Identification of biological pathways and putative candidate genes for residual feed intake in a tropically adapted beef cattle breed by plasma proteome analysis

IF 2.8 2区生物学 Q2 BIOCHEMICAL RESEARCH METHODS

Journal of proteomics Pub Date : 2024-12-03 DOI:10.1016/j.jprot.2024.105361

Jessica M. Malheiros , Henrique G. Reolon , Bruna G. Bosquini , Fernando Baldi , Daniela Lourenco , Breno O. Fragomeni , Rafael M.O. Silva , Claudia C.P. Paz , Nedenia B. Stafuzza

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引用次数: 0

Abstract

This study identified potential biomarkers for feed efficiency by blood plasma proteome analysis of a tropically adapted beef cattle breed. Two experimental groups were selected based on residual feed intake (RFI). The proteome was investigated by LC-MS/MS in a data-dependent acquisition mode. After quality control, 123 differentially abundant proteins (DAPs) were identified between the two experimental groups. Among DAPs with the highest absolute log-fold change values, the PRDM2, KRT5, UGGT1, DENND5B, B2M, SLC44A2, SLC7A2, PTPRC, and FETUB were highlighted as potential biomarkers because of their functions that may contribute to RFI. Furthermore, functional enrichment analysis revealed several biological processes, molecular functions and pathways that contributes to RFI, such as cell signaling, cellular responses to stimuli, immune system, calcium, hormones, metabolism and functions of proteins, lipids and carbohydrates. Protein-protein interaction analysis identified 32 and 11 DAPs as important nodes based on their interactions in the high- and low-RFI groups, respectively. This study represents the first comprehensive profiling of the blood plasma proteome of a tropically adapted beef cattle breed and provides valuable insights into the potential roles of these DAPs in key biological processes and pathways, contributing to our understanding of the mechanisms underlying feed efficiency in tropically adapted beef cattle.

Significance

LC-MS/MS analysis was performed to investigate changes in the blood plasma proteome associated with residual feed intake (RFI) in a tropically adapted beef cattle breed (Bos taurus taurus). Some putative biomarkers were identified to distinguish the high-RFI to low-RFI animals, based on their log-fold change value or on their protein-protein interaction network, which provide helpful sources in developing novel selection strategies for breeding programs. Our findings also revealed valuable insights into the metabolic pathways and biological processes that contribute to RFI in beef cattle, such as those closely linked to cell signaling, cellular responses to stimuli, immune system, calcium, hormones, metabolism and functions of proteins, lipids and carbohydrates.

Abstract Image

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通过血浆蛋白质组分析鉴定热带适应肉牛品种残采食量的生物学途径和可能的候选基因。

本研究通过对一个热带适应性肉牛品种的血浆蛋白质组分析，确定了饲料效率的潜在生物标志物。按剩余采食量（RFI）选择2个试验组。采用LC-MS/MS以数据依赖获取模式对蛋白质组进行研究。经质量控制，鉴定出123个差异丰富蛋白（DAPs）。在对数倍绝对值变化值最高的DAPs中，PRDM2、KRT5、UGGT1、DENND5B、B2M、SLC44A2、SLC7A2、PTPRC和FETUB被强调为潜在的生物标志物，因为它们的功能可能有助于RFI。此外，功能富集分析揭示了一些促进RFI的生物学过程、分子功能和途径，如细胞信号传导、细胞对刺激的反应、免疫系统、钙、激素、蛋白质、脂质和碳水化合物的代谢和功能。蛋白-蛋白相互作用分析发现，基于高rfi组和低rfi组中32个和11个DAPs的相互作用，它们分别是重要节点。该研究首次全面分析了热带适应性肉牛品种的血浆蛋白质组，并为这些DAPs在关键生物学过程和途径中的潜在作用提供了有价值的见解，有助于我们理解热带适应性肉牛饲料效率的潜在机制。意义：采用LC-MS/MS分析研究了热带适应肉牛品种（Bos taurus taurus）血浆蛋白质组与剩余采食量（RFI）相关的变化。基于对数倍变化值或蛋白质相互作用网络，我们确定了一些可能的生物标志物来区分高rfi和低rfi动物，这为制定新的育种计划选择策略提供了有用的来源。我们的研究结果还揭示了导致肉牛RFI的代谢途径和生物过程，例如与细胞信号、细胞对刺激的反应、免疫系统、钙、激素、蛋白质、脂质和碳水化合物的代谢和功能密切相关的代谢途径和生物过程。

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来源期刊

Journal of proteomics 生物-生化研究方法

CiteScore

7.10

自引率

3.00%

发文量

227

审稿时长

73 days

期刊介绍： Journal of Proteomics is aimed at protein scientists and analytical chemists in the field of proteomics, biomarker discovery, protein analytics, plant proteomics, microbial and animal proteomics, human studies, tissue imaging by mass spectrometry, non-conventional and non-model organism proteomics, and protein bioinformatics. The journal welcomes papers in new and upcoming areas such as metabolomics, genomics, systems biology, toxicogenomics, pharmacoproteomics. Journal of Proteomics unifies both fundamental scientists and clinicians, and includes translational research. Suggestions for reviews, webinars and thematic issues are welcome.