Cell State Transitions Drive Transcriptome-Proteome Alignment in a Minimal Photoautotroph

Abstract

The cyanobacterium Prochlorococcus marinus MED4 is a minimal photoautotroph that maintains circadian regulation despite its reduced circadian regulatory toolkit relative to other cyanobacteria. Moreover, MED4, like other small prokaryotes, has low transcript counts per cell and poor transcriptome-proteome alignment. A systems-level understanding of how MED4 uses its minimal regulatory machinery to achieve a well-coordinated circadian cycle is currently lacking. We address this knowledge gap by analyzing global proteomics, transcriptomics, metabolomics, and lipidomics collected across a circadian day. Integrating these data with statistical analyses, enzyme-constrained metabolic modeling, and stochastic mathematical modeling allows us to reveal and characterize six major population-level cell states. Here we present evidence that high-light response regulator RpaB plays an important night-time regulatory role in MED4 by inhibiting RpaA, the master transcriptional activator of dusk genes and HimA, a regulatory target of RpaA previously shown to influence DNA conformation, is highly correlated with global transcriptome-proteome alignment (R2 = 0.67, p < 0.001). We construct stochastic differential equations consistent with genome-wide promotion of transcription by HimA as a plausible mechanism. Our HimA-driven model recapitulates alignment dynamics (R2 = 0.59, p < 0.01) as one plausible explanation. Collectively, our results elucidate how a minimal circadian regulatory program achieves robust coordination across transcriptional, translational, and metabolic levels