Caroline M Weisman, Andrew W Murray, and Sean R Eddy. 5/18/2022. “Mixing genome annotation methods in a comparative analysis inflates the apparent number of lineage-specific genes.” Current Biology, 32, Pp. 1-8. Publisher's VersionAbstract

Comparisons of genomes of different species are used to identify lineage-specific genes, those genes that appear unique to one species or clade. Lineage-specific genes are often thought to represent genetic novelty that underlies unique adaptations. Identification of these genes depends not only on genome sequences, but also on inferred gene annotations. Comparative analyses typically use available genomes that have been annotated using different methods, increasing the risk that orthologous DNA sequences may be erroneously annotated as a gene in one species but not another, appearing lineage specific as a result. To evaluate the impact of such “annotation heterogeneity,” we identified four clades of species with sequenced genomes with more than one publicly available gene annotation, allowing us to compare the number of lineage-specific genes inferred when differing annotation methods are used to those resulting when annotation method is uniform across the clade. In these case studies, annotation heterogeneity increases the apparent number of lineage-specific genes by up to 15-fold, suggesting that annotation heterogeneity is a substantial source of potential artifact.

Andrea Giometto, David R. Nelson, and Andrew W Murray. 12/6/2021. “Antagonism between killer yeast strains as an experimental model for biological nucleation dynamics.” eLife, 10, e62932. Publisher's VersionAbstract
Antagonistic interactions are widespread in the microbial world and affect microbial evolutionary dynamics. Natural microbial communities often display spatial structure, which affects biological interactions, but much of what we know about microbial warfare comes from laboratory studies of well-mixed communities. To overcome this limitation, we manipulated two killer strains of the budding yeast Saccharomyces cerevisiae, expressing different toxins, to independently control the rate at which they released their toxins. We developed mathematical models that predict the experimental dynamics of competition between toxin-producing strains in both well-mixed and spatially structured populations. In both situations, we experimentally verified theory's prediction that a stronger antagonist can invade a weaker one only if the initial invading population exceeds a critical frequency or size. Finally, we found that toxin-resistant cells and weaker killers arose in spatially structured competitions between toxin-producing strains, suggesting that adaptive evolution can affect the outcome of microbial antagonism in spatial settings.
Severine Atis, Bryan T Weinstein, Andrew W Murray, and David R. Nelson. 11/15/2021. “Rocket yeast.” Physical Review Fluids, 6, 11, Pp. 110507-110510. Publisher's VersionAbstract
This paper is associated with a video winner of a 2020 American Physical Society's Division of Fluid Dynamics (DFD) Milton van Dyke Award for work presented at the DFD Gallery of Fluid Motion.
Marco Fumasoni and Andrew W Murray. 11/9/2021. “Ploidy and recombination proficiency shape the evolutionary adaptation to constitutive DNA replication stress.” PLOS Genetics, 17, 11. Publisher's VersionAbstract

In haploid budding yeast, evolutionary adaptation to constitutive DNA replication stress alters three genome maintenance modules: DNA replication, the DNA damage checkpoint, and sister chromatid cohesion. We asked how these trajectories depend on genomic features by comparing the adaptation in three strains: haploids, diploids, and recombination deficient haploids. In all three, adaptation happens within 1000 generations at rates that are correlated with the initial fitness defect of the ancestors. Mutations in individual genes are selected at different frequencies in populations with different genomic features, but the benefits these mutations confer are similar in the three strains, and combinations of these mutations reproduce the fitness gains of evolved populations. Despite the differences in the selected mutations, adaptation targets the same three functional modules despite differences in genomic features, revealing a common evolutionary response to constitutive DNA replication stress.

Sriram Srikant, Rachelle Gaudet, and Andrew W Murray. 9/28/2021. “Beyond the reach of homology: successive computational filters find yeast pheromone genes.” bioRxiv. Publisher's VersionAbstract
The mating of fungi depends on pheromones that mediate communication between two mating types. Most species use short peptides as pheromones, which are either unmodified (e.g., α-factor in Saccharomyces cerevisiae) or C-terminally farnesylated (e.g., a-factor in S. cerevisiae). Peptide pheromones have been found by genetics or biochemistry in small number of fungi, but their short sequences and modest conservation make it impossible to detect homologous sequences in most species. To overcome this problem, we used a four-step computational pipeline to identify candidate a-factor genes in sequenced genomes of the Saccharomycotina, the fungal clade that contains most of the yeasts: we require that candidate genes have a C-terminal prenylation motif, are fewer than 100 amino acids long, contain a proteolytic processing motif upstream of the potential mature pheromone sequence, and that closely related species contain highly conserved homologs of the potential mature pheromone sequence. Additional manual curation exploits the observation that many species carry more than one a-factor gene, encoding identical or nearly identical pheromones. From 332 fungal genomes, we identified strong candidate pheromone genes in 238 genomes, covering 13 clades that are separated from each other by at least 100 million years, the time required for evolution to remove detectable sequence homology. For one small clade, the Yarrowia, we demonstrated that our algorithm found the a-factor genes: deleting all four related genes in the a-mating type of Yarrowia lipolytica prevents mating.
Felix Barber, Jiseon Min, Andrew W. Murray, and Ariel Amir. 6/21/2021. “Modeling the impact of single-cell stochasticity and size control on the population growth rate in asymmetrically dividing cells.” PLOS Computational Biology, 17, 6. Publisher's VersionAbstract
Microbial populations show striking diversity in cell growth morphology and lifecycle; however, our understanding of how these factors influence the growth rate of cell populations remains limited. We use theory and simulations to predict the impact of asymmetric cell division, cell size regulation and single-cell stochasticity on the population growth rate. Our model predicts that coarse-grained noise in the single-cell growth rate decreases the population growth rate, as previously seen for symmetrically dividing cells. However, for a given noise in the single-cell growth rate we find that dividing asymmetrically can enhance the population growth rate for cells with strong size control (between a sizer and an adder). To reconcile this finding with the abundance of symmetrically dividing organisms in nature, we propose that additional constraints on cell growth and division must be present which are not included in our model, and we explore the effects of selected extensions thereof. Further, we find that within our model, epigenetically inherited generation times may arise due to size control in asymmetrically dividing cells, providing a possible explanation for recent experimental observations in budding yeast. Taken together, our findings provide insight into the complex effects generated by non-canonical growth morphologies.
Marco Fumasoni and Andrew Murray. 12/18/2020. “Genome architecture shapes evolutionary adaptation to DNA replication stress.” bioRxiv. Publisher's VersionAbstract

Evolutionary adaptation to perturbations in DNA replication follows reproducible trajectories that lead to changes in three important aspects of genome maintenance: DNA replication, the DNA damage checkpoint, and sister chromatid cohesion. We asked how these trajectories depend on a population's genome architecture by testing whether ploidy or the ability to perform homologous recombination influence the evolutionary fate of the budding yeast, Saccharomyces cerevisiae, as it adapts to constitutive DNA replication stress, a condition that characterizes many cancer cells. In all three genome architectures, adaptation happens within 1000 generations at rates that are linearly correlated with the initial fitness defect of the ancestors. Which genes are mutated depends on the frequency at which mutations occur and the selective advantage they confer. The recombination-deficient strain amplifies adaptive chromosomal regions less often, whereas the selective advantage of loss-of-function mutations, such as those that inactivate the DNA damage checkpoint, is reduced in diploids because of the presence of a second, wild-type copy of the gene. Despite these differences, selection targets the same three functional modules in all three architectures, suggesting that genome architecture controls which genes are mutated but not which modules are modified.

Caroline M. Weisman, Andrew W. Murray, and Sean R. Eddy. 11/2/2020. “Many, but not all, lineage-specific genes can be explained by homology detection failure.” PLOS Biology. Publisher's VersionAbstract

Genes for which homologs can be detected only in a limited group of evolutionarily

related species, called “lineage-specific genes,” are pervasive: essentially every

lineage has them, and they often comprise a sizable fraction of the group’s total genes.

Lineage-specific genes are often interpreted as “novel” genes, representing genetic

novelty born anew within that lineage. Here, we develop a simple method to test an

alternative null hypothesis: that lineage-specific genes do have homologs outside of

the lineage that, even while evolving at a constant rate in a novelty-free manner, have

merely become undetectable by search algorithms used to infer homology. We show

that this null hypothesis is sufficient to explain the lack of detected homologs of a large

number of lineage-specific genes in fungi and insects. However, we also find that a

minority of lineage-specific genes in both clades are not well-explained by this noveltyfree

model. The method provides a simple way of identifying which lineage-specific

genes call for special explanations beyond homology detection failure, highlighting

them as interesting candidates for further study.

Laura E. Bagamery, Quincey A. Justman, Ethan C. Garner, and Andrew W. Murray. 9/24/2020. “A putative bet hedging strategy buffers budding yeast against environmental instability.” Current Biology. Publisher's VersionAbstract

To grow and divide, cells must extract resources from dynamic and unpredictable environments. Many organisms use different metabolic strategies for distinct contexts. Budding yeast can produce ATP from carbon sources by mechanisms that prioritize either speed (fermentation) or yield (respiration). Withdrawing glucose from exponentially growing cells reveals variability in their ability to switch from fermentation to respiration. We observe two subpopulations of glucose-starved cells: recoverers, which rapidly adapt and resume growth, and arresters, which enter a shock state characterized by deformation of many cellular structures, including mitochondria. These states are heritable, and on high glucose, arresters grow and divide faster than recoverers. Recoverers have a fitness advantage during a carbon source shift but are less fit in a constant, high-glucose environment, and we observe natural variation in the frequency of the two states across wild yeast strains. These experiments suggest that bet hedging has evolved in budding yeast.

Felix Barber, Ariel Amir, and Andrew W Murray. 6/9/2020. “Cell size regulation in budding yeast does not depend on linear accumulation of Whi5.” PNAS, 117, 25. Publisher's VersionAbstract
Cells must couple cell cycle progress to their growth rate to restrict the spread of cell sizes present throughout a population. Linear, rather than exponential, accumulation of Whi5, was proposed to provide this coordination by causing a higher Whi5 concentration in cells born at smaller size. We tested this model using the inducible GAL1 promoter to make the Whi5 concentration independent of cell size. At an expression level that equalizes the mean cell size with that of wild-type cells, the size distributions of cells with galactose-induced Whi5 expression and wild-type cells are indistinguishable. Fluorescence microscopy confirms that the endogenous and GAL1 promoters produce different relationships between Whi5 concentration and cell volume without diminishing size control in the G1 phase. We also expressed Cln3 from the GAL1 promoter, finding that the spread in cell sizes for an asynchronous population is unaffected by this perturbation. Our findings contradict the previously proposed model for cell size control in budding yeast and demonstrate the need for a molecular mechanism that explains how cell size controls passage through Start.
Madhusudhan Srinivasan, Marco Fumasoni, Naomi J Petela, Andrew W Murray, and Kim A Nasmyth. 6/9/2020. “Cohesion is established during DNA replication by converting pre-existing chromosomal cohesin into cohesive structures as well as by de novo loading of cohesin onto nascent DNAs.” eLife. Publisher's VersionAbstract

Sister chromatid cohesion essential for mitotic chromosome segregation is thought to involve the co-entrapment of sister DNAs within cohesin rings. Though cohesin can load onto chromosomes throughout the cell cycle, it normally only builds cohesion during S phase. A key question is whether cohesion is generated by conversion of cohesin complexes associate with un-replicated DNAs ahead of replication forks into cohesive structures behind them, or from nucleoplasmic cohesin that is loaded de novo onto nascent DNAs associated with forks, a process that would be dependent on cohesin’s Scc2 subunit. We show here that in S. cerevisiae, both mechanisms exist and that each requires a different set of non-essential replisome-associated proteins. Cohesion produced by cohesin conversion requires Tof1/Csm3, Ctf4 and Chl1 (TCCC) but not Scc2 while that created by Scc2-dependent de novo loading at replication forks requires the Ctf18-RFC complex. Though inactivation of either pathway individually merely reduces the efficiency of cohesion establishment, simultaneous inactivation resembles the effect of cohesin ablation and is lethal. The association of specific replisome proteins with different types of cohesion establishment opens the way to a mechanistic understanding of an aspect of DNA replication unique to eukaryotic cells.

Andrew W Murray. 5/18/2020. “Can gene-inactivating mutations lead to evolutionary novelty?” Current Biology, 30, 10, Pp. R465. Publisher's VersionAbstract

Evolutionary novelty is difficult to define. It typically involves shifts in organismal or biochemical phenotypes that can be seen as qualitative as well as quantitative changes. In laboratory-based experimental evolution of novel phenotypes and the human domestication of crops, the majority of the mutations that lead to adaptation are loss of function mutations that impair or eliminate the function of genes rather than gain of function mutations that increase or qualitatively alter the function of proteins. I speculate that easier access to loss of function mutations has led them to play a major role in the adaptive radiations that occur when populations have access to many unoccupied ecological niches. I discuss four possible objections to this claim: that genes can only survive if they confer benefits to the organisms that bear them, antagonistic pleiotropy, the importance of pre-existing genetic variation in populations, and the danger that adaptation by breaking genes will, over long times, cause organisms to run out of genes.

Thomas LaBar, Yu-Ying Phoebe Hsieh, Marco Fumasoni, and Andrew W Murray. 5/18/2020. “Evolutionary repair experiments as a window to the molecular diversity of life.” Current Biology, 30, 10, Pp. R565. Publisher's VersionAbstract

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

Andrew Murray. 5/18/2020. “My Word: The easy way is hard enuff.” Current Biology, 30, 10, Pp. R419. Publisher's Version
Sriram Srikant, Rachelle Gaudet, and Andrew W Murray. 3/26/2020. “Selecting for altered substrate specificity reveals the evolutionary flexibility of ATP-binding cassette transporters.” Current Biology, 30, Pp. 1-14. Publisher's VersionAbstract
ABC transporters are the largest family of ATP-hydrolyzing transporters, with members in every sequenced genome, which transport substrates across membranes. Structural studies and biochemistry highlight the contrast between the global structural similarity of homologous transporters and the enormous diversity of their substrates. How do ABC transporters evolve to carry such diverse molecules and what variations in their amino acid sequence alter their substrate selectivity? We mutagenized the transmembrane domains of a conserved fungal ABC transporter that exports a mating pheromone and selected for mutants that export a non-cognate pheromone. Mutations that alter export selectivity cover a region that is larger than expected for a localized substrate-binding site. Individual selected clones have multiple mutations which have broadly additive contributions to specific transport activity. Our results suggest that multiple positions influence substrate selectivity, leading to alternative evolutionary paths towards selectivity for particular substrates, and explaining the number and diversity of ABC transporters.
Yu-Ying Phoebe Hsieh, Vasso Makrantoni, Daniel Robertson, Adele L Marston, and Andrew W Murray. 3/10/2020. “Evolutionary repair: changes in multiple functional modules allow meiotic cohesin to support mitosis.” PLOS Biology, 18, 3. Publisher's VersionAbstract
Different members of the same protein family often perform distinct cellular functions. How much are these differing functions due to changes in the biochemical activity of a protein itself versus changes in other proteins? We asked how the budding yeast, Saccharomyces cerevisiae, evolves when forced to use the meiosis-specific kleisin, Rec8, instead of the mitotic kleisin, Scc1, during the mitotic cell cycle. This perturbation impairs sister chromosome linkage and reduces reproductive fitness by 45%. We evolved 15 populations for 1750 generations, substantially increasing their fitness, and analyzed their genotypes and phenotypes. We found no mutations in Rec8, but many populations had mutations in the transcriptional mediator complex, cohesin-related genes, and cell cycle regulators that induce S phase. These mutations improve sister chromosome cohesion and slow genome replication in Rec8-expressing cells. We conclude that changes in known and novel partners allow proteins to improve their ability to perform new functions.
Patrick R. Stoddard, Eric M. Lynch, Daniel P. Farrell, Annie M. Dosey, Frank DiMaio, Tom A. Williams, Justin M. Kollman, Andrew W. Murray, and Ethan C. Garner. 2/28/2020. “Polymerization in the actin ATPase clan regulates hexokinase activity in yeast.” Science, 367, 6481, Pp. 1039-1042. Publisher's VersionAbstract

The actin protein fold is found in cytoskeletal polymers, chaperones, and various metabolic enzymes. Many actin-fold proteins, like the carbohydrate kinases, do not polymerize. We find that Glk1, a Saccharomyces cerevisiae glucokinase, forms two-stranded filaments with unique ultrastructure, distinct from that of cytoskeletal polymers. In cells, Glk1 polymerizes upon sugar addition and depolymerizes upon sugar withdrawal. Glk1 polymerization inhibits its enzymatic activity, thus the Glk1 monomer-polymer equilibrium sets a maximum rate of glucose phosphorylation regardless of Glk1 concentration. A mutation eliminating Glk1 polymerization alleviates concentration-dependent enzyme inhibition, causing glucokinase activity to become unconstrained. Polymerization-based regulation of Glk1 activity serves an important function in vivo: yeast containing non-polymerizing Glk1 are less fit when growing on sugars and more likely to die when refed glucose. Glucokinase polymerization arose within the ascomycete fungi and is conserved across a group of divergent (150-200 mya) yeast. We show that Glk1 polymerization arose independently from other actin-related filaments and allows yeast to rapidly modulate glucokinase activity as nutrient availability changes.

Marco Fumasoni and Andrew Murray. 2/2020. “The evolutionary plasticity of chromosome metabolism allows adaptation to DNA replication stress.” eLife. Publisher's VersionAbstract

Chromosome metabolism is defined by the pathways that collectively maintain the genome, including chromosome replication, repair and segregation. Because aspects of these pathways are conserved, chromosome metabolism is considered resistant to evolutionary change. We used the budding yeast, Saccharomyces cerevisiae, to investigate the evolutionary plasticity of chromosome metabolism. We experimentally evolved cells constitutively experiencing DNA replication stress caused by the absence of Ctf4, a protein that coordinates the activities at replication forks. Parallel populations adapted to replication stress, over 1000 generations, by acquiring multiple, successive mutations. Whole-genome sequencing and testing candidate mutations revealed adaptive changes in three aspects of chromosome metabolism: DNA replication, DNA damage checkpoint and sister chromatid cohesion. Although no gene was mutated in every population, the same pathways were sequentially altered, defining a functionally reproducible evolutionary trajectory. We propose that this evolutionary plasticity of chromosome metabolism has important implications for genome evolution in natural populations and cancer.

Miguel C Coelho, Ricardo M Pinto, and Andrew W Murray. 2019. “Heterozygous mutations cause genetic instability in yeast model of cancer evolution.” Nature, 566, Pp. 275–278. Publisher's VersionAbstract
Genetic instability, a heritable increase in the rate of genetic mutation, accelerates evolutionary adaptation1 and is widespread in cancer2,3. In mammals, instability can arise from damage to both copies of genes involved in DNA metabolism and cell cycle regulation4 or from inactivation of one copy of a gene whose product is present in limiting amounts (haploinsufficiency5); however, it has proved difficult to determine the relative importance of these two mechanisms. In Escherichia coli6, the application of repeated, strong selection enriches for genetic instability. Here we have used this approach to evolve genetic instability in diploid cells of the budding yeast Saccharomyces cerevisiae, and have isolated clones with increased rates of point mutation, mitotic recombination, and chromosome loss. We identified candidate, heterozygous, instability-causing mutations; engineering these mutations, as heterozygotes, into the ancestral diploid strain caused genetic instability. Mutations that inactivated one copy of haploinsufficient genes were more common than those that dominantly altered the function of the mutated gene copy. The mutated genes were enriched for genes functioning in transport, protein quality control, and DNA metabolism, and have revealed new targets for genetic instability7,8,9,10,11, including essential genes. Although only a minority (10 out of 57 genes with orthologues or close homologues) of the targets we identified have homologous human genes that have been implicated in cancer2, the remainder are candidates to contribute to human genetic instability. To test this hypothesis, we inactivated six examples in a near-haploid human cell line; five of these mutations increased instability. We conclude that single genetic events cause genetic instability in diploid yeast cells, and propose that similar, heterozygous mutations in mammalian homologues initiate genetic instability in cancer.
Severine Atis, Bryan T. Weinstein, Andrew W. Murray, and David R. Nelson. 2019. “Microbial range expansions on liquid substrates.” Physical Review X, 9, 2. Publisher's VersionAbstract

Despite the importance of flow for transporting and organizing populations, few laboratory systems exist to systematically investigate the impact of advection on their spatial evolutionary dynamics. To address this problem, we study the morphology and genetic spatial structure of microbial colonies growing on the surface of a nutrient-laden fluid 104 to 105 times more viscous than water in Petri dishes; the extreme but finite viscosity inhibits undesired thermal convection and allows populations to effectively live at the air-liquid interface due to capillary forces. We discover that S. cerevisiae (baker's yeast) growing on a viscous liquid behave like “active matter": they metabolically generate fluid flows many times larger than their unperturbed colony expansion speed, and that flow, in turn, can dramatically impact their colony morphology and spatial population genetics. We show that yeast cells generate fluid flows by consuming surrounding nutrients and decreasing the local substrate density, leading to misaligned fluid pressure and density contours  which ultimately generates vorticity via a thresholdless baroclinic instability. Numerical simulations with experimentally measured parameters demonstrate that an intense vortex ring is produced below the colony's edge. As the viscosity of the substrate is lowered and the self-induced flow intensifies, we observe three distinct morphologies: at the highest viscosity, cell proliferation and movement produces compact circular colonies with, however, a stretched regime of exponential expansion; intermediate viscosities give rise to compact colonies with “fingers" that are usually monoclonal and then break into smaller cell clusters; and at the lowest viscosity, the expanding colony fractures into many genetically-diverse, mutually repelling, island-like fragments that can colonize an entire 94 mm-diameter Petri dish within 36 hours. We propose a simple phenomenological model that predicts the early colony dynamics. Our results provide rich opportunities to study the interplay between fluid flow and spatial population genetics for future investigations.