microLife最新文献

{"title":"Proteome characterization of single gene deletion mutants lacking zinc finger µ-proteins in <i>Haloferax volcanii</i>.","authors":"Pedro H C Franco, Deniz Üresin, Andreas Borst, Leona A Rusling, Jörg Soppa, Julian D Langer","doi":"10.1093/femsml/uqag005","DOIUrl":"10.1093/femsml/uqag005","url":null,"abstract":"<p><p>Microproteins (≤70 amino acids) have important and often essential roles in all kingdoms of life, influencing cell motility, regulation of membrane transport and as transcription factors. In the halophilic archaeon and model system <i>Haloferax volcanii</i> a significant number of µ-proteins were predicted to be zinc finger proteins. Here we used mass spectrometry-based proteomics to systematically investigate the impact of single gene deletions of 19 zinc finger µ-proteins on the proteome of <i>H. volcanii</i> grown in synthetic medium with glucose as sole carbon and energy source. We employed a state-of-the-art dia-PASEF acquisition strategy, detecting over 3400 proteins across the 19 deletion strains and the wild type. The comprehensive proteome coverage enabled a systematic analysis of proteome remodeling. We found that in 11 out of the 19 mutants the proteome remodeling involved proteins annotated to play a role in cell motility, matching swarming and growth rate phenotypes we observed for these strains. Taken together, our data provide the most comprehensive proteome coverage of <i>H. volcanii</i> to date, and the effect of 19 different zinc-finger µ-proteins deletion strains on the proteome of this organism. The combined data (available via ProteomeXchange with identifier PXD066008) provide a valuable resource for future research in the field.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"7 ","pages":"uqag005"},"PeriodicalIF":0.0,"publicationDate":"2026-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12949519/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147328383","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":"Critical parameters of fungal pathogenicity at the epithelial interphase.","authors":"Anna Möslinger, Stefanie Allert, Slavena Vylkova, Bernhard Hube","doi":"10.1093/femsml/uqag001","DOIUrl":"10.1093/femsml/uqag001","url":null,"abstract":"<p><p>Modern medical advances have contributed to a growing population of immunocompromised individuals, increasing susceptibility to human fungal pathogens. The leading species for invasive fungal diseases are <i>Candida albicans</i> and <i>Aspergillus fumigatus</i>. While <i>C. albicans</i> is a common colonizer of mucosal sites that can cause endogenous infections, <i>A. fumigatus</i> is an environmental fungus that typically infects individuals through the inhalation of spores. As a first point of contact, the epithelial cell layers serve both as a physical barrier and a sentinel to alert the immune system. Numerous fungal and host-derived mediators have been described that facilitate fungal adherence, invasion into epithelial cells, and subsequent host tissue damage. In cases of systemic infection, this can lead to fungal dissemination. This review focusses on the early interactions-specifically adhesion and invasion-between epithelial cells and the fungal pathogens <i>C. albicans</i> and <i>A. fumigatus</i>.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"7 ","pages":"uqag001"},"PeriodicalIF":0.0,"publicationDate":"2026-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12919981/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147273313","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":"Caspofungin enhances antifungal immunity in human blood through transcriptional reprogramming.","authors":"Aia Shehata, Sascha Schäuble, Ronny Martin, Alexander Maximilian Aldejohann, Gianni Panagiotou, Oliver Kurzai, Kerstin Hünniger-Ast","doi":"10.1093/femsml/uqag004","DOIUrl":"10.1093/femsml/uqag004","url":null,"abstract":"<p><p><i>Candida albicans</i> is a leading cause of invasive candidiasis, a life-threatening infection with high mortality despite antifungal therapy. Echinocandins are first-line agents due to their fungicidal activity and low toxicity profile. Beyond direct killing, they may also modulate host immunity, e.g. through fungal cell wall remodeling. However, the systemic impact of echinocandins on human immune cells remains incompletely understood, particularly in the context of drug resistance. Using an <i>ex vivo</i> human whole-blood infection model, we assessed the effects of caspofungin during infection with echinocandin-susceptible (ECH^S/FKS^wt) and echinocandin-resistant (ECH^R/FKS^mut) <i>C. albicans</i> strains. Infection alone triggered a strong and conserved transcriptional immune program enriched for innate recognition and inflammatory pathways. Caspofungin treatment during infection with the susceptible strain selectively amplified these responses, engaging a sequential cascade of host defenses that linked pathogen recognition with innate effector functions and adaptive polarisation. In contrast, caspofungin induced only minimal transcriptional changes in resistant strain infections or in uninfected blood. These findings demonstrate that caspofungin efficacy arises not only from its fungicidal activity but also from amplification of host immunity, an effect primarily dependent on fungal susceptibility. This dual mode of action highlights a previously underappreciated role of echinocandins in shaping antifungal immunity and provides new mechanistic insight into drug-host-pathogen interactions during systemic candidiasis.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"7 ","pages":"uqag004"},"PeriodicalIF":0.0,"publicationDate":"2026-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12906344/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146204180","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 SliP4 deletion on the high-light acclimation in <i>Synechocystis</i> sp. PCC 6803.","authors":"Luna Alvarenga-Lucius, Sandra Maaß, Viktoria Reimann, Dörte Becher, Wolfgang R Hess, Martin Hagemann","doi":"10.1093/femsml/uqag003","DOIUrl":"10.1093/femsml/uqag003","url":null,"abstract":"<p><p>SliP4 is a small, 37 amino acids protein that is strongly induced when the cyanobacterium <i>Synechocystis</i> sp. PCC 6803 is exposed to high-light (HL) conditions. Deletion mutants manifest a light-sensitive phenotype due to impaired cyclic electron flow and state transitions. In this study, we aimed to investigate the consequences of SliP4 deficiency on the process of high-light acclimation on systems level. Transcriptomic data revealed that the deletion mutant Δ<i>sliP4</i> exhibited a wild-type-like gene regulatory response 30 minutes after the light intensity was increased from 50 to 250 μmol photons m^-2 s^-1, a process that is controlled by the RpaB-PsrR1 system. Proteome analysis showed consistent expression changes of many HL-regulated proteins. Metabolome analysis provided hints for a changed N and C metabolism in mutant cells compared to wild type. In addition, the mutant increased the production of extracellular polysaccharides causing the mutant cells to aggregate after the shift to HL. This effect corresponds to the upregulated expression of <i>xssA-E</i> and <i>xssN-P</i> genes for the production of the sulfated exopolysaccharide synechan. We interpret these observations as a response that counteracts the potential light stress effects caused by the impaired capacity for cyclic electron flow and state transitions in the Δ<i>sliP4</i> mutant. Our results demonstrate that the unicellular cyanobacterium <i>Synechocystis</i> compensates for the loss of SliP4 and its crucial role by activating a genetic program for a population-level response that helps the cells to cope with HL conditions.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"7 ","pages":"uqag003"},"PeriodicalIF":0.0,"publicationDate":"2026-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12850537/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146088150","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 complexity of multiple CRISPR arrays in strains with (co-occurring) CRISPR systems.","authors":"Axel Fehrenbach, Alexander Mitrofanov, Rolf Backofen, Franz Baumdicker","doi":"10.1093/femsml/uqaf042","DOIUrl":"10.1093/femsml/uqaf042","url":null,"abstract":"<p><p>CRISPR and their associated Cas proteins provide adaptive immunity in prokaryotes, protecting against invading genetic elements. These systems are categorized into types and are highly diverse. Genomes often harbor multiple CRISPR arrays varying in length and distance from Cas loci. However, the ecological roles of multiple CRISPR arrays and their interactions with multiple Cas loci remain poorly understood. We present a comprehensive analysis of CRISPR systems that uncovers variation between diverse Cas types regarding the occurrence of multiple arrays, the distribution of their lengths and positions relative to Cas loci, and the diversity of their repeat sequences. Some types tend to occur as the sole Cas locus present in the genome, but typically have two or more associated arrays, especially for types I-E and I-F. Multiple Cas types are also common, with some systems showing a preference for specific co-occurrence. Distinct array distributions and orientations around Cas loci indicate substantial differences in functionality and transcriptional behavior among Cas types. Our analysis suggests that arrays with identical repeats in the same genome acquire new spacers at comparable rates, irrespective of their proximity to the Cas locus. Furthermore, repeat similarities indicate that arrays of systems that often co-occur with other systems tend to have more diverse repeats than those mostly appearing alongside solitary systems. Our results indicate that co-occurring Cas-type pairs might not only collaborate in spacer acquisition but also maintain independent and complementary functions and that CRISPR systems distribute their defensive spacer repertoire equally across multiple CRISPR arrays.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"7 ","pages":"uqaf042"},"PeriodicalIF":0.0,"publicationDate":"2026-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12814883/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146013636","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"<i>Salmonella</i> relies on siderophore exploitation at low pH.","authors":"Manon Ferry, Connor Sharp, Isabelle J Schalk, Olivier Cunrath","doi":"10.1093/femsml/uqaf041","DOIUrl":"10.1093/femsml/uqaf041","url":null,"abstract":"<p><p><i>Salmonella enterica</i>, a prominent enteric pathogen, employs sophisticated iron acquisition mechanisms to overcome host-imposed iron limitation, notably through the production and uptake of siderophores-small, high-affinity iron-chelating compounds that scavenge iron from the host environment. In this study, we investigate how environmental pH influences <i>Salmonella's</i> preference for its endogenous siderophores versus exogenous siderophores within the physiological range of the gastrointestinal tract. Through competition assays, gene expression analysis, and siderophore quantification, we demonstrate that <i>Salmonella</i> increasingly relies on exogenous siderophores under acidic conditions. This shift is attributed to reduced production of its endogenous siderophores, enterobactin and salmochelin. Deletion of the sigma factor RpoS enhances iron acquisition through increased endogenous siderophore production at low pH, suggesting a role in iron homeostasis regulation. Our findings reveal a pH-dependent difference in <i>Salmonella's</i> iron acquisition strategy, highlighting the pathogen's versatility in nutrient acquisition across varying gastrointestinal conditions. This research provides insights into <i>Salmonella's</i> pathogenicity and may inform the development of targeted interventions for <i>Salmonella</i> infections.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"7 ","pages":"uqaf041"},"PeriodicalIF":0.0,"publicationDate":"2026-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12816392/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146020839","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":"Less missing values-evaluation of proteomics workflows for the quantification of (small) proteins.","authors":"Jürgen Bartel, Vaikhari Kale, Dennis Joshua Pyper, Harald Schwalbe, Sandra Maaß","doi":"10.1093/femsml/uqag002","DOIUrl":"10.1093/femsml/uqag002","url":null,"abstract":"<p><p>Quantitative information on protein abundance is crucial to understand biological processes and is therefore frequently gathered in proteomic studies. However, the quality of a quantitative proteomic dataset is greatly affected by the number of missing values, which need to be minimized to produce robust and meaningful data. In this context, small proteins (≤100 amino acids) pose specific analytical challenges, which hinder their efficient identification and quantitative characterization in complex proteomes. In this study, methods for sample preparation and MS-data processing are systematically evaluated for their contribution to identification and quantification of small proteins of <i>Clostridioides difficile</i> 630 Δ<i>erm</i>. Results show that small protein enrichment can enhance the number of identified and quantified proteins also for low abundant small proteins. Through application of spectral libraries for identification of MS spectra the number of robustly quantified proteins is increased and a lower limit of their detection is reached. Additionally, the dataset presented here is currently the most comprehensive protein repository for <i>C. difficile</i> covering 84.7% of the predicted proteome and 61.4% of all predicted small proteins of this important pathogen.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"7 ","pages":"uqag002"},"PeriodicalIF":0.0,"publicationDate":"2026-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12850539/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146088176","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":"Comprehensive analysis of CRISPR array repeat mutations reveals subtype-specific patterns and links to spacer dynamics.","authors":"Alexander Mitrofanov, Chase L Beisel, Franz Baumdicker, Omer S Alkhnbashi, Rolf Backofen","doi":"10.1093/femsml/uqaf050","DOIUrl":"https://doi.org/10.1093/femsml/uqaf050","url":null,"abstract":"<p><p>Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and their associated CRISPR-associated protein (Cas) systems are adaptive immune mechanisms in bacteria and archaea that protect against invading genetic elements by integrating short fragments of foreign DNA into CRISPR arrays. These arrays consist of repetitive sequences interspersed with unique spacers, guiding Cas proteins to recognize and degrade matching nucleic acids. The integrity of these repeat sequences is crucial for the proper function of CRISPR-Cas systems, yet their mutational dynamics remain poorly understood. In this study, we analyzed 56 343 CRISPR arrays across 25 628 diverse prokaryotic genomes to assess the mutation patterns in CRISPR array repeat sequences within and across different CRISPR subtypes. Our findings reveal, as expected to some extent, that mutation frequency is substantially higher in terminal repeat sequences compared to internal repeats consistently across system types. However, the mutation patterns exhibit an unexpected amount of variation among different CRISPR subtypes, suggesting that selective pressures and functional constraints shape repeat sequence evolution in distinct ways. Understanding these mutation dynamics provides insights into the stability and adaptability of CRISPR arrays across diverse bacterial and archaeal lineages. Additionally, we elucidate a novel relationship between repeat mutations and spacer dynamics, demonstrating that hotspots for terminal repeat mutations coincide with regions exhibiting higher spacer conservation. This observation corroborates recent findings indicating that spacer deletions occur at a frequency 374 times greater than that of mutations and are significantly influenced by repeat misalignment. Our findings suggest that repeat mutations might play a pivotal role in spacer retention or loss, or vice versa, thereby highlighting an evolutionary trade-off between the stability and adaptability of CRISPR arrays.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"7 ","pages":"uqaf050"},"PeriodicalIF":0.0,"publicationDate":"2026-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12839519/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146095124","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":"Enhanced ADP-heptose-dependent NF-κB activation by <i>Helicobacter pylori</i> CagA through cortactin-Src-dependent tyrosine phosphorylation of IKKβ.","authors":"Irshad Sharafutdinov, Nicole Tegtmeyer, Barbara Friedrich, Michael Naumann, Steffen Backert","doi":"10.1093/femsml/uqaf049","DOIUrl":"10.1093/femsml/uqaf049","url":null,"abstract":"<p><p>Nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) represents a family of important transcription factors in innate immunity. We have previously reported that the gastric pathogen <i>Helicobacter pylori</i> needs the actin-binding protein cortactin for efficient interleukin-8 (IL-8) secretion, which requires NF-κB activation. However, it remained unknown, which exact cortactin signaling mechanism contributes to IL-8 release. In fact, <i>H. pylori</i> profoundly activates NF-κB in wild-type AGS gastric epithelial cells by the effector molecule adenosine diphosphate (ADP)-β-d-manno-heptose (ADPH) in a type IV secretion system-dependent manner. However, the injected CagA protein might contribute to NF-κB activation. The ADPH-stimulated canonical NF-κB cascade involves alpha-kinase 1 and adapter protein TRAF-interacting protein with forkhead-associated domain (TIFA) to activate inhibitor of kappa B (IκB) kinases (IKKs), followed by phosphorylation-dependent degradation of IκBα and subsequent nuclear translocation of p65 NF-κB and IL-8 release. Here, we show that infection of cortactin knockout cells leads to reduced activation of focal adhesion kinase (FAK) and c-Sarcoma (Src) kinase resulting in diminished phosphorylation of IKKβ at tyrosine residue 199 and subsequently phosphorylation of p65 at serine residue 536, both of which are associated with downregulated NF-κB activity. Our results were further supported using FAK and TIFA knockout cells and treatments with purified ADPH and overexpression of CagA, showing cumulative effects in wild-type, but not in knockout cells. These data demonstrate that ADPH-dependent NF-κB activation and IL-8 secretion are enhanced by CagA. Together, we present here a novel CagA>cortactin>FAK>Src>IKKβ signaling cascade, contributing to proinflammatory responses by <i>H. pylori</i>.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"7 ","pages":"uqaf049"},"PeriodicalIF":0.0,"publicationDate":"2026-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12850538/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146088086","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":"CoMPaseD: advanced planning of proteomic experiments aiming to identify small proteins.","authors":"Jürgen Bartel, Philipp T Kaulich, Borja Ferrero-Bordera, Rick Gelhausen, Rolf Backofen, Andreas Tholey, Sandra Maaß","doi":"10.1093/femsml/uqaf043","DOIUrl":"10.1093/femsml/uqaf043","url":null,"abstract":"<p><p>In proteome studies, the application of alternative proteases, exclusively or in addition to trypsin, often increases protein sequence or proteome coverage. It has recently been shown that, in particular, the analysis of small proteins benefits from such multi-protease approaches. However, selecting the most optimal combination of proteases either requires laboursome experiments or the decision of an experienced user, which might be biased. In this manuscript, we present a protease score that enables the objective comparison of multiple-protease digestions and a Python-based tool named CoMPaseD (Comparison of Multiple Protease  Digestions), which utilizes Monte-Carlo simulations to predict this score for a user-defined set of proteases and any combination of these. By analysis of the small proteomes of the two model organisms <i>Bacillus subtilis</i> and <i>Methanosarcina mazei</i> with five proteases and different experimental setups, we demonstrate a good correlation between experimentally derived and predicted scores. This highlights the broad applicability of CoMPaseD, which can effectively guide the selection of proteases to enhance the characterization of specific subsets of the proteome, e.g. based on factors such as protein size, localization or isoelectric point. CoMPaseD is freely available at <i>https://github.com/MicrobialProteomics/CoMPaseD</i>.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"7 ","pages":"uqaf043"},"PeriodicalIF":0.0,"publicationDate":"2026-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12802878/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145992392","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}