Genome-wide identification and comparative analysis of EPSPS (aroA) genes in different plant species
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Dosyalar
Tarih
2016
Yazarlar
Dergi Başlığı
Dergi ISSN
Cilt Başlığı
Yayıncı
Springer India
Erişim Hakkı
info:eu-repo/semantics/closedAccess
Özet
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 pi: 0.29 and theta: 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.
Açıklama
Filiz, Ertugrul/0000-0001-9636-6389
WOS: 000368040500004
WOS: 000368040500004
Anahtar Kelimeler
Shikimate pathway, Aromatic amino acids, In silico analysis, 3Dstructure, Nucleotide diversity, Molecular docking
Kaynak
Journal Of Plant Biochemistry And Biotechnology
WoS Q Değeri
Q3
Scopus Q Değeri
Q2
Cilt
25
Sayı
1
