Molecular Microbiology最新文献

{"title":"MmoD and MmoG Are Crucial for the Synthesis of Soluble Methane Monooxygenase in Methanotrophs","authors":"Minggen Cheng, Yongchuang Liu, Xin Yan","doi":"10.1111/mmi.15345","DOIUrl":"https://doi.org/10.1111/mmi.15345","url":null,"abstract":"Soluble methane monooxygenase (sMMO) from methanotrophs has been extensively investigated for decades. However, major knowledge gaps persist regarding the synthesis mechanism of sMMO, particularly concerning the ambiguous roles of <i>mmoD</i> and <i>mmoG</i> in the sMMO gene cluster. Here, the functions of <i>mmoD</i> and <i>mmoG</i> were investigated in a model methanotrophic strain, <i>Methylotuvimicrobium buryatense</i> 5GB1C. Both genes were found to be essential for the functional expression of sMMO. Genetic and biochemical data supported the hypothesis that MmoG acts as a folding chaperone for both MmoX and MmoR, while MmoD serves as an assembly chaperone for the hydroxylase component. The functional expression of sMMO in <i>Escherichia coli</i> was achieved in an <i>mmoD-</i> and <i>mmoG-</i>dependent manner. In addition, deletion of <i>mmoD</i> dramatically reduced the transcription of the sMMO cluster in <i>M. buryatense</i> 5GB1C, implying that MmoD may regulate the sMMO cluster via an unknown mechanism. Knockout of neither <i>mmoD</i> nor <i>mmoG</i> abolished the essential feature of “copper switch”, indicating that they do not serve as the initial regulators of “copper switch”. These results demonstrate the crucial roles of <i>mmoD</i> and <i>mmoG</i> in sMMO synthesis and offer new insights into heterologous expression of sMMO.","PeriodicalId":19006,"journal":{"name":"Molecular Microbiology","volume":"1 1","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143385800","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":"Remote Regulation by VirB, the Transcriptional Anti‐Silencer of Shigella Virulence Genes, Provides Mechanistic Information","authors":"Cody Cris, Monika M. A. Karney, Juniper S. Rosen, Alexander D. Karabachev, Elizabeth N. Huezo, Helen J. Wing","doi":"10.1111/mmi.15344","DOIUrl":"https://doi.org/10.1111/mmi.15344","url":null,"abstract":"Classical models of bacterial transcription show regulators binding close to promoter elements to exert their effect. However, the scope for long‐range regulation exists, especially by nucleoid structuring proteins, like H‐NS. Here, long‐range regulation by VirB, a transcriptional regulator that alleviates H‐NS‐mediated silencing of key virulence genes in <jats:italic>Shigella</jats:italic> species, is explored in vivo to test the limits of long‐range regulation and provide further mechanistic insight. VirB‐dependent regulation of the well‐characterized <jats:italic>icsP</jats:italic> promoter persists if its cognate site is repositioned 1 kb, 3.3 kb, and even 4.7 kb further upstream than its native position in a plasmid reporter. VirB‐dependent regulation diminishes with binding site distance. While increasing cellular VirB pools elevated promoter activity in all constructs with wild‐type VirB binding sites, it did not generate a disproportionate increase in promoter activity from remote sites relative to the native site. Since VirB occludes a constitutively active promoter (PT5) when docked adjacent to its −35 element, we next moved the VirB binding site far outside the promoter region. We discovered that VirB still interfered with promoter activity. These findings and those generated from molecular roadblocks engineered around a distally located VirB‐binding site are reconciled with the various models of transcriptional regulation by VirB.","PeriodicalId":19006,"journal":{"name":"Molecular Microbiology","volume":"39 1","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143192107","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":"Distinct but Redundant Roles of ER Cargo Receptors p24 and Erv29 in Facilitating Proper Secretion of Cellulases in Trichoderma reesei","authors":"Zhixing Wang, Lin Liu, Yi Pu, Yu Fang, Wenhao Lv, Weifeng Liu","doi":"10.1111/mmi.15343","DOIUrl":"https://doi.org/10.1111/mmi.15343","url":null,"abstract":"<i>Trichoderma reesei</i> represents an important industrial workhorse for (hemi)cellulase production. However, relatively little is known about the details of its secretory pathway ensuring the extremely high-level enzyme secretion and how they might be leveraged for engineering improved protein production. Here, the functions of <i>T. reesei</i> ER cargo receptors p24 and Erv29 in trafficking cellulase were characterised. Whereas individual deletion of <i>p24</i> or <i>erv29</i> resulted in only a marginal effect on extracellular cellulase secretion, distinct intracellular trafficking pathways exist for individual hydrolytic enzyme in <i>T. reesei</i>. Notably, the simultaneous absence of p24 and Erv29 abolished the secreted production of cellulases but not xylanases. The secretion defect was accompanied by an apparent intracellular accumulation of cellulases. Mutations of residues on the cytosolic side of p24 and Erv29 supposed to mediate COPII coat recognition also compromised cellulase secretion although the overall ER exit sites (ERES) formation did not seem to be affected. We further revealed that a VPL motif following the signal peptide of CBH2 necessitates its efficient secretion mediated by Erv29. These results indicate that two specific ER cargo receptors complement each other to mediate the proper intracellular trafficking of cellulases and thus ensuring their extracellular secretion.","PeriodicalId":19006,"journal":{"name":"Molecular Microbiology","volume":"39 1","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143077201","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":"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}