microLife最新文献

{"title":"CRISPR-Cas targeting in <i>Haloferax volcanii</i> promotes within-species gene exchange by triggering homologous recombination.","authors":"Deepak Kumar Choudhary, Israela Turgeman-Grott, Shachar Robinzon, Uri Gophna","doi":"10.1093/femsml/uqaf047","DOIUrl":"10.1093/femsml/uqaf047","url":null,"abstract":"<p><p>CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-Cas (CRISPR-associated genes) systems provide adaptive immunity in bacteria and archaea against mobile genetic elements, but the role they play in gene exchange and speciation remains unclear. Here, we investigated how CRISPR-Cas targeting affects mating and gene exchange in the halophilic archaeon <i>Haloferax volcanii</i>. Surprisingly, we found that CRISPR-Cas targeting significantly increased mating efficiency between members of the same species, in contrast to its previously documented role in reducing interspecies mating. This enhanced mating efficiency was dependent on the Cas3 nuclease/helicase and extended beyond the targeted genomic regions. Further analysis revealed that CRISPR-Cas targeting promoted biased recombination in favor of the targeting strain (the strain containing the CRISPR-Cas system) during mating, resulting in an increased proportion of recombinant progeny that are positive for CRISPR-Cas. To test whether an increase in recombination is sufficient to increase mating efficiency, we tested whether strains lacking the Mre11-Rad50 complex, which are known to have elevated recombination activity, also exhibited higher mating success. Indeed, these strains showed higher mating, as did cells that were exposed to DNA damage using methyl methanesulfonate. These findings suggest that CRISPR-Cas systems in archaea play roles beyond their canonical immune function. They may contribute to speciation by facilitating within-species gene exchange while limiting between-species genetic transfer, thereby maintaining species boundaries.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"7 ","pages":"uqaf047"},"PeriodicalIF":0.0,"publicationDate":"2026-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12814878/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146013249","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 opposite effects of stringent response on phage infection of <i>Pseudomonas putida</i>.","authors":"Alicja Cecylia Lewańczyk, Mariliis Hinnu, Elise Mägi, Roger Rikberg, Age Brauer, Hedvig Tamman","doi":"10.1093/femsml/uqaf048","DOIUrl":"10.1093/femsml/uqaf048","url":null,"abstract":"<p><p>Guanosine tetra- and pentaphosphate ((p)ppGpp) are one of the key players in the stress response of bacteria. Accumulation of these alarmones activates the stringent response, usually triggered by different nutritional stresses. For <i>Pseudomonas putida</i>, there is only limited data available on the importance of the stringent response in stress situations. Also, in recent years, different specific phage defence systems have received much attention, but little is known about the involvement of stringent response in phage infection. Here, we show that <i>P. putida</i> PaW85 (p)ppGpp⁰ is prototrophic and tolerates chemical stress well. However, in the stationary phase <i>P. putida</i> cells deprived of (p)ppGpp have impaired membrane integrity. In addition, we conducted a large-scale screening of stringent response effects on phage infections using the CEPEST phage collection. We tested 67 phages of 22 different species and revealed that the lack of (p)ppGpp has opposing effects on phage infection with nearly half of the tested phages showing higher infection efficiency on the (p)ppGpp⁰ cells, whereas the other half shows reduced infection. We show that the differences in phage infection efficiency for phages Aura and Amme-3 are not caused by adsorption rate differences, but alterations in downstream steps of the infection cycle-prolonged latent period in the absence of (p)ppGpp or unproductive infection in the presence of (p)ppGpp. Altogether, results indicate that the role of stringent response in phage infection is highly diverse, and over half of the times the presence of (p)ppGpp facilitates phage infections rather than protects the cells.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"7 ","pages":"uqaf048"},"PeriodicalIF":0.0,"publicationDate":"2026-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12814882/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146013648","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":"A subset of type 4 secretion system effectors of <i>Brucella</i> spp. associates to outer membrane vesicles.","authors":"Maren Ketterer, Naadir Ganief, Petra Chiquet, Adélie Lannoy, Audrey Verhaeghe, Joanne Braunweiler, Marc Dieu, Xavier De Bolle, Maxime Québatte, Christoph Dehio","doi":"10.1093/femsml/uqaf046","DOIUrl":"10.1093/femsml/uqaf046","url":null,"abstract":"<p><p>The establishment of a replicative niche in the hostile environment of the host presents an enormous challenge for pathogens. Intracellular pathogens such as <i>Brucella</i> spp., the Gram-negative causative agents of Brucellosis, must subvert diverse host functions to ensure survival and replication. One of the key adaptations to achieve this is the translocation of effector proteins into host cells via its type 4 secretion system (T4SS). But effector identification in <i>Brucella</i> is particularly challenging, as previously identified effectors lack a conserved translocation signal, exhibit variable requirements for translocation, and in some cases appear to be translocated in a T4SS-independent manner. Here, we demonstrate that a subset of previously described T4SS effector proteins associates with outer membrane vesicles (OMVs) in different <i>Brucella</i> species. Most of these effector proteins encode predicted signal peptides for periplasmic export or transmembrane domains. Among them, BspC and VceA carry functional signal peptides that direct their export into the periplasm in a Sec-dependent manner. From the periplasm, these proteins are subsequently secreted into the extracellular milieu, likely via the formation and release of OMVs. Our findings provide new insights into protein secretion by <i>Brucella</i>, suggesting that OMVs may represent an alternative secretion pathway to the T4SS.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"7 ","pages":"uqaf046"},"PeriodicalIF":0.0,"publicationDate":"2026-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12794620/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145967896","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":"Obligate heterotrophy of hyperthermophilic archaea <i>Pyrobaculum arsenaticum</i> and <i>P. aerophilum</i>.","authors":"Eugenio Pettinato, Thomas M Steiner, Christian Seitz, Harald Huber, Wolfgang Eisenreich, Ivan A Berg","doi":"10.1093/femsml/uqaf045","DOIUrl":"10.1093/femsml/uqaf045","url":null,"abstract":"<p><p><i>Pyrobaculum arsenaticum</i> and <i>P. aerophilum</i> are two hyperthermophiles that belong to the phylum Thermoproteota (also known as Crenarchaeota), order <i>Thermoproteales. Pyrobaculum arsenaticum</i> is an obligate anaerobe, whereas <i>P. aerophilum</i> is a facultatively aerobic organism. Both species have been described as capable of autotrophic growth with molecular hydrogen. Because their genomes lack genes encoding key enzymes for known autotrophic CO₂ fixation pathways, they have been discussed as organisms that may use unknown pathways. To establish reliable autotrophic cultures, we gradually reduced the supplied concentrations of yeast extract but, in our hands, autotrophy was not attainable for either of the two species. Analysis of the ¹³C-labelling of the biomass of the obtained mixotrophic cultures of <i>P. arsenaticum</i> grown on ¹³CO₂ + H₂ (20:80, v/v), using isotopologue profiling, revealed that their amino acids contained <30% of ¹³C. Amino acids were mainly labelled only in carboxyl groups, demonstrating their purely heterotrophic nature. Our data suggest that the ability to grow autotrophically in currently known <i>Thermoproteales</i> is strictly correlated with the presence of the genes for the dicarboxylate/4-hydroxybutyrate cycle. We discuss the reasons that may lead to misinterpretation of the data on the ability of prokaryotes to grow autotrophically.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"7 ","pages":"uqaf045"},"PeriodicalIF":0.0,"publicationDate":"2025-12-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12794621/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145967975","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 role of microbiology in balancing nature during the Anthropocene.","authors":"Fernando Baquero, Roberto Kolter, Kenneth Timmis","doi":"10.1093/femsml/uqaf044","DOIUrl":"10.1093/femsml/uqaf044","url":null,"abstract":"","PeriodicalId":74189,"journal":{"name":"microLife","volume":"7 ","pages":"uqaf044"},"PeriodicalIF":0.0,"publicationDate":"2025-12-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12781888/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145954213","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":"Glucose metabolism controls oxidative burst and lipid mediator production in neutrophils upon microbial challenge.","authors":"Alexandra Freitag, Kerstin Günther, Miriam Campillo Prados, Sophia M Hochrein, Werner Schmitz, Katrin Sinning, Gunther Zischinsky, Bert Klebl, Knut Ohlsen, Joachim Morschhäuser, Oliver Werz, Paul M Jordan, Martin Vaeth","doi":"10.1093/femsml/uqaf040","DOIUrl":"10.1093/femsml/uqaf040","url":null,"abstract":"<p><p>Neutrophils are frontline responders against bacterial and fungal pathogens, requiring rapid energy and biosynthetic precursors to mount effective antimicrobial responses. To meet these demands, they primarily rely on aerobic glycolysis, making glucose uptake essential. Murine and human neutrophils express the glucose transporters GLUT1 and GLUT3; however, their specific roles in neutrophil immunobiology have not yet been fully elucidated. Here, we show that neutrophilic immune responses to <i>Candida albicans</i> and <i>Staphylococcus aureus</i> critically depend on GLUT1/3-dependent glucose uptake and glycolysis. Combined deletion of GLUT1 and GLUT3 almost completely abolished glucose uptake and aerobic glycolysis in murine neutrophils, yet did not impair granulopoiesis, indicating that homeostatic neutrophil development is largely independent of extracellular glucose. By contrast, during microbial challenge, loss of GLUT1/3 severely compromised NADPH-dependent ROS production, oxidative burst, and cyclooxygenase-derived lipid mediator (LM) biosynthesis, demonstrating that glucose uptake via GLUT1/3 controls inflammatory effector functions of neutrophils. Moreover, genetic and pharmacologic inhibition of GLUT1/3-mediated glucose utilization reprograms neutrophil metabolism and LM biosynthesis toward an immunomodulatory phenotype. These findings identify a conserved nutrient-sensing metabolic checkpoint that governs neutrophil reprogramming and highlight novel opportunities for therapeutic immunomodulation.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"6 ","pages":"uqaf040"},"PeriodicalIF":0.0,"publicationDate":"2025-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12721385/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145822233","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":"Exploring <i>Bacteroidota</i> strains from human stool and animal feces: phenotyping and functional diversity.","authors":"Lisa Ladewig, Birhanu M Kinfu, Hanna Fokt, Hendrik Bethge, Muhammad Aammar Tufail, John F Baines, Ruth A Schmitz","doi":"10.1093/femsml/uqaf039","DOIUrl":"10.1093/femsml/uqaf039","url":null,"abstract":"<p><p><i>Bacteroidota</i>, a diverse phylum of bacteria, includes classes whose members are increasingly recognized for their significant contributions to host health, particularly through their antimicrobial properties. This study investigates the functional diversity of 42 new <i>Bacteroidia</i> and <i>Sphingobacteriia</i> strains enriched and identified from diverse hosts, including mouse ceca and human stool samples. Using 16S rRNA gene sequencing, we phylogenetically characterized the strains of the genera <i>Bacteroides, Phocaeicola</i>, and <i>Sphingobacterium</i> and assessed their functional properties related to potential beneficial functions. The strains were evaluated concerning their ability to inhibit biofilm formation of the World Health Organization-declared clinically significant pathogens, including Gram-positive <i>Staphylococcus aureus</i> and <i>Staphylococcus epidermidis</i>, Gram-negative <i>Klebsiella oxytoca</i> and <i>Pseudomonas aeruginosa</i>, and the eukaryotic yeast <i>Candida albicans</i>. Additionally, we investigated bile salt hydrolase and quorum-quenching (QQ) activities of the strains, as these functions contribute to microbial community interactions and host-microbe dynamics. Our findings demonstrate that all examined <i>Bacteroidota</i> strains consistently exhibit a capacity to inhibit biofilm formation but to different extents. Furthermore, 14 strains showed QQ activity, and 39 bile salt hydrolase activity, indicating functional diversity among the isolates. High biofilm inhibition as well as QQ activity against both autoinducers, AHL and AI-2, were predominantly observed in <i>Bacteroides caecimuris</i> and <i>Bacteroides muris</i>. These traits suggest that such strains may play important roles in shaping microbial communities and interfering with pathogens and their communication. Overall, this study provides valuable insights into strain-specific functions that could support future microbiome-based strategies for pathogen control and host health modulation.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"7 ","pages":"uqaf039"},"PeriodicalIF":0.0,"publicationDate":"2025-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12767198/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145914048","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 <i>Brucella</i> type IV secretion system and effector proteins.","authors":"Chloé Dugelay, Jean Celli, Laurent Terradot","doi":"10.1093/femsml/uqaf036","DOIUrl":"10.1093/femsml/uqaf036","url":null,"abstract":"<p><p><i>Brucella</i> spp. are Gram-negative, facultative intracellular bacteria responsible for brucellosis, a globally prevalent zoonosis affecting both humans and animals. The genus includes several pathogenic species which primarily infect mammals but can cause chronic infections in humans through accidental transmission. As for most intracellular pathogens, <i>Brucella</i> pathogenicity relies on its capacity to invade host cells, evade immune defenses, and establish a replicative niche within a specialized organelle, the <i>Brucella</i>-containing vacuole (BCV). Central to this process is the VirB Type IV secretion system (T4SS), a highly conserved molecular apparatus used to translocate effector proteins (EPs) into host cells. These EPs manipulate diverse cellular pathways to promote bacterial survival, replication, and dissemination. This review provides an updated overview of the structure and function of the T4SS, based on a comparison with recent structural information gained on conjugative systems. The current repertoire of known effectors and their roles in host-pathogen interactions are also detailed, highlighting progress made in their identification. Finally, we discuss possible functions of T4SS and speculate on the mechanisms of effector translocation based on insights from other intracellular pathogens or secretion systems.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"6 ","pages":"uqaf036"},"PeriodicalIF":0.0,"publicationDate":"2025-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12676571/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145703077","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":"Guided tour through the small protein landscape of <i>Methanosarcina mazei</i> using proteomics and biochemical approaches.","authors":"Eva Herdering, Liam Cassidy, Philipp T Kaulich, Jürgen Bartel, Sandra Maaß, Katrin Weidenbach, Andreas Tholey, Ruth A Schmitz","doi":"10.1093/femsml/uqaf038","DOIUrl":"10.1093/femsml/uqaf038","url":null,"abstract":"<p><p>Small open reading frame (small ORF) encoded proteins fulfil important roles in many cellular processes. In the methanoarchaeon <i>Methanosarcina mazei</i>, numerous small proteins have previously been identified under different nitrogen-availabilities, with only few being subject to functional characterization. Consequently, a detailed expression analysis of small proteins translated under other stress conditions, in conjunction with conservation and sequence-based analyses, may reveal interesting candidates for future downstream analyses. Here, we investigated the small proteome of <i>M. mazei</i> under five growth conditions. By enriching the low molecular weight proteome and combining top-down and bottom-up proteomic analysis, a total of 234 small proteins were validated on protein level, of which 130 were found in top-down proteomics analysis, which were associated with 408 proteoforms. Aiming to unravel functions of the large number of small proteins, we performed sequence-based clustering with emphasis on the presence of characteristic motifs. Thereby, ferredoxin-like small proteins with putative iron-sulphur (Fe-S) cluster binding-sites, as well as possible zinc-binding proteins, both with distinct cysteine motifs, were identified. We further analysed heterologously expressed representatives of the ferredoxin-like and putative zinc-binding small proteins, confirming the zinc-binding capability of two small proteins of the latter group via inductively coupled plasma-mass spectrometry. Overall, the detailed analysis of the <i>M. mazei</i> small proteome under different growth conditions, using various proteomics approaches, as well as sequence-based analyses and biochemical approaches targeting specific protein candidates, represents a key step in systematically uncovering the functions of small proteins in <i>M. mazei</i>.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"6 ","pages":"uqaf038"},"PeriodicalIF":0.0,"publicationDate":"2025-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12704099/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145770175","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":"Impact of changed c-di-AMP levels and hypoosmotic stress on the transcriptome of <i>Haloferax volcanii</i> and on RCK domain-containing proteins.","authors":"Hongcheng Ren, Frank Braun, Felix Grünberger, Chris van der Does, Dina Grohmann, Sonja-Verena Albers","doi":"10.1093/femsml/uqaf037","DOIUrl":"10.1093/femsml/uqaf037","url":null,"abstract":"<p><p>We investigated the role of cyclic di-adenosine monophosphate (c-di-AMP) in the halophilic archaeon <i>Haloferax volcanii</i> by analysing transcriptomic changes in a strain with lowered c-di-AMP levels and by characterizing the function of key RCK (regulator-of-conductance-of-K⁺) domain proteins. The c-di-AMP-reduced mutant showed elevated expression of cell division genes and metabolic enzymes, whereas a Na⁺/H⁺ antiporter and an aspartate aminotransferase were strongly repressed. These patterns reveal previously unknown links between this messenger and both cell division and osmolyte homeostasis. To probe downstream effectors, we created deletion mutants of four RCK domain proteins and observed distinct phenotypes under potassium or sodium limitation. Deleting the primary RCK protein, linked to a high-affinity potassium importer, abolished growth under potassium limitation and caused extreme cell enlargement under hypoosmotic conditions, underscoring its essential role in potassium uptake and cell volume control. Removing a secondary transporter-associated RCK protein caused only mild defects, mainly under low sodium, indicating an auxiliary potassium acquisition system. Two stand-alone RCK proteins (unlinked to transporters) were dispensable for normal growth yet critical during osmotic stress: one knockout alleviated excessive swelling of c-di-AMP-reduced cells, whereas the other caused hypersensitivity to low-salt conditions. Biochemical assays revealed that only transporter-associated RCK proteins bound c-di-AMP, suggesting direct control of potassium transport, while stand-alone RCK proteins mediate osmotic adaptation through c-di-AMP-independent mechanisms. These findings define a novel osmotic stress regulatory network in <i>H. volcanii</i> integrating second-messenger signalling with ion homeostasis, highlighting the broader importance of cyclic nucleotide signalling in archaeal stress adaptation.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"6 ","pages":"uqaf037"},"PeriodicalIF":0.0,"publicationDate":"2025-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12699388/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145758317","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}