Transcriptome and proteome dynamics of a light-dark synchronized bacterial cell cycle

Natural ecosystems often impose periodic environmental changes, such as the daily light-dark cycle. In marine environments, Prochlorococcus, a cyanobacterium, dominates as a primary producer and synchronizes its growth with these cycles. Prior research has shown that gene expression patterns can vary with environmental rhythms. However, the relationship between mRNA and protein levels in response to such cycles remains unclear. This gap motivated an investigation into how transcriptome and proteome dynamics differ in Prochlorococcus. No prior work had resolved the extent to which mRNA and protein levels diverge in response to diel cycles. This uncertainty drove the need for paired transcriptomic and proteomic measurements. The study aimed to clarify how these levels interact in a natural, synchronized system. Understanding these dynamics could help interpret metatranscriptomic data in marine ecosystems. The lack of such data has limited the interpretation of gene expression in biogeochemical models.

The study aimed to quantify how transcriptome and proteome dynamics interact in Prochlorococcus under a natural 24-hour light-dark cycle. The researchers focused on the cyanobacterium’s synchronized growth and its response to energy supply oscillations. They sought to measure mRNA and protein levels for 312 genes every 2 hours. The goal was to determine the relationship between transcript and protein abundance over time. The study also aimed to identify which genes showed the strongest oscillations at the protein level. The researchers wanted to understand if mRNA and protein levels were in phase or antiphase. They also explored whether antisense RNA explained the observed differences. The study aimed to clarify how central carbon metabolism shifts between day and night.

The researchers used RNA-sequencing transcriptomics and mass spectrometry-based quantitative proteomics to measure gene expression. They collected timecourse data for 312 genes every 2 hours over a 24-hour cycle. This approach allowed them to compare mRNA and protein levels simultaneously. The study focused on Prochlorococcus, a cyanobacterium known for its synchronized growth. They analyzed temporal patterns of transcript and protein abundance to detect oscillations. The researchers looked for correlations between mRNA and protein levels across the cycle. They also examined whether antisense RNA could explain the observed divergence. The study included measurements of central carbon metabolism enzyme abundances.

Transcript abundance showed strong oscillations, but these were largely damped at the protein level. On average, mRNA levels varied 2.3 times more than their corresponding proteins. The strongest protein-level oscillation was observed in a ribonucleotide reductase. This enzyme’s peak abundance may reflect a defense strategy against phage infection. Most proteins peaked 2–8 hours after their transcripts. Some genes showed completely antiphase patterns between mRNA and protein levels. Abundant antisense RNA was detected but did not account for the observed divergence. Central carbon metabolism shifted from carbon fixation to respiration with minimal changes in enzyme abundance.

The study found that mRNA and protein levels in Prochlorococcus diverged significantly in response to the diel cycle. These differences suggest that transcript abundance does not always predict protein levels. The strongest protein oscillation was in a ribonucleotide reductase, possibly linked to phage defense. The lag between mRNA and protein peaks indicates post-transcriptional regulation. Some genes showed antiphase patterns, highlighting complex regulatory mechanisms. Antisense RNA was present but did not explain the divergence. Small changes in enzyme abundance were observed during shifts in carbon metabolism. The findings suggest that metatranscriptomic data may misrepresent cellular metabolism in marine ecosystems.