1
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Carlier F, Castro Ramirez S, Kilani J, Chehboub S, Loïodice I, Taddei A, Gladyshev E. Remodeling of perturbed chromatin can initiate de novo transcriptional and post-transcriptional silencing. Proc Natl Acad Sci U S A 2024; 121:e2402944121. [PMID: 39052837 PMCID: PMC11295056 DOI: 10.1073/pnas.2402944121] [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: 02/20/2024] [Accepted: 06/17/2024] [Indexed: 07/27/2024] Open
Abstract
In eukaryotes, repetitive DNA can become silenced de novo, either transcriptionally or post-transcriptionally, by processes independent of strong sequence-specific cues. The mechanistic nature of such processes remains poorly understood. We found that in the fungus Neurospora crassa, de novo initiation of both transcriptional and post-transcriptional silencing was linked to perturbed chromatin, which was produced experimentally by the aberrant activity of transcription factors at the tetO operator array. Transcriptional silencing was mediated by canonical constitutive heterochromatin. On the other hand, post-transcriptional silencing resembled repeat-induced quelling but occurred normally when homologous recombination was inactivated. All silencing of the tetO array was dependent on SAD-6, fungal ortholog of the SWI/SNF chromatin remodeler ATRX (Alpha Thalassemia/Mental Retardation Syndrome X-Linked), which was required to maintain nucleosome occupancy at the perturbed locus. In addition, we found that two other types of sequences (the lacO array and native AT-rich DNA) could also undergo recombination-independent quelling associated with perturbed chromatin. These results suggested a model in which the de novo initiation of transcriptional and post-transcriptional silencing is coupled to the remodeling of perturbed chromatin.
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Affiliation(s)
- Florian Carlier
- Institut Pasteur, Department of Mycology, Molecular Genetics and Epigenetics Unit, Université Paris Cité, Paris75015, France
| | - Sebastian Castro Ramirez
- Institut Pasteur, Department of Mycology, Molecular Genetics and Epigenetics Unit, Université Paris Cité, Paris75015, France
| | - Jaafar Kilani
- Institut Pasteur, Department of Mycology, Molecular Genetics and Epigenetics Unit, Université Paris Cité, Paris75015, France
| | - Sara Chehboub
- Institut Pasteur, Department of Mycology, Molecular Genetics and Epigenetics Unit, Université Paris Cité, Paris75015, France
| | - Isabelle Loïodice
- Institut Curie, UMR3664 Nuclear Dynamics, CNRS, Université Paris Sciences et Lettres, Sorbonne Université, Paris75005, France
| | - Angela Taddei
- Institut Curie, UMR3664 Nuclear Dynamics, CNRS, Université Paris Sciences et Lettres, Sorbonne Université, Paris75005, France
| | - Eugene Gladyshev
- Institut Pasteur, Department of Mycology, Molecular Genetics and Epigenetics Unit, Université Paris Cité, Paris75015, France
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2
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Spada M, Pugliesi C, Fambrini M, Pecchia S. Challenges and Opportunities Arising from Host- Botrytis cinerea Interactions to Outline Novel and Sustainable Control Strategies: The Key Role of RNA Interference. Int J Mol Sci 2024; 25:6798. [PMID: 38928507 PMCID: PMC11203536 DOI: 10.3390/ijms25126798] [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: 05/31/2024] [Revised: 06/18/2024] [Accepted: 06/18/2024] [Indexed: 06/28/2024] Open
Abstract
The necrotrophic plant pathogenic fungus Botrytis cinerea (Pers., 1794), the causative agent of gray mold disease, causes significant losses in agricultural production. Control of this fungal pathogen is quite difficult due to its wide host range and environmental persistence. Currently, the management of the disease is still mainly based on chemicals, which can have harmful effects not only on the environment and on human health but also because they favor the development of strains resistant to fungicides. The flexibility and plasticity of B. cinerea in challenging plant defense mechanisms and its ability to evolve strategies to escape chemicals require the development of new control strategies for successful disease management. In this review, some aspects of the host-pathogen interactions from which novel and sustainable control strategies could be developed (e.g., signaling pathways, molecules involved in plant immune mechanisms, hormones, post-transcriptional gene silencing) were analyzed. New biotechnological tools based on the use of RNA interference (RNAi) are emerging in the crop protection scenario as versatile, sustainable, effective, and environmentally friendly alternatives to the use of chemicals. RNAi-based fungicides are expected to be approved soon, although they will face several challenges before reaching the market.
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Affiliation(s)
- Maria Spada
- Department of Agriculture Food and Environment, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy
| | - Claudio Pugliesi
- Department of Agriculture Food and Environment, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy
| | - Marco Fambrini
- Department of Agriculture Food and Environment, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy
| | - Susanna Pecchia
- Department of Agriculture Food and Environment, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy
- Interdepartmental Research Center Nutrafood “Nutraceuticals and Food for Health”, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy
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3
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Jones G, Kleckner N, Zickler D. Meiosis through three centuries. Chromosoma 2024; 133:93-115. [PMID: 38730132 PMCID: PMC11180163 DOI: 10.1007/s00412-024-00822-0] [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] [Indexed: 05/12/2024]
Abstract
Meiosis is the specialized cellular program that underlies gamete formation for sexual reproduction. It is therefore not only interesting but also a fundamentally important subject for investigation. An especially attractive feature of this program is that many of the processes of special interest involve organized chromosomes, thus providing the possibility to see chromosomes "in action". Analysis of meiosis has also proven to be useful in discovering and understanding processes that are universal to all chromosomal programs. Here we provide an overview of the different historical moments when the gap between observation and understanding of mechanisms and/or roles for the new discovered molecules was bridged. This review reflects also the synergy of thinking and discussion among our three laboratories during the past several decades.
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Affiliation(s)
- Gareth Jones
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Nancy Kleckner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, 02138, USA.
| | - Denise Zickler
- Institute for Integrative Biology of the Cell (I2BC), Centre National de La Recherche Scientifique (CNRS), Université Paris-Sud, Université Paris-Saclay, 91198, Gif-Sur-Yvette, France
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4
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Sy VT, Boone EC, Xiao H, Vierling MM, Schmitz SF, Ung Q, Trawick SS, Hammond TM, Shiu PKT. A DEAD-box RNA helicase mediates meiotic silencing by unpaired DNA. G3 (BETHESDA, MD.) 2023; 13:jkad083. [PMID: 37052947 PMCID: PMC10411587 DOI: 10.1093/g3journal/jkad083] [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: 12/23/2022] [Revised: 03/22/2023] [Accepted: 04/03/2023] [Indexed: 04/14/2023]
Abstract
During the sexual phase of Neurospora crassa, unpaired genes are subject to a silencing mechanism known as meiotic silencing by unpaired DNA (MSUD). MSUD targets the transcripts of an unpaired gene and utilizes typical RNA interference factors for its process. Using a reverse genetic screen, we have identified a meiotic silencing gene called sad-9, which encodes a DEAD-box RNA helicase. While not essential for vegetative growth, SAD-9 plays a crucial role in both sexual development and MSUD. Our results suggest that SAD-9, with the help of the SAD-2 scaffold protein, recruits the SMS-2 Argonaute to the perinuclear region, the center of MSUD activity.
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Affiliation(s)
- Victor T Sy
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Erin C Boone
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Hua Xiao
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Michael M Vierling
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Shannon F Schmitz
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Quiny Ung
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Sterling S Trawick
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Thomas M Hammond
- School of Biological Sciences, Illinois State University, Normal, IL 61790, USA
| | - Patrick K T Shiu
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
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5
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Lohmar JM, Rhoades NA, Hammond TM, Brown DW. Gene drive by Fusarium SKC1 is dependent on its competing allele. Fungal Genet Biol 2022; 163:103749. [PMID: 36341840 DOI: 10.1016/j.fgb.2022.103749] [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: 08/05/2022] [Revised: 10/22/2022] [Accepted: 10/25/2022] [Indexed: 01/06/2023]
Abstract
The Fusarium verticillioides SKC1 gene driver is transmitted to offspring in a biased manner through spore killing. The mechanism that allows SKC1 to kill non-SKC1 offspring while sparing others is poorly understood. Here we report that gene drive by SKC1 is dependent on SKC1's competing allele. We propose that SKC1's competing allele influences the ability of a genome defense process to detect SKC1, and we provide evidence that this genome defense process is meiotic silencing by unpaired DNA (MSUD). Our findings suggest that the successful deployment of gene drivers to control pathogenic fungi will require researchers to consider how competing alleles influence the ability of gene drivers to be detected by genome defense processes.
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Affiliation(s)
- Jessica M Lohmar
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Unit, 1815 N. University St., Peoria, IL 61604, USA
| | - Nicholas A Rhoades
- School of Biological Sciences, Illinois State University, Normal, IL 61790, USA
| | - Thomas M Hammond
- School of Biological Sciences, Illinois State University, Normal, IL 61790, USA.
| | - Daren W Brown
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Unit, 1815 N. University St., Peoria, IL 61604, USA.
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6
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Carro MDLM, Grimson A, Cohen PE. Small RNAs and their protein partners in animal meiosis. Curr Top Dev Biol 2022; 151:245-279. [PMID: 36681472 DOI: 10.1016/bs.ctdb.2022.06.001] [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
Meiosis is characterized by highly regulated transitions in gene expression that require diverse mechanisms of gene regulation. For example, in male mammals, transcription undergoes a global shut-down in early prophase I of meiosis, followed by increasing transcriptional activity into pachynema. Later, as spermiogenesis proceeds, the histones bound to DNA are replaced with transition proteins, which are themselves replaced with protamines, resulting in a highly condensed nucleus with repressed transcriptional activity. In addition, two specialized gene silencing events take place during prophase I: meiotic silencing of unsynapsed chromatin (MSUC), and the sex chromatin specific mechanism, meiotic sex chromosome inactivation (MSCI). Notably, conserved roles for the RNA binding protein (RBP) machinery that functions with small non-coding RNAs have been described as participating in these meiosis-specific mechanisms, suggesting that RNA-mediated gene regulation is critical for fertility in many species. Here, we review roles of small RNAs and their associated RBPs in meiosis-related processes such as centromere function, silencing of unpaired chromatin and meiotic recombination. We will discuss the emerging evidence of non-canonical functions of these components in meiosis.
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Affiliation(s)
- María de Las Mercedes Carro
- Department of Biomedical Sciences, Cornell University, Ithaca, NY, United States; Cornell Reproductive Sciences Center (CoRe), Cornell University, Ithaca, NY, United States
| | - Andrew Grimson
- Cornell Reproductive Sciences Center (CoRe), Cornell University, Ithaca, NY, United States; Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY, United States.
| | - Paula E Cohen
- Department of Biomedical Sciences, Cornell University, Ithaca, NY, United States; Cornell Reproductive Sciences Center (CoRe), Cornell University, Ithaca, NY, United States.
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7
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Velazquez A, Webber E, O'Neil D, Hammond T, Rhoades N. Isolation of rfk-2 UV , a mutation that blocks spore killing by Neurospora Spore killer-3. MICROPUBLICATION BIOLOGY 2022; 2022:10.17912/micropub.biology.000604. [PMID: 35903779 PMCID: PMC9315408 DOI: 10.17912/micropub.biology.000604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/17/2022] [Accepted: 07/12/2022] [Indexed: 11/08/2022]
Abstract
Neurospora Spore killer-3 ( Sk-3 ) is a selfish genetic element that kills spores to achieve gene drive. Here, we describe the isolation and mapping of rfk-2 UV , a mutation that disrupts spore killing. The rfk-2 UV mutation is located 15.6 cM from mus-52 on Chromosome III. The significance of this discovery with respect to Sk-3 evolution is discussed.
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Affiliation(s)
- Abraham Velazquez
- Illinois State University, School of Biological Sciences, Normal, IL 61790 USA
| | - Elise Webber
- Illinois State University, School of Biological Sciences, Normal, IL 61790 USA
| | - Devonte O'Neil
- Illinois State University, School of Biological Sciences, Normal, IL 61790 USA
| | - Thomas Hammond
- Illinois State University, School of Biological Sciences, Normal, IL 61790 USA
,
Correspondence to: Thomas Hammond (
)
| | - Nicholas Rhoades
- Illinois State University, School of Biological Sciences, Normal, IL 61790 USA
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8
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Dicer promotes genome stability via the bromodomain transcriptional co-activator BRD4. Nat Commun 2022; 13:1001. [PMID: 35194019 PMCID: PMC8863982 DOI: 10.1038/s41467-022-28554-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 01/14/2022] [Indexed: 01/01/2023] Open
Abstract
RNA interference is required for post-transcriptional silencing, but also has additional roles in transcriptional silencing of centromeres and genome stability. However, these roles have been controversial in mammals. Strikingly, we found that Dicer-deficient embryonic stem cells have strong proliferation and chromosome segregation defects as well as increased transcription of centromeric satellite repeats, which triggers the interferon response. We conducted a CRISPR-Cas9 genetic screen to restore viability and identified transcriptional activators, histone H3K9 methyltransferases, and chromosome segregation factors as suppressors, resembling Dicer suppressors identified in independent screens in fission yeast. The strongest suppressors were mutations in the transcriptional co-activator Brd4, which reversed the strand-specific transcription of major satellite repeats suppressing the interferon response, and in the histone acetyltransferase Elp3. We show that identical mutations in the second bromodomain of Brd4 rescue Dicer-dependent silencing and chromosome segregation defects in both mammalian cells and fission yeast. This remarkable conservation demonstrates that RNA interference has an ancient role in transcriptional silencing and in particular of satellite repeats, which is essential for cell cycle progression and proper chromosome segregation. Our results have pharmacological implications for cancer and autoimmune diseases characterized by unregulated transcription of satellite repeats. While RNA interference is conserved across species, small RNA pathways are very diverse. In this study, Gutbrod et al. find that non-canonical roles of Dicer in genome stability are in fact deeply conserved from yeast to humans.
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9
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Lohmar JM, Rhoades NA, Patel TN, Proctor RH, Hammond TM, Brown DW. A-to-I mRNA editing controls spore death induced by a fungal meiotic drive gene in homologous and heterologous expression systems. Genetics 2022; 221:6528853. [PMID: 35166849 DOI: 10.1093/genetics/iyac029] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 02/06/2022] [Indexed: 11/13/2022] Open
Abstract
Spore killers are meiotic drive elements that can block development of sexual spores in fungi. In the maize ear rot and mycotoxin-producing fungus Fusarium verticillioides, a spore killer called SkK has been mapped to a 102-kb interval of chromosome V. Here, we show that a gene within this interval, SKC1, is required for SkK-mediated spore killing and meiotic drive. We also demonstrate that SKC1 is associated with at least four transcripts, two sense (sense-SKC1a and sense-SKC1b) and two antisense (antisense-SKC1a and antisense-SKC1b). Both antisense SKC1 transcripts lack obvious protein-coding sequences and thus appear to be non-coding RNAs. In contrast, sense-SKC1a is a protein-coding transcript that undergoes A-to-I editing to sense-SKC1b in sexual tissue. Translation of sense-SKC1a produces a 70 amino acid protein (Skc1a), whereas translation of sense-SKC1b produces an 84 amino acid protein (Skc1b). Heterologous expression analysis of SKC1 transcripts shows that sense-SKC1a also undergoes A-to-I editing to sense-SKC1b during the Neurospora crassa sexual cycle. Site directed mutagenesis studies indicate that Skc1b is responsible for spore killing in F. verticillioides and that it induces most meiotic cells to die in N. crassa. Finally, we report that SKC1 homologs are present in over 20 Fusarium species. Overall, our results demonstrate that fungal meiotic drive elements like SKC1 can influence the outcome of meiosis by hijacking a cell's A-to-I editing machinery and that the involvement of A-to-I editing in a fungal meiotic drive system does not preclude its horizontal transfer to a distantly related species.
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Affiliation(s)
- Jessica M Lohmar
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Unit, 1815 N. University St., Peoria, Illinois, 61604, USA
| | - Nicholas A Rhoades
- School of Biological Sciences, Illinois State University, Normal, Illinois, 61790, USA
| | - Tejas N Patel
- School of Biological Sciences, Illinois State University, Normal, Illinois, 61790, USA
| | - Robert H Proctor
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Unit, 1815 N. University St., Peoria, Illinois, 61604, USA
| | - Thomas M Hammond
- School of Biological Sciences, Illinois State University, Normal, Illinois, 61790, USA
| | - Daren W Brown
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Unit, 1815 N. University St., Peoria, Illinois, 61604, USA
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10
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Lütkenhaus R, Breuer J, Nowrousian M. Functional characterization of the developmental genes asm2, asm3, and spt3 required for fruiting body formation in the filamentous ascomycete Sordaria macrospora. Genetics 2021; 219:iyab103. [PMID: 34849873 PMCID: PMC8633134 DOI: 10.1093/genetics/iyab103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 06/30/2021] [Indexed: 01/10/2023] Open
Abstract
The formation of fruiting bodies is one of the most complex developmental processes in filamentous ascomycetes. It requires the development of sexual structures that give rise to meiosporangia (asci) and meiotic spores (ascospores) as well as surrounding structures for protection and dispersal of the spores. Previous studies have shown that these developmental processes are accompanied by significant changes of the transcriptome, and comparative transcriptomics of different fungi as well as the analysis of transcriptome changes in developmental mutants have aided in the identification of differentially regulated genes that are themselves involved in regulating fruiting body development. In previous analyses, we used transcriptomics to identify the genes asm2 and spt3, which result in developmental phenotypes when deleted in Sordaria macrospora. In this study, we identified another gene, asm3, required for fruiting body formation, and performed transcriptomics analyses of Δasm2, Δasm3, and Δspt3. Deletion of spt3, which encodes a subunit of the SAGA complex, results in a block at an early stage of development and drastic changes in the transcriptome. Deletion mutants of asm2 and asm3 are able to form fruiting bodies, but have defects in ascospore maturation. Transcriptomics analysis of fruiting bodies revealed a large overlap in differentially regulated genes in Δasm2 and Δasm3 compared to the wild type. Analysis of nuclear distribution during ascus development showed that both mutants undergo meiosis and postmeiotic divisions, suggesting that the transcriptomic and morphological changes might be related to defects in the morphogenesis of structural features of the developing asci and ascospores.
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Affiliation(s)
- Ramona Lütkenhaus
- Lehrstuhl für Molekulare und Zelluläre Botanik, Ruhr-Universität Bochum, Bochum 44801, Germany
| | - Jan Breuer
- Lehrstuhl für Molekulare und Zelluläre Botanik, Ruhr-Universität Bochum, Bochum 44801, Germany
| | - Minou Nowrousian
- Lehrstuhl für Molekulare und Zelluläre Botanik, Ruhr-Universität Bochum, Bochum 44801, Germany
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11
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Model and modelers provide an insight into pairing of homologous DNA duplexes. Proc Natl Acad Sci U S A 2021; 118:2114127118. [PMID: 34544880 DOI: 10.1073/pnas.2114127118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/18/2021] [Indexed: 11/18/2022] Open
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12
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Xiao H, Vierling MM, Kennedy RF, Boone EC, Decker LM, Sy VT, Haynes JB, Williams MA, Shiu PKT. Involvement of RNA granule proteins in meiotic silencing by unpaired DNA. G3 (BETHESDA, MD.) 2021; 11:jkab179. [PMID: 34568932 PMCID: PMC8482848 DOI: 10.1093/g3journal/jkab179] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 05/13/2021] [Indexed: 11/14/2022]
Abstract
In Neurospora crassa, expression from an unpaired gene is suppressed by a mechanism known as meiotic silencing by unpaired DNA (MSUD). MSUD utilizes common RNA interference (RNAi) factors to silence target mRNAs. Here, we report that Neurospora CAR-1 and CGH-1, homologs of two Caenorhabditis elegans RNA granule components, are involved in MSUD. These fungal proteins are found in the perinuclear region and P-bodies, much like their worm counterparts. They interact with components of the meiotic silencing complex (MSC), including the SMS-2 Argonaute. This is the first time MSUD has been linked to RNA granule proteins.
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Affiliation(s)
- Hua Xiao
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Michael M Vierling
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Rana F Kennedy
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Erin C Boone
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Logan M Decker
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Victor T Sy
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Jackson B Haynes
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Michelle A Williams
- Present address: Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Patrick K T Shiu
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
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13
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Recombination-independent recognition of DNA homology for meiotic silencing in Neurospora crassa. Proc Natl Acad Sci U S A 2021; 118:2108664118. [PMID: 34385329 DOI: 10.1073/pnas.2108664118] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The pairing of homologous chromosomes represents a critical step of meiosis in nearly all sexually reproducing species. In many organisms, pairing involves chromosomes that remain apparently intact. The mechanistic nature of homology recognition at the basis of such pairing is unknown. Using "meiotic silencing by unpaired DNA" (MSUD) as a model process, we demonstrate the existence of a cardinally different approach to DNA homology recognition in meiosis. The main advantage of MSUD over other experimental systems lies in its ability to identify any relatively short DNA fragment lacking a homologous allelic partner. Here, we show that MSUD does not rely on the canonical mechanism of meiotic recombination, yet it is promoted by REC8, a conserved component of the meiotic cohesion complex. We also show that certain patterns of interspersed homology are recognized as pairable during MSUD. Such patterns need to be colinear and must contain short tracts of sequence identity spaced apart at 21 or 22 base pairs. By using these periodicity values as a guiding parameter in all-atom molecular modeling, we discover that homologous DNA molecules can pair by forming quadruplex-based contacts with an interval of 2.5 helical turns. This process requires right-handed plectonemic coiling and additional conformational changes in the intervening double-helical segments. Our results 1) reconcile genetic and biophysical evidence for the existence of direct homologous double-stranded DNA (dsDNA)-dsDNA pairing, 2) identify a role for this process in initiating RNA interference, and 3) suggest that chromosomes can be cross-matched by a precise mechanism that operates on intact dsDNA molecules.
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14
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Girard C, Budin K, Boisnard S, Zhang L, Debuchy R, Zickler D, Espagne E. RNAi-Related Dicer and Argonaute Proteins Play Critical Roles for Meiocyte Formation, Chromosome-Axes Lengths and Crossover Patterning in the Fungus Sordaria macrospora. Front Cell Dev Biol 2021; 9:684108. [PMID: 34262901 PMCID: PMC8274715 DOI: 10.3389/fcell.2021.684108] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 06/01/2021] [Indexed: 11/29/2022] Open
Abstract
RNA interference (RNAi) is a cellular process involving small RNAs that target and regulate complementary RNA transcripts. This phenomenon has well-characterized roles in regulating gene and transposon expression. In addition, Dicer and Argonaute proteins, which are key players of RNAi, also have functions unrelated to gene repression. We show here that in the filamentous Ascomycete Sordaria macrospora, genes encoding the two Dicer (Dcl1 and Dcl2) and the two Argonaute (Sms2 and Qde2) proteins are dispensable for vegetative growth. However, we identified roles for all four proteins in the sexual cycle. Dcl1 and Sms2 are essential for timely and successful ascus/meiocyte formation. During meiosis per se, Dcl1, Dcl2, and Qde2 modulate, more or less severely, chromosome axis length and crossover numbers, patterning and interference. Additionally, Sms2 is necessary both for correct synaptonemal complex formation and loading of the pro-crossover E3 ligase-protein Hei10. Moreover, meiocyte formation, and thus meiotic induction, is completely blocked in the dcl1 dcl2 and dcl1 sms2 null double mutants. These results indicate complex roles of the RNAi machinery during major steps of the meiotic process with newly uncovered roles for chromosomes-axis length modulation and crossover patterning regulation.
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Affiliation(s)
- Chloe Girard
- Université Paris-Saclay, Commissariat à l'Énergie Atomiques et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Karine Budin
- Université Paris-Saclay, Commissariat à l'Énergie Atomiques et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Stéphanie Boisnard
- Université Paris-Saclay, Commissariat à l'Énergie Atomiques et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Liangran Zhang
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Robert Debuchy
- Université Paris-Saclay, Commissariat à l'Énergie Atomiques et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Denise Zickler
- Université Paris-Saclay, Commissariat à l'Énergie Atomiques et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Eric Espagne
- Université Paris-Saclay, Commissariat à l'Énergie Atomiques et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
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15
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Abstract
In order to survive, most organisms must deal with parasites. Such parasites can be other organisms or, sometimes, selfish genes found within the host genome itself. While much is known about parasitic organisms, the interaction with their hosts, and their ability to spread within and between species, much less is known about selfish genes. We here identify a selfish “spore killer” gene in the fungus Neurospora sitophila. The gene appears to have evolved within the genus but has entered the species through hybridization and introgression. We also show that the host can counteract the gene through RNA interference. These results shed light on the diversity of selfish genes in terms of origin, evolution, and host interactions. Meiotic drive elements cause their own preferential transmission following meiosis. In fungi, this phenomenon takes the shape of spore killing, and in the filamentous ascomycete Neurospora sitophila, the Sk-1 spore killer element is found in many natural populations. In this study, we identify the gene responsible for spore killing in Sk-1 by generating both long- and short-read genomic data and by using these data to perform a genome-wide association test. We name this gene Spk-1. Through molecular dissection, we show that a single 405-nt-long open reading frame generates a product that both acts as a poison capable of killing sibling spores and as an antidote that rescues spores that produce it. By phylogenetic analysis, we demonstrate that the gene has likely been introgressed from the closely related species Neurospora hispaniola, and we identify three subclades of N. sitophila, one where Sk-1 is fixed, another where Sk-1 is absent, and a third where both killer and sensitive strain are found. Finally, we show that spore killing can be suppressed through an RNA interference-based genome defense pathway known as meiotic silencing by unpaired DNA. Spk-1 is not related to other known meiotic drive genes, and similar sequences are only found within Neurospora. These results shed light on the diversity of genes capable of causing meiotic drive, their origin and evolution, and their interaction with the host genome.
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16
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Muyle A, Bachtrog D, Marais GAB, Turner JMA. Epigenetics drive the evolution of sex chromosomes in animals and plants. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200124. [PMID: 33866802 DOI: 10.1098/rstb.2020.0124] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
We review how epigenetics affect sex chromosome evolution in animals and plants. In a few species, sex is determined epigenetically through the action of Y-encoded small RNAs. Epigenetics is also responsible for changing the sex of individuals through time, even in species that carry sex chromosomes, and could favour species adaptation through breeding system plasticity. The Y chromosome accumulates repeats that become epigenetically silenced which leads to an epigenetic conflict with the expression of Y genes and could accelerate Y degeneration. Y heterochromatin can be lost through ageing, which activates transposable elements and lowers male longevity. Y chromosome degeneration has led to the evolution of meiotic sex chromosome inactivation in eutherians (placentals) and marsupials, and dosage compensation mechanisms in animals and plants. X-inactivation convergently evolved in eutherians and marsupials via two independently evolved non-coding RNAs. In Drosophila, male X upregulation by the male specific lethal (MSL) complex can spread to neo-X chromosomes through the transposition of transposable elements that carry an MSL-binding motif. We discuss similarities and possible differences between plants and animals and suggest future directions for this dynamic field of research. This article is part of the theme issue 'How does epigenetics influence the course of evolution?'
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Affiliation(s)
- Aline Muyle
- University of California Irvine, Irvine, CA 92697, USA
| | - Doris Bachtrog
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
| | - Gabriel A B Marais
- Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR 5558, F-69622 Villeurbanne, France.,LEAF- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, Portugal
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17
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Li WC, Liu HC, Lin YJ, Tung SY, Wang TF. Third-generation sequencing-based mapping and visualization of single nucleotide polymorphism, meiotic recombination, illegitimate mutation and repeat-induced point mutation. NAR Genom Bioinform 2020; 2:lqaa056. [PMID: 33575607 PMCID: PMC7671321 DOI: 10.1093/nargab/lqaa056] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 06/23/2020] [Accepted: 07/10/2020] [Indexed: 01/07/2023] Open
Abstract
Generation of new genetic diversity by crossover (CO) and non-crossover (NCO) is a fundamental process in eukaryotes. Fungi have played critical roles in studying this process because they permit tetrad analysis, which has been used by geneticists for several decades to determine meiotic recombination products. New genetic variations can also be generated in zygotes via illegitimate mutation (IM) and repeat-induced point mutation (RIP). RIP is a genome defense mechanism for preventing harmful expansion of transposable elements or duplicated sequences in filamentous fungi. Although the exact mechanism of RIP is unknown, the C:G to T:A mutations might result from DNA cytosine methylation. A comprehensive approach for understanding the molecular mechanisms underlying these important processes is to perform high-throughput mapping of CO, NCO, RIP and IM in zygotes bearing large numbers of heterozygous variant markers. To this aim, we developed ‘TSETA’, a versatile and user-friendly pipeline that utilizes high-quality and chromosome-level genome sequences involved in a single meiotic event of the industrial workhorse fungus Trichoderma reesei. TSETA not only can be applied to most sexual eukaryotes for genome-wide tetrad analysis, it also outcompetes most currently used methods for calling out single nucleotide polymorphisms between two or more intraspecies strains or isolates.
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Affiliation(s)
- Wan-Chen Li
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
| | - Hou-Cheng Liu
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
| | - Ying-Jyun Lin
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
| | - Shu-Yun Tung
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
| | - Ting-Fang Wang
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
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18
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Abstract
In the filamentous fungus Neurospora crassa, genes unpaired during meiosis are silenced by a process known as meiotic silencing by unpaired DNA (MSUD). MSUD utilizes common RNA interference (RNAi) proteins, such as Dicer and Argonaute, to target homologous mRNAs for silencing. Previously, we demonstrated that nuclear cap-binding proteins NCBP1 and NCBP2 are involved in MSUD. We report here that SAD-8, a protein similar to human NCBP3, also mediates silencing. Although SAD-8 is not essential for either vegetative or sexual development, it is required for MSUD. SAD-8 localizes predominantly in the nucleus and interacts with both NCBP1 and NCBP2. Similar to NCBP1 and NCBP2, SAD-8 interacts with a component (Argonaute) of the perinuclear meiotic silencing complex (MSC), further implicating the involvement of cap-binding proteins in silencing.
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19
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Gutbrod MJ, Martienssen RA. Conserved chromosomal functions of RNA interference. Nat Rev Genet 2020; 21:311-331. [PMID: 32051563 DOI: 10.1038/s41576-019-0203-6] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/26/2019] [Indexed: 12/21/2022]
Abstract
RNA interference (RNAi), a cellular process through which small RNAs target and regulate complementary RNA transcripts, has well-characterized roles in post-transcriptional gene regulation and transposon repression. Recent studies have revealed additional conserved roles for RNAi proteins, such as Argonaute and Dicer, in chromosome function. By guiding chromatin modification, RNAi components promote chromosome segregation during both mitosis and meiosis and regulate chromosomal and genomic dosage response. Small RNAs and the RNAi machinery also participate in the resolution of DNA damage. Interestingly, many of these lesser-studied functions seem to be more strongly conserved across eukaryotes than are well-characterized functions such as the processing of microRNAs. These findings have implications for the evolution of RNAi since the last eukaryotic common ancestor, and they provide a more complete view of the functions of RNAi.
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Affiliation(s)
- Michael J Gutbrod
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Robert A Martienssen
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA. .,Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
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20
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Hassing B, Eaton CJ, Winter D, Green KA, Brandt U, Savoian MS, Mesarich CH, Fleissner A, Scott B. Phosphatidic acid produced by phospholipase D is required for hyphal cell-cell fusion and fungal-plant symbiosis. Mol Microbiol 2020; 113:1101-1121. [PMID: 32022309 DOI: 10.1111/mmi.14480] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 01/23/2020] [Accepted: 01/27/2020] [Indexed: 12/15/2022]
Abstract
Although lipid signaling has been shown to serve crucial roles in mammals and plants, little is known about this process in filamentous fungi. Here we analyze the contribution of phospholipase D (PLD) and its product phosphatidic acid (PA) in hyphal morphogenesis and growth of Epichloë festucae and Neurospora crassa, and in the establishment of a symbiotic interaction between E. festucae and Lolium perenne. Growth of E. festucae and N. crassa PLD deletion strains in axenic culture, and for E. festucae in association with L. perenne, were analyzed by light-, confocal- and electron microscopy. Changes in PA distribution were analyzed in E. festucae using a PA biosensor and the impact of these changes on the endocytic recycling and superoxide production investigated. We found that E. festucae PldB, and the N. crassa ortholog, PLA-7, are required for polarized growth and cell fusion and contribute to ascospore development, whereas PldA/PLA-8 are dispensable for these functions. Exogenous addition of PA rescues the cell-fusion phenotype in E. festucae. PldB is also crucial for E. festucae to establish a symbiotic association with L. perenne. This study identifies a new component of the cell-cell communication and cell fusion signaling network for hyphal morphogenesis and growth of filamentous fungi.
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Affiliation(s)
- Berit Hassing
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand.,Bio-Protection Research Centre, Lincoln, New Zealand
| | - Carla J Eaton
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand.,Bio-Protection Research Centre, Lincoln, New Zealand
| | - David Winter
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand.,Bio-Protection Research Centre, Lincoln, New Zealand
| | - Kimberly A Green
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand.,Bio-Protection Research Centre, Lincoln, New Zealand
| | - Ulrike Brandt
- Institute for Genetics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Matthew S Savoian
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Carl H Mesarich
- Bio-Protection Research Centre, Lincoln, New Zealand.,School of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | - Andre Fleissner
- Institute for Genetics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Barry Scott
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand.,Bio-Protection Research Centre, Lincoln, New Zealand
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21
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Sun S, Coelho MA, Heitman J, Nowrousian M. Convergent evolution of linked mating-type loci in basidiomycete fungi. PLoS Genet 2019; 15:e1008365. [PMID: 31490920 PMCID: PMC6730849 DOI: 10.1371/journal.pgen.1008365] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 08/09/2019] [Indexed: 12/21/2022] Open
Abstract
Sexual development is a key evolutionary innovation of eukaryotes. In many species, mating involves interaction between compatible mating partners that can undergo cell and nuclear fusion and subsequent steps of development including meiosis. Mating compatibility in fungi is governed by the mating type (MAT) loci. In basidiomycetes, the ancestral state is hypothesized to be tetrapolar, with two genetically unlinked MAT loci containing homeodomain transcription factor genes (HD locus) and pheromone and pheromone receptor genes (P/R locus), respectively. Alleles at both loci must differ between mating partners for completion of sexual development. However, there are also basidiomycetes with bipolar mating systems, which can arise through genomic linkage of the HD and P/R loci. In the order Tremellales, bipolarity is found only in the pathogenic Cryptococcus species. Here, we describe the analysis of MAT loci from 24 species of the Trichosporonales, a sister order to the Tremellales. In all of the species analyzed, the MAT loci are fused and a single HD gene is present in each mating type, similar to the organization in the pathogenic Cryptococci. However, the HD and P/R allele combinations in the Trichosporonales are different from those in the pathogenic Cryptococci. This and the existence of tetrapolar species in the Tremellales suggest that fusion of the HD and P/R loci occurred independently in the Trichosporonales and pathogenic Cryptococci, supporting the hypothesis of convergent evolution towards fused MAT regions, similar to previous findings in other fungal groups. Unlike the fused MAT loci in several other basidiomycete lineages though, the gene content and gene order within the fused MAT loci are highly conserved in the Trichosporonales, and there is no apparent suppression of recombination extending from the MAT loci to adjacent chromosomal regions, suggesting different mechanisms for the evolution of physically linked MAT loci in these groups.
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Affiliation(s)
- Sheng Sun
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Marco A. Coelho
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Minou Nowrousian
- Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-Universität Bochum, Bochum, Germany
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22
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Kasbekar DP. A cross-eyed geneticist’s view IV. Neurospora genes and inversions collude to cheat Mendel. J Biosci 2019. [DOI: 10.1007/s12038-019-9902-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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23
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The Neurospora crassa Standard Oak Ridge Background Exhibits Atypically Efficient Meiotic Silencing by Unpaired DNA. G3-GENES GENOMES GENETICS 2019; 9:1487-1496. [PMID: 30842206 PMCID: PMC6505168 DOI: 10.1534/g3.119.400006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Meiotic silencing by unpaired DNA (MSUD), an RNAi-mediated gene silencing process, is efficient in crosses made in the Neurospora crassa standard Oak Ridge (OR) genetic background. However, MSUD was decidedly less efficient when the OR-derived MSUD testers were crossed with many wild-isolated strains (W), suggesting that either sequence heterozygosity in tester x W crosses suppresses MSUD, or that OR represents the MSUD-conducive extreme in the range of genetic variation in MSUD efficiency. Our results support the latter model. MSUD was less efficient in near-isogenic crosses made in the novel N. crassa B/S1 genetic background, and in N. tetrasperma strain 85. Possibly, in B/S1 and 85, additional regulatory cues, absent from OR, calibrate the MSUD response. A locus in distal chromosome 1R appears to underlie the OR vs. B/S1 difference. Repeat-induced point mutation (RIP) destroys duplicated genes by G:C to A:T mutation of duplicated DNA sequences. Chromosome segment duplications (Dps) dominantly suppress RIP, possibly by titrating out the RIP machinery. In Dp x N crosses, the Dp–borne genes cannot pair properly, hence efficient MSUD, as in OR, silences them and renders the crosses barren. We speculate that the increased productivity engendered by inefficient MSUD enables small duplications to escape RIP.
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24
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Identification of rfk-1, a Meiotic Driver Undergoing RNA Editing in Neurospora. Genetics 2019; 212:93-110. [PMID: 30918007 DOI: 10.1534/genetics.119.302122] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 03/21/2019] [Indexed: 11/18/2022] Open
Abstract
Sk-2 is a meiotic drive element that was discovered in wild populations of Neurospora fungi over 40 years ago. While early studies quickly determined that Sk-2 transmits itself through sexual reproduction in a biased manner via spore killing, the genetic factors responsible for this phenomenon have remained mostly unknown. Here, we identify and characterize rfk-1, a gene required for Sk-2-based spore killing. The rfk-1 gene contains four exons, three introns, and two stop codons, the first of which undergoes RNA editing to a tryptophan codon during sexual development. Translation of an unedited rfk-1 transcript in vegetative tissue is expected to produce a 102-amino acid protein, whereas translation of an edited rfk-1 transcript in sexual tissue is expected to produce a protein with 130 amino acids. These findings indicate that unedited and edited rfk-1 transcripts exist and that these transcripts could have different roles with respect to the mechanism of meiotic drive by spore killing. Regardless of RNA editing, spore killing only succeeds if rfk-1 transcripts avoid silencing caused by a genome defense process called meiotic silencing by unpaired DNA (MSUD). We show that rfk-1's MSUD avoidance mechanism is linked to the genomic landscape surrounding the rfk-1 gene, which is located near the Sk-2 border on the right arm of chromosome III. In addition to demonstrating that the location of rfk-1 is critical to spore-killing success, our results add to accumulating evidence that MSUD helps protect Neurospora genomes from complex meiotic drive elements.
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25
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Verdín J, Sánchez-León E, Rico-Ramírez AM, Martínez-Núñez L, Fajardo-Somera RA, Riquelme M. Off the wall: The rhyme and reason of Neurospora crassa hyphal morphogenesis. ACTA ACUST UNITED AC 2019; 5:100020. [PMID: 32743136 PMCID: PMC7389182 DOI: 10.1016/j.tcsw.2019.100020] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 02/07/2019] [Accepted: 02/10/2019] [Indexed: 12/11/2022]
Abstract
Chitin and β-1,3-glucan synthases are transported separately in chitosomes and macrovesicles. Chitin synthases occupy the core of the SPK; β-1,3-glucan synthases the outer layer. CHS-4 arrival to the SPK and septa is CSE-7 dependent. Rabs YPT-1 and YPT-31 localization at the SPK mimics that of chitosomes and macrovesicles. The exocyst acts as a tether between the SPK outer layer vesicles and the apical PM.
The fungal cell wall building processes are the ultimate determinants of hyphal shape. In Neurospora crassa the main cell wall components, β-1,3-glucan and chitin, are synthesized by enzymes conveyed by specialized vesicles to the hyphal tip. These vesicles follow different secretory routes, which are delicately coordinated by cargo-specific Rab GTPases until their accumulation at the Spitzenkörper. From there, the exocyst mediates the docking of secretory vesicles to the plasma membrane, where they ultimately get fused. Although significant progress has been done on the cellular mechanisms that carry cell wall synthesizing enzymes from the endoplasmic reticulum to hyphal tips, a lot of information is still missing. Here, the current knowledge on N. crassa cell wall composition and biosynthesis is presented with an emphasis on the underlying molecular and cellular secretory processes.
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Key Words
- BGT, β-1,3-glucan transferases
- CHS, chitin synthase
- CLSM, confocal laser scanning microscopy
- CWI, cell wall integrity
- CWP, cell wall proteins
- Cell wall
- ER, endoplasmic reticulum
- FRAP, fluorescence recovery after photobleaching
- GEF, guanine nucleotide exchange factor
- GFP, green fluorescent protein
- GH, glycosyl hydrolases
- GPI, glycosylphosphatidylinositol
- GSC, β-1,3-glucan synthase complex
- MMD, myosin-like motor domain
- MS, mass spectrometry
- MT, microtubule
- NEC, network of elongated cisternae
- PM, plasma membrane
- SPK, Spitzenkörper
- Spitzenkörper
- TIRFM, total internal reflection fluorescence microscopy
- TM, transmembrane
- Tip growth
- Vesicles
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Affiliation(s)
- Jorge Verdín
- Industrial Biotechnology, CIATEJ-Jalisco State Scientific Research and Technology Assistance Center, Mexico National Council for Science and Technology, Zapopan, Jalisco, Mexico
| | - Eddy Sánchez-León
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Adriana M Rico-Ramírez
- Department of Microbiology, Centro de Investigación Científica y de Educación Superior de Ensenada, CICESE Ensenada, Baja California, Mexico
| | - Leonora Martínez-Núñez
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Rosa A Fajardo-Somera
- Karlsruhe Institute of Technology (KIT) South Campus, Institute for Applied Biosciences, Department of Microbiology, Karlsruhe, Germany
| | - Meritxell Riquelme
- Department of Microbiology, Centro de Investigación Científica y de Educación Superior de Ensenada, CICESE Ensenada, Baja California, Mexico
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26
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Abstract
The evolution of heteromorphic sex chromosomes has occurred independently many times in different lineages. The differentiation of sex chromosomes leads to dramatic changes in sequence composition and function and guides the evolutionary trajectory and utilization of genes in pivotal sex determination and reproduction roles. In addition, meiotic recombination and pairing mechanisms are key in orchestrating the resultant impact, retention and maintenance of heteromorphic sex chromosomes, as the resulting exposure of unpaired DNA at meiosis triggers ancient repair and checkpoint pathways. In this review, we summarize the different ways in which sex chromosome systems are organized at meiosis, how pairing is affected, and differences in unpaired DNA responses. We hypothesize that lineage specific differences in meiotic organization is not only a consequence of sex chromosome evolution, but that the establishment of epigenetic changes on sex chromosomes contributes toward their evolutionary conservation.
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Affiliation(s)
- Tasman Daish
- Comparative Genome Biology Laboratory, Department of Molecular and Biomedical Science, School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - Frank Grützner
- Comparative Genome Biology Laboratory, Department of Molecular and Biomedical Science, School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia.
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27
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Xiao H, Hammond TM, Shiu PKT. Suppressors of Meiotic Silencing by Unpaired DNA. Noncoding RNA 2019; 5:ncrna5010014. [PMID: 30696000 PMCID: PMC6468904 DOI: 10.3390/ncrna5010014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 01/23/2019] [Accepted: 01/24/2019] [Indexed: 11/16/2022] Open
Abstract
Meiotic silencing by unpaired DNA (MSUD) is a gene silencing process that occurs within meiotic cells of Neurospora crassa and other fungi. We have previously developed a high-throughput screen to identify suppressors of this silencing pathway. Here, a list of MSUD suppressor candidates from a single pass of the first 84 plates of the Neurospora knockout library is provided.
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Affiliation(s)
- Hua Xiao
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA.
| | - Thomas M Hammond
- School of Biological Sciences, Illinois State University, Normal, IL 61790, USA.
| | - Patrick K T Shiu
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA.
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28
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Chen D, Wu C, Hao C, Huang P, Liu H, Bian Z, Xu JR. Sexual specific functions of Tub1 beta-tubulins require stage-specific RNA processing and expression in Fusarium graminearum. Environ Microbiol 2018; 20:4009-4021. [PMID: 30307105 DOI: 10.1111/1462-2920.14441] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 10/04/2018] [Accepted: 10/05/2018] [Indexed: 11/27/2022]
Abstract
The wheat head blight fungus Fusarium graminearum has two highly similar beta-tubulin genes with overlapping functions during vegetative growth but only TUB1 is important for sexual reproduction. To better understand their functional divergence during ascosporogenesis, in this study we characterized the sequence elements important for stage-specific functions of TUB1. Deletion of TUB1 blocked the late but not initial stages of perithecium formation. Perithecia formed by tub1 mutant had limited ascogenous hyphae and failed to develop asci. Silencing of TUB1 by MSUD also resulted in defects in ascospore formation. Interestingly, the 3'-UTR of TUB1 was dispensable for growth but essential for its function during sexual reproduction. RIP mutations that specifically affected Tub1 functions during sexual reproduction also were identified in two ascospore progeny. Furthermore, site-directed mutagenesis showed that whereas the non-editable mutations at three A-to-I RNA editing sites had no effects, the N347D (not T362D or I368V) edited mutation affected ascospore development. In addition, the F167Y, but not E198K or F200Y, mutation in TUB1 conferred tolerance to carbendazim and caused a minor defect in sexual reproduction. Taken together, our data indicate TUB1 plays an essential role in ascosporogenesis and sexual-specific functions of TUB1 require stage-specific RNA processing and Tub1 expression.
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Affiliation(s)
- Daipeng Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China.,Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA
| | - Chunlan Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Chaofeng Hao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Panpan Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Huiquan Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Zhuyun Bian
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA
| | - Jin-Rong Xu
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA
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29
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Abstract
Transposable elements have colonized the genomes of nearly all organisms, including fungi. Although transposable elements may sometimes provide beneficial functions to their hosts their overall impact is considered deleterious. As a result, the activity of transposable elements needs to be counterbalanced by the host genome defenses. In fungi, the primary genome defense mechanisms include repeat-induced point mutation (RIP) and methylation induced premeiotically, meiotic silencing by unpaired DNA, sex-induced silencing, cosuppression (also known as somatic quelling), and cotranscriptional RNA surveillance. Recent studies of the filamentous fungus Neurospora crassa have shown that the process of repeat recognition for RIP apparently involves interactions between coaligned double-stranded segments of chromosomal DNA. These studies have also shown that RIP can be mediated by the conserved pathway that establishes transcriptional (heterochromatic) silencing of repetitive DNA. In light of these new findings, RIP emerges as a specialized case of the general phenomenon of heterochromatic silencing of repetitive DNA.
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30
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An RNA Recognition Motif-Containing Protein Functions in Meiotic Silencing by Unpaired DNA. G3-GENES GENOMES GENETICS 2017; 7:2871-2882. [PMID: 28667016 PMCID: PMC5555490 DOI: 10.1534/g3.117.041848] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Meiotic silencing by unpaired DNA (MSUD) is a biological process that searches pairs of homologous chromosomes (homologs) for segments of DNA that are unpaired. Genes found within unpaired segments are silenced for the duration of meiosis. In this report, we describe the identification and characterization of Neurospora crassa sad-7, a gene that encodes a protein with an RNA recognition motif (RRM). Orthologs of sad-7 are found in a wide range of ascomycete fungi. In N. crassa, sad-7 is required for a fully efficient MSUD response to unpaired genes. Additionally, at least one parent must have a functional sad-7 allele for a cross to produce ascospores. Although sad-7-null crosses are barren, sad-7Δ strains grow at a wild-type (wt) rate and appear normal under vegetative growth conditions. With respect to expression, sad-7 is transcribed at baseline levels in early vegetative cultures, at slightly higher levels in mating-competent cultures, and is at its highest level during mating. These findings suggest that SAD-7 is specific to mating-competent and sexual cultures. Although the role of SAD-7 in MSUD remains elusive, green fluorescent protein (GFP)-based tagging studies place SAD-7 within nuclei, perinuclear regions, and cytoplasmic foci of meiotic cells. This localization pattern is unique among known MSUD proteins and raises the possibility that SAD-7 coordinates nuclear, perinuclear, and cytoplasmic aspects of MSUD.
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