The chronological lifespan of Saccharomyces cerevisiae has significantly contributed to our understanding of aging in eukaryotic cells. However, gaining a genome-wide perspective of this trait remains challenging due to substantial discrepancies observed across genome-wide gene-deletion screens. In this study, we systematically compiled nine chronological-lifespan datasets and evaluated how shared experimental variables influenced screen variability. Furthermore, we performed a meta-analysis to compile a ranked catalog of key processes and regulators driving chronological longevity in yeast, ensuring their robustness across diverse experimental setups. These consistent chronological aging factors were enriched in genes associated with yeast replicative lifespan and orthologs implicated in aging across other model organisms. Functional analysis revealed that the downstream cellular mechanisms underlying chronological longevity in yeast align with well-established, universal hallmarks of aging. Importantly, we identified transcriptional regulators associated with these consistent genetic factors, uncovering potential global and local modulators of chronological aging. Our findings provide an integrated view of the core genetic landscape underlying aging in yeast, highlighting the value of the chronological lifespan paradigm for investigating conserved mechanisms of aging.

Persister cells are a subpopulation of bacteria capable of surviving antibiotic treatments and are thought to contribute to disease chronicity and symptom relapse of chronic conditions. Crohn’s disease (CD) is a multifactorial chronic inflammatory condition of the gastrointestinal tract, and adherent-invasive Escherichia coli (AIEC) have emerged as a key contributor to its pathogenesis. AIEC can survive, replicate, and produce persister cells within macrophages; however, beyond the LF82 reference strain, little is known about the persistence phenotype and its variability among AIEC strains. In this study, the survival of two AIEC reference strains was analyzed following ciprofloxacin treatment, a fluoroquinolone antibiotic commonly used in CD therapy. In addition, four AIEC clinical isolates and two non-AIEC E. coli pathotypes were included for comparison. We investigated the roles of the resident antibiotic resistance plasmid, the stress response protein HtrA, and macrophage-induced persister formation. Our results revealed broad variability in persister cell formation among AIEC strains. Remarkably, the reference NRG857c strain exhibits a threateningly high-persistence phenotype, with persistence levels 200-fold higher than LF82 and certain clinical isolates. Neither the antibiotic resistance plasmid nor HtrA were required for this phenotype. Moreover, unlike LF82, NRG857c did not exhibit increased persistence following macrophage internalization. Overall, our findings demonstrate the presence of distinct persistence phenotypes among AIEC strains and identify NRG857c as a high-persistence variant. These observations underscore the need to consider bacterial persistence in the management of CD, particularly given the potential presence of AIEC strains with elevated persistence capabilities.

Trypanosoma cruzi, the causing agent of Chagas disease, is the only known trypanosomatid pathogenic to humans having a complete histidine to glutamate pathway, which involves a series of four enzymatic reactions that convert histidine into downstream metabolites, including urocanate, 4-imidazolone-5-propionate, N-formimino-L-glutamate and L-glutamate. Recent studies have highlighted the importance of this pathway in ATP production, redox balance, and the maintenance of cellular homeostasis in T. cruzi. In this work, we focus on the first step of the histidine degradation pathway, which is performed by the enzyme histidine ammonia lyase. Here we determined the kinetic and biochemical parameters of the T. cruzi histidine ammonia-lyase. By generating null mutants of this enzyme using CRISPR-Cas9 we observed that disruption of the first step of the histidine degradation pathway completely abolishes the capability of this parasite to metabolise histidine, compromising the use of this amino acid as an energy and carbon source. Additionally, we showed that the knockout of the histidine ammonia lyase affects metacyclogenesis when histidine is the only metabolizable source and diminishes trypomastigote infection in vitro.

TDP-43 is linked to human diseases such as amyotrophic lateral sclerosis (ALS) and frontotemporal degeneration (FTD). Expression of TDP-43 in yeast is known to be toxic, cause cells to elongate, form liquid-like aggregates, and inhibit autophagy and TOROID formation. Here, we used the apt1∆ aah1∆ yeast model of inborn errors of metabolism, previously shown to lead to intracellular adenine accumulation and adenine amyloid-like fiber formation, to explore interactions with TDP-43. Results show that the double deletion shifts the TDP-43 aggregates from liquid-like droplets toward a more amyloid-like state. At the same time the deletions reduce TDP-43’s effects on toxicity, cell morphology, autophagy, and TOROID formation without affecting the level of TDP-43. This suggests that the liquid-like droplets rather than amyloid-like TDP-43 aggregates are responsible for the deleterious effects in yeast. How the apt1∆ aah1∆ deletions alter TDP-43 aggregate formation is not clear. Possibly, it results from adenine and TDP-43 fiber interactions as seen for other heterologous fibers. This work offers new insights into the potential interactions between metabolite-based amyloids and pathological protein aggregates, with broad implications for understanding protein misfolding diseases.

Eucaryotic cell functioning and development depend on the concerted activity of its organelles. In the model fungus Podospora anserina, sexual development involves a dynamic regulation of mitochondria, peroxisomes and the endoplasmic reticulum (ER), suggesting that their activity during this process is coordinated. The ER-Mitochondria Encounter Structure (ERMES) is a tether complex composed of the ER protein Mmm1 and the mitochondrial proteins Mdm10, Mdm12 and Mdm34, which mediates membrane contact-site formation between these organelles. This complex also mediates interactions between mitochondria and peroxisomes. Here we analyzed the role of the ERMES complex during P. anserina development. By studying a thermosensitive MDM10 mutant, we show that MDM10 is required for mitochondrial morphology and distribution, as well as for peroxisome membrane-remodeling and motility. We discovered that lipid droplets exhibit a subapical hyphal localization, which depends on MDM10. MDM10 is also required for ER shaping and dynamics, notably of the apical ER domains of the polarized-growing hyphal region, in a process that involves the activity of the protein YOP1. We also show that apical ER shaping involves a Spitzenkörper-associated membrane traffic, which implicates MDM10, and that the mycelial growth defect of mdm10 mutants is exacerbated when the ER-shaping proteins YOP1 or RTN1 are loss. Finaly, we show that MMM1 is strictly required for mycelial growth and sexual development, suggesting that its activity is essential. Our results show that the activity of distinct organelles depends on the ERMES complex, and that the function of this complex is critical for P. anserina growth and development.

Programmed cell death (PCD) in unicellular organisms is not well characterized. This study investigated the transcriptomic response of Acanthamoeba castellanii to G418-induced PCD, focusing on the role of alternative splicing (AS). RNA sequencing revealed extensive transcriptional changes, affecting approximately 70% of annotated genes over six hours of treatment. This analysis also highlighted significant alterations in pathways related to cell cycle, proteolysis, and RNA splicing. Analysis of AS events identified 18,748 differentially spliced events, predominantly intron retention (IR). Interestingly, retained introns displayed a 3′ bias in untreated cells, a pattern that shifted towards uniform distribution throughout the gene body during PCD. Additionally, we characterized retained introns during trophozoite stage and during PCD of the amoeba. Correlational analysis revealed a significant negative correlation between IR and transcript levels, suggesting a complex interplay between transcriptional and post-transcriptional regulation. The predominance of IR, coupled with its dynamic positional shift during PCD, points to a novel regulatory mechanism in A. castellanii PCD. These findings provide insights into the molecular mechanisms underlying PCD in this organism, potentially identifying new therapeutic targets and allowing us a better understanding of such process in A. castellanii, a facultative human pathogen.

Mucormycosis is a life-threatening infection caused by certain members of the fungal order Mucorales, with increased incidence in recent years. Individuals with untreated diabetes mellitus, and patients treated with deferoxamine are particularly susceptible to this infection. Elevated free iron concentrations in serum contribute to the development of mucormycosis. Pathogenic fungi have evolved multiple mechanisms to acquire and utilize free iron or extract it from the various iron-binding molecules within the host. The utilization of hydroxamate siderophores as xenosiderophores may contribute to the development of mucormycosis. The genome of Mucor lusitanicus encodes one Sit1 siderophore transporter. In this study, the role of the sit1 gene was characterized by generating knockout mutants using CRISPR-Cas9. Relative transcript level of the sit1 gene significantly increased in the presence of deferoxamine- and deferasirox-iron complexes. Lack of sit1 resulted in altered germination of spores and growth ability, and decreased virulence. Furthermore, absence of the gene caused elevated transcript levels of a ferric reductase (FRE), a low-affinity iron permease (FET4) and a copper dependent iron oxidase (FET3). Our result suggests that expressions of the genes involved in iron uptake affect each other. The lack of Sit1 resulted in an increased transcript level of the FRE3 gene, which may be able to reduce iron from the siderophore-iron complex. The reduced and liberated iron may be then taken up by activated FET4a. This study highlights the significance of understanding the iron acquisition mechanisms of pathogenic fungi to develop effective treatments for fungal infections.

Glioblastoma is a malignant astrocytic tumor of the brain. A significantly decrease of glioblastoma cell proliferation and survival can be achieved by activating the M2 muscarinic acetylcholine receptor (a G protein-coupled receptor, or GPCR) with two agonist molecules, the orthosteric agonist Arecaidine Propargyl Ester (APE) and the dual-steric agonist Iper-8-naphthalimide (N-8-Iper). In glioblastoma cells, these agonists caused mitochondrial damage and an altered lipid profile. To characterize the mitochondrial dysfunction induced by the muscarinic agonists, we tested APE and N-8-Iper in S. cerevisiae, a yeast model system specifically suitable to study the activity of molecules of pharmaceutical interest on mitochondria. N-8-Iper, but not APE, induced mitochondrial dysfunction in S. cerevisiae cells in a time- and concentration-dependent manner. These results suggest that the agonist N-8-Iper on glioblastoma cell cultures has a direct effect on mitochondrial function. Moreover, since GPCRs are evolutionarily conserved from yeast to humans, these results confirm that the yeast system is a suitable model for studying human GPCRs.

The interaction between intratumoral microbiome and the tumor microenvironment (TME) has furthered our understanding of tumor ecology. Yet, the implications of their interaction for lung cancer management remain unclear. In the current work, we collected host transcriptome samples and matched intratumoral microbiome samples, as well as detailed clinical metadata from The Cancer Genome Atlas (TCGA) of 478 patients with lung adenocarcinoma (LUAD). Utilizing the multiomics integration approach, we comprehensively investigated the crosstalk between the TME and intratumoral microbiome in patients with LUAD. First, we developed a prognostic model based on the TME signatures (TMEindex) that clearly distinguished clinical, survival, and response to immunotherapy of patients with LUAD. Additionally, we found profound differences in intratumoral microbiota signatures, including alpha- and beta-diversity, among patients with different survival risks based on the TME signatures. In depth, we detected that genera Luteibacter and Chryseobacterium were strongly negatively and positively associated with patients’ survival risk, respectively, suggesting their opposing roles in cancer progression. Moreover, we developed a model that fused intratumoral microbial abundance information with TME signatures, called intratumoral microbiome-modified TMEindex (IMTMEindex), leading in predicting patient overall survival at 1-, 3-, and 5-years. Future clinical profiling of the specific intratumoral microbes in the TME could improve prognosis, inform immunotherapy, and facilitate the development of novel therapeutics for LUAD.

Ankylosing spondylitis (AS) is a chronic inflammatory disease with complex pathogenesis influenced by genetic, immunological and environmental factors. Recent evidence suggests that gut microbiota significantly contributes to AS etiopathogenesis. Dysbiosis and altered immune responses in the gut potentially trigger or exacerbate the disease through intestinal barrier disruption, alteration of the IL-23/17 axis and metabolite production. This review explores the growing role of gut microbiota in AS and its potential to reshape targeted treatment strategies and facilitate development of adjunct therapies to address disease onset and progression. AS is a multifactorial disease in which gut dysbiosis plays a significant role influencing immune regulation notably through the IL-23/17 pathway. Alterations in gut microbiota composition and its metabolites contribute to systemic inflammation, reinforcing a self-perpetuating feedback loop between gut and spinal inflammation that drives disease progression. Emerging evidence has linked microbial mechanisms to HLA-B27 misfolding promoting endoplasmic reticulum stress and triggering molecular mimicry through gut microbial-associated molecular patterns further contributing to AS pathogenesis. Given the crucial role of gut microbiota in AS, targeting microbiota imbalances presents a promising avenue for novel therapeutic strategies. Although it remains unclear whether gut inflammation and microbial changes precedes AS onset, current evidence suggests an ongoing cycle of autoimmune inflammation involving both the gut and joints. Further research, particularly longitudinal studies, are needed to better understand the gut-joint axis and its potential therapeutic implications in AS management.