Extreme Sensitivity of Fitness to Environmental Conditions: Lessons from #1BigBatch

Journal of Molecular Evolution, Год журнала: 2023, Номер 91(3), С. 293 - 310

Опубликована: Май 27, 2023

The phrase "survival of the fittest" has become an iconic descriptor how natural selection works. And yet, precisely measuring fitness, even for single-celled microbial populations growing in controlled laboratory conditions, remains a challenge. While numerous methods exist to perform these measurements, including recently developed utilizing DNA barcodes, all are limited their precision differentiate strains with small fitness differences. In this study, we rule out some major sources imprecision, but still find that measurements vary substantially from replicate replicate. Our data suggest very subtle and difficult avoid environmental differences between replicates create systematic variation across measurements. We conclude by discussing should be interpreted given extreme environment dependence. This work was inspired scientific community who followed us gave tips as live tweeted high-replicate measurement experiment at #1BigBatch.

Язык: Английский

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Trade-offs, trade-ups, and high mutational parallelism underlie microbial adaptation during extreme cycles of feast and famine

Current Biology, Год журнала: 2024, Номер 34(7), С. 1403 - 1413.e5

Опубликована: Март 8, 2024

Microbes are evolutionarily robust organisms capable of rapid adaptation to complex stress, which enables them colonize harsh environments. In nature, microbes regularly challenged by starvation, is a particularly stress because resource limitation often co-occurs with changes in pH, osmolarity, and toxin accumulation created metabolic waste. Often overlooked the additional complications introduced eventual replenishment, as successful must withstand environmental shifts before swiftly capitalizing on replenished resources avoid invasion competing species. To understand how navigate trade-offs between growth survival, ultimately adapting thrive environments extreme fluctuations, we experimentally evolved 16 Escherichia coli populations for 900 days repeated feast/famine conditions cycles 100-day starvation replenishment. Using longitudinal population-genomic analysis, found that evolution response characterized narrow adaptive trajectories high mutational parallelism notable order. Genetic reconstructions reveal early mutations result biofilm motility but trade-ups these conferred positively correlated advantages during both short-term long-term culture. Our results demonstrate can landscapes fluctuating follow confer benefits across diverse

Язык: Английский

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Identifying Targets of Selection in Laboratory Evolution Experiments

Journal of Molecular Evolution, Год журнала: 2023, Номер 91(3), С. 345 - 355

Опубликована: Фев. 21, 2023

Язык: Английский

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Evolutionary Constraints on RNA Polymerase Gene Positioning in the Genome of Fast-Growing Bacteria

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2025, Номер unknown

Опубликована: Апрель 14, 2025

Abstract How gene order along chromosomes affects cellular homeostasis and genome evolution remains poorly understood. Bacterial are organized the replication origin ( oriC )–terminus ter ) axis. The spatial arrengement of genes within this axis may influence physiology, evolution, transcriptional regulation. catalytic core sole bacterial RNA polymerase (RNAP) is encoded by rpoB rpoC universally conserved rplKAJL-rpoBC locus. In fast growing bacteria locus located near potentially linking organization to physiology. Here, we investigated functional relevance chromosomal positioning relocating it Vibrio cholerae genome. While viable, strains harboring far from exhibited nutrient-dependent fitness defects. These phenotypes correlated with reduced copy number RNAP abundance, without changes in its subcellular distribution. Introducing a second rpIKAJL-rpoBC at distal genomic location abolished phenotypes, demonstrating that replication-associated dosage effects were main mechanism behind observed physiological changes. Further uncoupling revealed costs specifically linked relocation. Our results reveal selective pressures act maintain RNAP-encoding optimize effects, ensuring efficient production during exponential growth. We discuss relationship between ecological strategies work underscores as an underestimated but critical factor shaping physiology evolution. Significance have highly plastic content importance their started be appreciated driver Growing evidence suggests genomes plays role expression, dynamics, fitness. study, demonstrate , encoding (RNAP), essential for optimal By show position directly impacts fitness, effects. findings suggest ensure output More broadly, our study highlights underappreciated beyond known roles operon structure Given fundamental RNAP, implications understanding strategies, adaptation, synthetic design. integrating positional genomics studies, provide theoretical experimental framework investigating how architecture shapes function.

Язык: Английский

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The role of NhaA protein in modulating antibiotic tolerance in Escherichia coli

International Journal of Biological Macromolecules, Год журнала: 2025, Номер unknown, С. 143721 - 143721

Опубликована: Апрель 1, 2025

Язык: Английский

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Single-cell heterogeneity in ribosome content and the consequences for the growth laws

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Апрель 23, 2024

Across species and environments, the ribosome content of cell populations correlates with population growth rate. The robustness universality this correlation have led to its classification as a "growth law." This law has fueled theories about how evolution selects for microbial organisms that maximize their rate based on nutrient availability, it informed models individual cells regulate rates ribosomal content. However, due methodological limitations, rarely been studied at level cells. While

Язык: Английский

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In Vitro Resistance-Predicting Studies and In Vitro Resistance-Related Parameters—A Hit-to-Lead Perspective

Pharmaceuticals, Год журнала: 2024, Номер 17(8), С. 1068 - 1068

Опубликована: Авг. 15, 2024

Despite the urgent need for new antibiotics, very few innovative antibiotics have recently entered clinics or clinical trials. To provide a constant supply of drug candidates optimized in terms their potential to select resistance natural settings, vitro resistance-predicting studies be improved and scaled up. In this review, following parameters are presented: frequency spontaneous mutant selection (FSMS), prevention concentration (MPC), dominant (MPC-D), inferior-mutant (MPC-F), minimal selective (MSC). The utility various adaptive laboratory evolution (ALE) approaches (serial transfer, continuous culture, spatiotemporal microenvironments) comparing hits level time required multistep emerge is discussed. We also consider how hit-to-lead stage can benefit from high-throughput ALE setups based on robotic workstations, do-it-yourself (DIY) cultivation systems, microbial growth arena (MEGA) plates, soft agar gradient (SAGE) microfluidic chips, microdroplet technology. Finally, evaluating fitness vitro-generated resistant mutants presented. This review aims draw attention newly emerged ideas improve forecasting compounds settings.

Язык: Английский

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Quantifying microbial fitness in high-throughput experiments

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Авг. 20, 2024

Few concepts are as central to evolution is fitness, and yet the quantification of fitness often ambiguous. In particular, high-throughput experiments measure mutant in microbes increasingly common but vary widely their definitions which makes results difficult compare. What consequences these different statistics, there a best way quantify given context? Here we systematize set possible statistics according following three choices: 1) encoding relative abundance (e.g., transforming by log or logit function), 2) time scale over change abundance, 3) choice reference subpopulation for calculating bulk competition experiments, such those using DNA-barcoded mutants. We show that choices can lead significantly interpretations affecting magnitude effects, presence epistasis, even ranking across This confound predictions evolutionary dynamics gene functions. Altogether our demonstrate importance consistent reproducible experiments.

Язык: Английский

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Evolution of pH-sensitive transcription termination in Escherichia coli during adaptation to repeated long-term starvation

Proceedings of the National Academy of Sciences, Год журнала: 2024, Номер 121(39)

Опубликована: Сен. 19, 2024

Fluctuating environments that consist of regular cycles co-occurring stress are a common challenge faced by cellular populations. For population to thrive in constantly changing conditions, an ability coordinate rapid response is essential. Here, we identify mutation conferring arginine-to-histidine (Arg His) substitution the transcription terminator Rho. The rho R109H frequently arose Escherichia coli populations experimentally evolved under repeated long-term starvation during which accumulation metabolic waste followed transfer into fresh media results drastic environmental pH fluctuations associated with feast and famine. Metagenomic sequencing revealed containing also possess putative loss-of-function mutations ydcI , encodes recently characterized factor homeostasis. Genetic reconstructions these show allele confers plasticity via alkaline-induced reduction Rho function that, when found tandem Δ allele, leads intracellular alkalization genetic assimilation mutant function. We further Arg His substitutions at analogous sites alleles from species regularly experience neutral alkaline their environments. Our suggest may serve rapidly complex physiological responses through sensing shed light on how use cues complex, fluctuating

Язык: Английский

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Site-selective modifications by lipid A phosphoethanolamine transferases linked to colistin resistance and bacterial fitness

mSphere, Год журнала: 2024, Номер unknown

Опубликована: Ноя. 29, 2024

ABSTRACT Genes encoding lipid A modifying phosphoethanolamine transferases (PETs) are genetically diverse and can confer resistance to colistin antimicrobial peptides. To better understand the functional diversity of PETs, we characterized three canonical mobile ( mcr ) alleles mcr-1 , -3 -9 ), one intrinsic pet eptA two -like genes petB petC in Escherichia coli . Using an isogenic expression system, show that mcr-3 similar phenotypes decreased susceptibility with low fitness costs. mcr-9 which is phylogenetically closely related only provide advantages presence sub-inhibitory concentrations significantly reduce media without colistin. PET-B PET-C were phenotypically distinct from bonafide PETs; neither impacted nor caused considerable cost. Strikingly, found for first time different PETs selectively modify phosphates A; MCR-1, MCR-3, 4′-phosphate, whereas MCR-9 EptA 1-phosphate. However, 4′-phosphate modifications facilitated by MCR-1 associated lowered toxicity. Our results suggest have a wide phenotypic increased specific modification patterns been largely unexplored thus far. IMPORTANCE Rising levels increasing numbers antimicrobials led revival last resort antibiotic Unfortunately, also spreading form genes, making it essential (i) improve identification resistant bacteria allow clinicians prescribe effective drug regimens (ii) develop new combination therapies at targeting bacteria. demonstrate including MCR variants, site-selective site-selectivity correlates level costs conferred certain PETs. Site selectivity given PET may not help predict but avenue combat colistin-resistant

Язык: Английский

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