Comparative analyses of the variation of the transcriptome and proteome of Rhodobacter sphaeroides throughout growth

Abstract

Background In 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. Results We 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. Conclusions The 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. Electronic supplementary material The online version of this article (10.1186/s12864-019-5749-3) contains supplementary material, which is available to authorized users.

Adaptation of the Alphaproteobacterium Rhodobacter sphaeroides to stationary phase

“…How does the organism translate this information into proteins from mRNAs? Discrepancies between mRNA and protein levels have been frequently noted in various organisms (Erdmann et al ., ; Bathke et al ., ). Bathke et al .…”

“…How does the organism translate this information into proteins from mRNAs? Discrepancies between mRNA and protein levels have been frequently noted in various organisms (Erdmann et al, 2018;Bathke et al, 2019). Bathke et al compared the proteome under low aerated growth with the transcriptome data used in this study.…”

“…Of the transcripts that are either increased or decreased in the transition phase, the accompanying protein levels (where detected) are provided in Table 2. Correlation between transcript and protein levels was generally low but was slightly improved by comparing transition phase mRNAs with proteins accumulated in the early stationary phase (Bathke et al, 2019). For example, the SitA protein showed strong accumulation, although this increase did not appear until the stationary phase (Table 2).…”

Adaptation to Photooxidative Stress: Common and Special Strategies of the Alphaproteobacteria Rhodobacter sphaeroides and Rhodobacter capsulatus

“…Protein sample preparation was performed as previously described [53]. For mass spectrometry (MS) analysis, peptides were eluted from STAGE tips by solvent B (80% acetonitrile, 0.1% formic acid), dried down in a SpeedVac Concentrator (Thermo Fisher Scientific, Schwerte, Germany) and dissolved in solvent a (0.1% formic acid).…”

Histone deacetylase inhibitors butyrate and bufexamac inhibitde novoHIV-1 infection in CD4 T-cells

“…While analysis of the transcriptome allows determination of ongoing intracellular changes, it usually does not correlate very well with protein abundancies as mRNA levels do not reflect protein half-lives or provide information about posttranslational modifications, which affect protein activity [51,52]. Thus, we additionally performed quantitative, TMT-based proteome analysis of Sb-treated CD4 + T-cells 48 h post treatment ( Figure 4A).…”