Abstract
BackgroundIn natural environments, bacteria must frequently cope with extremely scarce nutrients. Most studies focus on bacterial growth in nutrient replete conditions, while less is known about the stationary phase. Here, we are interested in global gene expression throughout all growth phases, including the adjustment to deep stationary phase.ResultsWe monitored both the transcriptome and the proteome in cultures of the alphaproteobacterium Rhodobacter sphaeroides, beginning with the transition to stationary phase and at different points of the stationary phase and finally during exit from stationary phase (outgrowth) following dilution with fresh medium. Correlation between the transcriptomic and proteomic changes was very low throughout the growth phases. Surprisingly, even in deep stationary phase, the abundance of many proteins continued to adjust, while the transcriptome analysis revealed fewer adjustments. This pattern was reversed during the first 90 min of outgrowth, although this depended upon the duration of the stationary phase. We provide a detailed analysis of proteomic changes based on the clustering of orthologous groups (COGs), and compare these with the transcriptome.ConclusionsThe low correlation between transcriptome and proteome supports the view that post-transcriptional processes play a major role in the adaptation to growth conditions. Our data revealed that many proteins with functions in transcription, energy production and conversion and the metabolism and transport of amino acids, carbohydrates, lipids, and secondary metabolites continually increased in deep stationary phase. Based on these findings, we conclude that the bacterium responds to sudden changes in environmental conditions by a radical and rapid reprogramming of the transcriptome in the first 90 min, while the proteome changes were modest. In response to gradually deteriorating conditions, however, the transcriptome remains mostly at a steady state while the bacterium continues to adjust its proteome. Even long after the population has entered stationary phase, cells are still actively adjusting their proteomes.
Highlights
In natural environments, bacteria must frequently cope with extremely scarce nutrients
A combined transcriptomic and proteomic approach has the advantage of providing deeper insights into the molecular changes underlying bacterial growth adaptation [4,5,6,7]
Changes in gene expression were detected by comparing expression levels at later phases to those obtained from exponential phase cultures and are referred to hereafter as log2 fold changes
Summary
Bacteria must frequently cope with extremely scarce nutrients. Most studies focus on bacterial growth in nutrient replete conditions, while less is known about the stationary phase. Transcriptomic approaches have been used to study the changes between the growth phases [2, 3]. A combined transcriptomic and proteomic approach has the advantage of providing deeper insights into the molecular changes underlying bacterial growth adaptation [4,5,6,7]. Evidence is emerging from a wide spectrum of organisms that RNA abundances do not generally correlate well with protein abundances [8]. Another goal of this study was to see if this is the case
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