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Islam SI, Mou MJ, Sanjida S, Mahfuj S. A review on molecular detection techniques of white spot syndrome virus: Perspectives of problems and solutions in shrimp farming. Vet Med Sci 2023; 9:778-801. [PMID: 36282009 PMCID: PMC10029913 DOI: 10.1002/vms3.979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
This review aims to provide an update on the current scientific understanding of various aspects of White Spot Syndrome Virus (WSSV) formation, diagnostic procedures, transmission, ecological effects, pathophysiology and management strategies. In terms of production and financial benefits, the WSSV has been the most virulent in shrimp and several other crustacean sectors around the globe. It spreads vertically from diseased broodstock to post-larvae and horizontally by cannibalism, invertebrate vectors, freshwater and sediments. In the transfer of white spot disease (WSD) in newly stocked ponds, the survivability of WSSV in sediment is the most important variable. In typical cultural conditions, it is a highly infectious pathogen capable of inflicting total death within 3-10 days after an outbreak. Some of the current biosecurity strategies used to keep diseases out of shrimp ponds such as pond water disinfection, quarantine of new stocks before stocking and broader usage of specific pathogen-free shrimp. The sequencing and characterisation of various WSSV strains have provided details about pathogen biology, pathogenicity and disease. To develop successful control methods, knowledge of these characteristics is essential. In several shrimp-producing countries in Asia and the Americas, the infections produced by the WSSV have had disastrous socio-economic consequences. As a result of international trade or migration of diseased species, the World Animal Health Organization recognised several illnesses as posing a substantial hazard to farmed shrimp. WSD is receiving much scientific research due to the potential economic effects of the virus. Research is now being done to understand better the molecular biology and pathophysiology of WSSV, as well as how to treat and prevent the virus. However, further study should be conducted in countries with more resilient host species to understand their role in mitigating disease impacts since these revelations may aid in developing a WSD treatment.
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Affiliation(s)
- Sk Injamamul Islam
- Department of Fisheries and Marine Bioscience, Faculty of Biological Science, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Moslema Jahan Mou
- Department of Genetic Engineering and Biotechnology, Faculty of Life and Earth Science, University of Rajshahi, Rajshahi, Bangladesh
| | - Saloa Sanjida
- Department of Environmental Science and Technology, Faculty of Applied Science and Technology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Sarower Mahfuj
- Department of Fisheries and Marine Bioscience, Faculty of Biological Science, Jashore University of Science and Technology, Jashore, Bangladesh
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Diwan AD, Harke SN, Panche AN. Application of proteomics in shrimp and shrimp aquaculture. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2022; 43:101015. [PMID: 35870418 DOI: 10.1016/j.cbd.2022.101015] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 07/11/2022] [Accepted: 07/11/2022] [Indexed: 06/15/2023]
Abstract
Since proteins play an important role in the life of an organism, many researchers are now looking at how genes and proteins interact to form different proteins. It is anticipated that the creation of adequate tools for rapid analysis of proteins will accelerate the determination of functional aspects of these biomolecules and develop new biomarkers and therapeutic targets for the diagnosis and treatment of various diseases. Though shrimp contains high-quality marine proteins, there are reports about the heavy losses to the shrimp industry due to the poor quality of shrimp production and many times due to mass mortality also. Frequent outbreaks of diseases, water pollution, and quality of feed are some of the most recognized reasons for such losses. In the seafood export market, shrimp occupies the top position in currency earnings and strengthens the economy of many developing nations. Therefore, it is vital for shrimp-producing companies they produce healthy shrimp with high-quality protein. Though aquaculture is a very competitive market, global awareness regarding the use of scientific knowledge and emerging technologies to obtain better-farmed organisms through sustainable production has enhanced the importance of proteomics in seafood biology research. Proteomics, as a powerful tool, has therefore been increasingly used to address several issues in shrimp aquaculture. In the present paper, efforts have been made to address some of them, particularly the role of proteomics in reproduction, breeding and spawning, immunological responses and disease resistance capacity, nutrition and health, microbiome and probiotics, quality and safety of shrimp production, bioinformatics applications in proteomics, the discovery of protein biomarkers, and mitigating biotic and abiotic stresses. Future challenges and research directions on proteomics in shrimp aquaculture have also been discussed.
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Affiliation(s)
- A D Diwan
- MGM Institute of Biosciences and Technology, Mahatma Gandhi Mission University N-6, CIDCO, Aurangabad-431003, Maharashtra, India.
| | - S N Harke
- MGM Institute of Biosciences and Technology, Mahatma Gandhi Mission University N-6, CIDCO, Aurangabad-431003, Maharashtra, India.
| | - Archana N Panche
- Novo Nordisk Centre for Biosustainability, Technical University of Denmark, B220 Kemitorvet, 2800 Kgs, Lyngby, Denmark.
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Aweya JJ, Zhuang K, Liu Y, Fan J, Yao D, Wang F, Chen X, Li S, Ma H, Zhang Y. The ARM repeat domain of hemocyanin interacts with MKK4 to modulate antimicrobial peptides expression. iScience 2022; 25:103958. [PMID: 35265821 PMCID: PMC8898971 DOI: 10.1016/j.isci.2022.103958] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 02/03/2022] [Accepted: 02/17/2022] [Indexed: 11/02/2022] Open
Abstract
The mitogen-activated protein kinase (MAPK) intracellular signaling pathway mediates numerous biological processes, including antimicrobial immune response by inducing antimicrobial peptides (AMPs) production. Although MAPK signaling cascade proteins have been identified in penaeid shrimp, their modulation via the MKK4-p38-c-Jun cascade and effect on AMPs production is unknown. Here, we show that hemocyanin (PvHMC), antimicrobial peptides (anti-lipopolysaccharide factor, crustin, and penaeidins), and MKK4-p38-c-Jun cascade proteins are simultaneously induced by pathogens (Vibrio parahaemolyticus, Staphylococcus aureus, and white spot syndrome virus) in Penaeus vannamei. Intriguingly, knockdown of PvHMC with or without pathogen challenge attenuated the expression of MKK4-p38-c-Jun cascade proteins and their phosphorylation level, which consequently decreased AMPs expression. Further analysis revealed that PvHMC interacts via its armadillo (ARM) repeat domain with PvMKK4 to modulate the p38 MAPK signaling pathway. Thus, the ARM repeat domain enables penaeid shrimp hemocyanin to modulate AMPs expression during antimicrobial response by activating the p38 MAPK signaling pathway. Pathogens induce hemocyanin, MKK4-p38-c-Jun proteins, and antimicrobial peptide genes Hemocyanin modulates MKK4-p38-c-Jun cascade proteins to regulate AMPs gene expression Hemocyanin interacts with MKK4 to modulate p38 MAPK signaling in penaeid shrimp Deletion of the ARM repeat domain attenuates the interaction of hemocyanin with MKK4
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Rojo-Arreola L, Navarrete del Toro M, Cordova-Murueta J, García-Carreño F. Techniques for protein digestion research in Decapoda: A review. Trends Food Sci Technol 2019. [DOI: 10.1016/j.tifs.2019.05.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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Guppy JL, Jones DB, Jerry DR, Wade NM, Raadsma HW, Huerlimann R, Zenger KR. The State of " Omics" Research for Farmed Penaeids: Advances in Research and Impediments to Industry Utilization. Front Genet 2018; 9:282. [PMID: 30123237 PMCID: PMC6085479 DOI: 10.3389/fgene.2018.00282] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 07/09/2018] [Indexed: 12/19/2022] Open
Abstract
Elucidating the underlying genetic drivers of production traits in agricultural and aquaculture species is critical to efforts to maximize farming efficiency. "Omics" based methods (i.e., transcriptomics, genomics, proteomics, and metabolomics) are increasingly being applied to gain unprecedented insight into the biology of many aquaculture species. While the culture of penaeid shrimp has increased markedly, the industry continues to be impeded in many regards by disease, reproductive dysfunction, and a poor understanding of production traits. Extensive effort has been, and continues to be, applied to develop critical genomic resources for many commercially important penaeids. However, the industry application of these genomic resources, and the translation of the knowledge derived from "omics" studies has not yet been completely realized. Integration between the multiple "omics" resources now available (i.e., genome assemblies, transcriptomes, linkage maps, optical maps, and proteomes) will prove critical to unlocking the full utility of these otherwise independently developed and isolated resources. Furthermore, emerging "omics" based techniques are now available to address longstanding issues with completing keystone genome assemblies (e.g., through long-read sequencing), and can provide cost-effective industrial scale genotyping tools (e.g., through low density SNP chips and genotype-by-sequencing) to undertake advanced selective breeding programs (i.e., genomic selection) and powerful genome-wide association studies. In particular, this review highlights the status, utility and suggested path forward for continued development, and improved use of "omics" resources in penaeid aquaculture.
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Affiliation(s)
- Jarrod L. Guppy
- Australian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, Australia
- College of Science and Engineering and Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, QLD, Australia
| | - David B. Jones
- Australian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, Australia
- College of Science and Engineering and Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, QLD, Australia
| | - Dean R. Jerry
- Australian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, Australia
- College of Science and Engineering and Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, QLD, Australia
| | - Nicholas M. Wade
- Australian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, Australia
- Aquaculture Program, CSIRO Agriculture & Food, Queensland Bioscience Precinct, St Lucia, QLD, Australia
| | - Herman W. Raadsma
- Australian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, Australia
- Faculty of Science, Sydney School of Veterinary Science, The University of Sydney, Camden, NSW, Australia
| | - Roger Huerlimann
- Australian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, Australia
- College of Science and Engineering and Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, QLD, Australia
| | - Kyall R. Zenger
- Australian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, Australia
- College of Science and Engineering and Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, QLD, Australia
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The response of glutathione peroxidase 1 and glutathione peroxidase 7 under different oxidative stresses in black tiger shrimp, Penaeus monodon. Comp Biochem Physiol B Biochem Mol Biol 2018; 217:1-13. [DOI: 10.1016/j.cbpb.2017.12.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 11/16/2017] [Accepted: 12/07/2017] [Indexed: 12/27/2022]
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Effect of acute salinity stress on ion homeostasis, Na +/K +-ATPase and histological structure in sea cucumber Apostichopus japonicus. SPRINGERPLUS 2016; 5:1977. [PMID: 27917349 PMCID: PMC5108739 DOI: 10.1186/s40064-016-3620-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 11/01/2016] [Indexed: 01/13/2023]
Abstract
Background Sea cucumbers (Apostichopus japonicus) are an imperiled fauna exposed to a variety of environmental condition such as salinity and studies are urgently needed to assess their effects to guide aquaculture efforts. The effects of acute salinity stress on coelomic fluid osmotic pressure, ion concentrations, the activity of Na+/K+-ATPase in respiratory trees and the histological variations were measured to evaluate the salinity tolerance of sea cucumbers. Results Significant correlations in osmotic pressure were observed between coelomic fluid and ambient environmental salinity. In coelomic fluid, Na+ concentration was observed fluctuated during salinity 18 psu and the inflection point presented at the 6 h. The Na+/K+-ATPase activity in respiratory trees indicated the “U-shaped” fluctuant change and the change trend was opposite with the Na+ concentration. The ions (K+, Cl−) concentration decreased and showed the same tendency at salinity 40 psu with salinity 18 psu. The total coelomocytes counts and phagocytosis of coelomic fluid Na+/K+-ATPase activity indicated fluctuating changes under different salinity stress. Histological variation revealed a negative relation between decreasing salt concentration and tissue integrity. Tissue damages were significantly observed in intestines, muscles and tube feet under low salinity environment (18, 23 and 27 psu). The connective tissue in intestines of A. japonicus exposed to 18 and 23 psu damaged and partly separated from the mucosal epithelium. The significant variations occurred in tube feet, which presented the swelling in connective tissue and a fracture in longitudinal muscles under low salinity (18 psu). The morphological change of tube feet showed the shrinkage of connective tissue under high salinity (40 psu). The amount of infusoria in the respiratory trees decreased or even disappeared in salinity treatment groups (18 and 23 psu). Conclusion The results inferred that osmoconformity and ionoregulation were seen in sea cucumbers, which contributed to understand the salinity regulatory mechanisms of A. japonicus under acute salinity stress.
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Havird JC, Mitchell RT, Henry RP, Santos SR. Salinity-induced changes in gene expression from anterior and posterior gills of Callinectes sapidus (Crustacea: Portunidae) with implications for crustacean ecological genomics. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2016; 19:34-44. [PMID: 27337176 DOI: 10.1016/j.cbd.2016.06.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 05/31/2016] [Accepted: 06/08/2016] [Indexed: 01/05/2023]
Abstract
Decapods represent one of the most ecologically diverse taxonomic groups within crustaceans, making them ideal to study physiological processes like osmoregulation. However, prior studies have failed to consider the entire transcriptomic response of the gill - the primary organ responsible for ion transport - to changing salinity. Moreover, the molecular genetic differences between non-osmoregulatory and osmoregulatory gill types, as well as the hormonal basis of osmoregulation, remain underexplored. Here, we identified and characterized differentially expressed genes (DEGs) via RNA-Seq in anterior (non-osmoregulatory) and posterior (osmoregulatory) gills during high to low salinity transfer in the blue crab Callinectes sapidus, a well-studied model for crustacean osmoregulation. Overall, we confirmed previous expression patterns for individual ion transport genes and identified novel ones with salinity-mediated expression. Notable, novel DEGs among salinities and gill types for C. sapidus included anterior gills having higher expression of structural genes such as actin and cuticle proteins while posterior gills exhibit elevated expression of ion transport and energy-related genes, with the latter likely linked to ion transport. Potential targets among recovered DEGs for hormonal regulation of ion transport between salinities and gill types included neuropeptide Y and a KCTD16-like protein. Using publically available sequence data, constituents for a "core" gill transcriptome among decapods are presented, comprising genes involved in ion transport and energy conversion and consistent with salinity transfer experiments. Lastly, rarefication analyses lead us to recommend a modest number of sequence reads (~10-15M), but with increased biological replication, be utilized in future DEG analyses of crustaceans.
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Affiliation(s)
- Justin C Havird
- Department of Biological Sciences, Molette Laboratory for Climate Change and Environmental Studies, Auburn University, 101 Rouse Life Sciences Bldg., Auburn, AL 36849, USA; Dept. of Biology, Colorado State University, Room E106 Anatomy/Zoology Building, Fort Collins, CO 80523, USA.
| | - Reed T Mitchell
- Dept. of Biological Sciences, Auburn University, 101 Rouse Life Sciences Bldg., Auburn, AL 36849, USA; Walter Reed Biosystematics Unit, 4210 Silver Hill Rd, Suitland, MD, 20746, USA
| | - Raymond P Henry
- Dept. of Biological Sciences, Auburn University, 101 Rouse Life Sciences Bldg., Auburn, AL 36849, USA
| | - Scott R Santos
- Department of Biological Sciences, Molette Laboratory for Climate Change and Environmental Studies, Auburn University, 101 Rouse Life Sciences Bldg., Auburn, AL 36849, USA
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Clark KF, Acorn AR, Wang H, Greenwood SJ. Comparative tissue expression of American lobster (Homarus americanus) immune genes during bacterial and scuticociliate challenge. FISH & SHELLFISH IMMUNOLOGY 2015; 47:1054-1066. [PMID: 26551049 DOI: 10.1016/j.fsi.2015.10.035] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Revised: 10/19/2015] [Accepted: 10/23/2015] [Indexed: 06/05/2023]
Abstract
The American lobster (Homarus americanus) fishery is the most economically significant fishery in Canada; although comparatively little is known about the lobsters' response to pathogenic challenge. This is the first study to investigate the expression of immune genes in tissues outside of the lobster hepatopancreas in response to challenges by the Gram-positive bacteria, Aerococcus viridans var. homari or the scuticociliate parasite, Anophryoides haemophila. The hepatopancreas has been regarded as the major humoral immune organ in crustaceans, but the contribution of other organs and tissues to the molecular immune response has largely been overlooked. This study used RT-qPCR to monitor the gene expression of several immune genes including three anti-lipopolysaccharide isoforms (ALF) Homame ALF-B1, Homame ALF-C1 and ALFHa-1, acute phase serum amyloid protein A (SAA), as well as thioredoxin and hexokinase, in antennal gland and gill tissues. Our findings indicate that the gene expression of the SAA and all ALF isoforms in the antennal gland and gill tissues increased in response to pathogenic challenge. However, there was differential expression of individual ALF isoforms that were dependent on both the tissue, and the pathogen used in the challenge. The gene expression changes of several immune genes were found to be higher in the antennal gland than have been previously reported for the hepatopancreas. This study demonstrates that increased immune gene expression from the gill and antennal gland over the course of pathogen induced disease contributes to the immune response of H. americanus.
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Affiliation(s)
- K Fraser Clark
- Department of Biomedical Sciences, Faculty of Veterinary Medicine, University of Prince Edward Island, 550 University Ave., Charlottetown, PEI, C1A 4P3, Canada; AVC Lobster Science Centre, Faculty of Veterinary Medicine, University of Prince Edward Island, 550 University Ave., Charlottetown, PEI, C1A 4P3, Canada; Department of Plant and Animal Sciences, Faculty of Agriculture, Dalhousie University, PO Box 500, Truro, Nova Scotia, B2N 5E3, Canada.
| | - Adam R Acorn
- Department of Biomedical Sciences, Faculty of Veterinary Medicine, University of Prince Edward Island, 550 University Ave., Charlottetown, PEI, C1A 4P3, Canada; AVC Lobster Science Centre, Faculty of Veterinary Medicine, University of Prince Edward Island, 550 University Ave., Charlottetown, PEI, C1A 4P3, Canada.
| | - Haili Wang
- Department of Biomedical Sciences, Faculty of Veterinary Medicine, University of Prince Edward Island, 550 University Ave., Charlottetown, PEI, C1A 4P3, Canada; AVC Lobster Science Centre, Faculty of Veterinary Medicine, University of Prince Edward Island, 550 University Ave., Charlottetown, PEI, C1A 4P3, Canada.
| | - Spencer J Greenwood
- Department of Biomedical Sciences, Faculty of Veterinary Medicine, University of Prince Edward Island, 550 University Ave., Charlottetown, PEI, C1A 4P3, Canada; AVC Lobster Science Centre, Faculty of Veterinary Medicine, University of Prince Edward Island, 550 University Ave., Charlottetown, PEI, C1A 4P3, Canada.
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Kim SH, Kim JH, Park MA, Hwang SD, Kang JC. The toxic effects of ammonia exposure on antioxidant and immune responses in Rockfish, Sebastes schlegelii during thermal stress. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2015; 40:954-959. [PMID: 26528677 DOI: 10.1016/j.etap.2015.10.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Revised: 10/15/2015] [Accepted: 10/16/2015] [Indexed: 06/05/2023]
Abstract
Rockfish, Sebastes schlegelii (mean weight 14.53 ± 1.14 cm, and mean weight 38.36 ± 3.45 g) were exposed for 4 weeks (2 weeks and 4 weeks) with the different levels of ammonia in the concentrations of 0, 0.1, 0.5, 1.0mg/L at 19 and 24°C. The ammonia exposure induced significant alterations in antioxidant responses. The activities of SOD, CAT, and GST were considerably increased by the ammonia exposure depending on water temperature, whereas the GSH level was notably decreased after 2 and 4 weeks. In the stress indicators, the cortisol and HSP 70 were significantly elevated by the exposure to ammonia depending on water temperature. In innate immune responses, the phagocytosis and lysozyme activity were notably decreased by ammonia exposure depending on water temperature after 2 and 4 weeks. The results suggest that ammonia exposure depending on water temperature can induce the considerable alterations in antioxidant responses, stress, and immune inhibition.
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Affiliation(s)
- Shin-Hu Kim
- Department of Aquatic Life Medicine, Pukyong National University, Busan 608-737, Republic of Korea
| | - Jun-Hwan Kim
- Department of Aquatic Life Medicine, Pukyong National University, Busan 608-737, Republic of Korea
| | - Myoung-Ae Park
- Aquatic life disease control division, National Fisheries Research and Development Institute, Busan 619-902, Republic of Korea
| | - Seong Don Hwang
- Aquatic life disease control division, National Fisheries Research and Development Institute, Busan 619-902, Republic of Korea
| | - Ju-Chan Kang
- Department of Aquatic Life Medicine, Pukyong National University, Busan 608-737, Republic of Korea.
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Nikapitiya C, Kim WS, Park K, Kim J, Lee MO, Kwak IS. Chitinase gene responses and tissue sensitivity in an intertidal mud crab (Macrophthalmus japonicus) following low or high salinity stress. Cell Stress Chaperones 2015; 20:517-26. [PMID: 25697403 PMCID: PMC4406927 DOI: 10.1007/s12192-015-0576-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 01/20/2015] [Accepted: 01/23/2015] [Indexed: 10/24/2022] Open
Abstract
Changes in salinity affect the physiological status of the marine habitat including that of the intertidal mud crab Macrophthalmus japonicus. Chitinases play significant biological roles in crustaceans such as morphogenesis, nutrient digestion, and pathogen defense. In this study, the osmoregulatory function of three chitinase gene transcripts was determined compared to seawater (SW, 31 ± 1 psu) in M. japonicus gills and hepatopancreas under different salinities (10, 25, and 40 psu) for 1, 4, and 7 days. In SW-exposed crab, quantitative real-time PCR analysis showed chitinase 1 (Mj-chi1) and chitinase 4 (Mj-chi4) transcripts constitutively expressed in all the tested tissues with strong expression in hepatopancreas, but chitinase 5 (Mj-chi5) showed highest expression in stomach. When exposed to different salinities, Mj-chi1 showed significant up-regulation at day 4 whereas Mj-chi4 showed late up-regulation (day 7) at all the salinities in hepatopancreas. In the gills, early up-regulation (day 1) in Mj-chi1 and time-dependent late up-regulation (day 7) in Mj-chi4 at high salinity were observed. These results indicate the possibility of using Mj-chi4 as a marker against salinity changes. Moreover, our results further suggest that Mj-chi1 and Mj-chi4 transcriptions were significantly affected by changes in salinity; however, Mj-chi5 in gills was less affected by salinity and showed no effect in hepatopancreas. Thus, chitinase transcription modulations in the gills are more sensitive than hepatopancreas to salinity stress. Further, present data indicate the possible existence of different physiological roles among chitinase gene families, which need to be clarified in more detail by future biochemical and physiological functional studies.
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Affiliation(s)
- Chamilani Nikapitiya
- />Department of Aqualife Medicine, Chonnam National University, Chonnam, 550-749 Korea
- />Faculty of Marine Technology, Chonnam National University, Chonnam, 550-749 Korea
| | - Won-Seok Kim
- />Faculty of Marine Technology, Chonnam National University, Chonnam, 550-749 Korea
| | - Kiyun Park
- />Faculty of Marine Technology, Chonnam National University, Chonnam, 550-749 Korea
| | - Jongkyu Kim
- />Faculty of Marine Technology, Chonnam National University, Chonnam, 550-749 Korea
| | - Moon-Ock Lee
- />Faculty of Marine Technology, Chonnam National University, Chonnam, 550-749 Korea
| | - Ihn-Sil Kwak
- />Faculty of Marine Technology, Chonnam National University, Chonnam, 550-749 Korea
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Hui M, Liu Y, Song C, Li Y, Shi G, Cui Z. Transcriptome changes in Eriocheir sinensis megalopae after desalination provide insights into osmoregulation and stress adaption in larvae. PLoS One 2014; 9:e114187. [PMID: 25470496 PMCID: PMC4254945 DOI: 10.1371/journal.pone.0114187] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 11/05/2014] [Indexed: 12/04/2022] Open
Abstract
Eriocheir sinensis, an extremely invasive alien crab species, has important economic value in China. It encounters different salinities during its life cycle, and at the megalopal stage it faces a turning point regarding the salinity in its environment. We applied RNA sequencing to E. sinensis megalopae before (MB) and after (MA) desalination, resulting in the discovery of 21,042 unigenes and 908 differentially expressed genes (DEGs, 4.32% of the unigenes). The DEGs primarily belonged to the Gene Ontology groups “Energy metabolism,” “Oxidoreductase activity,” “Translation,” “Transport,” “Metabolism,” and “Stress response.” In total, 33 DEGs related to transport processes were found, including 12 proton pump genes, three ATP-binding cassettes (ABCs), 13 solute carrier (SLC) family members, two sweet sugar transporter (ST) family members and three other substance transporters. Mitochondrial genes as well as genes involved in the tricarboxylic acid cycle, glycolytic pathway, or β-oxidation pathway, which can generate energy in the form of ATP, were typically up-regulated in MA. 11 unigenes related to amino acid metabolism and a large number of genes related to protein synthesis were differentially expressed in MB and MA, indicating that E. sinensis possibly adjusts its concentration of free amino acid osmolytes for hyper-osmoregulation. Additionally, 33 salinity and oxidative stress induced genes were found to be differentially expressed, such as the LEA2, HSPs, GST and coagulation factor genes. Notably, LEA2 is an extremely hydrophilic protein that responds to desiccation and reported for the first time in crabs. Therefore, we suppose that when the environment is hypo-osmotic, the megalopae might compensate for ion loss via hyper-osmoregulation by consuming more energy, accompanied by a series of stress induced adaptions. This study provides the first genome-wide transcriptome analysis of E. sinensis megalopae for studying its osmoregulation and stress adaption mechanisms.
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Affiliation(s)
- Min Hui
- EMBL, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Yuan Liu
- EMBL, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Chengwen Song
- EMBL, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yingdong Li
- EMBL, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Guohui Shi
- EMBL, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhaoxia Cui
- EMBL, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- National & Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao, 266071, China
- * E-mail:
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Nikapitiya C, Kim WS, Park K, Kwak IS. Identification of potential markers and sensitive tissues for low or high salinity stress in an intertidal mud crab (Macrophthalmus japonicus). FISH & SHELLFISH IMMUNOLOGY 2014; 41:407-416. [PMID: 25240977 DOI: 10.1016/j.fsi.2014.09.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 08/26/2014] [Accepted: 09/10/2014] [Indexed: 06/03/2023]
Abstract
Macrophthalmus japonicus is an intertidal mud crab is an ecologically important species in Korea, can tolerate a wide range of natural and anthropogenic stressors. Environmental changes especially salinity cause physiological stress to the marine habitats. Differential gene transcription of M. japonicus tissues provided information about tissue specific responses against salinity. Five potential genes were identified and their transcription levels were determined quantitatively comparison to seawater (SW: 31 ± 1 psu) in M. japonicus gills and hepatopancreas after exposed them to different salinities. Ecdysteroid receptor (Mj-EcR), trypsin (Mj-Tryp), arginine kinase (Mj-AK), lipopolysaccharide and β-1,3-glucan binding protein (Mj-LGBP) and peroxinectin (Mj-Prx) in hepatopancreas up-regulated against different salinities. In contrast, the gills, Mj-EcR, Mj-Tryp and Mj-AK showed late up-regulated responses to 40 psu compared to SW. All genes except Mj-LGBP showed up regulation in the gills as time dependent manner. These genes can be considered as potential markers to assess responses in salinity changes. This study suggests hepatopancreas is a suitable tissue for transcriptional, biochemical and physiological responses analysis on M. japonicus in low and high salinity stress.
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Affiliation(s)
- Chamilani Nikapitiya
- Department of Aqualife Medicine, Chonnam National University, Chonnam 550-749, Republic of Korea; Faculty of Marine Technology, Chonnam National University, Chonnam 550-749, Republic of Korea
| | - Won-Seok Kim
- Faculty of Marine Technology, Chonnam National University, Chonnam 550-749, Republic of Korea
| | - Kiyun Park
- Faculty of Marine Technology, Chonnam National University, Chonnam 550-749, Republic of Korea
| | - Ihn-Sil Kwak
- Faculty of Marine Technology, Chonnam National University, Chonnam 550-749, Republic of Korea.
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14
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Spicer JI. What can an ecophysiological approach tell us about the physiological responses of marine invertebrates to hypoxia? ACTA ACUST UNITED AC 2014; 217:46-56. [PMID: 24353203 DOI: 10.1242/jeb.090365] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Hypoxia (low O2) is a common and natural feature of many marine environments. However, human-induced hypoxia has been on the rise over the past half century and is now recognised as a major problem in the world's seas and oceans. Whilst we have information on how marine invertebrates respond physiologically to hypoxia in the laboratory, we still lack understanding of how they respond to such stress in the wild (now and in the future). Consequently, here the question 'what can an ecophysiological approach tell us about physiological responses of marine invertebrates to hypoxia' is addressed. How marine invertebrates work in the wild when challenged with hypoxia is explored using four case studies centred on different hypoxic environments. The recent integration of the various -omics into ecophysiology is discussed, and a number of advantages of, and challenges to, successful integration are suggested. The case studies and -omic/physiology integration data are used to inform the concluding part of the review, where it is suggested that physiological responses to hypoxia in the wild are not always the same as those predicted from laboratory experiments. This is due to behaviour in the wild modifying responses, and therefore more than one type of 'experimental' approach is essential to reliably determine the actual response. It is also suggested that assuming it is known what a measured response is 'for' can be misleading and that taking parodies of ecophysiology seriously may impede research progress. This review finishes with the suggestion that an -omics approach is, and is becoming, a powerful method of understanding the response of marine invertebrates to environmental hypoxia and may be an ideal way of studying hypoxic responses in the wild. Despite centring on physiological responses to hypoxia, the review hopefully serves as a contribution to the discussion of what (animal) ecophysiology looks like (or should look like) in the 21st century.
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Affiliation(s)
- John I Spicer
- Marine Biology and Ecology Research Centre, School of Marine Science and Engineering, Plymouth University, Drake Circus, Plymouth PL4 8AA, UK
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15
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High salinity induced expression profiling of differentially expressed genes in shrimp (Penaeus monodon). Mol Biol Rep 2014; 41:6275-89. [DOI: 10.1007/s11033-014-3510-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Accepted: 06/19/2014] [Indexed: 10/25/2022]
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16
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Feng F, Chen L, Lian C, Xia H, Zhou Y, Yao Q, Chen K. Comparative proteomic analysis reveals the suppressive effects of dietary high glucose on the midgut growth of silkworm. J Proteomics 2014; 108:124-32. [PMID: 24878427 DOI: 10.1016/j.jprot.2014.05.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2014] [Revised: 05/16/2014] [Accepted: 05/18/2014] [Indexed: 10/25/2022]
Abstract
UNLABELLED The silkworm, Bombyx mori, is an important model of lepidoptera insect, and it has been used for several models of human diseases. In human being, long-term high-sugar diet can induce the occurrence of diabetes and other related diseases. Interestingly, our experiments revealed the high glucose diet also has a suppressive effect on the development of silkworms. To investigate the molecular mechanism by which high-glucose diet inhibited the midgut growth in silkworms, we employed comparative proteomic analysis to globally identify proteins differentially expressed in normal and high-glucose diet group silkworms. In all, 28 differently proteins were suppressed and 5 proteins induced in high-glucose diet group. Gene ontology analysis showed that most of these differently proteins are mainly involved in metabolic process, catalytic and cellular process. A development related protein, imaginal disk growth factor (IDGF), was further confirmed by western blot exclusively expressing in the normal diet group silkworms. Taken together, our data suggests that IDGF plays a critical role in impairing the development of silkworms by a high-glucose diet. BIOLOGICAL SIGNIFICANCE Glucose has been thought to play essential roles in growth and development of silkworm. In this paper, we certified firstly that high-glucose diet can suppress the growth of silkworm, and comparative proteomic was employed to reveal the inhibition mechanism. Moreover, an important regulation related protein (IDGF) was found to involve in this inhibition process. These results will help us get a deeper understanding of the relationship between diet and healthy. Furthermore, IDGF may be the critical protein for reducing the blood sugar in silkworm, and it may be used for screening human hypoglycemic drug. The work has not been submitted elsewhere for publication, in whole or in part, and all the authors have approved the manuscript.
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Affiliation(s)
- Fan Feng
- School of Food and Biological Engineering, Jiangsu University, 301# Xuefu Road, Zhenjiang, Jiangsu Province 212013, PR China; Institute of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang, Jiangsu Province 212013, PR China
| | - Liang Chen
- Institute of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang, Jiangsu Province 212013, PR China
| | - Chaoqun Lian
- School of Food and Biological Engineering, Jiangsu University, 301# Xuefu Road, Zhenjiang, Jiangsu Province 212013, PR China
| | - Hengchuan Xia
- Institute of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang, Jiangsu Province 212013, PR China
| | - Yang Zhou
- Institute of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang, Jiangsu Province 212013, PR China
| | - Qin Yao
- Institute of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang, Jiangsu Province 212013, PR China
| | - Keping Chen
- School of Food and Biological Engineering, Jiangsu University, 301# Xuefu Road, Zhenjiang, Jiangsu Province 212013, PR China; Institute of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang, Jiangsu Province 212013, PR China.
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17
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Kniffin CD, Burnett LE, Burnett KG. Recovery from hypoxia and hypercapnic hypoxia: impacts on the transcription of key antioxidants in the shrimp Litopenaeus vannamei. Comp Biochem Physiol B Biochem Mol Biol 2014; 170:43-9. [PMID: 24509063 DOI: 10.1016/j.cbpb.2014.01.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Revised: 01/27/2014] [Accepted: 01/29/2014] [Indexed: 10/25/2022]
Abstract
Estuarine waters are prone to regular bouts of low oxygen (hypoxia) and high carbon dioxide (hypercapnia). In vertebrates, tissue hypoxia followed by reoxygenation can generate high levels of reactive oxygen species (ROS) that exceed cellular antioxidant capacity, leading to tissue damage. Here we quantified the expression of several antioxidant genes in the hepatopancreas of Pacific whiteleg shrimp, Litopenaeus vannamei, after exposure to hypoxia or hypercapnic hypoxia for 4h or 24h followed by recovery in air-saturated water (normoxia) for 0, 1, 6 or 24h, as compared to time-matched controls maintained only in normoxia. Transcripts of cytoplasmic Mn-superoxide dismutase (cMnSOD), glutathione peroxidase (GPX) and peptide-methionine (R)-S-oxide reductase (MsrB) increased after 4h exposure to either hypoxia or hypercapnic hypoxia; these elevated transcript levels persisted longer in animals recovering from hypercapnic hypoxia than hypoxia alone. cMnSOD transcripts generally increased, but GPX, MsrB, glutathione-S-transferase (GST), and thioredoxin 1 (TRX-1) decreased or did not change in most long-term (24h) treatment-recovery groups. Thus, the transcriptional responses of several antioxidant genes during recovery from tidally-driven hypoxia and hypercapnic hypoxia decrease or are muted by more persistent exposure to these conditions, leaving L. vannamei potentially vulnerable to ROS damage during recovery.
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Affiliation(s)
- Casey D Kniffin
- Grice Marine Laboratory, College of Charleston, 205 Fort Johnson, Charleston, SC 29412, USA; Hollings Marine Laboratory, 331 Fort Johnson, Charleston, SC 29412, USA
| | - Louis E Burnett
- Grice Marine Laboratory, College of Charleston, 205 Fort Johnson, Charleston, SC 29412, USA; Hollings Marine Laboratory, 331 Fort Johnson, Charleston, SC 29412, USA
| | - Karen G Burnett
- Grice Marine Laboratory, College of Charleston, 205 Fort Johnson, Charleston, SC 29412, USA; Hollings Marine Laboratory, 331 Fort Johnson, Charleston, SC 29412, USA.
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Constant diurnal temperature regime alters the impact of simulated climate warming on a tropical pseudoscorpion. Sci Rep 2014; 4:3706. [PMID: 24424082 PMCID: PMC3892181 DOI: 10.1038/srep03706] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Accepted: 11/13/2013] [Indexed: 12/31/2022] Open
Abstract
Recent theory suggests that global warming may be catastrophic for tropical ectotherms. Although most studies addressing temperature effects in ectotherms utilize constant temperatures, Jensen's inequality and thermal stress considerations predict that this approach will underestimate warming effects on species experiencing daily temperature fluctuations in nature. Here, we tested this prediction in a neotropical pseudoscorpion. Nymphs were reared in control and high-temperature treatments under a constant daily temperature regime, and results compared to a companion fluctuating-temperature study. At constant temperature, pseudoscorpions outperformed their fluctuating-temperature counterparts. Individuals were larger, developed faster, and males produced more sperm, and females more embryos. The greatest impact of temperature regime involved short-term, adult exposure, with constant temperature mitigating high-temperature effects on reproductive traits. Our findings demonstrate the importance of realistic temperature regimes in climate warming studies, and suggest that exploitation of microhabitats that dampen temperature oscillations may be critical in avoiding extinction as tropical climates warm.
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Shekhar MS, Kiruthika J, Ponniah AG. Identification and expression analysis of differentially expressed genes from shrimp (Penaeus monodon) in response to low salinity stress. FISH & SHELLFISH IMMUNOLOGY 2013; 35:1957-1968. [PMID: 24436977 DOI: 10.1016/j.fsi.2013.09.038] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Four suppression subtractive hybridization (SSH) cDNA libraries were constructed to identify differentially expressed salinity stress responsive genes of black tiger shrimp, Penaeus monodon exposed to low (3 ppt) salinity conditions. Forward and reverse SSH cDNA libraries were developed from the gill and gut tissues of shrimp and clones having inserts larger than 300 bp were unidirectionally sequenced. Based on the sequence homology search, the identified genes were categorized for their putative functions related to a wide range of biological roles, such as nucleic acid regulation and replication, immune response, energy and metabolism, cell signaling, cellular process, cytoskeleton and membrane structure, stress and osmoregulation. Gene expression levels in response to low salinity conditions at 2 weeks post salinity stress of thirteen selected differentially expressed genes identified from SSH cDNA libraries (14-3-3 like protein, crust in, lysozyme, arginine kinase, Naþ/Kþ-ATPase a-subunit, intracellular fatty acid binding protein, cathepsin B, anti-lipopolysaccharide factor, ferritin, ubiquitin conjugating enzyme E2, calreticulin, innexin 2 and heat shock protein 21) were analyzed by RT-PCR. The highest gene expression levels were observed for Naþ/Kþ-ATPase a-subunit (34.28-folds) in gill tissues, intracellular fatty acid binding protein (13.30-folds) in gut tissues and innexin 2 (14.43-folds) in muscle tissues respectively. The differential and significant levels of gene expression indicate the functional role of these genes in shrimp salinity stress adaptive mechanisms.
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20
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Sakaew W, Pratoomthai B, Pongtippatee P, Flegel TW, Withyachumnarnkul B. Discovery and partial characterization of a non-LTR retrotransposon that may be associated with abdominal segment deformity disease (ASDD) in the whiteleg shrimp Penaeus (Litopenaeus) vannamei. BMC Vet Res 2013; 9:189. [PMID: 24074037 PMCID: PMC3849965 DOI: 10.1186/1746-6148-9-189] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Accepted: 09/25/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Abdominal segment deformity disease (ASDD) of cultivated whiteleg shrimp Penaeus (Litopenaeus) vannamei causes economic loss of approximately 10% in affected specimens because of the unsightliness of distorted abdominal muscles. It is associated with the presence of viral-like particles seen by electron microscopy in the ventral nerve cords of affected shrimp. Thus, shotgun cloning was carried out to seek viral-like sequences in affected shrimp. RESULTS A new retrovirus-like element of 5052 bp (named abdominal segment deformity element or ASDE) was compiled by shotgun cloning and 3' and 5' RACE using RNA and DNA extracted from ventral nerve cords of ASDD shrimp. ASDE contained 7 putative open reading frames (ORF). One ORF (called the PENS sub-domain), had a deduced amino acid (aa) sequence homologous to the GIY-YIG endonuclease domain of penelope-like retrotransposons while two others were homologous to the reverse transcriptase (RT) and RNaseH domains of the pol gene of non-long terminal repeat (non-LTR) retrotransposons (called the NLRS sub-domain). No single amplicon of 5 kb containing both these elements was obtained by PCR or RT-PCR from ASDD shrimp. Subsequent analysis indicated that PENS and NLRS were not contiguous and that NLRS was a host genetic element. In situ hybridization using a dioxygenin-labeled NLRS probe revealed that NLRS gave positive reactions in abdominal-ganglion neurons of ASDD shrimp but not normal shrimp. Preliminary analysis indicated that long-term use of female broodstock after eyestalk ablation in the hatchery increased the intensity of RT-PCR amplicons for NLRS and also the prevalence of ASDD in mysis 3 offspring of the broodstock. The deformities persist upon further cultivation until shrimp harvest but do not increase in prevalence and do not affect growth or survival. CONCLUSIONS Our results suggested that NLRS is a shrimp genetic element associated with ASDD and that immediate preventative measures could include shorter-term use of broodstock after eyestalk ablation and/or discard of broodstock that give strong RT-PCR reactions for NLRS. In the longer term, it is recommended, if possible, that currently used, domesticated shrimp lines be selected for freedom from NLRS. The molecular tools developed in this work will facilitate the management and further study of ASDD.
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Affiliation(s)
- Waraporn Sakaew
- Department of Anatomy, Faculty of Science, Mahidol University, Bangkok 10400, Thailand.
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21
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Rathburn CK, Sharp NJ, Ryan JC, Neely MG, Cook M, Chapman RW, Burnett LE, Burnett KG. Transcriptomic responses of juvenile Pacific whiteleg shrimp, Litopenaeus vannamei, to hypoxia and hypercapnic hypoxia. Physiol Genomics 2013; 45:794-807. [DOI: 10.1152/physiolgenomics.00043.2013] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Estuarine crustaceans are often exposed to low dissolved O2 (hypoxia) accompanied by elevated CO2 (hypercapnia), which lowers water pH. Acclimatory responses to hypoxia have been widely characterized; responses to hypercapnia in combination with hypoxia (hypercapnic hypoxia) are less well known. Here we used oligonucleotide microarrays to characterize changes in global gene expression in the hepatopancreas of Pacific whiteleg shrimp, Litopenaeus vannamei, exposed to hypoxia or hypercapnic hypoxia for 4 or 24 h, compared with time-matched animals held in air-saturated water (normoxia). Unigenes whose expressions were significantly impacted by treatment and/or time were used to build artificial neural networks (ANNs) to identify genes with the greatest sensitivity in pairwise discriminations between treatments at each time point and between times for each treatment. ANN gene sets that discriminated hypoxia or hypercapnic hypoxia from normoxia shared functions of translation, mitochondrial energetics, and cellular defense. GO terms protein modification/phosphorylation/cellular protein metabolism and RNA processing/apoptosis/cell cycling occurred at highest frequency in discriminating hypercapnic hypoxia from hypoxia at 4 and 24 h, respectively. For 75.4% of the annotated ANN genes, exposure to hypercapnic hypoxia for 24 h reduced or reversed the transcriptional response to hypoxia alone. These results suggest that high CO2/low pH may interfere with transcriptionally based acclimation to hypoxia or elicit physiological or biochemical responses that relieve internal hypoxia. Whether these data reflect resilience or sensitivity of L. vannamei in the face of expanding hypoxic zones and rising levels of atmospheric CO2 may be important to understanding the survival of this and other estuarine species.
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Affiliation(s)
- Charles K. Rathburn
- Grice Marine Laboratory, College of Charleston, Charleston, South Carolina
- Center of Excellence in Oceans and Human Health, Hollings Marine Laboratory, Charleston, South Carolina
| | - Natasha J. Sharp
- Grice Marine Laboratory, College of Charleston, Charleston, South Carolina
- Center of Excellence in Oceans and Human Health, Hollings Marine Laboratory, Charleston, South Carolina
| | - James C. Ryan
- Center of Excellence in Oceans and Human Health, Hollings Marine Laboratory, Charleston, South Carolina
| | - Marion G. Neely
- Center of Excellence in Oceans and Human Health, Hollings Marine Laboratory, Charleston, South Carolina
- National Ocean Service, National Oceanic and Atmospheric Administration Hollings Marine Laboratory, Charleston, South Carolina; and
| | - Matthew Cook
- Grice Marine Laboratory, College of Charleston, Charleston, South Carolina
| | - Robert W. Chapman
- Center of Excellence in Oceans and Human Health, Hollings Marine Laboratory, Charleston, South Carolina
- Marine Resources Research Institute, South Carolina Department of Natural Resources, Charleston, South Carolina
| | - Louis E. Burnett
- Grice Marine Laboratory, College of Charleston, Charleston, South Carolina
- Center of Excellence in Oceans and Human Health, Hollings Marine Laboratory, Charleston, South Carolina
| | - Karen G. Burnett
- Grice Marine Laboratory, College of Charleston, Charleston, South Carolina
- Center of Excellence in Oceans and Human Health, Hollings Marine Laboratory, Charleston, South Carolina
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22
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Madeira D, Narciso L, Cabral HN, Diniz MS, Vinagre C. Thermal tolerance of the crab Pachygrapsus marmoratus: intraspecific differences at a physiological (CTMax) and molecular level (Hsp70). Cell Stress Chaperones 2012; 17:707-16. [PMID: 22619030 PMCID: PMC3468680 DOI: 10.1007/s12192-012-0345-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Revised: 05/02/2012] [Accepted: 05/04/2012] [Indexed: 10/28/2022] Open
Abstract
Temperature is one of the most important variables influencing organisms, especially in the intertidal zone. This work aimed to test physiological and molecular intraspecific differences in thermal tolerance of the crab Pachygrapsus marmoratus (Fabricius, 1787). The comparisons made focused on sex, size, and habitat (estuary and coast) differences. The physiological parameter was upper thermal limit, tested via the critical thermal maximum (CTMax) and the molecular parameter was total heat shock protein 70 (Hsp70 and Hsp70 plus Hsc70) production, quantified via an enzyme-linked imunosorbent assay. Results showed that CTMax values and Hsp70 production are higher in females probably due to different microhabitat use and potentially due to different hormonal regulation in males and females. Among females, non-reproducing ones showed a higher CTMax value, but no differences were found in Hsp70, even though reproducing females showed higher variability in Hsp70 amounts. As reproduction takes up a lot of energy, its allocation for other activities, including stress responses, is lower. Juveniles also showed higher CTMax and Hsp70 expression because they occur in greater shore heights and ageing leads to alterations in protein synthesis. Comparing estuarine and coastal crabs, no differences were found in CTMax but coastal crabs produce more Hsp70 than estuarine crabs because they occur in drier and hotter areas than estuarine ones, which occur in moister environments. This work shows the importance of addressing intraspecific differences in the stress response at different organizational levels. This study shows that these differences are key factors in stress research, climate research, and environmental monitoring.
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Affiliation(s)
- D Madeira
- Centro de Oceanografia, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisbon, Portugal.
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23
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Hardy KM, Follett CR, Burnett LE, Lema SC. Gene transcripts encoding hypoxia-inducible factor (HIF) exhibit tissue- and muscle fiber type-dependent responses to hypoxia and hypercapnic hypoxia in the Atlantic blue crab, Callinectes sapidus. Comp Biochem Physiol A Mol Integr Physiol 2012; 163:137-46. [DOI: 10.1016/j.cbpa.2012.05.195] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Revised: 05/19/2012] [Accepted: 05/21/2012] [Indexed: 11/28/2022]
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Veldhoen N, Ikonomou MG, Helbing CC. Molecular profiling of marine fauna: integration of omics with environmental assessment of the world's oceans. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2012; 76:23-38. [PMID: 22036265 DOI: 10.1016/j.ecoenv.2011.10.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Revised: 09/16/2011] [Accepted: 10/06/2011] [Indexed: 05/31/2023]
Abstract
Many species that contribute to the commercial and ecological richness of our marine ecosystems are harbingers of environmental change. The ability of organisms to rapidly detect and respond to changes in the surrounding environment represents the foundation for application of molecular profiling technologies towards marine sentinel species in an attempt to identify signature profiles that may reside within the transcriptome, proteome, or metabolome and that are indicative of a particular environmental exposure event. The current review highlights recent examples of the biological information obtained for marine sentinel teleosts, mammals, and invertebrates. While in its infancy, such basal information can provide a systems biology framework in the detection and evaluation of environmental chemical contaminant effects on marine fauna. Repeated evaluation across different seasons and local marine environs will lead to discrimination between signature profiles representing normal variation within the complex milieu of environmental factors that trigger biological response in a given sentinel species and permit a greater understanding of normal versus anthropogenic-associated modulation of biological pathways, which prove detrimental to marine fauna. It is anticipated that incorporation of contaminant-specific molecular signatures into current risk assessment paradigms will lead to enhanced wildlife management strategies that minimize the impacts of our industrialized society on marine ecosystems.
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Affiliation(s)
- Nik Veldhoen
- Department of Biochemistry and Microbiology, University of Victoria, P.O. Box 3055 Stn CSC, Victoria, B.C., Canada
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25
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Aoki T, Wang HC, Unajak S, Santos MD, Kondo H, Hirono I. Microarray analyses of shrimp immune responses. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2011; 13:629-638. [PMID: 20393773 DOI: 10.1007/s10126-010-9291-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2010] [Accepted: 03/16/2010] [Indexed: 05/29/2023]
Abstract
Shrimp aquaculture is one of the major foodproducing industries in the world. However, it is being impacted by several problems including diseases, antibiotic use, and environmental factors. The extent of the effects of these problems in the immune system of the shrimp at the molecular level is just beginning to be understood. Here, we review the gene expression profile of shrimp in response to some of these problems using the high-throughput microarray analysis, including white spot syndrome virus, yellow head virus, Vibrio spp., peptidoglycan, oxytetracycline, oxolinic acid, salinity, and temperature.
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Affiliation(s)
- Takashi Aoki
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Konan 4-5-7 Minato, Tokyo 108-8477, Japan.
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Flegel TW, Sritunyalucksana K. Shrimp molecular responses to viral pathogens. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2011; 13:587-607. [PMID: 20393775 DOI: 10.1007/s10126-010-9287-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2010] [Accepted: 03/10/2010] [Indexed: 05/29/2023]
Abstract
From almost negligible amounts in 1970, the quantity of cultivated shrimp (~3 million metric tons in 2007) has risen to approach that of the capture fishery and it constitutes a vital source of export income for many countries. Despite this success, viral diseases along the way have caused billions of dollars of losses for shrimp farmers. Desire to reduce the losses to white spot syndrome virus in particular, has stimulated much research since 2000 on the shrimp response to viral pathogens at the molecular level. The objective of the work is to develop novel, practical methods for improved disease control. This review covers the background and limitations of the current work, baseline studies and studies on humoral responses, on binding between shrimp and viral structural proteins and on intracellular responses. It also includes discussion of several important phenomena (i.e., the quasi immune response, viral co-infections, viral sequences in the shrimp genome and persistent viral infections) for which little or no molecular information is currently available, but is much needed.
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Affiliation(s)
- T W Flegel
- National Science and Technology Development Agency (NSTDA), Klong Luang, Pathumthani 12120, Thailand.
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27
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Towle DW, Henry RP, Terwilliger NB. Microarray-detected changes in gene expression in gills of green crabs (Carcinus maenas) upon dilution of environmental salinity. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2011; 6:115-25. [DOI: 10.1016/j.cbd.2010.11.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2010] [Revised: 11/04/2010] [Accepted: 11/10/2010] [Indexed: 10/18/2022]
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28
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Ellis RP, Parry H, Spicer JI, Hutchinson TH, Pipe RK, Widdicombe S. Immunological function in marine invertebrates: responses to environmental perturbation. FISH & SHELLFISH IMMUNOLOGY 2011; 30:1209-1222. [PMID: 21463691 DOI: 10.1016/j.fsi.2011.03.017] [Citation(s) in RCA: 122] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2011] [Revised: 03/20/2011] [Accepted: 03/27/2011] [Indexed: 05/30/2023]
Abstract
The inception of ecological immunology has led to an increase in the number of studies investigating the impact of environmental stressors on host immune defence mechanisms. This in turn has led to an increased understanding of the importance of invertebrate groups for immunological research. This review discusses the advances made within marine invertebrate ecological immunology over the past decade. By demonstrating the environmental stressors tested, the immune parameters typically investigated, and the species that have received the greatest level of investigation, this review provides a critical assessment of the field of marine invertebrate ecological immunology. In highlighting the methodologies employed within this field, our current inability to understand the true ecological significance of any immune dysfunction caused by environmental stressors is outlined. Additionally, a number of examples are provided in which studies successfully demonstrate a measure of immunocompetence through alterations in disease resistance and organism survival to a realized pathogenic threat. Consequently, this review highlights the potential to advance our current understanding of the ecological and evolutionary significance of environmental stressor related immune dysfunction. Furthermore, the potential for the advancement of our understanding of the immune system of marine invertebrates, through the incorporation of newly emerging and novel molecular techniques, is emphasized.
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Affiliation(s)
- R P Ellis
- Plymouth Marine Laboratory, Prospect Place, West Hoe, Plymouth, Devon PL1 3DH, UK.
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Fosmid library end sequencing reveals a rarely known genome structure of marine shrimp Penaeus monodon. BMC Genomics 2011; 12:242. [PMID: 21575266 PMCID: PMC3124438 DOI: 10.1186/1471-2164-12-242] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2011] [Accepted: 05/17/2011] [Indexed: 11/28/2022] Open
Abstract
Background The black tiger shrimp (Penaeus monodon) is one of the most important aquaculture species in the world, representing the crustacean lineage which possesses the greatest species diversity among marine invertebrates. Yet, we barely know anything about their genomic structure. To understand the organization and evolution of the P. monodon genome, a fosmid library consisting of 288,000 colonies and was constructed, equivalent to 5.3-fold coverage of the 2.17 Gb genome. Approximately 11.1 Mb of fosmid end sequences (FESs) from 20,926 non-redundant reads representing 0.45% of the P. monodon genome were obtained for repetitive and protein-coding sequence analyses. Results We found that microsatellite sequences were highly abundant in the P. monodon genome, comprising 8.3% of the total length. The density and the average length of microsatellites were evidently higher in comparison to those of other taxa. AT-rich microsatellite motifs, especially poly (AT) and poly (AAT), were the most abundant. High abundance of microsatellite sequences were also found in the transcribed regions. Furthermore, via self-BlastN analysis we identified 103 novel repetitive element families which were categorized into four groups, i.e., 33 WSSV-like repeats, 14 retrotransposons, 5 gene-like repeats, and 51 unannotated repeats. Overall, various types of repeats comprise 51.18% of the P. monodon genome in length. Approximately 7.4% of the FESs contained protein-coding sequences, and the Inhibitor of Apoptosis Protein (IAP) gene and the Innexin 3 gene homologues appear to be present in high abundance in the P. monodon genome. Conclusions The redundancy of various repeat types in the P. monodon genome illustrates its highly repetitive nature. In particular, long and dense microsatellite sequences as well as abundant WSSV-like sequences highlight the uniqueness of genome organization of penaeid shrimp from those of other taxa. These results provide substantial improvement to our current knowledge not only for shrimp but also for marine crustaceans of large genome size.
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Ren Q, Zhou J, Sun SS, Kang CJ, Zhao XF, Wang JX. Molecular cloning and expression pattern analysis of two novel disulfide isomerases in shrimp. Comp Biochem Physiol C Toxicol Pharmacol 2011; 153:301-9. [PMID: 21130898 DOI: 10.1016/j.cbpc.2010.11.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2010] [Revised: 11/26/2010] [Accepted: 11/28/2010] [Indexed: 01/14/2023]
Abstract
Protein disulfide isomerase (PDI) catalyzes formation and isomerization of disulfide bridges and has chaperone activity. Currently, increasing evidence suggests the significance of PDI in immune and stress responses. To clarify the role of PDIs in the innate immunity of shrimp, two PDI genes were isolated and identified from Fenneropenaeus chinensis (fleshy prawn). FcPDI1 is 1878bp in length and encodes a protein of 383 amino acids. It has 18-amino acid signal peptide, 3 thioredoxin domains with 3 active sites of CGHC, and KEDL retention signal at its C-end. FcPDI1 is an atypical PDI. The open reading frame of FcPDI2 encodes a 497-amino acid protein and shows the classical domain organization a-b-b'-a'. Phylogenic analysis and multiple alignments show that FcPDI1 is similar to PDI that contains 3 thioredoxin domains from other species including invertebrates and vertebrates. FcPDI2, LvPDI, and insect PDIs are grouped into one cluster and are similar to PDIs having a-b-b'-a' domain organization. Tissue distribution shows that FcPDI1 and FcPDI2 were expressed in all detected tissues at the mRNA level. Changes in FcPDI1 and FcPDI2 expression at the mRNA level in hemocytes, hepatopancreas, gills, and ovaries upon Vibrio or white spot syndrome virus challenge were also analyzed. The results suggest that FcPDI1 and FcPDI2 might have roles in the innate immunity of shrimp. FcPDI1 was also successfully expressed in Escherichia coli and the recombinant FcPDI1 showed insulin reductase activity. Results show that FcPDI might play an important role in the innate immunity of shrimp.
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Affiliation(s)
- Qian Ren
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Shandong University, Jinan, Shandong 250100, China
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Martinez-Cruz O, Garcia-Carreño F, Robles-Romo A, Varela-Romero A, Muhlia-Almazan A. Catalytic subunits atpα and atpβ from the Pacific white shrimp Litopenaeus vannamei F(O)F (1) ATP-synthase complex: cDNA sequences, phylogenies, and mRNA quantification during hypoxia. J Bioenerg Biomembr 2011; 43:119-33. [PMID: 21384180 DOI: 10.1007/s10863-011-9340-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2010] [Accepted: 12/08/2010] [Indexed: 01/13/2023]
Abstract
In the mitochondrial F(O)F(1) ATP-synthase/ATPase complex, subunits α and β are part of the extrinsic portion that catalyses ATP synthesis. Since there are no reports about genes and proteins from these subunits in crustaceans, we analyzed the cDNA sequences of both subunits in the whiteleg shrimp Litopenaeus vannamei and their phylogenetic relationships. We also investigated the effect of hypoxia on shrimp by measuring changes in the mRNA amounts of atpα and atpβ. Our results confirmed highly conserved regions for both subunits and underlined unique features among others. The ATPβ deduced protein of shrimp was less conserved in size and sequence than ATPα. The relative mRNA amounts of atpα and atpβ changed in shrimp pleopods; hypoxia at 1.5 mg/L caused an increase in atpβ transcripts and a subsequent decrease when shrimp were re-oxygenated. Results confirm that changes in the mRNAs of the ATP-synthase subunits are part of the mechanisms allowing shrimp to deal with the metabolic adjustment displayed to tolerate hypoxia.
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Affiliation(s)
- Oliviert Martinez-Cruz
- Molecular Biology Laboratory, Centro de Investigacion en Alimentacion y Desarrollo (CIAD), Hermosillo, Sonora, Mexico
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Immune responses and expression of immune-related genes in swimming crab Portunus trituberculatus exposed to elevated ambient ammonia-N stress. Comp Biochem Physiol A Mol Integr Physiol 2010; 157:246-51. [DOI: 10.1016/j.cbpa.2010.07.013] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2010] [Revised: 07/04/2010] [Accepted: 07/04/2010] [Indexed: 11/19/2022]
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Gorr T, Wichmann D, Hu J, Hermes‐Lima M, Welker A, Terwilliger N, Wren J, Viney M, Morris S, Nilsson G, Deten A, Soliz J, Gassmann M. Hypoxia Tolerance in Animals: Biology and Application. Physiol Biochem Zool 2010; 83:733-52. [DOI: 10.1086/648581] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Wilkins AS. The enemy within: an epigenetic role of retrotransposons in cancer initiation. Bioessays 2010; 32:856-65. [PMID: 20715060 DOI: 10.1002/bies.201000008] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This article proposes that cancers can be initiated by retrotransposon (RTN) activation through changes in the transcriptional regulation of nearby genes. I first detail the hypothesis and then discuss the nature of physiological stress(es) in RTN activation; the role of DNA demethylation in the initiation and propagation of new RTN states; the connection between ageing and cancer incidence and the involvement of activated RTNs in the chromosomal aberrations that feature in cancer progression. The hypothesis neither replaces nor invalidates other theories of cancer, in particular the somatic mutation theory, but helps clarify and unify much of the hitherto poorly integrated, complex phenomenology of cancer.
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Somboonwiwat K, Chaikeeratisak V, Wang HC, Fang Lo C, Tassanakajon A. Proteomic analysis of differentially expressed proteins in Penaeus monodon hemocytes after Vibrio harveyi infection. Proteome Sci 2010; 8:39. [PMID: 20626881 PMCID: PMC2915975 DOI: 10.1186/1477-5956-8-39] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2010] [Accepted: 07/13/2010] [Indexed: 01/24/2023] Open
Abstract
Background Viral and bacterial diseases can cause mass mortalities in commercial shrimp aquaculture. In contrast to studies on the antiviral response, the responses of shrimps to bacterial infections by high throughput techniques have been reported only at the transcriptional level and not at the translational level. In this study, a proteomic analysis of shrimp hemocytes to identify differentially expressed proteins in response to a luminous bacterium Vibrio harveyi was evaluated for its feasibility and is reported for the first time. Results The two-dimensional gel electrophoresis (2-DE) patterns of the hemocyte proteins from the unchallenged and V. harveyi challenged shrimp, Penaeus monodon, at 24 and 48 h post infection were compared. From this, 27 differentially expressed protein spots, and a further 12 weakly to non-differentially regulated control spots, were selected for further analyses by the LC-ESI-MS/MS. The 21 differentially expressed proteins that could be identified by homologous annotation were comprised of proteins that are directly involved in the host defense responses, such as hemocyanin, prophenoloxidase, serine proteinase-like protein, heat shock protein 90 and alpha-2-macroglobulin, and those involved in signal transduction, such as the14-3-3 protein epsilon and calmodulin. Western blot analysis confirmed the up-regulation of hemocyanin expression upon bacterial infection. The expression of the selected proteins which were the representatives of the down-regulated proteins (the 14-3-3 protein epsilon and alpha-2-macroglobulin) and of the up-regulated proteins (hemocyanin) was further assessed at the transcription level using real-time RT-PCR. Conclusions This work suggests the usefulness of a proteomic approach to the study of shrimp immunity and revealed hemocyte proteins whose expression were up regulated upon V. harveyi infection such as hemocyanin, arginine kinase and down regulated such as alpha-2-macroglobulin, calmodulin and 14-3-3 protein epsilon. The information is useful for understanding the immune system of shrimp against pathogenic bacteria.
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Affiliation(s)
- Kunlaya Somboonwiwat
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand.
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Knapen D, Vergauwen L, Laukens K, Blust R. Best practices for hybridization design in two-colour microarray analysis. Trends Biotechnol 2009; 27:406-14. [DOI: 10.1016/j.tibtech.2009.03.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2009] [Revised: 03/24/2009] [Accepted: 03/25/2009] [Indexed: 10/20/2022]
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Zeh DW, Zeh JA, Ishida Y. Transposable elements and an epigenetic basis for punctuated equilibria. Bioessays 2009; 31:715-26. [DOI: 10.1002/bies.200900026] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Piednoël M, Bonnivard E. DIRS1-like retrotransposons are widely distributed among Decapoda and are particularly present in hydrothermal vent organisms. BMC Evol Biol 2009; 9:86. [PMID: 19400949 PMCID: PMC2685390 DOI: 10.1186/1471-2148-9-86] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2008] [Accepted: 04/28/2009] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Transposable elements are major constituents of eukaryote genomes and have a great impact on genome structure and stability. Considering their mutational abilities, TEs can contribute to the genetic diversity and evolution of organisms. Knowledge of their distribution among several genomes is an essential condition to study their dynamics and to better understand their role in species evolution. DIRS1-like retrotransposons are a particular group of retrotransposons according to their mode of transposition that implies a tyrosine recombinase. To date, they have been described in a restricted number of species in comparison with the LTR retrotransposons. In this paper, we determine the distribution of DIRS1-like elements among 25 decapod species, 10 of them living in hydrothermal vents that correspond to particularly unstable environments. RESULTS Using PCR approaches, we have identified 15 new DIRS1-like families in 15 diverse decapod species (shrimps, lobsters, crabs and galatheid crabs). Hydrothermal organisms show a particularly great diversity of DIRS1-like elements with 5 families characterized among Alvinocarididae shrimps and 3 in the galatheid crab Munidopsis recta. Phylogenic analyses show that these elements are divergent toward the DIRS1-like families previously described in other crustaceans and arthropods and form a new clade called AlDIRS1. At larger scale, the distribution of DIRS1-like retrotransposons appears more or less patchy depending on the taxa considered. Indeed, a scattered distribution can be observed in the infraorder Brachyura whereas all the species tested in infraorders Caridea and Astacidea harbor some DIRS1-like elements. CONCLUSION Our results lead to nearly double both the number of DIRS1-like elements described to date, and the number of species known to harbor these ones. In this study, we provide the first degenerate primers designed to look specifically for DIRS1-like retrotransposons. They allowed for revealing for the first time a widespread distribution of these elements among a large phylum, here the order Decapoda. They also suggest some peculiar features of these retrotransposons in hydrothermal organisms where a great diversity of elements is already observed. Finally, this paper constitutes the first essential step which allows for considering further studies based on the dynamics of the DIRS1-like retrotransposons among several genomes.
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Affiliation(s)
- Mathieu Piednoël
- UMR 7138 Systématique Adaptation Evolution, Equipe Génétique et Evolution, Université Pierre et Marie Curie Paris 6, Case 5, Bâtiment A, porte 427, 7 quai St Bernard, 75252 Paris Cedex 05, France
| | - Eric Bonnivard
- UMR 7138 Systématique Adaptation Evolution, Equipe Génétique et Evolution, Université Pierre et Marie Curie Paris 6, Case 5, Bâtiment A, porte 427, 7 quai St Bernard, 75252 Paris Cedex 05, France
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Robalino J, Carnegie RB, O'Leary N, Ouvry-Patat SA, de la Vega E, Prior S, Gross PS, Browdy CL, Chapman RW, Schey KL, Warr G. Contributions of functional genomics and proteomics to the study of immune responses in the Pacific white leg shrimp Litopenaeus vannamei. Vet Immunol Immunopathol 2008; 128:110-8. [PMID: 19070907 DOI: 10.1016/j.vetimm.2008.10.329] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The need for better control of infectious diseases in shrimp aquaculture and the ecological importance of crustacea in marine ecosystems have prompted interest in the study of crustacean immune systems, particularly those of shrimp. As shrimp and other crustacea are poorly understood from the immunological point of view, functional genomic and proteomic approaches have been applied as a means of quickly obtaining molecular information regarding immune responses in these organisms. In this article, a series of results derived from transcriptomic and proteomic studies in shrimp (Litopenaeus vannamei) are discussed. Expressed Sequence Tag analysis, differential expression cloning through Suppression Subtractive Hybridization, expression profiling using microarrays, and proteomic studies using mass spectrometry, have provided a wealth of useful data and opportunities for new avenues of research. Examples of new research directions arising from these studies in shrimp include the molecular diversity of antimicrobial effectors, the role of double stranded RNA as an inducer of antiviral immunity, and the possible overlap between antibacterial and antiviral responses in the shrimp.
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Affiliation(s)
- Javier Robalino
- Marine Biomedicine and Environmental Sciences Center, Medical University of South Carolina, Hollings Marine Laboratory, United States
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Hizer SE, Tamulis WG, Robertson LM, Garcia DK. Evidence of multiple retrotransposons in two litopenaeid species. Anim Genet 2008; 39:363-73. [PMID: 18557973 DOI: 10.1111/j.1365-2052.2008.01739.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Retrotransposons encompass a specific class of mobile genetic elements that are widespread across eukaryotic genomes. The impact of the varied types of retrotransposons on these genomes is just beginning to be deciphered. In a step towards understanding their role in litopenaeid shrimp, we have herein identified nine non-LTR retrotransposons, among which several appear to exist outside the standard defined clades. Two Litopenaeus stylirostris elements were discovered through degenerate PCR amplification using previously defined non-LTR degenerate primers, and through primers designed from a RAPD-derived sequence. A third genomic L. stylirostris element was identified using specific priming from an amplification protocol. These three PCR-derived sequences showed conserved domains of the non-LTR reverse transcriptase gene. In silico searching of genome databases and subsequent contig construction yielded six non-LTR retrotransposons (both genomic and expressed) in the Litopenaeus vannamei genome that also exhibited the highly conserved domains found in our PCR-derived sequences. Phylogenetic placement among representatives from all non-LTR clades showed a possibly novel monophyletic group that included five of our nine sequences. This group, which included elements from both L. stylirostris and L. vannamei, appeared most closely related to the highly active RTE clade. Our remaining four sequences placed in the CR1 and I clades of retrotransposons, with one showing strong similarity to ancient Penelope elements. This research describes three newly discovered retrotransposons in the L. stylirostris genome. Phylogenetic analysis clusters these in a monophyletic grouping with retrotransposons previously described from two closely related species, L. vannamei and Penaeus monodon.
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Affiliation(s)
- S E Hizer
- Department of Biological Sciences, California State University, San Marcos, CA 920296, USA
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