Molecular Microbiology最新文献

Multifaceted Evolution of the PhoPQ Two-Component System in Salmonella enterica Enhanced the Expression of Horizontally Acquired Virulence Genes

IF 3.6 2区生物学

Molecular Microbiology Pub Date : 2025-03-24 DOI: 10.1111/mmi.15355

Luke A. F. Barretto, Casey C. Fowler

{"title":"Multifaceted Evolution of the PhoPQ Two-Component System in Salmonella enterica Enhanced the Expression of Horizontally Acquired Virulence Genes","authors":"Luke A. F. Barretto, Casey C. Fowler","doi":"10.1111/mmi.15355","DOIUrl":"https://doi.org/10.1111/mmi.15355","url":null,"abstract":"For a bacterium to adapt to a new environmental niche, its regulatory networks must evolve to effectively sense and respond to cues within that niche. For bacterial pathogens, which encounter harsh and dynamic host niches that require efficient coordination between detecting host cues and regulating virulence genes, this process is a key aspect of how virulence properties evolve. Here, we investigate how a widely conserved two-component regulatory system (TCS), PhoP/PhoQ (PhoPQ), evolved in Salmonella enterica to adopt a new role as a master regulator of gene expression within its species-specific intracellular niche: the Salmonella-containing vacuole (SCV). By comparing Salmonella PhoPQ with the closely related Escherichia coli PhoPQ ortholog, we demonstrate that optimizing virulence gene expression in Salmonella required a multifaceted evolution of several PhoPQ functional domains and establish that distinct genetic differences and mechanisms enhance virulence gene expression for different inducing cues. Interestingly, we find that the increased activity of the Salmonella PhoPQ system has a much more profound impact on the expression of H-NS-repressed, horizontally acquired virulence genes than on the ancestral members of the PhoP regulon. We observe that the PhoPQ systems of other related bacteria exhibit activity levels similar to the E. coli system, suggesting that the differences we observe are the result of Salmonella-specific adaptations that produced a more active PhoPQ system when encountering SCV conditions. Collectively, this study offers a window into the evolutionary adaptations of a TCS that enable it to assume an expanded regulatory role in a unique environment.","PeriodicalId":19006,"journal":{"name":"Molecular Microbiology","volume":"71 1","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143695667","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A Soluble Expression Construct of the Isolated Catalytic Domain of Plasmodium falciparum ATP4 Exhibits ATPase Activity Independent of a γ-Phosphate Receiving Aspartate

IF 3.6 2区生物学

Molecular Microbiology Pub Date : 2025-03-17 DOI: 10.1111/mmi.15358

Timo Beyer, Jesko Caliebe, Lara Kähler, Eric Beitz

{"title":"A Soluble Expression Construct of the Isolated Catalytic Domain of Plasmodium falciparum ATP4 Exhibits ATPase Activity Independent of a γ-Phosphate Receiving Aspartate","authors":"Timo Beyer, Jesko Caliebe, Lara Kähler, Eric Beitz","doi":"10.1111/mmi.15358","DOIUrl":"https://doi.org/10.1111/mmi.15358","url":null,"abstract":"The sodium/proton-exchanging ATPase of Plasmodium falciparum malaria parasites, PfATP4, is an emerging drug target. Inhibition results in detrimental cell swelling due to cytosolic accumulation of sodium and alkalization. PfATP4 is a sodium-releasing type II P-type ATPase restricted to apicomplexan parasites. Experimental data on structure–function relationships of the isolated protein are absent. Here, we produced and purified the soluble catalytic domain of PfATP4 and evaluated kinetic properties by in vitro phosphate colorimetry. The protein exhibited Mg2+-dependent ATPase activity at the same order of magnitude as the native cellular PfATP4 and was insensitive to the presence of sodium. AlphaFold 3-based structure and ATP/Mg2+ interaction predictions identified key residues of the nucleotide binding domain (Lys619, Lys652, Arg703). Replacement of the lysines by methionine decreased the enzymatic activity to one quarter. Individual mutation of the putative Mg2+-coordinating Asp865 of the phosphorylation domain was tolerated, while a joint replacement with Asp869 decreased ATPase again to one quarter. Mutation of the putative γ-phosphate receiving Asp451 maintained the rate of Pi release. Our data attribute typical functional roles for P-type ATPases to the basic and acidic residues of the soluble PfATP4 catalytic domain and show that its ATP hydrolysis is independent of phosphorylation of Asp451.","PeriodicalId":19006,"journal":{"name":"Molecular Microbiology","volume":"16 1","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143635181","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The Barrier Properties of Biological Membranes Dictate How Cells Experience Oxidative Stress

IF 3.6 2区生物学

Molecular Microbiology Pub Date : 2025-03-17 DOI: 10.1111/mmi.15353

James A. Imlay

引用次数: 0

Functional and Pangenomic Exploration of Roc Two-Component Regulatory Systems Identifies Novel Players Across Pseudomonas Species

IF 3.6 2区生物学

Molecular Microbiology Pub Date : 2025-03-14 DOI: 10.1111/mmi.15357

Victor Simon, Julian Trouillon, Ina Attrée, Sylvie Elsen

{"title":"Functional and Pangenomic Exploration of Roc Two-Component Regulatory Systems Identifies Novel Players Across Pseudomonas Species","authors":"Victor Simon, Julian Trouillon, Ina Attrée, Sylvie Elsen","doi":"10.1111/mmi.15357","DOIUrl":"https://doi.org/10.1111/mmi.15357","url":null,"abstract":"The opportunistic pathogen Pseudomonas aeruginosa relies on a large collection of two-component regulatory systems (TCSs) to sense and adapt to changing environments. Among them, the Roc (regulation of cup) system is a one-of-a-kind network of branched TCSs, composed of two histidine kinases (HKs—RocS1 and RocS2) interacting with three response regulators (RRs—RocA1, RocR, and RocA2), which regulate virulence, antibiotic resistance, and biofilm formation. Based on extensive work on the Roc system, previous data suggested the existence of other key regulators yet to be discovered. In this work, we identified PA4080, renamed RocA3, as a fourth RR that is activated by RocS1 and RocS2 and that positively controls the expression of the cupB operon. Comparative genomic analysis of the locus identified a gene—rocR3—adjacent to rocA3 in a subpopulation of strains that encodes a protein with structural and functional similarity to the c-di-GMP phosphodiesterase RocR. Furthermore, we identified a fourth branch of the Roc system consisting of the PA2583 HK, renamed RocS4, and the Hpt protein HptA. Using a bacterial two-hybrid system, we showed that RocS4 interacts with HptA, which in turn interacts with RocA1, RocA2, and RocR3. Finally, we mapped the pangenomic RRs repertoire, establishing a comprehensive view of the plasticity of such regulators among clades of the species. Overall, our work provides a comprehensive inter-species definition of the Roc system, nearly doubling the number of proteins known to be involved in this interconnected network of TCSs controlling pathogenicity in Pseudomonas species.","PeriodicalId":19006,"journal":{"name":"Molecular Microbiology","volume":"55 1","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143627472","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

MecA: A Multifunctional ClpP-Dependent and Independent Regulator in Gram-Positive Bacteria

IF 3.6 2区生物学

Molecular Microbiology Pub Date : 2025-03-11 DOI: 10.1111/mmi.15356

Zezhang T. Wen, Kassapa Ellepola, Hui Wu

引用次数: 0

Chromatin and gene regulation in archaea. 古细菌中的染色质和基因调控。

IF 2.6 2区生物学

Molecular Microbiology Pub Date : 2025-03-01 Epub Date: 2024-08-03 DOI: 10.1111/mmi.15302

Fabian Blombach, Finn Werner

{"title":"Chromatin and gene regulation in archaea.","authors":"Fabian Blombach, Finn Werner","doi":"10.1111/mmi.15302","DOIUrl":"10.1111/mmi.15302","url":null,"abstract":"The chromatinisation of DNA by nucleoid-associated proteins (NAPs) in archaea 'formats' the genome structure in profound ways, revealing both striking differences and analogies to eukaryotic chromatin. However, the extent to which archaeal NAPs actively regulate gene expression remains poorly understood. The dawn of quantitative chromatin mapping techniques and first NAP-specific occupancy profiles in different archaea promise a more accurate view. A picture emerges where in diverse archaea with very different NAP repertoires chromatin maintains access to regulatory motifs including the gene promoter independently of transcription activity. Our re-analysis of genome-wide occupancy data of the crenarchaeal NAP Cren7 shows that these chromatin-free regions are flanked by increased Cren7 binding across the transcription start site. While bacterial NAPs often form heterochromatin-like regions across islands with xenogeneic genes that are transcriptionally silenced, there is little evidence for similar structures in archaea and data from Haloferax show that the promoters of xenogeneic genes remain accessible. Local changes in chromatinisation causing wide-ranging effects on transcription restricted to one chromosomal interaction domain (CID) in Saccharolobus islandicus hint at a higher-order level of organisation between chromatin and transcription. The emerging challenge is to integrate results obtained at microscale and macroscale, reconciling molecular structure and function with dynamic genome-wide chromatin landscapes.","PeriodicalId":19006,"journal":{"name":"Molecular Microbiology","volume":" ","pages":"218-231"},"PeriodicalIF":2.6,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11894787/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141879066","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Polyphosphate: The "Dark Matter" of Bacterial Chromatin Structure.

IF 2.6 2区生物学

Molecular Microbiology Pub Date : 2025-03-01 Epub Date: 2025-02-18 DOI: 10.1111/mmi.15350

Lisa R Racki, Lydia Freddolino

引用次数: 0

In vivo assembly of bacterial partition condensates on circular supercoiled and linear DNA. 细菌在环形超卷曲 DNA 和线性 DNA 上的活体分区凝聚体组装。

IF 2.6 2区生物学

Molecular Microbiology Pub Date : 2025-03-01 Epub Date: 2024-08-07 DOI: 10.1111/mmi.15297

Hicham Sekkouri Alaoui, Valentin Quèbre, Linda Delimi, Jérôme Rech, Roxanne Debaugny-Diaz, Delphine Labourdette, Manuel Campos, François Cornet, Jean-Charles Walter, Jean-Yves Bouet

{"title":"In vivo assembly of bacterial partition condensates on circular supercoiled and linear DNA.","authors":"Hicham Sekkouri Alaoui, Valentin Quèbre, Linda Delimi, Jérôme Rech, Roxanne Debaugny-Diaz, Delphine Labourdette, Manuel Campos, François Cornet, Jean-Charles Walter, Jean-Yves Bouet","doi":"10.1111/mmi.15297","DOIUrl":"10.1111/mmi.15297","url":null,"abstract":"In bacteria, faithful DNA segregation of chromosomes and plasmids is mainly mediated by ParABS systems. These systems, consisting of a ParA ATPase, a DNA binding ParB CTPase, and centromere sites parS, orchestrate the separation of newly replicated DNA copies and their intracellular positioning. Accurate segregation relies on the assembly of a high-molecular-weight complex, comprising a few hundreds of ParB dimers nucleated from parS sites. This complex assembles in a multi-step process and exhibits dynamic liquid-droplet properties. Despite various proposed models, the complete mechanism for partition complex assembly remains elusive. This study investigates the impact of DNA supercoiling on ParB DNA binding profiles in vivo, using the ParABS system of the plasmid F. We found that variations in DNA supercoiling does not significantly affect any steps in the assembly of the partition complex. Furthermore, physical modeling, leveraging ChIP-seq data from linear plasmids F, suggests that ParB sliding is restricted to approximately 2 Kbp from parS, highlighting the necessity for additional mechanisms beyond ParB sliding over DNA for concentrating ParB into condensates nucleated at parS. Finally, explicit simulations of a polymer coated with bound ParB suggest a dominant role for ParB-ParB interactions in DNA compaction within ParB condensates.","PeriodicalId":19006,"journal":{"name":"Molecular Microbiology","volume":" ","pages":"232-244"},"PeriodicalIF":2.6,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141897798","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Identification, characterization and classification of prokaryotic nucleoid-associated proteins. 原核相关蛋白的鉴定、特征描述和分类。

IF 2.6 2区生物学

Molecular Microbiology Pub Date : 2025-03-01 Epub Date: 2024-07-22 DOI: 10.1111/mmi.15298

Samuel Schwab, Remus T Dame

引用次数: 0

The Human-Specific miR-6762-5p Is an Activator of RhoA GTPase Enhancing Shigella flexneri Intercellular Spreading

IF 3.6 2区生物学

Molecular Microbiology Pub Date : 2025-02-24 DOI: 10.1111/mmi.15352

Caroline Reisacher, Estelle Saifi, Elisabeth Ageron, Robert Theodor Mallmann, Norbert Klugbauer, David Skurnik, Laurence Arbibe

{"title":"The Human-Specific miR-6762-5p Is an Activator of RhoA GTPase Enhancing Shigella flexneri Intercellular Spreading","authors":"Caroline Reisacher, Estelle Saifi, Elisabeth Ageron, Robert Theodor Mallmann, Norbert Klugbauer, David Skurnik, Laurence Arbibe","doi":"10.1111/mmi.15352","DOIUrl":"https://doi.org/10.1111/mmi.15352","url":null,"abstract":"MicroRNAs have recently emerged as major players in host –bacterial pathogen interactions, either as part of the host defense mechanism to neutralize infection or as a bacterial arsenal aimed at subverting host cell functions. Here, we identify the newly evolved human microRNA miR-6762-5p as a new player in the host–Shigella interplay. A microarray analysis in infected epithelial cells allowed the detection of this miRNA exclusively during the late phase of infection. Conditional expression of miR-6762-5p combined with a transcriptome analysis indicated a role in cytoskeleton remodeling. Likewise, miR-6762-5p enhanced stress fiber formation through RhoA activation, and in silico analysis identified several regulators of RhoA activity as potential direct transcriptional targets. We further showed that miR-6762-5p expression induces an increase in Shigella intercellular spreading, while miR-6762-5p inhibition reduced bacterial dissemination. We propose a model in which the expression of miR-6762-5p induces cytoskeleton modifications through RhoA activation to achieve a successful dissemination of Shigella in the host.","PeriodicalId":19006,"journal":{"name":"Molecular Microbiology","volume":"51 1","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143477870","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0