang XB, Wu Q, Ito T, Cillo F, Li WX, Chen X, Yu JL, Ding SW (2010) RNAi-mediated viral immunity requires amplification of virus-derived siRNAs in Arabidopsis thaliana. Proc Natl Acad Sci USA 107:484–489. https://doi.org/10.1073/pnas.0904086107

    Article  PubMed  Google Scholar 

  54. Wang H, Jiao X, Kong X, Hamera S, Wu Y et al (2016) A signaling cascade from mir444 to RDR1 in rice antiviral RNA silencing pathway. Plant Physiol 170:2365–2377. https://doi.org/10.1104/pp.15.01283F

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Wassenegger M, Krczal G (2006) Nomenclature and functions of RNA-directed RNA polymerases. Trends Plant Sci 11:142–151. https://doi.org/10.1016/j.tplants.2006.01.003

    Article  CAS  PubMed  Google Scholar 

  56. Willmann MR, Endres MW, Cook RT, Gregory BD (2011) The functions of RNA-dependent RNA polymerases in Arabidopsis. Arabidopsis Book 9:e0146. https://doi.org/10.1199/tab.0146

    Article  PubMed  PubMed Central  Google Scholar 

  57. Xie Z, Fan B, Chen C, Chen Z (2001) An important role of an inducible RNA-dependent RNA polymerase in plant antiviral defense. Proc Natl Acad Sci USA 98:6516–6521. https://doi.org/10.1073/pnas.111440998

    Article  CAS  PubMed  Google Scholar 

  58. Yang SJ, Carter SA, Cole AB, Cheng NH, Nelson RS (2004) A natural variant of a host RNA-dependent RNA polymerase is associated with increased susceptibility to viruses by Nicotiana benthamiana. Proc Natl Acad Sci USA 101:6297–6302. https://doi.org/10.1073/pnas.0304346101

    Article  CAS  PubMed  Google Scholar 

  59. Yu D, Fan B, MacFarlane SA, Chen Z (2003) Analysis of the involvement of an inducible Arabidopsis RNA-dependent RNA polymerase in antiviral defense. Mol Plant Microbe Interact 16:206–216. https://doi.org/10.1094/MPMI.2003.16.3.206

    Article  CAS  PubMed  Google Scholar 

  60. Zong J, Yao X, Yin J, Zhang D, Ma H (2009) Evolution of the RNA-dependent RNA polymerase (RdRP) genes: duplications and possible losses before and after the divergence of major eukaryotic groups. Gene 447:29–39. https://doi.org/10.1016/j.gene.2009.07.004

    Article  CAS  PubMed  Google Scholar 

Download references

Funding

Funding was provided by UPE-II, UGC (Grant No. JNU/UPE-II/SLS/SC/13).

Author information

Affiliations

Authors

Corresponding author

Correspondence to Supriya Chakraborty.

Ethics declarations

Conflict of interest

The authors declare that they have no competing financial interests.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Fig. S1.

Phylogenetic analysis of RDR1, RDR2, RDR3, RDR4, RDR5 and RDR6 coding nucleotide sequences of various plant species. Maximum likelihood tree was generated by MEGA 7 with bootstrap method as the test of phylogeny (1000 replications). (TIFF 98 kb)

Fig. S2.

Schematic representation of transcription factor binding sites on the putative promoters of StRDR1, SlRDR1, CaRDR1, NtRDR1, NaRDR1, HaRDR1, GmRDR1, VvRDR1, PtRDR1, GhRDR1, CqRDR1, AtRDR1, MtRDR1, AhRDR1, PsRDR1 and OsRDR1 based on the default settings, i.e., core similarity 0.75 and optimal matrix similarity. SR2 gene of P. vulgaris was used as a control (‘P$’ denotes plants and ‘O$’ denotes general core promoter elements). (TIFF 1698 kb)

Fig. S3.

Schematic representation of transcription factor binding sites on the putative promoters of StRDR2, SlRDR2, CaRDR2, NtRDR2, NaRDR2, HaRDR2, GmRDR2, VvRDR2, PtRDR2, GhRDR2, CqRDR2, AtRDR2, MtRDR2, AhRDR2, PsRDR2 and OsRDR2 based on the default settings, i.e., core similarity 0.75 and optimal matrix similarity. SR2 gene of P. vulgaris was used as a control (‘P$’ denotes plants and ‘O$’ denotes general core promoter elements). (TIFF 1707 kb)

Fig. S4.

Schematic representation of transcription factor binding sites on the putative promoters of StRDR6, SlRDR6, CaRDR6, NtRDR6, NaRDR6, HaRDR6, GmRDR6, VvRDR6, PtRDR6, GhRDR6, CqRDR6, AtRDR6, MtRDR6, AhRDR6, PsRDR6 and OsRDR6 based on the default settings, i.e., core similarity 0.75 and optimal matrix similarity. SR2 gene of P. vulgaris was used as a control (‘P$’ denotes plants and ‘O$’ denotes general core promoter elements). (TIFF 1742 kb)

Fig. S5.

Schematic representation of transcription factor binding sites on the putative promoters of SlRDR3, CaRDR3, NtRDR3, HaRDR3, GmRDR3, PpRDR3, CqRDR3, SbRDR3, OsRDR3, AlRDR3, AhRDR3 and BvRDR3 based on the default settings, i.e., core similarity 0.75 and optimal matrix similarity. SR2 gene of P. vulgaris was used as a control (‘P$’ denotes plants and ‘O$’ denotes general core promoter elements). (TIFF 1371 kb)

Fig. S6.

Schematic representation of transcription factor binding sites on the putative promoters of SmRDR4, PpRDR4, OsRDR4 and AlRDR4 based on the default settings, i.e., core similarity 0.75 and optimal matrix similarity. SR2 gene of P. vulgaris was used as a control (‘P$’ denotes plants and ‘O$’ denotes general core promoter elements). (TIFF 618 kb)

Fig. S7.

Schematic representation of transcription factor binding sites on the putative promoters of StRDR5, SlRDR5, CaRDR5, NtRDR5, NaRDR5, HaRDR5, VvRDR5, PtRDR5, GhRDR5, CqRDR5, AlRDR5, MtRDR5, AhRDR5, and PsRDR5 based on the default settings, i.e., core similarity 0.75 and optimal matrix similarity. SR2 gene of P. vulgaris was used as a control (‘P$’ denotes plants and ‘O$’ denotes general core promoter elements). (TIFF 1551 kb)

Fig. S8.

Interactome of a-OsRDR1, b-OsRDR2, c-OsRDR3, d-OsRDR4 and e-OsRDR6 proteins with other proteins. Maximum degree of interaction was observed with the dicer like proteins (DCLs). Minimum required interaction score was medium confidence (0.400). (TIFF 24643 kb)

Table S1.

List of matrix families with details and summary of all of the matrix matches on the StRDR1, SlRDR1, CaRDR1, NtRDR1, NaRDR1, HaRDR1, GmRDR1, VvRDR1, PtRDR1, GhRDR1, CqRDR1, AtRDR1, MtRDR1, AhRDR1, PsRDR1 and OsRDR1 promoter sequences based on the MatInspector’s default as well as stringent settings. (XLSX 552 kb)

Table S2.

List of matrix families with details and summary of all of the matrix matches on the StRDR2, SlRDR2, CaRDR2, NtRDR2, NaRDR2, HaRDR2, GmRDR2, VvRDR2, PtRDR2, GhRDR2, CqRDR2, AtRDR2, MtRDR2, AhRDR2, PsRDR2 and OsRDR2 promoter sequences based on the MatInspector’s default as well as stringent settings. (XLSX 626 kb)

Table S3.

List of matrix families with details and summary of all of the matrix matches on the StRDR6, SlRDR6, CaRDR6, NtRDR6, NaRDR6, HaRDR6, GmRDR6, VvRDR6, PtRDR6, GhRDR6, CqRDR6, AtRDR6, MtRDR6, AhRDR6 and PsRDR6 promoter sequences based on the MatInspector’s default as well as stringent settings. (XLSX 655 kb)

Table S4.

List of matrix families with details and summary of all of the matrix matches on the SlRDR3, CaRDR3, NtRDR3, HaRDR3, GmRDR3, PpRDR3, CqRDR3, SbRDR3, OsRDR3, AlRDR3, AhRDR3 and BvRDR3 promoter sequences based on the MatInspector’s default as well as stringent settings. (XLSX 521 kb)

Table S5.

List of matrix families with details and summary of all of the matrix matches on the SmRDR4, PpRDR4, OsRDR4 and AlRDR4 promoter sequences based on the MatInspector’s default as well as stringent settings. (XLSX 197 kb)

Table S6.

List of matrix families with details and summary of all of the matrix matches on the StRDR5, SlRDR5, CaRDR5, NtRDR5, NaRDR5, HaRDR5, VvRDR5, PtRDR5, GhRDR5, CqRDR5, AlRDR5, MtRDR5, AhRDR5, and PsRDR5 promoter sequences based on the MatInspector’s default as well as stringent settings. (XLSX 495 kb)

Table S7.

List of probable interacting protein partners of SlRDRs and OsRDRs based on STRING database. Maximum degree of interaction was observed with the dicer like proteins (DCLs). Minimum required interaction score was medium confidence (0.400). (XLSX 74 kb)

Table S8.

Predicted protein partners of RDR3 and RDR5 of tomato and RDR3 and RDR4 of rice (top ten predicted partners are mentioned). Sequence information of RDR4 of tomato and RDR5 of rice are not available in the database (https://ncbi.nlm.nih.gov). (XLSX 38 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Prakash, V., Chakraborty, S. Identification of transcription factor binding sites on promoter of RNA dependent RNA polymerases (RDRs) and interacting partners of RDR proteins through in silico analysis. Physiol Mol Biol Plants 25, 1055–1071 (2019). https://doi.org/10.1007/s12298-019-00660-w

Download citation

Keywords

  • Promoter
  • RDRs
  • Interacting partners
  • In silico
  • Small RNA
  • Gene regulation