mLife最新文献

{"title":"Multi-target fluorescence staining of bacteria smears enables rapid machine learning-assisted species classification.","authors":"Maxence Galvan, Michael Fujarski, Can Beslendi, Frieder Schaumburg, Julian Varghese, Johannes Liesche","doi":"10.1002/mlf2.70076","DOIUrl":"10.1002/mlf2.70076","url":null,"abstract":"<p><p>Rapid identification of bacterial species from patient samples is crucial for clinical decision-making. In severe infections, such as bloodstream infections, the early start of an effective treatment is directly associated with reduced mortality rates. Current rapid species identification methods, such as matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) or multiplex PCR, require specialized hardware and extensive technical support that prevents application in resource-limited settings. Here, we present a staining and imaging procedure for bacterial smears using fluorescent dyes directed against intracellular structures and cell wall components. Data on relevant features were extracted from segmented images and used to train a machine learning (ML) model for species classification. The method was tested on clinical isolates from 126 patients. For the seven most common bacteria, the classification performance, indicated by area under the receiver operating characteristic (ROC) curve, ranged from 0.8 (<i>Klebsiella pneumoniae</i>) to 1 (<i>Pseudomonas aeruginosa</i>). Species that were not part of the training dataset, were reliably classified as unknown species. These results hold promise for the identification of further species, particularly <i>Enterobacterales</i>, and clinical application.</p>","PeriodicalId":94145,"journal":{"name":"mLife","volume":"5 2","pages":"229-238"},"PeriodicalIF":6.7,"publicationDate":"2026-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13131325/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147824937","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 signaling governs sunscreen biosynthesis to safeguard desert cyanobacteria against desiccation.","authors":"Lei Zhao, Hai-Feng Xu, Jin-Long Shang, Yong Li, Xiao-Yue Yin, Zhong-Chun Zhang, Huazhong Shi, Bao-Sheng Qiu","doi":"10.1002/mlf2.70075","DOIUrl":"10.1002/mlf2.70075","url":null,"abstract":"<p><p>Mycosporine-like amino acids (MAAs) are natural sunscreens synthesized by a wide range of organisms. Although the induction of MAA production by ultraviolet radiation is well established, the signaling pathways involved and specific functions of MAAs under other stress conditions remain poorly understood. We demonstrated that MAAs serve as effective osmoprotectants for desiccation tolerance in the desert cyanobacterium <i>Nostoc flagelliforme</i>. Genetic disruption of genes encoding MAA biosynthetic enzymes eliminated MAA production, resulting in elevated oxidative damage, increased lipid peroxidation, and impaired photosynthesis under dehydration. Biochemical assays revealed that MAAs stabilize proteins and scavenge reactive oxygen species, indicating dual roles as osmolytes and antioxidants. Furthermore, we identified a signaling pathway Dsp1-OrrA that mediates the osmotic induction of MAA biosynthesis. Genetic disruption of either gene of Dsp1 and OrrA abolished osmotic induction and severely reduced desiccation tolerance. Phylogenomic analysis suggests that MAA biosynthesis is an ancient trait conserved in desiccation-tolerant cyanobacteria. This work deepens our understanding of microbial adaptation to extreme environments and provides a foundation for synthetic biology applications of MAAs.</p>","PeriodicalId":94145,"journal":{"name":"mLife","volume":"5 2","pages":"164-179"},"PeriodicalIF":6.7,"publicationDate":"2026-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13131328/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147824949","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":"Recent advances in noncanonical inhibition mechanisms of anti-CRISPR proteins.","authors":"Lingguang Yang, Rongjun Luo, Wei Zhou, Peipei Yin, Yue Feng, Yi Zhang","doi":"10.1002/mlf2.70077","DOIUrl":"10.1002/mlf2.70077","url":null,"abstract":"<p><p>The CRISPR-Cas system constitutes an adaptive immune mechanism in prokaryotes that defends against mobile genetic elements. Within the perpetual co-evolutionary arms race between bacteria and their viral predators, bacteriophages encode anti-CRISPR (Acr) proteins that use sophisticated molecular strategies to sabotage CRISPR-Cas function. While canonical Acr proteins rely on steric blockade of Cas effectors, recent discoveries reveal unprecedented noncanonical mechanisms spanning CRISPR immunity stages. This review synthesizes recent mechanistic advances in this field since 2023, highlighting the expansion of noncanonical inhibition mechanisms beyond type I to include types II, V, and VI, as well as novel Acr interventions targeting multiple functional stages, such as spacer acquisition, translation-coupled inhibition, complex assembly/disassembly, and R-loop DNA binding. Structural insights demonstrate how Acr proteins achieve substoichiometric inhibition via conformational hijacking, catalytic repurposing, and molecular mimicry. Forged by the intense selective pressure of the phage-host conflict, these molecular innovations represent both remarkable evolutionary adaptations and versatile precision tools. They enable spatiotemporal control of CRISPR technologies, from engineered off-switches to diagnostic reset mechanisms, while posing critical challenges for therapeutic safety and microbiome management.</p>","PeriodicalId":94145,"journal":{"name":"mLife","volume":"5 2","pages":"133-147"},"PeriodicalIF":6.7,"publicationDate":"2026-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13131331/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147825107","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 oxygen-sensing FixLJ represses nitrogen fixation in <i>Rhodopseudomonas palustris</i> in response to oxygen.","authors":"Lingwei Cui, Yan Zeng, Mengmei Wang, Lu Huang, Zheyi Wang, Ying Liu, Yanning Zheng","doi":"10.1002/mlf2.70067","DOIUrl":"10.1002/mlf2.70067","url":null,"abstract":"<p><p>Biological nitrogen fixation in symbiotic diazotrophs is subject to oxygen regulation by an oxygen-sensing FixLJ two-component system under micro-oxic conditions. However, it remains unclear whether this mechanism is conserved in free-living diazotrophs. In this study, we discovered for the first time that FixLJ strongly inhibits the expression of <i>nifHDK</i> genes that encode molybdenum nitrogenase in response to oxygen. The deletion of <i>fixLJ</i> genes, whose expression was stimulated by oxygen, allowed a free-living photosynthetic diazotroph <i>Rhodopseudomonas palustris</i> to express active nitrogenase and grow diazotrophically even under oxic conditions. The unphosphorylated FixJ protein showed high-affinity binding to the promoter of nitrogenase gene cluster (P _<i>nifH</i> ) and strongly repressed the nitrogenase expression in response to oxygen. The transcriptional repression of <i>nifHDK</i> by FixJ reveals a new regulatory role for the FixLJ system. In addition, transcriptome analysis suggested that the FixLJ regulatory system also plays a role in the energy metabolism of <i>R. palustris</i>, probably through FixK regulation. This newly identified mechanism is speculated to allow <i>R. palustris</i> to rapidly shut down the synthesis of nitrogenase when exposed to oxygen, avoiding the build-up of nitrogenase with impaired activity due to the lack of protection from oxygen damage.</p>","PeriodicalId":94145,"journal":{"name":"mLife","volume":"5 3","pages":"312-324"},"PeriodicalIF":6.7,"publicationDate":"2026-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13327599/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148378799","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":"An infection and pathogenesis mouse model of SARS-CoV-2-related pangolin coronavirus GX_P2V(short_3UTR).","authors":"Lai Wei, Shuiqing Liu, Shanshan Lu, Shengdong Luo, Xiaoping An, Huahao Fan, Erguang Li, Lihua Song","doi":"10.1002/mlf2.12122","DOIUrl":"10.1002/mlf2.12122","url":null,"abstract":"<p><p>SARS-CoV-2-related pangolin coronavirus GX_P2V(short_3UTR) is highly attenuated, but can cause mortality in a specifically designed human <i>ACE2</i>-transgenic mouse model, making it a surrogate model for evaluating the efficacy of vaccines and drugs against SARS-CoV-2.</p>","PeriodicalId":94145,"journal":{"name":"mLife","volume":"5 2","pages":"259-262"},"PeriodicalIF":6.7,"publicationDate":"2026-03-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13131323/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147825220","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":"fCUT&Tag-Seq: An optimized CUT&Tag-based method for high-resolution profiling of histone modifications and chromatin-binding proteins in fungi.","authors":"Haiting Wang, Yongjunlin Tan, Jiayue Ma, Jie Yang, Mengran Liu, Peng Jiang, Shan Lu, Haoxue Xia, Guangfei Tang, Wende Liu, Hui-Shan Guo, Chun-Min Shan","doi":"10.1002/mlf2.70060","DOIUrl":"10.1002/mlf2.70060","url":null,"abstract":"<p><p>Histone modifications and chromatin-binding proteins play crucial roles in regulating gene expression in eukaryotes, with significant implications for fungal pathogenicity and development. However, profiling these modifications or proteins across the genome in fungi remains challenging due to the technical limitations of the traditional, widely used Chromatin Immunoprecipitation-Sequencing (ChIP-Seq) method. Here, we present an optimized fungal Cleavage Under Targets and Tagmentation-Sequencing (fCUT&Tag-Seq) protocol specifically designed for filamentous fungi and dimorphic fungi. Our approach involves the preparation of protoplasts and nuclear extraction to enhance antibody accessibility, along with formaldehyde crosslinking to improve protein-DNA binding efficiency. We then successfully applied fCUT&Tag-Seq to accurately profile multiple histone modifications like H3K9me3, H3K27me3, H3K4me3, and H3K18ac, across different plant pathogenic or model fungal species, including <i>Verticillium dahliae</i>, <i>Neurospora crassa, Fusarium graminearum</i>, and <i>Sporisorium scitamineum</i>, showing good signal-to-noise ratios, reproducibility, and detection sensitivity. Furthermore, we extended this method to profile chromatin-binding proteins, such as the histone acetyltransferase Gcn5. This study establishes fCUT&Tag-Seq as a robust and useful tool for fungal epigenetic research, enabling detailed exploration of chromatin dynamics and advancing our understanding of fungal gene regulation, development, and pathogenicity.</p>","PeriodicalId":94145,"journal":{"name":"mLife","volume":"5 2","pages":"239-253"},"PeriodicalIF":6.7,"publicationDate":"2026-03-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13131329/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147824909","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":"Genome-wide screen reveals a universal role of ATP in ciprofloxacin tolerance among genetically distinct <i>Escherichia coli</i> persisters.","authors":"Zhenfang Mei, Yawen Cai, Jianfeng Huang, Kedong Zhao, Zuqin Zhang, Dandan Yu, Shiyan Lu, Zeying Lai, Thomas K Wood, Xinmiao Fu","doi":"10.1002/mlf2.70072","DOIUrl":"10.1002/mlf2.70072","url":null,"abstract":"<p><p>Bacterial persisters show tolerance to bactericidal antibiotics and play essential roles in chronic infections; however, the general mechanisms underlying persister formation and antibiotic tolerance remain insufficiently characterized. In this study, the <i>Escherichia coli</i> Keio library was used to identify genes involved in ciprofloxacin tolerance by culturing each mutant to the late stationary phase (to induce persistence via starvation), followed by dilution into fresh medium for antibiotic exposure. This two-step, genome-wide screening approach enabled the identification of 37 ciprofloxacin-sensitive mutants with diverse biological functions and 11 ciprofloxacin-tolerant mutants related to amino acid and β-nicotinamide adenine dinucleotide (NAD⁺) biosynthesis, with 25 genes being identified as persister-related genes for the first time. Notably, sensitive mutants (Δ<i>atpC</i>, Δ<i>atpF</i>, Δ<i>ruvC</i>, and Δ<i>rnr</i>) were specifically sensitive to quinolone antibiotics, whereas tolerant mutants (Δ<i>metR</i>, Δ<i>leuB</i>, and Δ<i>nadB</i>) showed tolerance to ampicillin and gentamicin. Importantly, adenosine triphosphate (ATP) levels were downregulated in ciprofloxacin-tolerant mutants and upregulated in ciprofloxacin-sensitive mutants, implying a negative correlation between ATP levels and ciprofloxacin tolerance among these genetically distinct persisters. This negative correlation was further observed when ATP levels in different mutants were chemically modulated using specific metabolites, nutrients, and respiration inhibitors. In addition, ciprofloxacin persistence across different mutants was found to correlate closely with antibiotic uptake and reactive oxygen species (ROS) levels. Collectively, these findings establish a universal role for ATP in the ciprofloxacin tolerance of genetically diverse persisters under varying resuscitation conditions, conceivably through the modulation of antibiotic uptake and ROS accumulation, and it is implied that the provision of abundant nutrients is potentially beneficial for anti-persister chemotherapy in clinic settings.</p>","PeriodicalId":94145,"journal":{"name":"mLife","volume":"5 2","pages":"180-198"},"PeriodicalIF":6.7,"publicationDate":"2026-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13131330/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147824962","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":"Creation of bioactive non-natural flavonoids via combinatorial prenylation-glycosylation cascades.","authors":"Hongjiao Zhang, Anxin Zhang, Jiatong Ji, Wen-Bing Yin","doi":"10.1002/mlf2.70063","DOIUrl":"10.1002/mlf2.70063","url":null,"abstract":"<p><p>Flavonoids have significant medicinal potential; however, the reliance on plant extraction for their production poses a substantial barrier to their practical application. Innovative approaches like enzymatic cascade catalysis and microbial synthesis present promising avenues for the efficient production of these structurally complex compounds. In this study, two non-natural flavonoids (compounds <b>7</b> and <b>8</b>) were synthesized, with compound <b>7</b> displaying antifungal properties. This was achieved through the cascade enzymatic catalysis of naringenin, a key intermediate in flavonoid biosynthesis, using glycosyl- and prenyltransferases. Additionally, metabolic engineering was used to bolster the supply of the dimethylallyl pyrophosphate precursor via the isopentenol utilization pathway in <i>Escherichia coli</i>, facilitating the <i>de novo</i> creation of non-natural flavonoids. Consequently, the titers of compounds <b>7</b> and <b>8</b> reached 47.4 and 6.6 mg/l, respectively. This research highlights the potential of modular enzyme assembly in generating bioactive flavonoid derivatives and establishes a sustainable platform for the discovery of non-natural flavonoids.</p>","PeriodicalId":94145,"journal":{"name":"mLife","volume":"5 2","pages":"254-258"},"PeriodicalIF":6.7,"publicationDate":"2026-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13131324/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147825241","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":"Distinct actomyosin-septin coordination governs conidiation and septation in <i>Verticillium dahliae</i>.","authors":"Juan Tian, Mengli Pu, Bin Chen, Xiaxia Zhang, Yanjun Yu, Chunli Li, Haiyun Wang, Zhaosheng Kong","doi":"10.1002/mlf2.70062","DOIUrl":"10.1002/mlf2.70062","url":null,"abstract":"<p><p>Conidiation is the primary mode of reproduction in filamentous fungi and is essential for the dispersal of pathogenic species. However, the fundamental cellular mechanisms regulating conidiation in plant pathogenic fungi remain largely unexplored. Here, using <i>Verticillium dahliae</i> as a model, we investigated the dynamic assembly and function of the contractile actomyosin ring (CAR) and septins during conidiation through live-cell imaging. We show that septins, visualized via VdCdc11-GFP, first accumulate at the tip of budding hyphae during the transition from hyphal elongation to apical budding, and undergo an hourglass-to-double-ring transition at the bud neck. Following mitosis, myosin II and actin assemble simultaneously into a contractile ring to drive cytokinesis. Disruption of core septin function results in defective nuclear segregation and aberrant nuclear migration during mitosis, as well as delayed recruitment of myosin II to the bud neck, indicating that septins scaffold cytokinetic machinery and coordinate nuclear division during conidiation. In contrast, during hyphal septation, myosin II, actin, and septins appear simultaneously as a diffuse cortical band, with septin organization dependent on actin. Collectively, these findings reveal distinct spatial and temporal coordination between actomyosin and septins in two cytokinetic contexts-conidiation and hyphal septation-and define apical budding as a specialized cytokinesis mode in <i>V. dahliae</i>. Our study broadens the understanding of fungal cytokinesis beyond yeast models to multicellular filamentous fungi.</p>","PeriodicalId":94145,"journal":{"name":"mLife","volume":"5 1","pages":"35-50"},"PeriodicalIF":6.7,"publicationDate":"2026-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12948487/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147328750","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 microorganism-host interactions: Emerging organoid models and analytical approaches.","authors":"Yue Shi, Min Xu, Yanhong Huang, Jing Qu, Shumin Liao, Yingzi Liu, Liang Li","doi":"10.1002/mlf2.70053","DOIUrl":"10.1002/mlf2.70053","url":null,"abstract":"<p><p>Microorganisms play a vital role in human health through their interactions with the body. Studies of host-microbe mechanisms and interactions are crucial for advancing health management. Recently, the organoid-based models have provided new platforms in this field. Derived from human tissues, these models offer several advantages over traditional systems and, when combined with advanced analytical techniques, they enable deeper insights into host-microbe interactions. In this review, we summarize the different models and techniques used, with a particular focus on the newly developed organoid models. We discuss how these models can be effectively utilized in microorganism-host interaction studies and address their associated limitations.</p>","PeriodicalId":94145,"journal":{"name":"mLife","volume":"5 1","pages":"17-34"},"PeriodicalIF":6.7,"publicationDate":"2026-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12948489/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147328766","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}