School of Chemical and Biotechnology, SASTRA University, Thanjavur, 613401 India.
Centre for Advanced Research in Indian System of Medicine (CARISM), SASTRA University, Thanjavur, 613401 India.
Comput Biol Chem. 2018 Feb;72:181-191. doi: 10.1016/j.compbiolchem.2017.11.004. Epub 2017 Nov 13.
Plant secondary metabolites are widely used in human disease treatment; though primary metabolism provides precursors for secondary metabolism, not much has been studied to unravel the link connecting both the processes. Most common form of gene regulation interconnecting diverse metabolism occurs at the transcriptional and/or posttranscriptional level mediated by regulatory cis-elements. The present study aims at understanding the common cis-elements network connecting the major primary metabolic enzyme, cell wall invertase (CWIN) and secondary metabolism genes in Nicotiana benthamiana (N. benthamiana). The CWIN and thirty one other gene sequences were extracted from N. benthamiana genome, followed by cis-element analysis of their 5' upstream and 3' downstream region using different programs (Genomatix software suite; PLACE and PlantCARe). Comparative cis-element analysis of CWIN (N. benthamiana and other plant species) and other primary, secondary metabolism and transcription factor genes (N. benthamiana) revealed the occurrence of common stress associated cis-elements. Predominantly, AHBP, L1BX, MYBL, MADS, MYBS, GTBX, DOFF and CCAF were found in the 5' upstream region of all genes, whereas AHBP, MYBL, L1BX, HEAT, CCAF and KAN1 were largely occurring in the 3' downstream region of all genes; indicating common function of these elements in transcriptional and posttranscriptional gene regulation. Further, genomic analysis using FGENESH, GenScan and homology based methods (BlastX and BlastN) was performed on the N. benthamiana contigs harboring CWIN and PAL, in an attempt to identify genomic neighborhood genes. The 5' upstream and 3' downstream region of genes in the genomic neighborhood of CWIN and PAL were also subjected to similar cis-element analysis, and the results indicated cis-elements profile similar to CWIN, PAL and other primary, secondary metabolism and transcription factor genes. The results of evolutionary studies confirmed that the 5' upstream region of NbCWINs significantly showed more proximity to secondary metabolism genes 4CL and the redox gene SOD, followed by the phenylpropanoid pathway gene CHI. The 3' downstream regions of NbCWINs were more closely related to other plant CWINs, followed by the redox gene, SOD and primary metabolism gene FBA. Thus, the commonly found stress responsive cis-elements in our study can play a vital role in modulating key pathways of both primary and secondary metabolism; thereby postulating their role in regulating plant growth and metabolisms under unfavourable growth conditions.
植物次生代谢产物被广泛应用于人类疾病的治疗中；尽管初级代谢为次生代谢提供了前体，但对于连接这两个过程的联系，人们的研究还不多。最常见的基因调控形式是通过调节顺式元件在转录和/或转录后水平上连接不同的代谢。本研究旨在了解连接主要初级代谢酶细胞壁转化酶（CWIN）和烟草原生质体（Nicotiana benthamiana）中次生代谢基因的常见顺式元件网络。从烟草原生质体基因组中提取了 CWIN 和 31 个其他基因序列，然后使用不同的程序（Genomatix 软件套件；PLACE 和 PlantCARE）对其 5'上游和 3'下游区域进行顺式元件分析。对 CWIN（烟草原生质体和其他植物物种）和其他初级、次级代谢和转录因子基因（烟草原生质体）的顺式元件进行比较分析，揭示了常见的应激相关顺式元件的存在。AHBP、L1BX、MYBL、MADS、MYBS、GTBX、DOFF 和 CCAF 主要存在于所有基因的 5'上游区域，而 AHBP、MYBL、L1BX、HEAT、CCAF 和 KAN1 则主要存在于所有基因的 3'下游区域；表明这些元件在转录和转录后基因调控中具有共同的功能。此外，还使用 FGENESH、GenScan 和基于同源性的方法（BlastX 和 BlastN）对含有 CWIN 和 PAL 的烟草原生质体进行基因组分析，试图鉴定基因组邻近基因。CWIN 和 PAL 基因组邻近基因的 5'上游和 3'下游区域也进行了类似的顺式元件分析，结果表明顺式元件图谱与 CWIN、PAL 和其他初级、次级代谢和转录因子基因相似。进化研究的结果证实，NbCWINs 的 5'上游区域与次级代谢基因 4CL 和氧化还原基因 SOD 显著接近，其次是苯丙素途径基因 CHI。NbCWINs 的 3'下游区域与其他植物的 CWINs 更密切相关，其次是氧化还原基因 SOD 和初级代谢基因 FBA。因此，我们研究中发现的常见应激响应顺式元件可能在调节初级和次级代谢的关键途径中发挥重要作用；从而推测它们在调节植物在不利生长条件下的生长和代谢中的作用。
