101
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Chiapello H, Mallet L, Guérin C, Aguileta G, Amselem J, Kroj T, Ortega-Abboud E, Lebrun MH, Henrissat B, Gendrault A, Rodolphe F, Tharreau D, Fournier E. Deciphering Genome Content and Evolutionary Relationships of Isolates from the Fungus Magnaporthe oryzae Attacking Different Host Plants. Genome Biol Evol 2015; 7:2896-912. [PMID: 26454013 PMCID: PMC4684704 DOI: 10.1093/gbe/evv187] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Deciphering the genetic bases of pathogen adaptation to its host is a key question in ecology and evolution. To understand how the fungus Magnaporthe oryzae adapts to different plants, we sequenced eight M. oryzae isolates differing in host specificity (rice, foxtail millet, wheat, and goosegrass), and one Magnaporthe grisea isolate specific of crabgrass. Analysis of Magnaporthe genomes revealed small variation in genome sizes (39–43 Mb) and gene content (12,283–14,781 genes) between isolates. The whole set of Magnaporthe genes comprised 14,966 shared families, 63% of which included genes present in all the nine M. oryzae genomes. The evolutionary relationships among Magnaporthe isolates were inferred using 6,878 single-copy orthologs. The resulting genealogy was mostly bifurcating among the different host-specific lineages, but was reticulate inside the rice lineage. We detected traces of introgression from a nonrice genome in the rice reference 70-15 genome. Among M. oryzae isolates and host-specific lineages, the genome composition in terms of frequencies of genes putatively involved in pathogenicity (effectors, secondary metabolism, cazome) was conserved. However, 529 shared families were found only in nonrice lineages, whereas the rice lineage possessed 86 specific families absent from the nonrice genomes. Our results confirmed that the host specificity of M. oryzae isolates was associated with a divergence between lineages without major gene flow and that, despite the strong conservation of gene families between lineages, adaptation to different hosts, especially to rice, was associated with the presence of a small number of specific gene families. All information was gathered in a public database (http://genome.jouy.inra.fr/gemo).
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Affiliation(s)
- Hélène Chiapello
- INRA, UR 1404, Unité Mathématiques et Informatique Appliquées du Génome à l'Environnement, Jouy-en-Josas, France INRA, UR 875, Unité Mathématiques et Informatique Appliquées de Toulouse, Castanet-Tolosan, France
| | - Ludovic Mallet
- INRA, UR 1404, Unité Mathématiques et Informatique Appliquées du Génome à l'Environnement, Jouy-en-Josas, France INRA, UR 875, Unité Mathématiques et Informatique Appliquées de Toulouse, Castanet-Tolosan, France INRA, UR 1164, Unité de Recherche Génomique Info, Versailles, France
| | - Cyprien Guérin
- INRA, UR 1404, Unité Mathématiques et Informatique Appliquées du Génome à l'Environnement, Jouy-en-Josas, France
| | - Gabriela Aguileta
- CNRS, UMR 8079, Ecologie, Systématique et Evolution, Université Paris-Sud, Orsay, France Center for Genomic Regulation, Barcelona, Spain
| | - Joëlle Amselem
- INRA, UR 1164, Unité de Recherche Génomique Info, Versailles, France
| | - Thomas Kroj
- INRA, UMR 385, Biologie et Génétique des Interactions Plantes-Pathogènes BGPI, INRA-CIRAD-Montpellier SupAgro, Campus International de Baillarguet, Montpellier, France
| | - Enrique Ortega-Abboud
- CIRAD, UMR 385, Biologie et Génétique des Interactions Plantes-Pathogènes BGPI, INRA-CIRAD-Montpellier SupAgro, Campus International de Baillarguet, Montpellier, France
| | - Marc-Henri Lebrun
- INRA-AgroParisTech, UMR 1190, Biologie et Gestion des Risques en Agriculture BIOGER-CPP, Campus AgroParisTech, Thiverval-Grignon, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, Université d'Aix Marseille, France Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Annie Gendrault
- INRA, UR 1404, Unité Mathématiques et Informatique Appliquées du Génome à l'Environnement, Jouy-en-Josas, France
| | - François Rodolphe
- INRA, UR 1404, Unité Mathématiques et Informatique Appliquées du Génome à l'Environnement, Jouy-en-Josas, France
| | - Didier Tharreau
- CIRAD, UMR 385, Biologie et Génétique des Interactions Plantes-Pathogènes BGPI, INRA-CIRAD-Montpellier SupAgro, Campus International de Baillarguet, Montpellier, France
| | - Elisabeth Fournier
- INRA, UMR 385, Biologie et Génétique des Interactions Plantes-Pathogènes BGPI, INRA-CIRAD-Montpellier SupAgro, Campus International de Baillarguet, Montpellier, France
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102
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Ropars J, Rodríguez de la Vega RC, López-Villavicencio M, Gouzy J, Sallet E, Dumas É, Lacoste S, Debuchy R, Dupont J, Branca A, Giraud T. Adaptive Horizontal Gene Transfers between Multiple Cheese-Associated Fungi. Curr Biol 2015; 25:2562-9. [PMID: 26412136 PMCID: PMC4598740 DOI: 10.1016/j.cub.2015.08.025] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 07/09/2015] [Accepted: 08/11/2015] [Indexed: 11/29/2022]
Abstract
Domestication is an excellent model for studies of adaptation because it involves recent and strong selection on a few, identified traits [1–5]. Few studies have focused on the domestication of fungi, with notable exceptions [6–11], despite their importance to bioindustry [12] and to a general understanding of adaptation in eukaryotes [5]. Penicillium fungi are ubiquitous molds among which two distantly related species have been independently selected for cheese making—P. roqueforti for blue cheeses like Roquefort and P. camemberti for soft cheeses like Camembert. The selected traits include morphology, aromatic profile, lipolytic and proteolytic activities, and ability to grow at low temperatures, in a matrix containing bacterial and fungal competitors [13–15]. By comparing the genomes of ten Penicillium species, we show that adaptation to cheese was associated with multiple recent horizontal transfers of large genomic regions carrying crucial metabolic genes. We identified seven horizontally transferred regions (HTRs) spanning more than 10 kb each, flanked by specific transposable elements, and displaying nearly 100% identity between distant Penicillium species. Two HTRs carried genes with functions involved in the utilization of cheese nutrients or competition and were found nearly identical in multiple strains and species of cheese-associated Penicillium fungi, indicating recent selective sweeps; they were experimentally associated with faster growth and greater competitiveness on cheese and contained genes highly expressed in the early stage of cheese maturation. These findings have industrial and food safety implications and improve our understanding of the processes of adaptation to rapid environmental changes. New HTRs are found in cheese fungi HTRs are flanked by specific transposable elements HTRs have spread in cheese-associated fungi through recent selective sweeps Experiments link two HTRs to growth and competitive advantages on cheese
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Affiliation(s)
- Jeanne Ropars
- Ecologie, Systématique et Evolution, UMR8079, Univ. Paris-Sud, 91405 Orsay, France; Ecologie, Systématique et Evolution, UMR8079, CNRS, 91405 Orsay, France
| | - Ricardo C Rodríguez de la Vega
- Ecologie, Systématique et Evolution, UMR8079, Univ. Paris-Sud, 91405 Orsay, France; Ecologie, Systématique et Evolution, UMR8079, CNRS, 91405 Orsay, France
| | - Manuela López-Villavicencio
- Institut de Systématique, Evolution, Biodiversité, UMR 7205 CNRS-MNHN-UPMC-EPHE, Muséum national d'Histoire naturelle, Sorbonne Université, CP39, 57 Rue Cuvier, 75231 Paris Cedex 05, France
| | - Jérôme Gouzy
- Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, INRA, Castanet-Tolosan 31326, France; Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, CNRS, Castanet-Tolosan 31326, France
| | - Erika Sallet
- Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, INRA, Castanet-Tolosan 31326, France; Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, CNRS, Castanet-Tolosan 31326, France
| | - Émilie Dumas
- Ecologie, Systématique et Evolution, UMR8079, Univ. Paris-Sud, 91405 Orsay, France; Ecologie, Systématique et Evolution, UMR8079, CNRS, 91405 Orsay, France
| | - Sandrine Lacoste
- Institut de Systématique, Evolution, Biodiversité, UMR 7205 CNRS-MNHN-UPMC-EPHE, Muséum national d'Histoire naturelle, Sorbonne Université, CP39, 57 Rue Cuvier, 75231 Paris Cedex 05, France
| | - Robert Debuchy
- Institut de Génétique et Microbiologie, UMR8621, Univ. Paris-Sud, 91405 Orsay, France; Institut de Génétique et Microbiologie, UMR8621, CNRS, 91405 Orsay, France
| | - Joëlle Dupont
- Institut de Systématique, Evolution, Biodiversité, UMR 7205 CNRS-MNHN-UPMC-EPHE, Muséum national d'Histoire naturelle, Sorbonne Université, CP39, 57 Rue Cuvier, 75231 Paris Cedex 05, France
| | - Antoine Branca
- Ecologie, Systématique et Evolution, UMR8079, Univ. Paris-Sud, 91405 Orsay, France; Ecologie, Systématique et Evolution, UMR8079, CNRS, 91405 Orsay, France.
| | - Tatiana Giraud
- Ecologie, Systématique et Evolution, UMR8079, Univ. Paris-Sud, 91405 Orsay, France; Ecologie, Systématique et Evolution, UMR8079, CNRS, 91405 Orsay, France.
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103
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Almeida P, Barbosa R, Zalar P, Imanishi Y, Shimizu K, Turchetti B, Legras JL, Serra M, Dequin S, Couloux A, Guy J, Bensasson D, Gonçalves P, Sampaio JP. A population genomics insight into the Mediterranean origins of wine yeast domestication. Mol Ecol 2015; 24:5412-27. [PMID: 26248006 DOI: 10.1111/mec.13341] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2015] [Revised: 07/24/2015] [Accepted: 07/29/2015] [Indexed: 12/20/2022]
Abstract
The domestication of the wine yeast Saccharomyces cerevisiae is thought to be contemporary with the development and expansion of viticulture along the Mediterranean basin. Until now, the unavailability of wild lineages prevented the identification of the closest wild relatives of wine yeasts. Here, we enlarge the collection of natural lineages and employ whole-genome data of oak-associated wild isolates to study a balanced number of anthropic and natural S. cerevisiae strains. We identified industrial variants and new geographically delimited populations, including a novel Mediterranean oak population. This population is the closest relative of the wine lineage as shown by a weak population structure and further supported by genomewide population analyses. A coalescent model considering partial isolation with asymmetrical migration, mostly from the wild group into the Wine group, and population growth, was found to be best supported by the data. Importantly, divergence time estimates between the two populations agree with historical evidence for winemaking. We show that three horizontally transmitted regions, previously described to contain genes relevant to wine fermentation, are present in the Wine group but not in the Mediterranean oak group. This represents a major discontinuity between the two populations and is likely to denote a domestication fingerprint in wine yeasts. Taken together, these results indicate that Mediterranean oaks harbour the wild genetic stock of domesticated wine yeasts.
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Affiliation(s)
- Pedro Almeida
- UCIBIO@REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
| | - Raquel Barbosa
- UCIBIO@REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
| | - Polona Zalar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, SI-1000, Ljubljana, Slovenia
| | - Yumi Imanishi
- Department of Applied Material and Life Science, College of Engineering, Kanto Gakuin University, Mutsuura-higashi 1-50-1, Kanazawa-ku, Yokohama, 236-8501, Japan
| | - Kiminori Shimizu
- Medical Mycology Research Center, Chiba University, Inohana 1-8-1, Chuo-ku, Chiba, 260-8673, Japan
| | - Benedetta Turchetti
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali & Industrial Yeasts Collection DBVPG, Università degli Studi di Perugia, Borgo XX Giugno, 74 - 06121, Perugia, Italy
| | - Jean-Luc Legras
- Institut National de la Recherche Agronomique (INRA), UMR1083 Sciences pour l'Œnologie (SPO) 2, Place Viala, 34060, Montpellier, France
| | - Marta Serra
- UCIBIO@REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
| | - Sylvie Dequin
- Institut National de la Recherche Agronomique (INRA), UMR1083 Sciences pour l'Œnologie (SPO) 2, Place Viala, 34060, Montpellier, France
| | - Arnaud Couloux
- CEA, Institut de Génomique, Genoscope, Centre National de Séquençage, 2 rue Gaston Crémieux, CP5706 91057, Evry Cedex, France
| | - Julie Guy
- CEA, Institut de Génomique, Genoscope, Centre National de Séquençage, 2 rue Gaston Crémieux, CP5706 91057, Evry Cedex, France
| | - Douda Bensasson
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Paula Gonçalves
- UCIBIO@REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
| | - José Paulo Sampaio
- UCIBIO@REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
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104
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Gibbons JG, Rinker DC. The genomics of microbial domestication in the fermented food environment. Curr Opin Genet Dev 2015; 35:1-8. [PMID: 26338497 DOI: 10.1016/j.gde.2015.07.003] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 07/10/2015] [Accepted: 07/16/2015] [Indexed: 02/07/2023]
Abstract
Shortly after the agricultural revolution, the domestication of bacteria, yeasts, and molds, played an essential role in enhancing the stability, quality, flavor, and texture of food products. These domestication events were probably the result of human food production practices that entailed the continual recycling of isolated microbial communities in the presence of abundant agricultural food sources. We suggest that within these novel agrarian food niches the metabolic requirements of those microbes became regular and predictable resulting in rapid genomic specialization through such mechanisms as pseudogenization, genome decay, interspecific hybridization, gene duplication, and horizontal gene transfer. The ultimate result was domesticated strains of microorganisms with enhanced fermentative capacities.
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Affiliation(s)
- John G Gibbons
- Biology Department, Clark University, 950 Main Street, Worcester, MA, USA.
| | - David C Rinker
- Center for Human Genetics Research, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
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105
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Lee J, Kim Y, Lee S, Jo K. Visualization of large elongated DNA molecules. Electrophoresis 2015; 36:2057-71. [PMID: 25994517 DOI: 10.1002/elps.201400479] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 03/08/2015] [Accepted: 04/27/2015] [Indexed: 12/26/2022]
Abstract
Long and linear DNA molecules are the mainstream single-molecule analytes for a variety of biochemical analysis within microfluidic devices, including functionalized surfaces and nanostructures. However, for biochemical analysis, large DNA molecules have to be unraveled, elongated, and visualized to obtain biochemical and genomic information. To date, elongated DNA molecules have been exploited in the development of a number of genome analysis systems as well as for the study of polymer physics due to the advantage of direct visualization of single DNA molecule. Moreover, each single DNA molecule provides individual information, which makes it useful for stochastic event analysis. Therefore, numerous studies of enzymatic random motions have been performed on a large elongated DNA molecule. In this review, we introduce mechanisms to elongate DNA molecules using microfluidics and nanostructures in the beginning. Secondly, we discuss how elongated DNA molecules have been utilized to obtain biochemical and genomic information by direct visualization of DNA molecules. Finally, we reviewed the approaches used to study the interaction of proteins and large DNA molecules. Although DNA-protein interactions have been investigated for many decades, it is noticeable that there have been significant achievements for the last five years. Therefore, we focus mainly on recent developments for monitoring enzymatic activity on large elongated DNA molecules.
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Affiliation(s)
- Jinyong Lee
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Mapogu, Seoul, Republic of Korea
| | - Yongkyun Kim
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Mapogu, Seoul, Republic of Korea
| | - Seonghyun Lee
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Mapogu, Seoul, Republic of Korea
| | - Kyubong Jo
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Mapogu, Seoul, Republic of Korea
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106
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Marsit S, Mena A, Bigey F, Sauvage FX, Couloux A, Guy J, Legras JL, Barrio E, Dequin S, Galeote V. Evolutionary Advantage Conferred by an Eukaryote-to-Eukaryote Gene Transfer Event in Wine Yeasts. Mol Biol Evol 2015; 32:1695-707. [PMID: 25750179 PMCID: PMC4476156 DOI: 10.1093/molbev/msv057] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Although an increasing number of horizontal gene transfers have been reported in eukaryotes, experimental evidence for their adaptive value is lacking. Here, we report the recent transfer of a 158-kb genomic region between Torulaspora microellipsoides and Saccharomyces cerevisiae wine yeasts or closely related strains. This genomic region has undergone several rearrangements in S. cerevisiae strains, including gene loss and gene conversion between two tandemly duplicated FOT genes encoding oligopeptide transporters. We show that FOT genes confer a strong competitive advantage during grape must fermentation by increasing the number and diversity of oligopeptides that yeast can utilize as a source of nitrogen, thereby improving biomass formation, fermentation efficiency, and cell viability. Thus, the acquisition of FOT genes has favored yeast adaptation to the nitrogen-limited wine fermentation environment. This finding indicates that anthropic environments offer substantial ecological opportunity for evolutionary diversification through gene exchange between distant yeast species.
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Affiliation(s)
- Souhir Marsit
- INRA, UMR1083, SPO, F-34060 Montpellier, France Montpellier SupAgro, UMR1083, SPO, F-34060 Montpellier, France Montpellier University, UMR1083, SPO, F-34060 Montpellier, France
| | - Adriana Mena
- Department of Genetics, University of Valencia, and Department of Biotechnology, Institute of Agrochemistry and Food Technology, CSIC, Valencia, Spain
| | - Frédéric Bigey
- INRA, UMR1083, SPO, F-34060 Montpellier, France Montpellier SupAgro, UMR1083, SPO, F-34060 Montpellier, France Montpellier University, UMR1083, SPO, F-34060 Montpellier, France
| | - François-Xavier Sauvage
- INRA, UMR1083, SPO, F-34060 Montpellier, France Montpellier SupAgro, UMR1083, SPO, F-34060 Montpellier, France Montpellier University, UMR1083, SPO, F-34060 Montpellier, France
| | - Arnaud Couloux
- CEA, Institut de Génomique, Genoscope, Centre National de Séquençage, Evry, France
| | - Julie Guy
- CEA, Institut de Génomique, Genoscope, Centre National de Séquençage, Evry, France
| | - Jean-Luc Legras
- INRA, UMR1083, SPO, F-34060 Montpellier, France Montpellier SupAgro, UMR1083, SPO, F-34060 Montpellier, France Montpellier University, UMR1083, SPO, F-34060 Montpellier, France
| | - Eladio Barrio
- Department of Genetics, University of Valencia, and Department of Biotechnology, Institute of Agrochemistry and Food Technology, CSIC, Valencia, Spain
| | - Sylvie Dequin
- INRA, UMR1083, SPO, F-34060 Montpellier, France Montpellier SupAgro, UMR1083, SPO, F-34060 Montpellier, France Montpellier University, UMR1083, SPO, F-34060 Montpellier, France
| | - Virginie Galeote
- INRA, UMR1083, SPO, F-34060 Montpellier, France Montpellier SupAgro, UMR1083, SPO, F-34060 Montpellier, France Montpellier University, UMR1083, SPO, F-34060 Montpellier, France
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107
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Gillot G, Jany JL, Coton M, Le Floch G, Debaets S, Ropars J, López-Villavicencio M, Dupont J, Branca A, Giraud T, Coton E. Insights into Penicillium roqueforti Morphological and Genetic Diversity. PLoS One 2015; 10:e0129849. [PMID: 26091176 PMCID: PMC4475020 DOI: 10.1371/journal.pone.0129849] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 05/12/2015] [Indexed: 11/18/2022] Open
Abstract
Fungi exhibit substantial morphological and genetic diversity, often associated with cryptic species differing in ecological niches. Penicillium roqueforti is used as a starter culture for blue-veined cheeses, being responsible for their flavor and color, but is also a common spoilage organism in various foods. Different types of blue-veined cheeses are manufactured and consumed worldwide, displaying specific organoleptic properties. These features may be due to the different manufacturing methods and/or to the specific P. roqueforti strains used. Substantial morphological diversity exists within P. roqueforti and, although not taxonomically valid, several technological names have been used for strains on different cheeses (e.g., P. gorgonzolae, P. stilton). A worldwide P. roqueforti collection from 120 individual blue-veined cheeses and 21 other substrates was analyzed here to determine (i) whether P. roqueforti is a complex of cryptic species, by applying the Genealogical Concordance Phylogenetic Species Recognition criterion (GC-PSR), (ii) whether the population structure assessed using microsatellite markers correspond to blue cheese types, and (iii) whether the genetic clusters display different morphologies. GC-PSR multi-locus sequence analyses showed no evidence of cryptic species. The population structure analysis using microsatellites revealed the existence of highly differentiated populations, corresponding to blue cheese types and with contrasted morphologies. This suggests that the population structure has been shaped by different cheese-making processes or that different populations were recruited for different cheese types. Cheese-making fungi thus constitute good models for studying fungal diversification under recent selection.
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Affiliation(s)
- Guillaume Gillot
- Université de Brest, EA 3882 Laboratoire Universitaire de Biodiversité et d’Ecologie Microbienne, ESIAB, Technopôle Brest-Iroise, Plouzané, France
| | - Jean-Luc Jany
- Université de Brest, EA 3882 Laboratoire Universitaire de Biodiversité et d’Ecologie Microbienne, ESIAB, Technopôle Brest-Iroise, Plouzané, France
| | - Monika Coton
- Université de Brest, EA 3882 Laboratoire Universitaire de Biodiversité et d’Ecologie Microbienne, ESIAB, Technopôle Brest-Iroise, Plouzané, France
| | - Gaétan Le Floch
- Université de Brest, EA 3882 Laboratoire Universitaire de Biodiversité et d’Ecologie Microbienne, ESIAB, Technopôle Brest-Iroise, Plouzané, France
| | - Stella Debaets
- Université de Brest, EA 3882 Laboratoire Universitaire de Biodiversité et d’Ecologie Microbienne, ESIAB, Technopôle Brest-Iroise, Plouzané, France
| | - Jeanne Ropars
- Origine, Structure, Evolution de la Biodiversité, UMR 7205 CNRS-MNHN, Muséum National d’Histoire Naturelle, CP39, Paris Cedex 05, France
- Ecologie, Systématique et Evolution, Université Paris-Sud, Orsay cedex, France
- CNRS, Orsay cedex, France
| | - Manuela López-Villavicencio
- Origine, Structure, Evolution de la Biodiversité, UMR 7205 CNRS-MNHN, Muséum National d’Histoire Naturelle, CP39, Paris Cedex 05, France
| | - Joëlle Dupont
- Origine, Structure, Evolution de la Biodiversité, UMR 7205 CNRS-MNHN, Muséum National d’Histoire Naturelle, CP39, Paris Cedex 05, France
| | - Antoine Branca
- Ecologie, Systématique et Evolution, Université Paris-Sud, Orsay cedex, France
- CNRS, Orsay cedex, France
| | - Tatiana Giraud
- Ecologie, Systématique et Evolution, Université Paris-Sud, Orsay cedex, France
- CNRS, Orsay cedex, France
| | - Emmanuel Coton
- Université de Brest, EA 3882 Laboratoire Universitaire de Biodiversité et d’Ecologie Microbienne, ESIAB, Technopôle Brest-Iroise, Plouzané, France
- * E-mail:
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108
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Li B, Zong Y, Du Z, Chen Y, Zhang Z, Qin G, Zhao W, Tian S. Genomic Characterization Reveals Insights Into Patulin Biosynthesis and Pathogenicity in Penicillium Species. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2015; 28:635-47. [PMID: 25625822 DOI: 10.1094/mpmi-12-14-0398-fi] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Penicillium species are fungal pathogens that infect crop plants worldwide. P. expansum differs from P. italicum and P. digitatum, all major postharvest pathogens of pome and citrus, in that the former is able to produce the mycotoxin patulin and has a broader host range. The molecular basis of host-specificity of fungal pathogens has now become the focus of recent research. The present report provides the whole genome sequence of P. expansum (33.52 Mb) and P. italicum (28.99 Mb) and identifies differences in genome structure, important pathogenic characters, and secondary metabolite (SM) gene clusters in Penicillium species. We identified a total of 55 gene clusters potentially related to secondary metabolism, including a cluster of 15 genes (named PePatA to PePatO), that may be involved in patulin biosynthesis in P. expansum. Functional studies confirmed that PePatL and PePatK play crucial roles in the biosynthesis of patulin and that patulin production is not related to virulence of P. expansum. Collectively, P. expansum contains more pathogenic genes and SM gene clusters, in particular, an intact patulin cluster, than P. italicum or P. digitatum. These findings provide important information relevant to understanding the molecular network of patulin biosynthesis and mechanisms of host-specificity in Penicillium species.
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Affiliation(s)
- Boqiang Li
- 1 Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Yuanyuan Zong
- 1 Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Zhenglin Du
- 2 Core Genomic Facility, Beijing Institute of Genomics, Chinese Academy of Sciences
| | - Yong Chen
- 1 Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Zhanquan Zhang
- 1 Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Guozheng Qin
- 1 Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Wenming Zhao
- 2 Core Genomic Facility, Beijing Institute of Genomics, Chinese Academy of Sciences
| | - Shiping Tian
- 1 Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, China
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109
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Wolfe BE, Dutton RJ. Fermented foods as experimentally tractable microbial ecosystems. Cell 2015; 161:49-55. [PMID: 25815984 DOI: 10.1016/j.cell.2015.02.034] [Citation(s) in RCA: 213] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Indexed: 11/19/2022]
Abstract
Microbial communities of fermented foods have provided humans with tools for preservation and flavor development for thousands of years. These simple, reproducible, accessible, culturable, and easy-to-manipulate systems also provide opportunities for dissecting the mechanisms of microbial community formation. Fermented foods can be valuable models for processes in less tractable microbiota.
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Affiliation(s)
| | - Rachel J Dutton
- FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA.
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110
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A natural short pathway synthesizes roquefortine C but not meleagrin in three different Penicillium roqueforti strains. Appl Microbiol Biotechnol 2015; 99:7601-12. [PMID: 25998659 DOI: 10.1007/s00253-015-6676-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 05/03/2015] [Accepted: 05/05/2015] [Indexed: 10/23/2022]
Abstract
The production of mycotoxins and other secondary metabolites in Penicillium roqueforti is of great interest because of its long history of use in blue-veined cheese manufacture. In this article, we report the cloning and characterization of the roquefortine gene cluster in three different P. roqueforti strains isolated from blue cheese in the USA (the type strain), France, and the UK (Cheshire cheese). All three strains showed an identical roquefortine gene cluster organization and almost identical (98-99%) gene nucleotide sequences in the entire 16.6-kb cluster region. When compared with the Penicillium chrysogenum roquefortine/meleagrin seven-gene cluster, the P. roqueforti roquefortine cluster contains only four genes (rds, rdh, rpt, and gmt) encoding the roquefortine dipeptide synthetase, roquefortine D dehydrogenase, roquefortine prenyltransferase, and a methyltransferase, respectively. Silencing of the rds or rpt genes by the RNAi strategy reduced roquefortine C production by 50% confirming the involvement of these two key genes in roquefortine biosynthesis. An additional putative gene, orthologous of the MFS transporter roqT, is rearranged in all three strains as a pseudogene. The same four genes and a complete (not rearranged) roqT, encoding a MFS transporter containing 12 TMS domains, occur in the seven-gene cluster in P. chrysogenum although organized differently. Interestingly, the two "late" genes of the P. chrysogenum roquefortine/meleagrin gene cluster that convert roquefortine C to glandicoline B and meleagrin are absent in the P. roqueforti four-gene cluster. No meleagrin production was detected in P. roqueforti cultures grown in YES medium, while P. chrysogenum produces meleagrin in these conditions. No orthologous genes of the two missing meleagrin synthesizing genes were found elsewhere in the recently released P. roqueforti genome. Our data suggest that during evolution, the seven-gene cluster present in P. chrysogenum, and probably also in other glandicoline/meleagrin producing fungi, has been trimmed down to a short cluster in P. roqueforti leading to the synthesis of roquefortine C rather than meleagrin as a final product.
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111
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Dugat-Bony E, Straub C, Teissandier A, Onésime D, Loux V, Monnet C, Irlinger F, Landaud S, Leclercq-Perlat MN, Bento P, Fraud S, Gibrat JF, Aubert J, Fer F, Guédon E, Pons N, Kennedy S, Beckerich JM, Swennen D, Bonnarme P. Overview of a surface-ripened cheese community functioning by meta-omics analyses. PLoS One 2015; 10:e0124360. [PMID: 25867897 PMCID: PMC4395090 DOI: 10.1371/journal.pone.0124360] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Accepted: 03/02/2015] [Indexed: 11/18/2022] Open
Abstract
Cheese ripening is a complex biochemical process driven by microbial communities composed of both eukaryotes and prokaryotes. Surface-ripened cheeses are widely consumed all over the world and are appreciated for their characteristic flavor. Microbial community composition has been studied for a long time on surface-ripened cheeses, but only limited knowledge has been acquired about its in situ metabolic activities. We applied metagenomic, metatranscriptomic and biochemical analyses to an experimental surface-ripened cheese composed of nine microbial species during four weeks of ripening. By combining all of the data, we were able to obtain an overview of the cheese maturation process and to better understand the metabolic activities of the different community members and their possible interactions. Furthermore, differential expression analysis was used to select a set of biomarker genes, providing a valuable tool that can be used to monitor the cheese-making process.
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Affiliation(s)
- Eric Dugat-Bony
- INRA, UMR 782 Génie et Microbiologie des Procédés Alimentaires, F-78850, Thiverval-Grignon, France
- AgroParisTech, UMR 782 Génie et microbiologie des procédés alimentaires, F-78850, Thiverval-Grignon, France
| | - Cécile Straub
- INRA, UMR 782 Génie et Microbiologie des Procédés Alimentaires, F-78850, Thiverval-Grignon, France
- AgroParisTech, UMR 782 Génie et microbiologie des procédés alimentaires, F-78850, Thiverval-Grignon, France
| | - Aurélie Teissandier
- AgroParisTech, UMR 518 Mathématiques et Informatiques Appliquées, F-75231, Paris, France
- INRA, UMR 518 Mathématiques et Informatiques Appliquées, F-75231, Paris, France
| | - Djamila Onésime
- INRA, Institut Micalis, F-78352, Jouy-en-Josas, France
- AgroParisTech, Institut Micalis, F-78352, Jouy-en-Josas, France
| | - Valentin Loux
- INRA, UR1404 Mathématiques et Informatique Appliquées du Génome à l’Environnement, F-78352, Jouy-en-Josas, France
| | - Christophe Monnet
- INRA, UMR 782 Génie et Microbiologie des Procédés Alimentaires, F-78850, Thiverval-Grignon, France
- AgroParisTech, UMR 782 Génie et microbiologie des procédés alimentaires, F-78850, Thiverval-Grignon, France
| | - Françoise Irlinger
- INRA, UMR 782 Génie et Microbiologie des Procédés Alimentaires, F-78850, Thiverval-Grignon, France
- AgroParisTech, UMR 782 Génie et microbiologie des procédés alimentaires, F-78850, Thiverval-Grignon, France
| | - Sophie Landaud
- INRA, UMR 782 Génie et Microbiologie des Procédés Alimentaires, F-78850, Thiverval-Grignon, France
- AgroParisTech, UMR 782 Génie et microbiologie des procédés alimentaires, F-78850, Thiverval-Grignon, France
| | - Marie-Noëlle Leclercq-Perlat
- INRA, UMR 782 Génie et Microbiologie des Procédés Alimentaires, F-78850, Thiverval-Grignon, France
- AgroParisTech, UMR 782 Génie et microbiologie des procédés alimentaires, F-78850, Thiverval-Grignon, France
| | - Pascal Bento
- INRA, UR1404 Mathématiques et Informatique Appliquées du Génome à l’Environnement, F-78352, Jouy-en-Josas, France
| | | | - Jean-François Gibrat
- INRA, UR1404 Mathématiques et Informatique Appliquées du Génome à l’Environnement, F-78352, Jouy-en-Josas, France
| | - Julie Aubert
- AgroParisTech, UMR 518 Mathématiques et Informatiques Appliquées, F-75231, Paris, France
- INRA, UMR 518 Mathématiques et Informatiques Appliquées, F-75231, Paris, France
| | - Frédéric Fer
- INRA, UMR 782 Génie et Microbiologie des Procédés Alimentaires, F-78850, Thiverval-Grignon, France
- AgroParisTech, UMR 782 Génie et microbiologie des procédés alimentaires, F-78850, Thiverval-Grignon, France
- AgroParisTech, UMR 518 Mathématiques et Informatiques Appliquées, F-75231, Paris, France
- INRA, UMR 518 Mathématiques et Informatiques Appliquées, F-75231, Paris, France
| | - Eric Guédon
- INRA, Institut Micalis, F-78352, Jouy-en-Josas, France
- AgroParisTech, Institut Micalis, F-78352, Jouy-en-Josas, France
| | - Nicolas Pons
- INRA, US 1367 Metagenopolis, F-78352, Jouy-en-Josas, France
| | - Sean Kennedy
- INRA, US 1367 Metagenopolis, F-78352, Jouy-en-Josas, France
| | - Jean-Marie Beckerich
- INRA, UMR 782 Génie et Microbiologie des Procédés Alimentaires, F-78850, Thiverval-Grignon, France
- AgroParisTech, UMR 782 Génie et microbiologie des procédés alimentaires, F-78850, Thiverval-Grignon, France
| | - Dominique Swennen
- INRA, UMR 782 Génie et Microbiologie des Procédés Alimentaires, F-78850, Thiverval-Grignon, France
- AgroParisTech, UMR 782 Génie et microbiologie des procédés alimentaires, F-78850, Thiverval-Grignon, France
| | - Pascal Bonnarme
- INRA, UMR 782 Génie et Microbiologie des Procédés Alimentaires, F-78850, Thiverval-Grignon, France
- AgroParisTech, UMR 782 Génie et microbiologie des procédés alimentaires, F-78850, Thiverval-Grignon, France
- * E-mail:
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112
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Papadimitriou K, Pot B, Tsakalidou E. How microbes adapt to a diversity of food niches. Curr Opin Food Sci 2015. [DOI: 10.1016/j.cofs.2015.01.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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113
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Gil-Durán C, Rojas-Aedo JF, Medina E, Vaca I, García-Rico RO, Villagrán S, Levicán G, Chávez R. The pcz1 gene, which encodes a Zn(II)2Cys6 protein, is involved in the control of growth, conidiation, and conidial germination in the filamentous fungus Penicillium roqueforti. PLoS One 2015; 10:e0120740. [PMID: 25811807 PMCID: PMC4374774 DOI: 10.1371/journal.pone.0120740] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 01/26/2015] [Indexed: 12/26/2022] Open
Abstract
Proteins containing Zn(II)(2)Cys(6) domains are exclusively found in fungi and yeasts. Genes encoding this class of proteins are broadly distributed in fungi, but few of them have been functionally characterized. In this work, we have characterized a gene from the filamentous fungus Penicillium roqueforti that encodes a Zn(II)(2)Cys(6) protein, whose function to date remains unknown. We have named this gene pcz1. We showed that the expression of pcz1 is negatively regulated in a P. roqueforti strain containing a dominant active Gαi protein, suggesting that pcz1 encodes a downstream effector that is negatively controlled by Gαi. More interestingly, the silencing of pcz1 in P. roqueforti using RNAi-silencing technology resulted in decreased apical growth, the promotion of conidial germination (even in the absence of a carbon source), and the strong repression of conidiation, concomitant with the downregulation of the genes of the central conidiation pathway brlA, abaA and wetA. A model for the participation of pcz1 in these physiological processes in P. roqueforti is proposed.
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Affiliation(s)
- Carlos Gil-Durán
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Juan F. Rojas-Aedo
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Exequiel Medina
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Inmaculada Vaca
- Departmento de Química, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Ramón O. García-Rico
- GIMBIO Group, Department of Microbiology, Faculty of Basic Sciences, Universidad de Pamplona, Pamplona, Colombia
| | - Sebastián Villagrán
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Gloria Levicán
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Renato Chávez
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
- * E-mail: (RC)
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114
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Tannous J, Atoui A, El Khoury A, Kantar S, Chdid N, Oswald IP, Puel O, Lteif R. Development of a real-time PCR assay for Penicillium expansum quantification and patulin estimation in apples. Food Microbiol 2015; 50:28-37. [PMID: 25998812 DOI: 10.1016/j.fm.2015.03.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 01/19/2015] [Accepted: 03/02/2015] [Indexed: 10/23/2022]
Abstract
Due to the occurrence and spread of the fungal contaminants in food and the difficulties to remove their resulting mycotoxins, rapid and accurate methods are needed for early detection of these mycotoxigenic fungi. The polymerase chain reaction and the real time PCR have been widely used for this purpose. Apples are suitable substrates for fungal colonization mostly caused by Penicillium expansum, which produces the mycotoxin patulin during fruit infection. This study describes the development of a real-time PCR assay incorporating an internal amplification control (IAC) to specifically detect and quantify P. expansum. A specific primer pair was designed from the patF gene, involved in patulin biosynthesis. The selected primer set showed a high specificity for P. expansum and was successfully employed in a standardized real-time PCR for the direct quantification of this fungus in apples. Using the developed system, twenty eight apples were analyzed for their DNA content. Apples were also analyzed for patulin content by HPLC. Interestingly, a positive correlation (R(2) = 0.701) was found between P. expansum DNA content and patulin concentration. This work offers an alternative to conventional methods of patulin quantification and mycological detection of P. expansum and could be very useful for the screening of patulin in fruits through the application of industrial quality control.
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Affiliation(s)
- Joanna Tannous
- Université Saint-Joseph, Centre d'Analyses et de Recherche (Faculté des Sciences), Campus des Sciences et Technologies, Mar Roukos, Mkallès, P.O Box 11-514, Riad El Solh, 1107 2050 Beirut, Lebanon; INRA, UMR 1331 Toxalim, Research Centre in Food Toxicology, 180 Chemin de Tournefeuille, F-31027 Toulouse, Cedex, France; Université de Toulouse III, ENVT, INP, UMR 1331, Toxalim, F-31076, Toulouse, France
| | - Ali Atoui
- Laboratory of Microorganisms and Food Irradiation, Lebanese Atomic Energy Commission-CNRS, P.O. Box 11-8281, Riad El Solh, 1107 2260 Beirut, Lebanon.
| | - André El Khoury
- Université Saint-Joseph, Centre d'Analyses et de Recherche (Faculté des Sciences), Campus des Sciences et Technologies, Mar Roukos, Mkallès, P.O Box 11-514, Riad El Solh, 1107 2050 Beirut, Lebanon
| | - Sally Kantar
- Université Saint-Joseph, Centre d'Analyses et de Recherche (Faculté des Sciences), Campus des Sciences et Technologies, Mar Roukos, Mkallès, P.O Box 11-514, Riad El Solh, 1107 2050 Beirut, Lebanon
| | - Nader Chdid
- Université Saint-Joseph, Centre d'Analyses et de Recherche (Faculté des Sciences), Campus des Sciences et Technologies, Mar Roukos, Mkallès, P.O Box 11-514, Riad El Solh, 1107 2050 Beirut, Lebanon
| | - Isabelle P Oswald
- INRA, UMR 1331 Toxalim, Research Centre in Food Toxicology, 180 Chemin de Tournefeuille, F-31027 Toulouse, Cedex, France; Université de Toulouse III, ENVT, INP, UMR 1331, Toxalim, F-31076, Toulouse, France
| | - Olivier Puel
- INRA, UMR 1331 Toxalim, Research Centre in Food Toxicology, 180 Chemin de Tournefeuille, F-31027 Toulouse, Cedex, France; Université de Toulouse III, ENVT, INP, UMR 1331, Toxalim, F-31076, Toulouse, France
| | - Roger Lteif
- Université Saint-Joseph, Centre d'Analyses et de Recherche (Faculté des Sciences), Campus des Sciences et Technologies, Mar Roukos, Mkallès, P.O Box 11-514, Riad El Solh, 1107 2050 Beirut, Lebanon
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115
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Wisecaver JH, Rokas A. Fungal metabolic gene clusters-caravans traveling across genomes and environments. Front Microbiol 2015; 6:161. [PMID: 25784900 PMCID: PMC4347624 DOI: 10.3389/fmicb.2015.00161] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 02/11/2015] [Indexed: 11/13/2022] Open
Abstract
Metabolic gene clusters (MGCs), physically co-localized genes participating in the same metabolic pathway, are signature features of fungal genomes. MGCs are most often observed in specialized metabolism, having evolved in individual fungal lineages in response to specific ecological needs, such as the utilization of uncommon nutrients (e.g., galactose and allantoin) or the production of secondary metabolic antimicrobial compounds and virulence factors (e.g., aflatoxin and melanin). A flurry of recent studies has shown that several MGCs, whose functions are often associated with fungal virulence as well as with the evolutionary arms race between fungi and their competitors, have experienced horizontal gene transfer (HGT). In this review, after briefly introducing HGT as a source of gene innovation, we examine the evidence for HGT's involvement on the evolution of MGCs and, more generally of fungal metabolism, enumerate the molecular mechanisms that mediate such transfers and the ecological circumstances that favor them, as well as discuss the types of evidence required for inferring the presence of HGT in MGCs. The currently available examples indicate that transfers of entire MGCs have taken place between closely related fungal species as well as distant ones and that they sometimes involve large chromosomal segments. These results suggest that the HGT-mediated acquisition of novel metabolism is an ongoing and successful ecological strategy for many fungal species.
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Affiliation(s)
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University Nashville, TN, USA
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116
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Ballester AR, Marcet-Houben M, Levin E, Sela N, Selma-Lázaro C, Carmona L, Wisniewski M, Droby S, González-Candelas L, Gabaldón T. Genome, Transcriptome, and Functional Analyses of Penicillium expansum Provide New Insights Into Secondary Metabolism and Pathogenicity. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2015; 28:232-48. [PMID: 25338147 DOI: 10.1094/mpmi-09-14-0261-fi] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The relationship between secondary metabolism and infection in pathogenic fungi has remained largely elusive. The genus Penicillium comprises a group of plant pathogens with varying host specificities and with the ability to produce a wide array of secondary metabolites. The genomes of three Penicillium expansum strains, the main postharvest pathogen of pome fruit, and one Pencillium italicum strain, a postharvest pathogen of citrus fruit, were sequenced and compared with 24 other fungal species. A genomic analysis of gene clusters responsible for the production of secondary metabolites was performed. Putative virulence factors in P. expansum were identified by means of a transcriptomic analysis of apple fruits during the course of infection. Despite a major genome contraction, P. expansum is the Penicillium species with the largest potential for the production of secondary metabolites. Results using knockout mutants clearly demonstrated that neither patulin nor citrinin are required by P. expansum to successfully infect apples. Li et al. ( MPMI-12-14-0398-FI ) reported similar results and conclusions in their recently accepted paper.
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117
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Affiliation(s)
- Krishna Kant Sharma
- Laboratory of Enzymology and Recombinant DNA Technology, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, India
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118
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Perrone G, Samson RA, Frisvad JC, Susca A, Gunde-Cimerman N, Epifani F, Houbraken J. Penicillium salamii, a new species occurring during seasoning of dry-cured meat. Int J Food Microbiol 2015; 193:91-8. [DOI: 10.1016/j.ijfoodmicro.2014.10.023] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2014] [Revised: 09/29/2014] [Accepted: 10/20/2014] [Indexed: 11/28/2022]
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119
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Lacaze I, Lalucque H, Siegmund U, Silar P, Brun S. Identification of NoxD/Pro41 as the homologue of the p22phox NADPH oxidase subunit in fungi. Mol Microbiol 2014; 95:1006-24. [PMID: 25424886 DOI: 10.1111/mmi.12876] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/18/2014] [Indexed: 11/28/2022]
Abstract
NADPH oxidases (Nox) are membrane complexes that produce O2(-). Researches in mammals, plants and fungi highlight the involvement of Nox-generated ROS in cell proliferation, differentiation and defense. In mammals, the core enzyme gp91(phox)/Nox2 is associated with p22(phox) forming the flavocytochrome b558 ready for activation by a cytosolic complex. Intriguingly, no homologue of the p22(phox) gene has been found in fungal genomes, questioning how the flavoenzyme forms. Using whole genome sequencing combined with phylogenetic analysis and structural studies, we identify the fungal p22(phox) homologue as being mutated in the Podospora anserina mutant IDC(509). Functional studies show that the fungal p22(phox), PaNoxD, acts along PaNox1, but not PaNox2, a second fungal gp91(phox) homologue. Finally, cytological analysis of functional tagged versions of PaNox1, PaNoxD and PaNoxR shows clear co-localization of PaNoxD and PaNox1 and unravel a dynamic assembly of the complex in the endoplasmic reticulum and in the vacuolar system.
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Affiliation(s)
- Isabelle Lacaze
- Univ Paris Diderot, Sorbonne Paris Cité, Institut des Energies de Demain, case courrier 7040 Lamarck, 75205, Paris Cedex 13, France; Univ Paris Sud, Institut de Génétique et Microbiologie, UMR8621, 91405, Orsay Cedex, France
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120
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Monnet C, Landaud S, Bonnarme P, Swennen D. Growth and adaptation of microorganisms on the cheese surface. FEMS Microbiol Lett 2014; 362:1-9. [PMID: 25790503 DOI: 10.1093/femsle/fnu025] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Microbial communities living on cheese surfaces are composed of various bacteria, yeasts and molds that interact together, thus generating the typical sensory properties of a cheese. Physiological and genomic investigations have revealed important functions involved in the ability of microorganisms to establish themselves at the cheese surface. These functions include the ability to use the cheese's main energy sources, to acquire iron, to tolerate low pH at the beginning of ripening and to adapt to high salt concentrations and moisture levels. Horizontal gene transfer events involved in the adaptation to the cheese habitat have been described, both for bacteria and fungi. In the future, in situ microbial gene expression profiling and identification of genes that contribute to strain fitness by massive sequencing of transposon libraries will help us to better understand how cheese surface communities function.
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Affiliation(s)
- Christophe Monnet
- INRA, UMR782 Génie et Microbiologie des Procédés Alimentaires, 78850 Thiverval-Grignon, France AgroParisTech, UMR782 Génie et Microbiologie des Procédés Alimentaires, 78850 Thiverval-Grignon, France
| | - Sophie Landaud
- INRA, UMR782 Génie et Microbiologie des Procédés Alimentaires, 78850 Thiverval-Grignon, France AgroParisTech, UMR782 Génie et Microbiologie des Procédés Alimentaires, 78850 Thiverval-Grignon, France
| | - Pascal Bonnarme
- INRA, UMR782 Génie et Microbiologie des Procédés Alimentaires, 78850 Thiverval-Grignon, France AgroParisTech, UMR782 Génie et Microbiologie des Procédés Alimentaires, 78850 Thiverval-Grignon, France
| | - Dominique Swennen
- INRA, UMR 1319 Micalis, 78850 Thiverval-Grignon, France AgroParisTech, UMR 1319 Micalis, 78850 Thiverval-Grignon, France
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121
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Wolfe BE, Button JE, Santarelli M, Dutton RJ. Cheese rind communities provide tractable systems for in situ and in vitro studies of microbial diversity. Cell 2014; 158:422-433. [PMID: 25036636 DOI: 10.1016/j.cell.2014.05.041] [Citation(s) in RCA: 387] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 04/07/2014] [Accepted: 05/12/2014] [Indexed: 10/25/2022]
Abstract
Tractable microbial communities are needed to bridge the gap between observations of patterns of microbial diversity and mechanisms that can explain these patterns. We developed cheese rinds as model microbial communities by characterizing in situ patterns of diversity and by developing an in vitro system for community reconstruction. Sequencing of 137 different rind communities across 10 countries revealed 24 widely distributed and culturable genera of bacteria and fungi as dominant community members. Reproducible community types formed independent of geographic location of production. Intensive temporal sampling demonstrated that assembly of these communities is highly reproducible. Patterns of community composition and succession observed in situ can be recapitulated in a simple in vitro system. Widespread positive and negative interactions were identified between bacterial and fungal community members. Cheese rind microbial communities represent an experimentally tractable system for defining mechanisms that influence microbial community assembly and function.
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Affiliation(s)
- Benjamin E Wolfe
- FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
| | - Julie E Button
- FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
| | - Marcela Santarelli
- FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
| | - Rachel J Dutton
- FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA.
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Goarin A, Silar P, Malagnac F. Gene replacement in Penicillium roqueforti. Curr Genet 2014; 61:203-10. [PMID: 25315520 DOI: 10.1007/s00294-014-0456-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 10/06/2014] [Accepted: 10/09/2014] [Indexed: 11/30/2022]
Abstract
Most cheese-making filamentous fungi lack suitable molecular tools to improve their biotechnology potential. Penicillium roqueforti, a species of high industrial importance, would benefit from functional data yielded by molecular genetic approaches. This work provides the first example of gene replacement by homologous recombination in P. roqueforti, demonstrating that knockout experiments can be performed in this fungus. To do so, we improved the existing transformation method to integrate transgenes into P. roqueforti genome. In the meantime, we cloned the PrNiaD gene, which encodes a NADPH-dependent nitrate reductase that reduces nitrate to nitrite. Then, we performed a deletion of the PrNiaD gene from P. roqueforti strain AGO. The ΔPrNiaD mutant strain is more resistant to chlorate-containing medium than the wild-type strain, but did not grow on nitrate-containing medium. Because genomic data are now available, we believe that generating selective deletions of candidate genes will be a key step to open the way for a comprehensive exploration of gene function in P. roqueforti.
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Affiliation(s)
- Anne Goarin
- Institut des Energies de Demain (IED), LIED UMR 8236, Université Paris Diderot-Paris 7, Sorbonne Paris Cité, Case 7044-Lamarck, 35, rue Hélène Brion, 75205, Paris Cedex 13, France
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Yin LF, Wang F, Zhang Y, Kuang H, Schnabel G, Li GQ, Luo CX. Evolutionary analysis revealed the horizontal transfer of the Cyt b gene from Fungi to Chromista. Mol Phylogenet Evol 2014; 76:155-61. [DOI: 10.1016/j.ympev.2014.03.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Revised: 03/06/2014] [Accepted: 03/15/2014] [Indexed: 01/21/2023]
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Ropars J, López-Villavicencio M, Dupont J, Snirc A, Gillot G, Coton M, Jany JL, Coton E, Giraud T. Induction of sexual reproduction and genetic diversity in the cheese fungus Penicillium roqueforti. Evol Appl 2014; 7:433-41. [PMID: 24822078 PMCID: PMC4001442 DOI: 10.1111/eva.12140] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Accepted: 11/22/2013] [Indexed: 12/05/2022] Open
Abstract
The emblematic fungus Penicillium roqueforti is used throughout the world as a starter culture in the production of blue-veined cheeses. Like other industrial filamentous fungi, P. roqueforti was thought to lack a sexual cycle. However, an ability to induce recombination is of great economic and fundamental importance, as it would make it possible to transform and improve industrial strains, promoting the creation of novel phenotypes and eliminating the deleterious mutations that accumulate during clonal propagation. We report here, for the first time, the induction of the sexual structures of P. roqueforti — ascogonia, cleistothecia and ascospores. The progeny of the sexual cycle displayed clear evidence of recombination. We also used the recently published genome sequence for this species to develop microsatellite markers for investigating the footprints of recombination and population structure in a large collection of isolates from around the world and from different environments. Indeed, P. roqueforti also occurs in silage, wood and human-related environments other than cheese. We found tremendous genetic diversity within P. roqueforti, even within cheese strains and identified six highly differentiated clusters that probably predate the use of this species for cheese production. Screening for phenotypic and metabolic differences between these populations could guide future development strategies.
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Affiliation(s)
- Jeanne Ropars
- Ecologie, Systématique et Evolution, Université Paris-Sud Orsay Cedex, France ; CNRS Orsay Cedex, France
| | - Manuela López-Villavicencio
- Origine, Structure, Evolution de la Biodiversité, UMR 7205 CNRS-MNHN, Muséum National d'Histoire Naturelle Paris Cedex 05, France
| | - Joëlle Dupont
- Origine, Structure, Evolution de la Biodiversité, UMR 7205 CNRS-MNHN, Muséum National d'Histoire Naturelle Paris Cedex 05, France
| | - Alodie Snirc
- Ecologie, Systématique et Evolution, Université Paris-Sud Orsay Cedex, France ; CNRS Orsay Cedex, France
| | - Guillaume Gillot
- Université de Brest, EA 3882, Laboratoire Universitaire de Biodiversité et d'Ecologie Microbienne, ESIAB, Technopôle Brest-Iroise Plouzané, France
| | - Monika Coton
- Université de Brest, EA 3882, Laboratoire Universitaire de Biodiversité et d'Ecologie Microbienne, ESIAB, Technopôle Brest-Iroise Plouzané, France
| | - Jean-Luc Jany
- Université de Brest, EA 3882, Laboratoire Universitaire de Biodiversité et d'Ecologie Microbienne, ESIAB, Technopôle Brest-Iroise Plouzané, France
| | - Emmanuel Coton
- Université de Brest, EA 3882, Laboratoire Universitaire de Biodiversité et d'Ecologie Microbienne, ESIAB, Technopôle Brest-Iroise Plouzané, France
| | - Tatiana Giraud
- Ecologie, Systématique et Evolution, Université Paris-Sud Orsay Cedex, France ; CNRS Orsay Cedex, France
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125
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Maintaining two mating types: structure of the mating type locus and its role in heterokaryosis in Podospora anserina. Genetics 2014; 197:421-32. [PMID: 24558260 DOI: 10.1534/genetics.113.159988] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Pseudo-homothallism is a reproductive strategy elected by some fungi producing heterokaryotic sexual spores containing genetically different but sexually compatible nuclei. This lifestyle appears as a compromise between true homothallism (self-fertility with predominant inbreeding) and complete heterothallism (with exclusive outcrossing). However, pseudohomothallic species face the problem of maintaining heterokaryotic mycelia to fully benefit from this lifestyle, as homokaryons are self-sterile. Here, we report on the structure of chromosome 1 in mat+ and mat- isolates of strain S of the pseudohomothallic fungus Podospora anserina. Chromosome 1 contains either one of the mat+ and mat- mating types of P. anserina, which is mostly found in nature as a mat+/mat- heterokaryotic mycelium harboring sexually compatible nuclei. We identified a "mat" region ∼0.8 Mb long, devoid of meiotic recombination and containing the mating-type idiomorphs, which is a candidate to be involved in the maintenance of the heterokaryotic state, since the S mat+ and S mat- strains have different physiology that may enable hybrid-vigor-like phenomena in the heterokaryons. The mat region contains 229 coding sequences. A total of 687 polymorphisms were detected between the S mat+ and S mat- chromosomes. Importantly, the mat region is colinear between both chromosomes, which calls for an original mechanism of recombination inhibition. Microarray analyses revealed that 10% of the P. anserina genes have different transcriptional profiles in S mat+ and S mat-, in line with their different phenotypes. Finally, we show that the heterokaryotic state is faithfully maintained during mycelium growth of P. anserina, yet mat+/mat+ and mat-/mat- heterokaryons are as stable as mat+/mat- ones, evidencing a maintenance of heterokaryosis that does not rely on fitness-enhancing complementation between the S mat+ and S mat- strains.
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Gladieux P, Ropars J, Badouin H, Branca A, Aguileta G, Vienne DM, Rodríguez de la Vega RC, Branco S, Giraud T. Fungal evolutionary genomics provides insight into the mechanisms of adaptive divergence in eukaryotes. Mol Ecol 2014; 23:753-73. [DOI: 10.1111/mec.12631] [Citation(s) in RCA: 151] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 12/04/2013] [Indexed: 12/15/2022]
Affiliation(s)
- Pierre Gladieux
- Ecologie, Systématique et Evolution UMR8079 University of Paris‐Sud Orsay 91405 France
- Ecologie, Systématique et Evolution CNRS UMR8079 Orsay 91405 France
- Department of Plant and Microbial Biology University of California Berkeley CA 94720‐3102 USA
| | - Jeanne Ropars
- Ecologie, Systématique et Evolution UMR8079 University of Paris‐Sud Orsay 91405 France
- Ecologie, Systématique et Evolution CNRS UMR8079 Orsay 91405 France
| | - Hélène Badouin
- Ecologie, Systématique et Evolution UMR8079 University of Paris‐Sud Orsay 91405 France
- Ecologie, Systématique et Evolution CNRS UMR8079 Orsay 91405 France
| | - Antoine Branca
- Ecologie, Systématique et Evolution UMR8079 University of Paris‐Sud Orsay 91405 France
- Ecologie, Systématique et Evolution CNRS UMR8079 Orsay 91405 France
| | - Gabriela Aguileta
- Center for Genomic Regulation (CRG) Dr, Aiguader 88 Barcelona 08003 Spain
- Universitat Pompeu Fabra (UPF) Barcelona 08003 Spain
| | - Damien M. Vienne
- Center for Genomic Regulation (CRG) Dr, Aiguader 88 Barcelona 08003 Spain
- Universitat Pompeu Fabra (UPF) Barcelona 08003 Spain
- Laboratoire de Biométrie et Biologie Evolutive Université Lyon 1 CNRS UMR5558 Villeurbanne 69622 France
| | - Ricardo C. Rodríguez de la Vega
- Ecologie, Systématique et Evolution UMR8079 University of Paris‐Sud Orsay 91405 France
- Ecologie, Systématique et Evolution CNRS UMR8079 Orsay 91405 France
| | - Sara Branco
- Department of Plant and Microbial Biology University of California Berkeley CA 94720‐3102 USA
| | - Tatiana Giraud
- Ecologie, Systématique et Evolution UMR8079 University of Paris‐Sud Orsay 91405 France
- Ecologie, Systématique et Evolution CNRS UMR8079 Orsay 91405 France
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