RpoS-independent evolution reveals the importance of attenuated cAMP/CRP regulation in high hydrostatic pressure resistance acquisition in E. coli

RpoS-Regulated Genes and Phenotypes in the Phytopathogenic Bacterium Pectobacterium atrosepticum

The alternative sigma factor RpoS is considered to be one of the major regulators providing stress resistance and cross-protection in bacteria. In phytopathogenic bacteria, the effects of RpoS have not been analyzed with regard to cross-protection, and genes whose expression is directly or indirectly controlled by RpoS have not been determined at the whole-transcriptome level. Our study aimed to determine RpoS-regulated genes and phenotypes in the phytopathogenic bacterium Pectobacterium atrosepticum. Knockout of the rpoS gene in P. atrosepticum affected the long-term starvation response, cross-protection, and virulence toward plants with enhanced immune status. The whole-transcriptome profiles of the wild-type P. atrosepticum strain and its ΔrpoS mutant were compared under different experimental conditions, and functional gene groups whose expression was affected by RpoS were determined. The RpoS promoter motif was inferred within the promoter regions of the genes affected by rpoS deletion, and the P. atrosepticum RpoS regulon was predicted. Based on RpoS-controlled phenotypes, transcriptome profiles, and RpoS regulon composition, the regulatory role of RpoS in P. atrosepticum is discussed.

Association of resistance to quaternary ammonium compounds and organic acids with genetic markers and their relationship to Escherichia coli serogroup

Sanitizer resistance is being extensively investigated due to the potential for bacterial survival and cross-resistance with other antimicrobials. Similarly, organic acids are being used due to their microbial inactivation potential as well as being generally recognized as safe (GRAS). However, little is known about associations of genetic and phenotypic factors in Escherichia coli related to resistance to sanitizers and organic acids as well as differences between "Top 7" serogroups. Therefore, we investigated 746 E. coli isolates for resistance to lactic acid and two commercial sanitizers based on quaternary ammonium and peracetic acid. Furthermore, we correlated resistance to several genetic markers and investigated 44 isolates using Whole Genome Sequencing. Results indicate that factors related to motility, biofilm formation, and Locus of Heat Resistance played a role in resistance to sanitizers and lactic acid. In addition, Top 7 serogroups significantly differed in sanitizer and acid resistance, with O157 being the most consistently resistant to all treatments. Finally, mutations in rpoA, rpoC, and rpoS genes were observed, in addition to presence of a Gad gene with alpha-toxin formation in all O121 and O145 isolates, which may be related to increased resistance of these serogroups to the acids used in the present study.

Structural and functional diversity of bacterial cyclic nucleotide perception by CRP proteins

Cyclic AMP (cAMP) is a ubiquitous second messenger synthesized by most living organisms. In bacteria, it plays highly diverse roles in metabolism, host colonization, motility, and many other processes important for optimal fitness. The main route of cAMP perception is through transcription factors from the diverse and versatile CRP-FNR protein superfamily. Since the discovery of the very first CRP protein CAP in Escherichia coli more than four decades ago, its homologs have been characterized in both closely related and distant bacterial species. The cAMP-mediated gene activation for carbon catabolism by a CRP protein in the absence of glucose seems to be restricted to E. coli and its close relatives. In other phyla, the regulatory targets are more diverse. In addition to cAMP, cGMP has recently been identified as a ligand of certain CRP proteins. In a CRP dimer, each of the two cyclic nucleotide molecules makes contacts with both protein subunits and effectuates a conformational change that favors DNA binding. Here, we summarize the current knowledge on structural and physiological aspects of E. coli CAP compared with other cAMP- and cGMP-activated transcription factors, and point to emerging trends in metabolic regulation related to lysine modification and membrane association of CRP proteins.

The Effect of High-Pressure Processing on the Survival of Non-O157 Shiga Toxin-Producing Escherichia coli in Steak Tartare: The Good- or Best-Case Scenario?

Samples of steak tartare were artificially contaminated with a cocktail of Shiga toxin-producing Escherichia coli (STEC) O91, O146, O153, and O156 to the level of 3 log and 6 log CFU/g. Immediately after vacuum packing, high-pressure processing (HPP) was performed at 400 or 600 MPa/5 min. Some of the samples not treated with HPP were cooked under conditions of 55 °C for 1, 3, or 6 h. HPP of 400 MPa/5 min resulted in a 1-2 log reduction in the STEC count. In contrast, HPP of 600 MPa/5 min led to the elimination of STEC even when inoculated to 6 log CFU/g. Nevertheless, sub-lethally damaged cells were resuscitated after enrichment, and STEC was observed in all samples regardless of the pressure used. STEC was not detected in the samples cooked in a 55 °C water bath for 6 h, even after enrichment. Unfortunately, the temperature of 55 °C negatively affected the texture of the steak tartare. Further experiments are necessary to find an optimal treatment for steak tartare to assure its food safety while preserving the character and quality of this attractive product.

Dynamics of high hydrostatic pressure resistance development in RpoS-deficient Escherichia coli

High hydrostatic pressure (HHP) treatment is one of the most widely accepted non-thermal food processing methods, but HHP-resistance development in pathogenic or spoilage bacteria might compromise the safety and stability of HHP-treated foods. Charting the possible routes and mechanisms of HHP resistance development in foodborne bacteria is therefore essential to anticipate or prevent the appearance of resistant variants. While upregulation of the RpoS-governed general stress response is a well-established route for increased HHP resistance in Escherichia coli, previous work revealed that mutations causing attenuated cAMP/CRP activity or aggregation-prone TnaA variants can evolve to overcome the HHP-hypersensitivity of an E. coli ΔrpoS mutant. In this study, further directed evolution and genetic analysis approaches allowed us to demonstrate that both kinds of mutants tend to co-emerge and compete with each other in E. coli ΔrpoS populations evolving towards HHP resistance, because of the higher HHP resistance of cAMP/CRP mutants and the faster growth rate of the TnaA mutants. Moreover, closer scrutiny of evolving populations revealed RpoS, cAMP/CRP and TnaA independent routes of HHP resistance development, based on downregulation of YegW or RppH activity.

Experimental Evolution of Anticipatory Regulation in Escherichia coli

Environmental cues in an ecological niche are often temporal in nature. For instance, in temperate climates, temperature is higher in daytime compared to during night. In response to these temporal cues, bacteria have been known to exhibit anticipatory regulation, whereby triggering response to a yet to appear cue. Such an anticipatory response in known to enhance Darwinian fitness, and hence, is likely an important feature of regulatory networks in microorganisms. However, the conditions under which an anticipatory response evolves as an adaptive response are not known. In this work, we develop a quantitative model to study response of a population to two temporal environmental cues, and predict variables which are likely important for evolution of anticipatory regulatory response. We follow this with experimental evolution of Escherichia coli in alternating environments of rhamnose and paraquat for ∼850 generations. We demonstrate that growth in this cyclical environment leads to evolution of anticipatory regulation. As a result, pre-exposure to rhamnose leads to a greater fitness in paraquat environment. Genome sequencing reveals that this anticipatory regulation is encoded via mutations in global regulators. Overall, our study contributes to understanding of how environment shapes the topology of regulatory networks in an organism.

Gene Erosion Can Lead to Gain-of-Function Alleles That Contribute to Bacterial Fitness

Despite our extensive knowledge of the genetic regulation of heat shock proteins (HSPs), the evolutionary routes that allow bacteria to adaptively tune their HSP levels and corresponding proteostatic robustness have been explored less. In this report, directed evolution experiments using the Escherichia coli model system unexpectedly revealed that seemingly random single mutations in its tnaA gene can confer significant heat resistance. Closer examination, however, indicated that these mutations create folding-deficient and aggregation-prone TnaA variants that in turn can endogenously and preemptively trigger HSP expression to cause heat resistance. These findings, importantly, demonstrate that even erosive mutations with disruptive effects on protein structure and functionality can still yield true gain-of-function alleles with a selective advantage in adaptive evolution.

Modelling the piezo-protection effect exerted by lactate on the high pressure resistance of Listeria monocytogenes in cooked ham

Food safety is often based on the application of several preservative (hurdle) factors whose combination must be smartly selected. The aim of the present study was to evaluate the effect of lactate and diacetate on the high pressure processing (HPP) inactivation of three L. monocytogenes strains (CTC1011, CTC1034 and Scott A) in sliced cooked ham. Inoculated vacuum-packed slices of cooked ham formulated without organic acids and with lactate, diacetate or the combination of both were pressurized at 400 MPa for different holding times and the inactivation kinetics were characterised by fitting primary and secondary models. The shape of the inactivation curves for L. monocytogenes depended on both product formulation and strain. Interestingly, lactate caused a dose-dependent piezo-protection in all three strains, as the HPP inactivation rate decreased in cooked ham formulated with increasing amounts of lactate and in comparison with the control product. The design, validation and implementation of HPP requires a tailor-made approach, considering product formulation and selection of strain/s.

Synthetic reconstruction of extreme high hydrostatic pressure resistance in Escherichia coli

Although high hydrostatic pressure (HHP) is an interesting parameter to be applied in bioprocessing, its potential is currently limited by the lack of bacterial chassis capable of surviving and maintaining homeostasis under pressure. While several efforts have been made to genetically engineer microorganisms able to grow at sublethal pressures, there is little information for designing backgrounds that survive more extreme pressures. In this investigation, we analyzed the genome of an extreme HHP-resistant mutant of E. coli MG1655 (designated as DVL1), from which we identified four mutations (in the cra, cyaA, aceA and rpoD loci) causally linked to increased HHP resistance. Analysing the functional effect of these mutations we found that the coupled effect of downregulation of cAMP/CRP, Cra and the glyoxylate shunt activity, together with the upregulation of RpoH and RpoS activity, could mechanistically explain the increased HHP resistance of the mutant. Using combinations of three mutations, we could synthetically engineer E. coli strains able to comfortably survive pressures of 600-800 MPa, which could serve as genetic backgrounds for HHP-based biotechnological applications.

Evolutionary Repair Experiments as a Window to the Molecular Diversity of Life

Comparative genomics reveals an unexpected diversity in the molecular mechanisms underlying conserved cellular functions, such as DNA replication and cytokinesis. However, the genetic bases and evolutionary processes underlying this 'molecular diversity' remain to be explained. Here, we review a tool to generate alternative mechanisms for conserved cellular functions and test hypotheses concerning the generation of molecular diversity - evolutionary repair experiments, in which laboratory microbial populations adapt in response to a genetic perturbation. We summarize the insights gained from evolutionary repair experiments, the spectrum and dynamics of compensatory mutations, and the alternative molecular mechanisms used to repair perturbed cellular functions. We relate these experiments to the modifications of conserved functions that have occurred outside the laboratory. We end by proposing strategies to improve evolutionary repair experiments as a tool to explore the molecular diversity of life.