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Transcriptome and Redox Proteome Reveal Temporal Scales of Carbon Metabolism Regulation in Model Cyanobacteria Under Light Disturbance by Johnson, Connah G. M.; Johnson, Zachary; Mackey, Liam S.; Li, Xiaolu; Sadler, Natalie C.; Zhang, Tong; Qian, Wei-Jun; Bohutskyi, Pavlo; Feng, Song; Cheung, Margaret S. is a scholarly article available to read on EtoBox.

What is Transcriptome and Redox Proteome Reveal Temporal Scales of Carbon Metabolism Regulation in Model Cyanobacteria Under Light Disturbance about?

We develop a systems approach based on an energy-landscape concept to differentiate interactions involving redox activities and conformational changes of proteins and nucleic acids interactions in multi-layered protein-DNA regulatory networks under light disturbance. Our approach is a data-driven modeling workflow using a physics-informed machine learning algorithm to train a non-linear mathematical model for interpreting gene expression dynamics and to lead discovery for protein regulators using redox proteome analysis. We distinguish light-responsive elements within central carbon metabolism pathways from independent variables like circadian time using the publicly available transcriptome datasets of Synechococcus elongatus over diel cycles responding to light perturbations. Our approach provides interpretable de novo models for elucidating events of reactions in complex regulatory pathways in response to stressful disturbance from the environment. We discovered protein regulators in response to light disturbance in the proteome analysis involving shifts in protein abundance as well as cysteine redox states under constant illumination and after two hours of darkness. We discovere

Author

Johnson, Connah G. M.; Johnson, Zachary; Mackey, Liam S.; Li, Xiaolu; Sadler, Natalie C.; Zhang, Tong; Qian, Wei-Jun; Bohutskyi, Pavlo; Feng, Song; Cheung, Margaret S.

Published

2024

Language

EN