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Zhang Y, Wang J, Zhang M, Li X, Zhang F, Zhou M, Yang K, Chen W, Ding H, Tan X, Zhang Q, Qiao Z. Study on the Regulatory Mechanism of the PDK1-Mediated TGF-β/Smad Signaling Pathway in Hypoxia-Induced Yak Lungs. Animals (Basel) 2024; 14:2422. [PMID: 39199957 PMCID: PMC11350703 DOI: 10.3390/ani14162422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2024] [Revised: 08/10/2024] [Accepted: 08/20/2024] [Indexed: 09/01/2024] Open
Abstract
The aim of this study was to investigate the effects of hypoxia-induced phenotype, glucose metabolism, ROS levels, and the PDK1-mediated regulation of TGF-β/Smad signaling in yellow cattles, yaks, and those overexpressing PDK1 PASMCs using growth curves, flow cytometry, scratch experiments, glucose and lactic acid assays, RT-qPCR, and Western blotting. The results showed that hypoxia significantly promoted proliferation, migration, antiapoptosis, ROS levels, glucose consumption, and lactate production in yellow cattle PASMCs (p < 0.05), and the cells were dedifferentiated from the contractile phenotype; conversely, hypoxia had no significant effect on yak PASMCs (p > 0.05). PDK1 overexpression significantly promoted proliferation, antiapoptosis, glucose consumption, and lactate production in yak PASMCs under normoxia and hypoxia (p < 0.05), decreased their migration levels under hypoxia (p < 0.05), and dedifferentiated the contractile phenotype of the cells. Overexpression of PDK1 in yak PASMCs is detrimental to their adaptation to hypoxic environments. Yak PASMCs adapted to the effects of hypoxia on lung tissue by downregulating the expression of genes related to the PDK1 and TGF-β/Smad signaling pathways. Taken together, the regulation of PDK1-mediated TGF-β/Smad signaling may be involved in the process of yaks' adaptation to the hypoxic environment of the plateau, reflecting the good adaptive ability of yaks. The present study provides basic information to further elucidate the mechanism of PDK1-mediated TGF-β/Smad signaling induced by hypoxia in the lungs of yaks, as well as target genes for the treatment of plateau diseases in humans and animals.
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Affiliation(s)
- Yiyang Zhang
- Engineering Research Center of Key Technology and Industrialization of Cell-Based Vaccine, Ministry of Education, Northwest Minzu University, Lanzhou 730030, China; (Y.Z.); (X.L.); (F.Z.); (M.Z.); (Z.Q.)
- Gansu Tech Innovation Center of Animal Cell, Biomedical Research Center, Northwest Minzu University, Lanzhou 730030, China
- Key Laboratory of Biotechnology and Bioengineering of State Ethnic Affairs Commission, Biomedical Research Center, Northwest Minzu University, Lanzhou 730030, China
- Life Science and Engineering College, Northwest Minzu University, Lanzhou 730030, China; (J.W.); (M.Z.); (W.C.); (H.D.); (X.T.)
| | - Jun Wang
- Life Science and Engineering College, Northwest Minzu University, Lanzhou 730030, China; (J.W.); (M.Z.); (W.C.); (H.D.); (X.T.)
| | - Meng Zhang
- Life Science and Engineering College, Northwest Minzu University, Lanzhou 730030, China; (J.W.); (M.Z.); (W.C.); (H.D.); (X.T.)
| | - Xiaoyun Li
- Engineering Research Center of Key Technology and Industrialization of Cell-Based Vaccine, Ministry of Education, Northwest Minzu University, Lanzhou 730030, China; (Y.Z.); (X.L.); (F.Z.); (M.Z.); (Z.Q.)
- Gansu Tech Innovation Center of Animal Cell, Biomedical Research Center, Northwest Minzu University, Lanzhou 730030, China
- Key Laboratory of Biotechnology and Bioengineering of State Ethnic Affairs Commission, Biomedical Research Center, Northwest Minzu University, Lanzhou 730030, China
- Life Science and Engineering College, Northwest Minzu University, Lanzhou 730030, China; (J.W.); (M.Z.); (W.C.); (H.D.); (X.T.)
| | - Fan Zhang
- Engineering Research Center of Key Technology and Industrialization of Cell-Based Vaccine, Ministry of Education, Northwest Minzu University, Lanzhou 730030, China; (Y.Z.); (X.L.); (F.Z.); (M.Z.); (Z.Q.)
- Gansu Tech Innovation Center of Animal Cell, Biomedical Research Center, Northwest Minzu University, Lanzhou 730030, China
- Key Laboratory of Biotechnology and Bioengineering of State Ethnic Affairs Commission, Biomedical Research Center, Northwest Minzu University, Lanzhou 730030, China
- Life Science and Engineering College, Northwest Minzu University, Lanzhou 730030, China; (J.W.); (M.Z.); (W.C.); (H.D.); (X.T.)
| | - Manlin Zhou
- Engineering Research Center of Key Technology and Industrialization of Cell-Based Vaccine, Ministry of Education, Northwest Minzu University, Lanzhou 730030, China; (Y.Z.); (X.L.); (F.Z.); (M.Z.); (Z.Q.)
- Gansu Tech Innovation Center of Animal Cell, Biomedical Research Center, Northwest Minzu University, Lanzhou 730030, China
- Key Laboratory of Biotechnology and Bioengineering of State Ethnic Affairs Commission, Biomedical Research Center, Northwest Minzu University, Lanzhou 730030, China
- Life Science and Engineering College, Northwest Minzu University, Lanzhou 730030, China; (J.W.); (M.Z.); (W.C.); (H.D.); (X.T.)
| | - Kun Yang
- Engineering Research Center of Key Technology and Industrialization of Cell-Based Vaccine, Ministry of Education, Northwest Minzu University, Lanzhou 730030, China; (Y.Z.); (X.L.); (F.Z.); (M.Z.); (Z.Q.)
- Gansu Tech Innovation Center of Animal Cell, Biomedical Research Center, Northwest Minzu University, Lanzhou 730030, China
- Key Laboratory of Biotechnology and Bioengineering of State Ethnic Affairs Commission, Biomedical Research Center, Northwest Minzu University, Lanzhou 730030, China
- Life Science and Engineering College, Northwest Minzu University, Lanzhou 730030, China; (J.W.); (M.Z.); (W.C.); (H.D.); (X.T.)
| | - Weiji Chen
- Life Science and Engineering College, Northwest Minzu University, Lanzhou 730030, China; (J.W.); (M.Z.); (W.C.); (H.D.); (X.T.)
| | - Haie Ding
- Life Science and Engineering College, Northwest Minzu University, Lanzhou 730030, China; (J.W.); (M.Z.); (W.C.); (H.D.); (X.T.)
| | - Xiao Tan
- Life Science and Engineering College, Northwest Minzu University, Lanzhou 730030, China; (J.W.); (M.Z.); (W.C.); (H.D.); (X.T.)
| | - Qian Zhang
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China;
| | - Zilin Qiao
- Engineering Research Center of Key Technology and Industrialization of Cell-Based Vaccine, Ministry of Education, Northwest Minzu University, Lanzhou 730030, China; (Y.Z.); (X.L.); (F.Z.); (M.Z.); (Z.Q.)
- Gansu Tech Innovation Center of Animal Cell, Biomedical Research Center, Northwest Minzu University, Lanzhou 730030, China
- Key Laboratory of Biotechnology and Bioengineering of State Ethnic Affairs Commission, Biomedical Research Center, Northwest Minzu University, Lanzhou 730030, China
- Life Science and Engineering College, Northwest Minzu University, Lanzhou 730030, China; (J.W.); (M.Z.); (W.C.); (H.D.); (X.T.)
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Wu Z, Chai Z, Cai X, Wang J, Wang H, Yue B, Zhang M, Wang J, Wang H, Zhong J, Xin J. Protein Lactylation Profiles Provide Insights into Molecular Mechanisms Underlying Metabolism in Yak. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024. [PMID: 38850252 DOI: 10.1021/acs.jafc.4c01800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2024]
Abstract
Protein lysine lactylation, a recently discovered post-translational modification (PTM), is prevalent across tissues and cells of diverse species, serving as a regulator of glycolytic flux and biological metabolism. The yak (Bos grunniens), a species that has inhabited the Qinghai-Tibetan Plateau for millennia, has evolved intricate adaptive mechanisms to cope with the region's unique geographical and climatic conditions, exhibiting remarkable energy utilization and metabolic efficiency. Nonetheless, the specific landscape of lysine lactylation in yaks remains poorly understood. Herein, we present the first comprehensive lactylome profile of the yak, effectively identifying 421, 308, and 650 lactylated proteins in the heart, muscles, and liver, respectively. These lactylated proteins are involved in glycolysis/gluconeogenesis, the tricarboxylic acid cycle, oxidative phosphorylation, and metabolic process encompassing carbohydrates, lipids, and proteins during both anaerobic and aerobic glucose bio-oxidation, implying their crucial role in material and energy metabolism, as well as in maintaining homeostasis in yaks.
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Affiliation(s)
- Zhijuan Wu
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu, Sichuan 610225, China
| | - Zhixin Chai
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu, Sichuan 610225, China
| | - Xin Cai
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu, Sichuan 610225, China
| | - Jiabo Wang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu, Sichuan 610225, China
| | - Hui Wang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu, Sichuan 610225, China
| | - Binglin Yue
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu, Sichuan 610225, China
| | - Ming Zhang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu, Sichuan 610225, China
| | - Jikun Wang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu, Sichuan 610225, China
| | - Haibo Wang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu, Sichuan 610225, China
| | - Jincheng Zhong
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu, Sichuan 610225, China
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, Sichuan 610225, China
| | - Jinwei Xin
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, Tibet 850000, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Institute of Animal Science and Veterinary, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850009, China
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Jiang H, Chai ZX, Chen XY, Zhang CF, Zhu Y, Ji QM, Xin JW. Yak genome database: a multi-omics analysis platform. BMC Genomics 2024; 25:346. [PMID: 38580907 PMCID: PMC10998334 DOI: 10.1186/s12864-024-10274-6] [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: 10/30/2023] [Accepted: 03/31/2024] [Indexed: 04/07/2024] Open
Abstract
BACKGROUND The yak (Bos grunniens) is a large ruminant species that lives in high-altitude regions and exhibits excellent adaptation to the plateau environments. To further understand the genetic characteristics and adaptive mechanisms of yak, we have developed a multi-omics database of yak including genome, transcriptome, proteome, and DNA methylation data. DESCRIPTION The Yak Genome Database ( http://yakgenomics.com/ ) integrates the research results of genome, transcriptome, proteome, and DNA methylation, and provides an integrated platform for researchers to share and exchange omics data. The database contains 26,518 genes, 62 transcriptomes, 144,309 proteome spectra, and 22,478 methylation sites of yak. The genome module provides access to yak genome sequences, gene annotations and variant information. The transcriptome module offers transcriptome data from various tissues of yak and cattle strains at different developmental stages. The proteome module presents protein profiles from diverse yak organs. Additionally, the DNA methylation module shows the DNA methylation information at each base of the whole genome. Functions of data downloading and browsing, functional gene exploration, and experimental practice were available for the database. CONCLUSION This comprehensive database provides a valuable resource for further investigations on development, molecular mechanisms underlying high-altitude adaptation, and molecular breeding of yak.
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Affiliation(s)
- Hui Jiang
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, 850000, Lhasa, Tibet, China
- Institute of Animal Science and Veterinary, Tibet Academy of Agricultural and Animal Husbandry Sciences, 850000, Lhasa, Tibet, China
| | - Zhi-Xin Chai
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, 610041, Chengdu, Sichuan, China
| | - Xiao-Ying Chen
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, 850000, Lhasa, Tibet, China
- Institute of Animal Science and Veterinary, Tibet Academy of Agricultural and Animal Husbandry Sciences, 850000, Lhasa, Tibet, China
| | - Cheng-Fu Zhang
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, 850000, Lhasa, Tibet, China
- Institute of Animal Science and Veterinary, Tibet Academy of Agricultural and Animal Husbandry Sciences, 850000, Lhasa, Tibet, China
| | - Yong Zhu
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, 850000, Lhasa, Tibet, China
- Institute of Animal Science and Veterinary, Tibet Academy of Agricultural and Animal Husbandry Sciences, 850000, Lhasa, Tibet, China
| | - Qiu-Mei Ji
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, 850000, Lhasa, Tibet, China.
- Institute of Animal Science and Veterinary, Tibet Academy of Agricultural and Animal Husbandry Sciences, 850000, Lhasa, Tibet, China.
| | - Jin-Wei Xin
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, 850000, Lhasa, Tibet, China.
- Institute of Animal Science and Veterinary, Tibet Academy of Agricultural and Animal Husbandry Sciences, 850000, Lhasa, Tibet, China.
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Zhang Y, Zhou M, Liang Y, Li R, Zhang L, Chen S, Yang K, Ding H, Tan X, Zhang Q, Qiao Z. Study of Transcriptomic Analysis of Yak ( Bos grunniens) and Cattle ( Bos taurus) Pulmonary Artery Smooth Muscle Cells under Oxygen Concentration Gradients and Differences in Their Lung Histology and Expression of Pyruvate Dehydrogenase Kinase 1-Related Factors. Animals (Basel) 2023; 13:3450. [PMID: 38003068 PMCID: PMC10668684 DOI: 10.3390/ani13223450] [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: 08/29/2023] [Revised: 10/27/2023] [Accepted: 11/04/2023] [Indexed: 11/26/2023] Open
Abstract
The aim of this study was to investigate the molecular mechanisms by which hypoxia affects the biological behavior of yak PASMCs, the changes in the histological structure of yak and cattle lungs, and the relationships and regulatory roles that exist regarding the differences in the distribution and expression of PDK1 and its hypoxia-associated factors screened for their role in the adaptation of yak lungs to the plateau hypoxic environment. The results showed that, at the level of transcriptome sequencing, the molecular regulatory mechanisms of the HIF-1 signaling pathway, glucose metabolism pathway, and related factors (HK2/PGK1/ENO1/ENO3/ALDOC/ALDOA) may be closely related to the adaptation of yaks to the hypoxic environment of the plateau; at the tissue level, the presence of filled alveoli and semi-filled alveoli, thicker alveolar septa and basement membranes, a large number of erythrocytes, capillary distribution, and collagen fibers accounted for all levels of fine bronchioles in the lungs of yaks as compared to cattle. A higher percentage of goblet cells was found in the fine bronchioles of yaks, and PDK1, HIF-1α, and VEGF were predominantly distributed and expressed in the monolayers of ciliated columnar epithelium in the branches of the terminal fine bronchioles of yak and cattle lungs, with a small amount of it distributed in the alveolar septa; at the molecular level, the differences in PDK1 mRNA relative expression in the lungs of adult yaks and cattle were not significant (p > 0.05), the differences in HIF-1α and VEGF mRNA relative expression were significant (p < 0.05), and the expression of PDK1 and HIF-1α proteins in adult yaks was stronger than that in adult cattle. PDK1 and HIF-1α proteins were more strongly expressed in adult yaks than in adult cattle, and the difference was highly significant (p < 0.01); the relative expression of VEGF proteins was not significantly different between adult yaks and cattle (p > 0.05). The possible regulatory relationship between the above results and the adaptation of yak lungs to the plateau hypoxic environment paves the way for the regulatory mechanisms of PDK1, HIF-1α, and VEGF, and provides basic information for studying the mechanism of hypoxic adaptation of yaks in the plateau. At the same time, it provides a reference for human hypoxia adaptation and a target for the prevention and treatment of plateau diseases in humans and plateau animals.
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Affiliation(s)
- Yiyang Zhang
- Engineering Research Center of Key Technology and Industrialization of Cell-Based Vaccine, Ministry of Education, Northwest Minzu University, Lanzhou 730030, China; (Y.Z.); (M.Z.); (R.L.); (S.C.); (Z.Q.)
- Gansu Tech Innovation Center of Animal Cell, Biomedical Research Center, Northwest Minzu University, Lanzhou 730030, China
- Key Laboratory of Biotechnology and Bioengineering of State Ethnic Affairs Commission, Biomedical Research Center, Northwest Minzu University, Lanzhou 730030, China
- Life Science and Engineering College, Northwest Minzu University, Lanzhou 730030, China; (Y.L.); (L.Z.); (H.D.); (X.T.)
| | - Manlin Zhou
- Engineering Research Center of Key Technology and Industrialization of Cell-Based Vaccine, Ministry of Education, Northwest Minzu University, Lanzhou 730030, China; (Y.Z.); (M.Z.); (R.L.); (S.C.); (Z.Q.)
- Gansu Tech Innovation Center of Animal Cell, Biomedical Research Center, Northwest Minzu University, Lanzhou 730030, China
- Key Laboratory of Biotechnology and Bioengineering of State Ethnic Affairs Commission, Biomedical Research Center, Northwest Minzu University, Lanzhou 730030, China
- Life Science and Engineering College, Northwest Minzu University, Lanzhou 730030, China; (Y.L.); (L.Z.); (H.D.); (X.T.)
| | - Yuxin Liang
- Life Science and Engineering College, Northwest Minzu University, Lanzhou 730030, China; (Y.L.); (L.Z.); (H.D.); (X.T.)
| | - Rui Li
- Engineering Research Center of Key Technology and Industrialization of Cell-Based Vaccine, Ministry of Education, Northwest Minzu University, Lanzhou 730030, China; (Y.Z.); (M.Z.); (R.L.); (S.C.); (Z.Q.)
- Gansu Tech Innovation Center of Animal Cell, Biomedical Research Center, Northwest Minzu University, Lanzhou 730030, China
- Key Laboratory of Biotechnology and Bioengineering of State Ethnic Affairs Commission, Biomedical Research Center, Northwest Minzu University, Lanzhou 730030, China
- Life Science and Engineering College, Northwest Minzu University, Lanzhou 730030, China; (Y.L.); (L.Z.); (H.D.); (X.T.)
| | - Lan Zhang
- Life Science and Engineering College, Northwest Minzu University, Lanzhou 730030, China; (Y.L.); (L.Z.); (H.D.); (X.T.)
| | - Shuwu Chen
- Engineering Research Center of Key Technology and Industrialization of Cell-Based Vaccine, Ministry of Education, Northwest Minzu University, Lanzhou 730030, China; (Y.Z.); (M.Z.); (R.L.); (S.C.); (Z.Q.)
- Gansu Tech Innovation Center of Animal Cell, Biomedical Research Center, Northwest Minzu University, Lanzhou 730030, China
- Key Laboratory of Biotechnology and Bioengineering of State Ethnic Affairs Commission, Biomedical Research Center, Northwest Minzu University, Lanzhou 730030, China
- Life Science and Engineering College, Northwest Minzu University, Lanzhou 730030, China; (Y.L.); (L.Z.); (H.D.); (X.T.)
| | - Kun Yang
- Engineering Research Center of Key Technology and Industrialization of Cell-Based Vaccine, Ministry of Education, Northwest Minzu University, Lanzhou 730030, China; (Y.Z.); (M.Z.); (R.L.); (S.C.); (Z.Q.)
- Gansu Tech Innovation Center of Animal Cell, Biomedical Research Center, Northwest Minzu University, Lanzhou 730030, China
- Key Laboratory of Biotechnology and Bioengineering of State Ethnic Affairs Commission, Biomedical Research Center, Northwest Minzu University, Lanzhou 730030, China
- Life Science and Engineering College, Northwest Minzu University, Lanzhou 730030, China; (Y.L.); (L.Z.); (H.D.); (X.T.)
| | - Haie Ding
- Life Science and Engineering College, Northwest Minzu University, Lanzhou 730030, China; (Y.L.); (L.Z.); (H.D.); (X.T.)
| | - Xiao Tan
- Life Science and Engineering College, Northwest Minzu University, Lanzhou 730030, China; (Y.L.); (L.Z.); (H.D.); (X.T.)
| | - Qian Zhang
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China;
| | - Zilin Qiao
- Engineering Research Center of Key Technology and Industrialization of Cell-Based Vaccine, Ministry of Education, Northwest Minzu University, Lanzhou 730030, China; (Y.Z.); (M.Z.); (R.L.); (S.C.); (Z.Q.)
- Gansu Tech Innovation Center of Animal Cell, Biomedical Research Center, Northwest Minzu University, Lanzhou 730030, China
- Key Laboratory of Biotechnology and Bioengineering of State Ethnic Affairs Commission, Biomedical Research Center, Northwest Minzu University, Lanzhou 730030, China
- Life Science and Engineering College, Northwest Minzu University, Lanzhou 730030, China; (Y.L.); (L.Z.); (H.D.); (X.T.)
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Tian D, Sun D, Ren Q, Zhang P, Zhang Z, Zhang W, Luo H, Li X, Han B, Liu D, Zhao K. Genome-wide identification of candidate copy number polymorphism genes associated with complex traits of Tibetan-sheep. Sci Rep 2023; 13:17283. [PMID: 37828092 PMCID: PMC10570297 DOI: 10.1038/s41598-023-44402-1] [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: 03/28/2023] [Accepted: 10/07/2023] [Indexed: 10/14/2023] Open
Abstract
Copy number variation (CNV) is a genetic structural polymorphism important for phenotypic diversity and important economic traits of livestock breeds, and it plays an important role in the desired genetic variation. This study used whole genome sequencing to detect the CNV variation in the genome of 6 local Tibetan sheep groups. We detected 69,166 CNV events and 7230 copy number variable regions (CNVRs) after merging the overlapping CNVs, accounting for 2.72% of the reference genome. The CNVR length detected ranged from 1.1 to 1693.5 Kb, with a total length of 118.69 Mb and an average length of 16.42 Kb per CNVR. Functional GO cluster analysis showed that the CNVR genes were mainly involved in sensory perception systems, response to stimulus, and signal transduction. Through CNVR-based Vst analysis, we found that the CACNA2D3 and CTBP1 genes related to hypoxia adaptation, the HTR1A gene related to coat color, and the TRNAS-GGA and PIK3C3 genes related to body weight were all strongly selected. The findings of our study will contribute novel insights into the genetic structural variation underlying hypoxia adaptation and economically important traits in Tibetan sheep.
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Affiliation(s)
- Dehong Tian
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810001, Qinghai, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - De Sun
- Animal Husbandry and Veterinary Station of Huzhu County of Qinghai Province, Huzhu, 810500, Qinghai, China
| | - Qianben Ren
- Qinghai Sheep Breeding and Promotion Service Center, Gangcha, 812300, Qinghai, China
| | - Pei Zhang
- Qinghai Animal and Plant Quarantine Station, Xining, 810000, Qinghai, China
| | - Zian Zhang
- Qinghai Sheep Breeding and Promotion Service Center, Gangcha, 812300, Qinghai, China
| | - Wenkui Zhang
- Qinghai Sheep Breeding and Promotion Service Center, Gangcha, 812300, Qinghai, China
| | - Haizhou Luo
- Qinghai Sheep Breeding and Promotion Service Center, Gangcha, 812300, Qinghai, China
| | - Xue Li
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810001, Qinghai, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Buying Han
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810001, Qinghai, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dehui Liu
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810001, Qinghai, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kai Zhao
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810001, Qinghai, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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6
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Xin K, Tian K, Yu Q, Han L, Zang Z. Effects of altitude on meat quality difference and its relationship with HIF-1α during postmortem maturation of beef. J Food Biochem 2022; 46:e14470. [PMID: 36288466 DOI: 10.1111/jfbc.14470] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 09/22/2022] [Accepted: 09/26/2022] [Indexed: 01/14/2023]
Abstract
This study investigated the differences in meat quality during postmortem aging of yak meat from different altitudes as well as the relationship between the release of hypoxic factor HIF-1α and meat quality. The results showed that the HIF-1α increased with altitude but during aging process, there was an initial increase before a subsequent decrease (p < .05). Moreover, significant increases were showed in glycolytic potential, a* value, pH, HIF-1α mRNA expression, HIF-1α protein expression and shear force with altitude (p < .05). Additionally, the b* value, L* value, water holding power and MFI decreased significantly (p < .05). HIF-1α was shown, by PLS-DA method analysis, to be the main protein marker for differences in the quality during aging time of meat from three altitude groups. HIF-1α protein expression was high correlated with glycolytic potential, pH value, meat color, tenderness and water holding capacity during postmortem aging. The results demonstrated that HIF-1α is a novel marker protein that influences meat quality in yak from different altitudes and that HIF-1α-mediated glycolytic pathway was key to the meat quality during postmortem aging. PRACTICAL APPLICATIONS: Yak meat has the advantages of high protein, low fat, good amino acid and fatty acid composition, so the nutritional value of yak meat is in line with the current best-selling beef with less fat in domestic and foreign markets. But consumers often think that the meat tenderness of yak meat is worse than that of beef and improving the quality of yak meat was worthy of attention specifically. This study investigated the differences in meat quality during postmortem aging of yak meat at different altitudes and the relationship between hypoxic factor HIF-1α release and meat quality.
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Affiliation(s)
- Keqi Xin
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou, China
| | - Kai Tian
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou, China
| | - Qunli Yu
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou, China
| | - Ling Han
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou, China
| | - Zhixuan Zang
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou, China
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Zhang J, Cui Y. Integrative analysis identifies potential ferroptosis-related genes of hypoxia adaptation in yak. Front Vet Sci 2022; 9:1022972. [PMID: 36304416 PMCID: PMC9592977 DOI: 10.3389/fvets.2022.1022972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 09/13/2022] [Indexed: 11/04/2022] Open
Abstract
There are studies on the hypoxia adaptation in yak, but there are few studies on the regulation of ferroptosis by hypoxia. This study was the first time to explore ferroptosis-related genes about hypoxia in yak. In this study, the oviduct epithelial cells between yak and bovine are performed by integrative analysis for functions, regulating network and hub genes. The results showed 29 up-regulated ferroptosis genes and 67 down-regulated ferroptosis genes, and GO-KEGG analysis showed that up-regulated differentially expressed genes (DEGs) were significantly enriched in ribosome pathway and oxidative phosphorylation pathway. Down-regulated DEGs were significantly enriched in longevity regulating pathway-mammal pathway. Mitophagy-Animal Pathway was a significant enrichment pathway for the up-regulated differentially expressed ferroptosis genes (DE-FRGs). HIF-1 signaling pathway is a significant pathway for the down-regulated DE-FRGs. By constructing DE-FRGs protein-protein interaction (PPI) network, 10 hub DE-FRGs (Jun, STAT3, SP1, HIF1A, Mapk1, Mapk3, Rela, Ulk1, CDKN1A, EPAS1) were obtained. The bta-mir-21-5p, bta-mir-10a and bta-mir-17-5p related to STAT3 were predicted. The results of this study indicated the important genes and pathways of the hypoxia in yak, and it was the first time to study ferroptosis genes and pathways related to the hypoxia adaptation by bulk-seq in yak. This study provided sufficient transcriptome datas for hypoxia adaptation.
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Affiliation(s)
- Jian Zhang
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, China,Technology and Research Center of Gansu Province for Embryonic Engineering of Bovine and Sheep & Goat, Lanzhou, China
| | - Yan Cui
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, China,Technology and Research Center of Gansu Province for Embryonic Engineering of Bovine and Sheep & Goat, Lanzhou, China,*Correspondence: Yan Cui
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Qian S, Li X, Liu C, Zhang C, Blecker C. Proteomic changes involved in water holding capacity of frozen bovine longissimus dorsi muscles based on DIA strategy. J Food Biochem 2022; 46:e14330. [PMID: 35848392 DOI: 10.1111/jfbc.14330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/24/2022] [Accepted: 06/15/2022] [Indexed: 11/29/2022]
Abstract
As freeze/thaw procedure leads to inevitable drip loss, elucidation of mechanism on dynamic changes in water holding capacity (WHC) of muscle is urgently needed. In this study, the proteomic profile by DIA-based strategy, muscle microstructure, water mobility, and WHC indices of bovine longissimus dorsi muscles were investigated under different freezing conditions as well as the correlations among them. Results indicated that slow freezing (SF) sample exhibited significantly higher water mobility, thaw loss, total loss, and shear force value than the samples subjected to fast freezing (FF) and non-frozen control (CON). According to the protein profile, we have identified 272 differential abundance proteins (DAPs), in which more significant proteome changes were found in SF/CON samples as compared with FF/CON. Among the 132 DAPs in FF/SF comparison, correlation analysis revealed that MYL3, DES, SYNE2, EXR, RPL35A, RPS6, and Hsp40 were closely correlated with T23 , thaw loss, and total loss. Accordingly, we considered those seven proteins as potential biomarkers related to WHC of frozen muscle. Our study should give a further understanding on mechanisms behind the various WHC of muscle when subjected to different freezing conditions. PRACTICAL APPLICATIONS: Freezing plays a key role in the preservation method for meat and meat products. However, the drip loss during freezing and subsequent thawing procedure causes considerable economic and nutritional losses. To minimize the losses, elucidation of mechanism on the mechanism of thaw loss formation is urgently needed. DIA-based proteomics is a novel, robust method that provides further understanding on the mechanisms behind the dynamic changes in water holding capacity of muscle. The screened protein biomarkers in frozen muscle would play key roles in the development of WHC, especially for the thaw loss formation. Through this perspective, we can explain the origin of thaw loss and the variation under different freezing conditions, which should provide the meat industries with theoretical basis for reducing losses.
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Affiliation(s)
- Shuyi Qian
- Chinese Academy of Agricultural Sciences, Institute of Food Science and Technology, Beijing, China.,Unit of Food Science and Formulation, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Xia Li
- Chinese Academy of Agricultural Sciences, Institute of Food Science and Technology, Beijing, China
| | - Chengjiang Liu
- Institute of Agro-Products Processing Science and Technology, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
| | - Chunhui Zhang
- Chinese Academy of Agricultural Sciences, Institute of Food Science and Technology, Beijing, China
| | - Christophe Blecker
- Unit of Food Science and Formulation, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
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