scholarly journals 5'-Serial Analysis of Gene Expression studies reveal a transcriptomic switch during fruiting body development in Coprinopsis cinerea

BMC Genomics ◽  
2013 ◽  
Vol 14 (1) ◽  
pp. 195 ◽  
Author(s):  
Chi Keung Cheng ◽  
Chun Hang Au ◽  
Sarah K Wilke ◽  
Jason E Stajich ◽  
Miriam E Zolan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Fruiting Body ◽  
Coprinopsis Cinerea ◽  
Body Development ◽  
Expression Studies ◽  
Fruiting Body Development ◽  
Gene Expression Studies

scholarly journals Strand-Specific RNA-Seq Analyses of Fruiting Body Development in Coprinopsis cinerea

PLoS ONE ◽  
2015 ◽  
Vol 10 (10) ◽  
pp. e0141586 ◽  
Author(s):  
Hajime Muraguchi ◽  
Kiwamu Umezawa ◽  
Mai Niikura ◽  
Makoto Yoshida ◽  
Toshinori Kozaki ◽  
...  
Keyword(s):  
Fruiting Body ◽  
Rna Seq ◽  
Coprinopsis Cinerea ◽  
Body Development ◽  
Fruiting Body Development

scholarly journals Discovery of microRNA-like RNAs during early fruiting body development in the model mushroom Coprinopsis cinerea

PLoS ONE ◽  
2018 ◽  
Vol 13 (9) ◽  
pp. e0198234 ◽  
Author(s):  
Amy Yuet Ting Lau ◽  
Xuanjin Cheng ◽  
Chi Keung Cheng ◽  
Wenyan Nong ◽  
Man Kit Cheung ◽  
...  
Keyword(s):  
Fruiting Body ◽  
Coprinopsis Cinerea ◽  
Body Development ◽  
Fruiting Body Development

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

2013 ◽  
Vol 13 (1) ◽  
pp. 154-169 ◽  
Author(s):  
Zheng Wang ◽  
Francesc Lopez-Giraldez ◽  
Nina Lehr ◽  
Marta Farré ◽  
Ralph Common ◽  
...  
Keyword(s):  
Gene Expression ◽  
Neurospora Crassa ◽  
Sexual Development ◽  
Fruiting Body ◽  
Rna Silencing ◽  
Global Gene Expression ◽  
Gene Encoding ◽  
Content Type ◽  
Body Development ◽  
Fruiting Body Development

ABSTRACTFungi 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 inNeurospora crassa. We found that functionally unclassified proteins accounted for most upregulated genes, whereas downregulated genes were enriched for diverse functions. Moreover, genes associated with developmental traits exhibited stage-specific peaks of expression. Expression increased significantly across sexual development for mating type genemat a-1and format A-1specific pheromone precursorccg-4. In addition, expression of a gene encoding a protein similar to zinc finger,stc1, was highly upregulated early in perithecial development, and a strain with a knockout of this gene exhibited arrest at the same developmental stage. A similar expression pattern was observed for genes in RNA silencing and signaling pathways, and strains with knockouts of these genes were also arrested at stages of perithecial development that paralleled their peak in expression. The observed stage specificity allowed us to correlate expression upregulation and developmental progression and to identify regulators of sexual development. Bayesian networks inferred from our expression data revealed previously known and new putative interactions between RNA silencing genes and pathways. Overall, our analysis provides a fine-scale transcriptomic landscape and novel inferences regarding the control of the multistage development process of sexual crossing and fruiting body development inN. crassa.

scholarly journals Comparative Genomics and Transcriptomics To Analyze Fruiting Body Development in Filamentous Ascomycetes

Genetics ◽  
2019 ◽  
Vol 213 (4) ◽  
pp. 1545-1563 ◽  
Author(s):  
Ramona Lütkenhaus ◽  
Stefanie Traeger ◽  
Jan Breuer ◽  
Laia Carreté ◽  
Alan Kuo ◽  
...  
Keyword(s):  
Gene Expression ◽  
Fruiting Body ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Regulation Of Gene Expression ◽  
Comparative Transcriptomics ◽  
Fruiting Bodies ◽  
Body Development ◽  
Fruiting Body Development ◽  
Genes Encoding

Many filamentous ascomycetes develop three-dimensional fruiting bodies for production and dispersal of sexual spores. Fruiting bodies are among the most complex structures differentiated by ascomycetes; however, the molecular mechanisms underlying this process are insufficiently understood. Previous comparative transcriptomics analyses of fruiting body development in different ascomycetes suggested that there might be a core set of genes that are transcriptionally regulated in a similar manner across species. Conserved patterns of gene expression can be indicative of functional relevance, and therefore such a set of genes might constitute promising candidates for functional analyses. In this study, we have sequenced the genome of the Pezizomycete Ascodesmis nigricans, and performed comparative transcriptomics of developing fruiting bodies of this fungus, the Pezizomycete Pyronema confluens, and the Sordariomycete Sordaria macrospora. With only 27 Mb, the A. nigricans genome is the smallest Pezizomycete genome sequenced to date. Comparative transcriptomics indicated that gene expression patterns in developing fruiting bodies of the three species are more similar to each other than to nonsexual hyphae of the same species. An analysis of 83 genes that are upregulated only during fruiting body development in all three species revealed 23 genes encoding proteins with predicted roles in vesicle transport, the endomembrane system, or transport across membranes, and 13 genes encoding proteins with predicted roles in chromatin organization or the regulation of gene expression. Among four genes chosen for functional analysis by deletion in S. macrospora, three were shown to be involved in fruiting body formation, including two predicted chromatin modifier genes.

scholarly journals Nla18, a Key Regulatory Protein Required for Normal Growth and Development of Myxococcus xanthus

2006 ◽  
Vol 188 (5) ◽  
pp. 1733-1743 ◽  
Author(s):  
Michelle E. Diodati ◽  
Faisury Ossa ◽  
Nora B. Caberoy ◽  
Ivy R. Jose ◽  
Wataru Hiraiwa ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Fruiting Body ◽  
Vegetative Growth ◽  
Growth And Development ◽  
Expression Patterns ◽  
Myxococcus Xanthus ◽  
Body Development ◽  
Fruiting Body Development ◽  
Mutant Cells

ABSTRACT NtrC-like activators regulate the transcription of a wide variety of adaptive genes in bacteria. Previously, we demonstrated that a mutation in the ntrC-like activator gene nla18 causes defects in fruiting body development in Myxococcus xanthus. In this report, we describe the effect that nla18 inactivation has on gene expression patterns during development and vegetative growth. Gene expression in nla18 mutant cells is altered in the early stages of fruiting body development. Furthermore, nla18 mutant cells are defective for two of the earliest events in development, production of the intracellular starvation signal ppGpp and production of A-signal. Taken together, these results indicate that the developmental program in nla18 mutant cells goes awry very early. Inactivation of nla18 also causes a dramatic decrease in the vegetative growth rate of M. xanthus cells. DNA microarray analysis revealed that the vegetative expression patterns of more than 700 genes are altered in nla18 mutant cells. Genes coding for putative membrane and membrane-associated proteins are among the largest classes of genes whose expression is altered by nla18 inactivation. This result is supported by our findings that the profiles of membrane proteins isolated from vegetative nla18 mutant and wild-type cells are noticeably different. In addition to genes that code for putative membrane proteins, nla18 inactivation affects the expression of many genes that are likely to be important for protein synthesis and gene regulation. Our data are consistent with a model in which Nla18 controls vegetative growth and development by activating the expression of genes involved in gene regulation, translation, and membrane structure.

scholarly journals Discovery of microRNA-like RNAs during early fruiting body development in the model mushroom Coprinopsis cinerea

2018 ◽  
Author(s):  
Amy Yuet Ting Lau ◽  
Xuanjin Cheng ◽  
Chi Keung Cheng ◽  
Wenyan Nong ◽  
Man Kit Cheung ◽  
...  
Keyword(s):  
Fruiting Body ◽  
Developmental Stages ◽  
Expression Patterns ◽  
Regulation Of Gene Expression ◽  
Evolutionary Relationship ◽  
Mirna Biogenesis ◽  
Coprinopsis Cinerea ◽  
Stem Loop ◽  
Body Development ◽  
Fruiting Body Development

AbstractCoprinopsis cinerea is a model mushroom particularly suited to study fungal fruiting body development and the evolution of multicellularity in fungi. While microRNAs (miRNAs) are extensively studied in animals and plants for their essential roles in post-transcriptional regulation of gene expression, miRNAs in fungi are less well characterized and their potential roles in controlling mushroom development remain unknown. To identify miRNA-like RNAs (milRNAs) in C. cinerea and explore their expression patterns during the early developmental transition of mushroom development, small RNA libraries of vegetative mycelium and primordium were generated and putative milRNA candidates were identified following the standards of miRNA prediction in animals and plants. Two out of 22 novel predicted milRNAs, cci-milR-12c and cci-milR-13e-5p, were validated by northern blot and stem-loop reverse transcription real-time PCR. Cci-milR-12c was differentially expressed whereas the expression levels of cci-milR-13e-5p were similar in the two developmental stages. Target prediction of the validated milRNAs resulted in genes associated with fruiting body development, including pheromone, hydrophobin, cytochrome P450, and protein kinase. Besides, essential genes for miRNA biogenesis, including three coding for Dicer-like (DCL), two for Argonaute-like (AGO-like) and one for quelling deficient-2 (QDE-2) proteins, were identified in the C. cinerea genome. Phylogenetic analysis showed that the DCL and AGO-like proteins of C. cinerea were more closely related to those in other basidiomycetes and ascomycetes than to animals and plants. Taken together, our findings provided the first evidence of milRNAs in the model mushroom and their potential roles in regulating fruiting body development. Information on the evolutionary relationship of milRNA biogenesis proteins across kingdoms has also provided new insights into further functional and evolutionary studies of miRNAs.

scholarly journals Transcriptional profiling elucidates the essential role of glycogen synthase kinase 3 to fruiting body formation in Coprinopsis cinerea

2018 ◽  
Author(s):  
Kathy PoLam Chan ◽  
Jinhui Chang ◽  
Yichun Xie ◽  
Man Kit Cheung ◽  
Ka Lee Ma ◽  
...  
Keyword(s):  
Fruiting Body ◽  
Glycogen Synthase ◽  
Glycogen Synthase Kinase 3 ◽  
Coprinopsis Cinerea ◽  
Fruiting Body Formation ◽  
Body Formation ◽  
Body Development ◽  
Fruiting Body Development ◽  
Control Samples ◽  
Time Point

The functions of glycogen synthase kinase 3 (GSK3) have been well-studied in animal, plant and yeast. However, information on its roles in basidiomycetous fungi is still limited. In this study, we used the model mushroom Coprinopsis cinerea to study the characteristics of GSK3 in fruiting body development. Application of a GSK3 inhibitor Lithium chloride (LiCl) induced enhanced mycelial growth and inhibited fruiting body formation in C. cinerea. RNA-Seq of LiCl-treated C. cinerea resulted in a total of 14128 unigenes. There were 1210 differentially expressed genes (DEGs) between the LiCl-treated samples and control samples in the mycelium stage (first time point), whereas 1402 DEGs were detected at the stage when the control samples formed hyphal knots and the treatment samples were still in mycelium (second time point). Kyoto Encyclopedia of Genes and Genome (KEGG) pathway enrichment analysis of the DEGs revealed significant associations between the enhanced mycelium growth in LiCl treated C. cinerea and metabolism pathways such as “biosynthesis of secondary metabolite” and “biosynthesis of antibiotics”. In addition, DEGs involved in cellular process pathways, including “cell cycle-yeast” and “meiosis-yeast”, were identified in C. cinerea fruiting body formation suppressed by LiCl under favorable environmental conditions. Our findings suggest that GSK3 activity is essential for fruiting body formation as it affects the expression of fruiting body induction genes and genes in cellular processes. Further functional studies of GSK3 in basidiomycetous fungi may help understand the relationships between environmental signals and fruiting body development.

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