Marine proteomics

Abstract

A wealth of information is recorded in a protein's primary sequence, which can be used to determine its biological function and origin, and provide clues to the mechanisms of degradation. In contrast to DNA, proteins and their amino acid constituents have demonstrated a wide-spread presence outside the cell, preserved in the environment. In marine samples, proteins are present as mixtures from numerous sources in a salty, complex matrix at low concentrations. As a result of these factors, studies of this nitrogen-based component in the oceans have previously been limited to bulk elemental and amino acid analyses; these analyses were incapable of providing details regarding protein sequence, function and source information. Advances in biological mass spectrometry now allow for the analysis and characterization of the protein component from the marine environment. Proteomic mass spectrometry is a high-throughput analysis of protein mixtures that does not require any prior knowledge of the original protein structures in the mixture, making it an ideal technique for marine studies. Potential marine applications of proteomics include: analyzing organisms cultured under different nutrient conditions to examine cellular expression and adaptation, profiling the marine dissolved and particulate organic matter pools to determine source information and understand long-term carbon preservation, and verifying genomic findings with proteomic analyses to determine which genes are translated and to what extent the protein is expressed. Although some major advances in marine studies and mass spectrometry have been made, there remains a significant amount of methods development and community education before the full potential of proteomics is reached.

Iron biogeochemistry across marine systems – progress from the past decade

“…7. Further, our increasing ability to detect and characterize iron in seawater and in organisms (Mawji et al, 2008;Gledhill, 2007;Laglera and van den Berg, 2009;Vong et al, 2007) coupled to developments in techniques such as shotgun genomics Venter et al, 2004;Yooseph et al, 2007) and the potential of proteomics (Nunn and Timperman, 2007;Dupont et al, 2006) should lead to great advances over the coming years in our understanding of how organisms have adapted to low iron environments, and the implications of these adaptations to overall marine productivity and biodiversity. The development of in-situ measurement technology as for example suggested in the approach of Roy at al.…”

Genetic Variation Underlying Protein Expression in Eggs of the Marine Mussel Mytilus edulis

“…For example mussels are important for biomonitoring (24) and have been widely used in studies of population genetics and speciation (25,26). Given the increasing interest in the use of proteomics techniques in marine biology (27,28), mussels are thus positioned to play an important future role in this area. The technology for transcriptomics in Mytilus is being developed (29 -31), and several studies also indicate the feasibility of pursuing successful proteomics work in mussels and the identification of proteins differentially expressed between species (32)(33)(34)(35) and between different environments (36 -38).…”

Proteomic response of marine invertebrate larvae to ocean acidification and hypoxia during metamorphosis and calcification

“…In recent years, rapid developments in environmental molecular biology and chemical ecology have shed light on some key questions: how do larvae choose where to settle (Huang et al, 2012); what triggers the transformation from planktonic to benthic life (Dreanno et al, 2006); and what genes are involved in such transformations (Hayward et al, 2011)? Despite the rapid increase in proteomics studies on nonmodel (where the genome has not been completely sequenced) species (Diz and Skibinski, 2007;McDonagh and Sheehan, 2006;Nunn and Timperman, 2007;Tomanek, 2006;Tomanek, 2011), proteins and their post-translational modifications (PTMs) involved in larval metamorphosis and calcification are still largely unknown (Chandramouli et al, 2011).…”