1
|
Durand M, Besseau S, Papon N, Courdavault V. Unlocking plant bioactive pathways: omics data harnessing and machine learning assisting. Curr Opin Biotechnol 2024; 87:103135. [PMID: 38728826 DOI: 10.1016/j.copbio.2024.103135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 04/02/2024] [Accepted: 04/12/2024] [Indexed: 05/12/2024]
Abstract
Plant bioactives hold immense potential in the medicine and food industry. The recent advancements in omics applied in deciphering specialized metabolic pathways underscore the importance of high-quality genome releases and the wealth of data in metabolomics and transcriptomics. While harnessing data, whether integrated or standalone, has proven successful in unveiling plant natural product (PNP) biosynthetic pathways, the democratization of machine learning in biology opens exciting new opportunities for enhancing the exploration of these pathways. This review highlights the recent breakthroughs in disrupting plant-specialized biosynthetic pathways through the utilization of omics data harnessing and machine learning techniques.
Collapse
Affiliation(s)
- Mickael Durand
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200 Tours, France
| | - Sébastien Besseau
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200 Tours, France
| | - Nicolas Papon
- Univ Angers, Univ Brest, IRF, SFR ICAT, F-49000 Angers, France
| | - Vincent Courdavault
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200 Tours, France.
| |
Collapse
|
2
|
Courdavault V, Papon N. Metabolic engineering of plant medicines. Nat Rev Genet 2024; 25:307. [PMID: 38337018 DOI: 10.1038/s41576-024-00705-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2024]
Affiliation(s)
| | - Nicolas Papon
- University of Angers, University of Brest, IRF, Angers, France
| |
Collapse
|
3
|
Lezin E, Carqueijeiro I, Cuello C, Durand M, Jansen HJ, Vergès V, Birer Williams C, Oudin A, Dugé de Bernonville T, Petrignet J, Celton N, St-Pierre B, Papon N, Sun C, Dirks RP, O'Connor SE, Jensen MK, Besseau S, Courdavault V. A chromosome-scale genome assembly of Rauvolfia tetraphylla facilitates identification of the complete ajmaline biosynthetic pathway. Plant Commun 2024; 5:100784. [PMID: 38155576 PMCID: PMC11009098 DOI: 10.1016/j.xplc.2023.100784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 12/18/2023] [Accepted: 12/21/2023] [Indexed: 12/30/2023]
Affiliation(s)
- Enzo Lezin
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200 Tours, France
| | - Inês Carqueijeiro
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200 Tours, France
| | - Clément Cuello
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200 Tours, France
| | - Mickael Durand
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200 Tours, France
| | - Hans J Jansen
- Future Genomics Technologies, 2333 BE Leiden, the Netherlands
| | - Valentin Vergès
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200 Tours, France
| | | | - Audrey Oudin
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200 Tours, France
| | | | - Julien Petrignet
- Laboratoire Synthèse et Isolement de Molécules BioActives (SIMBA, EA 7502), Université de Tours, 37200 Tours, France
| | - Noémie Celton
- Laboratoire de Cytogénetique Constitutionnelle, CHRU de Tours - Hôpital Bretonneau, 37044 Tours, France
| | - Benoit St-Pierre
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200 Tours, France
| | - Nicolas Papon
- University Angers, University Brest, IRF, SFR ICAT, 49000 Angers, France; Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 2800, China
| | - Chao Sun
- University Angers, University Brest, IRF, SFR ICAT, 49000 Angers, France; Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 2800, China
| | - Ron P Dirks
- Future Genomics Technologies, 2333 BE Leiden, the Netherlands
| | - Sarah Ellen O'Connor
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
| | - Michael Krogh Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 100193 Kgs Lyngby, Denmark
| | - Sébastien Besseau
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200 Tours, France.
| | - Vincent Courdavault
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200 Tours, France.
| |
Collapse
|
4
|
Mahmoud DE, Herivaux A, Morio F, Briard B, Vigneau C, Desoubeaux G, Bouchara JP, Gangneux JP, Nevez G, Gal SLE, Papon N. The epidemiology of fungal infections in transplant patients. Biomed J 2024:100719. [PMID: 38580051 DOI: 10.1016/j.bj.2024.100719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 03/21/2024] [Accepted: 03/24/2024] [Indexed: 04/07/2024] Open
Abstract
Transplant patients, including solid-organ transplant (SOT) and hematopoietic stem cell transplant (HSCT) recipients, are exposed to various types of complications, particularly rejection. To prevent these outcomes, transplant recipients commonly receive long-term immunosuppressive regimens that in turn make them more susceptible to a wide array of infectious diseases, notably those caused by opportunistic pathogens. Among these, invasive fungal infections (IFIs) remain a major cause of mortality and morbidity in both SOT and HSCT recipients. Despite the continuing improvement in early diagnostics and treatments of IFIs, the management of these infections in transplant patients is still complicated. Here, we provide an overview concerning the most recent trends in the epidemiology of IFIs in SOT and HSCT recipients by describing the prominent yeasts and molds species involved, the timing of post-transplant IFIs and the risk factors associated with their occurrence in these particularly weak populations. We also give special emphasis into basic research advances in the field that recently suggested a role of the global and long-term prophylactic regimen in orchestrating various biological disturbances in the organism and conditioning the emergence of the most adapted fungal strains to the particular physiological profiles of transplant patients.
Collapse
Affiliation(s)
| | - Anaïs Herivaux
- Univ Angers, Univ Brest, IRF, SFR, ICAT, 49000, Angers, France
| | - Florent Morio
- Nantes Université, CHU Nantes, Cibles et Médicaments des Infections et de L'Immunité, UR1155, Nantes, France
| | - Benoit Briard
- INSERM, Centre D'Etude des Pathologies Respiratoires (CEPR), UMR 1100, Université de Tours, Faculté de Médecine de Tours, Tours, France; CHRU Tours, Parasitologie-Mycologie Médicale-Médecine Tropicale, 37044, Tours, France
| | - Cécile Vigneau
- Univ Rennes, CHU Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail), UMR_S 1085, F-35000, Rennes, France; Division of Nephrology, Rennes University Hospital, Rennes, France
| | - Guillaume Desoubeaux
- INSERM, Centre D'Etude des Pathologies Respiratoires (CEPR), UMR 1100, Université de Tours, Faculté de Médecine de Tours, Tours, France; CHRU Tours, Parasitologie-Mycologie Médicale-Médecine Tropicale, 37044, Tours, France
| | | | - Jean-Pierre Gangneux
- Univ Rennes, CHU Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail), UMR_S 1085, F-35000, Rennes, France; Laboratory of Parasitology and Medical Mycology, European Confederation of Medical Mycology (ECMM) Excellence Center, Centre National de Référence Aspergilloses Chroniques, Rennes University Hospital, F-35000, Rennes, France
| | - Gilles Nevez
- Laboratory of Parasitology and Mycology, Brest University Hospital, 29609, Brest, France; Univ Brest, Univ Angers, IRF, SFR, ICAT, Brest, France
| | - Soléne LE Gal
- Laboratory of Parasitology and Mycology, Brest University Hospital, 29609, Brest, France; Univ Brest, Univ Angers, IRF, SFR, ICAT, Brest, France
| | - Nicolas Papon
- Univ Angers, Univ Brest, IRF, SFR, ICAT, 49000, Angers, France.
| |
Collapse
|
5
|
Courdavault V, Papon N. Accessing natural vaccine adjuvants. Nat Chem Biol 2024; 20:401-403. [PMID: 38491321 DOI: 10.1038/s41589-024-01585-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2024]
Affiliation(s)
- Vincent Courdavault
- Biomolécules et Biotechnologies Végétales, Université de Tours, Tours, France.
| | - Nicolas Papon
- Université d'Angers, Université de Bretagne-Occidentale, IRF, SFR ICAT, Angers, France
| |
Collapse
|
6
|
Cuello C, Jansen HJ, Abdallah C, Zamar Mbadinga DL, Birer Williams C, Durand M, Oudin A, Papon N, Giglioli-Guivarc'h N, Dirks RP, Jensen MK, O'Connor SE, Besseau S, Courdavault V. The Madagascar palm genome provides new insights on the evolution of Apocynaceae specialized metabolism. Heliyon 2024; 10:e28078. [PMID: 38533072 PMCID: PMC10963385 DOI: 10.1016/j.heliyon.2024.e28078] [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: 12/01/2023] [Revised: 03/07/2024] [Accepted: 03/11/2024] [Indexed: 03/28/2024] Open
Abstract
Specialized metabolites possess diverse interesting biological activities and some cardenolides- and monoterpene indole alkaloids- (MIAs) derived pharmaceuticals are currently used to treat human diseases such as cancers or hypertension. While these two families of biocompounds are produced by specific subfamilies of Apocynaceae, one member of this medicinal plant family, the succulent tree Pachypodium lamerei Drake (also known as Madagascar palm), does not produce such specialized metabolites. To explore the evolutionary paths that have led to the emergence and loss of cardenolide and MIA biosynthesis in Apocynaceae, we sequenced and assembled the P. lamerei genome by combining Oxford Nanopore Technologies long-reads and Illumina short-reads. Phylogenomics revealed that, among the Apocynaceae whose genomes have been sequenced, the Madagascar palm is so far the species closest to the common ancestor between MIA producers/non-MIA producers. Transposable elements, constituting 72.48% of the genome, emerge as potential key players in shaping genomic architecture and influencing specialized metabolic pathways. The absence of crucial MIA biosynthetic genes such as strictosidine synthase in P. lamerei and non-Rauvolfioideae species hints at a transposon-mediated mechanism behind gene loss. Phylogenetic analysis not only showcases the evolutionary divergence of specialized metabolite biosynthesis within Apocynaceae but also underscores the role of transposable elements in this intricate process. Moreover, we shed light on the low conservation of enzymes involved in the final stages of MIA biosynthesis in the distinct MIA-producing plant families, inferring independent gains of these specialized enzymes along the evolution of these medicinal plant clades. Overall, this study marks a leap forward in understanding the genomic dynamics underpinning the evolution of specialized metabolites biosynthesis in the Apocynaceae family, with transposons emerging as potential architects of genomics restructuring and gene loss.
Collapse
Affiliation(s)
- Clément Cuello
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France
| | - Hans J. Jansen
- Future Genomics Technologies, 2333 BE, Leiden, the Netherlands
| | - Cécile Abdallah
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France
| | | | - Caroline Birer Williams
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France
| | - Mickael Durand
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France
| | - Audrey Oudin
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France
| | - Nicolas Papon
- Univ Angers, Univ Brest, IRF, SFR ICAT, F-49000, Angers, France
| | | | - Ron P. Dirks
- Future Genomics Technologies, 2333 BE, Leiden, the Netherlands
| | - Michael Krogh Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Sarah Ellen O'Connor
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, 07745, Germany
| | - Sébastien Besseau
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France
| | - Vincent Courdavault
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France
| |
Collapse
|
7
|
Perrot T, Marc J, Lezin E, Papon N, Besseau S, Courdavault V. Emerging trends in production of plant natural products and new-to-nature biopharmaceuticals in yeast. Curr Opin Biotechnol 2024; 87:103098. [PMID: 38452572 DOI: 10.1016/j.copbio.2024.103098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 02/07/2024] [Accepted: 02/07/2024] [Indexed: 03/09/2024]
Abstract
Natural products represent an inestimable source of valuable compounds for human health. Notably, those produced by plants remain challenging to access due to their low production. Potential shortages of plant-derived biopharmaceuticals caused by climate change or pandemics also regularly tense the market trends. Thus, biotechnological alternatives of supply based on synthetic biology have emerged. These innovative strategies mostly rely on the use of engineered microbial systems for compound synthesis. In this regard, yeasts remain the easiest-tractable eukaryotic models and a convenient chassis for reconstructing whole biosynthetic routes for the heterologous production of plant-derived metabolites. Here, we highlight the recent discoveries dedicated to the bioproduction of new-to-nature compounds in yeasts and provide an overview of emerging strategies for optimising bioproduction.
Collapse
Affiliation(s)
- Thomas Perrot
- Biomolécules et Biotechnologies Végétales, BBV, EA2106, Université de Tours, Tours, France
| | - Jillian Marc
- Biomolécules et Biotechnologies Végétales, BBV, EA2106, Université de Tours, Tours, France
| | - Enzo Lezin
- Biomolécules et Biotechnologies Végétales, BBV, EA2106, Université de Tours, Tours, France
| | - Nicolas Papon
- Univ Angers, Univ Brest, IRF, SFR ICAT, F-49000 Angers, France
| | - Sébastien Besseau
- Biomolécules et Biotechnologies Végétales, BBV, EA2106, Université de Tours, Tours, France
| | - Vincent Courdavault
- Biomolécules et Biotechnologies Végétales, BBV, EA2106, Université de Tours, Tours, France.
| |
Collapse
|
8
|
Zamar DL, Papon N, Courdavault V. SPOTLIGHT: Alpha carbonic anhydrases join the club of alkaloid biosynthetic enzymes. J Plant Physiol 2024; 293:154169. [PMID: 38184908 DOI: 10.1016/j.jplph.2023.154169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 12/29/2023] [Indexed: 01/09/2024]
Affiliation(s)
- Duchesse-Lacours Zamar
- Biomolécules et Biotechnologies Végétales, BBV, EA2106, Université de Tours, Tours, France
| | - Nicolas Papon
- Univ Angers, Univ Brest, IRF, SFR ICAT, F-49000, Angers, France
| | - Vincent Courdavault
- Biomolécules et Biotechnologies Végétales, BBV, EA2106, Université de Tours, Tours, France.
| |
Collapse
|
9
|
Mahmoud DE, Hanachi M, Yaakoub H, Blanchard S, Pignon P, Souiai O, Delneste Y, Bouchara JP, Papon N, Hérivaux A. Functional insights into human macrophage response against Scedosporium apiospermum and Scedosporium dehoogii. Cytokine 2023; 172:156384. [PMID: 37832161 DOI: 10.1016/j.cyto.2023.156384] [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: 07/19/2023] [Revised: 09/06/2023] [Accepted: 09/26/2023] [Indexed: 10/15/2023]
Abstract
Fungal infections caused by Scedosporium species are rising among immunocompromised and immunocompetent patients. Within the immunocompetent group, patients with cystic fibrosis (pwCF) are at high risk of developing a chronic airway colonization by these molds. While S. apiospermum is one of the major species encountered in the lungs of pwCF, S. dehoogii has rarely been reported. The innate immune response is believed to be critical for host defense against fungal infections. However, its role has only recently been elucidated and the immune mechanisms against Scedosporium species are currently unknown. In this context, we undertook a comparative investigation of macrophage-mediated immune responses toward S. apiospermum and S. dehoogii conidia. Our data showed that S. apiospermum and S. dehoogii conidia strongly stimulated the expression of a set of pro-inflammatory cytokines and chemokines such as IL-1β, IL-8, IL-6 and TNFα. We demonstrated that S. dehoogii was more potent in stimulating the early release of pro-inflammatory cytokines and chemokines while S. apiospermum induced a late inflammatory response at a higher level. Flow cytometry analysis showed that M1-like macrophages were able to internalize both S. apiospermum and S. dehoogii conidia, with a similar intracellular killing rate for both species. In conclusion, these results suggest that M1-like macrophages can rapidly initiate a strong immune response against both S. apiospermum and S. dehoogii. This response is characterized by a similar killing of internalized conidia, but a different time course of cytokine production.
Collapse
Affiliation(s)
| | - Mariem Hanachi
- Laboratory of Bioinformatics, Biomathematics and Biostatistics-LR16IPT09, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Hajar Yaakoub
- Univ Angers, Univ Brest, IRF, SFR ICAT, 49000 Angers, France
| | - Simon Blanchard
- Univ Angers, Nantes Université, Inserm, CNRS, CRCI2NA, SFR ICAT, F-49000 Angers, France
| | - Pascale Pignon
- Univ Angers, Nantes Université, Inserm, CNRS, CRCI2NA, SFR ICAT, F-49000 Angers, France
| | - Oussama Souiai
- Laboratory of Bioinformatics, Biomathematics and Biostatistics-LR16IPT09, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Yves Delneste
- Univ Angers, Nantes Université, Inserm, CNRS, CRCI2NA, SFR ICAT, F-49000 Angers, France; Immunology and Allergology Laboratory, University Hospital of Angers, Angers, France
| | | | - Nicolas Papon
- Univ Angers, Univ Brest, IRF, SFR ICAT, 49000 Angers, France
| | - Anaïs Hérivaux
- Univ Angers, Univ Brest, IRF, SFR ICAT, 49000 Angers, France.
| |
Collapse
|
10
|
Stander EA, Lehka B, Carqueijeiro I, Cuello C, Hansson FG, Jansen HJ, Dugé De Bernonville T, Birer Williams C, Vergès V, Lezin E, Lorensen MDBB, Dang TT, Oudin A, Lanoue A, Durand M, Giglioli-Guivarc'h N, Janfelt C, Papon N, Dirks RP, O'connor SE, Jensen MK, Besseau S, Courdavault V. The Rauvolfia tetraphylla genome suggests multiple distinct biosynthetic routes for yohimbane monoterpene indole alkaloids. Commun Biol 2023; 6:1197. [PMID: 38001233 PMCID: PMC10673892 DOI: 10.1038/s42003-023-05574-8] [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: 06/20/2023] [Accepted: 11/10/2023] [Indexed: 11/26/2023] Open
Abstract
Monoterpene indole alkaloids (MIAs) are a structurally diverse family of specialized metabolites mainly produced in Gentianales to cope with environmental challenges. Due to their pharmacological properties, the biosynthetic modalities of several MIA types have been elucidated but not that of the yohimbanes. Here, we combine metabolomics, proteomics, transcriptomics and genome sequencing of Rauvolfia tetraphylla with machine learning to discover the unexpected multiple actors of this natural product synthesis. We identify a medium chain dehydrogenase/reductase (MDR) that produces a mixture of four diastereomers of yohimbanes including the well-known yohimbine and rauwolscine. In addition to this multifunctional yohimbane synthase (YOS), an MDR synthesizing mainly heteroyohimbanes and the short chain dehydrogenase vitrosamine synthase also display a yohimbane synthase side activity. Lastly, we establish that the combination of geissoschizine synthase with at least three other MDRs also produces a yohimbane mixture thus shedding light on the complex mechanisms evolved for the synthesis of these plant bioactives.
Collapse
Affiliation(s)
- Emily Amor Stander
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France
| | - Beata Lehka
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Inês Carqueijeiro
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France
| | - Clément Cuello
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France
| | - Frederik G Hansson
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Hans J Jansen
- Future Genomics Technologies, 2333 BE, Leiden, The Netherlands
| | - Thomas Dugé De Bernonville
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France
- Limagrain, Centre de Recherche, Route d'Ennezat, Chappes, France
| | - Caroline Birer Williams
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France
| | - Valentin Vergès
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France
| | - Enzo Lezin
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France
| | | | - Thu-Thuy Dang
- Department of Chemistry, Irving K. Barber Faculty of Science, University of British Columbia, Kelowna, BC, Canada
| | - Audrey Oudin
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France
| | - Arnaud Lanoue
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France
| | - Mickael Durand
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France
| | | | - Christian Janfelt
- Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen, Denmark
| | - Nicolas Papon
- Univ Angers, Univ Brest, IRF, SFR ICAT, F-49000, Angers, France
| | - Ron P Dirks
- Future Genomics Technologies, 2333 BE, Leiden, The Netherlands
| | - Sarah Ellen O'connor
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, 07745, Germany.
| | - Michael Krogh Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs, Lyngby, Denmark.
| | - Sébastien Besseau
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France.
| | - Vincent Courdavault
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France.
| |
Collapse
|
11
|
Burlat V, Papon N, Courdavault V. Medicinal plants enter the single-cell multi-omics era. Trends Plant Sci 2023; 28:1205-1207. [PMID: 37625948 DOI: 10.1016/j.tplants.2023.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 08/07/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023]
Abstract
Elucidating biosynthetic pathways of plant specialized metabolites is a tricky but essential task for the biotechnological production of plant drugs. In a new report, Li et al. used a single-cell multi-omics approach to provide an integrative view of the architecture and regulation of anticancer alkaloid routes in Madagascar periwinkle.
Collapse
Affiliation(s)
- Vincent Burlat
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, Centre National de la Recherche Scientifique (CNRS), Université Paul Sabatier Toulouse 3, Institut National Polytechnique de Toulouse, 31320 Auzeville-Tolosane, France
| | - Nicolas Papon
- Univ Angers, Univ Brest, IRF, SFR ICAT, F-49000 Angers, France
| | - Vincent Courdavault
- Biomolécules et Biotechnologies Végétales, BBV, EA2106, Université de Tours, Tours, France.
| |
Collapse
|
12
|
Gangneux JP, Rhodes JL, Papon N. Airway microbiome: environmental exposure-respiratory health nexus. Trends Mol Med 2023; 29:875-877. [PMID: 37690859 DOI: 10.1016/j.molmed.2023.08.011] [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: 08/14/2023] [Revised: 08/27/2023] [Accepted: 08/28/2023] [Indexed: 09/12/2023]
Abstract
Toxicants such as smoke, biofuel, and pollutants constantly challenge our respiratory health, but little is known about the pathophysiological processes involved. In a new report, Lin et al. provide evidence that our bacterial and fungal lung populations orchestrate the interplay between environmental exposure and lung functions, thereby conditioning health outcomes.
Collapse
Affiliation(s)
- Jean-Pierre Gangneux
- Univ Rennes, CHU Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000 Rennes, France; Laboratory of Parasitology and Medical Mycology, European Confederation of Medical Mycology (ECMM) Excellence Center, Centre National de Référence Aspergilloses Chroniques, Rennes Teaching Hospital, F-35000 Rennes, France.
| | - Johanna L Rhodes
- MRC Centre for Global Infectious Disease Analysis, Imperial College School of Public Health, Imperial College London, South Kensington, London SW7 2BX, UK; Department of Medical Microbiology, Radboudumc, Nijmegen, The Netherlands.
| | - Nicolas Papon
- Univ Angers, Univ Brest, IRF, SFR ICAT, F-49000 Angers, France
| |
Collapse
|
13
|
Mongès A, Yaakoub H, Bidon B, Glévarec G, Héricourt F, Carpin S, Chauderon L, Drašarová L, Spíchal L, Binder BM, Papon N, Rochange S. Are Histidine Kinases of Arbuscular Mycorrhizal Fungi Involved in the Response to Ethylene and Cytokinins? Mol Plant Microbe Interact 2023; 36:656-665. [PMID: 37851914 DOI: 10.1094/mpmi-05-23-0056-r] [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] [Subscribe] [Scholar Register] [Indexed: 10/20/2023]
Abstract
Signals are exchanged at all stages of the arbuscular mycorrhizal (AM) symbiosis between fungi and their host plants. Root-exuded strigolactones are well-known early symbiotic cues, but the role of other phytohormones as interkingdom signals has seldom been investigated. Here we focus on ethylene and cytokinins, for which candidate receptors have been identified in the genome of the AM fungus Rhizophagus irregularis. Ethylene is known from the literature to affect asymbiotic development of AM fungi, and in the present study, we found that three cytokinin forms could stimulate spore germination in R. irregularis. Heterologous complementation of a Saccharomyces cerevisiae mutant strain with the candidate ethylene receptor RiHHK6 suggested that this protein can sense and transduce an ethylene signal. Accordingly, its N-terminal domain expressed in Pichia pastoris displayed saturable binding to radiolabeled ethylene. Thus, RiHHK6 displays the expected characteristics of an ethylene receptor. In contrast, the candidate cytokinin receptor RiHHK7 did not complement the S. cerevisiae mutant strain or Medicago truncatula cytokinin receptor mutants and seemed unable to bind cytokinins, suggesting that another receptor is involved in the perception of these phytohormones. Taken together, our results support the hypothesis that AM fungi respond to a range of phytohormones and that these compounds bear multiple functions in the rhizosphere beyond their known roles as internal plant developmental regulators. Our analysis of two phytohormone receptor candidates also sheds new light on the possible perception mechanisms in AM fungi. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
Collapse
Affiliation(s)
- Ayla Mongès
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, Centre National de la Recherche Scientifique, Université Paul Sabatier, INP Toulouse, 31326 Castanet-Tolosan, France
| | - Hajar Yaakoub
- UNIV Angers, IRF, SFR 4208 ICAT, F-49000 Angers, France
| | | | - Gaëlle Glévarec
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, Tours, France
| | - François Héricourt
- Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), Université d'Orléans, INRAE USC1328, 45067 Orléans Cedex 2, France
| | - Sabine Carpin
- Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), Université d'Orléans, INRAE USC1328, 45067 Orléans Cedex 2, France
| | - Lucie Chauderon
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, Centre National de la Recherche Scientifique, Université Paul Sabatier, INP Toulouse, 31326 Castanet-Tolosan, France
| | - Lenka Drašarová
- Isotope Laboratory, Institute of Experimental Botany, The Czech Academy of Sciences, Vídeňská, 1083, Prague, Czech Republic
| | - Lukáš Spíchal
- Czech Advanced Technology and Research Institute, Šlechtitelů 27, Olomouc CZ-783 71, Palacký University, Olomouc, Czech Republic
| | - Brad M Binder
- Department of Biochemistry and Cellular & Molecular Biology, University of Tennessee, Knoxville, TN, U.S.A
| | - Nicolas Papon
- UNIV Angers, IRF, SFR 4208 ICAT, F-49000 Angers, France
| | - Soizic Rochange
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, Centre National de la Recherche Scientifique, Université Paul Sabatier, INP Toulouse, 31326 Castanet-Tolosan, France
| |
Collapse
|
14
|
Zamar DL, Papon N, Courdavault V. The Evolutionary Pattern of Cocaine and Hyoscyamine Biosynthesis Provides Strategies To Produce Tropane Alkaloids. Chembiochem 2023; 24:e202300234. [PMID: 37249120 DOI: 10.1002/cbic.202300234] [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: 03/24/2023] [Revised: 05/25/2023] [Accepted: 05/26/2023] [Indexed: 05/31/2023]
Abstract
Cocaine and hyoscyamine are two tropane alkaloids (TA) from Erythroxylaceae and Solanaceae, respectively. These famous compounds possess anticholinergic properties that can be used to treat neuromuscular disorders. While the hyoscyamine biosynthetic pathway has been fully elucidated allowing its de novo synthesis in yeast, the cocaine pathway remained only partially elucidated. Recently, the Huang research group has completed the cocaine biosynthetic route by characterizing its two missing enzymes. This allowed the whole pathway to be transferring into Nicotiana benthamiana to achieve cocaine production. Here, besides highlighting the impact of this discovery, we discuss how TA biosynthesis evolved via the recruitment of two distinct and convergent pathways in Erythroxylaceae and Solanaceae. Finally, while enriching our knowledge on TA biosynthesis, this diversification of the molecular actors involved in cocaine and hyoscyamine biosynthesis opens perspectives in metabolic engineering by exploring enzyme biochemical plasticity that can ease and shorten TA pathway reconstitution in heterologous organisms.
Collapse
Affiliation(s)
- Duchesse-Lacours Zamar
- Université de Tours, Faculté de Pharmacie, EA2106 Biomolécules et Biotechnologies Végétales, 31, Avenue Monge, 37200, Tours, France
| | - Nicolas Papon
- Université d'Angers, Fungal Respiratory Infections Research Unit, University Hospital of Angers, 4 rue de Larrey, 49933, Angers Cedex 09, France
| | - Vincent Courdavault
- Université de Tours, Faculté de Pharmacie, EA2106 Biomolécules et Biotechnologies Végétales, 31, Avenue Monge, 37200, Tours, France
| |
Collapse
|
15
|
Hassoun N, Kassem II, Hamze M, El Tom J, Papon N, Osman M. Antifungal Use and Resistance in a Lower-Middle-Income Country: The Case of Lebanon. Antibiotics (Basel) 2023; 12:1413. [PMID: 37760710 PMCID: PMC10525119 DOI: 10.3390/antibiotics12091413] [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: 08/19/2023] [Revised: 08/31/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023] Open
Abstract
Antimicrobial resistance is a serious threat, particularly in low- and middle-income countries (LMICs). Antifungal resistance is often underestimated in both healthcare and non-clinical settings. In LMICs, it is believed that the inappropriate use of antifungals, limited surveillance systems, and low diagnostic capacities are significant drivers of resistance. Like other LMICs, Lebanon lacks antifungal use and resistance surveillance programs, and the impact of antifungal resistance in the country remains unclear, especially during the unfolding economic crisis that has severely affected medical care and access to safe food and water. Interestingly, the widespread use of antifungals in medicine and agriculture has raised concerns about the development of antifungal resistance in Lebanon. In this light, we aimed to survey available antifungal drugs in the country and evaluate susceptibility patterns of prevalent fungal species to guide empiric treatments and develop antifungal stewardship programs in Lebanon. We noted that the economic crisis resulted in significant increases in antifungal drug prices. Additionally, a comprehensive literature search across PubMed, ScienceDirect, and Google Scholar databases identified 15 studies on fungal infections and antifungal resistance conducted from 1998 to 2023 in Lebanon. While data on antifungal resistance are limited, 87% of available studies in Lebanon focused on candidiasis, while the remaining 13% were on aspergillosis. Overall, we observed a marked antimicrobial resistance among Candida and Aspergillus species. Additionally, incidences of Candida auris infections have increased in Lebanese hospitals during the COVID-19 pandemic, with a uniform resistance to fluconazole and amphotericin-B. Taken together, a One Health approach, reliable diagnostics, and prudent antifungal use are required to control the spread of resistant fungal pathogens in healthcare and agricultural settings.
Collapse
Affiliation(s)
- Nesrine Hassoun
- Faculty of Public Health, Lebanese University, Tripoli 1300, Lebanon;
| | - Issmat I. Kassem
- Center for Food Safety, Department of Food Science and Technology, University of Georgia, 1109 Experiment Street, Griffin, GA 30223, USA;
| | - Monzer Hamze
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli 1300, Lebanon;
| | - Jad El Tom
- School of Pharmacy, Lebanese American University, Byblos 1401, Lebanon;
| | - Nicolas Papon
- University of Angers, University of Brest, IRF, SFR ICAT, F-49000 Angers, France;
| | - Marwan Osman
- Cornell Atkinson Center for Sustainability, Cornell University, Ithaca, NY 14853, USA
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| |
Collapse
|
16
|
Perrot T, Besseau S, Papon N, Courdavault V. Gaining access to acetyl-CoA by peroxisomal surface display. Synth Syst Biotechnol 2023; 8:224-226. [PMID: 36936387 PMCID: PMC10020669 DOI: 10.1016/j.synbio.2023.02.003] [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: 12/14/2022] [Revised: 01/27/2023] [Accepted: 02/15/2023] [Indexed: 03/08/2023] Open
Abstract
Synthetic biology is constantly making progress for producing compounds on demand. Recently, Yocum and collaborators have developed an outstanding approach based on the anchoring of biosynthetic enzymes to the peroxisomal membrane. This allowed access to an untapped resource of acetyl-CoA and stimulated the synthesis of a valuable polyketide.
Collapse
Affiliation(s)
- Thomas Perrot
- Biomolécules et Biotechnologies Végétales, BBV, EA2106, Université de Tours, Tours, France
| | - Sébastien Besseau
- Biomolécules et Biotechnologies Végétales, BBV, EA2106, Université de Tours, Tours, France
| | - Nicolas Papon
- Univ Angers, Univ Brest, IRF, SFR ICAT, F-49000, Angers, France
| | - Vincent Courdavault
- Biomolécules et Biotechnologies Végétales, BBV, EA2106, Université de Tours, Tours, France
- Corresponding author.
| |
Collapse
|
17
|
Papon N, Courdavault V, Medema MH. Convergent evolution for antibiotic biosynthesis in bacteria and animals. Trends Genet 2023; 39:237-239. [PMID: 36822964 DOI: 10.1016/j.tig.2023.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 02/10/2023] [Indexed: 02/25/2023]
Abstract
Convergent evolution has been described for several metabolic pathways across the kingdoms of life. However, there is hitherto no evidence for such an interkingdom process for antimicrobials. A new report suggests that marine animals have evolved the ability to biosynthesize antimicrobial polyketides, in parallel with bacteria.
Collapse
Affiliation(s)
- Nicolas Papon
- Univ Angers, Univ Brest, IRF, SFR ICAT, F-49000 Angers, France.
| | - Vincent Courdavault
- Biomolécules et Biotechnologies Végétales, BBV, EA2106, Université de Tours, Tours, France.
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708, PB, Wageningen, The Netherlands; Institute of Biology, Leiden University, Sylviusweg 72, 2333BE Leiden, The Netherlands.
| |
Collapse
|
18
|
Gangneux JP, Hoenigl M, Papon N. How to lose resistance to Aspergillus infections. Trends Microbiol 2023; 31:222-224. [PMID: 36754763 DOI: 10.1016/j.tim.2023.01.008] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 01/24/2023] [Accepted: 01/24/2023] [Indexed: 02/08/2023]
Abstract
The distinct risk factors to deadly infections by Aspergillus fumigatus (Af) in intensive care unit (ICU) patients are well known; however, so far, the mechanistic link between these predisposing conditions has been unknown. Sarden et al. recently unraveled a shared B1a lymphocyte-natural antibody-neutrophil defense pathway to Af, opening new perspectives in diagnostics and therapeutics.
Collapse
Affiliation(s)
- Jean-Pierre Gangneux
- Univ Rennes, CHU Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail)-UMR_S 1085, F-35000 Rennes, France; Laboratoire de Parasitologie et Mycologie Médicale, LA-AspC Centre National de Référence des Mycoses et Antifongiques, European Excellence Center for Medical Mycology (ECMM), Centre hospitalier Universitaire de Rennes, F-35000 Rennes, France.
| | - Martin Hoenigl
- Division of Infectious Diseases, Department of Internal Medicine, Medical University of Graz, Graz, Austria; BioTechMed-Graz, Graz, Austria; Translational Medical Mycology Research Unit, European Confederation of Medical Mycology (ECMM) Excellence Center, Medical University of Graz, Graz, Austria
| | - Nicolas Papon
- Univ Angers, Univ Brest, IRF, SFR ICAT, F-49000 Angers, France
| |
Collapse
|
19
|
Lemos Cruz P, Carqueijeiro I, Koudounas K, Bomzan DP, Stander EA, Abdallah C, Kulagina N, Oudin A, Lanoue A, Giglioli-Guivarc'h N, Nagegowda DA, Papon N, Besseau S, Clastre M, Courdavault V. Identification of a second 16-hydroxytabersonine-O-methyltransferase suggests an evolutionary relationship between alkaloid and flavonoid metabolisms in Catharanthus roseus. Protoplasma 2023; 260:607-624. [PMID: 35947213 DOI: 10.1007/s00709-022-01801-x] [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] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 07/26/2022] [Indexed: 06/15/2023]
Abstract
The medicinal plant Catharanthus roseus biosynthesizes many important drugs for human health, including the anticancer monoterpene indole alkaloids (MIAs) vinblastine and vincristine. Over the past decades, the continuous increase in pharmaceutical demand has prompted several research groups to characterize MIA biosynthetic pathways for considering future metabolic engineering processes of supply. In line with previous work suggesting that diversification can potentially occur at various steps along the vindoline branch, we were here interested in investigating the involvement of distinct isoforms of tabersonine-16-O-methyltransferase (16OMT) which plays a pivotal role in the MIA biosynthetic pathway. By combining homology searches based on the previously characterized 16OMT1, phylogenetic analyses, functional assays in yeast, and biochemical and in planta characterizations, we identified a second isoform of 16OMT, referred to as 16OMT2. 16OMT2 appears to be a multifunctional enzyme working on both MIA and flavonoid substrates, suggesting that a constrained evolution of the enzyme for accommodating the MIA substrate has probably occurred to favor the apparition of 16OMT2 from an ancestral specific flavonoid-O-methyltransferase. Since 16OMT1 and 16OMT2 displays a high sequence identity and similar kinetic parameters for 16-hydroxytabersonine, we postulate that 16OMT1 may result from a later 16OMT2 gene duplication accompanied by a continuous neofunctionalization leading to an almost complete loss of flavonoid O-methyltransferase activity. Overall, these results participate in increasing our knowledge on the evolutionary processes that have likely led to enzyme co-optation for MIA synthesis.
Collapse
Affiliation(s)
- Pamela Lemos Cruz
- Université de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", Tours, France
| | - Ines Carqueijeiro
- Université de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", Tours, France
| | | | - Dikki Pedenla Bomzan
- Molecular Plant Biology and Biotechnology Lab, CSIR-Central Institute of Medicinal and Aromatic Plants, Research Centre, Bengaluru, 560065, India
| | - Emily Amor Stander
- Université de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", Tours, France
| | - Cécile Abdallah
- Université de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", Tours, France
| | - Natalja Kulagina
- Université de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", Tours, France
| | - Audrey Oudin
- Université de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", Tours, France
| | - Arnaud Lanoue
- Université de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", Tours, France
| | | | - Dinesh A Nagegowda
- Molecular Plant Biology and Biotechnology Lab, CSIR-Central Institute of Medicinal and Aromatic Plants, Research Centre, Bengaluru, 560065, India
| | - Nicolas Papon
- Univ Angers, Univ Brest, IRF, SFR, ICAT, F-49000, Angers, France
| | - Sébastien Besseau
- Université de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", Tours, France
| | - Marc Clastre
- Université de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", Tours, France
| | - Vincent Courdavault
- Université de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", Tours, France.
| |
Collapse
|
20
|
Peri KVR, Faria-Oliveira F, Larsson A, Plovie A, Papon N, Geijer C. Split-marker-mediated genome editing improves homologous recombination frequency in the CTG clade yeast Candida intermedia. FEMS Yeast Res 2023; 23:7074557. [PMID: 36893808 PMCID: PMC10035504 DOI: 10.1093/femsyr/foad016] [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: 11/23/2022] [Revised: 02/02/2023] [Accepted: 03/08/2023] [Indexed: 03/11/2023] Open
Abstract
Genome-editing toolboxes are essential for the exploration and exploitation of nonconventional yeast species as cell factories, as they facilitate both genome studies and metabolic engineering. The nonconventional yeast Candida intermedia is a biotechnologically interesting species due to its capacity to convert a wide range of carbon sources, including xylose and lactose found in forestry and dairy industry waste and side-streams, into added-value products. However, possibilities of genetic manipulation have so far been limited due to lack of molecular tools for this species. We describe here the development of a genome editing method for C. intermedia, based on electroporation and gene deletion cassettes containing the Candida albicans NAT1 dominant selection marker flanked by 1000 base pair sequences homologous to the target loci. Linear deletion cassettes targeting the ADE2 gene originally resulted in <1% targeting efficiencies, suggesting that C. intermedia mainly uses nonhomologous end joining for integration of foreign DNA fragments. By developing a split-marker based deletion technique for C. intermedia, we successfully improved the homologous recombination rates, achieving targeting efficiencies up to 70%. For marker-less deletions, we also employed the split-marker cassette in combination with a recombinase system, which enabled the construction of double deletion mutants via marker recycling. Overall, the split-marker technique proved to be a quick and reliable method for generating gene deletions in C. intermedia, which opens the possibility to uncover and enhance its cell factory potential.
Collapse
Affiliation(s)
- Kameshwara V R Peri
- Chalmers University of Technology, Department of Life Sciences, Division of Industrial Biotechnology, Kemigården 1, 41296 Gothenburg, Sweden
| | - Fábio Faria-Oliveira
- Chalmers University of Technology, Department of Life Sciences, Division of Industrial Biotechnology, Kemigården 1, 41296 Gothenburg, Sweden
| | - Adam Larsson
- Chalmers University of Technology, Department of Life Sciences, Division of Industrial Biotechnology, Kemigården 1, 41296 Gothenburg, Sweden
| | - Alexander Plovie
- Chalmers University of Technology, Department of Life Sciences, Division of Industrial Biotechnology, Kemigården 1, 41296 Gothenburg, Sweden
| | - Nicolas Papon
- University of Angers, Univ Brest, IRF, SFR ICAT, F-49000 Angers, France
| | - Cecilia Geijer
- Chalmers University of Technology, Department of Life Sciences, Division of Industrial Biotechnology, Kemigården 1, 41296 Gothenburg, Sweden
| |
Collapse
|
21
|
Méteignier LV, Nützmann HW, Papon N, Osbourn A, Courdavault V. Emerging mechanistic insights into the regulation of specialized metabolism in plants. Nat Plants 2023; 9:22-30. [PMID: 36564633 DOI: 10.1038/s41477-022-01288-7] [Citation(s) in RCA: 6] [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] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 10/25/2022] [Indexed: 06/17/2023]
Abstract
Plants biosynthesize a broad range of natural products through specialized and species-specific metabolic pathways that are fuelled by core metabolism, together forming a metabolic network. Specialized metabolites have important roles in development and adaptation to external cues, and they also have invaluable pharmacological properties. A growing body of evidence has highlighted the impact of translational, transcriptional, epigenetic and chromatin-based regulation and evolution of specialized metabolism genes and metabolic networks. Here we review the forefront of this research field and extrapolate to medicinal plants that synthetize rare molecules. We also discuss how this new knowledge could help in improving strategies to produce useful plant-derived pharmaceuticals.
Collapse
Affiliation(s)
| | - Hans-Wilhelm Nützmann
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Nicolas Papon
- IRF, SFR ICAT, Université Angers and Université de Bretagne-Occidentale, Angers, France
| | - Anne Osbourn
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich, UK.
| | - Vincent Courdavault
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, Tours, France.
| |
Collapse
|
22
|
Cuello C, Stander EA, Jansen HJ, Dugé De Bernonville T, Oudin A, Birer Williams C, Lanoue A, Giglioli Guivarc'h N, Papon N, Dirks RP, Jensen MK, O'Connor SE, Besseau S, Courdavault V. An updated version of the Madagascar periwinkle genome. F1000Res 2022; 11:1541. [PMID: 36761838 PMCID: PMC9902796 DOI: 10.12688/f1000research.129212.1] [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] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/13/2022] [Indexed: 12/24/2022] Open
Abstract
The Madagascar periwinkle, Catharanthus roseus, belongs to the Apocynaceae family. This medicinal plant, endemic to Madagascar, produces many important drugs including the monoterpene indole alkaloids (MIA) vincristine and vinblastine used to treat cancer worldwide. Here, we provide a new version of the C. roseus genome sequence obtained through the combination of Oxford Nanopore Technologies long-reads and Illumina short-reads. This more contiguous assembly consists of 173 scaffolds with a total length of 581.128 Mb and an N50 of 12.241 Mb. Using publicly available RNAseq data, 21,061 protein coding genes were predicted and functionally annotated. A total of 42.87% of the genome was annotated as transposable elements, most of them being long-terminal repeats. Together with the increasing access to MIA-producing plant genomes, this updated version should ease evolutionary studies leading to a better understanding of MIA biosynthetic pathway evolution.
Collapse
Affiliation(s)
- Clément Cuello
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, Tours, 37200, France
| | - Emily Amor Stander
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, Tours, 37200, France
| | - Hans J. Jansen
- Future Genomics Technologies, Leiden, 2333BE, The Netherlands
| | - Thomas Dugé De Bernonville
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, Tours, 37200, France,Present address: Centre de Recherche, Limagrain, Chappes, 07745, France
| | - Audrey Oudin
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, Tours, 37200, France
| | | | - Arnaud Lanoue
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, Tours, 37200, France
| | | | - Nicolas Papon
- IRF, SFR ICAT, Univ Angers, Univ Brest, Angers, 49000, France
| | - Ron P. Dirks
- Future Genomics Technologies, Leiden, 2333BE, The Netherlands
| | - Michael Krogh Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, 2800, Denmark
| | - Sarah Ellen O'Connor
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, 07745, Germany
| | - Sébastien Besseau
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, Tours, 37200, France
| | - Vincent Courdavault
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, Tours, 37200, France,
| |
Collapse
|
23
|
Perrin J, Besseau S, Papon N, Courdavault V. Boosting lignan-precursor synthesis in yeast cell factories through co-factor supply optimization. Front Bioeng Biotechnol 2022; 10:1079801. [DOI: 10.3389/fbioe.2022.1079801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 11/21/2022] [Indexed: 12/05/2022] Open
|
24
|
Stander EA, Cuello C, Birer-Williams C, Kulagina N, Jansen HJ, Carqueijeiro I, Méteignier LV, Vergès V, Oudin A, Papon N, Dirks RP, Jensen MK, O’Connor SE, Dugé de Bernonville T, Besseau S, Courdavault V. The Vinca minor genome highlights conserved evolutionary traits in monoterpene indole alkaloid synthesis. G3 (Bethesda) 2022; 12:jkac268. [PMID: 36200869 PMCID: PMC9713385 DOI: 10.1093/g3journal/jkac268] [Citation(s) in RCA: 4] [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] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 09/28/2022] [Indexed: 11/26/2023]
Abstract
Vinca minor, also known as the lesser periwinkle, is a well-known species from the Apocynaceae, native to central and southern Europe. This plant synthesizes monoterpene indole alkaloids, which are a class of specialized metabolites displaying a wide range of bioactive- and pharmacologically important properties. Within the almost 50 monoterpene indole alkaloids it produces, V. minor mainly accumulates vincamine, which is commercially used as a nootropic. Using a combination of Oxford Nanopore Technologies long read- and Illumina short-read sequencing, a 679,098 Mb V. minor genome was assembled into 296 scaffolds with an N50 scaffold length of 6 Mb, and encoding 29,624 genes. These genes were functionally annotated and used in a comparative genomic analysis to establish gene families and to investigate gene family expansion and contraction across the phylogenetic tree. Furthermore, homology-based monoterpene indole alkaloid gene predictions together with a metabolic analysis across 4 different V. minor tissue types guided the identification of candidate monoterpene indole alkaloid genes. These candidates were finally used to identify monoterpene indole alkaloid gene clusters, which combined with synteny analysis allowed for the discovery of a functionally validated vincadifformine-16-hydroxylase, reinforcing the potential of this dataset for monoterpene indole alkaloids gene discovery. It is expected that access to these resources will facilitate the elucidation of unknown monoterpene indole alkaloid biosynthetic routes with the potential of transferring these pathways to heterologous expression systems for large-scale monoterpene indole alkaloid production.
Collapse
Affiliation(s)
- Emily Amor Stander
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200 Tours, France
| | - Clément Cuello
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200 Tours, France
| | | | - Natalja Kulagina
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200 Tours, France
| | - Hans J Jansen
- Future Genomics Technologies, 2333 BE Leiden, The Netherlands
| | - Ines Carqueijeiro
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200 Tours, France
| | | | - Valentin Vergès
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200 Tours, France
| | - Audrey Oudin
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200 Tours, France
| | - Nicolas Papon
- Univ Angers, Univ Brest, IRF, SFR ICAT, F-49000 Angers, France
| | - Ron P Dirks
- Future Genomics Technologies, 2333 BE Leiden, The Netherlands
| | - Michael Krogh Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Sarah Ellen O’Connor
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena 07745, Germany
| | | | - Sébastien Besseau
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200 Tours, France
| | - Vincent Courdavault
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200 Tours, France
| |
Collapse
|
25
|
Cuello C, Stander EA, Jansen HJ, Dugé de Bernonville T, Lanoue A, Giglioli-Guivarc'h N, Papon N, Dirks RP, Jensen MK, O'Connor SE, Besseau S, Courdavault V. Genome Assembly of the Medicinal Plant Voacanga thouarsii. Genome Biol Evol 2022; 14:evac158. [PMID: 36300641 PMCID: PMC9673491 DOI: 10.1093/gbe/evac158] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/22/2022] [Indexed: 11/26/2023] Open
Abstract
The Apocynaceae tree Voacanga thouarsii, native to southern Africa and Madagascar, produces monoterpene indole alkaloids (MIA), which are specialized metabolites with a wide range of bioactive properties. Voacanga species mainly accumulates tabersonine in seeds making these species valuable medicinal plants currently used for industrial MIA production. Despite their importance, the MIA biosynthesis in Voacanga species remains poorly studied. Here, we report the first genome assembly and annotation of a Voacanga species. The combined assembly of Oxford Nanopore Technologies long-reads and Illumina short-reads resulted in 3,406 scaffolds with a total length of 1,354.26 Mb and an N50 of 3.04 Mb. A total of 33,300 protein-coding genes were predicted and functionally annotated. These genes were then used to establish gene families and to investigate gene family expansion and contraction across the phylogenetic tree. A transposable element (TE) analysis showed the highest proportion of TE in Voacanga thouarsii compared with all other MIA-producing plants. In a nutshell, this first reference genome of V. thouarsii will thus contribute to strengthen future comparative and evolutionary studies in MIA-producing plants leading to a better understanding of MIA pathway evolution. This will also allow the potential identification of new MIA biosynthetic genes for metabolic engineering purposes.
Collapse
Affiliation(s)
- Clément Cuello
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200 Tours, France
| | - Emily Amor Stander
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200 Tours, France
| | - Hans J Jansen
- Future Genomics Technologies, 2333 BE Leiden, The Netherlands
| | | | - Arnaud Lanoue
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200 Tours, France
| | | | - Nicolas Papon
- Univ Angers, Univ Brest, IRF, SFR ICAT, F-49000 Angers, France
| | - Ron P Dirks
- Future Genomics Technologies, 2333 BE Leiden, The Netherlands
| | - Michael Krogh Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Sarah Ellen O'Connor
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena 07745, Germany
| | - Sébastien Besseau
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200 Tours, France
| | - Vincent Courdavault
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200 Tours, France
| |
Collapse
|
26
|
Le Pogam P, Papon N, Beniddir MA, Courdavault V. Computer-Assisted Design of Sustainable Syntheses of Pharmaceuticals and Agrochemicals from Industrial Wastes. ChemSusChem 2022; 15:e202201125. [PMID: 35894947 DOI: 10.1002/cssc.202201125] [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] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/24/2022] [Indexed: 06/15/2023]
Abstract
Computer-based strategies vastly enhanced the field of analytical chemistry. The impact of data-driven technologies in shaping organic chemistry strategies long remained comparatively elusive but various tools recently emerged to computationally plan multistep organic syntheses. A recent study elegantly takes benefit of an in-house library of chemical reactions enriched with various metadata to provide numerous, reliable and realistic organic chemistry workflows to structurally-varied drugs of interest, from locally available industrial by-products. The retrieval of the different synthetic pathways and a scoring based on different features, especially comprising sustainability considerations, are also proposed.
Collapse
Affiliation(s)
- Pierre Le Pogam
- Équipe Chimie des Substances Naturelles, BioCIS, Université Paris-Saclay, CNRS, 92290, Châtenay-Malabry, France
| | - Nicolas Papon
- Univ Angers, Univ Brest, IRF, SFR ICAT, F-49000, Angers, France
| | - Mehdi A Beniddir
- Équipe Chimie des Substances Naturelles, BioCIS, Université Paris-Saclay, CNRS, 92290, Châtenay-Malabry, France
| | - Vincent Courdavault
- Biomolécules et Biotechnologies Végétales, BBV, EA2106, Université de Tours, 37200, Tours, France
| |
Collapse
|
27
|
Papon N, Govic YL, Havlíček V, Capilla J, Luptáková D, Dumas D, Gal SL, Nevez G, Vandeputte P, Bouchara JP. S10.5c Insight into the role of secondary metabolism in the pathogenesis of Scedosporium apiospermum. Med Mycol 2022. [PMCID: PMC9554670 DOI: 10.1093/mmy/myac072.s10.5c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
S10.5 Fungal respiratory infections in Cystic Fibrosis, September 24, 2022, 10:30 AM - 12:00 PM Secondary metabolism is a general term defining biosynthetic pathways that occur in plants, bacteria, and fungi and lead to the production of highly diversified molecular structures. Among the diverse functions that were attributed to these molecules, it is now obvious that they are predominantly involved in chemical warfare with competitors in their environments. In fungi, the two main classes of fungal secondary metabolites are polyketides (PKs) and nonribosomal peptides (NRPs). The biosynthesis of such bioactive molecules is performed by large multifunctional enzymes (NRP synthases, NRPS, and polyketide synthases, PKS) encoded by genes usually located within clusters. Conversely to Aspergillus fumigatus, only a few data are currently available for other pathogenic fungi. In this context, our research group is interested in delineating the role of secondary metabolism in Scedosporium apiospermum, a multi-resistant mold known to colonize chronically the airways of patients with cystic fibrosis (CF). Taking advantage of the availability of the S. apiospermum genome sequence, we first conducted an in silico analysis aiming at exploring the PKs and NRPs battery of the fungus. A total of 9 genes encoding PKs, 9 encoding NRPs, and 5 encoding hybrid NRPs/PKs enzymes were identified. All 3 of the PKs gene clusters presented homologies with those involved in the biosynthesis of pseurotin A. transbergamotene, and ovalicin, or the tremorgenic toxin b-aflatrem while a fourth one is involved in the biosynthesis of melanin. Among the NRPs encoding genes, 6 exhibited sufficient similarity scores with other fungal NRPs to predict the class of the generated peptide: siderophores (2), epidithiodioxopiperazines (2), and cyclopeptides (2). Nevertheless, substrate prediction methods for NRPs domains failed, thus questioning about the nature of the produced peptides. We thus focused our attention on the characterization of some NRP and PK biosynthetic pathways. Since iron acquisition is known to be crucial for the survival of microorganisms as for the virulence of numerous pathogens, we first investigated clusters predicted to be responsible for the biosynthesis of siderophores in S. apiospermum. For instance, we disrupted the SAPIO_CDS2806 gene, an ortholog of sidD which drives the production of the extracellular hydroxamate-type siderophore fusarinin C in Aspergillus fumigatus. A comparison of culture supernatants from sidD mutants and their parent strain revealed that S. apiospermum secretes a unique extracellular siderophore, namely Nα‐methylcoprogen B and that sidD gene was essential for the biosynthesis of this siderophore. sidD mutation resulted in the lack of growth under iron limiting conditions. Interestingly, pyoverdine supported the growth of the parent strain only, suggesting that Nα‐methylcoprogen B is required for iron acquisition from this Pseudomonas aeruginosa siderophore. Finally, the deletion of sidD resulted in the loss of virulence in a murine model of scedosporiosis. Altogether, our results demonstrate that S. apiospermum sidD gene drives the synthesis of a unique extracellular siderophore, namely Nα‐methylcoprogen B, which is essential for fungal growth and virulence. Above all, we also provide unprecedented data suggesting that this fungal siderophore scavenges iron from pyoverdine, which might explain the antagonism between S. apiospermum and P. aeruginosa in CF.
Collapse
Affiliation(s)
- Nicolas Papon
- ‘Fungal Respiratory Infections’ Research Unit , University of Angers, Angers , France
| | - Yohann Le Govic
- ‘Infectious Agents , Resistance and Chemotherapy’, UR 4294, University of Picardy Jules Verne, Amiens , France
- Parasitology-Mycology Department , Center for Human Biology, University Hospital of Amiens, Amiens , France
| | - Vladimir Havlíček
- Institute of Microbiology of the Czech Academy of Sciences , Prague , Czech Republic
| | - Javier Capilla
- Unitat de Microbiologia , Facultat de Medicina i Ciències de la Salut, Universitat Rovira i Virgili and Institut d'Investigació Sanitària Pere Virgili, Reus, Tarragona , Spain
| | - Dominika Luptáková
- Institute of Microbiology of the Czech Academy of Sciences , Prague , Czech Republic
| | - Dayana Dumas
- Unitat de Microbiologia , Facultat de Medicina i Ciències de la Salut, Universitat Rovira i Virgili and Institut d'Investigació Sanitària Pere Virgili, Reus, Tarragona , Spain
| | - Solène Le Gal
- ‘Fungal Respiratory Infections’ Research Unit , University of Angers, Angers , France
- Parasitology-Mycology Department , University Hospital of Brest, Brest , France
| | - Gilles Nevez
- ‘Fungal Respiratory Infections’ Research Unit , University of Angers, Angers , France
- Parasitology-Mycology Department , University Hospital of Brest, Brest , France
| | - Patrick Vandeputte
- ‘Fungal Respiratory Infections’ Research Unit , University of Angers, Angers , France
| | - J-P Bouchara
- ‘Fungal Respiratory Infections’ Research Unit , University of Angers, Angers , France
| |
Collapse
|
28
|
Mina S, Yaakoub H, Annweiler C, Dubée V, Papon N. COVID-19 and Fungal Infections: A Double Debacle. Microbes Infect 2022; 24:105039. [PMID: 36030024 PMCID: PMC9400371 DOI: 10.1016/j.micinf.2022.105039] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [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: 03/17/2022] [Revised: 08/08/2022] [Accepted: 08/09/2022] [Indexed: 12/15/2022]
Abstract
Fungal infections remain hardly treatable because of unstandardized diagnostic tests, limited antifungal armamentarium, and more specifically, potential toxic interactions between antifungals and immunosuppressants used during anti-inflammatory therapies, such as those set up in critically ill COVID-19 patients. Taking into account pre-existing difficulties in treating vulnerable COVID-19 patients, any co-occurrence of infectious diseases like fungal infections constitutes a double debacle for patients, healthcare experts, and the public economy. Since the first appearance of SARS-CoV-2, a significant rise in threatening fungal co-infections in COVID-19 patients has been testified in the scientific literature. Better management of fungal infections in COVID-19 patients is, therefore, a priority and requires highlighting common risk factors, relationships with immunosuppression, as well as challenges in fungal diagnosis and treatment. The present review attempts to highlight these aspects in the three most identified causative agents of fungal co-infections in COVID-19 patients: Aspergillus, Candida, and Mucorales species.
Collapse
Affiliation(s)
- Sara Mina
- Department of Medical Laboratory Sciences, Faculty of Health Sciences, Beirut Arab University, Beirut, Lebanon.
| | - Hajar Yaakoub
- Univ Angers, Univ Brest, IRF, SFR ICAT, F-49000, Angers, France
| | - Cédric Annweiler
- Department of Geriatric Medicine and Memory Clinic, Research Center on Autonomy and Longevity, University Hospital of Angers, Angers, France; Univ Angers, Université de Nantes, LPPL, SFR CONFLUENCES, F-49000 Angers, France
| | - Vincent Dubée
- Univ Angers, Université de Nantes, Inserm, CRCINA, INCIT, SFR ICAT, F-49000 Angers, France; Infectious Diseases Department, Angers University Hospital, Angers, France
| | - Nicolas Papon
- Univ Angers, Univ Brest, IRF, SFR ICAT, F-49000, Angers, France.
| |
Collapse
|
29
|
Courdavault V, Papon N. A new path for terpenoid biosynthesis. Trends Biochem Sci 2022; 47:906-908. [DOI: 10.1016/j.tibs.2022.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 07/17/2022] [Accepted: 07/19/2022] [Indexed: 10/31/2022]
|
30
|
Brassart PL, Thomas OP, Courdavault V, Papon N. Towards a Better Understanding of Toxin Biosynthesis in Seaweeds. Chembiochem 2022; 23:e202200223. [PMID: 35666802 DOI: 10.1002/cbic.202200223] [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: 04/19/2022] [Revised: 06/02/2022] [Indexed: 11/06/2022]
Abstract
Harmful algal blooms (HABs) represent both ecological and public health hazards in the marine environment. Indeed, some algae can produce metabolites that have negative effects on marine ecosystems and mammals. Kainoid derivatives such as kainic acid (KA) and domoic acid (DA) are considered some of the most toxic metabolites of marine origin biosynthesized by a limited number of micro- and macroalgae. While recent works have provided the first insights into the biosynthetic route of KA in red algae and DA in diatoms, the DA biosynthetic pathway has remained uncharacterized for red algae. In a recent work, the research groups of Chekan and Moore have not only elucidated the biosynthetic pathway of DA in the red alga Chondria armata but also shed light on its complex evolution among marine species. We discuss here the importance of pursuing active research in this area to gain insights into secondary biosynthetic pathways in marine organisms for diagnostic and metabolic engineering perspectives.
Collapse
Affiliation(s)
| | - Olivier P Thomas
- School of the Biological and Chemical Sciences, Ryan Institute, National University of Ireland Galway, H91TK33, Galway, Republic of Ireland
| | - Vincent Courdavault
- Biomolécules et Biotechnologies Végétales, BBV, EA2106, Université de Tours, Tours, France
| | - Nicolas Papon
- Univ Angers, Univ Brest, IRF, SFR ICAT, 49000, Angers, France
| |
Collapse
|
31
|
Kulagina N, Méteignier LV, Papon N, O'Connor SE, Courdavault V. More than a Catharanthus plant: A multicellular and pluri-organelle alkaloid-producing factory. Curr Opin Plant Biol 2022; 67:102200. [PMID: 35339956 DOI: 10.1016/j.pbi.2022.102200] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 02/14/2022] [Accepted: 02/20/2022] [Indexed: 06/14/2023]
Abstract
Plants represent a huge reservoir of natural products. A broad series of these compounds now find application for human health. In this respect, the monoterpene indole alkaloids (MIAs), particularly from Madagascar periwinkle, are a prominent example of plant specialized metabolites with an important therapeutic potential. However, the supply of MIA drugs has always been a challenge since the low-yield accumulation in planta. This mainly results from the complex architecture of the MIA biosynthetic pathway that involves several organs, tissue types and subcellular organelles. Here, we describe the most recent advances towards the elucidation of this pathway route as well as its spatial organization in planta. Besides allowing a better understanding of the MIA biosynthetic flux in the whole plant, such knowledge will also probably pave the way for the development of metabolic engineering strategies to sustain the MIA supply.
Collapse
Affiliation(s)
- Natalja Kulagina
- Université de Tours, EA2106 Biomolécules et Biotechnologies Végétales, Tours, France
| | | | - Nicolas Papon
- Univ Angers, Univ Brest, IRF, SFR ICAT, F-49000 Angers, France
| | - Sarah Ellen O'Connor
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena 07745, Germany.
| | - Vincent Courdavault
- Université de Tours, EA2106 Biomolécules et Biotechnologies Végétales, Tours, France.
| |
Collapse
|
32
|
Yaakoub H, Mina S, Calenda A, Bouchara JP, Papon N. Oxidative stress response pathways in fungi. Cell Mol Life Sci 2022; 79:333. [PMID: 35648225 PMCID: PMC11071803 DOI: 10.1007/s00018-022-04353-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [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: 02/09/2022] [Revised: 04/21/2022] [Accepted: 05/05/2022] [Indexed: 11/03/2022]
Abstract
Fungal response to any stress is intricate, specific, and multilayered, though it employs only a few evolutionarily conserved regulators. This comes with the assumption that one regulator operates more than one stress-specific response. Although the assumption holds true, the current understanding of molecular mechanisms that drive response specificity and adequacy remains rudimentary. Deciphering the response of fungi to oxidative stress may help fill those knowledge gaps since it is one of the most encountered stress types in any kind of fungal niche. Data have been accumulating on the roles of the HOG pathway and Yap1- and Skn7-related pathways in mounting distinct and robust responses in fungi upon exposure to oxidative stress. Herein, we review recent and most relevant studies reporting the contribution of each of these pathways in response to oxidative stress in pathogenic and opportunistic fungi after giving a paralleled overview in two divergent models, the budding and fission yeasts. With the concept of stress-specific response and the importance of reactive oxygen species in fungal development, we first present a preface on the expanding domain of redox biology and oxidative stress.
Collapse
Affiliation(s)
- Hajar Yaakoub
- Univ Angers, Univ Brest, IRF, SFR ICAT, 49000, Angers, France
| | - Sara Mina
- Department of Medical Laboratory Sciences, Faculty of Health Sciences, Beirut Arab University, Beirut, Lebanon
| | | | | | - Nicolas Papon
- Univ Angers, Univ Brest, IRF, SFR ICAT, 49000, Angers, France.
| |
Collapse
|
33
|
Affiliation(s)
- Yohann Le Govic
- Infectious Agents, Resistance and Chemotherapy (AGIR), University of Picardy Jules Verne, Amiens, France
- Parasitology-Mycology Department, Center for Human Biology, University Hospital of Amiens-Picardie, Amiens, France
| | - Baptiste Demey
- Infectious Agents, Resistance and Chemotherapy (AGIR), University of Picardy Jules Verne, Amiens, France
- Virology Department, Center for Human Biology, University Hospital of Amiens-Picardie, Amiens, France
| | - Julien Cassereau
- Department of Neurology, Angers University Hospital, Angers, France
- Univ Angers, Inserm, CNRS, MITOVASC, SFR ICAT, Angers, France
| | - Yong-Sun Bahn
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
- * E-mail: (Y-SB); (NP)
| | - Nicolas Papon
- Univ Angers, Univ Brest, IRF, SFR ICAT, Angers, France
- * E-mail: (Y-SB); (NP)
| |
Collapse
|
34
|
Koudounas K, Guirimand G, Hoyos LFR, Carqueijeiro I, Cruz PL, Stander E, Kulagina N, Perrin J, Oudin A, Besseau S, Lanoue A, Atehortùa L, St-Pierre B, Giglioli-Guivarc'h N, Papon N, O'Connor SE, Courdavault V. Tonoplast and Peroxisome Targeting of γ-tocopherol N-methyltransferase Homologs Involved in the Synthesis of Monoterpene Indole Alkaloids. Plant Cell Physiol 2022; 63:200-216. [PMID: 35166361 DOI: 10.1093/pcp/pcab160] [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] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 10/08/2021] [Accepted: 11/02/2021] [Indexed: 06/14/2023]
Abstract
Many plant species from the Apocynaceae, Loganiaceae and Rubiaceae families evolved a specialized metabolism leading to the synthesis of a broad palette of monoterpene indole alkaloids (MIAs). These compounds are believed to constitute a cornerstone of the plant chemical arsenal but above all several MIAs display pharmacological properties that have been exploited for decades by humans to treat various diseases. It is established that MIAs are produced in planta due to complex biosynthetic pathways engaging a multitude of specialized enzymes but also a complex tissue and subcellular organization. In this context, N-methyltransferases (NMTs) represent an important family of enzymes indispensable for MIA biosynthesis but their characterization has always remained challenging. In particular, little is known about the subcellular localization of NMTs in MIA-producing plants. Here, we performed an extensive analysis on the subcellular localization of NMTs from four distinct medicinal plants but also experimentally validated that two putative NMTs from Catharanthus roseus exhibit NMT activity. Apart from providing unprecedented data regarding the targeting of these enzymes in planta, our results point out an additional layer of complexity to the subcellular organization of the MIA biosynthetic pathway by introducing tonoplast and peroxisome as new actors of the final steps of MIA biosynthesis.
Collapse
Affiliation(s)
- Konstantinos Koudounas
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, 31 Av. Monge, Tours 37200, France
| | | | - Luisa Fernanda Rojas Hoyos
- Grupo de Biotransformación-Escuela de Microbiología, Universidad de Antioquia, Calle 70 No 52-21, A.A 1226, Medellín, Colombia
| | - Ines Carqueijeiro
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, 31 Av. Monge, Tours 37200, France
| | - Pamela Lemos Cruz
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, 31 Av. Monge, Tours 37200, France
| | - Emily Stander
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, 31 Av. Monge, Tours 37200, France
| | - Natalja Kulagina
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, 31 Av. Monge, Tours 37200, France
| | - Jennifer Perrin
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, 31 Av. Monge, Tours 37200, France
| | - Audrey Oudin
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, 31 Av. Monge, Tours 37200, France
| | - Sébastien Besseau
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, 31 Av. Monge, Tours 37200, France
| | - Arnaud Lanoue
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, 31 Av. Monge, Tours 37200, France
| | - Lucia Atehortùa
- Laboratorio de Biotecnología, Sede de Investigación Universitaria, Universidad de Antioquia, Medellin 50010, Colombia
| | - Benoit St-Pierre
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, 31 Av. Monge, Tours 37200, France
| | | | - Nicolas Papon
- GEIHP, SFR ICAT, University of Angers, Université de Bretagne Occidentale, 4 rue de Larrey - F49933, Angers 49000, France
| | - Sarah E O'Connor
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, Jena 07745, Germany
| | - Vincent Courdavault
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, 31 Av. Monge, Tours 37200, France
- Graduate School of Sciences, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| |
Collapse
|
35
|
Courdavault V, Papon N. Social amoebae as a new chassis for drug production. Trends Biotechnol 2022; 40:529-531. [DOI: 10.1016/j.tibtech.2022.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/10/2022] [Accepted: 02/11/2022] [Indexed: 11/26/2022]
|
36
|
Lorenz A, Papon N. New tools for the new bug Candida auris. Trends Microbiol 2022; 30:203-205. [PMID: 35115186 DOI: 10.1016/j.tim.2022.01.010] [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: 01/10/2022] [Revised: 01/17/2022] [Accepted: 01/17/2022] [Indexed: 10/19/2022]
Abstract
Candida auris is a recently emerged yeast pathogen of humans causing severe hospital-acquired systemic infections. It is of the utmost importance to understand the genetic and cellular basis of its virulence and pathogenicity. In a recent study, Santana and O'Meara generated forward and reverse genetic tools to manipulate C. auris.
Collapse
Affiliation(s)
- Alexander Lorenz
- Institute of Medical Sciences (IMS), University of Aberdeen, Aberdeen, UK.
| | - Nicolas Papon
- Univ Angers, Univ Brest, IRF, SFR ICAT, F-49000 Angers, France
| |
Collapse
|
37
|
Stander EA, Dugé de Bernonville T, Papon N, Courdavault V. Chromosome-scale genomes throw light on plant drug biosynthesis. Trends Pharmacol Sci 2022; 43:542-545. [DOI: 10.1016/j.tips.2022.01.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/14/2022] [Accepted: 01/20/2022] [Indexed: 01/18/2023]
|
38
|
Papon N, Courdavault V. ARResting cytokinin signaling for salt-stress tolerance. Plant Sci 2022; 314:111116. [PMID: 34895545 DOI: 10.1016/j.plantsci.2021.111116] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 11/08/2021] [Accepted: 11/12/2021] [Indexed: 06/14/2023]
Abstract
Cytokinins (CKs) are primarily known as a prominent type of plant hormones with pleiotropic functions such as the control of the cell division and morphogenesis. CKs are also well known to orchestrate plant responses to many types of environmental stresses. More specifically, CKs were previously shown to negatively regulate the response to salinity stress. However, the molecular mechanisms underlying this physiological process have not been investigated in detail. In a new report, Yan and colleagues show that salt stress interrupts the CK transduction pathway by promoting the degradation of some CK signaling modules. This represents an unprecedented advancement in our comprehension of how plants are able to inhibit their own development under stress conditions by interfering with the cell signaling circuitry of a growth hormone.
Collapse
Affiliation(s)
- Nicolas Papon
- Univ Angers, Univ Brest, GEIHP, SFR ICAT, F-49000, Angers, France.
| | - Vincent Courdavault
- Université de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", Tours, France.
| |
Collapse
|
39
|
Kasir D, Osman M, Hamze M, Bouchara JP, Courdavault V, Papon N. An Optimized Electroporation Procedure for Genetic Transformation of Candida auris. Methods Mol Biol 2022; 2517:89-94. [PMID: 35674947 DOI: 10.1007/978-1-0716-2417-3_7] [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: 06/15/2023]
Abstract
Candida auris is responsible for recent outbreaks with significant mortality in hospitalized and long-term care patients. As a highly transmissible and multidrug-resistant fungal pathogen, genetic tools are urgently needed for deciphering mechanisms involved in the host-pathogen interactions and potentially identifying new fungal targets for therapeutic development. Here, we provide a reliable transformation protocol based on an efficient electroporation procedure and the use of a mycophenolic acid resistance marker.
Collapse
Affiliation(s)
- Dalal Kasir
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Marwan Osman
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Monzer Hamze
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | | | - Vincent Courdavault
- Université de Tours, EA2106 Biomolécules et Biotechnologies Végétales, Tours, France
| | - Nicolas Papon
- Univ Angers, Univ Brest, IRF, SFR ICAT, Angers, France.
| |
Collapse
|
40
|
Yaakoub H, Sanchez NS, Ongay-Larios L, Courdavault V, Calenda A, Bouchara JP, Coria R, Papon N. The high osmolarity glycerol (HOG) pathway in fungi †. Crit Rev Microbiol 2021; 48:657-695. [PMID: 34893006 DOI: 10.1080/1040841x.2021.2011834] [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] [Indexed: 01/06/2023]
Abstract
While fungi are widely occupying nature, many species are responsible for devastating mycosis in humans. Such niche diversity explains how quick fungal adaptation is necessary to endow the capacity of withstanding fluctuating environments and to cope with host-imposed conditions. Among all the molecular mechanisms evolved by fungi, the most studied one is the activation of the phosphorelay signalling pathways, of which the high osmolarity glycerol (HOG) pathway constitutes one of the key molecular apparatus underpinning fungal adaptation and virulence. In this review, we summarize the seminal knowledge of the HOG pathway with its more recent developments. We specifically described the HOG-mediated stress adaptation, with a particular focus on osmotic and oxidative stress, and point out some lags in our understanding of its involvement in the virulence of pathogenic species including, the medically important fungi Candida albicans, Cryptococcus neoformans, and Aspergillus fumigatus, compared to the model yeast Saccharomyces cerevisiae. Finally, we also highlighted some possible applications of the HOG pathway modifications to improve the fungal-based production of natural products in the industry.
Collapse
Affiliation(s)
- Hajar Yaakoub
- Univ Angers, Univ Brest, GEIHP, SFR ICAT, Angers, France
| | - Norma Silvia Sanchez
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad Universitaria, Mexico City, Mexico
| | - Laura Ongay-Larios
- Unidad de Biología Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Vincent Courdavault
- EA2106 "Biomolécules et Biotechnologies Végétales", Université de Tours, Tours, France
| | | | | | - Roberto Coria
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad Universitaria, Mexico City, Mexico
| | - Nicolas Papon
- Univ Angers, Univ Brest, GEIHP, SFR ICAT, Angers, France
| |
Collapse
|
41
|
Papon N, Borman AM, Meyer W, Bouchara JP. Editorial: Fungal Respiratory Infections in Cystic Fibrosis. Front Cell Infect Microbiol 2021; 11:800847. [PMID: 34858886 PMCID: PMC8630675 DOI: 10.3389/fcimb.2021.800847] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 10/25/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Nicolas Papon
- Univ Angers, Univ Brest, GEIHP, SFR ICAT, Angers, France
| | - Andrew Mark Borman
- UK National Mycology Reference Laboratory, United Kingdom Health Security Agency South-West, Bristol, United Kingdom.,Medical Research Council Centre for Medical Mycology (MRC CMM), University of Exeter, Exeter, United Kingdom
| | - Wieland Meyer
- Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, NSW, Australia.,Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Westmead Clinical School, Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Westmead, Sydney, NSW, Australia.,Westmead Hospital (Research and Education Network), Westmead, NSW, Australia.,Westmead Institute for Medical Research, Westmead, NSW, Australia.,Curtin Medical School, Curtin University, Perth, WA, Australia
| | | |
Collapse
|
42
|
Briard B, Fontaine T, Kanneganti TD, Gow NAR, Papon N. Fungal cell wall components modulate our immune system. Cell Surf 2021; 7:100067. [PMID: 34825116 PMCID: PMC8603304 DOI: 10.1016/j.tcsw.2021.100067] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 10/16/2021] [Accepted: 10/27/2021] [Indexed: 11/28/2022] Open
Abstract
Invasive fungal infections remain highly problematic for human health. Collectively, they account for more than 1 million deaths a year in addition to more than 100 million mucosal infections and 1 billion skin infections. To be able to make progress it is important to understand the pathobiology of fungal interactions with the immune system. Here, we highlight new advancements pointing out the pivotal role of fungal cell wall components (β-glucan, mannan, galactosaminogalactan and melanin) in modulating host immunity and discuss how these open new opportunities for the development of immunomodulatory strategies to combat deadly fungal infectious diseases.
Collapse
Affiliation(s)
- Benoit Briard
- INSERM, Centre d'Etude des Pathologies Respiratoires (CEPR), UMR 1100, Université de Tours, Faculté de Médecine de Tours, Tours, France
| | - Thierry Fontaine
- Unité de Biologie et Pathogénicité Fongiques, Institut Pasteur, Paris, France
| | | | - Neil A R Gow
- The Aberdeen Fungal Group, School of Medicine, Medical Sciences & Nutrition, Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK.,Medical Research Council Centre for Medical Mycology at the University of Exeter, Exeter, UK
| | - Nicolas Papon
- Univ Angers, Univ Brest, GEIHP, SFR ICAT, F-49000 Angers, France
| |
Collapse
|
43
|
Papon N, Copp BR, Courdavault V. Marine drugs: Biology, pipelines, current and future prospects for production. Biotechnol Adv 2021; 54:107871. [PMID: 34801661 DOI: 10.1016/j.biotechadv.2021.107871] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 11/02/2021] [Accepted: 11/15/2021] [Indexed: 12/17/2022]
Abstract
The marine environment is a huge reservoir of biodiversity and represents an excellent source of chemical compounds, some of which have large economical values. In the urgent quest for new pharmaceuticals, marine-based drug discovery has progressed significantly over the past several decades and we now benefit from a series of approved marine natural products (MNPs) to treat cancer and pain while an additional collection of promising leads are in clinical trials. However, the discovery and supply of MNPs has always been challenging given their low bioavailability and structural complexity. Their manufacture for pre-clinical and clinical development but also commercialization mainly relies upon marine source extraction and chemical synthesis, which are associated with high costs, unsustainability and severe environmental problems. In this review, we discuss how metabolic engineering now raises reasonable expectations for the implementation of microbial cell factories, which may provide a sustainable approach for MNP-based drug supply in the near future.
Collapse
Affiliation(s)
- Nicolas Papon
- Univ. Angers, Univ. Brest, GEIHP, SFR ICAT, F-49000 Angers, France.
| | - Brent R Copp
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand.
| | - Vincent Courdavault
- Université de Tours, EA2106 Biomolécules et Biotechnologies Végétales, Tours, France.
| |
Collapse
|
44
|
Osman M, Kasir D, Rafei R, Kassem II, Ismail MB, El Omari K, Dabboussi F, Cazer C, Papon N, Bouchara JP, Hamze M. Trends in the epidemiology of dermatophytosis in the Middle East and North Africa region. Int J Dermatol 2021; 61:935-968. [PMID: 34766622 DOI: 10.1111/ijd.15967] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 08/31/2021] [Accepted: 10/15/2021] [Indexed: 12/28/2022]
Abstract
Dermatophytosis corresponds to a broad series of infections, mostly superficial, caused by a group of keratinophilic and keratinolytic filamentous fungi called dermatophytes. These mycoses are currently considered to be a major public health concern worldwide, particularly in developing countries such as those in the Middle East and North Africa (MENA) region. Here we compiled and discussed existing epidemiologic data on these infections in the MENA region. Most of the available studies were based on conventional diagnostic strategies and were published before the last taxonomic revision of dermatophytes. This has led to misidentifications, which might have resulted in the underestimation of the real burden of these infections in the MENA countries. Our analysis of the available literature highlights an urgent need for further studies based on reliable diagnostic tools and standard susceptibility testing methods for dermatophytosis, which represents a major challenge for these countries. This is crucial for guiding appropriate interventions and activating antifungal stewardship programs in the future.
Collapse
Affiliation(s)
- Marwan Osman
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon.,Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Dalal Kasir
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Rayane Rafei
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Issmat I Kassem
- Center for Food Safety and Department of Food Science and Technology, University of Georgia, Griffin, GA, USA
| | - Mohamad Bachar Ismail
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon.,Faculty of Science, Lebanese University, Tripoli, Lebanon
| | - Khaled El Omari
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon.,Quality Control Center Laboratories, Chamber of Commerce, Industry, and Agriculture of Tripoli and North Lebanon, Tripoli, Lebanon
| | - Fouad Dabboussi
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Casey Cazer
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Nicolas Papon
- Univ Angers, Univ Brest, GEIHP, SFR ICAT, Angers, France
| | | | - Monzer Hamze
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| |
Collapse
|
45
|
Kulagina N, Guirimand G, Melin C, Lemos‐Cruz P, Carqueijeiro I, De Craene J, Oudin A, Heredia V, Koudounas K, Unlubayir M, Lanoue A, Imbault N, St‐Pierre B, Papon N, Clastre M, Giglioli‐Guivarc’h N, Marc J, Besseau S, Courdavault V. Enhanced bioproduction of anticancer precursor vindoline by yeast cell factories. Microb Biotechnol 2021; 14:2693-2699. [PMID: 34302444 PMCID: PMC8601169 DOI: 10.1111/1751-7915.13898] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 07/10/2021] [Indexed: 11/28/2022] Open
Abstract
The pharmaceutical industry faces a growing demand and recurrent shortages in many anticancer plant drugs given their extensive use in human chemotherapy. Efficient alternative strategies of supply of these natural products such as bioproduction by microorganisms are needed to ensure stable and massive manufacturing. Here, we developed and optimized yeast cell factories efficiently converting tabersonine to vindoline, a precursor of the major anticancer alkaloids vinblastine and vincristine. First, fine-tuning of heterologous gene copies restrained side metabolites synthesis towards vindoline production. Tabersonine to vindoline bioconversion was further enhanced through a rational medium optimization (pH, composition) and a sequential feeding strategy. Finally, a vindoline titre of 266 mg l-1 (88% yield) was reached in an optimized fed-batch bioreactor. This precursor-directed synthesis of vindoline thus paves the way towards future industrial bioproduction through the valorization of abundant tabersonine resources.
Collapse
Affiliation(s)
- Natalja Kulagina
- Université de ToursEA2106 Biomolécules et Biotechnologies VégétalesToursFrance
| | - Grégory Guirimand
- Université de ToursEA2106 Biomolécules et Biotechnologies VégétalesToursFrance
- Graduate School of Sciences, Technology and InnovationKobe UniversityKobeJapan
- Le Studium Loire Valley Institute for Advanced StudiesOrléans & ToursFrance
| | - Céline Melin
- Université de ToursEA2106 Biomolécules et Biotechnologies VégétalesToursFrance
| | - Pamela Lemos‐Cruz
- Université de ToursEA2106 Biomolécules et Biotechnologies VégétalesToursFrance
| | - Ines Carqueijeiro
- Université de ToursEA2106 Biomolécules et Biotechnologies VégétalesToursFrance
| | | | - Audrey Oudin
- Université de ToursEA2106 Biomolécules et Biotechnologies VégétalesToursFrance
| | - Vladimir Heredia
- Université de ToursEA2106 Biomolécules et Biotechnologies VégétalesToursFrance
| | | | - Marianne Unlubayir
- Université de ToursEA2106 Biomolécules et Biotechnologies VégétalesToursFrance
| | - Arnaud Lanoue
- Université de ToursEA2106 Biomolécules et Biotechnologies VégétalesToursFrance
| | - Nadine Imbault
- Université de ToursEA2106 Biomolécules et Biotechnologies VégétalesToursFrance
| | - Benoit St‐Pierre
- Université de ToursEA2106 Biomolécules et Biotechnologies VégétalesToursFrance
| | - Nicolas Papon
- Université d'AngersEA3142 Groupe d'Etude des Interactions Hôte‐PathogèneAngersFrance
| | - Marc Clastre
- Université de ToursEA2106 Biomolécules et Biotechnologies VégétalesToursFrance
| | | | - Jillian Marc
- Université de ToursEA2106 Biomolécules et Biotechnologies VégétalesToursFrance
| | - Sébastien Besseau
- Université de ToursEA2106 Biomolécules et Biotechnologies VégétalesToursFrance
| | - Vincent Courdavault
- Université de ToursEA2106 Biomolécules et Biotechnologies VégétalesToursFrance
| |
Collapse
|
46
|
Al Kassaa I, El Omari S, Abbas N, Papon N, Drider D, Kassem II, Osman M. High association of COVID-19 severity with poor gut health score in Lebanese patients. PLoS One 2021; 16:e0258913. [PMID: 34673813 PMCID: PMC8530309 DOI: 10.1371/journal.pone.0258913] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 10/07/2021] [Indexed: 02/07/2023] Open
Abstract
Background Coronavirus disease 2019 (COVID-19) has affected millions of lives globally. However, the disease has presented more extreme challenges for developing countries that are experiencing economic crises. Studies on COVID-19 symptoms and gut health are scarce and have not fully analyzed possible associations between gut health and disease pathophysiology. Therefore, this study aimed to demonstrate a potential association between gut health and COVID-19 severity in the Lebanese community, which has been experiencing a severe economic crisis. Methods This cross-sectional study investigated SARS-CoV-2 PCR-positive Lebanese patients. Participants were interviewed and gut health, COVID-19 symptoms, and different metrics were analyzed using simple and multiple logistic regression models. Results Analysis of the data showed that 25% of participants were asymptomatic, while an equal proportion experienced severe symptoms, including dyspnea (22.7%), oxygen need (7.5%), and hospitalization (3.1%). The mean age of the participants was 38.3 ±0.8 years, and the majority were males (63.9%), married (68.2%), and currently employed (66.7%). A negative correlation was found between gut health score and COVID-19 symptoms (Kendall’s tau-b = -0.153, P = 0.004); indicating that low gut health was associated with more severe COVID-19 cases. Additionally, participants who reported unhealthy food intake were more likely to experience severe symptoms (Kendall’s tau-b = 0.118, P = 0.049). When all items were taken into consideration, multiple ordinal logistic regression models showed a significant association between COVID-19 symptoms and each of the following variables: working status, flu-like illness episodes, and gut health score. COVID-19 severe symptoms were more common among patients having poor gut health scores (OR:1.31, 95%CI:1.07–1.61; P = 0.008), experiencing more than one episode of flu-like illness per year (OR:2.85, 95%CI:1.58–5.15; P = 0.001), and owning a job (OR:2.00, 95%CI:1.1–3.65; P = 0.023). Conclusions To our knowledge, this is the first study that showed the impact of gut health and exposure to respiratory viruses on COVID-19 severity in Lebanon. These findings can facilitate combating the pandemic in Lebanon.
Collapse
Affiliation(s)
- Imad Al Kassaa
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Doctoral School of Science and Technology, Lebanese University, Beirut, Lebanon
- * E-mail: (IAK); , (MO)
| | - Sarah El Omari
- Department of Epidemiology and Population Health, Faculty of Health Sciences, American University of Beirut, Beirut, Lebanon
| | - Nada Abbas
- Department of Health Management and Policy, Faculty of Health Sciences, American University of Beirut, Beirut, Lebanon
| | - Nicolas Papon
- Univ Angers, Univ Brest, GEIHP, SFR ICAT, Angers, France
| | - Djamel Drider
- UMR Transfrontalière BioEcoAgro1158, Univ. Lille, INRAE, Univ. Liège, UPJV, YNCREA, Univ. Artois, Univ. Littoral Côte d’Opale, ICV—Institut Charles Viollette, Lille, France
| | - Issmat I. Kassem
- Center for Food Safety and Department of Food Science and Technology, University of Georgia, Griffin, GA, United States of America
| | - Marwan Osman
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States of America
- * E-mail: (IAK); , (MO)
| |
Collapse
|
47
|
Hoffmann CV, Nevez G, Moal MC, Quinio D, Le Nan N, Papon N, Bouchara JP, Le Meur Y, Le Gal S. Selection of Pneumocystis jirovecii Inosine 5'-Monophosphate Dehydrogenase Mutants in Solid Organ Transplant Recipients: Implication of Mycophenolic Acid. J Fungi (Basel) 2021; 7:jof7100849. [PMID: 34682270 PMCID: PMC8537117 DOI: 10.3390/jof7100849] [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: 09/15/2021] [Revised: 10/04/2021] [Accepted: 10/06/2021] [Indexed: 11/16/2022] Open
Abstract
Mycophenolic acid (MPA) targets the inosine 5'-monophosphate dehydrogenase (IMPDH) of human lymphocytes. It is widely used as an immunosuppressant to prevent rejection in solid organ transplant (SOT) recipients who, incidentally, are at risk for Pneumocystis pneumonia (PCP). We hypothesized that MPA exerts selective pressure on P. jirovecii microorganisms considering its in vitro antifungal activity on other fungi. Thus, we analysed impdh gene in P. jirovecii isolates from SOT recipients. P. jirovecii specimens from 26 patients diagnosed with PCP from 2010 to 2020 were retrospectively examined: 10 SOT recipients treated with MPA and 16 non-SOT patients without prior exposure to MPA. The P. jirovecii impdh gene was amplified and sequenced. Nucleotide sequences were aligned with the reference sequences retrieved from available P. jirovecii whole genomes. The deduced IMPDH protein sequences were aligned with available IMPDH proteins from Pneumocystis spp. and other fungal species known to be in vitro sensitive or resistant to MPA. A total of nine SNPs was identified. One SNP (G1020A) that results in an Ala261Thr substitution was identified in all SOT recipients and in none of the non-SOT patients. Considering that IMPDHs of other fungi, resistant to MPA, harbour Thr (or Ser) at the analogous position, the Ala261Thr mutation observed in MPA-treated patients was considered to represent the signature of P. jirovecii exposure to MPA. These results suggest that MPA may be involved in the selection of specific P. jirovecii strains that circulate in the SOT recipient population.
Collapse
Affiliation(s)
- Claire V. Hoffmann
- Laboratoire de Parasitologie et Mycologie, Hôpital de La Cavale Blanche, CHU de Brest, 29609 Brest, France; (C.V.H.); (D.Q.)
- Groupe d’Etude des Interactions Hôte-Pathogène (GEIHP), Université d’Angers, Université de Brest, 29238 Brest, France;
| | - Gilles Nevez
- Laboratoire de Parasitologie et Mycologie, Hôpital de La Cavale Blanche, CHU de Brest, 29609 Brest, France; (C.V.H.); (D.Q.)
- Groupe d’Etude des Interactions Hôte-Pathogène (GEIHP), Université d’Angers, Université de Brest, 29238 Brest, France;
- Correspondence: (G.N.); (S.L.G.); Tel.: +33-(0)-2-98-14-51-02 (G.N. & S.L.G.); Fax: +33-(0)-2-98-14-51-49 (G.N. & S.L.G.)
| | - Marie-Christine Moal
- Département de Néphrologie, CHU de Brest, 29609 Brest, France; (M.-C.M.); (Y.L.M.)
| | - Dorothée Quinio
- Laboratoire de Parasitologie et Mycologie, Hôpital de La Cavale Blanche, CHU de Brest, 29609 Brest, France; (C.V.H.); (D.Q.)
- Groupe d’Etude des Interactions Hôte-Pathogène (GEIHP), Université d’Angers, Université de Brest, 29238 Brest, France;
| | - Nathan Le Nan
- Groupe d’Etude des Interactions Hôte-Pathogène (GEIHP), Université d’Angers, Université de Brest, 29238 Brest, France;
| | - Nicolas Papon
- Groupe d’Etude des Interactions Hôte-Pathogène (GEIHP), Université de Brest, Université d’Angers, 49035 Angers, France; (N.P.); (J.-P.B.)
| | - Jean-Philippe Bouchara
- Groupe d’Etude des Interactions Hôte-Pathogène (GEIHP), Université de Brest, Université d’Angers, 49035 Angers, France; (N.P.); (J.-P.B.)
| | - Yannick Le Meur
- Département de Néphrologie, CHU de Brest, 29609 Brest, France; (M.-C.M.); (Y.L.M.)
- UMR1227, Lymphocytes B et Autoimmunité, Université de Brest, Inserm, Labex IGO, 20609 Brest, France
| | - Solène Le Gal
- Laboratoire de Parasitologie et Mycologie, Hôpital de La Cavale Blanche, CHU de Brest, 29609 Brest, France; (C.V.H.); (D.Q.)
- Groupe d’Etude des Interactions Hôte-Pathogène (GEIHP), Université d’Angers, Université de Brest, 29238 Brest, France;
- Correspondence: (G.N.); (S.L.G.); Tel.: +33-(0)-2-98-14-51-02 (G.N. & S.L.G.); Fax: +33-(0)-2-98-14-51-49 (G.N. & S.L.G.)
| |
Collapse
|
48
|
Kulagina N, Besseau S, Godon C, Goldman GH, Papon N, Courdavault V. Yeasts as Biopharmaceutical Production Platforms. Front Fungal Biol 2021; 2:733492. [PMID: 37744146 PMCID: PMC10512354 DOI: 10.3389/ffunb.2021.733492] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 08/26/2021] [Indexed: 09/26/2023]
Affiliation(s)
- Natalja Kulagina
- Université de Tours, EA2106 Biomolécules et Biotechnologies Végétales, Tours, France
| | - Sébastien Besseau
- Université de Tours, EA2106 Biomolécules et Biotechnologies Végétales, Tours, France
| | - Charlotte Godon
- Université d'Angers, EA3142 Groupe d'Etude des Interactions Hôte-Pathogène, Angers, France
| | - Gustavo H. Goldman
- Departamento de Ciências Farmacêuticas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Nicolas Papon
- Université d'Angers, EA3142 Groupe d'Etude des Interactions Hôte-Pathogène, Angers, France
| | - Vincent Courdavault
- Université de Tours, EA2106 Biomolécules et Biotechnologies Végétales, Tours, France
| |
Collapse
|
49
|
Annweiler C, Cao Z, Papon N, Kovacic H, Sabatier JM. Counter-Regulatory Renin-Angiotensin System: An Important Line of Research to Understand and Limit the Severity of COVID-19. Infect Disord Drug Targets 2021; 22:e100921196331. [PMID: 34515015 DOI: 10.2174/1871526521666210910063227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Cédric Annweiler
- Department of Geriatric Medicine and Memory Clinic, Research Center on Autonomy and Longevity, University Hospital, Angers, France; Laboratoire de Psychologie des Pays de la Loire, LPPL EA 4638, SFR Confluences, University of Angers. France
| | - Zhijian Cao
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan 430072. China
| | - Nicolas Papon
- Host-Pathogen Interaction Study Group (GEIHP, EA 3142), UNIV Angers, UNIV Brest, Angers. France
| | - Hervé Kovacic
- Université Aix-Marseille, Institut de Neuro-physiopathologie (INP), UMR 7051, Faculté de Pharmacie, 27 Bd Jean Moulin, 13385 Marseille Cedex. France
| | - Jean-Marc Sabatier
- Université Aix-Marseille, Institut de Neuro-physiopathologie (INP), UMR 7051, Faculté de Pharmacie, 27 Bd Jean Moulin, 13385 Marseille Cedex. France
| |
Collapse
|
50
|
Osman M, Papon N. Smoking-aggravated oral candidiasis: Nrf2 pathway dampens NLRP3 inflammasome. J Cell Mol Med 2021; 25:9473-9475. [PMID: 34486221 PMCID: PMC8500950 DOI: 10.1111/jcmm.16901] [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: 07/31/2021] [Revised: 08/18/2021] [Accepted: 08/23/2021] [Indexed: 12/15/2022] Open
Abstract
While cigarette smoke compounds are known to have immunosuppressive effects on the oral mucosa, the relationship between in vivo immune dysfunction caused by smoking and the development of oral Candida infections remains largely unexplored. In a recent issue of The Journal of Cellular and Molecular Medicine, Ye and colleagues provide evidence that smoking increases oral mucosa susceptibility to Candida albicans infection via the activation of the Nrf2 pathway, which in turn negatively regulates the NLRP3 inflammasome. This opens new perspective in considering Nrf2 as a relevant target for smoking‐induced C. albicans‐related oral diseases.
Collapse
Affiliation(s)
- Marwan Osman
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon.,Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Nicolas Papon
- GEIHP, SFR ICAT, University of Brest, University of Angers, Angers, France
| |
Collapse
|