Molecular Microbiology最新文献

{"title":"Rok from B. subtilis: Bridging genome structure and transcription regulation.","authors":"Amanda M Erkelens, Bert van Erp, Wilfried J J Meijer, Remus T Dame","doi":"10.1111/mmi.15250","DOIUrl":"10.1111/mmi.15250","url":null,"abstract":"<p><p>Bacterial genomes are folded and organized into compact yet dynamic structures, called nucleoids. Nucleoid orchestration involves many factors at multiple length scales, such as nucleoid-associated proteins and liquid-liquid phase separation, and has to be compatible with replication and transcription. Possibly, genome organization plays an intrinsic role in transcription regulation, in addition to classical transcription factors. In this review, we provide arguments supporting this view using the Gram-positive bacterium Bacillus subtilis as a model. Proteins BsSMC, HBsu and Rok all impact the structure of the B. subtilis chromosome. Particularly for Rok, there is compelling evidence that it combines its structural function with a role as global gene regulator. Many studies describe either function of Rok, but rarely both are addressed at the same time. Here, we review both sides of the coin and integrate them into one model. Rok forms unusually stable DNA-DNA bridges and this ability likely underlies its repressive effect on transcription by either preventing RNA polymerase from binding to DNA or trapping it inside DNA loops. Partner proteins are needed to change or relieve Rok-mediated gene repression. Lastly, we investigate which features characterize H-NS-like proteins, a family that, at present, lacks a clear definition.</p>","PeriodicalId":19006,"journal":{"name":"Molecular Microbiology","volume":" ","pages":"109-123"},"PeriodicalIF":2.6,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11841835/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140175601","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}

{"title":"Gene transfer agents: The ambiguous role of selfless viruses in genetic exchange and bacterial evolution.","authors":"Paul Christopher Michael Fogg","doi":"10.1111/mmi.15251","DOIUrl":"10.1111/mmi.15251","url":null,"abstract":"<p><p>Gene transfer agents (GTAs) are genetic elements derived from ancestral bacteriophages that have become domesticated by the host. GTAs are present in diverse prokaryotic organisms, where they can facilitate horizontal gene transfer under certain conditions. Unlike typical bacteriophages, GTAs do not exhibit any preference for the replication or transfer of the genes encoding them; instead, they exhibit a remarkable capacity to package chromosomal, and sometimes extrachromosomal, DNA into virus-like capsids and disseminate it to neighboring cells. Because GTAs resemble defective prophages, identification of novel GTAs is not trivial. The detection of candidates relies on the genetic similarity to known GTAs, which has been fruitful in α-proteobacterial lineages but challenging in more distant bacteria. Here we consider several fundamental questions: What is the true prevalence of GTAs in prokaryote genomes? Given there are high costs for GTA production, what advantage do GTAs provide to the bacterial host to justify their maintenance? How is the bacterial chromosome recognized and processed for inclusion in GTA particles? This article highlights the challenges in comprehensively understanding GTAs' prevalence, function and DNA packaging method. Going forward, broad study of atypical GTAs and use of ecologically relevant conditions are required to uncover their true impact on bacterial chromosome evolution.</p>","PeriodicalId":19006,"journal":{"name":"Molecular Microbiology","volume":" ","pages":"124-131"},"PeriodicalIF":2.6,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11841831/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140175600","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}

{"title":"A Systematic Targeted Genetic Screen Identifies Proteins Involved in Cytoadherence of the Malaria Parasite P. falciparum","authors":"Nina Küster, Lena Roling, Ardin Ouayoue, Katharina Steeg, Jude M. Przyborski","doi":"10.1111/mmi.15337","DOIUrl":"https://doi.org/10.1111/mmi.15337","url":null,"abstract":"Immediately after invading their chosen host cell, the mature human erythrocyte, malaria parasites begin to export an array of proteins to this compartment, where they initiate processes that are prerequisite for parasite survival and propagation, including nutrient import and immune evasion. One consequence of these activities is the emergence of novel adhesive phenotypes that can lead directly to pathology in the human host. To identify parasite proteins involved in this process, we used modern genetic tools to target genes encoding 15 exported parasite proteins, selected by an in silico workflow. This resulted in four genetically modified parasite lines that were then characterised in detail. Of these lines, three could be shown to have aberrations in adhesion, and of these one appears to have a block in the transport and/or correct folding of the major surface adhesin PfEMP1 (<jats:italic>Plasmodium falciparum</jats:italic> erythrocyte membrane protein 1). Our data expand the known factors involved in this important process and once again highlight the complexity of this phenomenon.","PeriodicalId":19006,"journal":{"name":"Molecular Microbiology","volume":"37 1","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142989809","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}

{"title":"In Vivo Nitrosative Stress‐Induced Expression of a Photolyase Promotes Vibrio cholerae Environmental Blue Light Resistance","authors":"Arkaprabha Banerjee, Hyuntae Byun, Andrew J. Hrycko, Qinqin Pu, Mary R. Brockett, Nathaniel C. Esteves, Jennifer R. Miller, Qiushi Li, Amy T. Ma, Jun Zhu","doi":"10.1111/mmi.15340","DOIUrl":"https://doi.org/10.1111/mmi.15340","url":null,"abstract":"Bacterial pathogens possess a remarkable capacity to sense and adapt to ever‐changing environments. For example, <jats:styled-content style=\"fixed-case\"><jats:italic>Vibrio cholerae</jats:italic></jats:styled-content>, the causative agent of the severe diarrheal disease cholera, thrives in aquatic ecosystems and human hosts through dynamic survival strategies. In this study, we investigated the role of three photolyases, enzymes that repair DNA damage caused by exposure to UV radiation and blue light, in the environmental survival of <jats:styled-content style=\"fixed-case\"><jats:italic>V. cholerae</jats:italic></jats:styled-content>. Among these, we identified <jats:italic>cry1</jats:italic> as critical for resistance to blue light, as mutations in this gene, but not in the other photolyase genes, rendered <jats:styled-content style=\"fixed-case\"><jats:italic>V. cholerae</jats:italic></jats:styled-content> susceptible to such stress. Expression of <jats:italic>cry1</jats:italic> was induced by blue light and regulated by RpoE and the anti‐sigma factor ChrR. We further showed that nitric oxide (NO), a host‐derived stressor encountered during infection, also activated <jats:italic>cry1</jats:italic> expression. We found that one of the two cysteine residues in ChrR was important for sensing reactive nitrogen species (RNS), thereby modulating <jats:italic>cry1</jats:italic> expression. While Cry1 was not required for <jats:styled-content style=\"fixed-case\"><jats:italic>V. cholerae</jats:italic></jats:styled-content> colonization in animal models, pre‐induction of Cry1 by RNS in vivo or in vitro enhanced <jats:styled-content style=\"fixed-case\"><jats:italic>V. cholerae</jats:italic></jats:styled-content> resistance to blue light. These findings suggest that host‐derived NO encountered during infection primes <jats:styled-content style=\"fixed-case\"><jats:italic>V. cholerae</jats:italic></jats:styled-content> for survival in blue‐light‐rich aquatic environments, supporting its transition between host and environmental niches.","PeriodicalId":19006,"journal":{"name":"Molecular Microbiology","volume":"14 1","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142986273","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}

{"title":"Autoregulation of the Master Regulator Spo0A Controls Cell-Fate Decisions in Bacillus subtilis","authors":"Brenda Zarazúa-Osorio, Priyanka Srivastava, Anuradha Marathe, Syeda Hira Zahid, Masaya Fujita","doi":"10.1111/mmi.15341","DOIUrl":"https://doi.org/10.1111/mmi.15341","url":null,"abstract":"Spo0A in <i>Bacillus subtilis</i> is activated by phosphorylation (Spo0A~P) upon starvation and differentially controls a set of genes involved in biofilm formation and sporulation. The <i>spo0A</i> gene is transcribed by two distinct promoters, a σ^A-recognized upstream promoter Pv during growth, and a σ^H-recognized downstream promoter Ps during starvation, and appears to be autoregulated by four Spo0A~P binding sites (0A1-4 boxes) localized between two promoters. However, the autoregulatory mechanisms and their impact on differentiation remain elusive. Here, we determined the relative affinity of Spo0A~P for each 0A box and dissected each promoter in combination with the systematic 0A box mutations. The data revealed that (1) the Pv and Ps promoters are on and off, respectively, under nutrient-rich conditions without Spo0A~P, (2) the Ps promoter is activated by first 0A3 and then 0A1 during early starvation with low Spo0A~P, (3) during later starvation with high Spo0A~P, the Pv promoter is repressed by first 0A1 and then 0A2 and 0A4, and (4) during prolonged starvation, both promoters are silenced by all 0A boxes with very high Spo0A~P. Our results indicate that the autoregulation of <i>spo0A</i> is one of the key determinants to achieve a developmental increase in Spo0A~P, leading to a temporal window for entry into biofilm formation or sporulation.","PeriodicalId":19006,"journal":{"name":"Molecular Microbiology","volume":"2 1","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142981669","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}

{"title":"Deciphering the Coupling State-Dependent Transcription Termination in the Escherichia coli Galactose Operon","authors":"Monford Paul Abishek N, Xun Wang, Heung Jin Jeon, Heon M. Lim","doi":"10.1111/mmi.15339","DOIUrl":"https://doi.org/10.1111/mmi.15339","url":null,"abstract":"The distance between the ribosome and the RNA polymerase active centers, known as the mRNA loop length, is crucial for transcription-translation coupling. Despite the existence of multiple expressomes with varying mRNA loop lengths, their in vivo roles remain largely unexplored. This study examines the mechanisms governing transcription termination in the <i>Escherichia coli</i> galactose operon, revealing a crucial role in the transcription and translation coupling state. The operon utilizes both Rho-independent and Rho-dependent terminators. Our findings demonstrate that long-loop coupled transcription-translation complexes preferentially terminate at the upstream Rho-independent terminator, while short-loop complexes bypass it, terminating at the downstream Rho-dependent terminator. The efficiency of the Rho-independent terminator is enhanced by an extended U-track, suggesting a novel mechanism to overcome ribosome inhibition. These results uncover a new regulatory layer in transcription termination, challenging the traditional view of this process as random and highlighting a predetermined mechanism based on the coupling state. We propose that tandem terminators may function as regulatory checkpoints under fluctuating ribosome-RNAP coupling conditions, which can occur due to specific cellular states or factors affecting ribosome or RNAP binding efficiency. This suggests a previously overlooked mechanism that could refine transcription termination choices and expand our understanding of transcription regulation.","PeriodicalId":19006,"journal":{"name":"Molecular Microbiology","volume":"6 1","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142937692","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}

{"title":"Leishmania mexicana N‐Acetyltransferease 10 Is Important for Polysome Formation and Cell Cycle Progression","authors":"Suellen Rodrigues Maran, Ariely Barbosa Leite, Gabriela Gomes Alves, Bruno Souza Bonifácio, Carlos Eduardo Alves, Paulo Otávio Lourenço Moreira, Giovanna Marques Panessa, Heloísa Monteiro do Amaral Prado, Angélica Hollunder Klippel, José Renato Cussiol, Katlin Brauer Massirer, Tiago Rodrigues Ferreira, David Sacks, Clara Lúcia Barbiéri, Marcelo Santos da Silva, Rubens Lima do Monte‐Neto, Nilmar Silvio Moretti","doi":"10.1111/mmi.15338","DOIUrl":"https://doi.org/10.1111/mmi.15338","url":null,"abstract":"<jats:italic>Leishmania</jats:italic> presents a complex life cycle that involves both invertebrate and vertebrate hosts. By regulating gene expression, protein synthesis, and metabolism, the parasite can adapt to various environmental conditions. This regulation occurs mainly at the post‐transcriptional level and may involve epitranscriptomic modifications of RNAs. Recent studies have shown that mRNAs in humans undergo a modification known as N4‐acetylcytidine (ac4C) catalyzed by the enzyme N‐acetyltransferase (NAT10), impacting mRNAs stability and translation. Here, we characterized the NAT10 homologue of <jats:styled-content style=\"fixed-case\"><jats:italic>L. mexicana</jats:italic></jats:styled-content>, finding that the enzyme exhibits all the conserved acetyltransferase domains although failed to functionally complement the Kre33 mutant in <jats:styled-content style=\"fixed-case\"><jats:italic>Saccharomyces cerevisiae</jats:italic></jats:styled-content>. We also discovered that LmexNAT10 is nuclear, and seems essential, as evidenced by unsuccessful attempts to obtain null mutant parasites. Phenotypic characterization of single‐knockout parasites revealed that LmexNAT10 affects the multiplication of procyclic forms and the promastigote‐amastigote differentiation. Additionally, in vivo infection studies using the invertebrate vector <jats:italic>Lutzomyia longipalpis</jats:italic> showed a delay in the parasite differentiation into metacyclics. Finally, we observed changes in the cell cycle progression and protein synthesis in the mutant parasites. Together, these results suggest that LmexNAT10 might be important for parasite differentiation, potentially by regulating ac4C levels.","PeriodicalId":19006,"journal":{"name":"Molecular Microbiology","volume":"34 1","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142925086","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}

{"title":"Environmental Control of Queuosine Levels in Streptococcus mutanstRNAs","authors":"Marshall Jaroch, Kathryn Savage, Paul Kuipers, Jo Marie Bacusmo, Jennifer Hu, Jingjing Sun, Peter C. Dedon, Kelly C. Rice, Valérie de Crécy‐Lagard","doi":"10.1111/mmi.15336","DOIUrl":"https://doi.org/10.1111/mmi.15336","url":null,"abstract":"Queuosine (Q) is a modification of the wobble base in tRNAs that decode NA(C/U) codons. It is ubiquitous in bacteria, including many pathogens. <jats:styled-content style=\"fixed-case\"><jats:italic>Streptococcus mutans</jats:italic></jats:styled-content> is an early colonizer of dental plaque biofilm and a key player in dental caries. Using a combination of genetic and physiological approaches, the predicted <jats:italic>Q</jats:italic> synthesis and salvage pathways were validated in this organism. These experiments confirmed that <jats:styled-content style=\"fixed-case\"><jats:italic>S. mutans</jats:italic></jats:styled-content> can synthesize <jats:italic>Q de novo</jats:italic> through similar pathways found in <jats:styled-content style=\"fixed-case\"><jats:italic>Bacillus subtilis</jats:italic></jats:styled-content> and <jats:styled-content style=\"fixed-case\"><jats:italic>Escherichia coli</jats:italic></jats:styled-content>. However, <jats:styled-content style=\"fixed-case\"><jats:italic>S. mutans</jats:italic></jats:styled-content> has a distinct salvage pathway compared to these model organisms, as it uses a transporter belonging to the energy coupling factor (ECF) family controlled by a preQ<jats:sub>1</jats:sub>‐dependent riboswitch. Furthermore, Q levels in this oral pathogen depended heavily on the media composition, suggesting that micronutrients can affect Q‐mediated translation efficiency.","PeriodicalId":19006,"journal":{"name":"Molecular Microbiology","volume":"8 1","pages":""},"PeriodicalIF":3.6,"publicationDate":"2024-12-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142884189","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}

{"title":"Regulation of DNA Topology in Archaea: State of the Art and Perspectives","authors":"Paul Villain, Tamara Basta","doi":"10.1111/mmi.15328","DOIUrl":"https://doi.org/10.1111/mmi.15328","url":null,"abstract":"DNA topology is a direct consequence of the double helical nature of DNA and is defined by how the two complementary DNA strands are intertwined. Virtually every reaction involving DNA is influenced by DNA topology or has topological effects. It is therefore of fundamental importance to understand how this phenomenon is controlled in living cells. DNA topoisomerases are the key actors dedicated to the regulation of DNA topology in cells from all domains of life. While significant progress has been made in the last two decades in understanding how these enzymes operate in vivo in Bacteria and Eukaryotes, studies in Archaea have been lagging behind. This review article aims to summarize what is currently known about DNA topology regulation by DNA topoisomerases in main archaeal model organisms. These model archaea exhibit markedly different lifestyles, genome organization and topoisomerase content, thus highlighting the diversity and the complexity of DNA topology regulation mechanisms and their evolution in this domain of life. The recent development of functional genomic assays supported by next-generation sequencing now allows to delve deeper into this timely and exciting, yet still understudied topic.","PeriodicalId":19006,"journal":{"name":"Molecular Microbiology","volume":"112 1","pages":""},"PeriodicalIF":3.6,"publicationDate":"2024-12-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142870016","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}

{"title":"ThyD Is a Thylakoid Membrane Protein Influencing Cell Division and Acclimation to High Light in the Multicellular Cyanobacterium Anabaena sp. Strain PCC 7120","authors":"Ana Valladares, Antonia Herrero","doi":"10.1111/mmi.15335","DOIUrl":"https://doi.org/10.1111/mmi.15335","url":null,"abstract":"Cyanobacteria developed oxygenic photosynthesis and represent the phylogenetic ancestors of chloroplasts. The model strain <i>Anabaena</i> sp. strain PCC 7120 grows as filaments of communicating cells and can form heterocysts, cells specialized for N₂ fixation. In the <i>Anabaena</i> genome, ORF all2390 is annotated as encoding a SulA homolog, but sequence similarity to SulA of model bacteria is insignificant. We generated strains that lacked or overexpressed all2390, both of which showed instances of increased cell size, and observed that purified All2390 protein interfered with the in vitro polymerization of FtsZ. Heterocyst frequency diminished by all2390 inactivation and increased by all2390 overexpression. Overexpression retarded the dismantlement of Z-ring structures that determines commitment in the differentiating cells. Thus, All2390 can influence cell division affecting heterocyst differentiation. An All2390-GFP fusion protein localized to the thylakoid membranes including the <i>honeycomb</i> membranes, which harbor photosynthetic complexes, in the heterocyst polar regions. Notably, all2390 expression strongly increased under high light, conditions under which growth of the null mutant is compromised. Thus, All2390 appears essential for adaptation to high light conditions. We named All2390 ThyD to reflect its thylakoidal localization and its dual role in cell division dynamics and acclimation of thylakoid membranes to increased light intensity.","PeriodicalId":19006,"journal":{"name":"Molecular Microbiology","volume":"12 1","pages":""},"PeriodicalIF":3.6,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142763483","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}