All methanogens that can fix nitrogen use molybdenum (Mo) nitrogenase. Some methanogens, including Methanosarcina acetivorans, also contain alternative vanadium- and iron-nitrogenases, encoded by the vnf and anf operons, respectively. These nitrogenases are produced when there is insufficient Mo to support Mo-nitrogenase activity. The factors that control the expression of the alternative nitrogenases in response to Mo availability are unknown in methanogens. Here we show that ModE is the regulator that represses transcription of the vnf and anf operons in M. acetivorans when cells are grown with Mo. CRISPRi repression of modE results in a significant increase in the transcription of the vnf and anf operons as well as the detection of Fe-nitrogenase during nitrogen fixation in the presence of Mo. Gel shift assays with recombinant ModE demonstrated that ModE binds a specific sequence motif upstream of the vnf and anf operons, as well as other genes and operons related to nitrogen fixation and Mo transport. However, purified ModE does not contain Mo, and the addition of Mo does not alter the affinity of ModE for DNA, indicating M. acetivorans ModE may not directly bind Mo. This study shows that ModE is the primary Mo-responsive regulator of alternative nitrogenase expression in M. acetivorans, but other factor(s) are likely involved in directly sensing Mo.
{"title":"ModE Regulates Alternative Nitrogenase Expression in the Methanogen Methanosarcina acetivorans.","authors":"Melissa Chanderban,Daniel J Lessner","doi":"10.1111/mmi.15377","DOIUrl":"https://doi.org/10.1111/mmi.15377","url":null,"abstract":"All methanogens that can fix nitrogen use molybdenum (Mo) nitrogenase. Some methanogens, including Methanosarcina acetivorans, also contain alternative vanadium- and iron-nitrogenases, encoded by the vnf and anf operons, respectively. These nitrogenases are produced when there is insufficient Mo to support Mo-nitrogenase activity. The factors that control the expression of the alternative nitrogenases in response to Mo availability are unknown in methanogens. Here we show that ModE is the regulator that represses transcription of the vnf and anf operons in M. acetivorans when cells are grown with Mo. CRISPRi repression of modE results in a significant increase in the transcription of the vnf and anf operons as well as the detection of Fe-nitrogenase during nitrogen fixation in the presence of Mo. Gel shift assays with recombinant ModE demonstrated that ModE binds a specific sequence motif upstream of the vnf and anf operons, as well as other genes and operons related to nitrogen fixation and Mo transport. However, purified ModE does not contain Mo, and the addition of Mo does not alter the affinity of ModE for DNA, indicating M. acetivorans ModE may not directly bind Mo. This study shows that ModE is the primary Mo-responsive regulator of alternative nitrogenase expression in M. acetivorans, but other factor(s) are likely involved in directly sensing Mo.","PeriodicalId":19006,"journal":{"name":"Molecular Microbiology","volume":"137 1","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143932897","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}
Cheyenne D. Lee, Arshad Rizvi, Zavier A. Carter, Adrianne N. Edwards, Shonna M. McBride
Clostridioides difficile is an anaerobic enteric pathogen that disseminates in the environment as a dormant spore. For C. difficile and other sporulating bacteria, the initiation of sporulation is a regulated process that prevents spore formation under favorable growth conditions. In Bacillus subtilis, one such mechanism for preventing sporulation is the prokaryotic 5-oxoprolinase, PxpB (KipI), which impedes the activation of the main sporulation kinase. In addition, PxpB functions as part of a complex that detoxifies the intermediate metabolite, 5-oxoproline (OP), a harmful by-product of glutamic acid and its derivatives. In this study, we investigate the orthologous Pxp proteins in C. difficile to determine their roles in the regulation of sporulation and metabolism. Through deletion of the pxpAGBC operon, we show that, unlike in B. subtilis, the Pxp (Kip) proteins have no significant impact on sporulation. However, we found that the pxp operon encodes a functional oxoprolinase that facilitates detoxification of OP. Furthermore, our data demonstrate that PxpAGBC not only detoxifies OP but also allows OP to be used as a nutrient source that supports the growth of C. difficile, thereby facilitating the conversion of a toxic by-product of metabolism into an energy source.
{"title":"The Pxp Complex Detoxifies 5-Oxoproline and Promotes the Growth of Clostridioides difficile","authors":"Cheyenne D. Lee, Arshad Rizvi, Zavier A. Carter, Adrianne N. Edwards, Shonna M. McBride","doi":"10.1111/mmi.15373","DOIUrl":"https://doi.org/10.1111/mmi.15373","url":null,"abstract":"<i>Clostridioides difficile</i> is an anaerobic enteric pathogen that disseminates in the environment as a dormant spore. For <i>C. difficile</i> and other sporulating bacteria, the initiation of sporulation is a regulated process that prevents spore formation under favorable growth conditions. In <i>Bacillus subtilis</i>, one such mechanism for preventing sporulation is the prokaryotic 5-oxoprolinase, PxpB (KipI), which impedes the activation of the main sporulation kinase. In addition, PxpB functions as part of a complex that detoxifies the intermediate metabolite, 5-oxoproline (OP), a harmful by-product of glutamic acid and its derivatives. In this study, we investigate the orthologous Pxp proteins in <i>C. difficile</i> to determine their roles in the regulation of sporulation and metabolism. Through deletion of the <i>pxpAGBC</i> operon, we show that, unlike in <i>B. subtilis,</i> the Pxp (Kip) proteins have no significant impact on sporulation. However, we found that the <i>pxp</i> operon encodes a functional oxoprolinase that facilitates detoxification of OP. Furthermore, our data demonstrate that PxpAGBC not only detoxifies OP but also allows OP to be used as a nutrient source that supports the growth of <i>C. difficile</i>, thereby facilitating the conversion of a toxic by-product of metabolism into an energy source.","PeriodicalId":19006,"journal":{"name":"Molecular Microbiology","volume":"37 1","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143920960","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}
Otmane Lamrabet, Raphael Munoz-Ruiz, Imen Ayadi, Alixia Bourbon, Erwann Pain, Joseph Oddy, Pierre Cosson
Phagocytic cells ingest bacteria and kill them in phagosomes. A variety of molecular mechanisms allow the killing and destruction of bacteria in phagosomes, but their complete list and relative importance remain poorly defined. Here we have used Dictyostelium discoideum amoebae as model phagocytic cells. Our results reveal that PldX, a luminal phospholipase D, plays an important role in the phagosomal destruction of ingested bacteria. Analysis of bacterial destruction in wild-type and pldX KO living cells suggests that PldX participates in the permeabilization of the bacterial membrane. The bacteriolytic activity of D. discoideum extracts was also measured in vitro: extracts from pldX KO cells exhibit significantly less bacteriolytic activity than wild-type cells, confirming the role of PldX in the lysis of bacterial membranes. These results identify luminal phospholipase D as a major player in the permeabilization of bacterial membranes in phagosomes.
{"title":"Luminal Phospholipase D Attacks Bacterial Membranes in Dictyostelium discoideum Phagosomes","authors":"Otmane Lamrabet, Raphael Munoz-Ruiz, Imen Ayadi, Alixia Bourbon, Erwann Pain, Joseph Oddy, Pierre Cosson","doi":"10.1111/mmi.15367","DOIUrl":"https://doi.org/10.1111/mmi.15367","url":null,"abstract":"Phagocytic cells ingest bacteria and kill them in phagosomes. A variety of molecular mechanisms allow the killing and destruction of bacteria in phagosomes, but their complete list and relative importance remain poorly defined. Here we have used <i>Dictyostelium discoideum</i> amoebae as model phagocytic cells. Our results reveal that PldX, a luminal phospholipase D, plays an important role in the phagosomal destruction of ingested bacteria. Analysis of bacterial destruction in wild-type and <i>pldX</i> KO living cells suggests that PldX participates in the permeabilization of the bacterial membrane. The bacteriolytic activity of <i>D. discoideum</i> extracts was also measured in vitro: extracts from <i>pldX</i> KO cells exhibit significantly less bacteriolytic activity than wild-type cells, confirming the role of PldX in the lysis of bacterial membranes. These results identify luminal phospholipase D as a major player in the permeabilization of bacterial membranes in phagosomes.","PeriodicalId":19006,"journal":{"name":"Molecular Microbiology","volume":"79 1","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-05-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143905431","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}
Actinobacillus pleuropneumoniae is the causative agent of pleuropneumonia in swine, a highly contagious and economically significant disease. The genetic variability of A. pleuropneumoniae complicates disease control efforts, as it enables rapid adaptation to various stressors, including antimicrobial treatments. To better understand the molecular mechanisms underlying this adaptability, we investigated the role of the bacterial defensome and its relationship with mobile genetic elements (MGEs), such as prophages, plasmids, and integrative conjugative elements (ICEs). Using bioinformatic tools, we identified a diverse and rich defensome in A. pleuropneumoniae, with an average of 16 different defense systems per strain. We found that CRISPR-Cas systems, along with other defense mechanisms, are actively involved in restricting the entry of foreign genetic material, playing a crucial role in bacterial adaptation. Additionally, we characterized several novel prophages and examined their distribution across different strains, revealing their potential contribution to the bacterium's evolutionary success. Our findings underscore the complex interplay between the bacterium's defense systems and MGEs, shedding light on how A. pleuropneumoniae maintains genetic diversity while also safeguarding itself against external threats. These insights provide a better understanding of the genetic factors that influence the pathogen's adaptability and highlight potential avenues for more effective disease control strategies.
{"title":"The Arms Race Between Actinobacillus pleuropneumoniae and Its Genetic Environment: A Comprehensive Analysis of Its Defensome and Mobile Genetic Elements","authors":"Giarlã Cunha da Silva, Ciro César Rossi","doi":"10.1111/mmi.15374","DOIUrl":"https://doi.org/10.1111/mmi.15374","url":null,"abstract":"<i>Actinobacillus pleuropneumoniae</i> is the causative agent of pleuropneumonia in swine, a highly contagious and economically significant disease. The genetic variability of <i>A. pleuropneumoniae</i> complicates disease control efforts, as it enables rapid adaptation to various stressors, including antimicrobial treatments. To better understand the molecular mechanisms underlying this adaptability, we investigated the role of the bacterial defensome and its relationship with mobile genetic elements (MGEs), such as prophages, plasmids, and integrative conjugative elements (ICEs). Using bioinformatic tools, we identified a diverse and rich defensome in <i>A. pleuropneumoniae</i>, with an average of 16 different defense systems per strain. We found that CRISPR-Cas systems, along with other defense mechanisms, are actively involved in restricting the entry of foreign genetic material, playing a crucial role in bacterial adaptation. Additionally, we characterized several novel prophages and examined their distribution across different strains, revealing their potential contribution to the bacterium's evolutionary success. Our findings underscore the complex interplay between the bacterium's defense systems and MGEs, shedding light on how <i>A. pleuropneumoniae</i> maintains genetic diversity while also safeguarding itself against external threats. These insights provide a better understanding of the genetic factors that influence the pathogen's adaptability and highlight potential avenues for more effective disease control strategies.","PeriodicalId":19006,"journal":{"name":"Molecular Microbiology","volume":"109 1","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143901813","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}
Brian Nguyen, Carly Ching, Ashley MacGuire, Pranav Casula, Connor Newman, Faith Finley, Veronica G. Godoy
Acinetobacter baumannii is an opportunistic pathogen causing several infections that are increasingly difficult to treat due to its ability to rapidly gain antibiotic resistances. These resistances can arise due to mutations through the activity of error-prone DNA polymerases, such as DNA polymerase V (DNA Pol V) in response to DNA damage. The regulation of the DNA damage response (DDR) in A. baumannii is not completely understood; the regulation of genes encoding multiple copies of DNA Pol V is not fully characterized. Through genome-wide mutagenesis, we have identified a novel TetR-like family regulator of the umuDC and umuC genes, which we have named Error-prone polymerase regulator (EppR). We have found that EppR represses the expression of the genes encoding DNA Pol V and itself through direct binding to an EppR motif in their promoters. Lastly, we show that EppR also regulates UmuDAb, previously identified as a regulator of genes encoding DNA Pol V. These two gene products are functionally required to ensure regulation of the expression of the two umuDC, the two umuC genes as well as the regulators umuDAb and eppR genes. With these results, we propose a model in which multiple transcription factors regulate the expression of all these genes.
鲍曼不动杆菌是一种机会致病菌，引起多种感染，由于其迅速获得抗生素耐药性的能力，这种感染越来越难以治疗。这些抗性可能是由于易出错的DNA聚合酶（如DNA聚合酶V (DNA Pol V)）响应DNA损伤而产生的突变而产生的。鲍曼不动杆菌DNA损伤反应（DDR）的调控机制尚不完全清楚；编码DNA多拷贝Pol V的基因调控尚未完全确定。通过全基因组诱变，我们鉴定出了umuDC和umuC基因的一种新的类似于rt的家族调节剂，我们将其命名为易出错聚合酶调节剂（Error-prone polymerase regulator, EppR）。我们发现EppR通过直接结合启动子中的EppR基序来抑制编码DNA Pol V及其自身的基因的表达。最后，我们发现EppR还能调控UmuDAb，而UmuDAb先前被认为是编码DNA Pol v的基因的调节因子。这两个基因产物在功能上是必需的，以确保调控两个umuDC、两个umuC基因以及调节因子UmuDAb和EppR基因的表达。根据这些结果，我们提出了一个模型，其中多个转录因子调节所有这些基因的表达。
{"title":"Identification of EppR, a Second Repressor of Error-Prone DNA Polymerase Genes in Acinetobacter baumannii","authors":"Brian Nguyen, Carly Ching, Ashley MacGuire, Pranav Casula, Connor Newman, Faith Finley, Veronica G. Godoy","doi":"10.1111/mmi.15368","DOIUrl":"https://doi.org/10.1111/mmi.15368","url":null,"abstract":"<i>Acinetobacter baumannii</i> is an opportunistic pathogen causing several infections that are increasingly difficult to treat due to its ability to rapidly gain antibiotic resistances. These resistances can arise due to mutations through the activity of error-prone DNA polymerases, such as DNA polymerase V (DNA Pol V) in response to DNA damage. The regulation of the DNA damage response (DDR) in <i>A. baumannii</i> is not completely understood; the regulation of genes encoding multiple copies of DNA Pol V is not fully characterized. Through genome-wide mutagenesis, we have identified a novel TetR-like family regulator of the <i>umuDC</i> and <i>umuC</i> genes, which we have named Error-prone polymerase regulator (EppR). We have found that EppR represses the expression of the genes encoding DNA Pol V and itself through direct binding to an EppR motif in their promoters. Lastly, we show that EppR also regulates UmuDAb, previously identified as a regulator of genes encoding DNA Pol V. These two gene products are functionally required to ensure regulation of the expression of the two <i>umuDC</i>, the two <i>umuC</i> genes as well as the regulators <i>umuDAb</i> and <i>eppR</i> genes. With these results, we propose a model in which multiple transcription factors regulate the expression of all these genes.","PeriodicalId":19006,"journal":{"name":"Molecular Microbiology","volume":"41 1","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-04-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143849527","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}
Biofilms are highly organized, cooperating communities of microorganisms encased in a self-produced extracellular matrix, providing resilience against external stress such as antimicrobial agents and host defenses. A hallmark of biofilms is their phenotypic heterogeneity, which enhances the overall growth and survival of the community. In this study, we demonstrate that removing the dnaK and tig genes encoding the core molecular chaperones DnaK (Hsp70 homolog) and Trigger factor disrupted protein homeostasis in Bacillus subtilis and resulted in the formation of an extremely mucoid biofilm with aberrant architecture, compromised structural integrity, and altered phenotypic heterogeneity. These changes include a large reduction in the motile subpopulation and an overrepresentation of matrix producers and endospores. Overproduction of poly-γ-glutamic acid contributed crucially to the mucoid phenotype and aberrant biofilm architecture. Homeostasis impairment, triggered by elevated temperatures, in wild-type cells led to mucoid and aberrant biofilm phenotypes similar to those observed in strains lacking both dnaK and tig. Our findings show that disruption of protein homeostasis, whether due to the absence of molecular chaperones or because of environmental factors, severely changes biofilm features.
{"title":"Protein Homeostasis Impairment Alters Phenotypic Heterogeneity of Biofilm Communities","authors":"Judith Matavacas, Claes von Wachenfeldt","doi":"10.1111/mmi.15366","DOIUrl":"https://doi.org/10.1111/mmi.15366","url":null,"abstract":"Biofilms are highly organized, cooperating communities of microorganisms encased in a self-produced extracellular matrix, providing resilience against external stress such as antimicrobial agents and host defenses. A hallmark of biofilms is their phenotypic heterogeneity, which enhances the overall growth and survival of the community. In this study, we demonstrate that removing the <i>dnaK</i> and <i>tig</i> genes encoding the core molecular chaperones DnaK (Hsp70 homolog) and Trigger factor disrupted protein homeostasis in <i>Bacillus subtilis</i> and resulted in the formation of an extremely mucoid biofilm with aberrant architecture, compromised structural integrity, and altered phenotypic heterogeneity. These changes include a large reduction in the motile subpopulation and an overrepresentation of matrix producers and endospores. Overproduction of poly-γ-glutamic acid contributed crucially to the mucoid phenotype and aberrant biofilm architecture. Homeostasis impairment, triggered by elevated temperatures, in wild-type cells led to mucoid and aberrant biofilm phenotypes similar to those observed in strains lacking both <i>dnaK</i> and <i>tig</i>. Our findings show that disruption of protein homeostasis, whether due to the absence of molecular chaperones or because of environmental factors, severely changes biofilm features.","PeriodicalId":19006,"journal":{"name":"Molecular Microbiology","volume":"63 1","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143841627","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}
Arnau Galan, Natalya Kraeva, Kristína Záhonová, Anzhelika Butenko, Alexei Yu Kostygov, Zdeněk Paris, Jiří Pergner, Claretta Bianchi, Fadel Fakih, Andreu Saura, Julius Lukeš, Vyacheslav Yurchenko
Blastocrithidia nonstop is a protist with a highly unusual nuclear genetic code, in which all three standard stop codons are reassigned to encode amino acids, with UAA also serving as a sole termination codon. In this study, we demonstrate that this parasitic flagellate is amenable to genetic manipulation, enabling gene ablation and protein tagging. Using preassembled Cas9 ribonucleoprotein complexes, we successfully disrupted and tagged the non-essential gene encoding catalase. These advances establish this single-celled eukaryote as a model organism for investigating the malleability and evolution of the genetic code in eukaryotes.
{"title":"Converting Blastocrithidia Nonstop, a Trypanosomatid With Non-Canonical Genetic Code, Into a Genetically-Tractable Model","authors":"Arnau Galan, Natalya Kraeva, Kristína Záhonová, Anzhelika Butenko, Alexei Yu Kostygov, Zdeněk Paris, Jiří Pergner, Claretta Bianchi, Fadel Fakih, Andreu Saura, Julius Lukeš, Vyacheslav Yurchenko","doi":"10.1111/mmi.15365","DOIUrl":"https://doi.org/10.1111/mmi.15365","url":null,"abstract":"<i>Blastocrithidia nonstop</i> is a protist with a highly unusual nuclear genetic code, in which all three standard stop codons are reassigned to encode amino acids, with UAA also serving as a sole termination codon. In this study, we demonstrate that this parasitic flagellate is amenable to genetic manipulation, enabling gene ablation and protein tagging. Using preassembled Cas9 ribonucleoprotein complexes, we successfully disrupted and tagged the non-essential gene encoding catalase. These advances establish this single-celled eukaryote as a model organism for investigating the malleability and evolution of the genetic code in eukaryotes.","PeriodicalId":19006,"journal":{"name":"Molecular Microbiology","volume":"3 1","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143813997","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}
Momoko Ito, Hideharu Yukitake, Paul D. Veith, Dhana G. Gorasia, Takashi Tominaga, Yuko Sasaki, Eric C. Reynolds, Koji Nakayama, Mariko Naito, Mikio Shoji
Porphyromonas gingivalis is an important bacterium associated with chronic periodontitis. The type IX secretion system (T9SS) in P. gingivalis secretes conserved C-terminal domain (CTD) containing proteins, which are also called T9SS cargo proteins, including gingipain proteinases, to the cell surface and extracellular milieu. We have shown that gene expression of some T9SS component proteins is regulated by a two-component regulatory system, PorX-PorY, an ECF sigma factor, SigP, and a T9SS cargo protein, PorA. As PorA has its own CTD, PorA is mainly localized as an A-LPS-bound form and PorV-bound form on the cell surface. However, it remains unclear how PorA can activate the PorXY-SigP signaling cascade. In this study, our results revealed that the CTD of PorA can activate the PorXY-SigP signaling cascade via interaction with PorY. It is well known that the canonical role of CTD is to act as a secretion signal for T9SS protein export. In here, we propose a novel concept that the CTD of PorA can play a dual role: as a secretion signal directing the secretion of PorA and as a positive regulator of T9SS gene expression by binding to PorY in the periplasm.
牙龈卟啉单胞菌是一种与慢性牙周炎相关的重要细菌。牙龈卟啉单胞菌的九型分泌系统（T9SS）向细胞表面和细胞外环境分泌含有保守的 C-末端结构域（CTD）的蛋白，这些蛋白也被称为 T9SS 货物蛋白，包括牙龈蛋白酶。我们的研究表明，一些 T9SS 组成蛋白的基因表达受双组分调控系统 PorX-PorY、ECF 西格玛因子 SigP 和 T9SS 货物蛋白 PorA 的调控。由于 PorA 有自己的 CTD，因此 PorA 主要以 A-LPS 结合型和 PorV 结合型的形式定位于细胞表面。然而，目前仍不清楚 PorA 如何激活 PorXY-SigP 信号级联。本研究的结果显示，PorA 的 CTD 可通过与 PorY 的相互作用激活 PorXY-SigP 信号级联。众所周知，CTD 的典型作用是作为 T9SS 蛋白质输出的分泌信号。在本文中，我们提出了一个新的概念，即 PorA 的 CTD 可以发挥双重作用：作为分泌信号指导 PorA 的分泌，以及通过与外质中的 PorY 结合成为 T9SS 基因表达的正向调节因子。
{"title":"PorA of the Type IX Secretion Is a Ligand of the PorXY Two-Component Regulatory System in Porphyromonas gingivalis","authors":"Momoko Ito, Hideharu Yukitake, Paul D. Veith, Dhana G. Gorasia, Takashi Tominaga, Yuko Sasaki, Eric C. Reynolds, Koji Nakayama, Mariko Naito, Mikio Shoji","doi":"10.1111/mmi.15363","DOIUrl":"https://doi.org/10.1111/mmi.15363","url":null,"abstract":"<i>Porphyromonas gingivalis</i> is an important bacterium associated with chronic periodontitis. The type IX secretion system (T9SS) in <i>P. gingivalis</i> secretes conserved C-terminal domain (CTD) containing proteins, which are also called T9SS cargo proteins, including gingipain proteinases, to the cell surface and extracellular milieu. We have shown that gene expression of some T9SS component proteins is regulated by a two-component regulatory system, PorX-PorY, an ECF sigma factor, SigP, and a T9SS cargo protein, PorA. As PorA has its own CTD, PorA is mainly localized as an A-LPS-bound form and PorV-bound form on the cell surface. However, it remains unclear how PorA can activate the PorXY-SigP signaling cascade. In this study, our results revealed that the CTD of PorA can activate the PorXY-SigP signaling cascade via interaction with PorY. It is well known that the canonical role of CTD is to act as a secretion signal for T9SS protein export. In here, we propose a novel concept that the CTD of PorA can play a dual role: as a secretion signal directing the secretion of PorA and as a positive regulator of T9SS gene expression by binding to PorY in the periplasm.","PeriodicalId":19006,"journal":{"name":"Molecular Microbiology","volume":"1 1","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143797989","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}
Yeast flocculation relies on cell surface flocculin proteins encoded by the sub-telomeric gene, FLO1. The expression of FLO1 is antagonistically regulated by the Tup1-Cyc8 repressor complex and the Swi-Snf co-activator complexes. The role of hyperacetylated N-terminal amino acid residues of histone H3 and H4 is well established in the transcription of FLO1 and other Tup1-Cyc8 regulated genes. However, sub-domains within the tails of histone H3 and H4 are yet to be identified and the mechanism by which they regulate the FLO1 transcription is completely unexplored. Upon screening of different H3 and H4 N-terminal stretch deletion mutants, we have identified a new region within the N-terminal tail of histone H3, H3Δ(17–24) regulating the transcription of FLO1 and FLO5. This N-terminal truncation mutant showed higher FLO1 and FLO5 expression by 68% and 41% respectively compared to wild-type H3. Further examination showed reduced Cyc8 and nucleosome occupancy in the upstream regulatory region of active flo1 in the H3Δ(17–24) mutant than in H3 wild-type cells. The findings also indicate that Hda1 assists in Cyc8 interaction at the active FLO1 template. Altogether we demonstrate that Tup1-independent interaction of Cyc8 with the active FLO1 gene acts as a transcription limiting factor and that the histone H3 N-terminal 17–24 stretch is essential for this interaction. In the absence of the 17–24 stretch, the Cyc8 restrictive effect is altered, resulting in over-expression of FLO1.
{"title":"An Uncharacterized Domain Within the N-Terminal Tail of Histone H3 Regulates the Transcription of FLO1 via Cyc8","authors":"Ranu Singh, Raghuvir Singh Tomar","doi":"10.1111/mmi.15362","DOIUrl":"https://doi.org/10.1111/mmi.15362","url":null,"abstract":"Yeast flocculation relies on cell surface flocculin proteins encoded by the sub-telomeric gene, <i>FLO1</i>. The expression of <i>FLO1</i> is antagonistically regulated by the Tup1-Cyc8 repressor complex and the Swi-Snf co-activator complexes. The role of hyperacetylated N-terminal amino acid residues of histone H3 and H4 is well established in the transcription of <i>FLO1</i> and other Tup1-Cyc8 regulated genes. However, sub-domains within the tails of histone H3 and H4 are yet to be identified and the mechanism by which they regulate the <i>FLO1</i> transcription is completely unexplored. Upon screening of different H3 and H4 N-terminal stretch deletion mutants, we have identified a new region within the N-terminal tail of histone H3, H3Δ(17–24) regulating the transcription of <i>FLO1</i> and <i>FLO5</i>. This N-terminal truncation mutant showed higher <i>FLO1</i> and <i>FLO5</i> expression by 68% and 41% respectively compared to wild-type H3. Further examination showed reduced Cyc8 and nucleosome occupancy in the upstream regulatory region of active <i>flo1</i> in the H3Δ(17–24) mutant than in H3 wild-type cells. The findings also indicate that Hda1 assists in Cyc8 interaction at the active <i>FLO1</i> template. Altogether we demonstrate that Tup1-independent interaction of Cyc8 with the active <i>FLO1</i> gene acts as a transcription limiting factor and that the histone H3 N-terminal 17–24 stretch is essential for this interaction. In the absence of the 17–24 stretch, the Cyc8 restrictive effect is altered, resulting in over-expression of <i>FLO1</i>.","PeriodicalId":19006,"journal":{"name":"Molecular Microbiology","volume":"4 1","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143798390","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}
Sara Moutacharrif, Feth El Zahar Haichar, Sam Meyer, Cecile Ribot, Sylvie Reverchon, William Nasser, Florence Hommais
In bacteria, the regulation of gene expression involves complex networks that integrate both transcriptional and posttranscriptional mechanisms. At the transcriptional level, nucleoid-associated proteins (NAPs) such as H-NS, HU, Lrp, IHF, Fis and Hfq are key players as they not only compact bacterial DNA but also regulate transcription. Small noncoding RNAs (sRNAs), on the other hand, are known to affect bacterial gene expression posttranscriptionally by base pairing with the target mRNA, but they can also be involved in nucleoid condensation. Interestingly, certain NAPs also influence the function of sRNAs and, conversely, sRNAs themselves can modulate the activity of NAPs, creating a complex bidirectional regulatory network. Here, we summarise the current knowledge of the major NAPs, focusing on the specific role of Hfq. Examples of the regulation of NAPs by sRNAs, the regulation of sRNAs by NAPs and the role of sRNAs in nucleoid structuring are also discussed. This review focuses on the cross-talk between NAPs and sRNAs in an attempt to understand how this interplay works to orchestrate the functioning of the cell.
{"title":"The Power Duo: How the Interplay Between Nucleoid-Associated Proteins and Small Noncoding RNAs Orchestrates the Cellular Regulatory Symphony","authors":"Sara Moutacharrif, Feth El Zahar Haichar, Sam Meyer, Cecile Ribot, Sylvie Reverchon, William Nasser, Florence Hommais","doi":"10.1111/mmi.15359","DOIUrl":"https://doi.org/10.1111/mmi.15359","url":null,"abstract":"In bacteria, the regulation of gene expression involves complex networks that integrate both transcriptional and posttranscriptional mechanisms. At the transcriptional level, nucleoid-associated proteins (NAPs) such as H-NS, HU, Lrp, IHF, Fis and Hfq are key players as they not only compact bacterial DNA but also regulate transcription. Small noncoding RNAs (sRNAs), on the other hand, are known to affect bacterial gene expression posttranscriptionally by base pairing with the target mRNA, but they can also be involved in nucleoid condensation. Interestingly, certain NAPs also influence the function of sRNAs and, conversely, sRNAs themselves can modulate the activity of NAPs, creating a complex bidirectional regulatory network. Here, we summarise the current knowledge of the major NAPs, focusing on the specific role of Hfq. Examples of the regulation of NAPs by sRNAs, the regulation of sRNAs by NAPs and the role of sRNAs in nucleoid structuring are also discussed. This review focuses on the cross-talk between NAPs and sRNAs in an attempt to understand how this interplay works to orchestrate the functioning of the cell.","PeriodicalId":19006,"journal":{"name":"Molecular Microbiology","volume":"20 1","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143784728","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}
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