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Stacy, C. L.

Publications and source records attributed to Stacy, C. L..

5 recordsLinked to original sources

Surprising regulatory plasticity for the conserved HOG pathway in diverse Saccharomyces cerevisiae strains

Mitogen-activated protein kinases (MAPKs) display remarkable regulatory plasticity across evolution, ranging from highly specialized pathways to broadly responsive global signaling hubs. In the budding yeast Saccharomyces cerevisiae, the high-osmolarity glycerol (HOG) network has served as a paradigm for largely stress-specific MAPK signaling, where the Hog1 MAPK coordinates osmoadaptation. This stands in sharp contrast to Hog1 orthologs in other fungi and humans, which respond not only to osmotic stress, but also diverse stresses including UV, heat shock, oxidative stress, and pathogen signals. Whether the relative osmospecificity of S. cerevisiae Hog1 represents an ancestral feature or lineage-specific evolution remains unclear. The majority of foundational work on S. cerevisiae HOG signaling has been performed in laboratory strains that are known to be genetic and phenotypic outliers, and we have been leveraging wild S. cerevisiae strains to understand aspects of stress signaling that may have been lost in laboratory strains. Here, we examined the phenotypic effects of hog1{Delta} mutations in a commonly-used laboratory S. cerevisiae strain and diverse wild strains on stress cross protection and gene expression. Our findings demonstrate an expanded role in cross-stress protection for Hog1 in wild yeast strains compared to the laboratory strain. More strikingly, we identified a large number of Hog1-dependent genes for non-osmotic stresses in the wild strains that were completely absent in the lab strain. Notably, the Hog1 regulon in wild strains responding to non-osmotic stresses is largely distinct from the canonical osmotic stress response, which we show likely occurs through non-canonical cytoplasmic functions. These findings reveal surprising within-species plasticity for the highly conserved HOG network, suggesting that evolutionary transitions between specialist to generalist stress signaling may occur with relative ease.

genetics↗

MIC*: A Framework for Interpretable Analysis of Ordinal Viability Data

Microbial survival assays frequently use ordered categorical (ordinal) scores, such as semi-quantitative viability scores across drug concentrations. While these ordinal data provide rich information about dose-response dynamics, they require appropriate statistical approaches for proper analysis. Proportional-odds (PO) ordinal regression is specifically designed for such data, modeling the ordered nature of scores while accommodating continuous variables such as concentration. However, despite its advantages, PO regression remains underutilized in microbiology because its cumulative log-odds outputs are abstract and biologically unintuitive. Consequently, researchers often resort to flawed alternatives: collapsing scores into binary outcomes (growth/no growth), treating scores as continuous values for t-tests or ANOVA, or applying nonparametric tests that ignore dose-response structure. Each approach sacrifices power or validity, risking unreliable conclusions. To allow researchers to better leverage the power of ordinal datasets, we introduce MIC*, a summary measure that translates PO regression results into biologically interpretable units. MIC* is defined as the treatment concentration where the predicted probability of "no viability" equals 0.5, and is thus conceptually related to the minimum inhibitory dose (MIC) widely used in antimicrobial research. MIC* retains the rigor of ordinal regression while providing more biologically intuitive effect size measures. The MIC* framework enables formal comparisons as absolute differences ({Delta}MIC*) or relative fold-changes ({Delta}log2MIC*), allowing for robust statistical comparisons between samples. Monte Carlo simulations demonstrate that MIC* yields robust estimates with superior power compared to conventional statistical methods, while case studies demonstrate practical utility. To ensure wide adoption, we provide a suite of open-source tools: a BLInded Scoring System (BLISS) for generating ordinal viability scores, and web-based (MICalculator) and R package (ordinalMIC) alternatives for performing complete MIC* analyses, thus reducing barriers to appropriate analysis of ordinal phenotypes in microbiology. ImportanceMicrobiologists routinely use visual scoring systems to assess cell viability for antimicrobial and stress resistance studies. However, current analysis approaches tend to be problematic, with researchers seeking simple approaches that either discard valuable information or violate important statistical assumptions. While rigorous and appropriate statistical approaches exist, they are rarely used in microbiology because they produce outputs that are non-intuitive and require specialized expertise to implement. Our MIC* framework overcomes these longstanding barriers by translating abstract outputs into an intuitive, concentration-based metric akin to the minimum inhibitory concentration (MIC) well Known to microbiologists. MIC* allows for biologically interpretable comparisons on both absolute ({Delta}MIC*) and relative ({Delta}log2MIC*) scales, allowing for facile between-sample comparisons. MIC* outperforms conventional statistical approaches, and we offer user-friendly software tools to enable broad adoption by the community.

microbiology↗

Stability Comparisons between Natural versus Engineered Archaeal Heat Shock Proteins

Crenarchaeal group II chaperonins (a.k.a., "heat shock" proteins, HSPs) are abundantly expressed in species of the family Sulfolobaceae. HSP and HSP{beta} expression is upregulated during thermal shock. HSPs are subunits of larger octadecameric complexes that function to protect intracellular proteins during thermal stress. Engineered HSPs have been constructed with the idea of protecting enzymes in industrial reactions. HSP{beta}-coh, a fusion protein comprised of HSP{beta} and type 1 cohesin from Clostridium thermocellum was used for proof-of-concept. Dockerin-endowed cellulolytic enzymes bind to the complex via cohesin-dockerin interactions. Enzymatic activity (i.e., hydrolysis of lignocellulose) is retained when the platform is used at high temperatures (e.g., 85-88{degrees}C). Moreover, enhancement persists on acid-pretreated substrates prompting the question: Are HSPs acid tolerant? In this study, HSP structural integrity is examined at different temperatures and pH. Far-UV circular dichroism and intrinsic fluorescence indicate HSP and HSP{beta} retain structural integrity at neutral pH over a range of temperatures (25-90{degrees}C) while HSP{beta}-coh is less tolerant to thermal stress. Structural integrity is compromised for all subunits at ultra-low pH (i.e., pH 2) with HSP showing the most susceptibility. Secondary structures of all HSPs are resilient under mildly acidic conditions (pH 4). ANS binding assays indicate a shift in tertiary structure for all subunits at ultra-low pH. Limited trypsin digestion reveals that the backbone of HSP{beta}-coh is the most flexible and HSP{beta} is the most resistant. Results suggest that HSP and HSP{beta} are more resilient than HSP{beta}-coh under thermal challenge and that there are limits to the acid tolerance of all HSPs.

biochemistry↗

Quantifying relative virulence: When μmax fails and AUC alone just isn't enough

AO_SCPLOWBSTRACTC_SCPLOWOne of the more challenging aspects in quantitative virology is quantifying relative virulence between two (or more) viruses that have different replication dynamics in a given susceptible host. Host growth curve analysis is often used to detail virus-host interactions and to determine the impact of viral infection on a host. Quantifying relative virulence using canonical parameters such as maximum specific growth rate (max) can fail to provide accurate information regarding experimental infection, especially for non-lytic viruses. Although area-under-the-curve (AUC) can be more robust by through calculation of a percent inhibition (PIAUC), this metric can be sensitive to limit selection. In this study, using empirical and extrapolated data from Sulfolobus Spindle-shaped Virus (SSV) infections, we introduce a novel, simple metric that is proven to be more robust and less sensitive than traditional measures for determining relative virulence. This metric (ISC) more accurately aligns biological phenomena with quantified metrics from growth curve analysis to determine trends in relative virulence. It also addresses a major gap in virology by allowing comparisons between non-lytic single-virus/single-host (SVSH) infections and between non-lytic versus lytic virus infection on a given host. How ISC may be applied to polymicrobial infection - both coinfection of a host culture and superinfection of a single cell with more than one virus (or other pathogen type) is a topic of ongoing investigation.

microbiology↗

Host-dependent differences in replication strategy of the Sulfolobus Spindle-shaped Virus strain SSV9 (a.k.a., SSVK1): Lytic replication in hosts of the family Sulfolobaceae

The Sulfolobus Spindle-shaped Virus (SSV) system has become a model for studying thermophilic virus biology, including archaeal host-virus interactions and biogeography. Several factors make the SSV system amenable to studying archaeal genetic mechanisms (e.g., CRISPRs) as well as virus-host interactions in high temperature acidic environments. First, it has been shown that endemic populations of Sulfolobus, the reported SSV host, exhibit biogeographic structure. Second, the acidic (pH<4.5) high temperature (65-88{degrees}C) SSV habitats have low biodiversity, thus, diminishing opportunities for host switching. Third, SSVs and their hosts are readily cultured in liquid media and on gellan gum plates. Fourth, given the wide geographic separation between the various SSV-Sulfolobus habitats, the system is amenable for studying allopatric versus sympatric virus-host interactions. Previously, we reported that SSVs exhibit differential infectivity on allopatric and sympatric hosts. We also noticed a wide host range for virus strain SSV9 (a.k.a., SSVK1). For decades, SSVs have been described as "non-lytic" dsDNA viruses that infect species of the genus Sulfolobus and release virions via "blebbing" or "budding" as a preferred strategy over host lysis. Here, we show that SSVs infect more than one genus of the family Sulfolobaceae and, in allopatric hosts, SSV9 does not appear to release virions by blebbing. Instead, SSV9 appears to lyse all susceptible allopatric hosts tested, while exhibiting canonical non-lytic viral release via "blebbing" (historically reported for all other SSVs), on a single sympatric host. Lytic versus non-lytic virion release does not appear to be driven by multiplicity of infection (MOI). Greater relative stability of SSV9 compared to other SSVs (i.e., SSV1) in high temperature, low pH environments may contribute to higher transmission rates. However, neither higher transmission rate nor relative virulence in SSV9 infection drives replication profile (i.e., lytic versus non-lytic) in susceptible hosts. Although it is known that CRISPR-Cas systems offer protection against viral infection in prokaryotes, CRISPRS are not reported to be a determinant virus replication strategy. Thus, the genetic/molecular mechanisms underlying SSV9-induced lysis are unknown. These results suggest that there are unknown genetic elements, resulting from allopatric evolution, that drive virion release strategy in specific host strain-SSV strain pairings.

microbiology↗