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.
Proteome_t0
Protein-level quantitative proteomics data (protXML format) of the diel proteome of Prochlorococcus MED4 for timepoint 0 hours. Includes peptide-spectrum matches generated by X!Tandem, OMSSA and Myrimatch (and combined with iProphet), and 15N-labeling-based quantifications performed with ASAPratio.
bAt0_14N_3way_MED4.prot.xml
Proteome_t2
Protein-level quantitative proteomics data (protXML format) of the diel proteome of Prochlorococcus MED4 for timepoint 2 hours. Includes peptide-spectrum matches generated by X!Tandem, OMSSA and Myrimatch (and combined with iProphet), and 15N-labeling-based quantifications performed with ASAPratio.
bAt2_14N_3way_MED4.prot.xml
Proteome_t4
Protein-level quantitative proteomics data (protXML format) of the diel proteome of Prochlorococcus MED4 for timepoint 4 hours. Includes peptide-spectrum matches generated by X!Tandem, OMSSA and Myrimatch (and combined with iProphet), and 15N-labeling-based quantifications performed with ASAPratio.
bAt4_14N_3way_MED4.prot.xml
Proteome_t6
Protein-level quantitative proteomics data (protXML format) of the diel proteome of Prochlorococcus MED4 for timepoint 6 hours. Includes peptide-spectrum matches generated by X!Tandem, OMSSA and Myrimatch (and combined with iProphet), and 15N-labeling-based quantifications performed with ASAPratio.
bAt6_14N_3way_MED4.prot.xml
Proteome_t8
Protein-level quantitative proteomics data (protXML format) of the diel proteome of Prochlorococcus MED4 for timepoint 8 hours. Includes peptide-spectrum matches generated by X!Tandem, OMSSA and Myrimatch (and combined with iProphet), and 15N-labeling-based quantifications performed with ASAPratio.
bAt8_14N_3way_MED4.prot.xml
Proteome_t10
Protein-level quantitative proteomics data (protXML format) of the diel proteome of Prochlorococcus MED4 for timepoint 10 hours. Includes peptide-spectrum matches generated by X!Tandem, OMSSA and Myrimatch (and combined with iProphet), and 15N-labeling-based quantifications performed with ASAPratio.
bAt10_14N_3way_MED4.prot.xml
Proteome_t12
Protein-level quantitative proteomics data (protXML format) of the diel proteome of Prochlorococcus MED4 for timepoint 12 hours. Includes peptide-spectrum matches generated by X!Tandem, OMSSA and Myrimatch (and combined with iProphet), and 15N-labeling-based quantifications performed with ASAPratio.
bAt12_14N_3way_MED4.prot.xml
Proteome_t14
Protein-level quantitative proteomics data (protXML format) of the diel proteome of Prochlorococcus MED4 for timepoint 14 hours. Includes peptide-spectrum matches generated by X!Tandem, OMSSA and Myrimatch (and combined with iProphet), and 15N-labeling-based quantifications performed with ASAPratio.
bAt14_14N_3way_MED4.prot.xml
Proteome_t16
Protein-level quantitative proteomics data (protXML format) of the diel proteome of Prochlorococcus MED4 for timepoint 16 hours. Includes peptide-spectrum matches generated by X!Tandem, OMSSA and Myrimatch (and combined with iProphet), and 15N-labeling-based quantifications performed with ASAPratio.
bAt16_14N_3way_MED4.prot.xml
Proteome_t18
Protein-level quantitative proteomics data (protXML format) of the diel proteome of Prochlorococcus MED4 for timepoint 18 hours. Includes peptide-spectrum matches generated by X!Tandem, OMSSA and Myrimatch (and combined with iProphet), and 15N-labeling-based quantifications performed with ASAPratio.
bAt18_14N_3way_MED4.prot.xml
Proteome_t20
Protein-level quantitative proteomics data (protXML format) of the diel proteome of Prochlorococcus MED4 for timepoint 20 hours. Includes peptide-spectrum matches generated by X!Tandem, OMSSA and Myrimatch (and combined with iProphet), and 15N-labeling-based quantifications performed with ASAPratio.
bAt20_14N_3way_MED4.prot.xml
Proteome_t22
Protein-level quantitative proteomics data (protXML format) of the diel proteome of Prochlorococcus MED4 for timepoint 22 hours. Includes peptide-spectrum matches generated by X!Tandem, OMSSA and Myrimatch (and combined with iProphet), and 15N-labeling-based quantifications performed with ASAPratio.
bAt22_14N_3way_MED4.prot.xml
Proteome_t24
Protein-level quantitative proteomics data (protXML format) of the diel proteome of Prochlorococcus MED4 for timepoint 24 hours. Includes peptide-spectrum matches generated by X!Tandem, OMSSA and Myrimatch (and combined with iProphet), and 15N-labeling-based quantifications performed with ASAPratio.
bAt24_14N_3way_MED4.prot.xml
Proteome_t26
Protein-level quantitative proteomics data (protXML format) of the diel proteome of Prochlorococcus MED4 for timepoint 26 hours. Includes peptide-spectrum matches generated by X!Tandem, OMSSA and Myrimatch (and combined with iProphet), and 15N-labeling-based quantifications performed with ASAPratio.
bAt26_14N_3way_MED4.prot.xml
RNAseq_t0
RNA-sequencing transcriptomics data of the diel cell cycle of Prochlorococcus MED4 for timepoint 0 hours. The compressed tar archive includes a Maq mapping file and pileup alignment.
t0_RNAseq.tgz
RNAseq_t2
RNA-sequencing transcriptomics data of the diel cell cycle of Prochlorococcus MED4 for timepoint 2 hours. The compressed tar archive includes a Maq mapping file and pileup alignment.
t2_RNAseq.tgz
RNAseq_t4
RNA-sequencing transcriptomics data of the diel cell cycle of Prochlorococcus MED4 for timepoint 4 hours. The compressed tar archive includes a Maq mapping file and pileup alignment.
t4_RNAseq.tgz
RNAseq_t6
RNA-sequencing transcriptomics data of the diel cell cycle of Prochlorococcus MED4 for timepoint 6 hours. The compressed tar archive includes a Maq mapping file and pileup alignment.
t6_RNAseq.tgz
RNAseq_t8
RNA-sequencing transcriptomics data of the diel cell cycle of Prochlorococcus MED4 for timepoint 8 hours. The compressed tar archive includes a Maq mapping file and pileup alignment.
t8_RNAseq.tgz
RNAseq_t10
RNA-sequencing transcriptomics data of the diel cell cycle of Prochlorococcus MED4 for timepoint 10 hours. The compressed tar archive includes a Maq mapping file and pileup alignment.
t10_RNAseq.tgz
RNAseq_t12
RNA-sequencing transcriptomics data of the diel cell cycle of Prochlorococcus MED4 for timepoint 12 hours. The compressed tar archive includes a Maq mapping file and pileup alignment.
t12_RNAseq.tgz
RNAseq_t14
RNA-sequencing transcriptomics data of the diel cell cycle of Prochlorococcus MED4 for timepoint 14 hours. The compressed tar archive includes a Maq mapping file and pileup alignment.
t14_RNAseq.tgz
RNAseq_t16
RNA-sequencing transcriptomics data of the diel cell cycle of Prochlorococcus MED4 for timepoint 16 hours. The compressed tar archive includes a Maq mapping file and pileup alignment.
t16_RNAseq.tgz
RNAseq_t18
RNA-sequencing transcriptomics data of the diel cell cycle of Prochlorococcus MED4 for timepoint 18 hours. The compressed tar archive includes a Maq mapping file and pileup alignment.
t18_RNAseq.tgz
RNAseq_t20
RNA-sequencing transcriptomics data of the diel cell cycle of Prochlorococcus MED4 for timepoint 20 hours. The compressed tar archive includes a Maq mapping file and pileup alignment.
t20_RNAseq.tgz
RNAseq_t22
RNA-sequencing transcriptomics data of the diel cell cycle of Prochlorococcus MED4 for timepoint 22 hours. The compressed tar archive includes a Maq mapping file and pileup alignment.
t22_RNAseq.tgz
RNAseq_t24
RNA-sequencing transcriptomics data of the diel cell cycle of Prochlorococcus MED4 for timepoint 24 hours. The compressed tar archive includes a Maq mapping file and pileup alignment.
t24_RNAseq.tgz
RNAseq_t26
RNA-sequencing transcriptomics data of the diel cell cycle of Prochlorococcus MED4 for timepoint 26 hours. The compressed tar archive includes a Maq mapping file and pileup alignment.
t26_RNAseq.tgz