Application of proteomics to ecology and population biology

Abstract

Proteomics is a relatively new scientific discipline that merges protein biochemistry, genome biology and bioinformatics to determine the spatial and temporal expression of proteins in cells, tissues and whole organisms. There has been very little application of proteomics to the fields of behavioral genetics, evolution, ecology and population dynamics, and has only recently been effectively applied to the closely allied fields of molecular evolution and genetics. However, there exists considerable potential for proteomics to impact in areas related to functional ecology; this review will introduce the general concepts and methodologies that define the field of proteomics and compare and contrast the advantages and disadvantages with other methods. Examples of how proteomics can aid, complement and indeed extend the study of functional ecology will be discussed including the main tool of ecological studies, population genetics with an emphasis on metapopulation structure analysis. Because proteomic analyses provide a direct measure of gene expression, it obviates some of the limitations associated with other genomic approaches, such as microarray and EST analyses. Likewise, in conjunction with associated bioinformatics and molecular evolutionary tools, proteomics can provide the foundation of a systems-level integration approach that can enhance ecological studies. It can be envisioned that proteomics will provide important new information on issues specific to metapopulation biology and adaptive processes in nature. A specific example of the application of proteomics to sperm ageing is provided to illustrate the potential utility of the approach.

Proteomic analysis of muscle between hybrid abalone and parental lines Haliotis gigantea Reeve and Haliotis discus hannai Ino

“…Recently, some studies suggest that hybridization between two parents can cause changes in gene expression, which may be responsible for heterosis (Xiang et al, 2013). Although relatively new genomics for genetic breeding studies concentrate on transcriptomics, the value of proteomic analysis is appreciated (Karr, 2007). Complex regulatory routes from posttranslational modifications to protein turnover cannot be studied at the cDNA level, and changes in gene expression do not necessarily reflect the changes in protein abundance (Xiang et al, 2013).…”

Proteomic characterization of a temperature-sensitive conditional lethal in Drosophila melanogaster

“…Proteome analysis is particularly well suited to characterize population-specific differences on a biological level very close to phenotypic fitness (Chevalier et al, 2004;Biron et al, 2006;Karr, 2008). In particular, genotypeenvironment interactions might be regulated by changes in cis/trans regulating factors, methylation status and post-translational modifications.…”

Gene-Expression Novelty in Allopolyploid Cotton: A Proteomic Perspective

“…However, the transcriptome itself is insufficient for understanding the end products of gene expression and phenotypic outcomes (Rose et al 2004;Thelen and Peck 2007;Karr 2008;Vogel and Marcotte 2012;Ponnala et al 2014). Because proteins are the major catalysts of cellular activities, the phenotype of an organism arguably may be more directly related to protein abundance and function than to transcriptional abundance (Karr 2008;Diz et al 2012). Thus, comparative proteomics offers an important perspective on evolutionary processes.…”