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Boulanger E, Benestan L, Guerin PE, Dalongeville A, Mouillot D, Manel S. Climate differently influences the genomic patterns of two sympatric marine fish species. J Anim Ecol 2021; 91:1180-1195. [PMID: 34716929 DOI: 10.1111/1365-2656.13623] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 10/21/2021] [Indexed: 12/19/2022]
Abstract
Climate influences population genetic variation in marine species. Capturing these impacts remains challenging for marine fishes which disperse over large geographical scales spanning steep environmental gradients. It requires the extensive spatial sampling of individuals or populations, representative of seascape heterogeneity, combined with a set of highly informative molecular markers capable of revealing climatic-associated genetic variations. We explored how space, dispersal and environment shape the genomic patterns of two sympatric fish species in the Mediterranean Sea, which ranks among the oceanic basins most affected by climate change and human pressure. We hypothesized that the population structure and climate-associated genomic signatures of selection would be stronger in the less mobile species, as restricted gene flow tends to facilitate the fixation of locally adapted alleles. To test our hypothesis, we genotyped two species with contrasting dispersal abilities: the white seabream Diplodus sargus and the striped red mullet Mullus surmuletus. We collected 823 individuals and used genotyping by sequencing (GBS) to detect 8,206 single nucleotide polymorphisms (SNPs) for the seabream and 2,794 for the mullet. For each species, we identified highly differentiated genomic regions (i.e. outliers) and disentangled the relative contribution of space, dispersal and environmental variables (climate, marine primary productivity) on the outliers' genetic structure to test the prevalence of gene flow and local adaptation. We observed contrasting patterns of gene flow and adaptive genetic variation between the two species. The seabream showed a distinct Alboran sea population and panmixia across the Mediterranean Sea. The mullet revealed additional differentiation within the Mediterranean Sea that was significantly correlated to summer and winter temperatures, as well as marine primary productivity. Functional annotation of the climate-associated outlier SNPs then identified candidate genes involved in heat tolerance that could be examined to further predict species' responses to climate change. Our results illustrate the key steps of a comparative seascape genomics study aiming to unravel the evolutionary processes at play in marine species, to better anticipate their response to climate change. Defining population adaptation capacities and environmental niches can then serve to incorporate evolutionary processes into species conservation planning.
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Affiliation(s)
- Emilie Boulanger
- CEFE, University of Montpellier, CNRS, EPHE-PSL University, IRD, Montpellier, France.,MARBEC, University of Montpellier, CNRS, Ifremer, IRD, Montpellier, France
| | - Laura Benestan
- CEFE, University of Montpellier, CNRS, EPHE-PSL University, IRD, Montpellier, France
| | - Pierre-Edouard Guerin
- CEFE, University of Montpellier, CNRS, EPHE-PSL University, IRD, Montpellier, France
| | | | - David Mouillot
- MARBEC, University of Montpellier, CNRS, Ifremer, IRD, Montpellier, France.,Institut Universitaire de France, Paris, France
| | - Stéphanie Manel
- CEFE, University of Montpellier, CNRS, EPHE-PSL University, IRD, Montpellier, France
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2
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Elowe C, Tomanek L. Circadian and circatidal rhythms of protein abundance in the California mussel (Mytilus californianus). Mol Ecol 2021; 30:5151-5163. [PMID: 34390513 DOI: 10.1111/mec.16122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 08/04/2021] [Accepted: 08/11/2021] [Indexed: 11/26/2022]
Abstract
Coastal habitats fluctuate with the 12.4 h tidal and 24 h light/dark cycle to predictably alter conditions such as air exposure, temperature, and food availability. Intertidal sessile bivalves exhibit behavioral and physiological adjustments to minimize the challenges of this environment. We investigated a high-resolution time course of the changes in protein abundance in the gill tissue of the intertidal mussel Mytilus californianus in a simulated tidal environment of 12:12 h light:dark cycles and a matching 6:6 h high:low tide cycle within each 12 h period. Approximately 38% of detected proteins showed significant rhythms in their abundances, with diversity in the phases of rhythmic isoforms. The circadian rhythm was dominant in protein abundance changes, particularly with oxidative metabolism. A tidal cycle elicited changes within functional groups, including in cytoskeletal proteins, chaperones, and oxidative stress proteins. In addition to protein abundance changes, we found the possibility for post-translational modifications driving rhythms, including methylation, mitochondrial peptide processing (proteolysis), and acylation. Dynamic changes in the proteome across functional categories demonstrate the importance of the tidal environment in entraining cellular processes, confirming that differential expression studies should not assume a static baseline of cellular conditions in intertidal organisms.
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Affiliation(s)
- Cory Elowe
- California Polytechnic State University, Department of Biological Sciences Environmental Proteomics Laboratory, Grand Avenue San Luis Obispo, CA, USA
| | - Lars Tomanek
- California Polytechnic State University, Department of Biological Sciences Environmental Proteomics Laboratory, Grand Avenue San Luis Obispo, CA, USA
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Vasquez MC, Joyner-Matos J, Vázquez-Medina JP, Zenteno-Savín T, Freitas R. Oxidative stress in aquatic ecosystems: Integrated responses to multiple stressors and preparation for oxidative stress. Selected papers from the 3rd international conference. Comp Biochem Physiol A Mol Integr Physiol 2020; 249:110770. [DOI: 10.1016/j.cbpa.2020.110770] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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4
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Multiple stressor responses are regulated by sirtuins in Mytilus congeners. Comp Biochem Physiol A Mol Integr Physiol 2020; 246:110719. [DOI: 10.1016/j.cbpa.2020.110719] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 04/28/2020] [Accepted: 04/29/2020] [Indexed: 02/06/2023]
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The Queen Conch (Lobatus gigas) Proteome: A Valuable Tool for Biological Studies in Marine Gastropods. Protein J 2020; 38:628-639. [PMID: 31399888 DOI: 10.1007/s10930-019-09857-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Queen conch (Lobatus gigas) is a marine gastropod endemic to the Caribbean. This species is a cultural symbol, being a significant local food source and the second largest commercial fishery in the region. However, over-exploitation and natural habitat degradation have exerted high survival pressure on this species. This work aims to provide novel proteomic data to highlight the metabolism of the species and to provide an important tool for the understanding of queen conch biology and physiology. Herein, we profiled the whole proteome from 3 organs (gills, digestive gland and muscle) of L. gigas combining gel-free and gel-based techniques. Overall 420 clusters of proteins were identified corresponding to the minimum identification requirement of protein sequence redundancy. Gene ontology and KEGG analysis highlighted 59 metabolic pathways between identified proteins. The most relevant routes according to the number of sequences found per pathway were purine and thiamine metabolism, closely related to nucleotide and carbohydrate metabolism. We also emphasize the high number of proteins associated to the biosynthesis of antibiotics (93 proteins and a total of 28 enzymes), which were among the top-twenty pathways identified by KEGG analysis. The proteomics approach allowed the identification and description of putative markers of oxidative stress, xenobiotic metabolism, heat shock response and respiratory chain for the first time in the species, which could be extremely useful in future investigations for diagnosing and monitoring L. gigas population health.
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Cadmium-Related Effects on Cellular Immunity Comprises Altered Metabolism in Earthworm Coelomocytes. Int J Mol Sci 2020; 21:ijms21020599. [PMID: 31963425 PMCID: PMC7013597 DOI: 10.3390/ijms21020599] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 01/09/2020] [Accepted: 01/13/2020] [Indexed: 12/13/2022] Open
Abstract
The heavy metal cadmium (Cd) is known to modulate the immune system, challenging soil-dwelling organisms where environmental Cd pollution is high. Since earthworms lack adaptive immunity, we determined Cd-related effects on coelomocytes, the cellular part of innate immunity, which is also the site of detoxification processes. A proteomics approach revealed a set of immunity-related proteins as well as gene products involved in energy metabolism changing in earthworms in response to Cd exposure. Based on these results, we conducted extracellular flux measurements of oxygen and acidification to reveal the effect of Cd on coelomocyte metabolism. We observed a significantly changing oxygen consumption rate, extracellular acidification, as well as metabolic potential, which can be defined as the response to an induced energy demand. Acute changes in intracellular calcium levels were also observed, indicating impaired coelomocyte activation. Lysosomes, the cell protein recycling center, and mitochondrial parameters did not change. Taken together, we were able to characterize coelomocyte metabolism to reveal a potential link to an impaired immune system upon Cd exposure.
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Comparative study of excretory-secretory proteins released by Schistosoma mansoni-resistant, susceptible and naïve Biomphalaria glabrata. Parasit Vectors 2019; 12:452. [PMID: 31521183 PMCID: PMC6744689 DOI: 10.1186/s13071-019-3708-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 09/05/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Schistosomiasis is a harmful neglected tropical disease caused by infection with Schistosoma spp., such as Schistosoma mansoni. Schistosoma must transition within a molluscan host to survive. Chemical analyses of schistosome-molluscan interactions indicate that host identification involves chemosensation, including naïve host preference. Proteomic technique advances enable sophisticated comparative analyses between infected and naïve snail host proteins. This study aimed to compare resistant, susceptible and naïve Biomphalaria glabrata snail-conditioned water (SCW) to identify potential attractants and deterrents. METHODS Behavioural bioassays were performed on S. mansoni miracidia to compare the effects of susceptible, F1 resistant and naïve B. glabrata SCW. The F1 resistant and susceptible B. glabrata SCW excretory-secretory proteins (ESPs) were fractionated using SDS-PAGE, identified with LC-MS/MS and compared to naïve snail ESPs. Protein-protein interaction (PPI) analyses based on published studies (including experiments, co-expression, text-mining and gene fusion) identified S. mansoni and B. glabrata protein interaction. Data are available via ProteomeXchange with identifier PXD015129. RESULTS A total of 291, 410 and 597 ESPs were detected in the susceptible, F1 resistant and naïve SCW, respectively. Less overlap in ESPs was identified between susceptible and naïve snails than F1 resistant and naïve snails. F1 resistant B. glabrata ESPs were predominately associated with anti-pathogen activity and detoxification, such as leukocyte elastase and peroxiredoxin. Susceptible B. glabrata several proteins correlated with immunity and anti-inflammation, such as glutathione S-transferase and zinc metalloproteinase, and S. mansoni sporocyst presence. PPI analyses found that uncharacterised S. mansoni protein Smp_142140.1 potentially interacts with numerous B. glabrata proteins. CONCLUSIONS This study identified ESPs released by F1 resistant, susceptible and naïve B. glabrata to explain S. mansoni miracidia interplay. Susceptible B. glabrata ESPs shed light on potential S. mansoni miracidia deterrents. Further targeted research on specific ESPs identified in this study could help inhibit B. glabrata and S. mansoni interactions and stop human schistosomiasis.
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Clark MS, Villota Nieva L, Hoffman JI, Davies AJ, Trivedi UH, Turner F, Ashton GV, Peck LS. Lack of long-term acclimation in Antarctic encrusting species suggests vulnerability to warming. Nat Commun 2019; 10:3383. [PMID: 31358752 PMCID: PMC6662708 DOI: 10.1038/s41467-019-11348-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 07/09/2019] [Indexed: 12/29/2022] Open
Abstract
Marine encrusting communities play vital roles in benthic ecosystems and have major economic implications with regards to biofouling. However, their ability to persist under projected warming scenarios remains poorly understood and is difficult to study under realistic conditions. Here, using heated settlement panel technologies, we show that after 18 months Antarctic encrusting communities do not acclimate to either +1 °C or +2 °C above ambient temperatures. There is significant up-regulation of the cellular stress response in warmed animals, their upper lethal temperatures decline with increasing ambient temperature and population genetic analyses show little evidence of differential survival of genotypes with treatment. By contrast, biofilm bacterial communities show no significant differences in community structure with temperature. Thus, metazoan and bacterial responses differ dramatically, suggesting that ecosystem responses to future climate change are likely to be far more complex than previously anticipated. Genetic adaptation and physiological acclimation can potentially buffer species against climate change. Here, the authors perform a long-term warming experiment of Antarctic encrusting communities and show that focal animal species failed to acclimate and lacked genetic variation in tolerance to warming.
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Affiliation(s)
- Melody S Clark
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge, CB3 0ET, UK.
| | - Leyre Villota Nieva
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge, CB3 0ET, UK.,School of Ocean Sciences, Bangor University, Menai Bridge, Anglesey, LL59 5AB, UK
| | - Joseph I Hoffman
- Department of Animal Behavior, University of Bielefeld, Postfach 100131, 33615, Bielefeld, Germany
| | - Andrew J Davies
- University of Rhode Island, Department of Biological Sciences, Woodward Hall, 9 East Alumni Avenue, Kingston, RI, 02881, USA
| | - Urmi H Trivedi
- Edinburgh Genomics (Genome Science), Ashworth Laboratories, Charlotte Auerbach Road, The King's Buildings, The University of Edinburgh, EH9 3FL, Edinburgh, UK
| | - Frances Turner
- Edinburgh Genomics (Genome Science), Ashworth Laboratories, Charlotte Auerbach Road, The King's Buildings, The University of Edinburgh, EH9 3FL, Edinburgh, UK
| | - Gail V Ashton
- Smithsonian Environmental Research Center, 647 Contees Wharf Road, Edgewater, MD, 21037-0028, USA
| | - Lloyd S Peck
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
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E GX, Basang WD, Zhu YB. Whole-genome analysis identifying candidate genes of altitude adaptive ecological thresholds in yak populations. J Anim Breed Genet 2019; 136:371-377. [PMID: 31062447 DOI: 10.1111/jbg.12403] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 04/10/2019] [Accepted: 04/11/2019] [Indexed: 12/30/2022]
Abstract
The domestic yak (Bos grunniens) is an iconic symbol of animal husbandry on the Qinghai-Tibet Plateau. Long-term domestication and natural selection have led to a wide distribution of yak, forming many ecological populations to adapt to the local ecological environment. High altitude is closely related to oxygen density, and it is an important environmental ecological factor for biological survival and livestock production. The aim of the present study was to perform a preliminary analysis to identify the candidate genes of altitude distribution adapted ecological thresholds in yak using next-generation sequence technology. A total of 15,762,829 SNPs were obtained from 29 yaks with high- and low-altitude distribution by genome-wide sequencing. According to the results of the selective sweep analysis with FST and ZHp, 21 candidate genes were identified. 14 genes (serine/threonine protein kinase TNNI3K, TEN1, DYM, ITPR1, ZC4H2, KNTC1, ADGRB3, CLYBL, TANGO6, ASCC3, KLHL3, PDE4D, DEPDC1B and AGBL4) were grouped into 32 Gene Ontology terms, and four genes (RPS6KA6, ITPR1, GNAO1 and PDE4D) annotated in 35 pathways, including seven environmental information processing and one environmental adaptation. Therefore, the novel candidate genes found in the current study do not only support new theories about high-altitude adaptation, but also further explain the molecular mechanisms of altitude adaptation threshold in yaks.
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Affiliation(s)
- Guang-Xin E
- Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, College of Animal Science and Technology, Southwest University, Chongqing, China.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Wang-Dui Basang
- State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement (Tibet Academy of Agricultural and Animal Husbandry Sciences (TAAAS)), Lhasa, China.,Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa, China
| | - Yan-Bin Zhu
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa, China
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Aguilar C, Raina JB, Fôret S, Hayward DC, Lapeyre B, Bourne DG, Miller DJ. Transcriptomic analysis reveals protein homeostasis breakdown in the coral Acropora millepora during hypo-saline stress. BMC Genomics 2019; 20:148. [PMID: 30786881 PMCID: PMC6381741 DOI: 10.1186/s12864-019-5527-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 02/13/2019] [Indexed: 11/18/2022] Open
Abstract
Background Coral reefs can experience salinity fluctuations due to rainfall and runoff; these events can have major impacts on the corals and lead to bleaching and mortality. On the Great Barrier Reef (GBR), low salinity events, which occur during summer seasons and can involve salinity dropping ~ 10 PSU correlate with declines in coral cover, and these events are predicted to increase in frequency and severity under future climate change scenarios. In other marine invertebrates, exposure to low salinity causes increased expression of genes involved in proteolysis, responses to oxidative stress, and membrane transport, but the effects that changes in salinity have on corals have so far received only limited attention. To better understand the coral response to hypo-osmotic stress, here we investigated the transcriptomic response of the coral Acropora millepora in both adult and juvenile life stages to acute (1 h) and more prolonged (24 h) exposure to low salinity. Results Differential gene expression analysis revealed the involvement of both common and specific response mechanisms in Acropora. The general response to environmental stressors included up-regulation of genes involved in the mitigation of macromolecular and oxidative damage, while up-regulation of genes involved in amino acid metabolism and transport represent specific responses to salinity stress. Conclusions This study is the first comprehensive transcriptomic analysis of the coral response to low salinity stress and provides important insights into the likely consequences of heavy rainfall and runoff events on coral reefs. Electronic supplementary material The online version of this article (10.1186/s12864-019-5527-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Catalina Aguilar
- AIMS@JCU and Department of Molecular and Cell Biology, James Cook University, Townsville, Queensland, 4811, Australia.,ARC Centre of Excellence for Coral Reef Studies and Department of Molecular and Cell Biology, James Cook University, Townsville, Queensland, 4811, Australia.,Cooperative Institute for Marine and Atmospheric Studies, Rosenstiel School of Marine & Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, Florida, 33149, USA.,Atlantic Oceanographic and Meteorological Laboratories (AOML), NOAA, 4301 Rickenbacker Causeway, Miami, Florida, 33149, USA
| | - Jean-Baptiste Raina
- AIMS@JCU and Department of Molecular and Cell Biology, James Cook University, Townsville, Queensland, 4811, Australia.,Climate Change Cluster (C3), University of Technology, Sydney, NSW, 2007, Australia
| | - Sylvain Fôret
- ARC Centre of Excellence for Coral Reef Studies and Department of Molecular and Cell Biology, James Cook University, Townsville, Queensland, 4811, Australia.,Division of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, ACT, 2601, Australia
| | - David C Hayward
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, ACT, 2601, Australia
| | - Bruno Lapeyre
- Laboratoire d'excellence CORAIL, Centre de Recherches Insulaires et Observatoire de l'Environnement (CRIOBE), Moorea, B.P.1013, Papeete, French Polynesia
| | - David G Bourne
- AIMS@JCU and Department of Molecular and Cell Biology, James Cook University, Townsville, Queensland, 4811, Australia.,Australian Institute of Marine Science, Townsville, Queensland, 4810, Australia.,College of Science and Engineering, James Cook University, Townsville, 4811, Australia
| | - David J Miller
- AIMS@JCU and Department of Molecular and Cell Biology, James Cook University, Townsville, Queensland, 4811, Australia. .,ARC Centre of Excellence for Coral Reef Studies and Department of Molecular and Cell Biology, James Cook University, Townsville, Queensland, 4811, Australia.
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Ertl NG, O'Connor WA, Elizur A. Molecular effects of a variable environment on Sydney rock oysters, Saccostrea glomerata: Thermal and low salinity stress, and their synergistic effect. Mar Genomics 2019; 43:19-32. [DOI: 10.1016/j.margen.2018.10.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Revised: 10/07/2018] [Accepted: 10/18/2018] [Indexed: 12/26/2022]
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iTRAQ-based proteome profiling of hyposaline responses in zygotes of the Pacific oyster Crassostrea gigas. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2018; 30:14-24. [PMID: 30771561 DOI: 10.1016/j.cbd.2018.12.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Revised: 12/06/2018] [Accepted: 12/07/2018] [Indexed: 11/22/2022]
Abstract
Low salinity treatment is proven to be the practical polyploidy inducing method for shellfish with advantages of lower cost, higher operability and reliable food security. However, little is known about the possible molecular mechanism of hypotonic induction. In this study, isobaric tags for relative and absolute quantitation (iTRAQ) based proteomic profiling was pursued to investigate the responses of zygotes of the Pacific oyster Crassostrea gigas to low salinity. A total of 2235 proteins were identified and 87 proteins were considered differentially expressed, of which 14 were up-regulated and 69 were down-regulated. Numerous functional proteins including ADP ribosylation factor 2, DNA repair protein Rad50, splicing factor 3B, tubulin-specific Chaperone D were significantly changed in abundance, and were involved in various biology processes including energy generation, vesicle trafficking, DNA/RNA/protein metabolism and cytoskeleton modification, indicating the prominent modulation of cell division and embryonic development. Parallel reaction monitoring (PRM) analyses were carried out for validation of the expression levels of differentially expressed proteins (DEPs), which indicated high reliability of the proteomic results. Our study not only demonstrated the proteomic alterations in oyster zygotes under low salinity, but also provided, in part, clues to the relatively lower hatching rate and higher mortality of induced larvae. Above all, this study presents a valuable foundation for further studies on mechanisms of hypotonic induction.
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Jeremias G, Barbosa J, Marques SM, De Schamphelaere KAC, Van Nieuwerburgh F, Deforce D, Gonçalves FJM, Pereira JL, Asselman J. Transgenerational Inheritance of DNA Hypomethylation in Daphnia magna in Response to Salinity Stress. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:10114-10123. [PMID: 30113818 DOI: 10.1021/acs.est.8b03225] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Epigenetic mechanisms have been found to play important roles in environmental stress response and regulation. These can, theoretically, be transmitted to future unexposed generations, yet few studies have shown persisting stress-induced transgenerational effects, particularly in invertebrates. Here, we focus on the aquatic microcrustacean Daphnia, a parthenogenetic model species, and its response to salinity stress. Salinity is a serious threat to freshwater ecosystems and a relevant form of environmental perturbation affecting freshwater ecosystems. We exposed one generation of D. magna to high levels of salinity (F0) and found that the exposure provoked specific methylation patterns that were transferred to the three consequent nonexposed generations (F1, F2, and F3). This was the case for the hypomethylation of six protein-coding genes with important roles in the organisms' response to environmental change: DNA damage repair, cytoskeleton organization, and protein synthesis. This suggests that epigenetic changes in Daphnia are particularly targeted to genes involved in coping with general cellular stress responses. Our results highlight that epigenetic marks are affected by environmental stressors and can be transferred to subsequent unexposed generations. Epigenetic marks could therefore prove to be useful indicators of past or historic pollution in this parthenogenetic model system. Furthermore, no life history costs seem to be associated with the maintenance of hypomethylation across unexposed generations in Daphnia following a single stress exposure.
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Affiliation(s)
- Guilherme Jeremias
- Department of Biology , University of Aveiro , 3810-193 , Aveiro , Portugal
| | - João Barbosa
- Department of Biology , University of Aveiro , 3810-193 , Aveiro , Portugal
| | - Sérgio M Marques
- Department of Biology , University of Aveiro , 3810-193 , Aveiro , Portugal
- CESAM (Centre for Environmental and Marine Studies) , University of Aveiro , 3810-193 , Aveiro , Portugal
| | - Karel A C De Schamphelaere
- Laboratory for Environmental Toxicology and Aquatic Ecology (GhEnToxLab) , Ghent University , 9000 , Ghent , Belgium
| | | | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology , Ghent University , 9000 , Ghent , Belgium
| | - Fernando J M Gonçalves
- Department of Biology , University of Aveiro , 3810-193 , Aveiro , Portugal
- CESAM (Centre for Environmental and Marine Studies) , University of Aveiro , 3810-193 , Aveiro , Portugal
| | - Joana Luísa Pereira
- Department of Biology , University of Aveiro , 3810-193 , Aveiro , Portugal
- CESAM (Centre for Environmental and Marine Studies) , University of Aveiro , 3810-193 , Aveiro , Portugal
| | - Jana Asselman
- Laboratory for Environmental Toxicology and Aquatic Ecology (GhEnToxLab) , Ghent University , 9000 , Ghent , Belgium
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Barros I, Froufe H, Marnellos G, Egas C, Delaney J, Clamp M, Santos RS, Bettencourt R. Metatranscriptomics profile of the gill microbial community during Bathymodiolus azoricus aquarium acclimatization at atmospheric pressure. AIMS Microbiol 2018; 4:240-260. [PMID: 31294213 PMCID: PMC6604929 DOI: 10.3934/microbiol.2018.2.240] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 03/05/2018] [Indexed: 12/04/2022] Open
Abstract
Background The deep-sea mussels Bathymodiolus azoricus (Bivalvia: Mytilidae) are the dominant macrofauna subsisting at the hydrothermal vents site Menez Gwen in the Mid-Atlantic Ridge (MAR). Their adaptive success in such challenging environments is largely due to their gill symbiotic association with chemosynthetic bacteria. We examined the response of vent mussels as they adapt to sea-level environmental conditions, through an assessment of the relative abundance of host-symbiont related RNA transcripts to better understand how the gill microbiome may drive host-symbiont interactions in vent mussels during hypothetical venting inactivity. Results The metatranscriptome of B. azoricus was sequenced from gill tissues sampled at different time-points during a five-week acclimatization experiment, using Next-Generation-Sequencing. After Illumina sequencing, a total of 181,985,262 paired-end reads of 150 bp were generated with an average of 16,544,115 read per sample. Metatranscriptome analysis confirmed that experimental acclimatization in aquaria accounted for global gill transcript variation. Additionally, the analysis of 16S and 18S rRNA sequences data allowed for a comprehensive characterization of host-symbiont interactions, which included the gradual loss of gill endosymbionts and signaling pathways, associated with stress responses and energy metabolism, under experimental acclimatization. Dominant active transcripts were assigned to the following KEGG categories: “Ribosome”, “Oxidative phosphorylation” and “Chaperones and folding catalysts” suggesting specific metabolic responses to physiological adaptations in aquarium environment. Conclusions Gill metagenomics analyses highlighted microbial diversity shifts and a clear pattern of varying mRNA transcript abundancies and expression during acclimatization to aquarium conditions which indicate change in bacterial community activity. This approach holds potential for the discovery of new host-symbiont associations, evidencing new functional transcripts and a clearer picture of methane metabolism during loss of endosymbionts. Towards the end of acclimatization, we observed trends in three major functional subsystems, as evidenced by an increment of transcripts related to genetic information processes; the decrease of chaperone and folding catalysts and oxidative phosphorylation transcripts; but no change in transcripts of gluconeogenesis and co-factors-vitamins.
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Affiliation(s)
- Inês Barros
- Department of Oceanography and Fisheries, University of the Azores, 9901-862 Horta, Portugal.,MARE-Marine and Environmental Sciences Centre, 9901-862 Horta, Portugal
| | - Hugo Froufe
- Next Generation Sequencing Unit-BIOCANT; Parque Tecnológico de Cantanhede, Núcleo 04, Lote 8, 3060-197 Cantanhede, Portugal
| | - George Marnellos
- Harvard University, Informatics and Scientific Applications, 38 Oxford Street, Cambridge, MA 02138-2020, United States
| | - Conceição Egas
- Next Generation Sequencing Unit-BIOCANT; Parque Tecnológico de Cantanhede, Núcleo 04, Lote 8, 3060-197 Cantanhede, Portugal
| | - Jennifer Delaney
- Harvard University, Informatics and Scientific Applications, 38 Oxford Street, Cambridge, MA 02138-2020, United States
| | - Michele Clamp
- Harvard University, Biological Laboratories, Room 3085, 16 Divinity Avenue, Cambridge, MA 02138-2020, United States
| | - Ricardo Serrão Santos
- Department of Oceanography and Fisheries, University of the Azores, 9901-862 Horta, Portugal.,MARE-Marine and Environmental Sciences Centre, 9901-862 Horta, Portugal.,OKEANOS Center, Faculty of Science and Technology, University of the Azores, 9901-862 Horta, Portugal
| | - Raul Bettencourt
- Department of Oceanography and Fisheries, University of the Azores, 9901-862 Horta, Portugal.,MARE-Marine and Environmental Sciences Centre, 9901-862 Horta, Portugal.,OKEANOS Center, Faculty of Science and Technology, University of the Azores, 9901-862 Horta, Portugal
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15
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Clark MS, Thorne MAS, King M, Hipperson H, Hoffman JI, Peck LS. Life in the intertidal: Cellular responses, methylation and epigenetics. Funct Ecol 2018. [DOI: 10.1111/1365-2435.13077] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Melody S. Clark
- British Antarctic SurveyNatural Environment Research Council Cambridge UK
| | | | - Michelle King
- British Antarctic SurveyNatural Environment Research Council Cambridge UK
| | - Helen Hipperson
- NERC Biomolecular Analysis FacilityDepartment of Animal and Plant SciencesUniversity of Sheffield Sheffield UK
| | - Joseph I. Hoffman
- Department of Animal BehaviourUniversity of Bielefeld Bielefeld Germany
| | - Lloyd S. Peck
- British Antarctic SurveyNatural Environment Research Council Cambridge UK
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16
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Moreira A, Freitas R, Figueira E, Volpi Ghirardini A, Soares AMVM, Radaelli M, Guida M, Libralato G. Combined effects of arsenic, salinity and temperature on Crassostrea gigas embryotoxicity. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2018; 147:251-259. [PMID: 28846930 DOI: 10.1016/j.ecoenv.2017.08.043] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 08/14/2017] [Accepted: 08/17/2017] [Indexed: 06/07/2023]
Abstract
The combined effects of different salinity and temperature levels on the toxicity of Arsenic (As) were studied on the embryonic development of the oyster Crassostrea gigas. A standardized embryotoxicity test was performed to assess the interactive effects of these stressors, in a full factorial design experiment including a range of salinities (15, 19, 24, 28 and 32), temperatures (16, 20, 24, 28 and 32°C) and As concentrations (100, 300, 600, 1200, 2400µgL-1). The embryotoxicity endpoint was about the determination of normal larvae development rates at various conditions, and median effect concentration (EC50) determination for each As exposure condition. Results showed that toxicity induced by As was characterized by retardation of embryonic development observing toxic effects at lower concentrations than previously reported studies. The presence of As in seawater resulted in a narrower range of tolerance to both salinity and temperature. These findings bring new insights on the impacts of a common contaminant on an important shellfish species having a planktonic early life stage development, with potential implications for population survival and ecosystem functioning in a changing environment.
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Affiliation(s)
- Anthony Moreira
- Departmento de Biologia & CESAM, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Rosa Freitas
- Departmento de Biologia & CESAM, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Etelvina Figueira
- Departmento de Biologia & CESAM, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Annamaria Volpi Ghirardini
- Department of Environmental Sciences, Informatics and Statistics, University Cà Foscari Venice, Via Torino 155, 30172 Venezia-Mestre, Italy
| | - Amadeu M V M Soares
- Departmento de Biologia & CESAM, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Marta Radaelli
- Department of Environmental Sciences, Informatics and Statistics, University Cà Foscari Venice, Via Torino 155, 30172 Venezia-Mestre, Italy
| | - Marco Guida
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, Via Cinthia ed. 7, 80126 Naples, Italy
| | - Giovanni Libralato
- Department of Environmental Sciences, Informatics and Statistics, University Cà Foscari Venice, Via Torino 155, 30172 Venezia-Mestre, Italy; Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, Via Cinthia ed. 7, 80126 Naples, Italy.
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17
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Goncalves P, Thompson EL, Raftos DA. Contrasting impacts of ocean acidification and warming on the molecular responses of CO 2-resilient oysters. BMC Genomics 2017; 18:431. [PMID: 28578697 PMCID: PMC5457604 DOI: 10.1186/s12864-017-3818-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 05/25/2017] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND This study characterises the molecular processes altered by both elevated CO2 and increasing temperature in oysters. Differences in resilience of marine organisms against the environmental stressors associated with climate change will have significant implications for the sustainability of coastal ecosystems worldwide. Some evidence suggests that climate change resilience can differ between populations within a species. B2 oysters represent a unique genetic resource because of their capacity to better withstand the impacts of elevated CO2 at the physiological level, compared to non-selected oysters from the same species (Saccostrea glomerata). Here, we used proteomic and transcriptomic analysis of gill tissue to evaluate whether the differential response of B2 oysters to elevated CO2 also extends to increased temperature. RESULTS Substantial and distinctive effects on protein concentrations and gene expression were evident among B2 oysters responding to elevated CO2 or elevated temperature. The combination of both stressors also altered oyster gill proteomes and gene expression. However, the impacts of elevated CO2 and temperature were not additive or synergistic, and may be antagonistic. CONCLUSIONS The data suggest that the simultaneous exposure of CO2-resilient oysters to near-future projected ocean pH and temperature results in complex changes in molecular processes in order to prevent stress-induced cellular damage. The differential response of B2 oysters to the combined stressors also indicates that the addition of thermal stress may impair the resilience of these oysters to decreased pH. Overall, this study reveals the intracellular mechanisms that might enable marine calcifiers to endure the emergent, adverse seawater conditions resulting from climate change.
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Affiliation(s)
- Priscila Goncalves
- Department of Biological Sciences, Macquarie University, Sydney, NSW, 2109, Australia. .,Sydney Institute of Marine Science, Chowder Bay, Sydney, NSW, 2088, Australia.
| | - Emma L Thompson
- Department of Biological Sciences, Macquarie University, Sydney, NSW, 2109, Australia.,Sydney Institute of Marine Science, Chowder Bay, Sydney, NSW, 2088, Australia.,Present Address: School of Life and Environmental Science, The University of Sydney, Sydney, NSW, 2006, Australia
| | - David A Raftos
- Department of Biological Sciences, Macquarie University, Sydney, NSW, 2109, Australia.,Sydney Institute of Marine Science, Chowder Bay, Sydney, NSW, 2088, Australia
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18
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Vasquez MC, Beam M, Blackwell S, Zuzow MJ, Tomanek L. Sirtuins regulate proteomic responses near thermal tolerance limits in the blue mussels Mytilus galloprovincialis and Mytilus trossulus. J Exp Biol 2017; 220:4515-4534. [DOI: 10.1242/jeb.160325] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 10/09/2017] [Indexed: 12/25/2022]
Abstract
The blue mussels Mytilus galloprovincialis and M. trossulus are competing species with biogeographical ranges set in part by environmental exposure to heat and hyposalinity. The underlying cellular mechanisms influencing interspecific differences in stress tolerance are unknown, but are believed to be under regulation by sirtuins, NAD-dependent deacylases that play a critical role in the cellular stress response. A comparison of the proteomic responses of M. galloprovincialis and M. trossulus to an acute heat shock in the presence and absence of the sirtuin inhibitor suramin (SIRT1, 2 and 5), showed that sirtuins affected molecular chaperones, oxidative stress proteins, metabolic enzymes, cytoskeletal and signaling proteins more in the heat-sensitive M. trossulus than in the heat-tolerant M. galloprovincialis. Interactions between sirtuin inhibition and changes in the abundance of proteins of β-oxidation and oxidative stress in M. trossulus suggest a greater role of sirtuins in shifting metabolism to reduce the production of reactive oxygen species near thermal limits. Furthermore, RNA-binding proteins initiating and inhibiting translation were affected by suramin in M. galloprovincialis and in M. trossulus, respectively. Western blot analysis showed that the levels of mitochondrial sirtuin 5 (SIRT5) were generally three times higher and increased with acute heat stress in response to sirtuin inhibition in M. trossulus but not in M. galloprovincialis, suggesting a possible feedback response in the former species and a greater reliance on SIRT5 for its stress response. Our findings suggest that SIRT5 plays an important role in setting interspecific differences in stress tolerance in Mytilus by affecting the stress proteome.
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Affiliation(s)
- M. Christina Vasquez
- California Polytechnic State University, Department of Biological Sciences, Center for Coastal Marine Sciences, Environmental Proteomics Laboratory, 1 Grand Ave., San Luis Obispo, CA 93407-0401, USA
| | - Michelle Beam
- California Polytechnic State University, Department of Biological Sciences, Center for Coastal Marine Sciences, Environmental Proteomics Laboratory, 1 Grand Ave., San Luis Obispo, CA 93407-0401, USA
| | - Shelley Blackwell
- California Polytechnic State University, Department of Biological Sciences, Center for Coastal Marine Sciences, Environmental Proteomics Laboratory, 1 Grand Ave., San Luis Obispo, CA 93407-0401, USA
| | - Marcus J. Zuzow
- California Polytechnic State University, Department of Biological Sciences, Center for Coastal Marine Sciences, Environmental Proteomics Laboratory, 1 Grand Ave., San Luis Obispo, CA 93407-0401, USA
| | - Lars Tomanek
- California Polytechnic State University, Department of Biological Sciences, Center for Coastal Marine Sciences, Environmental Proteomics Laboratory, 1 Grand Ave., San Luis Obispo, CA 93407-0401, USA
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19
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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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20
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Muraeva OA, Maltseva AL, Mikhailova NA, Granovitch AI. Mechanisms of adaption to salinity stress in marine gastropods Littorina saxatilis: a proteomic analysis. ACTA ACUST UNITED AC 2016. [DOI: 10.1134/s1990519x16020085] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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21
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Time course of lead induced proteomic changes in gill of the Antarctic limpet Nacella Concinna (Gastropoda: Patellidae). J Proteomics 2016; 151:145-161. [PMID: 27126604 DOI: 10.1016/j.jprot.2016.04.036] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 03/06/2016] [Accepted: 04/22/2016] [Indexed: 12/12/2022]
Abstract
The effect of increasing levels of metals from anthropogenic sources on Antarctic invertebrates is poorly understood. Here we exposed limpets (Nacella concinna) to 0, 0.12 and 0.25 μg L− 1 lead for 12, 24, 48 and 168 h. We subsequently quantified the changes in protein abundance from gill, using 2D gel electrophoresis and mass spectrometry. We identified several antioxidant proteins, including the metal binding Mn-superoxide dismutase and ferritin, increasing abundances early on. Chaperones involved in the redox-dependent maturation of proteins in the endoplasmic reticulum (ER) showed higher abundance with lead at 48 h. Lead also increased the abundance of Zn-binding carbonic anhydrase at 12 h, suggesting a challenge to acid-base balance. Metabolic proteins increased abundance at 168 h, suggesting a greater ATP demand during prolonged exposure. Changes in abundance of the small G-protein cdc42, a signaling protein modifying cytoskeleton, increased early and subsequently reversed during prolonged exposure, possibly leading to the modification of thick filament structure and function. We hypothesize that the replacement of metals initially affected antioxidant proteins and increased the production of reactive oxygen species. This disrupted the redox-sensitive maturation of proteins in the ER and caused increased ATP demand later on, accompanied by changes in cytoskeleton. SIGNIFICANCE Proteomic analysis of gill tissue in Antarctic limpets exposed to different concentrations of lead (Pb) over a 168 h time period showed that proteomic changes vary with time. These changes included an increase in the demand of scavenging reactive oxygen species, acid-base balance and a challenge to protein homeostasis in the endoplasmic reticulum early on and subsequently an increase in energy metabolism, cellular signaling, and cytoskeletal modifications. Based on this time course, we hypothesize that the main mode of action of lead is a replacement of metal-cofactors of key enzymes involved in the scavenging of reactive oxygen species and the regulation of acid-base balance.
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22
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Roland K, Kestemont P, Dieu M, Raes M, Silvestre F. Using a novel “Integrated Biomarker Proteomic” index to assess the effects of freshwater pollutants in European eel peripheral blood mononuclear cells. J Proteomics 2016; 137:83-96. [DOI: 10.1016/j.jprot.2016.01.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 12/30/2015] [Accepted: 01/05/2016] [Indexed: 01/04/2023]
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23
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Campos A, Danielsson G, Farinha AP, Kuruvilla J, Warholm P, Cristobal S. Shotgun proteomics to unravel marine mussel (Mytilus edulis) response to long-term exposure to low salinity and propranolol in a Baltic Sea microcosm. J Proteomics 2016; 137:97-106. [PMID: 26820222 DOI: 10.1016/j.jprot.2016.01.010] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 12/23/2015] [Accepted: 01/19/2016] [Indexed: 02/06/2023]
Abstract
UNLABELLED Pharmaceuticals, among them the β-adrenoceptor blocker propranolol, are an important group of environmental contaminants reported in European waters. Laboratory exposure to pharmaceuticals on marine species has been performed without considering the input of the ecosystem flow. To unravel the ecosystem response to long-term exposure to propranolol we have performed long-term exposure to propranolol and low salinity in microcosms. We applied shotgun proteomic analysis to gills of Mytilus edulis from those Baltic Sea microcosms and identified 2071 proteins with a proteogenomic strategy. The proteome profiling patterns from the 587 highly reproductive proteins among groups define salinity as a key factor in the mussel's response to propranolol. Exposure at low salinity drives molecular mechanisms of adaptation based on a decrease in the abundance of several cytoskeletal proteins, signalling and intracellular membrane trafficking pathway combined with a response towards the maintenance of transcription and translation. The exposure to propranolol combined with low salinity modulates the expression of structural proteins including cilia functions and decreases the expression of membrane protein transporters. This study reinforces the environment concerns of the impact of low salinity in combination with anthropogenic pollutants and anticipates critical physiological conditions for the survival of the blue mussel in the northern areas. BIOLOGICAL SIGNIFICANCE Applying shotgun proteomic analysis to M. edulis gills samples from a long-term microcosm exposure to propranolol and following a proteogenomic identification strategy, we have identified 2071 proteins. The proteomic analysis unrevealed which molecular mechanisms drive the adaptation to low salinity stress and how salinity modulates the effects of exposure to propranolol. These results reinforce the idea of the impact of low salinity in combination with anthropogenic pollutants and anticipate critical physiological condition.
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Affiliation(s)
- Alexandre Campos
- Department of Clinical and Experimental Medicine, Cell Biology, Faculty of Medicine, Linköping University, Linköping, Sweden
| | - Gabriela Danielsson
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Ana Paula Farinha
- Department of Clinical and Experimental Medicine, Cell Biology, Faculty of Medicine, Linköping University, Linköping, Sweden
| | - Jacob Kuruvilla
- Department of Clinical and Experimental Medicine, Cell Biology, Faculty of Medicine, Linköping University, Linköping, Sweden
| | - Per Warholm
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Susana Cristobal
- Department of Clinical and Experimental Medicine, Cell Biology, Faculty of Medicine, Linköping University, Linköping, Sweden; IKERBASQUE, Basque Foundation for Science, Bilbao, Bizkaia, Spain; Department of Physiology, Faculty of Medicine and Dentistry, University of Basque Country UPV/EHU, Bizkaia, Spain.
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24
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Marco-Ramell A, de Almeida AM, Cristobal S, Rodrigues P, Roncada P, Bassols A. Proteomics and the search for welfare and stress biomarkers in animal production in the one-health context. MOLECULAR BIOSYSTEMS 2016; 12:2024-35. [DOI: 10.1039/c5mb00788g] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Stress and welfare are important factors in animal production in the context of growing production optimization and scrutiny by the general public.
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Affiliation(s)
- A. Marco-Ramell
- Departament de Bioquímica i Biologia Molecular
- Facultat de Veterinària
- Universitat Autònoma de Barcelona
- 08193 Cerdanyola del Vallès
- Spain
| | - A. M. de Almeida
- Instituto de Biologia Experimental e Tecnologica
- Oeiras
- Portugal
- CIISA/FMV – Centro Interdisciplinar de Investigação em Sanidade Animal
- Faculdade de Medicina Veterinária
| | - S. Cristobal
- Department of Clinical and Experimental Medicine
- Cell Biology
- Faculty of Medicine
- Linköping University
- Linköping
| | - P. Rodrigues
- CCMAR
- Center of Marine Science
- University of Algarve
- 8005-139 Faro
- Portugal
| | - P. Roncada
- Istituto Sperimentale Italiano L. Spallanzani
- Milano
- Italy
| | - A. Bassols
- Departament de Bioquímica i Biologia Molecular
- Facultat de Veterinària
- Universitat Autònoma de Barcelona
- 08193 Cerdanyola del Vallès
- Spain
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25
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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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26
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Lockwood BL, Connor KM, Gracey AY. The environmentally tuned transcriptomes of Mytilus mussels. J Exp Biol 2015; 218:1822-33. [DOI: 10.1242/jeb.118190] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
ABSTRACT
Transcriptomics is a powerful tool for elucidating the molecular mechanisms that underlie the ability of organisms to survive and thrive in dynamic and changing environments. Here, we review the major contributions in this field, and we focus on studies of mussels in the genus Mytilus, which are well-established models for the study of ecological physiology in fluctuating environments. Our review is organized into four main sections. First, we illustrate how the abiotic forces of the intertidal environment drive the rhythmic coupling of gene expression to diel and tidal cycles in Mytilus californianus. Second, we discuss the challenges and pitfalls of conducting transcriptomic studies in field-acclimatized animals. Third, we examine the link between transcriptomic responses to environmental stress and biogeographic distributions in blue mussels, Mytilus trossulus and Mytilus galloprovincialis. Fourth, we present a comparison of transcriptomic datasets and identify 175 genes that share common responses to heat stress across Mytilus species. Taken together, these studies demonstrate that transcriptomics can provide an informative snapshot of the physiological state of an organism within an environmental context. In a comparative framework, transcriptomics can reveal how natural selection has shaped patterns of transcriptional regulation that may ultimately influence biogeography.
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Affiliation(s)
- Brent L. Lockwood
- Department of Biology, University of Vermont, 120 Marsh Life Science, 109 Carrigan Drive, Burlington, VT 05405, USA
| | - Kwasi M. Connor
- Marine Environmental Biology, University of Southern California, 3616 Trousdale Pkwy, Los Angeles, CA 90089, USA
| | - Andrew Y. Gracey
- Marine Environmental Biology, University of Southern California, 3616 Trousdale Pkwy, Los Angeles, CA 90089, USA
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27
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Abstract
ABSTRACT
Environmental (acute and chronic temperature, osmotic, hypoxic and pH) stress challenges the cellular redox balance and can lead to the increased production of reactive oxygen species (ROS). This review provides an overview of the reactions producing and scavenging ROS in the mitochondria, endoplasmic reticulum (ER) and peroxisome. It then compares these reactions with the findings of a number of studies investigating the proteomic responses of marine organisms to environmentally induced oxidative stress. These responses indicate that the thioredoxin–peroxiredoxin system is possibly more frequently recruited to scavenge H2O2 than the glutathione system. Isoforms of superoxide dismutase (SOD) are not ubiquitously induced in parallel, suggesting that SOD scavenging activity is sometimes sufficient. The glutathione system plays an important role in some organisms and probably also contributes to protecting protein thiols during environmental stress. Synthesis pathways of cysteine and selenocysteine, building blocks for glutathione and glutathione peroxidase, also play an important role in scavenging ROS during stress. The increased abundance of glutaredoxin and DyP-type peroxidase suggests a need for regulating the deglutathionylation of proteins and scavenging of peroxynitrite. Reducing equivalents for these scavenging reactions are generated by proteins of the pentose phosphate pathway and by NADP-dependent isocitrate dehydrogenase. Furthermore, proteins representing reactions of the tricarboxylic acid cycle and the electron transport system generating NADH and ROS, including those of complex I, II and III, are frequently reduced in abundance with stress. Protein maturation in the ER likely represents another source of ROS during environmental stress, as indicated by simultaneous changes in ER chaperones and antioxidant proteins. Although there are still too few proteomic analyses of non-model organisms exposed to environmental stress for a general pattern to emerge, hyposaline and low pH stress show different responses from temperature and hypoxic stress. Furthermore, comparisons of closely related congeners differing in stress tolerance start to provide insights into biochemical processes contributing to adaptive differences, but more of these comparisons are needed to draw general conclusions. To fully take advantage of a systems approach, studies with longer time courses, including several tissues and more species comparisons are needed.
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Turner BE, Basecke SM, Bazan GC, Dodge ES, Haire CM, Heussman DJ, Johnson CL, Mukai CK, Naccarati AM, Norton SJ, Sato JR, Talavera CO, Wade MV, Hillers KJ. Proteomic identification of germline proteins in Caenorhabditis elegans. WORM 2015; 4:e1008903. [PMID: 26435885 DOI: 10.1080/21624054.2015.1008903] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Revised: 11/30/2014] [Accepted: 01/13/2015] [Indexed: 01/06/2023]
Abstract
Sexual reproduction involves fusion of 2 haploid gametes to form diploid offspring with genetic contributions from both parents. Gamete formation represents a unique developmental program involving the action of numerous germline-specific proteins. In an attempt to identify novel proteins involved in reproduction and embryonic development, we have carried out a proteomic characterization of the process in Caenorhabditis elegans. To identify candidate proteins, we used 2D gel electrophoresis (2DGE) to compare protein abundance in nucleus-enriched extracts from wild-type C. elegans, and in extracts from mutant worms with greatly reduced gonads (glp-4(bn2) worms reared at 25°C); 84 proteins whose abundance correlated with germline presence were identified. To validate candidates, we used feeding RNAi to deplete candidate proteins, and looked for reduction in fertility and/or germline cytological defects. Of 20 candidates so screened for involvement in fertility, depletion of 13 (65%) caused a significant reduction in fertility, and 6 (30%) resulted in sterility (<5 % of wild-type fertility). Five of the 13 proteins with demonstrated roles in fertility have not previously been implicated in germline function. The high frequency of defects observed after RNAi depletion of candidate proteins suggests that this approach is effective at identifying germline proteins, thus contributing to our understanding of this complex organ.
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Affiliation(s)
- B Elizabeth Turner
- Department of Chemistry and Biochemistry; California Polytechnic State University ; San Luis Obispo, CA USA ; ; Department of Biological Sciences; California Polytechnic State University ; San Luis Obispo, CA USA
| | - Sophia M Basecke
- Department of Biological Sciences; California Polytechnic State University ; San Luis Obispo, CA USA
| | - Grace C Bazan
- Department of Biological Sciences; California Polytechnic State University ; San Luis Obispo, CA USA
| | - Eric S Dodge
- Department of Chemistry and Biochemistry; California Polytechnic State University ; San Luis Obispo, CA USA
| | - Cassy M Haire
- Department of Biological Sciences; California Polytechnic State University ; San Luis Obispo, CA USA
| | - Dylan J Heussman
- Department of Chemistry and Biochemistry; California Polytechnic State University ; San Luis Obispo, CA USA
| | - Chelsey L Johnson
- Department of Biological Sciences; California Polytechnic State University ; San Luis Obispo, CA USA
| | - Chelsea K Mukai
- Department of Biological Sciences; California Polytechnic State University ; San Luis Obispo, CA USA
| | - Adrianna M Naccarati
- Department of Biological Sciences; California Polytechnic State University ; San Luis Obispo, CA USA
| | - Sunny-June Norton
- Department of Biological Sciences; California Polytechnic State University ; San Luis Obispo, CA USA
| | - Jennifer R Sato
- Department of Biological Sciences; California Polytechnic State University ; San Luis Obispo, CA USA
| | - Chihara O Talavera
- Department of Chemistry and Biochemistry; California Polytechnic State University ; San Luis Obispo, CA USA
| | - Michael V Wade
- Department of Biological Sciences; California Polytechnic State University ; San Luis Obispo, CA USA
| | - Kenneth J Hillers
- Department of Biological Sciences; California Polytechnic State University ; San Luis Obispo, CA USA
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Garland MA, Stillman JH, Tomanek L. The proteomic response of cheliped myofibril tissue in the eurythermal porcelain crab Petrolisthes cinctipes to heat shock following acclimation to daily temperature fluctuations. J Exp Biol 2015; 218:388-403. [DOI: 10.1242/jeb.112250] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The porcelain crab Petrolisthes cinctipes lives under rocks and in mussel beds in the mid-intertidal zone where it experiences immersion during high tide and saturating humid conditions in air during low tide, which can increase habitat temperature by up to 20°C. To identify the biochemical changes affected by increasing temperature fluctuations and subsequent heat shock, we acclimated P. cinctipes for 30 days to one of three temperature regimes: (1) constant 10°C, (2) daily temperature fluctuations between 10 and 20°C (5 h up-ramp to 20°C, 1 h down-ramp to 10°C) and (3) 10–30°C (up-ramp to 30°C). After acclimation, animals were exposed to either 10°C or a 30°C heat shock to analyze the proteomic changes in claw muscle tissue. Following acclimation to 10–30°C (measured at 10°C), enolase and ATP synthase increased in abundance. Following heat shock, isoforms of arginine kinase and glycolytic enzymes such as aldolase, triose phosphate isomerase and glyceraldehyde 3-phosphate dehydrogenase increased across all acclimation regimes. Full-length isoforms of hemocyanin increased abundance following acclimation to 10–30°C, but hemocyanin fragments increased after heat shock following constant 10°C and fluctuating 10–20°C, possibly playing a role as antimicrobial peptides. Following constant 10°C and fluctuating 10–20°C, paramyosin and myosin heavy chain type-B increased in abundance, respectively, whereas myosin light and heavy chain decreased with heat shock. Actin-binding proteins, which stabilize actin filaments (filamin and tropomyosin), increased during heat shock following 10–30°C; however, actin severing and depolymerization proteins (gelsolin and cofilin) increased during heat shock following 10–20°C, possibly promoting muscle fiber restructuring. RAF kinase inhibitor protein and prostaglandin reductase increased during heat shock following constant 10°C and fluctuating 10–20°C, possibly inhibiting an immune response during heat shock. The results suggest that ATP supply, muscle fiber restructuring and immune responses are all affected by temperature fluctuations and subsequent acute heat shock in muscle tissue. Furthermore, although heat shock after acclimation to constant 10°C and fluctuating 10–30°C showed the greatest effects on the proteome, moderately fluctuating temperatures (10–20°C) broadened the temperature range over which claw muscle was able to respond to an acute heat shock with limited changes in the muscle proteome.
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Affiliation(s)
- Michael A. Garland
- California Polytechnic State University, Department of Biological Sciences, Center for Coastal Marine Studies, Environmental Proteomics Laboratory, 1 Grand Avenue, San Luis Obispo, CA 93407-0401, USA
| | - Jonathon H. Stillman
- Romberg Tiburon Center for Environmental Studies, San Francisco State University, 3152 Paradise Drive, Tiburon, CA 94920-1205, USA
| | - Lars Tomanek
- California Polytechnic State University, Department of Biological Sciences, Center for Coastal Marine Studies, Environmental Proteomics Laboratory, 1 Grand Avenue, San Luis Obispo, CA 93407-0401, USA
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Stekhoven FMAHS, van der Velde G, Lee TH, Bottrill AR. Proteomic study of the brackish water mussel Mytilopsis leucophaeata. Zool Stud 2015; 54:e22. [PMID: 31966109 PMCID: PMC6661436 DOI: 10.1186/s40555-014-0081-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 12/10/2014] [Indexed: 11/10/2022]
Abstract
BACKGROUND We encountered the opportunity to study proteochemically a brackish water invertebrate animal, Mytilopsis leucophaeata, belonging to the bivalves which stem from the second half of the Cambrian Period (about 510 million years ago). This way, we were able to compare it with the vertebrate animal, the frilled shark (Chlamydoselachus anguineus) that stems from a much later period of geologic time (Permian: 245-286 MYA). RESULTS The mussel contains a well-adapted system of protein synthesis on the ER, protein folding on the ER, protein trafficking via COPI or clathrin-coated vesicles from endoplasmic reticulum (ER) to Golgi and plasmalemma, an equally well-developed system of actin filaments that with myosin forms the transport system for vesicular proteins and tubulin, which is also involved in ATP-driven vesicular protein transport via microtubules or transport of chromosomes in mitosis and meiosis. A few of the systems that we could not detect in M. leucophaeata in comparison with C. anguineus are the synaptic vesicle cycle components as synaptobrevin, cellubrevin (v-snare) and synaptosomal associated protein 25-A (t-snare), although one component: Ras-related protein (O-Rab1) could be involved in synaptic vesicle traffic. Another component that we did not find in M. leucophaeata was Rab11 that is involved in the tubulovesicular recycling process of H+/K+-ATPase in C. anguineus. We have not been able to trace the H+/K+-ATPase of M. leucophaeata, but Na+/K+-ATPase was present. Furthermore, we have studied the increase of percent protein expression between 1,070 MYA (the generation of the Amoeba Dictyostelium discoideum) and present (the generation of the mammal Sus scrofa = wild boar). In this time span, three proteomic uprises did occur: 600 to 500 MYA, 47.5 to 4.75 MYA, and 1.4 to 0 MYA. The first uprise covers the generation of bivalves, the second covers gold fish, chicken, brine shrimp, house mouse, rabbit, Japanese medaka and Rattus norvegicus, and the third covers cow, chimpanzee, Homo sapiens, dog, goat, Puccinia graminis and wild boar. We hypothesise that the latter two uprises are related to geological and climate changes and their compensation in protein function expression. CONCLUSIONS The proteomic and evolutionary data demonstrate that M. leucophaeata is a highly educatioanal animal to study.
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Affiliation(s)
- Feico MAH Schuurmans Stekhoven
- Department of Animal Ecology and Ecophysiology, Faculty of Science, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Gerard van der Velde
- Department of Animal Ecology and Ecophysiology, Faculty of Science, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
- Naturalis Biodiversity Center, P.O. Box 9517,2300RA Leiden, The Netherlands
| | - Tsung-Han Lee
- Department of Life Sciences, National Chung-Hsing University, Taichung 402, Taiwan
| | - Andrew R Bottrill
- Protein and Nucleic Acid Chemistry Laboratory, Proteomics Facility, University of Leicester, Lancaster Road, Leicester LE1 9HN, UK
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Dong YW, Han GD, Huang XW. Stress modulation of cellular metabolic sensors: interaction of stress from temperature and rainfall on the intertidal limpet Cellana toreuma. Mol Ecol 2014; 23:4541-54. [PMID: 25130589 DOI: 10.1111/mec.12882] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 08/05/2014] [Accepted: 08/06/2014] [Indexed: 12/23/2022]
Abstract
In the natural environment, organisms are exposed to large variations in physical conditions. Quantifying such physiological responses is, however, often performed in laboratory acclimation studies, in which usually only a single factor is varied. In contrast, field acclimatization may expose organisms to concurrent changes in several environmental variables. The interactions of these factors may have strong effects on organismal function. In particular, rare events that occur stochastically and have relatively short duration may have strong effects. The present experiments studied levels of expression of several genes associated with cellular stress and metabolic regulation in a field population of limpet Cellana toreuma that encountered a wide range of temperatures plus periodic rain events. Physiological responses to these variable conditions were quantified by measuring levels of mRNA of genes encoding heat-shock proteins (Hsps) and metabolic sensors (AMPKs and Sirtuin 1). Our results reveal high ratios of individuals in upregulation group of stress-related gene expression at high temperature and rainy days, indicating the occurrence of stress from both prevailing high summer temperatures and occasional rainfall during periods of emersion. At high temperature, stress due to exposure to rainfall may be more challenging than heat stress alone. The highly variable physiological performances of limpets in their natural habitats indicate the possible differences in capability for physiological regulation among individuals. Our results emphasize the importance of studies of field acclimatization in unravelling the effects of environmental change on organisms, notably in the context of multiple changes in abiotic factors that are accompanying global change.
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Affiliation(s)
- Yun-Wei Dong
- State Key Laboratory of Marine Environmental Science, College of Marine and Earth Sciences, Xiamen University, Xiamen, 361102, China
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Tomanek L. Proteomics to study adaptations in marine organisms to environmental stress. J Proteomics 2014; 105:92-106. [PMID: 24788067 DOI: 10.1016/j.jprot.2014.04.009] [Citation(s) in RCA: 116] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2014] [Revised: 03/25/2014] [Accepted: 04/07/2014] [Indexed: 10/25/2022]
Abstract
Comparisons of proteomic responses of closely related congeners and populations have shown which cellular processes are critical to adapt to environmental stress. For example, several proteomic species comparisons showed that increasing abundances of oxidative stress proteins indicate that reactive oxygen species (ROS) represent a ubiquitous signal and possible co-stressor of warm and cold temperature, acute hyposaline and low pH stress, possibly causing a shift from pro-oxidant NADH-producing to anti-oxidant NADPH-producing and -consuming metabolic pathways. Changes in cytoskeletal and actin-binding proteins in response to several stressors, including ROS, suggest that both are important structural and functional elements in responding to stress. Disruption of protein homeostasis, e.g., increased abundance of molecular chaperones, was severe in response to acute heat stress, inducing proteolysis, but was also observed in response to chronic heat and cold stress and was concentrated to the endoplasmic reticulum during hyposaline stress. Small GTPases affecting vesicle formation and transport, Ca(2+)-signaling and ion transport responded to salinity stress in species- and population-specific ways. Aerobic energy metabolism was in general down-regulated in response to temperature, hypoxia, hyposalinity and low pH stress, but other metabolic pathways were activated to respond to increased oxidative stress or to switch metabolic fuels. Thus, comparative proteomics is a powerful approach to identify functionally adaptive variation. This article is part of a Special Issue entitled: Proteomics of non-model organisms.
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Affiliation(s)
- Lars Tomanek
- California Polytechnic State University, Department of Biological Sciences, Center for Coastal Marine Sciences, Environmental Proteomics Laboratory, 1 Grand Ave., San Luis Obispo, CA 93407-0401, USA.
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Suárez-Ulloa V, Fernández-Tajes J, Manfrin C, Gerdol M, Venier P, Eirín-López JM. Bivalve omics: state of the art and potential applications for the biomonitoring of harmful marine compounds. Mar Drugs 2013; 11:4370-89. [PMID: 24189277 PMCID: PMC3853733 DOI: 10.3390/md11114370] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Revised: 09/27/2013] [Accepted: 10/09/2013] [Indexed: 12/26/2022] Open
Abstract
The extraordinary progress experienced by sequencing technologies and bioinformatics has made the development of omic studies virtually ubiquitous in all fields of life sciences nowadays. However, scientific attention has been quite unevenly distributed throughout the different branches of the tree of life, leaving molluscs, one of the most diverse animal groups, relatively unexplored and without representation within the narrow collection of well established model organisms. Within this Phylum, bivalve molluscs play a fundamental role in the functioning of the marine ecosystem, constitute very valuable commercial resources in aquaculture, and have been widely used as sentinel organisms in the biomonitoring of marine pollution. Yet, it has only been very recently that this complex group of organisms became a preferential subject for omic studies, posing new challenges for their integrative characterization. The present contribution aims to give a detailed insight into the state of the art of the omic studies and functional information analysis of bivalve molluscs, providing a timely perspective on the available data resources and on the current and prospective applications for the biomonitoring of harmful marine compounds.
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Affiliation(s)
- Victoria Suárez-Ulloa
- Chromatin Structure and Evolution (CHROMEVOL) Group, Department of Biological Sciences, Florida International University, North Miami, FL 33181, USA; E-Mail:
| | - Juan Fernández-Tajes
- Wellcome Trust Center for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; E-Mail:
| | - Chiara Manfrin
- Department of Life Sciences, University of Trieste, Trieste 34127, Italy; E-Mails: (C.M.); (M.G.)
| | - Marco Gerdol
- Department of Life Sciences, University of Trieste, Trieste 34127, Italy; E-Mails: (C.M.); (M.G.)
| | - Paola Venier
- Department of Biology, University of Padova, Padova 35121, Italy; E-Mail:
| | - José M. Eirín-López
- Chromatin Structure and Evolution (CHROMEVOL) Group, Department of Biological Sciences, Florida International University, North Miami, FL 33181, USA; E-Mail:
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-305-919-4000; Fax: +1-305-919-4030
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