Gupta Dipinte, Ranjan Rajiv
Plant Biotechnology Lab, Department of Botany, Faculty of Science, Dayalbagh Educational Institute (Deemed University), Dayalbagh, Agra, 282005 India.
Virusdisease. 2017 Dec;28(4):416-421. doi: 10.1007/s13337-017-0410-8. Epub 2017 Nov 28.
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.
启动子是位于基因编码区上游的特定核苷酸序列，参与转录的起始和调控。多种顺式作用元件构成启动子的结构，反式作用核酸结合因子与之结合并调节其活性。自1980年以来，副逆转录病毒的基因组就被用于开发高效启动子。其中，花椰菜花叶病毒是基因表达中使用最广泛的启动子。启动子强度背后的基本原理在于顺式元件的序列以及它们之间的间隔核苷酸元件，因此可以通过改变这些核苷酸序列来调节这些启动子片段的强度。在本研究中，从美国国立生物技术信息中心（NCBI）网站检索了植物副逆转录病毒八个推定启动子的序列。这些序列经过多种生物信息学工具分析，包括Clustal W、Plant Care、Mathinspector、ModelInspector，分别用于建立系统发育相似性、识别现有顺式元件的数量和质量、查找各种常见转录因子结合位点以及确定各种特定功能模块的存在情况。在系统发育分析中观察到28.80%-56.0%的识别率范围，其中奇异果花叶病毒和大丽花花叶病毒的相似性最高。获得了广泛的顺式元件（51个）、转录因子结合位点（512个），并且观察到60%的模块与DOFF基序结合，这表明其与非生物胁迫诱导性具有功能相关性。本研究揭示了这些元件在副逆转录病毒基因组基因调控中的功能意义，也为设计新型合成启动子提供了总体思路。
