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

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dc.contributor.authorFiliz, Ertuğrul
dc.contributor.authorKoç, İbrahim
dc.date.accessioned2020-05-01T12:10:13Z
dc.date.available2020-05-01T12:10:13Z
dc.date.issued2016
dc.departmentDÜ, Çilimli Meslek Yüksekokulu, Bitkisel ve Hayvansal Üretim Bölümüen_US
dc.descriptionFiliz, Ertugrul/0000-0001-9636-6389en_US
dc.descriptionWOS: 000368040500004en_US
dc.description.abstractShikimate 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.en_US
dc.identifier.doi10.1007/s13562-015-0303-0en_US
dc.identifier.endpage29en_US
dc.identifier.issn0971-7811
dc.identifier.issn0974-1275
dc.identifier.issue1en_US
dc.identifier.scopusqualityQ2en_US
dc.identifier.startpage21en_US
dc.identifier.urihttps://doi.org/10.1007/s13562-015-0303-0
dc.identifier.urihttps://hdl.handle.net/20.500.12684/6087
dc.identifier.volume25en_US
dc.identifier.wosWOS:000368040500004en_US
dc.identifier.wosqualityQ3en_US
dc.indekslendigikaynakWeb of Scienceen_US
dc.indekslendigikaynakScopusen_US
dc.language.isoenen_US
dc.publisherSpringer Indiaen_US
dc.relation.ispartofJournal Of Plant Biochemistry And Biotechnologyen_US
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanıen_US
dc.rightsinfo:eu-repo/semantics/closedAccessen_US
dc.subjectShikimate pathwayen_US
dc.subjectAromatic amino acidsen_US
dc.subjectIn silico analysisen_US
dc.subject3Dstructureen_US
dc.subjectNucleotide diversityen_US
dc.subjectMolecular dockingen_US
dc.titleGenome-wide identification and comparative analysis of EPSPS (aroA) genes in different plant speciesen_US
dc.typeArticleen_US

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