microLife最新文献

{"title":"Phylogenetic diversity of core rumen microbiota as described by cryo-ET.","authors":"Benedikt H Wimmer,&nbsp;Sarah Moraïs,&nbsp;Ran Zalk,&nbsp;Itzhak Mizrahi,&nbsp;Ohad Medalia","doi":"10.1093/femsml/uqad010","DOIUrl":"https://doi.org/10.1093/femsml/uqad010","url":null,"abstract":"<p><p>Microbial taxonomy is critical for describing ecosystem composition, yet the link between taxonomy and properties of microbes, such as their cellular architecture, remains poorly defined. We hypothesized that the cellular architecture represents microbial niche adaptation. We used cryo-electron microscopy and tomography to analyze microbial morphology in order to associate cellular architecture with phylogeny and genomic contents. As a model system, we chose the core rumen microbiome and imaged a large isolate collection covering 90% of its richness at the order level. Based on quantifications of several morphological features, we found that the visual similarity of microbiota is significantly related to their phylogenetic distance. Up to the <i>Family</i> level, closely related microbes have similar cellular architectures, which are highly correlated with genome similarity. However, in more distantly related bacteria, the correlation both with taxonomy and genome similarity is lost. This is the first comprehensive study of microbial cellular architecture and our results highlight that structure remains an important parameter in classification of microorganisms, along with functional parameters such as metabolomics. Furthermore, the high-quality images presented in this study represent a reference database for the identification of bacteria in anaerobic ecosystems.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"4 ","pages":"uqad010"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/96/0c/uqad010.PMC10117717.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9518989","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":"<i>Streptomyces</i> development is involved in the efficient containment of viral infections.","authors":"Tom Luthe,&nbsp;Larissa Kever,&nbsp;Sebastian Hänsch,&nbsp;Aël Hardy,&nbsp;Natalia Tschowri,&nbsp;Stefanie Weidtkamp-Peters,&nbsp;Julia Frunzke","doi":"10.1093/femsml/uqad002","DOIUrl":"https://doi.org/10.1093/femsml/uqad002","url":null,"abstract":"<p><p>The formation of plaques represents the hallmark of phage infection visualizing the clearance of the bacterial lawn in structured environments. In this study, we have addressed the impact of cellular development on phage infection in <i>Streptomyces</i> undergoing a complex developmental life cycle. Analysis of plaque dynamics revealed, after a period of plaque size enlargement, a significant regrowth of transiently phage-resistant <i>Streptomyces</i> mycelium into the lysis zone. Analysis of <i>Streptomyces venezuelae</i> mutant strains defective at different stages of cellular development indicated that this regrowth was dependent on the onset of the formation of aerial hyphae and spores at the infection interface. Mutants restricted to vegetative growth (Δ<i>bldN</i>) featured no significant constriction of plaque area. Fluorescence microscopy further confirmed the emergence of a distinct zone of cells/spores with reduced cell permeability towards propidium iodide staining at the plaque periphery. Mature mycelium was further shown to be significantly less susceptible to phage infection, which is less pronounced in strains defective in cellular development. Transcriptome analysis revealed the repression of cellular development at the early stages of phage infection probably facilitating efficient phage propagation. We further observed an induction of the chloramphenicol biosynthetic gene cluster highlighting phage infection as a trigger of cryptic metabolism in <i>Streptomyces</i>. Altogether, our study emphasizes cellular development and the emergence of transient phage resistance as an important layer of <i>Streptomyces</i> antiviral immunity.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"4 ","pages":"uqad002"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10117723/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9518990","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":"Working together to fighting the bad guys.","authors":"Sarah Wettstadt","doi":"10.1093/femsml/uqad022","DOIUrl":"https://doi.org/10.1093/femsml/uqad022","url":null,"abstract":"When Sabine Ehrt first got into contact with bacteria in University lectures, she almost disregarded them as being too simple. But soon she realised that ‘they are actually not that simple; they are quite complicated, adapting to different environments, niches, and hosts.’ After finishing her Ph.D. on adaptation strategies of Acinetobacter calcoaceticus at the University of Erlangen in Germany, Sabine switched to human pathogens for her postdoc positions at Cornell University Medical College in New York and the University of California at Berkeley. She took the chance to work on bacteria that require a biosafety 3 lab set up and deep dived into the question of how the death-causing pathogen Mycobacterium tuberculosis adapts to humans. As an Assistant Professor in the Department of Microbiology and Immunology at Weill Medical College of Cornell University, Sabine started a substantial collaboration with Dirk Schnappinger to investigate the pathogen’s adaptation mechanisms. Mycobacterium tuberculosis comes into contact with a host via inhalation and infects macrophages in the lung. Within the macrophage cytosol, the pathogen resides within phagosomes, but prevents them from fusing with lysosomes and thereby from clearing the pathogen. To investigate how the pathogen adjusts to the macrophage environment and how macrophages respond to the infection, Sabine and her team set up two major studies ‘that used microarray techniques for the first time in tuberculosis research’. They found that M. tuberculosis senses the intraphagosomal environment through the presence of fatty acids and low pH. Hence, the pathogen responds by inducing anaerobic respiration, degradation of fatty acids, remodelling of its cell envelope and by producing siderophores for efficient iron acquisition (Schnappinger et al. 2003). Similarly, macrophages upregulate genes with functions related to immunity and inflammation to clear the invading pathogen. About 25% of the macrophage genome showed altered expression levels upon infection mainly driven by the macrophage-activating factor Interferon-γ (Ehrt et al. 2001). Her collaborative spirit became even more profound when Sabine was appointed Professor in 2010. She got involved in several global scientific projects, e.g. as chair of the Tuberculosis/Leprosy Panel of the USA–Japan Cooperative Medical Science Program, which fosters engagement between US and Asian scientists. Sabine was also involved on scientific advisory boards of several international research programs, including the Translational & Clinical Research Flagship Program Medical Research Council Singapore and the Research Unit at the University of Witwatersrand in Johannesburg. Being a member of the European Academy of Microbiology and section editor of their journal microLife fosters her belief that ‘science is and should not be limited to a single country or continent as it is important to collaborate with other scientists globally and exchange knowledge’.","PeriodicalId":74189,"journal":{"name":"microLife","volume":"4 ","pages":"uqad022"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/59/dd/uqad022.PMC10167628.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9522022","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":"Epigenetic effects of short-chain fatty acids from the large intestine on host cells.","authors":"Richard A Stein,&nbsp;Leise Riber","doi":"10.1093/femsml/uqad032","DOIUrl":"https://doi.org/10.1093/femsml/uqad032","url":null,"abstract":"<p><p>Adult humans harbor at least as many microbial cells as eukaryotic ones. The largest compartment of this diverse microbial population, <i>the gut microbiota</i>, encompasses the collection of bacteria, archaea, viruses, and eukaryotic organisms that populate the gastrointestinal tract, and represents a complex and dynamic ecosystem that has been increasingly implicated in health and disease. The gut microbiota carries ∼100-to-150-times more genes than the human genome and is intimately involved in development, homeostasis, and disease. Of the several microbial metabolites that have been studied, short-chain fatty acids emerge as a group of molecules that shape gene expression in several types of eukaryotic cells by multiple mechanisms, which include DNA methylation changes, histone post-translational modifications, and microRNA-mediated gene silencing. Butyric acid, one of the most extensively studied short-chain fatty acids, reaches higher concentrations in the colonic lumen, where it provides a source of energy for healthy colonocytes, and its concentrations decrease towards the bottom of the colonic crypts, where stem cells reside. The lower butyric acid concentration in the colonic crypts allows undifferentiated cells, such as stem cells, to progress through the cell cycle, pointing towards the importance of the crypts in providing them with a protective niche. In cancerous colonocytes, which metabolize relatively little butyric acid and mostly rely on glycolysis, butyric acid preferentially acts as a histone deacetylase inhibitor, leading to decreased cell proliferation and increased apoptosis. A better understanding of the interface between the gut microbiota metabolites and epigenetic changes in eukaryotic cells promises to unravel in more detail processes that occur physiologically and as part of disease, help develop novel biomarkers, and identify new therapeutic modalities.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"4 ","pages":"uqad032"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/5e/b1/uqad032.PMC10335734.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9817978","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":"Computer-aided design of a cyclic di-AMP synthesizing enzyme CdaA inhibitor.","authors":"Piotr Neumann,&nbsp;Patrick Kloskowski,&nbsp;Ralf Ficner","doi":"10.1093/femsml/uqad021","DOIUrl":"https://doi.org/10.1093/femsml/uqad021","url":null,"abstract":"<p><p>Cyclic di-AMP (c-di-AMP) is an essential secondary messenger regulating cell wall homeostasis and myriads of physiological processes in several Gram-positive and mycobacteria, including human pathogens. Hence, c-di-AMP synthesizing enzymes (DACs) have become a promising antibacterial drug target. To overcome a scarcity of small molecule inhibitors of c-di-AMP synthesizing enzyme CdaA, a computer-aided design of a new compound that should block the enzyme has been performed. This has led to the identification of a molecule comprising two thiazole rings and showing inhibitory potential based on ITC measurements. Thiazole scaffold is a good pharmacophore nucleus known due to its various pharmaceutical applications. It is contained in more than 18 FDA-approved drugs as well as in dozens of experimental drugs. Hence, the designed inhibitor can serve as a potent lead compound for further development of inhibitor against CdaA.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"4 ","pages":"uqad021"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10167629/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9516281","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":"Ancestral reconstruction of the MotA stator subunit reveals that conserved residues far from the pore are required to drive flagellar motility.","authors":"Md Imtiazul Islam,&nbsp;Pietro Ridone,&nbsp;Angela Lin,&nbsp;Katharine A Michie,&nbsp;Nicholas J Matzke,&nbsp;Georg Hochberg,&nbsp;Matthew A B Baker","doi":"10.1093/femsml/uqad011","DOIUrl":"https://doi.org/10.1093/femsml/uqad011","url":null,"abstract":"<p><p>The bacterial flagellar motor (BFM) is a rotary nanomachine powered by the translocation of ions across the inner membrane through the stator complex. The stator complex consists of two membrane proteins: MotA and MotB (in H⁺-powered motors), or PomA and PomB (in Na⁺-powered motors). In this study, we used ancestral sequence reconstruction (ASR) to probe which residues of MotA correlate with function and may have been conserved to preserve motor function. We reconstructed 10 ancestral sequences of MotA and found four of them were motile in combination with contemporary <i>Escherichia coli</i> MotB and in combination with our previously published functional ancestral MotBs. Sequence comparison between wild-type (WT) <i>E. coli</i> MotA and MotA-ASRs revealed 30 critical residues across multiple domains of MotA that were conserved among all motile stator units. These conserved residues included pore-facing, cytoplasm-facing, and MotA-MotA intermolecular facing sites. Overall, this work demonstrates the role of ASR in assessing conserved variable residues in a subunit of a molecular complex.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"4 ","pages":"uqad011"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10117855/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9518987","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":"Osmotic stress responses and the biology of the second messenger c-di-AMP in <i>Streptomyces</i>.","authors":"Sukanya Bhowmick,&nbsp;Mary L Shenouda,&nbsp;Natalia Tschowri","doi":"10.1093/femsml/uqad020","DOIUrl":"https://doi.org/10.1093/femsml/uqad020","url":null,"abstract":"<p><p><i>Streptomyces</i> are prolific antibiotic producers that thrive in soil, where they encounter diverse environmental cues, including osmotic challenges caused by rainfall and drought. Despite their enormous value in the biotechnology sector, which often relies on ideal growth conditions, how <i>Streptomyces</i> react and adapt to osmotic stress is heavily understudied. This is likely due to their complex developmental biology and an exceptionally broad number of signal transduction systems. With this review, we provide an overview of <i>Streptomyces</i>' responses to osmotic stress signals and draw attention to open questions in this research area. We discuss putative osmolyte transport systems that are likely involved in ion balance control and osmoadaptation and the role of alternative sigma factors and two-component systems (TCS) in osmoregulation. Finally, we highlight the current view on the role of the second messenger c-di-AMP in cell differentiation and the osmotic stress responses with specific emphasis on the two models, <i>S. coelicolor</i> and <i>S. venezuelae</i>.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"4 ","pages":"uqad020"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10117811/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9522026","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":"Local signaling enhances output specificity of bacterial c-di-GMP signaling networks.","authors":"Eike H Junkermeier,&nbsp;Regine Hengge","doi":"10.1093/femsml/uqad026","DOIUrl":"https://doi.org/10.1093/femsml/uqad026","url":null,"abstract":"<p><p>For many years the surprising multiplicity, signal input diversity, and output specificity of c-di-GMP signaling proteins has intrigued researchers studying bacterial second messengers. How can several signaling pathways act in parallel to produce specific outputs despite relying on the same diffusible second messenger maintained at a certain global cellular concentration? Such high specificity and flexibility arise from combining modes of local and global c-di-GMP signaling in complex signaling networks. Local c-di-GMP signaling can be experimentally shown by three criteria being met: (i) highly specific knockout phenotypes for particular c-di-GMP-related enzymes, (ii) actual cellular c-di-GMP levels that remain unchanged by such mutations and/or below the K_d's of the relevant c-di-GMP-binding effectors, and (iii) direct interactions between the signaling proteins involved. Here, we discuss the rationale behind these criteria and present well-studied examples of local c-di-GMP signaling in <i>Escherichia coli</i> and <i>Pseudomonas</i>. Relatively simple systems just colocalize a local source and/or a local sink for c-di-GMP, i.e. a diguanylate cyclase (DGC) and/or a specific phosphodiesterase (PDE), respectively, with a c-di-GMP-binding effector/target system. More complex systems also make use of regulatory protein interactions, e.g. when a \"trigger PDE\" responds to locally provided c-di-GMP, and thereby serves as a c-di-GMP-sensing effector that directly controls a target's activity, or when a c-di-GMP-binding effector recruits and directly activates its own \"private\" DGC. Finally, we provide an outlook into how cells can combine local and global signaling modes of c-di-GMP and possibly integrate those into other signaling nucleotides networks.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"4 ","pages":"uqad026"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/df/7c/uqad026.PMC10211494.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9546756","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":"Control of light-dependent behaviour in cyanobacteria by the second messenger cyclic di-GMP.","authors":"Gen Enomoto,&nbsp;Thomas Wallner,&nbsp;Annegret Wilde","doi":"10.1093/femsml/uqad019","DOIUrl":"https://doi.org/10.1093/femsml/uqad019","url":null,"abstract":"<p><p>Nucleotide-derived signalling molecules control a wide range of cellular processes in all organisms. The bacteria-specific cyclic dinucleotide c-di-GMP plays a crucial role in regulating motility-to-sessility transitions, cell cycle progression, and virulence. Cyanobacteria are phototrophic prokaryotes that perform oxygenic photosynthesis and are widespread microorganisms that colonize almost all habitats on Earth. In contrast to photosynthetic processes that are well understood, the behavioural responses of cyanobacteria have rarely been studied in detail. Analyses of cyanobacterial genomes have revealed that they encode a large number of proteins that are potentially involved in the synthesis and degradation of c-di-GMP. Recent studies have demonstrated that c-di-GMP coordinates many different aspects of the cyanobacterial lifestyle, mostly in a light-dependent manner. In this review, we focus on the current knowledge of light-regulated c-di-GMP signalling systems in cyanobacteria. Specifically, we highlight the progress made in understanding the most prominent behavioural responses of the model cyanobacterial strains <i>Thermosynechococcus vulcanus</i> and <i>Synechocystis</i> sp. PCC 6803. We discuss why and how cyanobacteria extract crucial information from their light environment to regulate ecophysiologically important cellular responses. Finally, we emphasize the questions that remain to be addressed.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"4 ","pages":"uqad019"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/f2/99/uqad019.PMC10124867.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10008578","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 mysterious diadenosine tetraphosphate (AP4A).","authors":"Victor Zegarra,&nbsp;Christopher-Nils Mais,&nbsp;Johannes Freitag,&nbsp;Gert Bange","doi":"10.1093/femsml/uqad016","DOIUrl":"https://doi.org/10.1093/femsml/uqad016","url":null,"abstract":"<p><p>Dinucleoside polyphosphates, a class of nucleotides found amongst all the Trees of Life, have been gathering a lot of attention in the past decades due to their putative role as cellular alarmones. In particular, diadenosine tetraphosphate (AP4A) has been widely studied in bacteria facing various environmental challenges and has been proposed to be important for ensuring cellular survivability through harsh conditions. Here, we discuss the current understanding of AP4A synthesis and degradation, protein targets, their molecular structure where possible, and insights into the molecular mechanisms of AP4A action and its physiological consequences. Lastly, we will briefly touch on what is known with regards to AP4A beyond the bacterial kingdom, given its increasing appearance in the eukaryotic world. Altogether, the notion that AP4A is a conserved second messenger in organisms ranging from bacteria to humans and is able to signal and modulate cellular stress regulation seems promising.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"4 ","pages":"uqad016"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10148737/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9516280","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}