Analysis of Proteins Associated with Quality Deterioration of Grouper Fillets Based on TMT Quantitative Proteomics during Refrigerated Storage

Zhang, Xicai; Xie, Jing

doi:10.3390/molecules24142641

Cited by 37 publications

(22 citation statements)

References 53 publications

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“…They cover several candidate genes related to economic and functional traits. The enriched biological processes including inner mitochondrial membrane organization and ATP-dependent chromatin remodeling are related to carcass traits, milk production, and reproduction in cattle ( Lu et al, 2016 ; Zhang and Xie, 2019 ; Shi et al, 2021 ). We also observed that the hybrids present more candidate regions related to heat response than the taurine populations, which is in line with the admixture with Zebu cattle known to tolerate high environmental heat loads ( Taye et al, 2017a ; Kim et al, 2020 ).…”

Section: Discussionmentioning

confidence: 99%

Unraveling Admixture, Inbreeding, and Recent Selection Signatures in West African Indigenous Cattle Populations in Benin

et al. 2021

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The Dwarf Lagune and the Savannah Somba cattle in Benin are typical representatives of the endangered West African indigenous Shorthorn taurine. The Lagune was previously exported to African and European countries and bred as Dahomey cattle, whereas the Somba contributed to the formation of two indigenous hybrids known as Borgou and Pabli cattle. These breeds are affected by demographic, economic, and environmental pressures in local production systems. Considering current and historical genomic data, we applied a formal test of admixture, estimated admixture proportions, and computed genomic inbreeding coefficients to characterize the five breeds. Subsequently, we unraveled the most recent selection signatures using the cross-population extended haplotype homozygosity approach, based on the current and historical genotypes. Results from principal component analyses and high proportion of Lagune ancestry confirm the Lagune origin of the European Dahomey cattle. Moreover, the Dahomey cattle displayed neither indicine nor European taurine (EUT) background, but they shared on average 40% of autozygosity from common ancestors, dated approximately eight generations ago. The Lagune cattle presented inbreeding coefficients larger than 0.13; however, the Somba and the hybrids (Borgou and Pabli) were less inbred (≤0.08). We detected evidence of admixture in the Somba and Lagune cattle, but they exhibited a similar African taurine (AFT) ancestral proportion (≥96%) to historical populations, respectively. A moderate and stable AFT ancestral proportion (62%) was also inferred for less admixed hybrid cattle including the Pabli. In contrast, the current Borgou samples displayed a lower AFT ancestral proportion (47%) than historical samples (63%). Irrespective of the admixture proportions, the hybrid populations displayed more selection signatures related to economic traits (reproduction, growth, and milk) than the taurine. In contrast, the taurine, especially the Somba, presented several regions known to be associated with adaptive traits (immunity and feed efficiency). The identified subregion of bovine leukocyte antigen (BoLA) class IIb (including DSB and BOLA-DYA) in Somba cattle is interestingly uncommon in other African breeds, suggesting further investigations to understand its association with specific adaptation to endemic diseases in Benin. Overall, our study provides deeper insights into recent evolutionary processes in the Beninese indigenous cattle and their aptitude for conservation and genetic improvement.

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Section: Discussionmentioning

confidence: 99%

Unraveling Admixture, Inbreeding, and Recent Selection Signatures in West African Indigenous Cattle Populations in Benin

et al. 2021

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“…Myosin heavy chain, myosin light chain 1 and myosin regulatory light chain 2 were all upregulated during cold storage, and this was related to shear force value. 39 The majority of myosin-binding protein C and myosin-binding protein H that were successfully identified also upregulated with the prolongation of storage time. Changes in these structural and functional proteins affected the texture of chicken breast and could be used as the key proteins to evaluate the freshness of prepared chicken breast.…”

Section: Discussionmentioning

confidence: 98%

Proteins associated with quality deterioration of prepared chicken breast based on differential proteomics during refrigerated storage

et al. 2020

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BACKGROUND: Prepared chicken breast deterioration is a complex biochemical process, of which protein change is one of the main features. The present research focuses on the analysis of proteins related to the deterioration in quality of prepared chicken breast through differential proteomics analysis. RESULTS:The physicochemical indexes of prepared chicken breast showed that quality gradually decreased at the second week of refrigerated storage, while the deterioration of chicken breast meat was obvious at the third week. Three key time points of quality change were determined to be at 0th, 2th and 5th week, respectively. In addition, 39 differential proteins were successfully identified using two-dimensional gel electrophoresis and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Most of the identified proteins showed significant differences in expression at the three key points of storage, of which actin, myosin, ⊍-1,4-glucan phosphorylase, phosphoglucomutase 1, heat shock protein ⊎-1, tubulin ⊎-7 chain and skeletal muscle type tropomodulin (fragment) were closely related to the quality deterioration of prepared chicken breast, and thus potential indicator proteins to evaluate the quality of chicken breast. CONCLUSION:The current study indicated that the physicochemical quality of prepared breast notably changed during refrigerated storage. Three key time points of quality change in the storage process of prepared chicken breast were determined. Furthermore, differential proteomics identified the key proteins related to freshness, which provides a theoretical basis for exploring the mechanism of chicken breast deterioration.

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“…Studies have shown that proteins in living cells do not exist as a single entity, but rather as functional associations within the cell [23]. It was of great significance to reveal the qualitative characteristics of proteins through the interaction between the formations of the network [24]. By using Cytoscape software against the S. oneidensis database, we explored protein interaction networks altered in the cold stress of S. putrefaciens by extracting a putative PPI network.…”

Section: Interaction Network Of Upregulated De Proteinsmentioning

confidence: 99%

TMT-Based Quantitative Proteomics Analysis of the Fish-Borne Spoiler Shewanella putrefaciens Subjected to Cold Stress Using LC-MS/MS

Gao

Mei

et al. 2021

Journal of Chemistry

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Shewanella putrefaciens is a specific spoilage bacterium for fish during cold storage. To better understand the molecular mechanisms of cold stress adaptation of S. putrefaciens, tandem mass tag- (TMT-) based quantitative proteomic analysis was performed to detect the effects of cold stress on protein expression profiles in S. putrefaciens which had been cultivated at 4°C and 30°C, respectively. A total of 266670 peptide spectrum matching numbers were quantified proteins after data analysis. Of the 2292 proteins quantitatively analyzed, a total of 274 were found to be differentially expressed (DE) under cold stress compared with the nonstress control. By integrating the results of Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, 9 common KEGG terms were found notable for the cold-responsive proteins. Generally, the DE proteins involved in carbohydrate, amino acid, and fatty acid biosynthesis and metabolism were significantly upregulated, leading to a specific energy conservation survival mode. The DE proteins related to DNA repair, transcription, and translation were upregulated, implicating change of gene expression and more protein biosynthesis needed in response to cold stress.

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Analysis of Proteins Associated with Quality Deterioration of Grouper Fillets Based on TMT Quantitative Proteomics during Refrigerated Storage

Cited by 37 publications

References 53 publications

Unraveling Admixture, Inbreeding, and Recent Selection Signatures in West African Indigenous Cattle Populations in Benin

Unraveling Admixture, Inbreeding, and Recent Selection Signatures in West African Indigenous Cattle Populations in Benin

Proteins associated with quality deterioration of prepared chicken breast based on differential proteomics during refrigerated storage

TMT-Based Quantitative Proteomics Analysis of the Fish-Borne Spoiler Shewanella putrefaciens Subjected to Cold Stress Using LC-MS/MS

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