Biology subjects

Johnson, A. E.

Publications and source records attributed to Johnson, A. E..

13 recordsLinked to original sources

bioRxiv2026

Individual-level social associations and social information use predict foraging success in winter mixed-species flocks

The acquisition of social information to improve foraging efficiency is considered one of the primary drivers of mixed-species flocks (MSFs). This flow of social information occurs among individuals of multiple species, but analyses of MSFs at the level of species fail to capture the nuances of this dynamic. We investigated how individual-level social associations in North American MSFs impact discovery of novel feeders presented alongside vocal cues. We used radio-frequency identification (RFID) data loggers to track arrivals of individually tagged black-capped chickadees (Poecile atricapillus), white-breasted nuthatches (Sitta carolinensis), and downy woodpeckers (Dryobates pubescens) at fixed feeders, and during novel feeder trials paired with chickadee, nuthatch, or white noise playbacks. For chickadees, a higher number of total associations and conspecific playbacks improved novel feeder discovery. The foraging benefits in nuthatches and woodpeckers were predicted by their individual-level associations with chickadees and these benefits only manifested during chickadee playbacks. We demonstrate that the advantages of mixed-species flocking are not uniformly distributed across species; rather, they are contingent upon individually maintained social associations and the presence of social information. These findings highlight the necessity of quantifying individual variation to accurately assess the evolutionary drivers and fitness consequences of species interactions.

animal behavior and cognition↗

bioRxiv2026

Release of BEC-1 from CED-9 stimulates lysosome tubulation in C. elegans by engaging Class III PI3K complex I

The anti-apoptotic protein CED-9 and the autophagy protein BEC-1 have been linked to autophagy regulation, but how their interaction modulates this process is not fully understood. Here, we find that the physical dissociation of BEC-1 from CED-9 influences lysosomal morphology in addition to autophagic activity in Caenorhabditis elegans. We present evidence that when autophagy is stimulated via dietary restriction, BEC-1 is released from CED-9 and assembles with VPS-34 and other members of the PI3K complex I to promote PI3P enrichment at lysosomal membranes and subsequent membrane tubulation. Mutation of two hydrophobic amino acids within a predicted BH-3 like motif of BEC-1 is sufficient to disrupt its interaction with CED-9, thereby constitutively inducing lysosomal tubulation and increasing autophagic cargo turnover. This phenotype is dependent on VPS-34 activity, linking the CED-9/BEC-1 dissociation to PI3K-dependent lysosomal remodeling. Collectively, our work identifies the CED-9/BEC-1 interaction as a molecular switch that governs apoptosis, autophagy, and lysosomal morphology.

cell biology↗

bioRxiv2026

ZDHHC17 Links S-Acylation, Huntington Disease, VCP-associated Multisystem Proteinopathy, and Amyotrophic Lateral Sclerosis.

Protein mislocalization is an important contributor to neurodegeneration. We have identified disrupted S-acylation as a driver of mislocalization. S11acylation, the addition of long-chain fatty acids to cysteine residues, is mediated by the ZDHHC family of S-acyltransferases, and regulates protein localization by modulating protein hydrophobicity. Among these enzymes, we have identified ZDHHC17 as a central node in neurodegenerative disease. Although decreased ZDHHC17 activity is correlated with Huntington disease (HD) pathology, its broader contributions to neurodegeneration remain poorly defined. Here, we present new evidence that ZDHHC17 S-acylates or interacts with multiple proteins implicated in amyotrophic lateral sclerosis (ALS), including Valosin-containing protein (VCP) and TAR DNA Binding Protein (TDP1143). We further confirm that VCP, TDP-43, FUS, C9ORF72, and SQSTM1 are S-acylated across rodent models of multiple neurodegenerative diseases, including HD, VCP-associated multisystem proteinopathy, and ALS. Using biochemical S-acylation assays and confocal microscopy, we show that ZDHHC17 S-acylates VCP, depletes the nuclear localization of both VCP and TDP-43, and modulates VCP-dependent toxicity via ER-stress. We additionally demonstrate that TDP-43 is S-acylated by ZDHHC9. Motivated by these findings, we investigated the functional significance of motor-neuronal (MN) ZDHHC17 by studying dHip14 (the fly analog of ZDHHC17) in Drosophila melanogaster. Here, we found that motor neuron-specific dHip14 knockdown (KD) in flies resulted in impaired motor function, whereas ubiquitous depletion led to pharate-adult lethality. Together, these results highlight a shared mechanism across neurodegenerative diseases. Collectively, our findings position ZDHHC17 as a critical enzyme that links fatty acylation, protein homeostasis, and neurodegeneration. Understanding how ZDHHC17 orchestrates S-acylation across different cellular pathways may reveal new therapeutic strategies to restore proteostasis in neurodegenerative disease.

molecular biology↗

bioRxiv2024

Clostridioides difficile colonization is not mediated by bile salts and requires Stickland fermentation of proline in an in vitro model of infection

Treatment with antibiotics is a major risk factor for Clostridioides difficile infection, likely due to depletion of the gastrointestinal microbiota. Two microbiota-mediated mechanisms thought to limit C. difficile colonization include conversion of conjugated primary bile salts into secondary bile salts toxic to C. difficile growth, and competition between the microbiota and C. difficile for limiting nutrients. Using a continuous flow model that simulates the nutrient conditions of the distal colon, we investigated how treatment with six clinically-used antibiotics influenced susceptibility to C. difficile infection in 12 different microbial communities cultivated from healthy individuals. Antibiotic treatment reduced microbial richness; disruption varied by antibiotic class and microbiota composition, but did not correlate with C. difficile susceptibility. Antibiotic treatment also disrupted microbial bile salt metabolism, increasing levels of the primary bile salt, cholate. However, changes in bile salt did not correlate with increased C. difficile susceptibility. Further, bile salts were not required to inhibit C. difficile colonization. We tested whether amino acid fermentation contributed to persistence of C. difficile in antibiotic- treated communities. C. difficile mutants unable to use proline as an electron acceptor in Stickland fermentation due to disruption of proline reductase (prdB-) had significantly lower levels of colonization than wild-type strains in four of six antibiotic-treated communities tested. Inability to ferment glycine or leucine as electron acceptors, however, was not sufficient to limit colonization in any communities. This data provides further support for the importance of bile salt-independent mechanisms in regulating colonization of C. difficile. IMPORTANCEC. difficile is one of the leading causes of hospital-acquired infections and antibiotic-associated diarrhea. Several potential mechanisms through which the microbiota can limit C. difficile infection have been identified and are potential targets for new therapeutics. However, it is unclear which mechanisms of C. difficile inhibition represent the best targets for development of new therapeutics. These studies demonstrate that in a complex in vitro model of C. difficile infection, colonization resistance is independent of microbial bile salt metabolism. Instead, the ability of C. difficile to colonize is dependent upon its ability to metabolize proline, although proline-dependent colonization is context-dependent and is not observed in all disrupted communities. Altogether, these studies support the need for further work to understand how bile- independent mechanisms regulate C. difficile colonization.

microbiology↗

bioRxiv2024

Modulatory Effects of IFN-γ and IL-22 on Inflammatory Signaling and Cellular Responses in Intestinal Epithelial Cells

Inflammatory bowel disease (IBD) continues to affect millions worldwide, with an increasing prevalence that highlights the urgent need for deeper understanding of its underlying immune mechanisms. The cytokine interactions, especially those mediated by cells from the TH1 and TH17 lymphocyte subsets, are crucial in orchestrating the immune landscape of IBD. TH1 cells are well known for producing TNF- and IFN{gamma}, which have been extensively studied for their roles in conjunction with each other within the context of IBD. TH17 cells secrete IL-22 and IL-17, with existing studies primarily focusing on IL-22s interaction with IL-17 rather than its interplay with other cytokines such as IFN{gamma}. Our study focuses on the co-stimulatory effects of IL-22 and IFN{gamma} using organoids derived from mouse small intestines to model epithelial interactions. We found that IFN{gamma} interferes with the capacity of IL-22 to up-regulate antimicrobial peptides, which is essential in mucosal defense. Additionally, higher concentrations of IL-22 enhance IFN{gamma}s ability to stimulate TNF- gene expression and CXCL10 protein production, indicating a dose-dependent relationship. This co-stimulation also led to an increased rate of cell death, influenced partly by TNF-. These findings suggest that IL-22, typically seen as an anti-inflammatory agent, can assume a pro-inflammatory role when combined with IFN{gamma}, complicating its effects on epithelial cells. This study highlights the need to consider specific cytokine interactions in developing more effective IBD treatments.

immunology↗

bioRxiv2023

A familial natural short sleep mutation promotes healthy aging and extends lifespan in Drosophila

Sleep loss typically imposes negative effects on animal health. However, humans with a rare genetic mutation in the dec2 gene (dec2P384R) present an exception; these individuals sleep less without the usual effects associated with sleep deprivation. Thus, it has been suggested that the dec2P384R mutation activates compensatory mechanisms that allows these individuals to thrive with less sleep. To test this directly, we used a Drosophila model to study the effects of the dec2P384Rmutation on animal health. Expression of human dec2P384R in fly sleep neurons was sufficient to mimic the short sleep phenotype and, remarkably, dec2P384R mutants lived significantly longer with improved health despite sleeping less. The improved physiological effects were enabled, in part, by enhanced mitochondrial fitness and upregulation of multiple stress response pathways. Moreover, we provide evidence that upregulation of pro-health pathways also contributes to the short sleep phenotype, and this phenomenon may extend to other pro-longevity models.

cell biology↗

bioRxiv2022

VCP acts downstream of tTAFs to downregulate mono-ubiquitinated H2A and promote spermatocyte differentiation in Drosophila

Valosin-containing protein (VCP) binds and extracts ubiquitinated cargo to regulate protein homeostasis. While VCP has been studied primarily in aging and disease contexts, it also affects germline development. However, the precise molecular functions of VCP in the germline, particularly in males, are poorly understood. Using the Drosophila male germline as a model system, we find that VCP translocates from the cytosol to the nucleus as germ cells transition into the meiotic spermatocyte stage. Importantly, nuclear translocation of VCP appears to be one critical event stimulated by testis-specific TBP-associated factors (tTAFs) to drive spermatocyte differentiation. Like tTAF mutants, spermatocyte gene expression fails to properly activate in VCP-RNAi testes, and germ cells arrest in early meiosis. At a molecular level, VCP activity supports spermatocyte gene expression by downregulating a repressive histone modification, mono-ubiquitinated H2A (H2Aub), at this developmental transition. Remarkably, experimentally blocking H2Aub in VCP-RNAi testes is sufficient to overcome the meiotic-arrest phenotype and to promote development through meiosis. Collectively, our data highlight VCP as a novel downstream effector of tTAFs that downregulates H2Aub to facilitate meiotic progression. SUMMARY STATEMENTVCP promotes the downregulation of mono-ubiquitinated H2A (H2Aub), potentially by driving H2A turnover. VCP-dependent downregulation of H2Aub occurs downstream of testis-specific TBP-associated factors and supports spermatocyte gene expression and differentiation.

developmental biology↗

bioRxiv2022

Ecological flexibility and selectivity in mixed-species flock participation in birds

Mixed-species groups are hypothesized to allow animals to minimize competitive interactions and maximize facilitative interactions. Individuals participation in mixed-species groups may reduce rates of competition and increase the social information available about predators or food availability. Behavioral plasticity may further increase these benefits as plastic species alter their rates of niche overlap with group mates. We investigate two axes of behavioral plasticity that may modulate how species interact with group mates in mixed-species groups--flexibility and selectivity. Specifically, we assess avian species patterns of selective preferences for participation in flocks of certain strata and whether behavioral flexibility in foraging strata corresponds with the foraging strata of flock mates. All species in our study maintained or increased their foraging strata overlap with flock mates, supporting the hypothesis that facilitation plays an important role in flock formation. Notably, the methods that species used varied: some species moved closer to flock mates via flexibly matching their flock mates behavior, some showed selectivity for flocks of certain stratums, and others did both. Ultimately, we show that species balance facilitative and competitive interactions with flock mates via multiple methods and that consideration of behavioral plasticity is integral to understanding the nuances of mixed-species flock interactions.

animal behavior and cognition↗

bioRxiv2022

A small molecule that inhibits the evolution of antibiotic resistance

Antimicrobial resistance (AMR) rapidly develops against almost all available therapeutics. New antibiotics target essential processes in bacteria but fail to address the root of the problem: mutagenesis and evolution. We recently proposed that inhibiting the molecular mechanisms underlying bacterial evolution is the ultimate solution to preventing AMR development. Here, we describe the first compound that inhibits the occurrence and progression of AMR by directly targeting a highly conserved bacterial evolvability factor, Mfd. We previously found that this RNA polymerase-associated translocase is required for rapid AMR development across highly divergent pathogens. Through an in vivo screen, we identified 43 potential Mfd-inhibiting compounds. Here we present on target validation, biochemical characterization, and in vivo efficacy studies of a lead compound, referred to as ARM-1. ARM-1 binds Mfd and modulates its RNA polymerase interaction. Inhibition of Mfd activity by ARM-1 delays the development of mutations and resistance acquisition, both in pure culture and during infection. Importantly, our data show that this compound prevents the evolution of AMR across highly divergent pathogens, including Pseudomonas aeruginosa, Staphylococcus aureus, Listeria monocytogenes, and Salmonella enterica serovar Typhimurium. The novel compound we present here has the potential to develop into a clinically useful "anti-evolution" drug. This work demonstrates that the molecular mechanisms of evolution are pharmaceutically targetable, and that this strategy could help prevent AMR development.

microbiology↗

bioRxiv2022

The high-resolution in vivo measurement of replication fork velocity and pausing

An important step towards understanding the mechanistic basis of the central dogma is the quantitative characterization of the dynamics of nucleic-acid-bound molecular motors in the context of the living cell, where a crowded cytoplasm as well as competing and potentially antagonistic processes may significantly affect their rapidity and reliability. To capture these dynamics, we develop a novel method, lag-time analysis, for measuring in vivo dynamics. The approach uses exponential growth as the stopwatch to resolve dynamics in an asynchronous culture and therefore circumvents the difficulties and potential artifacts associated with synchronization or fluorescent labeling. Although lag-time analysis has the potential to be widely applicable to the quantitative analysis of in vivo dynamics, we focus on an important application: characterizing replication dynamics. To benchmark the approach, we analyze replication dynamics in three different species and a collection of mutants. We provide the first quantitative locus-specific measurements of fork velocity, in units of kb per second, as well as replisome-pause durations, some with the precision of seconds. The measured fork velocity is observed to be both locus and time dependent, even in wild-type cells. In addition to quantitatively characterizing known phenomena, we detect brief, locus-specific pauses at rDNA in wild-type cells for the first time. We also observe temporal fork velocity oscillations in three highly-divergent bacterial species. Lag-time analysis not only has great potential to offer new insights into replication, as demonstrated in the paper, but also has potential to provide quantitative insights into other important processes.

biophysics↗

bioRxiv2022

Reproductive tradeoffs govern sexually dimorphic tubular lysosome induction in C. elegans

Animals of different sexes often exhibit unique behaviors that benefit their specific reproductive interests. In the nematode Caenorhabditis elegans, self-fertilizing hermaphrodites can reproduce without a mate and thus prioritize feeding to satisfy the high energetic costs of reproduction. However, males, which rely on finding potential mates for reproduction, sacrifice feeding and instead prioritize exploratory behavior. Here, we demonstrate that these differences in behavior are linked to sexual dimorphism at the cellular level; young males raised on a rich food source show constitutive induction of gut tubular lysosomes, a non-canonical lysosome morphology that typically forms in the gut of young hermaphrodites only when food is limited. We find that male-specific induction of gut tubular lysosomes on abundant food is due to self-imposed dietary restriction through daf-7/TGF{beta} signaling, which promotes mate-searching at the cost of feeding. While gut tubular lysosomes are largely absent from well-fed hermaphrodites at the start of adulthood, their induction accelerates in hermaphrodites in early aging, dependent on the presence of sperm and, partly, on embryo production. These findings identify tubular lysosome induction as a sexually dimorphic cellular event that may integrate animal physiology with sex-specific behavioral differences important for reproductive success.

cell biology↗

bioRxiv2021

Tubular lysosome induction couples animal starvation to healthy aging

Dietary restriction promotes longevity via autophagy activation. However, changes to lysosomes underlying this effect remain unclear. Using the nematode Caenorhabditis elegans, we show that induction of autophagic tubular lysosomes, which occurs upon dietary restriction or mTOR inhibition, is a critical event linking reduced food intake to lifespan extension. We find that starvation induces tubular lysosomes not only in affected individuals but also in well-fed descendants, and the presence of gut tubular lysosomes in well-fed progeny is predictive of enhanced lifespan. Furthermore, we demonstrate that expression of Drosophila SVIP, a tubular-lysosome activator in flies, artificially induces tubular lysosomes in well-fed worms and improves C. elegans health in old age. These findings identify tubular lysosomes as a new class of lysosomes that couples starvation to healthy aging. One-Sentence SummaryTubular lysosome induction promotes healthy aging.

cell biology↗

bioRxiv2018

Relief of the Dma1-mediated checkpoint requires Dma1 autoubiquitination and dynamic localization

Chromosome segregation and cell division are coupled to prevent aneuploidy and cell death. In the fission yeast Schizosaccharomyces pombe, the septation initiation network (SIN) promotes cytokinesis, but upon mitotic checkpoint activation, the SIN is actively inhibited to prevent cytokinesis from occurring before chromosomes have safely segregated. SIN inhibition during the mitotic checkpoint is mediated by the E3 ubiquitin ligase Dma1. Dma1 binds to the CK1-phosphorylated SIN scaffold protein, Sid4, at the SPB, and ubiquitinates it. Sid4 ubiquitination antagonizes the SPB localization of the Polo-like kinase Plo1, the major SIN activator, so that SIN signaling is delayed. How this checkpoint is silenced once spindle defects are resolved has not been clear. Here we establish that Dma1 transiently leaves SPBs during anaphase B due to extensive auto-ubiquitination. The SIN is required for Dma1 to return to SPBs later in anaphase. Blocking Dma1 removal from SPBs by permanently tethering it to Sid4 prevents SIN activation and cytokinesis. Therefore, controlling Dma1s SPB dynamics in anaphase is an essential step in S. pombe cell division and the silencing of the Dma1-dependent mitotic checkpoint.

cell biology↗