Modelling the response of FOXO transcription factors to multiple post-translational modifications made by ageing-related signalling pathways

• Published in: PloS one 2010-06, Vol.5 (6), p.e11092-e11092
• Main Authors: Smith, Graham R, Shanley, Daryl P
• Format: Article
• Language: English
• Subjects: Aging; Aging (artificial); Aging - metabolism; Amino Acid Sequence; Analysis; Apoptosis; Biochemistry/Bioinformatics; Biochemistry/Transcription and Translation; Bioinformatics; Cell cycle; Coffee; Computational Biology/Signaling Networks; Computational Biology/Systems Biology; Computational Biology/Transcriptional Regulation; Computer simulation; Deoxyribonucleic acid; DNA; DNA binding proteins; DNA damage; Drosophila; Forkhead protein; Forkhead Transcription Factors - chemistry; Forkhead Transcription Factors - metabolism; Gene expression; Genomics; Insects; Insulin resistance; Laboratories; Life span; Localization; Mathematical models; Metabolic disorders; Metabolism; Methods; Models, Molecular; Molecular Sequence Data; Phosphorylation; Physiological aspects; Post-translation; Programming Languages; Protein Processing, Post-Translational; Proteins; Proteomics; Radioactive half-life; Regulators; Sequence Homology, Amino Acid; Signal Transduction; Signaling; Stochasticity; Transcription factors; Translation; Xenopus
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0011092

FOXO transcription factors are an important, conserved family of regulators of cellular processes including metabolism, cell-cycle progression, apoptosis and stress resistance. They are required for the efficacy of several of the genetic interventions that modulate lifespan. FOXO activity is regulated by multiple post-translational modifications (PTMs) that affect its subcellular localization, half-life, DNA binding and transcriptional activity. Here, we show how a mathematical modelling approach can be used to simulate the effects, singly and in combination, of these PTMs. Our model is implemented using the Systems Biology Markup Language (SBML), generated by an ancillary program and simulated in a stochastic framework. The use of the ancillary program to generate the SBML is necessary because the possibility that many regulatory PTMs may be added, each independently of the others, means that a large number of chemically distinct forms of the FOXO molecule must be taken into account, and the program is used to generate them. Although the model does not yet include detailed representations of events upstream and downstream of FOXO, we show how it can qualitatively, and in some cases quantitatively, reproduce the known effects of certain treatments that induce various single and multiple PTMs, and allows for a complex spatiotemporal interplay of effects due to the activation of multiple PTM-inducing treatments. Thus, it provides an important framework to integrate current knowledge about the behaviour of FOXO. The approach should be generally applicable to other proteins experiencing multiple regulations.