Ribosome Protein Composition Mediates Translation during the Escherichia coli Stationary Phase

Bimodality in E. coli gene expression: Sources and robustness to genome-wide stresses

Bacteria evolved genes whose single-cell distributions of expression levels are broad, or even bimodal. Evidence suggests that they might enhance phenotypic diversity for coping with fluctuating environments. We identified seven genes in E. coli with bimodal (low and high) single-cell expression levels under standard growth conditions and studied how their dynamics are modified by environmental and antibiotic stresses known to target gene expression. We found that all genes lose bimodality under some, but not under all, stresses. Also, bimodality can reemerge upon cells returning to standard conditions, which suggests that the genes can switch often between high and low expression rates. As such, these genes could become valuable components of future multi-stable synthetic circuits. Next, we proposed models of bimodal transcription dynamics with realistic parameter values, able to mimic the outcome of the perturbations studied. We explored several models' tunability and boundaries of parameter values, beyond which it shifts to unimodal dynamics. From the model results, we predict that bimodality is robust, and yet tunable, not only by RNA and protein degradation rates, but also by the fraction of time that promoters remain unavailable for new transcription events. Finally, we show evidence that, although the empirical expression levels are influenced by many factors, the bimodality emerges during transcription initiation, at the promoter regions and, thus, may be evolvable and adaptable.

Ribosome-inactivation by a class of widely distributed C-tail anchored membrane proteins

Ribosome hibernation is a commonly used strategy that protects ribosomes under unfavorable conditions and regulates developmental processes. Multiple ribosome-hibernation factors have been identified in all domains of life, but due to their structural diversity and the lack of a common inactivation mechanism, it is currently unknown how many different hibernation factors exist. Here, we show that the YqjD/ElaB/YgaM paralogs, initially discovered as membrane-bound ribosome binding proteins in E. coli, constitute an abundant class of ribosome-hibernating proteins, which are conserved across all proteobacteria and some other bacterial phyla. Our data demonstrate that they inhibit in vitro protein synthesis by interacting with the 50S ribosomal subunit. In vivo cross-linking combined with mass spectrometry revealed their specific interactions with proteins surrounding the ribosomal tunnel exit and even their penetration into the ribosomal tunnel. Thus, YqjD/ElaB/YgaM inhibit translation by blocking the ribosomal tunnel and thus mimic the activity of antimicrobial peptides and macrolide antibiotics.

SILAC analysis of Escherichia coli proteome during progression of growth from exponential to prolonged stationary phase

The expression level of individual proteins varies markedly during the progression of the growth phase in bacteria. A set of proteins was quantified in Escherichia coli total proteome during 14 days of batch cultivation using pulse stable isotope labeled amino acids in cell culture (SILAC)-based quantitative mass spectrometry.

TRS: a method for determining transcript termini from RNAtag-seq sequencing data

In bacteria, determination of the 3' termini of transcripts plays an essential role in regulation of gene expression, affecting the functionality and stability of the transcript. Several experimental approaches were developed to identify the 3' termini of transcripts, however, these were applied only to a limited number of bacteria and growth conditions. Here we present a straightforward approach to identify 3' termini from widely available RNA-seq data without the need for additional experiments. Our approach relies on the observation that the RNAtag-seq sequencing protocol results in overabundance of reads mapped to transcript 3' termini. We present TRS (Termini by Read Starts), a computational pipeline exploiting this property to identify 3' termini in RNAtag-seq data, and show that the identified 3' termini are highly reliable. Since RNAtag-seq data are widely available for many bacteria and growth conditions, our approach paves the way for studying bacterial transcription termination in an unprecedented scope.

Coping with stress: How bacteria fine-tune protein synthesis and protein transport

Maintaining a functional proteome under different environmental conditions is challenging for every organism, in particular for unicellular organisms, such as bacteria. In order to cope with changing environments and stress conditions, bacteria depend on strictly coordinated proteostasis networks that control protein production, folding, trafficking, and degradation. Regulation of ribosome biogenesis and protein synthesis are cornerstones of this cellular adaptation in all domains of life, which is rationalized by the high energy demand of both processes and the increased resistance of translationally silent cells against internal or external poisons. Reduced protein synthesis ultimately also reduces the substrate load for protein transport systems, which are required for maintaining the periplasmic, inner, and outer membrane subproteomes. Consequences of impaired protein transport have been analyzed in several studies and generally induce a multifaceted response that includes the upregulation of chaperones and proteases and the simultaneous downregulation of protein synthesis. In contrast, generally less is known on how bacteria adjust the protein targeting and transport machineries to reduced protein synthesis, e.g., when cells encounter stress conditions or face nutrient deprivation. In the current review, which is mainly focused on studies using Escherichia coli as a model organism, we summarize basic concepts on how ribosome biogenesis and activity are regulated under stress conditions. In addition, we highlight some recent developments on how stress conditions directly impair protein targeting to the bacterial membrane. Finally, we describe mechanisms that allow bacteria to maintain the transport of stress-responsive proteins under conditions when the canonical protein targeting pathways are impaired.