The publication and scientific implementation of scholarly articles is a collaborative effort that unites readers, authors, editors, and referees. A scientific journal thereby serves as a vital platform, enabling these interactions and fostering a shared commitment to advancing the quality and impact of scientific communication. In this short editorial, we celebrate the milestone of publishing the 500th article in Microbial Cell by highlighting these collective efforts. Importantly, from the outset of the journal more than ten years ago, we have cultivated a handcrafted organ that is produced by scientists for scientists. In that frame, we have followed and advocated a radical open access approach that fuels interaction and visibility of such cooperative endeavors for the public good.

Molecular de-extinction has emerged as a novel strategy for studying biological molecules throughout evolutionary history. Among the myriad possibilities offered by ancient genomes and proteomes, antimicrobial peptides (AMPs) stand out as particularly promising alternatives to traditional antibiotics. Various strategies, including software tools and advanced deep learning models, have been used to mine these host defense peptides. For example, computational analysis of disulfide bond patterns has led to the identification of six previously uncharacterized β-defensins in extinct and critically endangered species. Additionally, artificial intelligence and machine learning have been utilized to uncover ancient antibiotics, revealing numerous candidates, including mammuthusin, and elephasin, which display inhibitory effects toward pathogens in vitro and in vivo. These innovations promise to discover novel antibiotics and deepen our insight into evolutionary processes.

Vaginal microbiota involves seven communities-state types (CST), four dominated by Lactobacillus. L. crispatus, particularly, offers enhanced protection against infections. Recurrent vulvovaginal candidiasis and trichomoniasis affect millions of people annually, often asymptomatically, facilitating infection spread and leading complications. Co-culture, the technique of cultivating different microbial populations together to mimic real-life conditions, enables the study of microorganism interactions, including inhibitory or promotive effects on pathogens. This review compiles data on co-culture techniques to analyze interactions among Lactobacillus spp., Candida spp., and Trichomonas vaginalis. PubMed was searched using medical subject headings (MESH) terms, ‘co-culture’, ‘coculture,’ ‘cocultivation,’ ‘co-incubation,’ and ‘Trichomonas vaginalis’, ‘Candida spp.’, ‘Lactobacillus spp.’. Articles were selected based on relevance to vaginal health, English language, availability, and use of co-culture or co-incubation techniques in the past 24 years. Co-culture and co-incubation studies over the past 24 years have advanced our understanding of microbiota-host, pathogen-host, and pathogen-host-microbiota interactions. These studies reveal that microbiota composition impacts infections, with the microbiota producing substances against pathogens and pathogens developing stress tolerance mechanisms. They elucidate pathogen virulence factors, interactions with immune cells, and how ecological relationships between microorganisms can enhance pathogenicity.

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.

The cervicovaginal microbiome (CVM) is increasingly being considered as an important aspect of women’s health, particularly in relation to the risk and progression of sexually transmitted infections (STIs). CVM composition varies significantly between individuals and is shaped by factors including diet, age, environmental exposures, and lifestyle. Understanding these influences may shed light on how microbial imbalances contribute to infection susceptibility and the development of reproductive health disorders. Five distinct community state types (CSTs) classify common CVM compositions. Most CSTs (I, II, III, V) are characterized by a dominant Lactobacillus species and are associated with better or neutral reproductive health, including reduced coincident detection of STIs such as Chlamydia trachomatis. In contrast, CST IV is composed of diverse, predominantly anaerobic, microbial species and is associated with CVM dysbiosis, bacterial vaginosis, and a heightened risk of STI acquisition. This review examines the complex interplay between the CVM, C. trachomatis infection, and host immune responses, highlighting the role of metabolites such as short-chain and long-chain fatty acids, indole, and iron in modulating pathogen survival and host defenses. Additionally, the impacts of CVM composition on C. trachomatis persistence, ascension, and clearance are discussed, alongside co-infection dynamics with pathogens like Neisseria gonorrhoeae and Mycoplasma genitalium.

Mitochondria are essential organelles that form a dynamic network within cells. The fusion, fission, and transport processes among mitochondria must reach a balance, which is achieved through complex regulatory mechanisms. These dynamic processes and regulatory pathways are highly conserved across species and are coordinated to help cells respond to environmental stress. The budding yeast Saccharomyces cerevisiae has become an important model organism for studying mitochondria dynamics due to its genetic tractability and the conservation of key mitochondrial regulators. Previous research on mitochondria dynamics in yeast has provided valuable insights into the regulatory pathways in eukaryotic cells. It has helped to elucidate the mechanisms related to diseases associated with disrupted mitochondria dynamics. This review explores the molecular mechanisms underlying mitochondria dynamics and their physiological roles in Saccharomyces cerevisiae. The knowledge we learned from the primary eukaryotic yeast cell will aid us in advancing future research on the regulatory mechanisms of mitochondria in both health and disease.

Acanthamoeba castellanii is a ubiquitous free-living amoeba that can cause severe infections in humans. Unlike most other organisms, A. castellanii possesses a “complete” mitochondrial respiratory chain, meaning it contains several additional enzymes that contribute to its metabolic versatility and survival in diverse environments. This review provides a comprehensive overview of the mitochondrial respiratory chain in A. castellanii, focusing on the key alternative components involved in oxidative phosphorylation and their roles in energy metabolism, stress response, and adaptation to various conditions. The functional characterization of the alternative oxidase (AOX), uncoupling protein (UCP), and alternative NAD(P)H dehydrogenases, highlight their roles in reducing oxidative stress, modulating proton gradients, and adapting to changes in temperature and nutrient availability. These proteins and systems serve a role in the survival of A. castellanii under stressful conditions such as starvation and cold conditions. Further knowledge of the respiratory chain of the amoeba has potential implications for understanding the evolution of mitochondrial respiration and developing new therapies for treating Acanthamoeba infections.

Cholelithiasis is one of the most common diseases of the biliary system. Neutrophil extracellular traps (NETs) in the liver play an important role in accelerating the formation of gallstones. The upstream mechanism of NETs formation remains unclear. In this study, 16S rRNA sequencing was used to screen the differential gut microbiota in mice with gallstones. Transcriptome sequencing was used to screen the differentially expressed core genes and signalling pathways of Clostridium scindens that acted on human colonic epithelial cells. Western blotting was used to verify the protein expression of TLR2 and the NF-κB pathway. RT-PCR was used to verify the mRNA expression of TLR2, CXCL1 and the NF-κB pathway. ELISA was used to verify CXCL1 expression in the supernatant or portal vein blood of mice. Immunofluorescence was used to detect NETs formation in cocultured neutrophils in vitro or in mouse livers. Clostridium scindens was the key differential strain in the formation of gallstones in mice. After treatment with Clostridium scindens, both in vitro and in vivo, the expression of TLR2 was upregulated, the secretion of CXCL1 was increased by regulating the NF-κB pathway. Finally, the formation of NETs and stones was significantly increased. This study reveals a new mechanism of the gut-liver immune axis in the formation of gallstones. Clostridium scindens acts on colonic epithelial cells through TLR2 to regulate the NF-κB pathway and increase the secretion of CXCL1. CXCL1 enters the liver via the portal vein and increases the formation of NETs in the liver, thereby accelerating gallstone formation.

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.

Persister cells are a clinically relevant sub-population of an isogenic bacterial culture that is tolerant to bactericidal antibiotics. With the aim to investigate the ribosomal protein content of persister cells, we employed the bacteriolytic properties of ampicillin to separate persister from sensitive cells. Thereby, we observed processing of several ribosomal proteins. Promisingly, we detected a variant of the large subunit protein uL2 that lacks the last 59 amino acids from its C-terminus (tL2) and which previously has been described as an inhibitor of DNA replication in vitro. Considering the increasing number of moonlighting functions described for ribosomal proteins, we investigated a potential regulatory role of tL2 in persister cells after ampicillin treatment. In contrast to our assumption, our findings show that the generation of tL2 after ampicillin treatment must be attributed to proteolysis upon cell lysis. Ultimately, no tL2 was detected intracellularly of purified persister cells isolated by an improved protocol employing proteinase K treatment. We therefore exclude the possibility of tL2 regulating DNA replication in ampicillin tolerant E. coli cells. Nevertheless, this study clearly highlights the necessity of further purification steps in addition to ampicillin treatment for the study of persister cells and invites for the careful re-examination of previously published results.

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.

Caffeine can modulate cell cycle progression, override DNA damage checkpoint signalling and increase chronological lifespan (CLS) in various model systems. Early studies suggested that caffeine inhibits the phosphatidylinositol 3-kinase-related kinase (PIKK) Rad3 to override DNA damage-induced cell cycle arrest in fission yeast. We have previously suggested that caffeine modulates cell cycle progression and lifespan by inhibiting the Target of Rapamycin Complex 1 (TORC1). Nevertheless, whether this inhibition is direct or not, has remained elusive. TORC1 controls metabolism and mitosis timing by integrating nutrients and environmental stress response (ESR) signalling. Nutritional or other stresses activate the Sty1-Ssp1-Ssp2 (AMP-activated protein kinase complex, AMPK) pathway, which inhibits TORC1 and accelerates mitosis through Sck2 inhibition. Additionally, activation of the ESR pathway can extend lifespan in fission yeast. Here, we demonstrate that caffeine indirectly activates Ssp1, Ssp2 and the AMPKβ regulatory subunit Amk2 to advance mitosis. Ssp2 is phosphorylated in an Ssp1-dependent manner following exposure to caffeine. Furthermore, Ssp1 and Amk2, are required for resistance to caffeine under conditions of prolonged genotoxic stress. The effects of caffeine on DNA damage sensitivity are uncoupled from mitosis in AMPK pathway mutants. We propose that caffeine interacts synergistically with other genotoxic agents to increase DNA damage sensitivity. Our findings show that caffeine accelerates mitotic division and is beneficial for CLS through AMPK. Direct pharmacological targeting of AMPK may serve towards healthspan and lifespan benefits beyond yeasts, given the highly conserved nature of this key regulatory cellular energy sensor.

Peroxisomes are organelles that are crucial for cellular metabolism, but they also play important roles in non-metabolic processes such as signalling, stress response or antiviral defense. To uncover the consequences of peroxisome deficiency, we compared Saccharomyces cerevisiae wild-type with pex3 cells, which lack peroxisomes, employing quantitative proteomics and transcriptomics technologies. Cells were grown on acetate, a carbon source that requires peroxisomal enzymes of the glyoxylate cycle to generate energy and essential carbohydrates, and that does not repress the expression of peroxisomal genes. Our integrative omics analysis reveals that the absence of peroxisomes induces distinct responses at the level of the transcriptome and proteome. Transcripts of genes and corresponding proteins that are associated with peroxisomal β-oxidation were mostly increased in pex3 cells. In contrast, levels of peroxins were regulated at protein but not at transcript level. Membrane-bound peroxins were reduced, whereas the soluble receptors Pex5 and Pex7 were increased in abundance in pex3 cells. Interestingly, we found several non-peroxisomal transcript and proteins regulated in pex3 cells including mitochondrial proteins involved in respiration or import processes, which led to the identification of the mitochondrial pyruvate carrier Mpc1/3 as so far unnoticed transporter present in the peroxisomal membrane. Our results reveal the impact of the absence of peroxisomes in pex3 yeast cells and represent a rich resource of genes/proteins for follow-up studies to obtain a deeper understanding of peroxisome biology in a cellular context.

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.

Shiga toxin-producing Escherichia coli (STEC) is a major food-borne pathogen causing human diseases ranging from diarrhea to life-threatening complications, mainly in young children. Colonization, virulence, and interactions of STEC strains with human gut microbiota are pivotal during infection but remain poorly described, particularly in children, the most affected population. In this work, we evaluated changes in the microbiota and metabolome composition in the in vitro gut model: Toddler ARtificial COLon (T-ARCOL) infected with EHEC O157:H7 strain EDL 933. Stool samples collected from children with STEC-positive diarrhea and stool from the same children after recovery from the diarrheal episode (n=5) were used to inoculate the T-ARCOL model. STEC colonization was progressively reduced throughout fermentation in T-ARCOL with diarrhea or recovery fecal samples. Beta diversity showed that the diarrhea-associated microbiota was significantly distinct from the recovery microbiota and exhibited a lower α-diversity. In contrast to recovery conditions, diarrheal conditions were characterized by an increased abundance of potential pathobionts such as members of the Clostridiaceae family and higher acetate, succinate, and N-acetylneuraminic acid levels. Our results provide new evidence of the impact of EHEC in the microbiota and metabolome dynamics in an in vitro gut model that could be useful in understanding their physiopathology in this at-risk population, considering inter-individual variabilities in gut microbiota.

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.

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.

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.

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.

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.

Nitrogen metabolism in Saccharomyces cerevisiae is tightly regulated to optimize the utilization of available nitrogen sources. Uga3 is a known transcription factor involved in the gamma-aminobutyric acid (GABA) pathway; however, its broader role in nitrogen metabolism remains unclear. Here, we demonstrate that Uga3 influences arginine biosynthesis, linking its function beyond GABA utilization when cells grow with proline as the sole and poor nitrogen source. Using a combination of intracellular amino acid quantification, proteomics, and gene expression analysis, we show that the absence of Uga3 leads to a significant increase in intracellular arginine levels and the up-regulation of ARG5,6, a key gene in the arginine biosynthesis pathway. Proteomic analysis of uga3∆ cells reveals differential expression of multiple nitrogen metabolism-related proteins, suggesting a broader regulatory role for Uga3. Surprisingly, chromatin immunoprecipitation (ChIP) assays indicate that Uga3 does not directly bind the ARG5,6 promoter, implying an indirect regulatory mechanism. These findings expand the known functions of Uga3, positioning it as a key player in the coordinated regulation of nitrogen metabolism. Given the impact of nitrogen availability on industrial fermentation processes, our results provide new insights into optimizing yeast performance under nitrogen-limited conditions.