-
Current Biology : CB Feb 2011
Topics: Fungal Proteins; Gene Expression Regulation, Fungal; Genome, Fungal; Mutation; Neurospora
PubMed: 21334288
DOI: 10.1016/j.cub.2011.01.006 -
Genetics Aug 2023A multinucleate syncytium is a common growth form in filamentous fungi. Comprehensive functions of the syncytial state remain unknown, but it likely allows for a wide...
A multinucleate syncytium is a common growth form in filamentous fungi. Comprehensive functions of the syncytial state remain unknown, but it likely allows for a wide range of adaptations to enable filamentous fungi to coordinate growth, reproduction, responses to the environment, and to distribute nuclear and cytoplasmic elements across a colony. Indeed, the underlying mechanistic details of how syncytia regulate cellular and molecular processes spatiotemporally across a colony are largely unexplored. Here, we implemented a strategy to analyze the relative fitness of different nuclear populations in syncytia of Neurospora crassa, including nuclei with loss-of-function mutations in essential genes, based on production of multinucleate asexual spores using flow cytometry of pairings between strains with differentially fluorescently tagged nuclear histones. The distribution of homokaryotic and heterokaryotic asexual spores in pairings was assessed between different auxotrophic and morphological mutants, as well as with strains that were defective in somatic cell fusion or were heterokaryon incompatible. Mutant nuclei were compartmentalized into both homokaryotic and heterokaryotic asexual spores, a type of bet hedging for maintenance and evolution of mutational events, despite disadvantages to the syncytium. However, in pairings between strains that were blocked in somatic cell fusion or were heterokaryon incompatible, we observed a "winner-takes-all" phenotype, where asexual spores originating from paired strains were predominantly one genotype. These data indicate that syncytial fungal cells are permissive and tolerate a wide array of nuclear functionality, but that cells/colonies that are unable to cooperate via syncytia formation actively compete for resources.
Topics: Neurospora crassa; Genes, Fungal; Permissiveness; Phenotype; Giant Cells; Fungal Proteins; Neurospora
PubMed: 37313736
DOI: 10.1093/genetics/iyad112 -
Advances in Genetics 2011This chapter describes our current understanding of the genetics of the Neurospora clock and summarizes the important findings in this area in the past decade.... (Review)
Review
This chapter describes our current understanding of the genetics of the Neurospora clock and summarizes the important findings in this area in the past decade. Neurospora is the most intensively studied clock system, and the reasons for this are listed. A discussion of the genetic interactions between clock mutants is included, highlighting the utility of dissecting complex mechanisms by genetic means. The molecular details of the Neurospora circadian clock mechanism are described, as well as the mutations that affect the key clock proteins, FRQ, WC-1, and WC-2, with an emphasis on the roles of protein phosphorylation. Studies on additional genes affecting clock properties are described and place these genes into two categories: those that affect the FRQ/WCC oscillator and those that do not. A discussion of temperature compensation and the mutants affecting this property is included. A section is devoted to the observations pertinent to the existence of other oscillators in this organism with respect to their properties, their effects, and their preliminary characterization. The output of the clock and the control of clock-controlled genes are discussed, emphasizing the phasing of these genes and the layers of control. In conclusion, the authors provide an outlook summarizing their suggestions for areas that would be fruitful for further exploration.
Topics: CLOCK Proteins; Circadian Rhythm; Fungal Proteins; Mutation; Neurospora
PubMed: 21924975
DOI: 10.1016/B978-0-12-387690-4.00003-9 -
Protein & Cell Apr 2010Circadian clocks are the internal time-keeping mechanisms for organisms to synchronize their cellular and physiological processes to the daily light/dark cycles. The... (Review)
Review
Circadian clocks are the internal time-keeping mechanisms for organisms to synchronize their cellular and physiological processes to the daily light/dark cycles. The molecular mechanisms underlying circadian clocks are remarkably similar in eukaryotes. Neurospora crassa, a filamentous fungus, is one of the best understood model organisms for circadian research. In recent years, accumulating data have revealed complex regulation in the Neurospora circadian clock at transcriptional, posttranscriptional, post-translational and epigenetic levels. Here we review the recent progress towards our understanding of the molecular mechanism of the Neurospora circadian oscillator. These advances have provided novel insights and furthered our understanding of the mechanism of eukaryotic circadian clocks.
Topics: Circadian Clocks; Epigenomics; Neurospora; Neurospora crassa
PubMed: 21203945
DOI: 10.1007/s13238-010-0053-7 -
Proceedings of the National Academy of... Apr 2021Meiotic drive elements cause their own preferential transmission following meiosis. In fungi, this phenomenon takes the shape of spore killing, and in the filamentous...
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 , the spore killer element is found in many natural populations. In this study, we identify the gene responsible for spore killing in 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 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 , and we identify three subclades of , one where is fixed, another where 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. is not related to other known meiotic drive genes, and similar sequences are only found within 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.
Topics: Chromosomes, Fungal; Genetic Introgression; Neurospora; RNA Interference; Repetitive Sequences, Nucleic Acid
PubMed: 33875604
DOI: 10.1073/pnas.2026605118 -
Evolution; International Journal of... Nov 2022Evolution of Bateson-Dobzhansky-Muller (BDM) incompatibilities is thought to represent a key step in the formation of separate species. They are incompatible alleles...
Evolution of Bateson-Dobzhansky-Muller (BDM) incompatibilities is thought to represent a key step in the formation of separate species. They are incompatible alleles that have evolved in separate populations and are exposed in hybrid offspring as hybrid sterility or lethality. In this study, we reveal a previously unconsidered mechanism promoting the formation of BDM incompatibilities, meiotic drive. Theoretical studies have evaluated the role that meiotic drive, the phenomenon whereby selfish elements bias their transmission to progeny at ratios above 50:50, plays in speciation, and have mostly concluded that drive could not result in speciation on its own. Using the model fungus Neurospora, we demonstrate that the large meiotic drive haplotypes, Sk-2 and Sk-3, contain putative sexual incompatibilities. Our experiments revealed that although crosses between Neurospora intermedia and Neurospora metzenbergii produce viable progeny at appreciable rates, when strains of N. intermedia carry Sk-2 or Sk-3 the proportion of viable progeny drops substantially. Additionally, it appears that Sk-2 and Sk-3 have accumulated different incompatibility phenotypes, consistent with their independent evolutionary history. This research illustrates how meiotic drive can contribute to reproductive isolation between populations, and thereby speciation.
Topics: Neurospora; Reproductive Isolation; Alleles; Phenotype
PubMed: 36148939
DOI: 10.1111/evo.14630 -
The ISME Journal Mar 2019Trade-offs among traits influencing fitness are predicted by life history theory because resources allocated to one function are unavailable to another. Here we examine...
Trade-offs among traits influencing fitness are predicted by life history theory because resources allocated to one function are unavailable to another. Here we examine the relationship between two such traits, asexual reproduction and growth rate, in the filamentous fungus Neurospora crassa, where shared genetic and physiological factors and a source-sink energetic relationship between growth and reproduction may constrain the evolution of these traits. To test growth-reproduction relationships in this species, we independently selected on mycelial growth rate or asexual spore production in a heterogeneous lab-derived population and evaluated the response of the non-selected traits. Combined with phenotypes for the 20 wild strains used to produce the heterogeneous population and the genome-wide genotypes of 468 strains, these data show that growth and reproduction are highly plastic in N. crassa and do not trade off either among wild strains or after laboratory selection in two environments. Rather, we find no predictable growth-reproduction relationship in the environments tested, indicating an effective absence of genetic constraint between these traits. Our results suggest that growth rate and asexual reproduction may not respond predictably to environmental change and suggest that reliance on a single trait as a proxy for fitness in fungal studies may be inadvisable.
Topics: Genotype; Life History Traits; Neurospora crassa; Phenotype; Reproduction, Asexual
PubMed: 30413765
DOI: 10.1038/s41396-018-0294-7 -
Proceedings of the National Academy of... Dec 2002One can imagine a variety of mechanisms that should result in self-perpetuating biological states. It is generally assumed that cytosine methylation is propagated in... (Review)
Review
One can imagine a variety of mechanisms that should result in self-perpetuating biological states. It is generally assumed that cytosine methylation is propagated in eukaryotes by enzymes that specifically methylate hemimethylated symmetrical sites (e.g., (5')CpGGpC(5') or (5')CpNpGGpNpC(5')). Although there is wide support for this model, we and others have found examples of methylation that must be propagated by a different mechanism. Most methylated regions of the Neurospora genome that have been examined are products of repeat-induced point mutation, a premeiotic genome defense system that litters duplicated sequences with C.G to T.A mutations and typically leaves them methylated at remaining cytosines. In general, such relics of repeat-induced point mutation are capable of triggering methylation de novo. Nevertheless, some reflect a mechanism that can propagate heterogeneous methylation at nonsymmetrical sites. We propose that de novo and maintenance methylation are manifestations of a single mechanism in Neurospora, catalyzed by the DIM-2 DNA methyltransferase. The action of DIM-2 is controlled by the DIM-5 histone H3 Lys-9 methyltransferase, which in turn is influenced by other modifications of histone H3. DNA methylation indirectly recruits histone deacetylases, providing the framework of a self-reinforcing system that could result in propagation of DNA methylation and the associated silenced chromatin state.
Topics: DNA Methylation; DNA, Fungal; Histone Deacetylases; Histone Methyltransferases; Histone-Lysine N-Methyltransferase; Histones; Methyltransferases; Neurospora; Protein Methyltransferases
PubMed: 12189210
DOI: 10.1073/pnas.182427299 -
PLoS Genetics Nov 2023Lineage-specific genes (LSGs) have long been postulated to play roles in the establishment of genetic barriers to intercrossing and speciation. In the genome of...
Lineage-specific genes (LSGs) have long been postulated to play roles in the establishment of genetic barriers to intercrossing and speciation. In the genome of Neurospora crassa, most of the 670 Neurospora LSGs that are aggregated adjacent to the telomeres are clustered with 61% of the HET-domain genes, some of which regulate self-recognition and define vegetative incompatibility groups. In contrast, the LSG-encoding proteins possess few to no domains that would help to identify potential functional roles. Possible functional roles of LSGs were further assessed by performing transcriptomic profiling in genetic mutants and in response to environmental alterations, as well as examining gene knockouts for phenotypes. Among the 342 LSGs that are dynamically expressed during both asexual and sexual phases, 64% were detectable on unusual carbon sources such as furfural, a wildfire-produced chemical that is a strong inducer of sexual development, and the structurally-related furan 5-hydroxymethyl furfural (HMF). Expression of a significant portion of the LSGs was sensitive to light and temperature, factors that also regulate the switch from asexual to sexual reproduction. Furthermore, expression of the LSGs was significantly affected in the knockouts of adv-1 and pp-1 that regulate hyphal communication, and expression of more than one quarter of the LSGs was affected by perturbation of the mating locus. These observations encouraged further investigation of the roles of clustered lineage-specific and HET-domain genes in ecology and reproduction regulation in Neurospora, especially the regulation of the switch from the asexual growth to sexual reproduction, in response to dramatic environmental conditions changes.
Topics: Neurospora; Genes, Fungal; Neurospora crassa; Phenotype; Gene Expression Profiling; Reproduction; Fungal Proteins
PubMed: 37934795
DOI: 10.1371/journal.pgen.1011019 -
Microbiology and Molecular Biology... Mar 2004We present an analysis of over 1,100 of the approximately 10,000 predicted proteins encoded by the genome sequence of the filamentous fungus Neurospora crassa. Seven... (Review)
Review
We present an analysis of over 1,100 of the approximately 10,000 predicted proteins encoded by the genome sequence of the filamentous fungus Neurospora crassa. Seven major areas of Neurospora genomics and biology are covered. First, the basic features of the genome, including the automated assembly, gene calls, and global gene analyses are summarized. The second section covers components of the centromere and kinetochore complexes, chromatin assembly and modification, and transcription and translation initiation factors. The third area discusses genome defense mechanisms, including repeat induced point mutation, quelling and meiotic silencing, and DNA repair and recombination. In the fourth section, topics relevant to metabolism and transport include extracellular digestion; membrane transporters; aspects of carbon, sulfur, nitrogen, and lipid metabolism; the mitochondrion and energy metabolism; the proteasome; and protein glycosylation, secretion, and endocytosis. Environmental sensing is the focus of the fifth section with a treatment of two-component systems; GTP-binding proteins; mitogen-activated protein, p21-activated, and germinal center kinases; calcium signaling; protein phosphatases; photobiology; circadian rhythms; and heat shock and stress responses. The sixth area of analysis is growth and development; it encompasses cell wall synthesis, proteins important for hyphal polarity, cytoskeletal components, the cyclin/cyclin-dependent kinase machinery, macroconidiation, meiosis, and the sexual cycle. The seventh section covers topics relevant to animal and plant pathogenesis and human disease. The results demonstrate that a large proportion of Neurospora genes do not have homologues in the yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe. The group of unshared genes includes potential new targets for antifungals as well as loci implicated in human and plant physiology and disease.
Topics: Animals; Computational Biology; Fungal Proteins; Gene Expression Regulation, Fungal; Genome, Fungal; Humans; Mycoses; Neurospora crassa; Plant Diseases
PubMed: 15007097
DOI: 10.1128/MMBR.68.1.1-108.2004