Department of Agricultural Genetic Engineering, Faculty of Agricultural Sciences and Technologies, Nigde Omer Halisdemir University, 51240, Nigde, Turkey.
Dept. of Biological Sciences, Middle East Technical University, 06800, Cankaya, Ankara, Turkey.
Mol Biol Rep. 2023 Aug;50(8):6783-6793. doi: 10.1007/s11033-023-08564-5. Epub 2023 Jul 1.
Bacterial 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.
Different bioinformatic analyses were performed to conduct homology, gene promoter analysis and determined protein structure. Antioxidant, MDA and HO 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.
This 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.
细菌病害是番茄生产的巨大威胁。在感染间隔期间，病原体影响番茄的生化、氧化和分子特性。因此，有必要研究番茄细菌感染过程中的抗氧化酶、氧化状态和相关基因。
对不同的生物信息学分析进行了同源性分析、基因启动子分析和蛋白质结构预测。在 Falcon、Rio grande 和 Sazlica 番茄品种中测量了抗氧化剂、MDA 和 HO 的响应。在这项研究中，鉴定并表征了 RNA 聚合酶 II（RNAP）C 端结构域磷酸酶样 3（SlCPL-3）基因。它包含 11 个外显子，编码两个蛋白质结构域，即 CPDCs 和 BRCT。使用 SOPMA 和 Phyre2 在线生物信息学工具预测二级结构。使用 CASTp 网络工具鉴定蛋白质口袋。使用 Netphos 和 Pondr 预测磷酸化位点和蛋白质无序区。启动子分析表明 SlCPL-3 参与防御相关机制。我们进一步扩增了 SlCPL-3 的两个不同区域并对其进行测序。它与参考番茄基因组具有同源性。我们的结果表明，SlCPL-3 基因在细菌胁迫下被触发。SlCPL-3 在不同时间间隔对细菌胁迫的响应而上调表达。Rio grande 在 72 hpi 后显示出高水平的 SICPL-3 基因表达。生化和基因表达分析表明，在生物胁迫下，Rio grande 品种对 Pst DC 3000 细菌更为敏感。
本研究为番茄品种中 SlCPL-3 基因的功能表征奠定了坚实的基础。所有这些发现都将有助于进一步分析 SlCPL-3 基因，并可能有助于开发具有弹性的番茄品种。
