Identification and characterization of RNA polymerase II (RNAP) C-Terminal domain phosphatase-like 3 (SlCPL3) in tomato under biotic stress

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dc.authoridSAEED, FAISAL/0000-0002-3508-1213
dc.authoridBakhsh, Allah/0000-0003-3561-7863
dc.authoridHashmi, Muneeb Hassan/0000-0002-2873-5661
dc.authoridDemirel, Ufuk/0000-0002-3457-5086
dc.contributor.authorSaeed, Faisal
dc.contributor.authorHashmi, Muneeb Hassan
dc.contributor.authorAksoy, Emre
dc.contributor.authorDemirel, Ufuk
dc.contributor.authorBakhsh, Allah
dc.date.accessioned2024-11-07T13:34:29Z
dc.date.available2024-11-07T13:34:29Z
dc.date.issued2023
dc.departmentNiğde Ömer Halisdemir Üniversitesi
dc.description.abstractBackgroundBacterial diseases are a huge threat to the production of tomatoes. During infection intervals, pathogens affect biochemical, oxidant and molecular properties of tomato. Therefore, it is necessary to study the antioxidant enzymes, oxidation state and genes involved during bacterial infection in tomato.Methods and resultsDifferent bioinformatic analyses were performed to conduct homology, gene promoter analysis and determined protein structure. Antioxidant, MDA and H2O2 response was measured in Falcon, Rio grande and Sazlica tomato cultivars. In this study, RNA Polymerase II (RNAP) C-Terminal Domain Phosphatase-like 3 (SlCPL-3) gene was identified and characterized. It contained 11 exons, and encoded for two protein domains i.e., CPDCs and BRCT. SOPMA and Phyre2, online bioinformatic tools were used to predict secondary structure. For the identification of protein pockets CASTp web-based tool was used. Netphos and Pondr was used for prediction of phosphorylation sites and protein disordered regions. Promoter analysis revealed that the SlCPL-3 is involved in defense-related mechanisms. We further amplified two different regions of SlCPL-3 and sequenced them. It showed homology respective to the reference tomato genome. Our results showed that SlCPL-3 gene was triggered during bacterial stress. SlCPL-3 expression was upregulated in response to bacterial stress during different time intervals. Rio grande showed a high level of SICPL-3 gene expression after 72 hpi. Biochemical and gene expression analysis showed that under biotic stress Rio grande cultivar is more sensitive to Pst DC 3000 bacteria.ConclusionThis study lays a solid foundation for the functional characterization of SlCPL-3 gene in tomato cultivars. All these findings would be beneficial for further analysis of SlCPL-3 gene and may be helpful for the development of resilient tomato cultivars.
dc.identifier.doi10.1007/s11033-023-08564-5
dc.identifier.endpage6793
dc.identifier.issn0301-4851
dc.identifier.issn1573-4978
dc.identifier.issue8
dc.identifier.pmid37392286
dc.identifier.scopus2-s2.0-85163791353
dc.identifier.scopusqualityQ2
dc.identifier.startpage6783
dc.identifier.urihttps://doi.org/10.1007/s11033-023-08564-5
dc.identifier.urihttps://hdl.handle.net/11480/16013
dc.identifier.volume50
dc.identifier.wosWOS:001020148800006
dc.identifier.wosqualityQ3
dc.indekslendigikaynakWeb of Science
dc.indekslendigikaynakScopus
dc.indekslendigikaynakPubMed
dc.language.isoen
dc.publisherSpringer
dc.relation.ispartofMolecular Biology Reports
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanı
dc.rightsinfo:eu-repo/semantics/closedAccess
dc.snmzKA_20241106
dc.subjectCPL-3
dc.subjectBiotic stress
dc.subjectTomato
dc.subjectRNAP II
dc.subjectPseudomonas syringae
dc.titleIdentification and characterization of RNA polymerase II (RNAP) C-Terminal domain phosphatase-like 3 (SlCPL3) in tomato under biotic stress
dc.typeArticle

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