You're using an outdated browser. Please upgrade to a modern browser for the best experience.
Submitted Successfully!
Thank you for your contribution! You can also upload a video entry or images related to this topic. For video creation, please contact our Academic Video Service.
Version Summary Created by Modification Content Size Created at Operation
1
Jayan Senevirathna
 -- 3199 2022-09-14 16:21:12 |
2 format change
Peter Tang
 Meta information modification 3199 2022-09-15 03:26:06 | |
3 format change
Peter Tang
 -1 word(s) 3198 2022-09-16 08:19:10 |

Video Upload Options

We provide professional Academic Video Service to translate complex research into visually appealing presentations. Would you like to try it?
No, upload directly Yes

Confirm

Are you sure to Delete?
Yes No
Cite
If you have any further questions, please contact Encyclopedia Editorial Office.
Gamage, N.T.G.;  Miyashita, R.;  Takahashi, K.;  Asakawa, S.;  Senevirathna, J.D.M. Proteomic Applications in Aquatic Environment Studies. Encyclopedia. Available online: https://encyclopedia.pub/entry/27173 (accessed on 11 July 2025).
Gamage NTG,  Miyashita R,  Takahashi K,  Asakawa S,  Senevirathna JDM. Proteomic Applications in Aquatic Environment Studies. Encyclopedia. Available at: https://encyclopedia.pub/entry/27173. Accessed July 11, 2025.
Gamage, Nadeeka Thushari Gajahin, Rina Miyashita, Kazutaka Takahashi, Shuichi Asakawa, Jayan Duminda Mahesh Senevirathna. "Proteomic Applications in Aquatic Environment Studies" Encyclopedia, https://encyclopedia.pub/entry/27173 (accessed July 11, 2025).
Gamage, N.T.G.,  Miyashita, R.,  Takahashi, K.,  Asakawa, S., & Senevirathna, J.D.M. (2022, September 14). Proteomic Applications in Aquatic Environment Studies. In Encyclopedia. https://encyclopedia.pub/entry/27173
Gamage, Nadeeka Thushari Gajahin, et al. "Proteomic Applications in Aquatic Environment Studies." Encyclopedia. Web. 14 September, 2022.
Proteomic Applications in Aquatic Environment Studies
Edit
This entry is adapted from the peer-reviewed paper 10.3390/proteomes10030032

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. 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.

aquatic proteomics biomarkers ecotoxicoproteomics protein fingerprinting multiomics

1. Introduction

The aquatic environment accounts for over 70% of the Earth’s land surface, with over 95% occurring as seawater. This extensive ecosystem comprises numerous biological, chemical, and physical energy resources. Aquatic proteins from fish, invertebrates, seaweeds, and algae largely contribute to human dietary requirements. Some protein discoveries from aquatic environments with special functions have been used in biotechnological studies for many decades. An example is the identification of green fluorescent protein in aquatic invertebrates by Shimomura in 1962, which is used as a protein marker in various biological studies [1]. Similarly, numerous proteins have been isolated and characterized from aquatic organisms and are used in various industries such as food, pharmaceutical, medical, and environmental monitoring. Key examples are aquatic proteins with repetitive motifs (e.g., the matrix proteins found in pearl oysters) with promising biomedical and biotechnological applications [2]. Aquatic organisms have adapted to various environmental changes. These adaptations could identify by using the diversity of proteoforms, which derives from a single gene within the context of aquatic evolutionary adaptations.
Pioneer protein-based research, which involved their modification through the addition of pentose sugar and phosphates after translation from a DNA fragment [3], led to various development opportunities. Subsequently, proteins became valuable resources contributing to the global economy, and for years, numerous industries have targeted protein-related research fields [4]. Numerous biotechnological companies have, in the past two decades, focused on expanding proteomic applications to solve various biological problems. Applying omics technologies, including genomics, transcriptomics, proteomics, and metabolomics in various studies on aquatic ecosystems, have been widely elaborated. Proteomic application has been reviewed in the field of mobile genetic elements research on microorganisms during their early development stage [5]. Protein markers were also applied in an ecotoxicogenomic study to determine hormonal changes in aquatic organisms because of various environmental contaminants [6]. Ecotoxicoproteomics studies are used to highlight the molecular responses of organisms to environmental stress to achieve the grand concept, “make our planet great again” [7]. Environmental proteomics can be applied to microorganisms and vertebrates; therefore, it is possible to study the long-term adverse effects of environmental toxins on humans and animals [8]. Proteins present in bones preserved in water offer excellent opportunities for forensic studies on aquatic environments.
Assessment of aquatic resources ensures that the status, exploitation level, diversity, and population dynamics are maintained. Basic concepts of stock assessment, processes, population dynamics, and fish stock assessment models can be applied to manage freshwater and marine fish resources using validated data collection techniques [9]. For commercial aquatic resources, novel technological approaches with value addition to fish and fishery or aquatic products are important to ensure safety and diversification. Aquatic byproducts, waste, and unutilized biomass can be converted into value-added beneficial byproducts with broad-spectrum applications because of their functional properties, diversified nutrient pool, and biopolymer composition [10].

2. Proteomics as a Biomonitoring Tool

All biological forms consist of a diverse array of proteins essential for their various functions. Proteomics identifies and studies total proteins in each tissue or cell [11]. Proteins are active molecules in an organism and are usually modified post-transcriptionally into different isoforms after mRNA synthesis from DNA fragments. Compared with nucleotides, protein diversity is very high, and a single gene can form more than 100 different proteins [12]. Thus, proteins have been used as monitoring tools in various sectors, such as medicine [13][14], forensic [15], aquaculture [16][17], environmental monitoring [18], and agriculture [19].
Significant progress has been made in proteomics, such as protein extraction and purification, quantification, characterization, sequence structure, and bioinformatic analysis [20]. Sample preparation and protein extraction are critical steps in proteomic studies. Consequently, novel protein extraction kits and protocols have been developed for various plant and animal tissues or cells. An ideal protein extraction protocol and kit should be simple, cost-effective, efficient, and rapid [21][22]. Currently, no universal protein extraction protocol is available for any biological sample from the aquatic environment [23]. A study on heart proteomics revealed that the in-solution digestion shotgun method was better than on-filter digestion or on-pellet digestion isolation methods for characterizing proteins from a dynamic range of tissues in a simple, inexpensive, straightforward, fast, and robust manner [24]. This technique could therefore be used to extract proteins in samples obtained from evolutionary-related aquatic organisms such as marine mammals. A study on aquatic animals showed that protocols, such as the TRIzol method, were suitable for protein extraction from the gill of Mytilus galloprovincialis and liver of Paralichthys olivaceus, whereas the trichloroacetic acid–acetone solvent method was better in extracting proteins from the soft tissue of Nereis diversicolor [25]. A combination of laboratory-made lysis buffers with sonication, followed by protein quantification by either bicinchoninic acid or Lowry assays, and silver staining has been suggested as the best protein extraction or characterization protocol in foraminifera [26]. Selecting or designing suitable buffers for protein isolation is critical, as they could easily damage proteins. Therefore, several aspects of laboratory-made buffers, including pH, buffering system, salts, and reducing and stabilizing agents have been investigated [27]. Some marine organisms, such as seaweed (Palmaria palmata), have high polysaccharide levels that require pretreatment to effectively extract proteins [28].
Proteomic analysis can be first categorized as gel-based and gel-free. The label-based and label-free strategies are both gel-free and mass spectrometry (MS)-based techniques. The gel-based technique is used for global protein separation and quantification. An older, two-dimensional gel electrophoresis (2D-GE) technique is popularly used; however, it exhibits some major limitations, including loss of all membrane proteins, the appearance of multiple proteins in a single spot, and the occurrence of a single protein in multiple spots. Consequently, MS techniques have become popular as the most reliable protein separation and quantification alternatives [29]. Label-based protein quantification methods require a stable labeling isotope for peptides, whereas label-free methods can determine the relative or absolute protein quantity using MS techniques. 
Liquid chromatography–mass spectrometry (LC–MS) is suggested as one of the most suitable novel techniques for protein characterization, with a wide use in proteomics because it overcomes major limitations of previous methods and can easily be automated. Common chemical label-based techniques include isotope-coded affinity tags, isotope-coded protein labeling, and isobaric tags for relative and absolute quantification (iTRAQ). The iTRAQ tags are mainly designed for peptides, and their reagents are extremely sensitive. Hence, the iTRAQ technique is more relevant for large-scale, bottom-up proteomics analysis of organism responses in aquatic environments. Tandem mass tag (TMT) labeling is also a label-based method that has been used to identify more than 5000 proteins in sea cucumbers [30] and can also be considered to be a suitable technique for comparative aquatic proteomic studies. Another study noted that the matrix-assisted laser desorption ionization–time-of-flight mass spectrometry (MALDI–TOF MS) is a less expensive and simple method for characterizing aquatic bacteria using protein extractions [31][32]. The MALDI–TOF technique has several applications in aquatic proteomics [33] and it shows great potentiality because the analyses are easy, rapid, robust, high-throughput, and cost-effective. It could represent an interesting alternative to traditional methods of identification of aquatic microorganisms/species despite the high initial cost of the mass spectrometer.
Protein extraction buffers might isolate a unique set of proteins with different hydrophobicity, pI (isoelectric point), aromaticity, and molecular weight. Therefore, this information might help develop enzyme-linked immunosorbent assay (ELISA) methods for assessing seafood allergies [23]. A recent study has developed a protocol for metagenomics applications to isolate proteins and DNA and to digest or extract peptides from microbial biomass in seawater [34]. Marine-based protein hydrolysates are common in food and fish feed composite; therefore, a standard protocol has been developed to characterize the abundance and diversity of their protein complexes, for example, in shrimp, tuna, krill, squid, tilapia, and salmon [35]. For decades, advanced technologies have been used to isolate and identify proteins from organisms. Assessments of protein structure similarities and differences are difficult because of their complexities that require keen bioinformatic analysis to correctly perform fingerprinting [36]. Recent advancements, such as dynamic structural vibration assessments, have been applied in protein fingerprinting (or peptide mass fingerprinting) [37]. However, structural vibrations are used as alternative analytical techniques for protein identification that cleave proteins into smaller peptides; then, their mass is measured and analyzed via mass spectrometry. Additionally, protein–protein interaction studies are essential for elucidating changes in metabolic pathways of aquatic organisms caused due to environmental stress. A recent study used protein fingerprinting to identify the intercellular protein mechanisms of H2O2 stress-mediated inhibition on algae, Scenedesmus obliquus [38].
Scientists have constructed protein databases to enhance protein identification and explore proteoforms complexity. Currently, UniProt is the most updated protein database (https://www.uniprot.org/, accessed on 27 January 2022), comprising two platforms, including Swiss-prot, with 565,928 reviewed data points by experts, and TrEMBL, which has 225,013,025 computationally generated data points. Pfam is another protein database that contains a total of 19,632 protein families and millions of sequences (http://pfam.xfam.org/, accessed on 27 January 2022). Protein Blast or BLASTP is another strategy for retrieving reliable, highly homologous protein sequences for the identification of unknown or new proteins (https://blast.ncbi.nlm.nih.gov/Blast.cgi, accessed on 27 January 2022). For structural analysis, 3D protein shapes can be predicted by several tools, such as the AlfaFold protein structure database (https://alphafold.ebi.ac.uk/, accessed on 2 February 2022), and Protein Data Bank (https://www.rcsb.org/, accessed on 2 February 2022). Additionally, Expasy is an online platform for various protein analyses and related studies (https://www.expasy.org/, accessed on 2 February 2022). For aquatic studies, a fish proteomic database has been developed and used for biomarker discovery (http://www.cifri.res.in/Fishprot/, accessed on 22 February 2022). Similarly, numerous protein data and analytical tools are currently available due to the rapid technological development, bioinformatics, and advancement in artificial intelligence. Therefore, proteomics is a promising biomonitoring tool that will offer numerous novel proteomics-based study opportunities in the aquatic environment.

3. Applications of Proteomics in Aquatic Studies

3.1. Proteomics in the Aquatic Food Industry

Aquatic foods largely contribute to the global food chain, and their diversity ranges from microorganisms to mammals. Proteins are basic nutritional components in seafood, and a wide variety of aquatic foods provides numerous opportunities for the development of various products [39]. According to a recent publication, aquatic animal source food consumption is expected to increase by 2030, whereas terrestrial animal meat consumption will reduce due to malnutrition, diet-related diseases [40], and cultural or religious perspectives.
Aquaculture is one of the sustainable approaches to acquiring valuable nutrients, such as eicosapentaenoic acid and docosahexaenoic acid from aquatic foods. Various types of fish, invertebrates (mainly shellfish), plants, and algae are well-known for their role in developing novel aquaculture practices. Contemporary aquaculture farming is currently undergoing growth to improve nutrient availability and sustainability [41]. Genomic information is available for some aquaculture fish species, and identifying causal genes is important for future aquaculture development [42]. Genomes of many cultured species are currently available because of the development of NGS technologies. Functional genomic approaches are essential for understanding gene and peptide functions. Therefore, the identification of active genes, proteins, and their expression dynamics are basic steps used in advanced proteomic techniques.
However, genomics and proteomics are still crucial for the discovery of novel aquaculture species and for assessing their development in the aquaculture system. Consequently, the past two decades have witnessed a significant increase in the application of proteomics to investigate aquatic species and their products. Proteomics is a powerful tool for addressing numerous challenges related to welfare, nutrition, health, production, safety, and quality in aquaculture systems [17]. Targeted and discovery proteomics are two critical approaches applied to enhance the welfare, health condition, nutritional composition, and well-being of cultured fish [43].
The rate of fish growth is a critical factor that affects aquaculture yield, and integrated proteomic techniques can be used to modify metabolic networks and pathways associated with fish growth. Proteomic techniques can also be applied to identify the relationship between genome and protein abundance for growth improvement. A previous report indicated that the incorporation of β-glucan in feed enhanced the growth efficiency and immunity of some fish species [44]. For example, β-glucan dietary supplementation for the rainbow trout, Oncorhynchus mykiss, resulted in increased levels of tropomyosin isoforms and a decrease in heavy- and light-chain isoforms of fish fillet myosin [45]. Another aspect is the development of sustainable, eco-friendly culture media for fish farming, since excess feed materials are potential environmental pollutants. Proper feed waste management can be achieved by proteomic techniques for identifying feed waste-degrading enzymes or microbes that can clean the culture environment.
Seafood allergy testing is one way of applying proteomics in an aquatic system. However, new protein-based biosensors are needed to improve the identification, detection, and quantification of seafood allergens [43]. Targeted proteomics was used as a rapid assessment tool to identify β-parvalbumin, a key allergen of fish [46]. Proteomic profiling of tropomyosin, which is a major allergen of shellfish species (mollusks and shrimps), was conducted to characterize its complete amino acid sequence [47]. Figure 1 presents a summarized overview of approaches to proteomic application toward sustainable aquaculture and aquatic or seafood safety.
Figure 1. Overview of proteomic applications in the aquaculture sector and seafood industry. Fish wellness and betterment is highly important in the sustainable aquaculture practices. Proteomics techniques can be applied to monitor and manage culture environments and fish feed development. After harvesting, fish processing and food safety can be advanced by proteomics.

3.2. Proteomics in Aquatic Environmental Pollution and Monitoring

Genome and environment are the two key factors that determine changes in the proteome of an organism. Proteins cause biochemical and functional changes in organisms as a response to environmental changes [48]. However, limited and incomplete genome sequences are still a barrier to identifying proteins for ecotoxicological studies on aquatic life [29]. Toxicity in the aquatic environment is a source of stress to aquatic life, and their stress responses can be detected and measured using proteomics. For example, the accumulation of human and veterinary active pharmaceutical ingredients, which alter aquatic phytoplankton protein profiles, has been widely examined using novel proteomics technologies [49].
Ecotoxicoproteomics is a trending study area that was developed approximately two decades ago, with the application of a 2D polyacrylamide gel electrophoresis, and to date, targeted proteins have been quantified using the selected reaction monitoring (SRM) method, which is a powerful tool for analyzing predetermined proteins across different samples; more details on this technique are reviewed elsewhere [50]. The toxicity of engineered nanomaterials (ENMs) has been identified in aquatic bivalves, and the materials can cross the cell membrane barriers and disrupt the intracellular environment, leading to DNA damage [51].
Next-generation proteomics using protein databases is a reliable tool for discovering biomarkers such as conserved and ubiquitous proteins. The previous absence of protein databases was a major challenge [52]; however, various protein databases have currently been developed, and proteomic techniques can now be used to identify novel biomarkers in aquatic pollution studies. Protein isoforms, post-translational modifications, and protein interactions are associated with chemical pollution in aquatic environments [53].
Plastic pollution is a severe threat to aquatic environments. Microplastics and nanoplastics highly contribute to the altered biological functions of aquatic life and have caused numerous environmental implications, such as the decreased photosynthetic ability of phytoplankton, cell growth inhibition, and heteroaggregate formation [54]. However, the cellular or molecular mechanism of microplastic- and nanoplastic-mediated changes in the biological processes of various aquatic organisms must still be explored on a large scale. Hence, recent proteomics technologies have a huge potential for future studies on the metabolic pathways’ modifications, biodistribution, and bioaccumulation caused by plastic molecules in aquatic environments.
Microplastics in aquatic ecosystems produce chemicals that change the homeostasis, osmoregulation, nutrition, reproduction, and molting of aquatic organisms and can be detected using proteomics techniques [55]. For example, a recent study using integrated proteomics and other omics strategies investigated the toxic effect of microplastics on edible shrimp, Litopenaeus vannamei, and the results showed that microplastics could change the protein profile of the hemolymph as well as the expression of immune-related proteins [56]. This indicates that proteomic technology is ideal for studying the impacts of microplastics and nanoplastics on edible aquatic animals and their potential health consequences in humans.

3.3. Natural Aquatic Proteins and Marine-Derived Medicine

Searching marine products for drug development is a remarkably developing industry that is interlinked with scientific research, the economy, and technological advances. Natural marine products have been described as valuable biomimetics and multifunctional raw materials for various industrial and biomedical development [57]. Common marine biomaterials are polysaccharides, such as chitin, alginates, fucoidans, carrageenans, ulvans, and agar; structural proteins, including spongin, collagens, gelatin, keratin, conchiolin, and conchixes; and biominerals, which include corals and shells. Aquatic proteins are directly or indirectly involved in the production of these biomaterials. Therefore, discovering such valuable proteins will be essential for the development of the biomaterials-related industries mentioned above.
A deep understanding of protein structure and domain specificities is important for functional product development. Chitin is a widely studied chemical compound that produces chitooligosaccharides and N-acetyl-D-glucosamine with various applications in agriculture, medicine, food, and cosmetic industries. Aquatic-based chitins are mainly derived from the cuticles of crustaceans such as crabs and shrimps. Chitin shows thermostability at 260–360 °C, which is a valuable trait for various industries [57]. However, chitin features are species-specific and can be altered depending on the chitin-degrading enzyme, chitinase, of the producing organism. A recent study identified 11 chitinolytic enzymes from Pseudoalteromonas flavipulchra and predicted their protein domain architecture to understand the chitinolytic enzyme secretion [58].
Marine-derived medicine is a rapidly developing field of aquatic science with the future aiming to apply proteomic strategies to enhance the discovery of aquatic-based natural drug products for use in human disease treatments. Marine-based gold nanoparticles such as chitosan have been used as a delivery drug for the diagnosis and treatment of cancers [59]. However, more proteomic-based studies on the roles of chitosan in oncology are still needed to potentially develop diagnostic kits and facilitate anticancer drug delivery.
Marine collagen is another sustainable area with potential biomedical applications in tissue engineering [60]. However, novel applications need exploration using proteomics and other omics technologies to determine the success of marine collagen as a scaffolding material in the biomedical sector. Metabolic pathways of natural marine products with drug potentials have been key objectives of marine medicine [61]. Reported studies between 2018 and 2021 identified 68 unique and patented natural marine products, and the majority will be used in biomedical applications [62]. Hence, there is a potential of growing aquatic proteomics-related sectors in the future.

References

  1. Swaminathan, S. GFP: The green revolution. Nat. Cell Biol. 2009, 11, S20.
  2. Yang, Y.J.; Jung, D.; Yang, B.; Hwang, B.H.; Cha, H.J. Aquatic proteins with repetitive motifs provide insights to bioengineering of novel biomaterials. Biotechnol. J. 2014, 9, 1493–1502.
  3. Swinbanks, D. Australia backs innovation, shuns telescope. Nature 1995, 378, 653.
  4. Phimister, B. Four companies announce discovery of β-secretase gene. Nat. Biotechnol. 2000, 18, 16.
  5. Smalla, K.; Sobecky, P.A. The prevalence and diversity of mobile genetic elements in bacterial communities of different environmental habitats: Insights gained from different methodological approaches. FEMS Microbiol. Ecol. 2002, 42, 165–175.
  6. Rotchell, J.M.; Ostrander, G.K. Molecular markers of endocrine disruption in aquatic organisms. J. Toxicol. Environ. Health—Part B Crit. Rev. 2003, 6, 453–495.
  7. Gouveia, D.; Almunia, C.; Cogne, Y.; Pible, O.; Degli-Esposti, D.; Salvador, A.; Cristobal, S.; Sheehan, D.; Chaumot, A.; Geffard, O.; et al. Ecotoxicoproteomics: A decade of progress in our understanding of anthropogenic impact on the environment. J. Proteom. 2019, 198, 66–77.
  8. Nesatyy, V.J.; Suter, M.J.F. Proteomics for the analysis of environmental stress responses in organisms. Environ. Sci. Technol. 2007, 41, 6891–6900.
  9. Gebremedhin, S.; Bruneel, S.; Getahun, A.; Anteneh, W.; Goethals, P. Scientific methods to understand fish population dynamics and support sustainable fisheries management. Water 2021, 13, 574.
  10. Rudovica, V.; Rotter, A.; Gaudêncio, S.P.; Novoveská, L.; Akgül, F.; Akslen-Hoel, L.K.; Alexandrino, D.A.M.; Anne, O.; Arbidans, L.; Atanassova, M.; et al. Valorization of Marine Waste: Use of Industrial By-Products and Beach Wrack Towards the Production of High Added-Value Products. Front. Mar. Sci. 2021, 8, 723333.
  11. Nyman, T.A. The role of mass spectrometry in proteome studies. Biomol. Eng. 2001, 18, 221–227.
  12. Ponomarenko, E.A.; Poverennaya, E.V.; Ilgisonis, E.V.; Pyatnitskiy, M.A.; Kopylov, A.T.; Zgoda, V.G.; Lisitsa, A.V.; Archakov, A.I. The Size of the Human Proteome: The Width and Depth. Int. J. Anal. Chem. 2016, 2016, 7436849.
  13. Avissar, S.; Schreiber, G. G protein measurements: An empirical tool for the diagnosis of affective disorders. Drug Dev. Res. 2000, 50, 316–323.
  14. Legutki, J.B.; Zhao, Z.G.; Greving, M.; Woodbury, N.; Johnston, S.A.; Stafford, P. Scalable high-density peptide arrays for comprehensive health monitoring. Nat. Commun. 2014, 5, 4785.
  15. Oonk, S.; Schuurmans, T.; Pabst, M.; de Smet, L.C.P.M.; de Puit, M. Proteomics as a new tool to study fingermark ageing in forensics. Sci. Rep. 2018, 8, 16425.
  16. Moreira, M.; Schrama, D.; Farinha, A.P.; Cerqueira, M.; de Magalhães, C.R.; Carrilho, R.; Rodrigues, P. Fish pathology research and diagnosis in aquaculture of farmed fish; a proteomics perspective. Animals 2021, 11, 125.
  17. Rodrigues, P.M.; Silva, T.S.; Dias, J.; Jessen, F. PROTEOMICS in aquaculture: Applications and trends. J. Proteom. 2012, 75, 4325–4345.
  18. Gouveia, D.; Chaumot, A.; Charnot, A.; Almunia, C.; François, A.; Navarro, L.; Armengaud, J.; Salvador, A.; Geffard, O. Ecotoxico-Proteomics for Aquatic Environmental Monitoring: First in Situ Application of a New Proteomics-Based Multibiomarker Assay Using Caged Amphipods. Environ. Sci. Technol. 2017, 51, 13417–13426.
  19. Bestel-Corre, G.; Dumas-Gaudot, E.; Gianinazzi, S. Proteomics as a tool to monitor plant-microbe endosymbioses in the rhizosphere. Mycorrhiza 2004, 14, 1–10.
  20. Aslam, B.; Basit, M.; Nisar, M.A.; Khurshid, M.; Rasool, M.H. Proteomics: Technologies and their applications. J. Chromatogr. Sci. 2017, 55, 182–196.
  21. Yadav, S.; Srivastava, A.; Biswas, S.; Chaurasia, N.; Singh, S.K.; Kumar, S.; Srivastava, V.; Mishra, Y. Comparison and optimization of protein extraction and two-dimensional gel electrophoresis protocols for liverworts. BMC Res. Notes 2020, 13, 60.
  22. An, Y.; Scherer, P. Mouse Adipose Tissue Protein Extraction. Bio-Protocol 2020, 10, e3631.
  23. Bose, U.; Broadbent, J.A.; Juhász, A.; Karnaneedi, S.; Johnston, E.B.; Stockwell, S.; Byrne, K.; Limviphuvadh, V.; Maurer-Stroh, S.; Lopata, A.L.; et al. Protein extraction protocols for optimal proteome measurement and arginine kinase quantitation from cricket Acheta domesticus for food safety assessment. Food Chem. 2021, 348, 129110.
  24. Rodrigues-Ribeiro, L.; Melo-Braga, M.N.; Kjeldsen, F.; Gómez-Mendoza, D.P.; Verano-Braga, T. Assessment of protein extraction and digestion efficiency of well-established shotgun protocols for heart proteomics. Anal. Biochem. 2019, 578, 51–59.
  25. Wu, H.; Ji, C.; Wei, L.; Zhao, J. Evaluation of protein extraction protocols for 2DE in marine ecotoxicoproteomics. Proteomics 2013, 13, 3205–3210.
  26. Betti, M.; Ciacci, C.; Abramovich, S.; Frontalini, F. Protein extractions from Amphistegina lessonii: Protocol development and optimization. Life 2021, 11, 418.
  27. Sedelnikova, S. Protocols and Tips in Protein Purification or How to Purify Protein in One Day; Department of Molecular Biology and Biotechnology of The University of Sheffield: Sheffield, UK, 2018.
  28. Harnedy, P.A.; FitzGerald, R.J. Extraction of protein from the macroalga Palmaria palmata. LWT—Food Sci. Technol. 2013, 51, 375–382.
  29. Sanchez, B.C.; Ralston-Hooper, K.; Sepúlveda, M.S. Review of recent proteomic applications in aquatic toxicology. Environ. Toxicol. Chem. 2011, 30, 274–282.
  30. Feng, J.; Zhang, L.; Xia, X.; Hu, W.; Zhou, P. Effect of geographic variation on the proteome of sea cucumber (Stichopus japonicus). Food Res. Int. 2020, 136, 109498.
  31. Popović, N.T.; Kazazić, S.P.; Strunjak-Perović, I.; Čož-Rakovac, R. Differentiation of environmental aquatic bacterial isolates by MALDI-TOF MS. Environ. Res. 2017, 152, 7–16.
  32. Rodriguez-Temporal, D.; Perez-Risco, D.; Struzka, E.A.; Mas, M.; Alcaide, F. Evaluation of two protein extraction protocols based on freezing and mechanical disruption for identifying nontuberculous mycobacteria by matrix-assisted laser desorption ionization–time of flight mass spectrometry from liquid and solid cultures. J. Clin. Microbiol. 2018, 56, 4.
  33. Dieme, C.; Yssouf, A.; Vega-Rúa, A.; Berenger, J.M.; Failloux, A.B.; Raoult, D.; Parola, P.; Almeras, L. Accurate identification of Culicidae at aquatic developmental stages by MALDI-TOF MS profiling. Parasites Vectors 2014, 7, 544.
  34. Colatriano, D.; Walsh, D.A. An aquatic microbial metaproteomics workflow: From cells to tryptic peptides suitable for tandem mass spectrometry-based analysis. J. Vis. Exp. 2015, 2015, e52827.
  35. Leduc, A.; Fournier, V.; Henry, J. A standardized, innovative method to characterize the structure of aquatic protein hydrolysates. Heliyon 2020, 6, e04170.
  36. Cui, X.; Li, S.C.; He, L.; Li, M. Fingerprinting protein structures effectively and efficiently. Bioinformatics 2014, 30, 949–955.
  37. Niessen, K.A.; Xu, M.; George, D.K.; Chen, M.C.; Ferré-D’Amaré, A.R.; Snell, E.H.; Cody, V.; Pace, J.; Schmidt, M.; Markelz, A.G. Protein and RNA dynamical fingerprinting. Nat. Commun. 2019, 10, 1026.
  38. Zhang, H.; Zong, R.; He, H.; Huang, T. Effects of hydrogen peroxide on Scenedesmus obliquus: Cell growth, antioxidant enzyme activity and intracellular protein fingerprinting. Chemosphere 2022, 287, 132185.
  39. Piñeiro, C.; Barros-Velázquez, J.; Vázquez, J.; Figueras, A.; Gallardo, J.M. Proteomics as a tool for the investigation of seafood and other marine products. J. Proteome Res. 2003, 2, 127–135.
  40. Golden, C.D.; Koehn, J.Z.; Shepon, A.; Passarelli, S.; Free, C.M.; Viana, D.F.; Matthey, H.; Eurich, J.G.; Gephart, J.A.; Fluet-Chouinard, E.; et al. Aquatic foods to nourish nations. Nature 2021, 598, 315–320.
  41. Fiorella, K.J.; Okronipa, H.; Baker, K.; Heilpern, S. Contemporary aquaculture: Implications for human nutrition. Curr. Opin. Biotechnol. 2021, 70, 83–90.
  42. Abdelrahman, H.; ElHady, M.; Alcivar-Warren, A.; Allen, S.; Al-Tobasei, R.; Bao, L.; Beck, B.; Blackburn, H.; Bosworth, B.; Buchanan, J.; et al. Aquaculture genomics, genetics and breeding in the United States: Current status, challenges, and priorities for future research. BMC Genom. 2017, 18, 191.
  43. Carrera, M.; Pazos, M.; Gasset, M. Proteomics-based methodologies for the detection and quantification of seafood allergens. Foods 2020, 9, 1134.
  44. Dalmo, R.A.; Bøgwald, J. ß-Glucans As Conductors of Immune Symphonies. Fish Shellfish Immunol. 2008, 25, 384–396.
  45. Ghaedi, G.; Keyvanshokooh, S.; Mohammadi Azarm, H.; Akhlaghi, M. Proteomic analysis of muscle tissue from rainbow trout (Oncorhynchus mykiss) fed dietary β-glucan. Iran. J. Vet. Res. 2016, 17, 184–189.
  46. Carrera, M.; Cañas, B.; Gallardo, J.M. Rapid direct detection of the major fish allergen, parvalbumin, by selected MS/MS ion monitoring mass spectrometry. J. Proteom. 2012, 75, 3211–3220.
  47. Rahman, A.M.A.; Kamath, S.; Lopata, A.L.; Helleur, R.J. Analysis of the allergenic proteins in black tiger prawn (Penaeus monodon) and characterization of the major allergen tropomyosin using mass spectrometry. Rapid Commun. Mass Spectrom. 2010, 24, 1457–1466.
  48. Tomanek, L. Proteomics to study adaptations in marine organisms to environmental stress. J. Proteom. 2014, 105, 92–106.
  49. Chia, M.A.; Lorenzi, A.S.; Ameh, I.; Dauda, S.; Cordeiro-Araújo, M.K.; Agee, J.T.; Okpanachi, I.Y.; Adesalu, A.T. Susceptibility of phytoplankton to the increasing presence of active pharmaceutical ingredients (APIs) in the aquatic environment: A review. Aquat. Toxicol. 2021, 234, 105809.
  50. Picotti, P.; Aebersold, R. Selected reaction monitoring-based proteomics: Workflows, potential, pitfalls and future directions. Nat. Methods 2012, 9, 555–566.
  51. De Marchi, L.; Coppola, F.; Soares, A.M.V.M.; Pretti, C.; Monserrat, J.M.; della Torre, C.; Freitas, R. Engineered nanomaterials: From their properties and applications, to their toxicity towards marine bivalves in a changing environment. Environ. Res. 2019, 178, 108683.
  52. Trapp, J.; Armengaud, J.; Salvador, A.; Chaumot, A.; Geffard, O. Next-generation proteomics: Toward customized biomarkers for environmental biomonitoring. Environ. Sci. Technol. 2014, 48, 13560–13572.
  53. López-Pedrouso, M.; Varela, Z.; Franco, D.; Fernández, J.A.; Aboal, J.R. Can proteomics contribute to biomonitoring of aquatic pollution? A critical review. Environ. Pollut. 2020, 267, 115473.
  54. Casabianca, S.; Bellingeri, A.; Capellacci, S.; Sbrana, A.; Russo, T.; Corsi, I.; Penna, A. Ecological implications beyond the ecotoxicity of plastic debris on marine phytoplankton assemblage structure and functioning. Environ. Pollut. 2021, 290, 118101.
  55. Liu, W.; Zhao, Y.; Shi, Z.; Li, Z.; Liang, X. Ecotoxicoproteomic assessment of microplastics and plastic additives in aquatic organisms: A review. Comp. Biochem. Physiol.—Part D Genom. Proteom. 2020, 36, 100713.
  56. Duan, Y.; Xiong, D.; Wang, Y.; Zhang, Z.; Li, H.; Dong, H.; Zhang, J. Toxicological effects of microplastics in Litopenaeus vannamei as indicated by an integrated microbiome, proteomic and metabolomic approach. Sci. Total Environ. 2021, 761, 143311.
  57. Khrunyk, Y.; Lach, S.; Petrenko, I.; Ehrlich, H. Progress in Modern Marine Biomaterials Research. Mar. Drugs 2020, 18, 589.
  58. Ren, X.B.; Dang, Y.R.; Liu, S.S.; Huang, K.X.; Qin, Q.L.; Chen, X.L. Identification and Characterization of Three Chitinases with Potential in Direct Conversion of Crystalline Chitin into N, N′-Diacetylchitobiose. Mar. Drugs 2022, 20, 165.
  59. Baghban, N.; Khoradmehr, A.; Nabipour, I.; Tamadon, A.; Ullah, M. The potential of marine-based gold nanomaterials in cancer therapy: A mini-review. Gold Bull. 2022, 55, 53–63.
  60. Liu, S.; Lau, C.S.; Liang, K.; Wen, F.; Teoh, S.H. Marine collagen scaffolds in tissue engineering. Curr. Opin. Biotechnol. 2022, 74, 92–103.
  61. Papon, N.; Copp, B.R.; Courdavault, V. Marine drugs: Biology, pipelines, current and future prospects for production. Biotechnol. Adv. 2022, 54, 107871.
  62. Banerjee, P.; Mandhare, A.; Bagalkote, V. Marine natural products as source of new drugs: An updated patent review (July 2018–July 2021). Expert Opin. Ther. Pat. 2022, 32, 317–363.
More
© Text is available under the terms and conditions of the Creative Commons Attribution (CC BY) license; additional terms may apply. By using this site, you agree to the Terms and Conditions and Privacy Policy.
Upload a video for this entry
Information
Subjects: Marine & Freshwater Biology
Contributors MDPI registered users' name will be linked to their SciProfiles pages. To register with us, please refer to https://encyclopedia.pub/register :
Nadeeka Thushari Gajahin Gamage
,
Rina Miyashita
,
Kazutaka Takahashi
,
Shuichi Asakawa
,
Jayan Duminda Mahesh Senevirathna
View Times: 807
Revisions: 3 times (View History)
Update Date: 20 Sep 2022
Table of Contents
    1000/1000
    Hot Most Recent
    Academic Video Service
    Feedback