Research Unit in Environmental and Evolutionary Biology (URBE), University of Namur (FUNDP), Rue de Bruxelles 61, B-5000, Namur, Belgium.
Integr Comp Biol. 2012 Nov;52(5):681-94. doi: 10.1093/icb/ics087. Epub 2012 May 28.
Nowadays, the unprecedented rates of anthropogenic changes in ecosystems suggest that organisms have to migrate to new distributional ranges or to adapt commensurately quickly to new conditions to avoid becoming extinct. Pollution and global warming are two of the most important threats aquatic organisms will have to face in the near future. If genetic changes in a population in response to natural selection are extensively studied, the role of acclimation through phenotypic plasticity (the property of a given genotype to produce different phenotypes in response to particular environmental conditions) in a species to deal with new environmental conditions remains largely unknown. Proteomics is the extensive study of the protein complement of a genome. It is dynamic and depends on the specific tissue, developmental stage, and environmental conditions. As the final product of gene expression, it is subjected to several regulatory steps from gene transcription to the functional protein. Consequently, there is a discrepancy between the abundance of mRNA and the abundance of the corresponding protein. Moreover, proteomics is closer to physiology and gives a more functional knowledge of the regulation of gene expression than does transcriptomics. The study of protein-expression profiles, however, gives a better portrayal of the cellular phenotype and is considered as a key link between the genotype and the organismal phenotype. Under new environmental conditions, we can observe a shift of the protein-expression pattern defining a new cellular phenotype that can possibly improve the fitness of the organism. It is now necessary to define a proteomic norm of reaction for organisms acclimating to environmental stressors. Its link to fitness will give new insights into how organisms can evolve in a changing environment. The proteomic literature bearing on chronic exposure to pollutants and on acclimation to heat stress in aquatic organisms, as well as potential application of proteomics in evolutionary issues, are outlined. While the transcriptome responses are commonly investigated, proteomics approaches now need to be intensified, with the new perspective of integrating the cellular phenotype with the organismal phenotype and with the mechanisms of the regulation of gene expression, such as epigenetics.
如今，生态系统中前所未有的人为变化速度表明，生物必须迁移到新的分布范围，或者快速适应新的条件，以避免灭绝。污染和全球变暖是水生生物在不久的将来将不得不面对的两个最重要的威胁。如果广泛研究种群对自然选择的遗传变化，那么物种通过表型可塑性（特定基因型在响应特定环境条件时产生不同表型的特性）来适应新环境条件的作用在很大程度上仍然未知。蛋白质组学是对基因组中蛋白质组的广泛研究。它是动态的，取决于特定的组织、发育阶段和环境条件。作为基因表达的最终产物，它受到从基因转录到功能蛋白的几个调节步骤的影响。因此，mRNA 的丰度与相应蛋白质的丰度之间存在差异。此外，蛋白质组学更接近生理学，并且比转录组学更能提供基因表达调控的功能知识。然而，蛋白质表达谱的研究更能描绘细胞表型，并被认为是基因型和生物体表型之间的关键联系。在新的环境条件下，我们可以观察到蛋白质表达模式的转变，定义新的细胞表型，这可能会提高生物体的适应性。现在有必要为适应环境胁迫的生物体定义一个蛋白质组反应规范。它与适应性的联系将为生物体如何在不断变化的环境中进化提供新的见解。本文概述了水生生物慢性暴露于污染物和热应激适应的蛋白质组文献，以及蛋白质组学在进化问题上的潜在应用。虽然转录组的反应通常被研究，但现在需要加强蛋白质组学的方法，从整合细胞表型和生物体表型以及基因表达调控机制（如表观遗传学）的新视角来进行研究。
