Protein Array-Based Approach to Evaluate Biomarkers of Beef Tenderness and Marbling in Cows: Understanding of the Underlying Mechanisms and Prediction
Abstract
:1. Introduction
2. Materials and Methods
2.1. Experimental Designs, Cows Handling and Slaughtering
2.2. Muscle and Meat Steaks Sampling
2.3. Intramuscular Fat Content Determination
2.4. Meat Tenderness Measurement by Warner–Bratzler Shear Force (WBSF)
2.5. Protein Extraction and Quantification
2.6. Reverse Phase Protein Array (RPPA) for Protein Biomarkers Quantification
2.7. Statistical Analyses
3. Results
3.1. Pearson Correlation Analyses between the Biomarkers and Meat Quality Traits
3.2. Discriminant Biomarkers of WBSF and Marbling
3.3. Partial Least Squares for the Prediction of WBSF and Marbling Using the Panel of 20 Protein Biomarkers
3.4. Summary of the Putative Common Protein Biomarkers from the Three Statistical Methods
4. Discussion
4.1. Common Biomarkers Explaining the Variation in WBSF (Tenderness) and IMF (Marbling)
4.2. Biomarkers Specific to WBSF
4.3. Biomarkers Specific to IMF
5. Conclusions
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Protein Biomarkers Name (Gene) | Uniprot ID | Monoclonal (Mo) or Polyclonal (Po) Antibodies References | Antibody Dilutions |
---|---|---|---|
Energy metabolic enzymes | |||
Malate dehydrogenase (MDH1) | Q3T145 | Mo. anti-pig Rockland 100-601-145 | 1/1000 |
β-enolase 3 (ENO3) | Q3ZC09 | Mo. anti-human Abnova Eno3 (M01), clone 5D1 | 1/30,000 |
Retinal dehydrogenase 1 (ALDH1A1) | P48644 | Po. anti-bovine Abcam ab23375 | 1/500 |
Triosephosphate isomerase (TPI1) | Q5E956 | Po. anti-human Novus NBP1-31470 | 1/50,000 |
Phosphoglycerate kinase 1 (PGK1) | Q3T0P6 | Po. anti-human Abcam ab90787 | 1/5000 |
Fructose-bisphosphate aldolase (ALDOA) | A6QLL8 | Po. anti-human Sigma AV48130 | 1/4000 |
Glycogen phosphorylase (PYGB) | Q3B7M9 | Po. anti-human Santa Cruz SC-46347 | 1/250 |
Heat shock proteins | |||
Alpha-crystallin B chain (CRYAB) | P02510 | Mo. anti-bovine Assay Designs SPA-222 | 1/1000 |
Heat shock protein beta-6, Hsp20 (HSPB6) | Q148F8 | Mo. anti-human Santa Cruz HSP20-11:SC51955 | 1/500 |
Heat shock protein beta-1, Hsp27 (HSPB1) | Q3T149 | Mo. anti-human Santa Cruz HSP27 (F-4):SC13132 | 1/3000 |
DnaJ homolog subfamily A member 1, Hsp40 (DNAJA1) | Q5E954 | Mo. anti-human Santa Cruz HSP40-4 (SPM251):SC-56400 | 1/250 |
Heat shock 70 kDa protein 1A, Hsp70-1A (HSPA1A) | Q27975 | Mo. anti-human RD Systems MAB1663 | 1/1000 |
Oxidative stress proteins | |||
Peroxiredoxin-6 (PRDX6) | O77834 | Mo. anti-human Abnova PRDX6 (M01), clone 3A10-2A11 | 1/500 |
Structural proteins | |||
Myosin light chain 1/3 (MYL1) | A0JNJ5 | Po. anti-human Abnova MYL1 (A01) | 1/1000 |
Myosin heavy chain-IIx (MYH1) | Q9BE40 | Mo anti-bovine Biocytex 8F4 | 1/500 |
Troponin T, slow skeletal muscle (TNNT1) | Q8MKH6 | Po. anti-human Sigma SAB2102501 | 1/4000 |
Titin (TTN) | Q8WZ42 | Mo. anti-human Novocastra NCL-TITIN | 1/100 |
Tubulin alpha-4A chain (TUBA4A) | P81948 | Mo anti-human Sigma T6074 | 1/1000 |
Cell death and protein binding | |||
Tripartite motif protein 72 (TRIM72) | E1BE77 | Po. anti-human Sigma SAB2102571 | 1/2000 |
Four and a half LIM domains 1 (FHL1) | F1MR86 | Po. anti-human Sigma AV34378 | 1/5000 |
Protein Biomarkers 1 | WBSF | IMF |
---|---|---|
Energy metabolic enzymes | ||
MDH1 | −0.29 *** | −0.18 * |
ENO3 | −0.21 ** | - |
ALDH1A1 | +0.34 *** | +0.38 *** |
TPI1 | - | - |
PGK1 | −0.15 * | - |
ALDOA | - | - |
PYGB | - | - |
Heat shock proteins | ||
CRYAB | +0.32 *** | +0.37 *** |
HSP20 (HSPB6) | +0.21 ** | +0.31 *** |
HSP27 (HSPB1) | +0.28 *** | +0.22 ** |
HSP40 (DNAJA1) | - | - |
HSP70-1A | - | - |
Oxidative stress proteins | ||
PRDX6 | - | +0.20 * |
Structural proteins | ||
MYL1 | −0.18 * | - |
MYH1 | −0.26 *** | −0.26 ** |
TNNT1 | +0.22 ** | +0.15 * |
TTN | - | - |
TUBA4A | - | - |
Cell death and protein binding | ||
TRIM72 | - | −0.33 *** |
FHL1 | +0.18 * | +0.22 ** |
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Gagaoua, M.; Bonnet, M.; Picard, B. Protein Array-Based Approach to Evaluate Biomarkers of Beef Tenderness and Marbling in Cows: Understanding of the Underlying Mechanisms and Prediction. Foods 2020, 9, 1180. https://doi.org/10.3390/foods9091180
Gagaoua M, Bonnet M, Picard B. Protein Array-Based Approach to Evaluate Biomarkers of Beef Tenderness and Marbling in Cows: Understanding of the Underlying Mechanisms and Prediction. Foods. 2020; 9(9):1180. https://doi.org/10.3390/foods9091180
Chicago/Turabian StyleGagaoua, Mohammed, Muriel Bonnet, and Brigitte Picard. 2020. "Protein Array-Based Approach to Evaluate Biomarkers of Beef Tenderness and Marbling in Cows: Understanding of the Underlying Mechanisms and Prediction" Foods 9, no. 9: 1180. https://doi.org/10.3390/foods9091180
APA StyleGagaoua, M., Bonnet, M., & Picard, B. (2020). Protein Array-Based Approach to Evaluate Biomarkers of Beef Tenderness and Marbling in Cows: Understanding of the Underlying Mechanisms and Prediction. Foods, 9(9), 1180. https://doi.org/10.3390/foods9091180