Year: 2015
Type: editorial
Abstract: 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 more comprehensive picture of how the various elements of the immune system act in concert. Consequently, two research articles focus on immune related proteins, one in fish and the other one in bivalves. Cordero et al. mapped the mucous proteome of the European Sea bass, Dicentrarchus labrax and identified numerous proteins directly or indirectly related to immunity. This allowed them to develop an integrative model of extracellular pathogen recognition by the complement pathway and intracellular processes in the skin, such as inflammatory reactions, as well as signalling across the epithelial barrier. Campos et al. mapped the proteome of the haemolymph of the Blue mussel, Mytilus edulis with a special regard to proteins and peptides from the haemocytes and soluble haemolymph factors implicated in innate immunity. Shotgun proteomics and an enlarged database of more than 80 000 sequences derived from transcriptomics of Mytilidae allowed for an increased proteome coverage of more than 1000 proteins from which around 600 could be annotated. Amongst these, numerous proteins involved in pathogen recognition, agglutination and killing could be identified. Organisms not only have to defend themselves against pathogens, but also against predators or competitors. Cone snails are venomous marine predators that use a vast array of peptide toxins to kill their prey. Jin et al., using transcriptomic and proteomics approaches, demonstrate that the conotoxins also serve for defensive purposes. LC-MS/MS revealed peptide profiles that are different from those used for predation and showed that the defensive venom is produced in different regions of the venom duct, but that both venoms act predominantly on nicotinic acetylcholine receptors responsible for fast signal transmission. Microalgae, dinoflagellates and cyanobacteria produce toxic secondary metabolites that are thought to play a defensive role against ‘grazing’ pressure and in competition for resources. Several toxins affect the nervous system of, notably, vertebrates causing neurodegeneration and paralysation. Zhang S.-F. et al. employed iTRAQ to compare the biosynthetic machinery of the toxic dinoflagellate Alexandrium catenella with a non-toxic mutant. They identified more than 3000 proteins, of which those involved in carbohydrate and amino acid metabolism were up-regulated in the toxic strain, thus pointing to a metabolism specifically dedicated to toxin production. Marine diatoms of the genus Pseudonitzschia produce domoic acid, which, in mammals crosses the brain-blood barrier and interferes with nerve signal transmission. California sea lions and other marine mammals show neurodegenerative disorders after feeding on prey that bioconcentrated this neurotoxin. Neely et al. used label-free LC-MS/MS to identify proteins that are characteristic of domoic acid toxicosis from the cerebrospinal fluid of California sea lions. They were able to identify and validate a number of proteins known to be involved in neurodegenerative diseases, thus advancing the understanding of the molecular pathology of domoic acid induced neurodegeneration, and providing candidate markers for the diagnosis of poisoning with this marine neurotoxin. Marine organisms provide many valuable models to study fundamental questions of neurobiology, regeneration and aging, egg and sperm activation, embryonic and larval development, or circadian rhythms. Nakazawa et al. used proteomic profiling of Ciona intestinalis sperms to investigate the sperm reaction initiated by the contact with the egg's vitelline coat. Successful fertilisation depends on proteins presented on the surface of, or released by, the sperm. In their study, Nakazawa et al. discovered novel sperm proteins implicated in fertilisation and confirmed receptors as well as kinases and phosphatases involved in various signalling pathways. Zhang Y. et al. report in their dataset brief upon the sperm proteome of Mytilus galloprovincialis, which they mapped using 1D SDS-PAGE coupled to LC-MS/MS. They identified more than 800 proteins, thus expanding the mussel sperm proteome, and compared orthologous sperm protein coding genes between M. galloprovincialis and the closely related species M. edulis, showing that fertilisation proteins are responsible for rapid interspecific divergence. Proteomics is particularly suitable to study fertilisation and early development, since the initial events after fertilisation and in the early embryo do not rely on transcription and translation, but rather on the proteins present and activated by, notably, phosphorylation. Guo et al. have chosen the sea urchin Strongylocentrotus purpuratus as a model, for this deuterstome provides a similar equipment of kinases and phosphatases as can be found in mammals. Highly conserved downstream events of egg activation were examined to disclose the complex patterns of phosphoprotein modification following egg activation. A comprehensive picture of novel signalling cascades could be drawn from the almost 3000 phosphoproteins and nearly 9000 phosphosite modifications identified in this exquisite study. Comparing successive developmental stages from oocyte maturation to early embryogenesis in the sequenced cnidarian Nematostella vectensis, Leviatan et al. were able to identify a number of stage-specific proteins, which share homology with proteins that are specific to bilaterian oocytes and embryos. Unravelling such proteins in a phylogenetically ancient organism provides information on the evolutionary origins of basic mechanisms in oocyte maturation. Furthermore, Leviatan et al. identified secreted mucins, lectins and zona pellicula proteins of the jelly sac mostly responsible for protection of the developing embryo until free-swimming larvae emerge and metamorphosis occurs. Post-embryonic development in flatfish entails dramatic anatomical modifications when the animals adopt an asymmetric morphology. Chicano-Galvez et al. investigated the proteomic profiles during metamorphosis of Solea senegalensis larvae and followed the dynamics of co-regulated proteins over several time points prior to and after completion of metamorphosis. Structural proteins, such as actin, tubulin and myosins showed dynamic changes, corresponding to the tissular transformations during asymmetric transformation. Interestingly, repeated identification of isoforms underscored the importance of post-translational modifications in larval metamorphosis. Ocean acidification has been identified as a menace to larval development of fish and shellfish as well as many other marine species. Bivalves are under particular pressure if the pH decreases during their early life stages when they form their shells. When analysing the proteomic changes in the oyster Crassostrea hongkongensis following a moderate decrease in pH using iTRAQ, Dineshram et al. found that although metamorphosis was normal, pediveligers experienced stress as indicated by up-regulation of proteins involved in energy production and metabolism. An increased metabolic rate may, in fact, be related to enhanced calcium transport and biomineralisation, thus allowing the oysters to cope with variable pH-levels in their natural environment. A compelling model organism is the unicellular marine alga Ostreococcus tauri, which has a minimal cellular organisation and a small genome. Le Bihan et al. used this green alga to study the role of conserved post-translational regulator proteins in circadian rhythmicity. Particularly, they examined how Casein Kinase 2 (CK2) phosphorylates proteins involved in circadian timekeeping. They show that overexpression of CK2 alters the circadian rhythm and that this effect is most pronounced at dusk. Comparisons between CK2-overexpressed and CK2-inhibited O. tauri at this time point revealed 447 unique CK2-responsive phosphopeptide motifs differentially regulated by CK2, which may also be of great interest for the regulation of circadian clocks in more complex organisms. Finally, two research articles explored organelle proteomics from species as different as a haptophyte alga and a marine angiosperm. Shi et al. were interested in the isolation of lipid bodies from the non-calcareous marine haptophyte Tisochrysis lutea, that produces long-chained ketones, so-called alkenones, and stores them in organelles of which little is known. Piro et al. were interested in chloroplast biochemistry of the seagrass Posidonia oceanica, in order to better understand adaption to low and fluctuating light conditions in their underwater habitats. In both cases, extraction protocols for the organelles had to be established or adapted, respectively, before the proteomes could be analysed by 1D SDS-PAGE and LC-MS/MS. Extraction in T. lutea is complicated by a four layer organelle membrane due to secondary endosymbiosis, whereas in P. oceanica, leaf tissue containing chloroplasts is limited and losses of organelle material must be minimised. Shi et al. describe a sub-cellular proteome for the lipid bodies in T. lutea, which is quite distinct from that of other microalgae and higher plants. Piro et al. inferred from the surprisingly low number of successful identifications for chloroplast proteins, which are considered to be highly homologous, that considerable adaptive modifications in photosynthetic biochemistry must have occurred when seagrasses conquered the marine habitat. This special issue was made possible by the great enthusiasm of all of the authors as well as the time and expertise so kindly provided by the numerous anonymous reviewers. I would like to thank the senior editor Thierry Rabilloud, who inspired me to this special issue, the editor Matthew Lock, the managing editor, Hans-Joachim Kraus as well as the editor-in-chief, Michael J. Dunn for their patience and unconditional support in producing this special issue. It has been a pleasure to discover and learn about the so many research topics to which proteomics and marine organisms can make a significant contribution. We hope that you will equally enjoy it and that this special issue will be stimulating for your own research! Thomas Knigge Guest Editor
Source: PROTEOMICS
Author: Thomas Knigge
Institution: Université de Reims Champagne-Ardenne
Language: English
Subfield: Spectroscopy
Field: Chemistry
Domain: Physical Sciences
SDG: Life below water
Open Access status: bronze
OpenAlex ID: W2193165456