DOI: 10.5061/dryad.8kk12
title: Data from: Transcriptome and proteome dynamics of a light-dark synchronized bacterial cell cycle

description: 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.
description: Proteome_t0Protein-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.xmlProteome_t2Protein-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.xmlProteome_t4Protein-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.xmlProteome_t6Protein-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.xmlProteome_t8Protein-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.xmlProteome_t10Protein-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.xmlProteome_t12Protein-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.xmlProteome_t14Protein-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.xmlProteome_t16Protein-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.xmlProteome_t18Protein-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.xmlProteome_t20Protein-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.xmlProteome_t22Protein-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.xmlProteome_t24Protein-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.xmlProteome_t26Protein-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.xmlRNAseq_t0RNA-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.tgzRNAseq_t2RNA-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.tgzRNAseq_t4RNA-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.tgzRNAseq_t6RNA-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.tgzRNAseq_t8RNA-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.tgzRNAseq_t10RNA-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.tgzRNAseq_t12RNA-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.tgzRNAseq_t14RNA-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.tgzRNAseq_t16RNA-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.tgzRNAseq_t18RNA-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.tgzRNAseq_t20RNA-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.tgzRNAseq_t22RNA-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.tgzRNAseq_t24RNA-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.tgzRNAseq_t26RNA-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