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Haque MA, Nath ND, Johnston TV, Haruna S, Ahn J, Ovissipour R, Ku S. Harnessing biotechnology for penicillin production: Opportunities and environmental considerations. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 946:174236. [PMID: 38942308 DOI: 10.1016/j.scitotenv.2024.174236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 06/20/2024] [Accepted: 06/21/2024] [Indexed: 06/30/2024]
Abstract
Since the discovery of antibiotics, penicillin has remained the top choice in clinical medicine. With continuous advancements in biotechnology, penicillin production has become cost-effective and efficient. Genetic engineering techniques have been employed to enhance biosynthetic pathways, leading to the production of new penicillin derivatives with improved properties and increased efficacy against antibiotic-resistant pathogens. Advances in bioreactor design, media formulation, and process optimization have contributed to higher yields, reduced production costs, and increased penicillin accessibility. While biotechnological advances have clearly benefited the global production of this life-saving drug, they have also created challenges in terms of waste management. Production fermentation broths from industries contain residual antibiotics, by-products, and other contaminants that pose direct environmental threats, while increased global consumption intensifies the risk of antimicrobial resistance in both the environment and living organisms. The current geographical and spatial distribution of antibiotic and penicillin consumption dramatically reveals a worldwide threat. These challenges are being addressed through the development of novel waste management techniques. Efforts are aimed at both upstream and downstream processing of antibiotic and penicillin production to minimize costs and improve yield efficiency while lowering the overall environmental impact. Yield optimization using artificial intelligence (AI), along with biological and chemical treatment of waste, is also being explored to reduce adverse impacts. The implementation of strict regulatory frameworks and guidelines is also essential to ensure proper management and disposal of penicillin production waste. This review is novel because it explores the key remaining challenges in antibiotic development, the scope of machine learning tools such as Quantitative Structure-Activity Relationship (QSAR) in modern biotechnology-driven production, improved waste management for antibiotics, discovering alternative path to reducing antibiotic use in agriculture through alternative meat production, addressing current practices, and offering effective recommendations.
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Affiliation(s)
- Md Ariful Haque
- Department of Food Science and Technology, Texas A&M University, College Station, USA.
| | - Nirmalendu Deb Nath
- Department of Biomedical and Diagnostic Sciences, University of Tennessee, Knoxville, USA.
| | - Tony Vaughn Johnston
- Fermentation Science Program, School of Agriculture, College of Basic and Applied Sciences, Middle Tennessee State University, Murfreesboro, USA.
| | - Samuel Haruna
- Fermentation Science Program, School of Agriculture, College of Basic and Applied Sciences, Middle Tennessee State University, Murfreesboro, USA.
| | - Jaehyun Ahn
- Department of Food Science and Technology, Texas A&M University, College Station, USA.
| | - Reza Ovissipour
- Department of Food Science and Technology, Texas A&M University, College Station, USA.
| | - Seockmo Ku
- Department of Food Science and Technology, Texas A&M University, College Station, USA.
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Lo Y, Bruxaux J, Rodríguez de la Vega RC, O'Donnell S, Snirc A, Coton M, Le Piver M, Le Prieur S, Roueyre D, Dupont J, Houbraken J, Debuchy R, Ropars J, Giraud T, Branca A. Domestication in dry-cured meat Penicillium fungi: Convergent specific phenotypes and horizontal gene transfers without strong genetic subdivision. Evol Appl 2023; 16:1637-1660. [PMID: 37752962 PMCID: PMC10519415 DOI: 10.1111/eva.13591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 07/17/2023] [Accepted: 08/18/2023] [Indexed: 09/28/2023] Open
Abstract
Some fungi have been domesticated for food production, with genetic differentiation between populations from food and wild environments, and food populations often acquiring beneficial traits through horizontal gene transfers (HGTs). Studying their adaptation to human-made substrates is of fundamental and applied importance for understanding adaptation processes and for further strain improvement. We studied here the population structures and phenotypes of two distantly related Penicillium species used for dry-cured meat production, P. nalgiovense, the most common species in the dry-cured meat food industry, and P. salamii, used locally by farms. Both species displayed low genetic diversity, lacking differentiation between strains isolated from dry-cured meat and those from other environments. Nevertheless, the strains collected from dry-cured meat within each species displayed slower proteolysis and lipolysis than their wild conspecifics, and those of P. nalgiovense were whiter. Phenotypically, the non-dry-cured meat strains were more similar to their sister species than to their conspecific dry-cured meat strains, indicating an evolution of specific phenotypes in dry-cured meat strains. A comparison of available Penicillium genomes from various environments revealed HGTs, particularly between P. nalgiovense and P. salamii (representing almost 1.5 Mb of cumulative length). HGTs additionally involved P. biforme, also found in dry-cured meat products. We further detected positive selection based on amino acid changes. Our findings suggest that selection by humans has shaped the P. salamii and P. nalgiovense populations used for dry-cured meat production, which constitutes domestication. Several genetic and phenotypic changes were similar in P. salamii, P. nalgiovense and P. biforme, indicating convergent adaptation to the same human-made environment. Our findings have implications for fundamental knowledge on adaptation and for the food industry: the discovery of different phenotypes and of two mating types paves the way for strain improvement by conventional breeding, to elucidate the genomic bases of beneficial phenotypes and to generate diversity.
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Affiliation(s)
- Ying‐Chu Lo
- IDEEV – Laboratoire Ecologie, Systématique et Evolution, CNRS, AgroParisTechUniversité Paris‐SaclayGif‐sur‐YvetteFrance
| | - Jade Bruxaux
- IDEEV – Laboratoire Ecologie, Systématique et Evolution, CNRS, AgroParisTechUniversité Paris‐SaclayGif‐sur‐YvetteFrance
- Department of Ecology and Environmental ScienceUmeå UniversityUmeåSweden
| | | | - Samuel O'Donnell
- IDEEV – Laboratoire Ecologie, Systématique et Evolution, CNRS, AgroParisTechUniversité Paris‐SaclayGif‐sur‐YvetteFrance
| | - Alodie Snirc
- IDEEV – Laboratoire Ecologie, Systématique et Evolution, CNRS, AgroParisTechUniversité Paris‐SaclayGif‐sur‐YvetteFrance
| | - Monika Coton
- Univ Brest, Laboratoire Universitaire de Biodiversité et Ecologie MicrobiennePlouzanéFrance
| | - Mélanie Le Piver
- Laboratoire Interprofessionnel de Production – SAS L.I.PAurillacFrance
| | - Stéphanie Le Prieur
- IDEEV – Laboratoire Ecologie, Systématique et Evolution, CNRS, AgroParisTechUniversité Paris‐SaclayGif‐sur‐YvetteFrance
| | - Daniel Roueyre
- Laboratoire Interprofessionnel de Production – SAS L.I.PAurillacFrance
| | - Joëlle Dupont
- Origine, Structure, Evolution de la Biodiversité, UMR 7205 CNRS‐MNHN, Muséum National d'Histoire NaturelleParis Cedex 05France
| | - Jos Houbraken
- Westerdijk Fungal Biodiversity InstituteUtrechtThe Netherlands
| | - Robert Debuchy
- Université Paris‐Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC)Gif‐sur‐YvetteFrance
| | - Jeanne Ropars
- IDEEV – Laboratoire Ecologie, Systématique et Evolution, CNRS, AgroParisTechUniversité Paris‐SaclayGif‐sur‐YvetteFrance
| | - Tatiana Giraud
- IDEEV – Laboratoire Ecologie, Systématique et Evolution, CNRS, AgroParisTechUniversité Paris‐SaclayGif‐sur‐YvetteFrance
| | - Antoine Branca
- IDEEV – Laboratoire Ecologie, Systématique et Evolution, CNRS, AgroParisTechUniversité Paris‐SaclayGif‐sur‐YvetteFrance
- IDEEV – Laboratoire Evolution, Génomes Comportement, EcologieCNRS Université Paris Saclay UMR 9191, IRD UMR 247Gif‐sur‐YvetteFrance
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3
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Ramšak B, Kück U. The Penicillium chrysogenum tom1 Gene a Major Target of Transcription Factor MAT1-1-1 Encodes a Nuclear Protein Involved in Sporulation. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:937023. [PMID: 37746180 PMCID: PMC10512297 DOI: 10.3389/ffunb.2022.937023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 06/13/2022] [Indexed: 09/26/2023]
Abstract
Fungal mating-type loci (MAT) encode transcription factors (TFs) MAT1-1-1 and MAT1-2-1, which govern sexual reproduction as well as other developmental processes. In Penicillium chrysogenum, the major producer of the beta-lactam antibiotic penicillin, a recent chromatin immunoprecipitation followed by sequencing (ChIP-seq) analysis identified 254 genes as direct targets of MAT1-1-1, many of which encode thus far uncharacterized proteins. Here, we characterized one of the major targets of MAT1-1-1, the tom1 gene, which encodes a protein highly conserved within the group of Eurotiomycetes fungi. Using fluorescence microscopy, we demonstrated binding of MAT1-1-1 to the tom1 promoter by reporter gene analysis. Extensive electrophoretic mobility shift assays (EMSAs) further showed that the promoter sequence of tom1 is bound in vitro by both MAT1-1-1 and MAT1-2-1. This indicated an interaction between the two TFs, which was verified by yeast two-hybrid analysis. The sequence of tom1 carries a nuclear localization sequence, and indeed its nuclear localization was verified by fluorescence microscopy. The in vivo function of tom1 was investigated using tom1 deletion strains, as well as a complementing strain where the wild-type tom1 gene was reintroduced. We found a clear sporulation defect in the deletion strain, which became more evident when the fungi were grown at an elevated temperature of 31°C.
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Affiliation(s)
| | - Ulrich Kück
- Allgemeine und Molekulare Botanik, Ruhr-Universität Bochum, Fakultät für Biologie und Biotechnologie, Bochum, Germany
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Fierro F, Vaca I, Castillo NI, García-Rico RO, Chávez R. Penicillium chrysogenum, a Vintage Model with a Cutting-Edge Profile in Biotechnology. Microorganisms 2022; 10:microorganisms10030573. [PMID: 35336148 PMCID: PMC8954384 DOI: 10.3390/microorganisms10030573] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 02/15/2022] [Accepted: 02/17/2022] [Indexed: 12/20/2022] Open
Abstract
The discovery of penicillin entailed a decisive breakthrough in medicine. No other medical advance has ever had the same impact in the clinical practise. The fungus Penicillium chrysogenum (reclassified as P. rubens) has been used for industrial production of penicillin ever since the forties of the past century; industrial biotechnology developed hand in hand with it, and currently P. chrysogenum is a thoroughly studied model for secondary metabolite production and regulation. In addition to its role as penicillin producer, recent synthetic biology advances have put P. chrysogenum on the path to become a cell factory for the production of metabolites with biotechnological interest. In this review, we tell the history of P. chrysogenum, from the discovery of penicillin and the first isolation of strains with high production capacity to the most recent research advances with the fungus. We will describe how classical strain improvement programs achieved the goal of increasing production and how the development of different molecular tools allowed further improvements. The discovery of the penicillin gene cluster, the origin of the penicillin genes, the regulation of penicillin production, and a compilation of other P. chrysogenum secondary metabolites will also be covered and updated in this work.
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Affiliation(s)
- Francisco Fierro
- Departamento de Biotecnología, Universidad Autónoma Metropolitana-Unidad Iztapalapa, Ciudad de México 09340, Mexico
- Correspondence:
| | - Inmaculada Vaca
- Departamento de Química, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile;
| | - Nancy I. Castillo
- Grupo de Investigación en Ciencias Biológicas y Químicas, Facultad de Ciencias, Universidad Antonio Nariño, Bogotá 110231, Colombia;
| | - Ramón Ovidio García-Rico
- Grupo de Investigación GIMBIO, Departamento De Microbiología, Facultad de Ciencias Básicas, Universidad de Pamplona, Pamplona 543050, Colombia;
| | - Renato Chávez
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago 9170020, Chile;
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Wilson AM, Wilken PM, Wingfield MJ, Wingfield BD. Genetic Networks That Govern Sexual Reproduction in the Pezizomycotina. Microbiol Mol Biol Rev 2021; 85:e0002021. [PMID: 34585983 PMCID: PMC8485983 DOI: 10.1128/mmbr.00020-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Sexual development in filamentous fungi is a complex process that relies on the precise control of and interaction between a variety of genetic networks and pathways. The mating-type (MAT) genes are the master regulators of this process and typically act as transcription factors, which control the expression of genes involved at all stages of the sexual cycle. In many fungi, the sexual cycle typically begins when the mating pheromones of one mating type are recognized by a compatible partner, followed by physical interaction and fertilization. Subsequently, highly specialized sexual structures are formed, within which the sexual spores develop after rounds of meiosis and mitosis. These spores are then released and germinate, forming new individuals that initiate new cycles of growth. This review provides an overview of the known genetic networks and pathways that are involved in each major stage of the sexual cycle in filamentous ascomycete fungi.
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Affiliation(s)
- Andi M. Wilson
- Forestry and Agricultural Biotechnology Institute, Department of Biochemistry, Genetics, and Microbiology, University of Pretoria, Pretoria, Gauteng, South Africa
| | - P. Markus Wilken
- Forestry and Agricultural Biotechnology Institute, Department of Biochemistry, Genetics, and Microbiology, University of Pretoria, Pretoria, Gauteng, South Africa
| | - Michael J. Wingfield
- Forestry and Agricultural Biotechnology Institute, Department of Biochemistry, Genetics, and Microbiology, University of Pretoria, Pretoria, Gauteng, South Africa
| | - Brenda D. Wingfield
- Forestry and Agricultural Biotechnology Institute, Department of Biochemistry, Genetics, and Microbiology, University of Pretoria, Pretoria, Gauteng, South Africa
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Mahmoudjanlou Y, Dahlmann TA, Kück U. Molecular analysis of mating type loci from the mycophenolic acid producer Penicillium brevicompactum: Phylogeny and MAT protein characterization suggest a cryptic sexual life cycle. Fungal Biol 2020; 124:821-833. [PMID: 32883432 DOI: 10.1016/j.funbio.2020.07.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 06/25/2020] [Accepted: 07/07/2020] [Indexed: 12/31/2022]
Abstract
The mycophenolic acid producing ascomycete Penicillium brevicompactum is considered to be an anamorphic (asexual) species, for which a sexual cycle was never observed. However, since recent reports of otherwise asexually propagating filamentous fungi have demonstrated a sexual cycle controlled by mating type loci, we carried out a molecular analysis of mating type loci from P. brevicompactum. Using data from extensive DNA sequencing analysis, we determined the mating type loci from 22 strains derived from various type culture collections. We found 8 strains carrying a MAT1-1 locus encoding a 362 amino acid alpha domain transcription factor. The other 14 possessed a MAT1-2 locus encoding a 298 amino acid HMG domain transcription factor. cDNA analysis confirmed that both mating type loci are transcriptionally expressed. The karyotype of six selected strains, determined using contour-clamped homogeneous electric field (CHEF) electrophoresis, demonstrated distinct differences in size and numbers of chromosomes between the strains investigated. Interestingly, our phylogenetic survey of 72 strains from 11 different Penicillium species revealed that MAT genes serve as excellent molecular markers to determine phylogenetic relationships among species closely related to P. brevicompactum. Based on our sequencing results, we constructed transformation vectors for site-specific deletion of mating type loci from two selected strains of opposite mating type. Complementation strains were constructed containing both the mating type locus deletion cassette and a MAT-egfp fusion gene. These strains were used for comparative phenotypic analyses between strains containing or lacking the mating type gene. Whereas all MAT1-2 strains were indistinguishable, the MAT1-1 and MAT1-1-1 deletion strains differed distinctly. The MAT1-1-1 deletion strain produced more conidiospores on solid media, but smaller pellets in liquid media. This is probably the consequence of fewer conidial germ tubes than with the wild type mating type strain. Finally, we showed that the MAT-EGPF fusion protein is localized to the nuclei and detectable in protein samples by Western analysis. Together, our results suggest that the asexually propagating fungus P. brevicompactum might be a heterothallic species with a cryptic sexual life cycle.
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Affiliation(s)
| | - Tim A Dahlmann
- Allgemeine und Molekulare Botanik, Ruhr-Universität Bochum, 44780 Bochum, Germany.
| | - Ulrich Kück
- Allgemeine und Molekulare Botanik, Ruhr-Universität Bochum, 44780 Bochum, Germany.
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Martín JF. Insight into the Genome of Diverse Penicillium chrysogenum Strains: Specific Genes, Cluster Duplications and DNA Fragment Translocations. Int J Mol Sci 2020; 21:E3936. [PMID: 32486280 PMCID: PMC7312703 DOI: 10.3390/ijms21113936] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 05/19/2020] [Accepted: 05/29/2020] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND There are eighteen species within the Penicillium genus section chrysogena, including the original penicillin producers Penicillium notatum (Fleming strain) and Penicillium chrysogenum NRRL 1951. Other wild type isolates of the Penicillium genus are relevant for the production of useful proteins and primary or secondary metabolites. The aim of this article is to characterize strain specific genes and those genes which are involved in secondary metabolite biosynthesis, particularly the mutations that have been introduced during the β-lactams strain improvement programs. RESULTS The available genomes of several classical and novel P. chrysogenum strains have been compared. The first genome sequenced was that of the reference strain P. chrysogenum Wis54-1255, which derives from the wild type P. chrysogenum NRRL 1951; its genome size is 32.19 Mb and it encodes 12,943 proteins. Four chromosomes were resolved in P. chrysogenum and P. notatum by pulse field gel electrophoresis. The genomes of three industrial strains have a similar size but contain gene duplications and truncations; the penicillin gene cluster copy number ranges from one in the wild type to twelve in the P. chrysogenum ASP-E1 industrial strain and is organized in head to tail tandem repeats. The genomes of two new strains, P. chrysogenum KF-25, a producer of antifungal proteins isolated from a soil sample, and P. chrysogenum HKF2, a strain with carbohydrate-converting activities isolated from a sludge treatment plant, showed strain specific genes. CONCLUSIONS The overall comparison of all available P. chrysogenum genomes indicates that there are a significant number of strain-specific genes, mutations of structural and regulatory genes, gene cluster duplications and DNA fragment translocations. This information provides important leads to improve the biosynthesis of enzymes, antifungal agents, prebiotics or different types of secondary metabolites.
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Affiliation(s)
- Juan F Martín
- Área de Microbiología, Departamento de Biología Molecular, Universidad de León, 24071 León, Spain
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8
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Mahmoudjanlou Y, Hoff B, Kück U. Construction of a Codon-Adapted Nourseotricin-Resistance Marker Gene for Efficient Targeted Gene Deletion in the Mycophenolic Acid Producer Penicillium brevicompactum. J Fungi (Basel) 2019; 5:E96. [PMID: 31658687 PMCID: PMC6958462 DOI: 10.3390/jof5040096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 10/01/2019] [Accepted: 10/06/2019] [Indexed: 11/16/2022] Open
Abstract
Penicillium brevicompactum is a filamentous ascomycete used in the pharmaceutical industry to produce mycophenolic acid, an immunosuppressant agent. To extend options for genetic engineering of this fungus, we have tested two resistance markers that have not previously been applied to P. brevicompactum. Although a generally available phleomycin resistance marker (ble) was successfully used in DNA-mediated transformation experiments, we were not able to use a commonly applicable nourseothricin resistance cassette (nat1). To circumvent this failure, we constructed a new nat gene, considering the codon bias for P. brevicompactum. We then used this modified nat gene in subsequent transformation experiments for the targeted disruption of two nuclear genes, MAT1-2-1 and flbA. For MAT1-2-1, we obtained deletion strains with a frequency of about 10%. In the case of flbA, the frequency was about 4%, and this disruption strain also showed reduced conidiospore formation. To confirm the deletion, we used ble to reintroduce the wild-type genes. This step restored the wild-type phenotype in the flbA deletion strain, which had a sporulation defect. The successful transformation system described here substantially extends options for genetically manipulating the biotechnologically relevant fungus P. brevicompactum.
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Affiliation(s)
| | - Birgit Hoff
- Allgemeine & Molekulare Botanik, Ruhr-Universität Bochum, 44780 Bochum, Germany.
| | - Ulrich Kück
- Allgemeine & Molekulare Botanik, Ruhr-Universität Bochum, 44780 Bochum, Germany.
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9
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Espeso EA, Villarino M, Carreras M, Alonso-Guirado L, Alonso JM, Melgarejo P, Larena I. Altered nitrogen metabolism in biocontrol strains of Penicillium rubens. Fungal Genet Biol 2019; 132:103263. [PMID: 31419528 DOI: 10.1016/j.fgb.2019.103263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 07/31/2019] [Accepted: 08/11/2019] [Indexed: 10/26/2022]
Abstract
The importance of the metabolic route of nitrogen in the fungus Penicillium rubens (strain PO212) is studied in relation to its biocontrol activity (BA). PO212 can resist a high concentration of chlorate anion and displays a classical nitrate-deficiency (nit-) phenotype resulting in poor colonial growth when nitrate is used as the main source of nitrogen. Analyses of genes implicated in nitrate assimilation evidenced the strong sequence conservation of PO212 and CH8 genome with penicillin producers such as reference strain P. rubens Wisconsin 54-1255, P2niaD18 and Pc3, however also revealed the presence of mutations. PO212 carries a mutation in the gene coding for zinc-binuclear cluster transcription factor NirA that specifically mediates the regulation of genes involved in nitrate assimilation. The nirA1 mutation causes an early stop of NirA factor, losing 66% of its sequence. The NirA1 mutant form is unable to mediate a nitrate-dependent regulation of nitrate and nitrite reductase coding genes. In this study, we study another isolate, CH8, with potential BA and nit- phenotype. A mutation in the nitrate permease coding gene crnA was found in CH8. An insertion of a guanine in the coding sequence cause a frameshift in CrnA with the loss of the last two transmembrane domains. Analysis of PO212 and CH8 isolates and complementation strains show the importance of NirA regulator in maintaining correct transcriptional levels of nitrate and nitrite reductases and suggest CrnA as the main nitrate transporter. the presence of alternative transporter for chlorate and the existence of a mechanism for preventing nitrite derived toxicity in Penicillum. BA of PO212 is partially altered when nirA1 mutation was complemented. This result and the finding of CH8, a novel biocontrol P. rubens strain with a nit- phenotype, suggest that nitrogen metabolism is a component of biocontrol capacity.
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Affiliation(s)
- E A Espeso
- Centro Investigaciones Biológicas, CSIC, Departamento de Biología Molecular y Celular, Ramiro de Maeztu, 9, Madrid 28040, Spain.
| | - M Villarino
- SGIT-INIA, Departamento de Protección Vegetal, Carretera de la Coruña, km 7, Madrid 28040, Spain.
| | - M Carreras
- SGIT-INIA, Departamento de Protección Vegetal, Carretera de la Coruña, km 7, Madrid 28040, Spain.
| | - L Alonso-Guirado
- Centro Investigaciones Biológicas, CSIC, Departamento de Biología Molecular y Celular, Ramiro de Maeztu, 9, Madrid 28040, Spain; Spanish National Cancer Research Centre CNIO, Genetic & Molecular Epidemiology Group, Madrid 28029, Spain(1).
| | - J M Alonso
- Centro Investigaciones Biológicas, CSIC, Departamento de Biología Molecular y Celular, Ramiro de Maeztu, 9, Madrid 28040, Spain
| | - P Melgarejo
- SGIT-INIA, Departamento de Protección Vegetal, Carretera de la Coruña, km 7, Madrid 28040, Spain.
| | - I Larena
- SGIT-INIA, Departamento de Protección Vegetal, Carretera de la Coruña, km 7, Madrid 28040, Spain.
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10
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Li X, Wang F, Liu Q, Li Q, Qian Z, Zhang X, Li K, Li W, Dong C. Developmental transcriptomics of Chinese cordyceps reveals gene regulatory network and expression profiles of sexual development-related genes. BMC Genomics 2019; 20:337. [PMID: 31054562 PMCID: PMC6500587 DOI: 10.1186/s12864-019-5708-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 04/17/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Chinese cordyceps, also known as Chinese caterpillar fungus (Ophiocordyceps sinensis, syn. Cordyceps sinensis), is of particular interest for its cryptic life cycle and economic and ecological importance. The large-scale artificial cultivation was succeeded recently after several decades of efforts and attempts. However, the induction of primordium, sexual development of O. sinensis and the molecular basis of its lifestyle still remain cryptic. RESULTS The developmental transcriptomes were analyzed for six stages covering the whole developmental process, including hyphae (HY), sclerotium (ST), primordium (PR), young fruiting body (YF), developed fruiting body (DF) and mature fruiting body (MF), with a focus on the expression of sexual development-related genes. Principal component analysis revealed that the gene expression profiles at the stages of primordium formation and fruiting body development are more similar than those of the undifferentiated HY stage. The PR and MF stages grouped together, suggesting that primordium differentiation and sexual maturation have similar expression patterns. Many more DEGs were identified between the ST and HY stages, covering 47.5% of the O. sinensis genome, followed by the comparisons between the ST and PR stages. Using pairwise comparisons and weighted gene coexpression network analysis, modules of coexpressed genes and candidate hub genes for each developmental stage were identified. The four mating type loci genes expressed during primordium differentiation and sexual maturation; however, spatiotemporal specificity of gene expression indicated that they also expressed during the anamorphic HY stage. The four mating type genes were not coordinately expressed, suggesting they may have divergent roles. The expression of the four mating type genes was highest in the fertile part and lowest in the sclerotium of the MF stage, indicating that there is tissue specificity. Half of genes related to mating signaling showed as the highest expression in the ST stage, indicating fruiting was initiated in the ST stage. CONCLUSIONS These results provide a new perspective to understanding of the key pathways and hub genes, and sexual development-related gene profile in the development of Chinese cordyceps. It will be helpful for underlying sexual reproduction, and add new information to existing models of fruiting body development in edible fungi.
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Affiliation(s)
- Xiao Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, NO. 3 Park 1, Beichen West Road, Chaoyang District, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100039 China
| | - Fen Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, NO. 3 Park 1, Beichen West Road, Chaoyang District, Beijing, 100101 China
| | - Qing Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, NO. 3 Park 1, Beichen West Road, Chaoyang District, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100039 China
| | - Quanping Li
- Key Laboratory of State Administration of Traditional Chinese Medicine, Sunshine Lake Pharma Co., LTD, Dongguan, 523850 Guangdong China
| | - Zhengming Qian
- Key Laboratory of State Administration of Traditional Chinese Medicine, Sunshine Lake Pharma Co., LTD, Dongguan, 523850 Guangdong China
| | - Xiaoling Zhang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, NO. 3 Park 1, Beichen West Road, Chaoyang District, Beijing, 100101 China
| | - Kuan Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, NO. 3 Park 1, Beichen West Road, Chaoyang District, Beijing, 100101 China
| | - Wenjia Li
- Key Laboratory of State Administration of Traditional Chinese Medicine, Sunshine Lake Pharma Co., LTD, Dongguan, 523850 Guangdong China
| | - Caihong Dong
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, NO. 3 Park 1, Beichen West Road, Chaoyang District, Beijing, 100101 China
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11
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It's All in the Genes: The Regulatory Pathways of Sexual Reproduction in Filamentous Ascomycetes. Genes (Basel) 2019; 10:genes10050330. [PMID: 31052334 PMCID: PMC6562746 DOI: 10.3390/genes10050330] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 04/17/2019] [Accepted: 04/24/2019] [Indexed: 12/23/2022] Open
Abstract
Sexual reproduction in filamentous ascomycete fungi results in the production of highly specialized sexual tissues, which arise from relatively simple, vegetative mycelia. This conversion takes place after the recognition of and response to a variety of exogenous and endogenous cues, and relies on very strictly regulated gene, protein, and metabolite pathways. This makes studying sexual development in fungi an interesting tool in which to study gene-gene, gene-protein, and protein-metabolite interactions. This review provides an overview of some of the most important genes involved in this process; from those involved in the conversion of mycelia into sexually-competent tissue, to those involved in the development of the ascomata, the asci, and ultimately, the ascospores.
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12
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Yu Y, Blachowicz A, Will C, Szewczyk E, Glenn S, Gensberger-Reigl S, Nowrousian M, Wang CCC, Krappmann S. Mating-type factor-specific regulation of the fumagillin/pseurotin secondary metabolite supercluster in Aspergillus fumigatus. Mol Microbiol 2018; 110:1045-1065. [PMID: 30240513 DOI: 10.1111/mmi.14136] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/17/2018] [Indexed: 12/13/2022]
Abstract
In the human pathogenic mold Aspergillus fumigatus, sexual identity is determined by the mating-type idiomorphs MAT1-1 and MAT1-2 residing at the MAT locus. Upon crossing of compatible partners, a heterothallic mating is executed to eventually form cleistothecia that contain recombinant ascospores. Given that the MAT1 gene products are DNA binding master regulators that govern this complex developmental process, we monitored the MAT1-driven transcriptomes of A. fumigatus by conditional overexpression of either MAT1 gene followed by RNA-seq analyses. Numerous genes related to the process of mating were found to be under transcriptional control, such as pheromone production and recognition. Substantial differences between the MAT1-1- and MAT1-2-driven transcriptomes could be detected by functional categorization of differentially expressed genes. Moreover, a significant and distinct impact on expression of genetic clusters of secondary metabolism became apparent, which could be verified on the product level. Unexpectedly, specific cross-regulation of the fumagillin/pseurotin supercluster was evident, thereby uncoupling its co-regulatory characteristic. These insights imply a tight interconnection of sexual development accompanied by ascosporogenesis with secondary metabolite production of a pathogenic fungus and impose evolutionary constraints that link these two fundamental aspects of the fungal lifestyle.
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Affiliation(s)
- Yidong Yu
- Mikrobiologisches Institut - Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen and Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany
| | - Adriana Blachowicz
- School of Pharmacy, John Staffer Pharmaceutical Sciences Center, University of Southern California, Los Angeles, CA, USA
| | - Cornelia Will
- Mikrobiologisches Institut - Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen and Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany
| | - Edyta Szewczyk
- Research Center for Infectious Diseases, Julius-Maximilians-Universität Würzburg, Germany
| | - Steven Glenn
- School of Pharmacy, John Staffer Pharmaceutical Sciences Center, University of Southern California, Los Angeles, CA, USA
| | - Sabrina Gensberger-Reigl
- Henriette Schmidt-Burkhardt Chair of Food Chemistry, Emil Fischer Center, Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany
| | - Minou Nowrousian
- Department of General and Molecular Botany, Ruhr University Bochum, Germany
| | - Clay C C Wang
- School of Pharmacy, John Staffer Pharmaceutical Sciences Center, University of Southern California, Los Angeles, CA, USA
| | - Sven Krappmann
- Mikrobiologisches Institut - Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen and Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany
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13
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Abstract
Approximately 20% of species in the fungal kingdom are only known to reproduce by asexual means despite the many supposed advantages of sexual reproduction. However, in recent years, sexual cycles have been induced in a series of emblematic "asexual" species. We describe how these discoveries were made, building on observations of evidence for sexual potential or "cryptic sexuality" from population genetic analyses; the presence, distribution, and functionality of mating-type genes; genome analyses revealing the presence of genes linked to sexuality; the functionality of sex-related genes; and formation of sex-related developmental structures. We then describe specific studies that led to the discovery of mating and sex in certain Candida, Aspergillus, Penicillium, and Trichoderma species and discuss the implications of sex including the beneficial exploitation of the sexual cycle. We next consider whether there might be any truly asexual fungal species. We suggest that, although rare, imperfect fungi may genuinely be present in nature and that certain human activities, combined with the genetic flexibility that is a hallmark of the fungal kingdom, might favor the evolution of asexuality under certain conditions. Finally, we argue that fungal species should not be thought of as simply asexual or sexual, but rather as being composed of isolates on a continuum of sexual fertility.
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14
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The mating type locus protein MAT1-2-1 of Trichoderma reesei interacts with Xyr1 and regulates cellulase gene expression in response to light. Sci Rep 2017; 7:17346. [PMID: 29229981 PMCID: PMC5725425 DOI: 10.1038/s41598-017-17439-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 11/27/2017] [Indexed: 12/17/2022] Open
Abstract
Cellulase production in the model cellulolytic fungus Trichoderma reesei is subject to a variety of environmental and physiological conditions involving an intricate regulatory network with multiple transcription factors. Here, we identified the mating type locus protein MAT1-2-1 as an interacting partner for the key transcriptional activator Xyr1 of T. reesei cellulase genes. Yeast two-hybrid and GST pulldown analyses revealed that MAT1-2-1 directly interacted with the putative transcription activation domain (AD, 767~940 aa) and the middle homology region (MHR2, 314~632 aa) of Xyr1. Disruption of the mat1-2-1 gene compromised the induced expression of cellulase genes with Avicel in response to light or with lactose. Chromatin immunoprecipitation (ChIP) demonstrated that MAT1-2-1 was recruited to the cbh1 (cellobiohydrolase 1-encoding) gene promoter in a Xyr1-dependent manner. These results strongly support an important role of MAT1-2-1 as a physiological cofactor of Xyr1, and suggest that MAT1-2-1 represents another regulatory node that integrates the light response with carbon source signaling to fine tune cellulase gene transcription.
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15
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Omics Analyses of Trichoderma reesei CBS999.97 and QM6a Indicate the Relevance of Female Fertility to Carbohydrate-Active Enzyme and Transporter Levels. Appl Environ Microbiol 2017; 83:AEM.01578-17. [PMID: 28916559 PMCID: PMC5666144 DOI: 10.1128/aem.01578-17] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 08/31/2017] [Indexed: 01/07/2023] Open
Abstract
The filamentous fungus Trichoderma reesei is found predominantly in the tropics but also in more temperate regions, such as Europe, and is widely known as a producer of large amounts of plant cell wall-degrading enzymes. We sequenced the genome of the sexually competent isolate CBS999.97, which is phenotypically different from the female sterile strain QM6a but can cross sexually with QM6a. Transcriptome data for growth on cellulose showed that entire carbohydrate-active enzyme (CAZyme) families are consistently differentially regulated between these strains. We evaluated backcrossed strains of both mating types, which acquired female fertility from CBS999.97 but maintained a mostly QM6a genetic background, and we could thereby distinguish between the effects of strain background and female fertility or mating type. We found clear regulatory differences associated with female fertility and female sterility, including regulation of CAZyme and transporter genes. Analysis of carbon source utilization, transcriptomes, and secondary metabolites in these strains revealed that only a few changes in gene regulation are consistently correlated with different mating types. Different strain backgrounds (QM6a versus CBS999.97) resulted in the most significant alterations in the transcriptomes and in carbon source utilization, with decreased growth of CBS999.97 on several amino acids (for example proline or alanine), which further correlated with the downregulation of genes involved in the respective pathways. In combination, our findings support a role of fertility-associated processes in physiology and gene regulation and are of high relevance for the use of sexual crossing in combining the characteristics of two compatible strains or quantitative trait locus (QTL) analysis.IMPORTANCETrichoderma reesei is a filamentous fungus with a high potential for secretion of plant cell wall-degrading enzymes. We sequenced the genome of the fully fertile field isolate CBS999.97 and analyzed its gene regulation characteristics in comparison with the commonly used laboratory wild-type strain QM6a, which is not female fertile. Additionally, we also evaluated fully fertile strains with genotypes very close to that of QM6a in order to distinguish between strain-specific and fertility-specific characteristics. We found that QM6a and CBS999.97 clearly differ in their growth patterns on different carbon sources, CAZyme gene regulation, and secondary metabolism. Importantly, we found altered regulation of 90 genes associated with female fertility, including CAZyme genes and transporter genes, but only minor mating type-dependent differences. Hence, when using sexual crossing in research and for strain improvement, it is important to consider female fertile and female sterile strains for comparison with QM6a and to achieve optimal performance.
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16
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Lu Y, Xia Y, Luo F, Dong C, Wang C. Functional convergence and divergence of mating-type genes fulfilling in Cordyceps militaris. Fungal Genet Biol 2016; 88:35-43. [DOI: 10.1016/j.fgb.2016.01.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 01/20/2016] [Accepted: 01/22/2016] [Indexed: 10/22/2022]
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17
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18
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Julca I, Droby S, Sela N, Marcet-Houben M, Gabaldón T. Contrasting Genomic Diversity in Two Closely Related Postharvest Pathogens: Penicillium digitatum and Penicillium expansum. Genome Biol Evol 2015; 8:218-27. [PMID: 26672008 PMCID: PMC4758248 DOI: 10.1093/gbe/evv252] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Penicillium digitatum and Penicillium expansum are two closely related fungal plant pathogens causing green and blue mold in harvested fruit, respectively. The two species differ in their host specificity, being P. digitatum restricted to citrus fruits and P. expansum able to infect a wide range of fruits after harvest. Although host-specific Penicillium species have been found to have a smaller gene content, it is so far unclear whether these different host specificities impact genome variation at the intraspecific level. Here we assessed genome variation across four P. digitatum and seven P. expansum isolates from geographically distant regions. Our results show very high similarity (average 0.06 SNPs [single nucleotide polymorphism] per kb) between globally distributed isolates of P. digitatum pointing to a recent expansion of a single lineage. This low level of genetic variation found in our samples contrasts with the higher genetic variability observed in the similarly distributed P. expansum isolates (2.44 SNPs per kb). Patterns of polymorphism in P. expansum indicate that recombination exists between genetically diverged strains. Consistent with the existence of sexual recombination and heterothallism, which was unknown for this species, we identified the two alternative mating types in different P. expansum isolates. Patterns of polymorphism in P. digitatum indicate a recent clonal population expansion of a single lineage that has reached worldwide distribution. We suggest that the contrasting patterns of genomic variation between the two species reflect underlying differences in population dynamics related with host specificities and related agricultural practices. It should be noted, however, that this results should be confirmed with a larger sampling of strains, as new strains may broaden the diversity so far found in P. digitatum.
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Affiliation(s)
- Irene Julca
- Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain Universitat Autònoma De Barcelona, Spain
| | - Samir Droby
- Department of Postharvest Science, ARO, the Volcani Center, Bet Dagan, Israel
| | - Noa Sela
- Department of Plant Pathology and Weed Research, The Volcani Center, Bet Dagan, Israel
| | - Marina Marcet-Houben
- Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Toni Gabaldón
- Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain Institució Catalana De Recerca I Estudis Avançats (ICREA), Barcelona, Spain
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19
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Dahlmann TA, Böhm J, Becker K, Kück U. Sexual recombination as a tool for engineering industrial Penicillium chrysogenum strains. Curr Genet 2015; 61:679-83. [PMID: 25993917 DOI: 10.1007/s00294-015-0497-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 05/14/2015] [Indexed: 12/13/2022]
Abstract
The recent discovery and functional characterization of opposite mating-type loci in the industrial penicillin producer Penicillium chrysogenum demonstrated their regulatory role in sexual as well as asexual development. Subsequent experiments further showed that a sexual life cycle can be induced in P. chrysogenum that was for long believed to reproduce exclusively by asexual propagation. Finally, crossing of wild type and production strains resulted in the generation of recombinant ascospore isolates. We predict from these recent findings that recombinant progeny for industrial applications can be obtained by sexual crossings and discuss experimental difficulties that occur when parental strains with karyotype heterogeneity are used for mating.
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Affiliation(s)
- Tim A Dahlmann
- Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-University Bochum, 44780, Bochum, Germany
| | - Julia Böhm
- Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-University Bochum, 44780, Bochum, Germany
| | - Kordula Becker
- Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-University Bochum, 44780, Bochum, Germany
| | - Ulrich Kück
- Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-University Bochum, 44780, Bochum, Germany.
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