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Andrews KR, Seaborn T, Egan JP, Fagnan MW, New DD, Chen Z, Hohenlohe PA, Waits LP, Caudill CC, Narum SR. Whole genome resequencing identifies local adaptation associated with environmental variation for redband trout. Mol Ecol 2023; 32:800-818. [PMID: 36478624 PMCID: PMC9905331 DOI: 10.1111/mec.16810] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 11/20/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022]
Abstract
Aquatic ectotherms are predicted to harbour genomic signals of local adaptation resulting from selective pressures driven by the strong influence of climate conditions on body temperature. We investigated local adaptation in redband trout (Oncorhynchus mykiss gairdneri) using genome scans for 547 samples from 11 populations across a wide range of habitats and thermal gradients in the interior Columbia River. We estimated allele frequencies for millions of single nucleotide polymorphism loci (SNPs) across populations using low-coverage whole genome resequencing, and used population structure outlier analyses to identify genomic regions under divergent selection between populations. Twelve genomic regions showed signatures of local adaptation, including two regions associated with genes known to influence migration and developmental timing in salmonids (GREB1L, ROCK1, SIX6). Genotype-environment association analyses indicated that diurnal temperature variation was a strong driver of local adaptation, with signatures of selection driven primarily by divergence of two populations in the northern extreme of the subspecies range. We also found evidence for adaptive differences between high-elevation desert vs. montane habitats at a smaller geographical scale. Finally, we estimated vulnerability of redband trout to future climate change using ecological niche modelling and genetic offset analyses under two climate change scenarios. These analyses predicted substantial habitat loss and strong genetic shifts necessary for adaptation to future habitats, with the greatest vulnerability predicted for high-elevation desert populations. Our results provide new insight into the complexity of local adaptation in salmonids, and important predictions regarding future responses of redband trout to climate change.
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Affiliation(s)
- Kimberly R Andrews
- Institute for Interdisciplinary Data Sciences (IIDS), University of Idaho, Moscow, Idaho, USA
| | - Travis Seaborn
- Department of Fish and Wildlife Sciences, College of Natural Resources, University of Idaho, Moscow, Idaho, USA
| | - Joshua P Egan
- Department of Biological Sciences, College of Science, University of Idaho, Moscow, Idaho, USA.,Bell Museum of Natural History, University of Minnesota, Saint Paul, Minnesota, USA
| | - Matthew W Fagnan
- Institute for Interdisciplinary Data Sciences (IIDS), University of Idaho, Moscow, Idaho, USA
| | - Daniel D New
- Institute for Interdisciplinary Data Sciences (IIDS), University of Idaho, Moscow, Idaho, USA
| | - Zhongqi Chen
- Aquaculture Research Institute, University of Idaho, Hagerman, Idaho, USA
| | - Paul A Hohenlohe
- Department of Biological Sciences, College of Science, University of Idaho, Moscow, Idaho, USA
| | - Lisette P Waits
- Department of Fish and Wildlife Sciences, College of Natural Resources, University of Idaho, Moscow, Idaho, USA
| | - Christopher C Caudill
- Department of Fish and Wildlife Sciences, College of Natural Resources, University of Idaho, Moscow, Idaho, USA
| | - Shawn R Narum
- Aquaculture Research Institute, University of Idaho, Hagerman, Idaho, USA.,Columbia River Inter-Tribal Fish Commission, Hagerman, Idaho, USA
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Aase-Remedios ME, Coll-Lladó C, Ferrier DEK. Amphioxus muscle transcriptomes reveal vertebrate-like myoblast fusion genes and a highly conserved role of insulin signalling in the metabolism of muscle. BMC Genomics 2022; 23:93. [PMID: 35105312 PMCID: PMC8805411 DOI: 10.1186/s12864-021-08222-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 11/25/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The formation and functioning of muscles are fundamental aspects of animal biology, and the evolution of 'muscle genes' is central to our understanding of this tissue. Feeding-fasting-refeeding experiments have been widely used to assess muscle cellular and metabolic responses to nutrition. Though these studies have focused on vertebrate models and only a few invertebrate systems, they have found similar processes are involved in muscle degradation and maintenance. Motivation for these studies stems from interest in diseases whose pathologies involve muscle atrophy, a symptom also triggered by fasting, as well as commercial interest in the muscle mass of animals kept for consumption. Experimentally modelling atrophy by manipulating nutritional state causes muscle mass to be depleted during starvation and replenished with refeeding so that the genetic mechanisms controlling muscle growth and degradation can be understood. RESULTS Using amphioxus, the earliest branching chordate lineage, we address the gap in previous work stemming from comparisons between distantly related vertebrate and invertebrate models. Our amphioxus feeding-fasting-refeeding muscle transcriptomes reveal a highly conserved myogenic program and that the pro-orthologues of many vertebrate myoblast fusion genes were present in the ancestral chordate, despite these invertebrate chordates having unfused mononucleate myocytes. We found that genes differentially expressed between fed and fasted amphioxus were orthologous to the genes that respond to nutritional state in vertebrates. This response is driven in a large part by the highly conserved IGF/Akt/FOXO pathway, where depleted nutrient levels result in activation of FOXO, a transcription factor with many autophagy-related gene targets. CONCLUSION Reconstruction of these gene networks and pathways in amphioxus muscle provides a key point of comparison between the distantly related groups assessed thus far, significantly refining the reconstruction of the ancestral state for chordate myoblast fusion genes and identifying the extensive role of duplicated genes in the IGF/Akt/FOXO pathway across animals. Our study elucidates the evolutionary trajectory of muscle genes as they relate to the increased complexity of vertebrate muscles and muscle development.
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Affiliation(s)
- Madeleine E Aase-Remedios
- The Scottish Oceans Institute, Gatty Marine Laboratory, School of Biology, University of St Andrews, St Andrews, Fife, KY16 8LB, UK
| | - Clara Coll-Lladó
- The Scottish Oceans Institute, Gatty Marine Laboratory, School of Biology, University of St Andrews, St Andrews, Fife, KY16 8LB, UK
| | - David E K Ferrier
- The Scottish Oceans Institute, Gatty Marine Laboratory, School of Biology, University of St Andrews, St Andrews, Fife, KY16 8LB, UK.
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Aravena-Canales D, Aedo JE, Molina A, Valdés JA. Regulation of the early expression of MAFbx/atrogin-1 and MuRF1 through membrane-initiated cortisol action in the skeletal muscle of rainbow trout. Comp Biochem Physiol B Biochem Mol Biol 2021; 253:110565. [PMID: 33497801 DOI: 10.1016/j.cbpb.2021.110565] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 12/18/2020] [Accepted: 01/13/2021] [Indexed: 11/17/2022]
Abstract
Glucocorticoids are key stress-related hormones in vertebrates, with cortisol being the main glucocorticoid in teleosts. Glucocorticoids exert their effects through two mechanisms of action: genomic/classic and membrane initiated. In mammals, cortisol-mediated stress has been found to be associated with increased expression of critical atrophy-related genes (atrogenes), such as MAFbx/atrogin-1 and murf1/trim63. However, the direct impact of cortisol on the early regulation of atrogene expression in teleost skeletal muscle and the contribution of membrane-initiated cortisol action to this process have not been identified. In this work, the mRNA levels of atrogin-1 and murf1 were assessed in isolated myotubes and skeletal muscle of rainbow trout administered with cortisol or cortisol-BSA. This latter compound is a membrane-impermeable cortisol analog that exclusively induces membrane-initiated effects. We found that cortisol (10 mg/kg) first decreased the expression of both atrogenes at 3 h of treatment and then increased their expression at 9 h of treatment in the skeletal muscle of rainbow trout. Additionally, the in vitro analysis suggested that membrane-initiated cortisol action regulates murf1 but not atrogin-1 in rainbow trout myotubes. Using RU486 to selectively block glucocorticoid receptor (GR), we found that early downregulation of murf1 is potentially mediated by membrane GR signaling in myotubes. Considering the results of both the in vivo and in vitro approaches, we suggest that membrane-initiated cortisol action regulates the early expression of atrophy-related processes in teleosts.
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Affiliation(s)
- Daniela Aravena-Canales
- Universidad Andrés Bello, Departamento Ciencias Biológicas, Facultad de Ciencias de la Vida, 8370146 Santiago, Chile; Interdisciplinary Center for Aquaculture Research (INCAR), 4030000 Concepción, Chile
| | - Jorge E Aedo
- Universidad Andrés Bello, Departamento Ciencias Biológicas, Facultad de Ciencias de la Vida, 8370146 Santiago, Chile; Interdisciplinary Center for Aquaculture Research (INCAR), 4030000 Concepción, Chile
| | - Alfredo Molina
- Universidad Andrés Bello, Departamento Ciencias Biológicas, Facultad de Ciencias de la Vida, 8370146 Santiago, Chile; Interdisciplinary Center for Aquaculture Research (INCAR), 4030000 Concepción, Chile
| | - Juan Antonio Valdés
- Universidad Andrés Bello, Departamento Ciencias Biológicas, Facultad de Ciencias de la Vida, 8370146 Santiago, Chile; Interdisciplinary Center for Aquaculture Research (INCAR), 4030000 Concepción, Chile.
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Lavajoo F, Perelló-Amorós M, Vélez EJ, Sánchez-Moya A, Balbuena-Pecino S, Riera-Heredia N, Fernández-Borràs J, Blasco J, Navarro I, Capilla E, Gutiérrez J. Regulatory mechanisms involved in muscle and bone remodeling during refeeding in gilthead sea bream. Sci Rep 2020; 10:184. [PMID: 31932663 PMCID: PMC6957526 DOI: 10.1038/s41598-019-57013-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 12/02/2019] [Indexed: 12/17/2022] Open
Abstract
The tolerance of fish to fasting offers a model to study the regulatory mechanisms and changes produced when feeding is restored. Gilthead sea bream juveniles were exposed to a 21-days fasting period followed by 2 h to 7-days refeeding. Fasting provoked a decrease in body weight, somatic indexes, and muscle gene expression of members of the Gh/Igf system, signaling molecules (akt, tor and downstream effectors), proliferation marker pcna, myogenic regulatory factors, myostatin, and proteolytic molecules such as cathepsins or calpains, while most ubiquitin-proteasome system members increased or remained stable. In bone, downregulated expression of Gh/Igf members and osteogenic factors was observed, whereas expression of the osteoclastic marker ctsk was increased. Refeeding recovered the expression of Gh/Igf system, myogenic and osteogenic factors in a sequence similar to that of development. Akt and Tor phosphorylation raised at 2 and 5 h post-refeeding, much faster than its gene expression increased, which occurred at day 7. The expression in bone and muscle of the inhibitor myostatin (mstn2) showed an inverse profile suggesting an inter-organ coordination that needs to be further explored in fish. Overall, this study provides new information on the molecules involved in the musculoskeletal system remodeling during the early stages of refeeding in fish.
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Affiliation(s)
- F Lavajoo
- Department of Cell Biology, Physiology and Immunology, Faculty of Biology, University of Barcelona, Barcelona, Spain
- Department of Marine Biology, Faculty of Marine Science and Technology, University of Hormozgan, Bandar Abbas, I.R., Iran
| | - M Perelló-Amorós
- Department of Cell Biology, Physiology and Immunology, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - E J Vélez
- Department of Cell Biology, Physiology and Immunology, Faculty of Biology, University of Barcelona, Barcelona, Spain
- Department of Veterinary Biomedical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, S7N 5B4, Canada
| | - A Sánchez-Moya
- Department of Cell Biology, Physiology and Immunology, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - S Balbuena-Pecino
- Department of Cell Biology, Physiology and Immunology, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - N Riera-Heredia
- Department of Cell Biology, Physiology and Immunology, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - J Fernández-Borràs
- Department of Cell Biology, Physiology and Immunology, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - J Blasco
- Department of Cell Biology, Physiology and Immunology, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - I Navarro
- Department of Cell Biology, Physiology and Immunology, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - E Capilla
- Department of Cell Biology, Physiology and Immunology, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - J Gutiérrez
- Department of Cell Biology, Physiology and Immunology, Faculty of Biology, University of Barcelona, Barcelona, Spain.
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Shaalan WM, El-Hameid NAA, El-Serafy SS, Salem M. Expressions and characterization of MuRFs, Atrogin-1, F-box25 genes in tilapia, Oreochromis niloticus, in response to starvation. FISH PHYSIOLOGY AND BIOCHEMISTRY 2019; 45:1321-1330. [PMID: 31190260 DOI: 10.1007/s10695-019-00667-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 05/24/2019] [Indexed: 06/09/2023]
Abstract
Muscle accretion is affected by the difference between protein synthesis and its degradation. Studies on different species revealed that muscle proteolysis is mediated by different pathways including the ubiquitin-proteasome pathway in which the ubiquitin protein ligases play an important role. These muscle atrophy associated ligases were not well studied in tilapia. In this study, we characterized the ubiquitin protein ligases MuRF1/2/3, Atrogin-1 and F-box25, members of the ubiquitin-proteasome pathway in tilapia, Oreochromis niloticus, and their expressions in the muscle of starved, fed, refed, and control fish. Sequences of these genes revealed presence of Ring finger, B-box, and Cos domains in all MuRF genes, as well as F-box domain in Atrogin-1 and F-box25 genes. Real-time qPCR data analysis showed that expression of MuRF1/2/3, Atrogin-1, F-box25, and proteasome complex genes was significantly upregulated in starved fish compared to fed fish. Concurrently, the proteasome activity was 1.7-folds elevated in the starved fish compared to fed fish. These results confirm the important role of these genes in muscle degradation and suggest potential usage as markers of muscle accretion in tilapia.
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Affiliation(s)
- Walaa M Shaalan
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, USA
- Department of Zoology, Faculty of Science, Benha University, Benha, Egypt
| | | | - Sabry S El-Serafy
- Department of Zoology, Faculty of Science, Benha University, Benha, Egypt
| | - Mohamed Salem
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, USA.
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Salmerón C, Navarro I, Johnston IA, Gutiérrez J, Capilla E. Characterisation and expression analysis of cathepsins and ubiquitin-proteasome genes in gilthead sea bream (Sparus aurata) skeletal muscle. BMC Res Notes 2015; 8:149. [PMID: 25880457 PMCID: PMC4431372 DOI: 10.1186/s13104-015-1121-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 04/02/2015] [Indexed: 12/02/2022] Open
Abstract
Background The proteolytic enzymes involved in normal protein turnover in fish muscle are also responsible for post-mortem softening of the flesh and are therefore potential determinants of product quality. The main enzyme systems involved are calpains, cathepsins, and the ubiquitin-proteasome (UbP). In this study on Sparus aurata (Sa), the coding sequences of cathepsins (SaCTSB and SaCTSDb) and UbP family members (SaN3 and SaUb) were cloned from fast skeletal muscle, and their expression patterns were examined during ontogeny and in a fasting/re-feeding experiment. Results The amino acid sequences identified shared 66-100% overall identity with their orthologues in other vertebrates, with well conserved characteristic functional domains and catalytic residues. SaCTSDb showed phylogenetic, sequence and tissue distribution differences with respect to its paralogue SaCTSDa, previously identified in the ovary. Expression of gilthead sea bream cathepsins (B, L, Da, Db) and UbP members (N3, Ub, MuRF1 and MAFbx) in fast skeletal muscle was determined at three different life-history stages and in response to fasting and re-feeding in juveniles. Most of the proteolytic genes analysed were significantly up-regulated during fasting, and down-regulated with re-feeding and, between the fingerling (15 g) and juvenile/adult stages (~50/500 g), consistent with a decrease in muscle proteolysis in both later contexts. In contrast, SaCTSDa and SaMuRF1 expression was relatively stable with ontogeny and SaUb had higher expression in fingerlings and adults than juveniles. Conclusions The data obtained in the present study suggest that cathepsins and UbP genes in gilthead sea bream are co-ordinately regulated during ontogeny to control muscle growth, and indicate that feeding regimes can modulate their expression, providing a potential dietary method of influencing post-mortem fillet tenderisation, and hence, product quality. Electronic supplementary material The online version of this article (doi:10.1186/s13104-015-1121-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Cristina Salmerón
- Department of Physiology and Immunology, Faculty of Biology, University of Barcelona, Av. Diagonal 643, Barcelona, 08028, Spain.
| | - Isabel Navarro
- Department of Physiology and Immunology, Faculty of Biology, University of Barcelona, Av. Diagonal 643, Barcelona, 08028, Spain.
| | - Ian A Johnston
- Scottish Oceans Institute, School of Biology, University of St Andrews, St Andrews Fife, KY16 8LB, Scotland, UK.
| | - Joaquim Gutiérrez
- Department of Physiology and Immunology, Faculty of Biology, University of Barcelona, Av. Diagonal 643, Barcelona, 08028, Spain.
| | - Encarnación Capilla
- Department of Physiology and Immunology, Faculty of Biology, University of Barcelona, Av. Diagonal 643, Barcelona, 08028, Spain.
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Macqueen DJ, Fuentes EN, Valdés JA, Molina A, Martin SA. The vertebrate muscle-specific RING finger protein family includes MuRF4 - A novel, conserved E3-ubiquitin ligase. FEBS Lett 2014; 588:4390-7. [DOI: 10.1016/j.febslet.2014.10.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Revised: 09/25/2014] [Accepted: 10/10/2014] [Indexed: 11/25/2022]
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9
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Li D, Lou Q, Zhai G, Peng X, Cheng X, Dai X, Zhuo Z, Shang G, Jin X, Chen X, Han D, He J, Yin Z. Hyperplasia and cellularity changes in IGF-1-overexpressing skeletal muscle of crucian carp. Endocrinology 2014; 155:2199-212. [PMID: 24617525 DOI: 10.1210/en.2013-1938] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The zebrafish skeletal muscle-specific promoter mylz2 was used to cause crucian carp overexpression of the zebrafish IGF-1 cDNA. In stable transgenic germline F1 progenies, a 5-fold increase in the level of IGF-1 in skeletal muscle was observed. Evident skeletal muscle hyperplasia was observed in the transgenic fish through histologic analysis. By analyzing the RNA sequencing transcriptome of the skeletal muscle of IGF-1 transgenic fish and nontransgenic control fish at 15 months of age, 10 966 transcripts with significant expression levels were identified with definite gene descriptions based on the corresponding zebrafish genome information. Based on the results of our RNA sequencing transcriptome profiling analysis and the results of the real-time quantitative PCR analysis performed to confirm the skeletal muscle transcriptomics analysis, several pathways, including IGF-1 signaling, aerobic metabolism, and protein degradation, were found to be activated in the IGF-1-overexpressing transgenic fish. Intriguingly, our transcriptional expression and protein assays indicated that the overexpression of IGF-1 stimulated a significant shift in the myofiber type toward a more oxidative slow muscle type. Although the body weight was surprisingly decreased by IGF-1 transgenic expression, significantly higher oxygen consumption rates were measured in IGF-1-overexpressing transgenic fish compared with their nontransgenic control fish. These results indicate that the sustained overexpression of IGF-1 in crucian carp skeletal muscle promotes myofiber hyperplasia and cellularity changes, which elicit alterations in the body energy metabolism and skeletal muscle growth.
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Affiliation(s)
- Dongliang Li
- Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences (D.L., Q.L., G.Z., X.P., X.C., X.D., Z.Z., G.S., X.J., X.C., D.H., J.H., Z.Y.), Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, China; and University of Chinese Academy of Sciences (D.L., G.Z., X.P., X.C., X.D., Z.Z., G.S.), Beijing, China
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10
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Li C, Beck BH, Peatman E. Nutritional impacts on gene expression in the surface mucosa of blue catfish (Ictalurus furcatus). DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2014; 44:226-234. [PMID: 24378224 DOI: 10.1016/j.dci.2013.12.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Revised: 12/20/2013] [Accepted: 12/21/2013] [Indexed: 06/03/2023]
Abstract
Short-term feed deprivation is a common occurrence in both wild and farmed fish species, due to reproductive processes, seasonal variations in temperature, or in response to a disease outbreak. Fasting can have dramatic physiological and biological consequences for fish, including impacts on mucosal immunity which can, in turn, change host susceptibility to pathogens. Culture and selection of blue catfish (Ictalurus furcatus) has gained importance as the production of a channel catfish×blue catfish (Ictalurus punctatus×I. furcatus) hybrid has increased in the Southeast US. Following a recent examination of fasting-induced impacts on mucosal immunity in channel catfish, here we utilized Illumina-based RNA-seq expression profiling to compare changes in blue catfish gill and skin after a brief (7 day) period of fasting. Transcriptome sequencing and de novo assembly of over 194 million 100 base-pair transcript reads was followed by differential expression analysis. Fasting altered a total of 530 genes in the surface mucosa, including genes regulating the immune response, energy metabolism, mucus production, cellular cytoskeletal structure, cell proliferation, and antioxidant responses. In particular, fasting perturbed arginine synthesis and metabolism pathways in a manner likely altering macrophage activation states and immune readiness. Our findings highlight key mediators of the critical interaction between nutrition and immunity at points of pathogen adherence and entry.
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Affiliation(s)
- Chao Li
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Benjamin H Beck
- United States Department of Agriculture, Agricultural Research Service, Stuttgart National Aquaculture Research Center, Stuttgart, AR 72160, USA
| | - Eric Peatman
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA.
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Salem M, Manor ML, Aussanasuwannakul A, Kenney PB, Weber GM, Yao J. Effect of sexual maturation on muscle gene expression of rainbow trout: RNA-Seq approach. Physiol Rep 2013; 1:e00120. [PMID: 24303187 PMCID: PMC3841051 DOI: 10.1002/phy2.120] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 09/10/2013] [Accepted: 09/11/2013] [Indexed: 11/28/2022] Open
Abstract
Muscle degradation occurs as a response to various physiological states that are regulated by specific molecular mechanisms. Previously, we characterized the metabolic changes of muscle deterioration of the female rainbow trout at full sexual maturity and spawning (Salem et al., Physiol. Genomics 2006;28:33–45; J. Proteomics 2010;73:778–789). Muscle deterioration in this model represents nutrient mobilization as a response to the energetic overdemands of the egg/ovarian growth phase. Our recent studies showed that most of the changes in muscle growth and quality start 2–3 months before spawning. Gravid fish exhibited reduced intramuscular fat that is lower in saturated and monounsaturated fatty acids and higher in polyunsaturated fatty acids compared to sterile fish. In this study, RNA-Seq was used to explain the mechanisms underlying changes during this phase of sexual maturity. Furthermore, to minimize changes due to nutrient deficits, fish were fed on a high-plane of nutrition. The RNA-Seq technique identified a gene expression signature that is consistent with metabolic changes of gravid fish. Gravid fish exhibited increased abundance of transcripts in metabolic pathways of fatty acid degradation and up-regulated expression of genes involved in biosynthesis of unsaturated fatty acids. In addition, increased expression of genes involved in the citric acid cycle and oxidative phosphorylation was observed for gravid fish. This muscle transcriptomic signature of fish fed on a high nutritional plane is quite distinct from that previously described for fish at terminal stages of maturity and suggest that female rainbow trout approaching spawning, on high nutritional planes, likely mobilize intramuscular fat rather than protein to support gonadal maturation.
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Affiliation(s)
- Mohamed Salem
- Department of Biology, Middle Tennessee State University Murfreesboro, Tennessee, 37132 ; Division of Animal and Nutritional Science, West Virginia University Morgantown, West Virginia, 26506-6108
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Liu L, Li C, Su B, Beck BH, Peatman E. Short-term feed deprivation alters immune status of surface mucosa in channel catfish (Ictalurus punctatus). PLoS One 2013; 8:e74581. [PMID: 24023952 PMCID: PMC3762756 DOI: 10.1371/journal.pone.0074581] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Accepted: 08/04/2013] [Indexed: 12/31/2022] Open
Abstract
Short-term feed deprivation (or fasting) is a common occurrence in aquacultured fish species whether due to season, production strategies, or disease. In channel catfish (Ictalurus punctatus) fasting impacts susceptibility to several bacterial pathogens including Flavobacterium columnare, the causative agent of columnaris disease. As columnaris gains entry through the gills and skin of fish, we examined here changes in transcriptional regulation induced in these surface mucosal tissues due to short-term (7 day) fasting. RNA-seq expression analysis revealed a total of 1,545 genes perturbed by fasting. Fasting significantly altered expression of critical innate immune factors in a manner consistent with lower immune fitness as well as dysregulating key genes involved in energy metabolism and cell cycling/proliferation. Downregulation of innate immune actors such as iNOS2b, Lysozyme C, and peptidoglycan recognition protein 6 is predicted to impact the delicate recognition/tolerance balance for commensal and pathogenic bacteria on the skin and gill. The highlighted expression profiles reveal potential mechanistic similarities between gut and surface mucosa and underscore the complex interrelationships between nutrition, mucosal integrity, and immunity in teleost fish.
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Affiliation(s)
- Lisa Liu
- Department of Chemistry and Chemical Biology, College of Arts and Sciences, Cornell University, Ithaca, New York, United States of America
| | - Chao Li
- Department of Fisheries and Allied Aquacultures, Auburn University, Auburn, Alabama, United States of America
| | - Baofeng Su
- Department of Fisheries and Allied Aquacultures, Auburn University, Auburn, Alabama, United States of America
| | - Benjamin H. Beck
- United States Department of Agriculture, Agricultural Research Service, Stuttgart National Aquaculture Research Center, Stuttgart, Arkansas, United States of America
| | - Eric Peatman
- Department of Fisheries and Allied Aquacultures, Auburn University, Auburn, Alabama, United States of America
- * E-mail:
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Seiliez I, Médale F, Aguirre P, Larquier M, Lanneretonne L, Alami-Durante H, Panserat S, Skiba-Cassy S. Postprandial regulation of growth- and metabolism-related factors in zebrafish. Zebrafish 2013; 10:237-48. [PMID: 23659367 DOI: 10.1089/zeb.2012.0835] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Zebrafish (Danio rerio) have been proposed as a possible model organism for nutritional physiology. However, this potential has not yet been realized and studies on the field remain scarce. In this work, we investigated in this species the effect of a single meal as well as that of an increase in the ratio of dietary carbohydrates/proteins on the postprandial expression of several hepatic and muscle metabolism-related genes and proteins. Fish were fed once either a commercial diet (experiment 1) or one of two experimental diets (experiment 2) containing different protein and carbohydrate levels after 72 h of starvation. Refeeding induced the postprandial expression of genes of glycolysis (GK, HK1) and lipogenesis (FAS, G6PDH, ACCa) and inhibited those of gluconeogenesis (cPEPCK) and beta-oxidation (CPT1b) in the viscera. In the muscle, refeeding increased transcript levels of myogenesis (Myf5, Myogenin), inhibited those of Ub-proteasomal proteolytic system (Atrogin1, Murf1a, Murf1b), and induced the activation of key signaling factors of protein synthesis (Akt, 4EBP1, S6K1, S6). However, diet composition had a low impact on the studied factors. Together, these results highlight some specificity of the zebrafish metabolism and demonstrate the interest and the limits of this species as a model organism for nutritional physiology studies.
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Affiliation(s)
- Iban Seiliez
- Institut National de la Recherche Agronomique , UR1067 Nutrition Métabolisme Aquaculture, St-Pée-sur-Nivelle, France.
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14
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Kong HJ, Lee YJ, Shin J, Cho HK, Kim WJ, Kim HS, Cheong J, Sohn YC, Lee SJ, Kim BS. Molecular characterization of tripartite motif protein 25 (TRIM25) involved in ERα-mediated transcription in the Korean rose bitterling Rhodeus uyekii. Comp Biochem Physiol B Biochem Mol Biol 2012; 163:147-53. [DOI: 10.1016/j.cbpb.2012.05.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Revised: 05/16/2012] [Accepted: 05/16/2012] [Indexed: 11/24/2022]
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15
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Ma H, Hostuttler M, Wei H, Rexroad CE, Yao J. Characterization of the rainbow trout egg microRNA transcriptome. PLoS One 2012; 7:e39649. [PMID: 22761856 PMCID: PMC3382587 DOI: 10.1371/journal.pone.0039649] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Accepted: 05/24/2012] [Indexed: 12/22/2022] Open
Abstract
MicroRNAs (miRNAs) are a class of endogenous small non-coding RNA molecules that regulate post-transcriptional expression of target genes and play important roles in animal development. The objectives of this study were to characterize the egg miRNA transcriptome and identify novel egg-predominant miRNAs in rainbow trout. Small RNAs isolated from mature unfertilized rainbow trout eggs were subjected to deep sequencing using an Illumina Genome Analyzer. The massive sequencing produced 24,621,741 quality reads, among which, 266 known miRNAs were identified and 230 putatively novel miRNAs were predicted. The most abundantly known miRNAs are let-7 and miR-21, accounting for 24.06% and 18.71% of the known miRNAs, respectively. Other known miRNAs which are abundantly present in eggs include miR-24, miR-202, miR-148, miR-30, miR-10, miR-146, miR-25, and miR-143. Real time PCR analysis using cDNAs derived from 10 tissues validated 87 out of 90 selected putative miRNAs and identified three novel miRNAs predominantly expressed in rainbow trout eggs. Each of these novel egg-predominant miRNAs is predicted to target a significant number of genes, most of which are significantly down-regulated in naturally ovulated rainbow trout eggs based on analysis of publicly available microarray data sets. Quantitative real time PCR analysis also demonstrated low expression of a selected number of target genes in eggs relative to liver and muscle tissues. This study represents the first complete survey of miRNAs in fish eggs and provides a starting point for future studies aimed at understanding the roles of miRNAs in controlling egg quality and early embryogenesis in rainbow trout.
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Affiliation(s)
- Hao Ma
- Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, West Virginia, United States of America
| | - Mark Hostuttler
- National Center for Cool and Cold Water Aquaculture, Kearneysville, West Virginia, United States of America
| | - Hairong Wei
- School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, Michigan, United States of America
| | - Caird E. Rexroad
- National Center for Cool and Cold Water Aquaculture, Kearneysville, West Virginia, United States of America
| | - Jianbo Yao
- Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, West Virginia, United States of America
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16
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Boussaid-Om Ezzine S, Métayer-Coustard S, Collin A, Rideau N, Leterrier C, Bouvarel I, Seiliez I, Tesseraud S. Regulators of protein metabolism are affected by cyclical nutritional treatments with diets varying in protein and energy content. J Nutr Biochem 2012; 23:1467-73. [PMID: 22305405 DOI: 10.1016/j.jnutbio.2011.09.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2011] [Revised: 09/12/2011] [Accepted: 09/22/2011] [Indexed: 10/14/2022]
Abstract
There is evidence that the E3 ubiquitin ligases muscle ring finger-1 (MuRF1) and atrogin-1, which mediate the ubiquitination of certain proteins and thereby their proteolysis, are regulated by cyclical nutritional treatments varying in lysine content. In order to explore further the regulatory mechanisms involved in metabolic adaptation to dietary changes, we investigated the effects of daily variations in energy [2800 (E-) followed by 3200 kcal/kg (E+)], protein [230 (P+) followed by 150g/kg (P-)] or both [E-P+ followed by E+P-] on muscle protein metabolism in 2-week-old male broiler chickens. Growth performance was similar for all treatments. Expression of atrogin-1 and MuRF1 was changed by alternation of diets varying in protein (higher expression with P- vs. P+) and energy content (higher expression with E- vs. E+). The expression of atrogin-1 was regulated with mixed diets (increase in E+P- vs. E-P+) but not that of MuRF1. Such regulation may involve the mammalian target of rapamycin (mTOR), which was more phosphorylated with P+ than with P-. Eukaryotic initiation factor 4E binding protein, p70S6 kinase and ribosomal protein S6, which are mTOR targets known to control protein synthesis, were highly activated by increased protein content (P+ vs. P-). The mechanisms coordinating the protein synthesis/proteolysis balance remain to be characterized.
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Cleveland BM, Weber GM. Effects of sex steroids on indices of protein turnover in rainbow trout (Oncorhynchusmykiss) white muscle. Gen Comp Endocrinol 2011; 174:132-42. [PMID: 21878334 DOI: 10.1016/j.ygcen.2011.08.011] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2011] [Revised: 08/12/2011] [Accepted: 08/15/2011] [Indexed: 01/26/2023]
Abstract
Effects of 17β-estradiol (E2), testosterone, and 5α-dihydrotestosterone (DHT) on protein turnover and proteolytic gene expression were determined in rainbow trout (Oncorhynchus mykiss) primary myocytes and white muscle tissue. E2 reduced rates of protein synthesis and increased rates of protein degradation in primary myocytes by 45% and 27%, respectively. DHT reduced rates of protein synthesis by 27%. Testosterone did not affect protein synthesis and neither testosterone nor DHT affected rates of protein degradation. Single injections of E2 increased expression of ubiquitin ligase genes fbxo32, fbxo25, and murf1, and the proteasome subunit psmd6 by 24h after injection. Within the cathepsin-lysosome pathway, E2 increased expression of cathepsins ctsd and ctsl, as well as autophagy-related genes atg4b and lc3b. Additionally, E2 injection up-regulated the expression of casp3 and casp9 caspase genes. Incubation of primary myocytes with E2 also increased expression of ubiquitin ligase genes. Therefore, catabolic effects of E2 on protein turnover result in part from E2-induced increases in proteolytic gene expression directly in muscle. Injection of testosterone increased milli-calpain (capn2) and casp3 expression, and DHT increased ctsd expression in vivo, whereas both androgens up-regulated fbxo32 expression in primary myocytes. These results suggest that effects of androgens on protein turnover in muscle are not driven primarily by direct effects of these hormones in this tissue.
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Affiliation(s)
- Beth M Cleveland
- United States Department of Agriculture, Agricultural Research Service, National Center for Cool and Cold Water Aquaculture, 11861 Leetown Rd., Kearneysville, WV 25430, USA.
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