Biology subjects

Gibney, P. A.

Publications and source records attributed to Gibney, P. A..

5 recordsLinked to original sources

bioRxiv2025

Electron transport chain disruption leads to failure of glucose derepression via the Snf1/AMPK pathway

When Saccharomyces cerevisiae cells transition from a glucose-rich environment to low glucose conditions, the expression of genes that were previously repressed by glucose is derepressed, enabling the cell to adapt metabolic processes to the available carbon source. The Snf1 pathway is one of the primary signaling pathways responsible for orchestrating glucose sensing and signaling. In this study, we investigate the impact of disrupted electron transport chain (ETC) function, a mitochondrial protein complex essential for respiratory energy generation, in glucose derepression. We observe that respiratory incompetent mutants exposed to glucose are unable to subsequently utilize galactose as a carbon source in minimal media. In contrast, ETC mutants that have been generated and maintained on galactose can effectively continue to metabolize galactose until glucose exposure. We define this phenomenon as a Failure of Glucose Derepression (FGD), wherein respiratory incompetent cells fail to fully reverse glucose repressed gene expression regulation. Through further characterization, we show how irregular localization patterns of crucial proteins within the Snf1 pathway are associated with FGD suggesting a potential novel connection between the ETC and the Snf1 pathway during carbon source transition. SIGNIFICANCE STATEMENTO_LIRespiratory incompetent electron-transport chain mutants are capable of metabolizing galactose as a carbon source. However, when ETC mutants encounter glucose, they lose this ability to metabolize galactose. C_LIO_LIThis study demonstrates that failure to derepress glucose repressed genes facilitated by the Snf1/AMPK pathway is primarily responsible for this phenotype in ETC mutants. C_LIO_LIThese results illustrate a novel signaling role for the ETC and suggest a possible metabolic intervention to certain disease phenotypes. C_LI

cell biology↗

bioRxiv2023

Identification of the yeast mannoprotein gene HZY1 as a key genetic determinant for yeast-derived haze in beer

With the sustained popularity of hazy IPAs, brewers have explored multiple approaches to maximizing stable haze that will remain in suspension throughout the shelf life of the beer. Our recent investigations into yeast-dependent haze have uncovered specific brewing yeast strains that promote the formation of haze in heavily dry-hopped beer styles. These brewing strains have been termed "haze-positive" and furthermore, the timing of dry hop additions has been found to be another key factor in producing this stable haze. Classical genetics have identified YIL169C (herein referred to as HZY1) as both necessary and sufficient for the haze-positive phenotype in the yeast strain most widely used for Hazy IPAs. HZY1 encodes a candidate glycoprotein and our recent findings suggest it is localized to the cell wall through a GPI anchor. Surprisingly, using long-read sequencing data we uncovered extensive genetic variation in HZY1 across brewing strains. The haze-positive phenotype correlates with an expansion in the N-terminal serine-rich region. We propose that the Hzy1 glycoprotein is a critical component to yeast-dependent colloidal haze and the genetic variation in this locus contributes the range of haze phenotypes observed across industrial brewing strains.

genetics↗

bioRxiv2023

Patulin contamination of hard apple cider by Paecilomyces niveus and other postharvest apple pathogens: assessing risk factors

Hard apple cider is considered to be a low-risk product for food spoilage and mycotoxin contamination due to its alcoholic nature and associated food sanitation measures. However, the thermotolerant mycotoxin-producing fungus Paecilomyces niveus may pose a significant threat to hard cider producers. Pa. niveus is known to infect apples (Malus xdomestica), and previous research indicates that it can survive thermal processing and contaminate finished apple juice with the mycotoxin patulin. To determine if hard apple cider is susceptible to a similar spoilage phenomenon, cider apples were infected with Pa. niveus or one of three patulin-producing Penicillium species and the infected fruits underwent benchtop fermentation. Cider was made with lab inoculated Dabinett and Medaille dOr apple cultivars, and patulin was quantified before and after fermentation. Results show that all four fungi can infect cider apples and produce patulin, some of which is lost during fermentation. Only Pa. niveus was able to actively grow throughout the fermentation process. To determine if apple cider can be treated to hinder Pa. niveus growth, selected industry-grade sanitation measures were tested, including chemical preservatives and pasteurization. High concentrations of preservatives inhibited Pa. niveus growth, but apple cider flash pasteurization was not found to significantly impact spore germination. This study confirms that hard apple cider is susceptible to fungal-mediated spoilage and patulin contamination. Pa. niveus should be of great concern to hard apple cider producers due to its demonstrated thermotolerance, survival in fermentative environments, and resistance to sanitation measures. HighlightsO_LIApple fruits of traditional cider cultivars Dabinett and Medaille dOr were found to be susceptible to infection by three patulin-producing Penicillium spp. and Paecilomyces niveus C_LIO_LIPa. niveus can grow in finished fermented hard cider at 5.22% ethanol C_LIO_LIPatulin levels in cider were reduced by fermentation but still exceeded 50 {micro}g/kg, a maximum limit set by various regulatory agencies C_LIO_LIPa. niveus was observed to be able to grow in low concentrations of three preservatives: potassium sorbate, sulfur dioxide, and sodium benzoate C_LI

microbiology↗

bioRxiv2018

Minor isozymes tailor yeast metabolism to carbon availability

Isozymes are enzymes that differ in sequence but catalyze the same chemical reactions. Despite their apparent redundancy, isozymes are often retained over evolutionary time for reasons that can be unclear. We find that, in yeast, isozymes are strongly enriched in central carbon metabolism. Using a gene expression compendium, we find that many isozyme pairs show anticorrelated expression during the respirofermentative shift, suggesting roles in adapting to changing carbon availability. Building on this observation, we assign function to two minor central carbon isozymes, aconitase 2 (ACO2) and pyruvate kinase 2 (PYK2). ACO2 is expressed during fermentation and proves advantageous when glucose is limiting. PYK2 is expressed during respiration and proves advantageous for growth on three-carbon substrates. PYK2s deletion is rescued by expressing the major pyruvate kinase, but only if that enzyme carries mutations mirroring PYK2s allosteric regulation. Thus, central carbon isozymes enable more precise tailoring of metabolism to changing nutrient availability.\n\nImportanceGene duplication is one of the main evolutionary drivers of new protein function. However, some gene duplicates have nevertheless persisted long-term without apparent divergence in biochemical function. Further, under standard lab conditions, many isozymes have subtle or no knockout phenotypes. These factors make it hard to assess the unique contributions of individual isozymes to fitness. We therefore developed a method to identify experimental perturbations that could expose such contributions, and applied it to yeast gene expression data, revealing a potential role for a set of yeast isozymes in adapting to changing carbon sources. Our experimental confirmation of distinct roles for two \"minor\" yeast isozymes, including one with no previously described knockout phenotype, highlight that even apparently redundant paralogs can have important and unique functions, with implications for genome-scale metabolic modeling and systems-level studies of quantitative genetics.

systems biology↗

bioRxiv2018

The Miniature-chemostat Aging Device: A new experimental platform facilitates assessment of the transcriptional and chromatin landscapes of replicatively aging yeast

Replicative aging of Saccharomyces cerevisiae is an established model system for eukaryotic cellular aging. A major limitation in yeast lifespan studies has been the difficulty of separating old cells from young cells in large quantities for in-depth comparative analyses. We engineered a new platform, the Miniature-chemostat Aging Device (MAD), that enables purification of aged cells at sufficient quantities to enable genomic and biochemical characterization of aging yeast populations. Using the MAD platform, we measured DNA accessibility (ATAC-Seq) and gene expression (RNA-Seq) changes in aging cells. Our data highlight an intimate connection between aging, growth rate, and stress, as many (but not all) genes that change with age have altered expression in cells that are subjected to stress. Stress-independent genes that change with age are highly enriched for targets of the signal recognition particle (SRP). By obtaining pure populations of old cells, we find that nucleosome occupancy does not change significantly with age; however, significant age-dependent changes in accessibility at ~12% of genomic loci reflect decreased replication and changing activities of cell cycle and metabolic regulators. Finally, ATAC-seq revealed that upregulating the proteasome by deleting UBR2 reduces rDNA instability usually observed in aging cells, demonstrating a connection between proteasome activity and genomic stability.

systems biology↗