1
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Arter M, Keeney S. Divergence and conservation of the meiotic recombination machinery. Nat Rev Genet 2024; 25:309-325. [PMID: 38036793 DOI: 10.1038/s41576-023-00669-8] [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] [Accepted: 10/03/2023] [Indexed: 12/02/2023]
Abstract
Sexually reproducing eukaryotes use recombination between homologous chromosomes to promote chromosome segregation during meiosis. Meiotic recombination is almost universally conserved in its broad strokes, but specific molecular details often differ considerably between taxa, and the proteins that constitute the recombination machinery show substantial sequence variability. The extent of this variation is becoming increasingly clear because of recent increases in genomic resources and advances in protein structure prediction. We discuss the tension between functional conservation and rapid evolutionary change with a focus on the proteins that are required for the formation and repair of meiotic DNA double-strand breaks. We highlight phylogenetic relationships on different time scales and propose that this remarkable evolutionary plasticity is a fundamental property of meiotic recombination that shapes our understanding of molecular mechanisms in reproductive biology.
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Affiliation(s)
- Meret Arter
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Scott Keeney
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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2
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Chou JY, Hsu PC, Leu JY. Enforcement of Postzygotic Species Boundaries in the Fungal Kingdom. Microbiol Mol Biol Rev 2022; 86:e0009822. [PMID: 36098649 PMCID: PMC9769731 DOI: 10.1128/mmbr.00098-22] [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: 01/01/2023] Open
Abstract
Understanding the molecular basis of speciation is a primary goal in evolutionary biology. The formation of the postzygotic reproductive isolation that causes hybrid dysfunction, thereby reducing gene flow between diverging populations, is crucial for speciation. Using various advanced approaches, including chromosome replacement, hybrid introgression and transcriptomics, population genomics, and experimental evolution, scientists have revealed multiple mechanisms involved in postzygotic barriers in the fungal kingdom. These results illuminate both unique and general features of fungal speciation. Our review summarizes experiments on fungi exploring how Dobzhansky-Muller incompatibility, killer meiotic drive, chromosome rearrangements, and antirecombination contribute to postzygotic reproductive isolation. We also discuss possible evolutionary forces underlying different reproductive isolation mechanisms and the potential roles of the evolutionary arms race under the Red Queen hypothesis and epigenetic divergence in speciation.
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Affiliation(s)
- Jui-Yu Chou
- Department of Biology, National Changhua University of Education, Changhua, Taiwan
| | - Po-Chen Hsu
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Jun-Yi Leu
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
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3
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Abstract
Spore killers are specific genetic elements in fungi that kill sexual spores that do not contain them. A range of studies in the last few years have provided the long-awaited first insights into the molecular mechanistic aspects of spore killing in different fungal models, including both yeast-forming and filamentous Ascomycota. Here we describe these recent advances, focusing on the wtf system in the fission yeast Schizosaccharomyces pombe; the Sk spore killers of Neurospora species; and two spore-killer systems in Podospora anserina, Spok and [Het-s]. The spore killers appear thus far mechanistically unrelated. They can involve large genomic rearrangements but most often rely on the action of just a single gene. Data gathered so far show that the protein domains involved in the killing and resistance processes differ among the systems and are not homologous. The emerging picture sketched by these studies is thus one of great mechanistic and evolutionary diversity of elements that cheat during meiosis and are thereby preferentially inherited over sexual generations.
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Affiliation(s)
- Sven J Saupe
- Institut de Biochimie et de Génétique Cellulaire, CNRS UMR 5095, Université de Bordeaux, Bordeaux, France;
| | - Hanna Johannesson
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden;
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4
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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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5
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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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6
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Rico-Ramírez AM, Pedro Gonçalves A, Louise Glass N. Fungal Cell Death: The Beginning of the End. Fungal Genet Biol 2022; 159:103671. [PMID: 35150840 DOI: 10.1016/j.fgb.2022.103671] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 01/04/2022] [Accepted: 01/29/2022] [Indexed: 11/04/2022]
Abstract
Death is an important part of an organism's existence and also marks the end of life. On a cellular level, death involves the execution of complex processes, which can be classified into different types depending on their characteristics. Despite their "simple" lifestyle, fungi carry out highly specialized and sophisticated mechanisms to regulate the way their cells die, and the pathways underlying these mechanisms are comparable with those of plants and metazoans. This review focuses on regulated cell death in fungi and discusses the evidence for the occurrence of apoptotic-like, necroptosis-like, pyroptosis-like death, and the role of the NLR proteins in fungal cell death. We also describe recent data on meiotic drive elements involved in "spore killing" and the molecular basis of allorecognition-related cell death during cell fusion of genetically dissimilar cells. Finally, we discuss how fungal regulated cell death can be relevant in developing strategies to avoid resistance and tolerance to antifungal agents.
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Affiliation(s)
- Adriana M Rico-Ramírez
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720
| | - A Pedro Gonçalves
- Department of Cell Biology and Anatomy, College of Medicine, National Cheng Kung University, Tainan City, 701, Taiwan
| | - N Louise Glass
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720.
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7
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Vogan AA, Martinossi-Allibert I, Ament-Velásquez SL, Svedberg J, Johannesson H. The spore killers, fungal meiotic driver elements. Mycologia 2022; 114:1-23. [PMID: 35138994 DOI: 10.1080/00275514.2021.1994815] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
During meiosis, both alleles of any given gene should have equal chances of being inherited by the progeny. There are a number of reasons why, however, this is not the case, with one of the most intriguing instances presenting itself as the phenomenon of meiotic drive. Genes that are capable of driving can manipulate the ratio of alleles among viable meiotic products so that they are inherited in more than half of them. In many cases, this effect is achieved by direct antagonistic interactions, where the driving allele inhibits or otherwise eliminates the alternative allele. In ascomycete fungi, meiotic products are packaged directly into ascospores; thus, the effect of meiotic drive has been given the nefarious moniker, "spore killing." In recent years, many of the known spore killers have been elevated from mysterious phenotypes to well-described systems at genetic, genomic, and molecular levels. In this review, we describe the known diversity of spore killers and synthesize the varied pieces of data from each system into broader trends regarding genome architecture, mechanisms of resistance, the role of transposable elements, their effect on population dynamics, speciation and gene flow, and finally how they may be developed as synthetic drivers. We propose that spore killing is common, but that it is under-observed because of a lack of studies on natural populations. We encourage researchers to seek new spore killers to build on the knowledge that these remarkable genetic elements can teach us about meiotic drive, genomic conflict, and evolution more broadly.
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Affiliation(s)
- Aaron A Vogan
- Systematic Biology, Department of Organismal Biology, Uppsala University, 752 36, Uppsala, Sweden
| | - Ivain Martinossi-Allibert
- Systematic Biology, Department of Organismal Biology, Uppsala University, 752 36, Uppsala, Sweden.,Institut de Biochimie et de Génétique Cellulaire, UMR 5095 CNRS, Université de Bordeaux, 33077, Bordeaux CEDEX, France
| | - S Lorena Ament-Velásquez
- Systematic Biology, Department of Organismal Biology, Uppsala University, 752 36, Uppsala, Sweden
| | - Jesper Svedberg
- Department of Biomolecular Engineering, University of California, -Santa Cruz, Santa Cruz, California 95064
| | - Hanna Johannesson
- Systematic Biology, Department of Organismal Biology, Uppsala University, 752 36, Uppsala, Sweden
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8
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Zanders S, Johannesson H. Molecular Mechanisms and Evolutionary Consequences of Spore Killers in Ascomycetes. Microbiol Mol Biol Rev 2021; 85:e0001621. [PMID: 34756084 PMCID: PMC8579966 DOI: 10.1128/mmbr.00016-21] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
In this review, we examine the fungal spore killers. These are meiotic drive elements that cheat during sexual reproduction to increase their transmission into the next generation. Spore killing has been detected in a number of ascomycete genera, including Podospora, Neurospora, Schizosaccharomyces, Bipolaris, and Fusarium. There have been major recent advances in spore killer research that have increased our understanding of the molecular identity, function, and evolutionary history of the known killers. The spore killers vary in the mechanism by which they kill and are divided into killer-target and poison-antidote drivers. In killer-target systems, the drive locus encodes an element that can be described as a killer, while the target is an allele found tightly linked to the drive locus but on the nondriving haplotype. The poison-antidote drive systems encode both a poison and an antidote element within the drive locus. The key to drive in this system is the restricted distribution of the antidote: only the spores that inherit the drive locus receive the antidote and are rescued from the toxicity of the poison. Spore killers also vary in their genome architecture and can consist of a single gene or multiple linked genes. Due to their ability to distort meiosis, spore killers gain a selective advantage at the gene level that allows them to increase in frequency in a population over time, even if they reduce host fitness, and they may have significant impact on genome architecture and macroevolutionary processes such as speciation.
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Affiliation(s)
- Sarah Zanders
- Stowers Institute for Medical Research, Kansas City, Kansas, USA
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Hanna Johannesson
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
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9
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Abstract
Diversity within the fungal kingdom is evident from the wide range of morphologies fungi display as well as the various ecological roles and industrial purposes they serve. Technological advances, particularly in long-read sequencing, coupled with the increasing efficiency and decreasing costs across sequencing platforms have enabled robust characterization of fungal genomes. These sequencing efforts continue to reveal the rampant diversity in fungi at the genome level. Here, we discuss studies that have furthered our understanding of fungal genetic diversity and genomic evolution. These studies revealed the presence of both small-scale and large-scale genomic changes. In fungi, research has recently focused on many small-scale changes, such as how hypermutation and allelic transmission impact genome evolution as well as how and why a few specific genomic regions are more susceptible to rapid evolution than others. High-throughput sequencing of a diverse set of fungal genomes has also illuminated the frequency, mechanisms, and impacts of large-scale changes, which include chromosome structural variation and changes in chromosome number, such as aneuploidy, polyploidy, and the presence of supernumerary chromosomes. The studies discussed herein have provided great insight into how the architecture of the fungal genome varies within species and across the kingdom and how modern fungi may have evolved from the last common fungal ancestor and might also pave the way for understanding how genomic diversity has evolved in all domains of life.
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Affiliation(s)
- Shelby J. Priest
- Department of Molecular Genetics and Microbiology, Duke University Medical Centre, Durham, NC, USA
| | - Vikas Yadav
- Department of Molecular Genetics and Microbiology, Duke University Medical Centre, Durham, NC, USA
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Centre, Durham, NC, USA
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10
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Kasbekar DP. A cross-eyed geneticist's view IV. Neurospora genes and inversions collude to cheat Mendel. J Biosci 2019; 44:83. [PMID: 31502561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
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11
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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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12
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Vogan AA, Ament-Velásquez SL, Granger-Farbos A, Svedberg J, Bastiaans E, Debets AJ, Coustou V, Yvanne H, Clavé C, Saupe SJ, Johannesson H. Combinations of Spok genes create multiple meiotic drivers in Podospora. eLife 2019; 8:46454. [PMID: 31347500 PMCID: PMC6660238 DOI: 10.7554/elife.46454] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 06/09/2019] [Indexed: 11/13/2022] Open
Abstract
Meiotic drive is the preferential transmission of a particular allele during sexual reproduction. The phenomenon is observed as spore killing in multiple fungi. In natural populations of Podospora anserina, seven spore killer types (Psks) have been identified through classical genetic analyses. Here we show that the Spok gene family underlies the Psks. The combination of Spok genes at different chromosomal locations defines the spore killer types and creates a killing hierarchy within a population. We identify two novel Spok homologs located within a large (74–167 kbp) region (the Spok block) that resides in different chromosomal locations in different strains. We confirm that the SPOK protein performs both killing and resistance functions and show that these activities are dependent on distinct domains, a predicted nuclease and kinase domain. Genomic and phylogenetic analyses across ascomycetes suggest that the Spok genes disperse through cross-species transfer, and evolve by duplication and diversification within lineages. In many organisms, most cells carry two versions of a given gene, one coming from the mother and the other from the father. An exception is sexual cells such as eggs, sperm, pollen or spores, which should only contain one variant of a gene. During their formation, these cells usually have an equal chance of inheriting one of the two gene versions. However, a certain class of gene variants called meiotic drivers can cheat this process and end up in more than half of the sexual cells; often, the cells that contain the drivers can kill sibling cells that do not carry these variants. This results in the selfish genetic elements spreading through populations at a higher rate, sometimes with severe consequences such as shifting the ratio of males to females. Meiotic drivers have been discovered in a wide range of organisms, from corn to mice to fruit flies and bread mold. They also exist in the fungus Podospora anserina, where they are called ‘spore killers’. Fungi are often used to study complex genetic processes, yet the identity and mode of action of spore killers in P. anserina were still unknown. Vogan, Ament-Velásquez et al. used a combination of genetic methods to identify three genes from the Spok family which are responsible for certain spores being able to kill their siblings. Two of these were previously unknown, and they could be found in different locations throughout the genome as part of a larger genetic region. Depending on the combination of Spok genes it carries, a spore can kill or be protected against other spores that contain different permutations of the genes. Copies of these genes were also shown to be present in other fungi, including species that are a threat to crops. Scientists have already started to create synthetic meiotic drivers to manipulate how certain traits are inherited within a population. This could be useful to control or eradicate pests and insects that transmit dangerous diseases. The results by Vogan, Ament-Velásquez et al. shine a light on the complex ways that natural meiotic drivers work, including how they can be shared between species; this knowledge could inform how to safely deploy synthetic drivers in the wild.
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Affiliation(s)
- Aaron A Vogan
- Organismal biology, Uppsala University, Uppsala, Sweden
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13
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Abstract
In sexual reproduction, opportunities are limited and the stakes are high. This inevitably leads to conflict. One pervasive conflict occurs within genomes between alternative alleles at heterozygous loci. Each gamete and thus each offspring will inherit only one of the two alleles from a heterozygous parent. Most alleles 'play fair' and have a 50% chance of being included in any given gamete. However, alleles can gain an enormous advantage if they act selfishly to force their own transmission into more than half, sometimes even all, of the functional gametes. These selfish alleles are known as 'meiotic drivers', and their cheating often incurs a high cost on the fertility of eukaryotes ranging from plants to mammals. Here, we review how several types of meiotic drivers directly and indirectly contribute to infertility, and argue that a complete picture of the genetics of infertility will require focusing on both the standard alleles - those that play fair - as well as selfish alleles involved in genetic conflict.
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Affiliation(s)
- Sarah E Zanders
- Stowers Institute for Medical Research, Kansas City, MO, USA; Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS, USA.
| | - Robert L Unckless
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, USA
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14
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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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15
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Svedberg J, Hosseini S, Chen J, Vogan AA, Mozgova I, Hennig L, Manitchotpisit P, Abusharekh A, Hammond TM, Lascoux M, Johannesson H. Convergent evolution of complex genomic rearrangements in two fungal meiotic drive elements. Nat Commun 2018; 9:4242. [PMID: 30315196 PMCID: PMC6185902 DOI: 10.1038/s41467-018-06562-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 09/12/2018] [Indexed: 12/31/2022] Open
Abstract
Meiotic drive is widespread in nature. The conflict it generates is expected to be an important motor for evolutionary change and innovation. In this study, we investigated the genomic consequences of two large multi-gene meiotic drive elements, Sk-2 and Sk-3, found in the filamentous ascomycete Neurospora intermedia. Using long-read sequencing, we generated the first complete and well-annotated genome assemblies of large, highly diverged, non-recombining regions associated with meiotic drive elements. Phylogenetic analysis shows that, even though Sk-2 and Sk-3 are located in the same chromosomal region, they do not form sister clades, suggesting independent origins or at least a long evolutionary separation. We conclude that they have in a convergent manner accumulated similar patterns of tandem inversions and dense repeat clusters, presumably in response to similar needs to create linkage between genes causing drive and resistance.
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Affiliation(s)
- Jesper Svedberg
- Department of Organismal Biology, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden
| | - Sara Hosseini
- Department of Organismal Biology, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden
| | - Jun Chen
- Department of Ecology and Genetics, Science for Life Laboratory, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden
| | - Aaron A Vogan
- Department of Organismal Biology, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden
| | - Iva Mozgova
- Department of Plant Biology and Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, PO-Box 7080, SE-75007, Uppsala, Sweden
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Opatovický mlýn, CZ-37981, Třeboň, Czech Republic
| | - Lars Hennig
- Department of Plant Biology and Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, PO-Box 7080, SE-75007, Uppsala, Sweden
| | | | - Anna Abusharekh
- 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
| | - Martin Lascoux
- Department of Ecology and Genetics, Science for Life Laboratory, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden
| | - Hanna Johannesson
- Department of Organismal Biology, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden.
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16
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Bravo Núñez MA, Nuckolls NL, Zanders SE. Genetic Villains: Killer Meiotic Drivers. Trends Genet 2018; 34:424-433. [PMID: 29499907 DOI: 10.1016/j.tig.2018.02.003] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Revised: 02/01/2018] [Accepted: 02/02/2018] [Indexed: 01/22/2023]
Abstract
Unbiased allele transmission into progeny is a fundamental genetic concept canonized as Mendel's Law of Segregation. Not all alleles, however, abide by the law. Killer meiotic drivers are ultra-selfish DNA sequences that are transmitted into more than half (sometimes all) of the meiotic products generated by a heterozygote. As their name implies, these loci gain a transmission advantage in heterozygotes by destroying otherwise viable meiotic products that do not inherit the driver. We review and classify killer meiotic drive genes across a wide spectrum of eukaryotes. We discuss how analyses of these ultra-selfish genes can lead to greater insight into the mechanisms of gametogenesis and the causes of infertility.
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Affiliation(s)
- María Angélica Bravo Núñez
- Stowers Institute for Medical Research, Kansas City, MO, USA; These authors contributed equally to this work
| | - Nicole L Nuckolls
- Stowers Institute for Medical Research, Kansas City, MO, USA; These authors contributed equally to this work
| | - Sarah E Zanders
- Stowers Institute for Medical Research, Kansas City, MO, USA; Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS, USA.
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17
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López Hernández JF, Zanders SE. Veni, vidi, vici: the success of wtf meiotic drivers in fission yeast. Yeast 2018; 35:447-453. [PMID: 29322557 PMCID: PMC6033644 DOI: 10.1002/yea.3305] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 11/30/2017] [Accepted: 12/22/2017] [Indexed: 12/20/2022] Open
Abstract
Meiotic drivers are selfish DNA loci that can bias their own transmission into gametes. Owing to their transmission advantages, meiotic drivers can spread in populations even if the drivers or linked variants decrease organismal fitness. Meiotic drive was first formally described in the 1950s and is thought to be a powerful force shaping eukaryotic genomes. Classic genetic analyses have detected the action of meiotic drivers in plants, filamentous fungi, insects and vertebrates. Several of these drive systems have limited experimental tractability and relatively little is known about the molecular mechanisms of meiotic drive. Recently, however, meiotic drivers were discovered in a yeast species. The Schizosaccharomyces pombe wtf gene family contains several active meiotic drive genes. This review summarizes what is known about the wtf family and highlights its potential as a highly tractable experimental model for molecular and evolutionary characterization of meiotic drive.
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Affiliation(s)
| | - Sarah E Zanders
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA.,Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
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Ailion M, Malik HS. Genetics: Master Regulator or Master of Disguise? Curr Biol 2017; 27:R844-R847. [PMID: 28898647 DOI: 10.1016/j.cub.2017.07.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The pha-1 gene of Caenorhabditis elegans was originally heralded as a master regulator of organ differentiation. A new study suggests instead that pha-1 actually serves no role in development and instead is a component of a selfish genetic element.
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Affiliation(s)
- Michael Ailion
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
| | - Harmit S Malik
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
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Hu W, Jiang ZD, Suo F, Zheng JX, He WZ, Du LL. A large gene family in fission yeast encodes spore killers that subvert Mendel's law. eLife 2017; 6:e26057. [PMID: 28631610 PMCID: PMC5478263 DOI: 10.7554/elife.26057] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 05/06/2017] [Indexed: 12/12/2022] Open
Abstract
Spore killers in fungi are selfish genetic elements that distort Mendelian segregation in their favor. It remains unclear how many species harbor them and how diverse their mechanisms are. Here, we discover two spore killers from a natural isolate of the fission yeast Schizosaccharomyces pombe. Both killers belong to the previously uncharacterized wtf gene family with 25 members in the reference genome. These two killers act in strain-background-independent and genome-location-independent manners to perturb the maturation of spores not inheriting them. Spores carrying one killer are protected from its killing effect but not that of the other killer. The killing and protecting activities can be uncoupled by mutation. The numbers and sequences of wtf genes vary considerably between S. pombe isolates, indicating rapid divergence. We propose that wtf genes contribute to the extensive intraspecific reproductive isolation in S. pombe, and represent ideal models for understanding how segregation-distorting elements act and evolve.
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Affiliation(s)
- Wen Hu
- National Institute of Biological Sciences, Beijing, China
| | - Zhao-Di Jiang
- National Institute of Biological Sciences, Beijing, China
- PTN Graduate Program, School of Life Sciences, Tsinghua University, Beijing, China
| | - Fang Suo
- National Institute of Biological Sciences, Beijing, China
| | - Jin-Xin Zheng
- National Institute of Biological Sciences, Beijing, China
| | - Wan-Zhong He
- National Institute of Biological Sciences, Beijing, China
| | - Li-Lin Du
- National Institute of Biological Sciences, Beijing, China
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20
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Nuckolls NL, Bravo Núñez MA, Eickbush MT, Young JM, Lange JJ, Yu JS, Smith GR, Jaspersen SL, Malik HS, Zanders SE. wtf genes are prolific dual poison-antidote meiotic drivers. eLife 2017. [PMID: 28631612 PMCID: PMC5478261 DOI: 10.7554/elife.26033] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Meiotic drivers are selfish genes that bias their transmission into gametes, defying Mendelian inheritance. Despite the significant impact of these genomic parasites on evolution and infertility, few meiotic drive loci have been identified or mechanistically characterized. Here, we demonstrate a complex landscape of meiotic drive genes on chromosome 3 of the fission yeasts Schizosaccharomyces kambucha and S. pombe. We identify S. kambucha wtf4 as one of these genes that acts to kill gametes (known as spores in yeast) that do not inherit the gene from heterozygotes. wtf4 utilizes dual, overlapping transcripts to encode both a gamete-killing poison and an antidote to the poison. To enact drive, all gametes are poisoned, whereas only those that inherit wtf4 are rescued by the antidote. Our work suggests that the wtf multigene family proliferated due to meiotic drive and highlights the power of selfish genes to shape genomes, even while imposing tremendous costs to fertility. DOI:http://dx.doi.org/10.7554/eLife.26033.001 Animals, plants and fungi produce sex cells – known as gametes – when they are preparing to reproduce. These cells are made when cells containing two copies of every gene in the organism divide to produce new cells that each only have one copy of each gene. Therefore, a particular gene copy usually has a 50% chance of being carried by each gamete. There is a group of genes that selfishly increase their chances of being transmitted to the next generation by destroying the gametes that do not carry them. These “gamete killer” genes can lead to infertility and other health problems. Fission yeast is a fungus that is widely used in research. Previous studies revealed that the yeast are likely to have several gamete killers, but the identities of these genes or how they work were not clear. Nuckolls, Bravo Núñez et al. sought to identify at least one gamete killer gene and understand how it works. The experiments found that a gene called wtf4 acts as a gamete killer in fission yeast. This gene encodes two different proteins, one that acts as a poison and one that acts as an antidote. The antidote remains inside the gametes that contain the wtf4 gene, while the poison is released in the surrounding environment. The poison is capable of killing all of the gametes, but the antidote protects the gametes that contain the wtf4 gene. Further experiments show that wtf4 is just one member of a large family of genes that are also likely to play roles in selectively killing gametes. A separate study by Hu et al. found that two other members of the wtf family also act as gamete killers in fission yeast. Together, these findings expand our understanding of the nature of gamete killers and how they can contribute to infertility. This may guide the search for gamete killers in humans and other organisms. In the future, gamete killers could potentially be used to eradicate populations of pests that damage crops or spread diseases in humans. DOI:http://dx.doi.org/10.7554/eLife.26033.002
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Affiliation(s)
| | | | | | - Janet M Young
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Jeffrey J Lange
- Stowers Institute for Medical Research, Kansas City, United States
| | - Jonathan S Yu
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Gerald R Smith
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Sue L Jaspersen
- Stowers Institute for Medical Research, Kansas City, United States.,Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, United States
| | - Harmit S Malik
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States.,Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Sarah E Zanders
- Stowers Institute for Medical Research, Kansas City, United States.,Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, United States
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Abstract
The filamentous fungus Neurospora crassa possesses a process called meiotic silencing by unpaired DNA (MSUD). MSUD has a remarkable ability to scan homologous chromosomes for unpaired DNA during meiosis. After unpaired DNA is identified, MSUD silences all RNA from the unpaired DNA along with any RNA transcribed from homologous sequences at other locations in the genome, regardless of their pairing state. The mechanism by which unpaired DNA is detected is unknown. Unpaired DNA segments can be as short as 1.3kb, if not shorter, and DNA sequences with only a small level of polymorphism (6%) can be considered unpaired by MSUD. MSUD research has identified nine proteins required for full efficiency of the process, three of which are homologs of the canonical RNA interference (RNAi) proteins Dicer, Argonaute, and RNA-dependent RNA polymerase. Most MSUD proteins, including the RNAi homologs, appear to dock outside of the nuclear envelope during early stages of meiosis. Only two have been observed inside the nucleus, a low number given that the identification of unpaired DNA and the triggering of silencing must begin within this location. These two proteins may participate in the unpaired DNA detection process. Recent evidence indicates that the search for unpaired DNA is spatially constrained, possibly because of restrictions on the arrangement of chromatin loops during or after homolog pairing. This review attempts to provide a complete analysis of past, present, and future directions of MSUD research, starting with its discovery during a search for a conserved regulator of fungal development and ending with some benefits the process may provide to MSUD capable organisms.
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Affiliation(s)
- T M Hammond
- Illinois State University, Normal, IL, United States.
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22
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Pyle J, Patel T, Merrill B, Nsokoshi C, McCall M, Proctor RH, Brown DW, Hammond TM. A Meiotic Drive Element in the Maize Pathogen Fusarium verticillioides Is Located Within a 102 kb Region of Chromosome V. G3 (BETHESDA, MD.) 2016; 6:2543-52. [PMID: 27317777 PMCID: PMC4978907 DOI: 10.1534/g3.116.029728] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Accepted: 06/06/2016] [Indexed: 11/24/2022]
Abstract
Fusarium verticillioides is an agriculturally important fungus because of its association with maize and its propensity to contaminate grain with toxic compounds. Some isolates of the fungus harbor a meiotic drive element known as Spore killer (Sk(K)) that causes nearly all surviving meiotic progeny from an Sk(K) × Spore killer-susceptible (Sk(S)) cross to inherit the Sk(K) allele. Sk(K) has been mapped to chromosome V but the genetic element responsible for meiotic drive has yet to be identified. In this study, we used cleaved amplified polymorphic sequence markers to genotype individual progeny from an Sk(K) × Sk(S) mapping population. We also sequenced the genomes of three progeny from the mapping population to determine their single nucleotide polymorphisms. These techniques allowed us to refine the location of Sk(K) to a contiguous 102 kb interval of chromosome V, herein referred to as the Sk region. Relative to Sk(S) genotypes, Sk(K) genotypes have one extra gene within this region for a total of 42 genes. The additional gene in Sk(K) genotypes, herein named SKC1 for Spore Killer Candidate 1, is the most highly expressed gene from the Sk region during early stages of sexual development. The Sk region also has three hyper-variable regions, the longest of which includes SKC1 The possibility that SKC1, or another gene from the Sk region, is an essential component of meiotic drive and spore killing is discussed.
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Affiliation(s)
- Jay Pyle
- School of Biological Sciences, Illinois State University, Normal, Illinois 61790
| | - Tejas Patel
- School of Biological Sciences, Illinois State University, Normal, Illinois 61790
| | - Brianna Merrill
- School of Biological Sciences, Illinois State University, Normal, Illinois 61790
| | - Chabu Nsokoshi
- School of Biological Sciences, Illinois State University, Normal, Illinois 61790
| | - Morgan McCall
- School of Biological Sciences, Illinois State University, Normal, Illinois 61790
| | - Robert H Proctor
- Mycotoxin Prevention and Applied Microbiology, National Center for Agricultural Utilization Research, U.S. Department of Agriculture, Agricultural Research Service, Peoria, Illinois 61604
| | - Daren W Brown
- Mycotoxin Prevention and Applied Microbiology, National Center for Agricultural Utilization Research, U.S. Department of Agriculture, Agricultural Research Service, Peoria, Illinois 61604
| | - Thomas M Hammond
- School of Biological Sciences, Illinois State University, Normal, Illinois 61790
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23
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Crosses Heterozygous for Hybrid Neurospora Translocation Strains Show Transmission Ratio Distortion Disfavoring Homokaryotic Ascospores Made Following Alternate Segregation. G3-GENES GENOMES GENETICS 2016; 6:2593-600. [PMID: 27317785 PMCID: PMC4978912 DOI: 10.1534/g3.116.030627] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
By introgressing Neurospora crassa translocations into N. tetrasperma, we constructed heterokaryons bearing haploid nuclei of opposite mating types, and either the translocation and normal sequence chromosomes (i.e., [T + N]) or a duplication and its complementary deficiency (i.e., [Dp + Df]). The [T + N] heterokaryons result from alternate segregation of homologous centromeres, whereas adjacent-1 segregation generates [Dp + Df]. Self-cross of either heterokaryon produces [T + N] and [Dp + Df] progeny. Occasionally during N. tetrasperma ascus development, a pair of smaller homokaryotic ascospores replaces a heterokaryotic ascospore. Crosses with the Eight-spore mutant increase such replacement, and can generate asci with eight homokaryotic ascospores, either 4T + 4N from alternate segregation, or 4Dp + 4Df from adjacent-1 segregation. Crosses of some of the introgressed translocation strains with normal sequence N. tetrasperma produced more Dp than T or N homokaryotic progeny. We suggest this is due to an insufficiency for a presumptive ascospore maturation factor, which increases the chance that, in asci with > 4 viable ascospores, none properly mature. Since only four viable ascospores (Dp or [Dp + Df]) share the limiting factor following adjacent-1 segregation, whereas four to eight ascospores compete for it following alternate segregation, this would explain why Dp homokaryons outnumber T and N types, whereas the heterokaryons are not as affected. We believe that this novel form of transmission ratio distortion is caused by a Bateson–Dobzhansky–Muller Incompatibility (BDMI) triggered by an N. crassa gene in the N. tetrasperma background. Heterokaryons tend not to out-cross, and crosses of Dp strains are barren, thus the BDMI impedes interspecies gene flow.
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Lindholm AK, Dyer KA, Firman RC, Fishman L, Forstmeier W, Holman L, Johannesson H, Knief U, Kokko H, Larracuente AM, Manser A, Montchamp-Moreau C, Petrosyan VG, Pomiankowski A, Presgraves DC, Safronova LD, Sutter A, Unckless RL, Verspoor RL, Wedell N, Wilkinson GS, Price TA. The Ecology and Evolutionary Dynamics of Meiotic Drive. Trends Ecol Evol 2016; 31:315-326. [DOI: 10.1016/j.tree.2016.02.001] [Citation(s) in RCA: 172] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 01/29/2016] [Accepted: 02/01/2016] [Indexed: 12/24/2022]
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Smith ZJ, Bedore S, Spingler S, Hammond TM. A mus-51 RIP allele for transformation of Neurospora crassa. FUNGAL GENETICS REPORTS 2016; 62. [PMID: 28729897 DOI: 10.4148/1941-4765.1001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
This report describes the construction and characterization of mus-51RIP70 , an allele for high-efficiency targeted integration of transgenes into the genome of the model eukaryote Neurospora crassa. Two of the mus-51RIP70 strains investigated in this work (RZS27.10 and RZS27.18) can be obtained from the Fungal Genetics Stock Center. The two deposited strains are, to our knowledge, genetically identical and neither one is preferred over the other for use in Neurospora research.
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Affiliation(s)
- Zachary J Smith
- School of Biological Sciences, Illinois State University, Normal, IL 61790
| | - Stacy Bedore
- School of Biological Sciences, Illinois State University, Normal, IL 61790
| | - Stephanie Spingler
- School of Biological Sciences, Illinois State University, Normal, IL 61790
| | - Thomas M Hammond
- School of Biological Sciences, Illinois State University, Normal, IL 61790
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26
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Li WC, Chuang YC, Chen CL, Wang TF. Hybrid Infertility: The Dilemma or Opportunity of Applying Sexual Development to Improve Trichoderma reesei Industrial Strains. Fungal Biol 2016. [DOI: 10.1007/978-3-319-27951-0_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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27
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Abstract
Genome defense likely evolved to curtail the spread of transposable elements and invading viruses. A combination of effective defense mechanisms has been shown to limit colonization of the Neurospora crassa genome by transposable elements. A novel DNA transposon named Sly1-1 was discovered in the genome of the most widely used laboratory "wild-type" strain FGSC 2489 (OR74A). Meiotic silencing by unpaired DNA, also simply called meiotic silencing, prevents the expression of regions of the genome that are unpaired during karyogamy. This mechanism is posttranscriptional and is proposed to involve the production of small RNA, so-called masiRNAs, by proteins homologous to those involved in RNA interference-silencing pathways in animals, fungi, and plants. Here, we demonstrate production of small RNAs when Sly1-1 was unpaired in a cross between two wild-type strains. These small RNAs are dependent on SAD-1, an RNA-dependent RNA polymerase necessary for meiotic silencing. We present the first case of endogenously produced masiRNA from a novel N. crassa DNA transposable element.
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28
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Chuang YC, Li WC, Chen CL, Hsu PWC, Tung SY, Kuo HC, Schmoll M, Wang TF. Trichoderma reesei meiosis generates segmentally aneuploid progeny with higher xylanase-producing capability. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:30. [PMID: 25729429 PMCID: PMC4344761 DOI: 10.1186/s13068-015-0202-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2014] [Accepted: 01/09/2015] [Indexed: 05/15/2023]
Abstract
BACKGROUND Hypocrea jecorina is the sexual form of the industrial workhorse fungus Trichoderma reesei that secretes cellulases and hemicellulases to degrade lignocellulosic biomass into simple sugars, such as glucose and xylose. H. jecorina CBS999.97 is the only T. reesei wild isolate strain that is sexually competent in laboratory conditions. It undergoes a heterothallic reproductive cycle and generates CBS999.97(1-1) and CBS999.97(1-2) haploids with MAT1-1 and MAT1-2 mating-type loci, respectively. T. reesei QM6a and its derivatives (RUT-C30 and QM9414) all have a MAT1-2 mating type locus, but they are female sterile. Sexual crossing of CBS999.97(1-1) with either CBS999.97(1-2) or QM6a produces fruiting bodies containing asci with 16 linearly arranged ascospores (the sexual spores specific to ascomycetes). This sexual crossing approach has created new opportunities for these biotechnologically important fungi. RESULTS Through genetic and genomic analyses, we show that the 16 ascospores are generated via meiosis followed by two rounds of postmeiotic mitosis. We also found that the haploid genomes of CBS999.97(1-2) and QM6a are similar to that of the ancestral T. reesei strain, whereas the CBS999.97(1-1) haploid genome contains a reciprocal arrangement between two scaffolds of the CBS999.97(1-2) genome. Due to sequence heterozygosity, most 16-spore asci (>90%) contain four or eight inviable ascospores and an equal number of segmentally aneuploid (SAN) ascospores. The viable SAN progeny produced higher levels of xylanases and white conidia due to segmental duplication and deletion, respectively. Moreover, they readily lost the duplicated segment approximately two weeks after germination. With better lignocellulosic biomass degradation capability, these SAN progeny gain adaptive advantages to the natural environment, especially in the early phase of colonization. CONCLUSIONS Our results have not only further elucidated T. reesei evolution and sexual development, but also provided new perspectives for improving T. reesei industrial strains.
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Affiliation(s)
- Yu-Chien Chuang
- />Taiwan International Graduate Program in Molecular and Cellular Biology, Academia Sinica, Taipei, 115 Taiwan
- />Institute of Life Sciences, National Defense Medical Center, Taipei, 115 Taiwan
- />Institute of Molecular Biology, Academia Sinica, Taipei, 115 Taiwan
| | - Wan-Chen Li
- />Institute of Molecular Biology, Academia Sinica, Taipei, 115 Taiwan
- />Institute of Genome Sciences, National Yang-Ming University, Taipei, 112 Taiwan
| | - Chia-Ling Chen
- />Institute of Molecular Biology, Academia Sinica, Taipei, 115 Taiwan
| | - Paul Wei-Che Hsu
- />Institute of Molecular Biology, Academia Sinica, Taipei, 115 Taiwan
| | - Shu-Yun Tung
- />Institute of Molecular Biology, Academia Sinica, Taipei, 115 Taiwan
| | - Hsiao-Che Kuo
- />Institute of Molecular Biology, Academia Sinica, Taipei, 115 Taiwan
- />Present address: Department of Forest Sciences, University of Helsinki, Helsinki, Finland
| | - Monika Schmoll
- />Austrian Institute of Technology, Health and Environment Department, Bioresources, University and Research Center, UFT Campus Tulln, Tulln/Donau, 3430 Austria
| | - Ting-Fang Wang
- />Taiwan International Graduate Program in Molecular and Cellular Biology, Academia Sinica, Taipei, 115 Taiwan
- />Institute of Molecular Biology, Academia Sinica, Taipei, 115 Taiwan
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Efficient detection of unpaired DNA requires a member of the rad54-like family of homologous recombination proteins. Genetics 2014; 198:895-904. [PMID: 25146971 DOI: 10.1534/genetics.114.168187] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Meiotic silencing by unpaired DNA (MSUD) is a process that detects unpaired regions between homologous chromosomes and silences them for the duration of sexual development. While the phenomenon of MSUD is well recognized, the process that detects unpaired DNA is poorly understood. In this report, we provide two lines of evidence linking unpaired DNA detection to a physical search for DNA homology. First, we have found that a putative SNF2-family protein (SAD-6) is required for efficient MSUD in Neurospora crassa. SAD-6 is closely related to Rad54, a protein known to facilitate key steps in the repair of double-strand breaks by homologous recombination. Second, we have successfully masked unpaired DNA by placing identical transgenes at slightly different locations on homologous chromosomes. This masking falls apart when the distance between the transgenes is increased. We propose a model where unpaired DNA detection during MSUD is achieved through a spatially constrained search for DNA homology. The identity of SAD-6 as a Rad54 paralog suggests that this process may be similar to the searching mechanism used during homologous recombination.
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