Global Gene Expression and Focused Knockout Analysis Reveals Genes Associated with Fungal Fruiting Body Development in Neurospora crassa

@article{Wang2013GlobalGE,
  title={Global Gene Expression and Focused Knockout Analysis Reveals Genes Associated with Fungal Fruiting Body Development in Neurospora crassa},
  author={Z. Wang and F. L{\'o}pez-Gir{\'a}ldez and Nina A. Lehr and M. Farr{\'e} and R. Common and F. Trail and J. Townsend},
  journal={Eukaryotic Cell},
  year={2013},
  volume={13},
  pages={154 - 169}
}
ABSTRACT Fungi can serve as highly tractable models for understanding genetic basis of sexual development in multicellular organisms. Applying a reverse-genetic approach to advance such a model, we used random and multitargeted primers to assay gene expression across perithecial development in Neurospora crassa. We found that functionally unclassified proteins accounted for most upregulated genes, whereas downregulated genes were enriched for diverse functions. Moreover, genes associated with… Expand
The ancestral levels of transcription and the evolution of sexual phenotypes in filamentous fungi
TLDR
This work examined differences in fruiting body morphology of five filamentous fungi in the Sordariomycetes, culturing them in a common garden environment and profiling genome-wide gene expression at five developmental stages, and reconstructed ancestral gene expression phenotypes, identifying genes with the largest evolved increases across development. Expand
Functional Profiling of Transcription Factor Genes in Neurospora crassa
TLDR
Analysis of available mRNA expression data for a time course of sexual development revealed mutants with sexual phenotypes that correlate with transcription factor transcript abundance in wild type, which implicated cryptic roles in sexual development for several cotranscribed transcription factor genes. Expand
Gene Expression Differences among Three Neurospora Species Reveal Genes Required for Sexual Reproduction in Neurospora crassa
TLDR
The results provide insight into the genetic basis of Neurospora sexual reproduction, which is also of great importance with regard to other multicellular ascomycetes, including perithecium-forming pathogens, such as Claviceps purpurea, Ophiostoma ulmi, and Glomerella graminicola. Expand
Neurospora crassa Female Development Requires the PACC and Other Signal Transduction Pathways, Transcription Factors, Chromatin Remodeling, Cell-To-Cell Fusion, and Autophagy
TLDR
Perithecia grafting experiments demonstrate that the autophagy genes and the cell-to-cell fusion genes (theMAK-1 and MAK-2 pathway genes) are needed for the mobilization and movement of nutrients from an established vegetative hyphal network into the developing protoperithecium. Expand
The Fast-Evolving phy-2 Gene Modulates Sexual Development in Response to Light in the Model Fungus Neurospora crassa
TLDR
Investigation of the evolution of red light sensors in ascomycetes and confirmed—using the model fungus Neurospora crassa—their roles in modulating the asexual-sexual reproduction balance in fungi, suggesting that further study of the function of phytochromes in fungi is critical to reveal the genetic basis of the a sexual-sexual switch responsible for fungal growth and distribution. Expand
Integrative Activity of Mating Loci, Environmentally Responsive Genes, and Secondary Metabolism Pathways during Sexual Development of Chaetomium globosum
TLDR
Bayesian networks indicated that gene interactions during sexual development have diverged in concert with the capacities both to reproduce asexually and to live a self-compatible versus self-incompatible life cycle, shifting the hierarchical roles of genes associated with conidiation and heterokaryon incompatibility in N. crassa and C. globosum. Expand
Using evolutionary genomics, transcriptomics, and systems biology to reveal gene networks underlying fungal development
TLDR
Recent advances in genome-wide analysis performed in representative multicellular fungal models and non-models have greatly improved upon the traditional reductive approaches in fungal evo-devo research by providing clues for focused knockout strategies. Expand
Clustering analysis of large-scale phenotypic data in the model filamentous fungus Neurospora crassa
TLDR
The results demonstrate that clustering analysis of phenotypes is a promising tool for generating new hypotheses regarding involvement of genes in cellular pathways in N. crassa and should be applicable to other filamentous fungi, including saprobes and pathogens. Expand
Dynamics of transcriptome evolution in the model eukaryote Neurospora
TLDR
It is hypothesized that rapid interspecies transcriptome evolution is shifting the mating types of Neurospora towards distinct female and male phenotypes, that is, sexual dimorphism. Expand
A-to-I RNA editing is developmentally regulated and generally adaptive for sexual reproduction in Neurospora crassa
TLDR
This study comprehensively analyzed A-to-I editing in N. crassa and showed that RNA editing is stage-specific and generally adaptive, and may be functionally related to repeat induced point mutation and meiotic silencing by unpaired DNA. Expand
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 91 REFERENCES
Sex-specific gene expression during asexual development of Neurospora crassa.
TLDR
Significant differences in overall gene expression between mating types across clonal development, especially at late development stages are observed, and significant up-regulation of expression was observed for many late light-responsive genes at late asexual development stages. Expand
Genome-Wide Gene Expression Profiling of Fertilization Competent Mycelium in Opposite Mating Types in the Heterothallic Fungus Podospora anserina
TLDR
This study represents the first comprehensive genome-wide analysis of mating-type direct and indirect target genes in a heterothallic filamentous fungus. Expand
Cross-species microarray hybridization to identify developmentally regulated genes in the filamentous fungus Sordaria macrospora
TLDR
Analysis of gene expression in double mutants revealed a complex network of interaction between the pro gene products, including genes encoding the pheromone precursors, enzymes involved in melanin biosynthesis and a lectin-like protein. Expand
Analyses of expressed sequence tags in Neurospora reveal rapid evolution of genes associated with the early stages of sexual reproduction in fungi
TLDR
This study represents a novel finding of a genome-wide pattern of rapid evolution of sex-associated genes in the fungal kingdom, and provides a list of candidate genes important for reproductive isolation in Neurospora. Expand
Gene expression shifts during perithecium development in Gibberella zeae (anamorph Fusarium graminearum), with particular emphasis on ion transport proteins.
TLDR
This is the first whole-genome analysis of differential transcript accumulation during sexual development in a filamentous fungus, and analysis of the 162 predicted ion transporter genes is reported in detail. Expand
A high-throughput gene knockout procedure for Neurospora reveals functions for multiple transcription factors
TLDR
This study describes a method for rapidly creating knockout mutants in which it makes use of yeast recombinational cloning, Neurospora mutant strains deficient in nonhomologous end-joining DNA repair, custom-written software tools, and robotics. Expand
Differential impact of nutrition on developmental and metabolic gene expression during fruiting body development in Neurospora crassa.
TLDR
Interestingly, metabolic effects of the media were also large in magnitude during late perithecial development, at which stage the lower expression in CA presumably reflected the continued intake of diverse complex initial compounds, diminishing the need for expression of anabolic pathways. Expand
Microarray analysis of transcript accumulation during perithecium development in the filamentous fungus Gibberella zeae (anamorph Fusarium graminearum)
TLDR
This study provides clear evidence that the sexual development in fungi is a complex, multigenic process and identifies genes involved in sexual development of this agriculturally important fungus. Expand
Multi-targeted priming for genome-wide gene expression assays
TLDR
Examining the response of Saccharomyces cerevisiae to nitrogen deficiency and profiling Neurospora crassa early sexual development, it is demonstrated that using multi-targeted primers in reverse transcription led to superior performance of microarray profiling and next-generation RNA tag sequencing. Expand
The genome sequence of the filamentous fungus Neurospora crassa
TLDR
A high-quality draft sequence of the N. crassa genome is reported, suggesting that RIP has had a profound impact on genome evolution, greatly slowing the creation of new genes through genomic duplication and resulting in a genome with an unusually low proportion of closely related genes. Expand
...
1
2
3
4
5
...