Long term anoxia in rainbow trout investigated by 2-DE and MS/MS

Proteomic Applications in Aquatic Environment Studies

Genome determines the unique individualities of organisms; however, proteins play significant roles in the generation of the colorful life forms below water. Aquatic systems are usually complex and multifaceted and can take on unique modifications and adaptations to environmental changes by altering proteins at the cellular level. Proteomics is an essential strategy for exploring aquatic ecosystems due to the diverse involvement of proteins, proteoforms, and their complexity in basic and advanced cellular functions. Proteomics can expedite the analysis of molecular mechanisms underlying biological processes in an aquatic environment. Previous proteomic studies on aquatic environments have mainly focused on pollution assessments, ecotoxicology, their role in the food industry, and extraction and identification of natural products. Aquatic protein biomarkers have been comprehensively reported and are currently extensively applied in the pharmaceutical and medical industries. Cellular- and molecular-level responses of organisms can be used as indicators of environmental changes and stresses. Conversely, environmental changes are expedient in predicting aquatic health and productivity, which are crucial for ecosystem management and conservation. Recent advances in proteomics have contributed to the development of sustainable aquaculture, seafood safety, and high aquatic food production. Proteomic approaches have expanded to other aspects of the aquatic environment, such as protein fingerprinting for species identification. In this review, we encapsulated current proteomic applications and evaluated the potential strengths, weaknesses, opportunities, and threats of proteomics for future aquatic environmental studies. The review identifies both pros and cons of aquatic proteomics and projects potential challenges and recommendations. We postulate that proteomics is an emerging, powerful, and integrated omics approach for aquatic environmental studies.

Identification of proteins differentially expressed in the gills of grass carp (Ctenopharyngodon idella) after hypoxic stress by two-dimensional gel electrophoresis analysis

Two-dimensional gel electrophoresis (2-DE) was combined with liquid chromatography-mass spectrometry (LC-MS/MS) to identify the differential proteomics of grass carp gills after hypoxic stress to better understand the roles of proteins in the hypoxic response and to explore the possible molecular mechanisms. Protein spots were obtained from a hypoxia-stressed group (372 ± 11 individuals) and a control group (406 ± 14 individuals) using the lmage Master 2D Platinum 7.0 analysis software. Fifteen protein spots were expressed differentially in the hypoxia-stressed group and varied significantly after exposure to the hypoxic conditions. In addition, these differential proteins were identified by mass spectrometry and then searched in a database. We found the expression and upregulation of the toll-like receptor 4, ephx1 protein, isocitrate dehydrogenase, L-lactate dehydrogenase, GTP-binding nuclear protein Ran, and glyceraldehyde-3-phosphate dehydrogenase; however, the expression of the keratin type II cytoskeletal 8, type I cytokeratin, ARP3 actin-related protein 3 homolog, thyroid hormone receptor alpha-A, ATP synthase subunit beta, citrate synthase, tropomyosin 2, and tropomyosin 3 were downregulated. Six proteins were found in the hypoxia-inducible factor-1 (HIF-1) signaling pathway. We concluded that the grass carp gill is involved in response processes, including energy generation, metabolic processes, cellular structure, antioxidation, immunity, and signal transduction, to hypoxic stress. To our knowledge, this is the first study to conduct a proteomics analysis of expressed proteins in the gills of grass carp, and this study will help increase the understanding of the molecular mechanisms involved in hypoxic stress responses in fish at the protein level.

Limited proteomic response in the marine snail Melarhaphe neritoides after long-term emersion

Rocky intertidal organisms are commonly exposed to environmental gradients, promoting adaptations to these conditions. Emersion time varies along the intertidal range and in the supralittoral zone is frequently larger than a single tidal cycle, even lasting for weeks. The planktonic-dispersing gastropod Melarhaphe neritoides is a common species of the high shore, adapted to reduce water loss in order to survive during long-term emersion. In this study, we investigated the molecular response, at the proteome level, of M. neritoides collected in high-shore tide pools to a series of emersion periods, from 8 to 24 days, in laboratory conditions. We compared this response to individuals maintained submerged during this period, because this was their original habitat. We also included a reversion treatment in the study, in which emersed individuals were returned to the submerged conditions. Although we detected an increase in overall protein concentration with longer emersion periods, contrary to general expectation, the two dimensional electrophoresis (2DE)-based proteomic analysis did not show significant differences between the treatments at the level of individual protein spots, even after an emersion period of 24 days. Our results suggest that the metabolism remains unaltered independent of the treatment carried out or the changes are very subtle and therefore difficult to detect with our experimental design. We conclude that M. neritoides could be equally adapted to emersion and submersion without drastic physiological changes.

Differential abundance of muscle proteome in cultured channel catfish (Ictalurus punctatus) subjected to ante-mortem stressors and its impact on fillet quality

The effects of environmental and handling stress during catfish (Ictalurus punctatus) aquaculture were evaluated to identify the biochemical alterations they induce in the muscle proteome and their impacts on fillet quality. Temperature (25°C and 33°C) and oxygen (~2.5mg/L [L] and >5mg/L [H]) were manipulated followed by sequential socking (S) and transport (T) stress to evaluate changes in quality when fish were subjected to handling (25-H-ST; temperature-oxygen-handling), oxygen stress (25-L-ST), temperature stress (33-H-ST) and severe stress (33-L-ST). Instrumental color and texture of fillets were evaluated, and muscle proteome profile was analyzed. Fillet redness, yellowness and chroma decreased, and hue angle increased in all treatments except temperature stress (33-H-ST). Alterations in texture compared to controls were observed when oxygen levels were held high. In general, changes in the abundance of structural proteins and those involved in protein regulation and energy metabolism were identified. Rearing under hypoxic conditions demonstrated a shift in metabolism to ketogenic pathways and a suppression of the stress-induced changes as the severity of the stress increased. Increased proteolytic activity observed through the down-regulation of various structural proteins could be responsible for the alterations in color and texture.

The effects of eating marine- or vegetable-fed farmed trout on the human plasma proteome profiles of healthy men

Most human intervention studies have examined the effects on a subset of risk factors, some of which may require long-term exposure. The plasma proteome may reflect the underlying changes in protein expression and activation, and this could be used to identify early risk markers. The aim of the present study was to evaluate the impact of regular fish intake on the plasma proteome. We recruited thirty healthy men aged 40 to 70 years, who were randomly allocated to a daily meal of chicken or trout raised on vegetable or marine feeds. Blood samples were collected before and after 8 weeks of intervention, and after the removal of the twelve most abundant proteins, plasma proteins were separated by two-dimensional gel electrophoresis. Protein spots < 66 kDa with a pI >4·3 visualised by silver staining were matched by two-dimensional imaging software. Within-subject changes in spots were compared between the treatment groups. Differentially affected spots were identified by matrix-assisted laser desorption ionisation-time of flight/time of flight MS and the human Swiss-Prot database. We found 23/681 abundant plasma protein spots, which were up- or down-regulated by the dietary treatment (P< 0·05, q< 0·30), and eighteen of these were identified. In each trout group, ten spots differed from those in subjects given the chicken meal, but only three of these were common, and only one spot differed between the two trout groups. In both groups, the affected plasma proteins were involved in biological processes such as regulation of vitamin A and haem transport, blood fibrinolysis and oxidative defence. Thus, regular fish intake affects the plasma proteome, and the changes may indicate novel mechanisms of effect.

Tissue damage in organic rainbow trout muscle investigated by proteomics and bioinformatics

The response to tissue damage is a complex process, which involves the coordinated regulation of multiple proteins to ensure tissue repair. In order to investigate the effect of tissue damage in a lower vertebrate, samples were taken from rainbow trout (Oncorhynchus mykiss) at day 7 after damage and proteins were separated using 2DE. The experimental design included two groups of rainbow trout, which were fed organic feed either with or without astaxanthin. In total, 96 proteins were found to be affected by tissue damage, clearly demonstrating in this lower vertebrate the complexity and magnitude of the cellular response, in the context of a regenerative process. Using a bioinformatics approach, the main biological function of these proteins were assigned, showing the regulation of proteins involved in processes such as apoptosis, iron homeostasis, and regulation of muscular structure. Interestingly, it was established that exclusively within the astaxanthin feed group, three members of the annexin protein family (annexin IV, V, and VI) were regulated in response to tissue damage.

PROTEOMICS in aquaculture: applications and trends

Over the last forty years global aquaculture presented a growth rate of 6.9% per annum with an amazing production of 52.5 million tonnes in 2008, and a contribution of 43% of aquatic animal food for human consumption. In order to meet the world's health requirements of fish protein, a continuous growth in production is still expected for decades to come. Aquaculture is, though, a very competitive market, and a global awareness regarding the use of scientific knowledge and emerging technologies to obtain a better farmed organism through a sustainable production has enhanced the importance of proteomics in seafood biology research. Proteomics, as a powerful comparative tool, has therefore been increasingly used over the last decade to address different questions in aquaculture, regarding welfare, nutrition, health, quality, and safety. In this paper we will give an overview of these biological questions and the role of proteomics in their investigation, outlining the advantages, disadvantages and future challenges. A brief description of the proteomics technical approaches will be presented. Special focus will be on the latest trends related to the aquaculture production of fish with defined nutritional, health or quality properties for functional foods and the integration of proteomics techniques in addressing this challenging issue.

Time-dependent changes in protein expression in rainbow trout muscle following hypoxia

Adaptation to hypoxia is a complex process, and individual proteins will be up- or down-regulated in order to address the main challenges at any given time. To investigate the dynamics of the adaptation, rainbow trout (Oncorhynchus mykiss) was exposed to 30% of normal oxygen tension for 1, 2, 5 and 24 h respectively, after which muscle samples were taken. The successful investigation of numerous proteins in a single study was achieved by selectively separating the sarcoplasmic proteins using 2-DE. In total 46 protein spots were identified as changing in abundance in response to hypoxia using one-way ANOVA and multivariate data analysis. Proteins of interest were subsequently identified by MS/MS following tryptic digestion. The observed regulation following hypoxia in skeletal muscle was determined to be time specific, as only a limited number of proteins were regulated in response to more than one time point. The cellular response to hypoxia included regulation of proteins involved in maintaining iron homeostasis, energy levels and muscle structure. In conclusion, this proteome-based study presents a comprehensive investigation of the expression profiles of numerous proteins at four different time points. This increases our understanding of timed changes in protein expression in rainbow trout muscle following hypoxia.

Brain proteome alterations of Atlantic cod (Gadus morhua) exposed to PCB 153

Polychlorinated biphenyls (PCBs) are still widespread environmental pollutants that bioaccumulate and biomagnify in the aquatic food chains despite the ban on their production. They constitute a class of 209 possible congeners with different chlorination pattern of the biphenyl ring structure resulting in many different toxicities and mechanisms of toxicity. The neurotoxicity of PCBs is relatively poorly understood, and biomarkers for their neurotoxic effects are lacking. We have carried out a proteomic analysis of brain tissue from Atlantic cod (Gadus morhua) exposed to 2,2',4,4',5,5'-hexachlorobiphenyl (PCB 153, ortho-substituted and non-coplanar), a previously demonstrated neurotoxic congener and the most prevalent congener in biological samples. The fish received 0, 0.5, 2 and 8 mg/kg PCB 153 by intraperitoneal injection, half of the dose on the first day and the second half after one week, and were exposed for two weeks in total. Using a 2-DE approach we found 56 protein spots to be 20% or more (≤ 0.8-fold or ≥ 1.2-fold) significantly different between at least one of the three PCB 153-exposed groups and the control group, and 27 of these were identified by MALDI-TOF MS and MS/MS. Approximately 80% of the differentially regulated proteins may be associated with a non stressor-specific response and/or have previously been classified as notoriously differentially regulated in 2-DE/MS based proteomics studies, such as alterations/responses in energy metabolism, cytoskeleton, protein synthesis, protein degradation (ubiquitin-proteasome system), cellular growth, cycle and death (14-3-3 protein), and (surprisingly) axon guidance (dihydropyrimidinase-like 2 (=collapsin response mediator protein 2, CRMP-2)). The six remaining affected proteins include the strongest up-regulated protein, pyridoxal kinase (essential for synthesis of neurotransmitters such as dopamine, serotonin and GABA), nicotinamide phosphoribosyl-transferase (involved in protection against axonal degeneration) and protein phosphatase 1 (controls brain recovery by synaptic plasticity). The last three of these six proteins (deltex, Rab14 and sorting nexin 6) may preliminarily identify involvement of the Notch signaling pathway and endosomal function in PCB 153-induced neurotoxicity. Our findings constitute novel clues for further research on PCB 153 mode of action in brain, and a proper selection of proteins may, following validation, be applicable in a panel of biomarkers for aquatic environmental monitoring.

Responses in the brain proteome of Atlantic cod (Gadus morhua) exposed to methylmercury

The molecular mechanisms underlying the neurotoxicity of methylmercury (MeHg), a ubiquitous environmental contaminant, are not yet fully understood. Furthermore, there is a lack of biomarkers of MeHg neurotoxicity for use in environmental monitoring. We have undertaken a proteomic analysis of brains from Atlantic cod (Gadus morhua) exposed to 0, 0.5 and 2 mg/kg MeHg administered by intraperitoneal injection. The doses were given in two injections, half of the dose on the first day and the second half after 1 week, and the total exposure period lasted 2 weeks. Using 2-DE coupled with MALDI-TOF MS and MS/MS, we observed the level of 71 protein spots to be 20% or more significantly altered following MeHg exposure, and successfully identified 40 of these protein spots. Many of these proteins are associated with main known molecular targets and mechanisms of MeHg-induced neurotoxicity in mammals, such as mitochondrial dysfunction, oxidative stress, altered calcium homeostasis and tubulin/disruption of microtubules. More interestingly, several of the affected proteins, with well-established or recently demonstrated critical functions in nervous system-specific processes, have not previously been associated with MeHg exposure in any species. These proteins include the strongest up-regulated protein, pyridoxal kinase (essential for synthesis of several neurotransmitters), G protein (coupled to neurotransmitter receptors), nicotinamide phosphoribosyl-transferase (protection against axonal degeneration), dihydropyrimidinase-like 5 (or collapsin response mediator protein 5, CRMP-5) (axon guidance and regeneration), septin (dendrite development), phosphatidylethanolamine binding protein (precursor for hippocampal cholinergic neurostimulating peptide) and protein phosphatase 1 (control of brain recovery by synaptic plasticity). The results of the present study aid our understanding of molecular mechanisms underlying MeHg neurotoxicity and defense responses, and provide a large panel of protein biomarker candidates for aquatic environmental monitoring.

A proteomic view of Caenorhabditis elegans caused by short-term hypoxic stress

Background

The nematode Caenorhabditis elegans is both sensitive and tolerant to hypoxic stress, particularly when the evolutionarily conserved hypoxia response pathway HIF-1/EGL-9/VHL is involved. Hypoxia-induced changes in the expression of a number of genes have been analyzed using whole genome microarrays in C. elegans, but the changes at the protein level in response to hypoxic stress still remain unclear.

Results

Here, we utilized a quantitative proteomic approach to evaluate changes in the expression patterns of proteins during the early response to hypoxia in C. elegans. Two-dimensional difference gel electrophoresis (2D-DIGE) was used to compare the proteomic maps of wild type C. elegans strain N2 under a 4-h hypoxia treatment (0.2% oxygen) and under normoxia (control). A subsequent analysis by MALDI-TOF-TOF-MS revealed nineteen protein spots that were differentially expressed. Nine of the protein spots were significantly upregulated, and ten were downregulated upon hypoxic stress. Three of the upregulated proteins were involved in cytoskeletal function (LEV-11, MLC-1, ACT-4), while another three upregulated (ATP-2, ATP-5, VHA-8) were ATP synthases functionally related to energy metabolism. Four ribosomal proteins (RPL-7, RPL-8, RPL-21, RPS-8) were downregulated, indicating a decrease in the level of protein translation upon hypoxic stress. The overexpression of tropomyosin (LEV-11) was further validated by Western blot. In addition, the mutant strain of lev-11(x12) also showed a hypoxia-sensitive phenotype in subsequent analyses, confirming the proteomic findings.

Conclusions

Taken together, our data suggest that altered protein expression, structural protein remodeling, and the reduction of translation might play important roles in the early response to oxygen deprivation in C. elegans, and this information will help broaden our knowledge on the mechanism of hypoxia response.

Fish as model systems for the study of vertebrate apoptosis

Apoptosis is a process of pivotal importance for multi-cellular organisms and due to its implication in the development of cancer and degenerative disease it is intensively studied in humans and mammalian model systems. Invertebrate models of apoptosis have been well-studied, especially in C. elegans and D. melanogaster, but as these are evolutionarily distant from mammals the relevance of findings for human research is sometimes limited. Presently, a non-mammalian vertebrate model for studying apoptosis is missing. However, in the past few years an increasing number of studies on cell death in fish have been published and thus new model systems may emerge. This review aims at highlighting the most important of these findings, showing similarities and dissimilarities between fish and mammals, and will suggest topics for future research. In addition, the outstanding usefulness of fish as research models will be pointed out, hoping to spark future research on this exciting, often underrated group of vertebrates.

Proteomic analysis of anoxia tolerance in the developing zebrafish embryo

While some species and tissue types are injured by oxygen deprivation, anoxia tolerant organisms display a protective response that has not been fully elucidated and is well-suited to genomic and proteomic analysis. However, such methodologies have focused on transcriptional responses, prolonged anoxia, or have used cultured cells or isolated tissues. In this study of intact zebrafish embryos, a species capable of >24 h survival in anoxia, we have utilized 2D difference in gel electrophoresis to identify changes in the proteomic profile caused by near-lethal anoxic durations as well as acute anoxia (1 h), a timeframe relevant to ischemic events in human disease when response mechanisms are largely limited to post-transcriptional and post-translational processes. We observed a general stabilization of the proteome in anoxia. Proteins involved in oxidative phosphorylation, antioxidant defense, transcription, and translation changed over this time period. Among the largest proteomic alterations was that of muscle cofilin 2, implicating the regulation of the cytoskeleton and actin assembly in the adaptation to acute anoxia. These studies in an intact embryo highlight proteomic components of an adaptive response to anoxia in a model organism amenable to genetic analysis to permit further mechanistic insight into the phenomenon of anoxia tolerance.