Biology subjects

Armstrong, J. O.

Publications and source records attributed to Armstrong, J. O..

6 recordsLinked to original sources

bioRxiv2026

Making sense of chaos: replication and segregation defects in the yeast mcm4Chaos3 mutant

Genome instability is a defining feature of cancer and is strongly influenced by alterations in the fidelity and timing of DNA replication. The conserved Mini-Chromosome Maintenance (MCM 2-7) helicase is a central component of the eukaryotic DNA replication machinery, playing critical roles in origin licensing and activation. Genetic screens for genome instability mutations in mice identified mcm4Chaos3, a hypomorphic allele of MCM4 associated with the formation of micronuclei and tumorigenesis, suggesting that the mcm4Chaos3 allele causes genome instability. To define the mechanistic basis of this instability, we examined the effects of the corresponding mutation in Saccharomyces cerevisiae. We found that mcm4Chaos3 selectively compromises origin firing at a subset of early S-phase origins, with pronounced effects at many centromere-proximal origins. Chromosome V, containing the sensitive centromere-adjacent ARS510, exhibited elevated loss rates that were rescued by replacement with the robust early-firing origin ARS305, restoring both origin activity and chromosome stability. Together these findings demonstrate that mcm4Chaos3 compromises genome stability by impairing a subset of early, centromere-proximal origins that are intrinsically sensitive to origin activation capacity. Our results establish that robust origin function near centromeres is critical for accurate chromosome segregation and reveal how subtle perturbations in helicase function can lead to chromosome instability.

genetics↗

bioRxiv2026

Beyond ERCs: exploring catastrophic forms of rDNA instability in aging yeast

Single-celled organisms grown in identical conditions have variable life spans. Identifying the factors that drive the inherent variability in life span is crucial for our understanding of aging at a fundamental level. Here, we revisit the role of chromosome XII instability as a source of life span variability in aging populations of the budding yeast, Saccharomyces cerevisiae. We followed populations of mother cells as they aged and quantified changes in karyotype, DNA content, and aberrant DNA structures, including the production of extrachromosomal rDNA circles (ERCs). We found that cells massively amplified their rDNA both as ERCs and as a structural form that could not be resolved on CHEF gels. We propose a model describing how these unresolved structures are generated. Our model, which we call CICR (Catastrophic IntraChromosomal Recombination), describes the consequences of recombination between repeats of different replication status. At the completion of replication, when all other replication forks have successfully terminated, CICR events leave behind a single, unopposed replication fork in a branched form of Chr XII that has profound consequences during mitosis and/or subsequent cycles. This form of instability within the ribosomal DNA can lead to a myriad of toxic recombination products that may contribute to the life span variability in isogenic populations of aging yeast. AUTHOR SUMMARYAging is an uphill battle against entropy. The wear and tear on biological processes in cells require surveillance mechanisms and repair processes to stave off the inevitable. A cells genome is constantly under external and internal insults that can ultimately lead to death. Known events that impact a cells DNA are damage from free radicals (produced by the very oxygen needed for survival), shortening of the caps on chromosomes (called telomeres) every time a cell divides, and mutations that accumulate over time that affect essential cell processes. Yeast is an excellent tool to examine specific causes of aging because of its asymmetric mode of cell division: a mother cell can divide a limited, but variable number of times before senescing. We have isolated cohorts of mother cells, examined their genomes over the course of their life span and find a new intrinsic insult that the genome must endure. We find, in addition to the accumulation of extrachromosomal copies of the genes that encode the RNA portion of ribosomes (rDNA), that cells accumulate a toxic product of genetic recombination within the rDNA. The chromosome that contains the rDNA becomes branched and/or fragmented which leads to cell death.

genetics↗

bioRxiv2025

Using Experimental Evolution to Correct Mother-Daughter Separation Defects in Brewing Yeast

The budding yeast, Saccharomyces cerevisiae, is the workhorse of the brewing industry. Brewers have domesticated a vast array of different strains with traits that complement the beers they wish to brew. Yet, some domesticated strains also harbor traits that are undesirable. One example of an undesirable trait in brewing strains is the mother-daughter separation defect (MDSD). MDSDs are a reproductive flaw present in a widely used brewing strain, London Ale III. MDSDs cause cells to form large clusters, possibly leading to the known requirement for more headspace during London Ale III fermentations that result in a lower fermentative yield. Because MDSDs can be caused by mutations to a number of genes, targeted genetic approaches to reduce MDSDs are experimentally challenging, especially for a tetraploid strain like London Ale III. To improve MDSDs in this strain, we employed experimental evolution and passaged populations from three biological replicates for over 200 generations to generate three independent evolved strains that form fewer clusters than the ancestral strain, as seen by microscopy. To confirm these results, we used flow cytometry to measure the average size of the clusters in clones of our evolved replicates and found them to be smaller on average than the ancestor. We also qualitatively assessed the aggregation phenotype using a settling assay and found that our evolved replicates settle slower than the ancestor. Finally, we characterized the mutations in our evolved replicates using whole genome sequencing and identified increased copy numbers of chromosome 1 and chromosome 14 in all three evolved clones. The best-performing strain generated by this project is now available commercially. This project demonstrates how experimental evolution can be used to select against less desirable traits in industrial yeast strains when targeted genetic approaches present considerable challenges. Future research could implement a similar approach to improve other traits in widely used brewing and baking strains.

genetics↗

bioRxiv2024

URA6 mutations provide an alternative mechanism for 5-FOA resistance in Saccharomyces cerevisiae

The URA3 gene is frequently used in the budding yeast community as the mutation target for 5-fluoroorotic acid (5-FOA) resistance. We identified a class of ura6 mutants that can grow in the presence of 5-FOA. Unlike ura3 mutants, ura6 mutants remain prototrophic and are able to grow in the absence of uracil. In addition to 5-FOA resistance, we found that ura6 mutants are also resistant to 5-fluorocytosine (5-FC) and 5-fluorouracil (5-FU). In total, we identified 50 unique missense mutations across 32 unique amino acid positions of Ura6 which confer resistance to 5-FOA. We found that 28 out of the 32 affected positions are located in regions conserved between Saccharomyces cerevisiae and three clinically relevant pathogenic fungi. Metabolic analysis revealed a build-up of uridine monophosphate (UMP) and 5-fluorouridine monophosphate (5-FUMP) in ura6 mutants, indicating a reduction in Ura6 activity. Despite the accumulation of UMP in ura6 mutants, uridine diphosphate and triphosphate (UDP, UTP) levels were similar across mutants and wild type. These findings suggest that missense mutations to URA6, can result in reduction of uridylate kinase activity and lead to cross resistance to fluorinated prodrugs that incorporate into both the de novo pyrimidine synthesis and the pyrimidine salvage pathway.

genetics↗

bioRxiv2023

Systematic Profiling of Ale Yeast Protein Dynamics across Fermentation and Repitching

Studying the genetic and molecular characteristics of brewing yeast strains is crucial for understanding their domestication history and adaptations accumulated over time in fermentation environments, and for guiding optimizations to the brewing process itself. Saccharomyces cerevisiae (brewing yeast) is amongst the most profiled organisms on the planet, yet the temporal molecular changes that underlie industrial fermentation and beer brewing remain understudied. Here, we characterized the genomic makeup of a Saccharomyces cerevisiae ale yeast widely used in the production of Hefeweizen beers, and applied shotgun mass spectrometry to systematically measure the proteomic changes throughout two fermentation cycles which were separated by 14 rounds of serial repitching. The resulting brewing yeast proteomics resource includes 64,740 protein abundance measurements. We found that this strain possesses typical genetic characteristics of Saccharomyces cerevisiae ale strains and displayed progressive shifts in molecular processes during fermentation based on protein abundance changes. We observed protein abundance differences between early fermentation batches compared to those separated by 14 rounds of serial repitching. The observed abundance differences occurred mainly in proteins involved in the metabolism of ergosterol and isobutyraldehyde. Our systematic profiling serves as a starting point for deeper characterization of how the yeast proteome changes during commercial fermentations and additionally serves as a resource to guide fermentation protocols, strain handling, and engineering practices in commercial brewing and fermentation environments. Finally, we created a web interface (https://brewing-yeast-proteomics.ccbb.utexas.edu/) to serve as a valuable resource for yeast geneticists, brewers, and biochemists to provide insights into the global trends underlying commercial beer production.

systems biology↗

bioRxiv2023

Multidimensional proteomics identifies molecular trajectories of cellular aging and rejuvenation

The declining capacity of cells to maintain a functional proteome is a major driver of cellular dysfunction and decreased fitness in aging. Here we assess the impact of aging on multiple proteome dimensions, which are reflective of function, across the replicative lifespan of Saccharomyces cerevisiae. We quantified protein abundance, protein turnover, protein thermal stability, and protein phosphorylation in mother yeast cells and their derived progeny at different ages. We find progressive and cumulative proteomic alterations that are reflective of dysregulation of complex assemblies, mitochondrial remodeling, post-translational activation of the AMPK/Snf1 energy sensor in mother cells, and an overall shift from biosynthetic to energy-metabolic processes. Our multidimensional proteomic study systematically corroborates previous findings of asymmetric segregation and daughter cell rejuvenation, and extends these concepts to protein complexes, protein phosphorylation, and activation of signaling pathways. Lastly, profiling age-dependent proteome changes in a caloric restriction model of yeast provided mechanistic insights into longevity, revealing minimal remodeling of energy-metabolic pathways, improved mitochondrial maintenance, ameliorated protein biogenesis, and decreased stress responses. Taken together, our study provides thousands of age-dependent molecular events that can be used to gain a holistic understanding of mechanisms of aging.

systems biology↗