Gene network centrality analysis identifies key regulators coordinating day-night metabolic transitions in Synechococcus elongatus PCC 7942 despite limited accuracy in predicting direct regulator-gene interactions DOI Creative Commons
Z. Johnson, David J. Anderson, Margaret S. Cheung

и другие.

Frontiers in Microbiology, Год журнала: 2025, Номер 16

Опубликована: Март 26, 2025

Synechococcus elongatus PCC 7942 is a model organism for studying circadian regulation and bioproduction, where precise temporal control of metabolism significantly impacts photosynthetic efficiency CO 2 -to-bioproduct conversion. Despite extensive research on core clock components, our understanding the broader regulatory network orchestrating genome-wide metabolic transitions remains incomplete. We address this gap by applying machine learning tools analysis to investigate transcriptional architecture governing circadian-controlled gene expression. While approach showed moderate accuracy in predicting individual transcription factor-gene interactions - common challenge with real expression data network-level topological successfully revealed organizational principles regulation. Our identified distinct modules coordinating day-night transitions, photosynthesis carbon/nitrogen controlled day-phase regulators, while nighttime orchestrate glycogen mobilization redox metabolism. Through centrality analysis, we potentially significant but previously understudied regulators: HimA as putative DNA regulator, TetR SrrB potential coordinators metabolism, working alongside established global regulators RpaA RpaB. This work demonstrates how can extract biologically meaningful insights despite limitations direct interactions. The uncovered here advance cyanobacteria coordinate complex may inform engineering strategies enhanced bioproduction from .

Язык: Английский

Gene network centrality analysis identifies key regulators coordinating day-night metabolic transitions in Synechococcus elongatus PCC 7942 despite limited accuracy in predicting direct regulator-gene interactions DOI Creative Commons
Z. Johnson, David J. Anderson, Margaret S. Cheung

и другие.

Frontiers in Microbiology, Год журнала: 2025, Номер 16

Опубликована: Март 26, 2025

Synechococcus elongatus PCC 7942 is a model organism for studying circadian regulation and bioproduction, where precise temporal control of metabolism significantly impacts photosynthetic efficiency CO 2 -to-bioproduct conversion. Despite extensive research on core clock components, our understanding the broader regulatory network orchestrating genome-wide metabolic transitions remains incomplete. We address this gap by applying machine learning tools analysis to investigate transcriptional architecture governing circadian-controlled gene expression. While approach showed moderate accuracy in predicting individual transcription factor-gene interactions - common challenge with real expression data network-level topological successfully revealed organizational principles regulation. Our identified distinct modules coordinating day-night transitions, photosynthesis carbon/nitrogen controlled day-phase regulators, while nighttime orchestrate glycogen mobilization redox metabolism. Through centrality analysis, we potentially significant but previously understudied regulators: HimA as putative DNA regulator, TetR SrrB potential coordinators metabolism, working alongside established global regulators RpaA RpaB. This work demonstrates how can extract biologically meaningful insights despite limitations direct interactions. The uncovered here advance cyanobacteria coordinate complex may inform engineering strategies enhanced bioproduction from .

Язык: Английский

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