Microbiology-Sgm最新文献

{"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":"170 7","pages":""},"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":"170 6","pages":""},"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":"170 6","pages":""},"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":"170 6","pages":""},"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":"170 6","pages":""},"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":"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":"170 6","pages":""},"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}

{"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":"170 6","pages":""},"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":"Stratifying macrophages based on their infectious burden identifies novel host targets for intervention during Crohn's disease associated adherent-invasive <i>Escherichia coli</i> infection.","authors":"Xiang Li, John Cole, Diane Vaughan, Yinbo Xiao, Daniel Walker, Daniel M Wall","doi":"10.1099/mic.0.001470","DOIUrl":"10.1099/mic.0.001470","url":null,"abstract":"<p><p>Bacterial infection is a dynamic process resulting in a heterogenous population of infected and uninfected cells. These cells respond differently based on their bacterial load and duration of infection. In the case of infection of macrophages with Crohn's disease (CD) associated adherent-invasive <i>Escherichia coli</i> (AIEC), understanding the drivers of pathogen success may allow targeting of cells where AIEC replicate to high levels. Here we show that stratifying immune cells based on their bacterial load identifies novel pathways and therapeutic targets not previously associated with AIEC when using a traditional homogeneous infected population approach. Using flow cytometry-based cell sorting we stratified cells into those with low or high intracellular pathogen loads, or those which were bystanders to infection. Immune cells transcriptomics revealed a diverse response to the varying levels of infection while pathway analysis identified novel intervention targets that were directly related to increasing intracellular AIEC numbers. Chemical inhibition of identified targets reduced AIEC intracellular replication or inhibited secretion of tumour necrosis factor alpha (TNFα), a key cytokine associated with AIEC infection. Our results have identified new avenues of intervention in AIEC infection that may also be applicable to CD through the repurposing of already available inhibitors. Additionally, they highlight the applicability of immune cell stratification post-infection as an effective approach for the study of microbial pathogens.</p>","PeriodicalId":49819,"journal":{"name":"Microbiology-Sgm","volume":"170 6","pages":""},"PeriodicalIF":2.6,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11261827/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141447407","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":"Characterization of MLST-99 <i>Salmonella</i> Typhimurium and the monophasic variant I:4,[5],12:i:- isolated from Canadian Atlantic coast shellfish.","authors":"Lisa M Hodges, Ashley Cooper, Adam Koziol, Catherine D Carrillo","doi":"10.1099/mic.0.001456","DOIUrl":"10.1099/mic.0.001456","url":null,"abstract":"<p><p><i>Salmonella enterica</i> subsp. <i>enterica</i> Typhimurium and its monophasic variant I 1;4,[5],12:i:- (MVST) are responsible for thousands of reported cases of salmonellosis each year in Canada, and countries worldwide. We investigated <i>S</i>. Typhimurium and MVST isolates recovered from raw shellfish harvested in Atlantic Canada by the Canadian Food Inspection Agency (CFIA) over the past decade, to assess the potential impact of these isolates on human illness and to explore possible routes of shellfish contamination. Whole-genome sequence analysis was performed on 210 isolates of <i>S</i>. Typhimurium and MVST recovered from various food sources, including shellfish. The objective was to identify genetic markers linked to ST-99, a sequence type specifically associated with shellfish, which could explain their high prevalence in shellfish. We also investigated the genetic similarity amongst CFIA ST-99 isolates recovered in different years and geographical locations. Finally, the study aimed to enhance the molecular serotyping of ST-99 isolates, as they are serologically classified as MVST but are frequently misidentified as <i>S</i>. Typhimurium through sequence analysis. To ensure recovery of ST-99 from shellfish was not due to favourable growth kinetics, we measured the growth rates of these isolates relative to other <i>Salmonella</i> and determined that ST-99 did not have a faster growth rate and/or shorter lag phase than other <i>Salmonella</i> evaluated. The CFIA ST-99 isolates from shellfish were highly clonal, with up to 81 high-quality single nucleotide variants amongst isolates. ST-99 isolates both within the CFIA collection and those isolated globally carried numerous unique deletions, insertions and mutations in genes, including some considered important for virulence, such as gene deletions in the type VI secretion system. Interestingly, several of these genetic characteristics appear to be unique to North America. Most notably was a large genomic region showing a high prevalence in genomes from Canadian isolates compared to those from the USA. Although the functions of the majority of the proteins encoded within this region remain unknown, the genes <i>umuC</i> and <i>umuD</i>, known to be protective against UV light damage, were present. While this study did not specifically examine the effects of mutations and insertions, results indicate that these isolates may be adapted to survive in specific environments, such as ocean water, where wild birds and/or animals serve as the natural hosts. Our hypothesis is reinforced by a global phylogenetic analysis, which indicates that isolates obtained from North American shellfish and wild birds are infrequently connected to isolates from human sources. These findings suggest a distinct ecological niche for ST-99, potentially indicating their specialization and adaptation to non-human hosts and environments, such as oceanic habitats.</p>","PeriodicalId":49819,"journal":{"name":"Microbiology-Sgm","volume":"170 4","pages":""},"PeriodicalIF":2.6,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11256474/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140946285","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":"A vector system for single and tandem expression of cloned genes and multi-colour fluorescent tagging in <i>Haloferax volcanii</i>.","authors":"Solenne Ithurbide, Roshali T de Silva, Hannah J Brown, Vinaya Shinde, Iain G Duggin","doi":"10.1099/mic.0.001461","DOIUrl":"10.1099/mic.0.001461","url":null,"abstract":"<p><p>Archaeal cell biology is an emerging field expected to identify fundamental cellular processes, help resolve the deep evolutionary history of cellular life, and contribute new components and functions in biotechnology and synthetic biology. To facilitate these, we have developed plasmid vectors that allow convenient cloning and production of proteins and fusion proteins with flexible, rigid, or semi-rigid linkers in the model archaeon <i>Haloferax volcanii</i>. For protein subcellular localization studies using fluorescent protein (FP) tags, we created vectors incorporating a range of codon-optimized fluorescent proteins for N- or C-terminal tagging, including GFP, mNeonGreen, mCherry, YPet, mTurquoise2 and mScarlet-I. Obtaining functional fusion proteins can be challenging with proteins involved in multiple interactions, mainly due to steric interference. We demonstrated the use of the new vector system to screen for improved function in cytoskeletal protein FP fusions, and identified FtsZ1-FPs that are functional in cell division and CetZ1-FPs that are functional in motility and rod cell development. Both the type of linker and the type of FP influenced the functionality of the resulting fusions. The vector design also facilitates convenient cloning and tandem expression of two genes or fusion genes, controlled by a modified tryptophan-inducible promoter, and we demonstrated its use for dual-colour imaging of tagged proteins in <i>H. volcanii</i> cells. These tools should promote further development and applications of archaeal molecular and cellular biology and biotechnology.</p>","PeriodicalId":49819,"journal":{"name":"Microbiology-Sgm","volume":"170 5","pages":""},"PeriodicalIF":2.6,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11165654/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141087743","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}