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Ott BD, Hulse-Kemp AM, Duke MV, Griffin MJ, Peterson BC, Scheffler BE, Torrans EL, Allen PJ. Hypothalamic transcriptome response to simulated diel earthen pond hypoxia cycles in channel catfish ( Ictalurus punctatus). Physiol Genomics 2024; 56:519-530. [PMID: 38808773 DOI: 10.1152/physiolgenomics.00007.2024] [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: 01/23/2024] [Revised: 05/03/2024] [Accepted: 05/27/2024] [Indexed: 05/30/2024] Open
Abstract
Commercial culture of channel catfish (Ictalurus punctatus) occurs in earthen ponds that are characterized by diel swings in dissolved oxygen concentration that can fall to severe levels of hypoxia, which can suppress appetite and lead to suboptimal growth. Given the significance of the hypothalamus in regulating these processes in other fishes, an investigation into the hypothalamus transcriptome was conducted to identify specific genes and expression patterns responding to hypoxia. Channel catfish in normoxic water were compared with catfish subjected to 12 h of hypoxia (20% oxygen saturation; 1.8 mg O2/L; 27°C) followed by 12 h of recovery in normoxia to mimic 24 h in a catfish aquaculture pond. Fish were sampled at 0-, 6-, 12-, 18-, and 24-h timepoints, with the 6- and 12-h samplings occurring during hypoxia. A total of 190 genes were differentially expressed during the experiment, with most occurring during hypoxia and returning to baseline values within 6 h of normoxia. Differentially expressed genes were sorted by function into Gene Ontology biological processes and revealed that most were categorized as "response to hypoxia," "sprouting angiogenesis," and "cellular response to xenobiotic stimulus." The patterns of gene expression reported here suggest that transcriptome responses to hypoxia are broad and quickly reversibly with the onset of normoxia. Although no genes commonly reported to modulate appetite were found to be differentially expressed in this experiment, several candidates were identified for future studies investigating the interplay between hypoxia and appetite in channel catfish, including adm, igfbp1a, igfbp7, and stc2b.NEW & NOTEWORTHY Channel catfish are an economically important species that experience diel episodic periods of hypoxia that can reduce appetite. This is the first study to investigate their transcriptome from the hypothalamus in a simulated 24-h span in a commercial catfish pond, with 12 h of hypoxia and 12 h of normoxia. The research revealed functional groups of genes relating to hypoxia, angiogenesis, and glycolysis as well as individual target genes possibly involved in appetite regulation.
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Affiliation(s)
- Brian D Ott
- Warmwater Aquaculture Research Unit, Agricultural Research Service, United States Department of Agriculture, Stoneville, Mississippi, United States
| | - Amanda M Hulse-Kemp
- Genomics and Bioinformatics Research Unit, Agricultural Research Service, United States Department of Agriculture, Stoneville, Mississippi, United States
| | - Mary V Duke
- Genomics and Bioinformatics Research Unit, Agricultural Research Service, United States Department of Agriculture, Stoneville, Mississippi, United States
| | - Matt J Griffin
- Aquatic Research and Diagnostic Laboratory, College of Veterinary Medicine, Mississippi State University, Stoneville, Mississippi, United States
| | - Brian C Peterson
- National Cold Water Marine Aquaculture Center, Agricultural Research Service, United States Department of Agriculture, Franklin, Maine, United States
| | - Brian E Scheffler
- Genomics and Bioinformatics Research Unit, Agricultural Research Service, United States Department of Agriculture, Stoneville, Mississippi, United States
| | - Eugene L Torrans
- Warmwater Aquaculture Research Unit, Agricultural Research Service, United States Department of Agriculture, Stoneville, Mississippi, United States
| | - Peter J Allen
- Department of Wildlife, Fisheries, and Aquaculture, Mississippi State University, Mississippi State, Mississippi, United States
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Murphy TE, Harris JC, Rees BB. Hypoxia-inducible factor 1 alpha protein increases without changes in mRNA during acute hypoxic exposure of the Gulf killifish, Fundulus grandis. Biol Open 2023; 12:bio060167. [PMID: 38116983 PMCID: PMC10805151 DOI: 10.1242/bio.060167] [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: 09/22/2023] [Accepted: 10/23/2023] [Indexed: 12/21/2023] Open
Abstract
The hypoxia inducible factor 1 (HIF1) is a central regulator of the molecular responses of animals to low oxygen. While the hypoxia-responsiveness of HIF1 is generally attributed to the stabilization of the alpha protein subunit (HIF1α) at low oxygen, several studies on fish report increased tissue levels of HIF1A mRNA during hypoxia, suggesting transcriptional regulation. In the current study, HIF1α protein and HIF1A mRNA were determined in parallel in tissues of Gulf killifish, Fundulus grandis, exposed to short-term hypoxia (24 h at 1 mg O2 l-1). HIF1α protein was higher in brain, ovary, and skeletal muscle from fish exposed to hypoxia compared with normoxic controls by 6 h, and it remained elevated in brain and ovary at 24 h. In contrast, HIF1A mRNA levels were unaffected by hypoxia in any tissue. Moreover, HIF1α protein and HIF1A mRNA levels in the same tissues were not correlated with one another during either normoxia or hypoxia. Hence, an increase in HIF1α protein does not depend upon an increase in HIF1A mRNA during acute exposure to low oxygen in this species. The results support the widely accepted mechanism of post-translational protein stabilization, rather than new transcription, during the initial response of fish to hypoxia.
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Affiliation(s)
- Taylor E. Murphy
- Department of Biological Sciences, University of New Orleans, New Orleans, LA, 70148, USA
| | - Jasmine C. Harris
- Department of Biological Sciences, University of New Orleans, New Orleans, LA, 70148, USA
| | - Bernard B. Rees
- Department of Biological Sciences, University of New Orleans, New Orleans, LA, 70148, USA
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3
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Shi X, Gao F, Zhao X, Pei C, Zhu L, Zhang J, Li C, Li L, Kong X. Role of HIF in fish inflammation. FISH & SHELLFISH IMMUNOLOGY 2023; 143:109222. [PMID: 37956798 DOI: 10.1016/j.fsi.2023.109222] [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: 09/21/2023] [Revised: 11/06/2023] [Accepted: 11/08/2023] [Indexed: 11/15/2023]
Abstract
The hypoxia-inducing factor (HIF) is a central transcription factor in cellular oxygen sensing and regulation. It is common that the inflammation always appears in many diseases, like infectious diseases in fishes, and the inflammation is often accompanied by hypoxia, as a hallmark of inflammation. Besides coordinating cellular responses to low oxygen, HIF-mediated hypoxia signaling pathway is also crucial for immune responses such as the regulations of innate immune cell phenotype and function, as well as metabolic reprogramming under the inflammation. However, the understanding of the molecular mechanisms by which HIFs regulate the inflammatory response in fish is still very limited. Here, we review the characteristics of HIF as well as its roles in innate immune cells and the infections caused by bacteria and viruses. The regulatory effects of HIF on the metabolic reprogramming of innate immune cells are also discussed and the future research directions are outlooked. This paper will serve as a reference for elucidating the molecular mechanism of HIF regulating inflammation and identifying treatment strategies to target HIF for fish disease.
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Affiliation(s)
- Xiaowei Shi
- Engineering Lab of Henan Province for Aquatic Animal Disease Control, College of Fisheries, Henan Normal University, Henan Province, PR China; Sanquan Medical College, Henan Province, PR China
| | - Feng Gao
- Engineering Lab of Henan Province for Aquatic Animal Disease Control, College of Fisheries, Henan Normal University, Henan Province, PR China
| | - Xianliang Zhao
- Engineering Lab of Henan Province for Aquatic Animal Disease Control, College of Fisheries, Henan Normal University, Henan Province, PR China
| | - Chao Pei
- Engineering Lab of Henan Province for Aquatic Animal Disease Control, College of Fisheries, Henan Normal University, Henan Province, PR China
| | - Lei Zhu
- Engineering Lab of Henan Province for Aquatic Animal Disease Control, College of Fisheries, Henan Normal University, Henan Province, PR China
| | - Jie Zhang
- Engineering Lab of Henan Province for Aquatic Animal Disease Control, College of Fisheries, Henan Normal University, Henan Province, PR China
| | - Chen Li
- Engineering Lab of Henan Province for Aquatic Animal Disease Control, College of Fisheries, Henan Normal University, Henan Province, PR China
| | - Li Li
- Engineering Lab of Henan Province for Aquatic Animal Disease Control, College of Fisheries, Henan Normal University, Henan Province, PR China
| | - Xianghui Kong
- Engineering Lab of Henan Province for Aquatic Animal Disease Control, College of Fisheries, Henan Normal University, Henan Province, PR China.
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4
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Li J, Li Y, Liang X, Yang Z, Peng Y, Zhang Y, Ning X, Zhang K, Ji J, Wang T, Zhang G, Yin S. Blood redistribution preferentially protects vital organs under hypoxic stress in Pelteobagrus vachelli. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2023; 258:106498. [PMID: 37001201 DOI: 10.1016/j.aquatox.2023.106498] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 03/13/2023] [Accepted: 03/14/2023] [Indexed: 06/19/2023]
Abstract
Blood redistribution occurs in mammals under hypoxia but has not been reported in fish. This study investigated the tissue damage, hypoxia-inducible factor (HIF) activation level, and blood flow changes in the brain, liver, and muscle of Pelteobagrus vachelli during the hypoxia process for normoxia-hypoxia-asphyxia. The results showed that P. vachelli has tissue specificity in response to hypoxic stress. Cerebral blood flow increased with less damage than in the liver and muscle, suggesting that P. vachelli may also have a blood redistribution mechanism in response to hypoxia. It is worth noting that severe hypoxia can lead to a sudden increase in the degree of brain tissue damage. In addition, higher dissolved oxygen levels activate HIF and may have contributed to the reduced damage observed in the brain. This study provides basic data for investigating hypoxic stress in fish.
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Affiliation(s)
- Jie Li
- College of Marine Science and Engineering, Nanjing Normal University, Nanjing, 210023, China; Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, 222005, China
| | - Yao Li
- College of Marine Science and Engineering, Nanjing Normal University, Nanjing, 210023, China; Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, 222005, China
| | - Xia Liang
- Key Laboratory for Physiology Biochemistry and Application, Heze University, Heze, 274015, China
| | - Zhiru Yang
- College of Marine Science and Engineering, Nanjing Normal University, Nanjing, 210023, China; Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, 222005, China
| | - Ye Peng
- College of Marine Science and Engineering, Nanjing Normal University, Nanjing, 210023, China; Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, 222005, China
| | - Yiran Zhang
- College of Marine Science and Engineering, Nanjing Normal University, Nanjing, 210023, China; Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, 222005, China
| | - Xianhui Ning
- College of Marine Science and Engineering, Nanjing Normal University, Nanjing, 210023, China; Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, 222005, China
| | - Kai Zhang
- College of Marine Science and Engineering, Nanjing Normal University, Nanjing, 210023, China; Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, 222005, China
| | - Jie Ji
- College of Marine Science and Engineering, Nanjing Normal University, Nanjing, 210023, China; Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, 222005, China
| | - Tao Wang
- College of Marine Science and Engineering, Nanjing Normal University, Nanjing, 210023, China; Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, 222005, China
| | - Guosong Zhang
- Key Laboratory for Physiology Biochemistry and Application, Heze University, Heze, 274015, China.
| | - Shaowu Yin
- College of Marine Science and Engineering, Nanjing Normal University, Nanjing, 210023, China; Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, 222005, China.
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Townley IK, Babin CH, Murphy TE, Summa CM, Rees BB. Genomic analysis of hypoxia inducible factor alpha in ray-finned fishes reveals missing Ohnologs and evidence of widespread positive selection. Sci Rep 2022; 12:22312. [PMID: 36566251 PMCID: PMC9789988 DOI: 10.1038/s41598-022-26876-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 12/20/2022] [Indexed: 12/25/2022] Open
Abstract
As aquatic hypoxia worsens on a global scale, fishes will become increasingly challenged by low oxygen, and understanding the molecular basis of their response to hypoxia may help to better define the capacity of fishes to cope with this challenge. The hypoxia inducible factor (HIF) plays a critical role in the molecular response to hypoxia by activating the transcription of genes that serve to improve oxygen delivery to the tissues or enhance the capacity of tissues to function at low oxygen. The current study examines the molecular evolution of genes encoding the oxygen-dependent HIFα subunit (HIFA) in the ray-finned fishes (Actinopterygii). Genomic analyses demonstrate that several lineages retain four paralogs of HIFA predicted from two rounds of genome duplication at the base of vertebrate evolution, broaden the known distribution of teleost-specific HIFA paralogs, and provide evidence for salmonid-specific HIFA duplicates. Evolution of the HIFA gene family is characterized by widespread episodic positive selection at amino acid sites that potentially mediate protein stability, protein-protein interactions, and transcriptional regulation. HIFA transcript abundance depends upon paralog, tissue, and fish lineage. A phylogenetically-informed gene nomenclature is proposed along with avenues for future research on this critical family of transcription factors.
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Affiliation(s)
- Ian K. Townley
- Science Department, Saint George’s School, Spokane, WA 99208 USA
| | - Courtney H. Babin
- grid.266835.c0000 0001 2179 5031Department of Biological Sciences, University of New Orleans, New Orleans, LA 70148 USA
| | - Taylor E. Murphy
- grid.266835.c0000 0001 2179 5031Department of Biological Sciences, University of New Orleans, New Orleans, LA 70148 USA
| | - Christopher M. Summa
- grid.266835.c0000 0001 2179 5031Department of Computer Sciences, University of New Orleans, New Orleans, LA 70148 USA
| | - Bernard B. Rees
- grid.266835.c0000 0001 2179 5031Department of Biological Sciences, University of New Orleans, New Orleans, LA 70148 USA
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6
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Gárriz A, Williamson SA, Shah AD, Evans RG, Deveson Lucas DS, Powell DR, Walton SL, Marques FZ, Reina RD. Transcriptomic analysis of pre-ovipositional embryonic arrest in a non-squamate reptile (Chelonia mydas). Mol Ecol 2022; 31:4319-4331. [PMID: 35762848 PMCID: PMC9540450 DOI: 10.1111/mec.16583] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 06/20/2022] [Accepted: 06/22/2022] [Indexed: 11/29/2022]
Abstract
After gastrulation, oviductal hypoxia maintains turtle embryos in an arrested state prior to oviposition. Subsequent exposure to atmospheric oxygen upon oviposition initiates recommencement of embryonic development. Arrest can be artificially extended for several days after oviposition by incubation of the egg under hypoxic conditions, with development recommencing in an apparently normal fashion after subsequent exposure to normoxia. To examine the transcriptomic events associated with embryonic arrest in green sea turtles (Chelonia mydas), RNA‐sequencing analysis was performed on embryos from freshly laid eggs and eggs incubated in either normoxia (oxygen tension ~159 mmHg) or hypoxia (<8 mmHg) for 36 h after oviposition (n = 5 per group). The patterns of gene expression differed markedly among the three experimental groups. Normal embryonic development in normoxia was associated with upregulation of genes involved in DNA replication, the cell cycle, and mitosis, but these genes were commonly downregulated after incubation in hypoxia. Many target genes of hypoxia inducible factors, including the gene encoding insulin‐like growth factor binding protein 1 (igfbp1), were downregulated by normoxic incubation but upregulated by incubation in hypoxia. Notably, some of the transcriptomic effects of hypoxia in green turtle embryos resembled those reported to be associated with hypoxia‐induced embryonic arrest in diverse taxa, including the nematode Caenorhabditis elegans and zebrafish (Danio rerio). Hypoxia‐induced preovipositional embryonic arrest appears to be a unique adaptation of turtles. However, our findings accord with the proposition that the mechanisms underlying hypoxia‐induced embryonic arrest per se are highly conserved across diverse taxa.
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Affiliation(s)
- Angela Gárriz
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Sean A Williamson
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Anup D Shah
- Monash Bioinformatics Platform, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.,Monash Proteomics & Metabolomics Facility, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Roger G Evans
- Cardiovascular Disease Program, Biomedicine Discovery Institute and Department of Physiology, Monash University, Clayton, Victoria 3800, Australia.,Pre-clinical Critical Care Unit, Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, Victoria, Australia
| | - Deanna S Deveson Lucas
- Monash Bioinformatics Platform, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - David R Powell
- Monash Bioinformatics Platform, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Sarah L Walton
- Cardiovascular Disease Program, Biomedicine Discovery Institute and Department of Physiology, Monash University, Clayton, Victoria 3800, Australia
| | - Francine Z Marques
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Richard D Reina
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
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7
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Jiang Z, Jia Y, Zhang J, Li X, Dong C. Effect of secondary attack by Aeromonas hydrophila on the expression level of hif genes in common carp (Cyprinus carpio). JOURNAL OF FISH DISEASES 2022; 45:907-917. [PMID: 35385592 DOI: 10.1111/jfd.13616] [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: 01/04/2022] [Revised: 03/09/2022] [Accepted: 03/11/2022] [Indexed: 06/14/2023]
Abstract
Hypoxia-inducible factors (hifs) are involved in infectious diseases inflammatory reactions, and immune regulation. Common carp, a representative allotetraploid species that has undergone genome-wide replication events, has important research value. In this study, common carp were infected twice with Aeromonas hydrophila. Liver tissues of common carp were collected at 4 h, 12 h, 24 h, 48 h, 3 days, 7 days post-first infection and 4 h, 12 h, 24 h post-second infection. The mRNA levels of hif genes were determined at different time points. The hif2a-2, hif3a-2, hif3b-1 and hif3b-2 expression levels in the infected group were upregulated when compared with those in the control group, whereas the expression levels of other genes were downregulated after the second infection. This indicates that the effect of A. hydrophila infection on gene expression pattern is dependent on the host, pathogen, infected tissue and gene. Pressure analysis of the hif gene family revealed that the non-synonymous substitution to synonymous substitution ratio of 12 hif genes was <1, which indicated that they were in a state of purification and selection. Combined with the differences between copy genes, the polyclonal antibodies against Hif1b-1 and Hif1b-2 were successfully prepared in this study. Western blot analysis showed that the protein expression of Hif1b-1 and Hif1b-2 reached to the highest level 48 h after the first infection. After the second A. hydrophila infection, the protein expression levels of Hif1b-1 and Hif1b-2 reached the highest levels at 4 and 48 h, respectively. This may indicate that the Hif1b-1 and Hif1b-2 genes in common carp play an important role in the immune mechanism at the protein level. The findings of this study will lay the foundation for future studies on the immune regulatory function of common carp hif genes, which may aid in devising novel therapeutic strategies for common carp diseases, such as A. hydrophila infection.
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Affiliation(s)
- Zhou Jiang
- Research Center on Legal Issues Concerning Agriculture, Countryside and Farmers, College of Fishery, Henan Normal University, Xinxiang, China
| | - Yingying Jia
- Research Center on Legal Issues Concerning Agriculture, Countryside and Farmers, College of Fishery, Henan Normal University, Xinxiang, China
| | - Jiangfan Zhang
- Research Center on Legal Issues Concerning Agriculture, Countryside and Farmers, College of Fishery, Henan Normal University, Xinxiang, China
| | - Xuejun Li
- Research Center on Legal Issues Concerning Agriculture, Countryside and Farmers, College of Fishery, Henan Normal University, Xinxiang, China
| | - Chuanju Dong
- Research Center on Legal Issues Concerning Agriculture, Countryside and Farmers, College of Fishery, Henan Normal University, Xinxiang, China
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Musilova Z, Indermaur A, Bitja‐Nyom AR, Omelchenko D, Kłodawska M, Albergati L, Remišová K, Salzburger W. Evolution of the visual sensory system in cichlid fishes from crater lake Barombi Mbo in Cameroon. Mol Ecol 2019; 28:5010-5031. [DOI: 10.1111/mec.15217] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 08/09/2019] [Accepted: 08/13/2019] [Indexed: 01/09/2023]
Affiliation(s)
- Zuzana Musilova
- Department of Zoology Charles University in Prague Prague Czech Republic
- Zoological Institute University of Basel Basel Switzerland
| | | | - Arnold Roger Bitja‐Nyom
- Department of Biological Sciences University of Ngaoundéré Ngaoundéré Cameroon
- Department of Management of Fisheries and Aquatic Ecosystems University of Douala Douala Cameroon
| | - Dmytro Omelchenko
- Department of Zoology Charles University in Prague Prague Czech Republic
| | - Monika Kłodawska
- Department of Zoology Charles University in Prague Prague Czech Republic
| | - Lia Albergati
- Zoological Institute University of Basel Basel Switzerland
| | - Kateřina Remišová
- Department of Physiology Charles University in Prague Prague Czech Republic
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Zhang J, Dong C, Feng J, Li J, Li S, Feng J, Duan X, Sun G, Xu P, Li X. Effects of dietary supplementation of three strains of Lactococcus lactis on HIFs genes family expression of the common carp following Aeromonas hydrophila infection. FISH & SHELLFISH IMMUNOLOGY 2019; 92:590-599. [PMID: 31252044 DOI: 10.1016/j.fsi.2019.06.040] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 06/23/2019] [Accepted: 06/23/2019] [Indexed: 06/09/2023]
Abstract
HIFs (Hypoxia inducible factors) are the main regulators of the expression change of oxygen-dependent genes, in addition, they also play important roles in immune regulation. HIFs participate in infectious diseases and inflammatory responses, providing us a new therapeutic target for the treatment of diseases. In this study, 16 HIFs were identified in common carp genome database. Comparative genomics analysis showed large expansion of HIF gene family and approved the four round whole genome duplication (WGD) event in common carp. To further understand the function of HIFs, the domain architectures were predicted. All HIF proteins had the conserved HLH-PAS domain, which were essential for them to form dimer and bind to the downstream targets. The differences in domain of HIFα and HIFβ might result in their different functions. Phylogenetic analysis revealed that all HIFs were divided into two subfamilies and the HIFs in common carp were clustered with their teleost counterparts indicating they are highly conservative during evolution. In addition, the tissue distribution was examined by RT-PCR showed that most of HIF genes had a wide range of tissue distribution but exhibited tissue-specific expression patterns. The expression divergences were observed between the copy genes, for example, HIF1A-1, HIF2A-1, ARNT-2 had wide tissue distribution while their copies had limited tissue distribution, proving the function divergence of copies post the WGD event. In order to find an effective activation of HIFs and apply to treatment of aquatic diseases, we investigate the dietary supplementation effects of different strains of Lactococcus lactis on the expression of HIFα subfamily members in kidney of common carp infected with A. hydrophila. In addition, all of the HIF genes have a high expression in the early stages of infection, and decreased in the treatment time point of 48 h in common carp. This phenomenon confirms that as a switch, the main function of HIFs is to regulate the production of immune response factors in early infection. So activation of the switch may be an effective method for infectious disease treatment. As expected, the treatment groups improved the expression of HIFs compared with the control group, and the effects of the three strains are different. The strain1 of L. lactis had a stronger induction on HIF genes than strain2 and strain3, and it might be applied as a potential activation of HIF genes for disease treatment. So, adding befitting L. lactis maybe a well method to activate the HIF genes to protect them from mycobacterial infection.
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Affiliation(s)
- Jiangfan Zhang
- College of Fishery, Henan Normal University, Xinxiang, Henan, 453007, China
| | - Chuanju Dong
- College of Fishery, Henan Normal University, Xinxiang, Henan, 453007, China; Key Laboratory of Tropical&;Subtropical Fishery Resource Application and Cultivation, Pearl River Fisheries Research Institute, CAFS, Guangzhou, 510380, China; State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361005, China.
| | - Junchang Feng
- College of Fishery, Henan Normal University, Xinxiang, Henan, 453007, China
| | - Junpeng Li
- Xinxiang Central Hospital, Xinxiang, Henan, 453000, China
| | - Shengjie Li
- Key Laboratory of Tropical&;Subtropical Fishery Resource Application and Cultivation, Pearl River Fisheries Research Institute, CAFS, Guangzhou, 510380, China
| | - Jianxin Feng
- Henan Academy of Fishery Science, Zhengzhou, 450044, China
| | - Xiaodi Duan
- College of Fishery, Henan Normal University, Xinxiang, Henan, 453007, China
| | - Gaigai Sun
- College of Fishery, Henan Normal University, Xinxiang, Henan, 453007, China
| | - Peng Xu
- College of Fishery, Henan Normal University, Xinxiang, Henan, 453007, China; State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361005, China.
| | - Xuejun Li
- College of Fishery, Henan Normal University, Xinxiang, Henan, 453007, China.
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10
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Borowiec BG, McClelland GB, Rees BB, Scott GR. Distinct metabolic adjustments arise from acclimation to constant hypoxia and intermittent hypoxia in estuarine killifish (Fundulus heteroclitus). J Exp Biol 2018; 221:221/23/jeb190900. [DOI: 10.1242/jeb.190900] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 10/16/2018] [Indexed: 12/15/2022]
Abstract
ABSTRACT
Many fish experience daily cycles of hypoxia in the wild, but the physiological strategies for coping with intermittent hypoxia are poorly understood. We examined how killifish adjust O2 supply and demand during acute hypoxia, and how these responses are altered after prolonged acclimation to constant or intermittent patterns of hypoxia exposure. We acclimated killifish to normoxia (∼20 kPa O2), constant hypoxia (2 kPa) or intermittent cycles of nocturnal hypoxia (12 h:12 h normoxia:hypoxia) for 28 days, and then compared whole-animal O2 consumption rates (ṀO2) and tissue metabolites during exposure to 12 h of hypoxia followed by reoxygenation in normoxia. Normoxia-acclimated fish experienced a pronounced 27% drop in ṀO2 during acute hypoxia, and modestly increased ṀO2 upon reoxygenation. They strongly recruited anaerobic metabolism during acute hypoxia, indicated by lactate accumulation in plasma, muscle, liver, brain, heart and digestive tract, as well as a transient drop in intracellular pH, and they increased hypoxia inducible factor (HIF)-1α protein abundance in muscle. Glycogen, glucose and glucose-6-phosphate levels suggested that glycogen supported brain metabolism in hypoxia, while the muscle used circulating glucose. Acclimation to constant hypoxia caused a stable ∼50% decrease in ṀO2 that persisted after reoxygenation, with minimal recruitment of anaerobic metabolism, suggestive of metabolic depression. By contrast, fish acclimated to intermittent hypoxia maintained sufficient O2 transport to support normoxic ṀO2, modestly recruited lactate metabolism and increased ṀO2 dramatically upon reoxygenation. Both groups of hypoxia-acclimated fish had similar glycogen, ATP, intracellular pH and HIF-1α levels as normoxic controls. We conclude that different patterns of hypoxia exposure favour distinct strategies for matching O2 supply and O2 demand.
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Affiliation(s)
| | - Grant B. McClelland
- Department of Biology, McMaster University, Hamilton, Ontario, Canada, L8S 4K1
| | - Bernard B. Rees
- Department of Biological Sciences, University of New Orleans, New Orleans, LA 70148, USA
| | - Graham R. Scott
- Department of Biology, McMaster University, Hamilton, Ontario, Canada, L8S 4K1
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Brennan RS, Healy TM, Bryant HJ, La MV, Schulte PM, Whitehead A. Integrative Population and Physiological Genomics Reveals Mechanisms of Adaptation in Killifish. Mol Biol Evol 2018; 35:2639-2653. [PMID: 30102365 PMCID: PMC11325861 DOI: 10.1093/molbev/msy154] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Adaptive divergence between marine and freshwater (FW) environments is important in generating phyletic diversity within fishes, but the genetic basis of this process remains poorly understood. Genome selection scans can identify adaptive loci, but incomplete knowledge of genotype-phenotype connections makes interpreting their significance difficult. In contrast, association mapping (genome-wide association mapping [GWAS], random forest [RF] analyses) links genotype to phenotype, but offer limited insight into the evolutionary forces shaping variation. Here, we combined GWAS, RF, and selection scans to identify loci important in adaptation to FW environments. We utilized FW-native and brackish water (BW)-native populations of Atlantic killifish (Fundulus heteroclitus) as well as a naturally admixed population between the two. We measured morphology and multiple physiological traits that differ between populations and may contribute to osmotic adaptation (salinity tolerance, hypoxia tolerance, metabolic rate, body shape) and used a reduced representation approach for genome-wide genotyping. Our results show patterns of population divergence in physiological capabilities that are consistent with local adaptation. Population genomic scans between BW-native and FW-native populations identified genomic regions evolving by natural selection, whereas association mapping revealed loci that contribute to variation for each trait. There was substantial overlap in the genomic regions putatively under selection and loci associated with phenotypic traits, particularly for salinity tolerance, suggesting that these regions and genes are important for adaptive divergence between BW and FW environments. Together, these data provide insight into the mechanisms that enable diversification of fishes across osmotic boundaries.
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Affiliation(s)
- Reid S Brennan
- Department of Environmental Toxicology, University of California-Davis, Davis, CA
- Department of Biology, University of Vermont, Burlington, VT
| | - Timothy M Healy
- Department of Zoology, The University of British Columbia, Vancouver, BC, Canada
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, CA
| | - Heather J Bryant
- Department of Zoology, The University of British Columbia, Vancouver, BC, Canada
| | - Man Van La
- Department of Environmental Toxicology, University of California-Davis, Davis, CA
| | - Patricia M Schulte
- Department of Zoology, The University of British Columbia, Vancouver, BC, Canada
| | - Andrew Whitehead
- Department of Environmental Toxicology, University of California-Davis, Davis, CA
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Pelster B, Egg M. Hypoxia-inducible transcription factors in fish: expression, function and interconnection with the circadian clock. J Exp Biol 2018; 221:221/13/jeb163709. [DOI: 10.1242/jeb.163709] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
ABSTRACT
The hypoxia-inducible transcription factors are key regulators for the physiological response to low oxygen availability. In vertebrates, typically three Hif-α isoforms, Hif-1α, Hif-2α and Hif-3α, are expressed, each of which, together with Hif-1β, may form a functional heterodimer under hypoxic conditions, controlling expression of hundreds of genes. A teleost-specific whole-genome duplication complicates the analysis of isoform-specific functions in fish, but recent studies suggest that the existence of paralogues of a specific isoform opens up the possibility for a subfunctionalization. In contrast to during development inside the uterus, fish eggs are freely accessible and studies analyzing Hif expression in fish embryos during development have revealed that Hif proteins are not only controlling the hypoxic response, but are also crucial for proper development and organ differentiation. Significant advances have been made in our knowledge about tissue-specific functions of Hif proteins, especially with respect to gill or gonadal tissue. The hypoxia signalling pathway is known to be tightly and mutually intertwined with the circadian clock in zebrafish and mammals. Recently, a mechanistic explanation for the hypoxia-induced dampening of the transcriptional clock was detected in zebrafish, including also metabolically induced alterations of cellular redox signalling. In turn, MAP kinase-mediated H2O2 signalling modulates the temporal expression of Hif-1α protein, similar to the redox regulation of the circadian clock itself. Once again, the zebrafish has emerged as an excellent model organism with which to explore these specific functional aspects of basic eukaryotic cell biology.
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Affiliation(s)
- Bernd Pelster
- Institute of Zoology, University of Innsbruck, Technikerstr. 25, A-6020 Innsbruck, Austria
- Center for Molecular Biosciences, University of Innsbruck, A-6020 Innsbruck, Austria
| | - Margit Egg
- Institute of Zoology, University of Innsbruck, Technikerstr. 25, A-6020 Innsbruck, Austria
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Amador MHB. Unearthing HIFs in a hardy marsh fish. J Exp Biol 2017. [DOI: 10.1242/jeb.147488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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