TMT-based quantitative proteomics analysis reveals the key proteins related with the differentiation process of goat intramuscular adipocytes

Du, Yuguang; Wang, Yong; Xu, Qiyou; Zhu, Jiangjiang; Lin, Yaqiu

doi:10.1186/s12864-021-07730-y

Cited by 15 publications

(10 citation statements)

References 65 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…These results were further confirmed by the protein-protein interaction network data ( Figure 8 ), suggesting that PPP3R1 and SPHK1 played a critical role on FA deposition. The results are consistent with the findings of previous studies ( 67 , 68 ). Additionally, it was noteworthy that the PPP3R1 was enriched in signaling pathways of the calcium (gga04020), VEGF (gga04370), MAPK (gga04010), and Wnt (gga04310) simultaneously.…”

Section: Discussionsupporting

confidence: 93%

Breast Meat Fatty Acid Profiling and Proteomic Analysis of Beijing-You Chicken During the Laying Period

et al. 2022

View full text Add to dashboard Cite

The disparity in fatty acids (FA) composition exhibits a significant impact on meat quality, however, the molecular regulatory mechanisms underlying this trait in chicken are far from clear. In this study, a total of 45 female Beijing-You chicken (BYC) hens, fed on the same diet, were collected at the slaughter age of 150, 300, or 450 days (D150, D300, and D450) from sexual maturation stage to culling stage (15 birds per age). Gas chromatography-mass spectrometry (GC-MS) and tandem mass tag labeling technology based on liquid chromatography mass spectrometry (TMT-LC-MS/MS) analysis strategies were applied to profile FA compositions and to compare differential expressed proteins (DEPs) between these different slaughter ages, respectively. The FA profiling showed that increasing hen ages resulted in increased contents of both saturated and unsaturated fatty acids. Proteomic analyses showed a total of 4,935 proteins in chicken breast muscle with the false discovery rate (FDR) < 1% and 664 of them were differentially expressed (fold change > 1.50 or < 0.67 and P < 0.01). There were 410 up- and 116 down-regulated proteins in D150 vs. D300 group, 32 up- and 20 down-regulated in D150 vs. D450 group, and 72 up- and 241 down-regulated in D300 vs. D450 group. A total of 57 DEPs related to FA/lipid-related metabolisms were obtained according to the enrichment analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). These DEPs were involved in 21 significantly enriched (P < 0.05) pathways, including well-known pathways for FA synthesis (metabolism, desaturation, and elongation) and the signaling pathways for lipid metabolism (PPAR, adipocytokine, calcium, VEGF, MAPK, and Wnt). In addition, there existed several representative DEPs (FABP, FABP3, apoA-I, apoA-IV, apoC-III, apoB, VTG1, and VTG2) involved in the regulation of FA/lipid transportation. The construction of the interaction networks indicated that HADH, ACAA2, HADHA, ACSL1, CD36, CPT1A, PPP3R1, and SPHK1 were the key core nodes. Finally, eight DEPs were quantified using parallel reaction monitoring (PRM) to validate the results from TMT analysis. These results expanded our understanding of how the laying age affects the FA compositions and metabolism in hen breast meat.

show abstract

Section: Discussionsupporting

confidence: 93%

Breast Meat Fatty Acid Profiling and Proteomic Analysis of Beijing-You Chicken During the Laying Period

et al. 2022

View full text Add to dashboard Cite

show abstract

“…Moreover, the association between genomic markers and IMF deposition is not always consistent, so it is essential to explore the potential molecular mechanisms related to IMF [ 32 ]. Up to now, some studies have identified candidate genes (protein-coding and noncoding genes) related to meat quality traits and used them in practical production [ 33 , 34 , 35 ]. Intramuscular fat is highly complex and metabolically active, which involves complex metabolic processes and pathways, and also involves multiple genes.…”

Section: Discussionmentioning

confidence: 99%

Systematic Identification and Comparison of the Expressed Profiles of lncRNAs, miRNAs, circRNAs, and mRNAs with Associated Co-Expression Networks in Pigs with Low and High Intramuscular Fat

Cheng

Liang

Yang

et al. 2021

Animals

View full text Add to dashboard Cite

Intramuscular fat (IMF) content is a complex trait that affects meat quality and determines pork quality. In order to explore the potential mechanisms that affect the intramuscular fat content of pigs, a Large white × Min pigs F2 resource populations were constructed, then whole-transcriptome profile analysis was carried out for five low-IMF and five high-IMF F2 individuals. In total, 218 messenger RNA (mRNAs), 213 long non-coding RNAs (lncRNAs), 18 microRNAs (miRNAs), and 59 circular RNAs (circRNAs) were found to be differentially expressed in the longissimus dorsi muscle. Gene ontology analysis and Kyoto Encyclopedia of Genes and Genomes annotations revealed that these differentially expressed (DE) genes or potential target genes (PTGs) of DE regulatory RNAs (lncRNAs, miRNAs, and circRNAs) are mainly involved in cell differentiation, fatty acid synthesis, system development, muscle fiber development, and regulating lipid metabolism. In total, 274 PTGs were found to be differentially expressed between low- and high-IMF pigs, which indicated that some DE regulatory RNAs may contribute to the deposition/metabolism of IMF by regulating their PTGs. In addition, we analyzed the quantitative trait loci (QTLs) of DE RNAs co-located in high- and low-IMF groups. A total of 97 DE regulatory RNAs could be found located in the QTLs related to IMF. Co-expression networks among different types of RNA and competing endogenous RNA (ceRNA) regulatory networks were also constructed, and some genes involved in type I diabetes mellitus were found to play an important role in the complex molecular process of intramuscular fat deposition. This study identified and analyzed some differential RNAs, regulatory RNAs, and PTGs related to IMF, and provided new insights into the study of IMF formation at the level of the genome-wide landscape.

show abstract

“…IMF plays a vital role in the quality of livestock meat, therefore, the identification of candidate proteins affecting IMF is essential for improving meat quality. Previous studies have applied proteomics to identify DAPs of IMF in other species including pigs ( 30 ) and goats ( 46 ). However, there is a paucity of research on candidate proteins for quality traits in donkey meat.…”

Section: Discussionmentioning

confidence: 99%

Comparative analysis of differentially abundant proteins between high and low intramuscular fat content groups in donkeys

Tan

He²,

Qin³

et al. 2022

Front. Vet. Sci.

View full text Add to dashboard Cite

Intramuscular fat (IMF) is an important regulator that determines meat quality, and its content is closely related to flavor, tenderness, and juiciness. Many studies have used quantitative proteomic analysis to identify proteins associated with meat quality traits in livestock, however, the potential candidate proteins that influence IMF in donkey muscle are not fully understood. In this study, we performed quantitative proteomic analysis, with tandem-mass-tagged (TMT) labeling, with samples from the longissimus dorsi (LD) muscle of the donkey. A total of 585,555 spectra were identified from the six muscle samples used in this study. In total, 20,583 peptides were detected, including 15,279 unique peptides, and 2,540 proteins were identified. We analyzed differentially abundant proteins (DAPs) between LD muscles of donkeys with high (H) and low (L) IMF content. We identified 30 DAPs between the H and L IMF content groups, of which 17 were upregulated and 13 downregulated in the H IMF group. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment analysis of these DAPs revealed many GO terms (e.g., bone morphogenetic protein (BMP) receptor binding) and pathways (e.g., Wnt signaling pathway and Hippo signaling pathway) involved in lipid metabolism and adipogenesis. The construction of protein–protein interaction networks identified 16 DAPs involved in these networks. Our data provide a basis for future investigations into candidate proteins involved in IMF deposition and potential new approaches to improve meat quality in the donkey.

show abstract

TMT-based quantitative proteomics analysis reveals the key proteins related with the differentiation process of goat intramuscular adipocytes

Cited by 15 publications

References 65 publications

Breast Meat Fatty Acid Profiling and Proteomic Analysis of Beijing-You Chicken During the Laying Period

Breast Meat Fatty Acid Profiling and Proteomic Analysis of Beijing-You Chicken During the Laying Period

Systematic Identification and Comparison of the Expressed Profiles of lncRNAs, miRNAs, circRNAs, and mRNAs with Associated Co-Expression Networks in Pigs with Low and High Intramuscular Fat

Comparative analysis of differentially abundant proteins between high and low intramuscular fat content groups in donkeys

Contact Info

Product

Resources

About