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Zhang D, Yue Y, Yuan C, An X, Guo T, Chen B, Liu J, Lu Z. DIA-Based Proteomic Analysis Reveals MYOZ2 as a Key Protein Affecting Muscle Growth and Development in Hybrid Sheep. Int J Mol Sci 2024; 25:2975. [PMID: 38474221 DOI: 10.3390/ijms25052975] [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: 12/18/2023] [Revised: 02/12/2024] [Accepted: 02/26/2024] [Indexed: 03/14/2024] Open
Abstract
Hybridization of livestock can be used to improve varieties, and different hybrid combinations produce unique breeding effects. In this study, male Southdown and Suffolk sheep were selected to hybridize with female Hu sheep to explore the effects of male parentage on muscle growth and the development of offspring. Using data-independent acquisition technology, we identified 119, 187, and 26 differentially abundant proteins (DAPs) between Hu × Hu (HH) versus Southdown × Hu (NH), HH versus Suffolk × Hu (SH), and NH versus SH crosses. Two DAPs, MYOZ2 and MYOM3, were common to the three hybrid groups and were mainly enriched in muscle growth and development-related pathways. At the myoblast proliferation stage, MYOZ2 expression decreased cell viability and inhibited proliferation. At the myoblast differentiation stage, MYOZ2 expression promoted myoblast fusion and enhanced the level of cell fusion. These findings provide new insights into the key proteins and metabolic pathways involved in the effect of male parentage on muscle growth and the development of hybrid offspring in sheep.
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Affiliation(s)
- Dan Zhang
- Key Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Yaojing Yue
- Key Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Chao Yuan
- Key Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Xuejiao An
- Key Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Tingting Guo
- Key Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Bowen Chen
- Key Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Jianbin Liu
- Key Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Zengkui Lu
- Key Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
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iTRAQ-based proteomic analysis reveals the underlying mechanism of postmortem tenderization of refrigerated porcine Longissimus thoracis et lumborum muscle. Meat Sci 2023; 197:109068. [PMID: 36495834 DOI: 10.1016/j.meatsci.2022.109068] [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: 10/24/2022] [Revised: 11/20/2022] [Accepted: 11/29/2022] [Indexed: 12/03/2022]
Abstract
The isobaric tags for relative and absolute quantitation (iTRAQ) technology was used for differential proteomic analysis of refrigerated porcine Longissimus thoracis et lumborum (LTL) muscle at different time points postmortem (45 min, 4 h, 8 h, 12 h, 24 h, 48 h, 72 h and 96 h) to mechanistically elucidate the postmortem tenderization. Compared with the proteins identified in porcine LTL muscle at 45 min postmortem (control), 862 proteins were significantly expressed at 4 h, 8 h, 12 h, 24 h, 48 h, 72 h and 96 h postmortem. Moreover, clustering and path analysis showed that the quality traits of porcine LTL muscle, including pH, shear force, myofibril fragmentation index, correlated significantly with 2, 6 and 6 differentially expressed proteins, respectively, with the lowest or highest expression at 8 h or 12 h postmortem. Overall, the tenderness of refrigerated porcine LTL muscle might be significantly affected by changes in quality traits at 8 h and 12 h postmortem.
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Zhao L, Zhang D, Li X, Zhang Y, Zhao Y, Xu D, Cheng J, Wang J, Li W, Lin C, Yang X, Ma Z, Cui P, Zhang X, Wang W. Comparative proteomics reveals genetic mechanisms of body weight in Hu sheep and Dorper sheep. J Proteomics 2022; 267:104699. [PMID: 35995385 DOI: 10.1016/j.jprot.2022.104699] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 08/06/2022] [Accepted: 08/08/2022] [Indexed: 10/15/2022]
Abstract
Body weight (BW) is a critical economic trait for meat production in sheep, and it is a complex trait affected by numerous elements. The aim of this study was to investigate the genetic mechanisms of sheep BW by a label-free proteomics approach. The result showed, a total of 27, 14, 61, and 65 differentially abundant proteins (DAPs) were identified in the Hu_HBW vs. Hu_LBW, DP_HBW vs. DP_LBW, Hu_HBW vs. DP_HBW, and Hu_LBW vs. DP_LBW comparisons, respectively. Five proteins (including ILK, AHCYL2, MLIP, CYB5A, and SMTNL1) related to fat synthesis and muscle development were detected in the Hu sheep group. In the Dorper sheep group, the screened DAPs strictly related to muscle development and fat synthesis were significantly enriched in MAP kinase activity (MAPK12), Arachidonic acid metabolism, and Steroid hormone biosynthesis (PGFS, LOC101107119) pathways. Several DAPs related to immune responses (SERPINA1, FGG, SERPINC1, and LOC101108131), fat deposition (APOH, GC, AHSG, SKP1, ACSL1, ACAT1, and ACADS), and muscle development (LMOD3 and LRRC39) were detected in the Hu vs. Dorper sheep comparison. These analyses indicated that the BW of sheep is regulated via a variety of pathways, and these DAPs can be further investigated as candidate markers for predicting the BW of sheep. SIGNIFICANCE: Body weight is one of the key traits in sheep and involves multiple coordinated regulatory mechanisms, but the genetic mechanism of BW is still unclear in sheep. In the current study, the label-free method was used to identify the proteins and pathways related to BW using LT muscle of Hu sheep and Dorper sheep with different BW. These findings will provide new candidate proteins and vital pathways into the molecular mechanisms involved growth traits in sheep.
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Affiliation(s)
- Liming Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Deyin Zhang
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu 730020, China
| | - Xiaolong Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Yukun Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Yuan Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Dan Xu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Jiangbo Cheng
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Jianghui Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Wenxin Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Changchun Lin
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Xiaobin Yang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Zongwu Ma
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Panpan Cui
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Xiaoxue Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China.
| | - Weimin Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China; The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu 730020, China.
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Integrated proteomic, phosphoproteomic, and N-glycoproteomic analyses of the longissimus thoracis of yaks. Curr Res Food Sci 2022; 5:1494-1507. [PMID: 36132491 PMCID: PMC9483648 DOI: 10.1016/j.crfs.2022.09.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 08/27/2022] [Accepted: 09/12/2022] [Indexed: 11/20/2022] Open
Abstract
Yaks (Bos mutus) live in the Qinghai–Tibet plateau. The quality of yak meat is unique due to its genetic and physiological characteristics. Identification of the proteome of yak muscle could help to reveal its meat-quality properties. The common proteome, phosphoproteome, and N-glycoproteome of yak longissimus thoracis (YLT) were analyzed by liquid chromatography-tandem mass spectrometry-based shotgun analysis. A total of 1812 common proteins, 1303 phosphoproteins (3918 phosphorylation sites), and 204 N-glycoproteins (285 N-glycosylation sites) were identified in YLT. The common proteins in YLT were involved mainly in myofibril structure and energy metabolism; phosphoproteins were associated primarily with myofibril organization, regulation of energy metabolism, and signaling; N-glycoproteins were engaged mainly in extracellular-matrix organization, cellular immunity, and organismal homeostasis. We reported, for the first time, the “panorama” of the YLT proteome, specifically the N-glycoproteome of YLT. Our results provide essential information for understanding post mortem physiology (rigor mortis and aging) and the quality of yak meat. A total of 2650 proteins were identified in yak longissimus thoracis. Common proteins were involved mainly in myofibril structure and energy metabolism. Phosphoproteins were associated with myofibrils, energy metabolism, and signaling. N-glycoproteins were engaged mainly in ECM organization, immunity, and homeostasis.
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YAN Z, LI W, HU R, MA Q, LU Z. Quantitative proteomic comparison of protein differences in different parts of yak meat. FOOD SCIENCE AND TECHNOLOGY 2022. [DOI: 10.1590/fst.62020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Zhongxin YAN
- Northwest A & F University, China; Qinghai University, China; Key Laboratory of Plateau Grazing Animal Nutrition and Feed Science of Qinghai Province, China
| | - Wei LI
- Qinghai University, China
| | | | - Qingmei MA
- Animal Husbandry and Veterinary Medicine Station of Haiyan County, China
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Honerlagen H, Reyer H, Oster M, Ponsuksili S, Trakooljul N, Kuhla B, Reinsch N, Wimmers K. Identification of Genomic Regions Influencing N-Metabolism and N-Excretion in Lactating Holstein- Friesians. Front Genet 2021; 12:699550. [PMID: 34335696 PMCID: PMC8318802 DOI: 10.3389/fgene.2021.699550] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 06/18/2021] [Indexed: 12/03/2022] Open
Abstract
Excreted nitrogen (N) of dairy cows contribute to environmental eutrophication. The main N-excretory metabolite of dairy cows is urea, which is synthesized as a result of N-metabolization in the liver and is excreted via milk and urine. Genetic variation in milk urea (MU) has been postulated but the complex physiology behind the trait as well as the tremendous diversity of processes regulating the N-metabolism impede the consistent determination of causal regions in the bovine genome. In order to map the genetic determinants affecting N-excretion, MU and eight other N-excretory metabolites in milk and urine were assessed in a genome-wide association study. Therefore phenotypes of 371 Holstein- Friesians were obtained in a trial on a dairy farm under near commercial conditions. Genotype data comprised SNP information of the Bovine 50K MD Genome chip (45,613 SNPs). Significantly associated genomic regions for MU concentration revealed GJA1 (BTA 9), RXFP1, and FRY1 (both BTA 12) as putative candidates. For milk urea yield (MUY) a promising QTL on BTA 17 including SH3D19 emerged, whereas RCAN2, CLIC5, ENPP4, and ENPP5 (BTA 23) are suggested to influence urinary urea concentration. Minor N-fractions in milk (MN) may be regulated by ELF2 and SLC7A11 (BTA 17), whilst ITPR2 and MYBPC1 (BTA 5), STIM2 (BTA 6), SGCD (BTA 7), SLC6A2 (BTA 18), TMCC2 and MFSD4A (BTA 16) are suggested to have an impact on various non-urea-N (NUN) fractions excreted via urine. Our results highlight genomic regions and candidate genes for N-excretory metabolites and provide a deeper insight into the predisposed component to regulate the N-metabolism in dairy cows.
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Affiliation(s)
- Hanne Honerlagen
- Genomics Unit, Institute for Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Henry Reyer
- Genomics Unit, Institute for Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Michael Oster
- Genomics Unit, Institute for Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Siriluck Ponsuksili
- Genomics Unit, Institute for Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Nares Trakooljul
- Genomics Unit, Institute for Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Björn Kuhla
- Metabolism Efficiency Unit, Institute of Nutritional Physiology "Oskar Kellner," Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Norbert Reinsch
- Livestock Genetics and Breeding Unit, Institute of Genetics and Biometry, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Klaus Wimmers
- Genomics Unit, Institute for Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany.,Faculty of Agricultural and Environmental Sciences, University of Rostock, Rostock, Germany
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Suh JK, Lee JS, Kong H, Lee Y, Lee HG. The effect of single-nucleotide polymorphisms within heat shock protein beta 1 on beef quantity in Korean native steers. Arch Anim Breed 2021; 63:417-422. [PMID: 33473366 PMCID: PMC7810230 DOI: 10.5194/aab-63-417-2020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 06/24/2020] [Indexed: 11/11/2022] Open
Abstract
Heat shock protein beta 1 (HSPB1), a member of the heat-shock family of protein, is a relatively small (27 kDa) molecular chaperone protein associated with cellular development. The relationship between HSPB1 expression and muscle growth in beef cattle has previously been reported, but there have been no reports of DNA markers related to meat quantity in Korean native steers. Therefore, the aim of this study was to evaluate the relationship of single-nucleotide polymorphisms (SNPs) within HSPB1 in terms of the carcass traits related to muscle growth in Korean native steers. Through direct sequencing, we discovered three SNPs: g.111 T > C SNP (rs208395876) and g.2548 C > G SNP (rs483014585) were respectively located in 5 ' UTR (untranslated region) and 3 ' UTR. Further, g.2352 T > C SNP (rs110832311) was located in the adjacent region of the RNA splicing site. The least square means of steers with a CC genotype of g.111 T > C SNP had a significantly higher meat ratio ( P = 0.04), while the least square means of steers with a CC genotype of g.2352 T > C SNP had a significantly higher meat ratio ( P = 0.002) and lower back-fat thickness ( P = 0.004) than those of the other genotype. Moreover, although the least square means of steers with CC-CC, CT-CC, and TT-CC genotypes were significantly decreased for back-fat thickness, they were significantly increased for the meat ratio. Therefore, our results suggested that g.111 T > C SNP and g.2352 T > C SNP could be a causal mutation related to an adipose metabolism in Korean cattle steer.
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Affiliation(s)
- Jung-Keun Suh
- Department of Animal Science and Technology, Sanghuh College of Life Sciences, Konkuk University, Seoul, 05029, Republic of Korea.,Team of An Educational Program for Specialists in Global Animal Science, Brain Korea 21 Plus Project, Sanghuh College of Life Sciences, Konkuk University, Seoul, 05029, Republic of Korea
| | - Jae-Sung Lee
- Department of Animal Science and Technology, Sanghuh College of Life Sciences, Konkuk University, Seoul, 05029, Republic of Korea
| | - Hongsik Kong
- Department of Biotechnology, Hankyung National University, Anseong-si, Gyeonggi-do, 17579, Republic of Korea
| | - Yoonseok Lee
- Department of Biotechnology, Hankyung National University, Anseong-si, Gyeonggi-do, 17579, Republic of Korea.,Center for Genetic Information, Hankyung National University, Anseong-si, Gyeonggi-do, 17579, Republic of Korea
| | - Hong-Gu Lee
- Department of Animal Science and Technology, Sanghuh College of Life Sciences, Konkuk University, Seoul, 05029, Republic of Korea.,Team of An Educational Program for Specialists in Global Animal Science, Brain Korea 21 Plus Project, Sanghuh College of Life Sciences, Konkuk University, Seoul, 05029, Republic of Korea
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Sun HZ, Zhu Z, Zhou M, Wang J, Dugan MER, Guan LL. Gene co-expression and alternative splicing analysis of key metabolic tissues to unravel the regulatory signatures of fatty acid composition in cattle. RNA Biol 2020; 18:854-862. [PMID: 32931715 DOI: 10.1080/15476286.2020.1824060] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Increasing the healthy/unhealthy fatty acid (FA) ratio in meat is one of the urgent tasks required to address consumer concerns. However, the regulatory mechanisms ultimately resulting in FA profiles vary among animals and remain largely unknown. In this study, using ~1.2 Tb high-quality RNA-Seq-based transcriptomic data of 188 samples from four key metabolic tissues (rumen, liver, muscle, and backfat) together with the contents of 49 FAs in backfat, the molecular regulatory mechanisms of these tissues contributing to FA formation in cattle were explored. Using this large dataset, the alternative splicing (AS) events, one of the transcriptional regulatory mechanisms in four tissues were identified. The highly conserved and absent AS events were detected in rumen tissue, which may contribute to its functional differences compared with the other three tissues. In addition, the healthy/unhealthy FA ratio related AS events, differential expressed (DE) genes, co-expressed genes, and their functions in four tissues were analysed. Eight key genes were identified from the integrated analysis of DE, co-expressed, and AS genes between animals with high and low healthy/unhealthy FA ratios. This study provides an applicable pipeline for AS events based on comprehensive RNA-Seq analysis and improves our understanding of the regulatory mechanism of FAs in beef cattle.
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Affiliation(s)
- Hui-Zeng Sun
- Institute of Dairy Science, Ministry of Education Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, China.,Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Zhi Zhu
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada.,Department of Animal Science, Southwest University, Chongqing, P.R. China
| | - Mi Zhou
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Jian Wang
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada.,Shaanxi Key Laboratory of Agricultural Molecular Biology, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Michael E R Dugan
- Shaanxi Key Laboratory of Agricultural Molecular Biology, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Le Luo Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
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Proteomic Analysis of Beef Tenderloin and Flank Assessed Using an Isobaric Tag for Relative and Absolute Quantitation (iTRAQ). Animals (Basel) 2020; 10:ani10010150. [PMID: 31963250 PMCID: PMC7022852 DOI: 10.3390/ani10010150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 01/10/2020] [Accepted: 01/13/2020] [Indexed: 01/10/2023] Open
Abstract
Simple Summary Amino acid composition is among the important indexes of the nutritional composition of meat nutrients. In this study, we performed a proteomic analysis of tenderloin and flank steaks from Simmental cattle using isobaric tags for a relative and absolute quantification (iTRAQ) approach. Seventeen amino acids were detected in tenderloin and flank steaks, including seven essential amino acids and 10 non-essential amino acids. A comparison of the expression patterns in steaks revealed 128 differentially expressed proteins (DEPs). Furthermore, 27 DEPs (p < 0.05) were subjected to Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. Abstract Herein, we performed a proteomic analysis of tenderloin and flank steaks from Simmental cattle using the isobaric tags for a relative and absolute quantification (iTRAQ) approach. We identified 17 amino acids in both steaks, and Gly, Cys, Ile, Lys, and Pro differed most in abundance between the steak types (p < 0.05). A comparison of the expression patterns in steaks revealed 128 differentially expressed proteins (DEPs), of which 44 were up-regulated and 84 were down-regulated. Furthermore, 27 DEPs (p < 0.05) were subjected to gene ontology (GO) analysis, and many were found to be related to oxidation-reduction, metabolism, hydrogen ion transmembrane transport, transport, the tricarboxylic acid (TCA) cycle, mitochondrial electron transport, and the conversion of nicotinamide adenine dinucleotide (NADH) to ubiquinone. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis also implicated these DEPs in various signalling pathways, including oxidative phosphorylation, cardiac muscle contraction, the TCA cycle, biosynthesis, and the metabolism. These findings provide a new insight into key proteins involved in the determination of amino acid composition in beef.
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Abstract
Genome-wide single nucleotide polymorphism (SNP) arrays can be used to explore homozygosity segments, where two haplotypes inherited from the parents are identical. In this study, we identified a total of 27,358 runs of homozygosity (ROH) with an average of 153 ROH events per animal in Chinese local cattle. The sizes of ROH events varied considerably ranging from 0.5 to 66 Mb, with an average length of 1.22 Mb. The highest average proportion of the genome covered by ROH (~11.54% of the cattle genome) was found in Nanda cattle (NDC) from South China, whereas the lowest average proportion (~3.1%) was observed in Yanhuang cattle (YHC). The average estimated FROH ranged from 0.03 in YHC to 0.12 in NDC. For each of three ROH classes with different sizes (Small 0.5-1 Mb, Medium 1-5 Mb and Large >5 Mb), the numbers and total lengths of ROH per individual showed considerable differences across breeds. Moreover, we obtained 993 to 3603 ROH hotspots (which were defined where ROH frequency at a SNP within each breed exceeded the 1% threshold) among eight cattle breeds. Our results also revealed several candidate genes embedded with ROH hotspots which may be related to environmental conditions and local adaptation. In conclusion, we generated baselines for homozygosity patterns in diverse Chinese cattle breeds. Our results suggested that selection has, at least partially, played a role with other factors in shaping the genomic patterns of ROH in Chinese local cattle and might provide valuable insights for understanding the genetic basis of economic and adaptive traits.
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Wei Y, Li X, Zhang D, Liu Y. Comparison of protein differences between high- and low-quality goat and bovine parts based on iTRAQ technology. Food Chem 2019; 289:240-249. [DOI: 10.1016/j.foodchem.2019.03.052] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 03/01/2019] [Accepted: 03/11/2019] [Indexed: 12/16/2022]
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Kim YS, Lee JS, Lee Y, Kim WS, Peng DQ, Bae MH, Jo YH, Baik M, Lee HG. Effect of glutamine on heat-shock protein beta 1 ( HSPB1) expression during myogenic differentiation in bovine embryonic fibroblast cells. Food Sci Biotechnol 2018; 27:829-835. [PMID: 30263808 PMCID: PMC6049688 DOI: 10.1007/s10068-018-0309-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 12/15/2017] [Accepted: 01/02/2018] [Indexed: 10/18/2022] Open
Abstract
The objective of this study was to examine the effects of glutamine on heat-shock protein beta 1 (HSPB1) expression in bovine embryonic fibroblast cells during myogenesis. First, to elucidate the role of glutamine on HSPB1 expression during myogenesis, we treated with glutamine in myogenic lineage determinant (MyoD) over-expressed bovine embryonic fibroblast cells (BEFS-MyoD cells). Second, knockdown of HSPB1 using small interference RNA was performed to evaluate whether muscle development by glutamine is dependent on HSPB1 in BEFS-MyoD cells. As a result, glutamine promoted the mRNA level of HSPB1, Myogenin, Desmin, and mTOR as well as myotube formation, and protein synthesis (p < 0.05). The inhibition of HSPB1 expression during myogenesis has shown to repress the expression of myogenic marker genes (MyoD, Myogenin, Desmin) (p < 0.01), formation of myotubes and protein synthesis (p < 0.05). According to the results, it is concluded that glutamine regulates HSPB1 expression during myogenesis.
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Affiliation(s)
- Young-Shin Kim
- Department of Animal Science and Technology, College of Animal Bioscience & Technology, Konkuk University, Seoul, 05029 Korea
- Team of An Educational Program for Specialists in Global Animal Science, Brain Korea 21 Plus Project, Konkuk University, Seoul, 05029 Korea
| | - Jae-Sung Lee
- Department of Animal Science and Technology, College of Animal Bioscience & Technology, Konkuk University, Seoul, 05029 Korea
- Team of An Educational Program for Specialists in Global Animal Science, Brain Korea 21 Plus Project, Konkuk University, Seoul, 05029 Korea
| | - Yoonseok Lee
- Department of Biotechnology, Hankyung National University, Anseong-si, Gyeonggi-do 17579 Korea
| | - Won-Seob Kim
- Department of Animal Science and Technology, College of Animal Bioscience & Technology, Konkuk University, Seoul, 05029 Korea
- Team of An Educational Program for Specialists in Global Animal Science, Brain Korea 21 Plus Project, Konkuk University, Seoul, 05029 Korea
| | - Dong-Qiao Peng
- Department of Animal Science and Technology, College of Animal Bioscience & Technology, Konkuk University, Seoul, 05029 Korea
- Team of An Educational Program for Specialists in Global Animal Science, Brain Korea 21 Plus Project, Konkuk University, Seoul, 05029 Korea
| | - Mun-Hee Bae
- Department of Animal Science and Technology, College of Animal Bioscience & Technology, Konkuk University, Seoul, 05029 Korea
- Team of An Educational Program for Specialists in Global Animal Science, Brain Korea 21 Plus Project, Konkuk University, Seoul, 05029 Korea
| | - Yong-Ho Jo
- Department of Animal Science and Technology, College of Animal Bioscience & Technology, Konkuk University, Seoul, 05029 Korea
- Team of An Educational Program for Specialists in Global Animal Science, Brain Korea 21 Plus Project, Konkuk University, Seoul, 05029 Korea
| | - Myunggi Baik
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826 Korea
| | - Hong-Gu Lee
- Department of Animal Science and Technology, College of Animal Bioscience & Technology, Konkuk University, Seoul, 05029 Korea
- Team of An Educational Program for Specialists in Global Animal Science, Brain Korea 21 Plus Project, Konkuk University, Seoul, 05029 Korea
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