microLife最新文献

{"title":"Dynamic optimization elucidates higher-level pathogenicity strategies of <i>Pseudomonas aeruginosa</i>.","authors":"Wassili Dimitriew, Stefan Schuster","doi":"10.1093/femsml/uqaf005","DOIUrl":"10.1093/femsml/uqaf005","url":null,"abstract":"<p><p>Multiple dangerous pathogens from the World Health Organization's priority list possess a plethora of virulence components, including the ability to survive inside macrophages. Often, the pathogens rely on a multi-layered defence strategy in order to defend themselves against the immune system. Here, a minimal model is proposed to study such a strategy. By way of example, we consider the interaction between <i>Pseudomonas aeruginosa</i> and the human host, in which the host and the pathogen counter each other in a back-and-forth interaction. In particular, the pathogen attacks the host, macrophages of the host engulf the pathogen and reduce its access to glucose, the pathogen activates the glyoxylate shunt, which is started by the enzyme isocitrate lyase (Icl), the host inhibits it by itaconic acid, and the pathogen metabolizes itaconic acid using the enzyme succinyl-CoA:itaconate CoA transferase (Ict). The flux through the glyoxylate shunt allows the pathogen to avoid carbon loss and oxidative stress. These functions are of utmost importance inside a phagolysosome. Therefore, the pathogen needs to allocate its limited protein resource between the enzymes Icl and Ict in order to maximize the time integral of a flux through the enzyme Icl. We use both random search and dynamic optimization to identify the enzyme Ict as a cost-effective means of counter-counter-counter-defence and as a possible drug target during the early phase of infection.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"6 ","pages":"uqaf005"},"PeriodicalIF":0.0,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11967335/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143781999","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Respiratory syncytial virus: health burden, disease prevention, and treatment-recent progress and lessons learned.","authors":"Harald Brüssow","doi":"10.1093/femsml/uqaf003","DOIUrl":"10.1093/femsml/uqaf003","url":null,"abstract":"<p><p>Respiratory syncytial virus (RSV), a negative-sense single-stranded RNA virus of the Pneumoviridae family, represents the most important pathogen of lower respiratory tract infections in young infants causing yearly epidemics. RSV is also an important respiratory viral pathogen for older subjects, which is second only to seasonal influenza virus infections. RSV represents a substantial public health burden with respect to morbidity and mortality, particularly in developing countries. Prevention and treatment options would therefore lessen the global disease burden. A formalin-inactivated RSV vaccine in the 1960s induced an enhanced disease upon exposure to natural RSV. After this tragical vaccine failure, it took nearly five decades of intensive research before prevention tools were approved by health authorities. The lead was taken by passive immunity approaches with injected monoclonal antibodies directed against the fusion protein F of RSV. The elucidation of the three-dimensional structure of the F protein revealed pre- and postfusion conformations. Subsequently, structure-based antigen engineering of the F protein paved the way for development of a prophylactic vaccine. In 2023, RSV vaccines were approved for maternal vaccination to protect young infants by placental transfer of antibodies and for vaccination in older subjects. Antiviral drugs that target the RSV fusion process, the RSV replicase, or the cytoplasmic viral factories are in development. Important research papers leading to these developments are reviewed here.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"6 ","pages":"uqaf003"},"PeriodicalIF":0.0,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12104812/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144152920","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"\"French Phage Network\" annual conference-eighth meeting report.","authors":"Carole Armal, Charles-Adrien Arnaud, Emilie Cenraud, Youn Le Cras, Pierre-Alexandre Pastouriaux, Callypso Pellegri, Laurent Debarbieux","doi":"10.1093/femsml/uqaf001","DOIUrl":"10.1093/femsml/uqaf001","url":null,"abstract":"<p><p>The French Phage Network organizes a scientific meeting every year in which the community of researchers from academia and industry, as well as clinicians participate due to the growing interest in phage therapy. Although centered on giving exposure to future generations of scientists from the French community with senior investigators invited as main speakers, the meeting has also welcomed participants from other countries. Covering almost every aspect of bacteriophage biology, the meeting is an opportunity not only to expose the youngest to a broad range of topics, but also to share their most recent \"work in progress\" without undergoing a stringent selection process to obtain an oral presentation slot. This report reflects the dynamism of the research field on bacteriophages across multiple disciplines, including molecular and structural biology, ecology, evolution, therapy, and biotechnology.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"6 ","pages":"uqaf001"},"PeriodicalIF":0.0,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11806420/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143384342","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction to: Compiling a versatile toolbox for inducible gene expression in <i>Methanosarcina mazei</i>.","authors":"","doi":"10.1093/femsml/uqae028","DOIUrl":"https://doi.org/10.1093/femsml/uqae028","url":null,"abstract":"<p><p>[This corrects the article DOI: 10.1093/femsml/uqae019.].</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"6 ","pages":"uqae028"},"PeriodicalIF":0.0,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11774203/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143061659","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Metagenomic analysis of pristine oil sheds new light on the global distribution of microbial genetic repertoire in hydrocarbon-associated ecosystems.","authors":"Julia Plewka, Armando Alibrandi, Till L V Bornemann, Sarah P Esser, Tom L Stach, Katharina Sures, Jannis Becker, Cristina Moraru, André Soares, Rolando di Primio, Jens Kallmeyer, Alexander J Probst","doi":"10.1093/femsml/uqae027","DOIUrl":"10.1093/femsml/uqae027","url":null,"abstract":"<p><p>Oil reservoirs are society's primary source of hydrocarbons. While microbial communities in industrially exploited oil reservoirs have been investigated in the past, pristine microbial communities in untapped oil reservoirs are little explored, as are distribution patterns of respective genetic signatures. Here, we show that a pristine oil sample contains a complex community consisting of bacteria and fungi for the degradation of hydrocarbons. We identified microorganisms and their pathways for the degradation of methane, <i>n</i>-alkanes, mono-aromatic, and polycyclic aromatic compounds in a metagenome retrieved from biodegraded petroleum encountered in a subsurface reservoir in the Barents Sea. Capitalizing on marker genes from metagenomes and public data mining, we compared the prokaryotes, putative viruses, and putative plasmids of the sampled site to those from 10 other hydrocarbon-associated sites, revealing a shared network of species and genetic elements across the globe. To test for the potential dispersal of the microbes and predicted elements via seawater, we compared our findings to the Tara Ocean dataset, resulting in a broad distribution of prokaryotic and viral signatures. Although frequently shared between hydrocarbon-associated sites, putative plasmids, however, showed little coverage in the Tara Oceans dataset, suggesting an undiscovered mode of transfer between hydrocarbon-affected ecosystems. Based on our analyses, genetic information is globally shared between oil reservoirs and hydrocarbon-associated sites, and we propose that currents and other physical occurrences within the ocean along with deep aquifers are major distributors of prokaryotes and viruses into these subsurface ecosystems.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"6 ","pages":"uqae027"},"PeriodicalIF":0.0,"publicationDate":"2025-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11774207/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143061628","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"New components of the community-based DNA-repair mechanism in Sulfolobales.","authors":"Alejandra Recalde, Alexander Wagner, Shamphavi Sivabalasarma, Anastasiya Yurmashava, Nayeli Phycilia Fehr, Rebecca Thurm, Thuong Ngoc Le, Christin Köebler, Bianca Wassmer, Sonja-Verena Albers, Marleen van Wolferen","doi":"10.1093/femsml/uqaf002","DOIUrl":"10.1093/femsml/uqaf002","url":null,"abstract":"<p><p>After exposure to ultraviolet (UV) light, <i>Sulfolobus acidocaldarius</i> cells aggregate in a species-specific manner to exchange DNA and repair double-strand breaks via homologous recombination. The formation of cell-cell interactions is mediated by Ups pili. DNA exchange subsequently occurs through the Crenarchaeal system for exchange of DNA (Ced), which imports DNA. To identify novel players in these processes, we investigated that several genes upregulated after UV exposure, by creating in-frame deletion mutants and performing cell aggregation and DNA exchange assays. This led to the identification of two novel components involved in the Ups and Ced systems: UpsC, a minor pilin of the Ups pili, and CedD, a VirD4-like ATPase essential for DNA import. Altogether, these findings provide new insights into the DNA damage response mechanisms in Sulfolobales.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"6 ","pages":"uqaf002"},"PeriodicalIF":0.0,"publicationDate":"2025-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11823120/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143416498","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Functional characterization of the DUF1127-containing small protein YjiS of <i>Salmonella</i> Typhimurium.","authors":"Elisa Venturini, Sandra Maaß, Thorsten Bischler, Dörte Becher, Jörg Vogel, Alexander J Westermann","doi":"10.1093/femsml/uqae026","DOIUrl":"10.1093/femsml/uqae026","url":null,"abstract":"<p><p>Bacterial small proteins impact diverse physiological processes, however, technical challenges posed by small size hampered their systematic identification and biochemical characterization. In our quest to uncover small proteins relevant for <i>Salmonella</i> pathogenicity, we previously identified YjiS, a 54 amino acid protein, which is strongly induced during this pathogen's intracellular infection stage. Here, we set out to further characterize the role of YjiS. Cell culture infection assays with <i>Salmonella</i> mutants lacking or overexpressing YjiS suggested this small protein to delay bacterial escape from macrophages. Mutant scanning of the protein's conserved, arginine-rich DUF1127 domain excluded a major effect of single amino acid substitutions on the infection phenotype. A comparative dual RNA-seq assay uncovered the molecular footprint of YjiS in the macrophage response to infection, with host effects related to oxidative stress and the cell cortex. Bacterial cell fractionation experiments demonstrated YjiS to associate with the inner membrane and proteins interacting with YjiS in pull-down experiments were enriched for inner membrane processes. Among the YjiS interactors was the two-component system SsrA/B, the master transcriptional activator of intracellular virulence genes and a suppressor of flagellar genes. Indeed, in the absence of YjiS, we observed elevated expression of motility genes and an increased number of flagella per bacterium. Together, our study points to a role for <i>Salmonella</i> YjiS as a membrane-associated timer of pathogen dissemination.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"6 ","pages":"uqae026"},"PeriodicalIF":0.0,"publicationDate":"2025-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11707872/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142959964","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Subtilosin A production is influenced by surfactin levels in <i>Bacillus subtilis</i>.","authors":"Caja Dinesen, Manca Vertot, Scott A Jarmusch, Carlos N Lozano-Andrade, Aaron J C Andersen, Ákos T Kovács","doi":"10.1093/femsml/uqae029","DOIUrl":"10.1093/femsml/uqae029","url":null,"abstract":"<p><p>Although not essential for their growth, the production of secondary metabolites increases the fitness of the producing microorganisms in their natural habitat by enhancing establishment, competition, and nutrient acquisition. The Gram-positive soil-dwelling bacterium, <i>Bacillus subtilis</i>, produces a variety of secondary metabolites. Here, we investigated the regulatory relationship between the non-ribosomal peptide surfactin and the sactipeptide bacteriocin subtilosin A. We discovered that <i>B. subtilis</i> mutants lacking surfactin production exhibited higher production of subtilosin A compared to their parental wild-type strain. Additionally, spatial visualization of <i>B. subtilis</i> production of metabolites demonstrated that surfactin secreted by a wild-type colony could suppress subtilosin A production in an adjacent mutant colony lacking surfactin production. Reporter assays were performed using mutants in specific transcriptional regulators, which confirmed the role of ResD as an activator of the subtilosin A encoding biosynthetic gene cluster (BGC), while the removal of Rok and AbrB repressors increased the expression of the BGC, which was further enhanced by additional deletion of surfactin, suggesting that a so-far-unidentified regulator might mediate the influence of surfactin on production of subtilosin A. Our study reveals a regulatory influence of one secondary metabolite on another, highlighting that the function of secondary metabolites could be more complex than its influence on other organisms and interactions among secondary metabolites could also contribute to their ecological significance.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"6 ","pages":"uqae029"},"PeriodicalIF":0.0,"publicationDate":"2025-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11756287/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143030268","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Did organs precede organisms in the origin of life?","authors":"Fernando Baquero, Gabriel S Bever, Victor de Lorenzo, Val Fernández-Lanza, Carlos Briones","doi":"10.1093/femsml/uqae025","DOIUrl":"10.1093/femsml/uqae025","url":null,"abstract":"<p><p>Evolutionary processes acting on populations of organized molecules preceded the origin of living organisms. These prebiotic entities were independently and repeatedly produced [i.e. (re)-produced] by the assembly of their components, following an iterative process giving rise to nearly but not fully identical replicas, allowing for a prebiotic form of Darwinian evolution. Natural selection favored the more persistent assemblies, some possibly modifying their own internal structure, or even their environment, thereby acquiring function. We refer to these assemblies as proto-organs. In association with other assemblies (e.g. in a coacervate or encapsulated within a vesicle), such proto-organs could evolve and acquire a role within the collective when their coexistence favored the selection of the ensemble. Along millions of years, an extraordinarily small number of successful combinations of those proto-organs co-occurring in spatially individualizing compartments might have co-evolved forming a proto-metabolic and proto-genetic informative network, eventually leading to the selfreplication of a very few. Thus, interactions between encapsulated proto-organs would have had a much higher probability of evolving into proto-organisms than interactions among simpler molecules. Multimolecular forms evolve functions; thus, functional organs would have preceded organisms.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"5 ","pages":"uqae025"},"PeriodicalIF":0.0,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11664216/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142883770","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The proteomic response of <i>Aspergillus fumigatus</i> to amphotericin B (AmB) reveals the involvement of the RTA-like protein RtaA in AmB resistance.","authors":"Ammar Abou-Kandil, Sophie Tröger-Görler, Annica Pschibul, Thomas Krüger, Maira Rosin, Franziska Schmidt, Parastoo Akbarimoghaddam, Arjun Sarkar, Zoltán Cseresnyés, Yana Shadkchan, Thorsten Heinekamp, Markus H Gräler, Amelia E Barber, Grit Walther, Marc Thilo Figge, Axel A Brakhage, Nir Osherov, Olaf Kniemeyer","doi":"10.1093/femsml/uqae024","DOIUrl":"10.1093/femsml/uqae024","url":null,"abstract":"<p><p>The polyene antimycotic amphotericin B (AmB) and its liposomal formulation AmBisome belong to the treatment options of invasive aspergillosis caused by <i>Aspergillus fumigatus</i>. Increasing resistance to AmB in clinical isolates of <i>Aspergillus</i> species is a growing concern, but mechanisms of AmB resistance remain unclear. In this study, we conducted a proteomic analysis of <i>A. fumigatus</i> exposed to sublethal concentrations of AmB and AmBisome. Both antifungals induced significantly increased levels of proteins involved in aromatic acid metabolism, transmembrane transport, and secondary metabolite biosynthesis. One of the most upregulated proteins was RtaA, a member of the RTA-like protein family, which includes conserved fungal membrane proteins with putative functions as transporters or translocases. Accordingly, we found that RtaA is mainly located in the cytoplasmic membrane and to a minor extent in vacuolar-like structures. Deletion of <i>rtaA</i> led to increased polyene sensitivity and its overexpression resulted in modest resistance. Interestingly, <i>rtaA</i> expression was only induced by exposure to the polyenes AmB and nystatin, but not by itraconazole and caspofungin. Orthologues of <i>rtaA</i> were also induced by AmB exposure in <i>A. lentulus</i> and <i>A. terreus</i>. Deletion of <i>rtaA</i> did not significantly change the ergosterol content of <i>A. fumigatus</i>, but decreased fluorescence intensity of the sterol-binding stain filipin. This suggests that RtaA is involved in sterol and lipid trafficking, possibly by transporting the target ergosterol to or from lipid droplets. These findings reveal the contribution of RtaA to polyene resistance in <i>A. fumigatus</i>, and thus provide a new putative target for antifungal drug development.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"6 ","pages":"uqae024"},"PeriodicalIF":0.0,"publicationDate":"2024-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11707875/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142959764","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}