mBio最新文献

{"title":"A novel mycovirus identified in clinical isolates of <i>Cryptococcus neoformans</i>.","authors":"Mysha N Turk, Abberly E Dela Rosa, J T Graham Solomons, Virginia E Glazier","doi":"10.1128/mbio.02060-26","DOIUrl":"https://doi.org/10.1128/mbio.02060-26","url":null,"abstract":"<p><p>Mycoviruses are widespread throughout the fungal kingdom and are known to infect diverse fungal taxa, including fungal species that are important plant and human pathogens. Although many mycoviruses have been found to have minimal effects on their host, several viruses have been found to modulate fungal physiology, and, as a result, impact fungal virulence. Screens for mycoviruses in clinically relevant fungi have identified numerous mycoviruses within several important human pathogens, but mycoviruses remain uncharacterized in the clinically relevant human pathogen <i>Cryptococcus neoformans. C. neoformans</i> is an opportunistic encapsulated yeast responsible for life-threatening cryptococcal meningitis, a leading cause of mortality among immunocompromised individuals, particularly those with HIV/AIDS. We performed a search for viral RNA-dependent RNA polymerase (RdRP) signatures in publicly available <i>C. neoformans</i> transcriptomic data. This search identified <i>Totiviridae</i> viral genomes within six clinical isolates of <i>C. neoformans</i> from Botswana. All six isolates originated from the cerebrospinal fluid (CSF) of HIV-positive individuals with cryptococcal meningitis. Reverse transcription PCR (RT-PCR) independently validated the continued presence of the virus in three of these clinical isolates. Subsequent analysis of the viral genome identified two genotypes of a single species of Totivirus. This new species possesses canonical features of the <i>Totiviridae</i> family, including a slippery heptamer and a predicted RNA pseudoknot structure involved in programmed -1 ribosomal frameshifting for RdRP expression. Taken together, these results provide evidence of a mycovirus capable of infecting <i>C. neoformans</i>.IMPORTANCEWe report the identification of a mycovirus capable of infecting <i>Cryptococcus neoformans</i>. While mycoviruses inhabit diverse fungal taxa, they have previously remained uncharacterized in this clinically significant fungal pathogen. The identification of the mycoviruses within <i>C. neoformans</i> isolated from the cerebrospinal fluid of individuals with cryptococcal meningitis places emphasis on the potential role of mycoviruses in the pathogenesis of <i>C. neoformans</i>.</p>","PeriodicalId":18315,"journal":{"name":"mBio","volume":" ","pages":"e0206026"},"PeriodicalIF":5.4,"publicationDate":"2026-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149220235","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Seasonal and evolutionary patterns of planktonic Hikarchaeia reveal ecological niches of marine rare biosphere constituents.","authors":"Fabian Wittmers, Nicole R Dames, Michelle Michelsen, Rachele Spezzano, Jacqueline Comstock, Kristin Bergauer, Kevin Vergin, Shuting Liu, Rachel Parsons, Ben Temperton, Mak A Saito, Craig A Carlson, Alexandra Z Worden","doi":"10.1128/mbio.01753-26","DOIUrl":"https://doi.org/10.1128/mbio.01753-26","url":null,"abstract":"<p><p>Members of Marine Group IV, now termed Hikarchaeia, hold an important transitional evolutionary position among Archaea but remain uncultivated, and their ecology remains uncharacterized. Over a 5-year period, we performed monthly profile sampling in the North Atlantic Subtropical Gyre and sequenced V4 16S rRNA gene amplicons, while also collecting additional size-fractionated and metagenomic samples. Hikarchaeal relative abundance annually peaked at ~1% of prokaryotic amplicons. Their relative abundances were significantly higher after deep winter mixing when thermal stratification isolated exported dissolved organic matter in the twilight zone (TZ), the boundary region between the epipelagic and mesopelagic. A diminutive 1.17 Mbp complete hikarchaeal genome was recovered by sequencing and co-assembling diel TZ metagenomes from 200 m during summer, where their relative abundances were highest. Phylogenomic reconstruction incorporating our new metagenome-assembled genome (MAG) and public MAGs established five clades. Clades I and III were in subtropical and tropical environments, with vertical partitioning: Clade I dominated the TZ, and Clade III detection initiated in the lower mesopelagic and extended into the bathypelagic. Clade V is polar-associated. Data sparsity makes Clade II and IV distributions unclear. All Hikarchaeia recovered thus far appear to be free-living aerobes capable of heterotrophy. Unlike MGI, MGII, and MGIII Archaea, and most marine pelagic bacteria, the Hikarchaeia encode bacterioruberin biosynthesis, except deep Clade III. Hikarchaeia also have nitrile hydratases alongside enzymes for carbon monoxide oxidation and menaquinone biosynthesis, suggesting previously unrecognized roles in nitrogen and carbon cycling. Collectively, our studies reveal niche partitioning of evolutionarily distinct uncultivated Hikarchaeia clades and patterning within the rare biosphere.IMPORTANCEThe ocean and its vertical water-column structure are changing with planetary warming; yet, there are many enigmatic microbes, especially those that inhabit the deep ocean. Here, we illuminate a group of uncultivated Archaea that were discovered over two decades ago but still lack clear distributions and habitat preferences. With the first complete hikarchaeal genome now in hand, we identified distinct lineages within the Hikarchaeia that occupy different marine niches. Strong reoccurring seasonal patterns were observed that closely followed the annual cycle of temperature-driven ocean stratification. Given rapid natural and anthropogenic perturbations at hand, establishing baselines for these Archaea is critical for improving our understanding and modeling of marine microbiomes and their biogeochemical functions.</p>","PeriodicalId":18315,"journal":{"name":"mBio","volume":" ","pages":"e0175326"},"PeriodicalIF":5.4,"publicationDate":"2026-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149220228","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Acetate modulates host physiology and bacterial energetics to improve antibiotic efficacy during obesity-associated infection.","authors":"Arsalan Hussain, Prateek Bhardwaj, Ashish Kumar Ray, Aakash Singh, Abhiroop Sett, Ranjana Pathania","doi":"10.1128/mbio.01630-26","DOIUrl":"https://doi.org/10.1128/mbio.01630-26","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Antibiotic efficacy is conventionally attributed to the susceptibility of the infecting pathogen. However, obese patients experience disproportionately poor infection outcomes despite receiving antibiotics to which pathogens remain genetically susceptible. These observations suggest that host-associated factors can influence treatment outcomes independently of the bacterial genotype, although the underlying mechanisms remain poorly understood. Using a mechanistic comparison of diet-induced obese and healthy mice infected with &lt;i&gt;Acinetobacter baumannii&lt;/i&gt;, we demonstrate that the effect of antibiotics is not solely a property of the pathogen but can be governed by a gut microbiota-derived metabolite acting on both host immunity and bacterial physiology. We identify obesity-associated acetate depletion as a key driver of antibiotic treatment failure, linking gut microbial metabolism to antibiotic activity during infection. We observed that this depletion impaired innate immune activation, reducing cytokine responses and neutrophil-mediated bacterial clearance. Under these conditions, &lt;i&gt;A. baumannii&lt;/i&gt; displayed enhanced tolerance to bactericidal antibiotics, particularly tobramycin. Given these findings, we investigated whether acetate could be leveraged therapeutically to restore antibiotic efficacy. We observed that oral acetate supplementation remodeled the dysbiotic microbiome, whereas systemic acetate restored innate immune competence and neutrophil-mediated bacterial clearance. Most importantly, acetate reversed antibiotic tolerance and restored aminoglycoside killing by directly sensitizing host-induced tolerant bacterial populations. Mechanistically, acetate directly reprogrammed bacterial physiology to enhance aminoglycoside-mediated killing. Combined acetate-tobramycin treatment resulted in eradication of tolerant populations and markedly improved bacterial clearance &lt;i&gt;in vivo&lt;/i&gt;. Our findings establish a mechanistic link between host metabolic state and antibiotic efficacy and identify acetate as a therapeutic intervention for obesity-associated gram-negative infections.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Importance: &lt;/strong&gt;Antibiotic treatment failure in obese patients remains poorly understood and therapeutically unaddressed. This study reveals that host metabolic state can control antibiotic response through a gut microbiota-derived metabolite that acts on both host defense and bacterial physiology. We identify obesity-driven depletion of microbiota-derived acetate as a previously unrecognized determinant of antibiotic failure, operating independently of bacterial resistance. By simultaneously restoring gut microbial balance, rescuing impaired innate immunity, and directly sensitizing pathogens to aminoglycoside killing through bacterial membrane alteration, acetate supplementation addresses the host-pathogen-microbiome axis through a single intervention. Given its established clinical safety, acetate represents a compelling combination ther","PeriodicalId":18315,"journal":{"name":"mBio","volume":" ","pages":"e0163026"},"PeriodicalIF":5.4,"publicationDate":"2026-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149195189","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Diversity of dirammox microorganisms.","authors":"Gantuya Khasbaatar, Qun Han, Xiao-Kang Wang, Lei Song, Chang Liu, Xin Sun, Ze-Shen Liu, Ying Liu, Cheng-Ying Jiang, Ji-Guo Qiu, Shuang-Jiang Liu, Yanning Zheng, De-Feng Li","doi":"10.1128/mbio.01645-26","DOIUrl":"https://doi.org/10.1128/mbio.01645-26","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Our knowledge of the nitrogen cycle has been advanced by the discovery of anammox bacteria, ammonia-oxidizing archaea, and comammox bacteria, along with their high diversity. Direct ammonia oxidation (dirammox), a recently discovered heterotrophic nitrification pathway, converts ammonium and organic nitrogen directly to N&lt;sub&gt;2&lt;/sub&gt; through the DnfABC multienzyme system, further expanding our understanding of the nitrogen cycle. However, the taxonomic distribution, prevalence, and nitrogen metabolic potential of microorganisms encoding dirammox genes remain poorly understood. Here, large-scale genome mining identified complete &lt;i&gt;dnfABC&lt;/i&gt; gene clusters in 690 genomes representing 3 phyla and 26 genera. The &lt;i&gt;dnfABC&lt;/i&gt; cluster showed a striking bimodal prevalence: it was nearly ubiquitous in &lt;i&gt;Alcaligenes&lt;/i&gt;, &lt;i&gt;Delftia&lt;/i&gt;, and &lt;i&gt;Microvirgula&lt;/i&gt; but occurred sporadically in most other genera. These microorganisms were recovered from diverse environments, particularly organic nitrogen-rich habitats. Comparative analyses of DnfABC phylogeny, gene cluster organization, GC content, and flanking mobile genetic elements indicate that the &lt;i&gt;dnfABC&lt;/i&gt; cluster is conserved within several core genera, whereas its sporadic distribution in other lineages suggests that horizontal gene transfer may have contributed to its dissemination. The &lt;i&gt;dnfABC&lt;/i&gt; cluster co-occurs with genes associated with assimilatory nitrate/nitrite reduction to ammonium, dissimilatory nitrate/nitrite reduction to ammonium, denitrification, and/or nitrogen fixation, but not with marker genes for nitrification or anammox, indicating diverse nitrogen metabolic potential among potential dirammox microorganisms. Functional assays further showed that diverse &lt;i&gt;dnfABC&lt;/i&gt; clusters consistently conferred ammonium- and glutamine-oxidizing activities in &lt;i&gt;Escherichia coli&lt;/i&gt;, despite exhibiting low activities in their native hosts. These results suggest that dirammox is a broadly distributed, metabolically flexible, and tightly regulated pathway and may represent an overlooked route of nitrogen transformation in organic-rich habitats.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Importance: &lt;/strong&gt;Nitrogen is essential for all life, and our understanding of the nitrogen cycle has advanced substantially with the discovery of anammox bacteria, ammonia-oxidizing archaea, and comammox bacteria, which exhibit remarkable taxonomic and metabolic diversity. This study suggests that the recently discovered dirammox pathway may be more widespread in nature than previously recognized. Potential dirammox microorganisms exhibit broad phylogenetic and ecological distributions, high genomic diversity, and notable metabolic versatility. Functional assays indicate that dirammox activity is tightly regulated in native hosts, suggesting that its ecological role depends on specific environmental conditions. Unlike canonical nitrification and anammox, dirammox operates under conditions where other nitrogen transformation","PeriodicalId":18315,"journal":{"name":"mBio","volume":" ","pages":"e0164526"},"PeriodicalIF":5.4,"publicationDate":"2026-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149195237","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Pre-existing systemic and nasal antibodies against avian H5 influenza A viruses vary according to childhood imprinting.","authors":"Peta Edler, Kevin J Selva, Ellie Reilly, Malet Aban, Ian G Barr, Jennifer A Juno, Adam K Wheatley, Amy W Chung, Stephen J Kent, David J Price, Marios Koutsakos","doi":"10.1128/mbio.01892-26","DOIUrl":"10.1128/mbio.01892-26","url":null,"abstract":"<p><p>Avian influenza A viruses (IAVs) pose a constant pandemic threat, with the recent 2.3.4.4b clade of the H5 subtype causing high pathogenicity and spreading across animal species and geographic locations. Understanding human pre-existing immunity to avian H5 IAV can inform on population susceptibility, a critical aspect of pandemic preparedness. To that end, we analyzed the IAV HA-specific antibodies across individuals born between 1928 and 1999 with different early life exposures to IAV subtypes. Individuals born prior to 1957 had the highest pre-existing serum antibodies to group 1 HA antigens, including the 2.3.4.4b H5 and a group 1 HA stem antigen. These birth year-specific patterns were not reflected in the limited pre-existing serum neutralizing antibodies detectable against a 2.3.4.4b H5 IAV or in H5-specific memory B cell populations. They were, however, evident in pre-existing nasal IgG and IgA titers to H5, which were greater in individuals born prior to 1957. Our findings demonstrate that the immunological biases afforded by early life exposure extend to antibodies detected in the nasal mucosa, the site of IAV replication.IMPORTANCEUnderstating pre-existing immunity to influenza A viruses (IAVs) of pandemic potential is an important aspect of pandemic preparedness. This includes an understanding of the heterogeneity of pre-existing immunity across the population. Here, we demonstrate that pre-existing antibodies to H5 IAV vary according to the year of birth and childhood imprinting. We demonstrate that this is the case for both systemic and nasal antibodies, highlighting the importance of understanding pre-existing mucosal immunity at the sites of influenza virus replication.</p>","PeriodicalId":18315,"journal":{"name":"mBio","volume":" ","pages":"e0189226"},"PeriodicalIF":5.4,"publicationDate":"2026-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148829768","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"IL-1α protects intestinal barrier in murine visceral leishmaniasis.","authors":"Laís A Sacramento, Pedro Alexandre Sampaio, Gabriela Castilho Martins, Luciana Benevides, Claudia Gonzalez-Lombana, Gabrielle B Trindade, Michely Mello, Fernando Q Cunha, Livia S Zaramela, João S Silva, Phillip Scott, Vanessa Carregaro","doi":"10.1128/mbio.00657-26","DOIUrl":"10.1128/mbio.00657-26","url":null,"abstract":"<p><p>Interleukin-1 (IL-1) is a pleiotropic cytokine important in inflammatory and infectious diseases, but its roles in visceral leishmaniasis (VL) remain poorly understood. Here, we evaluated the role of IL-1 cytokines during experimental visceral leishmaniasis. We showed that IL-1 receptor 1 (IL-1R1) deficiency enhanced the gamma interferon (IFNγ)-mediated response and restricted parasites in an IL-1α-dependent manner, whereas IL-1β deficiency had no effect. The absence of IL-1R1 and IL-1α led to intestinal microbiota dysbiosis. The infection induced IL-1α expression in the gut. The absence of IL-1α led to reduced expression of tight-junction molecules, increased intestinal permeability, and bacterial translocation. These alterations amplified non-<i>Leishmania</i>-specific IFN-γ production, which was reversed by broad-spectrum antibiotic treatment. Bone marrow chimeric transplantation showed that hematopoietic cells are the source of IL-1α during VL. Together, our findings reveal that IL-1α acts as a key regulator of gut barrier integrity in VL and indirectly restrains systemic IFNγ-driven inflammation. This work highlights IL-1α-dependent intestinal protection as an overlooked component of VL pathogenesis.IMPORTANCEVisceral leishmaniasis (VL) is a systemic and chronic disease caused by <i>Leishmania</i> parasites. Most infected individuals remain asymptomatic due to an appropriate IFNγ-mediated response. By contrast, the disease progression is characterized by excessive inflammation, with high levels of cytokines, among them IFNγ. IL-1 cytokines play a role in modulating immune responses and epithelial barriers. We report that IL-1α protects the intestinal environment and indirectly regulates the IFNγ-mediated response during experimental VL. The infection induces IL-1α expression in the intestine, and its absence leads to dysbiosis, gut permeability, and bacterial translocation. Overall, this study reveals the role of IL-1α in intestinal integrity during VL and in regulating the IFNγ-mediated response. Expanding the knowledge of IL-1α in intestinal protection may support therapeutic approaches to improve the outcomes of infection.</p>","PeriodicalId":18315,"journal":{"name":"mBio","volume":" ","pages":"e0065726"},"PeriodicalIF":5.4,"publicationDate":"2026-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148963520","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The catheterized urinary tract selects for <i>MRR1</i>-mediated efflux and fluconazole resistance in <i>Candida albicans</i> biofilms.","authors":"Shane A Cristy, Jennifer N Walker, Michael C Lorenz","doi":"10.1128/mbio.01785-26","DOIUrl":"10.1128/mbio.01785-26","url":null,"abstract":"<p><p>Catheter-associated urinary tract infections (CAUTIs) are the most common nosocomial infection in developed countries, and <i>Candida</i> species are among the most frequently isolated organisms. Despite this, little is known about the biology, host-pathogen interactions, or outcomes of these infections, and this has led to uncertain guidelines for clinical management of <i>Candida</i> CAUTIs. Here, we develop the first physiologically relevant artificial urine medium (AUM) that supports fungal growth in a manner similar to, but more consistent than, human urine samples. We demonstrate that human catheter-associated (CA) clinical isolates of <i>C. albicans</i> exhibit environment-dependent fluconazole resistance: many isolates determined to be susceptible by standard CLSI testing in RPMI (MIC ≤ 2 µg/mL) were fully resistant (MIC ≥ 128 µg/mL) when grown in pooled human urine or AUM, complicating clinical management, which is based on catheter exchange and fluconazole treatment. Transcriptomic profiling of biofilms formed in AUM revealed a remarkably convergent upregulation of efflux and detoxification processes across clinical isolates with diverse biofilm phenotypes. Whole-genome sequencing of the CA isolates identified variant alleles of transcriptional regulators of drug efflux, including <i>MRR1</i>, that have been previously associated with antifungal resistance. A competition assay confirmed that Mrr1 provides a fitness advantage in urine and AUM in a urea-dependent manner. Thus, we show that the urinary environment promotes a unique biofilm differentiation program and selects for adaptations that increase drug resistance and would be predicted to render standard treatment regimens ineffective.IMPORTANCECatheter-associated urinary tract infections are the most common nosocomial infection in the United States, and <i>Candida albicans</i> is one of the most frequently isolated organisms from these infections. Despite this high prevalence, few molecular studies have examined <i>C. albicans</i> biology in the urinary environment, and recommendations for clinical management lack robust evidence. Here, we show that clinical catheter-associated isolates of <i>C. albicans</i> identified as susceptible to fluconazole by standard clinical microbiology testing were resistant when grown in human or artificial urine. We identified transcriptional responses intrinsic to the urinary environment that produce this environment-specific resistance phenotype. Biofilm growth in the urinary environment induces cellular processes for efflux and detoxification. These findings suggest that standard susceptibility testing may not predict fluconazole efficacy in the urinary tract and underscore the need for niche-informed approaches to antifungal management of these common infections.</p>","PeriodicalId":18315,"journal":{"name":"mBio","volume":" ","pages":"e0178526"},"PeriodicalIF":5.4,"publicationDate":"2026-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148963528","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Resolution of viral R-loop by DHX9 promotes hepatitis B virus replication.","authors":"Yubo Pi, Huimin Luo, Kai Wang, Ni Tang, Ailong Huang, Yanmeng Chen","doi":"10.1128/mbio.01449-26","DOIUrl":"10.1128/mbio.01449-26","url":null,"abstract":"<p><p>Hepatitis B virus (HBV) is a hepatotropic DNA virus with a compact 3.2 kb genome that replicates via reverse transcription. HBV covalently closed circular DNA (cccDNA) transcription shares molecular features with R-loop. DExH-box helicase 9 (DHX9) has been shown to be associated with R-loop accumulation, genome instability, and HBV replication. However, the role of DHX9-mediated R-loop homeostasis in HBV transcription has not yet been elucidated. In this study, we identified a critical role of DHX9 in resolving R-loops at transcription termination during HBV transcription. We demonstrate that HBV replication promotes viral R-loop accumulation. DHX9 promotes HBV R-loop resolution, HBV cccDNA transcription termination, and subsequent nuclear export of the 3.5 kb HBV RNA, facilitating HBV DNA replication. These findings reveal DHX9-mediated R-loop resolution as a potential therapeutic target for antiviral intervention.IMPORTANCEThe persistence of HBV cccDNA poses a major challenge to achieving a cure for chronic hepatitis B. While R-loop structures have been implicated in the life cycles of viruses, their formation and functional significance in HBV replication have remained largely unexplored. This study provides the first evidence that the cellular helicase DHX9 resolves transcription-replication conflicts by dissolving R-loops formed during HBV replication. Our findings also identify DHX9-mediated R-loop resolution as a critical mechanism supporting the HBV life cycle. Consequently, targeting DHX9 presents a promising therapeutic strategy to silence the persistent HBV cccDNA reservoir.</p>","PeriodicalId":18315,"journal":{"name":"mBio","volume":" ","pages":"e0144926"},"PeriodicalIF":5.4,"publicationDate":"2026-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148990502","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cellular adaptations of fission yeast to inositol starvation.","authors":"Ana M Sanchez, Jill Babor, Michelle Saoi, Isabel Prucker, Henning J Jessen, Beate Schwer, Stewart Shuman","doi":"10.1128/mbio.01864-26","DOIUrl":"10.1128/mbio.01864-26","url":null,"abstract":"<p><p>Inositol is an essential nutrient and a precursor of phosphorylated metabolites that play important roles in cell physiology. Here we characterize the impact of intracellular inositol deficiency, taking advantage of fission yeast <i>Schizosaccharomyces pombe</i>, an obligate inositol auxotroph, as a model system. We find that cells deprived of inositol ceased growth after two or three rounds of division, with genome content indicative of a G2 arrest. Inositol starvation elicited (i) widespread changes in the expression of genes involved in lipid metabolism and inositol polyphosphate dynamics, associated with an across-the-board elevation of triacylglycerol lipids; (ii) depletion of glycerophosphoinositol and accumulation of glycerophosphocholine and choline; (iii) selective depletion of inositol pyrophosphate 1,5-IP₈, and depletion of polyphosphate; (iv) upregulation of autophagy genes; (v) downregulation of genes for the biogenesis and function of ribosomes and tRNAs, accompanied by conversion of polysomes to 80S monosomes; and (vi) large-magnitude changes in mRNAs encoding transcription factors. Our study underscores distinctive and shared features of the cellular responses to inositol deficiency versus phosphate deficiency that enhance our understanding of nutrient stress.</p><p><strong>Importance: </strong>Inositol is an essential precursor of diverse phosphorylated derivatives that govern cell signaling, glucose and lipid metabolism, and cellular phosphate homeostasis. To probe how cells adapt to inositol deprivation, we exploited the fission yeast <i>Schizosaccharomyces pombe</i>, which is unable to synthesize inositol and requires exogenous inositol for growth. Via genome-wide analysis of changes in mRNA levels and tracking the status of inositol-adjacent metabolites, we highlight adaptive responses specific to inositol starvation that affect lipid metabolism and inositol pyrophosphate signaling. Clues to the origins of the transcriptome remodeling during inositol starvation emerged from the large-magnitude increases in mRNAs encoding certain RNA polymerase II transcription factors, which correlated with increased expression of their putative client genes.</p>","PeriodicalId":18315,"journal":{"name":"mBio","volume":" ","pages":"e0186426"},"PeriodicalIF":5.4,"publicationDate":"2026-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149012358","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Single-cell analysis of StkP activity reveals the temporal dynamics of DivIVA phosphorylation in <i>Streptococcus pneumoniae</i>.","authors":"Sylvie Manuse, Léo Claude, Pedro M Alzari, Anne Marie Wehenkel, Christophe Grangeasse","doi":"10.1128/mbio.01648-26","DOIUrl":"10.1128/mbio.01648-26","url":null,"abstract":"<p><p>Serine/threonine phosphorylation has emerged as a central regulatory mechanism of the bacterial cell cycle. However, the dynamics and temporal selectivity of protein phosphorylation through the cell cycle remain unamenable to existing analytical tools. Although fluorescent phosphorylation biosensors are widely available in single eukaryotic cells, such tools have yet to be adapted for bacteria. To address this gap, we developed an <i>in vivo</i> fluorescent biosensor specifically designed to monitor serine/threonine phosphorylation in single bacterial cells. Specifically, this sensor reports protein phosphorylation mediated by the serine/threonine kinase StkP, the main regulator of cell division in <i>Streptococcus pneumoniae</i>. We showed that StkP activity is constitutive throughout the cell cycle. However, we observed that StkP-mediated protein phosphorylation is heterogeneous from cell to cell in early stages of the cell cycle. Importantly, our results revealed that the cell division protein DivIVA is found phosphorylated at the cell poles, suggesting an additional regulatory layer controlling its function at this location. Collectively, this work provides original insights into the temporal dynamics of StkP activity and the regulation of the pneumococcal cell cycle by phosphorylation.IMPORTANCEHow bacterial serine/threonine phosphorylation is dynamically regulated in living single cells remains inaccessible, largely because efficient reporters required to monitor phosphorylation <i>in vivo</i> are lacking. In this study, we designed a fluorescent biosensor approach that enables direct visualization of serine/threonine phosphorylation dynamics in single bacterial cells. Using this approach, we revealed that the activity of StkP, the serine/threonine kinase that regulates cell division in <i>Streptococcus pneumoniae</i>, is constitutive throughout the cell cycle, yet StkP-mediated protein phosphorylation is unexpectedly heterogeneous across individual cells in the early stages of division. Importantly, our reporter also showed that the phosphorylation of the key cell division protein DivIVA is highly dynamic. Together, these findings provide the conceptual basis to improve our understanding of the role of phosphorylation in pneumococcal cell division and pave the way for investigating phosphorylation dynamics in other bacterial species.</p>","PeriodicalId":18315,"journal":{"name":"mBio","volume":" ","pages":"e0164826"},"PeriodicalIF":5.4,"publicationDate":"2026-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149012542","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}