Modelling pathways to Rubisco degradation: a structural equation network modelling approach.
Modelling pathways to Rubisco degradation: a structural equation network modelling approach.
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DOI：
10.1371/journal.pone.0087597
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发表时间：
2014
期刊：
影响因子：
3.7
通讯作者：
Rushton S
中科院分区：
文献类型：
--
作者：
Tétard-Jones C;Gatehouse AM;Cooper J;Leifert C;Rushton S
组学分析（转录组学、蛋白质组学）量化基因/蛋白质表达的变化，提供生化途径随时间变化的快照。虽然研究基因/蛋白质之间关系所需的建模等工具已经存在，但很少使用。我们认为，使用结构方程模型研究蛋白质-蛋白质相互作用的建议Rubisco蛋白质降解途径，使用以前发表的数据从二维电泳和质谱蛋白质组分析的潜力。这些为先前模型的开发提供了信息，该模型假设Rubisco大亚基和小亚基降解的途径，产生初级和次级降解产物。虽然一些假定的途径得到了建模方法的证实，但该模型也展示了最初没有假设的特征。我们使用基于马尔可夫链蒙特卡罗模拟的贝叶斯分析来生成输出统计数据，表明该模型复制了由于蛋白质-蛋白质相互作用而导致的观察数据的变化。这项研究代表了早期的一步，在发展的方法，寻求使充分利用的信息，包含在蛋白质组学数据的生化途径的动态。随着这些方法获得关注，它们将指导实验的设计和实施，使组学建模成为分子生物学中的一种常见做法。
‘Omics analysis (transcriptomics, proteomics) quantifies changes in gene/protein expression, providing a snapshot of changes in biochemical pathways over time. Although tools such as modelling that are needed to investigate the relationships between genes/proteins already exist, they are rarely utilised. We consider the potential for using Structural Equation Modelling to investigate protein-protein interactions in a proposed Rubisco protein degradation pathway using previously published data from 2D electrophoresis and mass spectrometry proteome analysis. These informed the development of a prior model that hypothesised a pathway of Rubisco Large Subunit and Small Subunit degradation, producing both primary and secondary degradation products. While some of the putative pathways were confirmed by the modelling approach, the model also demonstrated features that had not been originally hypothesised. We used Bayesian analysis based on Markov Chain Monte Carlo simulation to generate output statistics suggesting that the model had replicated the variation in the observed data due to protein-protein interactions. This study represents an early step in the development of approaches that seek to enable the full utilisation of information regarding the dynamics of biochemical pathways contained within proteomics data. As these approaches gain attention, they will guide the design and conduct of experiments that enable ‘Omics modelling to become a common place practice within molecular biology.
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