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Genome-wide identification and comparative analysis of EPSPS (aroA) genes in different plant species

Abstract

Shikimate pathway produces aromatic amino acids such as phenylalanine, tyrosine and tryptophan, which is essential for plant life. EPSPS (5-enolpyruvylshikimate-3-phosphate synthase, EC 2.5.1.1.9) (aroA) that observed in plants and bacteria plays an important role in shikimate pathway as being the sixth crucial enzyme. In this study, genome-wide comparative analyses of EPSPS genes were performed in different plant species, including Glycine max, Medicago truncatula, Brachypodium disctahyon, Zea mays, Chlamydomonas reinhardtii (green alga), and Physcomitrella patens (moss). One EPSPS gene was identified in M. truncatula, B. distachyon, Z. mays, and C. reinhardtii while two EPSPS genes identified in G. max and P. patens. Based on nucleotide diversity analyses of EPSPS genes, nucleotide diversity was found to be π: 0.29 and θ: 0.34, respectively. Gene structure analysis revealed that 6 of 8 EPSPS genes (75 %) contained seven introns while the length of open reading frame (ORF) ranged from 1173 to 1611 bp. Two highly conserved motifs (LPGSKSLSNRILLLAAL and LFLGNAGTAMRPL) were detected in all plant species. All putative EPSPSs were predicted to be localized in chloroplast while 7 of 8 EPSPSs (87.5 %) contained N-glycosylation sites except for Chlamydomonas. Phylogenetic analyses showed that monocots, dicots, and moss were clustered in group A whereas green alga (C. reinhardtii) was located alone in group B. 3D structure analyses indicated that EPSP synthases contained N-terminal and C-terminal domains while electrostatic potential of EPSPSs were found to exhibit various patterns. In addition, ligand molecule glyphosate was docked with EPSPS of B. disctahyon and G. max. The result showed that there were strong favorable bonds between the proteins and the ligand with favorable conformation.

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Abbreviations

EPSPS:

5-enolpyruvylshikimate-3-phosphate synthase

DAHPS:

3-deoxy-d-arabino-heptulosonate-7-phosphate synthase

DHQS:

3-dehydroquinate synthase

SK:

Shikimate kinase

CS:

Chorismate synthase

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Correspondence to Ertugrul Filiz.

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Ertugrul Filiz holds a PhD in Duzce University.

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Filiz, E., Koc, I. Genome-wide identification and comparative analysis of EPSPS (aroA) genes in different plant species. J. Plant Biochem. Biotechnol. 25, 21–29 (2016). https://doi.org/10.1007/s13562-015-0303-0

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Keywords

  • Shikimate pathway
  • Aromatic amino acids
  • In silico analysis
  • 3D structure
  • Nucleotide diversity
  • Molecular docking