mBio最新文献

{"title":"Shared mechanisms of enhanced plasmid maintenance and antibiotic tolerance mediated by the VapBC toxin:antitoxin system.","authors":"Sarah Hollingshead, Gareth McVicker, Maria R Nielsen, YuGeng Zhang, Giulia Pilla, Rebekah A Jones, Jonathan C Thomas, Sarah E H Johansen, Rachel M Exley, Ditlev E Brodersen, Christoph M Tang","doi":"10.1128/mbio.02616-24","DOIUrl":"10.1128/mbio.02616-24","url":null,"abstract":"<p><p>Toxin:antitoxin (TA) systems are widespread in bacteria and were first identified as plasmid addiction systems that kill bacteria lacking a TA-encoding plasmid following cell division. TA systems have also been implicated in bacterial persistence and antibiotic tolerance, which can be precursors of antibiotic resistance. Here, we identified a clinical isolate of <i>Shigella sonnei</i> (CS14) with a remarkably stable pINV virulence plasmid; pINV is usually frequently lost from <i>S. sonnei</i>, but plasmid loss was not detected from CS14. We found that the plasmid in CS14 is stabilized by a single nucleotide polymorphism (SNP) in its <i>vapBC</i> TA system. VapBC TA systems are the most common Type II TA system in bacteria, and consist of a VapB antitoxin and VapC PIN domain-containing toxin. The plasmid stabilizing SNP leads to a Q12L substitution in the DNA-binding domain of VapB, which reduces VapBC binding to its own promoter, impairing <i>vapBC</i> autorepression. However, VapB^L12C mediates high-level plasmid stabilization because VapB^L12 is more prone to degradation by Lon than wild-type VapB; this liberates VapC to efficiently kill bacteria that no longer contain a plasmid. Of note, mutations that confer tolerance to antibiotics in <i>Escherichia coli</i> also map to the DNA-binding domain of VapBC encoded by the chromosomally integrated F plasmid. We demonstrate that the tolerance mutations also enhance plasmid stabilization by the same mechanism as VapB^L12. Our findings highlight the links between plasmid maintenance and antibiotic tolerance, both of which can promote the development of antimicrobial resistance.</p><p><strong>Importance: </strong>Our work addresses two processes, the maintenance of plasmids and antibiotic tolerance; both contribute to the development of antimicrobial resistance in bacteria that cause human disease. Here, we found a single nucleotide change in the vapBC toxin:antitoxin system that stabilizes the large virulence plasmid of <i>Shigella sonnei</i>. The mutation is in the vapB antitoxin gene and makes the antitoxin more likely to be degraded, releasing the VapC toxin to efficiently kill cells without the plasmid (and thus unable to produce more antitoxin as an antidote). We found that vapBC mutations in <i>E. coli</i> that lead to antibiotic tolerance (a precursor to resistance) also operate by the same mechanism (<i>i.e.</i>, generating VapB that is prone to cleavage); free VapC during tolerance will arrest bacterial growth and prevent susceptibility to antibiotics. This work shows the mechanistic links between plasmid maintenance and tolerance, and has applications in biotech and in the design and evaluation of vaccines against shigellosis.</p>","PeriodicalId":18315,"journal":{"name":"mBio","volume":" ","pages":"e0261624"},"PeriodicalIF":5.1,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11796401/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142864817","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Mla pathway promotes <i>Vibrio cholerae</i> re-expansion from stationary phase.","authors":"Deborah R Leitner, Franz G Zingl, Alexander A Morano, Hailong Zhang, Matthew K Waldor","doi":"10.1128/mbio.03433-24","DOIUrl":"10.1128/mbio.03433-24","url":null,"abstract":"<p><p>Bacteria have evolved diverse strategies to ensure survival under nutrient-limited conditions, where rapid energy generation is not achievable. Here, we performed a transposon insertion site sequencing loss-of-function screen to identify <i>Vibrio cholerae</i> genes that promote pathogen fitness in stationary phase. We discovered that the <u>m</u>aintenance of <u>l</u>ipid <u>a</u>symmetry (Mla) pathway, which is crucial for transferring phospholipids from the outer to the inner membrane, is critical for stationary phase fitness. Competition experiments with barcoded and fluorophore labeled wild-type (WT) and <i>mlaE</i> mutant <i>V. cholerae</i> revealed that the Mla pathway promotes re-expansion from 48 h stationary phase cultures. The mutant defect in transitioning out of stationary phase into active growth (culturability) was also observed in monocultures at 48 h. However, by 96 h the culturability of the WT and mutant strains were equivalent. By monitoring the abundances of genomically barcoded libraries of WT and ∆<i>mlaE</i> strains, we observed that a few barcodes dominated the mutant culture at 96 h, suggesting that the similarity of the population sizes at this time was caused by expansion of a subpopulation containing a mutation that suppressed the defect of ∆<i>mlaE</i>. Whole genome sequencing revealed that <i>mlaE</i> suppressors inactivated flagellar biosynthesis. Additional mechanistic studies support the idea that the Mla pathway is critical for maintaining the culturability of <i>V. cholerae</i> because it promotes energy homeostasis, likely due to its role in regulating outer membrane vesicle shedding. Together our findings provide insights into the cellular processes that control re-expansion from stationary phase and demonstrate a previously undiscovered role for the Mla pathway.</p><p><strong>Importance: </strong>Bacteria regularly encounter conditions with nutrient scarcity, where cell growth and division are minimal. Knowledge of the pathways that enable re-growth following nutrient restriction is limited. Here, using the cholera pathogen, we uncovered a role for the Mla pathway, a system that enables phospholipid re-cycling, in promoting <i>Vibrio cholerae</i> re-expansion from stationary phase cultures. Cells labeled with DNA barcodes or fluorophores were useful to demonstrate that though the abundances of wild-type and Mla mutant cells were similar in stationary phase cultures, they had marked differences in their capacities to regrow on plates. Of note, Mla mutant cells lose cell envelope components including high-energy phospholipids due to OMV shedding. Our findings suggest that the defects in cellular energy homeostasis that emerge in the absence of the Mla pathway underlie its importance in maintaining <i>V. cholerae</i> culturability.</p>","PeriodicalId":18315,"journal":{"name":"mBio","volume":" ","pages":"e0343324"},"PeriodicalIF":5.1,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11796348/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142877124","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Improving breast cancer treatments using pharmacomicrobiomics.","authors":"Aswin Anand Pai, Aadra Prashant Bhatt","doi":"10.1128/mbio.03422-24","DOIUrl":"10.1128/mbio.03422-24","url":null,"abstract":"<p><p>Tamoxifen is the mainstay treatment for estrogen-positive breast cancer for over half a century. However, a significant proportion of patients experience disease recurrence due to treatment failure attributed to various factors, including disease pathology, genetics, and drug metabolism. Alam et al. introduce gut microbiota as a key factor influencing tamoxifen pharmacokinetics (Y. Alam, S. Hakopian, L. Ortiz de Ora, I. Tamburini, et al., mBio 16:e01679-24, 2024, https://doi.org/10.1128/mbio.01679-24). The authors present compelling evidence that functional differences in the gut microbiota, specifically the bacterial enzyme β-glucuronidase, leads to inter-individual variability in systemic exposure of tamoxifen, affecting drug efficacy. This study provides novel insights into the impact of the gut microbiota on tamoxifen pharmacokinetics, the latest example of how pharmacomicrobiomics, or the study of drug-microbe interactions, can enhance precision medicine for numerous diseases.</p>","PeriodicalId":18315,"journal":{"name":"mBio","volume":" ","pages":"e0342224"},"PeriodicalIF":5.1,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11796342/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143007655","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Targets of influenza human T-cell response are mostly conserved in H5N1.","authors":"John Sidney, A-Reum Kim, Rory D de Vries, Bjoern Peters, Philip S Meade, Florian Krammer, Alba Grifoni, Alessandro Sette","doi":"10.1128/mbio.03479-24","DOIUrl":"10.1128/mbio.03479-24","url":null,"abstract":"<p><p>Frequent recent spillovers of subtype H5N1 clade 2.3.4.4b highly pathogenic avian influenza (HPAI) virus into poultry and mammals, especially dairy cattle, including several human cases, increased concerns over a possible future pandemic. Here, we performed an analysis of epitope data curated in the Immune Epitope Database (IEDB). We found that the patterns of immunodominance of seasonal influenza viruses circulating in humans and H5N1 are similar. We further conclude that a significant fraction of the T-cell epitopes is conserved at a level associated with cross-reactivity between avian and seasonal sequences, and we further experimentally demonstrate extensive cross-reactivity in the most dominant T-cell epitopes curated in the IEDB. Based on these observations, and the overall similarity of the neuraminidase (NA) N1 subtype encoded in both HPAI and seasonal H1N1 influenza virus as well as cross-reactive group 1 HA stalk-reactive antibodies, we expect that a degree of pre-existing immunity is present in the general human population that could blunt the severity of human H5N1 infections.IMPORTANCEInfluenza A viruses (IAVs) cause pandemics that can result in millions of deaths. The highly pathogenic avian influenza (HPAI) virus of the H5N1 subtype is presently among the top viruses of pandemic concern, according to the WHO and the National Institute of Allergy and Infectious Diseases (NIAID). Previous exposure by infection and/or vaccination to a given IAV subtype or clade influences immune responses to a different subtype or clade. Analysis of human CD4 and CD8 T-cell epitope conservation between HPAI H5N1 and seasonal IAV sequences revealed levels of identity and conservation conducive to T cell cross-reactivity, suggesting that pre-existing T cell immune memory should, to a large extent, cross-recognize avian influenza viruses. This observation was experimentally verified by testing responses from human T cells to non-avian IAV and their HPAI H5N1 counterparts. Accordingly, should a more widespread HPAI H5N1 outbreak occur, we hypothesize that cross-reactive T-cell responses might be able to limit disease severity.</p>","PeriodicalId":18315,"journal":{"name":"mBio","volume":" ","pages":"e0347924"},"PeriodicalIF":5.1,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11796400/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142877107","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transposon-sequencing across multiple <i>Mycobacterium abscessus</i> isolates reveals significant functional genomic diversity among strains.","authors":"Chidiebere Akusobi, Sanjeevani Choudhery, Bouchra S Benghomari, Ian D Wolf, Shreya Singhvi, Thomas R Ioerger, Eric J Rubin","doi":"10.1128/mbio.03376-24","DOIUrl":"10.1128/mbio.03376-24","url":null,"abstract":"<p><p><i>Mycobacterium abscessus (Mab</i>) is a clinically significant pathogen and a highly genetically diverse species due to its large accessory genome. The functional consequence of this diversity remains unknown mainly because, to date, functional genomic studies in <i>Mab</i> have been primarily performed on reference strains. Given the growing public health threat of <i>Mab</i> infections, understanding the functional genomic differences among <i>Mab</i> clinical isolates can provide more insight into how its genetic diversity influences gene essentiality, clinically relevant phenotypes, and importantly, potential drug targets. To determine the functional genomic diversity among <i>Mab</i> strains, we conducted transposon-sequencing (TnSeq) on 21 genetically diverse clinical isolates, including 15 <i>M</i>. <i>abscessus</i> subsp. <i>abscessus</i> isolates and 6 <i>M</i>. <i>abscessus</i> subsp. <i>massiliense</i> isolates, cataloging all the essential and non-essential genes in each strain. Pan-genome analysis revealed a core set of 3,845 genes and a large accessory genome of 11,507. We identified 259 core essential genes across the 21 clinical isolates and 425 differentially required genes, representing ~10% of the <i>Mab</i> core genome. We also identified genes whose requirements were subspecies, lineage, and isolate-specific. Finally, by correlating TnSeq profiles, we identified 19 previously uncharacterized genetic networks in <i>Mab</i>. Altogether, we find that <i>Mab</i> clinical isolates are not only genetically diverse but functionally diverse as well.</p><p><strong>Importance: </strong>This study investigates the genetic diversity of <i>Mycobacterium abscessus</i> (<i>Mab</i>), a bacteria known for causing difficult-to-treat infections. Researchers performed transposon-sequencing (TnSeq) on 21 different clinical isolates of <i>Mab</i> to identify essential and non-essential genes in each strain. Through this analysis, they identified core genes required for growth across all strains. Interestingly, they also identified genes whose requirement for growth or \"essentiality\" were subspecies, lineage, and isolate-specific. This study reveals that <i>Mab'</i>s genetic diversity translates into significant functional differences among clinical isolates. Insights from this paper lay essential groundwork for future studies exploring the biological and clinical implications of genetic diversity in <i>Mab</i> clinical isolates. Understanding this diversity could guide targeted therapies and offer new insights into managing infections caused by <i>Mab</i>, a growing public health concern.</p>","PeriodicalId":18315,"journal":{"name":"mBio","volume":" ","pages":"e0337624"},"PeriodicalIF":5.1,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11796383/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142914895","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The protein structurome of Orthornavirae and its dark matter.","authors":"Pascal Mutz, Antonio Pedro Camargo, Harutyun Sahakyan, Uri Neri, Anamarija Butkovic, Yuri I Wolf, Mart Krupovic, Valerian V Dolja, Eugene V Koonin","doi":"10.1128/mbio.03200-24","DOIUrl":"10.1128/mbio.03200-24","url":null,"abstract":"<p><p>Metatranscriptomics is uncovering more and more diverse families of viruses with RNA genomes comprising the viral kingdom Orthornavirae in the realm Riboviria. Thorough protein annotation and comparison are essential to get insights into the functions of viral proteins and virus evolution. In addition to sequence- and hmm profile‑based methods, protein structure comparison adds a powerful tool to uncover protein functions and relationships. We constructed an Orthornavirae \"structurome\" consisting of already annotated as well as unannotated (\"dark matter\") proteins and domains encoded in viral genomes. We used protein structure modeling and similarity searches to illuminate the remaining dark matter in hundreds of thousands of orthornavirus genomes. The vast majority of the dark matter domains showed either \"generic\" folds, such as single α-helices, or no high confidence structure predictions. Nevertheless, a variety of lineage-specific globular domains that were new either to orthornaviruses in general or to particular virus families were identified within the proteomic dark matter of orthornaviruses, including several predicted nucleic acid-binding domains and nucleases. In addition, we identified a case of exaptation of a cellular nucleoside monophosphate kinase as an RNA-binding protein in several virus families. Notwithstanding the continuing discovery of numerous orthornaviruses, it appears that all the protein domains conserved in large groups of viruses have already been identified. The rest of the viral proteome seems to be dominated by poorly structured domains including intrinsically disordered ones that likely mediate specific virus-host interactions.</p><p><strong>Importance: </strong>Advanced methods for protein structure prediction, such as AlphaFold2, greatly expand our capability to identify protein domains and infer their likely functions and evolutionary relationships. This is particularly pertinent for proteins encoded by viruses that are known to evolve rapidly and as a result often cannot be adequately characterized by analysis of the protein sequences. We performed an exhaustive structure prediction and comparative analysis for uncharacterized proteins and domains (\"dark matter\") encoded by viruses with RNA genomes. The results show the dark matter of RNA virus proteome consists mostly of disordered and all-α-helical domains that cannot be readily assigned a specific function and that likely mediate various interactions between viral proteins and between viral and host proteins. The great majority of globular proteins and domains of RNA viruses are already known although we identified several unexpected domains represented in individual viral families.</p>","PeriodicalId":18315,"journal":{"name":"mBio","volume":" ","pages":"e0320024"},"PeriodicalIF":5.1,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11796362/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142877178","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The <i>Rickettsia</i> actin-based motility effectors RickA and Sca2 contribute differently to cell-to-cell spread and pathogenicity.","authors":"Cuong J Tran, Zahra Zubair-Nizami, Ingeborg M Langohr, Matthew D Welch","doi":"10.1128/mbio.02563-24","DOIUrl":"10.1128/mbio.02563-24","url":null,"abstract":"<p><p><i>Rickettsia parkeri</i> is an obligate intracellular, tick-borne bacterial pathogen that can cause eschar-associated rickettsiosis in humans. <i>R. parkeri</i> invades host cells, escapes from vacuoles into the cytosol, and undergoes two independent modes of actin-based motility mediated by effectors RickA or Sca2. Actin-based motility of <i>R. parkeri</i> enables bacteria to enter protrusions of the host cell plasma membrane that are engulfed by neighboring host cells. However, whether and how RickA and Sca2 independently contribute to cell-to-cell spread <i>in vitro</i> or pathogenicity <i>in vivo</i> has been unclear. Using live cell imaging of <i>rickA</i>::Tn and <i>sca2</i>::Tn mutants, we discovered both RickA and Sca2 contribute to different modes of cell-to-cell spread. Compared with Sca2-spread, RickA-spread involves the formation of longer protrusions that exhibit larger fluctuations in length and take a longer time to be engulfed into neighboring cells. We further compared the roles of RickA and Sca2 <i>in vivo</i> following intradermal (i.d.) infection of <i>Ifnar1</i>^-/-; <i>Ifngr1</i>^-/- mice carrying knockout mutations in the genes encoding the receptors for IFN-I (<i>Ifnar1</i>) and IFN-γ (<i>Ifngr1</i>), which exhibit eschars and succumb to infection with wild-type (WT) <i>R. parkeri</i>. We observed that RickA is important for severe eschar formation, whereas Sca2 contributes to larger foci of infection in the skin and dissemination from the skin to the internal organs. Our results suggest that actin-based motility effectors RickA and Sca2 drive two distinct forms of cell-to-cell spread and contribute differently to pathogenicity in the mammalian host.IMPORTANCE<i>Rickettsia parkeri</i>, a bacterium in the spotted fever group of <i>Rickettsia</i> species, can be transmitted from ticks to humans, leading to symptoms including fever, rash, muscle aches, and a lesion at the site of the tick bite. During <i>Rickettsia parkeri</i> infection, bacteria invade cells within the animal host, proliferate in the host cell's cytosol, move using a process called actin-based motility, and spread to neighboring host cells. <i>Rickettsia parkeri</i> is unusual in having two bacterial proteins that mediate actin-based motility. The significance of our research is to reveal that each of these bacterial actin-based motility proteins contributes differently to spread between cells and to the signs of infection in a mouse model of spotted fever disease. Our results are important for understanding the contribution of actin-based motility to mammalian infection by <i>Rickettsia parkeri</i> as well as to infection by other bacterial and viral pathogens that require this process to spread between cells and cause disease.</p>","PeriodicalId":18315,"journal":{"name":"mBio","volume":" ","pages":"e0256324"},"PeriodicalIF":5.1,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11796396/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143007878","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Completely conserved VP2 residue K140 of KREMEN1-dependent enteroviruses is critical for virus-receptor interactions and viral infection.","authors":"Zeyu Liu, Xue Li, Xiaohong Li, Xingyu Yan, Yuan Tian, Yue Zhao, Kexin Liu, Pei Hao, Shuye Zhang, Chao Zhang","doi":"10.1128/mbio.03040-24","DOIUrl":"10.1128/mbio.03040-24","url":null,"abstract":"<p><p>The KREMEN1 (KRM1) protein is a cellular receptor for multiple enteroviruses that cause hand, foot, and mouth disease (HFMD), including coxsackievirus CVA2, CVA3, CVA4, CVA5, CVA6, CVA10, and CVA12. The molecular basis for the broad recognition of these viruses by the KRM1 receptor remains unclear. Here, we report the indispensable role of the completely conserved VP2 capsid protein residue K140 (designated K2140) in mediating receptor recognition and infection by CVA10 and other KRM1-dependent enteroviruses. Residue K2140 not only facilitates receptor recognition, cell attachment, and infection of CVA10 but also contributes to CVA10 pathogenicity <i>in vivo</i>. Notably, residue K2140 is completely conserved in all strains of the KRM1-dependent enteroviruses. Mutational analysis confirms the importance of K2140 for infection by CVA2-CVA6, and CVA12. Moreover, CVA8, an enterovirus for which the cellular receptor has not yet been identified, also possesses the conserved K2140 residue. We experimentally demonstrate that CVA8 utilizes KRM1 as its receptor, with K2140 being essential for viral infection. Additionally, residue D90 of KRM1 engages with residue K2140 and plays a crucial role in KRM1-mediated enterovirus infections. Collectively, our findings underscore the significance of the absolutely conserved K2140 residue in receptor interactions and infection of all KRM1-binding enteroviruses, providing novel insights into the molecular basis of enterovirus infection and informing the development of broad-spectrum therapies against HFMD.</p><p><strong>Importance: </strong>Hand, foot, and mouth disease (HFMD) annually affects millions of children worldwide. HFMD is caused by various enteroviruses, such as coxsackieviruses CVA6, CVA16, CVA10, and enterovirus 71 (EV-A71). Licensed inactivated EV-A71 vaccines do not provide cross-protection against other enteroviruses. There are no drugs specifically for HFMD. KREMEN1 (KRM1) serves as the cellular receptor for many HFMD-related enteroviruses, including CVA2-CVA6, CVA10, and CVA12. However, the molecular basis for broad recognition of these enteroviruses by the KRM1 receptor remains elusive. Here, we report that VP2 residue K140 (K2140) is completely conserved among all KRM1-dependent enteroviruses and is essential for virus-receptor binding and viral infection by interacting with residue D90 of KRM1. Overall, our findings provide a deeper understanding of the molecular basis of KRM1-dependent enterovirus infection <i>in vitro</i> and <i>in vivo</i> and may contribute to the development of broad-spectrum anti-enterovirus vaccines and treatments.</p>","PeriodicalId":18315,"journal":{"name":"mBio","volume":" ","pages":"e0304024"},"PeriodicalIF":5.1,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11796367/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143008153","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The <i>Campylobacter jejuni</i> BumS sensor phosphatase detects the branched short-chain fatty acids isobutyrate and isovalerate as direct cues for signal transduction.","authors":"Nestor Ruiz, Jiawei Xing, Igor B Zhulin, Chad A Brautigam, David R Hendrixson","doi":"10.1128/mbio.03278-24","DOIUrl":"10.1128/mbio.03278-24","url":null,"abstract":"<p><p>Two-component signal transduction systems (TCSs) are nearly ubiquitous across bacterial species and enable bacteria to sense and respond to specific cues for environmental adaptation. The <i>Campylobacter jejuni</i> BumSR TCS is unusual in that the BumS sensor exclusively functions as a phosphatase rather than a kinase to control phosphorylated levels of its cognate BumR response regulator (P-BumR). We previously found that BumSR directs a response to the short-chain fatty acid butyrate generated by resident microbiota so that <i>C. jejuni</i> identifies ideal lower intestinal niches in avian and human hosts for colonization. However, butyrate is an indirect cue for BumS and did not inhibit <i>in vitro</i> BumS phosphatase activity for P-BumR. In this work, we expanded the repertoire of lower intestinal metabolites that are cues sensed by BumS that modulate the expression of genes required for colonization to include the branched short-chain fatty acids isobutyrate and isovalerate. Unlike butyrate, isobutyrate and isovalerate inhibited <i>in vitro</i> BumS phosphatase activity for P-BumR, indicating that these metabolites are direct cues for BumS. Isobutyrate and isovalerate reduced the thermostability of BumS and caused a reorganization of protein structure to suggest how sensing these cues inhibits phosphatase activity. We also identified residues in the BumS sensory domain required to detect isobutyrate, isovalerate, and butyrate and for optimal colonization of hosts to reveal how gut bacteria can recognize these intestinal metabolites. Our work reveals how this unusual bacterial sensor phosphatase senses a repertoire of intestinal metabolites and how cues alter BumSR signal transduction to influence <i>C. jejuni</i> colonization of hosts.IMPORTANCETCSs are prevalent in many bacteria, but the cues sensed by each are not actually known for many of these systems. Microbiota-generated butyrate in human and avian hosts is detected by the <i>Campylobacter jejuni</i> BumS sensor phosphatase so that the bacterium identifies ideal lower intestinal niches for colonization. However, BumS only indirectly senses butyrate to inhibit dephosphorylation of its cognate BumR response regulator. Here, we expanded the repertoire of cues sensed by BumS to the branched-short chain fatty acids isobutyrate and isovalerate that are also abundant in the lower intestines. Both isobutyrate and isovalerate are potent, direct cues for BumS, whereas butyrate is an indirect cue. Leveraging isobutyrate and isovalerate as direct cues, we reveal BumS structure is altered upon cue detection to inhibit its phosphatase activity. We provide an understanding of the mechanics of an unusual mode of signal transduction executed by BumSR and other bacterial sensor phosphatase-driven TCSs.</p>","PeriodicalId":18315,"journal":{"name":"mBio","volume":" ","pages":"e0327824"},"PeriodicalIF":5.1,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11796366/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142818558","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A gut-derived <i>Streptococcus salivarius</i> produces the novel nisin variant designated nisin G and inhibits <i>Fusobacterium nucleatum</i> in a model of the human distal colon microbiome.","authors":"Garreth W Lawrence, Enriqueta Garcia-Gutierrez, A Kate O'Mahony, Calum J Walsh, Paula M O'Connor, Máire Begley, Caitriona M Guinane, Paul D Cotter","doi":"10.1128/mbio.01573-24","DOIUrl":"10.1128/mbio.01573-24","url":null,"abstract":"<p><p><i>Fusobacterium nucleatum</i> is a human pathogen associated with intestinal conditions including colorectal cancer. Screening for gut-derived strains that exhibit anti-<i>F</i>. <i>nucleatum</i> activity <i>in vitro</i> revealed <i>Streptococcus salivarius</i> DPC6487 as a strain of interest. Whole-genome sequencing of <i>S. salivarius</i> DPC6487 identified a nisin operon with a novel structural variant designated nisin G. The structural nisin G peptide differs from the prototypical nisin A with respect to seven amino acids (Ile4Tyr, Ala15Val, Gly18Ala, Asn20His, Met21Leu, His27Asn, and His31Ile), including differences that have not previously been associated with a natural nisin variant. The nisin G gene cluster consists of <i>nsgGEFABTCPRK</i> with transposases encoded between the nisin G structural gene (<i>nsgA</i>) and <i>nsgF</i>, notably lacking an equivalent to the <i>nisI</i> immunity determinant. <i>S. salivarius</i> DPC6487 exhibited a narrower spectrum of activity <i>in vitro</i> compared to the nisin A-producing <i>Lactococcus lactis</i> NZ9700. Nisin G-producing <i>S. salivarius</i> DPC6487 demonstrated the ability to control <i>F. nucleatum</i> DSM15643 in an <i>ex vivo</i> model colonic environment while exerting minimal impact on the surrounding microbiota. The production of this bacteriocin by a gut-derived <i>S. salivarius</i>, its narrow-spectrum activity, and its anti-<i>F. nucleatum</i> activity in a model colonic environment indicates that this strain merits further attention with a view to harnessing its probiotic potential.IMPORTANCE<i>Fusobacterium nucleatum</i> is a human pathogen associated with intestinal conditions, including colorectal cancer, making it a potentially important therapeutic target. Bacteriocin-producing probiotic bacteria demonstrate the potential to target disease-associated taxa <i>in situ</i> in the gut. A gut-derived strain <i>Streptococcus salivarius</i> DPC6487 was found to demonstrate anti-<i>F</i>. <i>nucleatum</i> activity, which was attributable to a gene encoding a novel nisin variant designated nisin G. Nisin G-producing <i>S. salivarius</i> DPC6487 demonstrated the ability to control an infection of <i>F. nucleatum</i> in a simulated model of the human distal colon while exerting minimal impact on the surrounding microbiota. Here, we describe this nisin variant produced by <i>S. salivarius</i>, a species that is frequently a focus for probiotic development. The production of nisin G by a gut-derived <i>S. salivarius</i>, its narrow-spectrum activity against <i>F. nucleatum</i>, and its anti-<i>F</i>. <i>nucleatum</i> activity in a model colonic environment warrants further research to determine its probiotic-related applications.</p>","PeriodicalId":18315,"journal":{"name":"mBio","volume":" ","pages":"e0157324"},"PeriodicalIF":5.1,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11796361/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142847113","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}