Molecular mechanisms involved in the regulation of mutation rates in bacteria

Microfluidics for adaptation of microorganisms to stress: design and application

Microfluidic systems have fundamentally transformed the realm of adaptive laboratory evolution (ALE) for microorganisms by offering unparalleled control over environmental conditions, thereby optimizing mutant generation and desired trait selection. This review summarizes the substantial influence of microfluidic technologies and their design paradigms on microbial adaptation, with a primary focus on leveraging spatial stressor concentration gradients to enhance microbial growth in challenging environments. Specifically, microfluidic platforms tailored for scaled-down ALE processes not only enable highly autonomous and precise setups but also incorporate novel functionalities. These capabilities encompass fostering the growth of biofilms alongside planktonic cells, refining selection gradient profiles, and simulating adaptation dynamics akin to natural habitats. The integration of these aspects enables shaping phenotypes under pressure, presenting an unprecedented avenue for developing robust, stress-resistant strains, a feat not easily attainable using conventional ALE setups. The versatility of these microfluidic systems is not limited to fundamental research but also offers promising applications in various areas of stress resistance. As microfluidic technologies continue to evolve and merge with cutting-edge methodologies, they possess the potential not only to redefine the landscape of microbial adaptation studies but also to expedite advancements in various biotechnological areas. KEY POINTS: • Microfluidics enable precise microbial adaptation in controlled gradients. • Microfluidic ALE offers insights into stress resistance and distinguishes between resistance and persistence. • Integration of adaptation-influencing factors in microfluidic setups facilitates efficient generation of stress-resistant strains.

Evolutionary and ecological role of extracellular contractile injection systems: from threat to weapon

Contractile injection systems (CISs) are phage tail-related structures that are encoded in many bacterial genomes. These devices encompass the cell-based type VI secretion systems (T6SSs) as well as extracellular CISs (eCISs). The eCISs comprise the R-tailocins produced by various bacterial species as well as related phage tail-like structures such as the antifeeding prophages (Afps) of Serratia entomophila, the Photorhabdus virulence cassettes (PVCs), and the metamorphosis-associated contractile structures (MACs) of Pseudoalteromonas luteoviolacea. These contractile structures are released into the extracellular environment upon suicidal lysis of the producer cell and play important roles in bacterial ecology and evolution. In this review, we specifically portray the eCISs with a focus on the R-tailocins, sketch the history of their discovery and provide insights into their evolution within the bacterial host, their structures and how they are assembled and released. We then highlight ecological and evolutionary roles of eCISs and conceptualize how they can influence and shape bacterial communities. Finally, we point to their potential for biotechnological applications in medicine and agriculture.

Microfluidic Evolution-On-A-Chip Reveals New Mutations that Cause Antibiotic Resistance

Microfluidic devices can mimic naturally occurring microenvironments and create microbial population heterogeneities ranging from planktonic cells to biofilm states. The exposure of such populations to spatially organized stress gradients can promote their adaptation into complex phenotypes, which are otherwise difficult to achieve with conventional experimental setups. Here a microfluidic chip that employs precise chemical gradients in consecutive microcompartments to perform microbial adaptive laboratory evolution (ALE), a key tool to study evolution in fundamental and applied contexts is described. In the chip developed here, microbial cells can be exposed to a defined profile of stressors such as antibiotics. By modulating this profile, stress adaptation in the chip through resistance or persistence can be specifically controlled. Importantly, chip-based ALE leads to the discovery of previously unknown mutations in Escherichia coli that confer resistance to nalidixic acid. The microfluidic device presented here can enhance the occurrence of mutations employing defined micro-environmental conditions to generate data to better understand the parameters that influence the mechanisms of antibiotic resistance.

Adapting the engine to the fuel: mutator populations can reduce the mutational load by reorganizing their genome structure

Background

Mutators are common in bacterial populations, both in natural isolates and in the lab. The fate of these lineages, which mutation rate is increased up to 100 ×, has long been studied using population genetics models, showing that they can spread in a population following an environmental change. However in stable conditions, they suffer from the increased mutational load, hence being overcome by non-mutators. However, these results don’t take into account the fact that an elevated mutation rate can impact the genetic structure, hence changing the sensitivity of the population to mutations. Here we used Aevol, an in silico experimental evolution platform in which genomic structures are free to evolve, in order to study the fate of mutator populations evolving for a long time in constant conditions.

Results

Starting from wild-types that were pre-evolved for 300,000 generations, we let 100 mutator populations (point mutation rate ×100) evolve for 100,000 further generations in constant conditions. As expected all populations initially undergo a fitness loss. However, after that the mutator populations started to recover. Most populations ultimately recovered their ancestors fitness, and a significant fraction became even fitter than the non-mutator control clones that evolved in parallel. By analyzing the genomes of the mutators, we show that the fitness recovery is due to two mechanisms: i. an increase in robustness through compaction of the coding part of the mutator genomes, ii. an increase of the selection coefficient that decreases the mean-fitness of the population. Strikingly the latter is due to the accumulation of non-coding sequences in the mutators genomes.

Conclusion

Our results show that the mutational burden that is classically thought to be associated with mutator phenotype is escapable. On the long run mutators adapted their genomes and reshaped the distribution of mutation effects. Therewith the lineage is able to recover fitness even though the population still suffers the elevated mutation rate. Overall these results change our view of mutator dynamics: by being able to reduce the deleterious effect of the elevated mutation rate, mutator populations may be able to last for a very long time; A situation commonly observed in nature.

Genetically distinct lineages of Salmonella Typhimurium ST313 and ST19 are present in Brazil

In sub-Saharan Africa, two genetically distinct lineages of multi-drug resistant non-typhoidal Salmonella (NTS) serovar Typhimurium sequence type 313 (ST313) are known to cause invasive disease among people. S. Typhimurium ST313 has evolved to become more human-adapted and is commonly isolated from systemic sites (eg., blood) from febrile patients in sub-Saharan Africa. Epidemiological studies indicate that S. Typhimurium is frequently isolated from systemic sites from human patients in Brazil, however, it is currently unknown if this pathogen has also evolved to become more invasive and human-adapted in this country. Here we determined genotypic and phenotypic divergence among clinical S. Typhimurium strains isolated from systemic and non-systemic sites from human patients in Brazil. We report that a subset (8/38, 20%) of epidemiologically diverse human clinical strains of S. Typhimurium recovered from systemic sites in Brazil show significantly higher intra-macrophage survival, indicating that this subset is likely more invasive. Using the whole genome sequencing and phylogenetic approaches, we identified S. Typhimurium ST313-lineage in Brazil that is genetically and phenotypically distinct from the known African ST313-lineages. We also report the identification of S. Typhimurium ST19-lineage in Brazil that is evolving similar to ST313 lineages from Africa but is genetically and phenotypically distinct from ST19-lineage commonly associated with the gastrointestinal disease worldwide. The identification of new S. Typhimurium ST313 and ST19 lineages responsible for human illnesses in Brazil warrants further epidemiological investigations to determine the incidence and spread of a genetically divergent population of this important human pathogen.

Key issues review: evolution on rugged adaptive landscapes

Adaptive landscapes represent a mapping between genotype and fitness. Rugged adaptive landscapes contain two or more adaptive peaks: allele combinations with higher fitness than any of their neighbors in the genetic space. How do populations evolve on such rugged landscapes? Evolutionary biologists have struggled with this question since it was first introduced in the 1930s by Sewall Wright. Discoveries in the fields of genetics and biochemistry inspired various mathematical models of adaptive landscapes. The development of landscape models led to numerous theoretical studies analyzing evolution on rugged landscapes under different biological conditions. The large body of theoretical work suggests that adaptive landscapes are major determinants of the progress and outcome of evolutionary processes. Recent technological advances in molecular biology and microbiology allow experimenters to measure adaptive values of large sets of allele combinations and construct empirical adaptive landscapes for the first time. Such empirical landscapes have already been generated in bacteria, yeast, viruses, and fungi, and are contributing to new insights about evolution on adaptive landscapes. In this Key Issues Review we will: (i) introduce the concept of adaptive landscapes; (ii) review the major theoretical studies of evolution on rugged landscapes; (iii) review some of the recently obtained empirical adaptive landscapes; (iv) discuss recent mathematical and statistical analyses motivated by empirical adaptive landscapes, as well as provide the reader with instructions and source code to implement simulations of evolution on adaptive landscapes; and (v) discuss possible future directions for this exciting field.

Errors in mutagenesis and the benefit of cell-to-cell signalling in the evolution of stress-induced mutagenesis

Stress-induced mutagenesis is a widely observed phenomenon. Theoretical models have shown that stress-induced mutagenesis can be favoured by natural selection due to the beneficial mutations it generates. These models, however, assumed an error-free regulation of mutation rate in response to stress. Here, we explore the effects of errors in the regulation of mutagenesis on the evolution of stress-induced mutagenesis, and consider the role of cell-to-cell signalling. Using theoretical models, we show (i) that stress-induced mutagenesis can be disadvantageous if errors are common; and (ii) that cell-to-cell signalling can allow stress-induced mutagenesis to be favoured by selection even when error rates are high. We conclude that cell-to-cell signalling can facilitate the evolution of stress-induced mutagenesis in microbes through second-order selection.