1
|
The Odilorhabdin Antibiotic Biosynthetic Cluster and Acetyltransferase Self-Resistance Locus Are Niche and Species Specific. mBio 2022; 13:e0282621. [PMID: 35012352 PMCID: PMC8749412 DOI: 10.1128/mbio.02826-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Antibiotic resistance is an increasing threat to human health. A direct link has been established between antimicrobial self-resistance determinants of antibiotic producers, environmental bacteria, and clinical pathogens. Natural odilorhabdins (ODLs) constitute a new family of 10-mer linear cationic peptide antibiotics inhibiting bacterial translation by binding to the 30S subunit of the ribosome. These bioactive secondary metabolites are produced by entomopathogenic bacterial symbiont Xenorhabdus (Morganellaceae), vectored by the soil-dwelling nematodes. ODL-producing Xenorhabdus nematophila symbionts have mechanisms of self-protection. In this study, we cloned the 44.5-kb odl biosynthetic gene cluster (odl-BGC) of the symbiont by recombineering and showed that the N-acetyltransferase-encoding gene, oatA, is responsible for ODL resistance. In vitro acetylation and liquid chromatography-tandem mass spectrometry (LC-MS/MS) analyses showed that OatA targeted the side chain amino group of ODL rare amino acids, leading to a loss of translation inhibition and antibacterial properties. Functional, genomic, and phylogenetic analyses of oatA revealed an exclusive cis-link to the odilorhabdin BGC, found only in X. nematophila and a specific phylogenetic clade of Photorhabdus. This work highlights the coevolution of antibiotic production and self-resistance as ancient features of this unique tripartite complex of host-vector-symbiont interactions without odl-BGC dissemination by lateral gene transfer. IMPORTANCE Odilorhabdins (ODLs) constitute a novel antibiotic family with promising properties for treating problematic multidrug-resistant Gram-negative bacterial infections. ODLs are 10-mer linear cationic peptides inhibiting bacterial translation by binding to the small subunit of the ribosome. These natural peptides are produced by Xenorhabdus nematophila, a bacterial symbiont of entomopathogenic nematodes well known to produce large amounts of specialized secondary metabolites. Like other antimicrobial producers, ODL-producing Xenorhabdus nematophila has mechanisms of self-protection. In this study, we cloned the ODL-biosynthetic gene cluster of the symbiont by recombineering and showed that the N-acetyltransferase-encoding gene, oatA, is responsible for ODL resistance. In vitro acetylation and LC-MS/MS analyses showed that OatA targeted the side chain amino group of ODL rare amino acids, leading to a loss of translation inhibition and antibacterial properties. Functional, genomic, and phylogenetic analyses of oatA revealed the coevolution of antibiotic production and self-resistance as ancient feature of this particular niche in soil invertebrates without resistance dissemination.
Collapse
|
2
|
Rimet F, Aylagas E, Borja Á, Bouchez A, Canino A, Chauvin C, Chonova T, Ciampor Jr F, Costa FO, Ferrari BJD, Gastineau R, Goulon C, Gugger M, Holzmann M, Jahn R, Kahlert M, Kusber WH, Laplace-Treyture C, Leese F, Leliaert F, Mann DG, Marchand F, Méléder V, Pawlowski J, Rasconi S, Rivera S, Rougerie R, Schweizer M, Trobajo R, Vasselon V, Vivien R, Weigand A, Witkowski A, Zimmermann J, Ekrem T. Metadata standards and practical guidelines for specimen and DNA curation when building barcode reference libraries for aquatic life. METABARCODING AND METAGENOMICS 2021. [DOI: 10.3897/mbmg.5.58056] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
DNA barcoding and metabarcoding is increasingly used to effectively and precisely assess and monitor biodiversity in aquatic ecosystems. As these methods rely on data availability and quality of barcode reference libraries, it is important to develop and follow best practices to ensure optimal quality and traceability of the metadata associated with the reference barcodes used for identification. Sufficient metadata, as well as vouchers, corresponding to each reference barcode must be available to ensure reliable barcode library curation and, thereby, provide trustworthy baselines for downstream molecular species identification. This document (1) specifies the data and metadata required to ensure the relevance, the accessibility and traceability of DNA barcodes and (2) specifies the recommendations for DNA harvesting and for the storage of both voucher specimens/samples and barcode data.
Collapse
|
3
|
Kahlert M, Kelly MG, Mann DG, Rimet F, Sato S, Bouchez A, Keck F. Connecting the morphological and molecular species concepts to facilitate species identification within the genus Fragilaria (Bacillariophyta). JOURNAL OF PHYCOLOGY 2019; 55:948-970. [PMID: 31106407 DOI: 10.1111/jpy.12886] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 04/24/2019] [Indexed: 06/09/2023]
Abstract
This paper explores the diversity and taxonomy of species within Fragilaria sensu stricto, an abundant and ecologically important diatom genus, taking advantage of cultured and DNA-barcoded material. The goal is to facilitate the identification of European taxa within this complex, providing a unified view on morphological and molecular diversity. There is a general agreement that the separation of species within the group of Fragilaria is difficult because morphological descriptions of species are not consistent between authorities, ongoing taxonomic revisions have resulted in species described with standards of the late 20th and 21st centuries alongside descriptions based on 19th century (light microscopical) criteria, and because not all diagnostic characters can be seen in all specimens encountered in routine analyses. Consequent confusion could blur potentially important ecological distinctions between species. Our study demonstrated that some species defined on morphological criteria could be confirmed using the rbcL chloroplast gene as a genetic marker, for example, Fragilaria gracilis, Fragilaria tenera, Fragilaria perminuta, and Fragilaria subconstricta. However, even for those species, preliminary identifications based on morphology often differed from identifications based on phylogenetic clustering combined with detailed morphological study. Clades were well-defined by rbcL, but based on morphology, the terminal taxa of these clades did not match the currently described Fragilaria species. To clarify recognition of these taxa, we describe three new species: Fragilaria agnesiae, Fragilaria heatherae, and Fragilaria joachimii.
Collapse
Affiliation(s)
- Maria Kahlert
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, PO Box 7050, SE-750 07, Uppsala, Sweden
| | - Martyn G Kelly
- Bowburn Consultancy, Bowburn, Durham, DH6 5QB, UK
- Department of Geography, University of Nottingham, Nottingham, NG7 2RD, UK
| | - David G Mann
- Royal Botanic Garden Edinburgh, Edinburgh, EH3 5LR, UK
- IRTA, Sant Carles de La Ràpita, Catalonia, E-43540, Spain
| | - Frédéric Rimet
- INRA, UMR CARRTEL, 75bis avenue de Corzent, F-74200, Thonon-les-Bains, France
| | - Shinya Sato
- Department of Marine Science and Technology, Fukui Prefectural University, 917-0003, Fukui, Japan
| | - Agnès Bouchez
- INRA, UMR CARRTEL, 75bis avenue de Corzent, F-74200, Thonon-les-Bains, France
| | - François Keck
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, PO Box 7050, SE-750 07, Uppsala, Sweden
- INRA, UMR CARRTEL, 75bis avenue de Corzent, F-74200, Thonon-les-Bains, France
| |
Collapse
|
4
|
Dubois O, Allanic C, Charvet CL, Guégnard F, Février H, Théry-Koné I, Cortet J, Koch C, Bouvier F, Fassier T, Marcon D, Magnin-Robert JB, Peineau N, Courtot E, Huau C, Meynadier A, Enguehard-Gueiffier C, Neveu C, Boudesocque-Delaye L, Sallé G. Lupin (Lupinus spp.) seeds exert anthelmintic activity associated with their alkaloid content. Sci Rep 2019; 9:9070. [PMID: 31227784 PMCID: PMC6588613 DOI: 10.1038/s41598-019-45654-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 06/12/2019] [Indexed: 12/20/2022] Open
Abstract
The growing range of drug resistant parasitic nematode populations threatens the sustainability of ruminant farming worldwide. In this context, nutraceuticals, animal feed that provides necessary dietary requirements while ensuring parasite control, could contribute to increase farming sustainability in developed and low resource settings. In this study, we evaluated the anthelmintic potential of lupin seed extracts against the major ruminant trichostrongylids, Haemonchus contortus and Teladorsagia circumcincta. In vitro observations showed that seed extracts from commercially available lupin varieties could significantly but moderately inhibit larval migration. This anthelmintic effect was mediated by the seed alkaloid content and was potent against both fully susceptible and multidrug resistant H. contortus isolates as well as a susceptible T. circumcincta isolate. Analytical chemistry revealed a set of four lupanine and sparteine-derivatives with anthelmintic activity, and electrophysiology assays on recombinant nematode acetylcholine receptors suggested an antagonistic mode of action for lupin alkaloids. An in vivo trial in H. contortus infected lupin-fed ewes and goats failed to demonstrate any direct anthelmintic effect of crude lupin seeds but infected lupin-fed goats suffered significantly less parasite-mediated blood losses. Altogether, our findings suggest that the anthelmintic potential of lupin remains limited. However, the potent alkaloids identified could lead to the development of novel drugs or may be used in combination with current anthelmintics to improve their efficacy.
Collapse
Affiliation(s)
- O Dubois
- UMR1282 Infectiologie et Santé Publique, INRA, Université de Tours, F-37380, Nouzilly, France.,EA 7502 SIMBA, Université de Tours, Faculté de Pharmacie, F-37000, Tours, France
| | - C Allanic
- UMR1282 Infectiologie et Santé Publique, INRA, Université de Tours, F-37380, Nouzilly, France
| | - C L Charvet
- UMR1282 Infectiologie et Santé Publique, INRA, Université de Tours, F-37380, Nouzilly, France
| | - F Guégnard
- UMR1282 Infectiologie et Santé Publique, INRA, Université de Tours, F-37380, Nouzilly, France
| | - H Février
- UMR1282 Infectiologie et Santé Publique, INRA, Université de Tours, F-37380, Nouzilly, France
| | - I Théry-Koné
- EA 7502 SIMBA, Université de Tours, Faculté de Pharmacie, F-37000, Tours, France
| | - J Cortet
- UMR1282 Infectiologie et Santé Publique, INRA, Université de Tours, F-37380, Nouzilly, France
| | - C Koch
- UMR1282 Infectiologie et Santé Publique, INRA, Université de Tours, F-37380, Nouzilly, France
| | - F Bouvier
- UE332 La Sapinière, INRA, F-18174, Osmoy, France
| | - T Fassier
- UE332 La Sapinière, INRA, F-18174, Osmoy, France
| | - D Marcon
- UE332 La Sapinière, INRA, F-18174, Osmoy, France
| | - J B Magnin-Robert
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, F-21000, Dijon, France
| | - N Peineau
- Département Physiologie Animale, Université de Tours, Faculté des Sciences et Techniques, F-37000, Tours, France
| | - E Courtot
- UMR1282 Infectiologie et Santé Publique, INRA, Université de Tours, F-37380, Nouzilly, France
| | - C Huau
- GenPhySE, INRA, Université de Toulouse, INPT, ENVT, F-31326, Castanet-Tolosan, France
| | - A Meynadier
- GenPhySE, INRA, Université de Toulouse, INPT, ENVT, F-31326, Castanet-Tolosan, France
| | | | - C Neveu
- UMR1282 Infectiologie et Santé Publique, INRA, Université de Tours, F-37380, Nouzilly, France
| | - L Boudesocque-Delaye
- EA 7502 SIMBA, Université de Tours, Faculté de Pharmacie, F-37000, Tours, France
| | - G Sallé
- UMR1282 Infectiologie et Santé Publique, INRA, Université de Tours, F-37380, Nouzilly, France.
| |
Collapse
|