1
|
Carobbi A, Di Nepi S, Fridman CM, Dar Y, Ben‐Yaakov R, Barash I, Salomon D, Sessa G. An antibacterial T6SS in Pantoea agglomerans pv. betae delivers a lysozyme-like effector to antagonize competitors. Environ Microbiol 2022; 24:4787-4802. [PMID: 35706135 PMCID: PMC9796082 DOI: 10.1111/1462-2920.16100] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 06/10/2022] [Indexed: 12/30/2022]
Abstract
The type VI secretion system (T6SS) is deployed by numerous Gram-negative bacteria to deliver toxic effectors into neighbouring cells. The genome of Pantoea agglomerans pv. betae (Pab) phytopathogenic bacteria contains a gene cluster (T6SS1) predicted to encode a complete T6SS. Using secretion and competition assays, we found that T6SS1 in Pab is a functional antibacterial system that allows this pathogen to outcompete rival plant-associated bacteria found in its natural environment. Computational analysis of the T6SS1 gene cluster revealed that antibacterial effector and immunity proteins are encoded within three genomic islands that also harbour arrays of orphan immunity genes or toxin and immunity cassettes. Functional analyses indicated that VgrG, a specialized antibacterial effector, contains a C-terminal catalytically active glucosaminidase domain that is used to degrade prey peptidoglycan. Moreover, we confirmed that a bicistronic unit at the end of the T6SS1 cluster encodes a novel antibacterial T6SS effector and immunity pair. Together, these results demonstrate that Pab T6SS1 is an antibacterial system delivering a lysozyme-like effector to eliminate competitors, and indicate that this bacterium contains additional novel T6SS effectors.
Collapse
Affiliation(s)
- Andrea Carobbi
- School of Plant Sciences and Food Security, The George S. Wise Faculty of Life SciencesTel‐Aviv UniversityTel‐Aviv
| | - Simone Di Nepi
- School of Plant Sciences and Food Security, The George S. Wise Faculty of Life SciencesTel‐Aviv UniversityTel‐Aviv
| | - Chaya M. Fridman
- Department of Clinical Microbiology and Immunology, Sackler Faculty of MedicineTel Aviv UniversityTel Aviv
| | - Yasmin Dar
- Department of Clinical Microbiology and Immunology, Sackler Faculty of MedicineTel Aviv UniversityTel Aviv
| | - Rotem Ben‐Yaakov
- Department of Clinical Microbiology and Immunology, Sackler Faculty of MedicineTel Aviv UniversityTel Aviv
| | - Isaac Barash
- School of Plant Sciences and Food Security, The George S. Wise Faculty of Life SciencesTel‐Aviv UniversityTel‐Aviv
| | - Dor Salomon
- Department of Clinical Microbiology and Immunology, Sackler Faculty of MedicineTel Aviv UniversityTel Aviv
| | - Guido Sessa
- School of Plant Sciences and Food Security, The George S. Wise Faculty of Life SciencesTel‐Aviv UniversityTel‐Aviv
| |
Collapse
|
2
|
Biochemical Characterizations of the Putative Endolysin Ecd09610 Catalytic Domain from Clostridioides difficile. Antibiotics (Basel) 2022; 11:antibiotics11081131. [PMID: 36010000 PMCID: PMC9405191 DOI: 10.3390/antibiotics11081131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/16/2022] [Accepted: 08/18/2022] [Indexed: 11/18/2022] Open
Abstract
Clostridioides difficile is the major pathogen of pseudomembranous colitis, and novel antimicrobial agents are sought after for its treatment. Phage-derived endolysins with species-specific lytic activity have potential as novel antimicrobial agents. We surveyed the genome of C. difficile strain 630 and identified an endolysin gene, Ecd09610, which has an uncharacterized domain at the N-terminus and two catalytic domains that are homologous to glucosaminidase and endopeptidase at the C-terminus. Genes containing the two catalytic domains, the glucosaminidase domain and the endopeptidase domain, were cloned and expressed in Escherichia coli as N-terminal histidine-tagged proteins. The purified domain variants showed lytic activity almost specifically for C. difficile, which has a unique peptide bridge in its peptidoglycan. This species specificity is thought to depend on substrate cleavage activity rather than binding. The domain variants were thermostable, and, notably, the glucosaminidase domain remained active up to 100 °C. In addition, we determined the optimal pH and salt concentrations of these domain variants. Their properties are suitable for formulating a bacteriolytic enzyme as an antimicrobial agent. This lytic enzyme can serve as a scaffold for the construction of high lytic activity mutants with enhanced properties.
Collapse
|
3
|
Sharma A, Sharma N, Gupta D, Lee HJ, Park YS. Comparative genome analysis of four Leuconostoc strains with a focus on carbohydrate-active enzymes and oligosaccharide utilization pathways. Comput Struct Biotechnol J 2022; 20:4771-4785. [PMID: 36147676 PMCID: PMC9465122 DOI: 10.1016/j.csbj.2022.08.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 07/30/2022] [Accepted: 08/13/2022] [Indexed: 11/03/2022] Open
Abstract
Comparative genomic analysis of four Leuconostoc strains was performed. Leuconostoc spp. shared genomic similarity, but their genetic content differed. Leuconostoc spp. showed different genes encoding CAZymes. Oligosaccharide’s utilization and folate biosynthesis pathways were investigated.
Leuconostoc is mostly found in food, plants, and dairy products. Due to their innate genomic features, such as the presence of carbohydrate-active enzymes, bacteriocins, and plasmids, Leuconostoc spp. have great biotechnological potential. In this study, four strains were isolated and identified as Leuconostoc mesenteroides SG315 (LA), L. citreum SG255 (LB), L. lactis CCK940 (LC), and L. lactis SBC001 (LD). Comparative analysis was performed using their draft genome sequences. Differences among the four strains were analyzed using the average nucleotide identity, dot plot, and multiple alignments of conserved genomic sequences. Functional profiling revealed 2134, 1917, 1751, and 1816 open reading frames; 2023, 1823, 1655, and 1699 protein-coding genes; 60, 57, 83, and 82 RNA-coding genes; and GC content of 37.5 %, 38.8 %, 43.3 %, and 43.2 %, in LA, LB, LC, and LD, respectively. The total number of genes encoding carbohydrate-active enzymes was 76 (LA), 73 (LB), 57 (LC), and 67 (LD). These results indicate that the four strains shared a large number of genes, but their gene content is different. Furthermore, most genes with unknown functions were observed in the prophage regions of the genome. This study also elucidated the oligosaccharide utilization and folate biosynthesis pathways in Leuconostoc spp. Taken together, our findings provide useful information on the genomic diversity of CAZymes in the four Leuconostoc strains and suggest that these species could be used for potent exploitation.
Collapse
|
4
|
Roig-Zamboni V, Barelier S, Dixon R, Galley NF, Ghanem A, Nguyen QP, Cahuzac H, Salamaga B, Davis PJ, Bourne Y, Mesnage S, Vincent F. Molecular basis for substrate recognition and septum cleavage by AtlA, the major N-acetylglucosaminidase of Enterococcus faecalis. J Biol Chem 2022; 298:101915. [PMID: 35398351 PMCID: PMC9108991 DOI: 10.1016/j.jbc.2022.101915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 04/04/2022] [Accepted: 04/05/2022] [Indexed: 11/26/2022] Open
Abstract
The cleavage of septal peptidoglycan at the end of cell division facilitates the separation of the two daughter cells. The hydrolases involved in this process (called autolysins) are potentially lethal enzymes that can cause cell death; their activity, therefore, must be tightly controlled during cell growth. In Enterococcus faecalis, the N-acetylglucosaminidase AtlA plays a predominant role in cell separation. atlA mutants form long cell chains and are significantly less virulent in the zebrafish model of infection. The attenuated virulence of atlA mutants is underpinned by a limited dissemination of bacterial chains in the host organism and a more efficient uptake by phagocytes that clear the infection. AtlA has structural homologs in other important pathogens, such as Listeria monocytogenes and Salmonella typhimurium, and therefore represents an attractive model to design new inhibitors of bacterial pathogenesis. Here, we provide a 1.45 Å crystal structure of the E. faecalis AtlA catalytic domain that reveals a closed conformation of a conserved β-hairpin and a complex network of hydrogen bonds that bring two catalytic residues to the ideal distance for an inverting mechanism. Based on the model of the AtlA-substrate complex, we identify key residues critical for substrate recognition and septum cleavage during bacterial growth. We propose that this work will provide useful information for the rational design of specific inhibitors targeting this enterococcal virulence factor and its orthologs in other pathogens.
Collapse
Affiliation(s)
| | | | - Robert Dixon
- School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | - Nicola F Galley
- School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | - Amani Ghanem
- CNRS, Aix Marseille University, AFMB, Marseille, France
| | | | - Héloize Cahuzac
- School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | | | - Peter J Davis
- School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | - Yves Bourne
- CNRS, Aix Marseille University, AFMB, Marseille, France
| | - Stéphane Mesnage
- School of Biosciences, University of Sheffield, Sheffield, United Kingdom.
| | | |
Collapse
|
5
|
Structure of the bacterial flagellar hook cap provides insights into a hook assembly mechanism. Commun Biol 2021; 4:1291. [PMID: 34785766 PMCID: PMC8595650 DOI: 10.1038/s42003-021-02796-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 10/06/2021] [Indexed: 11/14/2022] Open
Abstract
Assembly of bacterial flagellar hook requires FlgD, a protein known to form the hook cap. Symmetry mismatch between the hook and the hook cap is believed to drive efficient assembly of the hook in a way similar to the filament cap helping filament assembly. However, the hook cap dependent mechanism of hook assembly has remained poorly understood. Here, we report the crystal structure of the hook cap composed of five subunits of FlgD from Salmonella enterica at 3.3 Å resolution. The pentameric structure of the hook cap is divided into two parts: a stalk region composed of five N-terminal domains; and a petal region containing five C-terminal domains. Biochemical and genetic analyses show that the N-terminal domains of the hook cap is essential for the hook-capping function, and the structure now clearly reveals why. A plausible hook assembly mechanism promoted by the hook cap is proposed based on the structure.
Collapse
|
6
|
Xu H, Hu B, Flesher DA, Liu J, Motaleb MA. BB0259 Encompasses a Peptidoglycan Lytic Enzyme Function for Proper Assembly of Periplasmic Flagella in Borrelia burgdorferi. Front Microbiol 2021; 12:692707. [PMID: 34659138 PMCID: PMC8517470 DOI: 10.3389/fmicb.2021.692707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 08/19/2021] [Indexed: 11/18/2022] Open
Abstract
Assembly of the bacterial flagellar rod, hook, and filament requires penetration through the peptidoglycan (PG) sacculus and outer membrane. In most β- and γ-proteobacteria, the protein FlgJ has two functional domains that enable PG hydrolyzing activity to create pores, facilitating proper assembly of the flagellar rod. However, two distinct proteins performing the same functions as the dual-domain FlgJ are proposed in δ- and ε-proteobacteria as well as spirochetes. The Lyme disease spirochete Borrelia burgdorferi genome possesses a FlgJ and a PG lytic SLT enzyme protein homolog (BB0259). FlgJ in B. burgdorferi is crucial for flagellar hook and filament assembly but not for the proper rod assembly reported in other bacteria. However, BB0259 has never been characterized. Here, we use cryo-electron tomography to visualize periplasmic flagella in different bb0259 mutant strains and provide evidence that the E580 residue of BB0259 is essential for PG-hydrolyzing activity. Without the enzyme activity, the flagellar hook fails to penetrate through the pores in the cell wall to complete assembly of an intact periplasmic flagellum. Given that FlgJ and BB0259 interact with each other, they likely coordinate the penetration through the PG sacculus and assembly of a functional flagellum in B. burgdorferi and other spirochetes. Because of its role, we renamed BB0259 as flagellar-specific lytic transglycosylase or LTaseBb.
Collapse
Affiliation(s)
- Hui Xu
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, NC, United States
| | - Bo Hu
- Department of Microbiology and Molecular Genetics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - David A. Flesher
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, United States
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Jun Liu
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, United States
- Microbial Sciences Institute, Yale University, West Haven, CT, United States
| | - Md A. Motaleb
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, NC, United States
| |
Collapse
|
7
|
Integrated Phenotypic-Genotypic Analysis of Latilactobacillus sakei from Different Niches. Foods 2021; 10:foods10081717. [PMID: 34441495 PMCID: PMC8393274 DOI: 10.3390/foods10081717] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 07/22/2021] [Accepted: 07/23/2021] [Indexed: 11/16/2022] Open
Abstract
Increasing attention has been paid to the potential probiotic effects of Latilactobacillus sakei. To explore the genetic diversity of L. sakei, 14 strains isolated from different niches (feces, fermented kimchi, and meat products) and 54 published strains were compared and analyzed. The results showed that the average genome size and GC content of L. sakei were 1.98 Mb and 41.22%, respectively. Its core genome mainly encodes translation and transcription, amino acid synthesis, glucose metabolism, and defense functions. L. sakei has open pan-genomic characteristics, and its pan-gene curve shows an upward trend. The genetic diversity of L. sakei is mainly reflected in carbohydrate utilization, antibiotic tolerance, and immune/competition-related factors, such as clustering regular interval short palindromic repeat sequence (CRISPR)-Cas. The CRISPR system is mainly IIA type, and a few are IIC types. This work provides a basis for the study of this species.
Collapse
|
8
|
Sinclair TR, van den Hengel SK, Raza BG, Rutjes SA, de Roda Husman AM, Peijnenburg WJGM, Roesink HEDW, de Vos WM. Surface chemistry-dependent antiviral activity of silver nanoparticles. NANOTECHNOLOGY 2021; 32:365101. [PMID: 34020439 DOI: 10.1088/1361-6528/ac03d6] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 05/20/2021] [Indexed: 06/12/2023]
Abstract
The toxicity towards viruses of silver nanoparticles (AgNPs) has been reported to be dependent on several factors such as particle concentration, size, and shape. Although these factors may indeed contribute to the toxicity of AgNPs, the results presented in this work demonstrate that surface chemistry and especially surface charge is a crucial factor governing their antiviral activity. Here, this work investigated the influence of capping agents representing various surface charges ranging from negative to positive. These AgNPs were capped with citrate, polyethylene glycol (PEG), polyvinylpyrrolidone (PVP) mercaptoacetic acid (MAA) and (branched polyethyleneimine (BPEI). We show that AgNPs exhibited surface charge-dependent toxicity towards MS2 bacteriophages. Among the capping agents under investigation, BPEI capped AgNPs (Ag/BPEI) exhibited the highest reduction of MS2 resulting in ≥6 log10-units reductions, followed by 4-5 log10-units reductions with PVP and PEG capping's and 3-4 log10-units with MAA and citrate cappings. Bare nanoparticles reported a mere 1-2 log10-units reduction. Electrostatic interaction between the positively charged BPEI-coating and the negatively charged virus surface played a significant role in bringing the MS2 closer to toxic silver ions (Ag+). Further results obtained from TEM showed that Ag/BPEI nanoparticles could directly damage the structure of the MS2 bacteriophages. AgNPs and cationic capping agents' observed synergy can lead to much lower and much more efficient dosing of AgNPs for antiviral applications.
Collapse
Affiliation(s)
- Terica R Sinclair
- Membrane Science & Technology, MESA + Institute for Nanotechnology, University of Twente, Faculty of Science and Technology, PO Box 217, 7500 AE Enschede, The Netherlands
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA Leeuwarden, The Netherlands
| | - Sanne K van den Hengel
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA Leeuwarden, The Netherlands
- National Institute for Public health and the environment (RIVM), A van Leeuwenhoeklaan, 9, 3721 MA Bilthoven, The Netherlands
| | - Brahzil G Raza
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA Leeuwarden, The Netherlands
| | - Saskia A Rutjes
- National Institute for Public health and the environment (RIVM), A van Leeuwenhoeklaan, 9, 3721 MA Bilthoven, The Netherlands
| | - Ana Maria de Roda Husman
- National Institute for Public health and the environment (RIVM), A van Leeuwenhoeklaan, 9, 3721 MA Bilthoven, The Netherlands
- Institute of Risk Assessment Sciences, IRAS within the faculties of Veterinary Medicine, Medicine and Sciences of Utrecht University, The Netherlands
| | - Willie J G M Peijnenburg
- National Institute for Public health and the environment (RIVM), A van Leeuwenhoeklaan, 9, 3721 MA Bilthoven, The Netherlands
- Institute of Environmental Sciences (CML), Leiden University, PO Box 9518, 2300 RA Leiden, The Netherlands
| | - H Erik D W Roesink
- Membrane Science & Technology, MESA + Institute for Nanotechnology, University of Twente, Faculty of Science and Technology, PO Box 217, 7500 AE Enschede, The Netherlands
| | - Wiebe M de Vos
- Membrane Science & Technology, MESA + Institute for Nanotechnology, University of Twente, Faculty of Science and Technology, PO Box 217, 7500 AE Enschede, The Netherlands
| |
Collapse
|
9
|
Li C, Sun X, Niu B, Jiang Y, Yang J, Chen Q. Exopolysaccharide related gene bcsG affects biofilm formation of Cronobacter spp. Int Dairy J 2020. [DOI: 10.1016/j.idairyj.2020.104844] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
10
|
Structural Conservation and Adaptation of the Bacterial Flagella Motor. Biomolecules 2020; 10:biom10111492. [PMID: 33138111 PMCID: PMC7693769 DOI: 10.3390/biom10111492] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 10/26/2020] [Accepted: 10/27/2020] [Indexed: 02/07/2023] Open
Abstract
Many bacteria require flagella for the ability to move, survive, and cause infection. The flagellum is a complex nanomachine that has evolved to increase the fitness of each bacterium to diverse environments. Over several decades, molecular, biochemical, and structural insights into the flagella have led to a comprehensive understanding of the structure and function of this fascinating nanomachine. Notably, X-ray crystallography, cryo-electron microscopy (cryo-EM), and cryo-electron tomography (cryo-ET) have elucidated the flagella and their components to unprecedented resolution, gleaning insights into their structural conservation and adaptation. In this review, we focus on recent structural studies that have led to a mechanistic understanding of flagellar assembly, function, and evolution.
Collapse
|
11
|
Camarena L, Dreyfus G. Living in a Foster Home: The Single Subpolar Flagellum Fla1 of Rhodobacter sphaeroides. Biomolecules 2020; 10:E774. [PMID: 32429424 PMCID: PMC7277832 DOI: 10.3390/biom10050774] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 05/12/2020] [Accepted: 05/13/2020] [Indexed: 12/14/2022] Open
Abstract
Rhodobacter sphaeroides is an α-proteobacterium that has the particularity of having two functional flagellar systems used for swimming. Under the growth conditions commonly used in the laboratory, a single subpolar flagellum that traverses the cell membrane, is assembled on the surface. This flagellum has been named Fla1. Phylogenetic analyses have suggested that this flagellar genetic system was acquired from an ancient γ-proteobacterium. It has been shown that this flagellum has components homologous to those present in other γ-proteobacteria such as the H-ring characteristic of the Vibrio species. Other features of this flagellum such as a straight hook, and a prominent HAP region have been studied and the molecular basis underlying these features has been revealed. It has also been shown that FliL, and the protein MotF, mainly found in several species of the family Rhodobacteraceae, contribute to remodel the amphipathic region of MotB, known as the plug, in order to allow flagellar rotation. In the absence of the plug region of MotB, FliL and MotF are dispensable. In this review we have covered the most relevant aspects of the Fla1 flagellum of this remarkable photosynthetic bacterium.
Collapse
Affiliation(s)
- Laura Camarena
- Depto. Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CDMX 04510, Mexico
| | - Georges Dreyfus
- Depto. Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad Universitaria, CDMX 04510, Mexico
| |
Collapse
|
12
|
Coloma-Rivero RF, Gómez L, Alvarez F, Saitz W, Del Canto F, Céspedes S, Vidal R, Oñate AA. The Role of the Flagellar Protein FlgJ in the Virulence of Brucella abortus. Front Cell Infect Microbiol 2020; 10:178. [PMID: 32411617 PMCID: PMC7198779 DOI: 10.3389/fcimb.2020.00178] [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: 12/20/2019] [Accepted: 04/03/2020] [Indexed: 12/28/2022] Open
Abstract
Brucella abortus is a facultative intracellular pathogen that causes a zoonosis called brucellosis. This disease leads to abortion and infertility in cattle, and diverse complications in humans. B. abortus is a successful intracellular bacterium that has developed the ability to evade the host's immune system and it replicates in professional and non-professional phagocytic cells, persisting in the different tissues, and organs of its hosts. It has been described that Brucella expresses a polar flagellum under certain conditions, but its function is still unknown. In this study we evaluated the role of the FlgJ, a protein, presumably a peptidoglycan hydrolase involved in flagellum formation and in the virulence of B. abortus strain 2308. B. abortus 2308 ΔflgJ mutant and complemented strains were constructed to study the function of the FlgJ protein in the context of the virulence of this pathogen in in vitro and in vivo assays. The results showed that the elimination of the flgJ gene delays the growth rate of B. abortus in culture, reduces its intracellular survival capacity in professional and non-professional phagocytic cells, rendering it unable to escape from the endocytic route and not reaching the endoplasmic reticulum. It also negatively affects their persistence in BALB/c mice. Functionally, the B. abortus 2308 flgJ gene restored motility to an E. coli flgJ mutant gene. Furthermore, it was discovered that the production of FlgJ protein is associated with the bacterial adherence by B. abortus. Therefore, although the specific function of the polar flagellum for Brucella is unknown, the data indicates that the flagellar flgJ gene and its product are required for full virulence of B. abortus 2308, since its deletion significantly reduces the fitness of this pathogen in vitro and in vivo.
Collapse
Affiliation(s)
- Roberto F Coloma-Rivero
- Laboratory of Molecular Immunology, Department of Microbiology, Faculty of Biological Sciences, Universidad de Concepción, Concepción, Chile
| | - Leonardo Gómez
- Laboratory of Molecular Immunology, Department of Microbiology, Faculty of Biological Sciences, Universidad de Concepción, Concepción, Chile
| | - Francisco Alvarez
- Laboratory of Molecular Immunology, Department of Microbiology, Faculty of Biological Sciences, Universidad de Concepción, Concepción, Chile
| | - Waleska Saitz
- Laboratory of Molecular Immunology, Department of Microbiology, Faculty of Biological Sciences, Universidad de Concepción, Concepción, Chile.,Microbiology and Mycology Program, Institute of Biomedical Sciences, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Felipe Del Canto
- Microbiology and Mycology Program, Institute of Biomedical Sciences, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Sandra Céspedes
- Laboratory of Molecular Immunology, Department of Microbiology, Faculty of Biological Sciences, Universidad de Concepción, Concepción, Chile.,Microbiology and Mycology Program, Institute of Biomedical Sciences, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Roberto Vidal
- Microbiology and Mycology Program, Institute of Biomedical Sciences, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Angel A Oñate
- Laboratory of Molecular Immunology, Department of Microbiology, Faculty of Biological Sciences, Universidad de Concepción, Concepción, Chile
| |
Collapse
|
13
|
Zhang Q, Zhang L, Ross P, Zhao J, Zhang H, Chen W. Comparative Genomics of Lactobacillus crispatus from the Gut and Vagina Reveals Genetic Diversity and Lifestyle Adaptation. Genes (Basel) 2020; 11:genes11040360. [PMID: 32230824 PMCID: PMC7230607 DOI: 10.3390/genes11040360] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 03/23/2020] [Accepted: 03/25/2020] [Indexed: 12/20/2022] Open
Abstract
Lactobacillus crispatus colonizes the human feces, human vagina, and the crops and ceca of chicken. To explore the genetic characteristics and evolutionary relationships of L. crispatus isolated from different niches, we selected 37 strains isolated from the human vagina (n = 17), human feces (n = 11), and chicken feces (n = 9), and used comparative genomics to explore the genetic information of L. crispatus from the feces and vagina. No significant difference was found in the three sources of genomic features such as genome size, GC content, and number of protein coding sequences (CDS). However, in a phylogenetic tree constructed based on core genes, vagina-derived L. crispatus and feces-derived strains were each clustered separately. Therefore, the niche exerted an important impact on the evolution of L. crispatus. According to gene annotation, the L. crispatus derived from the vagina possessed a high abundance of genes related to acid tolerance, redox reactions, pullulanase, and carbohydrate-binding modules (CBMs). These genes helped L. crispatus to better adapt to the acidic environment of the vagina and obtain more nutrients, maintaining its dominance in the vagina in competition with other strains. In feces-derived bacteria, more genes encoding CRISPR/Cas system, glycoside hydrolases (GHs) family, and tetracycline/lincomycin resistance genes were found to adapt to the complex intestinal environment. This study highlights the evolutionary relationship of L. crispatus strains isolated from the vagina and feces, and the adaptation of L. crispatus to the host environment.
Collapse
Affiliation(s)
- Qiuxiang Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (Q.Z.); (L.Z.); (J.Z.); (H.Z.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- International Joint Research Center for Probiotics & Gut Health, Jiangnan University, Wuxi 214122, China
| | - Lili Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (Q.Z.); (L.Z.); (J.Z.); (H.Z.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Paul Ross
- International Joint Research Center for Probiotics & Gut Health, Jiangnan University, Wuxi 214122, China
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (Q.Z.); (L.Z.); (J.Z.); (H.Z.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (Q.Z.); (L.Z.); (J.Z.); (H.Z.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
- Wuxi Translational Medicine Research Center and Jiangsu Translational Medicine Research Institute Wuxi Branch, Wuxi 214122, China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (Q.Z.); (L.Z.); (J.Z.); (H.Z.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
- Beijing Innovation Centre of Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
- Correspondence: ; Tel.: +86-510-859-12155
| |
Collapse
|
14
|
Evaluation of Feasibility of Using the Bacteriophage T4 Lysozyme to Improve the Hydrolysis and Biochemical Methane Potential of Secondary Sludge. ENERGIES 2019. [DOI: 10.3390/en12193644] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Anaerobic digestion (AD) of secondary sludge is a rate-limiting step due to the bacterial cell wall. In this study, experiments were performed to characterize secondary sludges from three wastewater treatment plants (WWTPs), and to investigate the feasibility of using bacteriophage lysozymes to speed up AD by accelerating the degradation of bacterial cell walls. Protein was the main organic material (67.7% of volatile solids in the sludge). The bacteriophage T4 lysozyme (T4L) was tested for hydrolysis and biochemical methane potential. Variations in the volatile suspended solid (VSS) concentration and biogas production were monitored. The VSS reduction efficiencies by hydrolysis using T4L for 72 h increased and ranged from 17.8% to 26.4%. Biogas production using T4L treated sludges increased and biogas production was increased by as much as 82.4%. Biogas production rate also increased, and the average reaction rate coefficient of first-order kinetics was 0.56 ± 0.02/d, which was up to 47.5% higher compared to the untreated samples at the maximum. Alphaproteobacteria, Betaproteobacteria, Flavobacteriia, Gammaproteobacteria, and Sphingobacteriia were major microbial classes in all sludges. The interpretation of the microbial community structure indicated that T4L treatment is likely to increase the rate of cell wall digestion.
Collapse
|
15
|
Lyons BJE, Strynadka NCJ. On the road to structure-based development of anti-virulence therapeutics targeting the type III secretion system injectisome. MEDCHEMCOMM 2019; 10:1273-1289. [PMID: 31534650 PMCID: PMC6748289 DOI: 10.1039/c9md00146h] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 06/07/2019] [Indexed: 12/19/2022]
Abstract
The type III secretion system injectisome is a syringe-like multimembrane spanning nanomachine that is essential to the pathogenicity but not viability of many clinically relevant Gram-negative bacteria, such as enteropathogenic Escherichia coli, Salmonella enterica and Pseudomonas aeruginosa. Due to the rise in antibiotic resistance, new strategies must be developed to treat the growing spectre of drug resistant infections. Targeting the injectisome via an 'anti-virulence strategy' is a promising avenue to pursue as an alternative to the more commonly used bactericidal therapeutics, which have a high propensity for resulting resistance development and often more broad killing profile, including unwanted side effects in eliminating favourable members of the microbiome. Building on more than a decade of crystallographic work of truncated or isolated forms of the more than two dozen components of the secretion apparatus, recent advances in the field of single-particle cryo-electron microscopy have allowed for the elucidation of atomic resolution structures for many of the type III secretion system components in their assembled, oligomerized state including the needle complex, export apparatus and ATPase. Cryo-electron tomography studies have also advanced our understanding of the direct pathogen-host interaction between the type III secretion system translocon and host cell membrane. These new structural works that further our understanding of the myriad of protein-protein interactions that promote injectisome function will be highlighted in this review, with a focus on those that yield promise for future anti-virulence drug discovery and design. Recently developed inhibitors, including both synthetic, natural product and peptide inhibitors, as well as promising new developments of immunotherapeutics will be discussed. As our understanding of this intricate molecular machinery advances, the development of anti-virulence inhibitors can be enhanced through structure-guided drug design.
Collapse
Affiliation(s)
- Bronwyn J E Lyons
- Department of Biochemistry and Molecular Biology and Center for Blood Research , University of British Columbia , 2350 Health Sciences Mall , Vancouver , British Columbia V6T 1Z3 , Canada .
| | - Natalie C J Strynadka
- Department of Biochemistry and Molecular Biology and Center for Blood Research , University of British Columbia , 2350 Health Sciences Mall , Vancouver , British Columbia V6T 1Z3 , Canada .
| |
Collapse
|
16
|
Borišek J, Pintar S, Ogrizek M, Turk D, Perdih A, Novič M. A Water-Assisted Catalytic Mechanism in Glycoside Hydrolases Demonstrated on the Staphylococcus aureus Autolysin E. ACS Catal 2018. [DOI: 10.1021/acscatal.8b01064] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Jure Borišek
- National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
| | - Sara Pintar
- Department of Biochemistry, Molecular and Structural Biology, Jozef Stefan Institute, Jamova cesta 39, SI-1000 Ljubljana, Slovenia
- Jozef Stefan International Postgraduate School, Jamova cesta 39, SI-1000 Ljubljana, Slovenia
| | - Mitja Ogrizek
- National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
| | - Dušan Turk
- Department of Biochemistry, Molecular and Structural Biology, Jozef Stefan Institute, Jamova cesta 39, SI-1000 Ljubljana, Slovenia
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jamova cesta 39, SI-1000 Ljubljana, Slovenia
| | - Andrej Perdih
- National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
| | - Marjana Novič
- National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
| |
Collapse
|
17
|
Bacterial flagellar axial structure and its construction. Biophys Rev 2017; 10:559-570. [PMID: 29235079 DOI: 10.1007/s12551-017-0378-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 11/26/2017] [Indexed: 12/19/2022] Open
Abstract
The bacterial flagellum is a motile organelle composed of thousands of protein subunits. The filamentous part that extends from the cell membrane is called the axial structure and consists of three major parts, the filament, hook, and rod, and other minor components. Each of the three main parts shares a similar self-assembly mechanism and a common basic architecture of subunit arrangement while showing quite distinct mechanical properties to achieve its specific function. Structural and molecular mechanisms to produce these various mechanical properties of the axial structure, such as the filament, the hook, and the rod, have been revealed by the complementary use of X-ray crystallography and cryo-electron microscopy. In addition, the mechanism of growth of the axial structure is beginning to be revealed based on the molecular structure.
Collapse
|
18
|
Tamai E, Sekiya H, Goda E, Makihata N, Maki J, Yoshida H, Kamitori S. Structural and biochemical characterization of the Clostridium perfringens autolysin catalytic domain. FEBS Lett 2016; 591:231-239. [PMID: 27926788 DOI: 10.1002/1873-3468.12515] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 11/17/2016] [Accepted: 11/26/2016] [Indexed: 11/08/2022]
Abstract
Bacterial autolysins can partially hydrolyze cell wall peptidoglycans into small sections to regulate cell separation/division and the growth phase. Clostridium perfringens autolysin (Acp) has an N-terminal cell wall-binding domain and a C-terminal catalytic domain with glucosaminidase activity that belongs to the glycoside hydrolase 73 family. Here, we determined the X-ray structure of the Acp catalytic domain (AcpCD) at 1.76 Å resolution. AcpCD has a unique crescent-shaped structure, forming a deep groove for substrate-binding at the center of the protein. The modeling study of the enzyme/substrate complex demonstrated that the length of the substrate-binding groove is closely related to the glucosaminidase activity. Mutagenesis analysis showed that AcpCD likely adopts a neighboring-group mechanism for the catalytic reaction.
Collapse
Affiliation(s)
- Eiji Tamai
- Department of Infectious Disease, College of Pharmaceutical Science, Matsuyama University, Bunkyo-cho, Ehime, Japan.,Life Science Research Center and Faculty of Medicine, Kagawa University, Miki-cho, Kita-gun, Kagawa, Japan
| | - Hiroshi Sekiya
- Department of Infectious Disease, College of Pharmaceutical Science, Matsuyama University, Bunkyo-cho, Ehime, Japan
| | - Eri Goda
- Department of Infectious Disease, College of Pharmaceutical Science, Matsuyama University, Bunkyo-cho, Ehime, Japan
| | - Nahomi Makihata
- Department of Infectious Disease, College of Pharmaceutical Science, Matsuyama University, Bunkyo-cho, Ehime, Japan
| | - Jun Maki
- Department of Infectious Disease, College of Pharmaceutical Science, Matsuyama University, Bunkyo-cho, Ehime, Japan
| | - Hiromi Yoshida
- Life Science Research Center and Faculty of Medicine, Kagawa University, Miki-cho, Kita-gun, Kagawa, Japan
| | - Shigehiro Kamitori
- Life Science Research Center and Faculty of Medicine, Kagawa University, Miki-cho, Kita-gun, Kagawa, Japan
| |
Collapse
|
19
|
Herlihey FA, Clarke AJ. Controlling Autolysis During Flagella Insertion in Gram-Negative Bacteria. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 925:41-56. [PMID: 27722959 DOI: 10.1007/5584_2016_52] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The flagellum is an important macromolecular machine for many pathogenic bacteria. It is a hetero-oligomeric structure comprised of three major sub-structures: basal body, hook and thin helical filament. An important step during flagellum assembly is the localized and controlled degradation of the peptidoglycan sacculus to allow for the insertion of the rod as well as to facilitate anchoring for proper motor function. The peptidoglycan lysis events require specialized lytic enzymes, β-N-acetylglucosaminidases and lytic transglycosylases, which differ in flagellated proteobacteria. Due to their autolytic activity, these enzymes need to be controlled in order to prevent cellular lysis. This review summarizes are current understanding of the peptidoglycan lysis events required for flagellum assembly and motility with a main focus on Gram-negative bacteria.
Collapse
Affiliation(s)
- Francesca A Herlihey
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, N1G2W1, Canada
| | - Anthony J Clarke
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, N1G2W1, Canada.
| |
Collapse
|