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Fernandez-Cantos MV, Babu AF, Hanhineva K, Kuipers OP. Identification of metabolites produced by six gut commensal Bacteroidales strains using non-targeted LC-MS/MS metabolite profiling. Microbiol Res 2024; 283:127700. [PMID: 38518452 DOI: 10.1016/j.micres.2024.127700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 03/05/2024] [Accepted: 03/18/2024] [Indexed: 03/24/2024]
Abstract
As the most abundant gram-negative bacterial order in the gastrointestinal tract, Bacteroidales bacteria have been extensively studied for their contribution to various aspects of gut health. These bacteria are renowned for their involvement in immunomodulation and their remarkable capacity to break down complex carbohydrates and fibers. However, the human gut microbiota is known to produce many metabolites that ultimately mediate important microbe-host and microbe-microbe interactions. To gain further insights into the metabolites produced by the gut commensal strains of this order, we examined the metabolite composition of their bacterial cell cultures in the stationary phase. Based on their abundance in the gastrointestinal tract and their relevance in health and disease, we selected a total of six bacterial strains from the relevant genera Bacteroides, Phocaeicola, Parabacteroides, and Segatella. We grew these strains in modified Gifu anaerobic medium (mGAM) supplemented with mucin, which resembles the gut microbiota's natural environment. Liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based metabolite profiling revealed 179 annotated metabolites that had significantly differential abundances between the studied bacterial strains and the control growth medium. Most of them belonged to classes such as amino acids and derivatives, organic acids, and nucleot(s)ides. Of particular interest, Segatella copri DSM 18205 (previously referred to as Prevotella copri) produced substantial quantities of the bioactive metabolites phenylethylamine, tyramine, tryptamine, and ornithine. Parabacteroides merdae CL03T12C32 stood out due to its ability to produce cadaverine, histamine, acetylputrescine, and deoxycarnitine. In addition, we found that strains of the genera Bacteroides, Phocaeicola, and Parabacteroides accumulated considerable amounts of proline-hydroxyproline, a collagen-derived bioactive dipeptide. Collectively, these findings offer a more detailed comprehension of the metabolic potential of these Bacteroidales strains, contributing to a better understanding of their role within the human gut microbiome in health and disease.
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Affiliation(s)
- Maria Victoria Fernandez-Cantos
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Ambrin Farizah Babu
- School of Medicine, Institute of Public Health and Clinical Nutrition, University of Eastern Finland, 70211 Kuopio, Finland; Afekta Technologies Ltd., Microkatu 1, Kuopio 70210, Finland
| | - Kati Hanhineva
- School of Medicine, Institute of Public Health and Clinical Nutrition, University of Eastern Finland, 70211 Kuopio, Finland; Afekta Technologies Ltd., Microkatu 1, Kuopio 70210, Finland; Department of Life Technologies, Food Sciences Unit, University of Turku, Turku 20014, Finland
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands.
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2
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Lilge L, Kuipers OP. A two-step regulatory circuit involving Spo0A-AbrB activates mersacidin biosynthesis in Bacillus subtilis. Int J Antimicrob Agents 2024; 63:107155. [PMID: 38527561 DOI: 10.1016/j.ijantimicag.2024.107155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 03/13/2024] [Accepted: 03/20/2024] [Indexed: 03/27/2024]
Abstract
Due to intramolecular ring structures, the ribosomally produced and post-translationally modified peptide mersacidin shows antimicrobial properties comparable to those of vancomycin without exhibiting cross-resistance. Although the principles of mersacidin biosynthesis are known, there is no information on the molecular control processes for the initial stimulation of mersacidin bioproduction. By using Bacillus subtilis for heterologous biosynthesis, a considerable amount of mersacidin could be produced without the mersacidin-specific immune system and the mersacidin-activating secretory protease. By using the established laboratory strain Bacillus subtilis 168 and strain 3NA, which is used for high cell density fermentation processes, in combination with the construction of reporter strains to determine the promoter strengths within the mersacidin core gene cluster, the molecular regulatory circuit of Spo0A, a master regulator of cell differentiation including sporulation initiation, and the global transcriptional regulator AbrB, which is involved in cell adaptation processes in the transient growth phase, was identified to control the initial stimulation of the mersacidin core gene cluster. In a second downstream regulatory step, the activator MrsR1, encoded in the core gene cluster, acts as a stimulatory element for mersacidin biosynthesis. These findings are important to understand the mechanisms linking environmental conditions and microbial responses with respect to the bioproduction of bioactive metabolites including antimicrobials such as mersacidin. This information will also support the construction of production strains for bioactive metabolites with antimicrobial properties.
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Affiliation(s)
- Lars Lilge
- Department of Molecular Genetics, University of Groningen, AG Groningen, The Netherlands; Department of Bioprocess Engineering, Institute of Food Science and Biotechnology, University of Hohenheim, Stuttgart, Germany.
| | - Oscar P Kuipers
- Department of Molecular Genetics, University of Groningen, AG Groningen, The Netherlands
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3
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Guo L, Stoffels K, Broos J, Kuipers OP. Engineering hybrid lantibiotics yields the highly stable and bacteriocidal peptide cerocin V. Microbiol Res 2024; 282:127640. [PMID: 38350171 DOI: 10.1016/j.micres.2024.127640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 02/02/2024] [Accepted: 02/06/2024] [Indexed: 02/15/2024]
Abstract
Antimicrobial peptides (AMPs) show promise as alternatives to traditional antibiotics for treating drug-resistant infections. Their adaptability and diverse sequence possibilities allow for rational design by modulating physicochemical determinants to achieve desired biological properties, transforming them into peptides for potential new therapies. Nisin, one of the best-studied AMPs, is believed to have potential to be used as a therapeutic, particularly against antibiotic-resistant bacteria. However, its instability in physiological conditions limits its use in clinical applications and pharmaceutical development. Exploration of new natural variants of nisin has uncovered diverse properties using different domains. Shuffling peptide modules can fine-tune the chemical properties of these molecules, potentially enhancing stability while maintaining or improving antimicrobial activity. In this study, hybrid AMPs were created by combining domains from three unique nisin variants, i.e. nisin A, cesin and rombocin, leading to the identification of a promising variant, named cerocin A, which harbours only 25 amino acids compared to the typical 31-35 amino acid length of nisin. Cerocin A demonstrates potent antibacterial activity against methicillin-resistant Staphylococcus aureus (MRSA), approaching that of nisin itself. Cerocin A's mode of action involves a dual mechanism through the combination of two domains, consisting of a small ring/domain (6 amino acids) from the C-terminal end of rombocin attached to the preceding peptide of cesin, changing it from a bacteriostatic to a bactericidal peptide. Further mutation studies identified a new variant, cerocin V, with significantly improved resistance against trypsin degradation, while maintaining high potency. Importantly, cerocin V showed no undesired toxic effects on human red blood cells and remained stable in human plasma. In conclusion, we demonstrate that peptide construction using domain engineering is an effective strategy for manipulating both biological and physicochemical aspects, leading to the creation of novel bioactive molecules with desired properties. These constructs are appealing candidates for further optimization and development as novel antibiotics.
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Affiliation(s)
- Longcheng Guo
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Konstantin Stoffels
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Jaap Broos
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands.
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4
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Vargiu M, Xu Y, Kuipers OP, Roelfes G. Selective Aza-Michael Addition to Dehydrated Amino Acids in Natural Antimicrobial Peptides. Chembiochem 2024; 25:e202400043. [PMID: 38334959 DOI: 10.1002/cbic.202400043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/07/2024] [Accepted: 02/09/2024] [Indexed: 02/10/2024]
Abstract
We report the efficient and site selective modification of non-canonical dehydroamino acids in ribosomally synthesized and post-transationally modified peptides (RiPPs) by β-amination. The singly modified thiopeptide Thiostrepton showed an up to 35-fold increase in water solubility, and minimum inhibitory concentration (MIC) assays showed that antimicrobial activity remained good, albeit lower than the unmodified peptide. Also the lanthipeptide nisin could be modified using this method.
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Affiliation(s)
- Michela Vargiu
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747AG, Groningen, The Netherlands
| | - Yanli Xu
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747AG, Groningen, The Netherlands
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747AG, Groningen, The Netherlands
| | - Gerard Roelfes
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747AG, Groningen, The Netherlands
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Guo L, Stoffels K, Broos J, Kuipers OP. Altering Specificity and Enhancing Stability of the Antimicrobial Peptides Nisin and Rombocin through Dehydrated Amino Acid Residue Engineering. Peptides 2024; 174:171152. [PMID: 38220092 DOI: 10.1016/j.peptides.2024.171152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/08/2024] [Accepted: 01/09/2024] [Indexed: 01/16/2024]
Abstract
Nisin serves as the prototype within the lantibiotic group of antimicrobial peptides, exhibiting a broad-spectrum inhibition against Gram-positive bacteria, including important food-borne pathogens and clinically relevant antibiotic-resistant strains. The gene-encoded nature of nisin allows for gene-based bioengineering, enabling the generation of novel derivatives. It has been demonstrated that nisin mutants can be produced with improved functional properties. Here, we particularly focus on the uncommon amino acid residues dehydroalanine (Dha) and dehydrobutyrin (Dhb), whose functions are not yet fully elucidated. Prior to this study, we developed a new expression system that utilizes the nisin modification machinery NisBTC to advance expression, resulting in enhanced peptide dehydration efficiency. Through this approach, we discovered that the dehydrated amino acid Dhb at position 18 in the peptide rombocin, a short variant of nisin, displayed four times higher activity compared to the non-dehydrated peptide against the strain Lactococcus lactis. Furthermore, we observed that in the peptides nisin and rombocin, the dehydrated amino acid Dha at residue positon 18 exhibited superior activity compared to the dehydrated amino acid Dhb. Upon purifying the wild-type nisin and its variant nisinG18/Dha to homogeneity, the minimum inhibitory concentration (MIC) indicated that the variant exhibited activity similar to that of wild-type nisin in inhibiting the growth of Bacillus cereus but showed twice the MIC values against the other four tested Gram-positive strains. Further stability tests demonstrated that the dehydrated peptide exhibited properties similar to wild-type nisin under different temperatures but displayed higher resistance to proteolytic enzymes compared to wild-type nisin.
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Affiliation(s)
- Longcheng Guo
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Konstantin Stoffels
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Jaap Broos
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands.
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Liu F, van Heel AJ, Kuipers OP. Engineering circular bacteriocins: structural and functional effects of α-helix exchanges and disulfide introductions in circularin A. Front Microbiol 2024; 15:1337647. [PMID: 38435696 PMCID: PMC10905743 DOI: 10.3389/fmicb.2024.1337647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 01/29/2024] [Indexed: 03/05/2024] Open
Abstract
Circular bacteriocins form a distinct group of antimicrobial peptides (AMPs) characterized by their unique head-to-tail ligated circular structure and functional properties. They belong to the ribosomally synthesized and post-translationally modified peptide (RiPP) family. The ribosomal origin of these peptides facilitates rapid diversification through mutations in the precursor genes combined with specific modification enzymes. In this study, we primarily explored the bacteriocin engineering potential of circularin A, a circular bacteriocin produced by Clostridium beijerinckii ATCC 25752. Specifically, we employed strategies involving α-helix replacements and disulfide bond introductions to investigate their effects on both biosynthesis and bioactivity of the bacteriocin. The results show the feasibility of peptide engineering to introduce certain structural properties into circularin A through carefully designed approaches. The introduction of cysteines for potential disulfide bonds resulted in a substantial reduction in bacteriocin biosynthesis and/or bioactivity, indicating the importance of maintaining dynamic flexibility of α-helices in circularin A, while reduction of the potential disulfide in one case increased the activity. The 5 α-helices of circularin A were respectively replaced by corresponding helices from another circular peptide, enterocin AS-48, and modestly active peptides were obtained in a few cases. Overall, this study provides valuable insights into the engineering potential of circular bacteriocins as antimicrobial agents, including their structural and functional restrictions and their suitability as peptide engineering scaffolds. This helps to pave the way for the development of novel antimicrobial peptides with tailored properties based on circular bacteriocins.
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Affiliation(s)
- Fangfang Liu
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Auke J. van Heel
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
- Omnicin Therapeutics, Groningen, Netherlands
| | - Oscar P. Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
- Omnicin Therapeutics, Groningen, Netherlands
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7
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Garcia-Morena D, Fernandez-Cantos MV, Escalera SL, Lok J, Iannone V, Cancellieri P, Maathuis W, Panagiotou G, Aranzamendi C, Aidy SE, Kolehmainen M, El-Nezami H, Wellejus A, Kuipers OP. In Vitro Influence of Specific Bacteroidales Strains on Gut and Liver Health Related to Metabolic Dysfunction-Associated Fatty Liver Disease. Probiotics Antimicrob Proteins 2024:10.1007/s12602-024-10219-1. [PMID: 38319537 DOI: 10.1007/s12602-024-10219-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/17/2024] [Indexed: 02/07/2024]
Abstract
Metabolic dysfunction-associated fatty liver disease (MAFLD) has become a major health risk and a serious worldwide issue. MAFLD typically arises from aberrant lipid metabolism, insulin resistance, oxidative stress, and inflammation. However, subjacent causes are multifactorial. The gut has been proposed as a major factor in health and disease, and over the last decade, bacterial strains with potentially beneficial effects on the host have been identified. In vitro cell models have been commonly used as an early step before in vivo drug assessment and can confer complementary advantages in gut and liver health research. In this study, several selected strains of the order Bacteroidales were used in a three-cell line in vitro analysis (HT-29, Caco-2, and HepG2 cell lines) to investigate their potential as new-generation probiotics and microbiota therapeutics. Antimicrobial activity, a potentially useful trait, was studied, and the results showed that Bacteroidales can be a source of either wide- or narrow-spectrum antimicrobials targeting other closely related strains. Moreover, Bacteroides sp. 4_1_36 induced a significant decrease in gut permeability, as evidenced by the high TEER values in the Caco-2 monolayer assay, as well as a reduction in free fatty acid accumulation and improved fatty acid clearance in a steatosis HepG2 model. These results suggest that Bacteroidales may spearhead the next generation of probiotics to prevent or diminish MAFLD.
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Affiliation(s)
- Diego Garcia-Morena
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Maria Victoria Fernandez-Cantos
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Silvia Lopez Escalera
- Chr. Hansen A/S, Bøge Allé 10-12, 2970, Hørsholm, Denmark
- Friedrich-Schiller Universität Jena, Fakultät für Biowissenschaften, 18K, 07743, Bachstraβe, Germany
| | - Johnson Lok
- School of Medicine, Institute of Public Health and Clinical Nutrition, University of Eastern Finland, 70200, Kuopio, Finland
| | - Valeria Iannone
- School of Medicine, Institute of Public Health and Clinical Nutrition, University of Eastern Finland, 70200, Kuopio, Finland
| | - Pierluca Cancellieri
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Willem Maathuis
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Gianni Panagiotou
- Department of Microbiome Dynamics, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), 07745, Jena, Germany
- Department of Medicine and State Key Laboratory of Pharmaceutical Biotechnology, University of Hong Kong, Hong Kong, China
- Faculty of Biological Sciences, Friedrich Schiller University, 07745, Jena, Germany
| | - Carmen Aranzamendi
- Groningen Biomolecular Sciences and Biotechnology Institute, Host-Microbe Metabolic Interactions, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, the Netherlands
| | - Sahar El Aidy
- Groningen Biomolecular Sciences and Biotechnology Institute, Host-Microbe Metabolic Interactions, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, the Netherlands
| | - Marjukka Kolehmainen
- School of Medicine, Institute of Public Health and Clinical Nutrition, University of Eastern Finland, 70200, Kuopio, Finland
| | - Hani El-Nezami
- Molecular and Cell Biology Division, School of Biological Sciences, University of Hong Kong, Pok Fu Lam, Hong Kong SAR
| | - Anja Wellejus
- Chr. Hansen A/S, Bøge Allé 10-12, 2970, Hørsholm, Denmark
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.
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Guo L, Wambui J, Wang C, Broos J, Stephan R, Kuipers OP. Rombocin, a Short Stable Natural Nisin Variant, Displays Selective Antimicrobial Activity against Listeria monocytogenes and Employs a Dual Mode of Action to Kill Target Bacterial Strains. ACS Synth Biol 2024; 13:370-383. [PMID: 38194633 PMCID: PMC10804407 DOI: 10.1021/acssynbio.3c00612] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 12/26/2023] [Accepted: 12/27/2023] [Indexed: 01/11/2024]
Abstract
Nisin, with its unique mode of action and potent antimicrobial activity, serves as a remarkable inspiration for the design of novel antibiotics. However, peptides possess inherent weaknesses, particularly their susceptibility to proteolytic degradation, such as by trypsin, which limits their broader applications. This led us to speculate that natural variants of nisin produced by underexplored bacterial species can potentially overcome these limitations. We carried out genome mining of two Romboutsia sedimentorum strains, RC001 and RC002, leading to the discovery of rombocin A, which is a 25 amino acid residue short nisin variant that is predicted to have only four macrocycles compared to the known 31-35 amino acids long nisin variants with five macrocycles. Using the nisin-controlled expression system, we heterologously expressed fully modified and functional rombocin A in Lactococcus lactis and demonstrated its selective antimicrobial activity against Listeria monocytogenes. Rombocin A uses a dual mode of action involving lipid II binding activity and dissipation of the membrane potential to kill target bacteria. Stability tests confirmed its high stability at different pH values, temperatures, and in particular, against enzymatic degradation. With its gene-encoded characteristic, rombocin A is amenable to bioengineering to generate novel derivatives. Further mutation studies led to the identification of rombocin K, a mutant with enhanced bioactivity against L. monocytogenes. Our findings suggest that rombocin A and its bioengineered variant, rombocin K, are promising candidates for development as food preservatives or antibiotics against L. monocytogenes.
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Affiliation(s)
- Longcheng Guo
- Department
of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology
Institute, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Joseph Wambui
- Institute
for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich 8057, Switzerland
| | - Chenhui Wang
- Department
of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology
Institute, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Jaap Broos
- Department
of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology
Institute, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Roger Stephan
- Institute
for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich 8057, Switzerland
| | - Oscar P. Kuipers
- Department
of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology
Institute, University of Groningen, Groningen 9747 AG, The Netherlands
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Arias-Orozco P, Zhou L, Yi Y, Cebrián R, Kuipers OP. Uncovering the diversity and distribution of biosynthetic gene clusters of prochlorosins and other putative RiPPs in marine Synechococcus strains. Microbiol Spectr 2024; 12:e0361123. [PMID: 38088546 PMCID: PMC10783134 DOI: 10.1128/spectrum.03611-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 11/06/2023] [Indexed: 01/13/2024] Open
Abstract
IMPORTANCE Genome mining studies have revealed the remarkable combinatorial diversity of ribosomally synthesized and post-translationally modified peptides (RiPPs) in marine bacteria, including prochlorosins. However, mining strategies also prove valuable in investigating the genomic landscape of associated genes within biosynthetic gene cluster (BGC) specific to targeted RiPPs of interest. Our study contributes to the enrichment of knowledge regarding prochlorosin diversity. It offers insights into potential mechanisms involved in their biosynthesis and modification, such as hyper-modification, which may give rise to active lantibiotics. Additionally, our study uncovers putative novel promiscuous post-translational enzymes, thereby expanding the chemical space explored within the Synechococcus genus. Moreover, this research extends the applications of mining techniques beyond the discovery of new RiPP-like clusters, allowing for a deeper understanding of genomics and diversity. Furthermore, it holds the potential to reveal previously unknown functions within the intriguing RiPP families, particularly in the case of prochlorosins.
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Affiliation(s)
- Patricia Arias-Orozco
- Department of Molecular Genetics, University of Groningen, Nijenborgh, Groningen, The Netherlands
| | - Lu Zhou
- Department of Molecular Genetics, University of Groningen, Nijenborgh, Groningen, The Netherlands
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Yunhai Yi
- Department of Molecular Genetics, University of Groningen, Nijenborgh, Groningen, The Netherlands
| | - Rubén Cebrián
- Department of Molecular Genetics, University of Groningen, Nijenborgh, Groningen, The Netherlands
- Department of Clinical Microbiology, Instituto de Investigación Biosanitaria ibs.GRANADA, San Cecilio University Hospital, Granada, Spain
- CIBER de Enfermedades Infecciosas, CIBERINFEC, ISCIII, Madrid, Spain
| | - Oscar P. Kuipers
- Department of Molecular Genetics, University of Groningen, Nijenborgh, Groningen, The Netherlands
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Cebrián R, Lucas R, Fernández-Cantos MV, Slot K, Peñalver P, Martínez-García M, Párraga-Leo A, de Paz MV, García F, Kuipers OP, Morales JC. Synthesis and antimicrobial activity of aminoalkyl resveratrol derivatives inspired by cationic peptides. J Enzyme Inhib Med Chem 2023; 38:267-281. [PMID: 36600674 PMCID: PMC9828810 DOI: 10.1080/14756366.2022.2146685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Antimicrobial resistance is a global concern, far from being resolved. The need of new drugs against new targets is imminent. In this work, we present a family of aminoalkyl resveratrol derivatives with antibacterial activity inspired by the properties of cationic amphipathic antimicrobial peptides. Surprisingly, the newly designed molecules display modest activity against aerobically growing bacteria but show surprisingly good antimicrobial activity against anaerobic bacteria (Gram-negative and Gram-positive) suggesting specificity towards this bacterial group. Preliminary studies into the action mechanism suggest that activity takes place at the membrane level, while no cross-resistance with traditional antibiotics is observed. Actually, some good synergistic relations with existing antibiotics were found against Gram-negative pathogens. However, some cytotoxicity was observed, despite their low haemolytic activity. Our results show the importance of the balance between positively charged moieties and hydrophobicity to improve antimicrobial activity, setting the stage for the design of new drugs based on these molecules.
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Affiliation(s)
- Rubén Cebrián
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands,Department of Clinical Microbiology, Instituto de Investigación Biosanitaria ibs. GRANADA, University Hospital Clínico San Cecilio, Granada, Spain,CONTACT Rubén Cebrián University Hospital San Cecilio,Clinical Microbiology Department, Av. de la Innovación s/n, 18061, Granada, Spain
| | - Ricardo Lucas
- Department of Organic and Pharmaceutical Chemistry, School of Pharmacy, University of Seville, Seville, Spain
| | - María Victoria Fernández-Cantos
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Koen Slot
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Pablo Peñalver
- Department of Biochemistry and Molecular Pharmacology, Instituto de Parasitología y Biomedicina López Neyra, CSIC, PTS Granada, Armilla, Granada, Spain
| | - Marta Martínez-García
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Antonio Párraga-Leo
- Department of Organic and Pharmaceutical Chemistry, School of Pharmacy, University of Seville, Seville, Spain
| | - María Violante de Paz
- Department of Organic and Pharmaceutical Chemistry, School of Pharmacy, University of Seville, Seville, Spain
| | - Federico García
- Department of Clinical Microbiology, Instituto de Investigación Biosanitaria ibs. GRANADA, University Hospital Clínico San Cecilio, Granada, Spain
| | - Oscar P. Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands,Oscar P. Kuipers University of Groningen, Faculty of Science and Engineering, Department of Genetics, Nijenborgh 7, 9747AG, Groningen, The Netherlands
| | - Juan Carlos Morales
- Department of Biochemistry and Molecular Pharmacology, Instituto de Parasitología y Biomedicina López Neyra, CSIC, PTS Granada, Armilla, Granada, Spain,Juan Carlos Morales Instituto de Parasitología y Biomedicina López Neyra, CSIC, PTS Granada, Avda. del Conocimiento 17, Armilla, 18016Granada, Spain
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11
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Hammad M, Ali H, Hassan N, Tawab A, Salman M, Jawad I, de Jong A, Moreno CM, Kuipers OP, Feroz Y, Rashid MH. Food safety and biological control; genomic insights and antimicrobial potential of Bacillus velezensis FB2 against agricultural fungal pathogens. PLoS One 2023; 18:e0291975. [PMID: 37963161 PMCID: PMC10645337 DOI: 10.1371/journal.pone.0291975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 09/08/2023] [Indexed: 11/16/2023] Open
Abstract
Development of natural, broad-spectrum, and eco-friendly bio-fungicides is of high interest in the agriculture and food industries. In this context, Bacillus genus has shown great potential for producing a wide range of antimicrobial metabolites against various pathogens. A Bacillus velezensis strain FB2 was isolated from an agricultural field of National Institute for Biotechnology and Genetic Engineering (NIBGE) Faisalabad, Pakistan, exhibiting good antifungal properties. The complete genome of this strain was sequenced, and its antifungal potential was assayed by dual culture method. Moreover, structural characterization of its antifungal metabolites, produced in vitro, were studied. Genome analysis and mining revealed the secondary metabolite gene clusters, encoding non-ribosomal peptides (NRPs) production (e.g., surfactin, iturin and fengycin) and polyketide (PK) synthesis (e.g., difficidin, bacillaene and macrolactin). Furthermore, the Bacillus velezensis FB2 strain was observed to possess in vitro antifungal activity; 41.64, 40.38 and 26% growth inhibition against major fungal pathogens i.e. Alternaria alternata, Fusarium oxysporum and Fusarium solani respectively. Its lipopeptide extract obtained by acid precipitation method was also found effective against the above-mentioned fungal pathogens. The ESI-MS/MS analysis indicated various homologs of surfactin and iturin-A, responsible for their antifungal activities. Overall, this study provides a better understanding of Bacillus velezensis FB2, as a promising candidate for biocontrol purposes, acting in a safe and sustainable way, to control plant pathogens.
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Affiliation(s)
- Masooma Hammad
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Pakistan
| | - Hazrat Ali
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Pakistan
| | - Noor Hassan
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Pakistan
| | - Abdul Tawab
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Pakistan
| | - Mahwish Salman
- Department of Biochemistry, Government College University Faisalabad (GCUF), Faisalabad, Pakistan
| | - Iqra Jawad
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Pakistan
| | - Anne de Jong
- Groningen Molecular Biology and Biotechnology Institute (GBB), University of Groningen, Groningen, The Netherlands
| | - Claudia Munoz Moreno
- Groningen Molecular Biology and Biotechnology Institute (GBB), University of Groningen, Groningen, The Netherlands
| | - Oscar P. Kuipers
- Groningen Molecular Biology and Biotechnology Institute (GBB), University of Groningen, Groningen, The Netherlands
| | - Yusra Feroz
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Pakistan
| | - Muhammad Hamid Rashid
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Pakistan
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12
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Cacace E, Kim V, Varik V, Knopp M, Tietgen M, Brauer-Nikonow A, Inecik K, Mateus A, Milanese A, Mårli MT, Mitosch K, Selkrig J, Brochado AR, Kuipers OP, Kjos M, Zeller G, Savitski MM, Göttig S, Huber W, Typas A. Systematic analysis of drug combinations against Gram-positive bacteria. Nat Microbiol 2023; 8:2196-2212. [PMID: 37770760 PMCID: PMC10627819 DOI: 10.1038/s41564-023-01486-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 08/30/2023] [Indexed: 09/30/2023]
Abstract
Drug combinations can expand options for antibacterial therapies but have not been systematically tested in Gram-positive species. We profiled ~8,000 combinations of 65 antibacterial drugs against the model species Bacillus subtilis and two prominent pathogens, Staphylococcus aureus and Streptococcus pneumoniae. Thereby, we recapitulated previously known drug interactions, but also identified ten times more novel interactions in the pathogen S. aureus, including 150 synergies. We showed that two synergies were equally effective against multidrug-resistant S. aureus clinical isolates in vitro and in vivo. Interactions were largely species-specific and synergies were distinct from those of Gram-negative species, owing to cell surface and drug uptake differences. We also tested 2,728 combinations of 44 commonly prescribed non-antibiotic drugs with 62 drugs with antibacterial activity against S. aureus and identified numerous antagonisms that might compromise the efficacy of antimicrobial therapies. We identified even more synergies and showed that the anti-aggregant ticagrelor synergized with cationic antibiotics by modifying the surface charge of S. aureus. All data can be browsed in an interactive interface ( https://apps.embl.de/combact/ ).
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Affiliation(s)
- Elisabetta Cacace
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Vladislav Kim
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
- Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Vallo Varik
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Michael Knopp
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Manuela Tietgen
- Goethe University Frankfurt, University Hospital, Institute for Medical Microbiology and Infection Control, Frankfurt am Main, Germany
| | | | - Kemal Inecik
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - André Mateus
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Alessio Milanese
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
- Department of Biology, Institute of Microbiology, and Swiss Institute of Bioinformatics, ETH Zurich, Zurich, Switzerland
| | - Marita Torrissen Mårli
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Karin Mitosch
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Joel Selkrig
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
- Institute of Medical Microbiology, University Hospital of RWTH, Aachen, Germany
| | - Ana Rita Brochado
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Molecular Biology and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Morten Kjos
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Georg Zeller
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Mikhail M Savitski
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Stephan Göttig
- Goethe University Frankfurt, University Hospital, Institute for Medical Microbiology and Infection Control, Frankfurt am Main, Germany
| | - Wolfgang Huber
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Athanasios Typas
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany.
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany.
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13
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Guo L, Wambui J, Wang C, Muchaamba F, Fernandez-Cantos MV, Broos J, Tasara T, Kuipers OP, Stephan R. Cesin, a short natural variant of nisin, displays potent antimicrobial activity against major pathogens despite lacking two C-terminal macrocycles. Microbiol Spectr 2023; 11:e0531922. [PMID: 37754751 PMCID: PMC10581189 DOI: 10.1128/spectrum.05319-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 08/06/2023] [Indexed: 09/28/2023] Open
Abstract
Nisin is a widely used lantibiotic owing to its potent antimicrobial activity and its food-grade status. Its mode of action includes cell wall synthesis inhibition and pore formation, which are attributed to the lipid II binding and pore-forming domains, respectively. We discovered cesin, a short natural variant of nisin, produced by the psychrophilic anaerobe Clostridium estertheticum. Unlike other natural nisin variants, cesin lacks the two terminal macrocycles constituting the pore-forming domain. The current study aimed at heterologous expression and characterization of the antimicrobial activity and physicochemical properties of cesin. Following the successful heterologous expression of cesin in Lactococcus lactis, the lantibiotic demonstrated a broad and potent antimicrobial profile comparable to that of nisin. Determination of its mode of action using lipid II and lipoteichoic acid binding assays linked the potent antimicrobial activity to lipid II binding and electrostatic interactions with teichoic acids. Fluorescence microscopy showed that cesin lacks pore-forming ability in its natural form. Stability tests have shown the lantibiotic is highly stable at different pH values and temperature conditions, but that it can be degraded by trypsin. However, a bioengineered analog, cesin R15G, overcame the trypsin degradation, while keeping full antimicrobial activity. This study shows that cesin is a novel (small) nisin variant that efficiently kills target bacteria by inhibiting cell wall synthesis without pore formation. IMPORTANCE The current increase in antibiotic-resistant pathogens necessitates the discovery and application of novel antimicrobials. In this regard, we recently discovered cesin, which is a short natural variant of nisin produced by the psychrophilic Clostridium estertheticum. However, its suitability as an antimicrobial compound was in doubt due to its structural resemblance to nisin(1-22), a bioengineered short variant of nisin with low antimicrobial activity. Here, we show by heterologous expression, purification, and characterization that the potency of cesin is not only much higher than that of nisin(1-22), but that it is even comparable to the full-length nisin, despite lacking two C-terminal rings that are essential for nisin's activity. We show that cesin is a suitable scaffold for bioengineering to improve its applicability, such as resistance to trypsin. This study demonstrates the suitability of cesin for future application in food and/or for health as a potent and stable antimicrobial compound.
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Affiliation(s)
- Longcheng Guo
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Joseph Wambui
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Chenhui Wang
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Francis Muchaamba
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Maria Victoria Fernandez-Cantos
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Jaap Broos
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Taurai Tasara
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Oscar P. Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Roger Stephan
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
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14
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Fernandez-Cantos MV, Garcia-Morena D, Yi Y, Liang L, Gómez-Vázquez E, Kuipers OP. Bioinformatic mining for RiPP biosynthetic gene clusters in Bacteroidales reveals possible new subfamily architectures and novel natural products. Front Microbiol 2023; 14:1219272. [PMID: 37469430 PMCID: PMC10352776 DOI: 10.3389/fmicb.2023.1219272] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 06/16/2023] [Indexed: 07/21/2023] Open
Abstract
The Bacteroidales order, widely distributed among diverse human populations, constitutes a key component of the human microbiota. Members of this Gram-negative order have been shown to modulate the host immune system, play a fundamental role in the gut's microbial food webs, or be involved in pathogenesis. Bacteria inhabiting such a complex environment as the human microbiome are expected to display social behaviors and, hence, possess factors that mediate cooperative and competitive interactions. Different types of molecules can mediate interference competition, including non-ribosomal peptides (NRPs), polyketides, and bacteriocins. The present study investigates the potential of Bacteroidales bacteria to biosynthesize class I bacteriocins, which are ribosomally synthesized and post-translationally modified peptides (RiPPs). For this purpose, 1,136 genome-sequenced strains from this order were mined using BAGEL4. A total of 1,340 areas of interest (AOIs) were detected. The most commonly identified enzymes involved in RiPP biosynthesis were radical S-adenosylmethionine (rSAM), either alone or in combination with other biosynthetic enzymes such as YcaO. A more comprehensive analysis of a subset of 9 biosynthetic gene clusters (BGCs) revealed a consistent association in Bacteroidales BGCs between peptidase-containing ATP-binding transporters (PCATs) and precursor peptides with GG-motifs. This finding suggests a possibly shared mechanism for leader peptide cleavage and transport of mature products. Notably, human metagenomic studies showed a high prevalence and abundance of the RiPP BGCs from Phocaeicola vulgatus and Porphyromonas gulae. The mature product of P. gulae BGC is hypothesized to display γ-thioether linkages and a C-terminal backbone amidine, a potential new combination of post-translational modifications (PTM). All these findings highlight the RiPP biosynthetic potential of Bacteroidales bacteria, as a rich source of novel peptide structures of possible relevance in the human microbiome context.
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Affiliation(s)
- Maria Victoria Fernandez-Cantos
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Diego Garcia-Morena
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Yunhai Yi
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | | | - Emilio Gómez-Vázquez
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Oscar P. Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
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15
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Guo L, Wang C, Broos J, Kuipers OP. Lipidated variants of the antimicrobial peptide nisin produced via incorporation of methionine analogs for click chemistry show improved bioactivity. J Biol Chem 2023; 299:104845. [PMID: 37209826 PMCID: PMC10404616 DOI: 10.1016/j.jbc.2023.104845] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 05/10/2023] [Accepted: 05/14/2023] [Indexed: 05/22/2023] Open
Abstract
The increase in antibiotic resistance calls for accelerated molecular engineering strategies to diversify natural products for drug discovery. The incorporation of non-canonical amino acids (ncAAs) is an elegant strategy for this purpose, offering a diverse pool of building blocks to introduce desired properties into antimicrobial lanthipeptides. We here report an expression system using Lactococcus lactis as a host for non-canonical amino acid incorporation with high efficiency and yield. We show that incorporating the more hydrophobic analog ethionine (instead of methionine) into nisin improves its bioactivity against several Gram-positive strains we tested. New-to-nature variants were further created by click chemistry. By azidohomoalanine (Aha) incorporation and subsequent click chemistry, we obtained lipidated variants at different positions in nisin or in truncated nisin variants. Some of them show improved bioactivity and specificity against several pathogenic bacterial strains. These results highlight the ability of this methodology for lanthipeptide multi-site lipidation, to create new-to-nature antimicrobial products with diverse features, and extend the toolbox for (lanthi)peptide drug improvement and discovery.
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Affiliation(s)
- Longcheng Guo
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Chenhui Wang
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Jaap Broos
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands.
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16
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Zhao X, Zhong X, Yang S, Deng K, Liu L, Song X, Zou Y, Li L, Zhou X, Jia R, Lin J, Tang H, Ye G, Yang J, Zhao S, Lang Y, Wan H, Yin Z, Kuipers OP. Elucidating the Mechanism of Action of the Gram-Negative-Pathogen-Selective Cyclic Antimicrobial Lipopeptide Brevicidine. Antimicrob Agents Chemother 2023; 67:e0001023. [PMID: 36912655 PMCID: PMC10190627 DOI: 10.1128/aac.00010-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 02/13/2023] [Indexed: 03/14/2023] Open
Abstract
Due to the accelerated appearance of antimicrobial-resistant (AMR) pathogens in clinical infections, new first-in-class antibiotics, operating via novel modes of action, are desperately needed. Brevicidine, a bacterial nonribosomally produced cyclic lipopeptide, has shown potent and selective antimicrobial activity against Gram-negative pathogens. However, before our investigations, little was known about how brevicidine exerts its potent bactericidal effect against Gram-negative pathogens. In this study, we find that brevicidine has potent antimicrobial activity against AMR Enterobacteriaceae pathogens, with MIC values ranging between 0.5 μM (0.8 mg/L) and 2 μM (3.0 mg/L). In addition, brevicidine showed potent antibiofilm activity against the Enterobacteriaceae pathogens, with the same 100% inhibition and 100% eradication concentration of 4 μM (6.1 mg/L). Further mechanistic studies showed that brevicidine exerts its potent bactericidal activity by interacting with lipopolysaccharide in the outer membrane, targeting phosphatidylglycerol and cardiolipin in the inner membrane, and dissipating the proton motive force of bacteria. This results in metabolic perturbation, including the inhibition of ATP synthesis; the inhibition of the dehydrogenation of NADH; the accumulation of reactive oxygen species in bacteria; and the inhibition of protein synthesis. Finally, brevicidine showed a good therapeutic effect in a mouse peritonitis-sepsis model. Our findings pave the way for further research on the clinical applications of brevicidine to combat prevalent infections caused by AMR Gram-negative pathogens worldwide.
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Affiliation(s)
- Xinghong Zhao
- Lab for Sustainable Antimicrobials, Department of Pharmacy, Sichuan Agricultural University, Chengdu, China
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Xinyi Zhong
- Lab for Sustainable Antimicrobials, Department of Pharmacy, Sichuan Agricultural University, Chengdu, China
| | - Shinong Yang
- Lab for Sustainable Antimicrobials, Department of Pharmacy, Sichuan Agricultural University, Chengdu, China
| | - Kai Deng
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Lu Liu
- Lab for Sustainable Antimicrobials, Department of Pharmacy, Sichuan Agricultural University, Chengdu, China
| | - Xu Song
- Lab for Sustainable Antimicrobials, Department of Pharmacy, Sichuan Agricultural University, Chengdu, China
| | - Yuanfeng Zou
- Lab for Sustainable Antimicrobials, Department of Pharmacy, Sichuan Agricultural University, Chengdu, China
| | - Lixia Li
- Lab for Sustainable Antimicrobials, Department of Pharmacy, Sichuan Agricultural University, Chengdu, China
| | - Xun Zhou
- Lab for Sustainable Antimicrobials, Department of Pharmacy, Sichuan Agricultural University, Chengdu, China
| | - Renyong Jia
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Juchun Lin
- Lab for Sustainable Antimicrobials, Department of Pharmacy, Sichuan Agricultural University, Chengdu, China
| | - Huaqiao Tang
- Lab for Sustainable Antimicrobials, Department of Pharmacy, Sichuan Agricultural University, Chengdu, China
| | - Gang Ye
- Lab for Sustainable Antimicrobials, Department of Pharmacy, Sichuan Agricultural University, Chengdu, China
| | - Jianqing Yang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University at Wenjiang, Chengdu, Sichuan, China
| | - Shan Zhao
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Yifei Lang
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Hongping Wan
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Zhongqiong Yin
- Lab for Sustainable Antimicrobials, Department of Pharmacy, Sichuan Agricultural University, Chengdu, China
| | - Oscar P. Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
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17
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Fu Y, Xu Y, Ruijne F, Kuipers OP. Engineering lanthipeptides by introducing a large variety of RiPP modifications to obtain new-to-nature bioactive peptides. FEMS Microbiol Rev 2023; 47:7140522. [PMID: 37096385 PMCID: PMC10373908 DOI: 10.1093/femsre/fuad017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 04/21/2023] [Indexed: 04/26/2023] Open
Abstract
Natural bioactive peptide discovery is a challenging and time-consuming process. However, advances in synthetic biology are providing promising new avenues in peptide engineering that allow for the design and production of a large variety of new-to-nature peptides with enhanced or new bioactivities, using known peptides as templates. Lanthipeptides are ribosomally synthesized and post-translationally modified peptides (RiPPs). The modularity of posttranslational modification enzymes and ribosomal biosynthesis inherent to lanthipeptides, enable their engineering and screening in a high-throughput manner. The field of RiPPs research is rapidly evolving, with many novel post-translational modifications (PTMs) and their associated modification enzymes being identified and characterized. The modularity presented by these diverse and promiscuous modification enzymes has made them promising tools for further in vivo engineering of lanthipeptides, allowing for the diversification of their structures and activities. In this review, we explore the diverse modifications occurring in RiPPs and discuss the potential applications and feasibility of combining various modification enzymes for lanthipeptide engineering. We highlight the prospect of lanthipeptide- and RiPP engineering to produce and screen novel peptides, including mimics of potent non-ribosomally produced antimicrobial peptides (NRPs) such as daptomycin, vancomycin and teixobactin, which offer high therapeutic potential.
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Affiliation(s)
- Yuxin Fu
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Yanli Xu
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Fleur Ruijne
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen 9747 AG, The Netherlands
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18
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Morawska LP, Kuipers OP. Cell-to-cell non-conjugative plasmid transfer between Bacillus subtilis and lactic acid bacteria. Microb Biotechnol 2023; 16:784-798. [PMID: 36547214 PMCID: PMC10034627 DOI: 10.1111/1751-7915.14195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 11/15/2022] [Accepted: 11/25/2022] [Indexed: 12/24/2022] Open
Abstract
Bacillus subtilis is a soil-dwelling bacterium that can interact with a plethora of other microorganisms in its natural habitat. Due to the versatile interactions and its ability to form nanotubes, i.e., recently described membrane structures that trade cytoplasmic content between neighbouring cells, we investigated the potential of HGT from B. subtilis to industrially-relevant members of lactic acid bacteria (LAB). To explore the interspecies HGT events, we developed a co-culturing protocol and provided proof of transfer of a small high copy non-conjugative plasmid from B. subtilis to LABs. Interestingly, the plasmid transfer did not involve conjugation nor activation of the competent state by B. subtilis. Moreover, our study shows for the first time non-conjugative cell-to-cell intraspecies plasmid transfer for non-competent Lactococcus lactis sp. cremoris strains. Our study indicates that cell-to-cell transformation is a ubiquitous form of HGT and can be potentially utilized as an alternative tool for natural (non-GMO) strain improvement.
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Affiliation(s)
- Luiza P Morawska
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Oscar P Kuipers
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
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19
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Liu F, van Heel AJ, Kuipers OP. Leader- and Terminal Residue Requirements for Circularin A Biosynthesis Probed by Systematic Mutational Analyses. ACS Synth Biol 2023; 12:852-862. [PMID: 36857413 PMCID: PMC10028692 DOI: 10.1021/acssynbio.2c00661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
Circularin A is a circular bacteriocin belonging to a subgroup of the ribosomally synthesized and post-translationally modified peptide (RiPP) superfamily. The post-translational biosynthesis of circular bacteriocins primarily consists of leader cleavage, core peptide circularization, and bacteriocin secretion. However, none of these processes have been fully elucidated due to the complex biosynthesis of such bacteriocins and the lack of homology to the functions of other known biosynthetic enzymes. In this study, we investigated the leader- and terminal residue requirements for the biosynthesis of circularin A by systematic mutational analyses, including the mutational effects of variable leader lengths, as well as site-directed substitutions of residues at positions near the leader cleavage site and the circularization site. Results show that the leader with only one Met residue, the shortest leader possible, is sufficient to produce mature circularin A; helix-forming short-sidechain hydrophobic residues are required at positions Val1 and Ala2 of the N-terminus to form active peptide derivatives, indicating the possible steric hindrance effect at these two positions; and an aromatic residue is required at the C-terminal Tyr69 position to produce a mature circular derivative. However, the requirements for residues at position Ala68 are much more relaxed relative to the positions of Val1 and Ala2, since even substitution with the largest possible residue, i.e., tryptophan, still allows the generation of an active Ala68Trp derivative. Our findings provide new perspectives for the biosynthesis of this short-leader circular bacteriocin, which enables the application of circular bacteriocin biosynthesis in rational modified peptide engineering.
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Affiliation(s)
- Fangfang Liu
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Auke J van Heel
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
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20
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Cebrián R, Martínez-García M, Fernández M, García F, Martínez-Bueno M, Valdivia E, Kuipers OP, Montalbán-López M, Maqueda M. Advances in the preclinical characterization of the antimicrobial peptide AS-48. Front Microbiol 2023; 14:1110360. [PMID: 36819031 PMCID: PMC9936517 DOI: 10.3389/fmicb.2023.1110360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 01/11/2023] [Indexed: 02/05/2023] Open
Abstract
Antimicrobial resistance is a natural and inevitable phenomenon that constitutes a severe threat to global public health and economy. Innovative products, active against new targets and with no cross- or co-resistance with existing antibiotic classes, novel mechanisms of action, or multiple therapeutic targets are urgently required. For these reasons, antimicrobial peptides such as bacteriocins constitute a promising class of new antimicrobial drugs under investigation for clinical development. Here, we review the potential therapeutic use of AS-48, a head-to-tail cyclized cationic bacteriocin produced by Enterococcus faecalis. In the last few years, its potential against a wide range of human pathogens, including relevant bacterial pathogens and trypanosomatids, has been reported using in vitro tests and the mechanism of action has been investigated. AS-48 can create pores in the membrane of bacterial cells without the mediation of any specific receptor. However, this mechanism of action is different when susceptible parasites are studied and involves intracellular targets. Due to these novel mechanisms of action, AS-48 remains active against the antibiotic resistant strains tested. Remarkably, the effect of AS-48 against eukaryotic cell lines and in several animal models show little effect at the doses needed to inhibit susceptible species. The characteristics of this molecule such as low toxicity, microbicide activity, blood stability and activity, high stability at a wide range of temperatures or pH, resistance to proteases, and the receptor-independent effect make AS-48 unique to fight a broad range of microbial infections, including bacteria and some important parasites.
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Affiliation(s)
- Rubén Cebrián
- Department of Clinical Microbiology, Instituto de Investigación Biosanitaria Ibs.GRANADA, University Hospital San Cecilio, Granada, Spain,*Correspondence: Rubén Cebrián, ✉
| | | | | | - Federico García
- Department of Clinical Microbiology, Instituto de Investigación Biosanitaria Ibs.GRANADA, University Hospital San Cecilio, Granada, Spain,Biomedicinal Research Network Center, Infectious Diseases (CIBERINFEC), Madrid, Spain
| | | | - Eva Valdivia
- Department of Microbiology, University of Granada, Granada, Spain
| | - Oscar P. Kuipers
- Department of Molecular Genetics, University of Groningen, Groningen, Netherlands
| | - Manuel Montalbán-López
- Department of Microbiology, University of Granada, Granada, Spain,Manuel Montalbán-López, ✉
| | - Mercedes Maqueda
- Department of Microbiology, University of Granada, Granada, Spain
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21
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Mordhorst S, Ruijne F, Vagstad AL, Kuipers OP, Piel J. Emulating nonribosomal peptides with ribosomal biosynthetic strategies. RSC Chem Biol 2023; 4:7-36. [PMID: 36685251 PMCID: PMC9811515 DOI: 10.1039/d2cb00169a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022] Open
Abstract
Peptide natural products are important lead structures for human drugs and many nonribosomal peptides possess antibiotic activity. This makes them interesting targets for engineering approaches to generate peptide analogues with, for example, increased bioactivities. Nonribosomal peptides are produced by huge mega-enzyme complexes in an assembly-line like manner, and hence, these biosynthetic pathways are challenging to engineer. In the past decade, more and more structural features thought to be unique to nonribosomal peptides were found in ribosomally synthesised and posttranslationally modified peptides as well. These streamlined ribosomal pathways with modifying enzymes that are often promiscuous and with gene-encoded precursor proteins that can be modified easily, offer several advantages to produce designer peptides. This review aims to provide an overview of recent progress in this emerging research area by comparing structural features common to both nonribosomal and ribosomally synthesised and posttranslationally modified peptides in the first part and highlighting synthetic biology strategies for emulating nonribosomal peptides by ribosomal pathway engineering in the second part.
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Affiliation(s)
- Silja Mordhorst
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4 8093 Zürich Switzerland
| | - Fleur Ruijne
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen Nijenborgh 7, 9747 AG Groningen The Netherlands
| | - Anna L Vagstad
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4 8093 Zürich Switzerland
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen Nijenborgh 7, 9747 AG Groningen The Netherlands
| | - Jörn Piel
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4 8093 Zürich Switzerland
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22
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Arias-Orozco P, Yi Y, Ruijne F, Cebrián R, Kuipers OP. Investigating the Specificity of the Dehydration and Cyclization Reactions in Engineered Lanthipeptides by Synechococcal SyncM. ACS Synth Biol 2022; 12:164-177. [PMID: 36520855 PMCID: PMC9872173 DOI: 10.1021/acssynbio.2c00455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
ProcM-like enzymes are class II promiscuous lanthipeptide synthetases that are an attractive tool in synthetic biology for producing lanthipeptides with biotechnological or clinically desired properties. SyncM is a recently described modification enzyme from this family used to develop a versatile expression platform for engineering lanthipeptides. Most remarkably, SyncM can modify up to 79 SyncA substrates in a single strain. Six SyncAs were previously characterized from this pool of substrates. They showed particular characteristics, such as the presence of one or two lanthionine rings, different flanking residues influencing ring formation, and different ring directions, demonstrating the relaxed specificity of SyncM toward its precursor peptides. To gain a deeper understanding of the potential of SyncM as a biosynthetic tool, we further explored the enzyme's capabilities and limits in dehydration and ring formation. We used different SyncA scaffolds for peptide engineering, including changes in the ring's directionality (relative position of Ser/Thr to Cys in the peptide) and size. We further aimed to rationally design mimetics of cyclic antimicrobials and introduce macrocycles in prochlorosin-related and nonrelated substrates. This study highlights the largest lanthionine ring with 15 amino acids (ring-forming residues included) described to date. Taking advantage of the amino acid substrate tolerance of SyncM, we designed the first single-SyncA-based antimicrobial. The insights gained from this work will aid future bioengineering studies. Additionally, it broadens SyncM's application scope for introducing macrocycles in other bioactive molecules.
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Affiliation(s)
- Patricia Arias-Orozco
- Department
of Molecular Genetics, University of Groningen, Nijenborg 7, 9747 AG Groningen, The Netherlands
| | - Yunhai Yi
- Department
of Molecular Genetics, University of Groningen, Nijenborg 7, 9747 AG Groningen, The Netherlands
| | - Fleur Ruijne
- Department
of Molecular Genetics, University of Groningen, Nijenborg 7, 9747 AG Groningen, The Netherlands
| | - Rubén Cebrián
- Department
of Molecular Genetics, University of Groningen, Nijenborg 7, 9747 AG Groningen, The Netherlands,Department
of Clinical Microbiology, Instituto de Investigación Biosanitaria,
ibs. GRANADA, San Cecilio University Hospital, Av. De la Innovación s/n, 18016 Granada, Spain
| | - Oscar P. Kuipers
- Department
of Molecular Genetics, University of Groningen, Nijenborg 7, 9747 AG Groningen, The Netherlands,
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23
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Liu F, van Heel AJ, Chen J, Kuipers OP. Functional production of clostridial circularin A in Lactococcus lactis NZ9000 and mutational analysis of its aromatic and cationic residues. Front Microbiol 2022; 13:1026290. [PMID: 36504829 PMCID: PMC9726714 DOI: 10.3389/fmicb.2022.1026290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 11/07/2022] [Indexed: 11/24/2022] Open
Abstract
Circular bacteriocins, also known as bacterial head-to-tail cyclized peptides, are a subgroup of ribosomally synthesized and post-translationally modified peptides (RiPPs). Compared with their conventional linear counterparts, circular bacteriocins are highly stable over a broad temperature and pH range, and circularization decreases proteolytic degradation by exopeptidases. These features render them great potential as scaffold candidates to withstand strident conditions in food- and pharmaceutical applications. However, the biosynthesis and bioactivity of circular bacteriocins still remain largely unknown. To investigate and gain more insights into the biosynthesis of circular bacteriocins and to achieve efficient production and characterization of bacteriocin variants, we developed an efficient cloning and heterologous expression system for clostridial circularin A and successfully produced this circular peptide in Lactococcus lactis NZ9000. We report three system formats with single plasmid or plasmid combinations to achieve successful cloning and functional production of circularin A in L. lactis. These systematic varieties enabled us to choose the appropriate method to efficiently obtain various constructs with desired properties. With the established heterologous systems in L. lactis, we performed several mutagenesis studies in the precursor peptide to study its structure/function relationships. The overlay activity assay revealed that these mutant variants had variable effects on different indicator strains: lysine substitution for certain glutamine residue(s) greatly decreased its bioactivity against Clostridium perfringens and L. lactis NZ9000, and alanine replacement for the cationic residues significantly reduced the activity against Lactobacillus sake ATCC 15521, whereas alanine substitution for the aromatic residues decreased its bioactivity against all three testing strains dramatically. Moreover, the conditions for bacteriocin production were optimized. Results show that supplementing the minimal medium with extra glucose (or sucrose) and immediate nisin-induction improved the peptide yield significantly. Briefly, we developed an excellent system for the production of circularin A and a wide range of variant peptides in a convenient host, as well as a method for fast detection of peptide production and activity. This system facilitated our mutagenesis studies which provided valuable insights into the effects of mutating specific residues on its biosynthesis and bioactivity, and will eventually enable more complex research into the biosynthesis of circularin A.
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24
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Viel J, Kuipers OP. Modular Use of the Uniquely Small Ring A of Mersacidin Generates the Smallest Ribosomally Produced Lanthipeptide. ACS Synth Biol 2022; 11:3078-3087. [PMID: 36065523 PMCID: PMC9486960 DOI: 10.1021/acssynbio.2c00343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Mersacidin is an antimicrobial class II lanthipeptide. Lanthipeptides are a class of ribosomally synthesized and post-translationally modified peptides (RiPPs), characterized by intramolecular lanthionine rings. These rings give lanthipeptides their bioactive structure and stability. RiPPs are produced from a gene cluster that encodes a precursor peptide and its dedicated unique modification enzymes. The field of RiPP engineering aims to recombine modification enzymes from different RiPPs to modify new substrates, resulting in new-to-nature molecules with novel or improved functionality. The enzyme MrsM from the mersacidin gene cluster installs the four lanthionine rings of mersacidin, including the uniquely small ring A. By applying MrsM in RiPP engineering, this ring could be installed in linear peptides to achieve stabilization by a very small lanthionine or to create small lanthionine-stabilized modules for chemical modification. However, the formation of unique intramolecular structures like that of mersacidin's ring A can be very stringent. Here, the formation of ring A of mersacidin is characterized by mutagenesis. A range of truncated mersacidin variants was made to identify the smallest possible construct in which this ring could still be formed. Additionally, mutants were created to study the flexibility of ring A formation. It was found that although the formation of ring A is stringent, it can be formed in a core peptide as small as five amino acids. The truncated mersacidin core peptide CTFAL is the smallest ribosomally produced lanthipeptide reported to date, and it has exciting prospects as a new module for application in RiPP engineering.
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25
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Morawska LP, Kuipers OP. Antibiotic tolerance in environmentally stressed Bacillus subtilis: physical barriers and induction of a viable but nonculturable state. Microlife 2022; 3:uqac010. [PMID: 37223363 PMCID: PMC10117730 DOI: 10.1093/femsml/uqac010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 05/26/2022] [Indexed: 05/25/2023]
Abstract
Bacterial communities exposed to rapid changes in their habitat encounter different forms of stress. Fluctuating conditions of the microenvironment drive microorganisms to develop several stress responses to sustain growth and division, like altering gene expression and changing the cell's physiology. It is commonly known that these protection systems may give rise to differently adapted subpopulations and indirectly impact bacterial susceptibility to antimicrobials. This study focuses on the adaptation of a soil-dwelling bacterium, Bacillus subtilis, to sudden osmotic changes, including transient and sustained osmotic upshift. Here, we demonstrate that physiological changes caused by pre-exposure to osmotic stress facilitate B. subtilis' entry into a quiescent state, helping them survive when exposed to a lethal antibiotic concentration. We show that the adaptation to transient osmotic upshift with 0.6 M NaCl causes decreased metabolic rates and lowered antibiotic-mediated ROS production when cells were exposed to the aminoglycoside antibiotic kanamycin. Using a microfluidic platform combined with time-lapse microscopy, we followed the uptake of fluorescently labelled kanamycin and examined the metabolic activity of differently preadapted populations at a single-cell level. The microfluidics data revealed that under the conditions tested, B. subtilis escapes from the bactericidal activity of kanamycin by entering into a nongrowing dormant state. Combining single-cell studies and population-wide analysis of differently preadapted cultures, we demonstrate that kanamycin-tolerant B. subtilis cells are entrapped in a viable but nonculturable (VBNC) state.
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Affiliation(s)
- Luiza P Morawska
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, Netherlands
| | - Oscar P Kuipers
- Corresponding author: Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, Netherlands. Tel: +31 50 36 32093, E-mail:
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26
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Cebrián R, Li Q, Peñalver P, Belmonte-Reche E, Andrés-Bilbao M, Lucas R, de Paz MV, Kuipers OP, Morales JC. Chemically Tuning Resveratrol for the Effective Killing of Gram-Positive Pathogens. J Nat Prod 2022; 85:1459-1473. [PMID: 35621995 PMCID: PMC9237828 DOI: 10.1021/acs.jnatprod.1c01107] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Indexed: 06/12/2023]
Abstract
In the era of antimicrobial resistance, the identification of new compounds with strong antimicrobial activity and the development of alternative therapies to fight drug-resistant bacteria are urgently needed. Here, we have used resveratrol, a safe and well-known plant-derived stilbene with poor antimicrobial properties, as a scaffold to design several new families of antimicrobials by adding different chemical entities at specific positions. We have characterized the mode of action of the most active compounds prepared and have examined their synergistic antibacterial activity in combination with traditional antibiotics. Some alkyl- and silyl-resveratrol derivatives show bactericidal activity against Gram-positive bacteria in the same low micromolar range of traditional antibiotics, with an original mechanism of action that combines membrane permeability activity with ionophore-related activities. No cross-resistance or antagonistic effect was observed with traditional antibiotics. Synergism was observed for some specific general-use antibiotics, such as aminoglycosides and cationic antimicrobial peptide antibiotics. No hemolytic activity was observed at the active concentrations or above, although some low toxicity against an MRC-5 cell line was noted.
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Affiliation(s)
- Rubén Cebrián
- Department
of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology
Institute, University of Groningen, Nijenborgh 7, 9747AG Groningen, The Netherlands
| | - Qian Li
- Department
of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology
Institute, University of Groningen, Nijenborgh 7, 9747AG Groningen, The Netherlands
| | - Pablo Peñalver
- Department
of Biochemistry and Molecular Pharmacology and Instituto de Parasitología
y Biomedicina López Neyra, CSIC,
PTS Granada, Avenida del Conocimiento, 17, 18016 Armilla, Granada, Spain
| | - Efres Belmonte-Reche
- Department
of Biochemistry and Molecular Pharmacology and Instituto de Parasitología
y Biomedicina López Neyra, CSIC,
PTS Granada, Avenida del Conocimiento, 17, 18016 Armilla, Granada, Spain
| | - María Andrés-Bilbao
- Department
of Biochemistry and Molecular Pharmacology and Instituto de Parasitología
y Biomedicina López Neyra, CSIC,
PTS Granada, Avenida del Conocimiento, 17, 18016 Armilla, Granada, Spain
| | - Ricardo Lucas
- Department
of Organic and Pharmaceutical Chemistry, School of Pharmacy, University of Seville, 41012 Seville, Spain
| | - María Violante de Paz
- Department
of Organic and Pharmaceutical Chemistry, School of Pharmacy, University of Seville, 41012 Seville, Spain
| | - Oscar P. Kuipers
- Department
of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology
Institute, University of Groningen, Nijenborgh 7, 9747AG Groningen, The Netherlands
| | - Juan Carlos Morales
- Department
of Biochemistry and Molecular Pharmacology and Instituto de Parasitología
y Biomedicina López Neyra, CSIC,
PTS Granada, Avenida del Conocimiento, 17, 18016 Armilla, Granada, Spain
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27
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Ekkers DM, Tusso S, Moreno-Gamez S, Rillo MC, Kuipers OP, van Doorn GS. Trade-offs predicted by metabolic network structure give rise to evolutionary specialization and phenotypic diversification. Mol Biol Evol 2022; 39:msac124. [PMID: 35679426 PMCID: PMC9206417 DOI: 10.1093/molbev/msac124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 05/25/2022] [Accepted: 05/31/2022] [Indexed: 11/30/2022] Open
Abstract
Mitigating trade-offs between different resource-utilization functions is key to an organism's ecological and evolutionary success. These trade-offs often reflect metabolic constraints with a complex molecular underpinning; therefore, their consequences for evolutionary processes have remained elusive. Here, we investigate how metabolic architecture induces resource utilization constraints and how these constraints, in turn, elicit evolutionary specialization and diversification. Guided by the metabolic network structure of the bacterium Lactococcus cremoris, we selected two carbon sources (fructose and galactose) with predicted co-utilization constraints. By evolving L. cremoris on either fructose, galactose or a mix of both sugars, we imposed selection favoring divergent metabolic specializations or co-utilization of both resources, respectively. Phenotypic characterization revealed the evolution of either fructose or galactose specialists in the single-sugar treatments. In the mixed sugar regime, we observed adaptive diversification: both specialists coexisted, and no generalist evolved. Divergence from the ancestral phenotype occurred at key pathway junctions in the central carbon metabolism. Fructose specialists evolved mutations in the fbp and pfk genes that appear to balance anabolic and catabolic carbon fluxes. Galactose specialists evolved increased expression of pgmA (the primary metabolic bottleneck of galactose metabolism) and silencing of ptnABCD (the main glucose transporter) and ldh (regulator/enzyme of downstream carbon metabolism). Overall, our study shows how metabolic network architecture and historical contingency serve to predict targets of selection and inform the functional interpretation of evolved mutations. The elucidation of the relationship between molecular constraints and phenotypic trade-offs contributes to an integrative understanding of evolutionary specialization and diversification.
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Affiliation(s)
- David M Ekkers
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Sergio Tusso
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Grosshaderner Str. 2, 82152 Planegg-Martinsried, Germany
- Science for Life Laboratories and Department of Evolutionary Biology, Norbyvägen 18D, Uppsala University, 75236 Uppsala, Sweden
| | - Stefany Moreno-Gamez
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Marina C Rillo
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University Oldenburg, Schleusenstr. 1, 26382 Wilhelmshaven, Germany
| | - Oscar P Kuipers
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - G Sander van Doorn
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
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28
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de Jong A, Kuipers OP, Kok J. FUNAGE-Pro: comprehensive web server for gene set enrichment analysis of prokaryotes. Nucleic Acids Res 2022; 50:W330-W336. [PMID: 35641095 PMCID: PMC9252808 DOI: 10.1093/nar/gkac441] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 04/20/2022] [Accepted: 05/10/2022] [Indexed: 12/11/2022] Open
Abstract
Recent advances in the field of high throughput (meta-)transcriptomics and proteomics call for easy and rapid methods enabling to explore not only single genes or proteins but also extended biological systems. Gene set enrichment analysis is commonly used to find relations in a set of genes and helps to uncover the biological meaning in results derived from high-throughput data. The basis for gene set enrichment analysis is a solid functional classification of genes. Here, we describe a comprehensive database containing multiple functional classifications of genes of all (>55 000) publicly available complete bacterial genomes. In addition to the most common functional classes such as COG and GO, also KEGG, InterPro, PFAM, eggnog and operon classes are supported. As classification data for features is often not available, we offer fast annotation and classification of proteins in any newly sequenced bacterial genome. The web server FUNAGE-Pro enables fast functional analysis on single gene sets, multiple experiments, time series data, clusters, and gene network modules for any prokaryote species or strain. FUNAGE-Pro is freely available at http://funagepro.molgenrug.nl.
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Affiliation(s)
- Anne de Jong
- Department of Molecular Genetics, University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, the Netherlands
| | - Oscar P Kuipers
- Department of Molecular Genetics, University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, the Netherlands
| | - Jan Kok
- Department of Molecular Genetics, University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, the Netherlands
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29
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Morawska LP, Detert Oude Weme RGJ, Frenzel E, Dirkzwager M, Hoffmann T, Bremer E, Kuipers OP. Stress-induced activation of the proline biosynthetic pathway in Bacillus subtilis: a population-wide and single-cell study of the osmotically controlled proHJ promoter. Microb Biotechnol 2022; 15:2411-2425. [PMID: 35593133 PMCID: PMC9437891 DOI: 10.1111/1751-7915.14073] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/20/2022] [Accepted: 04/27/2022] [Indexed: 12/01/2022] Open
Abstract
Bacillus subtilis, in its natural habitat, is regularly exposed to rapid changes in the osmolarity of its surrounding. As its primary survival strategy, it accumulates large amounts of the compatible solute proline by activating the de novo proline biosynthesis pathway and exploiting the glutamate pools. This osmotically‐induced biosynthesis requires activation of a SigA‐type promoter that drives the expression of the proHJ operon. Population‐wide studies have shown that the activity of the proHJ promoter correlates with the increased osmotic pressure of the environment. Therefore, the activation of the proHJ transcription should be an adequate measure of the adaptation to osmotic stress through proline synthesis in the absence of other osmoprotectants. In this study, we investigate the kinetics of the proHJ promoter activation and the early adaptation to mild osmotic upshift at the single‐cell level. Under these conditions, we observed a switching point and heterogeneous proline biosynthesis gene expression, where the subpopulation of cells showing active proHJ transcription is able to continuously divide, and those unresponsive to osmotic stress remain dormant. Additionally, we demonstrate that bactericidal antibiotics significantly upregulate proHJ transcription in the absence of externally imposed osmotic pressure, suggesting that the osmotically‐controlled proline biosynthesis pathway is also involved in the antibiotic‐mediated stress response.
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Affiliation(s)
- Luiza P Morawska
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Ruud G J Detert Oude Weme
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Elrike Frenzel
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Maarten Dirkzwager
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Tamara Hoffmann
- Department of Biology, Laboratory for Microbiology, Philipps University Marburg, Karl-von-Frisch-Str.8, D-35032, Marburg, Germany.,Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Karl-von-Frisch Strasse 14, 35043, Marburg, Germany
| | - Erhard Bremer
- Department of Biology, Laboratory for Microbiology, Philipps University Marburg, Karl-von-Frisch-Str.8, D-35032, Marburg, Germany.,Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Karl-von-Frisch Strasse 14, 35043, Marburg, Germany
| | - Oscar P Kuipers
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
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30
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Abstract
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The class II lanthipeptide
mersacidin, a ribosomally synthesized
and post-translationally modified peptide (RiPP), displays unique
intramolecular structures, including a very small lanthionine ring.
When applied in the growing field of RiPP engineering, these can add
unique features to new-to-nature compounds with novel properties.
Recently, a heterologous expression system for mersacidin in Escherichia coli was developed to add its modification
enzymes to the RiPP engineering toolbox and further explore mersacidin
biosynthesis and leader-processing. The dedicated mersacidin transporter
and leader protease MrsT was shown to cleave the leader peptide only
partially upon export, transporting GDMEAA-mersacidin out of the cell.
The extracellular Bacillus amyloliquefaciens protease AprE was shown to release active mersacidin in a second
leader-processing step after transport. The conserved LanT cleavage
site in the mersacidin leader is present in many other class II lanthipeptides.
In contrast to mersacidin, the leader of these peptides is fully processed
in one step. This difference with mersacidin leader-processing raises
fundamentally interesting questions about the specifics of mersacidin
modification and processing, which is also crucial for its application
in RiPP engineering. Here, mutational studies of the mersacidin leader–core
interface were performed to answer these questions. Results showed
the GDMEAA sequence is crucial for both mersacidin modification and
leader processing, revealing a unique leader layout in which a LanM
recognition site is positioned downstream of the conserved leader-protease
LanT cleavage site. Moreover, by identifying residues and regions
that are crucial for mersacidin-type modifications, the wider application
of mersacidin modifications in RiPP engineering has been enabled.
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Affiliation(s)
- Jakob H. Viel
- Department of Molecular Genetics, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Oscar P. Kuipers
- Department of Molecular Genetics, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
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31
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Pinto JPC, Brouwer R, Zeyniyev A, Kuipers OP, Kok J. High-Resolution Chrono-Transcriptome of Lactococcus lactis Reveals That It Expresses Proteins with Adapted Size and pI upon Acidification and Nutrient Starvation. Appl Environ Microbiol 2022; 88:e0247621. [PMID: 35416684 PMCID: PMC9088255 DOI: 10.1128/aem.02476-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 02/26/2022] [Indexed: 12/04/2022] Open
Abstract
Whole-genome transcriptional analyses performed on microorganisms are traditionally based on a small number of samples. To map transient expression variations, and thoroughly characterize gene expression throughout the growth curve of the widely used model organism Lactococcus lactis MG1363, gene expression data were collected with unprecedented time resolution. The resulting gene expression patterns were globally analyzed in several different ways to demonstrate the richness of the data and the ease with which novel phenomena can be discovered. When the culture moves from one growth phase to another, gene expression patterns change to such an extent that we suggest that those patterns can be used to unequivocally distinguish growth phases from each other. Also, within the classically defined growth phases, subgrowth phases were distinguishable with a distinct expression signature. Apart from the global expression pattern shifts seen throughout the growth curve, several cases of short-lived transient gene expression patterns were clearly observed. These could help explain the gene expression variations frequently observed in biological replicates. A method was devised to estimate a measure of unnormalized/absolute gene expression levels and used to determine how global transcription patterns are influenced by nutrient starvation or acidification of the medium. Notably, we inferred that L. lactis MG1363 produces proteins with on average lower pIs and lower molecular weights as the medium acidifies and nutrients get scarcer. IMPORTANCE This data set is a rich resource for microbiologists interested in common mechanisms of gene expression, regulation and in particular the physiology of L. lactis. Thus, similar to the common use of genome sequence data by the scientific community, the data set constitutes an extensive data repository for mining and an opportunity for bioinformaticians to develop novel tools for in-depth analysis.
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Affiliation(s)
- João P. C. Pinto
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Rutger Brouwer
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Araz Zeyniyev
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Oscar P. Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Jan Kok
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
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32
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Morawska LP, Hernandez-Valdes JA, Kuipers OP. Diversity of bet-hedging strategies in microbial communities-Recent cases and insights. WIREs Mech Dis 2022; 14:e1544. [PMID: 35266649 PMCID: PMC9286555 DOI: 10.1002/wsbm.1544] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 10/05/2021] [Accepted: 10/07/2021] [Indexed: 12/12/2022]
Abstract
Microbial communities are continuously exposed to unpredictable changes in their environment. To thrive in such dynamic habitats, microorganisms have developed the ability to readily switch phenotypes, resulting in a number of differently adapted subpopulations expressing various traits. In evolutionary biology, a particular case of phenotypic heterogeneity that evolved in an unpredictably changing environment has been defined as bet‐hedging. Bet‐hedging is a risk‐spreading strategy where isogenic populations stochastically (randomly) diversify their phenotypes, often resulting in maladapted individuals that suffer lower reproductive success. This fitness trade‐off in a specific environment may have a selective advantage upon the sudden environmental shift. Thus, a bet‐hedging strategy allows populations to persist in very dynamic habitats, but with a particular fitness cost. In recent years, numerous examples of phenotypic heterogeneity in different microorganisms have been observed, some suggesting bet‐hedging. Here, we highlight the latest reports concerning bet‐hedging phenomena in various microorganisms to show how versatile this strategy is within the microbial realms. This article is categorized under:Infectious Diseases > Molecular and Cellular Physiology
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Affiliation(s)
- Luiza P Morawska
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, Groningen, The Netherlands
| | - Jhonatan A Hernandez-Valdes
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, Groningen, The Netherlands
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, Groningen, The Netherlands
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33
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Muñoz CY, Zhou L, Yi Y, Kuipers OP. Biocontrol properties from phyllospheric bacteria isolated from Solanum lycopersicum and Lactuca sativa and genome mining of antimicrobial gene clusters. BMC Genomics 2022; 23:152. [PMID: 35189837 PMCID: PMC8862347 DOI: 10.1186/s12864-022-08392-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 02/09/2022] [Indexed: 12/01/2022] Open
Abstract
BACKGROUND Biocontrol agents are sustainable eco-friendly alternatives for chemical pesticides that cause adverse effects in the environment and toxicity in animals including humans. An improved understanding of the phyllosphere microbiology is of vital importance for biocontrol development. Most studies have been directed towards beneficial plant-microbe interactions and ignore the pathogens that might affect humans when consuming vegetables. In this study we extended this perspective and investigated potential biocontrol strains isolated from tomato and lettuce phyllosphere that can promote plant growth and potentially antagonize human pathogens as well as plant pathogens. Subsequently, we mined into their genomes for discovery of antimicrobial biosynthetic gene clusters (BGCs), that will be further characterized. RESULTS The antimicrobial activity of 69 newly isolated strains from a healthy tomato and lettuce phyllosphere against several plant and human pathogens was screened. Three strains with the highest antimicrobial activity were selected and characterized (Bacillus subtilis STRP31, Bacillus velezensis SPL51, and Paenibacillus sp. PL91). All three strains showed a plant growth promotion effect on tomato and lettuce. In addition, genome mining of the selected isolates showed the presence of a large variety of biosynthetic gene clusters. A total of 35 BGCs were identified, of which several are already known, but also some putative novel ones were identified. Further analysis revealed that among the novel BGCs, one previously unidentified NRPS and two bacteriocins are encoded, the gene clusters of which were analyzed in more depth. CONCLUSIONS Three recently isolated strains of the Bacillus genus were identified that have high antagonistic activity against lettuce and tomato plant pathogens. Known and unknown antimicrobial BGCs were identified in these antagonistic bacterial isolates, indicating their potential to be used as biocontrol agents. Our study serves as a strong incentive for subsequent purification and characterization of novel antimicrobial compounds that are important for biocontrol.
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Affiliation(s)
- Claudia Y Muñoz
- Department of Molecular Genetics, University of Groningen, Groningen, The Netherlands
| | - Lu Zhou
- Department of Molecular Genetics, University of Groningen, Groningen, The Netherlands
| | - Yunhai Yi
- Department of Molecular Genetics, University of Groningen, Groningen, The Netherlands
| | - Oscar P Kuipers
- Department of Molecular Genetics, University of Groningen, Groningen, The Netherlands.
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34
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Cebrián R, Belmonte-Reche E, Pirota V, de Jong A, Morales JC, Freccero M, Doria F, Kuipers OP. G-Quadruplex DNA as a Target in Pathogenic Bacteria: Efficacy of an Extended Naphthalene Diimide Ligand and Its Mode of Action. J Med Chem 2021; 65:4752-4766. [PMID: 34928608 PMCID: PMC8958502 DOI: 10.1021/acs.jmedchem.1c01905] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
![]()
Guanidine DNA quadruplex
(G4-DNA) structures convey a distinctive
layer of epigenetic information that is critical for regulating key
biological activities and processes as transcription, replication,
and repair in living cells. The information regarding their role and
use as therapeutic drug targets in bacteria is still scarce. Here,
we tested the biological activity of a G4-DNA ligand library, based
on the naphthalene diimide (NDI) pharmacophore, against both Gram-positive
and Gram-negative bacteria. For the best compound identified, NDI-10, a different action mechanism was described for Gram-positive
or negative bacteria. This asymmetric activity profile could be related
to the different prevalence of putative G4-DNA structures in each
group, the influence that they can exert on gene expression, and the
different roles of the G4 structures in these bacteria, which seem
to promote transcription in Gram-positive bacteria and repress transcription
in Gram-negatives.
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Affiliation(s)
- Rubén Cebrián
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747AG Groningen, The Netherlands
| | - Efres Belmonte-Reche
- Advanced (magnetic) Theranostic Nanostructures Lab, International Iberian Nanotechnology Laboratory, Nanomedicine unit, Avenida Mestre José Veiga, s/n 4715-310 Braga, Portugal
| | - Valentina Pirota
- Department of Chemistry, University of Pavia, via Taramelli 10, I-27100 Pavia (PV), Italy
| | - Anne de Jong
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747AG Groningen, The Netherlands
| | - Juan Carlos Morales
- Department of Biochemistry and Molecular Pharmacology, Instituto de Parasitología y Biomedicina, CSIC, PTS Granada, Avda. del Conocimiento, 17, 18016 Armilla, Granada, Spain
| | - Mauro Freccero
- Department of Chemistry, University of Pavia, via Taramelli 10, I-27100 Pavia (PV), Italy
| | - Filippo Doria
- Department of Chemistry, University of Pavia, via Taramelli 10, I-27100 Pavia (PV), Italy
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747AG Groningen, The Netherlands
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35
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van Tilburg AY, Warmer P, van Heel AJ, Sauer U, Kuipers OP. Membrane composition and organization of Bacillus subtilis 168 and its genome-reduced derivative miniBacillus PG10. Microb Biotechnol 2021; 15:1633-1651. [PMID: 34856064 PMCID: PMC9049611 DOI: 10.1111/1751-7915.13978] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 10/13/2021] [Accepted: 11/14/2021] [Indexed: 11/30/2022] Open
Abstract
A form of lateral membrane compartmentalization in bacteria is represented by functional membrane microdomains (FMMs). FMMs are important for various cellular processes and offer application possibilities in microbial biotechnology. We designed a lipidomics method to directly measure relative abundances of lipids in detergent‐resistant and detergent‐sensitive membrane fractions of the model bacterium Bacillus subtilis 168 and the biotechnologically attractive miniBacillus PG10 strain. Our study supports previous work suggesting that cardiolipin and prenol lipids are enriched in FMMs of B. subtilis. Additionally, structural analysis of acyl chains of major phospholipids indicated that FMMs display increased order and thickness compared with the surrounding bilayer. Despite the 36% genome reduction, membrane and FMM integrity are largely preserved in miniBacillus PG10, as supported by analysis of membrane fluidity, flotillin distribution and gene expression data. The novel insights in FMM architecture reported here will contribute to further explore the biological significance of FMMs and the means by which FMMs can be exploited as heterologous production platforms. Moreover, our lipidomics method enables comparative FMM lipid profiling between different bacteria.
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Affiliation(s)
- Amanda Y van Tilburg
- Department of Molecular Genetics, University of Groningen, Groningen, The Netherlands
| | - Philipp Warmer
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland.,Life Science Zürich PhD Program on Systems Biology, Zürich, Switzerland
| | - Auke J van Heel
- Department of Molecular Genetics, University of Groningen, Groningen, The Netherlands
| | - Uwe Sauer
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Oscar P Kuipers
- Department of Molecular Genetics, University of Groningen, Groningen, The Netherlands
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36
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Viel JH, van Tilburg AY, Kuipers OP. Characterization of Leader Processing Shows That Partially Processed Mersacidin Is Activated by AprE After Export. Front Microbiol 2021; 12:765659. [PMID: 34777321 PMCID: PMC8581636 DOI: 10.3389/fmicb.2021.765659] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 10/05/2021] [Indexed: 11/26/2022] Open
Abstract
The ribosomally synthesized and post-translationally modified peptide mersacidin is a class II lanthipeptide with good activity against Gram-positive bacteria. The intramolecular lanthionine rings, that give mersacidin its stability and antimicrobial activity, are specific structures with potential applications in synthetic biology. To add the mersacidin modification enzymes to the synthetic biology toolbox, a heterologous expression system for mersacidin in Escherichia coli has recently been developed. While this system was able to produce fully modified mersacidin precursor peptide that could be activated by Bacillus amyloliquefaciens supernatant and showed that mersacidin was activated in an additional proteolytic step after transportation out of the cell, it lacked a mechanism for clean and straightforward leader processing. Here, the protease responsible for activating mersacidin was identified and heterologously produced in E. coli, improving the previously reported heterologous expression system. By screening multiple proteases, the stringency of proteolytic activity directly next to a very small lanthionine ring is demonstrated, and the full two-step proteolytic activation of mersacidin was elucidated. Additionally, the effect of partial leader processing on diffusion and antimicrobial activity is assessed, shedding light on the function of two-step leader processing.
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Affiliation(s)
- Jakob H Viel
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Amanda Y van Tilburg
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
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37
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Michalik S, Reder A, Richts B, Faßhauer P, Mäder U, Pedreira T, Poehlein A, van Heel AJ, van Tilburg AY, Altenbuchner J, Klewing A, Reuß DR, Daniel R, Commichau FM, Kuipers OP, Hamoen LW, Völker U, Stülke J. The Bacillus subtilis Minimal Genome Compendium. ACS Synth Biol 2021; 10:2767-2771. [PMID: 34587446 DOI: 10.1021/acssynbio.1c00339] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To better understand cellular life, it is essential to decipher the contribution of individual components and their interactions. Minimal genomes are an important tool to investigate these interactions. Here, we provide a database of 105 fully annotated genomes of a series of strains with sequential deletion steps of the industrially relevant model bacterium Bacillus subtilis starting with the laboratory wild type strain B. subtilis 168 and ending with B. subtilis PG38, which lacks approximately 40% of the original genome. The annotation is supported by sequencing of key intermediate strains as well as integration of literature knowledge for the annotation of the deletion scars and their potential effects. The strain compendium presented here represents a comprehensive genome library of the entire MiniBacillus project. This resource will facilitate the more effective application of the different strains in basic science as well as in biotechnology.
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Affiliation(s)
- Stephan Michalik
- C_FunGene, Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17487 Greifswald, Germany
| | - Alexander Reder
- C_FunGene, Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17487 Greifswald, Germany
| | - Björn Richts
- Institute of Microbiology and Genetics, GZMB, Georg-August University Göttingen, 37077 Göttingen, Germany
| | - Patrick Faßhauer
- Institute of Microbiology and Genetics, GZMB, Georg-August University Göttingen, 37077 Göttingen, Germany
| | - Ulrike Mäder
- C_FunGene, Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17487 Greifswald, Germany
| | - Tiago Pedreira
- Institute of Microbiology and Genetics, GZMB, Georg-August University Göttingen, 37077 Göttingen, Germany
| | - Anja Poehlein
- Institute of Microbiology and Genetics, GZMB, Georg-August University Göttingen, 37077 Göttingen, Germany
| | - Auke J. van Heel
- Department of Molecular Genetics, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Amanda Y. van Tilburg
- Department of Molecular Genetics, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Josef Altenbuchner
- Institute for Industrial Genetics, University of Stuttgart, 70569 Stuttgart, Germany
| | - Anika Klewing
- Institute of Microbiology and Genetics, GZMB, Georg-August University Göttingen, 37077 Göttingen, Germany
| | - Daniel R. Reuß
- Institute of Microbiology and Genetics, GZMB, Georg-August University Göttingen, 37077 Göttingen, Germany
| | - Rolf Daniel
- Institute of Microbiology and Genetics, GZMB, Georg-August University Göttingen, 37077 Göttingen, Germany
| | - Fabian M. Commichau
- Institute of Microbiology and Genetics, GZMB, Georg-August University Göttingen, 37077 Göttingen, Germany
- FG Synthetic Microbiology, Brandenburg University of Technology, 01958 Senftenberg, Germany
| | - Oscar P. Kuipers
- Department of Molecular Genetics, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Leendert W. Hamoen
- Swammerdam Institute for Life Sciences, University of Amsterdam, 1090 GE Amsterdam, The Netherlands
| | - Uwe Völker
- C_FunGene, Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17487 Greifswald, Germany
| | - Jörg Stülke
- Institute of Microbiology and Genetics, GZMB, Georg-August University Göttingen, 37077 Göttingen, Germany
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38
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Arias-Orozco P, Inklaar M, Lanooij J, Cebrián R, Kuipers OP. Functional Expression and Characterization of the Highly Promiscuous Lanthipeptide Synthetase SyncM, Enabling the Production of Lanthipeptides with a Broad Range of Ring Topologies. ACS Synth Biol 2021; 10:2579-2591. [PMID: 34554737 PMCID: PMC8524650 DOI: 10.1021/acssynbio.1c00224] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
![]()
Lanthipeptides are
ribosomally synthesized and post-translationally
modified peptides characterized by the presence of lanthionine rings
that provide stability and functionality. Genome mining techniques
have shown their huge diversity and potential for the discovery of
novel active molecules. However, in many cases, they are not easily
produced under laboratory conditions. The heterologous expression
of these molecules using well-characterized lanthipeptide biosynthetic
enzymes is rising as an alternative system for the design and production
of new lanthipeptides with biotechnological or clinical properties.
Nevertheless, the substrate-enzyme specificity limits the complete
modification of the desired peptides and hence, their full stability
and/or biological activity. New low substrate-selective biosynthetic
enzymes are therefore necessary for the heterologous production of
new-to-nature peptides. Here, we have identified, cloned, and heterologously
expressed in Lactococcus lactis the
most promiscuous lanthipeptide synthetase described to date, i.e.,
SyncM from the marine cyanobacteria Synechococcus MITS9509. We have characterized the functionality of SyncM by the
successful expression of 15 out of 18 different SyncA substrates,
subsequently determining the dehydration and cyclization processes
in six representatives of them. This characterization highlights the
very relaxed substrate specificity of SyncM toward its precursors
and the ability to catalyze the formation of exceptionally large rings
in a variety of topologies. Our results suggest that SyncM could be
an attractive enzyme to design and produce a wide variety of new-to-nature
lanthipeptides with a broad range of ring topologies.
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Affiliation(s)
- Patricia Arias-Orozco
- Department of Molecular Genetics, University of Groningen, Groningen 9747AG, The Netherlands
| | - Maartje Inklaar
- Department of Molecular Genetics, University of Groningen, Groningen 9747AG, The Netherlands
| | - Judith Lanooij
- Department of Molecular Genetics, University of Groningen, Groningen 9747AG, The Netherlands
| | - Rubén Cebrián
- Department of Molecular Genetics, University of Groningen, Groningen 9747AG, The Netherlands
| | - Oscar P. Kuipers
- Department of Molecular Genetics, University of Groningen, Groningen 9747AG, The Netherlands
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39
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Zhou L, Song C, Muñoz CY, Kuipers OP. Bacillus cabrialesii BH5 Protects Tomato Plants Against Botrytis cinerea by Production of Specific Antifungal Compounds. Front Microbiol 2021; 12:707609. [PMID: 34539606 PMCID: PMC8441496 DOI: 10.3389/fmicb.2021.707609] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 07/15/2021] [Indexed: 11/22/2022] Open
Abstract
The gray mold caused by the phytopathogen Botrytis cinerea presents a threat to global food security. For the biological regulation of several plant diseases, Bacillus species have been extensively studied. In this work, we explore the ability of a bacterial strain, Bacillus cabrialesii BH5, that was isolated from tomato rhizosphere soil, to control the fungal pathogen B. cinerea. Strain B. cabrialesii BH5 showed a strong antifungal activity against B. cinerea. A compound was isolated and identified as a cyclic lipopeptide of the fengycin family by high-performance liquid chromatography and tandem mass spectrometry (ESI-MS/MS) that we named fengycin H. The fengycin H-treated hyphae of B. cinerea displayed stronger red fluorescence than the control, which is clearly indicating that fengycin H triggered the hyphal cell membrane defects. Moreover, root inoculation of tomato seedlings with BH5 effectively promoted the growth of tomato plants. Transcription analysis revealed that both BH5 and fengycin H stimulate induced systemic resistance of tomato plants via the jasmonic acid signaling pathway and provide a strong biocontrol effect in vivo. Therefore, the strain BH5 and fengycin H are very promising candidates for biological control of B. cinerea and the associated gray mold.
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Affiliation(s)
- Lu Zhou
- Department of Molecular Genetics, University of Groningen, Groningen, Netherlands
| | - Chunxu Song
- Department of Molecular Genetics, University of Groningen, Groningen, Netherlands.,Key Laboratory of Plant-Soil Interactions, Ministry of Education, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing, China
| | - Claudia Y Muñoz
- Department of Molecular Genetics, University of Groningen, Groningen, Netherlands
| | - Oscar P Kuipers
- Department of Molecular Genetics, University of Groningen, Groningen, Netherlands
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40
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Cebrián R, Xu C, Xia Y, Wu W, Kuipers OP. The cathelicidin-derived close-to-nature peptide D-11 sensitises Klebsiella pneumoniae to a range of antibiotics in vitro, ex vivo and in vivo. Int J Antimicrob Agents 2021; 58:106434. [PMID: 34525402 DOI: 10.1016/j.ijantimicag.2021.106434] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 08/23/2021] [Accepted: 08/28/2021] [Indexed: 02/08/2023]
Abstract
The outer membrane of Gram-negative bacteria constitutes a permeability barrier that prevents certain antibiotics reaching their target, thus conferring a high tolerance to a wide range of antibiotics. Combined therapies of antibiotics and outer membrane-perturbing drugs have been proposed as an alternative treatment to extend the use of antibiotics active against Gram-positive bacteria to Gram-negative bacteria. Among the outer membrane-active compounds, the outer membrane-permeabilising peptides play a prominent role. They form a group of small cationic and amphipathic molecules with the ability to insert specifically into bacterial membranes, inducing their permeabilisation and/or disruption. Here we assessed the combined effect of several compounds belonging to the main antibiotic families and the cathelicidin close-to-nature outer membrane peptide D-11 against four clinically relevant Gram-negative bacteria. The results showed that peptide D-11 displays strong synergistic activity with several antibiotics belonging to different families, in particular against Klebsiella pneumoniae, even better than some other outer membrane-active peptides that are currently in clinical trials, such as SPR741. Notably, we observed this activity in vitro, ex vivo in a newly designed bacteraemia model, and in vivo in a mouse abscess infection model. Overall, our results suggest that D-11 is a good candidate to repurpose the activity of traditional antibiotics against K. pneumoniae.
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Affiliation(s)
- Rubén Cebrián
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, the Netherlands
| | - Congjuan Xu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 30071, China
| | - Yushan Xia
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, the Netherlands; State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 30071, China
| | - Weihui Wu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 30071, China
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, the Netherlands.
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41
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Zhou L, de Jong A, Yi Y, Kuipers OP. Identification, Isolation, and Characterization of Medipeptins, Antimicrobial Peptides From Pseudomonas mediterranea EDOX. Front Microbiol 2021; 12:732771. [PMID: 34594316 PMCID: PMC8477016 DOI: 10.3389/fmicb.2021.732771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 08/20/2021] [Indexed: 11/22/2022] Open
Abstract
The plant microbiome is a vastly underutilized resource for identifying new genes and bioactive compounds. Here, we used Pseudomonas sp. EDOX, isolated from the leaf endosphere of a tomato plant grown on a small farm in the Netherlands. To get more insight into its biosynthetic potential, the genome of Pseudomonas sp. EDOX was sequenced and subjected to bioinformatic analyses. The genome sequencing analysis identified strain EDOX as a member of the Pseudomonas mediterranea. In silico analysis for secondary metabolites identified a total of five non-ribosomally synthesized peptides synthetase (NRPS) gene clusters, related to the biosynthesis of syringomycin, syringopeptin, anikasin, crochelin A, and fragin. Subsequently, we purified and characterized several cyclic lipopeptides (CLPs) produced by NRPS, including some of the already known ones, which have biological activity against several plant and human pathogens. Most notably, mass spectrometric analysis led to the discovery of two yet unknown CLPs, designated medipeptins, consisting of a 22 amino acid peptide moiety with varying degrees of activity against Gram-positive and Gram-negative pathogens. Furthermore, we investigated the mode of action of medipeptin A. The results show that medipeptin A acts as a bactericidal antibiotic against Gram-positive pathogens, but as a bacteriostatic antibiotic against Gram-negative pathogens. Medipeptin A exerts its potent antimicrobial activity against Gram-positive bacteria via binding to both lipoteichoic acid (LTA) and lipid II as well as by forming pores in membranes. Collectively, our study provides important insights into the biosynthesis and mode of action of these novel medipeptins from P. mediterranea EDOX.
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Affiliation(s)
| | | | | | - Oscar P. Kuipers
- Department of Molecular Genetics, University of Groningen, Groningen, Netherlands
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42
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Xia Y, Cebrián R, Xu C, de Jong A, Wu W, Kuipers OP. Elucidating the mechanism by which synthetic helper peptides sensitize Pseudomonas aeruginosa to multiple antibiotics. PLoS Pathog 2021; 17:e1009909. [PMID: 34478485 PMCID: PMC8445441 DOI: 10.1371/journal.ppat.1009909] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 09/16/2021] [Accepted: 08/20/2021] [Indexed: 01/04/2023] Open
Abstract
The emergence and rapid spread of multi-drug resistant (MDR) bacteria pose a serious threat to the global healthcare. There is an urgent need for new antibacterial substances or new treatment strategies to deal with the infections by MDR bacterial pathogens, especially the Gram-negative pathogens. In this study, we show that a number of synthetic cationic peptides display strong synergistic antimicrobial effects with multiple antibiotics against the Gram-negative pathogen Pseudomonas aeruginosa. We found that an all-D amino acid containing peptide called D-11 increases membrane permeability by attaching to LPS and membrane phospholipids, thereby facilitating the uptake of antibiotics. Subsequently, the peptide can dissipate the proton motive force (PMF) (reducing ATP production and inhibiting the activity of efflux pumps), impairs the respiration chain, promotes the production of reactive oxygen species (ROS) in bacterial cells and induces intracellular antibiotics accumulation, ultimately resulting in cell death. By using a P. aeruginosa abscess infection model, we demonstrate enhanced therapeutic efficacies of the combination of D-11 with various antibiotics. In addition, we found that the combination of D-11 and azithromycin enhanced the inhibition of biofilm formation and the elimination of established biofilms. Our study provides a realistic treatment option for combining close-to-nature synthetic peptide adjuvants with existing antibiotics to combat infections caused by P. aeruginosa.
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Affiliation(s)
- Yushan Xia
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Rubén Cebrián
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Congjuan Xu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Anne de Jong
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Weihui Wu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
- * E-mail: (WW); (OPK)
| | - Oscar P. Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
- * E-mail: (WW); (OPK)
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43
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Abstract
A large number of antimicrobial peptides depend on intramolecular disulfide bonds for their biological activity. However, the relative instability of disulfide bonds has limited the potential of some of these peptides to be developed into therapeutics. Conversely, peptides containing intramolecular (methyl)lanthionine-based bonds, lanthipeptides, are highly stable under a broader range of biological and physical conditions. Here, the class-II lanthipeptide synthetase CinM, from the cinnamycin gene cluster, was employed to create methyllanthionine stabilized analogues of disulfide-bond-containing antimicrobial peptides. The resulting analogues were subsequently modified in vitro by adding lipid tails of variable lengths through chemical addition. Finally, the created compounds were characterized by MIC tests against several relevant pathogens, killing assays, membrane permeability assays, and hemolysis assays. It was found that CinM could successfully install methyllanthionine bonds at the intended positions of the analogues and that the lipidated macrocyclic core peptides have bactericidal activity against tested Gram-positive and Gram-negative pathogenic bacteria. Additionally, fluorescence microscopy assays revealed that the lipidated compounds disrupt the bacterial membrane and lyse bacterial cells, hinting toward a potential mode of action. Notably, the semisynthesized macrocyclic lipo-lanthipeptides show low hemolytic activity. These results show that the methods developed here extend the toolbox for novel antimicrobial development and might enable the further development of novel compounds with killing activity against relevant pathogenic bacteria.
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Affiliation(s)
- Xinghong Zhao
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Yanli Xu
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Jakob H. Viel
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Oscar P. Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen 9747 AG, The Netherlands
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44
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Teusink B, Kuipers OP, Moineau S. Symposium on Lactic Acid Bacteria-reading while waiting for a meeting. FEMS Microbiol Rev 2021; 45:5983770. [PMID: 33197931 PMCID: PMC7968516 DOI: 10.1093/femsre/fuaa049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 09/28/2020] [Indexed: 11/13/2022] Open
Affiliation(s)
- Bas Teusink
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, O2 building, location code 2E51, De Boelelaan 1085, NL-1081HV Amsterdam, The Netherlands
| | - Oscar P Kuipers
- Molecular Genetics, University of Groningen, Nijenborgh 7 (Linnaeusborg, building 5172, room 6.50), 9747AG Groningen the Netherlands, The Netherlands
| | - Sylvain Moineau
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie1045, avenue de la MédecineUniversité Laval, Québec, Canada, G1V 0A6
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45
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Shlla B, Gazioglu O, Shafeeq S, Manzoor I, Kuipers OP, Ulijasz A, Hiller NL, Andrew PW, Yesilkaya H. The Rgg1518 transcriptional regulator is a necessary facet of sugar metabolism and virulence in Streptococcus pneumoniae. Mol Microbiol 2021; 116:996-1008. [PMID: 34328238 DOI: 10.1111/mmi.14788] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 07/22/2021] [Accepted: 07/26/2021] [Indexed: 10/20/2022]
Abstract
Rggs are a group of transcriptional regulators with diverse roles in metabolism and virulence. Here, we present work on the Rgg1518/SHP1518 quorum sensing system of Streptococcus pneumoniae. The activity of Rgg1518 is induced by its cognate peptide, SHP1518. In vitro analysis showed that the Rgg1518 system is active in conditions rich in galactose and mannose, key nutrients during nasopharyngeal colonization. Rgg1518 expression is highly induced in the presence of these sugars and its isogenic mutant is attenuated in growth on galactose and mannose. When compared with other Rgg systems, Rgg1518 has the largest regulon on galactose. On galactose it controls up- or downregulation of a functionally diverse set of genes involved in galactose metabolism, capsule biosynthesis, iron metabolism, protein translation, as well as other metabolic functions, acting mainly as a repressor of gene expression. Rgg1518 is a repressor of capsule biosynthesis, and binds directly to the capsule regulatory region. Comparison with other Rggs revealed inter-regulatory interactions among Rggs. Finally, the rgg1518 mutant is attenuated in colonization and virulence in a mouse model of colonization and pneumonia. We conclude that Rgg1518 is a virulence determinant that contributes to a regulatory network composed of multiple Rgg systems.
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Affiliation(s)
- Bushra Shlla
- Department of Respiratory Sciences, University of Leicester, Leicester, UK.,Department of Biology, College of Science, University of Mosul, Mosul, Iraq
| | - Ozcan Gazioglu
- Department of Respiratory Sciences, University of Leicester, Leicester, UK
| | - Sulman Shafeeq
- Molecular Genetics, University of Groningen, Groningen, The Netherlands
| | - Irfan Manzoor
- Molecular Genetics, University of Groningen, Groningen, The Netherlands
| | - Oscar P Kuipers
- Molecular Genetics, University of Groningen, Groningen, The Netherlands
| | - Andrew Ulijasz
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, Illinois, USA
| | - N Luisa Hiller
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
| | - Peter W Andrew
- Department of Respiratory Sciences, University of Leicester, Leicester, UK
| | - Hasan Yesilkaya
- Department of Respiratory Sciences, University of Leicester, Leicester, UK
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46
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Abstract
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Lanthipeptides are
(methyl)lanthionine ring-containing ribosomally
synthesized and post-translationally modified peptides (RiPPs). Many
lanthipeptides show strong antimicrobial activity against bacterial
pathogens, including antibiotic-resistant bacterial pathogens. The
group of disulfide-bond-containing antimicrobial peptides (AMPs) is
well-known in nature and forms a rich source of templates for the
production of novel peptides with corresponding (methyl)lanthionine
analogues instead of disulfides. Here, we show that novel macrocyclic
lanthipeptides (termed thanacin and ripcin) can be synthesized using
the known antimicrobials thanatin and rip-thanatin as templates. Notably,
the synthesized nisin(1–20)–ripcin hybrid lanthipeptides
(ripcin B–G) showed selective antimicrobial activity against S. aureus, including an antibiotic-resistant MRSA
strain. Interestingly, ripcin B–G, which are hybrid peptides
of nisin(1–20) and ripcin that are each inactive against Gram-negative
pathogens, showed substantial antimicrobial activity against the tested
Gram-negative pathogens. Moreover, ripcin B–G was highly resistant
against the nisin resistance protein (NSR; a peptidase that removes
the C-terminal 6 amino acids of nisin and strongly reduces its antimicrobial
activity), opposed to nisin itself. This study provides an example
of converting disulfide-bond-based AMPs into (methyl)lanthionine-based
macrocyclic hybrid lanthipeptides and can yield antimicrobial peptides
with selective antimicrobial activity against S. aureus.
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Affiliation(s)
- Xinghong Zhao
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, 9747 AG, The Netherlands
| | - Oscar P. Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, 9747 AG, The Netherlands
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47
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Zhao X, Wang X, Shukla R, Kumar R, Weingarth M, Breukink E, Kuipers OP. Brevibacillin 2V Exerts Its Bactericidal Activity via Binding to Lipid II and Permeabilizing Cellular Membranes. Front Microbiol 2021; 12:694847. [PMID: 34335524 PMCID: PMC8322648 DOI: 10.3389/fmicb.2021.694847] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 06/28/2021] [Indexed: 11/14/2022] Open
Abstract
Lipo-tridecapeptides, a class of bacterial non-ribosomally produced peptides, show strong antimicrobial activity against Gram-positive pathogens, including antibiotic-resistant Staphylococcus aureus and Enterococcus spp. However, many of these lipo-tridecapeptides have shown high hemolytic activity and cytotoxicity, which has limited their potential to be developed into antibiotics. Recently, we reported a novel antimicrobial lipo-tridecapeptide, brevibacillin 2V, which showed no hemolytic activity against human red blood cells at a high concentration of 128 mg/L, opposite to other brevibacillins and lipo-tridecapeptides. In addition, brevibacillin 2V showed much lower cytotoxicity than the other members of the brevibacillin family. In this study, we set out to elucidate the antimicrobial mode of action of brevibacillin 2V. The results show that brevibacillin 2V acts as bactericidal antimicrobial agent against S. aureus (MRSA). Further studies show that brevibacillin 2V exerts its bactericidal activity by binding to the bacterial cell wall synthesis precursor Lipid II and permeabilizing the bacterial membrane. Combined solid-state NMR, circular dichroism, and isothermal titration calorimetry assays indicate that brevibacillin 2V binds to the GlcNAc-MurNAc moiety and/or the pentapeptide of Lipid II. This study provides an insight into the antimicrobial mode of action of brevibacillin 2V. As brevibacillin 2V is a novel and promising antibiotic candidate with low hemolytic activity and cytotoxicity, the here-elucidated mode of action will help further studies to develop it as an alternative antimicrobial agent.
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Affiliation(s)
- Xinghong Zhao
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Xiaoqi Wang
- Membrane Biochemistry and Biophysics, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Rhythm Shukla
- Membrane Biochemistry and Biophysics, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, Netherlands.,NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Raj Kumar
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Markus Weingarth
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Eefjan Breukink
- Membrane Biochemistry and Biophysics, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
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48
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Zhao X, Kuipers OP. Synthesis of silver-nisin nanoparticles with low cytotoxicity as antimicrobials against biofilm-forming pathogens. Colloids Surf B Biointerfaces 2021; 206:111965. [PMID: 34237525 DOI: 10.1016/j.colsurfb.2021.111965] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 06/02/2021] [Accepted: 07/01/2021] [Indexed: 10/20/2022]
Abstract
Wound infection is a serious threat to patients, in particular those with septic wound infections, which result in high mortality rates. Moreover, the treatment of wound infections with antimicrobial-resistant and/or biofilm-forming pathogens can be challenging. Nisin, a potent antimicrobial against Gram-positive bacterial pathogens, has been used in the food industry as a preservative for decades. Silver has been approved by the FDA as a topical antimicrobial. Here, we show that silver-nisin nanoparticles (Ag-nisin NP), with an average diameter of 60 nm, can be quickly synthesized with the assistance of a simple microwave. Ag-nisin NP act as bactericidal antibiotics against the tested pathogens. In contrast, resistance was observed in S. aureus and A. baumannii that were treated with silver nitrate alone. In addition, Ag-nisin NP showed potent antibiofilm activity against S. aureus, P. aeruginosa, A. baumannii, K. pneumoniae, and E. coli, which are pathogens occurring in wound infections. Notably, the synthesized Ag-nisin NP showed lower cytotoxicity than silver nitrate to human cells. This formulation provides an alternative and safe measurement for biofilm-infected wound control.
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Affiliation(s)
- Xinghong Zhao
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, 9747 AG, the Netherlands
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, 9747 AG, the Netherlands.
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49
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Fernandez-Cantos MV, Garcia-Morena D, Iannone V, El-Nezami H, Kolehmainen M, Kuipers OP. Role of microbiota and related metabolites in gastrointestinal tract barrier function in NAFLD. Tissue Barriers 2021; 9:1879719. [PMID: 34280073 PMCID: PMC8489918 DOI: 10.1080/21688370.2021.1879719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/13/2021] [Accepted: 01/18/2021] [Indexed: 11/06/2022] Open
Abstract
The Gastrointestinal (GI) tract is composed of four main barriers: microbiological, chemical, physical and immunological. These barriers play important roles in maintaining GI tract homeostasis. In the crosstalk between these barriers, microbiota and related metabolites have been shown to influence GI tract barrier integrity, and alterations of the gut microbiome might lead to an increase in intestinal permeability. As a consequence, translocation of bacteria and their products into the circulatory system increases, reaching proximal and distal tissues, such as the liver. One of the most prevalent chronic liver diseases, Nonalcoholic Fatty Liver Disease (NAFLD), has been associated with an altered gut microbiota and barrier integrity. However, the causal link between them has not been fully elucidated yet. In this review, we aim to highlight relevant bacterial taxa and their related metabolites affecting the GI tract barriers in the context of NAFLD, discussing their implications in gut homeostasis and in disease.
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Affiliation(s)
- Maria Victoria Fernandez-Cantos
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Diego Garcia-Morena
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Valeria Iannone
- Institute of Public Health and Clinical Nutrition, Department of Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Hani El-Nezami
- Molecular and Cell Biology Division, School of Biological Sciences, University of Hong Kong, Hong Kong SAR
| | - Marjukka Kolehmainen
- Institute of Public Health and Clinical Nutrition, Department of Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Oscar P. Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
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50
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Zhao X, Wang X, Shukla R, Kumar R, Weingarth M, Breukink E, Kuipers OP. Brevibacillin 2V, a Novel Antimicrobial Lipopeptide With an Exceptionally Low Hemolytic Activity. Front Microbiol 2021; 12:693725. [PMID: 34220785 PMCID: PMC8245773 DOI: 10.3389/fmicb.2021.693725] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 05/17/2021] [Indexed: 12/26/2022] Open
Abstract
Bacterial non-ribosomally produced peptides (NRPs) form a rich source of antibiotics, including more than 20 of these antibiotics that are used in the clinic, such as penicillin G, colistin, vancomycin, and chloramphenicol. Here we report the identification, purification, and characterization of a novel NRP, i.e., brevibacillin 2V (lipo-tridecapeptide), from Brevibacillus laterosporus DSM 25. Brevibacillin 2V has a strong antimicrobial activity against Gram-positive bacterial pathogens (minimum inhibitory concentration = 2 mg/L), including difficult-to-treat antibiotic-resistant Enterococcus faecium, Enterococcus faecalis, and Staphylococcus aureus. Notably, brevibacillin 2V has a much lower hemolytic activity (HC50 > 128 mg/L) and cytotoxicity (CC50 = 45.49 ± 0.24 mg/L) to eukaryotic cells than previously reported NRPs of the lipo-tridecapeptide family, including other brevibacillins, which makes it a promising candidate for antibiotic development. In addition, our results demonstrate that brevibacillins display a synergistic action with established antibiotics against Gram-negative bacterial pathogens. Probably due to the presence of non-canonical amino acids and D-amino acids, brevibacillin 2V showed good stability in human plasma. Thus, we identified and characterized a novel and promising antimicrobial candidate (brevibacillin 2V) with low hemolytic activity and cytotoxicity, which can be used either on its own or as a template for further total synthesis and modification.
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Affiliation(s)
- Xinghong Zhao
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Xiaoqi Wang
- Membrane Biochemistry and Biophysics, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Rhythm Shukla
- Membrane Biochemistry and Biophysics, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, Netherlands.,NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Raj Kumar
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Markus Weingarth
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Eefjan Breukink
- Membrane Biochemistry and Biophysics, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
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