In-silico analysis and expression profiling implicate diverse role of EPSPS family genes in regulating developmental and metabolic processes

Abstract

BackgroundThe EPSPS, EC 2.5.1.19 (5-enolpyruvylshikimate −3-phosphate synthase) is considered as one of the crucial enzyme in the shikimate pathway for the biosynthesis of essential aromatic amino acids and secondary metabolites in plants, fungi along with microorganisms. It is also proved as a specific target of broad spectrum herbicide glyphosate.ResultsOn the basis of structure analysis, this EPSPS gene family comprises the presence of EPSPS I domain, which is highly conserved among different plant species. Here, we followed an in-silico approach to identify and characterize the EPSPS genes from different plant species. On the basis of their phylogeny and sequence conservation, we divided them in to two groups. Moreover, the interacting partners and co-expression data of the gene revealed the importance of this gene family in maintaining cellular and metabolic functions in the cell. The present study also highlighted the highest accumulation of EPSPS transcript in mature leaves followed by young leaves, shoot and roots of tobacco. In order to gain the more knowledge about gene family, we searched for the previously reported motifs and studied its structural importance on the basis of homology modelling.ConclusionsThe results presented here is a first detailed in-silico study to explore the role of EPSPS gene in forefront of different plant species. The results revealed a great deal for the diversification and conservation of EPSPS gene family across different plant species. Moreover, some of the EPSPS from different plant species may have a common evolutionary origin and may contain same conserved motifs with related and important molecular function. Most importantly, overall analysis of EPSPS gene elucidated its pivotal role in immense function within the plant, both in regulating plant growth as well its development throughout the life cycle of plant. Since EPSPS is a direct target of herbicide glyphosate, understanding its mechanism for regulating developmental and cellular processes in different plant species would be a great revolution for developing glyphosate resistant crops.

Characterization of the Amaranthus palmeri Physiological Response to Glyphosate in Susceptible and Resistant Populations

“…Increases in EPSPS mRNA levels 321 after glyphosate have been reported previously, suggesting transcriptional regulation, in 322 resistant and sensitive biotypes of Eleusine indica, 50 Lolium rigidum 51 and tobacco. 52 By 323 contrast, in A. tuberculatus with multiple EPSPS copies, no increase in EPSPS expression was 324 detected after glyphosate application. 23…”

A 5-Enolpyruvylshikimate 3-Phosphate Synthase Functions as a Transcriptional Repressor in Populus

“…Although the proteins encoded by these two genes share 90.0% sequence similarity, Potri.002G146400, the candidate gene, carries an extra exon in the 5′ region, resulting in a longer cDNA transcript with a total of 1557 nucleotides and encoding a protein with 518 amino acids (∼56 kD), which is larger than the canonical EPSP synthase (∼46 kD) ( Figure 2A). By contrast, the transcript for the putative paralog Potri.014G068300 is 1173 nucleotides long and encodes a protein with 390 amino acids, corresponding to the canonical EPSP sequences reported in multiple organisms (Garg et al, 2014). To determine whether the two putative Populus paralogs retain EPSP synthase activity, we expressed GST-tagged proteins in Escherichia coli and purified them (GST-Potri.002G146400 and GST-Potri.014G068300; Figure 2B).…”

Multiple mechanism confers natural tolerance of three lilyturf species to glyphosate

“…Because of their high homology, the full length of EPSPS gene in LP was amplified according to that in LS. Additionally, sequences of plant EPSPS genes were obtained from GenBank, pooled, and redundancy was removed as in Garg et al (2014). Phylogenetic trees were created by MEGA software (http://www.megasoftware.net/) for homology analysis.…”