Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

An evolutionarily ancient transcription factor drives spore morphogenesis in mushroom-forming fungi

ABSTRACT: Sporulation is the most widespread means of reproduction and dispersal in fungi and, at the same time, an industrially important trait in crop mushrooms. In the Basidiomycota, sexual spores are produced on specialized cells known as basidia, from which they are forcibly discharged with the highest known acceleration in nature. However, the genetics of sporulation remains poorly known. Here, we identify a new, highly conserved transcription factor, sporulation-related regulator 1 (srr1), and systematically address the genetics of spore formation for the first time in the Basidiomycota. We show that Srr1 regulates postmeiotic spore morphogenesis, but not other aspects of fruiting body development or meiosis, and its role is conserved in the phylogenetically distant, but industrially important, Pleurotus spp. (oyster mushrooms). We used RNA sequencing to understand genes directly or indirectly regulated by Srr1 and identified a strongly supported binding motif for the protein. Using an inferred network of putative target genes regulated by Srr1 and comparative genomics, we identified genes lost in secondarily non-ballistosporic taxa, including a novel sporulation-specific chitinase gene. Overall, our study offers systematic insights into the genetics of spore morphogenesis in the Basidiomycota.

ORGANISM(S): Coprinopsis cinerea

PROVIDER: GSE269820 | GEO | 2025/02/26

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Induced homogenous sporulation by kinA-overexpression leads to altered Bacillus subtilis spore proteomes and spore properties

Project description:Summary To facilitate more accurate spore proteomic analysis, the current study focuses on inducing homogeneous sporulation by overexpressing kinA and assesses the effect of sporulation synchronization on spore resistance, structures, the germination behavior at single-spore level and the proteome. The results indicate that, in our set up, the synchronized sporulation by overexpressing kinA can generate a spore yield of 70% within 8 hours. The procedure increases spore wet heat resistance and thickness of the spore coat and cortex layers, whilst delaying the time to spore phase-darkening and burst after addition of germinant. The proteome analysis reveals that the upregulated proteins in the kinA induced spores, compared to spores without kinA induction as well as the wildtype spores, are mostly involved in spore formation. The downregulated proteins mostly belong to the categories of coping with stress, carbon and nitrogen metabolism, as well as regulation of sporulation. Thus, while kinA overexpression enhances sporulation synchronicity it also has profound effects on the central equilibrium of spore formation and spore germination through modulation of the spore molecular composition and stress resistance physiology.

2020-04-28 | MSV000085346 | MassIVE

Sporulation in yeast

Project description:Diploid cells of budding yeast produce haploid cells through the developmental program of sporulation, which consists of meiosis and spore morphogenesis. DNA microarrays containing nearly every yeast gene were used to assay changes in gene expression during sporulation. At least seven distinct temporal patterns of induction were observed. The transcription factor Ndt80 appeared to be important for induction of a large group of genes at the end of meiotic prophase. Consensus sequences known or proposed to be responsible for temporal regulation could be identified solely from analysis of sequences of coordinately expressed genes. The temporal expression pattern provided clues to potential functions of hundreds of previously uncharacterized genes, some of which have vertebrate homologs that may function during gametogenesis. This study is described in more detail in Chu S, et al. 1998. Science 282:699-705 Keywords: time-course

2002-02-12 | GSE27 | GEO

Alanine and glutamate catabolism collaborate to ensure the success of sporulation in Bacillus subtilis

Project description:Sporulation as a typical bacterial differentiation process has been studied for decades. However, two crucial aspects of sporulation, (i) the energy sources supporting the process, and (ii) the maintenance of spore dormancy throughout sporulation, are scarcely explored. Here, we reported the crucial role of RocG-mediated glutamate catabolism in regulating mother cell lysis, a critical step for successful sporulation of Bacillus subtilis, likely by providing energy metabolite ATP. Notably, rocG overexpression resulted in an excessive ATP accumulation in sporulating cells, leading to adverse effects on future spore properties, e.g. increased germination efficiency, reduced DPA content, and lowered heat resistance. Additionally, we revealed that Ald-mediated alanine metabolism was highly related to the inhibition of premature germination and the maintenance of spore dormancy during sporulation, which might be achieved by decreasing the typical germinant L-alanine concentration in sporulating environment. Our data inferred that sporulation of B. subtilis was a highly orchestrated biological process requiring a delicate balance in diverse metabolic pathways, hence ensuring both the completion of sporulation and production of high-quality spores.

2024-06-07 | PXD052983 |

Analysis of the messenger RNAs in Spores of Bacillus subtilis

Project description:Using RNA-seq, we cataloged messenger RNAs in highly purified dormant Bacillus subtilis spores prepared either on plates or in liquid. Almost all of the most abundant spore mRNAs are encoded by genes expressed only in the developing spore late in sporulation under control of the forespore-specific RNA polymerase sigma factor, sG. Given the levels of the ~40 most abundant mRNAs in dormant spores, we calculated the great majority of the low abundance mRNAs can be present in only a small fraction of the spore population.

2019-04-01 | GSE125530 | GEO

Time course of manganese treatment in LB

Project description:The SOS response to DNA damage in bacteria is a well-known component of the complex transcriptional responses to genotoxic environmental stresses such as exposure to reactive oxygen species, alkylating agents, and many of the antibiotics targeting DNA replication. However, bacteria such as Bacillus subtilis also respond to conditions that perturb DNA replication via a transcriptional response mediated by the replication initiation protein DnaA. In addition to regulating the initiation of DNA replication, DnaA directly regulates the transcription of specific genes. Conditions that perturb DNA replication can trigger the accumulation of active DnaA, activating or repressing transcription of genes in the DnaA regulon. We report here that simply growing B. subtilis in LB medium altered DnaA-dependent gene expression in a manner consistent with the accumulation of active DnaA, and that this was part of a general transcriptional response to manganese limitation. The SOS response to DNA damage was not induced under these conditions. One of the genes positively regulated by DnaA in Bacillus subtilis encodes a protein that inhibits the initiation of sporulation, Sda. Sda expression was induced as cells entered stationary phase in LB but not in LB supplemented with manganese, and induction of Sda inhibited sporulation-specific gene expression and the onset of spore morphogenesis. In the absence of Sda, manganese-limited cells initiated spore development but failed to form mature spores. These data highlight that DnaA-dependent gene expression may influence the response of bacteria to a range of environmental conditions, including conditions that are not obviously associated with genotoxic stress.

2010-06-12 | GSE22296 | GEO

High resolution time-lapse proteomic analysis of sporulation

Project description:Bacillus subtilis vegetative cells switch to sporulation upon nutrient limitation. To investigate the proteome changeover during sporulation, a time-lapse proteomic analysis was performed in a cell population that was induced to sporulate synchronously. Here, we are the first to comprehensively investigate the changeover of sporulation regulatory proteins, coat proteins and other proteins involved in sporulation and spore biogenesis. Protein co-expression analysis revealed four co-expressed modules. Modules brown and green are upregulated during sporulation and are annotated as associated with sporulation. Module blue, which is negatively correlated with modules brown and green, comprised ribosomal and metabolic proteins, and module yellow is co-expressed with module blue and modules brown & green. Notably, several proteins not belonging to any of the known transcription regulons were identified as co-expressed with modules brown and green. We speculate that they may also play roles during sporulation. Finally, amounts of some coat proteins, for example morphogenetic coat proteins, decreased late in sporulation. While we speculate on their possible role in guiding or helping assembly of other coat proteins, after which they can be disposed of, such a hypothesis remains to be experimentally addressed.

2021-04-03 | MSV000087154 | MassIVE

Embedding a ribonuclease in the spore crust couples gene expression to spore development in Bacillus subtilis

Project description:Faced with nutritional stress, some bacteria form endospores that can survive extreme conditions for long periods of time; yet the function of many proteins expressed during sporulation remains a mystery. We show that one such protein, KapD, is a 3 prime exoribonuclease expressed under control of the mother cell-specific transcription factors SigE and SigK in B. subtilis. KapD assembles dynamically over the spore surface through a direct interaction with the major crust protein CotY. KapD catalytic activity is required for the normal adhesiveness of spore surface layers. We identify the sigK mRNA as a key substrate for KapD and show that its sequestration by CotY controls the stability of the sigK transcript. SigK is controlled through excision of a prophage-like element, transcriptional regulation, and removal of an inhibitory pro-sequence. We reveal a fourth, posttranscriptional layer of control of sigK expression that couples late-stage gene expression in the mother cell to spore morphogenesis.

2024-12-10 | MSV000096627 | MassIVE

Gene expression during Bacillus subtilis spore germination and outgrowth (t=0-100)

Project description:Bacillus subtilis forms dormant spores upon nutrient depletion. Under favorable environmental conditions, the spore breaks its dormancy and resumes growth in a process called spore germination and outgrowth. To elucidate the physiological processes that occur during the transition of the dormant spore to an actively growing vegetative cell, we studied this process in a time-dependent manner by a combination of microscopy, analysis of extracellular metabolites and a genome-wide analysis of transcription. The results indicate the presence of abundant levels of late sporulation transcripts in dormant spores. In addition, results suggest the existence of a complex and well-regulated spore outgrowth program, involving the temporal expression of at least 30 % of the B. subtilis genome. Keywords: time course, spore outgrowth

2007-03-27 | GSE6865 | GEO

Genotyping of yeast spores to map meiotic crossovers and non-crossovers across the yeast genome

Project description:To map meiotic crossovers and noncrossovers across the yeast genome, we genotyped the four spores of 51 tetrads arising from sporulation of a YJM789/S96 hybrid strain. Sporulation was induced, tetrads were dissected, and genomic DNA from each spore was hybridized to microarrays, one array per spore. 12 YJM789 and 13 S96 hybridizations were also performed as a reference for genotyping. To analyze recombination mutants, we also hybridized DNA from 5 tetrads arising from a YJM789/S96 hybrid strain homozygous for a MSH4 deletion, and from 20 spores (6 dyads and 8 single spores) arising from a hybrid homozygous for a MMS4 deletion.

2009-08-04 | E-TABM-470 | biostudies-arrayexpress

RNA-seq of four Bacillus subtilis mutants during sporulation

Project description:Endospore (hereafter called spore) is a dormant, tough, and non-reproductive structure produced in a lack of nutrients by certain species of bacteria from the Firmicute phylum. Sporulation is tightly linked to cell cycle and involving by temporal and spatial regulation of hundreds genes. It has been suggested more than 500 genes are contributed to sporulation in B. subtilis, and there are certainly more. In our study, we identified four new sporulation genes and their mutants exhibited sporulation abnormal. RNA-seq of mutants compared to wild type during sporulation will reveal the regulation of sporulation related genes in the four mutants, and therefore shed the light to the functional role of the four new sporulation genes.

2020-03-18 | E-MTAB-8124 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data