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

BACKGROUND: Growth of the ocean’s most abundant primary producer, the
cyanobacterium Prochlorococcus, is tightly synchronized to the natural
24-hour light-dark cycle. We sought to quantify the relationship between
transcriptome and proteome dynamics that underlie this obligate
photoautotroph’s highly choreographed response to the daily oscillation in
energy supply. METHODOLOGY/PRINCIPAL FINDINGS: Using Illumina
RNA-sequencing transcriptomics and mass spectrometry-based quantitative
proteomics, we measured timecourses of paired mRNA-protein abundances for
312 genes every 2 hours over a light-dark cycle. These temporal expression
patterns reveal strong oscillations in transcript abundance that are
broadly damped at the protein level, with mRNA levels varying on average
2.3 times more than the corresponding protein. The single strongest
observed protein-level oscillation is in a ribonucleotide reductase, which
may reflect a defense strategy against phage infection. The peak in
abundance of most proteins also lags that of their transcript by 2-8
hours, and the two are completely antiphase for some genes. While abundant
antisense RNA was detected, it apparently does not account for the
observed divergences between expression levels. The redirection of flux
through central carbon metabolism from daytime carbon fixation to
nighttime respiration is associated with quite small changes in relative
enzyme abundances. CONCLUSIONS/SIGNIFICANCE: Our results indicate that
expression responses to periodic stimuli that are common in natural
ecosystems (such as the diel cycle) can diverge significantly between the
mRNA and protein levels. Protein expression patterns that are distinct
from those of cognate mRNA have implications for the interpretation of
transcriptome and metatranscriptome data in terms of cellular metabolism
and its biogeochemical impact.