A data-independent acquisition (DIA) assay library for quantitation of environmental effects on the kidney proteome of Oreochromis niloticus.
A data-independent acquisition (DIA) assay library for quantitation of environmental effects on the kidney proteome of Oreochromis niloticus.
复制标题
数据独立采集 (DIA) 检测库，用于定量环境对尼罗罗非鱼肾脏蛋白质组的影响。
DOI：
10.1111/1755-0998.13445
复制
发表时间：
2021
影响因子：
7.7
通讯作者：
Kültz,Dietmar
中科院分区：
文献类型：
--
作者：
Root,Larken;Campo,Aurora;MacNiven,Leah;Con,Pazit;Cnaani,Avner;Kültz,Dietmar
生物与环境的相互作用是复杂的，在生物组织的不同层次上的环境调节往往是非线性的。因此，从基因型到表现型的连续体需要在多个组织层次上进行研究。虽然转录组调控的研究现在对许多物种都很常见，但还需要对环境对蛋白质组的影响进行定量研究。在这里，我们报告了一个数据独立采集（DIA）测定文库的生成，该文库使用非常适合生态相关的现场样品的无标记和无凝胶工作流程，能够同时靶向蛋白质组学数千Oreochromis niloticus肾脏蛋白。我们通过辨别环境对肾脏蛋白质组ofO的影响来证明这种DIA测定库的有用性。尼罗河。此外，我们证明了DIA测定文库方法产生的数据是互补的，而不是多余的转录组数据。在2114个独特的基因的转录本和蛋白质丰度的差异，适应淡水和半咸水（25 g/kg）罗非鱼肾脏相关。转录组和蛋白质组的盐度依赖性调节中存在高度的非线性，表明环境盐度对尼罗罗非鱼肾功能的调节在很大程度上依赖于转录后机制。使用STRING和KEGG的功能富集分析在DIA测定数据集上的应用通过鉴定肌肌醇代谢、抗氧化剂和异源生物质功能以及信号传导机制作为罗非鱼肾脏中受盐度控制的关键元素来证明。DIA分析库资源可以用于其他组织和其他生物体，以研究在不断变化的生态环境中的蛋白质组动态。
Interactions of organisms with their environment are complex and environmental regulation at different levels of biological organization is often nonlinear. Therefore, the genotype to phenotype continuum requires study at multiple levels of organization. While studies of transcriptome regulation are now common for many species, quantitative studies of environmental effects on proteomes are needed. Here we report the generation of a data‐independent acquisition (DIA) assay library that enables simultaneous targeted proteomics of thousands ofOreochromis niloticuskidney proteins using a label‐ and gel‐free workflow that is well suited for ecologically relevant field samples. We demonstrate the usefulness of this DIA assay library by discerning environmental effects on the kidney proteome ofO. niloticus. Moreover, we demonstrate that the DIA assay library approach generates data that are complimentary rather than redundant to transcriptomic data. Transcript and protein abundance differences in kidneys of tilapia acclimated to freshwater and brackish water (25 g/kg) were correlated for 2114 unique genes. A high degree of non‐linearity in salinity‐dependent regulation of transcriptomes and proteomes was revealed suggesting that the regulation ofO.niloticusrenal function by environmental salinity relies heavily on post‐transcriptional mechanisms. The application of functional enrichment analyses using STRING and KEGG to DIA assay data sets is demonstrated by identifyingmyo‐inositol metabolism, antioxidant and xenobiotic functions, and signalling mechanisms as key elements controlled by salinity in tilapia kidneys. The DIA assay library resource presented here can be adopted for other tissues and other organisms to study proteome dynamics during changing ecological contexts.