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Maurer JJ, Cheng Y, Pedroso A, Thompson KK, Akter S, Kwan T, Morota G, Kinstler S, Porwollik S, McClelland M, Escalante-Semerena JC, Lee MD. Peeling back the many layers of competitive exclusion. Front Microbiol 2024; 15:1342887. [PMID: 38591029 PMCID: PMC11000858 DOI: 10.3389/fmicb.2024.1342887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 02/19/2024] [Indexed: 04/10/2024] Open
Abstract
Baby chicks administered a fecal transplant from adult chickens are resistant to Salmonella colonization by competitive exclusion. A two-pronged approach was used to investigate the mechanism of this process. First, Salmonella response to an exclusive (Salmonella competitive exclusion product, Aviguard®) or permissive microbial community (chicken cecal contents from colonized birds containing 7.85 Log10Salmonella genomes/gram) was assessed ex vivo using a S. typhimurium reporter strain with fluorescent YFP and CFP gene fusions to rrn and hilA operon, respectively. Second, cecal transcriptome analysis was used to assess the cecal communities' response to Salmonella in chickens with low (≤5.85 Log10 genomes/g) or high (≥6.00 Log10 genomes/g) Salmonella colonization. The ex vivo experiment revealed a reduction in Salmonella growth and hilA expression following co-culture with the exclusive community. The exclusive community also repressed Salmonella's SPI-1 virulence genes and LPS modification, while the anti-virulence/inflammatory gene avrA was upregulated. Salmonella transcriptome analysis revealed significant metabolic disparities in Salmonella grown with the two different communities. Propanediol utilization and vitamin B12 synthesis were central to Salmonella metabolism co-cultured with either community, and mutations in propanediol and vitamin B12 metabolism altered Salmonella growth in the exclusive community. There were significant differences in the cecal community's stress response to Salmonella colonization. Cecal community transcripts indicated that antimicrobials were central to the type of stress response detected in the low Salmonella abundance community, suggesting antagonism involved in Salmonella exclusion. This study indicates complex community interactions that modulate Salmonella metabolism and pathogenic behavior and reduce growth through antagonism may be key to exclusion.
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Affiliation(s)
- John J. Maurer
- School of Animal Sciences, College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Ying Cheng
- Department of Population Health, University of Georgia, Athens, GA, United States
| | - Adriana Pedroso
- Department of Population Health, University of Georgia, Athens, GA, United States
| | - Kasey K. Thompson
- Department of Population Health, University of Georgia, Athens, GA, United States
| | - Shamima Akter
- Department of Biomedical Sciences and Pathobiology, College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Tiffany Kwan
- Department of Population Health, University of Georgia, Athens, GA, United States
| | - Gota Morota
- School of Animal Sciences, College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Sydney Kinstler
- School of Animal Sciences, College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Steffen Porwollik
- Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, CA, United States
| | - Michael McClelland
- Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, CA, United States
| | | | - Margie D. Lee
- Department of Biomedical Sciences and Pathobiology, College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
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Lee HS, Nagahawatta DP, Jeon YJ, Lee MA, Heo CS, Park SJ, Shin HJ. Streptinone, a New Indanone Derivative from a Marine-Derived Streptomyces massiliensis, Inhibits Particulate Matter-Induced Inflammation. Mar Drugs 2023; 21:640. [PMID: 38132961 PMCID: PMC10744446 DOI: 10.3390/md21120640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 12/11/2023] [Accepted: 12/13/2023] [Indexed: 12/23/2023] Open
Abstract
Inflammatory diseases caused by air pollution, especially from particulate matter (PM) exposure, have increased daily. Accordingly, attention to treatment or prevention for these inflammatory diseases has grown. Natural products have been recognized as promising sources of cures and prevention for not only inflammatory but also diverse illnesses. As part of our ongoing study to discover bioactive compounds from marine microorganisms, we isolated streptinone, a new indanone derivative (1), along with three known diketopiperazines (2-4) and piericidin A (5), from a marine sediment-derived Streptomyces massiliensis by chromatographic methods. The structure of 1 was elucidated based on the spectroscopic data analysis. The relative and absolute configurations of 1 were determined by 1H-1H coupling constants, 1D NOESY, and ECD calculation. The anti-inflammatory activities of 1 were evaluated through enzyme-linked immunosorbent assay (ELISA), Western blot, and qPCR. Compound 1 suppressed the production of nitric oxide (NO), prostaglandin E2 (PGE2), and pro-inflammatory cytokines such as TNF-α, IL-6, and IL-1β, by inhibiting the Toll-like receptor (TLR)-mediated nuclear factor kappa B (NF-κB) signaling pathway. Therefore, compound 1 could potentially be used as an agent in the prevention and treatment of diverse inflammatory disorders caused by particulate matter.
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Affiliation(s)
- Hwa-Sun Lee
- Marine Natural Products Laboratory, Korea Institute of Ocean Science and Technology, 385 Haeyang-ro, Yeongdo-gu, Busan 49111, Republic of Korea; (H.-S.L.); (M.A.L.); (C.-S.H.)
- Department of Chemistry, Pukyong National University, 45 Yongso-ro, Nam-gu, Busan 48513, Republic of Korea;
| | - Dineth Pramuditha Nagahawatta
- Department of Marine Life Sciences, Jeju National University, 102 Jeju Daehak-ro, Jeju 63243, Republic of Korea; (D.P.N.); (Y.-J.J.)
| | - You-Jin Jeon
- Department of Marine Life Sciences, Jeju National University, 102 Jeju Daehak-ro, Jeju 63243, Republic of Korea; (D.P.N.); (Y.-J.J.)
| | - Min Ah Lee
- Marine Natural Products Laboratory, Korea Institute of Ocean Science and Technology, 385 Haeyang-ro, Yeongdo-gu, Busan 49111, Republic of Korea; (H.-S.L.); (M.A.L.); (C.-S.H.)
- Department of Chemistry, Pukyong National University, 45 Yongso-ro, Nam-gu, Busan 48513, Republic of Korea;
| | - Chang-Su Heo
- Marine Natural Products Laboratory, Korea Institute of Ocean Science and Technology, 385 Haeyang-ro, Yeongdo-gu, Busan 49111, Republic of Korea; (H.-S.L.); (M.A.L.); (C.-S.H.)
- Department of Marine Biotechnology, University of Science and Technology (UST), 217 Gajung-ro, Yuseong-gu, Daejeon 34113, Republic of Korea
| | - Sun Joo Park
- Department of Chemistry, Pukyong National University, 45 Yongso-ro, Nam-gu, Busan 48513, Republic of Korea;
| | - Hee Jae Shin
- Marine Natural Products Laboratory, Korea Institute of Ocean Science and Technology, 385 Haeyang-ro, Yeongdo-gu, Busan 49111, Republic of Korea; (H.-S.L.); (M.A.L.); (C.-S.H.)
- Department of Marine Biotechnology, University of Science and Technology (UST), 217 Gajung-ro, Yuseong-gu, Daejeon 34113, Republic of Korea
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Tang T, Martinenghi LD, Hounmanou YMG, Leisner JJ. Distribution and ecology of the generalist lactic acid bacterium Carnobacterium maltaromaticum in different freshwater habitats: Metabolic and antagonistic abilities. Environ Microbiol 2023; 25:3556-3576. [PMID: 37750577 DOI: 10.1111/1462-2920.16508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 09/05/2023] [Indexed: 09/27/2023]
Abstract
We explored the distribution, metabolic and antagonistic activities of Carnobacterium maltaromaticum, isolated from freshwater locations in Denmark during winter or early spring. This species was widely distributed in such habitats although it was relatively rare in low pH locations. Isolates possessed a diverse metabolism, potentially enabling functional capacities independent of habitat. The intraspecies competition showed a relatively high degree of mostly low-intensity interactions, which overall were not correlated with phylogeny or location. Only a few isolates exhibited broad-spectrum inhibition activity, targeting species from other genera and families, including one isolate that exhibited a broad inhibitory activity due to H2 O2 production. Bioinformatic analyses revealed that the frequency of bacteriocinogenic systems was low, and only one unmodified bacteriocin, piscicolin 126, correlated with phenotypic antagonistic activity. Furthermore, most potential bacteriocin gene complexes were not complete. Overall, this study showed C. maltaromaticum to be a generalist (nomadic) species with a constant presence in freshwater habitats, especially those with pH values >5. General metabolic properties did not suggest a strong degree of adaptation to the freshwater environment, and bacteriocin-mediated antagonistic activities appeared to play a minimal ecological role.
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Affiliation(s)
- Taya Tang
- Faculty of Health and Medical Sciences, Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Laura Daniela Martinenghi
- Faculty of Health and Medical Sciences, Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Yaovi Mahuton Gildas Hounmanou
- Faculty of Health and Medical Sciences, Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Jørgen J Leisner
- Faculty of Health and Medical Sciences, Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
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Akomoneh EA, Gestels Z, Abdellati S, Vereecken K, Bartholomeeusen K, Van den Bossche D, Kenyon C, Manoharan-Basil SS. Genome Mining Uncovers NRPS and PKS Clusters in Rothia dentocariosa with Inhibitory Activity against Neisseria Species. Antibiotics (Basel) 2023; 12:1592. [PMID: 37998794 PMCID: PMC10668837 DOI: 10.3390/antibiotics12111592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 10/31/2023] [Accepted: 11/02/2023] [Indexed: 11/25/2023] Open
Abstract
The growing global threat of antimicrobial resistance is reaching a crisis point as common bacterial infections, including those caused by pathogenic Neisseria species, are becoming increasingly untreatable. This is compelling the scientific community to search for new antimicrobial agents, taking advantage of computational mining and using whole genome sequences to discover natural products from the human microbiome with antibiotic effects. In this study, we investigated the crude extract from a Rothia dentocariosa strain with demonstrated antimicrobial activity against pathogenic Neisseria spp. by spot-on-lawn assay. The genomic DNA of the R. dentocariosa strain was sequenced, and bioinformatic evaluation was performed using antiSMASH and PRISM to search for biosynthetic gene clusters (BGCs). The crude extract with potential antimicrobial activity was run on Tricine-SDS-PAGE, and the putative peptides were characterised using liquid chromatography-tandem mass spectrometry (LC-MS). The crude extract inhibited the growth of the pathogenic Neisseria spp. Six BGCs were identified corresponding to non-ribosomal peptide synthases (NRPSs), polyketide synthases (PKSs), and ribosomally synthesised and post-translationally modified peptides. Three peptides were also identified corresponding to Actinorhodin polyketide putative beta-ketoacyl synthase 1. These findings serve as a useful reference to facilitate the research and development of NRPS and PKS as antimicrobial products against multidrug-resistant N. gonorrhoeae.
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Affiliation(s)
- Elvis Achondou Akomoneh
- HIV/STI Unit, Department of Clinical Sciences, Institute of Tropical Medicine Antwerp, 2000 Antwerp, Belgium; (E.A.A.); (Z.G.); (S.S.M.-B.)
- Department of Microbiology and Parasitology, University of Bamenda, Bambili P.O. Box 39, Cameroon
| | - Zina Gestels
- HIV/STI Unit, Department of Clinical Sciences, Institute of Tropical Medicine Antwerp, 2000 Antwerp, Belgium; (E.A.A.); (Z.G.); (S.S.M.-B.)
| | - Saïd Abdellati
- Clinical Reference Laboratory, Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium; (S.A.); (D.V.d.B.)
| | - Katleen Vereecken
- Virology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium; (K.V.); (K.B.)
| | - Koen Bartholomeeusen
- Virology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium; (K.V.); (K.B.)
| | - Dorien Van den Bossche
- Clinical Reference Laboratory, Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium; (S.A.); (D.V.d.B.)
| | - Chris Kenyon
- HIV/STI Unit, Department of Clinical Sciences, Institute of Tropical Medicine Antwerp, 2000 Antwerp, Belgium; (E.A.A.); (Z.G.); (S.S.M.-B.)
- Virology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium; (K.V.); (K.B.)
- Department of Medicine, University of Cape Town, Cape Town 7700, South Africa
| | - Sheeba Santhini Manoharan-Basil
- HIV/STI Unit, Department of Clinical Sciences, Institute of Tropical Medicine Antwerp, 2000 Antwerp, Belgium; (E.A.A.); (Z.G.); (S.S.M.-B.)
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Khabthani S, Rolain JM, Merhej V. Whole Genome Analysis of 335 New Bacterial Species from Human Microbiota Reveals a Huge Reservoir of Transferable Antibiotic Resistance Determinants. Int J Mol Sci 2022; 23:ijms23042137. [PMID: 35216256 PMCID: PMC8874588 DOI: 10.3390/ijms23042137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/06/2022] [Accepted: 02/12/2022] [Indexed: 02/04/2023] Open
Abstract
Background: The emergence and diffusion of strains of pathogenic bacteria resistant to antibiotics constitutes a real public health challenge. Antibiotic resistance genes (ARGs) can be carried by both pathogenic and non-pathogenic bacteria, including commensal bacteria from the human microbiota, which require special monitoring in the fight against antimicrobial resistance. Methods: We analyzed the proteomes of 335 new bacterial species from human microbiota to estimate its whole range of ARGs using the BLAST program against ARGs reference databases. Results: We found 278 bacteria that harbor a total of 883 potential ARGs with the following distribution: 264 macrolides-lincosamides-streptogramin, 195 aminoglycosides, 156 tetracyclines, 58 β-lactamases, 58 fosfomycin, 51 glycopeptides, 36 nitroimidazoles, 33 phenicols and 32 rifamycin. Furthermore, evolutionary analyses revealed the potential horizontal transfer with pathogenic bacteria involving mobile genetic elements such as transposase and plasmid. We identified many ARGs that may represent new variants in fosfomycin and β-lactams resistance. Conclusion: These findings show that new bacterial species from human microbiota should be considered as an important reservoir of ARGs that can be transferred to pathogenic bacteria. In vitro analyses of their phenotypic potential are required to improve our understanding of the functional role of this bacterial community in the development of antibiotic resistance.
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Affiliation(s)
- Sami Khabthani
- Faculté de Pharmacie, Aix-Marseille Université, 13005 Marseille, France; (S.K.); (J.-M.R.)
- IHU Méditerranée Infection, Institut de Recherche Pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Jean-Marc Rolain
- Faculté de Pharmacie, Aix-Marseille Université, 13005 Marseille, France; (S.K.); (J.-M.R.)
- IHU Méditerranée Infection, Institut de Recherche Pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Vicky Merhej
- IHU Méditerranée Infection, Institut de Recherche Pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), 19-21 Boulevard Jean Moulin, 13005 Marseille, France
- Faculté de Sciences Médicales et Paramédicales, Aix-Marseille Université, 13005 Marseille, France
- Correspondence:
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Adapted Protocol for Saccharibacteria Cocultivation: Two New Members Join the Club of Candidate Phyla Radiation. Microbiol Spectr 2021; 9:e0106921. [PMID: 35007432 PMCID: PMC8694215 DOI: 10.1128/spectrum.01069-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The growing application of metagenomics to different ecological and microbiome niches in recent years has enhanced our knowledge of global microbial biodiversity. Among these abundant and widespread microbes, the candidate phyla radiation (CPR) group has been recognized as representing a large proportion of the microbial kingdom (>26%). CPR are characterized by their obligate symbiotic or exoparasitic activity with other microbial hosts, mainly bacteria. Currently, isolating CPR is still considered challenging for microbiologists. The idea of this study was to develop an adapted protocol for the coculture of CPR with a suitable bacterial host. Based on various sputum samples, we tried to enrich CPR (Saccharibacteria members) and to cocultivate them with pure hosts (Schaalia odontolytica). This protocol was monitored by TaqMan real-time quantitative PCR (qPCR) using a system specific for Saccharibacteria designed in this study, as well as by electron microscopy and sequencing. We succeeded in coculturing and sequencing the complete genomes of two new Saccharibacteria species, "Candidatus Minimicrobia naudis" and "Candidatus Minimicrobia vallesae." In addition, we noticed a decrease in the CT values of Saccharibacteria and a significant multiplication through their physical association with Schaalia odontolytica strains in the enriched medium that we developed. This work may help bridge gaps in the genomic database by providing new CPR members, and in the future, their currently unknown characteristics may be revealed. IMPORTANCE In this study, the first TaqMan real-time quantitative PCR (qPCR) system, targeting Saccharibacteria phylum, has been developed. This technique can specifically quantify Saccharibacteria members in any sample of interest in order to investigate their prevalence. In addition, another easy, specific, and sensitive protocol has been developed to maintain the viability of Saccharibacteria cells in an enriched medium with their bacterial host. The use of this protocol facilitates subsequent studies of the phenotypic characteristics of CPR and their physical interactions with bacterial species, as well as the sequencing of new genomes to improve the current database.
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In Silico/In Vitro Strategies Leading to the Discovery of New Nonribosomal Peptide and Polyketide Antibiotics Active against Human Pathogens. Microorganisms 2021; 9:microorganisms9112297. [PMID: 34835423 PMCID: PMC8625390 DOI: 10.3390/microorganisms9112297] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 10/29/2021] [Accepted: 11/01/2021] [Indexed: 12/12/2022] Open
Abstract
Antibiotics are majorly important molecules for human health. Following the golden age of antibiotic discovery, a period of decline ensued, characterised by the rediscovery of the same molecules. At the same time, new culture techniques and high-throughput sequencing enabled the discovery of new microorganisms that represent a potential source of interesting new antimicrobial substances to explore. The aim of this review is to present recently discovered nonribosomal peptide (NRP) and polyketide (PK) molecules with antimicrobial activity against human pathogens. We highlight the different in silico/in vitro strategies and approaches that led to their discovery. As a result of technological progress and a better understanding of the NRP and PK synthesis mechanisms, these new antibiotic compounds provide an additional option in human medical treatment and a potential way out of the impasse of antibiotic resistance.
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Peterson SB, Bertolli SK, Mougous JD. The Central Role of Interbacterial Antagonism in Bacterial Life. Curr Biol 2021; 30:R1203-R1214. [PMID: 33022265 DOI: 10.1016/j.cub.2020.06.103] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The study of bacteria interacting with their environment has historically centered on strategies for obtaining nutrients and resisting abiotic stresses. We argue this focus has deemphasized a third facet of bacterial life that is equally central to their existence: namely, the threat to survival posed by antagonizing bacteria. The diversity and ubiquity of interbacterial antagonism pathways is becoming increasingly apparent, and the insidious manner by which interbacterial toxins disarm their targets emphasizes the highly evolved nature of these processes. Studies examining the role of antagonism in natural communities reveal it can serve many functions, from facilitating colonization of naïve habitats to maintaining bacterial community stability. The pervasiveness of antagonistic pathways is necessarily matched by an equally extensive array of defense strategies. These overlap with well characterized, central stress response pathways, highlighting the contribution of bacterial interactions to shaping cell physiology. In this review, we build the case for the ubiquity and importance of interbacterial antagonism.
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Affiliation(s)
- S Brook Peterson
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Savannah K Bertolli
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Joseph D Mougous
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington School of Medicine, Seattle, WA 98195, USA.
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Juettner NE, Bogen JP, Bauer TA, Knapp S, Pfeifer F, Huettenhain SH, Meusinger R, Kraemer A, Fuchsbauer HL. Decoding the Papain Inhibitor from Streptomyces mobaraensis as Being Hydroxylated Chymostatin Derivatives: Purification, Structure Analysis, and Putative Biosynthetic Pathway. JOURNAL OF NATURAL PRODUCTS 2020; 83:2983-2995. [PMID: 32998509 DOI: 10.1021/acs.jnatprod.0c00201] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Streptomyces mobaraensis produces the papain inhibitor SPI consisting of a 12 kDa protein and small active compounds (SPIac). Purification of the papain inhibitory compounds resulted in four diverse chymostatin derivatives that were characterized by NMR and MS analysis. Chymostatins are hydrophobic tetrapeptide aldehydes from streptomycetes, e.g., S. lavendulae and S. hygroscopicus, that reverse chymosin-mediated angiotensin activation and inhibit other serine and cysteine proteases. Chymotrypsin and papain were both inhibited by the SPIac compounds in the low nanomolar range. SPIac differs from the characterized chymostatins by the exchange of phenylalanine for tyrosine. The crystal structure of one of these chymostatin variants confirmed its molecular structure and revealed a S-configured hemithioacetal bond with the catalytic Cys25 thiolate as well as close interactions with hydrophobic S1 and S2 subsite amino acids. A model for chymostatin biosynthesis is provided based on the discovery of clustered genes encoding several putative nonribosomal peptide synthetases; among them, there is the unusual CstF enzyme that accommodates two canonical amino acid activation domains as well as three peptide carrier protein domains.
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Affiliation(s)
- Norbert E Juettner
- The Department of Chemical Engineering and Biotechnology, University of Applied Sciences of Darmstadt, Stephanstraße 7, 64295 Darmstadt, Germany
- The Department of Biology, Technische Universität Darmstadt, Schnittspahnstraße 10, 64287 Darmstadt, Germany
| | - Jan P Bogen
- The Department of Chemical Engineering and Biotechnology, University of Applied Sciences of Darmstadt, Stephanstraße 7, 64295 Darmstadt, Germany
| | - Tobias A Bauer
- The Department of Chemical Engineering and Biotechnology, University of Applied Sciences of Darmstadt, Stephanstraße 7, 64295 Darmstadt, Germany
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Max-von-Laue-Straße 15, 60438 Frankfurt am Main, Germany
| | - Felicitas Pfeifer
- The Department of Biology, Technische Universität Darmstadt, Schnittspahnstraße 10, 64287 Darmstadt, Germany
| | - Stefan H Huettenhain
- The Department of Chemical Engineering and Biotechnology, University of Applied Sciences of Darmstadt, Stephanstraße 7, 64295 Darmstadt, Germany
| | - Reinhard Meusinger
- The Department of Chemistry, Technische Universität Darmstadt, Alarich-Weiss-Straße 8, 64287 Darmstadt, Germany
| | - Andreas Kraemer
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany
| | - Hans-Lothar Fuchsbauer
- The Department of Chemical Engineering and Biotechnology, University of Applied Sciences of Darmstadt, Stephanstraße 7, 64295 Darmstadt, Germany
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Raoult D, Rolain JM. The living croquet theory: The Staphylococcus aureus paradigm. Int J Antimicrob Agents 2019; 53:724-725. [DOI: 10.1016/j.ijantimicag.2019.04.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 03/14/2019] [Accepted: 04/07/2019] [Indexed: 11/28/2022]
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Borsetto C, Amos GCA, da Rocha UN, Mitchell AL, Finn RD, Laidi RF, Vallin C, Pearce DA, Newsham KK, Wellington EMH. Microbial community drivers of PK/NRP gene diversity in selected global soils. MICROBIOME 2019; 7:78. [PMID: 31118083 PMCID: PMC6532259 DOI: 10.1186/s40168-019-0692-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 05/08/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND The emergence of antibiotic-resistant pathogens has created an urgent need for novel antimicrobial treatments. Advances in next-generation sequencing have opened new frontiers for discovery programmes for natural products allowing the exploitation of a larger fraction of the microbial community. Polyketide (PK) and non-ribosomal pepetide (NRP) natural products have been reported to be related to compounds with antimicrobial and anticancer activities. We report here a new culture-independent approach to explore bacterial biosynthetic diversity and determine bacterial phyla in the microbial community associated with PK and NRP diversity in selected soils. RESULTS Through amplicon sequencing, we explored the microbial diversity (16S rRNA gene) of 13 soils from Antarctica, Africa, Europe and a Caribbean island and correlated this with the amplicon diversity of the adenylation (A) and ketosynthase (KS) domains within functional genes coding for non-ribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs), which are involved in the production of NRP and PK, respectively. Mantel and Procrustes correlation analyses with microbial taxonomic data identified not only the well-studied phyla Actinobacteria and Proteobacteria, but also, interestingly, the less biotechnologically exploited phyla Verrucomicrobia and Bacteroidetes, as potential sources harbouring diverse A and KS domains. Some soils, notably that from Antarctica, provided evidence of endemic diversity, whilst others, such as those from Europe, clustered together. In particular, the majority of the domain reads from Antarctica remained unmatched to known sequences suggesting they could encode enzymes for potentially novel PK and NRP. CONCLUSIONS The approach presented here highlights potential sources of metabolic novelty in the environment which will be a useful precursor to metagenomic biosynthetic gene cluster mining for PKs and NRPs which could provide leads for new antimicrobial metabolites.
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Affiliation(s)
- Chiara Borsetto
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Gregory C. A. Amos
- School of Life Sciences, University of Warwick, Coventry, UK
- Present addresses: G.C.A.A National Institute for Biological Standards and Control (NIBSC), Potters Bar, UK
| | - Ulisses Nunes da Rocha
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research—UFZ, Leipzig, Germany
| | - Alex L. Mitchell
- EMBL-EBI European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Robert D. Finn
- EMBL-EBI European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | | | | | - David A. Pearce
- Applied Sciences, Faculty of Health and Life Sciences, Northumbria University at Newcastle, Ellison Building, Northumberland Road, Newcastle, NE1 8ST UK
- Natural Environment Research Council, British Antarctic Survey, Cambridge, UK
| | - Kevin K. Newsham
- Natural Environment Research Council, British Antarctic Survey, Cambridge, UK
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