In silico characterization of synthetic promoters designed from mirabilis mosaic virus and rice tungro bacilliform virus
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ORIGINAL ARTICLE
In silico characterization of synthetic promoters designed from mirabilis mosaic virus and rice tungro bacilliform virus Dipinte Gupta1 • Rajiv Ranjan1
Received: 21 April 2020 / Accepted: 25 July 2020 Ó Indian Virological Society 2020
Abstract CaMV35S is the most extensively used promoter for ectopic gene expression in plant system. However, multiple use of this promoter possesses several limitation i.e. homologous based gene silencing and differential suitability in monocot and dicot plants. The strength of a promoter is defined by the presence of cis-acting elements and trans acting nucleic binding factors, thus its strength can be regulated by changing the architecture of these regulatory elements. In the present study, eight hybrid promoters were designed from two parareteroviruses, rice tungro bacilliform viruses (RTBV) and mirabilis mosaic virus (MMV). The eight hybrid promoters, along with parental promoters were characterized for the presence of functional cis-elements and transcription factor binding sites (TFBS), which were predicted using bioinformatics tools such as PLACE and Matinspector. Presence of mirabilis mosaic virus modules for specific functions and overrepresented modules was determined using Model inspector. A broad range of cis-elements (85), TFBS (1471) was obtained. Presence of Dehydration responsive element binding factors, Apetala 2 (AP2), WRKY, DNA binding with one finger DOF (DOFF) motifs had shown the functional relevance of these designed promoters with abiotic stress inducibility. In addition to these stress regulating TFBS, the presence of some enhancer like motifs such as
Electronic supplementary material The online version of this article (https://doi.org/10.1007/s13337-020-00617-8) contains supplementary material, which is available to authorized users. & Rajiv Ranjan [email protected] 1
Plant Biotechnology Lab, Department of Botany, Faculty of Science, Dayalbagh Educational Institute, Dayalbagh, Agra 282005, India
P$OCSE, P$TERE, P$TODS, P$ASRC had shown the functional relevance of these promoters as a strong candidate for enhanced expression of ectopic gene. Keywords Synthetic promoter Cis-elements Transcription factor
Introduction One of the key determinants used in plant biotechnology experiments is the appropriate choice of the promoter, which confers constitutive spatio temporal transgene expression [23, 22]. For accurate decoding and manipulating the regulatory framework of the gene, it is essential to accomplish refined and targeted modification in the architecture of promoters, which can be achieved to an extent using the available sophisticated in silico promoter models [16, 5] and various bioinformatics tools and approaches [6, 7, 20, 21] Chimeric synthetic promoters can be designed to clarify the basal mechanism of fundamental gene with the interaction of the TFs and can be used to understand better expression of gene in the regulation of promoters [22]. Therefore, it may be noted that synthetic promoters are of high importance in th
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