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Xie Q, Yao T, Sun X, Liu X, Wang X. Whole genome identification of olive flounder (Paralichthys olivaceus) cathepsin genes: Provides insights into its regulation on biotic and abiotic stresses response. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2024; 266:106783. [PMID: 38064891 DOI: 10.1016/j.aquatox.2023.106783] [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: 08/15/2023] [Revised: 11/10/2023] [Accepted: 11/29/2023] [Indexed: 01/02/2024]
Abstract
Cathepsins are major lysosomal enzymes involved in essential physiological processes, including protein degradation, tissue differentiation, and innate or adaptive responses. Several kinds of cathepsins have been reported in teleost fishes, but no characterization have been performed for the inflammatory response of cathepsin family in olive flounder until now. In our current study, a total of 17 cathepsins in olive flounder were systematically identified and characterized. Phylogenetic analysis clearly indicated that the cathepsin genes was highly conserved. Analysis of structure and motifs exhibited high sequence similarity of cathepsin genes in olive flounder. Expression profiles of cathepsin genes in different tissues and developmental stages showed that cathepsins were temporally and spatially specific. RNA-seq analysis of bacteria and temperature stresses revealed that members of cathepsin were involved in inflammatory responses. Collectively, our findings would provide a further reference for understanding the molecular mechanisms of cathepsins in olive flounder.
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Affiliation(s)
- Qingping Xie
- Key Laboratory of Aquacultural Biotechnology (Ningbo University), Ministry of Education, Ningbo, Zhejiang, China
| | - Tingyan Yao
- Key Laboratory of Aquacultural Biotechnology (Ningbo University), Ministry of Education, Ningbo, Zhejiang, China
| | - Xuanyang Sun
- Key Laboratory of Aquacultural Biotechnology (Ningbo University), Ministry of Education, Ningbo, Zhejiang, China
| | - Xiumei Liu
- College of Life Sciences, Yantai University, Yantai, China
| | - Xubo Wang
- Key Laboratory of Aquacultural Biotechnology (Ningbo University), Ministry of Education, Ningbo, Zhejiang, China; National Engineering Research Laboratory of marine biotechnology and Engineering, Ningbo University; Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo University; Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China.
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2
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Hirano T, Saito T, Tsunamoto Y, Koseki J, Ye B, Do VT, Miura O, Suyama Y, Chiba S. Enigmatic incongruence between mtDNA and nDNA revealed by multi-locus phylogenomic analyses in freshwater snails. Sci Rep 2019; 9:6223. [PMID: 30996240 PMCID: PMC6470147 DOI: 10.1038/s41598-019-42682-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 04/05/2019] [Indexed: 02/08/2023] Open
Abstract
Phylogenetic incongruence has frequently been encountered among different molecular markers. Recent progress in molecular phylogenomics has provided detailed and important information for evolutionary biology and taxonomy. Here we focused on the freshwater viviparid snails (Cipangopaludina chinensis chinensis and C. c. laeta) of East Asia. We conducted phylogenetic analyses and divergence time estimation using two mitochondrial markers. We also performed population genetic analyses using genome-wide SNPs. We investigated how and which phylogenetic patterns reflect shell morphology. The results showed these two species could be separated into four major mitochondrial clades, whereas the nuclear clusters supported two groups. The phylogenetic patterns of both mtDNA and nDNA largely reflected the geographical distribution. Shell morphology reflected the phylogenetic clusters based on nDNA. The findings also showed these two species diversified in the Pliocene to early Pleistocene era, and occurred introgressive hybridisation. The results also raise the taxonomic issue of the two species.
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Affiliation(s)
- Takahiro Hirano
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, USA.
| | - Takumi Saito
- Graduate school of Life Sciences, Tohoku University, Miyagi, Japan
| | - Yoshihiro Tsunamoto
- Kawatabi Field Science Center, Graduate School of Agricultural Science, Tohoku University, Miyagi, Japan
| | - Joichiro Koseki
- Graduate school of Life Sciences, Tohoku University, Miyagi, Japan
| | - Bin Ye
- Graduate school of Life Sciences, Tohoku University, Miyagi, Japan
- Agricultural Experiment Station, Zhejiang University, Hangzhou, China
| | - Van Tu Do
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Osamu Miura
- Faculty of Agriculture and Marine Science, Kochi University, Kochi, Japan
| | - Yoshihisa Suyama
- Kawatabi Field Science Center, Graduate School of Agricultural Science, Tohoku University, Miyagi, Japan
| | - Satoshi Chiba
- Graduate school of Life Sciences, Tohoku University, Miyagi, Japan
- Center for Northeast Asian Studies, Tohoku University, Miyagi, Japan
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Healy TM, Schulte PM. Patterns of alternative splicing in response to cold acclimation in fish. ACTA ACUST UNITED AC 2019; 222:jeb.193516. [PMID: 30692167 DOI: 10.1242/jeb.193516] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 01/23/2019] [Indexed: 12/26/2022]
Abstract
Phenotypic plasticity is an important aspect of an organism's response to environmental change that often requires the modulation of gene expression. These changes in gene expression can be quantitative, as a result of increases or decreases in the amounts of specific transcripts, or qualitative, as a result of the expression of alternative transcripts from the same gene (e.g. via alternative splicing of pre-mRNAs). Although the role of quantitative changes in gene expression in phenotypic plasticity is well known, relatively few studies have examined the role of qualitative changes. Here, we use skeletal muscle RNA-seq data from Atlantic killifish (Fundulus heteroclitus), threespine stickleback (Gasterosteus aculeatus) and zebrafish (Danio rerio) to investigate the extent of qualitative changes in gene expression in response to cold acclimation. Fewer genes demonstrated alternative splicing than differential expression as a result of cold acclimation; however, differences in splicing were detected for 426 to 866 genes depending on species, indicating that large numbers of qualitative changes in gene expression are associated with cold acclimation. Many of these alternatively spliced genes were also differentially expressed, and there was functional enrichment for involvement in muscle contraction among the genes demonstrating qualitative changes in response to cold acclimation. Additionally, there was a common group of 29 genes with cold-acclimation-mediated changes in splicing in all three species, suggesting that there may be a set of genes with expression patterns that respond qualitatively to prolonged exposure to cold temperatures across fishes.
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Affiliation(s)
- Timothy M Healy
- The University of British Columbia, Department of Zoology, 6270 University Boulevard, Vancouver, British Columbia, Canada V6T 1Z4
| | - Patricia M Schulte
- The University of British Columbia, Department of Zoology, 6270 University Boulevard, Vancouver, British Columbia, Canada V6T 1Z4
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Nitzan T, Kokou F, Doron-Faigenboim A, Slosman T, Biran J, Mizrahi I, Zak T, Benet A, Cnaani A. Transcriptome Analysis Reveals Common and Differential Response to Low Temperature Exposure Between Tolerant and Sensitive Blue Tilapia ( Oreochromis aureus). Front Genet 2019; 10:100. [PMID: 30863423 PMCID: PMC6399464 DOI: 10.3389/fgene.2019.00100] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 01/29/2019] [Indexed: 12/14/2022] Open
Abstract
Tilapias are very important to the world's aquaculture. As befitting fish of their tropical origin, their distribution, and culture practices are highly affected by low temperatures. In this study, we used genetic and genomic methodologies to reveal pathways involved in the response and tolerance of blue tilapia (Oreochromis aureus) to low temperature stress. Cold tolerance was characterized in 66 families of blue tilapia. Fish from cold-tolerant and cold-sensitive families were sampled at 24 and 12°C, and the transcriptional responses to low-temperature exposure were measured in the gills and liver by high-throughput mRNA sequencing. Four hundred and ninety four genes displayed a similar temperature-dependent expression in both tolerant and sensitive fish and in the two tissues, representing the core molecular response to low temperature exposure. KEGG pathway analysis of these genes revealed down-regulation of focal-adhesion and other cell-extracellular matrix (ECM) interactions, and up-regulation of proteasome and various intra-cellular proteolytic activities. Differential responses between cold-tolerant and cold-sensitive fish were found with genes and pathways that were up-regulated in one group and down-regulated in the other. This reverse response was characterized by genes involved in metabolic pathways such as glycolysis/gluconeogenesis in the gills and biosynthesis of amino-acids in the liver, with low temperature down-regulation in tolerant fish and up-regulation in sensitive fish.
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Affiliation(s)
- Tali Nitzan
- Institute of Animal Science, Agricultural Research Organization, Rishon LeZion, Israel
| | - Fotini Kokou
- Institute of Animal Science, Agricultural Research Organization, Rishon LeZion, Israel.,Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Adi Doron-Faigenboim
- Institute of Animal Science, Agricultural Research Organization, Rishon LeZion, Israel
| | - Tatiana Slosman
- Institute of Animal Science, Agricultural Research Organization, Rishon LeZion, Israel
| | - Jakob Biran
- Institute of Animal Science, Agricultural Research Organization, Rishon LeZion, Israel
| | - Itzhak Mizrahi
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Tatyana Zak
- The Aquaculture Research Station, Ministry of Agriculture and Rural Development, Dor, Israel
| | - Ayana Benet
- The Aquaculture Research Station, Ministry of Agriculture and Rural Development, Dor, Israel
| | - Avner Cnaani
- Institute of Animal Science, Agricultural Research Organization, Rishon LeZion, Israel
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Kokou F, Sasson G, Nitzan T, Doron-Faigenboim A, Harpaz S, Cnaani A, Mizrahi I. Host genetic selection for cold tolerance shapes microbiome composition and modulates its response to temperature. eLife 2018; 7:e36398. [PMID: 30454554 PMCID: PMC6277203 DOI: 10.7554/elife.36398] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 11/06/2018] [Indexed: 01/19/2023] Open
Abstract
The hologenome concept proposes that microbes and their host organism are an independent unit of selection. Motivated by this concept, we hypothesized that thermal acclimation in poikilothermic organisms, owing to their inability to maintain their body temperature, is connected to their microbiome composition. To test this hypothesis, we used a unique experimental setup with a transgenerational selective breeding scheme for cold tolerance in tropical tilapias. We tested the effects of the selection on the gut microbiome and on host transcriptomic response. Interestingly, we found that host genetic selection for thermal tolerance shapes the microbiome composition and its response to cold. The microbiomes of cold-resistant fish showed higher resilience to temperature changes, indicating that the microbiome is shaped by its host's selection. These findings are consistent with the hologenome concept and highlight the connection between the host and its microbiome's response to the environment.
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Affiliation(s)
- Fotini Kokou
- Department of Life Sciences and the National Institute for Biotechnology in the NegevBen-Gurion University of the NegevBeer-ShevaIsrael
- Department of Poultry and Aquaculture, Institute of Animal SciencesAgricultural Research OrganizationRishon LeZionIsrael
| | - Goor Sasson
- Department of Life Sciences and the National Institute for Biotechnology in the NegevBen-Gurion University of the NegevBeer-ShevaIsrael
| | - Tali Nitzan
- Department of Poultry and Aquaculture, Institute of Animal SciencesAgricultural Research OrganizationRishon LeZionIsrael
| | - Adi Doron-Faigenboim
- Department of Vegetable and Field Crops, Institute of Plant ScienceAgricultural Research OrganizationRishon LeZionIsrael
| | - Sheenan Harpaz
- Department of Poultry and Aquaculture, Institute of Animal SciencesAgricultural Research OrganizationRishon LeZionIsrael
| | - Avner Cnaani
- Department of Poultry and Aquaculture, Institute of Animal SciencesAgricultural Research OrganizationRishon LeZionIsrael
| | - Itzhak Mizrahi
- Department of Life Sciences and the National Institute for Biotechnology in the NegevBen-Gurion University of the NegevBeer-ShevaIsrael
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Chung DJ, Sparagna GC, Chicco AJ, Schulte PM. Patterns of mitochondrial membrane remodeling parallel functional adaptations to thermal stress. J Exp Biol 2018; 221:221/7/jeb174458. [DOI: 10.1242/jeb.174458] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 02/14/2018] [Indexed: 01/07/2023]
Abstract
ABSTRACT
The effect of temperature on mitochondrial performance is thought to be partly due to its effect on mitochondrial membranes. Numerous studies have shown that thermal acclimation and adaptation can alter the amount of inner-mitochondrial membrane (IMM), but little is known about the capacity of organisms to modulate mitochondrial membrane composition. Using northern and southern subspecies of Atlantic killifish (Fundulus heteroclitus) that are locally adapted to different environmental temperatures, we assessed whether thermal acclimation altered liver mitochondrial respiratory capacity or the composition and amount of IMM. We measured changes in phospholipid headgroups and headgroup-specific fatty acid (FA) remodeling, and used respirometry to assess mitochondrial respiratory capacity. Acclimation to 5°C and 33°C altered mitochondrial respiratory capacity in both subspecies. Northern F. heteroclitus exhibited greater mitochondrial respiratory capacity across acclimation temperatures, consistent with previously observed subspecies differences in whole-organism aerobic metabolism. Mitochondrial phospholipids were altered following thermal acclimation, and the direction of these changes was largely consistent between subspecies. These effects were primarily driven by remodeling of specific phospholipid classes and were associated with shifts in metabolic phenotypes. There were also differences in membrane composition between subspecies that were driven largely by differences in phospholipid classes. Changes in respiratory capacity between subspecies and with acclimation were largely but not completely accounted for by alterations in the amount of IMM. Taken together, these results support a role for changes in liver mitochondrial function in the ectothermic response to thermal stress during both acclimation and adaptation, and implicate lipid remodeling as a mechanism contributing to these changes.
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Affiliation(s)
- Dillon J. Chung
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
| | - Genevieve C. Sparagna
- Department of Medicine/Division of Cardiology, University of Colorado Anschutz Medical Center, Aurora, CO 80045, USA
| | - Adam J. Chicco
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO 80523-1680, USA
| | - Patricia M. Schulte
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
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Pichaud N, Ekström A, Hellgren K, Sandblom E. Dynamic changes in cardiac mitochondrial metabolism during warm acclimation in rainbow trout. ACTA ACUST UNITED AC 2017; 220:1674-1683. [PMID: 28202582 DOI: 10.1242/jeb.152421] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Accepted: 02/13/2017] [Indexed: 01/06/2023]
Abstract
Although the mitochondrial metabolism responses to warm acclimation have been widely studied in fish, the time course of this process is less understood. Here, we characterized the changes of rainbow trout (Oncorhynchus mykiss) cardiac mitochondrial metabolism during acute warming from 10 to 16°C, and during the subsequent warm acclimation for 39 days. We repeatedly measured mitochondrial oxygen consumption in cardiac permeabilized fibers and the functional integrity of mitochondria (i.e. mitochondrial coupling and cytochrome c effect) at two assay temperatures (10 and 16°C), as well as the activities of citrate synthase (CS) and lactate dehydrogenase (LDH) at room temperature. LDH and CS activities significantly increased between day 0 (10°C acclimated fish) and day 1 (acute warming to 16°C) while mitochondrial oxygen consumption measured at respective in vivo temperatures did not change. Enzymatic activities and mitochondrial oxygen consumption rates significantly decreased by day 2, and remained stable during warm acclimation (days 2-39). The decrease in rates of oxygen between day 0 and day 1 coincided with an increased cytochrome c effect and a decreased mitochondrial coupling, suggesting a structural/functional impairment of mitochondria during acute warming. We suggest that after 2 days of warm acclimation, a new homeostasis is reached, which may involve the removal of dysfunctional mitochondria. Interestingly, from day 2 onwards, there was a lack of differences in mitochondrial oxygen consumption rates between the assay temperatures, suggesting that warm acclimation reduces the acute thermal sensitivity of mitochondria. This study provides significant knowledge on the thermal sensitivity of cardiac mitochondria that is essential to delineate the contribution of cellular processes to warm acclimation.
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Affiliation(s)
- Nicolas Pichaud
- Department of Chemistry and Biochemistry, University of Moncton, Moncton, New Brunswick, Canada E1A 3E9 .,Department of Biological and Environmental Sciences, University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | - Andreas Ekström
- Department of Biological and Environmental Sciences, University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | - Kim Hellgren
- Department of Biological and Environmental Sciences, University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | - Erik Sandblom
- Department of Biological and Environmental Sciences, University of Gothenburg, SE-405 30 Gothenburg, Sweden
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8
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Singh SP, Sharma J, Ahmad T, Chakrabarti R. Oxygen stress: impact on innate immune system, antioxidant defence system and expression of HIF-1α and ATPase 6 genes in Catla catla. FISH PHYSIOLOGY AND BIOCHEMISTRY 2016; 42:673-688. [PMID: 26588934 DOI: 10.1007/s10695-015-0168-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 11/13/2015] [Indexed: 06/05/2023]
Abstract
Catla catla catla (2.28 ± 0.1 g) were exposed to six different levels of dissolved oxygen: 1 (DO-1), 3 (DO-3), 5 (DO-5), 7 (DO-7), 9 (DO-9) and 11 (DO-11) mg/L. DO-5 served as control. In DO-1 and DO-3, the number of red blood cells (RBC), lysozyme, respiratory burst activity and nitric oxide synthase were significantly (p < 0.05) lower compared to the control one. In DO-7 and DO-9, RBC and lysozyme were significantly (p < 0.05) higher compared to the control one. Thiobarbituric acid reactive substances was significantly (p < 0.05) higher in catla exposed at low (1 and 3 mg/L) and high (9 and 11 mg/L) dissolved oxygen compared to others. In muscles and hepatopancreas, reduced glutathione was significantly (p < 0.05) higher in DO-5 and DO-7 and in gills of DO-5 compared to others after 1 h. In muscles, glutathione S-transferase (GST) was significantly (p < 0.05) lower in DO-5 and DO-7 compared to others. In hepatopancreas, GST and glutathione peroxidise (GPx) were significantly (p < 0.05) higher in DO-1 and DO-3 compared to others. In gills, GPx was higher in DO-9 and DO-11 after 48 h. In brain, hypoxia-inducible factor (HIF)-1α mRNA level was induced in DO-1 and DO-3 compared to others after 1 h of exposure. In gills and hepatopancreas, HIF-1α mRNA level was significantly (p < 0.05) higher in DO-1 compared to others after 1 h. The ATPase 6 mRNA level was significantly (p < 0.05) higher in brain and hepatopancreas of DO-1 after 1 h and in gills and hepatopancreas of DO-3 and DO-9, respectively, after 48 h compared to others.
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Affiliation(s)
- Samar Pal Singh
- Aqua Research Lab, Department of Zoology, University of Delhi, Delhi, 110007, India
| | - JaiGopal Sharma
- Department of Biotechnology, Delhi Technological University, Delhi, 110042, India
| | - Tauqueer Ahmad
- Aqua Research Lab, Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Rina Chakrabarti
- Aqua Research Lab, Department of Zoology, University of Delhi, Delhi, 110007, India.
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Transcriptome Analysis to Identify Cold-Responsive Genes in Amur Carp (Cyprinus carpio haematopterus). PLoS One 2015; 10:e0130526. [PMID: 26098567 PMCID: PMC4476670 DOI: 10.1371/journal.pone.0130526] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 05/21/2015] [Indexed: 11/19/2022] Open
Abstract
The adaptation of fish to low temperatures is the result of long-term evolution. Amur carp (Cyprinus carpio haematopterus) survives low temperatures (0-4°C) for six months per year. Therefore, we chose this fish as a model organism to study the mechanisms of cold-adaptive responses using high-throughput sequencing technology. This system provided an excellent model for exploring the relationship between evolutionary genomic changes and environmental adaptations. The Amur carp transcriptome was sequenced using the Illumina platform and was assembled into 163,121 cDNA contigs, with an average read length of 594 bp and an N50 length of 913 bp. A total of 162,339 coding sequences (CDSs) were identified and of 32,730 unique CDSs were annotated. Gene Ontology (GO), EuKaryotic Orthologous Groups (KOG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to classify all CDSs into different functional categories. A large number of cold-responsive genes were detected in different tissues at different temperatures. A total of 9,427 microsatellites were identified and classified, with 1952 identifying in cold-responsive genes. Based on GO enrichment analysis of the cold-induced genes, “protein localization” and “protein transport” were the most highly represented biological processes. “Circadian rhythm,” “protein processing in endoplasmic reticulum,” “endocytosis,” “insulin signaling pathway,” and “lysosome” were the most highly enriched pathways for the genes induced by cold stress. Our data greatly contribute to the common carp (C. carpio) transcriptome resource, and the identification of cold-responsive genes in different tissues at different temperatures will aid in deciphering the genetic basis of ecological and environmental adaptations in this species. Based on our results, the Amur carp has evolved special strategies to survive low temperatures, and these strategies include the system-wide or tissue-specific induction of gene expression during their six-month overwintering period.
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Barnes KR, Cozzi RRF, Robertson G, Marshall WS. Cold acclimation of NaCl secretion in a eurythermic teleost: mitochondrial function and gill remodeling. Comp Biochem Physiol A Mol Integr Physiol 2013; 168:50-62. [PMID: 24239670 DOI: 10.1016/j.cbpa.2013.11.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Revised: 10/30/2013] [Accepted: 11/06/2013] [Indexed: 10/26/2022]
Abstract
Active chloride secretion, measured as short-circuit current (Isc) in ionocytes of opercular epithelia (OE) in the eurythermic, euryoxic, and euryhaline killifish or mummichog (Fundulus heteroclitus) was studied in cold (5°C) and warm (20°C) acclimated fish to determine if homeoviscous adaptation aided chloride secretion in the cold. Isolated opercular epithelia were cooled from 30°C to 0.2°C for warm and cold acclimated fish; from 30 to 8°C, Isc decreased with Q10=1.68 for warm and Q10=1.56 for cold acclimated tissues. By Arrhenius plots, there is a critical temperature, 8°C, below which aerobic Isc decreased sharply (Q10=6.90 for warm and 4.23 for cold acclimated tissues), suggesting a shift in mitochondrial efficiency of oxidative phosphorylation. In anaerobic conditions (0.5mM NaCN; N2 saturation), chloride transport continued at a lower rate, and Isc decrease with cooling below 8°C was less pronounced (Q10=2.95 for warm and 3.08 for cold), suggesting a shift in transporter function in plasma membrane. Under anaerobic conditions, NaCl secretion at 20°C was reversibly inhibited by hypotonic shock, indicating normal regulation of transport. Chloride secretion in warm-acclimated fish was supported mostly (75% at 20°C) by aerobic metabolism, whereas that for cold-acclimated fish was lower (55% at 20°C), suggesting a greater reliance on anaerobic metabolism in the cold. Once acclimated to cold, ionocytes may be temporarily incapable of increasing their aerobic ATP supply, even when warmed to 30°C. In cold acclimated fish there was increased polyunsaturated fatty acid composition of gill epithelium (consistent with homeoviscous adaptation) and gill remodeling, wherein epithelial cells filled the interlamellar space (interlamellar cell mass, ILCM) by as much as 70%, thus increasing diffusion distance against passive ion gain. Most ionocytes in these thickened epithelial masses became taller, still connecting basal lamina with the environment, consistent with the continuing transport rates at low temperatures. Whereas the low aerobic scope of cold-acclimated fish and thickened gill epithelium is appropriate to winter inactivity, metabolic depression and anaerobiosis, the large aerobic scope of warm-acclimated fish favors active foraging at high temperatures.
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Affiliation(s)
- Katelyn R Barnes
- Department of Biology, St. Francis Xavier University, Antigonish, Nova Scotia B2G 2W5, Canada
| | - Regina R F Cozzi
- Department of Biology, St. Francis Xavier University, Antigonish, Nova Scotia B2G 2W5, Canada
| | - George Robertson
- Department of Biology, St. Francis Xavier University, Antigonish, Nova Scotia B2G 2W5, Canada
| | - William S Marshall
- Department of Biology, St. Francis Xavier University, Antigonish, Nova Scotia B2G 2W5, Canada.
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Bourdineaud JP, Rossignol R, Brèthes D. Zebrafish: a model animal for analyzing the impact of environmental pollutants on muscle and brain mitochondrial bioenergetics. Int J Biochem Cell Biol 2012; 45:16-22. [PMID: 22842533 DOI: 10.1016/j.biocel.2012.07.021] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2012] [Accepted: 07/18/2012] [Indexed: 12/26/2022]
Abstract
Mercury, anthropogenic release of uranium (U), and nanoparticles constitute hazardous environmental pollutants able to accumulate along the aquatic food chain with severe risk for animal and human health. The impact of such pollutants on living organisms has been up to now approached by classical toxicology in which huge doses of toxic compounds, environmentally irrelevant, are displayed through routes that never occur in the lifespan of organisms (for instance injecting a bolus of mercury to an animal although the main route is through prey and fish eating). We wanted to address the effect of such pollutants on the muscle and brain mitochondrial bioenergetics under realistic conditions, at unprecedented low doses, using an aquatic model animal, the zebrafish Danio rerio. We developed an original method to measure brain mitochondrial respiration: a single brain was put in 1.5 mL conical tube containing a respiratory buffer. Brains were gently homogenized by 13 strokes with a conical plastic pestle, and the homogenates were immediately used for respiration measurements. Skinned muscle fibers were prepared by saponin permeabilization. Zebrafish were contaminated with food containing 13 μg of methylmercury (MeHg)/g, an environmentally relevant dose. In permeabilized muscle fibers, we observed a strong inhibition of both state 3 mitochondrial respiration and cytochrome c oxidase activity after 49 days of MeHg exposure. We measured a dramatic decrease in the rate of ATP release by skinned muscle fibers. Contrarily to muscles, brain mitochondrial respiration was not modified by MeHg exposure although brain accumulated twice as much MeHg than muscles. When zebrafish were exposed to 30 μg/L of waterborne U, the basal mitochondrial respiratory control ratio was decreased in muscles after 28 days of exposure. This was due to an increase of the inner mitochondrial membrane permeability. The impact of a daily ration of food containing gold nanoparticles of two sizes (12 and 50 nm) was investigated at a very low dose for 60 days (40 ng gold/fish/day). Mitochondrial dysfunctions appeared in brain and muscle for both tested sizes. In conclusion, at low environmental doses, dietary or waterborne heavy metals impinged on zebrafish tissue mitochondrial respiration. Due to its incredible simplicity avoiding tedious and time-consuming mitochondria isolation, our one-pot method allowing brain respiratory analysis should give colleagues the incentive to use zebrafish brain as a model in bioenergetics. This article is part of a Directed Issue entitled: Bioenergetic dysfunction, adaptation and therapy.
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Affiliation(s)
- Jean-Paul Bourdineaud
- University of Bordeaux, CNRS, UMR 5805, Station marine d'Arcachon, Place du Dr Peyneau, 33120 Arcachon, France.
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The function of mitochondrial F(O)F(1) ATP-synthase from the whiteleg shrimp Litopenaeus vannamei muscle during hypoxia. Comp Biochem Physiol B Biochem Mol Biol 2012; 162:107-12. [PMID: 22507548 DOI: 10.1016/j.cbpb.2012.03.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Revised: 03/30/2012] [Accepted: 03/31/2012] [Indexed: 11/23/2022]
Abstract
The effect of hypoxia and re-oxygenation on the mitochondrial complex F(O)F(1)-ATP synthase was investigated in the whiteleg shrimp Litopenaeus vannamei. A 660 kDa protein complex isolated from mitochondria of the shrimp muscle was identified as the ATP synthase complex. After 10h at hypoxia (1.5-2.0 mg oxygen/L), the concentration of L-lactate in plasma increased significantly, but the ATP amount and the concentration of ATPβ protein remained unaffected. Nevertheless, an increase of 70% in the ATPase activity was detected, suggesting that the enzyme may be regulated at a post-translational level. Thus, during hypoxia shrimp are able to maintain ATP amounts probably by using some other energy sources as phosphoarginine when an acute lack of energy occurs. During re-oxygenation, the ATPase activity decreased significantly and the ATP production continued via the electron transport chain and oxidative phosphorylation. The results obtained showed that shrimp faces hypoxia partially by hydrolyzing the ATP through the reaction catalyzed by the mitochondrial ATPase which increases its activity.
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13
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Wu CL, Lin TH, Chang TL, Sun HW, Hui CF, Wu JL. Zebrafish HSC70 promoter to express carp muscle-specific creatine kinase for acclimation under cold condition. Transgenic Res 2011; 20:1217-26. [PMID: 21298478 DOI: 10.1007/s11248-011-9488-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2010] [Accepted: 01/18/2011] [Indexed: 01/28/2023]
Abstract
Zebrafish (Danio rerio) is used as a model system for in vivo studies. To expand the research scope of physical, biochemical and physiological studies, a cold-tolerant model of zebrafish was developed. The common carp (Cyprinus carpio) muscle form of creatine kinase (CK, EC 2.7.3.2) can maintain enzymatic activity at a temperature of around 15°C. However, a cold-inducible promoter of zebrafish, hsc 70 (heat shock protein 70 cognate), is able to increase the expression of gene product by 9.8 fold at a temperature of 16°C. Therefore, the carp CK gene was promoted by hsc 70 and transfected into zebrafish embryos. Resulting transgenic zebrafish survived and could maintain its swimming behavior at 13°C, which was not possible with the wild-type zebrafish. The swimming distance of the transgenic fish was 42% greater than that of the wild type at 13°C. This new transgenic fish model is ideal for studies of ectothermal vertebrates in low-temperature environments.
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Affiliation(s)
- Chih-Lu Wu
- Institute of Cellular and Organismic Biology, 128 Academia Road, Sect. 2 Academia Sinica, Taipei 115, Taiwan
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14
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Intraspecific variation in the mitochondrial genome among local populations of Medaka Oryzias latipes. Gene 2010; 457:13-24. [DOI: 10.1016/j.gene.2010.02.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2009] [Revised: 02/19/2010] [Accepted: 02/23/2010] [Indexed: 11/30/2022]
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15
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CHEVIRON ZACHARYA, WHITEHEAD ANDREW, BRUMFIELD ROBBT. Transcriptomic variation and plasticity in rufous-collared sparrows (Zonotrichia capensis) along an altitudinal gradient. Mol Ecol 2008; 17:4556-69. [DOI: 10.1111/j.1365-294x.2008.03942.x] [Citation(s) in RCA: 101] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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16
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Muhlia-Almazan A, Martinez-Cruz O, Navarrete del Toro MDLA, Garcia-Carreño F, Arreola R, Sotelo-Mundo R, Yepiz-Plascencia G. Nuclear and mitochondrial subunits from the white shrimp Litopenaeus vannamei F(0)F(1) ATP-synthase complex: cDNA sequence, molecular modeling, and mRNA quantification of atp9 and atp6. J Bioenerg Biomembr 2008; 40:359-69. [PMID: 18770013 DOI: 10.1007/s10863-008-9162-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2008] [Accepted: 05/16/2008] [Indexed: 01/29/2023]
Abstract
We studied for the first time the ATP-synthase complex from shrimp as a model to understand the basis of crustacean bioenergetics since they are exposed to endogenous processes as molting that demand high amount of energy. We analyzed the cDNA sequence of two subunits of the Fo sector from mitochondrial ATP-synthase in the white shrimp Litopenaeus vannamei. The nucleus encoded atp9 subunit presents a 773 bp sequence, containing a signal peptide sequence only observed in crustaceans, and the mitochondrial encoded atp6 subunit presents a sequence of 675 bp, and exhibits high identity with homologous sequences from invertebrate species. ATP9 and ATP6 protein structural models interaction suggest specific functional characteristics from both proteins in the mitochondrial enzyme. Differences in the steady-state mRNA levels of atp9 and atp6 from five different tissues correlate with tissue function. Moreover, significant changes in the mRNA levels of both subunits at different molt stages were detected. We discussed some insights about the enzyme structure and the regulation mechanisms from both ATP-synthase subunits related to the energy requirements of shrimp.
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Affiliation(s)
- Adriana Muhlia-Almazan
- Molecular Biology Lab, Centro de Investigación en Alimentación y Desarrollo (CIAD), A. C., Sonora, Mexico.
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17
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Li A, Denlinger DL. Rapid cold hardening elicits changes in brain protein profiles of the flesh fly, Sarcophaga crassipalpis. INSECT MOLECULAR BIOLOGY 2008; 17:565-572. [PMID: 18828842 DOI: 10.1111/j.1365-2583.2008.00827.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Rapid cold hardening (RCH) refers to the enhanced cold tolerance acquired by a brief exposure to a moderately low temperature. Although ecological aspects of this response have been well documented in insects, less is known about the physiological and biochemical mechanisms elicited by RCH. In this study we used two-dimensional electrophoresis to detect differences in brain protein abundance in pharate adults of the flesh fly Sarcophaga crassipalpis, in response to a 2 h RCH exposure at 0 degrees C. Fourteen high abundance proteins that responded to RCH were selected for mass spectrometric identification. Three proteins that increased in abundance during RCH included ATP synthase subunit alpha, a small heat shock protein (smHsp), and tropomyosin-1 isoforms 33/34. Eleven proteins that decreased in abundance or were missing following RCH included several proteins involved in energy metabolism, protein degradation, transcription, actin binding, and cytoskeleton organization. That several proteins increased in abundance during RCH underscores the dynamics of the RCH mechanism and suggests that more than one physiological response likely contribute to RCH. The increase in ATP synthase suggests an elevation of ATP during RCH, and the smHsp increase suggests that at least one of the Hsps is actually mobilized during RCH, rather than after RCH as previously assumed.
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Affiliation(s)
- A Li
- Department of Entomology, The Ohio State University, 318 West 12th Avenue, Columbus, OH 43210, USA
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18
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Cambier S, Bénard G, Mesmer-Dudons N, Gonzalez P, Rossignol R, Brèthes D, Bourdineaud JP. At environmental doses, dietary methylmercury inhibits mitochondrial energy metabolism in skeletal muscles of the zebra fish (Danio rerio). Int J Biochem Cell Biol 2008; 41:791-9. [PMID: 18765295 DOI: 10.1016/j.biocel.2008.08.008] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2008] [Revised: 07/29/2008] [Accepted: 08/07/2008] [Indexed: 10/21/2022]
Abstract
The neurotoxic compound methylmercury (MeHg) is a commonly encountered pollutant in the environment, and constitutes a hazard for human health through fish eating. To study the impact of MeHg on mitochondrial structure and function, we contaminated the model fish species Danio rerio with food containing 13 microg of MeHg per gram, an environmentally relevant dose. Mitochondria from contaminated zebrafish muscles presented structural abnormalities under electron microscopy observation. In permeabilized muscle fibers, we observed, a strong inhibition of both state 3 mitochondrial respiration and functionally isolated maximal cytochrome c oxidase (COX) activity after 49 days of MeHg exposure. However, the state 4 respiratory rate remained essentially unchanged. This suggested a defect at the level of ATP synthesis. Accordingly, we measured a dramatic decrease in the rate of ATP release by skinned muscle fibers using either pyruvate and malate or succinate as respiratory substrates. However, the amount and the assembly of the ATP synthase were identical in both control and contaminated muscle mitochondrial fractions. This suggests that MeHg induced a decoupling of mitochondrial oxidative phosphorylation in the skeletal muscle of zebrafish. Western blot analysis showed a 30% decrease of COX subunit IV levels, a 50% increase of ATP synthase subunit alpha, and a 40% increase of the succinate dehydrogenase Fe/S protein subunit in the contaminated muscles. This was confirmed by the analysis of gene expression levels, using RT-PCR. Our study provides a basis for further analysis of the deleterious effect of MeHg on fish health via mitochondrial impairment.
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Affiliation(s)
- S Cambier
- CNRS, UMR 5805, Ecotoxicologie des Systèmes Aquatiques, Université de Bordeaux 1, Place du Dr Peyneau, 33120 Arcachon, France
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19
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Lemieux H, Blier P, Tardif JC. Does membrane fatty acid composition modulate mitochondrial functions and their thermal sensitivities? Comp Biochem Physiol A Mol Integr Physiol 2008; 149:20-9. [DOI: 10.1016/j.cbpa.2007.09.015] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2007] [Revised: 09/26/2007] [Accepted: 09/27/2007] [Indexed: 11/25/2022]
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20
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McLean L, Young IS, Doherty MK, Robertson DHL, Cossins AR, Gracey AY, Beynon RJ, Whitfield PD. Global cooling: cold acclimation and the expression of soluble proteins in carp skeletal muscle. Proteomics 2007; 7:2667-81. [PMID: 17623276 DOI: 10.1002/pmic.200601004] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The common carp (Cyprinus carpio) has a well-developed capacity to modify muscle properties in response to changes in temperature. Understanding the mechanisms underpinning this phenotypic response at the protein level may provide fundamental insights into the molecular basis of adaptive processes in skeletal muscle. In this study, common carp were subjected to a cooling regimen and soluble extracts of muscle homogenates were separated by 1-D SDS-PAGE and 2-DE. Proteins were identified using MALDI-TOF-MS and de novo peptide sequencing using LC-MS/MS. The 2-D gel was populated with numerous protein spots that were fragments of all three muscle isoforms (M1, M2 and M3) of carp creatine kinase (CK). The accumulation of the CK fragments was enhanced when the carp were cooled to 10 degrees C. The protein changes observed in the skeletal muscle of carp subjected to cold acclimation were compared to changes described in a previous transcript analysis study. Genes encoding CK isoforms were downregulated and the genes encoding key proteins of the ubiquitin-proteasome pathway were upregulated. These findings are consistent with a specific cold-induced enhancement of proteolysis of CK.
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MESH Headings
- Acclimatization/physiology
- Animals
- Carps/genetics
- Carps/physiology
- Chromatography, Liquid
- Cold Temperature
- Creatine Kinase/genetics
- Creatine Kinase/isolation & purification
- Creatine Kinase/metabolism
- Electrophoresis, Gel, Two-Dimensional
- Electrophoresis, Polyacrylamide Gel
- Gene Expression Regulation, Enzymologic
- Isoenzymes
- Models, Molecular
- Muscle, Skeletal/chemistry
- Muscle, Skeletal/enzymology
- Peptide Mapping
- Proteins/genetics
- Proteins/metabolism
- Sequence Analysis, Protein
- Solubility
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
- Trypsin/pharmacology
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Affiliation(s)
- Lynn McLean
- Proteomics and Functional Genomics Research Group, Faculty of Veterinary Science, University of Liverpool, Liverpool, UK
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21
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Kraffe E, Marty Y, Guderley H. Changes in mitochondrial oxidative capacities during thermal acclimation of rainbow trout Oncorhynchus mykiss: roles of membrane proteins, phospholipids and their fatty acid compositions. ACTA ACUST UNITED AC 2007; 210:149-65. [PMID: 17170158 DOI: 10.1242/jeb.02628] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Changes in the properties of mitochondria from oxidative muscle of rainbow trout Oncorhynchus mykiss were examined during warm (5 degrees C to 15 degrees C) acclimation. Trout were studied shortly after the initial thermal change and after 8 weeks acclimation to 15 degrees C. To identify potential mechanisms by which oxidative capacities change, the modifications of phospholipid composition, membrane proteins and functional capacities of red muscle mitochondria were examined. Marked functional changes of isolated muscle mitochondria during warm acclimation of rainbow trout were reflected by a host of modifications in phospholipid composition, but by few shifts in protein components. Shortly after transfer of trout from 5 degrees C to 15 degrees C, the maximal oxidative capacity of mitochondria measured at 15 degrees C increased slightly, but rates at both assay temperatures (5 degrees C and 15 degrees C) decreased markedly after warm acclimation. The increase in capacity in short-term warm exposed trout was most pronounced when rates at 15 degrees C were expressed relative to cytochrome a and c(1) levels. Non-phosphorylating (State 4) rates of oxygen uptake increased with short-term warm exposure before returning to initial levels after warm acclimation. Cytochrome c oxidase (CCO) activity in the mitochondrial preparations decreased with warm acclimation. The thermal sensitivity of the ADP affinity was markedly modified during short-term warm exposure, when the ADP/O ratio increased, but warm acclimation returned these values to those observed initially. ADP affinity increased after warm acclimation. Changes in the mitochondrial content of cytochromes and adenine nucleotide translocase (ANT) could not explain these patterns. On the other hand, changes in the proportions of the lipid classes and in the acyl chain composition of certain phospholipid classes mirror the modifications in functional properties. Short-term exposure to 15 degrees C decreased the ratio of diacylphosphatidylethanolamine/diacylphosphatidylcholine (diacylPE/diacylPC), whereas warm acclimation led to restructuring of fatty acids (FA) and to increases of plasmalogen forms of PE and PC. Modification of overall membrane unsaturation did not appear to be the primary aim of restructuring membrane FA during warm acclimation, as total mitochondrial phospholipids and the major phospholipid classes only showed slight shifts of their acyl composition with warm acclimation. On the other hand, natural lysophosphatidylcholine (LysoPC) showed dramatic changes in FA content, as 16:0 and 18:1n-9 doubled whereas 22:6n-3 decreased from around 50% to 32% in warm acclimated trout. Similarly, in cardiolipin (CL), the levels of 16:0 and 18:1n-7 halved while 18:2n-6 increased to over 20% of the FA with warm acclimation. Given the central role of CL in modulating the activity of CCO, F(0)F(1)-ATPase and ANT, these changes suggest that specific compositional changes in CL are important modulators of mitochondrial capacities. The many structural changes in membrane lipids contrast with the limited modifications of the membrane protein components examined and support the concept of lipid structure modulating mitochondrial capacities.
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Affiliation(s)
- Edouard Kraffe
- Unité mixte CNRS 6521, Université de Bretagne Occidentale, C.S. 93837, 29238 Brest cedex 3, France.
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22
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Zakhartsev M, Lucassen M, Kulishova L, Deigweiher K, Smirnova YA, Zinov'eva RD, Mugue N, Baklushinskaya I, Pörtner HO, Ozernyuk ND. Differential expression of duplicated LDH-A genes during temperature acclimation of weatherfish Misgurnus fossilis. FEBS J 2007; 274:1503-13. [PMID: 17480202 DOI: 10.1111/j.1742-4658.2007.05692.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Temperature acclimation in poikilotherms entails metabolic rearrangements provided by variations in enzyme properties. However, in most cases the underlying molecular mechanisms that result in structural changes in the enzymes are obscure. This study reports that acclimation to low (5 degrees C) and high (18 degrees C) temperatures leads to differential expression of alternative forms of the LDH-A gene in white skeletal muscle of weatherfish, Misgurnus fossilis. Two isoforms of LDH-A mRNA were isolated and characterized: a short isoform (= 1332 bp) and a long isoform ( = 1550 bp), which both have 5'-UTRs and ORFs of the same length (333 amino acid residues), but differ in the length of the 3'-UTR. In addition, these two mRNAs have 44 nucleotide point mismatches of an irregular pattern along the complete sequence, resulting in three amino acid mismatches (Gly214Val; Val304Ile and Asp312Glu) between protein products from the short and long mRNA forms, correspondingly LDH-A(alpha) and LDH-A(beta) subunits. It is expected that the beta-subunit is more aliphatic due to the properties of the mismatched amino acids and therefore sterically more restricted. According to molecular modelling of M. fossilis LDH-A, the Val304Ile mismatch is located in the subunit contact area of the tetramer, whereas the remaining two mismatches surround the contact area; this is expected to manifest in the kinetic and thermodynamic properties of the assembled tetramer. In warm-acclimated fish the relative expression between alpha and beta isoforms of the LDH-A mRNA is around 5 : 1, whereas in cold-acclimated fish expression of is reduced almost to zero. This indicates that at low temperature the pool of total tetrameric LDH-A is more homogeneous in terms of alpha/beta-subunit composition. The temperature acclimation pattern of proportional pooling of subunits with different kinetic and thermodynamic properties of the tetrameric enzyme may result in fine-tuning of the properties of skeletal LDH-A, which is in line with previously observed kinetic and thermodynamic differences between 'cold' and 'warm' LDH-A purified from weatherfish. Also, an irregular pattern of nucleotide mismatches indicates that these mRNAs are the products of two independently evolving genes, i.e. paralogues. Karyotype analysis has confirmed that the experimental population of M. fossilis is tetraploid (2n = 100), therefore gene duplication, possibly through tetraploidy, may contribute to the adaptability towards temperature variation.
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Affiliation(s)
- Maxim Zakhartsev
- Alfred Wegener Institute for Polar and Marine Research, Am Handelshaven 12, 27570 Bremerhaven, Germany.
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23
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Ahsan MN, Aoki H, Watabe S. Characterization of cDNA clones encoding two distinct cathepsins with restricted expression pattern in a marine pelagic fish. Mol Biol Rep 2006; 33:233-41. [PMID: 16850193 DOI: 10.1007/s11033-005-0415-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/21/2005] [Indexed: 10/24/2022]
Abstract
Cathepsin L (EC 3.4.22.15) from aquatic animals are quite stable and active at neutral or alkaline pH values while their mammalian equivalents work at an acidic environment of the lysosomes. To understand the molecular properties at the gene level we employed a PCR-based strategy using degenerate oligonucleotide primers to isolate cathepsin L-like genes from anchovy Engraulis japonicus. As a result, we obtained two closely related genes encoding cathepsins (aCat1 and aCat2) similar to both cathepsins L and S from other organisms. The predicted precursor protein of 324 amino acid residues for genes differed in six residues and contained conserved residues characteristic of cathepsin L-like cysteine proteases. Phylogenetic analyses failed to produce any precise relationships of aCat1 and aCat2 with other cysteine proteases. However, with a bootstrap value less than 50, these two fish cathepsins formed a separate group to that bearing cathepsins L and S of various organisms. Interestingly, unlike mammalian cathepsin L transcripts of aCat1 and aCat2 were almost exclusively detected in the stomach suggesting that the fish homologues are non-lysosomal secretory enzymes present in the extracellular acidic environment of the stomach and that marine teleosts developed digestive cysteine proteases as a result of evolutionary pressure in response to varying dietary conditions.
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Affiliation(s)
- Md Nazmul Ahsan
- Laboratory of Aquatic Molecular Biology and Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
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24
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Ikeguchi K, Ineno T, Itoi S, Kondo H, Kinoshita S, Watabe S. Increased levels of mitochondrial gene transcripts in the thermally selected rainbow trout (Oncorhynchus mykiss) strain during embryonic development. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2006; 8:178-88. [PMID: 16505978 DOI: 10.1007/s10126-005-5110-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2005] [Accepted: 10/27/2005] [Indexed: 05/06/2023]
Abstract
To investigate molecular mechanisms involved in thermal resistance of rainbow trout, Oncorhynchus mykiss, embryos from thermally selected strain in various developmental stages were treated at 22 degrees C for 30 min and subsequently developed at 12 degrees C using the Donaldson strain as a reference. The embryos were evaluated for their hatching rate along with the ratio of embryos having an abnormal appearance and subjected to mRNA arbitrarily primed reverse transcription-polymerase chain reaction (RAP RT-PCR). One of the genes dominantly expressed in the thermally selected strain (COX II) coded for cytochrome c oxidase subunit II. Northern blot analysis revealed that the accumulated levels of COX II transcripts were more abundant in embryos and unfertilized eggs from the thermally selected strain than those from the Donaldson strain. Furthermore, the differential expression patterns of the ATPase 6-8 gene were similar to those of the COX II gene, whereas the ATP synthase beta-subunit gene showed no significant differences between the two strains.
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Affiliation(s)
- Koki Ikeguchi
- Laboratory of Aquatic Molecular Biology and Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan
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25
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Hirayama M, Mitani H, Watabe S. Temperature-dependent growth rates and gene expression patterns of various medaka Oryzias latipes cell lines derived from different populations. J Comp Physiol B 2005; 176:311-20. [PMID: 16341864 DOI: 10.1007/s00360-005-0053-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2005] [Revised: 10/22/2005] [Accepted: 11/08/2005] [Indexed: 11/30/2022]
Abstract
Medaka Oryzias latipes has several geographically and genetically distinct populations. We examined temperature acclimation response in various medaka cell lines derived from different populations. Measurement of cell growth at various temperatures suggested that 15 degrees Celsius was the permissive growth temperature in all cell lines from the Northern Japanese and East Korean populations, but not in those from the Southern Japanese population and medaka-related species Oryzias celebensis, which inhabits a tropical zone. RT-PCR for 102 temperature-responsive genes, previously reported in other species, revealed that the accumulated mRNA level of a gene encoding HSP47 was lower at 25 degrees Celsius than at 33 degrees Celsius, and vice versa for 12 genes including IkappaBalpha and Rab-1c, in OLHNI-1 cell line from the Northern Japanese population. Further analysis by real-time PCR demonstrated that the accumulated mRNA levels of IkappaBalpha and Rab-1c in OLHNI-1 and OLSOK-e7 cell lines from the East Korean population were increased when the culture temperature was shifted from 33 to 15 degrees Celsius, but not in OLHdrR-e3 cell line from the Southern Japanese population. Since IkappaBalpha and Rab-1c are related to the NFkappaB cascade and endoplasmic reticulum-to-Golgi transport, respectively, it is inferred that immune responses and intracellular transport are possibly critical to temperature adaptation for medaka.
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Affiliation(s)
- Makoto Hirayama
- Laboratory of Aquatic Molecular Biology and Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 113-8657, Bunkyo, Tokyo, Japan
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26
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Itoi S, Misaki R, Hirayama M, Nakaniwa M, Liang CS, Kondo H, Watabe S. Identification of three isoforms for mitochondrial adenine nucleotide translocator in the pufferfish Takifugu rubripes. Mitochondrion 2005; 5:162-72. [PMID: 16050982 DOI: 10.1016/j.mito.2005.01.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2004] [Revised: 12/20/2004] [Accepted: 01/26/2005] [Indexed: 11/21/2022]
Abstract
Three adenine nucleotide translocator (ANT) genes were identified through in silico data mining of the Fugu genome database along with isolation of their corresponding cDNAs in vivo from the pufferfish (Takifugu rubripes). As a result of phylogenetic analysis, the ANT gene on scaffold_254 corresponded to mammalian ANT1, whereas both of those on scaffold_6 and scaffold_598 to mammalian ANT3. The ANT gene encoded by scaffold_6 was expressed ubiquitously in various tissues, whereas the ANT genes encoded by scaffold_254 and scaffold_598 were predominantly expressed in skeletal muscle and heart, respectively.
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MESH Headings
- Amino Acid Sequence
- Animals
- Base Sequence
- Cloning, Molecular
- Computational Biology
- Conserved Sequence
- DNA, Complementary
- Genome
- Isoenzymes/chemistry
- Isoenzymes/genetics
- Isoenzymes/isolation & purification
- Mitochondria, Heart/enzymology
- Mitochondria, Muscle/enzymology
- Mitochondrial ADP, ATP Translocases/chemistry
- Mitochondrial ADP, ATP Translocases/genetics
- Mitochondrial ADP, ATP Translocases/isolation & purification
- Molecular Sequence Data
- Nucleic Acid Amplification Techniques
- Phylogeny
- Polymerase Chain Reaction
- Reverse Transcriptase Polymerase Chain Reaction
- Sequence Analysis, DNA
- Sequence Homology, Amino Acid
- Takifugu/genetics
- Tissue Distribution
- Transcription, Genetic
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Affiliation(s)
- Shiro Itoi
- Laboratory of Aquatic Molecular Biology and Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan
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27
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Gracey AY, Fraser EJ, Li W, Fang Y, Taylor RR, Rogers J, Brass A, Cossins AR. Coping with cold: An integrative, multitissue analysis of the transcriptome of a poikilothermic vertebrate. Proc Natl Acad Sci U S A 2004; 101:16970-5. [PMID: 15550548 PMCID: PMC534716 DOI: 10.1073/pnas.0403627101] [Citation(s) in RCA: 299] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2004] [Accepted: 10/19/2004] [Indexed: 11/18/2022] Open
Abstract
How do organisms respond adaptively to environmental stress? Although some gene-specific responses have been explored, others remain to be identified, and there is a very poor understanding of the system-wide integration of response, particularly in complex, multitissue animals. Here, we adopt a transcript screening approach to explore the mechanisms underpinning a major, whole-body phenotypic transition in a vertebrate animal that naturally experiences extreme environmental stress. Carp were exposed to increasing levels of cold, and responses across seven tissues were assessed by using a microarray composed of 13,440 cDNA probes. A large set of unique cDNAs (approximately 3,400) were affected by cold. These cDNAs included an expression signature common to all tissues of 252 up-regulated genes involved in RNA processing, translation initiation, mitochondrial metabolism, proteasomal function, and modification of higher-order structures of lipid membranes and chromosomes. Also identified were large numbers of transcripts with highly tissue-specific patterns of regulation. By unbiased profiling of gene ontologies, we have identified the distinctive functional features of each tissue's response and integrate them into a comprehensive view of the whole-body transition from one strongly adaptive phenotype to another. This approach revealed an expression signature suggestive of atrophy in cooled skeletal muscle. This environmental genomics approach by using a well studied but nongenomic species has identified a range of candidate genes endowing thermotolerance and reveals a previously unrecognized scale and complexity of responses that impacts at the level of cellular and tissue function.
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Affiliation(s)
- Andrew Y Gracey
- School of Biological Sciences, University of Liverpool, Biosciences Building, Crown Street, Liverpool L39 7ZB, United Kindgom.
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28
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