Biology subjects

Kimmey, J. M.

Publications and source records attributed to Kimmey, J. M..

7 recordsLinked to original sources

bioRxiv2026

Longitudinal tracking reveals developmental transitions in zebrafish clock gene expression

Circadian clocks coordinate physiological and behavioral rhythms by synchronizing biological processes with environmental cues. These rhythms emerge during development, but it remains unclear whether their component genes are activated by a common program or assembled through distinct regulatory pathways. To address this, we used longitudinal luciferase reporters to monitor per3 and per2 expression across zebrafish embryonic and larval development. Although both genes are canonical components of the circadian clock, they showed strikingly different developmental regulation. Two temporal frames of circadian gene expression were identified: an embryonic stage and a larval stage, each evident under different entrainment conditions. Per3 displayed early rhythmic expression in light/dark conditions, which was independent of per2 and cry1a light-entrainment regulation, but required bmal activity. Meanwhile, per2 displayed light-responsive transcription and remained largely bmal-independent. At the same time, both genes exhibited an endogenous embryonic expression that could not be explained solely by light-driven regulation, indicating that developmental inputs contribute to clock gene activation before mature larval rhythms are established. These findings demonstrate that the zebrafish circadian system is not assembled through a single synchronized onset of clock gene expression, but through gene-specific regulatory programs that shift across development.

cell biology↗

bioRxiv2026

An unrecognized host response to microbial exposure resets circadian timing

As ubiquitous features of every natural environment, microbes have profoundly shaped eukaryotic biology throughout evolution. Circadian clocks evolved in all domains of life as central regulators that align physiology with environmental cycles, yet whether they respond directly to microbial signals remains unknown. Here, we demonstrate that evolutionarily diverse microbes potently reset mammalian cellular clocks and can drive phase shifts in plants and algae, indicating cross-kingdom effects of microbes on circadian rhythms. In mammals, exposure to soluble bacterial components distinct from canonical innate immune ligands induces acute PER2 upregulation independently of Bmal1 or nascent transcription. A targeted inhibitor screen and biochemical assays implicate p38 MAPK as a modulator of this response. Taken together, this positions bacterial exposure as a previously unrecognized circadian clock input, revealing a new axis of host-microbe interaction that modulates biological timing at the cellular level.

cell biology↗

bioRxiv2024

Streptococcus pneumoniae augments circadian clock gene expression in zebrafish cells

The circadian clock is a highly coordinated, cell-autonomous process that regulates the daily internal rhythms of biological organisms. Circadian clocks have been identified in various organisms, including mammals, invertebrates, cyanobacteria, and plants. The zebrafish (Danio rerio) is a practical model for studying the vertebrate circadian clock due to its small size, ease of manipulation, gene tractability, and direct light responsiveness. Several studies have revealed that bacterial, viral, and parasitic infections can impact the expression of circadian genes in mammals. While some evidence suggests that this may also be the case in zebrafish, no studies have investigated the direct effects of bacterial exposure on the zebrafish clock. Here, using zebrafish Z3 cells, we show that exposure to heat-killed Streptococcus pneumoniae (HK-Spn) can augment the expression of core repressive factors, including per1b, per2, per3, and cry1a. Further investigation demonstrated that HK-Spn induces the production of reactive oxygen species (ROS) in Z3 cells and that the addition of NAC, a ROS antioxidant, blocks Spn-mediated induction of per2, cry1a, and per3. Additionally, HK-Spn augmented the expression of tefa and tefb, an effect NAC suppressed. These results suggest the involvement of a ROS-dependent pathway in the augmentation of per2, cry1a, and per3 by HK-Spn. Moreover, the activation of tefa and tefb by HK-Spn represents promising new targets for further investigation of the regulation of these genes.

microbiology↗

bioRxiv2023

ATG5 suppresses type I IFN-dependent neutrophil swarming and NETosis

Inflammation is critical for controlling infections, but when left unchecked can cause tissue damage and disease. For tuberculosis, the leading cause of death due to infection1, host inflammation is responsible for the clinical symptoms2, morbidity2, and mortality3,4. Specifically, neutrophil-dominated inflammation is associated with tuberculosis disease progression3,5,6. Therefore, understanding how neutrophil functions are regulated during infection is important for developing ways to prevent disease. Atg5 was the first gene shown to specifically function within neutrophils to promote control of Mycobacterium tuberculosis7, the causative agent of tuberculosis. ATG5 is best studied for its role in autophagy8-11, however, the protective activity of ATG5 in neutrophils was unexpectedly independent of other autophagy proteins and remained elusive7. We report here that ATG5, but not other autophagy proteins, is required in neutrophils to suppress neutrophil NETosis and swarming that occur due to elevated type I interferon levels during M. tuberculosis infection. The elevated level of NETosis that results from loss of ATG5 expression contributes to the early susceptibility of Atg5fl/fl-LysM-Cre mice during M. tuberculosis infection. NETosis is associated with poor disease outcomes in tuberculosis12,13 and COVID-19 patients14,15, as well as during other inflammatory diseases in humans16,17. Our studies identify an essential regulator of NETosis and elucidate previously unappreciated roles for ATG5 during infection, which may inform the design of host-directed therapeutics modulating these pathways.

immunology↗

bioRxiv2022

Autophagy is required in macrophages and dendritic cells to prevent early recruitment of neutrophils during Mycobacterium tuberculosis infection

The immune response to Mycobacterium tuberculosis infection determines tuberculosis disease outcomes, yet we have an incomplete understanding of what immune factors contribute to a protective immune response. Neutrophilic inflammation has been associated with poor disease prognosis in humans and in animal models during M. tuberculosis infection and, therefore, must be tightly regulated. ATG5 is an essential autophagy protein that is required in innate immune cells to control neutrophil-dominated inflammation and promote survival during M. tuberculosis infection, however, the mechanistic basis for how ATG5 regulates neutrophil recruitment is unknown. To interrogate what innate immune cells require ATG5 to control neutrophil recruitment during M. tuberculosis infection, we used different mouse strains that conditionally delete Atg5 in specific cell types. We found that ATG5 is required in CD11c+ cells (lung macrophages and dendritic cells) to control the production of proinflammatory cytokines and chemokines during M. tuberculosis infection, which would otherwise promote neutrophil recruitment. This role for ATG5 is autophagy-dependent, but independent of mitophagy, LC3-associated phagocytosis, and inflammasome activation, which are the most well-characterized ways that autophagy proteins regulate inflammation. In addition to the increase in proinflammatory cytokine production during M. tuberculosis infection, loss of ATG5 in innate immune cells also results in an early induction of TH17 responses. Despite prior published in vitro cell culture experiments supporting a role for autophagy in controlling M. tuberculosis replication in macrophages, loss of autophagy does not affect M. tuberculosis burden in macrophages in vivo and, therefore, the effects of autophagy on inflammatory responses occur without changes in pathogen numbers. These findings reveal new roles for autophagy proteins in lung resident macrophages and dendritic cells that are required to suppress inflammatory responses that are associated with poor control of M. tuberculosis infection.

immunology↗

bioRxiv2020

Role of Inflammasome-independent Activation of IL-1β by the Pseudomonas aeruginosa Protease LasB

Pulmonary damage by Pseudomonas aeruginosa during cystic fibrosis lung infection and ventilator-associated pneumonia is mediated both by pathogen virulence factors and host inflammation. Impaired immune function due to tissue damage and inflammation, coupled with pathogen multidrug resistance, complicates management of these deep-seated infections. Therefore, preservation of lung function and effective immune clearance may be enhanced by selectively controlling inflammation. Pathological inflammation during P. aeruginosa pneumonia is driven by interleukin-1{beta} (IL-1{beta}). This proinflammatory cytokine is canonically regulated by caspase-family inflammasome proteases, but we report that plasticity in IL-1{beta} proteolytic activation allows for its direct maturation by the pseudomonal protease LasB. LasB promotes IL-1{beta} activation, neutrophilic inflammation, and destruction of lung architecture characteristic of severe P. aeruginosa pulmonary infection. Discovery of this IL-1{beta} regulatory mechanism provides a distinct target for anti-inflammatory therapeutics, such that matrix metalloprotease inhibitors blocking LasB limit inflammation and pathology during P. aeruginosa pulmonary infections. HighlightsO_LIIL-1{beta} drives pathology during pulmonary infection by Pseudomonas aeruginosa. C_LIO_LIThe Pseudomonas protease LasB cleaves and activates IL-1{beta} independent of canonical and noncanonical inflammasomes C_LIO_LIMetalloprotease inhibitors active against LasB limit inflammation and bacterial growth C_LI Research in ContextInflammation is highly damaging during lung infections by the opportunistic pathogen Pseudomonas aeruginosa. Sun et al. demonstrate that the Pseudomonas LasB protease directly activates IL-1{beta} in an inflammasome-independent manner. Inhibition of IL-1{beta} conversion by LasB protects against neutrophilic inflammation and destruction of the lung. Adjunctive therapeutics that limit pathological inflammation induced by infection would be beneficial for the treatment of pulmonary infections when used with conventional antibiotics.

microbiology↗

bioRxiv2020

Exploration of bacterial bottlenecks and Streptococcus pneumoniae pathogenesis by CRISPRi-seq

Streptococcus pneumoniae is a commensal bacterium of the human nasopharynx, but can cause harmful infections if it spreads to other parts of the body, such as pneumonia, sepsis or meningitis. To facilitate pathogenesis studies, we constructed a doxycycline-inducible pooled CRISPR interference (CRISPRi) library targeting all operons in protypical S. pneumoniae strain D39V. Our library design allows fitness within the pool to be assessed by a one-step PCR reaction directly followed by Illumina sequencing (CRISPRi-seq). The doxycycline-inducible CRISPRi system is tightly controllable and suitable for both bottleneck exploration and evaluation of gene fitness in vitro and in vivo. Here, we applied CRISPRi-seq to identify genetic factors important for causing pneumococcal pneumonia. Mice were infected intratracheally with our CRISPRi library and bacteria collected at 24 h (from lung) and 48 h (from both lung and blood) post-infection. CRISPRi-seq showed a critical bottleneck at 48 h after intratracheal infection, with only a few bacteria surviving the brunt of the innate immune response to cause systemic infection. However, earlier at 24 h post-infection, many significant differences in gene fitness cost between in vitro and in vivo conditions were identified, including genes encoding known and putative novel virulence factors, genes essential only in vivo, and genes essential only in vitro. A key advantage of CRISPRi-seq over traditional transposon-based genetic screens is that all genes, including essential genes, can be tested for their role in virulence and pathogenicity. The approaches developed here should be generally applicable to study infection bottlenecks and in vivo fitness for other important human and animal pathogens.

microbiology↗