1
|
Rbbani G, Murshed R, Siriyappagouder P, Sharko F, Nedoluzhko A, Joshi R, Galindo-Villegas J, Raeymaekers JAM, Fernandes JMO. Embryonic temperature has long-term effects on muscle circRNA expression and somatic growth in Nile tilapia. Front Cell Dev Biol 2024; 12:1369758. [PMID: 39149515 PMCID: PMC11324953 DOI: 10.3389/fcell.2024.1369758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 07/11/2024] [Indexed: 08/17/2024] Open
Abstract
Embryonic temperature has a lasting impact on muscle phenotype in vertebrates, involving complex molecular mechanisms that encompass both protein-coding and non-coding genes. Circular RNAs (circRNAs) are a class of regulatory RNAs that play important roles in various biological processes, but the effect of variable thermal conditions on the circRNA transcriptome and its long-term impact on muscle growth plasticity remains largely unexplored. To fill this knowledge gap, we performed a transcriptomic analysis of circRNAs in fast muscle of Nile tilapia (Oreochromis niloticus) subjected to different embryonic temperatures (24°C, 28°C and 32°C) and then reared at a common temperature (28°C) for 4 months. Nile tilapia embryos exhibited faster development and subsequently higher long-term growth at 32°C compared to those reared at 28°C and 24°C. Next-generation sequencing data revealed a total of 5,141 unique circRNAs across all temperature groups, of which 1,604, 1,531, and 1,169 circRNAs were exclusively found in the 24°C, 28°C and 32°C groups, respectively. Among them, circNexn exhibited a 1.7-fold (log2) upregulation in the 24°C group and a 1.3-fold (log2) upregulation in the 32°C group when compared to the 28°C group. Conversely, circTTN and circTTN_b were downregulated in the 24°C groups compared to their 28°C and 32°C counterparts. Furthermore, these differentially expressed circRNAs were found to have multiple interactions with myomiRs, highlighting their potential as promising candidates for further investigation in the context of muscle growth plasticity. Taken together, our findings provide new insights into the molecular mechanisms that may underlie muscle growth plasticity in response to thermal variation in fish, with important implications in the context of climate change, fisheries and aquaculture.
Collapse
Affiliation(s)
- Golam Rbbani
- Genomics Division, Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Riaz Murshed
- Genomics Division, Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | | | - Fedor Sharko
- Paleogenomics Laboratory, European University at Saint Petersburg, Saint Petersburg, Russia
- Paleogenomics Laboratory, National Research Center "Kurchatov Institute", Moscow, Russia
| | - Artem Nedoluzhko
- Paleogenomics Laboratory, European University at Saint Petersburg, Saint Petersburg, Russia
| | | | - Jorge Galindo-Villegas
- Genomics Division, Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Joost A M Raeymaekers
- Genomics Division, Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Jorge M O Fernandes
- Genomics Division, Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
- Institute of Marine Sciences, Spanish National Research Council, Barcelona, Spain
| |
Collapse
|
2
|
Xie X, Wang Y, Ma F, Ma R, Du L, Chen X. High-Temperature-Induced Differential Expression of miRNA Mediates Liver Inflammatory Response in Tsinling Lenok Trout (Brachymystax lenok tsinlingensis). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2024; 26:526-538. [PMID: 38647909 DOI: 10.1007/s10126-024-10315-x] [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: 11/14/2023] [Accepted: 04/10/2024] [Indexed: 04/25/2024]
Abstract
High-temperature stress poses a significant environmental challenge for aquatic organisms, including tsinling lenok trout (Brachymystax lenok tsinlingensis). This study aimed to investigate the role of microRNAs (miRNAs) in inducing liver inflammation in tsinling lenok trout under high-temperature stress. Tsinling lenok trout were exposed to high-temperature conditions (24 °C) for 8 h, and liver samples were collected for analysis. Through small RNA sequencing, we identified differentially expressed miRNAs in the liver of high-temperature-stressed tsinling lenok trout compared to the control group (maintained at 16 °C). Several miRNAs, including novel-m0105-5p and miR-8159-x, showed significant changes in expression levels. Additionally, we conducted bioinformatics analysis to explore the potential target genes of these differentially expressed miRNAs. Our findings revealed that these miRNA target genes are involved in inflammatory response pathways, such as NFKB1 and MAP3K5. The downregulation of novel-m0105-5p and miR-8159-x in the liver of high-temperature-stressed tsinling lenok trout suggests their role in regulating liver inflammatory responses. To validate this, we performed a dual-luciferase reporter assay to confirm the regulatory relationship between miRNAs and target genes. Our results demonstrated that novel-m0105-5p and miR-8159-x enhance the inflammatory response of hepatocytes by promoting the expression of NFKB1 and MAP3K5, respectively. In conclusion, our study provides evidence that high-temperature stress induces liver inflammation in tsinling lenok trout through dysregulation of miRNAs. Understanding the molecular mechanisms underlying the inflammatory response in tsinling lenok trout under high-temperature stress is crucial for developing strategies to mitigate the negative impacts of environmental stressors on fish health and aquaculture production.
Collapse
Affiliation(s)
- Xiaobin Xie
- Key Laboratory of Resource Utilization of Agricultural Solid Waste in Gansu Province, Tianshui Normal University, South Xihe Road, Qinzhou District, Tianshui, 741000, Gansu Province, People's Republic of China
| | - Yibo Wang
- Key Laboratory of Resource Utilization of Agricultural Solid Waste in Gansu Province, Tianshui Normal University, South Xihe Road, Qinzhou District, Tianshui, 741000, Gansu Province, People's Republic of China
| | - Fang Ma
- Key Laboratory of Resource Utilization of Agricultural Solid Waste in Gansu Province, Tianshui Normal University, South Xihe Road, Qinzhou District, Tianshui, 741000, Gansu Province, People's Republic of China.
| | - Ruilin Ma
- Key Laboratory of Resource Utilization of Agricultural Solid Waste in Gansu Province, Tianshui Normal University, South Xihe Road, Qinzhou District, Tianshui, 741000, Gansu Province, People's Republic of China
| | - Leqiang Du
- Key Laboratory of Resource Utilization of Agricultural Solid Waste in Gansu Province, Tianshui Normal University, South Xihe Road, Qinzhou District, Tianshui, 741000, Gansu Province, People's Republic of China
| | - Xin Chen
- Key Laboratory of Resource Utilization of Agricultural Solid Waste in Gansu Province, Tianshui Normal University, South Xihe Road, Qinzhou District, Tianshui, 741000, Gansu Province, People's Republic of China
| |
Collapse
|
3
|
Zhang J, Wang QH, Miao BB, Wu RX, Li QQ, Tang BG, Liang ZB, Niu SF. Liver transcriptome analysis reveal the metabolic and apoptotic responses of Trachinotus ovatus under acute cold stress. FISH & SHELLFISH IMMUNOLOGY 2024; 148:109476. [PMID: 38447780 DOI: 10.1016/j.fsi.2024.109476] [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: 12/13/2023] [Revised: 02/07/2024] [Accepted: 03/03/2024] [Indexed: 03/08/2024]
Abstract
Trachinotus ovatus is an economically important fish and has been recommended as a high-quality aquaculture fish breed for the high-quality development of sea ranches in the South China Sea. However, T. ovatus shows intolerance to low temperature, greatly limiting the extension of farming scale, reducing production efficiency in winter, and increasing farming risks. In this study, liver transcriptome analysis was investigated in T. ovatus under acute low temperature conditions (20 and 15 °C) using RNA sequencing (RNA-Seq) technology. Inter-groups differential expression analysis and trend analysis screened 1219 DEGs and four significant profiles (profiles 0, 3, 4, and 7), respectively. GO enrichment analysis showed that these DEGs were mainly related to metabolic process and cell growth and death process. KEGG enrichment analysis found that DEGs were mainly associated with lipid metabolism, carbohydrate metabolism, and cell growth and death, such as gluconeogenesis, glycolysis, fatty acid oxidation, cholesterol biosynthesis, p53 signaling pathway, cell cycle arrest, and apoptotic cell death. Moreover, protein-protein interaction networks identified two hub genes (FOS and JUNB) and some important genes related to metabolic process and cell growth and death process, that corresponding to enrichment analysis. Overall, gluconeogenesis, lipid mobilization, and fatty acid oxidation in metabolic process and cell cycle arrest and apoptotic cell death in cell growth and death process were enhanced, while glycolysis, liver glycogen synthesis and cholesterol biosynthesis in metabolic process were inhibited. The enhancement or attenuatment of metabolic process and cell growth and death process is conducive to maintain energy balance, normal fluidity of cell membrane, normal physiological functions of liver cell, enhancing the tolerance of T. ovatus to cold stress. These results suggested that metabolic process and cell growth and death process play important roles in response to acute cold stress in the liver of T. ovatus. Gene expreesion level analysis showed that acute cold stress at 15 °C was identified as a critical temperature point for T. ovatus in term of cellular metabolism alteration and apoptosis inducement, and rewarming intervention should be timely implemented above 15 °C. Our study can provide theoretical support for breeding cold-tolerant cultivars of T. ovatus, which is contributed to high-quality productions fish production.
Collapse
Affiliation(s)
- Jing Zhang
- College of Fisheries, Guangdong Ocean University, Zhanjiang, 524088, China; Southern Marine Science and Engineering Guangdong Laboratory, Zhanjiang, 524025, China
| | - Qing-Hua Wang
- College of Fisheries, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Ben-Ben Miao
- College of Fisheries, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Ren-Xie Wu
- College of Fisheries, Guangdong Ocean University, Zhanjiang, 524088, China; Southern Marine Science and Engineering Guangdong Laboratory, Zhanjiang, 524025, China
| | - Qian-Qian Li
- College of Fisheries, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Bao-Gui Tang
- College of Fisheries, Guangdong Ocean University, Zhanjiang, 524088, China; Southern Marine Science and Engineering Guangdong Laboratory, Zhanjiang, 524025, China
| | - Zhen-Bang Liang
- College of Fisheries, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Su-Fang Niu
- College of Fisheries, Guangdong Ocean University, Zhanjiang, 524088, China; Southern Marine Science and Engineering Guangdong Laboratory, Zhanjiang, 524025, China.
| |
Collapse
|
4
|
Ren X, Zhao J, Hu J. Non-concordant epigenetic and transcriptional responses to acute thermal stress in western mosquitofish (Gambusia affinis). Mol Ecol 2024:e17332. [PMID: 38529738 DOI: 10.1111/mec.17332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 02/28/2024] [Accepted: 03/18/2024] [Indexed: 03/27/2024]
Abstract
Climate change is intensifying the frequency and severity of extreme temperatures. Understanding the molecular mechanisms underlying the ability to cope with acute thermal stress is key for predicting species' responses to extreme temperature events. While many studies have focused on the individual roles of gene expression, post-transcriptional processes and epigenetic modifications in response to acute thermal stress, the relative contribution of these molecular mechanisms remains unclear. The wide range of thermal limits of western mosquitofish (Gambusia affinis) provides an opportunity to explore this interplay. Here, we quantified changes in gene expression, alternative splicing, DNA methylation and microRNA (miRNA) expression in muscle tissue dissected from mosquitofish immediately after reaching high (CTmax) or low thermal limit (CTmin). Although the numbers of genes showing expression and splicing changes in response to acute temperature stress were small, we found a possibly larger and non-redundant role of splicing compared to gene expression, with more genes being differentially spliced (DSGs) than differentially expressed (DEGs), and little overlap between DSGs and DEGs. We also identified a small proportion of CpGs showing significant methylation change (i.e. differentially methylated cytosines, DMCs) in fish at thermal limits; however, there was no overlap between DEGs and genes annotated with DMCs in both CTmax and CTmin experiments. The weak interplay between epigenetic modifications and gene expression was further supported by our discoveries of no differentially expressed miRNAs. These findings provide novel insights into the relative role of different molecular mechanisms underlying immediate responses to extreme temperatures and demonstrate non-concordant responses of epigenetic and transcriptional mechanisms to acute temperature stress.
Collapse
Affiliation(s)
- Xingyue Ren
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, P. R. China
| | - Junjie Zhao
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, P. R. China
| | - Juntao Hu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, P. R. China
| |
Collapse
|
5
|
Hu S, Chen L, Bai Y, He Q, Liu Y, Xu P. Epigenetic mechanisms of lncRNA in response to thermal stress during embryogenesis of allotetraploid Cyprinus carpio. Genomics 2023; 115:110698. [PMID: 37595932 DOI: 10.1016/j.ygeno.2023.110698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 07/24/2023] [Accepted: 08/15/2023] [Indexed: 08/20/2023]
Abstract
Embryogenesis and epigenetic mechanisms of lncRNA may play an important role in the formation of temperature tolerance in allotetraploid Cyprinus carpio. To investigate the response of lncRNA to thermal stress during embryogenesis of C. carpio, transcriptome sequencing was performed on 81 embryo or larva samples from different early development stages and temperatures. We identified 45,097 lncRNAs and analyzed transcriptome variation during embryogenesis. Stage-specific and temperature-specific DE lncRNAs and DEGs were screened. GO and KEGG analysis identified numerous pathways involved in thermal stress. Temperature-specific regulation of cis-/trans-/antisense lncRNAs was analyzed. Interaction network analysis identified 6 hub lncRNAs and many hub genes, such as cdk1 and hsf1. Decreased expression of many essential genes regulated by lncRNAs may lead to the death of embryos at 33 °C. Our findings provide new insights into the regulation of lncRNA in thermal stress response during embryogenesis and contribute to the understanding of environmental adaptation of allotetraploid species.
Collapse
Affiliation(s)
- Shuimu Hu
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Lin Chen
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Yulin Bai
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Qian He
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Yue Liu
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Peng Xu
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China.
| |
Collapse
|
6
|
Nandanpawar P, Sahoo L, Sahoo B, Murmu K, Chaudhari A, Pavan kumar A, Das P. Identification of differentially expressed genes and SNPs linked to harvest body weight of genetically improved rohu carp, Labeo rohita. Front Genet 2023; 14:1153911. [PMID: 37359361 PMCID: PMC10285081 DOI: 10.3389/fgene.2023.1153911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 05/25/2023] [Indexed: 06/28/2023] Open
Abstract
In most of the aquaculture selection programs, harvest body weight has been a preferred performance trait for improvement. Molecular interplay of genes linked to higher body weight is not elucidated in major carp species. The genetically improved rohu carp with 18% average genetic gain per generation with respect to harvest body weight is a promising candidate for studying genes' underlying performance traits. In the present study, muscle transcriptome sequencing of two groups of individuals, with significant difference in breeding value, belonging to the tenth generation of rohu carp was performed using the Illumina HiSeq 2000 platform. A total of 178 million paired-end raw reads were generated to give rise to 173 million reads after quality control and trimming. The genome-guided transcriptome assembly and differential gene expression produced 11,86,119 transcripts and 451 upregulated and 181 downregulated differentially expressed genes (DEGs) between high-breeding value and low-breeding value (HB & LB) groups, respectively. Similarly, 39,158 high-quality coding SNPs were identified with the Ts/Tv ratio of 1.23. Out of a total of 17 qPCR-validated transcripts, eight were associated with cellular growth and proliferation and harbored 13 SNPs. The gene expression pattern was observed to be positively correlated with RNA-seq data for genes such as myogenic factor 6, titin isoform X11, IGF-1 like, acetyl-CoA, and thyroid receptor hormone beta. A total of 26 miRNA target interactions were also identified to be associated with significant DETs (p-value < 0.05). Genes such as Myo6, IGF-1-like, and acetyl-CoA linked to higher harvest body weight may serve as candidate genes in marker-assisted breeding and SNP array construction for genome-wide association studies and genomic selection.
Collapse
Affiliation(s)
- P. Nandanpawar
- ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha, India
| | - L. Sahoo
- ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha, India
| | - B. Sahoo
- ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha, India
| | - K. Murmu
- ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha, India
| | - A. Chaudhari
- ICAR-Central Institute of Fisheries Education, Mumbai, Maharashtra, India
| | - A. Pavan kumar
- ICAR-Central Institute of Fisheries Education, Mumbai, Maharashtra, India
| | - P. Das
- ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha, India
| |
Collapse
|
7
|
Blödorn EB, Domingues WB, Martins AWS, Dellagostin EN, Komninou ER, Remião MH, Silveira TLR, Collares GL, Giongo JL, Vaucher RA, Campos VF. MicroRNA qPCR normalization in Nile tilapia (Oreochromis niloticus): Effects of acute cold stress on potential reference targets. FISH PHYSIOLOGY AND BIOCHEMISTRY 2023; 49:409-423. [PMID: 37074474 DOI: 10.1007/s10695-023-01190-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 04/05/2023] [Indexed: 05/03/2023]
Abstract
The Nile tilapia (Oreochromis niloticus) is one of the most important cultured fish worldwide, but tilapia culture is largely affected by low temperatures. Recent studies suggest that microRNAs (miRNAs) regulate cold tolerance traits in fish. In general, qPCR-based methods are the simplest and most accurate forms of miRNA quantification. However, qPCR data heavily depends on appropriate normalization. Therefore, the aim of the present study is to determine whether the expression of previously tested, stably expressed miRNAs are affected by acute cold stress in Nile tilapia. For this purpose, one small nuclear RNA (U6) and six candidate reference miRNAs (miR-23a, miR-25-3, Let-7a, miR-103, miR-99-5, and miR-455) were evaluated in four tissues (blood, brain, liver, and gills) under two experimental conditions (acute cold stress and control) in O. niloticus. The stability of the expression of each candidate reference miRNA was analyzed by four independent methods (the delta Ct method, geNorm, NormFinder, and BestKeeper). Further, consensual comprehensive ranking of stability was built with RefFinder. Overall, miR-103 was the most stable reference miRNA in this study, and miR-103 and Let-7a were the best combination of reference targets. Equally important, Let-7a, miR-23a, and miR-25-3 remained consistently stable across different tissues and experimental groups. Considering all variables, U6, miR-99-5, and miR-455 were the least stable candidates under acute cold stress. Most important, suitable reference miRNAs were validated in O. niloticus, facilitating further accurate miRNA quantification in this species.
Collapse
Affiliation(s)
- Eduardo B Blödorn
- Laboratório de Genômica Estrutural, Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - William B Domingues
- Laboratório de Genômica Estrutural, Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Amanda W S Martins
- Laboratório de Genômica Estrutural, Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Eduardo N Dellagostin
- Laboratório de Genômica Estrutural, Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Eliza R Komninou
- Laboratório de Genômica Estrutural, Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Mariana H Remião
- Laboratório de Genômica Estrutural, Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Tony L R Silveira
- Instituto de Ciências Biológicas, Universidade Federal do Rio Grande, Rio Grande, RS, Brazil
| | - Gilberto L Collares
- Agência de Desenvolvimento da Bacia da Lagoa Mirim, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Janice L Giongo
- Laboratório de Pesquisa em Bioquímica e Biologia Molecular de Micro-Organismos, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Rodrigo A Vaucher
- Laboratório de Pesquisa em Bioquímica e Biologia Molecular de Micro-Organismos, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Vinicius Farias Campos
- Laboratório de Genômica Estrutural, Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil.
| |
Collapse
|
8
|
Cao Q, Zhang H, Li T, He L, Zong J, Shan H, Huang L, Zhang Y, Liu H, Jiang J. Profiling miRNAs of Teleost Fish in Responses to Environmental Stress: A Review. BIOLOGY 2023; 12:biology12030388. [PMID: 36979079 PMCID: PMC10045198 DOI: 10.3390/biology12030388] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 02/11/2023] [Accepted: 02/24/2023] [Indexed: 03/05/2023]
Abstract
miRNAs are a class of endogenous and evolutionarily conserved noncoding short RNA molecules that post-transcriptionally regulate gene expression through sequence-specific interactions with mRNAs and are capable of controlling gene expression by binding to miRNA targets and interfering with the final protein output. The miRNAs of teleost were firstly reported in zebrafish development, but there are recent studies on the characteristics and functions of miRNAs in fish, especially when compared with mammals. Environmental factors including salinity, oxygen concentration, temperature, feed, pH, environmental chemicals and seawater metal elements may affect the transcriptional and posttranscriptional regulators of miRNAs, contributing to nearly all biological processes. The survival of aquatic fish is constantly challenged by the changes in these environmental factors. Environmental factors can influence miRNA expression, the functions of miRNAs and their target mRNAs. Progress of available information is reported on the environmental effects of the identified miRNAs, miRNA targets and the use of miRNAs in fish.
Collapse
Affiliation(s)
- Quanquan Cao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
- MARBEC, University Montpellier, CNRS, IFREMER, IRD, 34090 Montpellier, France
- Correspondence: or (Q.C.); (H.L.); (J.J.); Tel./Fax: +86-28-86291010 (J.J.)
| | - Hailong Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Tong Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Lingjie He
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jiali Zong
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Hongying Shan
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Lishi Huang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Yupeng Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Haifeng Liu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Correspondence: or (Q.C.); (H.L.); (J.J.); Tel./Fax: +86-28-86291010 (J.J.)
| | - Jun Jiang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Correspondence: or (Q.C.); (H.L.); (J.J.); Tel./Fax: +86-28-86291010 (J.J.)
| |
Collapse
|
9
|
Thermal Stress Induces Metabolic Responses in Juvenile Qingtian Paddy Field Carp Cyprinus carpio var qingtianensis. Animals (Basel) 2022; 12:ani12233395. [PMID: 36496916 PMCID: PMC9739747 DOI: 10.3390/ani12233395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 11/24/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022] Open
Abstract
Extreme fluctuations in water temperature lead to significant economic losses for the aquaculture industry. Cyprinus carpio var qingtianensis (locally called Qingtian paddy field carp), is a local variety commonly found in Zhejiang province, China. Unlike traditional aquaculture environments, the water temperature range between day and night in the rice field environment is much larger, and the high temperature in summer may exceed the growth threshold of fish because there is no manual intervention; therefore, the study of how the Qingtian paddy field carp (PF carp) adapts to high-temperature conditions can shed light how the species adapt to the rice field environment. To investigate the molecular mechanisms of this fish under thermal stress, the liver metabolomics of Qiangtian paddy field carp (PF carp) were analyzed. In this study, metabolomics was used to examine the metabolic reaction of PF carp (102 days old, 104.69 ± 3.08 g in weight, 14.65 ± 0.46 cm in length) at water temperatures of 28 °C (control group, CG), 34 °C (experimental group (EG) 34), and 38 °C (EG38). The results show that 175 expression profile metabolites (DEMs), including 115 upregulated and 60 downregulated metabolites, were found in the CG vs. EG34. A total of 354 DEMs were inspected in CG vs. EG38, with 85 metabolites downregulated and 269 metabolites upregulated. According to the pathway enrichment study, various pathways were altered by thermal stress, including those of lipid, amino-acid, and carbohydrate metabolism. Our study presents a potential metabolic profile for PF carp under thermal stress. It also demonstrates how the host responds to thermal stress on a metabolic and molecular level.
Collapse
|
10
|
Zhao W, Cheng J, Luo Y, Fu W, Zhou L, Wang X, Wang Y, Yang Z, Yao X, Ren M, Zhong Z, Wu X, Ren Z, Li Y. MicroRNA let-7f-5p regulates PI3K/AKT/COX2 signaling pathway in bacteria-induced pulmonary fibrosis via targeting of PIK3CA in forest musk deer. PeerJ 2022; 10:e14097. [PMID: 36217380 PMCID: PMC9547585 DOI: 10.7717/peerj.14097] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 08/31/2022] [Indexed: 01/25/2023] Open
Abstract
Background Recent studies have characterized that microRNA (miRNA) is a suitable candidate for the study of bleomycin/LPS-induced pulmonary fibrosis, but the knowledge on miRNA in bacteria-induced pulmonary fibrosis (BIPF) is limited. Forest musk deer (Moschus berezovskii, FMD) is an important endangered species that has been seriously affected by BIPF. We sought to determine whether miRNA exist that modulates the pathogenesis of BIPF in FMD. Methods High-throughput sequencing and RT-qPCR were used to determine the differentially expressed miRNAs (DEmiRNAs) in the blood of BIPF FMD. The DEmiRNAs were further detected in the blood and lung of BIPF model rat by RT-qPCR, and the targeting relationship between candidate miRNA and its potential target gene was verified by dual-luciferase reporter activity assay. Furthermore, the function of the candidate miRNA was verified in the FMD lung fibroblast cells (FMD-C1). Results Here we found that five dead FMD were suffered from BIPF, and six circulating miRNAs (miR-30g, let-7f-5p, miR-27-3p, miR-25-3p, miR-9-5p and miR-652) were differentially expressed in the blood of the BIPF FMD. Of these, let-7f-5p showed reproducibly lower level in the blood and lung of the BIPF model rat, and the expression levels of PI3K/AKT/COX2 signaling pathway genes (PIK3CA, PDK1, Akt1, IKBKA, NF-κB1 and COX2) were increased in the lung of BIPF model rats, suggesting that there is a potential correlation between BIPF and the PI3K/AKT/COX2 signaling pathway. Notably, using bioinformatic prediction and experimental verification, we demonstrated that let-7f-5p is conserved across mammals, and the seed sequence of let-7f-5p displays perfect complementarity with the 3' UTR of PIK3CA gene and the expression of the PIK3CA gene was regulated by let-7f-5p. In order to determine the regulatory relationship between let-7f-5p and the PI3K/AKT/COX2 signaling pathway in FMD, we successfully cultured FMD-C1, and found that let-7f-5p could act as a negative regulator for the PI3K/Akt/COX2 signaling pathway in FMD-C1. Collectively, this study not only provided a study strategy for non-invasive research in pulmonary disease in rare animals, but also laid a foundation for further research in BIPF.
Collapse
Affiliation(s)
- Wei Zhao
- College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Sichuan Province, China
| | - Jianguo Cheng
- Sichuan Institute of Musk Deer Breeding, Dujiangyan, Sichuan Province, China
| | - Yan Luo
- College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Sichuan Province, China
| | - Wenlong Fu
- Sichuan Institute of Musk Deer Breeding, Dujiangyan, Sichuan Province, China
| | - Lei Zhou
- Sichuan Institute of Musk Deer Breeding, Dujiangyan, Sichuan Province, China
| | - Xiang Wang
- College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Sichuan Province, China
| | - Yin Wang
- College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Sichuan Province, China
| | - Zexiao Yang
- College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Sichuan Province, China
| | - Xueping Yao
- College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Sichuan Province, China
| | - Meishen Ren
- College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Sichuan Province, China
| | - Zhijun Zhong
- College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Sichuan Province, China
| | - Xi Wu
- College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Sichuan Province, China
| | - Ziwei Ren
- College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Sichuan Province, China
| | - Yimeng Li
- College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Sichuan Province, China
| |
Collapse
|
11
|
Chen J, Song C, Wen H, Liu G, Wu N, Li H, Xue M, Xu P. miR-1/AMPK-Mediated Glucose and Lipid Metabolism under Chronic Hypothermia in the Liver of Freshwater Drum, Aplodinotus grunniens. Metabolites 2022; 12:metabo12080697. [PMID: 36005571 PMCID: PMC9415528 DOI: 10.3390/metabo12080697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 07/23/2022] [Accepted: 07/25/2022] [Indexed: 12/10/2022] Open
Abstract
Our previous study demonstrated that low temperature could induce hepatic inflammation and suppress the immune and oxidation resistance of freshwater drum. However, the metabolism, especially the glucose and lipid metabolism involved, is poorly studied. To further explore the chronic hypothermia response of freshwater drum, an 8-day hypothermia experiment was conducted at 10 °C to investigate the effect of chronic hypothermia on glucose and lipid metabolism via biochemical and physiological indexes, and metabolic enzyme activities, miRNAs and mRNA-miRNA integrate analysis in the liver. Plasma and hepatic biochemical parameters reveal chronic hypothermia-promoted energy expenditure. Metabolic enzyme levels uncover that glycolysis was enhanced but lipid metabolism was suppressed. Differentially expressed miRNAs induced by hypothermia were mainly involved in glucose and lipid metabolism, programmed cell death, disease, and cancerization. Specifically, KEGG enrichment indicates that AMPK signaling was dysregulated. mRNA-miRNA integrated analysis manifests miR-1 and AMPK, which were actively co-related in the regulatory network. Furthermore, transcriptional expression of key genes demonstrates hypothermia-activated AMPK signaling by miR-1 and subsequently inhibited the downstream glucogenic and glycogenic gene expression and gene expression of fatty acid synthesis. However, glycogenesis was alleviated to the control level while fatty acid synthesis was still suppressed at 8 d. Meanwhile, the gene expressions of glycolysis and fatty acid oxidation were augmented under hypothermia. In conclusion, these results suggest that miR-1/AMPK is an important target for chronic hypothermia control. It provides a theoretical basis for hypothermia resistance on freshwater drum.
Collapse
Affiliation(s)
- Jianxiang Chen
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; (J.C.); (C.S.); (H.W.); (G.L.); (N.W.); (M.X.)
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Changyou Song
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; (J.C.); (C.S.); (H.W.); (G.L.); (N.W.); (M.X.)
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Haibo Wen
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; (J.C.); (C.S.); (H.W.); (G.L.); (N.W.); (M.X.)
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Guangxiang Liu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; (J.C.); (C.S.); (H.W.); (G.L.); (N.W.); (M.X.)
| | - Ningyuan Wu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; (J.C.); (C.S.); (H.W.); (G.L.); (N.W.); (M.X.)
| | - Hongxia Li
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; (J.C.); (C.S.); (H.W.); (G.L.); (N.W.); (M.X.)
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
- Correspondence: (H.L.); (P.X.)
| | - Miaomiao Xue
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; (J.C.); (C.S.); (H.W.); (G.L.); (N.W.); (M.X.)
| | - Pao Xu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; (J.C.); (C.S.); (H.W.); (G.L.); (N.W.); (M.X.)
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
- Correspondence: (H.L.); (P.X.)
| |
Collapse
|
12
|
Liu Z, Ma F, Kang Y, Liu X. Gene ssa-miR-301a-3p improves rainbow trout ( Oncorhynchus mykiss) resistance to heat stress by targeting hsp90b2. PeerJ 2022; 10:e13476. [PMID: 35811807 PMCID: PMC9266697 DOI: 10.7717/peerj.13476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 05/01/2022] [Indexed: 01/17/2023] Open
Abstract
Rainbow trout (Oncorhynchus mykiss) is a cold-water fish that is commonly harmed by high temperatures. MicroRNAs (miRNAs) are being investigated intensively because they act as essential metabolic regulators and have a role in the heat stress response. Although there have been numerous studies on rainbow trout heat stress, research on miRNA implicated in rainbow trout heat stress is quite restricted. Rainbow trout were sampled at 18 and 24 °C, respectively, to examine the mechanism of miRNA under heat stress, and we identified a heat stress-induced miRNA, ssa-miR-301a-3p, for further investigation based on our bioinformatics analysis of rainbow trout small RNA sequencing data. Bioinformatics research suggested that hsp90b2 is a probable target gene for ssa-miR-301a-3p. QRT-PCR was used to confirm the expression levels of ssa-miR-301a-3p and hsp90b2. Meanwhile, the dual-luciferase reporter assay was employed to validate the ssa-miR-301a-3p-hsp90b2 targeted connection. The results indicated that at 24 °C, the relative expression of ssa-miR-301a-3p was considerably lower than at 18 °C. On the other hand, hsp90b2 expression, followed the opposite pattern. The binding of ssa-miR-301a-3p to the 3'-UTR of hsp90b2 resulted in a substantial decrease in luciferase activity. The findings showed that ssa-miR-301a-3p was implicated in heat stress, and our findings provide fresh insights into the processes of miRNA in response to heat stress in rainbow trout.
Collapse
Affiliation(s)
- Zhe Liu
- Gansu Agricultural University, Lanzhou, China
| | - Fang Ma
- Tianshui Normal University, Tianshui, China
| | - Yujun Kang
- Gansu Agricultural University, Lanzhou, China
| | - Xiaoxia Liu
- Gansu Agricultural University, Lanzhou, China
| |
Collapse
|
13
|
Shen F, Geng Y, Zhang L, Luo L, Yan G, Hou R, Yue B, Zhang X. Transcriptome Analysis Reveals the Alternative Splicing Changes in the Immune-Related Genes of the Giant Panda (Ailuropoda melanoleuca), in Response to the Canine Distemper Vaccine. Zoolog Sci 2022; 39:275-285. [DOI: 10.2108/zs210078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 01/18/2022] [Indexed: 11/17/2022]
Affiliation(s)
- Fujun Shen
- The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China
| | - Yang Geng
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Liang Zhang
- The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China
| | - Li Luo
- The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China
| | - Guoqiang Yan
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Rong Hou
- The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China
| | - Bisong Yue
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Xiuyue Zhang
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China
| |
Collapse
|
14
|
Mugwanya M, Dawood MA, Kimera F, Sewilam H. Anthropogenic temperature fluctuations and their effect on aquaculture: A comprehensive review. AQUACULTURE AND FISHERIES 2022. [DOI: 10.1016/j.aaf.2021.12.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
|
15
|
Opinion AGR, Çakir R, De Boeck G. Better together: Cross-tolerance induced by warm acclimation and nitrate exposure improved the aerobic capacity and stress tolerance of common carp Cyprinus carpio. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 225:112777. [PMID: 34534834 DOI: 10.1016/j.ecoenv.2021.112777] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/08/2021] [Accepted: 09/10/2021] [Indexed: 06/13/2023]
Abstract
Climate warming is a threat of imminent concern that may exacerbate the impact of nitrate pollution on fish fitness. These stressors can individually affect the aerobic capacity and stress tolerance of fish. In combination, they may interact in unexpected ways where exposure to one stressor may heighten or reduce the resilience to another stressor and their interactive effects may not be uniform across species. Here, we examined how nitrate pollution under a warming scenario affects the aerobic scope (AS), and the hypoxia and heat stress susceptibility of a generally tolerant fish species, common carp Cyprinus carpio. We used a 3 × 2 factorial design, where fish were exposed to one of three ecologically relevant levels of nitrate (0, 50, or 200 mg NO3- L-1) and one of two temperatures (18 °C or 26 °C) for 5 weeks. Warm acclimation increased the AS by 11% due to the maintained standard metabolic rate and increased maximum metabolic rate at higher temperature, and the AS improvement seemed greater at higher nitrate concentration. Warm-acclimated fish exposed to 200 mg NO3- L-1 were less susceptible to acute hypoxia, and fish acclimated at higher temperature exhibited improved heat tolerance (critical thermal maxima, CTMax) by 5 °C. This cross-tolerance can be attributed to the hematological results including maintained haemoglobin and increased haematocrit levels that may have compensated for the initial surge in methaemoglobin at higher nitrate exposure.
Collapse
Affiliation(s)
- April Grace R Opinion
- University of Antwerp, Department of Biology, Systemic Physiological and Ecotoxicological Research (SPHERE), Groenenborgerlaan 171, 2020 Antwerp, Belgium.
| | - Rümeysa Çakir
- University of Antwerp, Department of Biology, Systemic Physiological and Ecotoxicological Research (SPHERE), Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Gudrun De Boeck
- University of Antwerp, Department of Biology, Systemic Physiological and Ecotoxicological Research (SPHERE), Groenenborgerlaan 171, 2020 Antwerp, Belgium
| |
Collapse
|
16
|
Zhao L, He K, Xiao Q, Liu Q, Luo W, Luo J, Fu H, Li J, Wu X, Du J, Gong Q, Wang X, Yang S. Comparative transcriptome profiles of large and small bodied large-scale loaches cultivated in paddy fields. Sci Rep 2021; 11:4936. [PMID: 33654201 PMCID: PMC7925675 DOI: 10.1038/s41598-021-84519-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 02/03/2021] [Indexed: 01/31/2023] Open
Abstract
Fish culture in paddy fields is a traditional aquaculture mode, which has a long history in East Asia. Large-scale loach (Paramisgurnus dabryanus) fast growth is suitable for paddy fields aquaculture in China. The objective of this study was to identify differential expression genes (DEGs) in the brain, liver and muscle tissues between large (LG, top 5% of maximum total length) and small (SG, top 5% of minimum total length) groups using RNA-seq. In total, 150 fish were collected each week and 450 fish were collected at twelfth week from three paddy fields for all the experimental. Histological observation found that the muscle fibre diameter of LG loaches was greater than that of SG loaches. Transcriptome results revealed that the high expression genes (HEGs) in LG loaches (fold change ≥ 2, p < 0.05) were mainly concentrated in metabolic pathways, such as "Thyroid hormone signalling pathway", "Citrate cycle (TCA cycle)", "Carbon metabolism", "Fatty acid metabolism", and "Cholesterol metabolism", and the HEGs in SG loaches were enriched in the pathways related to environmental information processing such as "Cell adhesion molecules (CAMs)", "ECM- receptor interaction" and "Rap1 signalling pathway"; cellular processes such as "Tight junction", "Focal adhesion", "Phagosome" and "Adherens junction". Furthermore, IGFs gene family may play an important role in loach growth for their different expression pattern between the two groups. These findings can enhance our understanding about the molecular mechanism of different growth and development levels of loaches in paddy fields.
Collapse
Affiliation(s)
- Liulan Zhao
- grid.80510.3c0000 0001 0185 3134College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130 China
| | - Kuo He
- grid.80510.3c0000 0001 0185 3134College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130 China
| | - Qing Xiao
- grid.80510.3c0000 0001 0185 3134College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130 China
| | - Qiao Liu
- grid.80510.3c0000 0001 0185 3134College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130 China
| | - Wei Luo
- grid.80510.3c0000 0001 0185 3134College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130 China
| | - Jie Luo
- grid.80510.3c0000 0001 0185 3134College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130 China
| | - Hongmei Fu
- grid.80510.3c0000 0001 0185 3134College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130 China
| | - Jiayao Li
- grid.412514.70000 0000 9833 2433Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, 200090 China
| | - Xugan Wu
- grid.412514.70000 0000 9833 2433Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, 200090 China
| | - Jun Du
- grid.465230.60000 0004 1777 7721Fisheries Institute, Sichuan Academy of Agricultural Science, Chengdu, 611731 China
| | - Quan Gong
- grid.465230.60000 0004 1777 7721Fisheries Institute, Sichuan Academy of Agricultural Science, Chengdu, 611731 China
| | - Xun Wang
- grid.80510.3c0000 0001 0185 3134College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130 China
| | - Song Yang
- grid.80510.3c0000 0001 0185 3134College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130 China
| |
Collapse
|
17
|
Sun JL, Zhao LL, He K, Liu Q, Luo J, Zhang DM, Liang J, Liao L, Ma JD, Yang S. MicroRNA regulation in hypoxic environments: differential expression of microRNAs in the liver of largemouth bass (Micropterus salmoides). FISH PHYSIOLOGY AND BIOCHEMISTRY 2020; 46:2227-2242. [PMID: 32948974 DOI: 10.1007/s10695-020-00877-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 09/08/2020] [Indexed: 06/11/2023]
Abstract
Environmental changes in intensive aquaculture commonly lead to hypoxic stress for cultured largemouth bass (Micropterus salmoides). To better to understand the hypoxic stress response mechanisms, the miRNA expression profiles of the livers of largemouth bass exposed for 24 h to three different dissolved oxygen levels (7.0 ± 0.2 mg/L as control, 3.0 ± 0.2 mg/L and 1.2 ± 0.2 mg/L) were compared. In this study, a total of 266 known miRNAs were identified, 84 of which were differentially expressed compared with the control group. Thirteen of the differentially expressed miRNAs (miR-15b-5p, miR-30a-3p, miR-133a-3p, miR-19d-5p, miR-1288-3p, miR456, miR-96-5p, miR-23a-3p, miR-23b-5p, miR-214, miR-24, miR-20a-3p, and miR-2188-5p) were significantly enriched in VEGF signaling pathway, MAPK signaling pathway, and phosphatidylinositol signaling system. These miRNAs were significantly downregulated during stress, especially after a 4-h exposure to hypoxia. In contrast, their target genes (vegfa, pla2g4a, raf1a, pik3c2a, clam2a, inpp1, pi4k2b, mtmr14, ip6k, itpkca, map3k7, and Jun) were significant upregulated after 4 h of hypoxic stress. Moreover, two potential hypoxia-tolerance signal transduction pathways (MAPK signaling pathway and phosphatidylinositol signaling system) were revealed, both of which may play important roles in responding to acute hypoxic stress. We see that miRNAs played an important role in regulating gene expression related to physiological responses to hypoxia. Potential functional network regulated by miRNAs under hypoixic stress in the liver of largemouth bass (Micropterus salmoides). Blue boxes indicated that the expression of miRNA or target genes were down-regulated. Red boxes indicated that the expression of miRNA or target genes wasere up-regulated.
Collapse
Affiliation(s)
- Jun Long Sun
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan Aquaculture Breeding Engineering Research Center, Hainan University, Haikou, 570228, Hainan, China
| | - Liu Lan Zhao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Kuo He
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Qiao Liu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Jie Luo
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Dong Mei Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Ji Liang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Lei Liao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Ji Deng Ma
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Song Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
| |
Collapse
|
18
|
Zhao LL, Wu H, Sun JL, Liao L, Cui C, Liu Q, Luo J, Tang XH, Luo W, Ma JD, Ye X, Li SJ, Yang S. MicroRNA-124 regulates lactate transportation in the muscle of largemouth bass (micropterus salmoides) under hypoxia by targeting MCT1. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2020; 218:105359. [PMID: 31765944 DOI: 10.1016/j.aquatox.2019.105359] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 11/11/2019] [Accepted: 11/14/2019] [Indexed: 06/10/2023]
Abstract
Carbohydrate metabolism switches from aerobic to anaerobic (glycolysis) to supply energy in response to acute hypoxic stress. Acute hypoxic stress with dissolved oxygen (DO) levels of 1.2 ± 0.1 mg/L for 24 h and 12 h re-oxygenation was used to investigate the response of the anaerobic glycolytic pathway in Micropterus salmoides muscle. The results showed that the glucose concentration was significantly lower in muscle, while the lactic acid and pyruvic acid concentrations tended to increase during hypoxic stress. No significant difference was observed in muscle glycogen, and ATP content fluctuated significantly. The activities of gluconeogenesis-related enzymes were slightly elevated, such as phosphoenolpyruvate carboxykinase (PEPCK). The activities of the glycolytic enzymes increased after the induction of hypoxia, such as hexokinase (HK), pyruvate kinase (PK), and lactate dehydrogenase (LDH). Curiously, phosphofructokinase (PFK) activity was significantly down-regulated within 4 h during hypoxia, although these effects were transient, and most indices returned to control levels after 12 h of re-oxygenation. Upregulated hif-1α, ampkα, hk, glut1, and ldh mRNA expression suggested that carbohydrate metabolism was reprogrammed under hypoxia. Lactate transport was regulated by miR-124-5p according to quantitative polymerase chain reaction and dual luciferase reporter assays. Our findings provide new insight into the molecular regulatory mechanism of hypoxia in Micropterus salmoides muscle.
Collapse
Affiliation(s)
- L L Zhao
- College of Animal Science and Technology, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, China.
| | - H Wu
- College of Animal Science and Technology, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, China; Hunan Fisheries Science Institute, Changsha, 410153, China.
| | - J L Sun
- College of Animal Science and Technology, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, China.
| | - L Liao
- College of Animal Science and Technology, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, China.
| | - C Cui
- College of Animal Science and Technology, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, China.
| | - Q Liu
- College of Animal Science and Technology, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, China.
| | - J Luo
- College of Animal Science and Technology, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, China.
| | - X H Tang
- College of Animal Science and Technology, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, China.
| | - W Luo
- College of Animal Science and Technology, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, China.
| | - J D Ma
- College of Animal Science and Technology, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, China.
| | - X Ye
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, GuangZhou 510380, China.
| | - S J Li
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, GuangZhou 510380, China.
| | - S Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, China.
| |
Collapse
|
19
|
Sun J, Liu Q, Zhao L, Cui C, Wu H, Liao L, Tang G, Yang S, Yang S. Potential regulation by miRNAs on glucose metabolism in liver of common carp (Cyprinus carpio) at different temperatures. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2019; 32:100628. [PMID: 31677400 DOI: 10.1016/j.cbd.2019.100628] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 09/13/2019] [Accepted: 09/13/2019] [Indexed: 12/12/2022]
Abstract
Water temperature can affect the metabolism of fish. Common carp (Cyprinus carpio) is a representative eurythermic fish that can survive at a wide range of ambient temperatures, allowing it to live in an extensive geographical range. The goal of this work was to study the glucose metabolism of common carp at different temperatures and determine the miRNAs involved in the regulation of glucose metabolism. We determined the indicators related to glucose metabolism after long-term temperature stress and constructed nine small RNA libraries of livers under different temperature stress (5 °C, 17 °C, and 30 °C, with three biological replicates for each temperature), and subjected these samples to high-throughput sequencing. A positive relationship was observed between weight gain rate (WGR) and temperature increase after 18 days of temperature stress. However, the glucose level in the plasma maintained a gentle decrease. Unexpectedly, liver lactic acid levels were elevated in HTG (high temperature group) and LTG (low temperature group). Six down-regulated miRNAs (miR-122, miR-30b, miR-15b-5p, miR-20a-5p, miR-1, and miR-7b) were identified as involved in the regulation of glycolysis. Twelve genes were predicted as targets of these miRNAs, and these genes are in pathways related to pyruvate metabolism, glycolysis/gluconeogenesis, and the citrate cycle (TCA cycle). The results allowed prediction of a potential regulatory network of miRNAs involved in the regulation of glycolysis. The target genes of six down-regulated miRNAs were up-regulated under temperature stress, including Aldolase C, fructose-bisphosphate, b (ALDOCB), multiple inositol-polyphosphate phosphatase 1 (MINPP1), phosphoenolpyruvate carboxykinase 1 (PCK1), pyruvate dehydrogenase E1 alpha 1 (PDHA1), aldehyde dehydrogenase 9 family member A1a (ALDH9A1A), Acetyl-coenzyme A synthetase (ACSS), lactate dehydrogenase b (LDH-b), and glyoxylate reductase/hydroxypyruvate reductase (GRHPR). Other key genes of glycolysis, glucose transporter 1 (GLUT-1), pyruvate kinase PKM (PKM), and mitochondrial pyruvate carrier (MPC) were significantly up-regulated in LTG and HTG. Overall, the results suggest that miRNAs maintain their energy requirements by regulating glycolysis and play an important role in the molecular response to cold and heat stress of common carp. These data provide the foundation for further studies of the role of miRNAs in environmental adaptation in fish.
Collapse
Affiliation(s)
- JunLong Sun
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Qiao Liu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - LiuLan Zhao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Can Cui
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Hao Wu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Lei Liao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Gang Tang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - ShiYong Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Song Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China.
| |
Collapse
|
20
|
Ma F, Liu Z, Huang J, Li Y, Kang Y, Liu X, Wang J. High-throughput sequencing reveals microRNAs in response to heat stress in the head kidney of rainbow trout (Oncorhynchus mykiss). Funct Integr Genomics 2019; 19:775-786. [PMID: 31076931 DOI: 10.1007/s10142-019-00682-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 02/11/2019] [Accepted: 04/30/2019] [Indexed: 12/26/2022]
Abstract
Recently, the research of animal microRNAs (miRNAs) has attracted wide attention for its regulatory effect in the development process and the response to abiotic stresses. Rainbow trout is a commercially and cold water fish species, and usually encounters heat stress, which affects its growth and leads to a huge economic loss. But there were few investigations about the roles of miRNAs in heat stress in rainbow trout. In this study, miRNAs of rainbow trout which were involved in heat stress were identified by high-throughput sequencing of six small RNA libraries from head kidney tissues under control (18 °C) and heat-treated (24 °C) conditions. A total of 392 conserved miRNAs and 989 novel miRNAs were identified, of which 78 miRNAs were expressed in different response to heat stress. Ten of these miRNAs were further validated by quantitative real-time PCR. In addition to, including 393 negative correlation miRNA-target gene pairs, several important regulatory pathways were involved in heat stress of the potential target genes, including protein processing in endoplasmic reticulum, NOD-like receptor signaling pathway, and phagosome. Our data significantly advance understanding of heat stress regulatory mechanism of miRNA in the head kidney of rainbow trout, which provide a useful resource for the cultivation of rainbow trout.
Collapse
Affiliation(s)
- Fang Ma
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Zhe Liu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China.
| | - Jinqiang Huang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Yongjuan Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Yujun Kang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Xiaoxia Liu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Jianfu Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| |
Collapse
|