Abstract
‘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.
Highlights
Transcriptome and more recently proteome analysis are capable of producing vast amounts of data that provide snapshots of changes in gene expression through time in relation to developmental or environmental variation [1,2,3,4,5,6,7,8,9,10]
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
We assumed that if a degradation product contained a portion of the whole protein sequence of a particular Rubisco subunit (either Rubisco Large Subunit (RLS) or Small Subunit (RSS)), this indicated a link between that intact subunit and the primary degradation product
Summary
Transcriptome and more recently proteome analysis are capable of producing vast amounts of data that provide snapshots of changes in gene expression through time in relation to developmental or environmental variation [1,2,3,4,5,6,7,8,9,10]. To understand the dynamics of the protein degradation process there is need for a statistical modelling approach that makes testable predictions and tests hypotheses regarding the relationships between the protein and its degradation products. This would address important questions such as how many stages of degradation does Rubisco go through and how the degradation process is affected by the proteins’ environment (e.g. plant nutritional status). 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
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