Marine Proteomics: A Critical Assessment of an Emerging Technology

Abstract

The application of proteomics to marine sciences has increased in recent years because the proteome represents the interface between genotypic and phenotypic variability and, thus, corresponds to the broadest possible biomarker for eco-physiological responses and adaptations. Likewise, proteomics can provide important functional information regarding biosynthetic pathways, as well as insights into mechanism of action, of novel marine natural products. The goal of this review is to (1) explore the application of proteomics methodologies to marine systems, (2) assess the technical approaches that have been used, and (3) evaluate the pros and cons of this proteomic research, with the intent of providing a critical analysis of its future roles in marine sciences. To date, proteomics techniques have been utilized to investigate marine microbe, plant, invertebrate, and vertebrate physiology, developmental biology, seafood safety, susceptibility to disease, and responses to environmental change. However, marine proteomics studies often suffer from poor experimental design, sample processing/optimization difficulties, and data analysis/interpretation issues. Moreover, a major limitation is the lack of available annotated genomes and proteomes for most marine organisms, including several "model species". Even with these challenges in mind, there is no doubt that marine proteomics is a rapidly expanding and powerful integrative molecular research tool from which our knowledge of the marine environment, and the natural products from this resource, will be significantly expanded.

Proteomic Analysis of Eggs from Mytilus edulis Females Differing in Mitochondrial DNA Transmission Mode

“…Proteomics has made a rapid progress when applied to model species where genomic databases are well developed, but recent reviews have pointed to the growing interest in applying proteomics to nonmodel species in areas such as evolutionary ecology (1), aquatic toxicology (2), aquatic pollution (3), aquaculture (4), and marine biology (5). In the marine mussel genus Mytilus, an unusual system of mtDNA inheritance occurs characterized by the presence of two mitochondrial genomes (called F and M) one of which is inherited maternally and the other paternally (6 -9).…”

Proteomic profiling of healthy and diseased hybrid soft corals Sinularia maxima × S. polydactyla

“…Several other proteins, including glutathione peroxidase (which is an oxidative stress response protein), chaperone proteins and proteins involved in metabolism and biosynthesis were also identified in the soft coral samples, but these did not exhibit significant up-or down-regulation in the diseased soft corals. This may be an artefact of the limited number of annotated cnidarian proteins within existing proteomic databases and represents an interpretative challenge for researchers working with non-model marine organisms (Slattery et al 2012, Weston et al 2012.…”

“…Specifically, expression proteomics, or proteomic profiling, provides information about the differentially expressed proteins between 2 conditions under consideration (e.g. healthy and diseased), while functional proteomics deals with the study of the biological functions of proteins and their relationships to disease processes (reviewed in Slattery et al 2012).…”

Perspectives on Chemical Oceanography in the 21st century: Participants of the COME ABOARD Meeting examine aspects of the field in the context of 40 years of DISCO

“…Research on the cycling of specific organic compounds through proteomics, metabolomics, lipidomics and the chemical and structural characterization of organic matter represent Emerging areas of Chemical Oceanography. These types of measurements (e.g., Collins et al, 2016;Heal et al, 2017;Kharbush et al, 2016;Kido Soule et al, 2015;Koch et al, 2005;Pearson, 2014;Slattery et al, 2012) may have a solid theoretical basis but their interpretive power is currently limited by the extent of application. For example, marine proteomics studies have revealed physiological responses of Southern Ocean phytoplankton to changing environmental conditions (Boyd et al, 2016), identified combined nutrient stressors in the Pacific Ocean , and been used to track organic nitrogen sources from the water column to sediment burial in the Bering Sea (Moore et al, 2012), demonstrating the field's emerging interpretive power.…”