Proteomics in evolutionary ecology: linking the genotype with the phenotype

Abstract

The study of the proteome (proteomics), which includes the dynamics of protein expression, regulation, interactions and its function, has played a less prominent role in evolutionary and ecological investigations in comparison with the study of the genome and transcriptome. There are, however, a number of arguments suggesting that this situation should change. First, the proteome is closer to the phenotype than the genome or the transcriptome, and as such may be more directly responsive to natural selection, and thus closely linked to adaptation. Second, there is evidence of a low correlation between protein and transcript expression levels across genes in many different organisms. Finally, there have been some recent important technological improvements in proteomics methods that make them feasible, practical and useful to address a wide range of evolutionary questions even in nonmodel organisms. The different proteomic methods, their limitations and problems when interpreting empirical data are described and discussed. In addition, the proteomic literature pertaining to evolutionary ecology is reviewed with examples, and potential applications of proteomics in a variety of evolutionary contexts are outlined. New proteomic research trends such as the study of posttranslational modifications and protein-protein interactions, as well as the combined use of the different -omics approaches, are discussed in relation to the development of a more functional and integrated perspective, needed for achieving a more comprehensive knowledge of evolutionary change.

Expression Differentiation Is Constrained to Low-Expression Proteins over Ecological Timescales

“…Expression is typically measured at the mRNA level (Rokyta et al 2012;Margres et al 2013;Rokyta et al 2013). The proteome, however, is more representative of the actual phenotype (Diz et al 2012), particularly for venoms (Casewell et al 2014), and the specialization of the venom gland makes venom genetically tractable (Margres et al 2014(Margres et al , 2015a. Because venom is a secretion (Gibbs et al 2009), protein expression can be measured directly by reversed-phase high-performance liquid chromatography (RP-HPLC).…”

As formigas poneromorfas do Brasil

“…Além disso, possibilita a obtenção de informações quantitativas de proteínas expressas e modifi cações pós-transducionais que não podem ser deduzidas através do estudo do genoma (DIZ et al, 2012). Vale ressaltar, no entanto, que os bancos de dados genômicos e transcriptômicos facilitam as análises proteômi-cas, especialmente na identifi cação de proteínas.…”

Proteome response to heat stress in the Antarctic clam Laternula elliptica

“…In addition, it is likely that some changes occurring in mRNA expression do not result in changes at the corresponding protein level. Several studies have shown that predictions on protein expression levels based on changes in the corresponding mRNA abundance are not always met (reviewed in [5]). It is also possible that there is a time lag between the generation of mRNAs and subsequent protein production in response to changes in temperature.…”

“…In ecologically relevant non-model species, a greater number of investigations on the mechanisms underlying phenotypic change have focused on the transcriptome. Recent work has demonstrated that new hypotheses can be tested in proteomics studies in non-model organisms, opening the possibility of "addressing old problems, from a new perspective" (reviewed in [5]). e present paper demonstrates the application of an exploratory proteomics approach in the study of the physiologically important stress response in a non-model Antarctic species.…”