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Suleman M, Yaseen AR, Ahmed S, Khan Z, Irshad A, Pervaiz A, Rahman HH, Azhar M. Pyocins and Beyond: Exploring the World of Bacteriocins in Pseudomonas aeruginosa. Probiotics Antimicrob Proteins 2024:10.1007/s12602-024-10322-3. [PMID: 39023701 DOI: 10.1007/s12602-024-10322-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/08/2024] [Indexed: 07/20/2024]
Abstract
Pseudomonas aeruginosa significantly induces health-associated infections in a variety of species other than humans. Over the years, the opportunistic pathogen has developed resistance against commonly used antibiotics. Since most P. aeruginosa strains are multi-drug resistant, regular antibiotic treatment of its infections is becoming a dire concern, shifting the global focus towards the development of alternate antimicrobial approaches. Pyocins are one of the most diverse antimicrobial peptide combinations produced by bacteria. They have potent antimicrobial properties, mainly against bacteria from the same phylogenetic group. P. aeruginosa, whether from clinical or environmental origins, produce several different pyocins that show inhibitory activity against other multi-drug-resistant strains of P. aeruginosa. They are, therefore, good candidates for alternate therapeutic antimicrobials because they have a unique mode of action that kills antibiotic-resistant bacteria by attacking their biofilms. Here, we review pseudomonas-derived antimicrobial pyocins with great therapeutic potential against multi-drug-resistant P. aeruginosa.
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Affiliation(s)
- Muhammad Suleman
- School of Biological Sciences, Faculty of Life Sciences, University of the Punjab, Lahore, 54590, Pakistan.
| | - Allah Rakha Yaseen
- School of Biological Sciences, Faculty of Life Sciences, University of the Punjab, Lahore, 54590, Pakistan
| | - Shahbaz Ahmed
- School of Biological Sciences, Faculty of Life Sciences, University of the Punjab, Lahore, 54590, Pakistan
| | - Zoha Khan
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, 54590, Pakistan
| | - Asma Irshad
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, 54590, Pakistan
| | - Afsah Pervaiz
- Institute of Microbiology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Hafiza Hiba Rahman
- Department of Pathology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Muteeba Azhar
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, 54590, Pakistan
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2
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Antimicrobial Weapons of Pseudomonas aeruginosa. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1386:223-256. [DOI: 10.1007/978-3-031-08491-1_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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3
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Chai R, Rooney WM, Milner JJ, Walker D. Challenges of using protein antibiotics for pathogen control. PEST MANAGEMENT SCIENCE 2021; 77:3836-3840. [PMID: 33527621 DOI: 10.1002/ps.6312] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/18/2021] [Accepted: 02/02/2021] [Indexed: 06/12/2023]
Abstract
Bacterial phytopathogens represent a significant threat to many economically important crops. Current control measures often inflict harm on the environment and may ultimately impact on human health through the spread of antibiotic resistance. Antimicrobial proteins such as bacteriocins have been suggested as the next generation of disease control agents since they are able to specifically target the pathogen of interest with minimal impact on the wider microbial community and environment. However, substantial gaps in knowledge with regards to the efficacy and application of bacteriocins to combat phytopathogenic bacteria remain. Here we highlight the immediate challenges the community must address to ensure maximum exploitation of antimicrobial proteins in the field. © 2021 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Ray Chai
- College of Medical, Veterinary & Life Sciences, Institute of Infection, Immunity & Inflammation, University of Glasgow, Glasgow, UK
| | - William M Rooney
- College of Medical, Veterinary & Life Sciences, Institute of Infection, Immunity & Inflammation, University of Glasgow, Glasgow, UK
- Plant Science Group, College of Molecular, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - Joel J Milner
- Plant Science Group, College of Molecular, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - Daniel Walker
- College of Medical, Veterinary & Life Sciences, Institute of Infection, Immunity & Inflammation, University of Glasgow, Glasgow, UK
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Rooney WM, Chai R, Milner JJ, Walker D. Bacteriocins Targeting Gram-Negative Phytopathogenic Bacteria: Plantibiotics of the Future. Front Microbiol 2020; 11:575981. [PMID: 33042091 PMCID: PMC7530242 DOI: 10.3389/fmicb.2020.575981] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 08/25/2020] [Indexed: 12/12/2022] Open
Abstract
Gram-negative phytopathogenic bacteria are a significant threat to food crops. These microbial invaders are responsible for a plethora of plant diseases and can be responsible for devastating losses in crops such as tomatoes, peppers, potatoes, olives, and rice. Current disease management strategies to mitigate yield losses involve the application of chemicals which are often harmful to both human health and the environment. Bacteriocins are small proteinaceous antibiotics produced by bacteria to kill closely related bacteria and thereby establish dominance within a niche. They potentially represent a safer alternative to chemicals when used in the field. Bacteriocins typically show a high degree of selectivity toward their targets with no off-target effects. This review outlines the current state of research on bacteriocins active against Gram-negative phytopathogenic bacteria. Furthermore, we will examine the feasibility of weaponizing bacteriocins for use as a treatment for bacterial plant diseases.
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Affiliation(s)
- William M. Rooney
- Plant Science Group, School of Life Sciences, Institute of Molecular, Cell and Systems Biology, University of Glasgow, Glasgow, United Kingdom
- College of Medical, Veterinary and Life Sciences, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Ray Chai
- College of Medical, Veterinary and Life Sciences, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Joel J. Milner
- Plant Science Group, School of Life Sciences, Institute of Molecular, Cell and Systems Biology, University of Glasgow, Glasgow, United Kingdom
| | - Daniel Walker
- College of Medical, Veterinary and Life Sciences, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
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Rooney WM, Grinter RW, Correia A, Parkhill J, Walker DC, Milner JJ. Engineering bacteriocin-mediated resistance against the plant pathogen Pseudomonas syringae. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:1296-1306. [PMID: 31705720 PMCID: PMC7152609 DOI: 10.1111/pbi.13294] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 10/16/2019] [Accepted: 10/27/2019] [Indexed: 05/20/2023]
Abstract
The plant pathogen, Pseudomonas syringae (Ps), together with related Ps species, infects and attacks a wide range of agronomically important crops, including tomato, kiwifruit, pepper, olive and soybean, causing economic losses. Currently, chemicals and introduced resistance genes are used to protect plants against these pathogens but have limited success and may have adverse environmental impacts. Consequently, there is a pressing need to develop alternative strategies to combat bacterial disease in crops. One such strategy involves using narrow-spectrum protein antibiotics (so-called bacteriocins), which diverse bacteria use to compete against closely related species. Here, we demonstrate that one bacteriocin, putidacin L1 (PL1), can be expressed in an active form at high levels in Arabidopsis and in Nicotiana benthamiana in planta to provide effective resistance against diverse pathovars of Ps. Furthermore, we find that Ps strains that mutate to acquire tolerance to PL1 lose their O-antigen, exhibit reduced motility and still cannot induce disease symptoms in PL1-transgenic Arabidopsis. Our results provide proof-of-principle that the transgene-mediated expression of a bacteriocin in planta can provide effective disease resistance to bacterial pathogens. Thus, the expression of bacteriocins in crops might offer an effective strategy for managing bacterial disease, in the same way that the genetic modification of crops to express insecticidal proteins has proven to be an extremely successful strategy for pest management. Crucially, nearly all genera of bacteria, including many plant pathogenic species, produce bacteriocins, providing an extensive source of these antimicrobial agents.
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Affiliation(s)
- William M. Rooney
- Plant Science GroupInstitute of Molecular, Cell and Systems Biology & School of Life SciencesUniversity of GlasgowGlasgowUK
- Institute of Infection, Immunity & InflammationCollege of Medical, Veterinary & Life SciencesUniversity of GlasgowGlasgowUK
| | - Rhys W. Grinter
- Institute of Infection, Immunity & InflammationCollege of Medical, Veterinary & Life SciencesUniversity of GlasgowGlasgowUK
- Present address:
School of Biological SciencesCentre for Geometric BiologyMonash UniversityClaytonVictoria3800Australia
| | - Annapaula Correia
- Wellcome Trust Sanger InstituteWellcome Trust Genome CampusHinxtonUK
- Present address:
Department of ZoologyUniversity of OxfordSouth Parks RoadOxfordOX1 3PSUK
| | - Julian Parkhill
- Wellcome Trust Sanger InstituteWellcome Trust Genome CampusHinxtonUK
- Present address:
Department of Veterinary MedicineUniversity of CambridgeMadingley RoadCambridgeCB3 0ESUK
| | - Daniel C. Walker
- Institute of Infection, Immunity & InflammationCollege of Medical, Veterinary & Life SciencesUniversity of GlasgowGlasgowUK
| | - Joel J. Milner
- Plant Science GroupInstitute of Molecular, Cell and Systems Biology & School of Life SciencesUniversity of GlasgowGlasgowUK
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6
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Victorio-De Los Santos M, Vibanco-Pérez N, Soto-Rodriguez S, Pereyra A, Zenteno E, Cano-Sánchez P. The B Subunit of PirAB vp Toxin Secreted from Vibrio parahaemolyticus Causing AHPND Is an Amino Sugar Specific Lectin. Pathogens 2020; 9:E182. [PMID: 32138213 PMCID: PMC7157558 DOI: 10.3390/pathogens9030182] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 02/17/2020] [Accepted: 02/29/2020] [Indexed: 11/26/2022] Open
Abstract
Vibrio parahaemolyticus (Vp) is the etiological agent of the acute hepatopancreatic necrosis disease (AHPND) in Penaeus vannamei shrimp. Vp possesses a 63-70 kb conjugative plasmid that encodes the binary toxin PirAvp/PirBvp. The 250 kDa PirABvp complex was purified by affinity chromatography with galactose-sepharose 4B and on a stroma from glutaraldehyde-fixed rat erythrocytes column, as a heterotetramer of PirAvp and PirBvp subunits. In addition, recombinant pirB (rPirBvp) and pirA (rPirAvp) were obtained. The homogeneity of the purified protein was determined by SDS-PAGE analysis, and the yield of protein was 488 ng/100 μg of total protein of extracellular products. The PirABvp complex and the rPirBvp showed hemagglutinating activity toward rat erythrocytes. The rPirAvp showed no hemagglutinating capacity toward the animal red cells tested. Among different mono and disaccharides tested, only GalNH2 and GlcNH2 were able to inhibit hemagglutination of the PirABvp complex and the rPirBvp. Glycoproteins showed inhibitory specificity, and fetuin was the glycoprotein that showed the highest inhibition. Other glycoproteins, such as mucin, and glycosaminoglycans, such as heparin, also inhibited the activity. Desialylation of erythrocytes enhanced the hemagglutinating activity. This confirms that Gal or Gal (β1,4) GlcNAc are the main ligands for PirABvp. The agglutinating activity of the PirABvp complex and the rPirBvp is not dependent on cations, because addition of Mg2+ or Ca2+ showed no effect on the protein capacity. Our results strongly suggest that the PirBvp subunit is a lectin, which is part of the PirA/PirBvp complex, and it seems to participate in bacterial pathogenicity.
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Affiliation(s)
- Marcelo Victorio-De Los Santos
- Laboratorio de Bacteriología. Centro de Investigación en Alimentación y Desarrollo, A.C. Unidad de Acuacultura y Manejo Ambiental, Av. Sábalo-Cerritos S/N A.P. 711, Mazatlán, Sinaloa 82112, Mexico
- Laboratorio de Investigación en Biología Molecular e Inmunología, Unidad Académica de Ciencias Químico Biológicas y Farmacéuticas, Universidad Autónoma de Nayarit, Ciudad de la Cultura, Tepic, Nayarit 63190, Mexico
| | - Norberto Vibanco-Pérez
- Laboratorio de Investigación en Biología Molecular e Inmunología, Unidad Académica de Ciencias Químico Biológicas y Farmacéuticas, Universidad Autónoma de Nayarit, Ciudad de la Cultura, Tepic, Nayarit 63190, Mexico
| | - Sonia Soto-Rodriguez
- Laboratorio de Bacteriología. Centro de Investigación en Alimentación y Desarrollo, A.C. Unidad de Acuacultura y Manejo Ambiental, Av. Sábalo-Cerritos S/N A.P. 711, Mazatlán, Sinaloa 82112, Mexico
| | - Ali Pereyra
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, Coyoacan, CDMX 04510, Mexico; (A.P.); (E.Z.)
| | - Edgar Zenteno
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, Coyoacan, CDMX 04510, Mexico; (A.P.); (E.Z.)
| | - Patricia Cano-Sánchez
- Laboratorio de Biología Molecular, Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, Coyoacan, CDMX 04510, Mexico;
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MacNair CR, Tsai CN, Brown ED. Creative targeting of the Gram-negative outer membrane in antibiotic discovery. Ann N Y Acad Sci 2019; 1459:69-85. [PMID: 31762048 DOI: 10.1111/nyas.14280] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 10/30/2019] [Accepted: 10/31/2019] [Indexed: 12/13/2022]
Abstract
The rising threat of multidrug-resistant Gram-negative bacteria is exacerbated by the scarcity of new antibiotics in the development pipeline. Permeability through the outer membrane remains one of the leading hurdles in discovery efforts. However, the essentiality of a robust outer membrane makes itself an intriguing antimicrobial target. Herein, we review drug discovery efforts targeting the outer membrane and the prospective antimicrobial leads identified.
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Affiliation(s)
- Craig R MacNair
- Michael G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Caressa N Tsai
- Michael G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Eric D Brown
- Michael G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
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Ghequire MGK, De Mot R. LlpB represents a second subclass of lectin-like bacteriocins. Microb Biotechnol 2019; 12:567-573. [PMID: 30702207 PMCID: PMC6465234 DOI: 10.1111/1751-7915.13373] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 01/14/2019] [Accepted: 01/15/2019] [Indexed: 12/11/2022] Open
Abstract
Bacteriocins are secreted bacterial proteins that selectively kill related strains. Lectin-like bacteriocins are atypical bacteriocins not requiring a cognate immunity factor and have been primarily studied in Pseudomonas. These so-called LlpAs are composed of a tandem of B-lectin domains. One domain interacts with d-rhamnose residues in the common polysaccharide antigen of Pseudomonas lipopolysaccharide (LPS). The other lectin domain is crucial for interference with the outer membrane protein assembly machinery by interacting with surface-exposed loops of its central component BamA. Via genome mining, we identified a second subclass of Pseudomonas lectin-like proteins, termed LlpB, consisting of a single B-lectin domain. We show that these proteins also display bactericidal activity. Among LlpB-resistant transposon mutants of an LlpB-susceptible Pseudomonas strain, a major subset was hit in an acyltransferase gene, predicted to be involved in LPS core modification, hereby suggesting that LlpBs equally attach to LPS for surface anchoring. This indicates that LPS binding and target strain specificity are condensed in a single B-lectin domain. The identification of this second subclass of lectin-like bacteriocins further expands the toolbox of antibacterial warfare deployed by bacteria and holds potential for their integration in biotechnological applications.
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Affiliation(s)
- Maarten G. K. Ghequire
- Centre of Microbial and Plant GeneticsKU LeuvenKasteelpark Arenberg 20 bus 24603001HeverleeBelgium
| | - René De Mot
- Centre of Microbial and Plant GeneticsKU LeuvenKasteelpark Arenberg 20 bus 24603001HeverleeBelgium
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Robinson JA. Folded Synthetic Peptides and Other Molecules Targeting Outer Membrane Protein Complexes in Gram-Negative Bacteria. Front Chem 2019; 7:45. [PMID: 30788339 PMCID: PMC6372539 DOI: 10.3389/fchem.2019.00045] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 01/17/2019] [Indexed: 02/06/2023] Open
Abstract
Conformationally constrained peptidomimetics have been developed to mimic interfacial epitopes and target a wide selection of protein-protein interactions. ß-Hairpin mimetics based on constrained macrocyclic peptides have provided access to excellent structural mimics of ß-hairpin epitopes and found applications as interaction inhibitors in many areas of biology and medicinal chemistry. Recently, ß-hairpin peptidomimetics and naturally occurring ß-hairpin-shaped peptides have also been discovered with potent antimicrobial activity and novel mechanisms of action, targeting essential outer membrane protein (OMP) complexes in Gram-negative bacteria. This includes the Lpt complex, required for transporting LPS to the cell surface during OM biogenesis and the BAM complex that folds OMPs and inserts them into the OM bilayer. The Lpt complex is a macromolecular superstructure comprising seven different proteins (LptA-LptG) that spans the entire bacterial cell envelope, whereas the BAM complex is a folding machine comprising a ß-barrel OMP (BamA) and four different lipoproteins (BamB-BamE). Folded synthetic and natural ß-hairpin-shaped peptides appear well-suited for interacting with proteins within the Lpt and BAM complexes that are rich in ß-structure. Recent progress in identifying antibiotics targeting these complexes are reviewed here. Already a clinical candidate has been developed (murepavadin) that targets LptD, with potent antimicrobial activity specifically against pseudmonads. The ability of folded synthetic ß-hairpin epitope mimetics to interact with ß-barrel and ß-jellyroll domains in the Lpt and Bam complexes represent new avenues for antibiotic discovery, which may lead to the development of much needed new antimicrobials to combat the rise of drug-resistant pathogenic Gram-negative bacteria.
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Affiliation(s)
- John A Robinson
- Department of Chemistry, University of Zurich, Zurich, Switzerland
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10
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Barre A, Bourne Y, Van Damme EJM, Rougé P. Overview of the Structure⁻Function Relationships of Mannose-Specific Lectins from Plants, Algae and Fungi. Int J Mol Sci 2019; 20:E254. [PMID: 30634645 PMCID: PMC6359319 DOI: 10.3390/ijms20020254] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 12/29/2018] [Accepted: 12/31/2018] [Indexed: 01/05/2023] Open
Abstract
To date, a number of mannose-binding lectins have been isolated and characterized from plants and fungi. These proteins are composed of different structural scaffold structures which harbor a single or multiple carbohydrate-binding sites involved in the specific recognition of mannose-containing glycans. Generally, the mannose-binding site consists of a small, central, carbohydrate-binding pocket responsible for the "broad sugar-binding specificity" toward a single mannose molecule, surrounded by a more extended binding area responsible for the specific recognition of larger mannose-containing N-glycan chains. Accordingly, the mannose-binding specificity of the so-called mannose-binding lectins towards complex mannose-containing N-glycans depends largely on the topography of their mannose-binding site(s). This structure⁻function relationship introduces a high degree of specificity in the apparently homogeneous group of mannose-binding lectins, with respect to the specific recognition of high-mannose and complex N-glycans. Because of the high specificity towards mannose these lectins are valuable tools for deciphering and characterizing the complex mannose-containing glycans that decorate both normal and transformed cells, e.g., the altered high-mannose N-glycans that often occur at the surface of various cancer cells.
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Affiliation(s)
- Annick Barre
- UMR 152 PharmaDev, Institut de Recherche et Développement, Faculté de Pharmacie, Université Paul Sabatier, 35 Chemin des Maraîchers, 31062 Toulouse, France.
| | - Yves Bourne
- Centre National de la Recherche Scientifique, Aix-Marseille Univ, Architecture et Fonction des Macromolécules Biologiques, 163 Avenue de Luminy, 13288 Marseille, France.
| | - Els J M Van Damme
- Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, B-9000 Ghent, Belgium.
| | - Pierre Rougé
- UMR 152 PharmaDev, Institut de Recherche et Développement, Faculté de Pharmacie, Université Paul Sabatier, 35 Chemin des Maraîchers, 31062 Toulouse, France.
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Ghequire MGK, Öztürk B, De Mot R. Lectin-Like Bacteriocins. Front Microbiol 2018; 9:2706. [PMID: 30483232 PMCID: PMC6240691 DOI: 10.3389/fmicb.2018.02706] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 10/23/2018] [Indexed: 12/22/2022] Open
Abstract
Bacteria produce a diverse array of antagonistic compounds to restrict growth of microbial rivals. Contributing to this warfare are bacteriocins: secreted antibacterial peptides, proteins and multi-protein complexes. These compounds typically eliminate competitors closely related to the producer. Lectin-like bacteriocins (LlpAs) constitute a distinct class of such proteins, produced by Pseudomonas as well as some other proteobacterial genera. LlpAs share a common architecture consisting of two B-lectin domains, followed by a short carboxy-terminal extension. Two surface-exposed moieties on susceptible Pseudomonas cells are targeted by the respective lectin modules. The carboxy-terminal domain binds D-rhamnose residues present in the lipopolysaccharide layer, whereas the amino-terminal domain interacts with a polymorphic external loop of the outer-membrane protein insertase BamA, hence determining selectivity. The absence of a toxin-immunity module as found in modular bacteriocins and other polymorphic toxin systems, hints toward a novel mode of killing initiated at the cellular surface, not requiring bacteriocin import. Despite significant progress in understanding the function of LlpAs, outstanding questions include the secretion machinery recruited by lectin-like bacteriocins for their release, as well as a better understanding of the environmental signals initiating their expression.
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Affiliation(s)
| | - Başak Öztürk
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany
| | - René De Mot
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
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12
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Rojas-Rojas FU, Salazar-Gómez A, Vargas-Díaz ME, Vásquez-Murrieta MS, Hirsch AM, De Mot R, Ghequire MGK, Ibarra JA, Estrada-de los Santos P. Broad-spectrum antimicrobial activity by Burkholderia cenocepacia TAtl-371, a strain isolated from the tomato rhizosphere. Microbiology (Reading) 2018; 164:1072-1086. [DOI: 10.1099/mic.0.000675] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Affiliation(s)
- Fernando Uriel Rojas-Rojas
- 1Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Prol. Carpio y Plan de Ayala s/n, Col. Santo Tomas, Del. Miguel Hidalgo. México, Cd. de, México
| | - Anuar Salazar-Gómez
- 1Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Prol. Carpio y Plan de Ayala s/n, Col. Santo Tomas, Del. Miguel Hidalgo. México, Cd. de, México
| | - María Elena Vargas-Díaz
- 1Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Prol. Carpio y Plan de Ayala s/n, Col. Santo Tomas, Del. Miguel Hidalgo. México, Cd. de, México
| | - María Soledad Vásquez-Murrieta
- 1Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Prol. Carpio y Plan de Ayala s/n, Col. Santo Tomas, Del. Miguel Hidalgo. México, Cd. de, México
| | - Ann M. Hirsch
- 2Dept. of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA
- 3Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA, USA
| | - René De Mot
- 4Centre of Microbial and Plant Genetics, University of Leuven, Kasteelpark Arenberg 20 box 2460, 3001, Heverlee-Leuven, Belgium
| | - Maarten G. K. Ghequire
- 4Centre of Microbial and Plant Genetics, University of Leuven, Kasteelpark Arenberg 20 box 2460, 3001, Heverlee-Leuven, Belgium
| | - J. Antonio Ibarra
- 1Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Prol. Carpio y Plan de Ayala s/n, Col. Santo Tomas, Del. Miguel Hidalgo. México, Cd. de, México
| | - Paulina Estrada-de los Santos
- 1Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Prol. Carpio y Plan de Ayala s/n, Col. Santo Tomas, Del. Miguel Hidalgo. México, Cd. de, México
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Abstract
Lectin-like bacteriocins (LlpAs) are secreted by proteobacteria and selectively kill strains of their own or related species, and they are composed of two B-lectin domains with divergent sequences. In Pseudomonas spp., initial binding of these antibacterial proteins to cells is mediated by the carboxy-terminal domain through d-rhamnose residues present in the common polysaccharide antigen of their lipopolysaccharide, whereas the amino-terminal domain accounts for strain selectivity of killing. Here, we show that spontaneous LlpA-resistant mutants carry mutations in one of three surface-exposed moieties of the essential β-barrel outer membrane protein insertase BamA, the core component of the BAM complex. Polymorphism of this loop in different Pseudomonas groups is linked to LlpA susceptibility, and targeted cells all share the same signature motif in this loop. Since heterologous expression of such a bamA gene confers LlpA susceptibility upon a resistant strain, BamA represents the primary bacteriocin selectivity determinant in pseudomonads. Contrary to modular bacteriocins that require uptake via the Tol or Ton system, parasitism of BamA as an LlpA receptor advocates a novel bacteriocin killing mechanism initiated by impairment of the BAM machinery. Bacteria secrete a variety of molecules to eliminate microbial rivals. Bacteriocins are a pivotal group of peptides and proteins that assist in this fight, specifically killing related bacteria. In Gram-negative bacteria, these antibacterial proteins often comprise distinct domains for initial binding to a target cell’s surface and subsequent killing via enzymatic or pore-forming activity. Here, we show that lectin-like bacteriocins, a family of bacteriocins that lack the prototypical modular toxin architecture, also stand out by parasitizing BamA, the core component of the outer membrane protein assembly machinery. A particular surface-exposed loop of BamA, critical for its function, serves as a key discriminant for cellular recognition, and polymorphisms in this loop determine whether a strain is susceptible or immune to a particular bacteriocin. These findings suggest a novel mechanism of contact-dependent killing that does not require cellular uptake. The evolutionary advantage of piracy of an essential cellular compound is highlighted by the observation that contact-dependent growth inhibition, a distinct antagonistic system, can equally take advantage of this receptor.
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Moonens K, Remaut H. Evolution and structural dynamics of bacterial glycan binding adhesins. Curr Opin Struct Biol 2017; 44:48-58. [DOI: 10.1016/j.sbi.2016.12.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 11/30/2016] [Accepted: 12/05/2016] [Indexed: 01/25/2023]
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Ghequire MGK, Kemland L, De Mot R. Novel Immunity Proteins Associated with Colicin M-like Bacteriocins Exhibit Promiscuous Protection in Pseudomonas. Front Microbiol 2017; 8:93. [PMID: 28194143 PMCID: PMC5277000 DOI: 10.3389/fmicb.2017.00093] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 01/13/2017] [Indexed: 01/08/2023] Open
Abstract
Bacteriocins related to colicin M, acting via cleavage of the cell wall precursor lipid II, have been characterized in γ- and β-proteobacteria. Depending on the species, immunity is provided by either an inner membrane-anchored periplasmic protein or by an integral membrane protein. In Pseudomonas however, the immunity partner of colicin M-like bacteriocins remains unknown. Based on an in silico analysis in pseudomonad genomes, we here identify a gene encoding a putative immunity partner that represents a novel type of integral membrane protein (PmiA, Pseudomonas colicin M-like immunity type A). By heterologous expression of pmiA genes in susceptible strains, we show that immunity to colicin M-like bacteriocins is indeed provided by the cognate PmiA. Sequence homology among PmiA proteins is essentially absent, except for a short motif with a conserved periplasm-exposed aspartate residue. However, PmiA's protective function is not abolished by changing this acidic residue to the uncharged alanine. Immunity by PmiAs appears promiscuous to the extent that PmiA homologs from a clade sharing <40% pairwise amino acid identity, equally provide protection against the bacteriocin linked to the original PmiA. This study shows that multiple immunity factors have evolved independently to silence lipid II-targeting enzymatic bacteriocins. Their relaxed bacteriocin immunization capacity contrasts to the strict specificity of immunity proteins shielding the enzymatic domain of nuclease bacteriocins. The nature of associated immune functions needs consideration when using such natural protein antibiotics or designing novel variants.
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Affiliation(s)
- Maarten G K Ghequire
- Centre of Microbial and Plant Genetics, KU LeuvenHeverlee, Belgium; National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesda, MD, USA
| | | | - René De Mot
- Centre of Microbial and Plant Genetics, KU Leuven Heverlee, Belgium
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Draft Genome Sequence of Pseudomonas putida BW11M1, a Banana Rhizosphere Isolate with a Diversified Antimicrobial Armamentarium. GENOME ANNOUNCEMENTS 2016; 4:4/2/e00251-16. [PMID: 27081131 PMCID: PMC4832159 DOI: 10.1128/genomea.00251-16] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
In this study, we report the draft genome of Pseudomonas putida BW11M1, a banana rhizosphere isolate producing various antimicrobial compounds, including a lectin-like bacteriocin, an R-type tailocin, the cyclic lipopeptide xantholysin, and the fatty acid–derived pseudopyronine.
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Dingemans J, Ghequire MGK, Craggs M, De Mot R, Cornelis P. Identification and functional analysis of a bacteriocin, pyocin S6, with ribonuclease activity from a Pseudomonas aeruginosa cystic fibrosis clinical isolate. Microbiologyopen 2016; 5:413-23. [PMID: 26860427 PMCID: PMC4905994 DOI: 10.1002/mbo3.339] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2015] [Revised: 11/30/2015] [Accepted: 01/05/2016] [Indexed: 01/28/2023] Open
Abstract
S‐type pyocins are bacteriocins produced by Pseudomonas aeruginosa isolates to antagonize or kill other strains of the same species. They have a modular organization comprising a receptor‐binding domain recognizing a surface constituent of the target bacterium, a domain for translocation through the periplasm, and a killing or toxic domain with DNase, tRNase, or pore‐forming activity. Pyocins S2, S3, S4, and S5 recognize TonB‐dependent ferri‐siderophore receptors in the outer membrane. We here describe a new nuclease bacteriocin, pyocin S6, encoded in the genome of a P. aeruginosa cystic fibrosis (CF) clinical isolate, CF_PA39. Similarly to pyocins S1 and S2, the S6 toxin–immunity gene tandem was recruited to the genomic region encoding exotoxin A. The pyocin S6 receptor‐binding and translocation domains are identical to those of pyocin S1, whereas the killing domain is similar to the 16S ribonuclease domain of Escherichia coli colicin E3. The cytotoxic activity was abolished in pyocin S6 forms with a mutation in the colicin E3‐equivalent catalytic motif. The CF_PA39 S6 immunity gene displays a higher expression level than the gene encoding the killing protein, the latter being only detected when bacteria are grown under iron‐limiting conditions. In the S1‐pyocinogenic strain P. aeruginosa ATCC 25324 and pyocin S2 producer P. aeruginosa PAO1, a remnant of the pyocin S6 killing domain and an intact S6‐type immunity gene are located downstream of their respective pyocin operons. Strain PAO1 is insensitive for pyocin S6, and its S6‐type immunity gene provides protection against pyocin S6 activity. Purified pyocin S6 inhibits one‐fifth of 110 P. aeruginosa CF clinical isolates tested, showing clearer inhibition zones when the target cells are grown under iron limitation. In this panel, about half of the CF clinical isolates were found to host the S6 genes. The pyocin S6 locus is also present in the genome of some non‐CF clinical isolates.
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Affiliation(s)
- Jozef Dingemans
- Department of Bioengineering Sciences, Research group Microbiology and VIB Department of Structural Biology, Vrije Universiteit Brussel, Pleinlaan 2, Brussels, 1050, Belgium
| | - Maarten G K Ghequire
- Department Microbial and Molecular Systems, Centre of Microbial and Plant Genetics, KU Leuven Kasteelpark Arenberg 20 - bus 2460, Heverlee, B-3001, Belgium
| | - Michael Craggs
- Department of Bioengineering Sciences, Research group Microbiology and VIB Department of Structural Biology, Vrije Universiteit Brussel, Pleinlaan 2, Brussels, 1050, Belgium
| | - René De Mot
- Department Microbial and Molecular Systems, Centre of Microbial and Plant Genetics, KU Leuven Kasteelpark Arenberg 20 - bus 2460, Heverlee, B-3001, Belgium
| | - Pierre Cornelis
- Department of Bioengineering Sciences, Research group Microbiology and VIB Department of Structural Biology, Vrije Universiteit Brussel, Pleinlaan 2, Brussels, 1050, Belgium
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18
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Godino A, Príncipe A, Fischer S. A ptsP deficiency in PGPR Pseudomonas fluorescens SF39a affects bacteriocin production and bacterial fitness in the wheat rhizosphere. Res Microbiol 2015; 167:178-89. [PMID: 26708985 DOI: 10.1016/j.resmic.2015.12.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 12/04/2015] [Accepted: 12/07/2015] [Indexed: 11/26/2022]
Abstract
Pseudomonas fluorescens SF39a is a plant-growth-promoting bacterium isolated from wheat rhizosphere. In this report, we demonstrate that this native strain secretes bacteriocins that inhibit growth of phytopathogenic strains of the genera Pseudomonas and Xanthomonas. An S-type pyocin gene was detected in the genome of strain SF39a and named pys. A non-polar pys::Km mutant was constructed. The bacteriocin production was impaired in this mutant. To identify genes involved in bacteriocin regulation, random transposon mutagenesis was carried out. A miniTn5Km1 mutant, called P. fluorescens SF39a-451, showed strongly reduced bacteriocin production. This phenotype was caused by inactivation of the ptsP gene which encodes a phosphoenolpyruvate phosphotransferase (EI(Ntr)) of the nitrogen-related phosphotransferase system (PTS(Ntr)). In addition, this mutant showed a decrease in biofilm formation and protease production, and an increase in surface motility and pyoverdine production compared with the wild-type strain. Moreover, we investigated the ability of strain SF39a-451 to colonize the wheat rhizosphere under greenhouse conditions. Interestingly, the mutant was less competitive than the wild-type strain in the rhizosphere. To our knowledge, this study provides the first evidence of both the relevance of the ptsP gene in bacteriocin production and functional characterization of a pyocin S in P. fluorescens.
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Affiliation(s)
- Agustina Godino
- Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Ruta 36-Km 601-5800, Río Cuarto, Córdoba, Argentina.
| | - Analía Príncipe
- Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Ruta 36-Km 601-5800, Río Cuarto, Córdoba, Argentina.
| | - Sonia Fischer
- Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Ruta 36-Km 601-5800, Río Cuarto, Córdoba, Argentina.
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Distinct colicin M-like bacteriocin-immunity pairs in Burkholderia. Sci Rep 2015; 5:17368. [PMID: 26610609 PMCID: PMC4661593 DOI: 10.1038/srep17368] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 10/28/2015] [Indexed: 11/30/2022] Open
Abstract
The Escherichia coli bacteriocin colicin M (ColM) acts via degradation of the cell wall precursor lipid II in target cells. ColM producers avoid self-inhibition by a periplasmic immunity protein anchored in the inner membrane. In this study, we identified colM-like bacteriocin genes in genomes of several β-proteobacterial strains belonging to the Burkholderia cepacia complex (Bcc) and the Burkholderia pseudomallei group. Two selected Burkholderia ambifaria proteins, designated burkhocins M1 and M2, were produced recombinantly and showed antagonistic activity against Bcc strains. In their considerably sequence-diverged catalytic domain, a conserved aspartate residue equally proved pivotal for cytotoxicity. Immunity to M-type burkhocins is conferred upon susceptible strains by heterologous expression of a cognate gene located either upstream or downstream of the toxin gene. These genes lack homology with currently known ColM immunity genes and encode inner membrane-associated proteins of two distinct types, differing in predicted transmembrane topology and moiety exposed to the periplasm. The addition of burkhocins to the bacteriocin complement of Burkholderia reveals a wider phylogenetic distribution of ColM-like bacteriotoxins, beyond the γ-proteobacterial genera Escherichia, Pectobacterium and Pseudomonas, and illuminates the diversified nature of immunity-providing proteins.
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Bauer JS, Ghequire MGK, Nett M, Josten M, Sahl HG, De Mot R, Gross H. Biosynthetic Origin of the Antibiotic Pseudopyronines A and B in Pseudomonas putida BW11M1. Chembiochem 2015; 16:2491-7. [PMID: 26507104 DOI: 10.1002/cbic.201500413] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Indexed: 11/08/2022]
Abstract
Within the framework of our effort to discover new antibiotics from pseudomonads, pseudopyronines A and B were isolated from the plant-derived Pseudomonas putida BW11M1. Pseudopyronines are 3,6-dialkyl-4-hydroxy-2-pyrones and displayed high in vitro activities against several human pathogens, and in our hands also towards the plant pathogen Pseudomonas savastanoi. Here, the biosynthesis of pseudopyronine B was studied by a combination of feeding experiments with isotopically labeled precursors, genomic sequence analysis, and gene deletion experiments. The studies resulted in the deduction of all acetate units and revealed that the biosynthesis of these α-pyrones occurs with a single PpyS-homologous ketosynthase. It fuses, with some substrate flexibility, a 3-oxo-fatty acid and a further unbranched saturated fatty acid, both of medium chain-length and provided by primary metabolism.
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Affiliation(s)
- Judith S Bauer
- Department of Pharmaceutical Biology, Pharmaceutical Institute, University of Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany.,German Centre for Infection Research (DZIF), Partner site Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany
| | - Maarten G K Ghequire
- Centre of Microbial and Plant Genetics, Department of Microbial and Molecular Systems, University of Leuven, Kasteelpark Arenberg 20, 3001, Heverlee-Leuven, Belgium
| | - Markus Nett
- Junior Research Group "Secondary Metabolism of Predatory Bacteria", Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institut, Beutenbergstrasse 11 A, 07745, Jena, Germany
| | - Michaele Josten
- Institute for Medical Microbiology, Immunology and Parasitology (IMMIP), Pharmaceutical Microbiology Unit, University of Bonn, Meckenheimer Allee 168, 53115, Bonn, Germany.,German Centre for Infection Research (DZIF), Partner site Bonn-Cologne, Meckenheimer Allee 168, 53115, Bonn, Germany
| | - Hans-Georg Sahl
- Institute for Medical Microbiology, Immunology and Parasitology (IMMIP), Pharmaceutical Microbiology Unit, University of Bonn, Meckenheimer Allee 168, 53115, Bonn, Germany.,German Centre for Infection Research (DZIF), Partner site Bonn-Cologne, Meckenheimer Allee 168, 53115, Bonn, Germany
| | - René De Mot
- Centre of Microbial and Plant Genetics, Department of Microbial and Molecular Systems, University of Leuven, Kasteelpark Arenberg 20, 3001, Heverlee-Leuven, Belgium.
| | - Harald Gross
- Department of Pharmaceutical Biology, Pharmaceutical Institute, University of Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany. .,German Centre for Infection Research (DZIF), Partner site Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany.
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21
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Ghequire MGK, Dillen Y, Lambrichts I, Proost P, Wattiez R, De Mot R. Different Ancestries of R Tailocins in Rhizospheric Pseudomonas Isolates. Genome Biol Evol 2015; 7:2810-28. [PMID: 26412856 PMCID: PMC4684702 DOI: 10.1093/gbe/evv184] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Bacterial genomes accommodate a variety of mobile genetic elements, including bacteriophage-related clusters that encode phage tail-like protein complexes playing a role in interactions with eukaryotic or prokaryotic cells. Such tailocins are unable to replicate inside target cells due to the lack of a phage head with associated DNA. A subset of tailocins mediate antagonistic activities with bacteriocin-like specificity. Functional characterization of bactericidal tailocins of two Pseudomonas putida rhizosphere isolates revealed not only extensive similarity with the tail assembly module of the Pseudomonas aeruginosa R-type pyocins but also differences in genomic integration site, regulatory genes, and lytic release modules. Conversely, these three features are quite similar between strains of the P. putida and Pseudomonas fluorescens clades, although phylogenetic analysis of tail genes suggests them to have evolved separately. Unlike P. aeruginosa R pyocin elements, the tailocin gene clusters of other pseudomonads frequently carry cargo genes, including bacteriocins. Compared with P. aeruginosa, the tailocin tail fiber sequences that act as specificity determinants have diverged much more extensively among the other pseudomonad species, mostly isolates from soil and plant environments. Activity of the P. putida antibacterial particles requires a functional lipopolysaccharide layer on target cells, but contrary to R pyocins from P. aeruginosa, strain susceptibilities surpass species boundaries.
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Affiliation(s)
- Maarten G K Ghequire
- Centre of Microbial and Plant Genetics (CMPG), University of Leuven, Heverlee, Belgium
| | - Yörg Dillen
- Group of Morphology, Biomedical Research Institute (BIOMED), Hasselt University, Diepenbeek, Leuven, Belgium
| | - Ivo Lambrichts
- Group of Morphology, Biomedical Research Institute (BIOMED), Hasselt University, Diepenbeek, Leuven, Belgium
| | - Paul Proost
- Laboratory of Molecular Immunology, Department of Microbiology and Immunology, Rega Institute, University of Leuven, Belgium
| | - Ruddy Wattiez
- Proteomics and Microbiology Laboratory, Research Institute for Biosciences, University of Mons, Mons, Belgium
| | - René De Mot
- Centre of Microbial and Plant Genetics (CMPG), University of Leuven, Heverlee, Belgium
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22
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Nahalka J, Hrabarova E, Talafova K. Protein-RNA and protein-glycan recognitions in light of amino acid codes. Biochim Biophys Acta Gen Subj 2015; 1850:1942-52. [PMID: 26145579 DOI: 10.1016/j.bbagen.2015.06.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 06/18/2015] [Accepted: 06/22/2015] [Indexed: 12/13/2022]
Abstract
BACKGROUND RNA-binding proteins, in cooperation with non-coding RNAs, play important roles in post-transcriptional regulation. Non-coding micro-RNAs control information flow from the genome to the glycome by interacting with glycan-synthesis enzymes. Glycan-binding proteins read the cell surface and cytoplasmic glycome and transfer signals back to the nucleus. The profiling of the protein-RNA and protein-glycan interactomes is of significant medicinal importance. SCOPE OF REVIEW This review discusses the state-of-the-art research in the protein-RNA and protein-glycan recognition fields and proposes the application of amino acid codes in profiling and programming the interactomes. MAJOR CONCLUSIONS The deciphered PUF-RNA and PPR-RNA amino acid recognition codes can be explained by the protein-RNA amino acid recognition hypothesis based on the genetic code. The tripartite amino acid code is also involved in protein-glycan interactions. At present, the results indicate that a system of four codons ("gnc", where n=g - guanine, c - cytosine, u - uracil or a - adenine) and four amino acids (G - glycine, A - alanine, V - valine, D - aspartic acid) could be the original genetic code that imprinted "rules" into both recognition processes. GENERAL SIGNIFICANCE Amino acid recognition codes have provocative potential in the profiling and programming of the protein-RNA and protein-glycan interactomes. The profiling and even programming of the interactomes will play significant roles in diagnostics and the development of therapeutic procedures against cancer and neurodegenerative, developmental and other diseases.
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Affiliation(s)
- Jozef Nahalka
- Institute of Chemistry, Centre for Glycomics, Slovak Academy of Sciences, Dubravska cesta 9, SK-84538 Bratislava, Slovak Republic; Institute of Chemistry, Centre of Excellence for White-green Biotechnology, Slovak Academy of Sciences, Trieda Andreja Hlinku 2, SK-94976 Nitra, Slovak Republic.
| | - Eva Hrabarova
- Institute of Chemistry, Centre for Glycomics, Slovak Academy of Sciences, Dubravska cesta 9, SK-84538 Bratislava, Slovak Republic; Institute of Chemistry, Centre of Excellence for White-green Biotechnology, Slovak Academy of Sciences, Trieda Andreja Hlinku 2, SK-94976 Nitra, Slovak Republic
| | - Klaudia Talafova
- Institute of Chemistry, Centre for Glycomics, Slovak Academy of Sciences, Dubravska cesta 9, SK-84538 Bratislava, Slovak Republic; Institute of Chemistry, Centre of Excellence for White-green Biotechnology, Slovak Academy of Sciences, Trieda Andreja Hlinku 2, SK-94976 Nitra, Slovak Republic
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23
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Taylor ME, Drickamer K. Convergent and divergent mechanisms of sugar recognition across kingdoms. Curr Opin Struct Biol 2014; 28:14-22. [PMID: 25102772 PMCID: PMC4444583 DOI: 10.1016/j.sbi.2014.07.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Revised: 06/23/2014] [Accepted: 07/16/2014] [Indexed: 12/03/2022]
Abstract
Protein modules that bind specific oligosaccharides are found across all kingdoms of life from single-celled organisms to man. Different, overlapping and evolving designations for sugar-binding domains in proteins can sometimes obscure common features that often reflect convergent solutions to the problem of distinguishing sugars with closely similar structures and binding them with sufficient affinity to achieve biologically meaningful results. Structural and functional analysis has revealed striking parallels between protein domains with widely different structures and evolutionary histories that employ common solutions to the sugar recognition problem. Recent studies also demonstrate that domains descended from common ancestors through divergent evolution appear more widely across the kingdoms of life than had previously been recognized.
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Affiliation(s)
- Maureen E Taylor
- Department of Life Sciences, Imperial College, London SW7 2AZ, United Kingdom
| | - Kurt Drickamer
- Department of Life Sciences, Imperial College, London SW7 2AZ, United Kingdom.
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Ghequire MGK, Dingemans J, Pirnay JP, De Vos D, Cornelis P, De Mot R. O serotype-independent susceptibility of Pseudomonas aeruginosa to lectin-like pyocins. Microbiologyopen 2014; 3:875-84. [PMID: 25224846 PMCID: PMC4263511 DOI: 10.1002/mbo3.210] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Revised: 07/25/2014] [Accepted: 07/28/2014] [Indexed: 11/08/2022] Open
Abstract
Lectin-like bacteriocins of the LlpA family, originally identified in plant-associated bacteria, are narrow-spectrum antibacterial proteins composed of two tandemly organized monocot mannose-binding lectin (MMBL) domains. The LlpA-like bacteriocin of Pseudomonas aeruginosa C1433, pyocin L1, lacks any similarity to known P. aeruginosa bacteriocins. The initial interaction of pyocin L1 with target cells is mediated by binding to d-rhamnose, present in the common polysaccharide antigen of lipopolysaccharides (LPS), but the actual cytotoxic mechanism is unknown. In this study, we characterized the activity range of pyocin L1 and two additional L pyocins revealed by genome mining, representing two highly diverged LlpA groups in P. aeruginosa. The recombinant proteins exhibit species-specific antagonistic activities down to nanomolar concentrations against clinical and environmental P. aeruginosa strains, including several multidrug-resistant isolates. The overlap in target strain spectrum between two close homologues of the pyocin L1 group is only minimal, contrasting with the considerable spectral redundancy of LlpA proteins reported for other Pseudomonas species. No correlation was found between L pyocin susceptibility and phylogenetic relatedness of P. aeruginosa isolates. Sensitive strains were retrieved in 13 out of 15 O serotypes tested, excluding the possibility that the highly variable and immunogenic O serotype antigen of the LPS coating would represent a dominant susceptibility-discriminating factor.
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Affiliation(s)
- Maarten G K Ghequire
- Centre of Microbial and Plant Genetics, University of Leuven, 3001, Heverlee, Belgium
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25
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Ghequire MGK, De Mot R. Ribosomally encoded antibacterial proteins and peptides from Pseudomonas. FEMS Microbiol Rev 2014; 38:523-68. [PMID: 24923764 DOI: 10.1111/1574-6976.12079] [Citation(s) in RCA: 139] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 05/05/2014] [Accepted: 05/16/2014] [Indexed: 12/26/2022] Open
Abstract
Members of the Pseudomonas genus produce diverse secondary metabolites affecting other bacteria, fungi or predating nematodes and protozoa but are also equipped with the capacity to secrete different types of ribosomally encoded toxic peptides and proteins, ranging from small microcins to large tailocins. Studies with the human pathogen Pseudomonas aeruginosa have revealed that effector proteins of type VI secretion systems are part of the antibacterial armamentarium deployed by pseudomonads. A novel class of antibacterial proteins with structural similarity to plant lectins was discovered by studying antagonism among plant-associated Pseudomonas strains. A genomic perspective on pseudomonad bacteriocinogeny shows that the modular architecture of S pyocins of P. aeruginosa is retained in a large diversified group of bacteriocins, most of which target DNA or RNA. Similar modularity is present in as yet poorly characterized Rhs (recombination hot spot) proteins and CDI (contact-dependent inhibition) proteins. Well-delimited domains for receptor recognition or cytotoxicity enable the design of chimeric toxins with novel functionalities, which has been applied successfully for S and R pyocins. Little is known regarding how these antibacterials are released and ultimately reach their targets. Other remaining issues concern the identification of environmental triggers activating these systems and assessment of their ecological impact in niches populated by pseudomonads.
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26
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Patra D, Mishra P, Surolia A, Vijayan M. Structure, interactions and evolutionary implications of a domain-swapped lectin dimer from Mycobacterium smegmatis. Glycobiology 2014; 24:956-65. [DOI: 10.1093/glycob/cwu059] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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27
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McCaughey LC, Grinter R, Josts I, Roszak AW, Waløen KI, Cogdell RJ, Milner J, Evans T, Kelly S, Tucker NP, Byron O, Smith B, Walker D. Lectin-like bacteriocins from Pseudomonas spp. utilise D-rhamnose containing lipopolysaccharide as a cellular receptor. PLoS Pathog 2014; 10:e1003898. [PMID: 24516380 PMCID: PMC3916391 DOI: 10.1371/journal.ppat.1003898] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 12/10/2013] [Indexed: 11/24/2022] Open
Abstract
Lectin-like bacteriocins consist of tandem monocot mannose-binding domains and display a genus-specific killing activity. Here we show that pyocin L1, a novel member of this family from Pseudomonas aeruginosa, targets susceptible strains of this species through recognition of the common polysaccharide antigen (CPA) of P. aeruginosa lipopolysaccharide that is predominantly a homopolymer of d-rhamnose. Structural and biophysical analyses show that recognition of CPA occurs through the C-terminal carbohydrate-binding domain of pyocin L1 and that this interaction is a prerequisite for bactericidal activity. Further to this, we show that the previously described lectin-like bacteriocin putidacin L1 shows a similar carbohydrate-binding specificity, indicating that oligosaccharides containing d-rhamnose and not d-mannose, as was previously thought, are the physiologically relevant ligands for this group of bacteriocins. The widespread inclusion of d-rhamnose in the lipopolysaccharide of members of the genus Pseudomonas explains the unusual genus-specific activity of the lectin-like bacteriocins. Due to rapidly increasing rates of antibiotic resistance observed among Gram-negative pathogens, such as Pseudomonas aeruginosa, there is an urgent requirement for novel approaches to the treatment of bacterial infections. Lectin-like bacteriocins are highly potent protein antibiotics that display an unusual ability to kill a select group of bacteria within a specific genus. In this work, we show how the lectin-like protein antibiotic, pyocin L1, can kill Pseudomonas aeruginosa with extraordinary potency through specific binding to the common polysaccharide antigen (CPA) of P. aeruginosa lipopolysaccharide. The CPA is predominantly a homopolymer of the sugar d-rhamnose that although generally rare in nature is found frequently as a component of the lipopolysaccharide of members of the genus Pseudomonas. The targeting of d-rhamnose containing polysaccharides by pyocin L1 and a related lectin-like protein antibiotic, putidacin L1, explains the unusual genus- specific killing activity of the lectin-like bacteriocins. As we learn more about the link between changes to the microbiome and a range of chronic diseases there is a growing realisation that the ability to target specific bacterial pathogens while maintaining the normal gut flora is a desirable property for next generation antibiotics.
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Affiliation(s)
- Laura C. McCaughey
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Rhys Grinter
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Inokentijs Josts
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Aleksander W. Roszak
- WestCHEM, School of Chemistry, College of Science and Engineering, University of Glasgow, Glasgow, United Kingdom
- Institute of Molecular Cell and Systems Biology, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Kai I. Waløen
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- School of Life Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Richard J. Cogdell
- Institute of Molecular Cell and Systems Biology, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Joel Milner
- Institute of Molecular Cell and Systems Biology, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Tom Evans
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Sharon Kelly
- Institute of Molecular Cell and Systems Biology, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Nicholas P. Tucker
- Strathclyde Institute for Pharmaceutical and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Olwyn Byron
- School of Life Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Brian Smith
- Institute of Molecular Cell and Systems Biology, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Daniel Walker
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- * E-mail:
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Ghequire MGK, De Canck E, Wattiau P, Van Winge I, Loris R, Coenye T, De Mot R. Antibacterial activity of a lectin-like Burkholderia cenocepacia protein. Microbiologyopen 2013; 2:566-75. [PMID: 23737242 PMCID: PMC3831624 DOI: 10.1002/mbo3.95] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Revised: 04/29/2013] [Accepted: 05/06/2013] [Indexed: 12/13/2022] Open
Abstract
Bacteriocins of the LlpA family have previously been characterized in the γ-proteobacteria Pseudomonas and Xanthomonas. These proteins are composed of two MMBL (monocot mannose-binding lectin) domains, a module predominantly and abundantly found in lectins from monocot plants. Genes encoding four different types of LlpA-like proteins were identified in genomes from strains belonging to the Burkholderia cepacia complex (Bcc) and the Burkholderia pseudomallei group. A selected recombinant LlpA-like protein from the human isolate Burkholderia cenocepacia AU1054 displayed narrow-spectrum genus-specific antibacterial activity, thus representing the first functionally characterized bacteriocin within this β-proteobacterial genus. Strain-specific killing was confined to other members of the Bcc, with mostly Burkholderia ambifaria strains being susceptible. In addition to killing planktonic cells, this bacteriocin also acted as an antibiofilm agent.
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Affiliation(s)
- Maarten G K Ghequire
- Centre of Microbial and Plant Genetics, University of Leuven, Kasteelpark Arenberg 20 box 2460, 3001, Heverlee-Leuven, Belgium
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29
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Li W, Rokni-Zadeh H, De Vleeschouwer M, Ghequire MGK, Sinnaeve D, Xie GL, Rozenski J, Madder A, Martins JC, De Mot R. The antimicrobial compound xantholysin defines a new group of Pseudomonas cyclic lipopeptides. PLoS One 2013; 8:e62946. [PMID: 23690965 PMCID: PMC3656897 DOI: 10.1371/journal.pone.0062946] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Accepted: 03/27/2013] [Indexed: 12/17/2022] Open
Abstract
The rhizosphere isolate Pseudomonas putida BW11M1 produces a mixture of cyclic lipopeptide congeners, designated xantholysins. Properties of the major compound xantholysin A, shared with several other Pseudomonas lipopeptides, include antifungal activity and toxicity to Gram-positive bacteria, a supportive role in biofilm formation, and facilitation of surface colonization through swarming. Atypical is the lipopeptide’s capacity to inhibit some Gram-negative bacteria, including several xanthomonads. The lipotetradecadepsipeptides are assembled by XtlA, XtlB and XtlC, three co-linearly operating non-ribosomal peptide synthetases (NRPSs) displaying similarity in modular architecture with the entolysin-producing enzymes of the entomopathogenic Pseudomonas entomophila L48. A shifted serine-incorporating unit in the eight-module enzyme XtlB elongating the central peptide moiety not only generates an amino acid sequence differing at several equivalent positions from entolysin, but also directs xantholysin’s macrocyclization into an octacyclic structure, distinct from the pentacyclic closure in entolysin. Relaxed fatty acid specificity during lipoinitiation by XtlA (acylation with 3-hydroxydodec-5-enoate instead of 3-hydroxydecanoate) and for incorporation of the ultimate amino acid by XtlC (valine instead of isoleucine) account for the production of the minor structural variants xantholysin C and B, respectively. Remarkably, the genetic backbones of the xantholysin and entolysin NRPS systems also bear pronounced phylogenetic similarity to those of the P. putida strains PCL1445 and RW10S2, albeit generating the seemingly structurally unrelated cyclic lipopeptides putisolvin (undecapeptide containing a cyclotetrapeptide) and WLIP (nonapeptide containing a cycloheptapeptide), respectively. This similarity includes the linked genes encoding the cognate LuxR-family regulator and tripartite export system components in addition to individual modules of the NRPS enzymes, and probably reflects a common evolutionary origin. Phylogenetic scrutiny of the modules used for selective amino acid activation by these synthetases indicates that bacteria such as pseudomonads recruit and reshuffle individual biosynthetic units and blocks thereof to engineer reorganized or novel NRPS assembly lines for diversified synthesis of lipopeptides.
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Affiliation(s)
- Wen Li
- Centre of Microbial and Plant Genetics, Department of Microbial and Molecular Systems, University of Leuven, Heverlee-Leuven, Belgium
| | - Hassan Rokni-Zadeh
- Centre of Microbial and Plant Genetics, Department of Microbial and Molecular Systems, University of Leuven, Heverlee-Leuven, Belgium
| | - Matthias De Vleeschouwer
- NMR and Structure Analysis Unit, Department of Organic Chemistry, Ghent University, Gent, Belgium
- Organic and Biomimetic Chemistry Research Group, Department of Organic Chemistry, Ghent University, Gent, Belgium
| | - Maarten G. K. Ghequire
- Centre of Microbial and Plant Genetics, Department of Microbial and Molecular Systems, University of Leuven, Heverlee-Leuven, Belgium
| | - Davy Sinnaeve
- NMR and Structure Analysis Unit, Department of Organic Chemistry, Ghent University, Gent, Belgium
| | - Guan-Lin Xie
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Jef Rozenski
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, University of Leuven, Leuven, Belgium
| | - Annemieke Madder
- Organic and Biomimetic Chemistry Research Group, Department of Organic Chemistry, Ghent University, Gent, Belgium
| | - José C. Martins
- NMR and Structure Analysis Unit, Department of Organic Chemistry, Ghent University, Gent, Belgium
| | - René De Mot
- Centre of Microbial and Plant Genetics, Department of Microbial and Molecular Systems, University of Leuven, Heverlee-Leuven, Belgium
- * E-mail:
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