Biology subjects

Pentz, J. T.

Publications and source records attributed to Pentz, J. T..

5 recordsLinked to original sources

bioRxiv2024

Metabolic trade-offs in response to increased acetate metabolism in Escherichia coli

Adaptive laboratory evolution (ALE) is a powerful tool to improve phenotypes in microbial cell factories for biotechnological processes. For example, ALE can be utilized to improve growth on alternative carbon sources such as acetate. Acetate is becoming a promising alternative feedstock to produce a variety of bio-products, but growth on acetate is slow relative to other preferred carbon sources and can be toxic to cells. However, ALE in a homogenous environment can lead to evolutionary trade-offs for growth on other carbon sources, which might be detrimental for feedstocks that contain multiple sugars. Here, we evolved Escherichia coli for [~]100 generations using continuous culturing in turbidostats in media containing acetate as the sole carbon source to rapidly select for increased growth in acetate. We measured absolute fitness of 119 clones in acetate and glucose separately to characterize trade-offs and found that trade-off patterns were heterogenous amongst measured clones, with 45% of clones showing significantly reduced growth in glucose. Sequencing revealed that the trade-offs were a result of antagonistic pleiotropic effects of early adaptive mutations, but not all high-effect mutations conferred a trade-off, consistent with the model that mutations accumulated in the selected environment can display a range of pleiotropic effects in other environments. Together, these results suggest that ALE in a homogeneous environment needs to be carefully considered for the improvement of metabolic traits in microbial cells as this could limit the use of evolved strains in complex feedstocks that contain multiple sugars.

evolutionary biology↗

bioRxiv2024

Competition and cooperation: The plasticity of bacteria interactions across environments

Bacteria live in diverse communities, forming complex networks of interacting species. A central question in bacterial ecology is why some species engage in cooperative interactions, whereas others compete. But this question often neglects the role of the environment. Here, we use genome-scale metabolic networks from two different open-access collections (AGORA and CarveMe) to assess pairwise interactions of different microbes in varying environmental conditions (provision of different environmental compounds). By scanning thousands of environments for 10,000 pairs of bacteria from each collection, we found that most pairs were able to both compete and cooperate depending on the availability of environmental resources. This approach allowed us to determine commonalities between environments that could facilitate the potential for cooperation or competition between a pair of species. Namely, cooperative interactions, especially obligate, were most common in less diverse environments. Further, as compounds were removed from the environment, we found interactions tended to degrade towards obligacy. However, we also found that on average at least one compound could be removed from an environment to switch the interaction from competition to facultative cooperation or vice versa. Together our approach indicates a high degree of plasticity in microbial interactions to the availability of environmental resources.

microbiology↗

bioRxiv2024

Forecasting of phenotypic and genetic outcomes of experimental evolution in Pseudomonas syringae and Pseudomonas savastanoi

Microbial experimental evolution is commonly highly repeatable under identical conditions, indicating a potential for short-term evolutionary forecasting. However, it is unclear to what extent evolutionary predictions can be extrapolated to related species adapting in similar environments, which would enable direct testing of general forecasting models and biological assumptions. To further develop a model system for evolutionary forecasting based on adaptation to static culture conditions, we experimentally tested previous predictions for Pseudomonas syringae and Pseudomonas savastanoi. In addition to sequence divergence, these species also differ in their repertoire of diguanylate cyclases that can be mutationally activated to produce the adaptive wrinkly spreader (WS) phenotype and genes for biosynthesis of exopolysaccharides. After experimental evolution, we isolated 32 independent WS mutants for P. syringae and 37 WS mutants for P. savastanoi that had increased ability to colonize the air-liquid interface and reduced motility. As predicted, most mutants had mutations in the wsp operon followed by rarer promoter mutations upstream of uncharacterized diguanylate cyclases. Surprisingly, no mutations were found in wspF, the most commonly mutated gene in the previously characterized species, which was explained by differences in relative fitness. While prediction of mutated regions was largely successful for WspA, mutations in WspE had a divergent pattern for both species. Surprisingly, deletion of known exopolysaccharide loci previously shown to contribute to the adaptive WS phenotype in other species did not reduce fitness, suggesting the presence of additional adhesive components under c-di-GMP control. This study shows that evolutionary forecasts can be extended to related species, but that differences in the genotype-phenotype-fitness map and mutational biases limit predictability on a detailed molecular level. Author summaryBiological evolution is often observed to be repeatable in the short-term, which suggests that it might be possible to forecast and ultimately steer evolution. Evolutionary processes are fundamental to biology but are also central to major societal problems, including antibiotic resistance, cancer, and adaptation to climate change. Experimental evolution with microbes makes it possible to study evolutionary processes in real-time over many generations to allow direct tests of evolutionary forecasts. However, a fundamental problem is that predictive models are usually based on previous experimental data which limits the novelty of the prediction beyond simple repeatability. A more challenging issue is to predict to what degree similar species evolve in similar ways in similar environments. Here we show that one of the best characterized bacterial experimental evolution model systems, biofilm formation at the surface of static tubes in Pseudomonas, can be extended to related species evolving in similar environments. This allowed us to directly test previous evolutionary forecasts to show that similar phenotypes evolved in similar environments, but that predictions of molecular details often fail. This study also elucidates the causes for failed forecasts to allow continuous improvements in predictive models and to delineate the limits of evolutionary forecasting.

evolutionary biology↗

bioRxiv2022

Clonal development, not aggregation, drives the transition to multicellularity in an isogenic model system

A key step in the evolutionary transition to multicellularity is the origin of multicellular groups as biological individuals capable of adaptation. Comparative work, supported by theory, suggests clonal development should facilitate this transition, though this hypothesis has never been tested in a single model system. We evolved 20 replicate populations of otherwise isogenic clonally-reproducing snowflake yeast ({Delta}ace2/{Delta}ace2) and aggregative floc yeast (GAL1p::FLO1/ GAL1p::FLO1) with daily selection for rapid growth in liquid media, which favors faster cell division, followed by selection for rapid sedimentation, which favors larger multicellular groups. While both genotypes adapted to this regime, growing faster and having higher survival during the group-selection phase, there was a stark difference in evolutionary dynamics. Aggregative floc yeast obtained nearly all of their increased fitness from faster growth, not improved group survival; indicating that selection acted primarily at the level of cells. In contrast, clonal snowflake yeast mainly benefited from higher group-dependent fitness, indicating a shift in the level of biological individuality from cells to groups. Through genome sequencing and mathematical modeling, we show that the genetic bottlenecks in a clonal life cycle also drive much higher rates of genetic drift--a result with complex implications for this evolutionary transition. Our results highlight the central role that early multicellular life cycles play in the process of multicellular adaptation.

evolutionary biology↗

bioRxiv2018

Ecological advantages and evolutionary limitations of aggregative multicellular development

All multicellular organisms develop through one of two basic routes: they either aggregate from free-living cells, creating potentially-chimeric multicellular collectives, or they develop clonally via mother-daughter cellular adhesion. While evolutionary theory makes clear predictions about trade-offs between these developmental modes, these have never been experimentally tested in otherwise genetically-identical organisms. We engineered unicellular bakers yeast (Saccharomyces cerevisiae) to develop either clonally ( snowflake, {Delta}ace2), or aggregatively ( floc, GAL1p::FLO1), and examined their fitness in a fluctuating environment characterized by periods of growth and selection for rapid sedimentation. When cultured independently, aggregation was far superior to clonal development, providing a 35% advantage during growth, and a 2.5-fold advantage during settling selection. Yet when competed directly, clonally-developing snowflake yeast rapidly displaced aggregative floc. This was due to unexpected social exploitation: snowflake yeast, which do not produce adhesive FLO1, nonetheless become incorporated into flocs at a higher frequency than floc cells themselves. Populations of chimeric clusters settle much faster than floc alone, providing snowflake yeast with a fitness advantage during competition. Mathematical modeling suggests that such developmental cheating may be difficult to circumvent; hypothetical choosy floc that avoid exploitation by maintaining clonality pay an ecological cost when rare, often leading to their extinction. Our results highlight the conflict at the heart of aggregative development: non-specific cellular binding provides a strong ecological advantage - the ability to quickly form groups - but this very feature leads to its exploitation.

evolutionary biology↗