Microbiology-Sgm最新文献

{"title":"RelQ-mediated alarmone signalling regulates growth, stress-induced biofilm formation and spore accumulation in <i>Clostridioides difficile</i>.","authors":"Areej Malik, Adenrele Oludiran, Asia Poudel, Orlando Berumen Alvarez, Charles Woodward, Erin B Purcell","doi":"10.1099/mic.0.001479","DOIUrl":"10.1099/mic.0.001479","url":null,"abstract":"<p><p>The bacterial stringent response (SR) is a conserved transcriptional reprogramming pathway mediated by the nucleotide signalling alarmones, (pp)pGpp. The SR has been implicated in antibiotic survival in <i>Clostridioides difficile</i>, a biofilm- and spore-forming pathogen that causes resilient, highly recurrent <i>C. difficile</i> infections. The role of the SR in other processes and the effectors by which it regulates <i>C. difficile</i> physiology are unknown. <i>C. difficile</i> RelQ is a clostridial alarmone synthetase. Deletion of <i>relQ</i> dysregulates <i>C. difficile</i> growth in unstressed conditions, affects susceptibility to antibiotic and oxidative stressors and drastically reduces biofilm formation. While wild-type <i>C. difficile</i> displays increased biofilm formation in the presence of sublethal stress, the Δ<i>relQ</i> strain cannot upregulate biofilm production in response to stress. Deletion of <i>relQ</i> slows spore accumulation in planktonic cultures but accelerates it in biofilms. This work establishes biofilm formation and spore accumulation as alarmone-mediated processes in <i>C. difficile</i> and reveals the importance of RelQ in stress-induced biofilm regulation.</p>","PeriodicalId":49819,"journal":{"name":"Microbiology-Sgm","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11317968/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141724855","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"OxyR is required for oxidative stress resistance of the entomopathogenic bacterium <i>Xenorhabdus nematophila</i> and has a minor role during the bacterial interaction with its hosts.","authors":"Victoria Bientz, Anne Lanois, Nadège Ginibre, Sylvie Pagès, Jean-Claude Ogier, Simon George, Stéphanie Rialle, Julien Brillard","doi":"10.1099/mic.0.001481","DOIUrl":"10.1099/mic.0.001481","url":null,"abstract":"<p><p><i>Xenorhabdus nematophila</i> is a Gram-negative bacterium, mutualistically associated with the soil nematode <i>Steinernema carpocapsae</i>, and this nemato-bacterial complex is parasitic for a broad spectrum of insects. The transcriptional regulator OxyR is widely conserved in bacteria and activates the transcription of a set of genes that influence cellular defence against oxidative stress. It is also involved in the virulence of several bacterial pathogens. The aim of this study was to identify the <i>X. nematophila</i> OxyR regulon and investigate its role in the bacterial life cycle. An <i>oxyR</i> mutant was constructed in <i>X. nematophila</i> and phenotypically characterized <i>in vitro</i> and <i>in vivo</i> after reassociation with its nematode partner. OxyR plays a major role during the <i>X. nematophila</i> resistance to oxidative stress <i>in vitro</i>. Transcriptome analysis allowed the identification of 59 genes differentially regulated in the <i>oxyR</i> mutant compared to the parental strain. <i>In vivo</i>, the <i>oxyR</i> mutant was able to reassociate with the nematode as efficiently as the control strain. These nemato-bacterial complexes harbouring the <i>oxyR</i> mutant symbiont were able to rapidly kill the insect larvae in less than 48 h after infestation, suggesting that factors other than OxyR could also allow <i>X. nematophila</i> to cope with oxidative stress encountered during this phase of infection in insect. The significantly increased number of offspring of the nemato-bacterial complex when reassociated with the <i>X. nematophila oxyR</i> mutant compared to the control strain revealed a potential role of OxyR during this symbiotic stage of the bacterial life cycle.</p>","PeriodicalId":49819,"journal":{"name":"Microbiology-Sgm","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11281485/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141762105","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Generation of tools for expression and purification of the phage-encoded Type I restriction enzyme inhibitor, Ocr.","authors":"Joana Alves, Inga Dry, John H White, David T F Dryden, Nicola N Lynskey","doi":"10.1099/mic.0.001465","DOIUrl":"10.1099/mic.0.001465","url":null,"abstract":"<p><p>DNA manipulation is an essential tool in molecular microbiology research that is dependent on the ability of bacteria to take up and preserve foreign DNA by horizontal gene transfer. This process can be significantly impaired by the activity of bacterial restriction modification systems; bacterial operons comprising paired enzymatic activities that protectively methylate host DNA, while cleaving incoming unmodified foreign DNA. Ocr is a phage-encoded protein that inhibits Type I restriction modification systems, the addition of which significantly improves bacterial transformation efficiency. We recently established an improved and highly efficient transformation protocol for the important human pathogen group A <i>Streptococcus</i> using commercially available recombinant Ocr protein, manufacture of which has since been discontinued. In order to ensure the continued availability of Ocr protein within the research community, we have generated tools and methods for in-house Ocr production and validated the activity of the purified recombinant protein.</p>","PeriodicalId":49819,"journal":{"name":"Microbiology-Sgm","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11317969/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141749529","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mapping the <i>Escherichia coli</i> DnaA-binding landscape reveals a preference for binding pairs of closely spaced DNA sites.","authors":"Anne M Stringer, Devon M Fitzgerald, Joseph T Wade","doi":"10.1099/mic.0.001474","DOIUrl":"10.1099/mic.0.001474","url":null,"abstract":"<p><p>DnaA is a widely conserved DNA-binding protein that is essential for the initiation of DNA replication in many bacterial species, including <i>Escherichia coli</i>. Cooperative binding of ATP-bound DnaA to multiple 9mer sites ('DnaA boxes') at the origin of replication results in local unwinding of the DNA and recruitment of the replication machinery. DnaA also functions as a transcription regulator by binding to DNA sites upstream of target genes. Previous studies have identified many sites of direct positive and negative regulation by <i>E. coli</i> DnaA. Here, we use a ChIP-seq to map the <i>E. coli</i> DnaA-binding landscape. Our data reveal a compact regulon for DnaA that coordinates the initiation of DNA replication with expression of genes associated with nucleotide synthesis, replication, DNA repair and RNA metabolism. We also show that DnaA binds preferentially to pairs of DnaA boxes spaced 2 or 3 bp apart. Mutation of either the upstream or downstream site in a pair disrupts DnaA binding, as does altering the spacing between sites. We conclude that binding of DnaA at almost all target sites requires a dimer of DnaA, with each subunit making critical contacts with a DnaA box.</p>","PeriodicalId":49819,"journal":{"name":"Microbiology-Sgm","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11317965/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141621590","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"'Queer in Microbiology': a Microbiology Society members' endeavour for creating a safe and inclusive environment for LGBTQIA+ microbiologists.","authors":"Bruno Francesco Rodrigues de Oliveira, I'ah Donovan-Banfield, Rebekah Penrice-Randal, Rowan Casey, Daniel Gonçalves-Carneiro","doi":"10.1099/mic.0.001468","DOIUrl":"10.1099/mic.0.001468","url":null,"abstract":"<p><p>The past decade has seen growing awareness of the challenges faced by LGBTQIA+ scientists, including discrimination in the workplace and the lack of representation. Initiatives such as 500 Queer Scientists, Pride in STEM and the Microbiology Society's LGBTQIA+ events have been instrumental in promoting inclusivity in science, technology, engineering, mathematics and medicine (STEMM). The Microbiology Society and its members have played a pivotal role in these efforts and summarized here are their initiatives towards safer and more inclusive scientific and research environments. Starting with a series of interviews and blog posts about the experiences of LGBTQIA+ microbiologists in research, the Society has promoted the organization of networking and social events and developed guidelines for creating more inclusive scientific conferences. These initiatives have not only improved the representation and visibility of LGBTQIA+ individuals in microbiology, but have also served as a blueprint for similar efforts in other scientific areas. Nevertheless, despite improvements in some areas, full inclusion of LGBTQIA+ scientists is still hindered by societal and institutional policies around the world. Here, we propose novel measures to support and empower LGBTQIA+ microbiological communities within learned societies.</p>","PeriodicalId":49819,"journal":{"name":"Microbiology-Sgm","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11261901/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141301976","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Special collection to commemorate 40 years of antimicrobial efflux.","authors":"Ayush Kumar, Jessica M A Blair","doi":"10.1099/mic.0.001466","DOIUrl":"10.1099/mic.0.001466","url":null,"abstract":"","PeriodicalId":49819,"journal":{"name":"Microbiology-Sgm","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11261860/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141332363","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Development of a split-luciferase assay to establish optimal protein secretion conditions for protein production by <i>Bacillus subtilis</i>.","authors":"Mariah B M J Kes, Biwen Wang, Peter van Ulsen, Leendert W Hamoen, Joen Luirink","doi":"10.1099/mic.0.001460","DOIUrl":"10.1099/mic.0.001460","url":null,"abstract":"<p><p><i>Bacillus subtilis</i> is a Gram-positive bacterium that is frequently used in the bioindustry for the production of various proteins, because of its superior protein secretion capacities. To determine optimal conditions for protein secretion by <i>B. subtilis</i>, a quick and sensitive method for measuring protein secretion is crucial. A fast and universal assay is most useful for detecting diverse proteins in a high-throughput manner. In this study, we introduce a split-luciferase-based method for measuring protein secretion by <i>B. subtilis</i>. The NanoBiT system was used to monitor secretion of four different proteins: xylanase A, amylase M, protein glutaminase A, and GFP nanobody. Our findings underscore the split-luciferase system as a quick, sensitive, and user-friendly method.</p>","PeriodicalId":49819,"journal":{"name":"Microbiology-Sgm","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11261832/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141285167","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Broadening the application of <i>Yarrowia lipolytica</i> synthetic biology tools to explore the potential of <i>Yarrowia</i> clade diversity.","authors":"Young-Kyoung Park, Tristan Rossignol","doi":"10.1099/mic.0.001472","DOIUrl":"10.1099/mic.0.001472","url":null,"abstract":"<p><p>Yeasts have established themselves as prominent microbial cell factories, and the availability of synthetic biology tools has led to breakthroughs in the rapid development of industrial chassis strains. The selection of a suitable microbial host is critical in metabolic engineering applications, but it has been largely limited to a few well-defined strains. However, there is growing consideration for evaluating strain diversity, as a wide range of specific traits and phenotypes have been reported even within a specific yeast genus or species. Moreover, with the advent of synthetic biology tools, non-type strains can now be easily and swiftly reshaped. The yeast <i>Yarrowia lipolytica</i> has been extensively studied for various applications such as fuels, chemicals, and food. Additionally, other members of the <i>Yarrowia</i> clade are currently being evaluated for their industrial potential. In this study, we demonstrate the versatility of synthetic biology tools originally developed for <i>Y. lipolytica</i> by repurposing them for engineering other yeasts belonging to the <i>Yarrowia</i> clade. Leveraging the Golden Gate <i>Y. lipolytica</i> tool kit, we successfully expressed fluorescent proteins as well as the carotenoid pathway in at least five members of the clade, serving as proof of concept. This research lays the foundation for conducting more comprehensive investigations into the uncharacterized strains within the <i>Yarrowia</i> clade and exploring their potential applications in biotechnology.</p>","PeriodicalId":49819,"journal":{"name":"Microbiology-Sgm","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11261841/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141443604","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Benchmarking short-, long- and hybrid-read assemblers for metagenome sequencing of complex microbial communities.","authors":"Gleb Goussarov, Mohamed Mysara, Ilse Cleenwerck, Jürgen Claesen, Natalie Leys, Peter Vandamme, Rob Van Houdt","doi":"10.1099/mic.0.001469","DOIUrl":"10.1099/mic.0.001469","url":null,"abstract":"<p><p>Metagenome community analyses, driven by the continued development in sequencing technology, is rapidly providing insights in many aspects of microbiology and becoming a cornerstone tool. Illumina, Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio) are the leading technologies, each with their own advantages and drawbacks. Illumina provides accurate reads at a low cost, but their length is too short to close bacterial genomes. Long reads overcome this limitation, but these technologies produce reads with lower accuracy (ONT) or with lower throughput (PacBio high-fidelity reads). In a critical first analysis step, reads are assembled to reconstruct genomes or individual genes within the community. However, to date, the performance of existing assemblers has never been challenged with a complex mock metagenome. Here, we evaluate the performance of current assemblers that use short, long or both read types on a complex mock metagenome consisting of 227 bacterial strains with varying degrees of relatedness. We show that many of the current assemblers are not suited to handle such a complex metagenome. In addition, hybrid assemblies do not fulfil their potential. We conclude that ONT reads assembled with CANU and Illumina reads assembled with SPAdes offer the best value for reconstructing genomes and individual genes of complex metagenomes, respectively.</p>","PeriodicalId":49819,"journal":{"name":"Microbiology-Sgm","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11261854/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141447406","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effects of quorum sensing-interfering agents, including macrolides and furanone C-30, and an efflux pump inhibitor on nitrosative stress sensitivity in <i>Pseudomonas aeruginosa</i>.","authors":"Shin Suzuki, Yuji Morita, Shota Ishige, Kiyohiro Kai, Kenji Kawasaki, Kazuyuki Matsushita, Kohei Ogura, Tohru Miyoshi-Akiyama, Takeshi Shimizu","doi":"10.1099/mic.0.001464","DOIUrl":"10.1099/mic.0.001464","url":null,"abstract":"<p><p>Long-term administration of certain macrolides is efficacious in patients with persistent pulmonary <i>Pseudomonas aeruginosa</i> infection, despite how limited the clinically achievable concentrations are, being far below their MICs. An increase in the sub-MIC of macrolide exposure-dependent sensitivity to nitrosative stress is a typical characteristic of <i>P. aeruginosa</i>. However, a few <i>P. aeruginosa</i> clinical isolates do not respond to sub-MIC of macrolide treatment. Therefore, we examined the effects of sub-MIC of erythromycin (EM) on the sensitivity to nitrosative stress together with an efflux pump inhibitor (EPI) phenylalanine arginyl β-naphthylamide (PAβN). The sensitivity to nitrosative stress increased, suggesting that the efflux pump was involved in inhibiting the sub-MIC of macrolide effect. Analysis using efflux pump-mutant <i>P. aeruginosa</i> revealed that MexAB-OprM, MexXY-OprM, and MexCD-OprJ are factors in reducing the sub-MIC of macrolide effect. Since macrolides interfere with quorum sensing (QS), we demonstrated that the QS-interfering agent furanone C-30 (C-30) producing greater sensitivity to nitric oxide (NO) stress than EM. The effect of C-30 was decreased by overproduction of MexAB-OprM. To investigate whether the increase in the QS-interfering agent exposure-dependent sensitivity to nitrosative stress is characteristic of <i>P. aeruginosa</i> clinical isolates, we examined the viability of <i>P. aeruginosa</i> treated with NO. Although treatment with EM could reduce cell viability, a high variability in EM effects was observed. Conversely, C-30 was highly effective at reducing cell viability. Treatment with both C-30 and PAβN was sufficiently effective against the remaining isolates. Therefore, the combination of a QS-interfering agent and an EPI could be effective in treating <i>P. aeruginosa</i> infections.</p>","PeriodicalId":49819,"journal":{"name":"Microbiology-Sgm","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11263931/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141428090","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}