Proteomics in Marine Organisms

Thomas Knigge In the vast seas of proteomics research, work on marine organisms is merely a drop in the ocean. This appears to be inversely proportional to the importance of marine environments, which cover almost 71% of the Earth's surface and harbour an immense diversity of life forms and species. This vital resource to the planet provides us with seafood as well as chemical compounds that can be made into various products. Marine phytoplankton is responsible for half of primary productivity, driving important global nutrient cycles as well as the Earth's climate. Macroalgae, seagrass and corals provide habitats for many other species forming highly complex ecosystems altogether. Many of them are characterised by fluctuating environmental conditions, thus confronting the organisms with various stresses to which they have to adapt. Moreover, life in the oceans provides scientists with very interesting ‘model-organisms’ that can help to understand evolutionary and biological processes. At the same time these resources, ecosystems and life forms are threatened in many ways: pollution, global warming and ocean acidification or habitat destruction, to mention but the most important. This special issue on ‘Proteomics in Marine Organisms’ comprises a total of 20 exciting contributions from all fields of research and about all kinds of organisms ranging from bacteria to mammals and from microalgae to flowering plants, providing a small, but hopefully representative, compendium on marine proteomics. Firstly, two review articles sum up the achievements in proteomics on marine bacteria and diatoms, which have a key position in the oceans’ carbon and nutrient cycle. Using the example of the Roseobacter lineage, Christie-Oleza and Armengaud describe how proteomics can enhance knowledge on the metabolic physiology of these mixotroph marine bacteria. Notably, the exoproteome is involved in planktonic interaction by degrading organic matter into small molecules that can be taken up by a striking diversity of active membrane transporters. Christie-Oleza and Armengaud, also point to the value of proteomics data for taxonomic identification and improved annotation of genomes. Muhseen et al. give an overview on proteomics studies that shed light on the proteins involved in biochemical processes allowing diatoms to cope with deficiencies in nutrients, such as nitrogen, phosphorus, iron and silicon. Importantly, diatoms have evolved specific thylakoid protein complexes to adapt to light attenuation and fluctuation in the aquatic environment (see also Mazzuca et al. this issue). Due to their high primary productivity, diatoms may also constitute a natural source of energy-rich oils for biotechnical exploitation (see also Shi et al. this issue). Both reviews underline how recent technological developments, notably in mass spectrometry, have advanced research in these fields. Secondly, 17 research articles and one dataset brief display the current state of research in proteomics applied to marine organisms. Coastal areas represent dynamic interfaces between land and water with periodical or gradual changes of habitat conditions, such as oxygen supply, salinity or temperature. Many proteomics studies focus on the adaptations necessary to face these natural stressors. López-Cristoffanini et al. studied such physiological adaptations in the ‘red algae’ Pyropia orbicularis, regularly exposed to solar radiation and desiccation. Their results point to the highly conserved stress responses, such as increased antioxidative capacity and heat shock proteins also evoked (see also Muhseen et al. this issue). But López-Cristoffanini et al. also confirmed that responses of land plants to desiccation, which are essential for preserving the cellular integrity, such as regulation of water content, cell volume and cell wall structure constitute ancient responses already present in algae. Neuropeptides play an important role in the regulation of many biological functions in invertebrates. Zhang Y. et al. investigated the neurohormonal regulation of salinity stress in the euryhaline shore crab, Carcinus maenas by duplex dimethyl labelling and MALDI-MS. Interestingly, phenotypic differences in RFamides, RYamides, allatostatins and orcokinins were revealed between colour morphs better adapted to osmotic stress, or better performing in terms of growth and reproduction. Phenotypic differences in neuropeptides between the two morphs were also confirmed by imaging mass spectrometry. Tolerance to low salinity has allowed many marine species to gradually colonise freshwater environments. An example is provided by the three-spined stickleback, Gasterosteus aculeatus, of which genetically and morphologically different ecotypes inhabit marine and freshwater habitats. Kültz et al. used quantitative nano-LC-MS/MS to characterise the plasma proteome of marine and freshwater forms for the first time, revealing a composition similar to that of other vertebrates, however, with less albumins and globulins as in mammals. Proteins related to immunity and defence (see also Cordero et al. this issue) had significantly higher levels in plasma from marine sticklebacks. Also, up-regulated proteins could be linked to the morphological differences in body armour between the two ecotypes. Phenotypic variability was also studied in Mytilus galloprovincialis by Atasaral-Şahin et al., who investigated mussel populations from different geographical areas in a common garden experiment. Proteomics detected subtle differences between these populations, which could not be seen in genetic analyses, but persisted even after they were reared in a common environment for up to two months. Notably, proteins of the general stress response seem to be involved in the adaptation to local differences in temperature, oxygen, salinity or food availability. The immune response in fish, and even more so in invertebrates, is only partly characterised and proteomics could provide a