1
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Li M, Xiong L, Chen W, Li Y, Khan A, Powell CA, Chen B, Zhang M. VirB11, a traffic ATPase, mediated flagella assembly and type IV pilus morphogenesis to control the motility and virulence of Xanthomonas albilineans. MOLECULAR PLANT PATHOLOGY 2024; 25:e70001. [PMID: 39223938 PMCID: PMC11369208 DOI: 10.1111/mpp.70001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Revised: 07/29/2024] [Accepted: 08/13/2024] [Indexed: 09/04/2024]
Abstract
Xanthomonas albilineans (Xal) is a gram-negative bacterial pathogen responsible for developing sugarcane leaf scald disease, which engenders significant economic losses within the sugarcane industry. In the current study, homologous recombination exchange was carried out to induce mutations within the virB/D4-like type IV secretion system (T4SS) genes of Xal. The results revealed that the virB11-deletion mutant (ΔvirB11) exhibited a loss in swimming and twitching motility. Application of transmission electron microscopy analysis further demonstrated that the ΔvirB11 failed to develop flagella formation and type IV pilus morphology and exhibited reduced swarming behaviour and virulence. However, these alterations had no discernible impact on bacterial growth. Comparative transcriptome analysis between the wild-type Xal JG43 and the deletion-mutant ΔvirB11 revealed 123 differentially expressed genes (DEGs), of which 28 and 10 DEGs were notably associated with flagellar assembly and chemotaxis, respectively. In light of these findings, we postulate that virB11 plays an indispensable role in regulating the processes related to motility and chemotaxis in Xal.
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Affiliation(s)
- Meilin Li
- Guangxi Key Laboratory for Sugarcane Biology & State Key Laboratory of Conservation and Utilization for Subtropical Agri‐Biological ResourcesGuangxi UniversityNanningGuangxiChina
| | - Liya Xiong
- Guangxi Key Laboratory for Sugarcane Biology & State Key Laboratory of Conservation and Utilization for Subtropical Agri‐Biological ResourcesGuangxi UniversityNanningGuangxiChina
| | - Wenhan Chen
- Guangxi Key Laboratory for Sugarcane Biology & State Key Laboratory of Conservation and Utilization for Subtropical Agri‐Biological ResourcesGuangxi UniversityNanningGuangxiChina
| | - YiSha Li
- Guangxi Key Laboratory for Sugarcane Biology & State Key Laboratory of Conservation and Utilization for Subtropical Agri‐Biological ResourcesGuangxi UniversityNanningGuangxiChina
| | - Abdullah Khan
- Guangxi Key Laboratory for Sugarcane Biology & State Key Laboratory of Conservation and Utilization for Subtropical Agri‐Biological ResourcesGuangxi UniversityNanningGuangxiChina
| | | | - Baoshan Chen
- Guangxi Key Laboratory for Sugarcane Biology & State Key Laboratory of Conservation and Utilization for Subtropical Agri‐Biological ResourcesGuangxi UniversityNanningGuangxiChina
| | - Muqing Zhang
- Guangxi Key Laboratory for Sugarcane Biology & State Key Laboratory of Conservation and Utilization for Subtropical Agri‐Biological ResourcesGuangxi UniversityNanningGuangxiChina
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2
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Jamal GA, Jahangirian E, Hamblin MR, Mirzaei H, Tarrahimofrad H, Alikowsarzadeh N. Proteases, a powerful biochemical tool in the service of medicine, clinical and pharmaceutical. Prep Biochem Biotechnol 2024:1-25. [PMID: 38909284 DOI: 10.1080/10826068.2024.2364234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/24/2024]
Abstract
Proteases, enzymes that hydrolyze peptide bonds, have various applications in medicine, clinical applications, and pharmaceutical development. They are used in cancer treatment, wound debridement, contact lens cleaning, prion degradation, biofilm removal, and fibrinolytic agents. Proteases are also crucial in cardiovascular disease treatment, emphasizing the need for safe, affordable, and effective fibrinolytic drugs. Proteolytic enzymes and protease biosensors are increasingly used in diagnostic and therapeutic applications. Advanced technologies, such as nanomaterials-based sensors, are being developed to enhance the sensitivity, specificity, and versatility of protease biosensors. These biosensors are becoming effective tools for disease detection due to their precision and rapidity. They can detect extracellular and intracellular proteases, as well as fluorescence-based methods for real-time and label-free detection of virus-related proteases. The active utilization of proteolytic enzymatic biosensors is expected to expand significantly in biomedical research, in-vitro model systems, and drug development. We focused on journal articles and books published in English between 1982 and 2024 for this study.
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Affiliation(s)
- Ghadir A Jamal
- Faculty of Allied Health Sciences, Kuwait University, Kuwait City, Kuwait
| | - Ehsan Jahangirian
- Department of Molecular, Zist Tashkhis Farda Company (tBioDx), Tehran, Iran
| | - Michael R Hamblin
- Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Faculty of Health Science, Laser Research Center, University of Johannesburg, Doornfontein, South Africa
| | - Hamed Mirzaei
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
| | | | - Neda Alikowsarzadeh
- Molecular and Life Science Department, Han University of Applied Science, Arnhem, Nederland
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3
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Little JI, Singh PK, Zhao J, Dunn S, Matz H, Donnenberg MS. Type IV pili of Enterobacteriaceae species. EcoSal Plus 2024:eesp00032023. [PMID: 38294234 DOI: 10.1128/ecosalplus.esp-0003-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 12/01/2023] [Indexed: 02/01/2024]
Abstract
Type IV pili (T4Ps) are surface filaments widely distributed among bacteria and archaea. T4Ps are involved in many cellular functions and contribute to virulence in some species of bacteria. Due to the diversity of T4Ps, different properties have been observed for homologous proteins that make up T4Ps in various organisms. In this review, we highlight the essential components of T4Ps, their functions, and similarities to related systems. We emphasize the unique T4Ps of enteric pathogens within the Enterobacteriaceae family, which includes pathogenic strains of Escherichia coli and Salmonella. These include the bundle-forming pilus (BFP) of enteropathogenic E. coli (EPEC), longus (Lng) and colonization factor III (CFA/III) of enterotoxigenic E. coli (ETEC), T4P of Salmonella enterica serovar Typhi, Colonization Factor Citrobacter (CFC) of Citrobacter rodentium, T4P of Yersinia pseudotuberculosis, a ubiquitous T4P that was characterized in enterohemorrhagic E. coli (EHEC), and the R64 plasmid thin pilus. Finally, we highlight areas for further study.
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Affiliation(s)
- Janay I Little
- School of Medicine, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Pradip K Singh
- School of Medicine, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Jinlei Zhao
- School of Medicine, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Shakeera Dunn
- Internal Medicine Residency, Bayhealth Medical Center, Dover, Delaware, USA
| | - Hanover Matz
- Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
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4
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Mom J, Chouikha I, Valette O, Pieulle L, Pelicic V. Systematic functional analysis of the Com pilus in Streptococcus sanguinis: a minimalistic type 4 filament dedicated to DNA uptake in monoderm bacteria. mBio 2024; 15:e0266723. [PMID: 38095871 PMCID: PMC10790768 DOI: 10.1128/mbio.02667-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 11/07/2023] [Indexed: 01/17/2024] Open
Abstract
IMPORTANCE Type 4 filaments (T4F) are nanomachines ubiquitous in prokaryotes, centered on filamentous polymers of type 4 pilins. T4F are exceptionally versatile and widespread virulence factors in bacterial pathogens. The mechanisms of filament assembly and the many functions they facilitate remain poorly understood because of the complexity of T4F machineries. This hinders the development of anti-T4F drugs. The significance of our research lies in characterizing the simplest known T4F-the Com pilus that mediates DNA uptake in competent monoderm bacteria-and showing that four protein components universally conserved in T4F are sufficient for filament assembly. The Com pilus becomes a model for elucidating the mechanisms of T4F assembly.
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Affiliation(s)
- Jeremy Mom
- Laboratoire de Chimie Bactérienne, Aix-Marseille Université-CNRS (UMR 7283), Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Iman Chouikha
- Laboratoire de Chimie Bactérienne, Aix-Marseille Université-CNRS (UMR 7283), Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Odile Valette
- Laboratoire de Chimie Bactérienne, Aix-Marseille Université-CNRS (UMR 7283), Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Laetitia Pieulle
- Laboratoire de Chimie Bactérienne, Aix-Marseille Université-CNRS (UMR 7283), Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Vladimir Pelicic
- Laboratoire de Chimie Bactérienne, Aix-Marseille Université-CNRS (UMR 7283), Institut de Microbiologie de la Méditerranée, Marseille, France
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5
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Cheng M, Chen R, Liao L. T2SS-peptidase XcpA associated with LasR evolutional phenotypic variations provides a fitness advantage to Pseudomonas aeruginosa PAO1. Front Microbiol 2023; 14:1256785. [PMID: 37954251 PMCID: PMC10637944 DOI: 10.3389/fmicb.2023.1256785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 10/06/2023] [Indexed: 11/14/2023] Open
Abstract
The Gram-negative opportunistic pathogen Pseudomonas aeruginosa possesses hierarchical quorum sensing (QS) systems. The intricate QS network of P. aeruginosa synchronizes a suite of virulence factors, contributing to the mortality and morbidity linked to the pathogenicity of this bacterium. Previous studies have revealed that variations in the lasR gene are frequently observed in chronic isolates of cystic fibrosis (CF). Specifically, LasRQ45stop was identified as a common variant among CF, lasR mutants during statistical analysis of the clinical lasR mutants in the database. In this study, we introduced LasRQ45stop into the chromosome of P. aeruginosa PAO1 through allelic replacement. The social traits of PAO1 LasRQ45stop were found to be equivalent to those of PAO1 LasR-null isolates. By co-evolving with the wild-type in caseinate broth, elastase-phenotypic-variability variants were derived from the LasRQ45stop subpopulation. Upon further examination of four LasRQ45stop sublines, we determined that the variation of T2SS-peptidase xcpA and mexT genes plays a pivotal role in the divergence of various phenotypes, including public goods elastase secretion and other pathogenicity traits. Furthermore, XcpA mutants demonstrated a fitness advantage compared to parent strains during co-evolution. Numerous phenotypic variations were associated with subline-specific genetic alterations. Collectively, these findings suggest that even within the same parental subline, there is ongoing microevolution of individual mutational trajectory diversity during adaptation.
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Affiliation(s)
- Mengmeng Cheng
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Ruiyi Chen
- Department of Microbiology, University of Washington, Seattle, WA, United States
| | - Lisheng Liao
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
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6
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Pelicic V. Mechanism of assembly of type 4 filaments: everything you always wanted to know (but were afraid to ask). MICROBIOLOGY (READING, ENGLAND) 2023; 169. [PMID: 36947586 DOI: 10.1099/mic.0.001311] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
Type 4 filaments (T4F) are a superfamily of filamentous nanomachines - virtually ubiquitous in prokaryotes and functionally versatile - of which type 4 pili (T4P) are the defining member. T4F are polymers of type 4 pilins, assembled by conserved multi-protein machineries. They have long been an important topic for research because they are key virulence factors in numerous bacterial pathogens. Our poor understanding of the molecular mechanisms of T4F assembly is a serious hindrance to the design of anti-T4F therapeutics. This review attempts to shed light on the fundamental mechanistic principles at play in T4F assembly by focusing on similarities rather than differences between several (mostly bacterial) T4F. This holistic approach, complemented by the revolutionary ability of artificial intelligence to predict protein structures, led to an intriguing mechanistic model of T4F assembly.
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Affiliation(s)
- Vladimir Pelicic
- Laboratoire de Chimie Bactérienne, UMR 7283 CNRS/Aix-Marseille Université, Institut de Microbiologie de la Méditerranée, Marseille, France
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7
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Abstract
Type IV pili (T4P) are retractable multifunctional nanofibers present on the surface of numerous bacterial and archaeal species. Their importance to microbiology is difficult to overstate. The scientific journey leading to our current understanding of T4P structure and function has included many innovative research milestones. Although multiple T4P reviews over the years have emphasized recent advances, we find that current reports often omit many of the landmark discoveries in this field. Here, we attempt to highlight chronologically the most important work on T4P, from the discovery of pili to the application of sophisticated contemporary methods, which has brought us to our current state of knowledge. As there remains much to learn about the complex machine that assembles and retracts T4P, we hope that this review will increase the interest of current researchers and inspire innovative progress.
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8
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Linhartová M, Skotnicová P, Hakkila K, Tichý M, Komenda J, Knoppová J, Gilabert JF, Guallar V, Tyystjärvi T, Sobotka R. Mutations Suppressing the Lack of Prepilin Peptidase Provide Insights Into the Maturation of the Major Pilin Protein in Cyanobacteria. Front Microbiol 2021; 12:756912. [PMID: 34712217 PMCID: PMC8546353 DOI: 10.3389/fmicb.2021.756912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 09/14/2021] [Indexed: 11/24/2022] Open
Abstract
Type IV pili are bacterial surface-exposed filaments that are built up by small monomers called pilin proteins. Pilins are synthesized as longer precursors (prepilins), the N-terminal signal peptide of which must be removed by the processing protease PilD. A mutant of the cyanobacterium Synechocystis sp. PCC 6803 lacking the PilD protease is not capable of photoautotrophic growth because of the impaired function of Sec translocons. Here, we isolated phototrophic suppressor strains of the original ΔpilD mutant and, by sequencing their genomes, identified secondary mutations in the SigF sigma factor, the γ subunit of RNA polymerase, the signal peptide of major pilin PilA1, and in the pilA1-pilA2 intergenic region. Characterization of suppressor strains suggests that, rather than the total prepilin level in the cell, the presence of non-glycosylated PilA1 prepilin is specifically harmful. We propose that the restricted lateral mobility of the non-glycosylated PilA1 prepilin causes its accumulation in the translocon-rich membrane domains, which attenuates the synthesis of membrane proteins.
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Affiliation(s)
- Markéta Linhartová
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia.,Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Petra Skotnicová
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | - Kaisa Hakkila
- Biotechnology/Molecular Plant Biology, University of Turku, Turku, Finland
| | - Martin Tichý
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | - Josef Komenda
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | - Jana Knoppová
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | | | - Victor Guallar
- Barcelona Supercomputing Center, Barcelona, Spain.,ICREA: Institucio Catalana de Recerca i Estudis Avançats Passeig Lluis Companys, Barcelona, Spain
| | - Taina Tyystjärvi
- Biotechnology/Molecular Plant Biology, University of Turku, Turku, Finland
| | - Roman Sobotka
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
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9
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Activity of CcpA-Regulated GH18 Family Glycosyl Hydrolases That Contributes to Nutrient Acquisition and Fitness in Enterococcus faecalis. Infect Immun 2021; 89:e0034321. [PMID: 34424752 DOI: 10.1128/iai.00343-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The ability of Enterococcus faecalis to colonize host anatomical sites is dependent on its adaptive response to host conditions. Three glycosyl hydrolase gene clusters, each belonging to glycosyl hydrolase family 18 (GH18) (ef0114, ef0361, and ef2863), in E. faecalis were previously found to be upregulated under glucose-limiting conditions. The GH18 catalytic domain is present in proteins that are classified as either chitinases or β-1,4 endo-β-N-acetylglucosaminidases (ENGases) based on their β-1,4 endo-N-acetyl-β-d-glucosaminidase activity, and ENGase activity is commonly associated with cleaving N-linked glycoprotein, an abundant glycan structure on host epithelial surfaces. Here, we show that all three hydrolases are negatively regulated by the transcriptional regulator carbon catabolite protein A (CcpA). Additionally, we demonstrate that a constitutively active CcpA variant represses the expression of CcpA-regulated genes irrespective of glucose availability. Previous studies showed that the GH18 catalytic domains of EndoE (EF0114) and EfEndo18A (EF2863) were capable of deglycosylating RNase B, a model high-mannose-type glycoprotein. However, it remained uncertain which glycosidase is primarily responsible for the deglycosylation of high-mannose-type glycoproteins. In this study, we show by mutation analysis as well as a dose-dependent analysis of recombinant protein expression that EfEndo18A is primarily responsible for deglycosylating high-mannose glycoproteins and that the glycans removed by EfEndo18A support growth under nutrient-limiting conditions in vitro. In contrast, IgG is representative of a complex-type glycoprotein, and we demonstrate that the GH18 domain of EndoE is primarily responsible for the removal of this glycan decoration. Finally, our data highlight the combined contribution of glycosidases to the virulence of E. faecalis in vivo.
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10
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Potteth US, Upadhyay T, Saini S, Saraogi I. Novel Antibacterial Targets in Protein Biogenesis Pathways. Chembiochem 2021; 23:e202100459. [PMID: 34643994 DOI: 10.1002/cbic.202100459] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/12/2021] [Indexed: 11/11/2022]
Abstract
Antibiotic resistance has emerged as a global threat due to the ability of bacteria to quickly evolve in response to the selection pressure induced by anti-infective drugs. Thus, there is an urgent need to develop new antibiotics against resistant bacteria. In this review, we discuss pathways involving bacterial protein biogenesis as attractive antibacterial targets since many of them are essential for bacterial survival and virulence. We discuss the structural understanding of various components associated with bacterial protein biogenesis, which in turn can be utilized for rational antibiotic design. We highlight efforts made towards developing inhibitors of these pathways with insights into future possibilities and challenges. We also briefly discuss other potential targets related to protein biogenesis.
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Affiliation(s)
- Upasana S Potteth
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhauri, Bhopal Bypass Road, Bhopal, 462066, Madhya Pradesh, India
| | - Tulsi Upadhyay
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhauri, Bhopal Bypass Road, Bhopal, 462066, Madhya Pradesh, India
| | - Snehlata Saini
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhauri, Bhopal Bypass Road, Bhopal, 462066, Madhya Pradesh, India
| | - Ishu Saraogi
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhauri, Bhopal Bypass Road, Bhopal, 462066, Madhya Pradesh, India.,Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhauri, Bhopal Bypass Road, Bhopal - 462066, Madhya Pradesh, India
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11
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Artificial sweeteners stimulate horizontal transfer of extracellular antibiotic resistance genes through natural transformation. ISME JOURNAL 2021; 16:543-554. [PMID: 34465899 PMCID: PMC8776823 DOI: 10.1038/s41396-021-01095-6] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 08/11/2021] [Accepted: 08/13/2021] [Indexed: 12/22/2022]
Abstract
Antimicrobial resistance has emerged as a global threat to human health. Natural transformation is an important pathway for horizontal gene transfer, which facilitates the dissemination of antibiotic resistance genes (ARGs) among bacteria. Although it is suspected that artificial sweeteners could exert antimicrobial effects, little is known whether artificial sweeteners would also affect horizontal transfer of ARGs via transformation. Here we demonstrate that four commonly used artificial sweeteners (saccharin, sucralose, aspartame, and acesulfame potassium) promote transfer of ARGs via natural transformation in Acinetobacter baylyi ADP1, a model organism for studying competence and transformation. Such phenomenon was also found in a Gram-positive human pathogen Bacillus subtilis and mice faecal microbiome. We reveal that exposure to these sweeteners increases cell envelope permeability and results in an upregulation of genes encoding DNA uptake and translocation (Com) machinery. In addition, we find that artificial sweeteners induce an increase in plasmid persistence in transformants. We propose a mathematical model established to predict the long-term effects on transformation dynamics under exposure to these sweeteners. Collectively, our findings offer insights into natural transformation promoted by artificial sweeteners and highlight the need to evaluate these environmental contaminants for their antibiotic-like side effects.
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12
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PilB from Streptococcus sanguinis is a bimodular type IV pilin with a direct role in adhesion. Proc Natl Acad Sci U S A 2021; 118:2102092118. [PMID: 34031252 PMCID: PMC8179133 DOI: 10.1073/pnas.2102092118] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Type IV pili (T4P) are functionally versatile filaments widespread in prokaryotes, composed of type IV pilins and assembled by conserved multiprotein machineries. It remains unclear how such rather simple filaments can be so versatile. Our structure/function analysis of PilB, a minor pilin of Streptococcus sanguinis T4P, offers an elegant explanation for this paradox. We show that PilB is a modular pilin with a bulky module “grafted” onto a small pilin module, which directly mediates adhesion of S. sanguinis to host cells/proteins. This evolutionary tinkering strategy appears to be prevalent in bacteria since a global analysis reveals that modular pilins are widespread and exhibit an astonishing variety of architectures. Type IV pili (T4P) are functionally versatile filamentous nanomachines, nearly ubiquitous in prokaryotes. They are predominantly polymers of one major pilin but also contain minor pilins whose functions are often poorly defined and likely to be diverse. Here, we show that the minor pilin PilB from the T4P of Streptococcus sanguinis displays an unusual bimodular three-dimensional structure with a bulky von Willebrand factor A–like (vWA) module “grafted” onto a small pilin module via a short loop. Structural modeling suggests that PilB is only compatible with a localization at the tip of T4P. By performing a detailed functional analysis, we found that 1) the vWA module contains a canonical metal ion–dependent adhesion site, preferentially binding Mg2+ and Mn2+, 2) abolishing metal binding has no impact on the structure of PilB or piliation, 3) metal binding is important for S. sanguinis T4P–mediated twitching motility and adhesion to eukaryotic cells, and 4) the vWA module shows an intrinsic binding ability to several host proteins. These findings reveal an elegant yet simple evolutionary tinkering strategy to increase T4P functional versatility by grafting a functional module onto a pilin for presentation by the filaments. This strategy appears to have been extensively used by bacteria, in which modular pilins are widespread and exhibit an astonishing variety of architectures.
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13
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Rozman V, Accetto T, Duncan SH, Flint HJ, Vodovnik M. Type IV pili are widespread among non-pathogenic Gram-positive gut bacteria with diverse carbohydrate utilization patterns. Environ Microbiol 2021; 23:1527-1540. [PMID: 33331146 DOI: 10.1111/1462-2920.15362] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 12/15/2020] [Indexed: 12/23/2022]
Abstract
Type IV pili (T4P) are bacterial surface-exposed appendages that have been extensively studied in Gram-negative pathogenic bacteria. Despite recent sequencing efforts, little is known regarding these structures in non-pathogenic anaerobic Gram-positive species, particularly commensals of the mammalian gut. Early studies revealed that T4P in two ruminal Gram-positive species are associated with growth on cellulose, suggesting possible associations of T4P with substrate utilization patterns. In the present study, genome sequences of 118 taxonomically diverse, mainly Gram-positive, bacterial strains isolated from anaerobic (gastrointestinal) environments, have been analysed. The genes likely to be associated with T4P biogenesis were analysed and grouped according to T4P genetic organization. In parallel, consortia of Carbohydrate Active enZYmes (CAZymes) were also analysed and used to predict carbohydrate utilization abilities of selected strains. The predictive power of this approach was additionally confirmed by experimental assessment of substrate-related growth patterns of selected strains. Our analysis revealed that T4P systems with diverse genetic organization are widespread among Gram-positive anaerobic non-pathogenic bacteria isolated from different environments, belonging to two phylogenetically distantly related phyla: Firmicutes and Actinobacteria.
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Affiliation(s)
- Vita Rozman
- Chair of Microbiology and Microbial Biotechnology, Biotechnical Faculty, University of Ljubljana, Domžale, Slovenia
| | - Tomaž Accetto
- Chair of Microbiology and Microbial Biotechnology, Biotechnical Faculty, University of Ljubljana, Domžale, Slovenia
| | - Sylvia H Duncan
- Gut Health Group, Rowett Institute, University of Aberdeen, Aberdeen, UK
| | - Harry J Flint
- Gut Health Group, Rowett Institute, University of Aberdeen, Aberdeen, UK
| | - Maša Vodovnik
- Chair of Microbiology and Microbial Biotechnology, Biotechnical Faculty, University of Ljubljana, Domžale, Slovenia
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14
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Spitz C, Schlosser C, Guschtschin-Schmidt N, Stelzer W, Menig S, Götz A, Haug-Kröper M, Scharnagl C, Langosch D, Muhle-Goll C, Fluhrer R. Non-canonical Shedding of TNFα by SPPL2a Is Determined by the Conformational Flexibility of Its Transmembrane Helix. iScience 2020; 23:101775. [PMID: 33294784 PMCID: PMC7689174 DOI: 10.1016/j.isci.2020.101775] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 10/21/2020] [Accepted: 11/03/2020] [Indexed: 12/22/2022] Open
Abstract
Ectodomain (EC) shedding defines the proteolytic removal of a membrane protein EC and acts as an important molecular switch in signaling and other cellular processes. Using tumor necrosis factor (TNF)α as a model substrate, we identify a non-canonical shedding activity of SPPL2a, an intramembrane cleaving aspartyl protease of the GxGD type. Proline insertions in the TNFα transmembrane (TM) helix strongly increased SPPL2a non-canonical shedding, while leucine mutations decreased this cleavage. Using biophysical and structural analysis, as well as molecular dynamic simulations, we identified a flexible region in the center of the TNFα wildtype TM domain, which plays an important role in the processing of TNFα by SPPL2a. This study combines molecular biology, biochemistry, and biophysics to provide insights into the dynamic architecture of a substrate's TM helix and its impact on non-canonical shedding. Thus, these data will provide the basis to identify further physiological substrates of non-canonical shedding in the future.
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Affiliation(s)
- Charlotte Spitz
- Biochemistry and Molecular Biology, Institute of Theoretical Medicine, Medical Faculty, University of Augsburg, Universitätsstrasse 2, 86159 Augsburg, Germany
| | - Christine Schlosser
- Biochemistry and Molecular Biology, Institute of Theoretical Medicine, Medical Faculty, University of Augsburg, Universitätsstrasse 2, 86159 Augsburg, Germany
| | - Nadja Guschtschin-Schmidt
- Karlsruhe Institute of Technology, Institute for Biological Interfaces 4, 76344 Eggenstein- Leopoldshafen, Germany and Karlsruhe Institute of Technology, Institute of Organic Chemistry, 76131 Karlsruhe, Germany
| | - Walter Stelzer
- Lehrstuhl für Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany
| | - Simon Menig
- Physics of Synthetic Biological Systems, Technische Universität München, Maximus-von-Imhof Forum 4, 85340 Freising, Germany
| | - Alexander Götz
- Present Address: Leibniz Supercomputing Centre, Boltzmannstr. 1, 85748 Garching, Germany
| | - Martina Haug-Kröper
- Biochemistry and Molecular Biology, Institute of Theoretical Medicine, Medical Faculty, University of Augsburg, Universitätsstrasse 2, 86159 Augsburg, Germany
| | - Christina Scharnagl
- Physics of Synthetic Biological Systems, Technische Universität München, Maximus-von-Imhof Forum 4, 85340 Freising, Germany
| | - Dieter Langosch
- Lehrstuhl für Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany
| | - Claudia Muhle-Goll
- Karlsruhe Institute of Technology, Institute for Biological Interfaces 4, 76344 Eggenstein- Leopoldshafen, Germany and Karlsruhe Institute of Technology, Institute of Organic Chemistry, 76131 Karlsruhe, Germany
| | - Regina Fluhrer
- Biochemistry and Molecular Biology, Institute of Theoretical Medicine, Medical Faculty, University of Augsburg, Universitätsstrasse 2, 86159 Augsburg, Germany
- DZNE – German Center for Neurodegenerative Diseases, Feodor-Lynen-Str 17, 81377 Munich, Germany
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15
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Heywood A, Lamont IL. Cell envelope proteases and peptidases of Pseudomonas aeruginosa: multiple roles, multiple mechanisms. FEMS Microbiol Rev 2020; 44:857-873. [PMID: 32804218 DOI: 10.1093/femsre/fuaa036] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 08/05/2020] [Indexed: 12/15/2022] Open
Abstract
Pseudomonas aeruginosa is a Gram-negative bacterium that is commonly isolated from damp environments. It is also a major opportunistic pathogen, causing a wide range of problematic infections. The cell envelope of P. aeruginosa, comprising the cytoplasmic membrane, periplasmic space, peptidoglycan layer and outer membrane, is critical to the bacteria's ability to adapt and thrive in a wide range of environments. Over 40 proteases and peptidases are located in the P. aeruginosa cell envelope. These enzymes play many crucial roles. They are required for protein secretion out of the cytoplasm to the periplasm, outer membrane, cell surface or the environment; for protein quality control and removal of misfolded proteins; for controlling gene expression, allowing adaptation to environmental changes; for modification and remodelling of peptidoglycan; and for metabolism of small molecules. The key roles of cell envelope proteases in ensuring normal cell functioning have prompted the development of inhibitors targeting some of these enzymes as potential new anti-Pseudomonas therapies. In this review, we summarise the current state of knowledge across the breadth of P. aeruginosa cell envelope proteases and peptidases, with an emphasis on recent findings, and highlight likely future directions in their study.
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Affiliation(s)
- Astra Heywood
- Department of Biochemistry, University of Otago, Dunedin 9054, New Zealand
| | - Iain L Lamont
- Department of Biochemistry, University of Otago, Dunedin 9054, New Zealand
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16
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Sheppard D, Berry JL, Denise R, Rocha EPC, Matthews S, Pelicic V. The major subunit of widespread competence pili exhibits a novel and conserved type IV pilin fold. J Biol Chem 2020; 295:6594-6604. [PMID: 32273343 PMCID: PMC7212644 DOI: 10.1074/jbc.ra120.013316] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/07/2020] [Indexed: 12/12/2022] Open
Abstract
Type IV filaments (T4F), which are helical assemblies of type IV pilins, constitute a superfamily of filamentous nanomachines virtually ubiquitous in prokaryotes that mediate a wide variety of functions. The competence (Com) pilus is a widespread T4F, mediating DNA uptake (the first step in natural transformation) in bacteria with one membrane (monoderms), an important mechanism of horizontal gene transfer. Here, we report the results of genomic, phylogenetic, and structural analyses of ComGC, the major pilin subunit of Com pili. By performing a global comparative analysis, we show that Com pili genes are virtually ubiquitous in Bacilli, a major monoderm class of Firmicutes. This also revealed that ComGC displays extensive sequence conservation, defining a monophyletic group among type IV pilins. We further report ComGC solution structures from two naturally competent human pathogens, Streptococcus sanguinis (ComGCSS) and Streptococcus pneumoniae (ComGCSP), revealing that this pilin displays extensive structural conservation. Strikingly, ComGCSS and ComGCSP exhibit a novel type IV pilin fold that is purely helical. Results from homology modeling analyses suggest that the unusual structure of ComGC is compatible with helical filament assembly. Because ComGC displays such a widespread distribution, these results have implications for hundreds of monoderm species.
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Affiliation(s)
- Devon Sheppard
- Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom
| | - Jamie-Lee Berry
- Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom
| | - Rémi Denise
- Microbial Evolutionary Genomics, Institut Pasteur, CNRS UMR3525, Paris 75015, France
- Sorbonne Université, Collège doctoral, Paris 75005, France
| | - Eduardo P C Rocha
- Microbial Evolutionary Genomics, Institut Pasteur, CNRS UMR3525, Paris 75015, France
| | - Steve Matthews
- Centre for Structural Biology, Imperial College London, London SW7 2AZ, United Kingdom
| | - Vladimir Pelicic
- Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom
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17
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Effect of changes at the conserved + 3 position of mature archaellins on in vitro cleavage by the pre-archaellin peptidase FlaK of Methanococcus maripaludis. Arch Microbiol 2020; 202:1669-1675. [PMID: 32285165 DOI: 10.1007/s00203-020-01873-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 01/28/2020] [Accepted: 04/01/2020] [Indexed: 10/24/2022]
Abstract
Archaea swim using archaella that are domain-specific rotary type IV pilus-like appendages. The structural components of the archaellum filament are archaellins, initially made as preproteins with type IV pilin-like signal peptides which are removed by signal peptidases that are homologues of prepilin peptidases that remove signal peptides from type IV pilins. N-terminal sequences of archaellins, including the signal peptide cleavage site, are conserved and various positions have been previously shown to be critical for signal peptide removal. Archaellins have an absolute conservation of glycine at the + 3 position from the signal peptide cleavage site. To investigate its role in signal peptide cleavage, I used archaellin variants in which the + 3 glycine was mutated to all other possibilities in in vitro cleavage reactions. Cleavage was observed with ten different amino acids at the + 3 position, indicating that the observed glycine conservation is not required for this essential processing step.
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18
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González D, Álamos P, Rivero M, Orellana O, Norambuena J, Chávez R, Levicán G. Deciphering the Role of Multiple Thioredoxin Fold Proteins of Leptospirillum sp. in Oxidative Stress Tolerance. Int J Mol Sci 2020; 21:E1880. [PMID: 32164170 PMCID: PMC7084401 DOI: 10.3390/ijms21051880] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 03/04/2020] [Accepted: 03/05/2020] [Indexed: 12/22/2022] Open
Abstract
Thioredoxin fold proteins (TFPs) form a family of diverse proteins involved in thiol/disulfide exchange in cells from all domains of life. Leptospirillum spp. are bioleaching bacteria naturally exposed to extreme conditions like acidic pH and high concentrations of metals that can contribute to the generation of reactive oxygen species (ROS) and consequently the induction of thiol oxidative damage. Bioinformatic studies have predicted 13 genes that encode for TFP proteins in Leptospirillum spp. We analyzed the participation of individual tfp genes from Leptospirillum sp. CF-1 in the response to oxidative conditions. Genomic context analysis predicted the involvement of these genes in the general thiol-reducing system, cofactor biosynthesis, carbon fixation, cytochrome c biogenesis, signal transduction, and pilus and fimbria assembly. All tfp genes identified were transcriptionally active, although they responded differentially to ferric sulfate and diamide stress. Some of these genes confer oxidative protection to a thioredoxin-deficient Escherichia coli strain by restoring the wild-type phenotype under oxidative stress conditions. These findings contribute to our understanding of the diversity and complexity of thiol/disulfide systems, and of adaptations that emerge in acidophilic microorganisms that allow them to thrive in highly oxidative environments. These findings also give new insights into the physiology of these microorganisms during industrial bioleaching operations.
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Affiliation(s)
- Daniela González
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Avenida Libertador Bernardo O’Higgins 3363, Estación Central Santiago 917022, Chile; (D.G.); (P.Á.); (M.R.); (J.N.); (R.C.)
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago 8380453, Chile;
| | - Pamela Álamos
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Avenida Libertador Bernardo O’Higgins 3363, Estación Central Santiago 917022, Chile; (D.G.); (P.Á.); (M.R.); (J.N.); (R.C.)
| | - Matías Rivero
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Avenida Libertador Bernardo O’Higgins 3363, Estación Central Santiago 917022, Chile; (D.G.); (P.Á.); (M.R.); (J.N.); (R.C.)
| | - Omar Orellana
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago 8380453, Chile;
| | - Javiera Norambuena
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Avenida Libertador Bernardo O’Higgins 3363, Estación Central Santiago 917022, Chile; (D.G.); (P.Á.); (M.R.); (J.N.); (R.C.)
| | - Renato Chávez
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Avenida Libertador Bernardo O’Higgins 3363, Estación Central Santiago 917022, Chile; (D.G.); (P.Á.); (M.R.); (J.N.); (R.C.)
| | - Gloria Levicán
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Avenida Libertador Bernardo O’Higgins 3363, Estación Central Santiago 917022, Chile; (D.G.); (P.Á.); (M.R.); (J.N.); (R.C.)
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19
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Wolfe MS. Unraveling the complexity of γ-secretase. Semin Cell Dev Biol 2020; 105:3-11. [PMID: 31980377 PMCID: PMC7371508 DOI: 10.1016/j.semcdb.2020.01.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 11/26/2019] [Accepted: 01/15/2020] [Indexed: 01/07/2023]
Abstract
γ-Secretase was initially defined as a proteolytic activity that cleaves within the transmembrane of the amyloid precursor protein (APP) to produce the amyloid β-peptide of Alzheimer's disease. The discovery of mutations in APP and the presenilins associated with familial Alzheimer's disease and their effects on APP processing dovetailed with pharmacological studies on γ-secretase, leading to the revelation that presenilins are unprecedented membrane-embedded aspartyl proteases. Other members of what became known as the γ-secretase complex were subsequently identified. In parallel with these advances, connections between presenilins and Notch receptors essential to metazoan development became evident, resulting in the concurrent realization that γ-secretase also carries out intramembrane proteolysis of Notch as part of its signaling mechanism. Substantial progress has been made toward elucidating how γ-secretase carries out complex processing of transmembrane domains, how it goes awry in familial Alzheimer's disease, the scope of its substrates, and the atomic details of its structure. Critical questions remain for future study, toward further unraveling the complexity of this unique membrane-embedded proteolytic machine and its roles in biology and disease.
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Affiliation(s)
- Michael S Wolfe
- Department of Medicinal Chemistry, University of Kansas, Lawrence, KS 66045, USA.
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20
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McCallum M, Benlekbir S, Nguyen S, Tammam S, Rubinstein JL, Burrows LL, Howell PL. Multiple conformations facilitate PilT function in the type IV pilus. Nat Commun 2019; 10:5198. [PMID: 31729381 PMCID: PMC6858323 DOI: 10.1038/s41467-019-13070-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 10/18/2019] [Indexed: 12/13/2022] Open
Abstract
Type IV pilus-like systems are protein complexes that polymerize pilin fibres. They are critical for virulence in many bacterial pathogens. Pilin polymerization and depolymerization are powered by motor ATPases of the PilT/VirB11-like family. This family is thought to operate with C2 symmetry; however, most of these ATPases crystallize with either C3 or C6 symmetric conformations. The relevance of these conformations is unclear. Here, we determine the X-ray structures of PilT in four unique conformations and use these structures to classify the conformation of available PilT/VirB11-like family member structures. Single particle electron cryomicroscopy (cryoEM) structures of PilT reveal condition-dependent preferences for C2, C3, and C6 conformations. The physiologic importance of these conformations is validated by coevolution analysis and functional studies of point mutants, identifying a rare gain-of-function mutation that favours the C2 conformation. With these data, we propose a comprehensive model of PilT function with broad implications for PilT/VirB11-like family members.
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Affiliation(s)
- Matthew McCallum
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Program in Molecular Structure & Function, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Samir Benlekbir
- Program in Molecular Structure & Function, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Sheryl Nguyen
- Program in Molecular Structure & Function, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Stephanie Tammam
- Program in Molecular Structure & Function, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - John L Rubinstein
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada.
- Program in Molecular Structure & Function, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1l7, Canada.
| | - Lori L Burrows
- Department of Biochemistry and Biomedical Sciences and the Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, L8S 4K1, Canada.
| | - P Lynne Howell
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada.
- Program in Molecular Structure & Function, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.
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21
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Hsu T, Gemmell MR, Franzosa EA, Berry S, Mukhopadhya I, Hansen R, Michaud M, Nielsen H, Miller WG, Nielsen H, Bajaj-Elliott M, Huttenhower C, Garrett WS, Hold GL. Comparative genomics and genome biology of Campylobacter showae. Emerg Microbes Infect 2019; 8:827-840. [PMID: 31169073 PMCID: PMC6567213 DOI: 10.1080/22221751.2019.1622455] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Campylobacter showae a bacterium historically linked to gingivitis and periodontitis, has recently been associated with inflammatory bowel disease and colorectal cancer. Our aim was to generate genome sequences for new clinical C. showae strains and identify functional properties explaining their pathogenic potential. Eight C. showae genomes were assessed, four strains isolated from inflamed gut tissues from paediatric Crohn’s disease patients, three strains from colonic adenomas, and one from a gastroenteritis patient stool. Genome assemblies were analyzed alongside the only 3 deposited C. showae genomes. The pangenome from these 11 strains consisted of 4686 unique protein families, and the core genome size was estimated at 1050 ± 15 genes with each new genome contributing an additional 206 ± 16 genes. Functional assays indicated that colonic strains segregated into 2 groups: adherent/invasive vs. non-adherent/non-invasive strains. The former possessed Type IV secretion machinery and S-layer proteins, while the latter contained Cas genes and other CRISPR associated proteins. Comparison of gene profiles with strains in Human Microbiome Project metagenomes showed that gut-derived isolates share genes specific to tongue dorsum and supragingival plaque counterparts. Our findings indicate that C. showae strains are phenotypically and genetically diverse and suggest that secretion systems may play an important role in virulence potential.
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Affiliation(s)
- Tiffany Hsu
- a Department of Biostatistics , Harvard T. H. Chan School of Public Health , Boston , USA
| | - Matthew R Gemmell
- b School of Medicine, Medical Sciences and Nutrition , Centre for Genome Enabled Biology and Medicine, University of Aberdeen , Aberdeen , UK
| | - Eric A Franzosa
- a Department of Biostatistics , Harvard T. H. Chan School of Public Health , Boston , USA
| | - Susan Berry
- c School of Medicine, Medical Sciences and Nutrition , GI Research Group, University of Aberdeen , Aberdeen , UK
| | - Indrani Mukhopadhya
- c School of Medicine, Medical Sciences and Nutrition , GI Research Group, University of Aberdeen , Aberdeen , UK
| | - Richard Hansen
- d Department of Paediatric Gastroenterology , Royal Hospital for Children , Glasgow , UK
| | - Monia Michaud
- e Departments of Genetics and Complex Diseases and Immunology and Infectious Diseases , Harvard T. H. Chan School of Public Health , Boston , USA
| | - Hans Nielsen
- f Department of Clinical Microbiology , Aalborg University Hospital , Aalborg , Denmark
| | - William G Miller
- g Produce Safety and Microbiology Research Unit, U.S. Department of Agriculture , Agricultural Research Service , Albany , USA
| | - Henrik Nielsen
- h Department of Infectious Diseases , Aalborg University Hospital Aalborg , Denmark
| | - Mona Bajaj-Elliott
- i Infection, Immunity, Inflammation Programme , UCL Great Ormond Street Institute of Child Health , London , UK
| | - Curtis Huttenhower
- a Department of Biostatistics , Harvard T. H. Chan School of Public Health , Boston , USA
| | - Wendy S Garrett
- e Departments of Genetics and Complex Diseases and Immunology and Infectious Diseases , Harvard T. H. Chan School of Public Health , Boston , USA
| | - Georgina L Hold
- a Department of Biostatistics , Harvard T. H. Chan School of Public Health , Boston , USA.,c School of Medicine, Medical Sciences and Nutrition , GI Research Group, University of Aberdeen , Aberdeen , UK.,e Departments of Genetics and Complex Diseases and Immunology and Infectious Diseases , Harvard T. H. Chan School of Public Health , Boston , USA.,j St George and Sutherland Clinical School , Microbiome Research Centre, University of New South Wales , Sydney , Australia
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22
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Abstract
γ-Secretase is a membrane-embedded protease complex, with presenilin as the catalytic component containing two transmembrane aspartates in the active site. With more than 90 known substrates, the γ-secretase complex is considered "the proteasome of the membrane", with central roles in biology and medicine. The protease carries out hydrolysis within the lipid bilayer to cleave the transmembrane domain of the substrate multiple times before releasing secreted products. For many years, elucidation of γ-secretase structure and function largely relied on small-molecule probes and mutagenesis. Recently, however, advances in cryo-electron microscopy have led to the first detailed structures of the protease complex. Two new reports of structures of γ-secretase bound to membrane protein substrates provide great insight into the nature of substrate recognition and how Alzheimer's disease-causing mutations in presenilin might alter substrate binding and processing. These new structures offer a powerful platform for elucidating enzyme mechanisms, deciphering effects of disease-causing mutations, and advancing Alzheimer's disease drug discovery.
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Affiliation(s)
- Michael S Wolfe
- Department of Medicinal Chemistry , University of Kansas , Lawrence , Kansas 66045 , United States
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23
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Abstract
Type IV pilus (T4P)-like systems have been identified in almost every major phylum of prokaryotic life. They include the type IVa pilus (T4aP), type II secretion system (T2SS), type IVb pilus (T4bP), Tad/Flp pilus, Com pilus, and archaeal flagellum (archaellum). These systems are used for adhesion, natural competence, phage adsorption, folded-protein secretion, surface sensing, swimming motility, and twitching motility. The T4aP allows for all of these functions except swimming and is therefore a good model system for understanding T4P-like systems. Recent structural analyses have revolutionized our understanding of how the T4aP machinery assembles and functions. Here we review the structure and function of the T4aP.
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24
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Berry JL, Gurung I, Anonsen JH, Spielman I, Harper E, Hall AMJ, Goosens VJ, Raynaud C, Koomey M, Biais N, Matthews S, Pelicic V. Global biochemical and structural analysis of the type IV pilus from the Gram-positive bacterium Streptococcus sanguinis. J Biol Chem 2019; 294:6796-6808. [PMID: 30837269 PMCID: PMC6497953 DOI: 10.1074/jbc.ra118.006917] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/27/2019] [Indexed: 11/06/2022] Open
Abstract
Type IV pili (Tfp) are functionally versatile filaments, widespread in prokaryotes, that belong to a large class of filamentous nanomachines known as type IV filaments (Tff). Although Tfp have been extensively studied in several Gram-negative pathogens where they function as key virulence factors, many aspects of their biology remain poorly understood. Here, we performed a global biochemical and structural analysis of Tfp in a recently emerged Gram-positive model, Streptococcus sanguinis In particular, we focused on the five pilins and pilin-like proteins involved in Tfp biology in S. sanguinis We found that the two major pilins, PilE1 and PilE2, (i) follow widely conserved principles for processing by the prepilin peptidase PilD and for assembly into filaments; (ii) display only one of the post-translational modifications frequently found in pilins, i.e. a methylated N terminus; (iii) are found in the same heteropolymeric filaments; and (iv) are not functionally equivalent. The 3D structure of PilE1, solved by NMR, revealed a classical pilin-fold with a highly unusual flexible C terminus. Intriguingly, PilE1 more closely resembles pseudopilins forming shorter Tff than bona fide Tfp-forming major pilins, underlining the evolutionary relatedness among different Tff. Finally, we show that S. sanguinis Tfp contain a low abundance of three additional proteins processed by PilD, the minor pilins PilA, PilB, and PilC. These findings provide the first global biochemical and structural picture of a Gram-positive Tfp and have fundamental implications for our understanding of a widespread class of filamentous nanomachines.
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Affiliation(s)
- Jamie-Lee Berry
- From the Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom
| | - Ishwori Gurung
- From the Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom
| | - Jan Haug Anonsen
- the Department of Biological Sciences, Proteomics and Mass Spectrometry Unit, University of Oslo, 0371 Oslo, Norway.,the Department of Biological Sciences, Center for Integrative Microbial Evolution, University of Oslo, 0371 Oslo, Norway
| | - Ingrid Spielman
- the Department of Biology, Brooklyn College of the City University of New York, New York, New York 11210.,The Graduate Center of the City University of New York, New York, New York 10016, and
| | - Elliot Harper
- From the Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom
| | - Alexander M J Hall
- From the Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom
| | - Vivianne J Goosens
- From the Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom
| | - Claire Raynaud
- From the Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom
| | - Michael Koomey
- the Department of Biological Sciences, Center for Integrative Microbial Evolution, University of Oslo, 0371 Oslo, Norway
| | - Nicolas Biais
- the Department of Biology, Brooklyn College of the City University of New York, New York, New York 11210.,The Graduate Center of the City University of New York, New York, New York 10016, and
| | - Steve Matthews
- the Centre for Structural Biology, Imperial College London, London SW7 2AZ, United Kingdom
| | - Vladimir Pelicic
- From the Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom,
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25
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Montánchez I, Ogayar E, Plágaro AH, Esteve-Codina A, Gómez-Garrido J, Orruño M, Arana I, Kaberdin VR. Analysis of Vibrio harveyi adaptation in sea water microcosms at elevated temperature provides insights into the putative mechanisms of its persistence and spread in the time of global warming. Sci Rep 2019; 9:289. [PMID: 30670759 PMCID: PMC6343004 DOI: 10.1038/s41598-018-36483-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 11/22/2018] [Indexed: 12/12/2022] Open
Abstract
Discovering the means to control the increasing dissemination of pathogenic vibrios driven by recent climate change is challenged by the limited knowledge of the mechanisms in charge of Vibrio spp. persistence and spread in the time of global warming. To learn about physiological and gene expression patterns associated with the long-term persistence of V. harveyi at elevated temperatures, we studied adaptation of this marine bacterium in seawater microcosms at 30 °C which closely mimicked the upper limit of sea surface temperatures around the globe. We found that nearly 90% of cells lost their culturability and became partly damaged after two weeks, thus suggesting a negative impact of the combined action of elevated temperature and shortage of carbon on V. harveyi survival. Moreover, further gene expression analysis revealed that major adaptive mechanisms were poorly coordinated and apparently could not sustain cell fitness. On the other hand, elevated temperature and starvation promoted expression of many virulence genes, thus potentially reinforcing the pathogenicity of this organism. These findings suggest that the increase in disease outbreaks caused by V. harveyi under rising sea surface temperatures may not reflect higher cell fitness, but rather an increase in virulence enabling V. harveyi to escape from adverse environments to nutrient rich, host-pathogen associations.
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Affiliation(s)
- Itxaso Montánchez
- Department of Immunology, Microbiology and Parasitology, University of the Basque Country UPV/EHU, 48940, Leioa, Spain
| | - Elixabet Ogayar
- Department of Immunology, Microbiology and Parasitology, University of the Basque Country UPV/EHU, 48940, Leioa, Spain
| | - Ander Hernández Plágaro
- Department of Immunology, Microbiology and Parasitology, University of the Basque Country UPV/EHU, 48940, Leioa, Spain
| | - Anna Esteve-Codina
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Catalonia, 08028, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Catalonia, 08003, Spain
| | - Jèssica Gómez-Garrido
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Catalonia, 08028, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Catalonia, 08003, Spain
| | - Maite Orruño
- Department of Immunology, Microbiology and Parasitology, University of the Basque Country UPV/EHU, 48940, Leioa, Spain.,Research Centre for Experimental Marine Biology and Biotechnology (PIE-UPV/EHU), 48620, Plentzia, Spain
| | - Inés Arana
- Department of Immunology, Microbiology and Parasitology, University of the Basque Country UPV/EHU, 48940, Leioa, Spain.,Research Centre for Experimental Marine Biology and Biotechnology (PIE-UPV/EHU), 48620, Plentzia, Spain
| | - Vladimir R Kaberdin
- Department of Immunology, Microbiology and Parasitology, University of the Basque Country UPV/EHU, 48940, Leioa, Spain. .,Research Centre for Experimental Marine Biology and Biotechnology (PIE-UPV/EHU), 48620, Plentzia, Spain. .,IKERBASQUE, Basque Foundation for Science, Maria Diaz de Haro 3, 48013, Bilbao, Spain.
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pH dependent membrane binding of the Solanum tuberosum plant specific insert: An in silico study. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:2608-2618. [PMID: 30291921 DOI: 10.1016/j.bbamem.2018.10.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 09/27/2018] [Accepted: 10/01/2018] [Indexed: 01/07/2023]
Abstract
The Solanum tuberosum plant-specific insert (StPSI) has been shown to possess potent antimicrobial activity against both human and plant pathogens. Furthermore, in vitro, the StPSI is capable of fusing phospholipid vesicles, provided the conditions of net anionic vesicle charge and acidic pH are met. Constant pH replica-exchange simulations indicate several acidic residues on the dimer have highly perturbed pKas (<3.0; E15, D28, E85 & E100) due to involvement in salt bridges. After setting the pH of the system to either 3.0 or 7.4, all-atom simulations provided details of the effect of pH on secondary structural elements, particularly in the previously unresolved crystallographic structure of the loop section. Coarse-grained dimer-bilayer simulations demonstrated that at pH 7.4, the dimer had no affinity for neutral or anionic membranes over the course of 1 μs simulations. Conversely, at pH 3.0 two binding modes were observed. Mode 1 is mediated primarily via strong N-terminal interactions on one monomer only, whereas in mode 2, N- and C-terminal residues of one monomer and numerous polar and basic residues on the second monomer, particularly in the third helix, participate in membrane interactions. Mode 2 was accompanied by re-orientation of the dimer to a more vertical position with respect to helices 1 and 4, positioning the dimer for membrane interactions. These results offer the first examination at near-atomic resolution of residues mediating the StPSI-membrane interactions, and allow for the postulation of a possible fusion mechanism.
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Gurung I, Berry JL, Hall A, Pelicic V. Cloning-independent markerless gene editing in Streptococcus sanguinis: novel insights in type IV pilus biology. Nucleic Acids Res 2017; 45:e40. [PMID: 27903891 PMCID: PMC5389465 DOI: 10.1093/nar/gkw1177] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 11/14/2016] [Indexed: 11/14/2022] Open
Abstract
Streptococcus sanguinis, a naturally competent opportunistic human pathogen, is a Gram-positive workhorse for genomics. It has recently emerged as a model for the study of type IV pili (Tfp)—exceptionally widespread and important prokaryotic filaments. To enhance genetic manipulation of Streptococcus sanguinis, we have developed a cloning-independent methodology, which uses a counterselectable marker and allows sophisticated markerless gene editing in situ. We illustrate the utility of this methodology by answering several questions regarding Tfp biology by (i) deleting single or mutiple genes, (ii) altering specific bases in genes of interest, and (iii) engineering genes to encode proteins with appended affinity tags. We show that (i) the last six genes in the pil locus harbouring all the genes dedicated to Tfp biology play no role in piliation or Tfp-mediated motility, (ii) two highly conserved Asp residues are crucial for enzymatic activity of the prepilin peptidase PilD and (iii) that pilin subunits with a C-terminally appended hexa-histidine (6His) tag are still assembled into functional Tfp. The methodology for genetic manipulation we describe here should be broadly applicable.
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Affiliation(s)
- Ishwori Gurung
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
| | - Jamie-Lee Berry
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
| | - Alexander M. J. Hall
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
| | - Vladimir Pelicic
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
- To whom correspondence should be addressed. Tel: +44 20 7594 2080;
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28
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Motility and adhesion through type IV pili in Gram-positive bacteria. Biochem Soc Trans 2017; 44:1659-1666. [PMID: 27913675 DOI: 10.1042/bst20160221] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 09/27/2016] [Accepted: 09/29/2016] [Indexed: 12/23/2022]
Abstract
Type IV pili are hair-like bacterial surface appendages that play a role in diverse processes such as cellular adhesion, colonization, twitching motility, biofilm formation, and horizontal gene transfer. These extracellular fibers are composed exclusively or primarily of many copies of one or more pilin proteins, tightly packed in a helix so that the highly hydrophobic amino-terminus of the pilin is buried in the pilus core. Type IV pili have been characterized extensively in Gram-negative bacteria, and recent advances in high-throughput genomic sequencing have revealed that they are also widespread in Gram-positive bacteria. Here, we review the current state of knowledge of type IV pilus systems in Gram-positive bacterial species and discuss them in the broader context of eubacterial type IV pili.
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Goosens VJ, Busch A, Georgiadou M, Castagnini M, Forest KT, Waksman G, Pelicic V. Reconstitution of a minimal machinery capable of assembling periplasmic type IV pili. Proc Natl Acad Sci U S A 2017; 114:E4978-E4986. [PMID: 28588140 PMCID: PMC5488919 DOI: 10.1073/pnas.1618539114] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Type IV pili (Tfp), which are key virulence factors in many bacterial pathogens, define a large group of multipurpose filamentous nanomachines widespread in Bacteria and Archaea. Tfp biogenesis is a complex multistep process, which relies on macromolecular assemblies composed of 15 conserved proteins in model gram-negative species. To improve our limited understanding of the molecular mechanisms of filament assembly, we have used a synthetic biology approach to reconstitute, in a nonnative heterologous host, a minimal machinery capable of building Tfp. Here we show that eight synthetic genes are sufficient to promote filament assembly and that the corresponding proteins form a macromolecular complex at the cytoplasmic membrane, which we have purified and characterized biochemically. Our results contribute to a better mechanistic understanding of the assembly of remarkable dynamic filaments nearly ubiquitous in prokaryotes.
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Affiliation(s)
- Vivianne J Goosens
- Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom
| | - Andreas Busch
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, London WC1E 7HX, United Kingdom
| | - Michaella Georgiadou
- Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom
| | - Marta Castagnini
- Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom
| | - Katrina T Forest
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706
| | - Gabriel Waksman
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, London WC1E 7HX, United Kingdom
| | - Vladimir Pelicic
- Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom;
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Signal peptide peptidase and SPP-like proteases - Possible therapeutic targets? BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2017. [PMID: 28624439 DOI: 10.1016/j.bbamcr.2017.06.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Signal peptide peptidase (SPP) and the four homologous SPP-like proteases SPPL2a, SPPL2b, SPPL2c and SPPL3 are GxGD-type intramembrane-cleaving proteases (I-CLIPs). In addition to divergent subcellular localisations, distinct differences in the mechanistic properties and substrate requirements of individual family members have been unravelled. SPP/SPPL proteases employ a catalytic mechanism related to that of the γ-secretase complex. Nevertheless, differential targeting of SPP/SPPL proteases and γ-secretase by inhibitors has been demonstrated. Furthermore, also within the SPP/SPPL family significant differences in the sensitivity to currently available inhibitory compounds have been reported. Though far from complete, our knowledge on pathophysiological functions of SPP/SPPL proteases, in particular based on studies in mice, has been significantly increased over the last years. Based on this, inhibition of distinct SPP/SPPL proteases has been proposed as a novel therapeutic concept e.g. for the treatment of autoimmunity and viral or protozoal infections, as we will discuss in this review. This article is part of a Special Issue entitled: Proteolysis as a Regulatory Event in Pathophysiology edited by Stefan Rose-John.
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Saldaña-Ahuactzi Z, Rodea GE, Cruz-Córdova A, Rodríguez-Ramírez V, Espinosa-Mazariego K, González-Montalvo MA, Ochoa SA, González-Pedrajo B, Eslava-Campos CA, López-Villegas EO, Hernández-Castro R, Arellano-Galindo J, Patiño-López G, Xicohtencatl-Cortes J. Effects of lng Mutations on LngA Expression, Processing, and CS21 Assembly in Enterotoxigenic Escherichia coli E9034A. Front Microbiol 2016; 7:1201. [PMID: 27536289 PMCID: PMC4971541 DOI: 10.3389/fmicb.2016.01201] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 07/19/2016] [Indexed: 12/22/2022] Open
Abstract
Enterotoxigenic Escherichia coli (ETEC) is a major cause of morbidity in children under 5 years of age in low- and middle-income countries and a leading cause of traveler's diarrhea worldwide. The ability of ETEC to colonize the intestinal epithelium is mediated by fimbrial adhesins, such as CS21 (Longus). This adhesin is a type IVb pilus involved in adherence to intestinal cells in vitro and bacterial self-aggregation. Fourteen open reading frames have been proposed to be involved in CS21 assembly, hitherto only the lngA and lngB genes, coding for the major (LngA) and minor (LngB) structural subunit, have been characterized. In this study, we investigated the role of the LngA, LngB, LngC, LngD, LngH, and LngP proteins in the assembly of CS21 in ETEC strain E9034A. The deletion of the lngA, lngB, lngC, lngD, lngH, or lngP genes, abolished CS21 assembly in ETEC strain E9034A and the adherence to HT-29 cells was reduced 90%, compared to wild-type strain. Subcellular localization prediction of CS21 proteins was similar to other well-known type IV pili homologs. We showed that LngP is the prepilin peptidase of LngA, and that ETEC strain E9034A has another peptidase capable of processing LngA, although with less efficiency. Additionally, we present immuno-electron microscopy images to show that the LngB protein could be localized at the tip of CS21. In conclusion, our results demonstrate that the LngA, LngB, LngC, LngD, LngH, and LngP proteins are essential for CS21 assembly, as well as for bacterial aggregation and adherence to HT-29 cells.
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Affiliation(s)
- Zeus Saldaña-Ahuactzi
- Laboratorio de Investigación en Bacteriología Intestinal, Hospital Infantil de México Federico GómezCiudad de México, Mexico; Instituto de Fisiología Celular at the Universidad Nacional Autónoma de MéxicoCiudad de México, Mexico
| | - Gerardo E Rodea
- Laboratorio de Investigación en Bacteriología Intestinal, Hospital Infantil de México Federico GómezCiudad de México, Mexico; Instituto de Fisiología Celular at the Universidad Nacional Autónoma de MéxicoCiudad de México, Mexico
| | - Ariadnna Cruz-Córdova
- Laboratorio de Investigación en Bacteriología Intestinal, Hospital Infantil de México Federico Gómez Ciudad de México, Mexico
| | - Viridiana Rodríguez-Ramírez
- Laboratorio de Investigación en Bacteriología Intestinal, Hospital Infantil de México Federico Gómez Ciudad de México, Mexico
| | - Karina Espinosa-Mazariego
- Laboratorio de Investigación en Bacteriología Intestinal, Hospital Infantil de México Federico Gómez Ciudad de México, Mexico
| | - Martín A González-Montalvo
- Laboratorio de Investigación en Bacteriología Intestinal, Hospital Infantil de México Federico Gómez Ciudad de México, Mexico
| | - Sara A Ochoa
- Laboratorio de Investigación en Bacteriología Intestinal, Hospital Infantil de México Federico Gómez Ciudad de México, Mexico
| | - Bertha González-Pedrajo
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México Ciudad de México, Mexico
| | - Carlos A Eslava-Campos
- Departamento de Salud Pública, Facultad de Medicina, Universidad Nacional Autónoma de México Ciudad de México, Mexico
| | - Edgar O López-Villegas
- Laboratorio Central de Microscopía, Departamento de Investigación-SEPI, Instituto Politecnico Nacional Ciudad de México, Mexico
| | - Rigoberto Hernández-Castro
- Departamento de Ecología de Agentes Patógenos, Hospital General "Dr. Manuel Gea González" Ciudad de México, Mexico
| | - José Arellano-Galindo
- Departamento de Infectología, Hospital Infantil de México Federico Gómez Ciudad de México, Mexico
| | - Genaro Patiño-López
- Laboratorio de Investigación en Inmunología y Proteómica, Hospital Infantil de México Federico Gómez Ciudad de México, Mexico
| | - Juan Xicohtencatl-Cortes
- Laboratorio de Investigación en Bacteriología Intestinal, Hospital Infantil de México Federico Gómez Ciudad de México, Mexico
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Abstract
During the first step of biofilm formation, initial attachment is dictated by physicochemical and electrostatic interactions between the surface and the bacterial envelope. Depending on the nature of these interactions, attachment can be transient or permanent. To achieve irreversible attachment, bacterial cells have developed a series of surface adhesins promoting specific or nonspecific adhesion under various environmental conditions. This article reviews the recent advances in our understanding of the secretion, assembly, and regulation of the bacterial adhesins during biofilm formation, with a particular emphasis on the fimbrial, nonfimbrial, and discrete polysaccharide adhesins in Gram-negative bacteria.
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Coburger I, Schaub Y, Roeser D, Hardes K, Maeder P, Klee N, Steinmetzer T, Imhof D, Diederich WE, Than ME. Identification of inhibitors of the transmembrane protease FlaK of Methanococcus maripaludis. Microbiologyopen 2016; 5:637-46. [PMID: 27038342 PMCID: PMC4985597 DOI: 10.1002/mbo3.358] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 02/23/2016] [Accepted: 03/07/2016] [Indexed: 01/17/2023] Open
Abstract
GxGD‐type intramembrane cleaving proteases (I‐CLiPs) form a family of proteolytic enzymes that feature an aspartate‐based catalytic mechanism. Yet, they structurally and functionally largely differ from the classical pepsin‐like aspartic proteases. Among them are the archaeal enzyme FlaK, processing its substrate FlaB2 during the formation of flagella and γ‐secretase, which is centrally involved in the etiology of the neurodegenerative Alzheimer's disease. We developed an optimized activity assay for FlaK and based on screening of a small in‐house library and chemical synthesis, we identified compound 9 as the first inhibitor of this enzyme. Our results show that this intramembrane protease differs from classical pepsin‐like aspartic proteases and give insights into the substrate recognition of this enzyme. By providing the needed tools to further study the enzymatic cycle of FlaK, our results also enable further studies towards a functional understanding of other GxGD‐type I‐CLiPs.
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Affiliation(s)
- Ina Coburger
- Leibniz Institute on Aging (FLI), Protein Crystallography Group, Beutenbergstr. 11, Jena, 07745, Germany
| | - Yvonne Schaub
- Leibniz Institute on Aging (FLI), Protein Crystallography Group, Beutenbergstr. 11, Jena, 07745, Germany
| | - Dirk Roeser
- Leibniz Institute on Aging (FLI), Protein Crystallography Group, Beutenbergstr. 11, Jena, 07745, Germany
| | - Kornelia Hardes
- Department of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, Marburg, 35032, Germany
| | - Patrick Maeder
- Department of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, Marburg, 35032, Germany
| | - Nina Klee
- Department of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, Marburg, 35032, Germany
| | - Torsten Steinmetzer
- Department of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, Marburg, 35032, Germany
| | - Diana Imhof
- Institute of Pharmacy, Pharmaceutical Chemistry I, University of Bonn, Brühler Str. 7, Bonn, 53119, Germany
| | - Wibke E Diederich
- Department of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, Marburg, 35032, Germany
| | - Manuel E Than
- Leibniz Institute on Aging (FLI), Protein Crystallography Group, Beutenbergstr. 11, Jena, 07745, Germany
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34
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Affiliation(s)
- Alain Filloux
- Alain Filloux, MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK; E-mail:
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35
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Buddelmeijer N. The molecular mechanism of bacterial lipoprotein modification—How, when and why? FEMS Microbiol Rev 2015; 39:246-61. [DOI: 10.1093/femsre/fuu006] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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36
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Abstract
Recent studies on archaeal motility have shown that the archaeal motility structure is unique in several aspects. Although it fulfills the same swimming function as the bacterial flagellum, it is evolutionarily and structurally related to the type IV pilus. This was the basis for the recent proposal to term the archaeal motility structure the "archaellum." This review illustrates the key findings that led to the realization that the archaellum was a novel motility structure and presents the current knowledge about the structural composition, mechanism of assembly and regulation, and the posttranslational modifications of archaella.
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Affiliation(s)
- Sonja-Verena Albers
- Molecular Biology of Archaea, Institute of Biology II-Microbiology, University of Freiburg , Freiburg, Germany ; Molecular Biology of Archaea, Max Planck Institute for Terrestrial Microbiology , Marburg, Germany
| | - Ken F Jarrell
- Department of Biomedical and Molecular Sciences, Queen's University , Kingston, ON, Canada
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37
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Berry JL, Pelicic V. Exceptionally widespread nanomachines composed of type IV pilins: the prokaryotic Swiss Army knives. FEMS Microbiol Rev 2014; 39:134-54. [PMID: 25793961 PMCID: PMC4471445 DOI: 10.1093/femsre/fuu001] [Citation(s) in RCA: 178] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Prokaryotes have engineered sophisticated surface nanomachines that have allowed them to colonize Earth and thrive even in extreme environments. Filamentous machineries composed of type IV pilins, which are associated with an amazing array of properties ranging from motility to electric conductance, are arguably the most widespread since distinctive proteins dedicated to their biogenesis are found in most known species of prokaryotes. Several decades of investigations, starting with type IV pili and then a variety of related systems both in bacteria and archaea, have outlined common molecular and structural bases for these nanomachines. Using type IV pili as a paradigm, we will highlight in this review common aspects and key biological differences of this group of filamentous structures. Using type IV pili as a paradigm, we review common genetic, structural and mechanistic features (many) as well as differences (few) of the exceptionally widespread and functionally versatile prokaryotic nano-machines composed of type IV pilins.
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Affiliation(s)
- Jamie-Lee Berry
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK
| | - Vladimir Pelicic
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK
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38
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Henche AL, van Wolferen M, Ghosh A, Albers SV. Dissection of key determinants of cleavage activity in signal peptidase III (SPaseIII) PibD. Extremophiles 2014; 18:905-13. [PMID: 25102813 DOI: 10.1007/s00792-014-0675-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 07/06/2014] [Indexed: 10/24/2022]
Abstract
In Archaea, type IV prepilins and prearchaellins are processed by designated signal peptidase III (SPaseIII) prior to their incorporation into pili and the archaellum, respectively. These peptidases belong to the family of integral membrane aspartic acid proteases that contain two essential aspartate residues of which the second aspartate is located in a conserved GxGD motif. To this group also bacterial type IV prepilin peptidases, Alzheimer disease-related secretases, signal peptide peptidases and signal peptide peptidase-like proteases in humans belong. Here we have performed detailed in vivo analyses to understand the cleavage activity of PibD, SPaseIII from the thermoacidophilic crenarchaeon Sulfolobus acidocaldarius. Using an already established in vivo heterologous system cleavage assay, we could successfully identify the key amino acid residues essential for catalysis of PibD. Furthermore, in trans complementation of a pibD S. acidocaldarius deletion mutant with PibD variants having substituted key amino acids has consolidated our observations of the importance of these residues in catalysis. Based on our data, we propose to re-define class III peptidases/type IV prepilin/prearchaellin peptidases as GxHyD group (rather than GxGD) of proteases [Hy-hydrophobic amino acid].
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Affiliation(s)
- Anna-Lena Henche
- Molecular Biology of Archaea, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Strasse 10, 35043, Marburg, Germany
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Type II secretion system: A magic beanstalk or a protein escalator. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1843:1568-77. [DOI: 10.1016/j.bbamcr.2013.12.020] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 12/13/2013] [Accepted: 12/23/2013] [Indexed: 12/12/2022]
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Abstract
Type IV pili (T4P) are surface-exposed fibers that mediate many functions in bacteria, including locomotion, adherence to host cells, DNA uptake (competence), and protein secretion and that can act as nanowires carrying electric current. T4P are composed of a polymerized protein, pilin, and their assembly apparatuses share protein homologs with type II secretion systems in eubacteria and the flagella of archaea. T4P are found throughout Gram-negative bacterial families and have been studied most extensively in certain model Gram-negative species. Recently, it was discovered that T4P systems are also widespread among Gram-positive species, in particular the clostridia. Since Gram-positive and Gram-negative bacteria have many differences in cell wall architecture and other features, it is remarkable how similar the T4P core proteins are between these organisms, yet there are many key and interesting differences to be found as well. In this review, we compare the two T4P systems and identify and discuss the features they have in common and where they differ to provide a very broad-based view of T4P systems across all eubacterial species.
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41
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Rao C V S, De Waelheyns E, Economou A, Anné J. Antibiotic targeting of the bacterial secretory pathway. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1843:1762-83. [PMID: 24534745 DOI: 10.1016/j.bbamcr.2014.02.004] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Revised: 01/27/2014] [Accepted: 02/06/2014] [Indexed: 02/06/2023]
Abstract
Finding new, effective antibiotics is a challenging research area driven by novel approaches required to tackle unconventional targets. In this review we focus on the bacterial protein secretion pathway as a target for eliminating or disarming pathogens. We discuss the latest developments in targeting the Sec-pathway for novel antibiotics focusing on two key components: SecA, the ATP-driven motor protein responsible for driving preproteins across the cytoplasmic membrane and the Type I signal peptidase that is responsible for the removal of the signal peptide allowing the release of the mature protein from the membrane. We take a bird's-eye view of other potential targets in the Sec-pathway as well as other Sec-dependent or Sec-independent protein secretion pathways as targets for the development of novel antibiotics. This article is part of a Special Issue entitled: Protein trafficking and secretion in bacteria. Guest Editors: Anastassios Economou and Ross Dalbey.
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Affiliation(s)
- Smitha Rao C V
- Laboratory of Molecular Bacteriology, Rega Institute, Department of Microbiology and Immunology, KU Leuven, O&N1, 6th floor, Herestraat 49, P.O. Box 1037, B-3000 Leuven, Belgium.
| | - Evelien De Waelheyns
- Laboratory of Molecular Bacteriology, Rega Institute, Department of Microbiology and Immunology, KU Leuven, O&N1, 6th floor, Herestraat 49, P.O. Box 1037, B-3000 Leuven, Belgium.
| | - Anastassios Economou
- Laboratory of Molecular Bacteriology, Rega Institute, Department of Microbiology and Immunology, KU Leuven, O&N1, 6th floor, Herestraat 49, P.O. Box 1037, B-3000 Leuven, Belgium; Institute of Molecular Biology and Biotechnology, FORTH, University of Crete, P.O. Box 1385, GR-711 10 Iraklio, Crete, Greece; Department of Biology, University of Crete, P.O. Box 1385, GR-71110 Iraklio, Crete, Greece.
| | - Jozef Anné
- Laboratory of Molecular Bacteriology, Rega Institute, Department of Microbiology and Immunology, KU Leuven, O&N1, 6th floor, Herestraat 49, P.O. Box 1037, B-3000 Leuven, Belgium.
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Voss M, Schröder B, Fluhrer R. Mechanism, specificity, and physiology of signal peptide peptidase (SPP) and SPP-like proteases. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:2828-39. [PMID: 24099004 DOI: 10.1016/j.bbamem.2013.03.033] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2012] [Revised: 03/25/2013] [Accepted: 03/29/2013] [Indexed: 01/09/2023]
Abstract
Signal peptide peptidase (SPP) and the homologous SPP-like (SPPL) proteases SPPL2a, SPPL2b, SPPL2c and SPPL3 belong to the family of GxGD intramembrane proteases. SPP/SPPLs selectively cleave transmembrane domains in type II orientation and do not require additional co-factors for proteolytic activity. Orthologues of SPP and SPPLs have been identified in other vertebrates, plants, and eukaryotes. In line with their diverse subcellular localisations ranging from the ER (SPP, SPPL2c), the Golgi (SPPL3), the plasma membrane (SPPL2b) to lysosomes/late endosomes (SPPL2a), the different members of the SPP/SPPL family seem to exhibit distinct functions. Here, we review the substrates of these proteases identified to date as well as the current state of knowledge about the physiological implications of these proteolytic events as deduced from in vivo studies. Furthermore, the present knowledge on the structure of intramembrane proteases of the SPP/SPPL family, their cleavage mechanism and their substrate requirements are summarised. This article is part of a Special Issue entitled: Intramembrane Proteases.
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Affiliation(s)
- Matthias Voss
- Adolf Butenandt Institute for Biochemistry, Ludwig-Maximilians University Munich, Schillerstr. 44, 80336 Munich, Germany
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43
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Abstract
Type IV pili (T4P) are multifunctional protein fibers produced on the surfaces of a wide variety of bacteria and archaea. The major subunit of T4P is the type IV pilin, and structurally related proteins are found as components of the type II secretion (T2S) system, where they are called pseudopilins; of DNA uptake/competence systems in both Gram-negative and Gram-positive species; and of flagella, pili, and sugar-binding systems in the archaea. This broad distribution of a single protein family implies both a common evolutionary origin and a highly adaptable functional plan. The type IV pilin is a remarkably versatile architectural module that has been adopted widely for a variety of functions, including motility, attachment to chemically diverse surfaces, electrical conductance, acquisition of DNA, and secretion of a broad range of structurally distinct protein substrates. In this review, we consider recent advances in this research area, from structural revelations to insights into diversity, posttranslational modifications, regulation, and function.
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44
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Tomita T, Iwatsubo T. Structural biology of presenilins and signal peptide peptidases. J Biol Chem 2013; 288:14673-80. [PMID: 23585568 DOI: 10.1074/jbc.r113.463281] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Presenilin and signal peptide peptidase are multispanning intramembrane-cleaving proteases with a conserved catalytic GxGD motif. Presenilin comprises the catalytic subunit of γ-secretase, a protease responsible for the generation of amyloid-β peptides causative of Alzheimer disease. Signal peptide peptidase proteins are implicated in the regulation of the immune system. Both protease family proteins have been recognized as druggable targets for several human diseases, but their detailed structure still remains unknown. Recently, the x-ray structures of some archaeal GxGD proteases have been determined. We review the recent progress in biochemical and biophysical probing of the structure of these atypical proteases.
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Affiliation(s)
- Taisuke Tomita
- Department of Neuropathology and Neuroscience, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan.
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45
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Strisovsky K. Structural and mechanistic principles of intramembrane proteolysis--lessons from rhomboids. FEBS J 2013; 280:1579-603. [PMID: 23432912 DOI: 10.1111/febs.12199] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Revised: 02/11/2013] [Accepted: 02/18/2013] [Indexed: 02/03/2023]
Abstract
Intramembrane proteases cleave membrane proteins in their transmembrane helices to regulate a wide range of biological processes. They catalyse hydrolytic reactions within the hydrophobic environment of lipid membranes where water is normally excluded. How? Do the different classes of intramembrane proteases share any mechanistic principles? In this review these questions will be discussed in view of the crystal structures of prokaryotic members of the three known catalytic types of intramembrane proteases published over the past 7 years. Rhomboids, the intramembrane serine proteases that are the best understood family, will be the initial area of focus, and the principles that have arisen from a number of structural and biochemical studies will be considered. The site-2 metalloprotease and GXGD-type aspartyl protease structures will then be discussed, with parallels drawn and differences highlighted between these enzymes and the rhomboids. Despite the significant advances achieved so far, to obtain a detailed understanding of the mechanism of any intramembrane protease, high-resolution structural information on the substrate-enzyme complex is required. This remains a major challenge for the field.
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Affiliation(s)
- Kvido Strisovsky
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic.
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46
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Kolappan S, Craig L. Structure of the cytoplasmic domain of TcpE, the inner membrane core protein required for assembly of the Vibrio cholerae toxin-coregulated pilus. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:513-9. [PMID: 23519659 DOI: 10.1107/s0907444912050330] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Accepted: 12/10/2012] [Indexed: 11/10/2022]
Abstract
Type IV pili are long thin surface-displayed polymers of the pilin subunit that are present in a diverse group of bacteria. These multifunctional filaments are critical to virulence for pathogens such as Vibrio cholerae, which use them to form microcolonies and to secrete the colonization factor TcpF. The type IV pili are assembled from pilin subunits by a complex inner membrane machinery. The core component of the type IV pilus-assembly platform is an integral inner membrane protein belonging to the GspF superfamily of secretion proteins. These proteins somehow convert chemical energy from ATP hydrolysis by an assembly ATPase on the cytoplasmic side of the inner membrane to mechanical energy for extrusion of the growing pilus filament out of the inner membrane. Most GspF-family inner membrane core proteins are predicted to have N-terminal and central cytoplasmic domains, cyto1 and cyto2, and three transmembrane segments, TM1, TM2 and TM3. Cyto2 and TM3 represent an internal repeat of cyto1 and TM1. Here, the 1.88 Å resolution crystal structure of the cyto1 domain of V. cholerae TcpE, which is required for assembly of the toxin-coregulated pilus, is reported. This domain folds as a monomeric six-helix bundle with a positively charged membrane-interaction face at one end and a hydrophobic groove at the other end that may serve as a binding site for partner proteins in the pilus-assembly complex.
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47
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Aly KA, Beebe ET, Chan CH, Goren MA, Sepúlveda C, Makino SI, Fox BG, Forest KT. Cell-free production of integral membrane aspartic acid proteases reveals zinc-dependent methyltransferase activity of the Pseudomonas aeruginosa prepilin peptidase PilD. Microbiologyopen 2012; 2:94-104. [PMID: 23255525 PMCID: PMC3584216 DOI: 10.1002/mbo3.51] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Revised: 10/30/2012] [Accepted: 11/05/2012] [Indexed: 12/25/2022] Open
Abstract
Integral membrane aspartic acid proteases are receiving growing recognition for their fundamental roles in cellular physiology of eukaryotes and prokaryotes, and may be medically important pharmaceutical targets. The Gram-negative Pseudomonas aeruginosa PilD and the archaeal Methanococcus voltae FlaK were synthesized in the presence of unilamellar liposomes in a cell-free translation system. Cosynthesis of PilD with its full-length substrate, PilA, or of FlaK with its full-length substrate, FlaB2, led to complete cleavage of the substrate signal peptides. Scaled-up synthesis of PilD, followed by solubilization in dodecyl-β-d-maltoside and chromatography, led to a pure enzyme that retained both of its known biochemical activities: cleavage of the PilA signal peptide and S-adenosyl methionine-dependent methylation of the mature pilin. X-ray fluorescence scans show for the first time that PilD is a zinc-binding protein. Zinc is required for the N-terminal methylation of the mature pilin, but not for signal peptide cleavage. Taken together, our work identifies the P. aeruginosa prepilin peptidase PilD as a zinc-dependent N-methyltransferase and provides a new platform for large-scale synthesis of PilD and other integral membrane proteases important for basic microbial physiology and virulence.
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Affiliation(s)
- Khaled A Aly
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
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48
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Roux N, Spagnolo J, de Bentzmann S. Neglected but amazingly diverse type IVb pili. Res Microbiol 2012; 163:659-73. [PMID: 23103334 DOI: 10.1016/j.resmic.2012.10.015] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Accepted: 10/19/2012] [Indexed: 01/12/2023]
Abstract
This review provides an overview of current knowledge concerning type IVb pili in Gram-negative bacteria. The number of these pili identified is steadily increasing with genome sequencing and mining studies, but studies of these pili are somewhat uneven, because their expression is tightly regulated and the signals or regulators controlling expression need to be identified. However, as illustrated here, they have a number of interesting functional, assembly-related and regulatory features.
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Affiliation(s)
- Nicolas Roux
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, CNRS UMR7255 - Aix Marseille University, Institut de Microbiologie de la Méditerranée, 31 Chemin Joseph Aiguier, 13402, cédex 20, Marseille, France
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49
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Membrane proteases in the bacterial protein secretion and quality control pathway. Microbiol Mol Biol Rev 2012; 76:311-30. [PMID: 22688815 DOI: 10.1128/mmbr.05019-11] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Proteolytic cleavage of proteins that are permanently or transiently associated with the cytoplasmic membrane is crucially important for a wide range of essential processes in bacteria. This applies in particular to the secretion of proteins and to membrane protein quality control. Major progress has been made in elucidating the structure-function relationships of many of the responsible membrane proteases, including signal peptidases, signal peptide hydrolases, FtsH, the rhomboid protease GlpG, and the site 1 protease DegS. These enzymes employ very different mechanisms to cleave substrates at the cytoplasmic and extracytoplasmic membrane surfaces or within the plane of the membrane. This review highlights the different ways that bacterial membrane proteases degrade their substrates, with special emphasis on catalytic mechanisms and substrate delivery to the respective active sites.
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50
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The type II secretion system: biogenesis, molecular architecture and mechanism. Nat Rev Microbiol 2012; 10:336-51. [PMID: 22466878 DOI: 10.1038/nrmicro2762] [Citation(s) in RCA: 347] [Impact Index Per Article: 28.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Many gram-negative bacteria use the sophisticated type II secretion system (T2SS) to translocate a wide range of proteins from the periplasm across the outer membrane. The inner-membrane platform of the T2SS is the nexus of the system and orchestrates the secretion process through its interactions with the periplasmic filamentous pseudopilus, the dodecameric outer-membrane complex and a cytoplasmic secretion ATPase. Here, recent structural and biochemical information is reviewed to describe our current knowledge of the biogenesis and architecture of the T2SS and its mechanism of action.
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