Evolution of penicillin-binding protein 2 concentration and cell shape during a long-term experiment with Escherichia coli

Fitness benefits of a synonymous substitution in an ancient EF-Tu gene depend on the genetic background

Synonymous mutations are changes to DNA sequence, which occur within translated genes but which do not affect the protein sequence. Although often referred to as silent mutations, evidence suggests that synonymous mutations can affect gene expression, mRNA stability, and even translation efficiency. A collection of both experimental and bioinformatic data has shown that synonymous mutations can impact cell phenotype, yet less is known about the molecular mechanisms and potential of beneficial or adaptive effects of such changes within evolved populations. Here, we report a beneficial synonymous mutation acquired via experimental evolution in an essential gene variant encoding the translation elongation factor protein EF-Tu. We demonstrate that this particular synonymous mutation increases EF-Tu mRNA and protein levels as well as global polysome abundance on RNA transcripts. Although presence of the synonymous mutation is clearly causative of such changes, we also demonstrate that fitness benefits are highly contingent on other potentiating mutations present within the genetic background in which the mutation arose. Our results underscore the importance of beneficial synonymous mutations, especially those that affect levels of proteins that are key for cellular processes.IMPORTANCEThis study explores the degree to which synonymous mutations in essential genes can influence adaptation in bacteria. An experimental system whereby an Escherichia coli strain harboring an engineered translation protein elongation factor-Tu (EF-Tu) was subjected to laboratory evolution. We find that a synonymous mutation acquired on the gene encoding for EF-Tu is conditionally beneficial for bacterial fitness. Our findings provide insight into the importance of the genetic background when a synonymous substitution is favored by natural selection and how such changes have the potential to impact evolution when critical cellular processes are involved.

Linking genotypic and phenotypic changes in the E. coli long-term evolution experiment using metabolomics

Changes in an organism's environment, genome, or gene expression patterns can lead to changes in its metabolism. The metabolic phenotype can be under selection and contributes to adaptation. However, the networked and convoluted nature of an organism's metabolism makes relating mutations, metabolic changes, and effects on fitness challenging. To overcome this challenge, we use the long-term evolution experiment (LTEE) with E. coli as a model to understand how mutations can eventually affect metabolism and perhaps fitness. We used mass spectrometry to broadly survey the metabolomes of the ancestral strains and all 12 evolved lines. We combined this metabolic data with mutation and expression data to suggest how mutations that alter specific reaction pathways, such as the biosynthesis of nicotinamide adenine dinucleotide, might increase fitness in the system. Our work provides a better understanding of how mutations might affect fitness through the metabolic changes in the LTEE and thus provides a major step in developing a complete genotype-phenotype map for this experimental system.

A beneficial synonymous substitution in EF-Tu is contingent on genetic background

Synonymous mutations are changes to DNA sequence that occur within translated genes but which do not affect the protein sequence. Although often referred to as silent mutations, evidence suggests that synonymous mutations can affect gene expression, mRNA stability, and even translation efficiency. A collection of both experimental and bioinformatic data has shown that synonymous mutations can impact cell phenotype, yet less is known about the molecular mechanisms and potential of beneficial or adaptive effects of such changes within evolved populations. Here, we report a beneficial synonymous mutation acquired via experimental evolution in an essential gene variant encoding the translation Elongation Factor protein EF-Tu. We demonstrate that this particular synonymous mutation increases EF-Tu mRNA and protein levels, as well as the polysome abundance on global transcripts. Although presence of the synonymous mutation is clearly causative of such changes, we also demonstrate that fitness benefits are highly contingent on other potentiating mutations present within the genetic background in which the mutation arose. Our results underscore the importance of beneficial synonymous mutations, especially those that affect levels of proteins that are key for cellular processes.

Penicillin-Binding Protein 5/6 Acting as a Decoy Target in Pseudomonas aeruginosa Identified by Whole-Cell Receptor Binding and Quantitative Systems Pharmacology

The β-lactam antibiotics have been successfully used for decades to combat susceptible Pseudomonas aeruginosa, which has a notoriously difficult to penetrate outer membrane (OM). However, there is a dearth of data on target site penetration and covalent binding of penicillin-binding proteins (PBP) for β-lactams and β-lactamase inhibitors in intact bacteria. We aimed to determine the time course of PBP binding in intact and lysed cells and estimate the target site penetration and PBP access for 15 compounds in P. aeruginosa PAO1. All β-lactams (at 2 × MIC) considerably bound PBPs 1 to 4 in lysed bacteria. However, PBP binding in intact bacteria was substantially attenuated for slow but not for rapid penetrating β-lactams. Imipenem yielded 1.5 ± 0.11 log10 killing at 1h compared to <0.5 log10 killing for all other drugs. Relative to imipenem, the rate of net influx and PBP access was ~ 2-fold slower for doripenem and meropenem, 7.6-fold for avibactam, 14-fold for ceftazidime, 45-fold for cefepime, 50-fold for sulbactam, 72-fold for ertapenem, ~ 249-fold for piperacillin and aztreonam, 358-fold for tazobactam, ~547-fold for carbenicillin and ticarcillin, and 1,019-fold for cefoxitin. At 2 × MIC, the extent of PBP5/6 binding was highly correlated (r2 = 0.96) with the rate of net influx and PBP access, suggesting that PBP5/6 acted as a decoy target that should be avoided by slowly penetrating, future β-lactams. This first comprehensive assessment of the time course of PBP binding in intact and lysed P. aeruginosa explained why only imipenem killed rapidly. The developed novel covalent binding assay in intact bacteria accounts for all expressed resistance mechanisms.

Identifying Targets of Selection in Laboratory Evolution Experiments

Adaptive evolution navigates a balance between chance and determinism. The stochastic processes of mutation and drift generate phenotypic variation; however, once mutations reach an appreciable frequency in the population, their fate is governed by the deterministic action of selection, enriching for favorable genotypes and purging the less-favorable ones. The net result is that replicate populations will traverse similar-but not identical-pathways to higher fitness. This parallelism in evolutionary outcomes can be leveraged to identify the genes and pathways under selection. However, distinguishing between beneficial and neutral mutations is challenging because many beneficial mutations will be lost due to drift and clonal interference, and many neutral (and even deleterious) mutations will fix by hitchhiking. Here, we review the best practices that our laboratory uses to identify genetic targets of selection from next-generation sequencing data of evolved yeast populations. The general principles for identifying the mutations driving adaptation will apply more broadly.

Linking genotypic and phenotypic changes in the E. coli Long-Term Evolution Experiment using metabolomics

Changes in an organism's environment, genome, or gene expression patterns can lead to changes in its metabolism. The metabolic phenotype can be under selection and contributes to adaptation. However, the networked and convoluted nature of an organism's metabolism makes relating mutations, metabolic changes, and effects on fitness challenging. To overcome this challenge, we use the Long-Term Evolution Experiment (LTEE) with E. coli as a model to understand how mutations can eventually affect metabolism and perhaps fitness. We used mass-spectrometry to broadly survey the metabolomes of the ancestral strains and all 12 evolved lines. We combined this metabolic data with mutation and expression data to suggest how mutations that alter specific reaction pathways, such as the biosynthesis of nicotinamide adenine dinucleotide, might increase fitness in the system. Our work provides a better understanding of how mutations might affect fitness through the metabolic changes in the LTEE and thus provides a major step in developing a complete genotype-phenotype map for this experimental system.

Extracellular Vesicles from 50,000 Generation Clones of the Escherichia coli Long-Term Evolution Experiment

Extracellular vesicles (EVs) are critical elements of cell-cell communication. Here, we characterized the outer membrane vesicles (OMVs) released by specific clones of Escherichia coli isolated from the Long-Term Evolution Experiment after 50,000 generations (50K) of adaptation to glucose minimal medium. Compared with their ancestor, the evolved clones produce small OMVs but also larger ones which display variable amounts of both OmpA and LPS. Tracking ancestral, fluorescently labelled OMVs revealed that they fuse with both ancestral- and 50K-evolved cells, albeit in different proportions. We quantified that less than 2% of the cells from one 50K-evolved clone acquired the fluorescence delivered by OMVs from the ancestral strain but that one cell concomitantly fuses with several OMVs. Globally, our results showed that OMV production in E. coli is a phenotype that varies along bacterial evolution and question the contribution of OMVs-mediated interactions in bacterial adaptation.

The landscape of transcriptional and translational changes over 22 years of bacterial adaptation

Organisms can adapt to an environment by taking multiple mutational paths. This redundancy at the genetic level, where many mutations have similar phenotypic and fitness effects, can make untangling the molecular mechanisms of complex adaptations difficult. Here, we use the Escherichia coli long-term evolution experiment (LTEE) as a model to address this challenge. To understand how different genomic changes could lead to parallel fitness gains, we characterize the landscape of transcriptional and translational changes across 12 replicate populations evolving in parallel for 50,000 generations. By quantifying absolute changes in mRNA abundances, we show that not only do all evolved lines have more mRNAs but that this increase in mRNA abundance scales with cell size. We also find that despite few shared mutations at the genetic level, clones from replicate populations in the LTEE are remarkably similar in their gene expression patterns at both the transcriptional and translational levels. Furthermore, we show that the majority of the expression changes are due to changes at the transcriptional level with very few translational changes. Finally, we show how mutations in transcriptional regulators lead to consistent and parallel changes in the expression levels of downstream genes. These results deepen our understanding of the molecular mechanisms underlying complex adaptations and provide insights into the repeatability of evolution.

Role of Penicillin-Binding Protein 1b in the Biofilm Inhibitory Efficacy of Ceftazidime Against Escherichia coli

Penicillin-binding proteins (PBPs) play an important role in bacterial biofilm formation and are the targets of β-lactam antibiotics. This study aimed to investigate the effect of the β-lactam antibiotic ceftazidime (CAZ) at subminimal inhibitory concentration (sub-MIC) on the biofilm formation of Escherichia coli by targeting PBPs. In this study, PBP1a (encoded by mrcA), PBP1b (encoded by mrcB) and PBP3 (encoded by ftsI), which have high affinity for CAZ, were deleted from the E. coli strain. The mrcB mutant showed lower adhesion, biofilm formation and swimming motility, whereas the knockout of mrcA or ftsI had no obvious influence on the biofilm-associated indicators mentioned above. After treatment with sub-MIC of CAZ, the adhesion, biofilm formation and swimming motility of the mrcB-mutant strain were not different or were slightly reduced compared with those of the untreated group. However, sub-MIC of CAZ still significantly inhibited these biofilm-associated indicators in mrcA- and ftsI-mutant strains. In addition, consistent with the bacterial motility results, the deletion of the mrcB gene reduced the flagellar numbers and the expression of flagellar structural genes, but flagellum-related indicators in the mrcB-mutant strain treated with CAZ were similar to those in the untreated group. Bioinformatic analysis showed that CAZ binds to Lys287, Lys274, Glu281, and Arg286 in PBP1b. Taken together, these results suggest that CAZ reduced flagellar synthesis and bacterial motility by binding with PBP1b and thereby inhibited the adhesion and biofilm formation of E. coli.

Advantages of laboratory natural selection in the applied sciences

In the past three decades, laboratory natural selection has become a widely used technique in biological research. Most studies which have utilized this technique are in the realm of basic science, often testing hypotheses related to mechanisms of evolutionary change or ecological dynamics. While laboratory natural selection is currently utilized heavily in this setting, there is a significant gap with its usage in applied studies, especially when compared to the other selection experiment methodologies like artificial selection and directed evolution. This is despite avenues of research in the applied sciences which seem well suited to laboratory natural selection. In this review, we place laboratory natural selection in context with other selection experiments, identify the characteristics which make it well suited for particular kinds of applied research and briefly cover key examples of the usefulness of selection experiments within applied science. Finally, we identify three promising areas of inquiry for laboratory natural selection in the applied sciences: bioremediation technology, identifying mechanisms of drug resistance and optimizing biofuel production. Although laboratory natural selection is currently less utilized in applied science when compared to basic research, the method has immense promise in the field moving forward.

Bottom-up controls, ecological revolutions and diversification in the oceans through time

Animals originated in the oceans and evolved there for hundreds of millions of years before adapting to terrestrial environments. Today, oceans cover more than two-thirds of Earth and generate as much primary production as land. The path from the first macrobiota to modern marine biodiversity involved parallel increases in terrestrial nutrient input, marine primary production, species' abundance, metabolic rates, ecotypic diversity and taxonomic diversity. Bottom-up theories of ecosystem cascades arrange these changes in a causal sequence. At the base of marine food webs, nutrient fluxes and atmosphere-ocean chemistry interact with phytoplankton to regulate production. First-order consumers (e.g., zooplankton) might propagate changes in quantity and quality of phytoplankton to changes in abundance and diversity of larger predators (e.g., nekton). However, many uncertainties remain about the mechanisms and effect size of bottom-up control, particularly in oceans across the entire history of animal life. Here, we review modern and fossil evidence for hypothesized bottom-up pathways, and we assess the ramifications of these processes for four key intervals in marine ecosystems: the Ediacaran-Cambrian (635-485 million years ago), the Ordovician (485-444 million years ago), the Devonian (419-359 million years ago) and the Mesozoic (252-66 million years ago). We advocate for a clear articulation of bottom-up hypotheses to better understand causal relationships and proposed effects, combined with additional ecological experiments, paleontological documentation, isotope geochemistry and geophysical reconstructions. How small-scale ecological change transitions into large-scale evolutionary change remains an outstanding question for empirical and theoretical research.

Quantifying rapid bacterial evolution and transmission within the mouse intestine

Due to limitations on high-resolution strain tracking, selection dynamics during gut microbiota colonization and transmission between hosts remain mostly mysterious. Here, we introduced hundreds of barcoded Escherichia coli strains into germ-free mice and quantified strain-level dynamics and metagenomic changes. Mutations in genes involved in motility and metabolite utilization are reproducibly selected within days. Even with rapid selection, coprophagy enforced similar barcode distributions across co-housed mice. Whole-genome sequencing of hundreds of isolates revealed linked alleles that demonstrate between-host transmission. A population-genetics model predicts substantial fitness advantages for certain mutants and that migration accounted for ∼10% of the resident microbiota each day. Treatment with ciprofloxacin suggests interplay between selection and transmission. While initial colonization was mostly uniform, in two mice a bottleneck reduced diversity and selected for ciprofloxacin resistance in the absence of drug. These findings highlight the interplay between environmental transmission and rapid, deterministic selection during evolution of the intestinal microbiota.

Seven Years at High Salinity-Experimental Evolution of the Extremely Halotolerant Black Yeast Hortaea werneckii

The experimental evolution of microorganisms exposed to extreme conditions can provide insight into cellular adaptation to stress. Typically, stress-sensitive species are exposed to stress over many generations and then examined for improvements in their stress tolerance. In contrast, when starting with an already stress-tolerant progenitor there may be less room for further improvement, it may still be able to tweak its cellular machinery to increase extremotolerance, perhaps at the cost of poorer performance under non-extreme conditions. To investigate these possibilities, a strain of extremely halotolerant black yeast Hortaea werneckii was grown for over seven years through at least 800 generations in a medium containing 4.3 M NaCl. Although this salinity is well above the optimum (0.8–1.7 M) for the species, the growth rate of the evolved H. werneckii did not change in the absence of salt or at high concentrations of NaCl, KCl, sorbitol, or glycerol. Other phenotypic traits did change during the course of the experimental evolution, including fewer multicellular chains in the evolved strains, significantly narrower cells, increased resistance to caspofungin, and altered melanisation. Whole-genome sequencing revealed the occurrence of multiple aneuploidies during the experimental evolution of the otherwise diploid H. werneckii. A significant overrepresentation of several gene groups was observed in aneuploid regions. Taken together, these changes suggest that long-term growth at extreme salinity led to alterations in cell wall and morphology, signalling pathways, and the pentose phosphate cycle. Although there is currently limited evidence for the adaptive value of these changes, they offer promising starting points for future studies of fungal halotolerance.

Salt Tolerance Mechanism of the Rhizosphere Bacterium JZ-GX1 and Its Effects on Tomato Seed Germination and Seedling Growth

Salinity is one of the strongest abiotic factors in nature and has harmful effects on plants and microorganisms. In recent years, the degree of soil salinization has become an increasingly serious problem, and the use of plant growth-promoting rhizobacteria has become an option to improve the stress resistance of plants. In the present study, the salt tolerance mechanism of the rhizosphere bacterium Rahnella aquatilis JZ-GX1 was investigated through scanning electron microscopy observations and analysis of growth characteristics, compatible solutes, ion distribution and gene expression. In addition, the effect of JZ-GX1 on plant germination and seedling growth was preliminarily assessed through germination experiments. R. aquatilis JZ-GX1 was tolerant to 0-9% NaCl and grew well at 3%. Strain JZ-GX1 promotes salt tolerance by stimulating the production of exopolysaccharides, and can secrete 60.6983 mg/L of exopolysaccharides under the high salt concentration of 9%. Furthermore, the accumulation of the compatible solute trehalose in cells as the NaCl concentration increased was shown to be the primary mechanism of resistance to high salt concentrations in JZ-GX1. Strain JZ-GX1 could still produce indole-3-acetic acid (IAA) and siderophores and dissolve inorganic phosphorus under salt stress, characteristics that promote the ability of plants to resist salt stress. When the salt concentration was 100 mmol/L, strain JZ-GX1 significantly improved the germination rate, germination potential, fresh weight, primary root length and stem length of tomato seeds by 10.52, 125.56, 50.00, 218.18, and 144.64%, respectively. Therefore, R. aquatilis JZ-GX1 is a moderately halophilic bacterium with good growth-promoting function that has potential for future development as a microbial agent and use in saline-alkali land resources.

Changes in Cell Size and Shape during 50,000 Generations of Experimental Evolution with Escherichia coli

Bacteria adopt a wide variety of sizes and shapes, with many species exhibiting stereotypical morphologies. How morphology changes, and over what timescales, is less clear. Previous work examining cell morphology in an experiment with Escherichia coli showed that populations evolved larger cells and, in some cases, cells that were less rod-like. That experiment has now run for over two more decades. Meanwhile, genome sequence data are available for these populations, and new computational methods enable high-throughput microscopic analyses. In this study, we measured stationary-phase cell volumes for the ancestor and 12 populations at 2,000, 10,000, and 50,000 generations, including measurements during exponential growth at the last time point. We measured the distribution of cell volumes for each sample using a Coulter counter and microscopy, the latter of which also provided data on cell shape. Our data confirm the trend toward larger cells while also revealing substantial variation in size and shape across replicate populations. Most populations first evolved wider cells but later reverted to the ancestral length-to-width ratio. All but one population evolved mutations in rod shape maintenance genes. We also observed many ghost-like cells in the only population that evolved the novel ability to grow on citrate, supporting the hypothesis that this lineage struggles with maintaining balanced growth. Lastly, we show that cell size and fitness remain correlated across 50,000 generations. Our results suggest that larger cells are beneficial in the experimental environment, while the reversion toward ancestral length-to-width ratios suggests partial compensation for the less favorable surface area-to-volume ratios of the evolved cells.IMPORTANCE Bacteria exhibit great morphological diversity, yet we have only a limited understanding of how their cell sizes and shapes evolve and of how these features affect organismal fitness. This knowledge gap reflects, in part, the paucity of the fossil record for bacteria. In this study, we revived and analyzed samples extending over 50,000 generations from 12 populations of experimentally evolving Escherichia coli to investigate the relation between cell size, shape, and fitness. Using this "frozen fossil record," we show that all 12 populations evolved larger cells concomitant with increased fitness, with substantial heterogeneity in cell size and shape across the replicate lines. Our work demonstrates that cell morphology can readily evolve and diversify, even among populations living in identical environments.

Evolution of Pseudomonas aeruginosa toward higher fitness under standard laboratory conditions

Identifying genetic factors that contribute to the evolution of adaptive phenotypes in pathogenic bacteria is key to understanding the establishment of infectious diseases. In this study, we performed mutation accumulation experiments to record the frequency of mutations and their effect on fitness in hypermutator strains of the environmental bacterium Pseudomonas aeruginosa in comparison to the host-niche-adapted Salmonella enterica. We demonstrate that P. aeruginosa, but not S. enterica, hypermutators evolve toward higher fitness under planktonic conditions. Adaptation to increased growth performance was accompanied by a reversible perturbing of the local genetic context of membrane and cell wall biosynthesis genes. Furthermore, we observed a fine-tuning of complex regulatory circuits involving multiple di-guanylate modulating enzymes that regulate the transition between fast growing planktonic and sessile biofilm-associated lifestyles. The redundancy and local specificity of the di-guanylate signaling pathways seem to allow a convergent shift toward increased growth performance across niche-adapted clonal P. aeruginosa lineages, which is accompanied by a pronounced heterogeneity of their motility, virulence, and biofilm phenotypes.

Insertion-sequence-mediated mutations both promote and constrain evolvability during a long-term experiment with bacteria

Insertion sequences (IS) are ubiquitous bacterial mobile genetic elements, and the mutations they cause can be deleterious, neutral, or beneficial. The long-term dynamics of IS elements and their effects on bacteria are poorly understood, including whether they are primarily genomic parasites or important drivers of adaptation by natural selection. Here, we investigate the dynamics of IS elements and their contribution to genomic evolution and fitness during a long-term experiment with Escherichia coli. IS elements account for ~35% of the mutations that reached high frequency through 50,000 generations in those populations that retained the ancestral point-mutation rate. In mutator populations, IS-mediated mutations are only half as frequent in absolute numbers. In one population, an exceptionally high ~8-fold increase in IS150 copy number is associated with the beneficial effects of early insertion mutations; however, this expansion later slowed down owing to reduced IS150 activity. This population also achieves the lowest fitness, suggesting that some avenues for further adaptation are precluded by the IS150-mediated mutations. More generally, across all populations, we find that higher IS activity becomes detrimental to adaptation over evolutionary time. Therefore, IS-mediated mutations can both promote and constrain evolvability.

Insertion sequences (IS) are common mobile genetic elements in bacteria, but their effects on bacterial evolution are not well understood. Here, Consuegra and colleagues investigate the dynamics and fitness consequences of IS elements in E. coli over 50,000 generations.

Genetics of Adaptation of the Ascomycetous Fungus Podospora anserina to Submerged Cultivation

Podospora anserina is a model ascomycetous fungus which shows pronounced phenotypic senescence when grown on solid medium but possesses unlimited lifespan under submerged cultivation. In order to study the genetic aspects of adaptation of P. anserina to submerged cultivation, we initiated a long-term evolution experiment. In the course of the first 4 years of the experiment, 125 single-nucleotide substitutions and 23 short indels were fixed in eight independently evolving populations. Six proteins that affect fungal growth and development evolved in more than one population; in particular, in the G-protein alpha subunit FadA, new alleles fixed in seven out of eight experimental populations, and these fixations affected just four amino acid sites, which is an unprecedented level of parallelism in experimental evolution. Parallel evolution at the level of genes and pathways, an excess of nonsense and missense substitutions, and an elevated conservation of proteins and their sites where the changes occurred suggest that many of the observed fixations were adaptive and driven by positive selection.

Experimental Design, Population Dynamics, and Diversity in Microbial Experimental Evolution

In experimental evolution, laboratory-controlled conditions select for the adaptation of species, which can be monitored in real time. Despite the current popularity of such experiments, nature's most pervasive biological force was long believed to be observable only on time scales that transcend a researcher's life-span, and studying evolution by natural selection was therefore carried out solely by comparative means. Eventually, microorganisms' propensity for fast evolutionary changes proved us wrong, displaying strong evolutionary adaptations over a limited time, nowadays massively exploited in laboratory evolution experiments. Here, we formulate a guide to experimental evolution with microorganisms, explaining experimental design and discussing evolutionary dynamics and outcomes and how it is used to assess ecoevolutionary theories, improve industrially important traits, and untangle complex phenotypes. Specifically, we give a comprehensive overview of the setups used in experimental evolution. Additionally, we address population dynamics and genetic or phenotypic diversity during evolution experiments and expand upon contributing factors, such as epistasis and the consequences of (a)sexual reproduction. Dynamics and outcomes of evolution are most profoundly affected by the spatiotemporal nature of the selective environment, where changing environments might lead to generalists and structured environments could foster diversity, aided by, for example, clonal interference and negative frequency-dependent selection. We conclude with future perspectives, with an emphasis on possibilities offered by fast-paced technological progress. This work is meant to serve as an introduction to those new to the field of experimental evolution, as a guide to the budding experimentalist, and as a reference work to the seasoned expert.

Biosynthesis of selenium nanoparticles and effects of selenite, selenate, and selenomethionine on cell growth and morphology in Rahnella aquatilis HX2

Rahnella aquatilis HX2 (proteobacteria) shows tolerance to selenium (Se). The minimum inhibitory concentrations of selenomethionine (Se-Met), selenite [Se (IV)], and selenate [Se (VI)] to HX2 are 4.0, 85.0, and 590.0 mM, respectively. HX2 shows the ability to reduce Se (IV) and Se (VI) to elemental Se nanoparticles (SeNPs). The maximum production of SeNPs by HX2 strain is 1.99 and 3.85 mM in Luria-Bertani (LB) broth with 5 mM Se (IV) and 10 mM Se (VI), respectively. The morphology of SeNPs and cells were observed by transmission electron microscope, environmental scanning electron microscope, and selected area electric diffraction detector. Spherical SeNPs with amorphous structure were found in the cytoplasm, membrane, and exterior of cells. Morphological variations of the cell membrane were further confirmed by the release of cellular materials absorbed at 260 nm. Flagella were inhibited and cell sizes were 1.8-, 1.6-, and 1.2-fold increases with the Se-Met, Se (VI), and Se (IV) treatments, respectively. The real-time quantitative PCR analysis indicated that some of the genes controlling Se metabolism or cell morphology, including cysA, cysP, rodA, ZntA, and ada, were significantly upregulated, while grxA, fliO, flgE, and fliC genes were significantly downregulated in those Se treatments. This study provided novel valuable information concerning the cell morphology along with biological synthesis process of SeNPs in R. aquatilis and demonstrated that the strain HX2 could be applied in both biosynthesis of SeNPs and in management of environmental Se pollution.

Thinking big: the tunability of bacterial cell size

The determination of cell size is a fundamental challenge for all living organisms. In a given growth condition, cell size for a particular bacterial species typically falls within a narrow distribution. Nonetheless, size can vary enormously across species, and the size of a single bacterium can even vary substantially across growth conditions. Recent phenomenological studies have revived classic interest in how cells maintain their size and how they adjust their size with changes in growth rate. However, the mechanisms by which cells establish a particular size are relatively enigmatic. Here, we review existing knowledge on how size in rod-shaped bacteria is shaped by nutrient, mechanical, and genetic factors. We also examine obstacles to accurate size measurement and recent technologies that help to overcome these hurdles. Finally, we discuss the relevance of cell size to bacterial physiology.

Bacterial Cell Mechanics

Cellular mechanical properties play an integral role in bacterial survival and adaptation. Historically, the bacterial cell wall and, in particular, the layer of polymeric material called the peptidoglycan were the elements to which cell mechanics could be primarily attributed. Disrupting the biochemical machinery that assembles the peptidoglycan (e.g., using the β-lactam family of antibiotics) alters the structure of this material, leads to mechanical defects, and results in cell lysis. Decades after the discovery of peptidoglycan-synthesizing enzymes, the mechanisms that underlie their positioning and regulation are still not entirely understood. In addition, recent evidence suggests a diverse group of other biochemical elements influence bacterial cell mechanics, may be regulated by new cellular mechanisms, and may be triggered in different environmental contexts to enable cell adaptation and survival. This review summarizes the contributions that different biomolecular components of the cell wall (e.g., lipopolysaccharides, wall and lipoteichoic acids, lipid bilayers, peptidoglycan, and proteins) make to Gram-negative and Gram-positive bacterial cell mechanics. We discuss the contribution of individual proteins and macromolecular complexes in cell mechanics and the tools that make it possible to quantitatively decipher the biochemical machinery that contributes to bacterial cell mechanics. Advances in this area may provide insight into new biology and influence the development of antibacterial chemotherapies.

Transposable Elements Mediate Adaptive Debilitation of Flagella in Experimental Escherichia coli Populations

Although insertion sequence (IS) elements are generally considered genomic parasites, they can mediate adaptive genetic changes in bacterial genomes. We discovered that among 12 laboratory-evolved Escherichia coli populations, three had experienced at least six different IS1-mediated deletions of flagellar genes. These deletions all involved the master flagellar regulator flhDC, and as such completely incapacitate motility. Two lines of evidence strongly suggest that these deletions were adaptive in our evolution experiment: (1) parallel evolution in three independent populations is highly unlikely just by chance, and (2) one of these deletion mutations swept to fixation within ~1000 generations, which is over two million times faster than expected if this deletion was instead selectively neutral and thus evolving by genetic drift. Because flagella are energetically expensive to synthesize and operate, we suspect that debilitating their construction conferred a fitness advantage in our well-stirred evolution experiment. These findings underscore the important role that IS elements can play in mediating adaptive loss-of-function mutations in bacteria.

Convergence and Divergence in a Long-Term Experiment with Bacteria

Suitably designed experiments offer the possibility of quantifying evolutionary convergence because the fraction of replicate populations that converge is known. Here I review an experiment with Escherichia coli, in which 12 populations were founded from the same ancestral strain and have evolved for almost 30 years and more than 65,000 generations under the same conditions. The tension between divergence and convergence has been a major focus of this experiment. I summarize analyses of competitive fitness, correlated responses to different environments, cell morphology, the capacity to use a previously untapped resource, mutation rates, genomic changes, and within-population polymorphisms. These analyses reveal convergence, divergence, and often a complicated mix thereof. Complications include concordance in the direction of evolutionary change with sustained quantitative variation among populations, and the potential for a given trait to exhibit divergence on one timescale and convergence on another. Despite these complications, which also occur in nature, experiments provide a powerful way to study evolutionary convergence based on analyzing replicate lineages that experience the same environment.

Specificity of genome evolution in experimental populations of Escherichia coli evolved at different temperatures

Isolated populations derived from a common ancestor are expected to diverge genetically and phenotypically as they adapt to different local environments. To examine this process, 30 populations of Escherichia coli were evolved for 2,000 generations, with six in each of five different thermal regimes: constant 20 °C, 32 °C, 37 °C, 42 °C, and daily alternations between 32 °C and 42 °C. Here, we sequenced the genomes of one endpoint clone from each population to test whether the history of adaptation in different thermal regimes was evident at the genomic level. The evolved strains had accumulated ∼5.3 mutations, on average, and exhibited distinct signatures of adaptation to the different environments. On average, two strains that evolved under the same regime exhibited ∼17% overlap in which genes were mutated, whereas pairs that evolved under different conditions shared only ∼4%. For example, all six strains evolved at 32 °C had mutations in nadR, whereas none of the other 24 strains did. However, a population evolved at 37 °C for an additional 18,000 generations eventually accumulated mutations in the signature genes strongly associated with adaptation to the other temperature regimes. Two mutations that arose in one temperature treatment tended to be beneficial when tested in the others, although less so than in the regime in which they evolved. These findings demonstrate that genomic signatures of adaptation can be highly specific, even with respect to subtle environmental differences, but that this imprint may become obscured over longer timescales as populations continue to change and adapt to the shared features of their environments.

A case study in evolutionary contingency

Biological evolution is a fundamentally historical phenomenon in which intertwined stochastic and deterministic processes shape lineages with long, continuous histories that exist in a changing world that has a history of its own. The degree to which these characteristics render evolution historically contingent, and evolutionary outcomes thereby unpredictably sensitive to history has been the subject of considerable debate in recent decades. Microbial evolution experiments have proven among the most fruitful means of empirically investigating the issue of historical contingency in evolution. One such experiment is the Escherichia coli Long-Term Evolution Experiment (LTEE), in which twelve populations founded from the same clone of E. coli have evolved in parallel under identical conditions. Aerobic growth on citrate (Cit(+)), a novel trait for E. coli, evolved in one of these populations after more than 30,000 generations. Experimental replays of this population's evolution from various points in its history showed that the Cit(+) trait was historically contingent upon earlier mutations that potentiated the trait by rendering it mutationally accessible. Here I review this case of evolutionary contingency and discuss what it implies about the importance of historical contingency arising from the core processes of evolution.

Evolved plasmid-host interactions reduce plasmid interference cost

Antibiotic selection drives adaptation of antibiotic resistance plasmids to new bacterial hosts, but the molecular mechanisms are still poorly understood. We previously showed that a broad-host-range plasmid was poorly maintained in Shewanella oneidensis, but rapidly adapted through mutations in the replication initiation gene trfA1. Here we examined if these mutations reduced the fitness cost of TrfA1, and whether this was due to changes in interaction with the host's DNA helicase DnaB. The strains expressing evolved TrfA1 variants showed a higher growth rate than those expressing ancestral TrfA1. The evolved TrfA1 variants showed a lower affinity to the helicase than ancestral TrfA1 and were no longer able to activate the helicase at the oriV without host DnaA. Moreover, persistence of the ancestral plasmid was increased upon overexpression of DnaB. Finally, the evolved TrfA1 variants generated higher plasmid copy numbers than ancestral TrfA1. The findings suggest that ancestral plasmid instability can at least partly be explained by titration of DnaB by TrfA1. Thus under antibiotic selection resistance plasmids can adapt to a novel bacterial host through partial loss of function mutations that simultaneously increase plasmid copy number and decrease unfavorably high affinity to one of the hosts' essential proteins.

Nanofiber scaffolds influence organelle structure and function in bone marrow stromal cells

Recent work demonstrates that osteoprogenitor cell culture on nanofiber scaffolds can promote differentiation. This response may be driven by changes in cell morphology caused by the three-dimensional (3D) structure of nanofibers. We hypothesized that nanofiber effects on cell behavior may be mediated by changes in organelle structure and function. To test this hypothesis, human bone marrow stromal cells (hBMSCs) were cultured on poly(ε-caprolactone) (PCL) nanofibers scaffolds and on PCL flat spuncoat films. After 1 day-culture, hBMSCs were stained for actin, nucleus, mitochondria, and peroxisomes, and then imaged using 3D confocal microscopy. Imaging revealed that the hBMSC cell body (actin) and peroxisomal volume were reduced during culture on nanofibers. In addition, the nucleus and peroxisomes occupied a larger fraction of cell volume during culture on nanofibers than on films, suggesting enhancement of the nuclear and peroxisomal functional capacity. Organelles adopted morphologies with greater 3D-character on nanofibers, where the Z-Depth (a measure of cell thickness) was increased. Comparisons of organelle positions indicated that the nucleus, mitochondria, and peroxisomes were closer to the cell center (actin) for nanofibers, suggesting that nanofiber culture induced active organelle positioning. The smaller cell volume and more centralized organelle positioning would reduce the energy cost of inter-organelle vesicular transport during culture on nanofibers. Finally, hBMSC bioassay measurements (DNA, peroxidase, bioreductive potential, lactate, and adenosine triphosphate (ATP)) indicated that peroxidase activity may be enhanced during nanofiber culture. These results demonstrate that culture of hBMSCs on nanofibers caused changes in organelle structure and positioning, which may affect organelle functional capacity and transport. Published 2016. This article is a U.S. Government work and is in the public domain in the USA. J Biomed Mater Res Part B: Appl Biomater, 2016. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 105B: 989-1001, 2017.

Diverse phenotypic and genetic responses to short-term selection in evolving Escherichia coli populations

Beneficial mutations fuel adaptation by altering phenotypes that enhance the fit of organisms to their environment. However, the phenotypic effects of mutations often depend on ecological context, making the distribution of effects across multiple environments essential to understanding the true nature of beneficial mutations. Studies that address both the genetic basis and ecological consequences of adaptive mutations remain rare. Here, we characterize the direct and pleiotropic fitness effects of a collection of 21 first-step beneficial mutants derived from naïve and adapted genotypes used in a long-term experimental evolution of Escherichia coli. Whole-genome sequencing was able to identify the majority of beneficial mutations. In contrast to previous studies, we find diverse fitness effects of mutations selected in a simple environment and few cases of genetic parallelism. The pleiotropic effects of these mutations were predominantly positive but some mutants were highly antagonistic in alternative environments. Further, the fitness effects of mutations derived from the adapted genotypes were dramatically reduced in nearly all environments. These findings suggest that many beneficial variants are accessible from a single point on the fitness landscape, and the fixation of alternative beneficial mutations may have dramatic consequences for niche breadth reduction via metabolic erosion.

High-throughput, Highly Sensitive Analyses of Bacterial Morphogenesis Using Ultra Performance Liquid Chromatography

The bacterial cell wall is a network of glycan strands cross-linked by short peptides (peptidoglycan); it is responsible for the mechanical integrity of the cell and shape determination. Liquid chromatography can be used to measure the abundance of the muropeptide subunits composing the cell wall. Characteristics such as the degree of cross-linking and average glycan strand length are known to vary across species. However, a systematic comparison among strains of a given species has yet to be undertaken, making it difficult to assess the origins of variability in peptidoglycan composition. We present a protocol for muropeptide analysis using ultra performance liquid chromatography (UPLC) and demonstrate that UPLC achieves resolution comparable with that of HPLC while requiring orders of magnitude less injection volume and a fraction of the elution time. We also developed a software platform to automate the identification and quantification of chromatographic peaks, which we demonstrate has improved accuracy relative to other software. This combined experimental and computational methodology revealed that peptidoglycan composition was approximately maintained across strains from three Gram-negative species despite taxonomical and morphological differences. Peptidoglycan composition and density were maintained after we systematically altered cell size in Escherichia coli using the antibiotic A22, indicating that cell shape is largely decoupled from the biochemistry of peptidoglycan synthesis. High-throughput, sensitive UPLC combined with our automated software for chromatographic analysis will accelerate the discovery of peptidoglycan composition and the molecular mechanisms of cell wall structure determination.

Evolutionary dynamics of morphological stability in a long-term experiment with Escherichia coli

To investigate the questions in morphological evolution, some biologists seek to carry out evolution experiments owing to the incompleteness and uncontrollability of the fossil record and natural populations. To quantitatively analyse the morphology (cell size) evolution observed from a long-term experiment with Escherichia coli, the authors present three mathematical approximations to the Wright-Fisher model of the morphological evolution. They firstly use a deterministic approximation, which fails to predict evolutionary dynamics of cell size and proves the importance of stochasticity in large populations. Then, they develop a stochastic approximation and derive an analytic expression for the anticipated waiting time to reach the stability of cell size. The results show that the calculation of this waiting time is in good agreement with the experimental data and that the selective advantage plays a prominent role in cell size evolution, with mutation rate and population size having less impact. Finally, they employ a multistep process to approximate the Wright-Fisher model of cell size evolution and acquire an analytical formula for the median waiting time until the stability of cell size. This median time supports the idea that the selective advantage is the dominant force for the morphological evolution in the long-term experiment.

Detecting rare structural variation in evolving microbial populations from new sequence junctions using breseq

New mutations leading to structural variation (SV) in genomes—in the form of mobile element insertions, large deletions, gene duplications, and other chromosomal rearrangements—can play a key role in microbial evolution. Yet, SV is considerably more difficult to predict from short-read genome resequencing data than single-nucleotide substitutions and indels (SN), so it is not yet routinely identified in studies that profile population-level genetic diversity over time in evolution experiments. We implemented an algorithm for detecting polymorphic SV as part of the breseq computational pipeline. This procedure examines split-read alignments, in which the two ends of a single sequencing read match disjoint locations in the reference genome, in order to detect structural variants and estimate their frequencies within a sample. We tested our algorithm using simulated Escherichia coli data and then applied it to 500- and 1000-generation population samples from the Lenski E. coli long-term evolution experiment (LTEE). Knowledge of genes that are targets of selection in the LTEE and mutations present in previously analyzed clonal isolates allowed us to evaluate the accuracy of our procedure. Overall, SV accounted for ~25% of the genetic diversity found in these samples. By profiling rare SV, we were able to identify many cases where alternative mutations in key genes transiently competed within a single population. We also found, unexpectedly, that mutations in two genes that rose to prominence at these early time points always went extinct in the long term. Because it is not limited by the base-calling error rate of the sequencing technology, our approach for identifying rare SV in whole-population samples may have a lower detection limit than similar predictions of SNs in these data sets. We anticipate that this functionality of breseq will be useful for providing a more complete picture of genome dynamics during evolution experiments with haploid microorganisms.

Systematic perturbation of cytoskeletal function reveals a linear scaling relationship between cell geometry and fitness

Diversification of cell size is hypothesized to have occurred through a process of evolutionary optimization, but direct demonstrations of causal relationships between cell geometry and fitness are lacking. Here, we identify a mutation from a laboratory-evolved bacterium that dramatically increases cell size through cytoskeletal perturbation and confers a large fitness advantage. We engineer a library of cytoskeletal mutants of different sizes and show that fitness scales linearly with respect to cell size over a wide physiological range. Quantification of the growth rates of single cells during the exit from stationary phase reveals that transitions between "feast-or-famine" growth regimes are a key determinant of cell-size-dependent fitness effects. We also uncover environments that suppress the fitness advantage of larger cells, indicating that cell-size-dependent fitness effects are subject to both biophysical and metabolic constraints. Together, our results highlight laboratory-based evolution as a powerful framework for studying the quantitative relationships between morphology and fitness.

Molecular surveillance of the subtle septum: discovering a new mode of peptidoglycan synthesis in streptococci

The process of septation requires precise temporal and spatial organization of penicillin binding proteins (PBPs) and associated proteins for the deposition of new cell wall material. In most bacteria, the filamentous protein FtsZ organises PBPs into assemblies at the midcell which then constrict inwards as peptidoglycan is synthesised, eventually closing the septa. Tsui et al. (2014), through the use of fluorescent d-amino acids and high resolution microscopy, report that PBP2x of Streptococcus pneumoniae is directed to a discrete location within the septal aperture during the later stages of cell division. Once at this new site, PBP2x catalyses the de novo synthesis of peptidoglycan, which is imaged by the authors as a central 'spot', distinct from material made by other PBPs at the outer ring. This discovery, which represents a novel mode of cell wall assembly, was made in a directed capsular knockout of strain D39, thereby avoiding potential mechanistic complications in commonly used laboratory strain R6. These findings prompt not only a partial rethink of septum formation in S. pneumoniae, but consideration of the modes of PBP localization and the subtleties that can influence phenotypic study.

Escherichia coli genes and pathways involved in surviving extreme exposure to ionizing radiation

To further an improved understanding of the mechanisms used by bacterial cells to survive extreme exposure to ionizing radiation (IR), we broadly screened nonessential Escherichia coli genes for those involved in IR resistance by using transposon-directed insertion sequencing (TraDIS). Forty-six genes were identified, most of which become essential upon heavy IR exposure. Most of these were subjected to direct validation. The results reinforced the notion that survival after high doses of ionizing radiation does not depend on a single mechanism or process, but instead is multifaceted. Many identified genes affect either DNA repair or the cellular response to oxidative damage. However, contributions by genes involved in cell wall structure/function, cell division, and intermediary metabolism were also evident. About half of the identified genes have not previously been associated with IR resistance or recovery from IR exposure, including eight genes of unknown function.

A dynamically assembled cell wall synthesis machinery buffers cell growth

Assembly of protein complexes is a key mechanism for achieving spatial and temporal coordination in processes involving many enzymes. Growth of rod-shaped bacteria is a well-studied example requiring such coordination; expansion of the cell wall is thought to involve coordination of the activity of synthetic enzymes with the cytoskeleton via a stable complex. Here, we use single-molecule tracking to demonstrate that the bacterial actin homolog MreB and the essential cell wall enzyme PBP2 move on timescales orders of magnitude apart, with drastically different characteristic motions. Our observations suggest that PBP2 interacts with the rest of the synthesis machinery through a dynamic cycle of transient association. Consistent with this model, growth is robust to large fluctuations in PBP2 abundance. In contrast to stable complex formation, dynamic association of PBP2 is less dependent on the function of other components of the synthesis machinery, and buffers spatially distributed growth against fluctuations in pathway component concentrations and the presence of defective components. Dynamic association could generally represent an efficient strategy for spatiotemporal coordination of protein activities, especially when excess concentrations of system components are inhibitory to the overall process or deleterious to the cell.

The reproducibility of adaptation in the light of experimental evolution with whole genome sequencing

A key question in evolutionary biology is the reproducibility of adaptation. This question can now be quantitatively analyzed using experimental evolution coupled to whole genome sequencing (WGS). With complete sequence data, one can assess convergence among replicate populations. In turn, convergence reflects the action of natural selection and also the breadth of the field of possible adaptive solutions. That is, it provides insight into how many genetic solutions or adaptive paths may lead to adaptation in a given environment. Convergence is both a property of an adaptive landscape and, reciprocally, a tool to study that landscape. In this chapter we present the links between convergence and the properties of adaptive landscapes with respect to two types of microbial experimental evolution. The first tries to reconstruct a full adaptive landscape using a handful of carefully identified mutations (the reductionist approach), while the second uses WGS of replicate experiments to infer properties of the adaptive landscape. Reductionist approaches have highlighted the importance of epistasis in shaping the adaptive landscape, but have also uncovered a wide diversity of landscape architectures. The WGS approach has uncovered a very high diversity of beneficial mutations that affect a limited set of genes or functions and also suggests some shortcomings of the reductionist approach. We conclude that convergence may be better defined at an integrated level, such as the genic level or even at a phenotypic level, and that integrated mechanistic models derived from systems biology may offer an interesting perspective for the analysis of convergence at all levels.

Characterization of osmotically induced filaments of Salmonella enterica

Salmonella enterica forms aseptate filaments with multiple nucleoids when cultured in hyperosmotic conditions. These osmotic-induced filaments are viable and form single colonies on agar plates even though they contain multiple genomes and have the potential to divide into multiple daughter cells. Introducing filaments that are formed during osmotic stress into culture conditions without additional humectants results in the formation of septa and their division into individual cells, which could present challenges to retrospective analyses of infectious dose and risk assessments. We sought to characterize the underlying mechanisms of osmotic-induced filament formation. The concentration of proteins and chromosomal DNA in filaments and control cells was similar when standardized by biomass. Furthermore, penicillin-binding proteins in the membrane of salmonellae were active in vitro. The activity of penicillin-binding protein 2 was greater in filaments than in control cells, suggesting that it may have a role in osmotic-induced filament formation. Filaments contained more ATP than did control cells in standardized cell suspensions, though the levels of two F(0)F(1)-ATP synthase subunits were reduced. Furthermore, filaments could septate and divide within 8 h in 0.2 × Luria-Bertani broth at 23°C, while nonfilamentous control cells did not replicate. Based upon the ability of filaments to septate and divide in this diluted broth, a method was developed to enumerate by plate count the number of individual, viable cells within a population of filaments. This method could aid in retrospective analyses of infectious dose of filamented salmonellae.

Escherichia coli ATCC 8739 Adapts to the Presence of Sodium Chloride, Monosodium Glutamate, and Benzoic Acid after Extended Culture

Escherichia coli is commonly found in intestine of human, and any changes in their adaptation or evolution may affect the human body. The relationship between E. coli and food additives is less studied as compared to antibiotics. E. coli within our human gut are consistently interacting with the food additives; thus, it is important to investigate this relationship. In this paper, we observed the evolution of E. coli cultured in different concentration of food additives (sodium chloride, benzoic acid, and monosodium glutamate), singly or in combination, over 70 passages. Adaptability over time was estimated by generation time and cell density at stationary phase. Polymerase chain reaction (PCR)/restriction fragments length polymorphism (RFLP) using 3 primers and restriction endonucleases, each was used to characterize adaptation/evolution at genomic level. The amplification and digestion profiles were tabulated and analyzed by Nei-Li dissimilarity index. Our results demonstrate that E. coli in every treatment had adapted over 465 generations. The types of stress were discovered to be different even though different concentrations of same additives were used. However, RFLP shows a convergence of genetic distances, suggesting the presence of global stress response. In addition, monosodium glutamate may be a nutrient source and support acid resistance in E. coli.

Hypermutation and stress adaptation in bacteria

Hypermutability is a phenotype characterized by a moderate to high elevation of spontaneous mutation rates and could result from DNA replication errors, defects in error correction mechanisms and many other causes. The elevated mutation rates are helpful to organisms to adapt to sudden and unforeseen threats to survival. At the same time hypermutability also leads to the generation of many deleterious mutations which offset its adaptive value and therefore disadvantageous. Nevertheless, it is very common in nature, especially among clinical isolates of pathogens. Hypermutability is inherited by indirect (second order) selection along with the beneficial mutations generated. At large population sizes and high mutation rates many cells in the population could concurrently acquire beneficial mutations of varying adaptive (fitness) values. These lineages compete with the ancestral cells and also among themselves for fixation. The one with the 'fittest' mutation gets fixed ultimately while the others are lost. This has been called 'clonal interference' which puts a speed limit on adaptation. The original clonal interference hypothesis has been modified recently. Nonheritable (transient) hypermtability conferring significant adaptive benefits also occur during stress response although its molecular basis remains controversial. The adaptive benefits of heritable hypermutability are discussed with emphasis on host-pathogen interactions.

Mechanisms for maintaining cell shape in rod-shaped Gram-negative bacteria

For the rod-shaped Gram-negative bacterium Escherichia coli, changes in cell shape have critical consequences for motility, immune system evasion, proliferation and adhesion. For most bacteria, the peptidoglycan cell wall is both necessary and sufficient to determine cell shape. However, how the synthesis machinery assembles a peptidoglycan network with a robustly maintained micron-scale shape has remained elusive. To explore shape maintenance, we have quantified the robustness of cell shape in three Gram-negative bacteria in different genetic backgrounds and in the presence of an antibiotic that inhibits division. Building on previous modelling suggesting a prominent role for mechanical forces in shape regulation, we introduce a biophysical model for the growth dynamics of rod-shaped cells to investigate the roles of spatial regulation of peptidoglycan synthesis, glycan-strand biochemistry and mechanical stretching during insertion. Our studies reveal that rod-shape maintenance requires insertion to be insensitive to fluctuations in cell-wall density and stress, and even a simple helical pattern of insertion is sufficient for over sixfold elongation without significant loss in shape. In addition, we demonstrate that both the length and pre-stretching of newly inserted strands regulate cell width. In sum, we show that simple physical rules can allow bacteria to achieve robust, shape-preserving cell-wall growth.

Adaptation of Saccharomyces cerevisiae to saline stress through laboratory evolution

Most laboratory evolution studies that characterize evolutionary adaptation genomically focus on genetically simple traits that can be altered by one or few mutations. Such traits are important, but they are few compared with complex, polygenic traits influenced by many genes. We know much less about complex traits, and about the changes that occur in the genome and in gene expression during their evolutionary adaptation. Salt stress tolerance is such a trait. It is especially attractive for evolutionary studies, because the physiological response to salt stress is well-characterized on the molecular and transcriptome level. This provides a unique opportunity to compare evolutionary adaptation and physiological adaptation to salt stress. The yeast Saccharomyces cerevisiae is a good model system to study salt stress tolerance, because it contains several highly conserved pathways that mediate the salt stress response. We evolved three replicate lines of yeast under continuous salt (NaCl) stress for 300 generations. All three lines evolved faster growth rate in high salt conditions than their ancestor. In these lines, we studied gene expression changes through microarray analysis and genetic changes through next generation population sequencing. We found two principal kinds of gene expression changes, changes in basal expression (82 genes) and changes in regulation (62 genes). The genes that change their expression involve several well-known physiological stress-response genes, including CTT1, MSN4 and HLR1. Next generation sequencing revealed only one high-frequency single-nucleotide change, in the gene MOT2, that caused increased fitness when introduced into the ancestral strain. Analysis of DNA content per cell revealed ploidy increases in all the three lines. Our observations suggest that evolutionary adaptation of yeast to salt stress is associated with genome size increase and modest expression changes in several genes.

Identification and dynamics of a beneficial mutation in a long-term evolution experiment with Escherichia coli

BACKGROUND

Twelve populations of E. coli were serially propagated for 20,000 generations in a glucose-supplemented minimal medium in order to study the dynamics of evolution. We sought to find and characterize one of the beneficial mutations responsible for the adaptation and other phenotypic changes, including increased cell size, in one of these populations.

RESULTS

We used transposon-tagging followed by P1-transduction into the ancestor, screening for increased cell size and fitness, co-transduction analysis, and DNA sequencing. We identified a 1-bp insertion in the BoxG1 region located upstream of glmUS, an operon involved in cell-wall biosynthesis. When transduced into the ancestor, this mutation increased competitive fitness by about 5%. This mutation spread through its population of origin between 500 and 1500 generations. Mutations in this region were not found in the other 11 evolving populations, even after 20,000 generations.

CONCLUSION

The 1-bp insertion in the BoxG1 region near glmUS was demonstrably beneficial in the environment in which it arose. The absence of similar mutations in the other evolved populations suggests that they substituted other mutations that rendered this particular mutation unimportant. These results show the unpredictability of adaptive evolution, whereas parallel substitutions at other loci in these same populations reveal the predictability.

Genome-wide mutational diversity in an evolving population of Escherichia coli

The level of genetic variation in a population is the result of a dynamic tension between evolutionary forces. Mutations create variation, certain frequency-dependent interactions may preserve diversity, and natural selection purges variation. New sequencing technologies offer unprecedented opportunities to discover and characterize the diversity present in evolving microbial populations on a whole-genome scale. By sequencing mixed-population samples, we have identified single-nucleotide polymorphisms (SNPs) present at various points in the history of an Escherichia coli population that has evolved for almost 20 years from a founding clone. With 50-fold genome coverage, we were able to catch beneficial mutations as they swept to fixation, discover contending beneficial alleles that were eliminated by clonal interference, and detect other minor variants possibly adapted to a new ecological niche. Additionally, there was a dramatic increase in genetic diversity late in the experiment after a mutator phenotype evolved. Still finer-resolution details of the structure of genetic variation and how it changes over time in microbial evolution experiments will enable new applications and quantitative tests of population genetic theory.