Proteomics Reveals the Obstruction of Cellular ATP Synthesis in the Ruminal Epithelium of Growth-Retarded Yaks
Abstract
:Simple Summary
Abstract
1. Introduction
2. Material and Methods
2.1. Animal Ethics Approval
2.2. Experimental Design
2.3. Sample Collection
2.4. Mass Spectrometry
2.5. Bioinformatic Analysis
2.6. Relative Mitochondrial DNA Copy Number
2.7. Metabolite Concentrations in ATP Synthesis
2.8. The Activity of Key Enzymes of MRCC and LDHA
2.9. Quantitative Real-Time (qPCR) Detected mRNA Expressions of MRCC and LDHA
2.10. Statistical Analysis
3. Results
3.1. Significantly Differentially Expressed Proteins
3.2. Gene Ontology (GO) Analysis of DEPs
3.3. Kyoto Encyclopedia of Genes and Genomes (KEGG) Analysis of DEPs
3.4. Mitochondrial Number and Metabolite Concentrations of ATP Synthesis
3.5. Enzymatic Activity in a Tricarboxylic Acid Cycle and Electron Transport Chain
3.6. mRNA Expressions of MRCC and LDHA
3.7. Correlation Analysis between Ruminal Epithelial Morphology and ATP Synthesis
4. Discussion
4.1. Proteome Analysis
4.2. ATP Synthesis in Ruminal Epithelium
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Gene Name | Accession Number | Forward and Reverse Primer Sequence (5′-3′) | Product Length (bp) |
---|---|---|---|
18S | XM_005891364.2 | F: TCCTGCTCGGACCAC | 147 |
R: CAATGCCAACACAAGTCA | |||
COQ9 | XM_005899884.2 | F: ATACCCGCCGAGCAGT | 164 |
R: CTCTCCGGTGGACTTGACCT | |||
COX4 | XM_005892420.2 | F: TGGCAACCAGAGTATTTAGCCT | 127 |
R: TAGTCACGCCGGTCCAC | |||
ATP5F1 | XM_005905667.2 | F: TGGTTCAAAAGCGCCAT | 160 |
R: TGTTCCTTCTGACGCATC | |||
LDHA | XM_014479751.1 | F: AATACAGCCCAAATTGCAAG | 70 |
R: TTCCAAGCCACATAGGTCA |
No. | Accession Number | Protein ID | Gene ID | GRY/GNY Ratio | p-Value |
---|---|---|---|---|---|
1 | XP014338291.1 | Collagen alpha-1(VII) chain | COL7A1 | 2.615 | 0.000 |
2 | XP014332664.1 | Urea transporter 1 isoform X2 | SLC14A1 | 2.590 | 0.004 |
3 | XP005894969.1 | Alpha-endosulfine | ENSA | 2.178 | 0.007 |
4 | XP005896989.1 | Charged multivesicular body protein 4b | CHMP4B | 2.077 | 0.009 |
5 | XP005888708.1 | 4-Trimethylaminobutyraldehyde dehydrogenase | ALDH9A1 | 5.974 | 0.013 |
6 | XP005897961.1 | Gamma-interferon-inducible lysosomal thiol reductase | IFI30 | 3.025 | 0.013 |
7 | XP014336324.1 | Septin-8 isoform X6 | SEPTIN8 | 3.395 | 0.013 |
8 | XP005887104.1 | 26S proteasome non-ATPase regulatory subunit 1 | PSMD1 | 1.834 | 0.014 |
9 | XP005899315.1 | Transmembrane 9 superfamily member 2 | TM9SF2 | 1.952 | 0.020 |
10 | XP005905989.1 | Heterogeneous nuclear ribonucleoprotein H | HNRNPH1 | 1.509 | 0.022 |
11 | XP005887576.1 | Splicing factor 3A subunit 1 | SF3A1 | 2.443 | 0.028 |
12 | XP014338421.1 | Serine/arginine-rich splicing factor 6 | SRSF6 | 1.512 | 0.028 |
13 | XP014337469.1 | Protein SCO1 homolog, mitochondrial | LOC102285116 | 2.121 | 0.031 |
14 | XP005903851.1 | elafin | PI3 | 4.408 | 0.036 |
15 | XP005891798.1 | ER membrane protein complex subunit 2 | EMC2 | 1.666 | 0.036 |
16 | XP005898898.1 | Low molecular weight phosphotyrosine protein phosphatase isoform X2 | ACP1 | 1.748 | 0.043 |
17 | XP005887779.1 | Threonine--tRNA ligase, cytoplasmic isoform X2 | TARS1 | 1.953 | 0.043 |
18 | XP005903557.1 | Lymphocyte-specific protein 1 | LSP1 | 1.555 | 0.044 |
19 | XP005896048.1 | Histone H2A type 1-like | LOC102280777 | 1.511 | 0.046 |
20 | XP005901593.1 | Dihydrolipoyllysine-residue acetyltransferase component of pyruvate−dehydrogenase complex, mitochondrial isoform X2 | DLAT | 1.558 | 0.046 |
21 | XP005911546.1 | V-type proton ATPase subunit D | ATP6V1D | 0.357 | 0.001 |
22 | XP005909437.2 | Glutathione peroxidase 1 | GPX1 | 0.125 | 0.002 |
23 | XP005887951.1 | Short palate, lung, and nasal epithelium carcinoma-associated protein 2A | LOC102271013 | 0.349 | 0.003 |
24 | XP005902818.2 | 2-oxoisovalerate dehydrogenase subunit beta, mitochondrial | BCKDHB | 0.347 | 0.003 |
25 | XP005906367.1 | V-type proton ATPase catalytic subunit A | ATP6V1A | 0.491 | 0.004 |
26 | XP005898873.1 | Alcohol dehydrogenase 6 | LOC102284246 | 0.262 | 0.008 |
27 | XP005895336.1 | Hydroxymethylglutaryl-CoA synthase, mitochondrial | HMGCS2 | 0.593 | 0.010 |
28 | XP005910791.1 | Microtubule-associated protein 4 isoform X2 | MAP4 | 0.381 | 0.010 |
29 | XP005891129.1 | Catenin beta-1 | CTNNB1 | 0.613 | 0.011 |
30 | XP005896630.1 | Cocaine esterase | CES2 | 0.435 | 0.011 |
31 | XP005892792.2 | basigin | BSG | 0.554 | 0.012 |
32 | XP005905265.1 | Alkaline phosphatase, tissue-nonspecific isozyme | ALPL | 0.458 | 0.013 |
33 | XP014334225.1 | Prolactin-inducible protein homolog isoform X3 | LOC102271568 | 0.418 | 0.014 |
34 | XP005897415.1 | UDP-glucose 6-dehydrogenase isoform X1 | UGDH | 0.645 | 0.015 |
35 | XP005901484.1 | Chloride anion exchanger | SLC26A3 | 0.325 | 0.016 |
36 | XP005910259.1 | Lactadherin isoform X1 | MFGE8 | 0.560 | 0.016 |
37 | XP005906507.2 | Glutathione S-transferase A1 | LOC102274807 | 0.465 | 0.022 |
38 | XP005900452.1 | Acetyl-CoA acetyltransferase, cytosolic isoform X1 | ACAT2 | 0.538 | 0.023 |
39 | XP005896890.2 | Oxygen-dependent coproporphyrinogen-III oxidase, mitochondrial | CPOX | 0.520 | 0.023 |
40 | XP005906127.1 | Mitochondrial 2-oxoglutarate/malate carrier protein isoform X3 | SLC25A11 | 0.471 | 0.025 |
41 | XP014335386.1 | Tenascin | TNC | 0.552 | 0.031 |
42 | XP005899319.1 | Propionyl-CoA carboxylase alpha chain, mitochondrial isoform X3 | PCCA | 0.667 | 0.034 |
43 | XP014335094.1 | Ladinin-1 | LAD1 | 0.660 | 0.034 |
44 | XP014331756.1 | 1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase | ADI1 | 0.393 | 0.037 |
45 | XP005901352.1 | Ferritin heavy chain isoform X2 | FTH1 | 0.145 | 0.041 |
46 | XP005894555.1 | Eukaryotic translation initiation factor 3 subunit C | LOC102275797 | 0.657 | 0.042 |
47 | XP005897085.1 | Endoplasmic reticulum resident protein 44 | ERP44 | 0.630 | 0.045 |
48 | XP005889654.1 | SCY1-like protein 2 | SCYL2 | 0.554 | 0.047 |
49 | XP014337951.1 | 14-3-3 protein eta | YWHAH | 0.658 | 0.048 |
50 | XP005892436.1 | Inositol monophosphatase 2 | IMPA2 | 0.420 | 0.048 |
51 | XP005901633.1 | Sulfhydryl oxidase 1 | QSOX1 | 0.592 | 0.048 |
52 | XP005890379.1 | Acyl-CoA synthetase family member 2, mitochondrial isoform X2 | ACSF2 | 0.591 | 0.049 |
Categories | Subcategories | Pathway | DEPs | p-Value |
---|---|---|---|---|
Metabolism | Amino acid metabolism | Valine, leucine and isoleucine degradation | BCKDHB↓, HMGCS2↓, ALDH9A1↑, ACAT2↓, PCCA↓ | 0.002 |
Metabolism | Metabolism of cofactors and vitamins | Thiamine metabolism | ALPL↓, ACP1↑ | 0.006 |
Metabolism | Lipid metabolism | Synthesis and degradation of ketone bodies | HMGCS2↓, ACAT2↓ | 0.012 |
Metabolism | Carbohydrate metabolism | Propanoate metabolism | BCKDHB↓, ACAT2↓, PCCA↓ | 0.018 |
Metabolism | Carbohydrate metabolism | Pyruvate metabolism | ALDH9A1↑, ACAT2↓, DLAT↑ | 0.020 |
Metabolism | Lipid metabolism | Fatty acid degradation | ADH 6↓, ALDH9A1↑, ACAT2↓ | 0.022 |
Metabolism | Metabolism of terpenoids and polyketides | Terpenoid backbone biosynthesis | HMGCS2↓, ACAT2↓ | 0.024 |
Metabolism | Carbohydrate metabolism | Ascorbate and aldarate metabolism | ALDH9A1↑, UGDH↓ | 0.024 |
Organismal Systems | Excretory system | Collecting duct acid secretion | ATP6V1D↓, ATP6V1A↓ | 0.024 |
Organismal Systems | Digestive system | Mineral absorption | SLC26A3↓, FTH1↓ | 0.034 |
Metabolism | Global and overview maps | Metabolic pathways | ATP6V1D↓, BCKDHB↓, ATP6V1A↓, ADH 6↓, HMGCS2↓, ALDH9A1↑, ALPL↓, UGDH↓, ACAT2↓, CPOX↓, PCCA↓, ADI1↓, ACP1↑, DLAT↑, IMPA2↓ | 0.039 |
Metabolism | Carbohydrate metabolism | Glycolysis/Gluconeogenesis | ADH 6↓, ALDH9A1↑, DLAT↑ | 0.042 |
Metabolism | Carbohydrate metabolism | Butanoate metabolism | HMGCS2↓, ACAT2↓ | 0.045 |
Human Diseases | Cancers: Specific types | Basal cell carcinoma | CTNNB1↓ | 0.049 |
Items | Groups | SEM | p-Value | |
---|---|---|---|---|
GRY | GNY | |||
Mitochondrial DNA copy number | 7.27 a | 23.73 b | 4.994 | 0.009 |
α-Ketoglutarate (μg/g) | 1.50 a | 1.13 b | 0.127 | 0.005 |
Succinate (mg/g) | 4.43 | 3.84 | 0.826 | 0.490 |
Lactate (μmol/g) | 15.89 b | 22.13 a | 5.627 | 0.034 |
AMP (μg/g) | 258.75 b | 505.18 a | 3.731 | 0.000 |
ADP (μg/g) | 11.16 | 11.08 | 0.240 | 0.766 |
ATP (μg/g) | 49.27 b | 63.82 a | 0.788 | 0.000 |
AMP/ATP | 7.92 a | 5.25 b | 0.117 | 0.000 |
Items | Groups | SEM | p-Value | |
---|---|---|---|---|
GRY | GNY | |||
CS (U/mg) | 0.08 b | 0.12 a | 0.007 | <0.001 |
ICD (U/mg) | 0.96 b | 1.36 a | 0.800 | <0.001 |
α-KGDHC (U/mg) | 0.78 b | 1.09 a | 0.070 | 0.020 |
MRCC I (U/g) | 1882.25 b | 2308.22 a | 84.144 | 0.004 |
MRCC II (U/g) | 2042.14 b | 3487.05 a | 283.318 | 0.003 |
MRCC III (U/g) | 264.74 b | 367.52 a | 19.116 | 0.001 |
MRCC IV (U/g) | 189.18 b | 249.15 a | 12.852 | 0.011 |
MRCC V (U/g) | 581.73 b | 858.10 a | 55.301 | 0.005 |
LDH-A (U/g) | 101.01 b | 135.74 a | 34.728 | 0.001 |
Items | Groups | SEM | p-Value | |
---|---|---|---|---|
GRY | GNY | |||
COQ9 | 1.23 b | 5.24 a | 0.784 | 0.029 |
COX4 | 0.79 b | 3.01 a | 0.203 | 0.016 |
ATP5 F1 | 0.95 | 1.59 | 0.299 | 0.248 |
LDHA | 0.99 b | 6.43 a | 0.899 | 0.03 |
Item | Mitochondrial DNA Copy Number | ATP Concentrations | LA Concentrations |
---|---|---|---|
ADG | 0.772 ** | 0.728 ** | 0.182 |
Rumen weight | 0.631 * | 0.957 ** | 0.181 |
Papillae height | 0.186 | 0.770 ** | 0.158 |
Papillae width | 0.046 | −0.102 | −0.418 |
Papillae surface area | 0.208 | 0.493 | −0.223 |
Muscular thickness | 0.018 | 0.131 | 0.291 |
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Hu, R.; Shah, A.M.; Han, Q.; Ma, J.; Dai, P.; Meng, Y.; Peng, Q.; Jiang, Y.; Kong, X.; Wang, Z.; et al. Proteomics Reveals the Obstruction of Cellular ATP Synthesis in the Ruminal Epithelium of Growth-Retarded Yaks. Animals 2024, 14, 1243. https://doi.org/10.3390/ani14081243
Hu R, Shah AM, Han Q, Ma J, Dai P, Meng Y, Peng Q, Jiang Y, Kong X, Wang Z, et al. Proteomics Reveals the Obstruction of Cellular ATP Synthesis in the Ruminal Epithelium of Growth-Retarded Yaks. Animals. 2024; 14(8):1243. https://doi.org/10.3390/ani14081243
Chicago/Turabian StyleHu, Rui, Ali Mujtaba Shah, Qiang Han, Jian Ma, Peng Dai, Yukun Meng, Quanhui Peng, Yahui Jiang, Xiangying Kong, Zhisheng Wang, and et al. 2024. "Proteomics Reveals the Obstruction of Cellular ATP Synthesis in the Ruminal Epithelium of Growth-Retarded Yaks" Animals 14, no. 8: 1243. https://doi.org/10.3390/ani14081243
APA StyleHu, R., Shah, A. M., Han, Q., Ma, J., Dai, P., Meng, Y., Peng, Q., Jiang, Y., Kong, X., Wang, Z., & Zou, H. (2024). Proteomics Reveals the Obstruction of Cellular ATP Synthesis in the Ruminal Epithelium of Growth-Retarded Yaks. Animals, 14(8), 1243. https://doi.org/10.3390/ani14081243