School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China; Centre for Sustainable Aquatic Ecosystems, Harry Butler Institute, School of Veterinary & Life Sciences, Murdoch University, South Street, Murdoch, Western Australia, 6150, Australia.
Centre for Sustainable Aquatic Ecosystems, Harry Butler Institute, School of Veterinary & Life Sciences, Murdoch University, South Street, Murdoch, Western Australia, 6150, Australia.
Fish Shellfish Immunol. 2023 Jan;132:108506. doi: 10.1016/j.fsi.2022.108506. Epub 2022 Dec 24.
Recently, Vibrio anguillarum, a Gram-negative pathogenic bacterium, has been becoming a major constraint on the development of the turbot aquaculture industry because of its characteristics of worldwide distribution, broad host range and potentially devastating impacts. Although the functions of protein-coding mRNAs in the immune response against bacterial infection have been reported, as well as several non-coding RNAs (ncRNAs), such as circular RNAs (circRNAs) and microRNAs (miRNAs), the relationships between mRNAs and ncRNAs in the immune system of turbot liver are still limited during bacterial infection. In present study, the comprehensive analyses of whole-transcriptome sequencing were conducted in turbot liver infected by V. anguillarum. The differential expression was analyzed in the data of circRNAs, miRNAs, and mRNAs. The interactions of miRNA-circRNA pairs and miRNA-mRNA pairs were predicted basing on the negative regulatory relationships between miRNAs and their target circRNAs\mRNAs. The circRNA-related ceRNA regulatory networks were constructed for the analyses of regulated mechanism in turbot immune system. Subsequently, the RT-qPCR was carried out to verify the results of sequencing. Finally, we identified 31 circRNAs, 53 miRNAs and 948 mRNAs with differential expression. Gene set enrichment analyses using Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways showed that innate immunity was principally activated at the early stages of infection, while adaptive immunity was activated after 24 h. Finally, 65 circRNA-miRNA-mRNA pathways were constructed, based on the hypothesis of ceRNA regulatory networks. In conclusion, our findings provide new insights on the underlying immune response to bacterial infection and identify novel target genes for the prevention and control of disease in turbot.
最近，一种革兰氏阴性致病性细菌鳗弧菌由于其分布广泛、宿主范围广和潜在的破坏性影响，成为了大菱鲆养殖业发展的主要制约因素。虽然已经报道了蛋白质编码 mRNA 在免疫反应中对抗细菌感染的功能，以及几种非编码 RNA（ncRNA），如环状 RNA（circRNA）和 microRNA（miRNA），但在细菌感染期间，大菱鲆肝脏的免疫系统中 mRNA 和 ncRNA 之间的关系仍然有限。在本研究中，对鳗弧菌感染的大菱鲆肝脏进行了全转录组测序的综合分析。分析了 circRNA、miRNA 和 mRNA 的差异表达。基于 miRNA 和其靶 circRNA/mRNA 之间的负调控关系，预测了 miRNA-circRNA 对和 miRNA-mRNA 对的相互作用。构建了 circRNA 相关的 ceRNA 调控网络，用于分析大菱鲆免疫系统的调控机制。随后，进行了 RT-qPCR 验证测序结果。最后，我们鉴定出 31 个 circRNA、53 个 miRNA 和 948 个 mRNA 具有差异表达。使用基因本体论（GO）和京都基因与基因组百科全书（KEGG）通路的基因集富集分析表明，固有免疫在感染早期主要被激活，而适应性免疫在 24 小时后被激活。最后，构建了 65 个 circRNA-miRNA-mRNA 通路，基于 ceRNA 调控网络的假设。总之，我们的研究结果为细菌感染的潜在免疫反应提供了新的见解，并为大菱鲆疾病的预防和控制鉴定了新的靶基因。
