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Lee Y, Kim DH, Lee JS, Lee MC, Kim HS, Maszczyk P, Sakakura Y, Yang Z, Hagiwara A, Park HG, Lee JS. Oxidative stress-mediated deleterious effects of hypoxia in the brackish water flea Diaphanosoma celebensis. MARINE POLLUTION BULLETIN 2024; 205:116633. [PMID: 38936003 DOI: 10.1016/j.marpolbul.2024.116633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 03/25/2024] [Accepted: 06/18/2024] [Indexed: 06/29/2024]
Abstract
In this study, we investigated the acute toxicity, in vivo effects, oxidative stress, and gene expression changes caused by hypoxia on the brackish water flea Diaphanosoma celebensis. The no-observed-effect concentration (NOEC) of 48 h of hypoxia exposure was found to be 2 mg/L O2. Chronic exposure to NOEC caused a significant decline in lifespan but had no effect on total fecundity. The induction of reactive oxygen species increased in a time-dependent manner over 48 h, whereas the content of antioxidant enzymes (superoxide dismutase and catalase) decreased. The transcription and translation levels were modulated by hypoxia exposure. In particular, a significant increase in hemoglobin level was followed by up-regulation of hypoxia-inducible factor 1α gene expression and activation of the mitogen-activated protein kinase pathway. In conclusion, our findings provide a better understanding of the molecular mechanism of the adverse effects of hypoxia in brackish water zooplankton.
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Affiliation(s)
- Yoseop Lee
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Duck-Hyun Kim
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Jin-Sol Lee
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, South Korea
| | - Min-Chul Lee
- Department of Food and Nutrition, College of Bio-Nano Technology, Gachon University, Seongnam 13120, South Korea
| | - Hyung Sik Kim
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, South Korea
| | - Piotr Maszczyk
- Department of Hydrobiology, Institute of Functional Biology and Ecology, Faculty of Biology, University of Warsaw, Warsaw 02-089, Poland
| | - Yoshitaka Sakakura
- Graduate School of Integrated Science and Technology, Nagasaki University, Nagasaki 852-8521, Japan
| | - Zhou Yang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Biological Sciences, 8 Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China
| | - Atsushi Hagiwara
- Graduate School of Integrated Science and Technology, Nagasaki University, Nagasaki 852-8521, Japan
| | - Heum Gi Park
- Department of Marine Ecology and Environment, College of Life Sciences, Gangneung-Wonju National University, Gangneung 25457, South Korea
| | - Jae-Seong Lee
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea.
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Lee Y, Byeon E, Kim DH, Maszczyk P, Wang M, Wu RSS, Jeung HD, Hwang UK, Lee JS. Hypoxia in aquatic invertebrates: Occurrence and phenotypic and molecular responses. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2023; 263:106685. [PMID: 37690363 DOI: 10.1016/j.aquatox.2023.106685] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 08/27/2023] [Accepted: 09/01/2023] [Indexed: 09/12/2023]
Abstract
Global deoxygenation in aquatic systems is an increasing environmental problem, and substantial oxygen loss has been reported. Aquatic animals have been continuously exposed to hypoxic environments, so-called "dead zones," in which severe die-offs among organisms are driven by low-oxygen events. Multiple studies of hypoxia exposure have focused on in vivo endpoints, metabolism, oxidative stress, and immune responses in aquatic invertebrates such as molluscs, crustaceans, echinoderms, and cnidarians. They have shown that acute and chronic exposure to hypoxia induces significant decreases in locomotion, respiration, feeding, growth, and reproduction rates. Also, several studies have examined the molecular responses of aquatic invertebrates, such as anaerobic metabolism, reactive oxygen species induction, increased antioxidant enzymes, immune response mechanisms, regulation of hypoxia-inducible factor 1-alpha (HIF-1α) genes, and differently expressed hemoglobin/hemocyanin. The genetic basis of those molecular responses involves HIF-1α pathway genes, which are highly expressed in hypoxic conditions. However, the identification of HIF-1α-related genes and understanding of their applications in some aquatic invertebrates remain inadequate. Also, some species of crustaceans, rotifers, sponges, and ctenophores that lack HIF-1α are thought to have alternative defense mechanisms to cope with hypoxia, but those factors are still unclear. This review covers the formation of hypoxia in aquatic environments and the various adverse effects of hypoxia on aquatic invertebrates. The limitations of current hypoxia research and genetic information about the HIF-1α pathway are also discussed. Finally, this paper explains the underlying processes of the hypoxia response and presents an integrated program for research about the molecular mechanisms of hypoxic stresses in aquatic invertebrates.
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Affiliation(s)
- Yoseop Lee
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Eunjin Byeon
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Duck-Hyun Kim
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Piotr Maszczyk
- Department of Hydrobiology, Institute of Functional Biology and Ecology, Faculty of Biology, University of Warsaw, Żwirki i Wigury 101, Warsaw 02-089, Poland
| | - Minghua Wang
- Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies/College of the Environment & Ecology, Xiamen University, Xiamen 361102, China
| | - Rudolf Shiu Sun Wu
- Department of Science and Environmental Studies, The Education University of Hong Kong, Hong Kong, China; State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon, Hong Kong, China
| | - Hee-Do Jeung
- Tidal Flat Research Center, National Institute of Fisheries Science, Gunsan 54001, South Korea
| | - Un-Ki Hwang
- Tidal Flat Research Center, National Institute of Fisheries Science, Gunsan 54001, South Korea
| | - Jae-Seong Lee
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea.
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Xie XD, Zhou Y, Sun YB, Yi SL, Zhao Y, Chen Q, Xie YH, Cao MX, Yu ML, Wei YY, Zhang L, Hu TJ. RNA-Seq and 16S rRNA Reveals That Tian-Dong-Tang-Gan Powder Alleviates Environmental Stress-Induced Decline in Immune and Antioxidant Function and Gut Microbiota Dysbiosis in Litopenaeus vannami. Antioxidants (Basel) 2023; 12:1262. [PMID: 37371991 DOI: 10.3390/antiox12061262] [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: 05/05/2023] [Revised: 06/07/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
Ammonia stress and nitrite stress can induce immune depression and oxidative stress in Litopenaeus vannami (L. vannamei). Earlier reports showed that L. vannamei immunity, resistance to ammonia stress, and resistance to nitrite stress improved after Tian-Dong-Tang-Gan Powder (TDTGP) treatment, but the mechanism is not clear. In this study, three thousand L. vannamei were fed different doses of TDTGP for 35 days and then subjected to ammonia and nitrite stress treatments for 72 h. Transcriptome and 16-Seq ribosomal RNA gene sequencing (16S rRNA-seq) were used to analyze hepatopancreas gene expression and changes in gut microbiota abundance in each group. The results showed that after TDTGP treatment, hepatopancreas mRNA expression levels of immunity- and antioxidant-related genes were increased, the abundance of Vibrionaceae in the gut microbiota was decreased, and the abundance of Rhodobacteraceae and Flavobacteriaceae was increased. In addition, after TDTGP treatment, the effects of ammonia and nitrite stress on the mRNA expression of Pu, cat-4, PPAF2, HO, Hsp90b1, etc. were reduced and the disruption of the gut microbiota was alleviated. In short, TDTGP can regulate the immunity and antioxidant of L. vannamei by increasing the expression levels of immunity- and antioxidant-related genes and regulating the abundance of Rhodobacteraceae and Flavobacteriaceae in the gut microbiota.
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Affiliation(s)
- Xiao-Dong Xie
- College of Animal Science and Technology, Guangxi University, Nanning 530005, China
| | - Ying Zhou
- College of Animal Science and Technology, Guangxi University, Nanning 530005, China
| | - Yu-Bo Sun
- College of Animal Science and Technology, Guangxi University, Nanning 530005, China
| | - Shou-Li Yi
- College of Animal Science and Technology, Guangxi University, Nanning 530005, China
| | - Yi Zhao
- College of Animal Science and Technology, Guangxi University, Nanning 530005, China
| | - Qi Chen
- College of Animal Science and Technology, Guangxi University, Nanning 530005, China
| | - Ying-Hong Xie
- College of Animal Science and Technology, Guangxi University, Nanning 530005, China
| | - Mi-Xia Cao
- College of Animal Science, Anhui Science and Technology University, Chuzhou 233100, China
| | - Mei-Ling Yu
- College of Animal Science and Technology, Guangxi University, Nanning 530005, China
| | - Ying-Yi Wei
- College of Animal Science and Technology, Guangxi University, Nanning 530005, China
| | - Ling Zhang
- Guangxi Scientific Research Center of Traditional Chinese Medicine, Guangxi University of Chinese Medicine, Nanning 530200, China
| | - Ting-Jun Hu
- College of Animal Science and Technology, Guangxi University, Nanning 530005, China
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Burnett KG, Burnett LE. Immune Defense in Hypoxic Waters: Impacts of CO 2 Acidification. THE BIOLOGICAL BULLETIN 2022; 243:120-133. [PMID: 36548972 DOI: 10.1086/721322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
AbstractPeriodic episodes of low oxygen (hypoxia) and elevated CO2 (hypercapnia) accompanied by low pH occur naturally in estuarine environments. Under the influence of climate change, the geographic range and intensity of hypoxia and hypercapnic hypoxia are predicted to increase, potentially jeopardizing the survival of economically and ecologically important organisms that use estuaries as habitat and nursery grounds. In this review we synthesize data from published studies that evaluate the impact of hypoxia and hypercapnic hypoxia on the ability of crustaceans and bivalve molluscs to defend themselves against potential microbial pathogens. Available data indicate that hypoxia generally has suppressive effects on host immunity against bacterial pathogens as measured by in vitro and in vivo assays. Few studies have documented the effects of hypercapnic hypoxia on crustaceans or bivalve immune defense, with a range of outcomes suggesting that added CO2 might have additive, negative, or no interactions with the effects of hypoxia alone. This synthesis points to the need for more partial pressure of O2 × low pH factorial design experiments and recommends the development of new host∶pathogen challenge models incorporating natural transmission of a wide range of viruses, bacteria, and parasites, along with novel in vivo tracking systems that better quantify how pathogens interact with their hosts in real time under laboratory and field conditions.
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Woods HA, Moran AL, Atkinson D, Audzijonyte A, Berenbrink M, Borges FO, Burnett KG, Burnett LE, Coates CJ, Collin R, Costa-Paiva EM, Duncan MI, Ern R, Laetz EMJ, Levin LA, Lindmark M, Lucey NM, McCormick LR, Pierson JJ, Rosa R, Roman MR, Sampaio E, Schulte PM, Sperling EA, Walczyńska A, Verberk WCEP. Integrative Approaches to Understanding Organismal Responses to Aquatic Deoxygenation. THE BIOLOGICAL BULLETIN 2022; 243:85-103. [PMID: 36548975 DOI: 10.1086/722899] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
AbstractOxygen bioavailability is declining in aquatic systems worldwide as a result of climate change and other anthropogenic stressors. For aquatic organisms, the consequences are poorly known but are likely to reflect both direct effects of declining oxygen bioavailability and interactions between oxygen and other stressors, including two-warming and acidification-that have received substantial attention in recent decades and that typically accompany oxygen changes. Drawing on the collected papers in this symposium volume ("An Oxygen Perspective on Climate Change"), we outline the causes and consequences of declining oxygen bioavailability. First, we discuss the scope of natural and predicted anthropogenic changes in aquatic oxygen levels. Although modern organisms are the result of long evolutionary histories during which they were exposed to natural oxygen regimes, anthropogenic change is now exposing them to more extreme conditions and novel combinations of low oxygen with other stressors. Second, we identify behavioral and physiological mechanisms that underlie the interactive effects of oxygen with other stressors, and we assess the range of potential organismal responses to oxygen limitation that occur across levels of biological organization and over multiple timescales. We argue that metabolism and energetics provide a powerful and unifying framework for understanding organism-oxygen interactions. Third, we conclude by outlining a set of approaches for maximizing the effectiveness of future work, including focusing on long-term experiments using biologically realistic variation in experimental factors and taking truly cross-disciplinary and integrative approaches to understanding and predicting future effects.
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Hall ER, Wickes L, Burnett LE, Scott GI, Hernandez D, Yates KK, Barbero L, Reimer JJ, Baalousha M, Mintz J, Cai WJ, Craig JK, DeVoe MR, Fisher WS, Hathaway TK, Jewett EB, Johnson Z, Keener P, Mordecai RS, Noakes S, Phillips C, Sandifer PA, Schnetzer A, Styron J. Acidification in the U.S. Southeast: Causes, Potential Consequences and the Role of the Southeast Ocean and Coastal Acidification Network. FRONTIERS IN MARINE SCIENCE 2020; 7:1-548. [PMID: 32802822 PMCID: PMC7424514 DOI: 10.3389/fmars.2020.00548] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Coastal acidification in southeastern U.S. estuaries and coastal waters is influenced by biological activity, run-off from the land, and increasing carbon dioxide in the atmosphere. Acidification can negatively impact coastal resources such as shellfish, finfish, and coral reefs, and the communities that rely on them. Organismal responses for species located in the U.S. Southeast document large negative impacts of acidification, especially in larval stages. For example, the toxicity of pesticides increases under acidified conditions and the combination of acidification and low oxygen has profoundly negative influences on genes regulating oxygen consumption. In corals, the rate of calcification decreases with acidification and processes such as wound recovery, reproduction, and recruitment are negatively impacted. Minimizing the changes in global ocean chemistry will ultimately depend on the reduction of carbon dioxide emissions, but adaptation to these changes and mitigation of the local stressors that exacerbate global acidification can be addressed locally. The evolution of our knowledge of acidification, from basic understanding of the problem to the emergence of applied research and monitoring, has been facilitated by the development of regional Coastal Acidification Networks (CANs) across the United States. This synthesis is a product of the Southeast Coastal and Ocean Acidification Network (SOCAN). SOCAN was established to better understand acidification in the coastal waters of the U.S. Southeast and to foster communication among scientists, resource managers, businesses, and governments in the region. Here we review acidification issues in the U.S. Southeast, including the regional mechanisms of acidification and their potential impacts on biological resources and coastal communities. We recommend research and monitoring priorities and discuss the role SOCAN has in advancing acidification research and mitigation of and adaptation to these changes.
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Affiliation(s)
- Emily R. Hall
- Mote Marine Laboratory, Sarasota, FL, United States
- Correspondence: Emily R. Hall
| | - Leslie Wickes
- Thrive Blue Consulting, Charleston, SC, United States
| | - Louis E. Burnett
- Grice Marine Laboratory, College of Charleston, Charleston, SC, United States
| | - Geoffrey I. Scott
- Arnold School of Public Health, University of South Carolina, Columbia, SC, United States
| | - Debra Hernandez
- Southeastern Coastal Ocean Observing and Research Regional Association, Charleston, SC, United States
| | | | - Leticia Barbero
- National Oceanic and Atmospheric Administration, Atlantic Oceanographic and Meteorological Laboratory, Miami, FL, United States
| | - Janet J. Reimer
- College of Earth, Ocean and Environment, University of Delaware, Newark, DE, United States
| | - Mohammed Baalousha
- Arnold School of Public Health, University of South Carolina, Columbia, SC, United States
| | - Jennifer Mintz
- National Oceanic and Atmospheric Administration, Ocean Acidification Program, Silver Spring, MD, United States
| | - Wei-Jun Cai
- College of Earth, Ocean and Environment, University of Delaware, Newark, DE, United States
| | - J. Kevin Craig
- National Oceanic and Atmospheric Administration, National Marine Fisheries Service, Southeast Fisheries Science Center, Beaufort, NC, United States
| | - M. Richard DeVoe
- South Carolina Sea Grant Consortium, Charleston, SC, United States
| | - William S. Fisher
- United States Environmental Protection Agency, Gulf Ecology Laboratory, Gulf Breeze, FL, United States
| | | | - Elizabeth B. Jewett
- National Oceanic and Atmospheric Administration, Ocean Acidification Program, Silver Spring, MD, United States
| | - Zackary Johnson
- Nicholas School of the Environment and Biology Department, Duke University, Beaufort, NC, United States
| | - Paula Keener
- Global Ocean Visions, LLC, Charleston, SC, United States
| | | | - Scott Noakes
- Center for Applied Isotope Studies, The University of Georgia, Athens, GA, United States
| | - Charlie Phillips
- Phillips Seafood, Sapelo Sea Farms, South Atlantic Fisheries Management Council, Townsend, GA, United States
| | - Paul A. Sandifer
- Hollings Marine Laboratory, College of Charleston, Charleston, SC, United States
| | - Astrid Schnetzer
- Marine, Earth and Atmospheric Sciences, North Carolina State University, Raleigh, NC, United States
| | - Jay Styron
- Carolina Mariculture Company, Cedar Island, NC, United States
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Mendoza-Porras O, Kamath S, Harris JO, Colgrave ML, Huerlimann R, Lopata AL, Wade NM. Resolving hemocyanin isoform complexity in haemolymph of black tiger shrimp Penaeus monodon - implications in aquaculture, medicine and food safety. J Proteomics 2020; 218:103689. [PMID: 32088355 DOI: 10.1016/j.jprot.2020.103689] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 02/10/2020] [Accepted: 02/14/2020] [Indexed: 01/21/2023]
Abstract
Hemocyanin (Hc) is a multifunctional macromolecule involved in oxygen transport and non-specific immunity in shrimp. Hc is crucial in physiology and nutrition linked with optimal performance in aquaculture production systems. In medicine, Hc has been approved for clinical use in humans as adjuvant and anticancer therapeutic. In contrast, Hc has also been identified as one of the proteins causing anaphylaxis following shrimp consumption. The role of individual Hc isoforms remains unknown due to a lack of resolved Hc isoforms. We successfully identified eleven different Penaeus monodon hemocyanin (PmoHc) γ isoforms including two truncated isoforms (50 and 20 kDa) and one PmoHc β isoform in haemolymph using proteomics informed by transcriptomics. Amino acid sequence homology ranged from 24 to 97% between putative PmoHc gene isoforms. Hc isoforms showed specific patterns of transcript expression in shrimp larval stages and adult hepatopancreas. These findings enable isoform level investigations aiming to define molecular mechanisms underpinning Hc functionality in shrimp physiology and immunity, as well as their individual immunogenic role in human allergy. Our research demonstrates the power of proteomics informed by transcriptomics to resolve isoform complexity in non-model organisms and lay the foundations for improved performance within the aquaculture industry and advance allergenic applications in medicine. SIGNIFICANCE: The roles of hemocyanin (Hc) in shrimp homeostasis and immunity as well as in human allergy are not well understood because the complexity of Hc isoforms has remained unresolved. Our results have confirmed the existence of at least 12 individual Hc isoforms in shrimp haemolymph and validated putative Hc gene assemblies from transcriptomics. Our findings will enable monitoring the expression of specific Hc isoforms in shrimp haemolymph during different environmental, nutritional and pathogenic conditions, thus providing insights into isoform specific functional roles. In medicine, the potential allergenicity of each Hc isoform could be determined and advance allergenic applications. Lastly, since Hc comprises up to 95% of the total protein in haemolymph, these isoforms become ideal targets for prawn provenance, traceability and food contamination studies.
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Affiliation(s)
- Omar Mendoza-Porras
- CSIRO Livestock and Aquaculture, Queensland Bioscience Precinct, 306 Carmody Rd, St Lucia, QLD, Australia.
| | - Sandip Kamath
- James Cook University, Molecular Allergy Research Laboratory, College of Public Health, Medical and Veterinary Sciences, James Cook Drive, Townsville, QLD 4811, Australia; James Cook University, Australian Institute of Tropical Health and Medicine, James Cook Drive, Townsville, QLD 4811, Australia
| | - James O Harris
- Flinders University, College of Science and Engineering, GPO Box 2100, Adelaide, SA 5001, Australia
| | - Michelle L Colgrave
- CSIRO Livestock and Aquaculture, Queensland Bioscience Precinct, 306 Carmody Rd, St Lucia, QLD, Australia
| | - Roger Huerlimann
- James Cook University, College of Science and Engineering, James Cook Drive, Townsville, QLD 4811, Australia; Australian Research Council Industrial Transformation Research Hub for Advanced Shrimp Breeding, Australia
| | - Andreas L Lopata
- James Cook University, Molecular Allergy Research Laboratory, College of Public Health, Medical and Veterinary Sciences, James Cook Drive, Townsville, QLD 4811, Australia; James Cook University, Australian Institute of Tropical Health and Medicine, James Cook Drive, Townsville, QLD 4811, Australia
| | - Nicholas M Wade
- CSIRO Livestock and Aquaculture, Queensland Bioscience Precinct, 306 Carmody Rd, St Lucia, QLD, Australia; James Cook University, College of Science and Engineering, James Cook Drive, Townsville, QLD 4811, Australia; Australian Research Council Industrial Transformation Research Hub for Advanced Shrimp Breeding, Australia
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8
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Regulation of glyceraldehyde-3-phosphate dehydrogenase by hypoxia inducible factor 1 in the white shrimp Litopenaeus vannamei during hypoxia and reoxygenation. Comp Biochem Physiol A Mol Integr Physiol 2019; 235:56-65. [PMID: 31100464 DOI: 10.1016/j.cbpa.2019.05.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 05/08/2019] [Accepted: 05/09/2019] [Indexed: 12/15/2022]
Abstract
Hypoxia is a frequent source of stress in the estuarine habitat of the white shrimp Litopenaeus vannamei. During hypoxia, L. vannamei gill cells rely more heavily on anaerobic glycolysis to obtain ATP. This is mediated by transcriptional up-regulation of glycolytic enzymes including glyceraldehyde-3-phosphate dehydrogenase (GAPDH). The hypoxia inducible factor 1 (HIF-1) is an important transcriptional activator of several glycolytic enzymes during hypoxia in diverse animals, including crustaceans. In this work, we cloned and sequenced a fragment corresponding to the 5' flank of the GAPDH gene and identified a putative HIF-1 binding site, as well as sites for other transcription factors involved in the hypoxia signaling pathway. To investigate the role of HIF-1 in GAPDH regulation, we simultaneously injected double-stranded RNA (dsRNA) into shrimp to silence HIF-1α and HIF-1β under normoxia, hypoxia, and hypoxia followed by reoxygenation, and then measured gill HIF-1α, HIF-1β expression, GAPDH expression and activity, and glucose and lactate concentrations at 0, 3, 24 and 48 h. During normoxia, HIF-1 silencing induced up-regulation of GAPDH transcripts and activity, suggesting that expression is down-regulated via HIF-1 under these conditions. In contrast, HIF-1 silencing during hypoxia abolished the increases in GAPDH expression and activity, glucose and lactate concentrations. Finally, HIF-1 silencing during hypoxia-reoxygenation prevented the increase in GAPDH expression, however, those changes were not reflected in GAPDH activity and lactate accumulation. Altogether, these results indicate that GAPDH and glycolysis are transcriptionally regulated by HIF-1 in gills of white shrimp.
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9
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Jimenez AG, Braun E, Tobin K. How does chronic temperature exposure affect hypoxia tolerance in sheepshead minnows' (Cyprinodon variegatus variegatus) ability to tolerate oxidative stress? FISH PHYSIOLOGY AND BIOCHEMISTRY 2019; 45:499-510. [PMID: 30397840 DOI: 10.1007/s10695-018-0583-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 10/23/2018] [Indexed: 06/08/2023]
Abstract
Estuarine environments are characterized by cyclical fluctuations in tides, with tidal shifts drastically, frequently, and acutely altering temperature, dissolved oxygen, and salinity. Despite these ecological challenges, the sheepshead minnow, Cyprinodon variegatus, seems to dominate estuarine landscapes. Here, we held sheepshead minnows to four temperature treatment groups for 1 month. We then tested whether temperature exposure had an effect on acute hypoxia tolerance via oxidative stress. We measured superoxide dismutase (SOD), catalase (CAT), and glutathione peroxidase (GPx) activities, as well as total antioxidant capacity and lipid peroxidation (LPO) damage in white muscle. We found that exposure to increasing temperatures (15, 20, 25, and 30 °C) for 1 month led to significantly higher CTmax in sheepshead minnows. We also found that CAT activity significantly increased in the 20 and 25 °C temperature treatment groups, whereas it did not change between control and hypoxia trials. SOD activity was significantly higher in control groups of the 15 and 30 °C temperature treatment groups compared with hypoxia groups of these same temperature treatments. GPx activity was significantly lower in the 30 °C temperature treatment group regardless of control or hypoxia trials. Hydroxyl scavenging capacity varied across temperature treatment and control/hypoxia groups. Peroxyl scavenging capacity and LPO damage showed no significant differences across temperature treatment groups or between control and hypoxia trials.
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Affiliation(s)
- Ana Gabriela Jimenez
- Department of Biology, Colgate University, 13 Oak Dr., Hamilton, NY, 13346, USA.
| | - Evan Braun
- Department of Biology, Colgate University, 13 Oak Dr., Hamilton, NY, 13346, USA
| | - Kailey Tobin
- Department of Biology, Colgate University, 13 Oak Dr., Hamilton, NY, 13346, USA
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10
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Zeng D, Chen X, Peng J, Yang C, Peng M, Zhu W, Xie D, He P, Wei P, Lin Y, Zhao Y, Chen X. Single-molecule long-read sequencing facilitates shrimp transcriptome research. Sci Rep 2018; 8:16920. [PMID: 30446694 PMCID: PMC6240054 DOI: 10.1038/s41598-018-35066-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 10/31/2018] [Indexed: 12/26/2022] Open
Abstract
Although shrimp are of great economic importance, few full-length shrimp transcriptomes are available. Here, we used Pacific Biosciences single-molecule real-time (SMRT) long-read sequencing technology to generate transcripts from the Pacific white shrimp (Litopenaeus vannamei). We obtained 322,600 full-length non-chimeric reads, from which we generated 51,367 high-quality unique full-length transcripts. We corrected errors in the SMRT sequences by comparison with Illumina-produced short reads. We successfully annotated 81.72% of all unique SMRT transcripts against the NCBI non-redundant database, 58.63% against Swiss-Prot, 45.38% against Gene Ontology, 32.57% against Clusters of Orthologous Groups of proteins (COG), and 47.83% against Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Across all transcripts, we identified 3,958 long non-coding RNAs (lncRNAs) and 80,650 simple sequence repeats (SSRs). Our study provides a rich set of full-length cDNA sequences for L. vannamei, which will greatly facilitate shrimp transcriptome research.
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Affiliation(s)
- Digang Zeng
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Sciences, Nanning, Guangxi, P.R. China
| | - Xiuli Chen
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Sciences, Nanning, Guangxi, P.R. China
| | - Jinxia Peng
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Sciences, Nanning, Guangxi, P.R. China
| | - Chunling Yang
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Sciences, Nanning, Guangxi, P.R. China
| | - Min Peng
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Sciences, Nanning, Guangxi, P.R. China
| | - Weilin Zhu
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Sciences, Nanning, Guangxi, P.R. China
| | - Daxiang Xie
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Sciences, Nanning, Guangxi, P.R. China
| | - Pingping He
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Sciences, Nanning, Guangxi, P.R. China
| | - Pinyuan Wei
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Sciences, Nanning, Guangxi, P.R. China
| | - Yong Lin
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Sciences, Nanning, Guangxi, P.R. China
| | - Yongzhen Zhao
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Sciences, Nanning, Guangxi, P.R. China.
| | - Xiaohan Chen
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Sciences, Nanning, Guangxi, P.R. China.
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11
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Camacho-Jiménez L, Peregrino-Uriarte AB, Martínez-Quintana JA, Yepiz-Plascencia G. The glyceraldehyde-3-phosphate dehydrogenase of the shrimp Litopenaeus vannamei: Molecular cloning, characterization and expression during hypoxia. MARINE ENVIRONMENTAL RESEARCH 2018; 138:65-75. [PMID: 29699713 DOI: 10.1016/j.marenvres.2018.04.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 04/15/2018] [Accepted: 04/16/2018] [Indexed: 06/08/2023]
Abstract
Some marine crustaceans like the white shrimp Litopenaeus vannamei are tolerant to environmental hypoxia. Under oxygen deprivation, shrimp tissues obtain energy by enhancing anaerobic glycolysis. In mammals, hypoxia increases the expression of the glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase (GAPDH), which has been shown a "moonlighting" role in cells. However, the effect of hypoxia on the GAPDH expression has not been studied in crustaceans. In the present work, we obtained a 2744 bp gene sequence with a 999 bp ORF split by a single intron. The deduced protein is 332 amino acids and corresponds to the L. vannamei GAPDH (LvGAPDH), which is highly similar in sequence and structure to other animal GAPDHs. During hypoxia, LvGAPDH expression is significantly induced in gills but not in hepatopancreas, suggesting that it may play a role in the molecular and cellular response of shrimp to hypoxia.
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Affiliation(s)
- Laura Camacho-Jiménez
- Centro de Investigación en Alimentación y Desarrollo (CIAD), A.C., Carretera a Ejido La Victoria Km. 0.6, Hermosillo, Sonora, C.P. 83304, Mexico
| | - Alma B Peregrino-Uriarte
- Centro de Investigación en Alimentación y Desarrollo (CIAD), A.C., Carretera a Ejido La Victoria Km. 0.6, Hermosillo, Sonora, C.P. 83304, Mexico
| | - José A Martínez-Quintana
- Facultad de Zootecnia y Ecología, Universidad Autónoma de Chihuahua, Periférico Francisco R. Almada Km. 1, Chihuahua, C.P. 33820, Mexico
| | - Gloria Yepiz-Plascencia
- Centro de Investigación en Alimentación y Desarrollo (CIAD), A.C., Carretera a Ejido La Victoria Km. 0.6, Hermosillo, Sonora, C.P. 83304, Mexico.
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Das S, Shyamal S, Durica DS. Analysis of Annotation and Differential Expression Methods used in RNA-seq Studies in Crustacean Systems. Integr Comp Biol 2018; 56:1067-1079. [PMID: 27940611 DOI: 10.1093/icb/icw117] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
In the field of crustacean biology, usage of RNA-seq to study gene expression is rapidly growing. Major advances in sequencing technology have contributed to the ability to examine complex patterns of genome activity in a wide range of organisms that are extensively used for comparative physiology, ecology and evolution, environmental monitoring, and commercial aquaculture. Relative to insect and vertebrate model organisms, however, information on the organization of crustacean genomes is virtually nonexistent, making de novo transcriptome assembly, annotation and quantification problematic and challenging. We present here a summary of the methodologies and software analyses employed in 23 recent publications, which describe de novo transcriptome assembly, annotation, and differential gene expression in a variety of crustacean experimental systems. We focus on establishing a series of best practices that will allow for investigators to produce datasets that are understandable, reproducible, and of general utility for related analyses and cross-study comparisons.
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Affiliation(s)
- Sunetra Das
- *Department of Biology, Colorado State University, 1878 Campus Delivery Fort Collins, CO 80523, USA;
| | | | - David S Durica
- Department of Biology, University of Oklahoma, Norman, OK 73019, USA
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13
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McCormick LR, Levin LA. Physiological and ecological implications of ocean deoxygenation for vision in marine organisms. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2017; 375:rsta.2016.0322. [PMID: 28784712 PMCID: PMC5559417 DOI: 10.1098/rsta.2016.0322] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 05/18/2017] [Indexed: 05/04/2023]
Abstract
Climate change has induced ocean deoxygenation and exacerbated eutrophication-driven hypoxia in recent decades, affecting the physiology, behaviour and ecology of marine organisms. The high oxygen demand of visual tissues and the known inhibitory effects of hypoxia on human vision raise the questions if and how ocean deoxygenation alters vision in marine organisms. This is particularly important given the rapid loss of oxygen and strong vertical gradients in oxygen concentration in many areas of the ocean. This review evaluates the potential effects of low oxygen (hypoxia) on visual function in marine animals and their implications for marine biota under current and future ocean deoxygenation based on evidence from terrestrial and a few marine organisms. Evolutionary history shows radiation of eye designs during a period of increasing ocean oxygenation. Physiological effects of hypoxia on photoreceptor function and light sensitivity, in combination with morphological changes that may occur throughout ontogeny, have the potential to alter visual behaviour and, subsequently, the ecology of marine organisms, particularly for fish, cephalopods and arthropods with 'fast' vision. Visual responses to hypoxia, including greater light requirements, offer an alternative hypothesis for observed habitat compression and shoaling vertical distributions in visual marine species subject to ocean deoxygenation, which merits further investigation.This article is part of the themed issue 'Ocean ventilation and deoxygenation in a warming world'.
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Affiliation(s)
- Lillian R McCormick
- Integrative Oceanography Division, Scripps Institution of Oceanography, La Jolla, CA 92093-0218, USA
| | - Lisa A Levin
- Integrative Oceanography Division, Scripps Institution of Oceanography, La Jolla, CA 92093-0218, USA
- Center for Marine Biodiversity and Conservation, Scripps Institution of Oceanography, La Jolla, CA 92093-0218, USA
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14
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Mykles DL, Burnett KG, Durica DS, Joyce BL, McCarthy FM, Schmidt CJ, Stillman JH. Resources and Recommendations for Using Transcriptomics to Address Grand Challenges in Comparative Biology. Integr Comp Biol 2016; 56:1183-1191. [PMID: 27639274 PMCID: PMC5146710 DOI: 10.1093/icb/icw083] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
High-throughput RNA sequencing (RNA-seq) technology has become an important tool for studying physiological responses of organisms to changes in their environment. De novo assembly of RNA-seq data has allowed researchers to create a comprehensive catalog of genes expressed in a tissue and to quantify their expression without a complete genome sequence. The contributions from the "Tapping the Power of Crustacean Transcriptomics to Address Grand Challenges in Comparative Biology" symposium in this issue show the successes and limitations of using RNA-seq in the study of crustaceans. In conjunction with the symposium, the Animal Genome to Phenome Research Coordination Network collated comments from participants at the meeting regarding the challenges encountered when using transcriptomics in their research. Input came from novices and experts ranging from graduate students to principal investigators. Many were unaware of the bioinformatics analysis resources currently available on the CyVerse platform. Our analysis of community responses led to three recommendations for advancing the field: (1) integration of genomic and RNA-seq sequence assemblies for crustacean gene annotation and comparative expression; (2) development of methodologies for the functional analysis of genes; and (3) information and training exchange among laboratories for transmission of best practices. The field lacks the methods for manipulating tissue-specific gene expression. The decapod crustacean research community should consider the cherry shrimp, Neocaridina denticulata, as a decapod model for the application of transgenic tools for functional genomics. This would require a multi-investigator effort.
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Affiliation(s)
- Donald L Mykles
- *Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Karen G Burnett
- Grice Marine Laboratory, College of Charleston, Charleston, SC 29412, USA
- Hollings Marine Laboratory, Charleston, SC 29412, USA
| | - David S Durica
- Department of Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Blake L Joyce
- BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Fiona M McCarthy
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Carl J Schmidt
- Department of Animal and Food Sciences, University of Delaware, Newark, DE 19716
| | - Jonathon H Stillman
- Romberg Tiburon Center for Environmental Studies and Department of Biology, San Francisco State University, Tiburon, CA 94920, USA
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
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15
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Johnson JG, Burnett LE, Burnett KG. Uncovering Hemocyanin Subunit Heterogeneity in Penaeid Shrimp using RNA-Seq. Integr Comp Biol 2016; 56:1080-1091. [DOI: 10.1093/icb/icw088] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
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Armstrong EJ, Stillman JH. Construction and Characterization of Two Novel Transcriptome Assemblies in the Congeneric Porcelain Crabs Petrolisthes cinctipes and P. manimaculis. Integr Comp Biol 2016; 56:1092-1102. [PMID: 27375271 DOI: 10.1093/icb/icw043] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Crustaceans have commonly been used as non-model systems in basic biological research, especially physiological regulation. With the recent and rapid adoption of functional genomic tools, crustaceans are increasingly becoming model systems for ecological investigations of development and evolution and for mechanistic examinations of genotype-phenotype interactions and molecular pathways of response to environmental stressors. Comparative transcriptomic approaches, however, remain constrained by a lack of sequence data in closely related crustacean taxa. We identify challenges in the use of functional genomics tools in comparative analysis among decapod crustacean in light of recent advances. We present RNA-seq data from two congeneric species of porcelain crabs (Petrolisthes cinctipes and P. manimaculis) used to construct two de novo transcriptome assemblies with ∼194K and ∼278K contigs, respectively. We characterize and contrast these assemblies and compare them to a previously generated EST sequence library for P. cinctipes We also discuss the potential use of these data as a case-study system in the broader context of crustacean comparative transcriptomics.
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Affiliation(s)
- Eric J Armstrong
- *Department of Integrative Biology, University of California, 3040 Valley Life Sciences Bldg, Berkeley, CA 94720, USA .,Romberg Tiburon Center for Environmental Studies, San Francisco State University, 3152 Paradise Drive, Tiburon, CA 94920, USA
| | - Jonathon H Stillman
- *Department of Integrative Biology, University of California, 3040 Valley Life Sciences Bldg, Berkeley, CA 94720, USA.,Romberg Tiburon Center for Environmental Studies, San Francisco State University, 3152 Paradise Drive, Tiburon, CA 94920, USA
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