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Li Y, Wu S, Huang J, Zhao L. Integration of physiological, miRNA-mRNA interaction and functional analysis reveals the molecular mechanism underlying hypoxia stress tolerance in crucian carp (Carassius auratus). FASEB J 2024; 38:e23722. [PMID: 38934365 DOI: 10.1096/fj.202302629rr] [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: 12/19/2023] [Revised: 04/23/2024] [Accepted: 05/21/2024] [Indexed: 06/28/2024]
Abstract
Hypoxia has become one of the most critical factors limiting the development of aquaculture. Crucian carp (Carassius auratus) is widely consumed fish in China, with excellent tolerance to hypoxic environment. However, the molecular mechanisms underlying hypoxia adaptation and tolerance in crucian carp remain unclear. Compared with the control, increased T-SOD, CAT, GSH-Px, T-AOC, ALT, and AST activities and MDA, TCHO, and TG contents, and decreased TP and ATP contents were observed after hypoxia stress. Based on RNA-seq, 2479 differentially expressed (DE) mRNAs and 60 DE miRNAs were identified, and numerous DE mRNAs involved in HIF signaling pathway (hif-1α, epo, vegfa, and ho), anaerobic metabolism (hk1/hk2, pfk, gapdh, pk, and ldh) and immune response (nlrp12, cxcr1, cxcr4, ccr9, and cxcl12) were significantly upregulated after hypoxia exposure. Integrated analysis found that ho, igfbp1, hsp70, and hk2 were predicted to be regulated by novel_867, dre-miR-125c-3p/novel_173, dre-miR-181b-5p, and dre-miR-338-5p/dre-miR-17a-3p, respectively, and targets of DE miRNAs were significantly enriched in MAPK signaling pathway, FoxO signaling pathway, and glycolysis/gluconeogenesis. Expression analysis showed that the mRNA levels of vegfa, epo, ho, hsp70, hsp90aa.1, igfbp1, ldh, hk1, pfk, pk, and gapdh exhibited a remarkable increase, whereas sdh and mdh were downregulated in the H3h, H12h, and H24h groups compared with the control. Furthermore, research found that hk2 is a target of dre-miR-17a-3p, overexpression of dre-miR-17a-3p significantly decreased the expression level of hk2, while the opposite results were obtained after dre-miR-17a-3p silencing. These results contribute to our understanding of the molecular mechanisms of hypoxia tolerance in crucian carp.
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Affiliation(s)
- Yongjuan Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
- College of Science, Gansu Agricultural University, Lanzhou, China
| | - Shenji Wu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Jinqiang Huang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Lu Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
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Huo D, Liu S, Zhang L, Yang H, Sun L. Importance of the ECM-receptor interaction for adaptive response to hypoxia based on integrated transcription and translation analysis. Mol Ecol 2024:e17352. [PMID: 38624130 DOI: 10.1111/mec.17352] [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: 05/25/2023] [Revised: 03/28/2024] [Accepted: 04/03/2024] [Indexed: 04/17/2024]
Abstract
Low dissolved oxygen (LO) conditions represent a major environmental challenge to marine life, especially benthic animals. For these organisms, drastic declines in oxygen availability (hypoxic events) can trigger mass mortality events and thus, act as agents of selection influencing the evolution of adaptations. In sea cucumbers, one of the most successful groups of benthic invertebrates, the exposure to hypoxic conditions triggers adaptive adjustments in metabolic rates and behaviour. It is unclear, however, how these adaptive responses are regulated and the genetic mechanisms underpinning them. Here, we addressed this knowledge gap by assessing the genetic regulation (transcription and translation) of hypoxia exposure in the sea cucumber Apostichopus japonicus. Transcriptional and translational gene expression profiles under short- and long-term exposure to low oxygen conditions are tightly associated with extracellular matrix (ECM)-receptor interaction in which laminin and collagen likely have important functions. Finding revealed that genes with a high translational efficiency (TE) had a relatively short upstream open reading frame (uORF) and a high uORF normalized minimal free energy, suggesting that sea cucumbers may respond to hypoxic stress via altered TE. These results provide valuable insights into the regulatory mechanisms that confer adaptive capacity to holothurians to survive oxygen deficiency conditions and may also be used to inform the development of strategies for mitigating the harmful effects of hypoxia on other marine invertebrates facing similar challenges.
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Affiliation(s)
- Da Huo
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
- Shandong Province Key Laboratory of Experimental Marine Biology, Qingdao, China
| | - Shilin Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
- Shandong Province Key Laboratory of Experimental Marine Biology, Qingdao, China
| | - Libin Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
- Shandong Province Key Laboratory of Experimental Marine Biology, Qingdao, China
| | - Hongsheng Yang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
- Shandong Province Key Laboratory of Experimental Marine Biology, Qingdao, China
| | - Lina Sun
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
- Shandong Province Key Laboratory of Experimental Marine Biology, Qingdao, China
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Raposo de Magalhães C, Sandoval K, Kagan F, McCormack G, Schrama D, Carrilho R, Farinha AP, Cerqueira M, Rodrigues PM. Transcriptomic changes behind Sparus aurata hepatic response to different aquaculture challenges: An RNA-seq study and multiomics integration. PLoS One 2024; 19:e0300472. [PMID: 38517901 PMCID: PMC10959376 DOI: 10.1371/journal.pone.0300472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 02/13/2024] [Indexed: 03/24/2024] Open
Abstract
Gilthead seabream (Sparus aurata) is an important species in Mediterranean aquaculture. Rapid intensification of its production and sub-optimal husbandry practices can cause stress, impairing overall fish performance and raising issues related to sustainability, animal welfare, and food safety. The advent of next-generation sequencing technologies has greatly revolutionized the study of fish stress biology, allowing a deeper understanding of the molecular stress responses. Here, we characterized for the first time, using RNA-seq, the different hepatic transcriptome responses of gilthead seabream to common aquaculture challenges, namely overcrowding, net handling, and hypoxia, further integrating them with the liver proteome and metabolome responses. After reference-guided transcriptome assembly, annotation, and differential gene expression analysis, 7, 343, and 654 genes were differentially expressed (adjusted p-value < 0.01, log2|fold-change| >1) in the fish from the overcrowding, net handling, and hypoxia challenged groups, respectively. Gene set enrichment analysis (FDR < 0.05) suggested a scenario of challenge-specific responses, that is, net handling induced ribosomal assembly stress, whereas hypoxia induced DNA replication stress in gilthead seabream hepatocytes, consistent with proteomics and metabolomics' results. However, both responses converged upon the downregulation of insulin growth factor signalling and induction of endoplasmic reticulum stress. These results demonstrate the high phenotypic plasticity of this species and its differential responses to distinct challenging environments at the transcriptomic level. Furthermore, it provides significant resources for characterizing and identifying potentially novel genes that are important for gilthead seabream resilience and aquaculture production efficiency with regard to fish welfare.
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Affiliation(s)
- Cláudia Raposo de Magalhães
- Centre of Marine Sciences (CCMAR), Universidade do Algarve, Campus de Gambelas, Faro, Portugal
- Universidade do Algarve, Campus de Gambelas, Faro, Portugal
| | - Kenneth Sandoval
- Molecular Evolution and Systematics Laboratory, Zoology, Ryan Institute & School of Natural Sciences, University of Galway, Galway, Ireland
| | | | - Grace McCormack
- Molecular Evolution and Systematics Laboratory, Zoology, Ryan Institute & School of Natural Sciences, University of Galway, Galway, Ireland
| | - Denise Schrama
- Centre of Marine Sciences (CCMAR), Universidade do Algarve, Campus de Gambelas, Faro, Portugal
- Universidade do Algarve, Campus de Gambelas, Faro, Portugal
| | - Raquel Carrilho
- Centre of Marine Sciences (CCMAR), Universidade do Algarve, Campus de Gambelas, Faro, Portugal
- Universidade do Algarve, Campus de Gambelas, Faro, Portugal
| | - Ana Paula Farinha
- Centre of Marine Sciences (CCMAR), Universidade do Algarve, Campus de Gambelas, Faro, Portugal
- Universidade do Algarve, Campus de Gambelas, Faro, Portugal
- Escola Superior Agrária de Santarém, Santarém, Portugal
| | - Marco Cerqueira
- Centre of Marine Sciences (CCMAR), Universidade do Algarve, Campus de Gambelas, Faro, Portugal
- Universidade do Algarve, Campus de Gambelas, Faro, Portugal
| | - Pedro M. Rodrigues
- Centre of Marine Sciences (CCMAR), Universidade do Algarve, Campus de Gambelas, Faro, Portugal
- Universidade do Algarve, Campus de Gambelas, Faro, Portugal
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Zhang Y, Shen W, Ding J, Gao X, Wu X, Zhu J. Comparative Transcriptome Analysis of Head Kidney of Aeromonas hydrophila-infected Hypoxia-tolerant and Normal Large Yellow Croaker. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2022; 24:1039-1054. [PMID: 36129638 DOI: 10.1007/s10126-022-10158-4] [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: 06/18/2022] [Accepted: 08/16/2022] [Indexed: 06/15/2023]
Abstract
The large yellow croaker (Larimichthys crocea) is one of the most economically important marine fish on the southeast coast of China and much of its yield is usually lost by hypoxia. To address this problem and lay a foundation for culturing a new strain of large yellow croaker with hypoxia tolerance, our research group screened a hypoxia-tolerant population of L. crocea. Surprisingly, we also found that hypoxia-tolerant population exhibited higher survival when infected with pathogens compared to the normal population during the farming operation. In order to understand the mechanism underlying the higher survival rate of the hypoxia-tolerant population and enrich the head kidney immune mechanism of L. crocea infected with pathogens, we compared and analyzed the head kidney transcriptome of the hypoxia-tolerant and normal individuals under Aeromonas hydrophila infection. We obtained 159.68 GB high-quality reads, of which more than 87.61% were successfully localized to the reference genome of L. crocea. KEGG analysis revealed differentially expressed genes in the signaling pathways involving immunity, cell growth and death, transport and catabolism, and metabolism. Among these, the toll-like receptor signaling pathway, Nod-like receptor signaling pathway, cytokine-cytokine receptor interaction, phagosome, apoptosis, and OXPHOS pathways were enriched in both groups after infection compared to before, and were enriched in infected tolerant individuals compared to normal individuals. In addition, we found that the expression of hif1α and its downstream genes were higher in the hypoxia-sensitive group of fish than in the normal group. In conclusion, our results showed some signaling pathways and hub genes, which may participate in A. hydrophila defense in the head kidney of two populations, and may contribute to the higher survival rate in the hypoxia-tolerant population. Overall, these findings increase our understanding of the defense mechanism within the head kidney of L. crocea under A. hydrophila infection, and suggest a preliminary hypothesis for why hypoxia-tolerant individuals may exhibit a higher survival rates after infection. Our study provides scientific evidence for the breeding of a new hypoxia-tolerant strain of L. crocea for aquaculture.
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Affiliation(s)
- Yibo Zhang
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, College of Marine Sciences, Ningbo University, Ningbo, Zhejiang, China
- Zhejiang Key Laboratory of Aquatic Germplasm Resources, Ningbo Academy of Oceanology and Fishery, Ningbo, Zhejiang, China
| | - Weiliang Shen
- Zhejiang Key Laboratory of Aquatic Germplasm Resources, Ningbo Academy of Oceanology and Fishery, Ningbo, Zhejiang, China.
| | - Jie Ding
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, College of Marine Sciences, Ningbo University, Ningbo, Zhejiang, China
- Zhejiang Key Laboratory of Aquatic Germplasm Resources, Ningbo Academy of Oceanology and Fishery, Ningbo, Zhejiang, China
| | - Xinming Gao
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, College of Marine Sciences, Ningbo University, Ningbo, Zhejiang, China
| | - Xiongfei Wu
- Zhejiang Key Laboratory of Aquatic Germplasm Resources, Ningbo Academy of Oceanology and Fishery, Ningbo, Zhejiang, China
| | - Junquan Zhu
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, College of Marine Sciences, Ningbo University, Ningbo, Zhejiang, China
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Jiang JY, Li WH, Wu YY, Cheng CX, Ye QQ, Feng JX, Xie ZX. Effects of cadmium exposure on intestinal microflora of Cipangopaludina cathayensis. Front Microbiol 2022; 13:984757. [PMID: 36003941 PMCID: PMC9393624 DOI: 10.3389/fmicb.2022.984757] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 07/21/2022] [Indexed: 01/04/2023] Open
Abstract
As one of the most environmentally toxic heavy metals, cadmium (Cd) has attracted the attention of researchers globally. In particular, Guangxi, a province in southwestern China, has been subjected to severe Cd pollution due to geogenic processes and anthropogenic activities. Cd can be accumulated in aquatic animals and transferred to the human body through the food chain, with potential health risks. The aim of the present study was to explore the effects of waterborne Cd exposure (0.5 mg/L and 1.5 mg/L) on the intestinal microbiota of mudsnail, Cipangopaludina cathayensis, which is favored by farmers and consumers in Guangxi. Gut bacterial community composition was investigated using high-throughput sequencing of the V3–V4 segment of the bacterial 16S rRNA gene. Our results indicated that C. cathayensis could tolerate low Cd (0.5 mg/L) stress, while Cd exposure at high doses (1.5 mg/L) exerted considerable effects on microbiota composition. At the phylum level, Proteobacteria, Bacteroidetes, and Firmicutes were the dominant phyla in the mudsnail gut microbiota. The relative abundances of Bacteroidetes increased significantly under high Cd exposure (H14) (p < 0.01), with no significant change in the low Cd exposure (L14) treatment. The dominant genera with significant differences in relative abundance were Pseudomonas, Cloacibacterium, Acinetobacter, Dechloromonas, and Rhodobacter. In addition, Cd exposure could significantly alter the pathways associated with metabolism, cellular processes, environmental information processing, genetic information processing, human diseases, and organismal systems. Notably, compared to the L14 treatment, some disease-related pathways were enriched, while some xenobiotic and organic compound biodegradation and metabolism pathways were significantly inhibited in the H14 group. Overall, Cd exposure profoundly influenced community structure and function of gut microbiota, which may in turn influence C. cathayensis gut homeostasis and health.
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Affiliation(s)
- Jiao-yun Jiang
- College of Life Science and Technology, Guangxi University, Nanning, China
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, China
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education, Guangxi Normal University, Guilin, China
| | - Wen-hong Li
- College of Life Science and Technology, Guangxi University, Nanning, China
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Yang-yang Wu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education, Guangxi Normal University, Guilin, China
| | - Chun-xing Cheng
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education, Guangxi Normal University, Guilin, China
| | - Quan-qing Ye
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education, Guangxi Normal University, Guilin, China
| | - Jia-xun Feng
- College of Life Science and Technology, Guangxi University, Nanning, China
| | - Zhi-xun Xie
- College of Life Science and Technology, Guangxi University, Nanning, China
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, China
- *Correspondence: Zhi-xun Xie,
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