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Wang H, Su B, Zhang Y, Shang M, Wang J, Johnson A, Dilawar H, Bruce TJ, Dunham RA, Wang X. Transcriptome analysis revealed potential mechanisms of channel catfish growth advantage over blue catfish in a tank culture environment. Front Genet 2024; 15:1341555. [PMID: 38742167 PMCID: PMC11089159 DOI: 10.3389/fgene.2024.1341555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 03/27/2024] [Indexed: 05/16/2024] Open
Abstract
Channel catfish (Ictalurus punctatus) and blue catfish (Ictalurus furcatus) are two economically important freshwater aquaculture species in the United States, with channel catfish contributing to nearly half of the country's aquaculture production. While differences in economic traits such as growth rate and disease resistance have been noted, the extent of transcriptomic variance across various tissues between these species remains largely unexplored. The hybridization of female channel catfish with male blue catfish has led to the development of superior hybrid catfish breeds that exhibit enhanced growth rates and improved disease resistance, which dominate more than half of the total US catfish production. While hybrid catfish have significant growth advantages in earthen ponds, channel catfish were reported to grow faster in tank culture environments. In this study, we confirmed channel fish's superiority in growth over blue catfish in 60-L tanks at 10.8 months of age (30.3 g and 11.6 g in this study, respectively; p < 0.001). In addition, we conducted RNA sequencing experiments and established transcriptomic resources for the heart, liver, intestine, mucus, and muscle of both species. The number of expressed genes varied across tissues, ranging from 5,036 in the muscle to over 20,000 in the mucus. Gene Ontology analysis has revealed the functional specificity of differentially expressed genes within their respective tissues, with significant pathway enrichment in metabolic pathways, immune activity, and stress responses. Noteworthy tissue-specific marker genes, including lrrc10, fabp2, myog, pth1a, hspa9, cyp21a2, agt, and ngtb, have been identified. This transcriptome resource is poised to support future investigations into the molecular mechanisms underlying environment-dependent heterosis and advance genetic breeding efforts of hybrid catfish.
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Affiliation(s)
- Haolong Wang
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
- Auburn University Center for Advanced Science, Innovation, and Commerce, Alabama Agricultural Experiment Station, Auburn, AL, United States
| | - Baofeng Su
- Auburn University Center for Advanced Science, Innovation, and Commerce, Alabama Agricultural Experiment Station, Auburn, AL, United States
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, United States
| | - Ying Zhang
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
- Auburn University Center for Advanced Science, Innovation, and Commerce, Alabama Agricultural Experiment Station, Auburn, AL, United States
| | - Mei Shang
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, United States
| | - Jinhai Wang
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, United States
| | - Andrew Johnson
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, United States
| | - Hamza Dilawar
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, United States
| | - Timothy J. Bruce
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, United States
| | - Rex A. Dunham
- Auburn University Center for Advanced Science, Innovation, and Commerce, Alabama Agricultural Experiment Station, Auburn, AL, United States
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, United States
| | - Xu Wang
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
- Auburn University Center for Advanced Science, Innovation, and Commerce, Alabama Agricultural Experiment Station, Auburn, AL, United States
- Scott-Ritchey Research Center, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
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Chen X, Gao Y, Wu G, Gu J, Cai Y, Xu J, Cheng H. Molecular cloning, tissue expression, and transcriptional regulation of fabp1 and fabp2 in javelin goby (Synechogobius hasta) in response to starvation stress. Comp Biochem Physiol B Biochem Mol Biol 2020; 250:110484. [PMID: 32745520 DOI: 10.1016/j.cbpb.2020.110484] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 07/20/2020] [Accepted: 07/27/2020] [Indexed: 01/15/2023]
Abstract
Fatty acid binding proteins (FABPs) are intracellular lipid chaperones with low molecular weight, which are widely distributed in a variety of tissues, participating in fatty acid transport, cell proliferation, and angiogenesis. In this study, full-length sequences of two fabp genes (fabp1 and fabp2) from javelin goby (Synechogobius hasta) were cloned via RACE PCR, followed by bioinformatic analyses and gene expression evaluation. The fabp1 and fabp2 cDNA sequences were 493 and 626 bp in length, encoding 126 and 132 amino acids, respectively. Phylogenetic analysis revealed that both genes from S. hasta were clustered with those of other fish species in accordance with their known taxonomic relationships. fabp1 and fabp2 mRNA showed distinct expression patterns in different tissues, with fabp1 being most expressed in the liver and fabp2 in the intestine. Furthermore, the expression of fabp1 in the liver was significantly up-regulated during starvation, whereas fabp2 mRNA level in the intestine initially increased and then decreased, indicating that the transcriptional responses of the two genes could be influenced by malnourishment/starvation. Changes in the transcriptional levels of fabp1 and fabp2 also suggested that glycogen was catabolized in the liver of S. hasta at the beginning of starvation prior to lipid depletion, whereas lipids served as fuel reserves in the intestine during short-term starvation. In conclusion, this study provides fundamental insights into the role of Fabps in S. hasta lipid metabolism.
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Affiliation(s)
- Xiangning Chen
- Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222005, China; Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222005, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Lianyungang 222005, China.
| | - Yingli Gao
- Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222005, China; Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222005, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Lianyungang 222005, China
| | - Guanju Wu
- College of Marine Science and Fisheries, Jiangsu Ocean University, Lianyungang 222005, China
| | - Jiaze Gu
- College of Marine Science and Fisheries, Jiangsu Ocean University, Lianyungang 222005, China
| | - Yuefeng Cai
- College of Marine Science and Fisheries, Jiangsu Ocean University, Lianyungang 222005, China
| | - Jianhe Xu
- College of Marine Science and Fisheries, Jiangsu Ocean University, Lianyungang 222005, China
| | - Hanliang Cheng
- College of Marine Science and Fisheries, Jiangsu Ocean University, Lianyungang 222005, China
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Zhang Y, Zhang J, Ren Y, Lu R, Yang L, Nie G. Tracing the evolution of fatty acid-binding proteins (FABPs) in organisms with a heterogeneous fat distribution. FEBS Open Bio 2020; 10:861-872. [PMID: 32170849 PMCID: PMC7193176 DOI: 10.1002/2211-5463.12840] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 02/22/2020] [Accepted: 03/12/2020] [Indexed: 11/28/2022] Open
Abstract
The distribution of fat among both invertebrate and vertebrate groups is heterogeneous. Studies have shown that fatty acid‐binding proteins (FABPs), which mainly bind and transport fatty acids, play important roles in the regulation of fat storage and distribution. However, the systematic and genome‐wide investigation of FABP genes in organisms with a heterogeneous fat distribution remains in its infancy. The availability of the complete genomes of Caenorhabditis elegans, Callorhinchus milii, and other organisms with a heterogeneous fat distribution allowed us to systematically investigate the gene structure and phylogeny of FABP genes across a wide range of phyla. In this study, we analyzed the number, structure, chromosomal location, and phylogeny of FABP genes in 18 organisms from C. elegans to Homo sapiens. A total of 12 types of FABP genes were identified in the 18 species, and no single organism exhibited all 12 fatty acid‐binding genes (FABPs). The absence of a specific FABP gene in tissue may be related to the absence of fat storage in the corresponding tissue. The genomic loci of the FABP genes were diverse, and their gene structures varied. The results of the phylogenetic analysis and the observation of conserved gene synthesis of FABP family genes/proteins suggest that all FABP genes may have evolved from a common ancestor through tandem duplication. This study not only lays a strong theoretical foundation for the study of fat deposition in different organisms, but also provides a new perspective regarding metabolic disease prevention and control and the improvement of agricultural product quality.
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Affiliation(s)
- Yuru Zhang
- College of Fisheries, Henan Normal University, Xinxiang, China.,College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, China
| | - Junmei Zhang
- College of Fisheries, Henan Normal University, Xinxiang, China.,College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, China
| | - Yanhua Ren
- College of Fisheries, Henan Normal University, Xinxiang, China.,College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, China
| | - Ronghua Lu
- College of Fisheries, Henan Normal University, Xinxiang, China.,College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, China
| | - Liping Yang
- College of Fisheries, Henan Normal University, Xinxiang, China.,College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, China
| | - Guoxing Nie
- College of Fisheries, Henan Normal University, Xinxiang, China.,College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, China
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Wang Z, Yue YX, Liu ZM, Yang LY, Li H, Li ZJ, Li GX, Wang YB, Tian YD, Kang XT, Liu XJ. Genome-Wide Analysis of the FABP Gene Family in Liver of Chicken (Gallus gallus): Identification,Dynamic Expression Profile, and RegulatoryMechanism. Int J Mol Sci 2019; 20:E5948. [PMID: 31779219 PMCID: PMC6928644 DOI: 10.3390/ijms20235948] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 11/19/2019] [Accepted: 11/22/2019] [Indexed: 02/07/2023] Open
Abstract
The fatty acid-binding protein (FABP) gene family, which encodes a group of fatty acid-trafficking molecules that affect cellular functions, has been studied extensively in mammals. However, little is known about the gene structure, expression profile, and regulatory mechanism of the gene family in chickens. In the present study, bioinformatics-based methods were used to identify the family members and investigate their evolutionary history and features of gene structure. Real-time PCR combined with in vivo and in vitro experiments were used to examine the spatiotemporal expression pattern, and explore the regulatory mechanism of FABP genes. The results show that nine members of the FABP gene family, which branched into two clusters and shared a conserved FATTYACIDBP domain, exist in the genome of chickens. Of these, seven FABP genes, including FABP1, FABP3-7, and FABP10 were abundantly expressed in the liver of hens. The expression levels of FABP1, FABP3, and FABP10 were significantly increased, FABP5 and FABP7 were significantly decreased, and FABP4 and FABP6 remained unchanged in hens at the peak laying stage in comparison to those at the pre-laying stage. Transcription of FABP1 and FABP3 were activated by estrogen via estrogen receptor (ER) α, whilst FABP10 was activated by estrogen via ERβ. Meanwhile, the expression of FABP1 was regulated by peroxisome proliferator activated receptor (PPAR) isoforms, of which tested PPARα and PPARβ agonists significantly inhibited the expression of FABP1, while tested PPARγ agonists significantly increased the expression of FABP1, but downregulated it when the concentration of the PPARγ agonist reached 100 nM. The expression of FABP3 was upregulated via tested PPARβ and PPARγ agonists, and the expression of FABP7 was selectively promoted via PPARγ. The expression of FABP10 was activated by all of the three tested PPAR agonists, but the expression of FABP4-6 was not affected by any of the PPAR agonists. In conclusion, members of the FABP gene family in chickens shared similar functional domains, gene structures, and evolutionary histories with mammalian species, but exhibited varying expression profiles and regulatory mechanisms. The results provide a valuable resource for better understanding the biological functions of individual FABP genes in chickens.
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Affiliation(s)
- Zhang Wang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China; (Z.W.); (Y.-X.Y.); (Z.-M.L.); (L.-Y.Y.); (H.L.); (Z.-J.L.); (G.-X.L.); (Y.-B.W.); (Y.-D.T.); (X.-T.K.)
| | - Ya-Xin Yue
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China; (Z.W.); (Y.-X.Y.); (Z.-M.L.); (L.-Y.Y.); (H.L.); (Z.-J.L.); (G.-X.L.); (Y.-B.W.); (Y.-D.T.); (X.-T.K.)
| | - Zi-Ming Liu
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China; (Z.W.); (Y.-X.Y.); (Z.-M.L.); (L.-Y.Y.); (H.L.); (Z.-J.L.); (G.-X.L.); (Y.-B.W.); (Y.-D.T.); (X.-T.K.)
| | - Li-Yu Yang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China; (Z.W.); (Y.-X.Y.); (Z.-M.L.); (L.-Y.Y.); (H.L.); (Z.-J.L.); (G.-X.L.); (Y.-B.W.); (Y.-D.T.); (X.-T.K.)
| | - Hong Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China; (Z.W.); (Y.-X.Y.); (Z.-M.L.); (L.-Y.Y.); (H.L.); (Z.-J.L.); (G.-X.L.); (Y.-B.W.); (Y.-D.T.); (X.-T.K.)
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou 450002, China
- International Joint Research Laboratory for Poultry Breeding of Henan, Zhengzhou 450002, China
| | - Zhuan-Jian Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China; (Z.W.); (Y.-X.Y.); (Z.-M.L.); (L.-Y.Y.); (H.L.); (Z.-J.L.); (G.-X.L.); (Y.-B.W.); (Y.-D.T.); (X.-T.K.)
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou 450002, China
- International Joint Research Laboratory for Poultry Breeding of Henan, Zhengzhou 450002, China
| | - Guo-Xi Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China; (Z.W.); (Y.-X.Y.); (Z.-M.L.); (L.-Y.Y.); (H.L.); (Z.-J.L.); (G.-X.L.); (Y.-B.W.); (Y.-D.T.); (X.-T.K.)
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou 450002, China
- International Joint Research Laboratory for Poultry Breeding of Henan, Zhengzhou 450002, China
| | - Yan-Bin Wang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China; (Z.W.); (Y.-X.Y.); (Z.-M.L.); (L.-Y.Y.); (H.L.); (Z.-J.L.); (G.-X.L.); (Y.-B.W.); (Y.-D.T.); (X.-T.K.)
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou 450002, China
- International Joint Research Laboratory for Poultry Breeding of Henan, Zhengzhou 450002, China
| | - Ya-Dong Tian
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China; (Z.W.); (Y.-X.Y.); (Z.-M.L.); (L.-Y.Y.); (H.L.); (Z.-J.L.); (G.-X.L.); (Y.-B.W.); (Y.-D.T.); (X.-T.K.)
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou 450002, China
- International Joint Research Laboratory for Poultry Breeding of Henan, Zhengzhou 450002, China
| | - Xiang-Tao Kang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China; (Z.W.); (Y.-X.Y.); (Z.-M.L.); (L.-Y.Y.); (H.L.); (Z.-J.L.); (G.-X.L.); (Y.-B.W.); (Y.-D.T.); (X.-T.K.)
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou 450002, China
- International Joint Research Laboratory for Poultry Breeding of Henan, Zhengzhou 450002, China
| | - Xiao-Jun Liu
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China; (Z.W.); (Y.-X.Y.); (Z.-M.L.); (L.-Y.Y.); (H.L.); (Z.-J.L.); (G.-X.L.); (Y.-B.W.); (Y.-D.T.); (X.-T.K.)
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou 450002, China
- International Joint Research Laboratory for Poultry Breeding of Henan, Zhengzhou 450002, China
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Chen W, Wang K, Liu S. Molecular cloning and tissue distribution of fatty acid binding protein-3 in goldfish (Carassius auratus) and its mRNA expression in response to cadmium and PAMPs. Comp Biochem Physiol A Mol Integr Physiol 2018; 224:68-75. [PMID: 30008387 DOI: 10.1016/j.cbpa.2018.06.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Revised: 06/25/2018] [Accepted: 06/25/2018] [Indexed: 12/13/2022]
Abstract
Fatty acid binding proteins (FABPs) are members of the conserved, multigene family of intracellular lipid binding proteins. In this study, the full-length cDNA of goldfish (Carassius auratus) FABP-3 (gfFABP-3) was successfully cloned. gfFABP-3 had an open reading frame of 402 bp and encoded a 133 amino acid polypeptide. The predicted gfFABP-3 protein included a lipocalin domain and displayed typical conserved FABP tertiary structures. Reverse transcription-PCR (RT-PCR) revealed that the gfFABP-3 gene was expressed in all tested tissues, with higher levels of expression in the testis, liver, heart, fat and kidney. After 24 h of cadmium exposure, gfFABP-3 was significantly upregulated in the gill, liver and spleen, but downregulated in the intestine, as compared to unexposed controls. gfFABP-3 expression was significantly downregulated in the spleen in goldfish challenged with LPS and Poly I:C. Our study provides a molecular characterization of goldfish FABP-3 and indicated that gfFABP-3 was potentially associated with the toxic effects of cadmium on lipid metabolism, and with the immune response to pathogenic infection.
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Affiliation(s)
- Wenbo Chen
- Department of Biology, Institute of Resources and Environment, Henan Polytechnic University, Jiaozuo 454000, Henan, China.
| | - Kaimeng Wang
- Department of Biology, Institute of Resources and Environment, Henan Polytechnic University, Jiaozuo 454000, Henan, China
| | - Shiyu Liu
- Department of Biology, Institute of Resources and Environment, Henan Polytechnic University, Jiaozuo 454000, Henan, China
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