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Pérez-Ramos A, Madi-Moussa D, Coucheney F, Drider D. Current Knowledge of the Mode of Action and Immunity Mechanisms of LAB-Bacteriocins. Microorganisms 2021; 9:2107. [PMID: 34683428 PMCID: PMC8538875 DOI: 10.3390/microorganisms9102107] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 09/28/2021] [Accepted: 09/29/2021] [Indexed: 12/31/2022] Open
Abstract
Bacteriocins produced by lactic acid bacteria (LAB-bacteriocins) may serve as alternatives for aging antibiotics. LAB-bacteriocins can be used alone, or in some cases as potentiating agents to treat bacterial infections. This approach could meet the different calls and politics, which aim to reduce the use of traditional antibiotics and develop novel therapeutic options. Considering the clinical applications of LAB-bacteriocins as a reasonable and desirable therapeutic approach, it is therefore important to assess the advances achieved in understanding their modes of action, and the resistance mechanisms developed by the producing bacteria to their own bacteriocins. Most LAB-bacteriocins act by disturbing the cytoplasmic membrane through forming pores, or by cell wall degradation. Nevertheless, some of these peptides still have unknown modes of action, especially those that are active against Gram-negative bacteria. Regarding immunity, most bacteriocin-producing strains have an immunity mechanism involving an immunity protein and a dedicated ABC transporter system. However, these immunity mechanisms vary from one bacteriocin to another.
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Affiliation(s)
| | | | | | - Djamel Drider
- UMR Transfrontalière BioEcoAgro 1158, Univ. Lille, INRAE, Univ. Liège, UPJV, YNCREA, Univ. Artois, Univ. Littoral Côte d’Opale, ICV—Institut Charles Viollette, F-59000 Lille, France; (A.P.-R.); (D.M.-M.); (F.C.)
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Geiger C, Korn SM, Häsler M, Peetz O, Martin J, Kötter P, Morgner N, Entian KD. LanI-Mediated Lantibiotic Immunity in Bacillus subtilis: Functional Analysis. Appl Environ Microbiol 2019; 85:e00534-19. [PMID: 30952662 PMCID: PMC6532034 DOI: 10.1128/aem.00534-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 03/26/2019] [Indexed: 01/09/2023] Open
Abstract
Lantibiotics subtilin and nisin are produced by Bacillus subtilis and Lactococcus lactis, respectively. To prevent toxicity of their own lantibiotic, both bacteria express specific immunity proteins, called SpaI and NisI. In addition, ABC transporters SpaFEG and NisFEG prevent lantibiotic toxicity by transporting the respective peptides to the extracellular space. Although the three-dimensional structures of SpaI and NisI have been solved, very little is known about the molecular function of either lipoprotein. Using laser-induced liquid bead ion desorption (LILBID)-mass spectrometry, we show here that subtilin interacts with SpaI monomers. The expression of either SpaI or NisI in a subtilin-nonproducing B. subtilis strain resulted in the respective strain being more resistant against either subtilin or nisin. Furthermore, pore formation provided by subtilin and nisin was prevented specifically upon the expression of either SpaI or NisI. As shown with a nisin-subtilin hybrid molecule, the C-terminal part of subtilin but not any particular lanthionine ring was needed for SpaI-mediated immunity. With respect to growth, SpaI provided less immunity against subtilin than is provided by the ABC transporter SpaFEG. However, SpaI prevented pore formation much more efficiently than SpaFEG. Taken together, our data show the physiological function of SpaI as a fast immune response to protect the cellular membrane.IMPORTANCE The two lantibiotics nisin and subtilin are produced by Lactococcus lactis and Bacillus subtilis, respectively. Both peptides have strong antimicrobial activity against Gram-positive bacteria, and therefore, appropriate protection mechanisms are required for the producing strains. To prevent toxicity of their own lantibiotic, both bacteria express immunity proteins, called SpaI and NisI, and in addition, ABC transporters SpaFEG and NisFEG. Whereas it has been shown that the ABC transporters protect the producing strains by transporting the toxic peptides to the extracellular space, the exact mode of action and the physiological function of the lipoproteins during immunity are still unknown. Understanding the exact role of lantibiotic immunity proteins is of major importance for improving production rates and for the design of newly engineered peptide antibiotics. Here, we show (i) the specificity of each lipoprotein for its own lantibiotic, (ii) the specific physical interaction of subtilin with its lipoprotein SpaI, (iii) the physiological function of SpaI in protecting the cellular membrane, and (iv) the importance of the C-terminal part of subtilin for its interaction with SpaI.
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Affiliation(s)
- Christoph Geiger
- Molecular Genetics and Cellular Microbiology, Institute for Molecular Biosciences, University of Frankfurt, Frankfurt, Germany
| | - Sophie Marianne Korn
- Molecular Genetics and Cellular Microbiology, Institute for Molecular Biosciences, University of Frankfurt, Frankfurt, Germany
| | - Michael Häsler
- Molecular Genetics and Cellular Microbiology, Institute for Molecular Biosciences, University of Frankfurt, Frankfurt, Germany
| | - Oliver Peetz
- Institute of Physical and Theoretical Chemistry, Goethe University, Frankfurt, Germany
| | - Janosch Martin
- Institute of Physical and Theoretical Chemistry, Goethe University, Frankfurt, Germany
| | - Peter Kötter
- Molecular Genetics and Cellular Microbiology, Institute for Molecular Biosciences, University of Frankfurt, Frankfurt, Germany
| | - Nina Morgner
- Institute of Physical and Theoretical Chemistry, Goethe University, Frankfurt, Germany
| | - Karl-Dieter Entian
- Molecular Genetics and Cellular Microbiology, Institute for Molecular Biosciences, University of Frankfurt, Frankfurt, Germany
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Casados-Vázquez LE, Bideshi DK, Barboza-Corona JE. Regulator ThnR and the ThnDE ABC transporter proteins confer autoimmunity to thurincin H in Bacillus thuringiensis. Antonie Van Leeuwenhoek 2018; 111:2349-2360. [DOI: 10.1007/s10482-018-1124-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 07/06/2018] [Indexed: 10/28/2022]
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Crystal Structure of NisI in a Lipid-Free Form, the Nisin Immunity Protein, from Lactococcus lactis. Antimicrob Agents Chemother 2018; 62:AAC.01966-17. [PMID: 29311076 DOI: 10.1128/aac.01966-17] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 12/18/2017] [Indexed: 11/20/2022] Open
Abstract
Nisin is a lantibiotic, a member of a family of polypeptides containing lanthionine with antimicrobial activity. Nisin-producing microorganisms require immunity proteins for self-protection from nisin itself. Lactococcus lactis, a microorganism that synthesizes nisin, has an integral NisFEG ABC transporter and an NisI lipoprotein that function in nisin immunity. Here, we present the crystal structure of the full length of NisI22-C, a lipid-free form of NisI, determined at 1.9-Å resolution. As with the nuclear magnetic resonance (NMR) structures of the N- and C-terminal domains of NisI, NisI22-C is composed of N- and C-terminal domains, both of which display a fold similar to that found in SpaI, a lipoprotein with immunity against subtilin in Bacillus subtilis The full-length structure of NisI22-c reveals a large, deep cleft by the interdomain association, one side of which is occupied by the residues important for immunity. Opposite the cleft, a shallow groove is found where nisin-interacting residues are distributed in the periphery composed of the C-terminal negative patch. Based on a sulfate ion found in the large and deep cleft, a model of NisI in complex with a farnesyl diphosphate backbone of lipid II is proposed, suggesting a mechanism for increasing the chances of encountering nisin.
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Repka LM, Chekan JR, Nair SK, van der Donk WA. Mechanistic Understanding of Lanthipeptide Biosynthetic Enzymes. Chem Rev 2017; 117:5457-5520. [PMID: 28135077 PMCID: PMC5408752 DOI: 10.1021/acs.chemrev.6b00591] [Citation(s) in RCA: 320] [Impact Index Per Article: 45.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
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Lanthipeptides
are ribosomally synthesized and post-translationally
modified peptides (RiPPs) that display a wide variety of biological
activities, from antimicrobial to antiallodynic. Lanthipeptides that
display antimicrobial activity are called lantibiotics. The post-translational
modification reactions of lanthipeptides include dehydration of Ser
and Thr residues to dehydroalanine and dehydrobutyrine, a transformation
that is carried out in three unique ways in different classes of lanthipeptides.
In a cyclization process, Cys residues then attack the dehydrated
residues to generate the lanthionine and methyllanthionine thioether
cross-linked amino acids from which lanthipeptides derive their name.
The resulting polycyclic peptides have constrained conformations that
confer their biological activities. After installation of the characteristic
thioether cross-links, tailoring enzymes introduce additional post-translational
modifications that are unique to each lanthipeptide and that fine-tune
their activities and/or stability. This review focuses on studies
published over the past decade that have provided much insight into
the mechanisms of the enzymes that carry out the post-translational
modifications.
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Affiliation(s)
- Lindsay M Repka
- Howard Hughes Medical Institute and Department of Chemistry, ‡Department of Biochemistry, and §Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Jonathan R Chekan
- Howard Hughes Medical Institute and Department of Chemistry, ‡Department of Biochemistry, and §Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Satish K Nair
- Howard Hughes Medical Institute and Department of Chemistry, ‡Department of Biochemistry, and §Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Wilfred A van der Donk
- Howard Hughes Medical Institute and Department of Chemistry, ‡Department of Biochemistry, and §Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
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Nawrocki KL, Crispell EK, McBride SM. Antimicrobial Peptide Resistance Mechanisms of Gram-Positive Bacteria. Antibiotics (Basel) 2014; 3:461-92. [PMID: 25419466 PMCID: PMC4239024 DOI: 10.3390/antibiotics3040461] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Revised: 09/25/2014] [Accepted: 09/28/2014] [Indexed: 01/09/2023] Open
Abstract
Antimicrobial peptides, or AMPs, play a significant role in many environments as a tool to remove competing organisms. In response, many bacteria have evolved mechanisms to resist these peptides and prevent AMP-mediated killing. The development of AMP resistance mechanisms is driven by direct competition between bacterial species, as well as host and pathogen interactions. Akin to the number of different AMPs found in nature, resistance mechanisms that have evolved are just as varied and may confer broad-range resistance or specific resistance to AMPs. Specific mechanisms of AMP resistance prevent AMP-mediated killing against a single type of AMP, while broad resistance mechanisms often lead to a global change in the bacterial cell surface and protect the bacterium from a large group of AMPs that have similar characteristics. AMP resistance mechanisms can be found in many species of bacteria and can provide a competitive edge against other bacterial species or a host immune response. Gram-positive bacteria are one of the largest AMP producing groups, but characterization of Gram-positive AMP resistance mechanisms lags behind that of Gram-negative species. In this review we present a summary of the AMP resistance mechanisms that have been identified and characterized in Gram-positive bacteria. Understanding the mechanisms of AMP resistance in Gram-positive species can provide guidelines in developing and applying AMPs as therapeutics, and offer insight into the role of resistance in bacterial pathogenesis.
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Affiliation(s)
- Kathryn L Nawrocki
- Department of Microbiology and Immunology, Emory University School of Medicine, 1510 Clifton Rd, Atlanta, GA 30322, USA; (K.L.N.); (E.K.C.)
| | - Emily K Crispell
- Department of Microbiology and Immunology, Emory University School of Medicine, 1510 Clifton Rd, Atlanta, GA 30322, USA; (K.L.N.); (E.K.C.)
| | - Shonna M McBride
- Department of Microbiology and Immunology, Emory University School of Medicine, 1510 Clifton Rd, Atlanta, GA 30322, USA; (K.L.N.); (E.K.C.)
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Christ NA, Bochmann S, Gottstein D, Duchardt-Ferner E, Hellmich UA, Düsterhus S, Kötter P, Güntert P, Entian KD, Wöhnert J. The First structure of a lantibiotic immunity protein, SpaI from Bacillus subtilis, reveals a novel fold. J Biol Chem 2012; 287:35286-35298. [PMID: 22904324 PMCID: PMC3471728 DOI: 10.1074/jbc.m112.401620] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Revised: 08/16/2012] [Indexed: 11/06/2022] Open
Abstract
Lantibiotics are peptide-derived antibiotics that inhibit the growth of Gram-positive bacteria via interactions with lipid II and lipid II-dependent pore formation in the bacterial membrane. Due to their general mode of action the Gram-positive producer strains need to express immunity proteins (LanI proteins) for protection against their own lantibiotics. Little is known about the immunity mechanism protecting the producer strain against its own lantibiotic on the molecular level. So far, no structures have been reported for any LanI protein. We solved the structure of SpaI, a LanI protein from the subtilin producing strain Bacillus subtilis ATCC 6633. SpaI is a 16.8-kDa lipoprotein that is attached to the outside of the cytoplasmic membrane via a covalent diacylglycerol anchor. SpaI together with the ABC transporter SpaFEG protects the B. subtilis membrane from subtilin insertion. The solution-NMR structure of a 15-kDa biologically active C-terminal fragment reveals a novel fold. We also demonstrate that the first 20 N-terminal amino acids not present in this C-terminal fragment are unstructured in solution and are required for interactions with lipid membranes. Additionally, growth tests reveal that these 20 N-terminal residues are important for the immunity mediated by SpaI but most likely are not part of a possible subtilin binding site. Our findings are the first step on the way of understanding the immunity mechanism of B. subtilis in particular and of other lantibiotic producing strains in general.
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Affiliation(s)
- Nina A Christ
- Institute for Molecular Biosciences, Goethe University, 60438 Frankfurt am Main, Germany; Center of Biomolecular Magnetic Resonance, Goethe University, 60438 Frankfurt am Main, Germany
| | - Sophie Bochmann
- Institute for Molecular Biosciences, Goethe University, 60438 Frankfurt am Main, Germany
| | - Daniel Gottstein
- Center of Biomolecular Magnetic Resonance, Goethe University, 60438 Frankfurt am Main, Germany; Institute of Biophysical Chemistry, Goethe University, 60438 Frankfurt am Main, Germany
| | - Elke Duchardt-Ferner
- Institute for Molecular Biosciences, Goethe University, 60438 Frankfurt am Main, Germany; Center of Biomolecular Magnetic Resonance, Goethe University, 60438 Frankfurt am Main, Germany
| | - Ute A Hellmich
- Institute for Molecular Biosciences, Goethe University, 60438 Frankfurt am Main, Germany; Center of Biomolecular Magnetic Resonance, Goethe University, 60438 Frankfurt am Main, Germany; Institute of Biophysical Chemistry, Goethe University, 60438 Frankfurt am Main, Germany
| | - Stefanie Düsterhus
- Institute for Molecular Biosciences, Goethe University, 60438 Frankfurt am Main, Germany
| | - Peter Kötter
- Institute for Molecular Biosciences, Goethe University, 60438 Frankfurt am Main, Germany
| | - Peter Güntert
- Center of Biomolecular Magnetic Resonance, Goethe University, 60438 Frankfurt am Main, Germany; Institute of Biophysical Chemistry, Goethe University, 60438 Frankfurt am Main, Germany
| | - Karl-Dieter Entian
- Institute for Molecular Biosciences, Goethe University, 60438 Frankfurt am Main, Germany; Cluster of Excellence "Macromolecular Complexes," Goethe University, 60438 Frankfurt am Main, Germany.
| | - Jens Wöhnert
- Institute for Molecular Biosciences, Goethe University, 60438 Frankfurt am Main, Germany; Center of Biomolecular Magnetic Resonance, Goethe University, 60438 Frankfurt am Main, Germany; Cluster of Excellence "Macromolecular Complexes," Goethe University, 60438 Frankfurt am Main, Germany.
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Christ NA, Duchardt-Ferner E, Düsterhus S, Kötter P, Entian KD, Wöhnert J. NMR resonance assignment of the autoimmunity protein SpaI from Bacillus subtilis ATCC 6633. BIOMOLECULAR NMR ASSIGNMENTS 2012; 6:9-13. [PMID: 21643970 DOI: 10.1007/s12104-011-9314-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Accepted: 05/23/2011] [Indexed: 05/30/2023]
Abstract
Bacillus subtilis ATCC 6633 produces the lipid II targeting lantibiotic subtilin. For self-protection these gram-positive bacteria express a cluster of four self-immunity proteins named SpaIFEG. SpaI is a 16.8 kDa lipoprotein which is attached to the outside of the cytoplasmic membrane via a covalently linked diacylglycerol anchor. Together with the ABC-transporter SpaFEG, SpaI protects the membrane from subtilin insertion and there is evidence for a direct interaction of SpaI with subtilin. As a prerequisite for further structural studies of SpaI and the SpaI/subtilin complex we report here the full (1)H, (15)N, (13)C chemical shift assignment for a stable 14.9 kDa C-terminal fragment of SpaI.
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Affiliation(s)
- Nina Alexandra Christ
- Institut für Molekulare Biowissenschaften, Johann-Wolfgang-Goethe-Universität Frankfurt/M., Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
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Entianin, a novel subtilin-like lantibiotic from Bacillus subtilis subsp. spizizenii DSM 15029T with high antimicrobial activity. Appl Environ Microbiol 2011; 77:1698-707. [PMID: 21239550 DOI: 10.1128/aem.01962-10] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Lantibiotics, such as nisin and subtilin, are lanthionine-containing peptides that exhibit antimicrobial as well as pheromone-like autoinducing activity. Autoinduction is specific for each lantibiotic, and reporter systems for nisin and subtilin autoinduction are available. In this report, we used the previously reported subtilin autoinduction bioassay in combination with mass spectrometric analyses to identify the novel subtilin-like lantibiotic entianin from Bacillus subtilis subsp. spizizenii DSM 15029(T). Linearization of entianin using Raney nickel-catalyzed reductive cleavage enabled, for the first time, the use of tandem mass spectrometry for the fast and efficient determination of an entire lantibiotic primary structure, including posttranslational modifications. The amino acid sequence determined was verified by DNA sequencing of the etnS structural gene, which confirmed that entianin differs from subtilin at 3 amino acid positions. In contrast to B. subtilis ATCC 6633, which produces only small amounts of unsuccinylated subtilin, B. subtilis DSM 15029(T) secretes considerable amounts of unsuccinylated entianin. Entianin was very active against several Gram-positive pathogens, such as Staphylococcus aureus and Enterococcus faecalis. The growth-inhibiting activity of succinylated entianin (S-entianin) was much lower than that of unsuccinylated entianin: a 40-fold higher concentration was required for inhibition. For succinylated subtilin (S-subtilin), a concentration 100-fold higher than that of unsuccinylated entianin was required to inhibit the growth of a B. subtilis test strain. This finding was in accordance with a strongly reduced sensing of cellular envelope stress provided by S-entianin relative to that of entianin. Remarkably, S-entianin and S-subtilin showed considerable autoinduction activity, clearly demonstrating that autoinduction and antibiotic activity underlie different molecular mechanisms.
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