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Dobretsov S, Rittschof D. "Omics" Techniques Used in Marine Biofouling Studies. Int J Mol Sci 2023; 24:10518. [PMID: 37445696 DOI: 10.3390/ijms241310518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/16/2023] [Accepted: 06/19/2023] [Indexed: 07/15/2023] Open
Abstract
Biofouling is the growth of organisms on wet surfaces. Biofouling includes micro- (bacteria and unicellular algae) and macrofouling (mussels, barnacles, tube worms, bryozoans, etc.) and is a major problem for industries. However, the settlement and growth of some biofouling species, like oysters and corals, can be desirable. Thus, it is important to understand the process of biofouling in detail. Modern "omic" techniques, such as metabolomics, metagenomics, transcriptomics, and proteomics, provide unique opportunities to study biofouling organisms and communities and investigate their metabolites and environmental interactions. In this review, we analyze the recent publications that employ metagenomic, metabolomic, and proteomic techniques for the investigation of biofouling and biofouling organisms. Specific emphasis is given to metagenomics, proteomics and publications using combinations of different "omics" techniques. Finally, this review presents the future outlook for the use of "omics" techniques in marine biofouling studies. Like all trans-disciplinary research, environmental "omics" is in its infancy and will advance rapidly as researchers develop the necessary expertise, theory, and technology.
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Affiliation(s)
- Sergey Dobretsov
- Department of Marine Science and Fisheries, College of Agricultural and Marine Sciences, Sultan Qaboos University, Al Khoud 123, Muscat P.O. Box 34, Oman
| | - Daniel Rittschof
- Nicholas School of the Environment, Duke University, Beaufort, NC 28516, USA
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2
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Carroll SL, Coyne VE. A proteomic analysis of the effect of ocean acidification on the haemocyte proteome of the South African abalone Haliotis midae. FISH & SHELLFISH IMMUNOLOGY 2021; 117:274-290. [PMID: 34411749 DOI: 10.1016/j.fsi.2021.08.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 08/02/2021] [Accepted: 08/10/2021] [Indexed: 06/13/2023]
Abstract
As a result of increasing CO2 emissions and the prevalence of global climate change, ocean acidification (OA) is becoming more pervasive, affecting many trophic levels, particularly those that rely on succinctly balanced ocean chemistry. This ultimately threatens community structures, as well as the future sustainability of the fishing/aquaculture industry. Understanding the molecular stress response of key organisms will aid in predicting their future survivability under changing environmental conditions. This study sought to elucidate the molecular stress response of the South African abalone, Haliotis midae, an understudied organism with high economic value, utilising a high throughput iTRAQ-based proteomics methodology. Adult abalone were exposed to control (pH 7.9) and experimental (pH 7.5) conditions for 12, 72 and 168 h, following which protein was isolated from sampled haemocytes and subsequently processed. iTRAQ-labelled peptides were analysed using mass spectrometry, while an array of bioinformatics tools was utilised for analysing the proteomic data. COG analysis identified "Cytoskeleton", "Translation, ribosomal structure and biogenesis", "Post-translational modification, protein turnover, chaperones", and "Intracellular trafficking, secretion and vesicular transport" to be the most enriched functional classes, while statistical analysis identified a total of 33 up-regulated and 23 down-regulated effectors of OA stress in abalone. Several of the up-regulated proteins that were identified function in central metabolism (ENO1, PGK, DUOX1, GPD2), the stress/immune response (CAMKI, HSPA5/GRP78, MAPKI), and cytoskeleton, protein sorting and signal transduction (IQGAP1, MYO9B, TLN1, RDX, TCP-1/CCT, SNX6, CHMP1a, VPS13a). Protein-protein interactions were predicted using STRING DB, Cytoscape and Ingenuity Pathway Analysis, providing a model of the effects of OA on the H. midae haemocyte proteome. The data indicated that H. midae underwent a metabolic shift under OA conditions to utilize more energy-efficient mechanisms of ATP generation, while attempts at restoring haemocyte stabilisation and homeostasis were reflected by up-regulation of oxidative stress and cytoskeletal proteins. Our results support other molluscan studies that report a complex array of overlapping functions of both the stress and immune response systems. This interplay of the mounted stress and immune response is maintained and observed through the up-regulation of proteins involved in protein synthesis and turnover, as well as intracellular signalling and transport. The data presented in this study highlight the value of employing sensitive and robust -omics technologies for assessing the effects of changing environmental conditions on marine organisms.
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Affiliation(s)
- Sarah L Carroll
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, 7700, South Africa
| | - Vernon E Coyne
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, 7700, South Africa.
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3
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Beltran CGG, Coyne VE. iTRAQ-based quantitative proteomic profiling of the immune response of the South African abalone, Haliotis midae. FISH & SHELLFISH IMMUNOLOGY 2020; 99:130-143. [PMID: 32045637 DOI: 10.1016/j.fsi.2020.02.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 01/30/2020] [Accepted: 02/03/2020] [Indexed: 06/10/2023]
Abstract
The South African abalone Haliotis midae is a commercially important species farmed at high densities in land-based aquaculture systems. Disease outbreaks have had a severe financial impact on the abalone industry yet the molecular mechanisms underlying the immune response of H. midae remain obscure. In this study, a comparative shotgun proteomics approach using iTRAQ coupled with LC-MS/MS was employed to investigate H. midae proteome changes in response to Vibrio anguillarum challenge. A total of 118 non-redundant, unique haemocyte proteins were identified and quantified, with 16 proteins significantly regulated. Hierarchical clustering and pathway analysis uncovered a coordinated response dominated by calcium and cAMP signalling via activation of MAPK cascades. Early up-regulated biological processes involve phagocytosis, nitric oxide production and ATP-synthesis, whilst down-regulated responses were predominantly involved in the regulation of apoptosis. The late up-regulated response involved protein kinase activity and detoxification processes. Expression of selected proteins was validated by Western blot. A putative allograft inflammatory factor-1 protein was further selected to establish its functional molecular role in haemocytes. Confocal imaging revealed that allograft inflammatory factor-1 regulates phagocytosis via a functional interaction with filamentous actin. This is the first time a high-throughput proteomics approach has been used to investigate the immune response of H. midae.
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Affiliation(s)
- Caroline G G Beltran
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, 7700, South Africa
| | - Vernon E Coyne
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, 7700, South Africa.
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4
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Bioinformatics for Marine Products: An Overview of Resources, Bottlenecks, and Perspectives. Mar Drugs 2019; 17:md17100576. [PMID: 31614509 PMCID: PMC6835618 DOI: 10.3390/md17100576] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 10/01/2019] [Accepted: 10/02/2019] [Indexed: 12/13/2022] Open
Abstract
The sea represents a major source of biodiversity. It exhibits many different ecosystems in a huge variety of environmental conditions where marine organisms have evolved with extensive diversification of structures and functions, making the marine environment a treasure trove of molecules with potential for biotechnological applications and innovation in many different areas. Rapid progress of the omics sciences has revealed novel opportunities to advance the knowledge of biological systems, paving the way for an unprecedented revolution in the field and expanding marine research from model organisms to an increasing number of marine species. Multi-level approaches based on molecular investigations at genomic, metagenomic, transcriptomic, metatranscriptomic, proteomic, and metabolomic levels are essential to discover marine resources and further explore key molecular processes involved in their production and action. As a consequence, omics approaches, accompanied by the associated bioinformatic resources and computational tools for molecular analyses and modeling, are boosting the rapid advancement of biotechnologies. In this review, we provide an overview of the most relevant bioinformatic resources and major approaches, highlighting perspectives and bottlenecks for an appropriate exploitation of these opportunities for biotechnology applications from marine resources.
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Di G, Li Y, Zhao X, Wang N, Fu J, Li M, Huang M, You W, Kong X, Ke C. Differential proteomic profiles and characterizations between hyalinocytes and granulocytes in ivory shell Babylonia areolata. FISH & SHELLFISH IMMUNOLOGY 2019; 92:405-420. [PMID: 31212011 DOI: 10.1016/j.fsi.2019.06.036] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 06/11/2019] [Accepted: 06/13/2019] [Indexed: 06/09/2023]
Abstract
The haemocytes of the ivory shell, Babylonia areolata are classified by morphologic observation into the following types: hyalinocytes (H) and granulocytes (G). Haemocytes comprise diverse cell types with morphological and functional heterogene and play indispensable roles in immunological homeostasis of invertebrates. In the present study, two types of haemocytes were morphologically identified and separated as H and G by Percoll density gradient centrifugation. The differentially expressed proteins were investigated between H and G using mass spectrometry. The results showed that total quantitative proteins between H and G samples were 1644, the number of up-regulated proteins in G was 215, and the number of down-regulated proteins in G was 378. Among them, cathepsin, p38 MAPK, toll-interacting protein-like and beta-adrenergic receptor kinase 2-like were up-regulated in G; alpha-2-macroglobulin-like protein, C-type lectin, galectin-2-1, galectin-3, β-1,3-glucan-binding protein, ferritin, mega-hemocyanin, mucin-17-like, mucin-5AC-like and catalytic subunit of protein kinase A were down-regulated in G. The results showed that the most significantly enriched KEGG pathways were the pathways related to ribosome, phagosome, endocytosis, carbon metabolism, protein processing in endoplasmic reticulum and oxidative phosphorylation. For phagosome and endocytosis pathway, the number of down-regulation proteins in G was more than that of up-regulation proteins. For lysosome pathway, the number of up-regulation proteins in G was more than that of down-regulation proteins. These results suggested that two sub-population haemocytes perform the different immune functions in B. areolata.
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Affiliation(s)
- Guilan Di
- College of Fisheries, Henan Normal University, Xinxiang, 453007, China
| | - Yanfei Li
- College of Fisheries, Henan Normal University, Xinxiang, 453007, China
| | - Xianliang Zhao
- College of Fisheries, Henan Normal University, Xinxiang, 453007, China
| | - Ning Wang
- College of Fisheries, Henan Normal University, Xinxiang, 453007, China
| | - Jingqiang Fu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Min Li
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Miaoqin Huang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Weiwei You
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Xianghui Kong
- College of Fisheries, Henan Normal University, Xinxiang, 453007, China.
| | - Caihuan Ke
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.
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Barranger A, Langan LM, Sharma V, Rance GA, Aminot Y, Weston NJ, Akcha F, Moore MN, Arlt VM, Khlobystov AN, Readman JW, Jha AN. Antagonistic Interactions between Benzo[a]pyrene and Fullerene (C 60) in Toxicological Response of Marine Mussels. NANOMATERIALS (BASEL, SWITZERLAND) 2019; 9:E987. [PMID: 31288459 PMCID: PMC6669530 DOI: 10.3390/nano9070987] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 06/25/2019] [Accepted: 06/28/2019] [Indexed: 12/12/2022]
Abstract
This study aimed to assess the ecotoxicological effects of the interaction of fullerene (C60) and benzo[a]pyrene (B[a]P) on the marine mussel, Mytilus galloprovincialis. The uptake of nC60, B[a]P and mixtures of nC60 and B[a]P into tissues was confirmed by Gas Chromatography-Mass Spectrometry (GC-MS), Liquid Chromatography-High Resolution Mass Spectrometry (LC-HRMS) and Inductively Coupled Plasma Mass Spectrometer (ICP-MS). Biomarkers of DNA damage as well as proteomics analysis were applied to unravel the interactive effect of B[a]P and C60. Antagonistic responses were observed at the genotoxic and proteomic level. Differentially expressed proteins (DEPs) were only identified in the B[a]P single exposure and the B[a]P mixture exposure groups containing 1 mg/L of C60, the majority of which were downregulated (~52%). No DEPs were identified at any of the concentrations of nC60 (p < 0.05, 1% FDR). Using DEPs identified at a threshold of (p < 0.05; B[a]P and B[a]P mixture with nC60), gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis indicated that these proteins were enriched with a broad spectrum of biological processes and pathways, including those broadly associated with protein processing, cellular processes and environmental information processing. Among those significantly enriched pathways, the ribosome was consistently the top enriched term irrespective of treatment or concentration and plays an important role as the site of biological protein synthesis and translation. Our results demonstrate the complex multi-modal response to environmental stressors in M. galloprovincialis.
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Affiliation(s)
- Audrey Barranger
- School of Biological and Marine Sciences, University of Plymouth, Plymouth PL4 8AA, UK
| | - Laura M Langan
- School of Biological and Marine Sciences, University of Plymouth, Plymouth PL4 8AA, UK
| | - Vikram Sharma
- School of Biomedical Sciences, University of Plymouth, Plymouth PL4 8AA, UK
| | - Graham A Rance
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK
- Nanoscale and Microscale Research Centre, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Yann Aminot
- Centre for Chemical Sciences, University of Plymouth, Plymouth PL4 8AA, UK
| | - Nicola J Weston
- Nanoscale and Microscale Research Centre, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Farida Akcha
- Ifremer, Laboratory of Ecotoxicology, F-44311, CEDEX 03 Nantes, France
| | - Michael N Moore
- School of Biological and Marine Sciences, University of Plymouth, Plymouth PL4 8AA, UK
- Plymouth Marine Laboratory, Prospect Place, The Hoe, Plymouth PL1 3HD, UK
- European Centre for Environment & Human Health (ECEHH), University of Exeter Medical School, Knowledge Spa, Royal Cornwall Hospital, Cornwall TR1 3LJ, UK
| | - Volker M Arlt
- Department of Analytical, Environmental and Forensic Sciences, King's College London, MRC-PHE Centre for Environmental & Health, London SE1 9NH, UK
- NIHR Health Protection Research Unit in Health Impact of Environmental Hazards at King's College London in partnership with Public Health England and Imperial College London, London SE1 9NH, UK
| | - Andrei N Khlobystov
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK
- Nanoscale and Microscale Research Centre, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - James W Readman
- Centre for Chemical Sciences, University of Plymouth, Plymouth PL4 8AA, UK
| | - Awadhesh N Jha
- School of Biological and Marine Sciences, University of Plymouth, Plymouth PL4 8AA, UK.
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7
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Artifon V, Zanardi-Lamardo E, Fillmann G. Aquatic organic matter: Classification and interaction with organic microcontaminants. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 649:1620-1635. [PMID: 30308930 DOI: 10.1016/j.scitotenv.2018.08.385] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 08/13/2018] [Accepted: 08/27/2018] [Indexed: 06/08/2023]
Abstract
Organic matter (OM) in aquatic system is originated from autochthonous and allochthonous natural sources as well as anthropogenic inputs, and can be found in dissolved, particulate or colloidal form. According to the type/composition, OM can be divided in non-humic substances (NHS) or humic substances (HS). The present review focuses on the main groups that constitute the NHS (carbohydrates, proteins, lipids, and lignin) and their role as chemical biomarkers, as well as the main characteristics of HS are presented. HS functions, properties and mechanisms are discussed, in addition to their association to the fate, bioavailability, and toxicity of organic microcontaminants in the aquatic systems. Despite the growing diversity and potential impacts of organic microcontaminants to the aquatic environment, limited information is available about their association with OM. A protective effect is, however, normally seen since the presence of OM (HS mainly) may reduce bioavailability and, consequently, the concentration of organic microcontaminants within the organism. It may also affect the toxicity by either absorbing ultraviolet radiation incidence and, then, reducing the formation of phototoxic compounds, or by increasing the oxygen reactive species and, thus, affecting the decomposition of natural and anthropogenic organic compounds. In addition, the outcome data is hard to compare since each study follows unique experimental protocols. The often use of commercial humic acid (Aldrich) as a generic source of OM in studies can also hinder comparisons since differences in composition makes this type of OM not representative of any aquatic environment. Thus, the current challenge is find out how this clear fragmentation can be overcome.
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Affiliation(s)
- Vanda Artifon
- Laboratório de Microcontaminantes Orgânicos e Ecotoxicologia Aquática, Instituto de Oceanografia, Universidade Federal do Rio Grande, Rio Grande 96203-900, RS, Brazil
| | - Eliete Zanardi-Lamardo
- Laboratório de Compostos Orgânicos em Ecossistemas Costeiros e Marinhos, Departamento de Oceanografia, Universidade Federal de Pernambuco, Recife 50740-550, PE, Brazil
| | - Gilberto Fillmann
- Laboratório de Microcontaminantes Orgânicos e Ecotoxicologia Aquática, Instituto de Oceanografia, Universidade Federal do Rio Grande, Rio Grande 96203-900, RS, Brazil.
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8
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Yu N, Ding Q, Li E, Qin JG, Chen L, Wang X. Growth, energy metabolism and transcriptomic responses in Chinese mitten crab (Eriocheir sinensis) to benzo[α]pyrene (BaP) toxicity. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2018; 203:150-158. [PMID: 30138799 DOI: 10.1016/j.aquatox.2018.08.014] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 08/14/2018] [Accepted: 08/14/2018] [Indexed: 06/08/2023]
Abstract
Benzo(a)pyrene (BaP) is a highly toxic polycyclic aromatic hydrocarbon and has strong affinity to suspended materials and sediments in the aquatic environment. Most crustaceans are benthic species and are easily affected by the pollution in the sediments, but there is little information on the response mechanism of crustaceans to BaP exposure. This study compared the growth and hepatopancreas transcriptomic responses of the Chinse mitten crab (Eriocheir sinensis) exposed to 0, 0.15 (BaP1) and 0.45 μg /L (BaP2) for 28 days. Crab survival and weight gain were reduced in the water born BaP in a dose-dependent way. The contents of hepatopancreas glycogen, triglyceride, total amino acids and lactic acid were all decreased after BaP exposure, indicating possible more energy consumption during detoxification. In the transcriptome analysis, a total of 106.65 million clean reads were obtained and assembled into 81,714 unigenes with an average length of 594 bp and N50 of 808 bp. Under 0.15 or 0.45 μg /L BaP exposure, 922 and 1129 unigenes in crabs were significantly expressed, annotated to 676 and 802 Gene Ontology (GO) terms respectively. The "cellular process" was the leading category for both concentrations. Thirteen significantly changed pathways were identified in both Control vs BaP1 and Control vs BaP2 groups. These pathways were divided into four different parts according to their reported functions, including metabolism, environmental information processing, organismal systems and cellular processes. Nice out of thirteen pathways in BaP1 were related to metabolism, containing amino acid metabolism, phenylpropanoid biosynthesis, monobactam biosynthesis and styrene degradation. Almost all the pathways related with the biosynthesis processes were down-regulated, while the degradation pathways were up-regulated. Seven out of thirteen pathways were classified into metabolism category in BaP2. These pathways were mostly associated with stress resistance rather than supplying energy. This study indicates that both concentrations of BaP disturbed nutrient metabolism, immune response and defense system in the crabs, while exposure to a higher concentration had a greater impact on immunity system than on metabolism. This study provides a better understanding of the underlying molecular and regulatory mechanisms in crustaceans coping with BaP toxicity.
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Affiliation(s)
- Na Yu
- East China Normal University, Shanghai, 200241, China
| | - Qingqing Ding
- East China Normal University, Shanghai, 200241, China
| | - Erchao Li
- East China Normal University, Shanghai, 200241, China; Department of Aquaculture, College of Marine Sciences, Hainan University, Haikou, Hainan, 570228, China
| | - Jian G Qin
- School of Biological Sciences, Flinders University, Adelaide, SA, 5001, Australia
| | - Liqiao Chen
- East China Normal University, Shanghai, 200241, China
| | - Xiaodan Wang
- East China Normal University, Shanghai, 200241, China.
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9
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Chen H, Diao X, Wang H, Zhou H. An integrated metabolomic and proteomic study of toxic effects of Benzo[a]pyrene on gills of the pearl oyster Pinctada martensii. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2018; 156:330-336. [PMID: 29573723 DOI: 10.1016/j.ecoenv.2018.03.040] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 03/11/2018] [Accepted: 03/13/2018] [Indexed: 06/08/2023]
Abstract
Benzo[a]pyrene (BaP) is one of the most important polycyclic aromatic hydrocarbons (PAHs), which are widely present in the marine environment. Because of its teratogenic, mutagenic, and carcinogenic effects on various organisms, the toxicity of BaP is of great concern. In this study, we focused on the toxic effects of BaP (1 µg/L and 10 µg/L) on gills of the pearl oyster Pinctada martensii using combined metabolomic and proteomic approaches. At the metabolome level, the high concentration of BaP mainly caused abnormal energy metabolism, osmotic regulation and immune response marked by significantly altered metabolites in gills. At the proteome level, both concentrations of BaP mainly induced signal transduction, transcription regulation, cell growth, stress response, and energy metabolism. Overall, the research demonstrated that the combination of proteomic and metabolomic approaches could provide a significant way to elucidate toxic effects of BaP on P. martensii.
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Affiliation(s)
- Hao Chen
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China; Institute of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China.
| | - Xiaoping Diao
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China; Institute of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China.
| | - Haihua Wang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China; Institute of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China.
| | - Hailong Zhou
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China; Institute of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China.
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10
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Dhakal D, Pokhrel AR, Shrestha B, Sohng JK. Marine Rare Actinobacteria: Isolation, Characterization, and Strategies for Harnessing Bioactive Compounds. Front Microbiol 2017; 8:1106. [PMID: 28663748 PMCID: PMC5471306 DOI: 10.3389/fmicb.2017.01106] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Accepted: 05/31/2017] [Indexed: 12/28/2022] Open
Abstract
Actinobacteria are prolific producers of thousands of biologically active natural compounds with diverse activities. More than half of these bioactive compounds have been isolated from members belonging to actinobacteria. Recently, rare actinobacteria existing at different environmental settings such as high altitudes, volcanic areas, and marine environment have attracted attention. It has been speculated that physiological or biochemical pressures under such harsh environmental conditions can lead to the production of diversified natural compounds. Hence, marine environment has been focused for the discovery of novel natural products with biological potency. Many novel and promising bioactive compounds with versatile medicinal, industrial, or agricultural uses have been isolated and characterized. The natural compounds cannot be directly used as drug or other purposes, so they are structurally modified and diversified to ameliorate their biological or chemical properties. Versatile synthetic biological tools, metabolic engineering techniques, and chemical synthesis platform can be used to assist such structural modification. This review summarizes the latest studies on marine rare actinobacteria and their natural products with focus on recent approaches for structural and functional diversification of such microbial chemicals for attaining better applications.
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Affiliation(s)
- Dipesh Dhakal
- Department of Life Science and Biochemical Engineering, Sun Moon UniversityAsan-si, South Korea
| | - Anaya Raj Pokhrel
- Department of Life Science and Biochemical Engineering, Sun Moon UniversityAsan-si, South Korea
| | - Biplav Shrestha
- Department of Life Science and Biochemical Engineering, Sun Moon UniversityAsan-si, South Korea
| | - Jae Kyung Sohng
- Department of Life Science and Biochemical Engineering, Sun Moon UniversityAsan-si, South Korea.,Department of BT-Convergent Pharmaceutical Engineering, Sun Moon University Asan-siSouth Korea
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11
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Dineshram R, Quan Q, Sharma R, Chandramouli K, Yalamanchili HK, Chu I, Thiyagarajan V. Comparative and quantitative proteomics reveal the adaptive strategies of oyster larvae to ocean acidification. Proteomics 2016; 15:4120-34. [PMID: 26507238 DOI: 10.1002/pmic.201500198] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Revised: 10/08/2015] [Accepted: 10/15/2015] [Indexed: 01/01/2023]
Abstract
Decreasing pH due to anthropogenic CO2 inputs, called ocean acidification (OA), can make coastal environments unfavorable for oysters. This is a serious socioeconomical issue for China which supplies >70% of the world's edible oysters. Here, we present an iTRAQ-based protein profiling approach for the detection and quantification of proteome changes under OA in the early life stage of a commercially important oyster, Crassostrea hongkongensis. Availability of complete genome sequence for the pacific oyster (Crassostrea gigas) enabled us to confidently quantify over 1500 proteins in larval oysters. Over 7% of the proteome was altered in response to OA at pHNBS 7.6. Analysis of differentially expressed proteins and their associated functional pathways showed an upregulation of proteins involved in calcification, metabolic processes, and oxidative stress, each of which may be important in physiological adaptation of this species to OA. The downregulation of cytoskeletal and signal transduction proteins, on the other hand, might have impaired cellular dynamics and organelle development under OA. However, there were no significant detrimental effects in developmental processes such as metamorphic success. Implications of the differentially expressed proteins and metabolic pathways in the development of OA resistance in oyster larvae are discussed. The MS proteomics data have been deposited to the ProteomeXchange with identifiers PXD002138 (http://proteomecentral.proteomexchange.org/dataset/PXD002138).
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Affiliation(s)
- R Dineshram
- The Swire Institute of Marine Sciences and School of Biological Sciences, The University of Hong Kong, Hong Kong Special Administrative Region, P. R. China
| | - Q Quan
- Department of Chemistry, The University of Hong Kong, Hong Kong Special Administrative Region, P. R. China
| | - Rakesh Sharma
- Department of Biochemistry, L.K.S Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, P. R. China.,Department of Biology and Chemistry, City University of Hong Kong, Kowloon Tong, Hong Kong
| | - Kondethimmanahalli Chandramouli
- Biological, Environmental Sciences & Engineering, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | | | - Ivan Chu
- Department of Chemistry, The University of Hong Kong, Hong Kong Special Administrative Region, P. R. China
| | - Vengatesen Thiyagarajan
- The Swire Institute of Marine Sciences and School of Biological Sciences, The University of Hong Kong, Hong Kong Special Administrative Region, P. R. China
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Upadhyay A, Thiyagarajan V, Tong Y. Proteomic characterization of oyster shell organic matrix proteins (OMP). Bioinformation 2016; 12:266-278. [PMID: 28246460 PMCID: PMC5295041 DOI: 10.6026/97320630012266] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 07/19/2016] [Accepted: 07/20/2016] [Indexed: 12/31/2022] Open
Abstract
Oysters are economically and ecologically important bivalves, with its calcareous shell and delicious meat. The shell composition is a blend of inorganic crystals and shell proteins that form an organic matrix which protects the soft inner tissue of the oyster. The objective of the study was to compare the composition of organic matrix proteins (OMP) of two phylogenetically related species: the Hong Kong oyster (Crassostrea hongkongensis) and the Portuguese oyster (Crassostrea angulata) which differ in their shell hardness and mechanical properties. C. hongkongensis shells are comparatively stronger than C. angulata. Modern shotgun proteomics has been used to understand the nature of the OMP and the variations observed in the mechanical properties of these two species of oyster shells. After visualizing proteins on the one (1DE) and two-dimensional electrophoresis (2DE) gels, the protein spots and their intensities were compared using PDQuest software and 14 proteins of C. hongkongensis were found to be significantly different (student׳s t-test; p<0.05) when compared to the C. angulata. Furthermore, shell OMP separated on 1DE gels were processed using Triple TOF5600 mass spectrometry and 42 proteins of C. hongkongensis and 37 of C. angulata identified. A Circos based comparative analysis of the shell proteins of both oyster species were prepared against the shell proteome of other shell forming gastropods and molluscs to study the evolutionary conservation of OMP and their function. This comparative proteomics expanded our understating of the molecular mechanism behind the shells having different hardness and mechanical properties.
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Affiliation(s)
- Abhishek Upadhyay
- The Swire Institute of Marine Science (SWIMS), The University of Hong Kong (HKU), Hong Kong
- School of Biological Sciences (SBS), The University of Hong Kong (HKU), Hong Kong
| | - Vengatesen Thiyagarajan
- The Swire Institute of Marine Science (SWIMS), The University of Hong Kong (HKU), Hong Kong
- School of Biological Sciences (SBS), The University of Hong Kong (HKU), Hong Kong
| | - Ying Tong
- School of Biological Sciences (SBS), The University of Hong Kong (HKU), Hong Kong
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13
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Dineshram R, Chandramouli K, Ko GWK, Zhang H, Qian PY, Ravasi T, Thiyagarajan V. Quantitative analysis of oyster larval proteome provides new insights into the effects of multiple climate change stressors. GLOBAL CHANGE BIOLOGY 2016; 22:2054-2068. [PMID: 26990129 DOI: 10.1111/gcb.13249] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 01/26/2016] [Accepted: 01/27/2016] [Indexed: 06/05/2023]
Abstract
The metamorphosis of planktonic larvae of the Pacific oyster (Crassostrea gigas) underpins their complex life-history strategy by switching on the molecular machinery required for sessile life and building calcite shells. Metamorphosis becomes a survival bottleneck, which will be pressured by different anthropogenically induced climate change-related variables. Therefore, it is important to understand how metamorphosing larvae interact with emerging climate change stressors. To predict how larvae might be affected in a future ocean, we examined changes in the proteome of metamorphosing larvae under multiple stressors: decreased pH (pH 7.4), increased temperature (30 °C), and reduced salinity (15 psu). Quantitative protein expression profiling using iTRAQ-LC-MS/MS identified more than 1300 proteins. Decreased pH had a negative effect on metamorphosis by down-regulating several proteins involved in energy production, metabolism, and protein synthesis. However, warming switched on these down-regulated pathways at pH 7.4. Under multiple stressors, cell signaling, energy production, growth, and developmental pathways were up-regulated, although metamorphosis was still reduced. Despite the lack of lethal effects, significant physiological responses to both individual and interacting climate change related stressors were observed at proteome level. The metamorphosing larvae of the C. gigas population in the Yellow Sea appear to have adequate phenotypic plasticity at the proteome level to survive in future coastal oceans, but with developmental and physiological costs.
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Affiliation(s)
- Ramadoss Dineshram
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Pok Fu Lam Road, Hong Kong Island, Hong Kong SAR, China
| | - Kondethimmanahalli Chandramouli
- Division of Biological, Environmental Sciences & Engineering, Division of Applied Mathematics and Computer Sciences and KAUST Environmental Epigenetic Program (KEEP), King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Ginger Wai Kuen Ko
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Pok Fu Lam Road, Hong Kong Island, Hong Kong SAR, China
| | - Huoming Zhang
- Division of Biological, Environmental Sciences & Engineering, Division of Applied Mathematics and Computer Sciences and KAUST Environmental Epigenetic Program (KEEP), King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Pei-Yuan Qian
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Timothy Ravasi
- Division of Biological, Environmental Sciences & Engineering, Division of Applied Mathematics and Computer Sciences and KAUST Environmental Epigenetic Program (KEEP), King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Vengatesen Thiyagarajan
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Pok Fu Lam Road, Hong Kong Island, Hong Kong SAR, China
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14
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Kim BM, Kim J, Choi IY, Raisuddin S, Au DWT, Leung KMY, Wu RSS, Rhee JS, Lee JS. Omics of the marine medaka (Oryzias melastigma) and its relevance to marine environmental research. MARINE ENVIRONMENTAL RESEARCH 2016; 113:141-152. [PMID: 26716363 DOI: 10.1016/j.marenvres.2015.12.004] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 12/11/2015] [Accepted: 12/12/2015] [Indexed: 06/05/2023]
Abstract
In recent years, the marine medaka (Oryzias melastigma), also known as the Indian medaka or brackish medaka, has been recognized as a model fish species for ecotoxicology and environmental research in the Asian region. O. melastigma has several promising features for research, which include a short generation period (3-4 months), daily spawning, small size (3-4 cm), transparent embryos, sexual dimorphism, and ease of mass culture in the laboratory. There have been extensive transcriptome and genome studies on the marine medaka in the past decade. Such omics data can be useful in understanding the signal transduction pathways of small teleosts in response to environmental stressors. An omics-integrated approach in the study of the marine medaka is important for strengthening its role as a small fish model for marine environmental studies. In this review, we present current omics information about the marine medaka and discuss its potential applications in the study of various molecular pathways that can be targets of marine environmental stressors, such as chemical pollutants. We believe that this review will encourage the use of this small fish as a model species in marine environmental research.
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Affiliation(s)
- Bo-Mi Kim
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon, 16419, South Korea
| | - Jaebum Kim
- Department of Animal Biotechnology, College of Animal Bioscience & Technology, Konkuk University, Seoul, 05029, South Korea
| | - Ik-Young Choi
- National Instrumentation Center for Environmental Management, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Sheikh Raisuddin
- Department of Medical Elementology & Toxicology, Hamdard University, 110062, New Delhi, India
| | - Doris W T Au
- State Key Laboratory on Marine Pollution, City University of Hong Kong, Kowloon, Hong Kong, China
| | - Kenneth M Y Leung
- School of Biological Sciences, University of Hong Kong, Hong Kong, China
| | - Rudolf S S Wu
- School of Biological Sciences, University of Hong Kong, Hong Kong, China
| | - Jae-Sung Rhee
- Department of Marine Science, College of Natural Sciences, Incheon National University, Incheon, 22012, South Korea.
| | - Jae-Seong Lee
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon, 16419, South Korea.
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15
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Provan F, Nilsen MM, Larssen E, Uleberg KE, Sydnes MO, Lyng E, Øysæd KB, Baussant T. An evaluation of coral lophelia pertusa mucus as an analytical matrix for environmental monitoring: A preliminary proteomic study. JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH. PART A 2016; 79:647-657. [PMID: 27484144 DOI: 10.1080/15287394.2016.1210494] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
For the environmental monitoring of coral, mucus appears to be an appropriate biological matrix due to its array of functions in coral biology and the non-intrusive manner in which it can be collected. The aim of the present study was to evaluate the feasibility of using mucus of the stony coral Lophelia pertusa (L. pertusa) as an analytical matrix for discovery of biomarkers used for environmental monitoring. More specifically, to assess whether a mass-spectrometry-based proteomic approach can be applied to characterize the protein composition of coral mucus and changes related to petroleum discharges at the seafloor. Surface-enhanced laser desorption/ionization-time of flight mass spectrometry (SELDI-TOF MS) screening analyses of orange and white L. pertusa showed that the mucosal protein composition varies significantly with color phenotype, a pattern not reported prior to this study. Hence, to reduce variability from phenotype difference, L. pertusa white individuals only were selected to characterize in more detail the basal protein composition in mucus using liquid chromatography, mass spectrometry, mass spectrometry (LC-MS/MS). In total, 297 proteins were identified in L. pertusa mucus of unexposed coral individuals. Individuals exposed to drill cuttings in the range 2 to 12 mg/L showed modifications in coral mucus protein composition compared to unexposed corals. Although the results were somewhat inconsistent between individuals and require further validation in both the lab and the field, this study demonstrated preliminary encouraging results for discovery of protein markers in coral mucus that might provide more comprehensive insight into potential consequences attributed to anthropogenic stressors and may be used in future monitoring of coral health.
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Affiliation(s)
- Fiona Provan
- a International Research Institute of Stavanger (IRIS), Biomiljø , Randaberg , Norway
| | - Mari Mæland Nilsen
- a International Research Institute of Stavanger (IRIS), Biomiljø , Randaberg , Norway
| | - Eivind Larssen
- a International Research Institute of Stavanger (IRIS), Biomiljø , Randaberg , Norway
| | - Kai-Erik Uleberg
- a International Research Institute of Stavanger (IRIS), Biomiljø , Randaberg , Norway
| | - Magne O Sydnes
- a International Research Institute of Stavanger (IRIS), Biomiljø , Randaberg , Norway
- b Faculty of Science and Technology, Department of Mathematics and Natural Science , University of Stavanger , Stavanger , Norway
| | - Emily Lyng
- a International Research Institute of Stavanger (IRIS), Biomiljø , Randaberg , Norway
| | - Kjell Birger Øysæd
- a International Research Institute of Stavanger (IRIS), Biomiljø , Randaberg , Norway
| | - Thierry Baussant
- a International Research Institute of Stavanger (IRIS), Biomiljø , Randaberg , Norway
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16
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Gochfeld DJ, Ankisetty S, Slattery M. Proteomic profiling of healthy and diseased hybrid soft corals Sinularia maxima × S. polydactyla. DISEASES OF AQUATIC ORGANISMS 2015; 116:133-141. [PMID: 26480916 DOI: 10.3354/dao02910] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Emerging diseases of marine invertebrates have been implicated as one of the major causes of the continuing decline in coral reefs worldwide. To date, most of the focus on marine diseases has been aimed at hard (scleractinian) corals, which are the main reef builders worldwide. However, soft (alcyonacean) corals are also essential components of tropical reefs, representing food, habitat and the 'glue' that consolidates reefs, and they are subject to the same stressors as hard corals. Sinularia maxima and S. polydactyla are the dominant soft corals on the shallow reefs of Guam, where they hybridize. In addition to both parent species, the hybrid soft coral population in Guam is particularly affected by Sinularia tissue loss disease. Using label-free shotgun proteomics, we identified differences in protein expression between healthy and diseased colonies of the hybrid S. maxima × S. polydactyla. This study provided qualitative and quantitative data on specific proteins that were differentially expressed under the stress of disease. In particular, metabolic proteins were down-regulated, whereas proteins related to stress and to symbiont photosynthesis were up-regulated in the diseased soft corals. These results indicate that soft corals are responding to pathogenesis at the level of the proteome, and that this label-free approach can be used to identify and quantify protein biomarkers of sub-lethal stress in studies of marine disease.
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Affiliation(s)
- Deborah J Gochfeld
- National Center for Natural Products Research, and Department of BioMolecular Sciences, University of Mississippi, PO Box 1848, University, MS 38677-1848, USA
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17
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Suarez-Ulloa V, Gonzalez-Romero R, Eirin-Lopez JM. Environmental epigenetics: A promising venue for developing next-generation pollution biomonitoring tools in marine invertebrates. MARINE POLLUTION BULLETIN 2015; 98:5-13. [PMID: 26088539 DOI: 10.1016/j.marpolbul.2015.06.020] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Revised: 06/04/2015] [Accepted: 06/11/2015] [Indexed: 06/04/2023]
Abstract
Environmental epigenetics investigates the cause-effect relationships between specific environmental factors and the subsequent epigenetic modifications triggering adaptive responses in the cell. Given the dynamic and potentially reversible nature of the different types of epigenetic marks, environmental epigenetics constitutes a promising venue for developing fast and sensible biomonitoring programs. Indeed, several epigenetic biomarkers have been successfully developed and applied in traditional model organisms (e.g., human and mouse). Nevertheless, the lack of epigenetic knowledge in other ecologically and environmentally relevant organisms has hampered the application of these tools in a broader range of ecosystems, most notably in the marine environment. Fortunately, that scenario is now changing thanks to the growing availability of complete reference genome sequences along with the development of high-throughput DNA sequencing and bioinformatic methods. Altogether, these resources make the epigenetic study of marine organisms (and more specifically marine invertebrates) a reality. By building on this knowledge, the present work provides a timely perspective highlighting the extraordinary potential of environmental epigenetic analyses as a promising source of rapid and sensible tools for pollution biomonitoring, using marine invertebrates as sentinel organisms. This strategy represents an innovative, groundbreaking approach, improving the conservation and management of natural resources in the oceans.
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Affiliation(s)
- Victoria Suarez-Ulloa
- CHROMEVOL Group, Department of Biological Sciences, Florida International University, Miami, FL, USA
| | - Rodrigo Gonzalez-Romero
- CHROMEVOL Group, Department of Biological Sciences, Florida International University, Miami, FL, USA
| | - Jose M Eirin-Lopez
- CHROMEVOL Group, Department of Biological Sciences, Florida International University, Miami, FL, USA.
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18
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Helmholz H, Lassen S, Ruhnau C, Pröfrock D, Erbslöh HB, Prange A. Investigation on the proteome response of transplanted blue mussel (Mytilus sp.) during a long term exposure experiment at differently impacted field stations in the German Bight (North Sea). MARINE ENVIRONMENTAL RESEARCH 2015; 110:69-80. [PMID: 26275755 DOI: 10.1016/j.marenvres.2015.07.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 07/28/2015] [Accepted: 07/30/2015] [Indexed: 06/04/2023]
Abstract
In a pilot field study the proteome response of Mytilus sp. was analyzed in relation to the concentration of different trace metal contaminants. Over a period of eight month test organisms have been exposed at a near-shore station in the anthropogenic impacted estuary of the river Elbe and at an off-shore station in the vicinity of the Island of Helgoland in the German Bight (North Sea). The stations differ in their hydrological as well as chemical characteristics. The physiological biomarkers, such as condition index which have been continuously monitored during the experiment clearly indicate the effects of the different environmental conditions. Multiple protein abundance changes were detected utilizing the techniques of two dimensional gel electrophoresis (2dGE) and consequently proteins arising as potential candidates for ecotoxicological monitoring have been identified by MALDI-ToF and ToF/ToF mass spectrometry. Different cytoskeletal proteins, enzymes of energy metabolism, stress proteins and one protein relevant for metal detoxification have been pointed out.
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Affiliation(s)
- Heike Helmholz
- Helmholtz-Zentrum Geesthacht, Centre for Materials and Coastal Research, Institute of Coastal Research, Department Marine Bioanalytical Chemistry, Max-Planck St. 1, D-21502 Geesthacht, Germany.
| | - Stephan Lassen
- Helmholtz-Zentrum Geesthacht, Centre for Materials and Coastal Research, Institute of Coastal Research, Department Marine Bioanalytical Chemistry, Max-Planck St. 1, D-21502 Geesthacht, Germany
| | - Christiane Ruhnau
- Helmholtz-Zentrum Geesthacht, Centre for Materials and Coastal Research, Institute of Coastal Research, Department Marine Bioanalytical Chemistry, Max-Planck St. 1, D-21502 Geesthacht, Germany
| | - Daniel Pröfrock
- Helmholtz-Zentrum Geesthacht, Centre for Materials and Coastal Research, Institute of Coastal Research, Department Marine Bioanalytical Chemistry, Max-Planck St. 1, D-21502 Geesthacht, Germany
| | - Hans-Burkhard Erbslöh
- Helmholtz-Zentrum Geesthacht, Centre for Materials and Coastal Research, Institute of Coastal Research, Department Marine Bioanalytical Chemistry, Max-Planck St. 1, D-21502 Geesthacht, Germany
| | - Andreas Prange
- Helmholtz-Zentrum Geesthacht, Centre for Materials and Coastal Research, Institute of Coastal Research, Department Marine Bioanalytical Chemistry, Max-Planck St. 1, D-21502 Geesthacht, Germany
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19
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Mathé-Hubert H, Gatti JL, Colinet D, Poirié M, Malausa T. Statistical analysis of the individual variability of 1D protein profiles as a tool in ecology: an application to parasitoid venom. Mol Ecol Resour 2015; 15:1120-32. [PMID: 25691098 DOI: 10.1111/1755-0998.12389] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 02/12/2015] [Accepted: 02/13/2015] [Indexed: 02/03/2023]
Abstract
Understanding the forces that shape eco-evolutionary patterns often requires linking phenotypes to genotypes, allowing characterization of these patterns at the molecular level. DNA-based markers are less informative in this aim compared to markers associated with gene expression and, more specifically, with protein quantities. The characterization of eco-evolutionary patterns also usually requires the analysis of large sample sizes to accurately estimate interindividual variability. However, the methods used to characterize and compare protein samples are generally expensive and time-consuming, which constrains the size of the produced data sets to few individuals. We present here a method that estimates the interindividual variability of protein quantities based on a global, semi-automatic analysis of 1D electrophoretic profiles, opening the way to rapid analysis and comparison of hundreds of individuals. The main original features of the method are the in silico normalization of sample protein quantities using pictures of electrophoresis gels at different staining levels, as well as a new method of analysis of electrophoretic profiles based on a median profile. We demonstrate that this method can accurately discriminate between species and between geographically distant or close populations, based on interindividual variation in venom protein profiles from three endoparasitoid wasps of two different genera (Psyttalia concolor, Psyttalia lounsburyi and Leptopilina boulardi). Finally, we discuss the experimental designs that would benefit from the use of this method.
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Affiliation(s)
- H Mathé-Hubert
- INRA, UMR 1355 Institut Sophia Agrobiotech, 06903, Sophia Antipolis, France.,Univ. Nice Sophia Antipolis, UMR 7254 Institut Sophia Agrobiotech, 06903, Sophia Antipolis, France.,CNRS, UMR 7254 Institut Sophia Agrobiotech, 06903, Sophia Antipolis, France
| | - J-L Gatti
- INRA, UMR 1355 Institut Sophia Agrobiotech, 06903, Sophia Antipolis, France.,Univ. Nice Sophia Antipolis, UMR 7254 Institut Sophia Agrobiotech, 06903, Sophia Antipolis, France.,CNRS, UMR 7254 Institut Sophia Agrobiotech, 06903, Sophia Antipolis, France
| | - D Colinet
- INRA, UMR 1355 Institut Sophia Agrobiotech, 06903, Sophia Antipolis, France.,Univ. Nice Sophia Antipolis, UMR 7254 Institut Sophia Agrobiotech, 06903, Sophia Antipolis, France.,CNRS, UMR 7254 Institut Sophia Agrobiotech, 06903, Sophia Antipolis, France
| | - M Poirié
- INRA, UMR 1355 Institut Sophia Agrobiotech, 06903, Sophia Antipolis, France.,Univ. Nice Sophia Antipolis, UMR 7254 Institut Sophia Agrobiotech, 06903, Sophia Antipolis, France.,CNRS, UMR 7254 Institut Sophia Agrobiotech, 06903, Sophia Antipolis, France
| | - T Malausa
- INRA, UMR 1355 Institut Sophia Agrobiotech, 06903, Sophia Antipolis, France.,Univ. Nice Sophia Antipolis, UMR 7254 Institut Sophia Agrobiotech, 06903, Sophia Antipolis, France.,CNRS, UMR 7254 Institut Sophia Agrobiotech, 06903, Sophia Antipolis, France
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20
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Hogle SL, Barbeau KA, Gledhill M. Heme in the marine environment: from cells to the iron cycle. Metallomics 2015; 6:1107-20. [PMID: 24811388 DOI: 10.1039/c4mt00031e] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Hemes are iron containing heterocyclic molecules important in many cellular processes. In the marine environment, hemes participate as enzymatic cofactors in biogeochemically significant processes like photosynthesis, respiration, and nitrate assimilation. Further, hemoproteins, hemes, and their analogs appear to be iron sources for some marine bacterioplankton under certain conditions. Current oceanographic analytical methodologies allow for the extraction and measurement of heme b from marine material, and a handful of studies have begun to examine the distribution of heme b in ocean basins. The study of heme in the marine environment is still in its infancy, but some trends can be gleaned from the work that has been published so far. In this review, we summarize what is known or might be inferred about the roles of heme in marine microbes as well as the few studies on heme in the marine environment that have been conducted to date. We conclude by presenting some future questions and challenges for the field.
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Affiliation(s)
- Shane L Hogle
- Geoscience Research Division, Scripps Institution of Oceanography, La Jolla, California, USA.
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21
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Emerging strategies and integrated systems microbiology technologies for biodiscovery of marine bioactive compounds. Mar Drugs 2014; 12:3516-59. [PMID: 24918453 PMCID: PMC4071589 DOI: 10.3390/md12063516] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 05/21/2014] [Accepted: 05/22/2014] [Indexed: 12/30/2022] Open
Abstract
Marine microorganisms continue to be a source of structurally and biologically novel compounds with potential use in the biotechnology industry. The unique physiochemical properties of the marine environment (such as pH, pressure, temperature, osmolarity) and uncommon functional groups (such as isonitrile, dichloroimine, isocyanate, and halogenated functional groups) are frequently found in marine metabolites. These facts have resulted in the production of bioactive substances with different properties than those found in terrestrial habitats. In fact, the marine environment contains a relatively untapped reservoir of bioactivity. Recent advances in genomics, metagenomics, proteomics, combinatorial biosynthesis, synthetic biology, screening methods, expression systems, bioinformatics, and the ever increasing availability of sequenced genomes provides us with more opportunities than ever in the discovery of novel bioactive compounds and biocatalysts. The combination of these advanced techniques with traditional techniques, together with the use of dereplication strategies to eliminate known compounds, provides a powerful tool in the discovery of novel marine bioactive compounds. This review outlines and discusses the emerging strategies for the biodiscovery of these bioactive compounds.
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22
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Hartmann EM, Durighello E, Pible O, Nogales B, Beltrametti F, Bosch R, Christie-Oleza JA, Armengaud J. Proteomics meets blue biotechnology: a wealth of novelties and opportunities. Mar Genomics 2014; 17:35-42. [PMID: 24780860 DOI: 10.1016/j.margen.2014.04.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Revised: 04/11/2014] [Accepted: 04/12/2014] [Indexed: 10/25/2022]
Abstract
Blue biotechnology, in which aquatic environments provide the inspiration for various products such as food additives, aquaculture, biosensors, green chemistry, bioenergy, and pharmaceuticals, holds enormous promise. Large-scale efforts to sequence aquatic genomes and metagenomes, as well as campaigns to isolate new organisms and culture-based screenings, are helping to push the boundaries of known organisms. Mass spectrometry-based proteomics can complement 16S gene sequencing in the effort to discover new organisms of potential relevance to blue biotechnology by facilitating the rapid screening of microbial isolates and by providing in depth profiles of the proteomes and metaproteomes of marine organisms, both model cultivable isolates and, more recently, exotic non-cultivable species and communities. Proteomics has already contributed to blue biotechnology by identifying aquatic proteins with potential applications to food fermentation, the textile industry, and biomedical drug development. In this review, we discuss historical developments in blue biotechnology, the current limitations to the known marine biosphere, and the ways in which mass spectrometry can expand that knowledge. We further speculate about directions that research in blue biotechnology will take given current and near-future technological advancements in mass spectrometry.
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Affiliation(s)
- Erica M Hartmann
- CEA, DSV, IBEB, Lab Biochim System Perturb, Bagnols-sur-Cèze, F-30207, France
| | - Emie Durighello
- CEA, DSV, IBEB, Lab Biochim System Perturb, Bagnols-sur-Cèze, F-30207, France
| | - Olivier Pible
- CEA, DSV, IBEB, Lab Biochim System Perturb, Bagnols-sur-Cèze, F-30207, France
| | - Balbina Nogales
- Microbiologia, Departament de Biologia, Universitat de les Illes Balears, Palma de Mallorca, Spain
| | | | - Rafael Bosch
- Microbiologia, Departament de Biologia, Universitat de les Illes Balears, Palma de Mallorca, Spain
| | - Joseph A Christie-Oleza
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV47AL, United Kingdom
| | - Jean Armengaud
- CEA, DSV, IBEB, Lab Biochim System Perturb, Bagnols-sur-Cèze, F-30207, France.
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23
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Abstract
This review covers the literature published in 2012 for marine natural products, with 1035 citations (673 for the period January to December 2012) referring to compounds isolated from marine microorganisms and phytoplankton, green, brown and red algae, sponges, cnidarians, bryozoans, molluscs, tunicates, echinoderms, mangroves and other intertidal plants and microorganisms. The emphasis is on new compounds (1241 for 2012), together with the relevant biological activities, source organisms and country of origin. Biosynthetic studies, first syntheses, and syntheses that lead to the revision of structures or stereochemistries, have been included.
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Affiliation(s)
- John W Blunt
- Department of Chemistry, University of Canterbury, Christchurch, New Zealand.
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24
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Altmäe S, Esteban FJ, Stavreus-Evers A, Simón C, Giudice L, Lessey BA, Horcajadas JA, Macklon NS, D'Hooghe T, Campoy C, Fauser BC, Salamonsen LA, Salumets A. Guidelines for the design, analysis and interpretation of 'omics' data: focus on human endometrium. Hum Reprod Update 2014; 20:12-28. [PMID: 24082038 PMCID: PMC3845681 DOI: 10.1093/humupd/dmt048] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Revised: 08/04/2013] [Accepted: 08/19/2013] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND 'Omics' high-throughput analyses, including genomics, epigenomics, transcriptomics, proteomics and metabolomics, are widely applied in human endometrial studies. Analysis of endometrial transcriptome patterns in physiological and pathophysiological conditions has been to date the most commonly applied 'omics' technique in human endometrium. As the technologies improve, proteomics holds the next big promise for this field. The 'omics' technologies have undoubtedly advanced our knowledge of human endometrium in relation to fertility and different diseases. Nevertheless, the challenges arising from the vast amount of data generated and the broad variation of 'omics' profiling according to different environments and stimuli make it difficult to assess the validity, reproducibility and interpretation of such 'omics' data. With the expansion of 'omics' analyses in the study of the endometrium, there is a growing need to develop guidelines for the design of studies, and the analysis and interpretation of 'omics' data. METHODS Systematic review of the literature in PubMed, and references from relevant articles were investigated up to March 2013. RESULTS The current review aims to provide guidelines for future 'omics' studies on human endometrium, together with a summary of the status and trends, promise and shortcomings in the high-throughput technologies. In addition, the approaches presented here can be adapted to other areas of high-throughput 'omics' studies. CONCLUSION A highly rigorous approach to future studies, based on the guidelines provided here, is a prerequisite for obtaining data on biological systems which can be shared among researchers worldwide and will ultimately be of clinical benefit.
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Affiliation(s)
- Signe Altmäe
- Competence Centre on Reproductive Medicine and Biology, Tartu, Estonia
- School of Medicine, Department of Paediatrics, University of Granada, 18012 Granada, Spain
| | | | - Anneli Stavreus-Evers
- Department of Women's and Children's Health, Uppsala University, Akademiska Sjukhuset, 75185 Uppsala, Sweden
| | - Carlos Simón
- Fundación Instituto Valenciano de Infertilidad (FIVI) and Instituto Universitario IVI/INCLIVA, Valencia University, 46021 Valencia, Spain
| | - Linda Giudice
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143-0132, USA
| | - Bruce A. Lessey
- Division of Reproductive Endocrinology, Department of Obstetrics and Gynecology, University Medical Group, Greenville Hospital System, Greenville, South Carolina, SC 29605, USA
| | - Jose A. Horcajadas
- Araid-Hospital Miguel Servet, 50004 Zaragoza, Spain
- Department of Genetics, Universidad Pablo de Olavide, 41013 Sevilla, Spain
| | - Nick S. Macklon
- Department of Obstetrics and Gynaecology, Division of Developmental Origins of Adult Disease, University of Southampton, Princess Anne Hospital, SO16 5YA Southampton, UK
- Department of Reproductive Medicine and Gynaecology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
| | - Thomas D'Hooghe
- Leuven University Fertility Center, Department of Obstetrics and Gynecology, University Hospital Leuven, Leuven, Belgium
- Department of Development and Regeneration, KU Leuven (Leuven University), 3000 Leuven, Belgium
| | - Cristina Campoy
- School of Medicine, Department of Paediatrics, University of Granada, 18012 Granada, Spain
| | - Bart C. Fauser
- Department of Reproductive Medicine and Gynaecology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
| | - Lois A. Salamonsen
- Prince Henry's Institute of Medical Research, Melbourne, Victoria 3168, Australia
| | - Andres Salumets
- Competence Centre on Reproductive Medicine and Biology, Tartu, Estonia
- Department of Obstetrics and Gynaecology, University of Tartu, 51014 Tartu, Estonia
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Schofield MM, Sherman DH. Meta-omic characterization of prokaryotic gene clusters for natural product biosynthesis. Curr Opin Biotechnol 2013; 24:1151-8. [PMID: 23731715 PMCID: PMC3797859 DOI: 10.1016/j.copbio.2013.05.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Revised: 04/14/2013] [Accepted: 05/07/2013] [Indexed: 01/04/2023]
Abstract
Microorganisms produce a remarkable selection of bioactive small molecules. The study and exploitation of these secondary metabolites have traditionally been restricted to the cultivable minority of bacteria. Rapid advances in meta-omics challenge this paradigm. Breakthroughs in metagenomic library methodologies, direct sequencing, single cell genomics, and natural product-specific bioinformatic tools now facilitate the retrieval of previously inaccessible biosynthetic gene clusters. Similarly, metaproteomic developments enable the direct study of biosynthetic enzymes from complex microbial communities. Additional methods within and beyond meta-omics are also in development. This review discusses recent reports in these arenas and how they can be utilized to characterize natural product biosynthetic gene clusters and pathways.
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Affiliation(s)
- Michael M. Schofield
- Life Sciences Institute and Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - David H. Sherman
- Life Sciences Institute and Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
- Departments of Medicinal Chemistry, and Chemistry, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109
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26
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Matrix-assisted laser desorption ionization mass spectrometry for identification of shrimp. Anal Chim Acta 2013; 794:55-9. [DOI: 10.1016/j.aca.2013.07.014] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Revised: 06/19/2013] [Accepted: 07/05/2013] [Indexed: 11/18/2022]
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Mukherjee J, Po BHK, Chiu JMY, Wu RSS, Qian PY, Thiyagarajan V. Polybrominated diphenyl ethers do not affect metamorphosis but alter the proteome of the invasive slipper limpet Crepidula onyx. MARINE POLLUTION BULLETIN 2013; 73:273-281. [PMID: 23743271 DOI: 10.1016/j.marpolbul.2013.05.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2013] [Revised: 04/28/2013] [Accepted: 05/06/2013] [Indexed: 06/02/2023]
Abstract
Man-made polybrominated diphenyl ethers (PBDEs) used as flame retardants in various consumer products may be harmful to marine organisms. Larvae of some marine invertebrates, especially invasive species, can develop resistance to PBDEs through altered protein expression patterns or proteome plasticity. This is the first report of a proteomics approach to study BDE-47 induced molecular changes in the invasive limpet Crepidula onyx. Larvae of C. onyx were cultured for 5 days (hatching to metamorphosis) in the presence of BDE-47 (1 μg L(-1)). Using a 2-DE proteomics approach with triple quadrupole and high-resolution TOF-MS, we showed that BDE-47 altered the proteome structure but not the growth or metamorphosis of C. onyx larvae. We found eight significant differentially expressed proteins in response to BDE-47, deemed the protein expression signature, consisting of cytoskeletal, stress tolerance, metabolism and energy production related proteins. Our data suggest C. onyx larvae have adequate proteome plasticity to tolerate BDE-47 toxicity.
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Affiliation(s)
- Joy Mukherjee
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Hong Kong Special Administrative Region
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Diz AP, Dudley E, Cogswell A, MacDonald BW, Kenchington ELR, Zouros E, Skibinski DOF. Proteomic analysis of eggs from Mytilus edulis females differing in mitochondrial DNA transmission mode. Mol Cell Proteomics 2013; 12:3068-80. [PMID: 23869045 DOI: 10.1074/mcp.m113.031401] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Many bivalves have an unusual mechanism of mitochondrial DNA (mtDNA) inheritance called doubly uniparental inheritance (DUI) in which distinctly different genomes are inherited through the female (F genome) and male (M genome) lineages. In fertilized eggs that will develop into male embryos, the sperm mitochondria remain in an aggregation, which is believed to be delivered to the primordial germ cells and passed to the next generation through the sperm. In fertilized eggs that will develop into female embryos, the sperm mitochondria are dispersed throughout the developing embryo and make little if any contribution to the next generation. The frequency of embryos with the aggregated or dispersed mitochondrial type varies among females. Previous models of DUI have predicted that maternal nuclear factors cause molecular differences among unfertilized eggs from females producing embryos with predominantly dispersed or aggregated mitochondria. We test this hypothesis using females of each of the two types from a natural population. We have found small, yet detectable, differences of the predicted type at the proteome level. We also provide evidence that eggs of females giving the dispersed pattern have consistently lower expression for different proteasome subunits than eggs of females giving the aggregated pattern. These results, combined with those of an earlier study in which we used hatchery lines of Mytilus, and with a transcriptomic study in a clam that has the DUI system of mtDNA transmission, reinforce the hypothesis that the ubiquitin-proteasome system plays a key role in the mechanism of DUI and sex determination in bivalves. We also report that eggs of females giving the dispersed pattern have higher expression for arginine kinase and enolase, enzymes involved in energy production, whereas ferritin, which is involved in iron homeostasis, has lower expression. We discuss these results in the context of genetic models for DUI and suggest experimental methods for further understanding the role of these proteins in DUI.
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Affiliation(s)
- Angel P Diz
- Institute of Life Science, College of Medicine, Swansea University, Swansea SA28PP, Wales UK
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Differential in gel electrophoresis (DIGE) comparative proteomic analysis of macrophages cell cultures in response to perthamide C treatment. Mar Drugs 2013; 11:1288-99. [PMID: 23595056 PMCID: PMC3705404 DOI: 10.3390/md11041288] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Revised: 03/19/2013] [Accepted: 04/01/2013] [Indexed: 12/17/2022] Open
Abstract
Secondary metabolites contained in marine organisms disclose diverse pharmacological activities, due to their intrinsic ability to recognize bio-macromolecules, which alter their expression and modulate their function. Thus, the identification of the cellular pathways affected by marine natural products is crucial to provide important functional information concerning their mechanism of action at the molecular level. Perthamide C, a marine sponge metabolite isolated from the polar extracts of Theonella swinhoei and endowed with a broad and interesting anti-inflammatory profile, was found in a previous study to specifically interact with heat shock protein-90 and glucose regulated protein-94, also disclosing the ability to reduce cisplatin-mediated apoptosis. In this paper, we evaluated the effect of this compound on the whole proteome of murine macrophages cells by two-dimensional DIGE proteomics. Thirty-three spots were found to be altered in expression by at least 1.6-fold and 29 proteins were identified by LC ESI-Q/TOF-MS. These proteins are involved in different processes, such as metabolism, structural stability, protein folding assistance and gene expression. Among them, perthamide C modulates the expression of several chaperones implicated in the folding of proteins correlated to apoptosis, such as Hsp90 and T-complexes, and in this context our data shed more light on the cellular effects and pathways altered by this marine cyclo-peptide.
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