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Metagenomic analysis of pristine oil sheds new light on the global distribution of microbial genetic repertoire in hydrocarbon-associated ecosystems. 原始原油的宏基因组分析为烃类生态系统中微生物遗传库的全球分布提供了新的思路。
microLife Pub Date : 2025-01-23 eCollection Date: 2025-01-01 DOI: 10.1093/femsml/uqae027
Julia Plewka, Armando Alibrandi, Till L V Bornemann, Sarah P Esser, Tom L Stach, Katharina Sures, Jannis Becker, Cristina Moraru, André Soares, Rolando di Primio, Jens Kallmeyer, Alexander J Probst
{"title":"Metagenomic analysis of pristine oil sheds new light on the global distribution of microbial genetic repertoire in hydrocarbon-associated ecosystems.","authors":"Julia Plewka, Armando Alibrandi, Till L V Bornemann, Sarah P Esser, Tom L Stach, Katharina Sures, Jannis Becker, Cristina Moraru, André Soares, Rolando di Primio, Jens Kallmeyer, Alexander J Probst","doi":"10.1093/femsml/uqae027","DOIUrl":"10.1093/femsml/uqae027","url":null,"abstract":"<p><p>Oil reservoirs are society's primary source of hydrocarbons. While microbial communities in industrially exploited oil reservoirs have been investigated in the past, pristine microbial communities in untapped oil reservoirs are little explored, as are distribution patterns of respective genetic signatures. Here, we show that a pristine oil sample contains a complex community consisting of bacteria and fungi for the degradation of hydrocarbons. We identified microorganisms and their pathways for the degradation of methane, <i>n</i>-alkanes, mono-aromatic, and polycyclic aromatic compounds in a metagenome retrieved from biodegraded petroleum encountered in a subsurface reservoir in the Barents Sea. Capitalizing on marker genes from metagenomes and public data mining, we compared the prokaryotes, putative viruses, and putative plasmids of the sampled site to those from 10 other hydrocarbon-associated sites, revealing a shared network of species and genetic elements across the globe. To test for the potential dispersal of the microbes and predicted elements via seawater, we compared our findings to the Tara Ocean dataset, resulting in a broad distribution of prokaryotic and viral signatures. Although frequently shared between hydrocarbon-associated sites, putative plasmids, however, showed little coverage in the Tara Oceans dataset, suggesting an undiscovered mode of transfer between hydrocarbon-affected ecosystems. Based on our analyses, genetic information is globally shared between oil reservoirs and hydrocarbon-associated sites, and we propose that currents and other physical occurrences within the ocean along with deep aquifers are major distributors of prokaryotes and viruses into these subsurface ecosystems.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"6 ","pages":"uqae027"},"PeriodicalIF":0.0,"publicationDate":"2025-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11774207/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143061628","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}
引用次数: 0
New components of the community-based DNA-repair mechanism in Sulfolobales. 邻苯二甲酸乙酯中社区dna修复机制的新成分。
microLife Pub Date : 2025-01-20 eCollection Date: 2025-01-01 DOI: 10.1093/femsml/uqaf002
Alejandra Recalde, Alexander Wagner, Shamphavi Sivabalasarma, Anastasiya Yurmashava, Nayeli Phycilia Fehr, Rebecca Thurm, Thuong Ngoc Le, Christin Köebler, Bianca Wassmer, Sonja-Verena Albers, Marleen van Wolferen
{"title":"New components of the community-based DNA-repair mechanism in Sulfolobales.","authors":"Alejandra Recalde, Alexander Wagner, Shamphavi Sivabalasarma, Anastasiya Yurmashava, Nayeli Phycilia Fehr, Rebecca Thurm, Thuong Ngoc Le, Christin Köebler, Bianca Wassmer, Sonja-Verena Albers, Marleen van Wolferen","doi":"10.1093/femsml/uqaf002","DOIUrl":"10.1093/femsml/uqaf002","url":null,"abstract":"<p><p>After exposure to ultraviolet (UV) light, <i>Sulfolobus acidocaldarius</i> cells aggregate in a species-specific manner to exchange DNA and repair double-strand breaks via homologous recombination. The formation of cell-cell interactions is mediated by Ups pili. DNA exchange subsequently occurs through the Crenarchaeal system for exchange of DNA (Ced), which imports DNA. To identify novel players in these processes, we investigated that several genes upregulated after UV exposure, by creating in-frame deletion mutants and performing cell aggregation and DNA exchange assays. This led to the identification of two novel components involved in the Ups and Ced systems: UpsC, a minor pilin of the Ups pili, and CedD, a VirD4-like ATPase essential for DNA import. Altogether, these findings provide new insights into the DNA damage response mechanisms in Sulfolobales.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"6 ","pages":"uqaf002"},"PeriodicalIF":0.0,"publicationDate":"2025-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11823120/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143416498","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}
引用次数: 0
Functional characterization of the DUF1127-containing small protein YjiS of Salmonella Typhimurium. 鼠伤寒沙门菌duf1127小蛋白YjiS的功能表征
microLife Pub Date : 2025-01-03 eCollection Date: 2025-01-01 DOI: 10.1093/femsml/uqae026
Elisa Venturini, Sandra Maaß, Thorsten Bischler, Dörte Becher, Jörg Vogel, Alexander J Westermann
{"title":"Functional characterization of the DUF1127-containing small protein YjiS of <i>Salmonella</i> Typhimurium.","authors":"Elisa Venturini, Sandra Maaß, Thorsten Bischler, Dörte Becher, Jörg Vogel, Alexander J Westermann","doi":"10.1093/femsml/uqae026","DOIUrl":"10.1093/femsml/uqae026","url":null,"abstract":"<p><p>Bacterial small proteins impact diverse physiological processes, however, technical challenges posed by small size hampered their systematic identification and biochemical characterization. In our quest to uncover small proteins relevant for <i>Salmonella</i> pathogenicity, we previously identified YjiS, a 54 amino acid protein, which is strongly induced during this pathogen's intracellular infection stage. Here, we set out to further characterize the role of YjiS. Cell culture infection assays with <i>Salmonella</i> mutants lacking or overexpressing YjiS suggested this small protein to delay bacterial escape from macrophages. Mutant scanning of the protein's conserved, arginine-rich DUF1127 domain excluded a major effect of single amino acid substitutions on the infection phenotype. A comparative dual RNA-seq assay uncovered the molecular footprint of YjiS in the macrophage response to infection, with host effects related to oxidative stress and the cell cortex. Bacterial cell fractionation experiments demonstrated YjiS to associate with the inner membrane and proteins interacting with YjiS in pull-down experiments were enriched for inner membrane processes. Among the YjiS interactors was the two-component system SsrA/B, the master transcriptional activator of intracellular virulence genes and a suppressor of flagellar genes. Indeed, in the absence of YjiS, we observed elevated expression of motility genes and an increased number of flagella per bacterium. Together, our study points to a role for <i>Salmonella</i> YjiS as a membrane-associated timer of pathogen dissemination.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"6 ","pages":"uqae026"},"PeriodicalIF":0.0,"publicationDate":"2025-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11707872/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142959964","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}
引用次数: 0
Subtilosin A production is influenced by surfactin levels in Bacillus subtilis. 枯草芽孢杆菌表面素水平影响草抑菌素A的生产。
microLife Pub Date : 2025-01-02 eCollection Date: 2025-01-01 DOI: 10.1093/femsml/uqae029
Caja Dinesen, Manca Vertot, Scott A Jarmusch, Carlos N Lozano-Andrade, Aaron J C Andersen, Ákos T Kovács
{"title":"Subtilosin A production is influenced by surfactin levels in <i>Bacillus subtilis</i>.","authors":"Caja Dinesen, Manca Vertot, Scott A Jarmusch, Carlos N Lozano-Andrade, Aaron J C Andersen, Ákos T Kovács","doi":"10.1093/femsml/uqae029","DOIUrl":"10.1093/femsml/uqae029","url":null,"abstract":"<p><p>Although not essential for their growth, the production of secondary metabolites increases the fitness of the producing microorganisms in their natural habitat by enhancing establishment, competition, and nutrient acquisition. The Gram-positive soil-dwelling bacterium, <i>Bacillus subtilis</i>, produces a variety of secondary metabolites. Here, we investigated the regulatory relationship between the non-ribosomal peptide surfactin and the sactipeptide bacteriocin subtilosin A. We discovered that <i>B. subtilis</i> mutants lacking surfactin production exhibited higher production of subtilosin A compared to their parental wild-type strain. Additionally, spatial visualization of <i>B. subtilis</i> production of metabolites demonstrated that surfactin secreted by a wild-type colony could suppress subtilosin A production in an adjacent mutant colony lacking surfactin production. Reporter assays were performed using mutants in specific transcriptional regulators, which confirmed the role of ResD as an activator of the subtilosin A encoding biosynthetic gene cluster (BGC), while the removal of Rok and AbrB repressors increased the expression of the BGC, which was further enhanced by additional deletion of surfactin, suggesting that a so-far-unidentified regulator might mediate the influence of surfactin on production of subtilosin A. Our study reveals a regulatory influence of one secondary metabolite on another, highlighting that the function of secondary metabolites could be more complex than its influence on other organisms and interactions among secondary metabolites could also contribute to their ecological significance.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"6 ","pages":"uqae029"},"PeriodicalIF":0.0,"publicationDate":"2025-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11756287/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143030268","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}
引用次数: 0
Did organs precede organisms in the origin of life? 在生命的起源中,器官先于有机体吗?
microLife Pub Date : 2024-12-23 eCollection Date: 2024-01-01 DOI: 10.1093/femsml/uqae025
Fernando Baquero, Gabriel S Bever, Victor de Lorenzo, Val Fernández-Lanza, Carlos Briones
{"title":"Did organs precede organisms in the origin of life?","authors":"Fernando Baquero, Gabriel S Bever, Victor de Lorenzo, Val Fernández-Lanza, Carlos Briones","doi":"10.1093/femsml/uqae025","DOIUrl":"10.1093/femsml/uqae025","url":null,"abstract":"<p><p>Evolutionary processes acting on populations of organized molecules preceded the origin of living organisms. These prebiotic entities were independently and repeatedly produced [i.e. (re)-produced] by the assembly of their components, following an iterative process giving rise to nearly but not fully identical replicas, allowing for a prebiotic form of Darwinian evolution. Natural selection favored the more persistent assemblies, some possibly modifying their own internal structure, or even their environment, thereby acquiring function. We refer to these assemblies as proto-organs. In association with other assemblies (e.g. in a coacervate or encapsulated within a vesicle), such proto-organs could evolve and acquire a role within the collective when their coexistence favored the selection of the ensemble. Along millions of years, an extraordinarily small number of successful combinations of those proto-organs co-occurring in spatially individualizing compartments might have co-evolved forming a proto-metabolic and proto-genetic informative network, eventually leading to the selfreplication of a very few. Thus, interactions between encapsulated proto-organs would have had a much higher probability of evolving into proto-organisms than interactions among simpler molecules. Multimolecular forms evolve functions; thus, functional organs would have preceded organisms.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"5 ","pages":"uqae025"},"PeriodicalIF":0.0,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11664216/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142883770","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}
引用次数: 0
The proteomic response of Aspergillus fumigatus to amphotericin B (AmB) reveals the involvement of the RTA-like protein RtaA in AmB resistance. 烟曲霉对两性霉素B (AmB)的蛋白质组学反应揭示了rta样蛋白RtaA参与AmB抗性。
microLife Pub Date : 2024-12-05 eCollection Date: 2025-01-01 DOI: 10.1093/femsml/uqae024
Ammar Abou-Kandil, Sophie Tröger-Görler, Annica Pschibul, Thomas Krüger, Maira Rosin, Franziska Schmidt, Parastoo Akbarimoghaddam, Arjun Sarkar, Zoltán Cseresnyés, Yana Shadkchan, Thorsten Heinekamp, Markus H Gräler, Amelia E Barber, Grit Walther, Marc Thilo Figge, Axel A Brakhage, Nir Osherov, Olaf Kniemeyer
{"title":"The proteomic response of <i>Aspergillus fumigatus</i> to amphotericin B (AmB) reveals the involvement of the RTA-like protein RtaA in AmB resistance.","authors":"Ammar Abou-Kandil, Sophie Tröger-Görler, Annica Pschibul, Thomas Krüger, Maira Rosin, Franziska Schmidt, Parastoo Akbarimoghaddam, Arjun Sarkar, Zoltán Cseresnyés, Yana Shadkchan, Thorsten Heinekamp, Markus H Gräler, Amelia E Barber, Grit Walther, Marc Thilo Figge, Axel A Brakhage, Nir Osherov, Olaf Kniemeyer","doi":"10.1093/femsml/uqae024","DOIUrl":"10.1093/femsml/uqae024","url":null,"abstract":"<p><p>The polyene antimycotic amphotericin B (AmB) and its liposomal formulation AmBisome belong to the treatment options of invasive aspergillosis caused by <i>Aspergillus fumigatus</i>. Increasing resistance to AmB in clinical isolates of <i>Aspergillus</i> species is a growing concern, but mechanisms of AmB resistance remain unclear. In this study, we conducted a proteomic analysis of <i>A. fumigatus</i> exposed to sublethal concentrations of AmB and AmBisome. Both antifungals induced significantly increased levels of proteins involved in aromatic acid metabolism, transmembrane transport, and secondary metabolite biosynthesis. One of the most upregulated proteins was RtaA, a member of the RTA-like protein family, which includes conserved fungal membrane proteins with putative functions as transporters or translocases. Accordingly, we found that RtaA is mainly located in the cytoplasmic membrane and to a minor extent in vacuolar-like structures. Deletion of <i>rtaA</i> led to increased polyene sensitivity and its overexpression resulted in modest resistance. Interestingly, <i>rtaA</i> expression was only induced by exposure to the polyenes AmB and nystatin, but not by itraconazole and caspofungin. Orthologues of <i>rtaA</i> were also induced by AmB exposure in <i>A. lentulus</i> and <i>A. terreus</i>. Deletion of <i>rtaA</i> did not significantly change the ergosterol content of <i>A. fumigatus</i>, but decreased fluorescence intensity of the sterol-binding stain filipin. This suggests that RtaA is involved in sterol and lipid trafficking, possibly by transporting the target ergosterol to or from lipid droplets. These findings reveal the contribution of RtaA to polyene resistance in <i>A. fumigatus</i>, and thus provide a new putative target for antifungal drug development.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"6 ","pages":"uqae024"},"PeriodicalIF":0.0,"publicationDate":"2024-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11707875/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142959764","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}
引用次数: 0
Accessing microbial natural products of the past. 获取过去的微生物天然产物。
microLife Pub Date : 2024-11-19 eCollection Date: 2024-01-01 DOI: 10.1093/femsml/uqae023
Martin Klapper, Pierre Stallforth
{"title":"Accessing microbial natural products of the past.","authors":"Martin Klapper, Pierre Stallforth","doi":"10.1093/femsml/uqae023","DOIUrl":"10.1093/femsml/uqae023","url":null,"abstract":"<p><p>Microbial natural products-low molecular weight compounds biosynthesized by microorganisms-form the foundation of important modern therapeutics, including antibiotics, immunomodulators, and anti-cancer agents. This perspective discusses and contrasts two emerging approaches for uncovering natural products of the past. On the one hand, ancestral sequence reconstruction allows recreating biosynthetic pathways that date back hundreds of millions of years. On the other hand, sequencing and <i>de novo</i> assembly of ancient DNA reveals the biosynthetic potential of ancient microbial communities up to 100 000 years. Together, these approaches unveil an otherwise hidden reservoir of functional and structural molecular diversity. They also offer new opportunities to study the biological function and evolution of these molecules within an archaeological context.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"5 ","pages":"uqae023"},"PeriodicalIF":0.0,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11630838/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142808869","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}
引用次数: 0
Tracking the uptake of labelled host-derived extracellular vesicles by the human fungal pathogen Aspergillus fumigatus. 追踪人类真菌病原体烟曲霉对标记宿主来源的细胞外囊泡的摄取。
microLife Pub Date : 2024-11-06 eCollection Date: 2024-01-01 DOI: 10.1093/femsml/uqae022
Corissa Visser, Flora Rivieccio, Thomas Krüger, Franziska Schmidt, Zoltán Cseresnyés, Manfred Rohde, Marc Thilo Figge, Olaf Kniemeyer, Matthew G Blango, Axel A Brakhage
{"title":"Tracking the uptake of labelled host-derived extracellular vesicles by the human fungal pathogen <i>Aspergillus fumigatus</i>.","authors":"Corissa Visser, Flora Rivieccio, Thomas Krüger, Franziska Schmidt, Zoltán Cseresnyés, Manfred Rohde, Marc Thilo Figge, Olaf Kniemeyer, Matthew G Blango, Axel A Brakhage","doi":"10.1093/femsml/uqae022","DOIUrl":"10.1093/femsml/uqae022","url":null,"abstract":"<p><p>Extracellular vesicles (EVs) have gained attention as facilitators of intercellular as well as interkingdom communication during host-microbe interactions. Recently we showed that upon infection, host polymorphonuclear leukocytes produce antifungal EVs targeting the clinically important fungal pathogen <i>Aspergillus fumigatus</i>; however, the small size of EVs (<1 µm) complicates their functional analysis. Here, we employed a more tractable, reporter-based system to label host alveolar epithelial cell-derived EVs and enable their visualization during <i>in vitro A. fumigatus</i> interaction. Fusion of EV marker proteins (CD63, CD9, and CD81) with a Nanoluciferase (NLuc) and a green fluorescent protein (GFP) facilitated their relative quantification by luminescence and visualization by a fluorescence signal. The use of an NLuc fused with a GFP is advantageous as it allows for quantification and visualization of EVs simultaneously without additional external manipulation and to distinguish subpopulations of EVs. Using this system, visualization and tracking of EVs was possible using confocal laser scanning microscopy and advanced imaging analysis. These experiments revealed the propensity of host cell-derived EVs to associate with the fungal cell wall and ultimately colocalize with the cell membrane of <i>A. fumigatus</i> hyphae in large numbers. In conclusion, we have created a series of tools to better define the complex interplay of host-derived EVs with microbial pathogens.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"5 ","pages":"uqae022"},"PeriodicalIF":0.0,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11631206/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142808870","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}
引用次数: 0
Pyoverdine-antibiotic combination treatment: its efficacy and effects on resistance evolution in Escherichia coli. Pyoverdine 抗生素联合疗法:其疗效及其对大肠杆菌耐药性演变的影响。
microLife Pub Date : 2024-10-15 eCollection Date: 2024-01-01 DOI: 10.1093/femsml/uqae021
Vera Vollenweider, Flavie Roncoroni, Rolf Kümmerli
{"title":"Pyoverdine-antibiotic combination treatment: its efficacy and effects on resistance evolution in <i>Escherichia coli</i>.","authors":"Vera Vollenweider, Flavie Roncoroni, Rolf Kümmerli","doi":"10.1093/femsml/uqae021","DOIUrl":"10.1093/femsml/uqae021","url":null,"abstract":"<p><p>Antibiotic resistance is a growing concern for global health, demanding innovative and effective strategies to combat pathogenic bacteria. Pyoverdines, iron-chelating siderophores produced by environmental <i>Pseudomonas</i> spp., present a novel class of promising compounds to induce growth arrest in pathogens through iron starvation. While we previously demonstrated the efficacy of pyoverdines as antibacterials, our understanding of how these molecules interact with antibiotics and impact resistance evolution remains unknown. Here, we investigated the propensity of three <i>Escherichia coli</i> strains to evolve resistance against pyoverdine, the cephalosporin antibiotic ceftazidime, and their combination. We used a naive <i>E. coli</i> wildtype strain and two isogenic variants carrying the <i>bla</i> <sub>TEM-1</sub> β-lactamase gene on either the chromosome or a costly multicopy plasmid to explore the influence of genetic background on selection for resistance. We found that strong resistance against ceftazidime and weak resistance against pyoverdine evolved in all <i>E. coli</i> variants under single treatment. Ceftazidime resistance was linked to mutations in outer membrane porin genes (<i>envZ</i> and <i>ompF</i>), whereas pyoverdine resistance was associated with mutations in the oligopeptide permease (<i>opp</i>) operon. In contrast, ceftazidime resistance phenotypes were attenuated under combination treatment, especially for the <i>E. coli</i> variant carrying <i>bla</i> <sub>TEM-1</sub> on the multicopy plasmid. Altogether, our results show that ceftazidime and pyoverdine interact neutrally and that pyoverdine as an antibacterial is particularly potent against plasmid-carrying <i>E. coli</i> strains, presumably because iron starvation compromises both cellular metabolism and plasmid replication.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"5 ","pages":"uqae021"},"PeriodicalIF":0.0,"publicationDate":"2024-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11536758/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142585270","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}
引用次数: 0
Compiling a versatile toolbox for inducible gene expression in Methanosarcina mazei. 为迷宫甲烷虫的诱导基因表达编译多功能工具箱。
microLife Pub Date : 2024-10-10 eCollection Date: 2024-01-01 DOI: 10.1093/femsml/uqae019
Johanna Hüttermann, Ruth Schmitz
{"title":"Compiling a versatile toolbox for inducible gene expression in <i>Methanosarcina mazei</i>.","authors":"Johanna Hüttermann, Ruth Schmitz","doi":"10.1093/femsml/uqae019","DOIUrl":"10.1093/femsml/uqae019","url":null,"abstract":"<p><p><i>Methanosarcina mazei</i> is a model organism, providing a platform to explore methanoarchaeal regulation mechanisms on the transcriptional and translational level. This study investigates and evaluates various molecular tools to allow inducible gene expression in <i>M. mazei</i>. (i) The TetR/TetO system was utilized to induce expression of a designed antisense RNA directed against sRNA<sub>154</sub> allowing to increase transcripts of asRNA<sub>154</sub> (500-fold), resulting in a significant decrease of sRNA<sub>154</sub> levels (tetracycline-induced knockdown mutant). Strong reduction of sRNA<sub>154</sub> was further confirmed in the knockdown mutant by up to 50-fold decreased transcript levels of the genes <i>nifH, glnK<sub>1</sub></i> , and <i>glnA<sub>1</sub></i> , the stability of which is increased by sRNA<sub>154</sub>. (ii) For translational regulation, an RNA thermometer was designed and first-ever utilized in an archaeon, inserted into the 5'-untranslated region of a reporter gene, which showed enhanced protein expression upon a temperature shift from 30°C to 40°C. (iii) The long 5'-UTR of a trimethylamine (TMA)-inducible polycistronic mRNA was evaluated and studied as a potential genetic tool for induced gene expression on the translational level. However, we discovered TMA-dependent regulation occurs most likely on the transcript level. (iv) A new selection marker (nourseothricin resistance) was established for <i>M. mazei</i> using the streptothricin acetyltransferase gene. Taken together, our findings provide a foundation for future exploration of genetic regulation and inducible gene expression in <i>M. mazei</i> and other methanoarchaea, advancing genetic studies in these organisms and enhancing their potential for biotechnology applications.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"5 ","pages":"uqae019"},"PeriodicalIF":0.0,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11549558/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142633518","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}
引用次数: 0
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