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Berasategui A, Salem H, Moller AG, Christopher Y, Vidaurre Montoya Q, Conn C, Read TD, Rodrigues A, Ziemert N, Gerardo N. Genomic insights into the evolution of secondary metabolism of Escovopsis and its allies, specialized fungal symbionts of fungus-farming ants. mSystems 2024; 9:e0057624. [PMID: 38904377 PMCID: PMC11265373 DOI: 10.1128/msystems.00576-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Accepted: 05/14/2024] [Indexed: 06/22/2024] Open
Abstract
The metabolic intimacy of symbiosis often demands the work of specialists. Natural products and defensive secondary metabolites can drive specificity by ensuring infection and propagation across host generations. But in contrast to bacteria, little is known about the diversity and distribution of natural product biosynthetic pathways among fungi and how they evolve to facilitate symbiosis and adaptation to their host environment. In this study, we define the secondary metabolism of Escovopsis and closely related genera, symbionts in the gardens of fungus-farming ants. We ask how the gain and loss of various biosynthetic pathways correspond to divergent lifestyles. Long-read sequencing allowed us to define the chromosomal features of representative Escovopsis strains, revealing highly reduced genomes composed of seven to eight chromosomes. The genomes are highly syntenic with macrosynteny decreasing with increasing phylogenetic distance, while maintaining a high degree of mesosynteny. An ancestral state reconstruction analysis of biosynthetic pathways revealed that, while many secondary metabolites are shared with non-ant-associated Sordariomycetes, 56 pathways are unique to the symbiotic genera. Reflecting adaptation to diverging ant agricultural systems, we observe that the stepwise acquisition of these pathways mirrors the ecological radiations of attine ants and the dynamic recruitment and replacement of their fungal cultivars. As different clades encode characteristic combinations of biosynthetic gene clusters, these delineating profiles provide important insights into the possible mechanisms underlying specificity between these symbionts and their fungal hosts. Collectively, our findings shed light on the evolutionary dynamic nature of secondary metabolism in Escovopsis and its allies, reflecting adaptation of the symbionts to an ancient agricultural system.IMPORTANCEMicrobial symbionts interact with their hosts and competitors through a remarkable array of secondary metabolites and natural products. Here, we highlight the highly streamlined genomic features of attine-associated fungal symbionts. The genomes of Escovopsis species, as well as species from other symbiont genera, many of which are common with the gardens of fungus-growing ants, are defined by seven chromosomes. Despite a high degree of metabolic conservation, we observe some variation in the symbionts' potential to produce secondary metabolites. As the phylogenetic distribution of the encoding biosynthetic gene clusters coincides with attine transitions in agricultural systems, we highlight the likely role of these metabolites in mediating adaptation by a group of highly specialized symbionts.
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Affiliation(s)
- Aileen Berasategui
- Department of Biology, Emory University, Atlanta, Georgia, USA
- Cluster of Excellence-Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
- Mutualisms Research Group, Max Planck Institute for Biology, Tübingen, Germany
- Amsterdam Institute for Life and Environment, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Hassan Salem
- Department of Biology, Emory University, Atlanta, Georgia, USA
- Mutualisms Research Group, Max Planck Institute for Biology, Tübingen, Germany
| | - Abraham G. Moller
- Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Yuliana Christopher
- Instituto de Investigaciones Científicas y Servicios de Alta Tecnología, Ciudad del Saber, Panamá City, Panama
| | - Quimi Vidaurre Montoya
- Department of General and Applied Biology, São Paulo State University (UNESP), Institute of Biosciences, Rio Claro, São Paulo, Brazil
| | - Caitlin Conn
- Department of Biology, Emory University, Atlanta, Georgia, USA
- Department of Biology, Berry College, Mount Berry, Georgia, USA
| | - Timothy D. Read
- Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Andre Rodrigues
- Department of General and Applied Biology, São Paulo State University (UNESP), Institute of Biosciences, Rio Claro, São Paulo, Brazil
| | - Nadine Ziemert
- Cluster of Excellence-Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
- Translational Genome Mining for Natural Products, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Interfaculty Institute for Biomedical Informatics (IBMI), University of Tübingen, Tübingen, Germany
| | - Nicole Gerardo
- Department of Biology, Emory University, Atlanta, Georgia, USA
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Jovanska L, Lin IC, Yao JS, Chen CL, Liu HC, Li WC, Chuang YC, Chuang CN, Yu ACH, Lin HN, Pong WL, Yu CI, Su CY, Chen YP, Chen RS, Hsueh YP, Yuan HS, Timofejeva L, Wang TF. DNA cytosine methyltransferases differentially regulate genome-wide hypermutation and interhomolog recombination in Trichoderma reesei meiosis. Nucleic Acids Res 2024:gkae611. [PMID: 39021337 DOI: 10.1093/nar/gkae611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 06/20/2024] [Accepted: 07/01/2024] [Indexed: 07/20/2024] Open
Abstract
Trichoderma reesei is an economically important enzyme producer with several unique meiotic features. spo11, the initiator of meiotic double-strand breaks (DSBs) in most sexual eukaryotes, is dispensable for T. reesei meiosis. T. reesei lacks the meiosis-specific recombinase Dmc1. Rad51 and Sae2, the activator of the Mre11 endonuclease complex, promote DSB repair and chromosome synapsis in wild-type and spo11Δ meiosis. DNA methyltransferases (DNMTs) perform multiple tasks in meiosis. Three DNMT genes (rid1, dim2 and dimX) differentially regulate genome-wide cytosine methylation and C:G-to-T:A hypermutations in different chromosomal regions. We have identified two types of DSBs: type I DSBs require spo11 or rid1 for initiation, whereas type II DSBs do not rely on spo11 and rid1 for initiation. rid1 (but not dim2) is essential for Rad51-mediated DSB repair and normal meiosis. rid1 and rad51 exhibit a locus heterogeneity (LH) relationship, in which LH-associated proteins often regulate interconnectivity in protein interaction networks. This LH relationship can be suppressed by deleting dim2 in a haploid rid1Δ (but not rad51Δ) parental strain, indicating that dim2 and rid1 share a redundant function that acts earlier than rad51 during early meiosis. In conclusion, our studies provide the first evidence of the involvement of DNMTs during meiotic initiation and recombination.
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Affiliation(s)
| | - I-Chen Lin
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
- Chi-Mei Medical Center, Tainan 71004, Taiwan
| | - Jhong-Syuan Yao
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Chia-Ling Chen
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Hou-Cheng Liu
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Wan-Chen Li
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Yu-Chien Chuang
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Chi-Ning Chuang
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | | | - Hsin-Nan Lin
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Wen-Li Pong
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Chang-I Yu
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Ching-Yuan Su
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Yi-Ping Chen
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Ruey-Shyang Chen
- Department of Biochemical Science and Technology, National Chiayi University, Chiayi, Taiwan
| | - Yi-Ping Hsueh
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Hanna S Yuan
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Ljudmilla Timofejeva
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
- Centre of Estonian Rural Research and Knowledge, J. Aamisepa 1, Jõgeva 48309, Estonia
| | - Ting-Fang Wang
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
- Department of Biochemical Science and Technology, National Chiayi University, Chiayi, Taiwan
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Zong X, Lou Y, Xia M, Zhao K, Chen J, Huang J, Yang S, Wang L. Recombination and repeat-induced point mutation landscapes reveal trade-offs between the sexual and asexual cycles of Magnaporthe oryzae. J Genet Genomics 2024; 51:723-734. [PMID: 38490361 DOI: 10.1016/j.jgg.2024.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/01/2024] [Accepted: 03/06/2024] [Indexed: 03/17/2024]
Abstract
The fungal disease caused by Magnaporthe oryzae is one of the most devastating diseases that endanger many crops worldwide. Evidence shows that sexual reproduction can be advantageous for fungal diseases as hybridization facilitates host-jumping. However, the pervasive clonal lineages of M. oryzae observed in natural fields contradict this expectation. A better understanding of the roles of recombination and the fungi-specific repeat-induced point mutation (RIP) in shaping its evolutionary trajectory is essential to bridge this knowledge gap. Here we systematically investigate the RIP and recombination landscapes in M. oryzae using a whole genome sequencing data from 252 population samples and 92 cross progenies. Our data reveal that the RIP can robustly capture the population history of M. oryzae, and we provide accurate estimations of the recombination and RIP rates across different M. oryzae clades. Significantly, our results highlight a parent-of-origin bias in both recombination and RIP rates, tightly associating with their sexual potential and variations of effector proteins. This bias suggests a critical trade-off between generating novel allelic combinations in the sexual cycle to facilitate host-jumping and stimulating transposon-associated diversification of effectors in the asexual cycle to facilitate host coevolution. These findings provide unique insights into understanding the evolution of blast fungus.
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Affiliation(s)
- Xifang Zong
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210000, China
| | - Yaxin Lou
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210000, China
| | - Mengshuang Xia
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210000, China
| | - Kunyang Zhao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210000, China
| | - Jingxuan Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210000, China
| | - Ju Huang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, Jiangsu 210000, China
| | - Sihai Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210000, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210000, China.
| | - Long Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210000, China.
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Shi J, Liu J, Li H, Tang Y, Liu S, Sun Z, Yu Z, Ji X. DNA methylation plays important roles in lifestyle transition of Arthrobotrys oligospora. IET Syst Biol 2024; 18:92-102. [PMID: 38760669 PMCID: PMC11179157 DOI: 10.1049/syb2.12094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 04/24/2024] [Accepted: 05/06/2024] [Indexed: 05/19/2024] Open
Abstract
Trap formation is the key indicator of carnivorous lifestyle transition of nematode-trapping fungi (NTF). Here, the DNA methylation profile was explored during trap induction of Arthrobotrys oligospora, a typical NTF that captures nematodes by developing adhesive networks. Whole-genome bisulfite sequencing identified 871 methylation sites and 1979 differentially methylated regions (DMRs). This first-of-its-kind investigation unveiled the widespread presence of methylation systems in NTF, and suggested potential regulation of ribosomal RNAs through DNA methylation. Functional analysis indicated DNA methylation's involvement in complex gene regulations during trap induction, impacting multiple biological processes like response to stimulus, transporter activity, cell reproduction and molecular function regulator. These findings provide a glimpse into the important roles of DNA methylation in trap induction and offer new insights for understanding the molecular mechanisms driving carnivorous lifestyle transition of NTF.
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Affiliation(s)
- Jiajia Shi
- Smart Health Big Data Analysis and Location Services Engineering Lab of Jiangsu Province, Nanjing University of Posts and Telecommunications, Nanjing, China
| | - Jiaxin Liu
- Smart Health Big Data Analysis and Location Services Engineering Lab of Jiangsu Province, Nanjing University of Posts and Telecommunications, Nanjing, China
| | - Heng Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, China
| | - Yao Tang
- Smart Health Big Data Analysis and Location Services Engineering Lab of Jiangsu Province, Nanjing University of Posts and Telecommunications, Nanjing, China
| | - Shuqun Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
| | - Zhirong Sun
- Institute of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China
| | - Zefen Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
| | - Xinglai Ji
- Smart Health Big Data Analysis and Location Services Engineering Lab of Jiangsu Province, Nanjing University of Posts and Telecommunications, Nanjing, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
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Stahr MN, Parada-Rojas C, Childs KL, Alfenas RF, Fernandes FM, Avila K, Quesada-Ocampo LM. Long-Read Sequencing Genome Assembly of Ceratocystis fimbriata Enables Development of Molecular Diagnostics for Sweetpotato Black Rot. PHYTOPATHOLOGY 2024; 114:1411-1420. [PMID: 38264989 DOI: 10.1094/phyto-09-23-0341-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Abstract
Ceratocystis fimbriata is a destructive fungal pathogen of sweetpotato (Ipomoea batatas) that leads to losses at all stages of sweetpotato production. Accurate detection of C. fimbriata would allow for more efficient deployment of management tactics in sweetpotato production. To develop a diagnostic assay, a hybrid genome assembly of C. fimbriata isolate AS236 was generated. The resulting 31.7-MB assembly was near-chromosome level, with 18 contigs, 6,481 predicted genes, and a BUSCO completion score of 98.4% when compared with the fungus-specific lineage database. Additional Illumina DNA reads from C. manginecans, C. platani, and a second C. fimbriata isolate (C1421) were then mapped to the assembled genome using BOWTIE2 and counted using HTSeq, which identified 148 genes present only within C. fimbriata as molecular diagnostic candidates; 6 single-copy and 35 highly multi-copy (>40 BLAST hits), as determined through a self-BLAST-P alignment. Primers for PCR were designed in the 200-bp flanking region of the first exon for each candidate, and the candidates were validated against a diverse DNA panel containing Ceratocystis species, sweetpotato pathogens, and plants. After validation, two diagnostic candidates amplified only C. fimbriata DNA and were considered to be highly specific to the species. These genetic markers will serve as valuable diagnostic tools with multiple applications including the detection of C. fimbriata in seed, soil, and wash water in sweetpotato production.
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Affiliation(s)
- M N Stahr
- Department of Entomology and Plant Pathology and NC Plant Sciences Initiative, North Carolina State University, Raleigh, NC 27695-7825, U.S.A
| | - C Parada-Rojas
- Department of Entomology and Plant Pathology and NC Plant Sciences Initiative, North Carolina State University, Raleigh, NC 27695-7825, U.S.A
| | - K L Childs
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, U.S.A
| | - R F Alfenas
- Department of Plant Pathology, Universidade Federal de Viçosa, Minas Gerais State, 36570-900, Brazil
| | - F M Fernandes
- Department of Plant Pathology, Universidade Federal de Viçosa, Minas Gerais State, 36570-900, Brazil
| | - K Avila
- Department of Entomology and Plant Pathology and NC Plant Sciences Initiative, North Carolina State University, Raleigh, NC 27695-7825, U.S.A
| | - L M Quesada-Ocampo
- Department of Entomology and Plant Pathology and NC Plant Sciences Initiative, North Carolina State University, Raleigh, NC 27695-7825, U.S.A
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6
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Stajich JE, Lovett B, Lee E, Macias AM, Hajek AE, de Bivort BL, Kasson MT, De Fine Licht HH, Elya C. Signatures of transposon-mediated genome inflation, host specialization, and photoentrainment in Entomophthora muscae and allied entomophthoralean fungi. eLife 2024; 12:RP92863. [PMID: 38767950 PMCID: PMC11105155 DOI: 10.7554/elife.92863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024] Open
Abstract
Despite over a century of observations, the obligate insect parasites within the order Entomophthorales remain poorly characterized at the genetic level. In this manuscript, we present a genome for a laboratory-tractable Entomophthora muscae isolate that infects fruit flies. Our E. muscae assembly is 1.03 Gb, consists of 7810 contigs and contains 81.3% complete fungal BUSCOs. Using a comparative approach with recent datasets from entomophthoralean fungi, we show that giant genomes are the norm within Entomophthoraceae owing to extensive, but not recent, Ty3 retrotransposon activity. In addition, we find that E. muscae and its closest allies possess genes that are likely homologs to the blue-light sensor white-collar 1, a Neurospora crassa gene that has a well-established role in maintaining circadian rhythms. We uncover evidence that E. muscae diverged from other entomophthoralean fungi by expansion of existing families, rather than loss of particular domains, and possesses a potentially unique suite of secreted catabolic enzymes, consistent with E. muscae's species-specific, biotrophic lifestyle. Finally, we offer a head-to-head comparison of morphological and molecular data for species within the E. muscae species complex that support the need for taxonomic revision within this group. Altogether, we provide a genetic and molecular foundation that we hope will provide a platform for the continued study of the unique biology of entomophthoralean fungi.
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Affiliation(s)
- Jason E Stajich
- Department of Microbiology and Plant Pathology, University of California-RiversideRiversideUnited States
| | - Brian Lovett
- Emerging Pests and Pathogens Research Unit, USDA-ARSIthacaUnited States
| | - Emily Lee
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
| | - Angie M Macias
- Division of Plant and Soil Sciences, West Virginia UniversityMorgantownUnited States
| | - Ann E Hajek
- Department of Entomology, Cornell UniversityIthacaUnited States
| | - Benjamin L de Bivort
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
| | - Matt T Kasson
- Division of Plant and Soil Sciences, West Virginia UniversityMorgantownUnited States
| | - Henrik H De Fine Licht
- Section for Organismal Biology, Department of Plant and Environmental Sciences, University of CopenhagenCopenhagenDenmark
| | - Carolyn Elya
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
- Department of Molecular and Cellular Biology, Harvard UniversityCambridgeUnited States
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Moin AT, Robin TB, Patil RB, Rani NA, Prome AA, Sakif TI, Hossain M, Chowdhury DUS, Rashid SS, Mollah AKMM, Islam S, Uddin MH, Khalequzzaman M, Islam T, Islam NN. Antifungal plant flavonoids identified in silico with potential to control rice blast disease caused by Magnaporthe oryzae. PLoS One 2024; 19:e0301519. [PMID: 38578751 PMCID: PMC10997076 DOI: 10.1371/journal.pone.0301519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Accepted: 03/14/2024] [Indexed: 04/07/2024] Open
Abstract
Rice blast disease, caused by the fungus Magnaporthe oryzae, poses a severe threat to rice production, particularly in Asia where rice is a staple food. Concerns over fungicide resistance and environmental impact have sparked interest in exploring natural fungicides as potential alternatives. This study aimed to identify highly potent natural fungicides against M. oryzae to combat rice blast disease, using advanced molecular dynamics techniques. Four key proteins (CATALASE PEROXIDASES 2, HYBRID PKS-NRPS SYNTHETASE TAS1, MANGANESE LIPOXYGENASE, and PRE-MRNA-SPLICING FACTOR CEF1) involved in M. oryzae's infection process were identified. A list of 30 plant metabolites with documented antifungal properties was compiled for evaluation as potential fungicides. Molecular docking studies revealed that 2-Coumaroylquinic acid, Myricetin, Rosmarinic Acid, and Quercetin exhibited superior binding affinities compared to reference fungicides (Azoxystrobin and Tricyclazole). High throughput molecular dynamics simulations were performed, analyzing parameters like RMSD, RMSF, Rg, SASA, hydrogen bonds, contact analysis, Gibbs free energy, and cluster analysis. The results revealed stable interactions between the selected metabolites and the target proteins, involving important hydrogen bonds and contacts. The SwissADME server analysis indicated that the metabolites possess fungicide properties, making them effective and safe fungicides with low toxicity to the environment and living beings. Additionally, bioactivity assays confirmed their biological activity as nuclear receptor ligands and enzyme inhibitors. Overall, this study offers valuable insights into potential natural fungicides for combating rice blast disease, with 2-Coumaroylquinic acid, Myricetin, Rosmarinic Acid, and Quercetin standing out as promising and environmentally friendly alternatives to conventional fungicides. These findings have significant implications for developing crop protection strategies and enhancing global food security, particularly in rice-dependent regions.
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Affiliation(s)
- Abu Tayab Moin
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram, Bangladesh
| | - Tanjin Barketullah Robin
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, Bangladesh
| | - Rajesh B. Patil
- Department of Pharmaceutical Chemistry, Sinhgad Technical Education Society’s, Sinhgad College of Pharmacy, Pune, Maharashtra, India
| | - Nurul Amin Rani
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, Bangladesh
| | - Anindita Ash Prome
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, Bangladesh
| | - Tahsin Islam Sakif
- Department of Computer Science and Electrical Engineering, West Virginia University, Morgantown, WV, United States of America
| | - Mohabbat Hossain
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram, Bangladesh
| | - Dil Umme Salma Chowdhury
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram, Bangladesh
| | - Shah Samiur Rashid
- Department of Biochemistry and Biotechnology, University of Science and Technology Chittagong (USTC), Chattogram, Bangladesh
| | | | - Saiful Islam
- Chattogram Laboratories, Bangladesh Council of Scientific and Industrial Research (BCSIR), Chattogram, Bangladesh
| | - Mohammad Helal Uddin
- Department of Applied Chemistry and Chemical Engineering, University of Chittagong, Chittagong, Bangladesh
| | | | - Tofazzal Islam
- Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh
| | - Nazneen Naher Islam
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram, Bangladesh
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Cohen AB, Cai G, Price DC, Molnar TJ, Zhang N, Hillman BI. The massive 340 megabase genome of Anisogramma anomala, a biotrophic ascomycete that causes eastern filbert blight of hazelnut. BMC Genomics 2024; 25:347. [PMID: 38580927 PMCID: PMC10998396 DOI: 10.1186/s12864-024-10198-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 03/07/2024] [Indexed: 04/07/2024] Open
Abstract
BACKGROUND The ascomycete fungus Anisogramma anomala causes Eastern Filbert Blight (EFB) on hazelnut (Corylus spp.) trees. It is a minor disease on its native host, the American hazelnut (C. americana), but is highly destructive on the commercially important European hazelnut (C. avellana). In North America, EFB has historically limited commercial production of hazelnut to west of the Rocky Mountains. A. anomala is an obligately biotrophic fungus that has not been grown in continuous culture, rendering its study challenging. There is a 15-month latency before symptoms appear on infected hazelnut trees, and only a sexual reproductive stage has been observed. Here we report the sequencing, annotation, and characterization of its genome. RESULTS The genome of A. anomala was assembled into 108 scaffolds totaling 342,498,352 nt with a GC content of 34.46%. Scaffold N50 was 33.3 Mb and L50 was 5. Nineteen scaffolds with lengths over 1 Mb constituted 99% of the assembly. Telomere sequences were identified on both ends of two scaffolds and on one end of another 10 scaffolds. Flow cytometry estimated the genome size of A. anomala at 370 Mb. The genome exhibits two-speed evolution, with 93% of the assembly as AT-rich regions (32.9% GC) and the other 7% as GC-rich (57.1% GC). The AT-rich regions consist predominantly of repeats with low gene content, while 90% of predicted protein coding genes were identified in GC-rich regions. Copia-like retrotransposons accounted for more than half of the genome. Evidence of repeat-induced point mutation (RIP) was identified throughout the AT-rich regions, and two copies of the rid gene and one of dim-2, the key genes in the RIP mutation pathway, were identified in the genome. Consistent with its homothallic sexual reproduction cycle, both MAT1-1 and MAT1-2 idiomorphs were found. We identified a large suite of genes likely involved in pathogenicity, including 614 carbohydrate active enzymes, 762 secreted proteins and 165 effectors. CONCLUSIONS This study reveals the genomic structure, composition, and putative gene function of the important pathogen A. anomala. It provides insight into the molecular basis of the pathogen's life cycle and a solid foundation for studying EFB.
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Affiliation(s)
- Alanna B Cohen
- Department of Plant Biology, Rutgers The State University of New Jersey, New Brunswick, NJ, 08901, USA
- Graduate Program in Microbial Biology, Rutgers The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Guohong Cai
- Crop Production and Pest Control Research Unit, USDA-ARS, West Lafayette, IN, 47907, USA.
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA.
| | - Dana C Price
- Department of Entomology, Rutgers The State University of New Jersey, New Brunswick, NJ, 08901, USA
- Center for Vector Biology, Rutgers The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Thomas J Molnar
- Department of Plant Biology, Rutgers The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Ning Zhang
- Department of Plant Biology, Rutgers The State University of New Jersey, New Brunswick, NJ, 08901, USA
- Graduate Program in Microbial Biology, Rutgers The State University of New Jersey, New Brunswick, NJ, 08901, USA
- Department of Biochemistry and Microbiology, Rutgers The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Bradley I Hillman
- Department of Plant Biology, Rutgers The State University of New Jersey, New Brunswick, NJ, 08901, USA.
- Graduate Program in Microbial Biology, Rutgers The State University of New Jersey, New Brunswick, NJ, 08901, USA.
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9
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Waheed A, Chen Y, Rizwan HM, Adnan M, Ma X, Liu G. Genomic characterization and expression profiling of the lytic polysaccharide monooxygenases AA9 family in thermophilic fungi Thermothelomyces fergusii in response to carbon source media. Int J Biol Macromol 2024; 265:130740. [PMID: 38462117 DOI: 10.1016/j.ijbiomac.2024.130740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 02/16/2024] [Accepted: 03/06/2024] [Indexed: 03/12/2024]
Abstract
Enhancing enzyme activity and stability in biomass degradation can improve substrate saccharification and, increases biorefinery efficiency. For the first time, we identified 20 lytic polysaccharide monooxygenases (LPMOs) AA9 genes in the genome of Thermothelomyces fergusii. Our results showed that TfAA9 was categorized into LPMOs1, LPMOs2, and LPMOs3 subgroups based on protein diversity. Protein- 3D structure analysis showed strong interactions between Myceliophthora thermophila AA9 proteins and 17 TfAA9 proteins. Gene ontology analysis indicated a high enrichment of cellulase activity in TfAA9 genes. KEGG pathways analysis revealed the role of TfAA9 proteins in the endohydrolysis of 1,4-beta-D-glucosidic linkages in cellulose. Numerous TfAA9s gene transcripts were up-regulated on avicel, cellobiose, and glucose, with a higher proportion on avicel. Protein concentration, endoglucanase, and cellulase activity were also boosted on avicel. However, limited fungal biomass was observed on avicel, despite the abundance of AA9 LPMOs in the T. fergusii genome. These findings expand our understanding of fungal AA9 genes and their role in lignocellulolytic degradation. The disparity between biomass and enzymatic activity suggests screening TfAA9 genes for highly active enzymes and redundant genes via heterologous expression. In short, functional characterization of these genes could contribute to improving the saccharification process of industrial raw materials.
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Affiliation(s)
- Abdul Waheed
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China; College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Yi Chen
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Hafiz Muhammad Rizwan
- College of Civil and Transportation Engineering, Shenzhen University, Shenzhen 518060, China; Shenzhen Key Laboratory of Food Nutrition and Health, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, China
| | - Muhammad Adnan
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Xuekun Ma
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Gang Liu
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China.
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10
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Kumakura N, Singkaravanit-Ogawa S, Gan P, Tsushima A, Ishihama N, Watanabe S, Seo M, Iwasaki S, Narusaka M, Narusaka Y, Takano Y, Shirasu K. Guanosine-specific single-stranded ribonuclease effectors of a phytopathogenic fungus potentiate host immune responses. THE NEW PHYTOLOGIST 2024; 242:170-191. [PMID: 38348532 DOI: 10.1111/nph.19582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 01/06/2024] [Indexed: 03/08/2024]
Abstract
Plants activate immunity upon recognition of pathogen-associated molecular patterns. Although phytopathogens have evolved a set of effector proteins to counteract plant immunity, some effectors are perceived by hosts and induce immune responses. Here, we show that two secreted ribonuclease effectors, SRN1 and SRN2, encoded in a phytopathogenic fungus, Colletotrichum orbiculare, induce cell death in a signal peptide- and catalytic residue-dependent manner, when transiently expressed in Nicotiana benthamiana. The pervasive presence of SRN genes across Colletotrichum species suggested the conserved roles. Using a transient gene expression system in cucumber (Cucumis sativus), an original host of C. orbiculare, we show that SRN1 and SRN2 potentiate host pattern-triggered immunity responses. Consistent with this, C. orbiculare SRN1 and SRN2 deletion mutants exhibited increased virulence on the host. In vitro analysis revealed that SRN1 specifically cleaves single-stranded RNAs at guanosine, leaving a 3'-end phosphate. Importantly, the potentiation of C. sativus responses by SRN1 and SRN2, present in the apoplast, depends on ribonuclease catalytic residues. We propose that the pathogen-derived apoplastic guanosine-specific single-stranded endoribonucleases lead to immunity potentiation in plants.
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Affiliation(s)
- Naoyoshi Kumakura
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
| | | | - Pamela Gan
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Ayako Tsushima
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
- Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Nobuaki Ishihama
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Shunsuke Watanabe
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Mitsunori Seo
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
- Tropical Biosphere Research Center, University of the Ryukyus, Nakagami, Okinawa, 903-0213, Japan
| | - Shintaro Iwasaki
- RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8561, Japan
| | - Mari Narusaka
- Okayama Prefectural Technology Center for Agriculture, Forestry, and Fisheries, Research Institute for Biological Sciences, Kaga, Okayama, 716-1241, Japan
| | - Yoshihiro Narusaka
- Okayama Prefectural Technology Center for Agriculture, Forestry, and Fisheries, Research Institute for Biological Sciences, Kaga, Okayama, 716-1241, Japan
| | - Yoshitaka Takano
- Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Ken Shirasu
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
- Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
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11
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Stajich JE, Lovett B, Lee E, Macias AM, Hajek AE, de Bivort BL, Kasson MT, De Fine Licht HH, Elya C. Signatures of transposon-mediated genome inflation, host specialization, and photoentrainment in Entomophthora muscae and allied entomophthoralean fungi. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.13.557621. [PMID: 37745330 PMCID: PMC10515909 DOI: 10.1101/2023.09.13.557621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Despite over a century of observations, the obligate insect parasites within the order Entomophthorales remain poorly characterized at the genetic level. This is in part due to their large genome sizes and difficulty in obtaining sequenceable material. In this manuscript, we leveraged a recently-isolated, laboratory-tractable Entomophthora muscae isolate and improved long-read sequencing to obtain a largely-complete entomophthoralean genome. Our E. muscae assembly is 1.03 Gb, consists of 7,810 contigs and contains 81.3% complete fungal BUSCOs. Using a comparative approach with other available (transcriptomic and genomic) datasets from entomophthoralean fungi, we provide new insight into the biology of these understudied pathogens. We offer a head-to-head comparison of morphological and molecular data for species within the E. muscae species complex. Our findings suggest that substantial taxonomic revision is needed to define species within this group and we provide recommendations for differentiating strains and species in the context of the existing body of E. muscae scientific literature. We show that giant genomes are the norm within Entomophthoraceae owing to extensive, but not recent, Ty3 retrotransposon activity, despite the presence of machinery to defend against transposable elements(RNAi). In addition, we find that E. muscae and its closest allies are enriched for M16A peptidases and possess genes that are likely homologs to the blue-light sensor white-collar 1, a Neurospora crassa gene that has a well-established role in maintaining circadian rhythms. We find that E. muscae has an expanded group of acid-trehalases, consistent with trehalose being the primary sugar component of fly (and insect) hemolymph. We uncover evidence that E. muscae diverged from other entomophthoralean fungi by expansion of existing families, rather than loss of particular domains, and possesses a potentially unique suite of secreted catabolic enzymes, consistent with E. muscae's species-specific, biotrophic lifestyle. Altogether, we provide a genetic and molecular foundation that we hope will provide a platform for the continued study of the unique biology of entomophthoralean fungi.
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Affiliation(s)
- Jason E. Stajich
- Department of Microbiology and Plant Pathology, University of California-Riverside, Riverside, CA United States
| | - Brian Lovett
- Emerging Pests and Pathogens Research Unit, USDA-ARS, Ithaca, NY, United States
| | - Emily Lee
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States
| | - Angie M. Macias
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, United States
| | - Ann E. Hajek
- Department of Entomology, Cornell University, Ithaca, NY, United States
| | - Benjamin L. de Bivort
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States
| | - Matt T. Kasson
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, United States
| | - Henrik H. De Fine Licht
- Section for Organismal Biology, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Carolyn Elya
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, United States
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12
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Yeadon PJ, Bowring FJ, Catcheside DEA. Recombination hotspots in Neurospora crassa controlled by idiomorphic sequences and meiotic silencing. Genetics 2024; 226:iyad213. [PMID: 38124387 DOI: 10.1093/genetics/iyad213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 12/11/2023] [Accepted: 12/12/2023] [Indexed: 12/23/2023] Open
Abstract
Genes regulating recombination in specific chromosomal intervals of Neurospora crassa were described in the 1960s, but the mechanism is still unknown. For each of the rec-1, rec-2, and rec-3 genes, a single copy of the putative dominant allele, for example, rec-2SL found in St Lawrence OR74 A wild type, reduces recombination in chromosomal regions specific to that gene. However, when we sequenced the recessive allele, rec-2LG (derived from the Lindegren 1A wild type), we found that a 10 kb region in rec-2SL strains was replaced by a 2.7 kb unrelated sequence, making the "alleles" idiomorphs. When we introduced sad-1, a mutant lacking the RNA-dependent RNA polymerase that silences unpaired coding regions during meiosis into crosses heterozygous rec-2SL/rec-2LG, it increased recombination, indicating that meiotic silencing of a gene promoting recombination is responsible for dominant suppression of recombination. Consistent with this, mutation of rec-2LG by Repeat-Induced Point mutation generated an allele with multiple stop codons in the predicted rec-2 gene, which does not promote recombination and is recessive to rec-2LG. Sad-1 also relieves suppression of recombination in relevant target regions, in crosses heterozygous for rec-1 alleles and in crosses heterozygous for rec-3 alleles. We conclude that for all 3 known rec genes, 1 allele appears dominant only because meiotic silencing prevents the product of the active, "recessive," allele from stimulating recombination during meiosis. In addition, the proposed amino acid sequence of REC-2 suggests that regulation of recombination in Neurospora differs from any currently known mechanism.
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Affiliation(s)
- Patricia Jane Yeadon
- College of Science and Engineering, Flinders University, Sturt Road, Bedford Park, South Australia 5042, Australia
| | - Frederick J Bowring
- College of Science and Engineering, Flinders University, Sturt Road, Bedford Park, South Australia 5042, Australia
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13
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Garcia JF, Morales-Cruz A, Cochetel N, Minio A, Figueroa-Balderas R, Rolshausen PE, Baumgartner K, Cantu D. Comparative Pangenomic Insights into the Distinct Evolution of Virulence Factors Among Grapevine Trunk Pathogens. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2024; 37:127-142. [PMID: 37934016 DOI: 10.1094/mpmi-09-23-0129-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
The permanent organs of grapevines (Vitis vinifera L.), like those of other woody perennials, are colonized by various unrelated pathogenic ascomycete fungi secreting cell wall-degrading enzymes and phytotoxic secondary metabolites that contribute to host damage and disease symptoms. Trunk pathogens differ in the symptoms they induce and the extent and speed of damage. Isolates of the same species often display a wide virulence range, even within the same vineyard. This study focuses on Eutypa lata, Neofusicoccum parvum, and Phaeoacremonium minimum, causal agents of Eutypa dieback, Botryosphaeria dieback, and Esca, respectively. We sequenced 50 isolates from viticulture regions worldwide and built nucleotide-level, reference-free pangenomes for each species. Through examination of genomic diversity and pangenome structure, we analyzed intraspecific conservation and variability of putative virulence factors, focusing on functions under positive selection and recent gene family dynamics of contraction and expansion. Our findings reveal contrasting distributions of putative virulence factors in the core, dispensable, and private genomes of each pangenome. For example, carbohydrate active enzymes (CAZymes) were prevalent in the core genomes of each pangenome, whereas biosynthetic gene clusters were prevalent in the dispensable genomes of E. lata and P. minimum. The dispensable fractions were also enriched in Gypsy transposable elements and virulence factors under positive selection (polyketide synthase genes in E. lata and P. minimum, glycosyltransferases in N. parvum). Our findings underscore the complexity of the genomic architecture in each species and provide insights into their adaptive strategies, enhancing our understanding of the underlying mechanisms of virulence. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Jadran F Garcia
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, U.S.A
| | - Abraham Morales-Cruz
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, U.S.A
- U.S. Department of Energy, Joint Genome Institute, Lawrence Berkeley National Lab, Berkeley, CA, U.S.A
| | - Noé Cochetel
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, U.S.A
| | - Andrea Minio
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, U.S.A
| | - Rosa Figueroa-Balderas
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, U.S.A
| | - Philippe E Rolshausen
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, U.S.A
| | - Kendra Baumgartner
- Crops Pathology and Genetics Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Davis, CA, U.S.A
| | - Dario Cantu
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, U.S.A
- Genome Center, University of California, Davis, Davis, CA, U.S.A
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14
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Breuer J, Busche T, Kalinowski J, Nowrousian M. Histone binding of ASF1 is required for fruiting body development but not for genome stability in the filamentous fungus Sordaria macrospora. mBio 2024; 15:e0289623. [PMID: 38112417 PMCID: PMC10790691 DOI: 10.1128/mbio.02896-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 10/27/2023] [Indexed: 12/21/2023] Open
Abstract
IMPORTANCE Histone chaperones are proteins that are involved in nucleosome assembly and disassembly and can therefore influence all DNA-dependent processes including transcription, DNA replication, and repair. ASF1 is a histone chaperone that is conserved throughout eukaryotes. In contrast to most other multicellular organisms, a deletion mutant of asf1 in the fungus Sordaria macrospora is viable; however, the mutant is sterile. In this study, we could show that the histone-binding ability of ASF1 is required for fertility in S. macrospora, whereas the function of ASF1 in maintenance of genome stability does not require histone binding. We also showed that the histone modifications H3K27me3 and H3K56ac are misregulated in the Δasf1 mutant. Furthermore, we identified a large duplication on chromosome 2 of the mutant strain that is genetically linked to the Δasf1 allele present on chromosome 6, suggesting that viability of the mutant might depend on the presence of the duplicated region.
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Affiliation(s)
- Jan Breuer
- Department of Molecular and Cellular Botany, Ruhr University Bochum, Bochum, Germany
| | - Tobias Busche
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
- Medical School OWL, Bielefeld University, Bielefeld, Germany
| | - Jörn Kalinowski
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Minou Nowrousian
- Department of Molecular and Cellular Botany, Ruhr University Bochum, Bochum, Germany
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15
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De Vos L, van der Nest MA, Santana QC, van Wyk S, Leeuwendaal KS, Wingfield BD, Steenkamp ET. Chromosome-Level Assemblies for the Pine Pitch Canker Pathogen Fusarium circinatum. Pathogens 2024; 13:70. [PMID: 38251377 PMCID: PMC10819268 DOI: 10.3390/pathogens13010070] [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: 12/03/2023] [Revised: 12/26/2023] [Accepted: 01/09/2024] [Indexed: 01/23/2024] Open
Abstract
The pine pitch canker pathogen, Fusarium circinatum, is globally regarded as one of the most important threats to commercial pine-based forestry. Although genome sequences of this fungus are available, these remain highly fragmented or structurally ill-defined. Our overall goal was to provide high-quality assemblies for two notable strains of F. circinatum, and to characterize these in terms of coding content, repetitiveness and the position of telomeres and centromeres. For this purpose, we used Oxford Nanopore Technologies MinION long-read sequences, as well as Illumina short sequence reads. By leveraging the genomic synteny inherent to F. circinatum and its close relatives, these sequence reads were assembled to chromosome level, where contiguous sequences mostly spanned from telomere to telomere. Comparative analyses unveiled remarkable variability in the twelfth and smallest chromosome, which is known to be dispensable. It presented a striking length polymorphism, with one strain lacking substantial portions from the chromosome's distal and proximal regions. These regions, characterized by a lower gene density, G+C content and an increased prevalence of repetitive elements, contrast starkly with the syntenic segments of the chromosome, as well as with the core chromosomes. We propose that these unusual regions might have arisen or expanded due to the presence of transposable elements. A comparison of the overall chromosome structure revealed that centromeric elements often underpin intrachromosomal differences between F. circinatum strains, especially at chromosomal breakpoints. This suggests a potential role for centromeres in shaping the chromosomal architecture of F. circinatum and its relatives. The publicly available genome data generated here, together with the detailed metadata provided, represent essential resources for future studies of this important plant pathogen.
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Affiliation(s)
- Lieschen De Vos
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria (UP), Pretoria 0002, South Africa; (L.D.V.); (K.S.L.); (B.D.W.)
| | - Magriet A. van der Nest
- Hans Merensky Chair in Avocado Research, Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute FABI, University of Pretoria, Pretoria 0002, South Africa;
| | - Quentin C. Santana
- Biotechnology Platform, Agricultural Research Council, 100 Old Soutpan Road, Onderstepoort, Pretoria 0010, South Africa;
| | - Stephanie van Wyk
- Collaborating Centre for Optimising Antimalarial Therapy (CCOAT), Mitigating Antimalarial Resistance Consortium in South-East Africa (MARC SEA), Department of Medicine, Division of Clinical Pharmacology, University of Cape Town, Cape Town 7925, South Africa;
| | - Kyle S. Leeuwendaal
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria (UP), Pretoria 0002, South Africa; (L.D.V.); (K.S.L.); (B.D.W.)
| | - Brenda D. Wingfield
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria (UP), Pretoria 0002, South Africa; (L.D.V.); (K.S.L.); (B.D.W.)
| | - Emma T. Steenkamp
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria (UP), Pretoria 0002, South Africa; (L.D.V.); (K.S.L.); (B.D.W.)
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16
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Zhang Y, Nada B, Baker SE, Evans JE, Tian C, Benz JP, Tamayo E. Unveiling a classical mutant in the context of the GH3 β-glucosidase family in Neurospora crassa. AMB Express 2024; 14:4. [PMID: 38180602 PMCID: PMC10770018 DOI: 10.1186/s13568-023-01658-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 12/23/2023] [Indexed: 01/06/2024] Open
Abstract
Classical fungal mutant strains obtained by mutagenesis have helped to elucidate fundamental metabolic pathways in the past. In the filamentous fungus Neurospora crassa, the gluc-1 strain was isolated long ago and characterized by its low level of β-glucosidase activity, which is essential for the degradation of cellulose, the most abundant biopolymer on Earth and the main polymeric component of the plant cell wall. Based on genomic resequencing, we hypothesized that the causative mutation resides in the β-glucosidase gene gh3-3 (bgl6, NCU08755). In this work, growth patterns, enzymatic activities and sugar utilization rates were analyzed in several mutant and overexpression strains related to gluc-1 and gh3-3. In addition, different mutants affected in the degradation and transport of cellobiose were analyzed. While overexpression of gh3-3 led to the recovery of β-glucosidase activity in the gluc-1 mutant, as well as normal utilization of cellobiose, the full gene deletion strain Δgh3-3 was found to behave differently than gluc-1 with lower secreted β-glucosidase activity, indicating a dominant role of the amino acid substitution in the point mutated gh3-3 gene of gluc-1. Our results furthermore confirm that GH3-3 is the major extracellular β-glucosidase in N. crassa and demonstrate that the two cellodextrin transporters CDT-1 and CDT-2 are essential for growth on cellobiose when the three main N. crassa β-glucosidases are absent. Overall, these findings provide valuable insight into the mechanisms of cellulose utilization in filamentous fungi, being an essential step in the efficient production of biorefinable sugars from agricultural and forestry plant biomass.
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Affiliation(s)
- Yuxin Zhang
- Fungal Biotechnology in Wood Science, Holzforschung München, TUM School of Life Sciences, Technical University of Munich, 85354, Freising, Germany
| | - Basant Nada
- Fungal Biotechnology in Wood Science, Holzforschung München, TUM School of Life Sciences, Technical University of Munich, 85354, Freising, Germany
| | - Scott E Baker
- DOE Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Microbial Molecular Phenotyping Group, Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - James E Evans
- Microbial Molecular Phenotyping Group, Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Chaoguang Tian
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - J Philipp Benz
- Fungal Biotechnology in Wood Science, Holzforschung München, TUM School of Life Sciences, Technical University of Munich, 85354, Freising, Germany
| | - Elisabeth Tamayo
- Fungal Biotechnology in Wood Science, Holzforschung München, TUM School of Life Sciences, Technical University of Munich, 85354, Freising, Germany.
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17
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Miao Z, Wang H, Tu X, Huang Z, Huang S, Zhang X, Wang F, Huang Z, Li H, Jiao Y, Gao S, Zhou Z, Shan CM, Li J, Yue JX. GetPrimers: A generalized PCR-based genetic targeting primer designer enabling easy and standardized targeted gene modification across multiple systems. Yeast 2024; 41:19-34. [PMID: 38041528 DOI: 10.1002/yea.3916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/02/2023] [Accepted: 11/17/2023] [Indexed: 12/03/2023] Open
Abstract
Genetic targeting (e.g., gene knockout and tagging) based on polymerase chain reaction (PCR) is a simple yet powerful approach for studying gene functions. Although originally developed in classic budding and fission yeast models, the same principle applies to other eukaryotic systems with efficient homologous recombination. One-step PCR-based genetic targeting is conventionally used but the sizes of the homologous arms that it generates for recombination-mediated genetic targeting are usually limited. Alternatively, gene targeting can also be performed via fusion PCR, which can create homologous arms that are orders of magnitude larger, therefore substantially increasing the efficiency of recombination-mediated genetic targeting. Here, we present GetPrimers (https://www.evomicslab.org/app/getprimers/), a generalized computational framework and web tool to assist automatic targeting and verification primer design for both one-step PCR-based and fusion PCR-based genetic targeting experiments. Moreover, GetPrimers by design runs for any given genetic background of any species with full genome scalability. Therefore, GetPrimers is capable of empowering high-throughput functional genomic assays at multipopulation and multispecies levels. Comprehensive experimental validations have been performed for targeting and verification primers designed by GetPrimers across multiple organism systems and experimental setups. We anticipate GetPrimers to become a highly useful and popular tool to facilitate easy and standardized gene modification across multiple systems.
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Affiliation(s)
- Zepu Miao
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Haiting Wang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xinyu Tu
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Zhengshen Huang
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Shujing Huang
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xinxin Zhang
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Fan Wang
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Zhishen Huang
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Huihui Li
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yue Jiao
- Development Center of Science and Technology, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Song Gao
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Zhipeng Zhou
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Chun-Min Shan
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jing Li
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jia-Xing Yue
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
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18
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Bonometti L, De Bellis F, Cros-Arteil S, Gueret E, Gladieux P. Draft genome sequences of Neurospora crassa clade B, isolated from burned Cytisus sp. plants in France. Microbiol Resour Announc 2023; 12:e0062723. [PMID: 37943031 PMCID: PMC10720570 DOI: 10.1128/mra.00627-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 10/04/2023] [Indexed: 11/10/2023] Open
Abstract
Neurospora crassa clade A is a model system for genetics, biochemistry, molecular biology, and experimental evolution. Here, we present the draft genome sequences of four isolates of N. crassa clade B. These data represent a valuable resource to investigate the population biology and evolutionary history of N. crassa sensu lato.
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Affiliation(s)
- Lucas Bonometti
- PHIM Plant Health Institute, University of Montpellier, INRAE, CIRAD, Institut Agro, Montpellier, France
| | - Fabien De Bellis
- CIRAD, UMR AGAP Institut, Montpellier, France
- AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Sandrine Cros-Arteil
- PHIM Plant Health Institute, University of Montpellier, INRAE, CIRAD, Institut Agro, Montpellier, France
| | - Elise Gueret
- MGX-Montpellier GenomiX, University of Montpellier, CNRS, INSERM, Montpellier, France
| | - Pierre Gladieux
- PHIM Plant Health Institute, University of Montpellier, INRAE, CIRAD, Institut Agro, Montpellier, France
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19
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Hensen N, Bonometti L, Westerberg I, Brännström IO, Guillou S, Cros-Aarteil S, Calhoun S, Haridas S, Kuo A, Mondo S, Pangilinan J, Riley R, LaButti K, Andreopoulos B, Lipzen A, Chen C, Yan M, Daum C, Ng V, Clum A, Steindorff A, Ohm RA, Martin F, Silar P, Natvig DO, Lalanne C, Gautier V, Ament-Velásquez SL, Kruys Å, Hutchinson MI, Powell AJ, Barry K, Miller AN, Grigoriev IV, Debuchy R, Gladieux P, Hiltunen Thorén M, Johannesson H. Genome-scale phylogeny and comparative genomics of the fungal order Sordariales. Mol Phylogenet Evol 2023; 189:107938. [PMID: 37820761 DOI: 10.1016/j.ympev.2023.107938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 09/28/2023] [Accepted: 10/04/2023] [Indexed: 10/13/2023]
Abstract
The order Sordariales is taxonomically diverse, and harbours many species with different lifestyles and large economic importance. Despite its importance, a robust genome-scale phylogeny, and associated comparative genomic analysis of the order is lacking. In this study, we examined whole-genome data from 99 Sordariales, including 52 newly sequenced genomes, and seven outgroup taxa. We inferred a comprehensive phylogeny that resolved several contentious relationships amongst families in the order, and cleared-up intrafamily relationships within the Podosporaceae. Extensive comparative genomics showed that genomes from the three largest families in the dataset (Chaetomiaceae, Podosporaceae and Sordariaceae) differ greatly in GC content, genome size, gene number, repeat percentage, evolutionary rate, and genome content affected by repeat-induced point mutations (RIP). All genomic traits showed phylogenetic signal, and ancestral state reconstruction revealed that the variation of the properties stems primarily from within-family evolution. Together, the results provide a thorough framework for understanding genome evolution in this important group of fungi.
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Affiliation(s)
- Noah Hensen
- Stockholm University, Department of Ecology, Environment and Plants Sciences, Stockholm, Sweden
| | - Lucas Bonometti
- University of Montpellier, PHIM Plant Health Institute, Montpellier, France
| | - Ivar Westerberg
- Stockholm University, Department of Ecology, Environment and Plants Sciences, Stockholm, Sweden
| | - Ioana Onut Brännström
- Oslo University, Natural History Museum, Oslo, Norway; Uppsala University, Department of Ecology and Genetics, Uppsala, Sweden
| | - Sonia Guillou
- University of Montpellier, PHIM Plant Health Institute, Montpellier, France
| | | | - Sara Calhoun
- Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Sajeet Haridas
- Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Alan Kuo
- Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Stephen Mondo
- Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Jasmyn Pangilinan
- Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Robert Riley
- Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Kurt LaButti
- Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Bill Andreopoulos
- Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Anna Lipzen
- Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Cindy Chen
- Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Mi Yan
- Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Chris Daum
- Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Vivian Ng
- Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Alicia Clum
- Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Andrei Steindorff
- Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Robin A Ohm
- Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | | | - Philippe Silar
- Université de Paris Cité, Laboratoire Interdisciplinaire des Energies de Demain, Paris, France
| | - Donald O Natvig
- University of New Mexico, Department of Biology, Albuquerque, USA
| | - Christophe Lalanne
- Université de Paris Cité, Laboratoire Interdisciplinaire des Energies de Demain, Paris, France
| | - Valérie Gautier
- Université de Paris Cité, Laboratoire Interdisciplinaire des Energies de Demain, Paris, France
| | | | - Åsa Kruys
- Uppsala University, Museum of Evolution, Uppsala, Sweden
| | | | - Amy Jo Powell
- Sandia National Laboratories, Dept. of Systems Design and Architecture, Albuquerque, USA
| | - Kerrie Barry
- Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Andrew N Miller
- University of Illinois Urbana-Champaign, Illinois Natural History Survey, USA
| | - Igor V Grigoriev
- Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA; University of California Berkeley, Department of Plant and Microbial Biology, Berkeley, CA, USA
| | - Robert Debuchy
- Université Paris-Saclay, Institute for Integrative Biology of the Cell, Gif-sur-Yvette, France
| | - Pierre Gladieux
- University of Montpellier, PHIM Plant Health Institute, Montpellier, France
| | - Markus Hiltunen Thorén
- Stockholm University, Department of Ecology, Environment and Plants Sciences, Stockholm, Sweden; The Royal Swedish Academy of Sciences, Stockholm, Sweden
| | - Hanna Johannesson
- Stockholm University, Department of Ecology, Environment and Plants Sciences, Stockholm, Sweden; The Royal Swedish Academy of Sciences, Stockholm, Sweden.
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20
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Poinsignon T, Gallopin M, Grognet P, Malagnac F, Lelandais G, Poulain P. 3D models of fungal chromosomes to enhance visual integration of omics data. NAR Genom Bioinform 2023; 5:lqad104. [PMID: 38058589 PMCID: PMC10696920 DOI: 10.1093/nargab/lqad104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 10/11/2023] [Accepted: 11/17/2023] [Indexed: 12/08/2023] Open
Abstract
The functions of eukaryotic chromosomes and their spatial architecture in the nucleus are reciprocally dependent. Hi-C experiments are routinely used to study chromosome 3D organization by probing chromatin interactions. Standard representation of the data has relied on contact maps that show the frequency of interactions between parts of the genome. In parallel, it has become easier to build 3D models of the entire genome based on the same Hi-C data, and thus benefit from the methodology and visualization tools developed for structural biology. 3D modeling of entire genomes leverages the understanding of their spatial organization. However, this opportunity for original and insightful modeling is underexploited. In this paper, we show how seeing the spatial organization of chromosomes can bring new perspectives to omics data integration. We assembled state-of-the-art tools into a workflow that goes from Hi-C raw data to fully annotated 3D models and we re-analysed public omics datasets available for three fungal species. Besides the well-described properties of the spatial organization of their chromosomes (Rabl conformation, hypercoiling and chromosome territories), our results highlighted (i) in Saccharomyces cerevisiae, the backbones of the cohesin anchor regions, which were aligned all along the chromosomes, (ii) in Schizosaccharomyces pombe, the oscillations of the coiling of chromosome arms throughout the cell cycle and (iii) in Neurospora crassa, the massive relocalization of histone marks in mutants of heterochromatin regulators. 3D modeling of the chromosomes brings new opportunities for visual integration of omics data. This holistic perspective supports intuition and lays the foundation for building new concepts.
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Affiliation(s)
- Thibault Poinsignon
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
| | - Mélina Gallopin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Pierre Grognet
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Fabienne Malagnac
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Gaëlle Lelandais
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Pierre Poulain
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
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21
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Xue F, Zhao Z, Gu S, Chen M, Xu J, Luo X, Li J, Tian C. The transcriptional factor Clr-5 is involved in cellulose degradation through regulation of amino acid metabolism in Neurospora crassa. BMC Biotechnol 2023; 23:50. [PMID: 38031036 PMCID: PMC10687990 DOI: 10.1186/s12896-023-00823-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 11/23/2023] [Indexed: 12/01/2023] Open
Abstract
BACKGROUND Filamentous fungi are efficient degraders of plant biomass and the primary producers of commercial cellulolytic enzymes. While the transcriptional regulation mechanisms of cellulases have been continuously explored in lignocellulolytic fungi, the induction of cellulase production remains a complex multifactorial system, with several aspects still largely elusive. RESULTS In this study, we identified a Zn2Cys6 transcription factor, designated as Clr-5, which regulates the expression of cellulase genes by influencing amino acid metabolism in Neurospora crassa during growth on cellulose. The deletion of clr-5 caused a significant decrease in secreted protein and cellulolytic enzyme activity of N. crassa, which was partially alleviated by supplementing with yeast extract. Transcriptomic profiling revealed downregulation of not only the genes encoding main cellulases but also those related to nitrogen metabolism after disruption of Clr-5 under Avicel condition. Clr-5 played a crucial role in the utilization of multiple amino acids, especially leucine and histidine. When using leucine or histidine as the sole nitrogen source, the Δclr-5 mutant showed significant growth defects on both glucose and Avicel media. Comparative transcriptomic analysis revealed that the transcript levels of most genes encoding carbohydrate-active enzymes and those involved in the catabolism and uptake of histidine, branched-chain amino acids, and aromatic amino acids, were remarkably reduced in strain Δclr-5, compared with the wild-type N. crassa when grown in Avicel medium with leucine or histidine as the sole nitrogen source. These findings underscore the important role of amino acid metabolism in the regulation of cellulase production in N. crassa. Furthermore, the function of Clr-5 in regulating cellulose degradation is conserved among ascomycete fungi. CONCLUSIONS These findings regarding the novel transcription factor Clr-5 enhance our comprehension of the regulatory connections between amino acid metabolism and cellulase production, offering fresh prospects for the development of fungal cell factories dedicated to cellulolytic enzyme production in bio-refineries.
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Affiliation(s)
- Fanglei Xue
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Zhen Zhao
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Shuying Gu
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Meixin Chen
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Jing Xu
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Xuegang Luo
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Jingen Li
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China.
| | - Chaoguang Tian
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China.
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22
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Scadden AW, Graybill AS, Hull-Crew C, Lundberg TJ, Lande NM, Klocko AD. Histone deacetylation and cytosine methylation compartmentalize heterochromatic regions in the genome organization of Neurospora crassa. Proc Natl Acad Sci U S A 2023; 120:e2311249120. [PMID: 37963248 PMCID: PMC10666030 DOI: 10.1073/pnas.2311249120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 10/11/2023] [Indexed: 11/16/2023] Open
Abstract
Chromosomes must correctly fold in eukaryotic nuclei for proper genome function. Eukaryotic organisms hierarchically organize their genomes, including in the fungus Neurospora crassa, where chromatin fiber loops compact into Topologically Associated Domain-like structures formed by heterochromatic region aggregation. However, insufficient data exist on how histone posttranslational modifications (PTMs), including acetylation, affect genome organization. In Neurospora, the HCHC complex [composed of the proteins HDA-1, CDP-2 (Chromodomain Protein-2), Heterochromatin Protein-1, and CHAP (CDP-2 and HDA-1 Associated Protein)] deacetylates heterochromatic nucleosomes, as loss of individual HCHC members increases centromeric acetylation, and alters the methylation of cytosines in DNA. Here, we assess whether the HCHC complex affects genome organization by performing Hi-C in strains deleted of the cdp-2 or chap genes. CDP-2 loss increases intra- and interchromosomal heterochromatic region interactions, while loss of CHAP decreases heterochromatic region compaction. Individual HCHC mutants exhibit different patterns of histone PTMs genome-wide, as CDP-2 deletion increases heterochromatic H4K16 acetylation, yet smaller heterochromatic regions lose H3K9 trimethylation and gain interheterochromatic region interactions; CHAP loss produces minimal acetylation changes but increases heterochromatic H3K9me3 enrichment. Loss of both CDP-2 and the DIM-2 DNA methyltransferase causes extensive genome disorder as heterochromatic-euchromatic contacts increase despite additional H3K9me3 enrichment. Our results highlight how the increased cytosine methylation in HCHC mutants ensures genome compartmentalization when heterochromatic regions become hyperacetylated without HDAC activity.
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Affiliation(s)
- Ashley W. Scadden
- Department of Chemistry and Biochemistry, University of Colorado Colorado Springs, Colorado Springs, CO80918
| | - Alayne S. Graybill
- Department of Chemistry and Biochemistry, University of Colorado Colorado Springs, Colorado Springs, CO80918
| | - Clayton Hull-Crew
- Department of Chemistry and Biochemistry, University of Colorado Colorado Springs, Colorado Springs, CO80918
| | - Tiffany J. Lundberg
- Department of Chemistry and Biochemistry, University of Colorado Colorado Springs, Colorado Springs, CO80918
| | - Nickolas M. Lande
- Department of Chemistry and Biochemistry, University of Colorado Colorado Springs, Colorado Springs, CO80918
| | - Andrew D. Klocko
- Department of Chemistry and Biochemistry, University of Colorado Colorado Springs, Colorado Springs, CO80918
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23
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Wang Z, Wang YW, Kasuga T, Lopez-Giraldez F, Zhang Y, Zhang Z, Wang Y, Dong C, Sil A, Trail F, Yarden O, Townsend JP. Lineage-specific genes are clustered with HET-domain genes and respond to environmental and genetic manipulations regulating reproduction in Neurospora. PLoS Genet 2023; 19:e1011019. [PMID: 37934795 PMCID: PMC10684091 DOI: 10.1371/journal.pgen.1011019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 11/28/2023] [Accepted: 10/16/2023] [Indexed: 11/09/2023] Open
Abstract
Lineage-specific genes (LSGs) have long been postulated to play roles in the establishment of genetic barriers to intercrossing and speciation. In the genome of Neurospora crassa, most of the 670 Neurospora LSGs that are aggregated adjacent to the telomeres are clustered with 61% of the HET-domain genes, some of which regulate self-recognition and define vegetative incompatibility groups. In contrast, the LSG-encoding proteins possess few to no domains that would help to identify potential functional roles. Possible functional roles of LSGs were further assessed by performing transcriptomic profiling in genetic mutants and in response to environmental alterations, as well as examining gene knockouts for phenotypes. Among the 342 LSGs that are dynamically expressed during both asexual and sexual phases, 64% were detectable on unusual carbon sources such as furfural, a wildfire-produced chemical that is a strong inducer of sexual development, and the structurally-related furan 5-hydroxymethyl furfural (HMF). Expression of a significant portion of the LSGs was sensitive to light and temperature, factors that also regulate the switch from asexual to sexual reproduction. Furthermore, expression of the LSGs was significantly affected in the knockouts of adv-1 and pp-1 that regulate hyphal communication, and expression of more than one quarter of the LSGs was affected by perturbation of the mating locus. These observations encouraged further investigation of the roles of clustered lineage-specific and HET-domain genes in ecology and reproduction regulation in Neurospora, especially the regulation of the switch from the asexual growth to sexual reproduction, in response to dramatic environmental conditions changes.
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Affiliation(s)
- Zheng Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Yen-Wen Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Takao Kasuga
- College of Biological Sciences, University of California, Davis, California, United States of America
| | | | - Yang Zhang
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Zhang Zhang
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Yaning Wang
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Caihong Dong
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Anita Sil
- Department of Microbiology and Immunology, University of California, San Francisco, California, United States of America
| | - Frances Trail
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan, United States of America
| | - Oded Yarden
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Jeffrey P. Townsend
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, United States of America
- Department of Ecology and Evolutionary Biology, Program in Microbiology, and Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America
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24
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Nambiar A, Dubinkina V, Liu S, Maslov S. FUN-PROSE: A deep learning approach to predict condition-specific gene expression in fungi. PLoS Comput Biol 2023; 19:e1011563. [PMID: 37971967 PMCID: PMC10653424 DOI: 10.1371/journal.pcbi.1011563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 09/30/2023] [Indexed: 11/19/2023] Open
Abstract
mRNA levels of all genes in a genome is a critical piece of information defining the overall state of the cell in a given environmental condition. Being able to reconstruct such condition-specific expression in fungal genomes is particularly important to metabolically engineer these organisms to produce desired chemicals in industrially scalable conditions. Most previous deep learning approaches focused on predicting the average expression levels of a gene based on its promoter sequence, ignoring its variation across different conditions. Here we present FUN-PROSE-a deep learning model trained to predict differential expression of individual genes across various conditions using their promoter sequences and expression levels of all transcription factors. We train and test our model on three fungal species and get the correlation between predicted and observed condition-specific gene expression as high as 0.85. We then interpret our model to extract promoter sequence motifs responsible for variable expression of individual genes. We also carried out input feature importance analysis to connect individual transcription factors to their gene targets. A sizeable fraction of both sequence motifs and TF-gene interactions learned by our model agree with previously known biological information, while the rest corresponds to either novel biological facts or indirect correlations.
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Affiliation(s)
- Ananthan Nambiar
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, Illinois, United States of America
- Carl R. Woese Institute for Genomic Biology, Urbana, Illinois, United States of America
| | - Veronika Dubinkina
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, Illinois, United States of America
- Carl R. Woese Institute for Genomic Biology, Urbana, Illinois, United States of America
- The Gladstone Institute of Data Science and Biotechnology, San Francisco, California, United States of America
| | - Simon Liu
- Carl R. Woese Institute for Genomic Biology, Urbana, Illinois, United States of America
- Department of Computer Science, University of Illinois Urbana-Champaign, Urbana, Illinois, United States of America
| | - Sergei Maslov
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, Illinois, United States of America
- Carl R. Woese Institute for Genomic Biology, Urbana, Illinois, United States of America
- Department of Physics, University of Illinois Urbana-Champaign, Urbana, Illinois, United States of America
- Computing, Environment and Life Sciences, Argonne National Laboratory, Lemont, Illinois, United States of America
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25
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Wang Z, Wang YW, Kasuga T, Hassler H, Lopez-Giraldez F, Dong C, Yarden O, Townsend JP. Origins of lineage-specific elements via gene duplication, relocation, and regional rearrangement in Neurospora crassa. Mol Ecol 2023. [PMID: 37843462 DOI: 10.1111/mec.17168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 09/20/2023] [Accepted: 09/27/2023] [Indexed: 10/17/2023]
Abstract
The origin of new genes has long been a central interest of evolutionary biologists. However, their novelty means that they evade reconstruction by the classical tools of evolutionary modelling. This evasion of deep ancestral investigation necessitates intensive study of model species within well-sampled, recently diversified, clades. One such clade is the model genus Neurospora, members of which lack recent gene duplications. Several Neurospora species are comprehensively characterized organisms apt for studying the evolution of lineage-specific genes (LSGs). Using gene synteny, we documented that 78% of Neurospora LSG clusters are located adjacent to the telomeres featuring extensive tracts of non-coding DNA and duplicated genes. Here, we report several instances of LSGs that are likely from regional rearrangements and potentially from gene rebirth. To broadly investigate the functions of LSGs, we assembled transcriptomics data from 68 experimental data points and identified co-regulatory modules using Weighted Gene Correlation Network Analysis, revealing that LSGs are widely but peripherally involved in known regulatory machinery for diverse functions. The ancestral status of the LSG mas-1, a gene with roles in cell-wall integrity and cellular sensitivity to antifungal toxins, was investigated in detail alongside its genomic neighbours, indicating that it arose from an ancient lysophospholipase precursor that is ubiquitous in lineages of the Sordariomycetes. Our discoveries illuminate a "rummage region" in the N. crassa genome that enables the formation of new genes and functions to arise via gene duplication and relocation, followed by fast mutation and recombination facilitated by sequence repeats and unconstrained non-coding sequences.
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Affiliation(s)
- Zheng Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, USA
| | - Yen-Wen Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, USA
| | - Takao Kasuga
- College of Biological Sciences, University of California, Davis, Davis, California, USA
| | - Hayley Hassler
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, USA
| | | | - Caihong Dong
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Oded Yarden
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Jeffrey P Townsend
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, USA
- Department of Ecology and Evolutionary Biology, Program in Microbiology, and Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, USA
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26
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Scadden AW, Graybill AS, Hull-Crew C, Lundberg TJ, Lande NM, Klocko AD. Histone deacetylation and cytosine methylation compartmentalize heterochromatic regions in the genome organization of Neurospora crassa. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.03.547530. [PMID: 37461718 PMCID: PMC10349943 DOI: 10.1101/2023.07.03.547530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
Chromosomes must correctly fold in eukaryotic nuclei for proper genome function. Eukaryotic organisms hierarchically organize their genomes, including in the fungus Neurospora crassa, where chromatin fiber loops compact into Topologically Associated Domain (TAD)-like structures formed by heterochromatic region aggregation. However, insufficient data exists on how histone post-translational modifications, including acetylation, affect genome organization. In Neurospora, the HCHC complex (comprised of the proteins HDA-1, CDP-2, HP1, and CHAP) deacetylates heterochromatic nucleosomes, as loss of individual HCHC members increases centromeric acetylation and alters the methylation of cytosines in DNA. Here, we assess if the HCHC complex affects genome organization by performing Hi-C in strains deleted of the cdp-2 or chap genes. CDP-2 loss increases intra- and inter-chromosomal heterochromatic region interactions, while loss of CHAP decreases heterochromatic region compaction. Individual HCHC mutants exhibit different patterns of histone post-translational modifications genome-wide: without CDP-2, heterochromatic H4K16 acetylation is increased, yet smaller heterochromatic regions lose H3K9 trimethylation and gain inter-heterochromatic region interactions; CHAP loss produces minimal acetylation changes but increases heterochromatic H3K9me3 enrichment. Loss of both CDP-2 and the DIM-2 DNA methyltransferase causes extensive genome disorder, as heterochromatic-euchromatic contacts increase despite additional H3K9me3 enrichment. Our results highlight how the increased cytosine methylation in HCHC mutants ensures genome compartmentalization when heterochromatic regions become hyperacetylated without HDAC activity.
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Affiliation(s)
- Ashley W. Scadden
- University of Colorado Colorado Springs, Department of Chemistry & Biochemistry, Colorado Springs, CO 80918, USA
| | - Alayne S. Graybill
- University of Colorado Colorado Springs, Department of Chemistry & Biochemistry, Colorado Springs, CO 80918, USA
| | - Clayton Hull-Crew
- University of Colorado Colorado Springs, Department of Chemistry & Biochemistry, Colorado Springs, CO 80918, USA
| | - Tiffany J. Lundberg
- University of Colorado Colorado Springs, Department of Chemistry & Biochemistry, Colorado Springs, CO 80918, USA
| | - Nickolas M. Lande
- University of Colorado Colorado Springs, Department of Chemistry & Biochemistry, Colorado Springs, CO 80918, USA
| | - Andrew D. Klocko
- University of Colorado Colorado Springs, Department of Chemistry & Biochemistry, Colorado Springs, CO 80918, USA
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Gutiérrez-Corona JF, González-Hernández GA, Padilla-Guerrero IE, Olmedo-Monfil V, Martínez-Rocha AL, Patiño-Medina JA, Meza-Carmen V, Torres-Guzmán JC. Fungal Alcohol Dehydrogenases: Physiological Function, Molecular Properties, Regulation of Their Production, and Biotechnological Potential. Cells 2023; 12:2239. [PMID: 37759461 PMCID: PMC10526403 DOI: 10.3390/cells12182239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/27/2023] [Accepted: 08/31/2023] [Indexed: 09/29/2023] Open
Abstract
Fungal alcohol dehydrogenases (ADHs) participate in growth under aerobic or anaerobic conditions, morphogenetic processes, and pathogenesis of diverse fungal genera. These processes are associated with metabolic operation routes related to alcohol, aldehyde, and acid production. The number of ADH enzymes, their metabolic roles, and their functions vary within fungal species. The most studied ADHs are associated with ethanol metabolism, either as fermentative enzymes involved in the production of this alcohol or as oxidative enzymes necessary for the use of ethanol as a carbon source; other enzymes participate in survival under microaerobic conditions. The fast generation of data using genome sequencing provides an excellent opportunity to determine a correlation between the number of ADHs and fungal lifestyle. Therefore, this review aims to summarize the latest knowledge about the importance of ADH enzymes in the physiology and metabolism of fungal cells, as well as their structure, regulation, evolutionary relationships, and biotechnological potential.
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Affiliation(s)
- J. Félix Gutiérrez-Corona
- Departamento de Biología, DCNE, Universidad de Guanajuato, Guanajuato C.P. 36050, Mexico; (G.A.G.-H.); (I.E.P.-G.); (V.O.-M.); (A.L.M.-R.)
| | - Gloria Angélica González-Hernández
- Departamento de Biología, DCNE, Universidad de Guanajuato, Guanajuato C.P. 36050, Mexico; (G.A.G.-H.); (I.E.P.-G.); (V.O.-M.); (A.L.M.-R.)
| | - Israel Enrique Padilla-Guerrero
- Departamento de Biología, DCNE, Universidad de Guanajuato, Guanajuato C.P. 36050, Mexico; (G.A.G.-H.); (I.E.P.-G.); (V.O.-M.); (A.L.M.-R.)
| | - Vianey Olmedo-Monfil
- Departamento de Biología, DCNE, Universidad de Guanajuato, Guanajuato C.P. 36050, Mexico; (G.A.G.-H.); (I.E.P.-G.); (V.O.-M.); (A.L.M.-R.)
| | - Ana Lilia Martínez-Rocha
- Departamento de Biología, DCNE, Universidad de Guanajuato, Guanajuato C.P. 36050, Mexico; (G.A.G.-H.); (I.E.P.-G.); (V.O.-M.); (A.L.M.-R.)
| | - J. Alberto Patiño-Medina
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo (UMSNH), Morelia C.P. 58030, Mexico; (J.A.P.-M.); (V.M.-C.)
| | - Víctor Meza-Carmen
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo (UMSNH), Morelia C.P. 58030, Mexico; (J.A.P.-M.); (V.M.-C.)
| | - Juan Carlos Torres-Guzmán
- Departamento de Biología, DCNE, Universidad de Guanajuato, Guanajuato C.P. 36050, Mexico; (G.A.G.-H.); (I.E.P.-G.); (V.O.-M.); (A.L.M.-R.)
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Baruah D, Tamuli R. The cell functions of phospholipase C-1, Ca 2+/H + exchanger-1, and secretory phospholipase A 2 in tolerance to stress conditions and cellulose degradation in Neurospora crassa. Arch Microbiol 2023; 205:327. [PMID: 37676310 DOI: 10.1007/s00203-023-03662-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 08/13/2023] [Accepted: 08/17/2023] [Indexed: 09/08/2023]
Abstract
We investigated the cell functions of the Ca2+ signaling genes phospholipase C-1 (plc-1), Ca2+/H+ exchanger (cpe-1), and secretory phospholipase A2 (splA2) for stress responses and cellulose utilization in Neurospora crassa. The Δplc-1, Δcpe-1, and ΔsplA2 mutants displayed increased sensitivity to the alkaline pH and reduced survival during induced thermotolerance. The ΔsplA2 mutant also exhibited hypersensitivity to the DTT-induced endoplasmic reticulum (ER) stress, increased microcrystalline cellulose utilization, increased protein secretion, and glucose accumulation in the culture supernatants. Moreover, the ΔsplA2 mutant could not grow on microcrystalline cellulose during ER stress. Furthermore, plc-1, cpe-1, and splA2 synthetically regulate the acquisition of thermotolerance induced by heat shock, responses to alkaline pH and ER stress, and utilization of cellulose and other alternate carbon sources in N. crassa. In addition, expression of the alkaline pH regulator, pac-3, and heat shock proteins, hsp60, and hsp80 was reduced in the Δplc-1, Δcpe-1, and ΔsplA2 single and double mutants. The expression of the unfolded protein response (UPR) markers grp-78 and pdi-1 was also significantly reduced in the mutants showing growth defect during ER stress. The increased cellulolytic activities of the ΔsplA2 and Δcpe-1; ΔsplA2 mutants were due to increased cbh-1, cbh-2, and endo-2 expression in N. crassa. Therefore, plc-1, cpe-1, and splA2 are involved in stress responses and cellulose utilization in N. crassa.
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Affiliation(s)
- Darshana Baruah
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781 039, India
| | - Ranjan Tamuli
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781 039, India.
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Montenegro-Montero A, Goity A, Canessa PF, Larrondo LF. Identification of a common secondary mutation in the Neurospora crassa knockout collection conferring a cell fusion-defective phenotype. Microbiol Spectr 2023; 11:e0208723. [PMID: 37623742 PMCID: PMC10580951 DOI: 10.1128/spectrum.02087-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 07/12/2023] [Indexed: 08/26/2023] Open
Abstract
Gene-deletion mutants represent a powerful tool to study gene function. The filamentous fungus Neurospora crassa is a well-established model organism, and features a comprehensive gene knockout strain collection. While these mutant strains have been used in numerous studies, resulting in the functional annotation of many Neurospora genes, direct confirmation of gene-phenotype relationships is often lacking, which is particularly relevant given the possibility of background mutations, sample contamination, and/or strain mislabeling. Indeed, spontaneous mutations resulting in phenotypes resembling many cell fusion mutants have long been known to occur at relatively high frequency in N. crassa, and these secondary mutations are common in the Neurospora deletion collection. The identity of these mutations, however, is largely unknown. Here, we report that the Δada-3 strain from the N. crassa knockout collection, which exhibits a cell fusion defect, harbors a secondary mutation responsible for this phenotype. Through whole-genome sequencing and genetic analyses, we found a ~30-Kb deletion in this strain affecting a known cell fusion-related gene, so/ham-1, and show that it is the absence of this gene-and not of ada-3-that underlies its cell fusion defect. We additionally found three other knockout strains harboring the same deletion, suggesting that this mutation may be common in the collection and could have impacted previous studies. Our findings provide a cautionary note and highlight the importance of proper functional validation of strains from mutant collections. We discuss our results in the context of the spread of cell fusion-defective cheater variants in N. crassa cultures. IMPORTANCE This study emphasizes the need for careful and detailed characterization of strains from mutant collections. Specifically, we found a common deletion in various strains from the Neurospora crassa gene knockout collection that results in a cell fusion-defective phenotype. This is noteworthy because this collection is known to contain background mutations-of a largely unclear nature-that produce cell fusion-defective phenotypes. Our results describe an example of such mutations, and highlight how this common genetic defect could have impacted previous studies that have used the affected strains. Furthermore, they provide a cautionary note about the use of Neurospora strains with similar phenotypes. Lastly, these findings offer additional details relevant to our understanding of the origin and spread of cell fusion-defective cheater variants in N. crassa cultures.
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Affiliation(s)
- Alejandro Montenegro-Montero
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Agencia Nacional de Investigación y Desarrollo-Millennium Science Initiative Program, Millennium Institute for Integrative Biology, Santiago, Chile
| | - Alejandra Goity
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Agencia Nacional de Investigación y Desarrollo-Millennium Science Initiative Program, Millennium Institute for Integrative Biology, Santiago, Chile
| | - Paulo F. Canessa
- Agencia Nacional de Investigación y Desarrollo-Millennium Science Initiative Program, Millennium Institute for Integrative Biology, Santiago, Chile
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Luis F. Larrondo
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Agencia Nacional de Investigación y Desarrollo-Millennium Science Initiative Program, Millennium Institute for Integrative Biology, Santiago, Chile
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Talbi N, Fokkens L, Audran C, Petit‐Houdenot Y, Pouzet C, Blaise F, Gay EJ, Rouxel T, Balesdent M, Rep M, Fudal I. The neighbouring genes AvrLm10A and AvrLm10B are part of a large multigene family of cooperating effector genes conserved in Dothideomycetes and Sordariomycetes. MOLECULAR PLANT PATHOLOGY 2023; 24:914-931. [PMID: 37128172 PMCID: PMC10346447 DOI: 10.1111/mpp.13338] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 03/22/2023] [Accepted: 03/26/2023] [Indexed: 05/03/2023]
Abstract
Fungal effectors (small-secreted proteins) have long been considered as species or even subpopulation-specific. The increasing availability of high-quality fungal genomes and annotations has allowed the identification of trans-species or trans-genera families of effectors. Two avirulence effectors, AvrLm10A and AvrLm10B, of Leptosphaeria maculans, the fungus causing stem canker of oilseed rape, are members of such a large family of effectors. AvrLm10A and AvrLm10B are neighbouring genes, organized in divergent transcriptional orientation. Sequence searches within the L. maculans genome showed that AvrLm10A/AvrLm10B belong to a multigene family comprising five pairs of genes with a similar tail-to-tail organization. The two genes, in a pair, always had the same expression pattern and two expression profiles were distinguished, associated with the biotrophic colonization of cotyledons and/or petioles and stems. Of the two protein pairs further investigated, AvrLm10A_like1/AvrLm10B_like1 and AvrLm10A_like2/AvrLm10B_like2, the second one had the ability to physically interact, similarly to what was previously described for the AvrLm10A/AvrLm10B pair, and cross-interactions were also detected for two pairs. AvrLm10A homologues were identified in more than 30 Dothideomycete and Sordariomycete plant-pathogenic fungi. One of them, SIX5, is an effector from Fusarium oxysporum f. sp. lycopersici physically interacting with the avirulence effector Avr2. We found that AvrLm10A/SIX5 homologues were associated with at least eight distinct putative effector families, suggesting that AvrLm10A/SIX5 is able to cooperate with different effectors. These results point to a general role of the AvrLm10A/SIX5 proteins as "cooperating proteins", able to interact with diverse families of effectors whose encoding gene is co-regulated with the neighbouring AvrLm10A homologue.
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Affiliation(s)
- Nacera Talbi
- BIOGER, INRAEUniversité Paris‐SaclayPalaiseauFrance
| | - Like Fokkens
- Molecular Plant PathologyUniversity of AmsterdamAmsterdamNetherlands
- Present address:
Laboratory of PhytopathologyWageningen University and ResearchWageningenNetherlands
| | - Corinne Audran
- UMR LIPMEUniversité de Toulouse, INRAE, CNRSCastanet‐TolosanFrance
| | | | - Cécile Pouzet
- FRAIB‐TRI Imaging Platform Facilities, FR AIBUniversité de Toulouse, CNRSCastanet‐TolosanFrance
| | | | - Elise J. Gay
- BIOGER, INRAEUniversité Paris‐SaclayPalaiseauFrance
| | | | | | - Martijn Rep
- Molecular Plant PathologyUniversity of AmsterdamAmsterdamNetherlands
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Maseko NN, Steenkamp ET, Wingfield BD, Wilken PM. An in Silico Approach to Identifying TF Binding Sites: Analysis of the Regulatory Regions of BUSCO Genes from Fungal Species in the Ceratocystidaceae Family. Genes (Basel) 2023; 14:genes14040848. [PMID: 37107606 PMCID: PMC10137650 DOI: 10.3390/genes14040848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/26/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
Transcriptional regulation controls gene expression through regulatory promoter regions that contain conserved sequence motifs. These motifs, also known as regulatory elements, are critically important to expression, which is driving research efforts to identify and characterize them. Yeasts have been the focus of such studies in fungi, including in several in silico approaches. This study aimed to determine whether in silico approaches could be used to identify motifs in the Ceratocystidaceae family, and if present, to evaluate whether these correspond to known transcription factors. This study targeted the 1000 base-pair region upstream of the start codon of 20 single-copy genes from the BUSCO dataset for motif discovery. Using the MEME and Tomtom analysis tools, conserved motifs at the family level were identified. The results show that such in silico approaches could identify known regulatory motifs in the Ceratocystidaceae and other unrelated species. This study provides support to ongoing efforts to use in silico analyses for motif discovery.
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Hossain MM, Sultana F, Li W, Tran LSP, Mostofa MG. Sclerotinia sclerotiorum (Lib.) de Bary: Insights into the Pathogenomic Features of a Global Pathogen. Cells 2023; 12:cells12071063. [PMID: 37048136 PMCID: PMC10093061 DOI: 10.3390/cells12071063] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 03/11/2023] [Accepted: 03/23/2023] [Indexed: 04/03/2023] Open
Abstract
Sclerotinia sclerotiorum (Lib.) de Bary is a broad host-range fungus that infects an inclusive array of plant species and afflicts significant yield losses globally. Despite being a notorious pathogen, it has an uncomplicated life cycle consisting of either basal infection from myceliogenically germinated sclerotia or aerial infection from ascospores of carpogenically germinated sclerotia. This fungus is unique among necrotrophic pathogens in that it inevitably colonizes aging tissues to initiate an infection, where a saprophytic stage follows the pathogenic phase. The release of cell wall-degrading enzymes, oxalic acid, and effector proteins are considered critical virulence factors necessary for the effective pathogenesis of S. sclerotiorum. Nevertheless, the molecular basis of S. sclerotiorum pathogenesis is still imprecise and remains a topic of continuing research. Previous comprehensive sequencing of the S. sclerotiorum genome has revealed new insights into its genome organization and provided a deeper comprehension of the sophisticated processes involved in its growth, development, and virulence. This review focuses on the genetic and genomic aspects of fungal biology and molecular pathogenicity to summarize current knowledge of the processes utilized by S. sclerotiorum to parasitize its hosts. Understanding the molecular mechanisms regulating the infection process of S. sclerotiorum will contribute to devising strategies for preventing infections caused by this destructive pathogen.
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Liu Z, Cong Y, Sossah FL, Lu Y, Kang J, Li Y. Characterization and Genome Analysis of Cladobotryum mycophilum, the Causal Agent of Cobweb Disease of Morchella sextelata in China. J Fungi (Basel) 2023; 9:jof9040411. [PMID: 37108865 PMCID: PMC10145569 DOI: 10.3390/jof9040411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 03/08/2023] [Accepted: 03/21/2023] [Indexed: 03/29/2023] Open
Abstract
Cobweb disease is a fungal disease that can cause serious damage to edible mushrooms worldwide. To investigate cobweb disease in Morchella sextelata in Guizhou Province, China, we isolated and purified the pathogen responsible for the disease. Through morphological and molecular identification and pathogenicity testing on infected M. sextelata, we identified Cladobotryum mycophilum as the cause of cobweb disease in this region. This is the first known occurrence of this pathogen causing cobweb disease in M. sextelata anywhere in the world. We then obtained the genome of C. mycophilum BJWN07 using the HiFi sequencing platform, resulting in a high-quality genome assembly with a size of 38.56 Mb, 10 contigs, and a GC content of 47.84%. We annotated 8428 protein-coding genes in the genome, including many secreted proteins, host interaction-related genes, and carbohydrate-active enzymes (CAZymes) related to the pathogenesis of the disease. Our findings shed new light on the pathogenesis of C. mycophilum and provide a theoretical basis for developing potential prevention and control strategies for cobweb disease.
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Affiliation(s)
- Zhenghui Liu
- Engineering and Research Center for Southwest Bio-pharmaceutical Resources of National Education Ministry, Guizhou University, Guiyang 550025, China
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
| | - Yunlong Cong
- Research Institute of Science and Technology, Guizhou University, Guiyang 550025, China
| | - Frederick Leo Sossah
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
- Council for Scientific and Industrial Research (CSIR), Oil Palm Research Institute, Coconut Research Programme, Sekondi P.O. Box 245, Ghana
| | - Yongzhong Lu
- School of Food and Pharmaceutical Engineering, Guizhou Institute of Technology, Guiyang 550003, China
| | - Jichuan Kang
- Engineering and Research Center for Southwest Bio-pharmaceutical Resources of National Education Ministry, Guizhou University, Guiyang 550025, China
- Correspondence: (J.K.); (Y.L.)
| | - Yu Li
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
- Correspondence: (J.K.); (Y.L.)
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Yu H, Yang H, Haridas S, Hayes RD, Lynch H, Andersen S, Newman M, Li G, Martínez-Soto D, Milo-Cochavi S, Hazal Ayhan D, Zhang Y, Grigoriev IV, Ma LJ. Conservation and Expansion of Transcriptional Factor Repertoire in the Fusarium oxysporum Species Complex. J Fungi (Basel) 2023; 9:359. [PMID: 36983527 PMCID: PMC10056406 DOI: 10.3390/jof9030359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/11/2023] [Accepted: 03/13/2023] [Indexed: 03/17/2023] Open
Abstract
The Fusarium oxysporum species complex (FOSC) includes both plant and human pathogens that cause devastating plant vascular wilt diseases and threaten public health. Each F. oxysporum genome comprises core chromosomes (CCs) for housekeeping functions and accessory chromosomes (ACs) that contribute to host-specific adaptation. This study inspects global transcription factor profiles (TFomes) and their potential roles in coordinating CC and AC functions to accomplish host-specific interactions. Remarkably, we found a clear positive correlation between the sizes of TFomes and the proteomes of an organism. With the acquisition of ACs, the FOSC TFomes were larger than the other fungal genomes included in this study. Among a total of 48 classified TF families, 14 families involved in transcription/translation regulations and cell cycle controls were highly conserved. Among the 30 FOSC expanded families, Zn2-C6 and Znf_C2H2 were most significantly expanded to 671 and 167 genes per family including well-characterized homologs of Ftf1 (Zn2-C6) and PacC (Znf_C2H2) that are involved in host-specific interactions. Manual curation of characterized TFs increased the TFome repertoires by 3% including a disordered protein Ren1. RNA-Seq revealed a steady pattern of expression for conserved TF families and specific activation for AC TFs. Functional characterization of these TFs could enhance our understanding of transcriptional regulation involved in FOSC cross-kingdom interactions, disentangle species-specific adaptation, and identify targets to combat diverse diseases caused by this group of fungal pathogens.
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Affiliation(s)
- Houlin Yu
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - He Yang
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Sajeet Haridas
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, University of California Berkeley, Berkeley, CA 94720, USA
| | - Richard D. Hayes
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, University of California Berkeley, Berkeley, CA 94720, USA
| | - Hunter Lynch
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Sawyer Andersen
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Madison Newman
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Gengtan Li
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Domingo Martínez-Soto
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Shira Milo-Cochavi
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Dilay Hazal Ayhan
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Yong Zhang
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Igor V. Grigoriev
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, University of California Berkeley, Berkeley, CA 94720, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94598, USA
| | - Li-Jun Ma
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
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Wang R, Arioka M. Glucuronoyl esterase facilitates biomass degradation in Neurospora crassa by upregulating the expression of plant biomass-degrading enzymes. J GEN APPL MICROBIOL 2023; 68:278-286. [PMID: 35858815 DOI: 10.2323/jgam.2022.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Glucuronoyl esterase (GE) is a promising agent for the delignification of plant biomass since it has been shown to cleave the linkage between xylan and lignin in vitro. In this study, we demonstrate that NcGE, a GE from Neurospora crassa, stimulates plant biomass degradation. In vitro, NcGE synergistically increased the release of reducing sugars from plant biomass when added together with cellulase or xylanase. In vivo, overexpression of NcGE in N. crassa resulted in an increase in xylanolytic activity. Consistently, elevated transcription of genes encoding the major plant biomass degrading-enzymes (PBDEs) was observed in the NcGE overexpression strain. Increased xylanolytic activity and transcription of PDBE genes were largely abolished when the transcription factors clr-1, clr-2, or xlr-1 were deleted. Interestingly, the expression of some PBDE genes was increased when the hydrolysate of plant biomass by NcGE was added to the culture medium. We propose that NcGE boosts the production of PBDEs through the activation of key transcription factors, which is presumably caused by NcGE-mediated generation of hypothetical inducer(s) from plant biomass.
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Affiliation(s)
- Ruijie Wang
- Department of Biotechnology, The University of Tokyo
| | - Manabu Arioka
- Department of Biotechnology, The University of Tokyo.,Collaborative Research Institute for Innovative Microbiology (CRIIM), The University of Tokyo
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Vittorelli N, Rodríguez de la Vega RC, Snirc A, Levert E, Gautier V, Lalanne C, De Filippo E, Gladieux P, Guillou S, Zhang Y, Tejomurthula S, Grigoriev IV, Debuchy R, Silar P, Giraud T, Hartmann FE. Stepwise recombination suppression around the mating-type locus in an ascomycete fungus with self-fertile spores. PLoS Genet 2023; 19:e1010347. [PMID: 36763677 PMCID: PMC9949647 DOI: 10.1371/journal.pgen.1010347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 02/23/2023] [Accepted: 01/17/2023] [Indexed: 02/12/2023] Open
Abstract
Recombination is often suppressed at sex-determining loci in plants and animals, and at self-incompatibility or mating-type loci in plants and fungi. In fungal ascomycetes, recombination suppression around the mating-type locus is associated with pseudo-homothallism, i.e. the production of self-fertile dikaryotic sexual spores carrying the two opposite mating types. This has been well studied in two species complexes from different families of Sordariales: Podospora anserina and Neurospora tetrasperma. However, it is unclear whether this intriguing association holds in other species. We show here that Schizothecium tetrasporum, a fungus from a third family in the order Sordariales, also produces mostly self-fertile dikaryotic spores carrying the two opposite mating types. This was due to a high frequency of second meiotic division segregation at the mating-type locus, indicating the occurrence of a single and systematic crossing-over event between the mating-type locus and the centromere, as in P. anserina. The mating-type locus has the typical Sordariales organization, plus a MAT1-1-1 pseudogene in the MAT1-2 haplotype. High-quality genome assemblies of opposite mating types and segregation analyses revealed a suppression of recombination in a region of 1.47 Mb around the mating-type locus. We detected three evolutionary strata, indicating a stepwise extension of recombination suppression. The three strata displayed no rearrangement or transposable element accumulation but gene losses and gene disruptions were present, and precisely at the strata margins. Our findings indicate a convergent evolution of self-fertile dikaryotic sexual spores across multiple ascomycete fungi. The particular pattern of meiotic segregation at the mating-type locus was associated with recombination suppression around this locus, that had extended stepwise. This association between pseudo-homothallism and recombination suppression across lineages and the presence of gene disruption at the strata limits are consistent with a recently proposed mechanism of sheltering deleterious alleles to explain stepwise recombination suppression.
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Affiliation(s)
- Nina Vittorelli
- Ecologie Systematique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
- Laboratoire Interdisciplinaire des Energies de Demain, Université Paris Cité, Paris, France
- Département de Biologie, École Normale Supérieure, PSL Université Paris, Paris, France
| | | | - Alodie Snirc
- Ecologie Systematique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
| | - Emilie Levert
- Ecologie Systematique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
- Laboratoire Interdisciplinaire des Energies de Demain, Université Paris Cité, Paris, France
| | - Valérie Gautier
- Laboratoire Interdisciplinaire des Energies de Demain, Université Paris Cité, Paris, France
| | - Christophe Lalanne
- Laboratoire Interdisciplinaire des Energies de Demain, Université Paris Cité, Paris, France
| | - Elsa De Filippo
- Ecologie Systematique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
- Laboratoire Interdisciplinaire des Energies de Demain, Université Paris Cité, Paris, France
| | - Pierre Gladieux
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Sonia Guillou
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Yu Zhang
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Sravanthi Tejomurthula
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Igor V. Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Robert Debuchy
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Philippe Silar
- Laboratoire Interdisciplinaire des Energies de Demain, Université Paris Cité, Paris, France
| | - Tatiana Giraud
- Ecologie Systematique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
| | - Fanny E. Hartmann
- Ecologie Systematique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
- * E-mail:
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Yu H, Yang H, Haridas S, Hayes RD, Lynch H, Andersen S, Li G, Mart Nez-Soto D, Milo-Cochavi S, Hazal Ayhan D, Zhang Y, Grigoriev IV, Ma LJ. Conservation and Expansion of Transcriptional Factor Repertoire in the Fusarium oxysporum Species Complex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.09.527873. [PMID: 36798233 PMCID: PMC9934661 DOI: 10.1101/2023.02.09.527873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
The Fusarium oxysporum species complex (FOSC) includes both plant and human pathogens that cause devastating plant vascular wilt diseases and threaten public health. Each F. oxysporum genome comprises core chromosomes (CCs) for housekeeping functions and accessory chromosomes (ACs) that contribute to host-specific adaptation. This study inspected global transcription factor profiles (TFomes) and their potential roles in coordinating CCs and ACs functions to accomplish host-specific pathogenicity. Remarkably, we found a clear positive correlation between the sizes of TFome and proteome of an organism, and FOSC TFomes are larger due to the acquisition of ACs. Among a total of 48 classified TF families, 14 families involved in transcription/translation regulations and cell cycle controls are highly conserved. Among 30 FOSC expanded families, Zn2-C6 and Znf_C2H2 are most significantly expanded to 671 and 167 genes per family, including well-characterized homologs of Ftf1 (Zn2-C6) and PacC (Znf_C2H2) involved in host-specific interactions. Manual curation of characterized TFs increased the TFome repertoires by 3%, including a disordered protein Ren1. Expression profiles revealed a steady expression of conserved TF families and specific activation of AC TFs. Functional characterization of these TFs could enhance our understanding of transcriptional regulation involved in FOSC cross-kingdom interactions, disentangle species-specific adaptation, and identify targets to combat diverse diseases caused by this group of fungal pathogens.
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38
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The Botrytis cinerea Gene Expression Browser. J Fungi (Basel) 2023; 9:jof9010084. [PMID: 36675905 PMCID: PMC9861337 DOI: 10.3390/jof9010084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 12/29/2022] [Accepted: 12/30/2022] [Indexed: 01/07/2023] Open
Abstract
For comprehensive gene expression analyses of the phytopathogenic fungus Botrytis cinerea, which infects a number of plant taxa and is a cause of substantial agricultural losses worldwide, we developed BEB, a web-based B. cinerea gene Expression Browser. This computationally inexpensive web-based application and its associated database contain manually curated RNA-Seq data for B. cinerea. BEB enables expression analyses of genes of interest under different culture conditions by providing publication-ready heatmaps depicting transcript levels, without requiring advanced computational skills. BEB also provides details of each experiment and user-defined gene expression clustering and visualization options. If needed, tables of gene expression values can be downloaded for further exploration, including, for instance, the determination of differentially expressed genes. The BEB implementation is based on open-source computational technologies that can be deployed for other organisms. In this case, the new implementation will be limited only by the number of transcriptomic experiments that are incorporated into the platform. To demonstrate the usability and value of BEB, we analyzed gene expression patterns across different conditions, with a focus on secondary metabolite gene clusters, chromosome-wide gene expression, previously described virulence factors, and reference genes, providing the first comprehensive expression overview of these groups of genes in this relevant fungal phytopathogen. We expect this tool to be broadly useful in B. cinerea research, providing a basis for comparative transcriptomics and candidate gene identification for functional assays.
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Kobayashi Y, Shibata TF, Hirakawa H, Nishiyama T, Yamada A, Hasebe M, Shigenobu S, Kawaguchi M. The genome of Lyophyllum shimeji provides insight into the initial evolution of ectomycorrhizal fungal genomes. DNA Res 2023; 30:6969780. [PMID: 36610744 PMCID: PMC9896470 DOI: 10.1093/dnares/dsac053] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 11/29/2022] [Accepted: 01/04/2023] [Indexed: 01/09/2023] Open
Abstract
Mycorrhizae are one of the most fundamental symbioses between plants and fungi, with ectomycorrhizae being the most widespread in boreal forest ecosystems. Ectomycorrhizal fungi are hypothesized to have evolved convergently from saprotrophic ancestors in several fungal clades, especially members of the subdivision Agaricomycotina. Studies on fungal genomes have identified several typical characteristics of mycorrhizal fungi, such as genome size expansion and decreases in plant cell-wall degrading enzymes (PCWDEs). However, genomic changes concerning the evolutionary transition to the ectomycorrhizal lifestyle are largely unknown. In this study, we sequenced the genome of Lyophyllum shimeji, an ectomycorrhizal fungus that is phylogenetically related to saprotrophic species and retains some saprotroph-like traits. We found that the genome of Ly. shimeji strain AT787 lacks both incremental increases in genome size and reduced numbers of PCWDEs. Our findings suggest that the previously reported common genomic traits of mycorrhizal fungi are not essential for the ectomycorrhizal lifestyle, but are a result of abolishing saprotrophic activity. Since Ly. shimeji is commercially consumed as an edible mushroom, the newly available genomic information may also impact research designed to enhance the cultivation of this mushroom.
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Affiliation(s)
- Yuuki Kobayashi
- To whom correspondence should be addressed. Tel.: +81-0564-55-7672, (Y.K.)
| | - Tomoko F Shibata
- Division of Evolutionary Biology, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Hideki Hirakawa
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Tomoaki Nishiyama
- Research Center for Experimental Modeling of Human Disease, Kanazawa University, Kanazawa, Ishikawa 920-0934, Japan
| | - Akiyoshi Yamada
- Faculty of Agriculture, Shinshu University, Kamiina, Nagano 399-4598, Japan
| | - Mitsuyasu Hasebe
- Division of Evolutionary Biology, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan,Department of Basic Biology, SOKENDAI, Okazaki, Aichi 444-8585, Japan
| | - Shuji Shigenobu
- Laboratory of Evolutionary Genomics, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan,Department of Basic Biology, SOKENDAI, Okazaki, Aichi 444-8585, Japan,Trans-omics Facility, National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan
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40
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Islam MD, Harrison BD, Li JJY, McLoughlin AG, Court DA. Do mitochondria use efflux pumps to protect their ribosomes from antibiotics? MICROBIOLOGY (READING, ENGLAND) 2023; 169:001272. [PMID: 36748523 PMCID: PMC9993110 DOI: 10.1099/mic.0.001272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Fungal environments are rich in natural and engineered antimicrobials, and this, combined with the fact that fungal genomes are rich in coding sequences for transporters, suggests that fungi are an intriguing group in which to search for evidence of antimicrobial efflux pumps in mitochondria. Herein, the range of protective mechanisms used by fungi against antimicrobials is introduced, and it is hypothesized, based on the susceptibility of mitochondrial and bacterial ribosomes to the same antibiotics, that mitochondria might also contain pumps that efflux antibiotics from these organelles. Preliminary evidence of ethidium bromide efflux is presented and several candidate efflux pumps are identified in fungal mitochondrial proteomes.
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Affiliation(s)
- Md Deen Islam
- Department of Microbiology, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - Brian D Harrison
- Department of Microbiology, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - Judy J-Y Li
- Department of Microbiology, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - Austein G McLoughlin
- Department of Microbiology, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
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41
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Lozy F, Meetro J, Simon R, Calabrese P, Whiteley JM. Genotoxicity, acute, and subchronic toxicity evaluation of dried Neurospora crassa protein-rich biomass. Toxicol Res (Camb) 2022; 11:1003-1017. [PMID: 36569482 PMCID: PMC9773060 DOI: 10.1093/toxres/tfac069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 07/06/2022] [Accepted: 09/12/2022] [Indexed: 11/13/2022] Open
Abstract
Filamentous fungus biomass is a protein-rich food, which can serve as an alternative to animal, plant, and legume protein sources. Neurospora crassa is a filamentous fungus that typically grows in tropical and sub-tropical regions. Traditionally, N. crassa has served as a model eukaryotic organism due to its ease of growth and propagation and suitability for genetic manipulation. However, filamentous fungi, such as Neurospora, have also been consumed or used to produce fermented foods for centuries and have been developed into protein-rich biomass ingredients to be used in conventional foods and meat substitutes. A panel of toxicological tests including genotoxic, acute, and subchronic studies were conducted on dried N. crassa biomass to support its safe use in food. The dried N. crassa biomass was found to be not genotoxic in a bacterial reverse mutation (Ames) assay, an in vitro chromosomal aberration test, and an in vivo micronucleus test. In the acute and subchronic toxicity studies, rats were orally gavaged with N. crassa biomass at concentrations of 0, 1,000, 2,500, and 5,000 mg/kg body weight/day for 14 and 90 days, respectively. At the conclusion of the studies, there were no test article-related toxicity results observed in clinical observations, body weight, food consumption, ophthalmology, hematology, clinical chemistry, coagulation, thyroid hormone, urinalysis, and macroscopic and microscopic findings. The no-observed-adverse-effect level for the dried N. crassa biomass ingredient was determined to be 5,000 mg/kg body weight/day, the highest dose tested.
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Affiliation(s)
- Fred Lozy
- Intertek Health Sciences Inc., 2233 Argentia Road, Suite 201, Mississauga, ON L5N 2X7, Canada
| | - Jwar Meetro
- Intertek Health Sciences Inc., 2233 Argentia Road, Suite 201, Mississauga, ON L5N 2X7, Canada
| | - Ryan Simon
- Intertek Health Sciences Inc., 2233 Argentia Road, Suite 201, Mississauga, ON L5N 2X7, Canada
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42
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Regulation of Hsp80 involved in the acquisition of induced thermotolerance, and NCA-2 involved in calcium stress tolerance by the calcineurin-CRZ-1 signaling pathway in Neurospora crassa. Mycol Prog 2022. [DOI: 10.1007/s11557-022-01833-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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43
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Ji J, Yu J, Ye Y, Sheng L, Fang J, Yang Y, Sun X. Biodegradation methods and product analysis of zearalenone and its future development trend: A review. Food Control 2022. [DOI: 10.1016/j.foodcont.2022.109469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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44
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Anand G, Gupta R, Marash I, Leibman-Markus M, Bar M. Cytokinin production and sensing in fungi. Microbiol Res 2022; 262:127103. [DOI: 10.1016/j.micres.2022.127103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/07/2022] [Accepted: 06/22/2022] [Indexed: 10/17/2022]
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45
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Chuang YC, Smith GR. Meiotic crossover interference: Methods of analysis and mechanisms of action. Curr Top Dev Biol 2022; 151:217-244. [PMID: 36681471 PMCID: PMC10063388 DOI: 10.1016/bs.ctdb.2022.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Segregation of chromosomes during meiosis, to form haploid gametes from diploid precursor cells, requires in most species formation of crossovers physically connecting homologous chromosomes. Along with sister chromatid cohesion, crossovers allow tension to be generated when chromosomes begin to segregate; tension signals that chromosome movement is proceeding properly. But crossovers too close to each other might result in less sister chromatid cohesion and tension and thus failed meiosis. Interference describes the non-random distribution of crossovers, which occur farther apart than expected from independence. We discuss both genetic and cytological methods of assaying crossover interference and models for interference, whose molecular mechanism remains to be elucidated. We note marked differences among species.
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Affiliation(s)
| | - Gerald R Smith
- Fred Hutchinson Cancer Center, Seattle, WA, United States.
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46
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Bartholomai BM, Ruwe KM, Thurston J, Jha P, Scaife K, Simon R, Abdelmoteleb M, Goodman RE, Farhi M. Safety evaluation of Neurospora crassa mycoprotein for use as a novel meat alternative and enhancer. Food Chem Toxicol 2022; 168:113342. [PMID: 35963473 DOI: 10.1016/j.fct.2022.113342] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 07/26/2022] [Accepted: 07/29/2022] [Indexed: 10/15/2022]
Abstract
Cultivation of filamentous fungi to produce sustainable, nutrient rich meat replacements has recently attracted significant commercial and research interest. Here, we report evidence for the safety and nutritional value of Neurospora crassa mycoprotein, a whole mycelium food ingredient produced by fermentation and minimal downstream processing. N. crassa has a long history of human use in fermented foods and in molecular biology research. A survey of studies that used N. crassa in animal feed revealed no adverse effects to the health of the animals. Furthermore, a review of the literature found no reports of confirmed allergenicity or toxicity in humans involving N. crassa. Genomic toxigenicity analysis and in vitro testing did not identify any toxins in N. crassa mycoprotein. Two independent genomic allergenicity studies did not identify proteins that would be considered a particular risk for allergenic potential. Furthermore, nutritional analysis demonstrated that N. crassa mycoprotein is a good source of complete protein and is rich in fiber, potassium, and iron. Taken together, the presented data and the history of human use without evidence of human or animal harm indicate that foods containing N. crassa can generally be regarded as safe.
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Affiliation(s)
| | | | | | - Prachi Jha
- The Better Meat Co., West Sacramento, CA, USA
| | - Kevin Scaife
- Intertek Health Sciences Inc., Mississauga, ON, Canada
| | - Ryan Simon
- Intertek Health Sciences Inc., Mississauga, ON, Canada
| | | | - Richard E Goodman
- Food Allergy Research and Resource Program, University of Nebraska, Lincoln, NE, USA
| | - Moran Farhi
- The Better Meat Co., West Sacramento, CA, USA
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47
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Meunier C, Darolti I, Reimegård J, Mank JE, Johannesson H. Nuclear-specific gene expression in heterokaryons of the filamentous ascomycete Neurospora tetrasperma. Proc Biol Sci 2022; 289:20220971. [PMID: 35946150 PMCID: PMC9363985 DOI: 10.1098/rspb.2022.0971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Heterokaryosis is a system in which genetically distinct nuclei coexist within the same cytoplasm. While heterokaryosis dominates the life cycle of many fungal species, the transcriptomic changes associated with the transition from homokaryosis to heterokaryosis is not well understood. Here, we analyse gene expression profiles of homokaryons and heterokaryons from three phylogenetically and reproductively isolated lineages of the filamentous ascomycete Neurospora tetrasperma. We show that heterokaryons are transcriptionally distinct from homokaryons in the sexual stage of development, but not in the vegetative stage, suggesting that the phenotypic switch to fertility in heterokaryons is associated with major changes in gene expression. Heterokaryon expression is predominantly defined by additive effects of its two nuclear components. Furthermore, allele-specific expression analysis of heterokaryons with varying nuclear ratios show patterns of expression ratios strongly dependent on nuclear ratios in the vegetative stage. By contrast, in the sexual stage, strong deviations of expression ratios indicate a co-regulation of nuclear gene expression in all three lineages. Taken together, our results show two levels of expression control: additive effects suggest a nuclear level of expression, whereas co-regulation of gene expression indicate a heterokaryon level of control.
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Affiliation(s)
- Cécile Meunier
- Department ECOBIO, UMR CNRS 6553, Université Rennes 1, Rennes, France
| | - Iulia Darolti
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
| | - Johan Reimegård
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Judith E. Mank
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, Canada,Centre for Ecology and Conservation, University of Exeter, Penryn Campus, UK
| | - Hanna Johannesson
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden,The Royal Swedish Academy of Sciences and Department of Ecology, Environment and Plant Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
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48
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Neurospora crassa is a potential source of anti-cancer agents against breast cancer. Breast Cancer 2022; 29:1032-1041. [PMID: 35881300 DOI: 10.1007/s12282-022-01383-9] [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: 05/07/2022] [Accepted: 06/23/2022] [Indexed: 11/02/2022]
Abstract
Fungi are an excellent source of pharmaceuticals including anti-tumor agents. Neurospora crassa generates metabolites with diverse structural classes, however, its potential as an anti-tumor agent source has not been explored. The purpose of this study aimed to investigate the potential of Neurospora crassa mixture against breast cancer. The in vitro T-47D and MDA-MB-231 experiments showed that N. crassa mixture at the concentrations of both 1.7 and 0.85 µg/ml significantly inhibited tumor cell proliferation, migration and invasion, and 3D spheroid formation. However, the inhibition rates of MCF-10A ranged 10-20% at concentrations of 0.85 and 1.7 µg/ml. The mixture at the concentration of 0.85 µg/ml could significantly downregulate the expressions of transcription factors of E2F1 and E2F3, cancer stem cell-related genes of LIN28, HIWI, and CD133, and onco-lncRNA HOTAIR, and increase CASP3 activity in either T-47D or MDA-MD-231 breast cancer cell lines. In vivo breast cancer C3H mouse model results showed that N. crassa mixture significantly inhibited tumor growth. These findings suggest that N. crassa contains an antitumor component(s) against breast cancer invasiveness, which may inhibit the self-renewal and differentiation of breast cancer stem cells possibly by downregulating cancer stem cell-associated and/or transcription factor genes and oncogenes, and promoting apoptosis.
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49
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Secondary Metabolism Gene Clusters Exhibit Increasingly Dynamic and Differential Expression during Asexual Growth, Conidiation, and Sexual Development in Neurospora crassa. mSystems 2022; 7:e0023222. [PMID: 35638725 PMCID: PMC9239088 DOI: 10.1128/msystems.00232-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Secondary metabolite clusters (SMCs) encode the machinery for fungal toxin production. However, understanding their function and analyzing their products requires investigation of the developmental and environmental conditions in which they are expressed. Gene expression is often restricted to specific and unexamined stages of the life cycle. Therefore, we applied comparative genomics analyses to identify SMCs in Neurospora crassa and analyzed extensive transcriptomic data spanning nine independent experiments from diverse developmental and environmental conditions to reveal their life cycle-specific gene expression patterns. We reported 20 SMCs comprising 177 genes-a manageable set for investigation of the roles of SMCs across the life cycle of the fungal model N. crassa-as well as gene sets coordinately expressed in 18 predicted SMCs during asexual and sexual growth under three nutritional and two temperature conditions. Divergent activity of SMCs between asexual and sexual development was reported. Of 126 SMC genes that we examined for knockout phenotypes, al-2 and al-3 exhibited phenotypes in asexual growth and conidiation, whereas os-5, poi-2, and pmd-1 exhibited phenotypes in sexual development. SMCs with annotated function in mating and crossing were actively regulated during the switch between asexual and sexual growth. Our discoveries call for attention to roles that SMCs may play in the regulatory switches controlling mode of development, as well as the ecological associations of those developmental stages that may influence expression of SMCs. IMPORTANCE Secondary metabolites (SMs) are low-molecular-weight compounds that often mediate interactions between fungi and their environments. Fungi enriched with SMs are of significant research interest to agriculture and medicine, especially from the aspects of pathogen ecology and environmental epidemiology. However, SM clusters (SMCs) that have been predicted by comparative genomics alone have typically been poorly defined and insufficiently functionally annotated. Therefore, we have investigated coordinate expression in SMCs in the model system N. crassa, and our results suggest that SMCs respond to environmental signals and to stress that are associated with development. This study examined SMC regulation at the level of RNA to integrate observations and knowledge of these genes in various growth and development conditions, supporting combining comparative genomics and inclusive transcriptomics to improve computational annotation of SMCs. Our findings call for detailed study of the function of SMCs during the asexual-sexual switch, a key, often-overlooked developmental stage.
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50
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Abstract
Gene expression divergence through evolutionary processes is thought to be important for achieving programmed development in multicellular organisms. To test this premise in filamentous fungi, we investigated transcriptional profiles of 3,942 single-copy orthologous genes (SCOGs) in five related sordariomycete species that have morphologically diverged in the formation of their flask-shaped perithecia. We compared expression of the SCOGs to inferred gene expression levels of the most recent common ancestor of the five species, ranking genes from their largest increases to smallest increases in expression during perithecial development in each of the five species. We found that a large proportion of the genes that exhibited evolved increases in gene expression were important for normal perithecial development in Fusarium graminearum. Many of these genes were previously uncharacterized, encoding hypothetical proteins without any known functional protein domains. Interestingly, the developmental stages during which aberrant knockout phenotypes appeared largely coincided with the elevated expression of the deleted genes. In addition, we identified novel genes that affected normal perithecial development in Magnaporthe oryzae and Neurospora crassa, which were functionally and transcriptionally diverged from the orthologous counterparts in F. graminearum. Furthermore, comparative analysis of developmental transcriptomes and phylostratigraphic analysis suggested that genes encoding hypothetical proteins are generally young and transcriptionally divergent between related species. This study provides tangible evidence of shifts in gene expression that led to acquisition of novel function of orthologous genes in each lineage and demonstrates that several genes with hypothetical function are crucial for shaping multicellular fruiting bodies. IMPORTANCE The fungal class Sordariomycetes includes numerous important plant and animal pathogens. It also provides model systems for studying fungal fruiting body development, as its members develop fruiting bodies with a few well-characterized tissue types on common growth media and have rich genomic resources that enable comparative and functional analyses. To understand transcriptional divergence of key developmental genes between five related sordariomycete fungi, we performed targeted knockouts of genes inferred to have evolved significant upward shifts in expression. We found that many previously uncharacterized genes play indispensable roles at different stages of fruiting body development, which have undergone transcriptional activation in specific lineages. These novel genes are predicted to be phylogenetically young and tend to be involved in lineage- or species-specific function. Transcriptional activation of genes with unknown function seems to be more frequent than ever thought, which may be crucial for rapid adaption to changing environments for successful sexual reproduction.
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