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Han P, Chen J, Sun Z, Ren S, Wang X. Evaluation of reference genes for gene expression analysis in Japanese flounder (Paralichthys olivaceus) under temperature stress. BMC Genomics 2025; 26:117. [PMID: 39920593 PMCID: PMC11804088 DOI: 10.1186/s12864-025-11285-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2024] [Accepted: 01/23/2025] [Indexed: 02/09/2025] Open
Abstract
BACKGROUND Quantitative Real-time PCR (qRT-PCR) is a powerful technique to analyze gene expression patterns by measuring the relative abundance of mRNA transcription levels. The most crucial step in obtaining accurate results of qRT-PCR is to select suitable reference genes. Water temperature is an important factor that affects various physiological processes of fish. Presently, Japanese flounder is a commercially important marine culture species and the study of its gene expression is increasing rapidly. However, the reference genes used for Japanese flounder in previous studies, especially under temperature stress, only focused on those well-known genes widely reported in vertebrates, which might not be the proper reference genes. RESULTS In this study, we evaluated the suitability of eight genes including ribosomal protein L6 (rpl6), ribosomal protein L9 (rpl9), delta (4)-desaturase, sphingolipid 1 (degs1), cathepsin L (ctsl), eukaryotic translation elongation factor 1 gamma (eef1g), NSA2 ribosome biogenesis homolog (nsa2), eukaryotic translation initiation factor 3, subunit E, a (eif3ea), glutamine amidotransferase class 1 domain containing 1 (gatd1) analyzed from RNA sequencing (RNA-Seq) data and two genes including β-actin (actb) and 18S rRNA ribosomal RNA (18S RNA) selected from literature to obtain the best internal controls in qRT-PCR analysis of Japanese flounder under temperature stress. The statistical analysis methods (delta-Ct, BestKeeper, geNorm, and NormFinder) were further used to determine candidate reference gene stability. Initial results showed the suitability of eight genes from RNA-Seq data, which exhibited more stable expression levels than two commonly reported reference genes. Further analysis revealed that gatd1 and rpl6 were the best reference genes in Japanese flounder exposed to temperature stress. CONCLUSION This study transcriptome-wide identified reference genes in different tissues of Japanese flounder exposed to temperature stress for the first time, providing a basis for gene expression research in flatfish.
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Affiliation(s)
- Ping Han
- Key Laboratory of Aquacultural Biotechnology (Ningbo University), Ministry of Education, Ningbo, Zhejiang, China
| | - Jianming Chen
- College of Life Sciences and Technology, Tarim University, Alaer, Xinjiang, China.
| | - Zhennan Sun
- Key Laboratory of Aquacultural Biotechnology (Ningbo University), Ministry of Education, Ningbo, Zhejiang, China
| | - Shengjie Ren
- College of Life Sciences and Technology, Tarim University, Alaer, Xinjiang, China
| | - Xubo Wang
- Key Laboratory of Aquacultural Biotechnology (Ningbo University), Ministry of Education, Ningbo, Zhejiang, China.
- National Engineering Research Laboratory of Marine Biotechnology and Engineering, Ningbo University, Ningbo, Zhejiang, China.
- Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo University, Ningbo, Zhejiang, China.
- Key Laboratory of Green Mariculture (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural, Ningbo University, Ningbo, Zhejiang, China.
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Zhu X, Ren X, Xiong L, Liu T, Bai X. Genetic dissection of crayfish (Procambarus clarkii) high temperature tolerance and assessment of the potential application in breeding of the HSP genes. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2024; 52:101330. [PMID: 39293144 DOI: 10.1016/j.cbd.2024.101330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 09/12/2024] [Accepted: 09/13/2024] [Indexed: 09/20/2024]
Abstract
Red swamp crayfish (Procambarus clarkii) is an important freshwater aquaculture species in China. In the process of crayfish aquaculture, high temperature stress is common, which seriously affects its yield and quality. It is urgently recommended to improve these traits in the breed. However, the application of high-temperature tolerance genes in molecular breeding of crayfish has not been reported. In this study, transcriptome analysis was used to explore the high-temperature tolerance genes of crayfish. The results showed that genes related to energy metabolism, antioxidant, immunity and body restoration were involved in high temperature adaptation of crayfish. Based on the selected high temperature tolerance genes Heat Stress Protein 70 and Heat Stress Protein 90 (HSP70 and HSP90), the genetic variation of their open reading frames was investigated. Totally, three and four SNPs of HSP70 and HSP90, were obtained respectively. In addition, three high-temperature stress experiments were conducted on crayfish to identify favoured haplotypes. HSP70-1 and HSP90-1 are the favoured haplotypes of HSP70 and HSP90, respectively. Furthermore, a series of molecular markers were developed to identify the favoured haplotype combinations of HSP70 and HSP90. Finally, we propose a molecular breeding strategy to improve crayfish tolerance to high temperature, thereby providing a potential to increase crayfish yield. Together, this study provides a theoretical basis and molecular markers for the breeding of high-temperature tolerant crayfish.
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Affiliation(s)
- Xi Zhu
- National Key Laboratory of Crop Genetic Improvement, Shuangshui Shuanglü Institute, Huazhong Agricultural University, Wuhan 430070, China; College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Xin Ren
- National Key Laboratory of Crop Genetic Improvement, Shuangshui Shuanglü Institute, Huazhong Agricultural University, Wuhan 430070, China; College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Lijing Xiong
- National Key Laboratory of Crop Genetic Improvement, Shuangshui Shuanglü Institute, Huazhong Agricultural University, Wuhan 430070, China; College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Tiantian Liu
- National Key Laboratory of Crop Genetic Improvement, Shuangshui Shuanglü Institute, Huazhong Agricultural University, Wuhan 430070, China; College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Xufeng Bai
- National Key Laboratory of Crop Genetic Improvement, Shuangshui Shuanglü Institute, Huazhong Agricultural University, Wuhan 430070, China; College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China; Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan 430070, China.
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Giffard-Mena I, Ponce-Rivas E, Sigala-Andrade HM, Uranga-Solís C, Re AD, Díaz F, Camacho-Jiménez L. Evaluation of the osmoregulatory capacity and three stress biomarkers in white shrimp Penaeus vannamei exposed to different temperature and salinity conditions: Na +/K + ATPase, Heat Shock Proteins (HSP), and Crustacean Hyperglycemic Hormones (CHHs). Comp Biochem Physiol B Biochem Mol Biol 2024; 271:110942. [PMID: 38224831 DOI: 10.1016/j.cbpb.2024.110942] [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: 09/13/2023] [Revised: 01/11/2024] [Accepted: 01/11/2024] [Indexed: 01/17/2024]
Abstract
Salinity and temperature influence growth, survival, and reproduction of crustacean species such as Penaeus vannamei where Na +/K+-ATPase plays a key role in maintaining osmotic homeostasis in different salinity conditions. This ability is suggested to be mediated by other proteins including neuropeptides such as the crustacean hyperglycemic hormones (CHHs), and heat shock proteins (HSPs). The mRNA expression of Na+/K+-ATPase, HSP60, HSP70, CHH-A, and CHH-B1, was analyzed by qPCR in shrimp acclimated to different salinities (10, 26, and 40 PSU) and temperature conditions (20, 23, 26, 29, and 32 °C) to evaluate their uses as molecular stress biomarkers. The results showed that the hemolymph osmoregulatory capacity in shrimp changed with exposure to the different salinities. From 26 to 32 °C the Na+/K+-ATPase expression increased significantly at 10 PSU relative to shrimp acclimated at 26 PSU and at 20 °C increased at similar values independently of salinity. The highest HSP expression levels were obtained by HSP70 at 20 °C, suggesting a role in protecting proteins such as Na+/K+ -ATPase under low-temperature and salinity conditions. CHH-A was not expressed in the gill under any condition, but CHH-B1 showed the highest expression at the lowest temperatures and salinities, suggesting its participation in the Na+/K+-ATPase induction. Since Na+/K+-ATPase, HSPs, and CHHs seem to participate in maintaining the osmo-ionic balance and homeostasis in P. vannamei, their expression levels may be used as a stress biomarkers to monitor marine crustacean health status when acclimated in low salinity and temperature conditions.
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Affiliation(s)
- Ivone Giffard-Mena
- Laboratorio de Ecología Molecular, Facultad de Ciencias Marinas, Universidad Autónoma de Baja California (UABC), Ensenada, Baja California C.P. 22860, Mexico. https://twitter.com/igiffard28
| | - Elizabeth Ponce-Rivas
- Departamento de Biotecnología Marina, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Ensenada, Baja California C.P. 22860, Mexico.
| | - Héctor M Sigala-Andrade
- Departamento de Biotecnología Marina, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Ensenada, Baja California C.P. 22860, Mexico
| | - Carla Uranga-Solís
- Laboratorio de Ecología Molecular, Facultad de Ciencias Marinas, Universidad Autónoma de Baja California (UABC), Ensenada, Baja California C.P. 22860, Mexico. https://twitter.com/carla_uranga
| | - Ana Denisse Re
- Departamento de Biotecnología Marina, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Ensenada, Baja California C.P. 22860, Mexico
| | - Fernando Díaz
- Departamento de Biotecnología Marina, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Ensenada, Baja California C.P. 22860, Mexico
| | - Laura Camacho-Jiménez
- Laboratorio de Biología Molecular y Bioquímica, Centro de Investigación en Alimentación y Desarrollo (CIAD), A.C., Hermosillo, Sonora, Mexico
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Ferrer-Chujutalli K, Sernaqué-Jacinto J, Reyes-Avalos W. Optimal temperature and thermal tolerance of postlarvae of the freshwater prawn Cryphiops (Cryphiops) caementarius acclimated to different temperatures. Heliyon 2024; 10:e25850. [PMID: 38434307 PMCID: PMC10907542 DOI: 10.1016/j.heliyon.2024.e25850] [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: 07/27/2023] [Revised: 01/30/2024] [Accepted: 02/04/2024] [Indexed: 03/05/2024] Open
Abstract
In this study, the optimum temperature and thermal tolerance of postlarvae of the commercially important freshwater prawn Cryphiops (Cryphiops) caementarius were determined after acclimation to six different rearing temperatures (19 °C, 22 °C, 24 °C, 26 °C, 28 °C, and 30 °C) during a 45 day-culture period. Best growth parameter values were obtained within the temperature range of 24 °C to 28 °C, where the optimum temperature for growth was found to be at 26 °C (weight gain 81.70%; specific growth rate 1.33 %/day) but had not significant effect (p > 0.05) on survival (64%-71%) of postlarvae. Increasing the acclimation temperature significantly (p < 0.05) increased both the critical thermal maximum (CTMax: from 33.82 °C to 38.48 °C) and minimum (CTMin: from 9.27 °C to 14.58 °C). The thermal tolerance interval increased (p < 0.05) from 24.55 °C to 25.48 °C in postlarvae acclimated at 28 °C but decreased (p < 0.05) to 23.90 °C in those acclimated at 30 °C. The acclimation response rate was lower for CTMax and higher for CTMin. The current (12.48 °C) and future (9.48 °C) thermal safety margins were like those reported for other tropical crustaceans. A thermal tolerance polygon over the range of 19-30 °C resulted in a calculated area of 242.25 °C2. The presented results can be used for aquaculture activities and also to help to protect this species against expected climate warming impacts.
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Affiliation(s)
- Karla Ferrer-Chujutalli
- Escuela Profesional de Biología en Acuicultura, Universidad Nacional del Santa, Ancash, 02712, Perú
| | - José Sernaqué-Jacinto
- Escuela Profesional de Biología en Acuicultura, Universidad Nacional del Santa, Ancash, 02712, Perú
| | - Walter Reyes-Avalos
- Laboratorio de Acuicultura Ornamental, Departamento Académico de Biología, Microbiología y Biotecnología, Universidad Nacional del Santa, Ancash, 02712, Perú
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Wang L, Jiang Y, Fang L, Guan C, Xu Y. Heat-shock protein 90 alleviates oxidative stress and reduces apoptosis in liver of Seriola aureovittata (yellowtail kingfish) under high-temperature stress. Comp Biochem Physiol B Biochem Mol Biol 2024; 270:110927. [PMID: 38040327 DOI: 10.1016/j.cbpb.2023.110927] [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: 07/27/2023] [Revised: 11/27/2023] [Accepted: 11/27/2023] [Indexed: 12/03/2023]
Abstract
Hsp90s are molecular chaperones that enhance fish tolerance to high-temperature stress. However, the function of Hsp90s in Seriola aureovittata (yellowtail kingfish) under high-temperature stress remains largely unknown. Here, two Hsp90 isoforms were identified in S. aureovittata by bioinformatics analysis: SaHsp90α and SaHsp90β. The coding sequence of SaHsp90α was 2193-bp long and encoded a polypeptide of 730 amino acids; SaHsp90β was 2178-bp long and encoded a polypeptide of 725 amino acids. SaHsp90α and SaHsp90β both contained a HATPase domain and a HSP90 domain. Their transcripts were detected in all examined S. aureovittata tissues, with relatively high levels in the gonads, head kidney, and intestine. During high-temperature stress at 28 °C, the expression levels of SaHsp90α and SaHsp90β transcripts were significantly increased in liver. After simultaneously knocking down the expression of the SaHsp90s, there was a significant decrease in liver superoxide dismutase (SOD) activity and a remarkable increase of malondialdehyde content in liver after high-temperature stress. The expression levels of the key caspase family genes caspase-3 and caspase-7 were also significantly upregulated by high-temperature stress in SaHsp90-knockdown liver. TUNEL labeling demonstrated that the number of apoptotic cells significantly increased in the SaHsp90-knockdown group when high-temperature treatment lasted for 48 h. Protein-protein docking analysis predicted that SaHsp90α and SaHsp90β can bind to S. aureovittata SOD and survivin, which are key proteins for maintenance of redox homeostasis and inhibition of apoptosis. These findings demonstrate that SaHsp90α and SaHsp90β play a crucial role in resistance to high-temperature stress by regulating redox homeostasis and apoptosis in yellowtail kingfish.
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Affiliation(s)
- Lin Wang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Joint Laboratory for Deep Blue Fishery Engineering, Qingdao, Shandong 266071, China
| | - Yan Jiang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Joint Laboratory for Deep Blue Fishery Engineering, Qingdao, Shandong 266071, China
| | - Lu Fang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Changtao Guan
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Joint Laboratory for Deep Blue Fishery Engineering, Qingdao, Shandong 266071, China
| | - Yongjiang Xu
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Joint Laboratory for Deep Blue Fishery Engineering, Qingdao, Shandong 266071, China.
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Liu J, Lin J, Chen L. Heat shock protein 40 of Streptococcus pneumoniae induces immune response of human dendritic cells via TLR4-dependent p38 MAPK and JNK signaling pathways. Immun Inflamm Dis 2022; 10:e735. [PMID: 36444618 PMCID: PMC9695094 DOI: 10.1002/iid3.735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 10/19/2022] [Accepted: 10/21/2022] [Indexed: 11/27/2022] Open
Abstract
INTRODUCTION Heat shock protein 40 (HSP40) is a vaccine adjuvant candidate for Streptococcus pneumoniae. The mechanism by which HSP40 activates the human dendritic cells (DCs) is unclear. METHODS DCs were isolated from human peripheral blood and their markers (HLA-DR, CD86, CD83, and CD80) were detected by flow cytometry. The messenger RNA (mRNA) and secretion levels of inflammary cytokines were measured after DCs were stimulated with recombinant HSP40 (rHSP40). Short hairpin RNAs were used to knock down toll-like receptor 2 (TLR2) and TLR4. The TLR2- or TLR4-deficient DCs were treated with lipopolysaccharides, rHSP40, or peptidoglycan, and then the secretion levels of tumor necrosis factor-α (TNF-α) and interleukin-6 (IL-6) were measured. Moreover, the secretion levels of TNF-α and IL-6 were measured after DCs were treated with mitogen-activated protein kinase (MAPK) inhibitors including SB203580, SP600125, and U0126. In addition, the phosphorylation levels of p38 MAPK and Jun N-terminal kinase (JNK) in DC cells were determined using western blot analysis after treatment with rHSP40 for different times. RESULTS DCs were successfully isolated and cultured. rHSP40 treatment significantly increased cytokine levels in a concentration-dependent manner. TLR4 deficiency, but not TLR2 deficiency, significantly suppressed the rHSP40-induced secretion of tumor necrosis factor-α (TNF-α) and interleukin-6 (IL-6). SB203580 and SP600125 significantly inhibited the rHSP40-induced secretion of TNF-α and IL-6. rHSP40 significantly enhanced the phosphorylation of p38 MAPK and JNK. CONCLUSION HPS40 stimulates the immune response of DCs via the p38 MAPK and JNK signaling pathways, which depend on TLR4.
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Affiliation(s)
- Jing‐jing Liu
- Clinical LaboratoryXiamen Children's HospitalXiamenChina
| | - Jian‐cheng Lin
- Clinical LaboratoryXiamen Children's HospitalXiamenChina
| | - Li‐na Chen
- Clinical LaboratoryXiamen Children's HospitalXiamenChina
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Effects of Low Temperature on Antioxidant and Heat Shock Protein Expression Profiles and Transcriptomic Responses in Crayfish ( Cherax destructor). Antioxidants (Basel) 2022; 11:antiox11091779. [PMID: 36139854 PMCID: PMC9495765 DOI: 10.3390/antiox11091779] [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: 08/08/2022] [Revised: 09/04/2022] [Accepted: 09/06/2022] [Indexed: 11/20/2022] Open
Abstract
Low temperature is a critical factor restricting the growth and survival of aquatic animals, but research on the mechanism of response to low temperature in Cherax destructor is limited. C. destructor is one of the most important freshwater crustaceans with strong adaptability in Australia, and it has been commercialized gradually in recent years. Here, growth indicators, antioxidant parameters, anti-stress gene expression, and transcriptome sequencing were used on crayfish following 8 weeks of low-temperature acclimation. The results showed that weight gain, length gain, and molting rates decreased as the temperature decreased. The activity of antioxidant enzymes decreased, while the content of antioxidant substances and the expression of anti-stress genes increased. Transcriptome sequencing identified 589 differentially expressed genes, 279 of which were upregulated and 310 downregulated. The gene functions and pathways for endocrine disorders, glucose metabolism, antioxidant defense, and immune responses were identified. In conclusion, although low-temperature acclimation inhibited the basal metabolism and immune ability of crayfish, it also increased the antioxidant substance content and anti-stress-gene expression to protect the organism from low-temperature damage. This study provided molecular insights into the study of low-temperature responses of low-temperature-tolerant crustacean species.
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