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PLOS Genetics: A Network of HMG-box Transcription Factors Regulates Sexual Cycle in the Fungus Podospora anserina

PLOS Genetics: A Network of HMG-box Transcription Factors Regulates Sexual Cycle in the Fungus Podospora anserina | The Mycology | Scoop.it
Podospora anserina, a coprophilous fungus, is used extensively as a model organism to address questions of sexual development and mating-type functions. Its mating-type locus contains three HMGB genes that encode transcription factors involved in fertilization and fruit-body development. We present the functional characterization of the remaining HMGB genes, which revealed that 11 of 12 HMGB genes were involved in sexual development. An analysis of the relationships between these genes uncovered a regulatory network governing the expression of mating-type genes. PaHMG5 is a key transcription factor that operates upstream of mating-type genes in this network. A homolog of PaHMG5 performs a similar function in the fission yeast Schizosaccharomyces pombe, which diverged from P. anserina 550 million years ago. The conservation of a regulatory circuit over such a prolonged timeframe is a striking exception to the general observation that sex developmental pathways are highly variable, even across closely related lineages. A module consisting of two HMGB transcription factors (Sry and Sox9) is a key regulator of sex determination in mammals. We propose that the module containing PaHMG5 and mating-type HMGB genes is the fungal counterpart of the mammalian module, revealing a commonality of sex regulation in animals and fungi.
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Fungal siderophore biosynthesis is partially localized in peroxisomes - Gründlinger - 2013 - Molecular Microbiology - Wiley Online Library

Fungal siderophore biosynthesis is partially localized in peroxisomes - Gründlinger - 2013 - Molecular Microbiology - Wiley Online Library | The Mycology | Scoop.it

Siderophores play a central role in iron metabolism and virulence of most fungi. Both Aspergillus fumigatus and Aspergillus nidulans excrete the siderophore triacetylfusarinine C (TAFC) for iron acquisition. In A. fumigatus, green fluorescence protein-tagging revealed peroxisomal localization of the TAFC biosynthetic enzymes SidI (mevalonyl-CoA ligase), SidH (mevalonyl-CoA hydratase) and SidF (anhydromevalonyl-CoA transferase), while elimination of the peroxisomal targeting signal (PTS) impaired both, peroxisomal SidH-targeting and TAFC biosynthesis. The analysis of A. nidulans mutants deficient in peroxisomal biogenesis, ATP import or protein import revealed that cytosolic mislocalization of one or two but, interestingly, not all three enzymes impairs TAFC production during iron starvation. The PTS motifs are conserved in fungal orthologues of SidF, SidH and SidI. In agreement with the evolutionary conservation of the partial peroxisomal compartmentalization of fungal siderophore biosynthesis, the SidI orthologue of coprogen-type siderophore-producing Neurospora crassa was confirmed to be peroxisomal. Taken together, this study identified and characterized a novel, evolutionary conserved metabolic function of peroxisomes.

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PLOS Genetics: The NDR Kinase Scaffold HYM1/MO25 Is Essential for MAK2 MAP Kinase Signaling in Neurospora crassa

PLOS Genetics: The NDR Kinase Scaffold HYM1/MO25 Is Essential for MAK2 MAP Kinase Signaling in Neurospora crassa | The Mycology | Scoop.it

Intercellular communication and cellular morphogenesis are essential for eukaryotic development. Our knowledge of molecules and mechanisms associated with these processes is, however, fragmentary. In particular, the molecular connection between signal sensing and regulation of cell polarity is poorly understood. Fungal hyphae share with neurons and pollen tubes the distinction of being amongst the most highly polarized cells in biology. The robust genetic tractability of filamentous fungi provides an unparalleled opportunity to determine common principles that underlie polarized growth and its regulation through cell communication. In Neurospora crassa, germinating spores mutually attract each other, establish physical contact through polarized tropic growth, and fuse. During this process, the cells rapidly alternate between two different physiological states, probably associated with signal delivery and response. Here, we show that the conserved scaffolding protein HYM1/MO25 interacts with the polarity and cell shape-regulating NDR kinase complex as well as a MAP kinase module, which is essential for cell communication during the tropic interaction. We propose that this dual use of a common regulator in both molecular complexes may represent an intriguing mechanism of linking the perception of external cues with the polarization machinery to coordinate communication and tropic growth of interacting cells.

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PLoS Genetics: Advances in Quantitative Trait Analysis in Yeast (and more)

PLoS Genetics: Advances in Quantitative Trait Analysis in Yeast (and more) | The Mycology | Scoop.it

If you are teaching a Genetics course you might like this article - it describes how yeast are being used to invesigate quantitative trait loci (QTL). It's a nice complement for discussions about QTLs in crop breeding. 

 

A few other articles of note in this issue of PLOS Genetics:

Arabidopsis G1/S phase control (http://tinyurl.com/8pgxzwm)

Epigenetic Remodeling of Meiotic Crossover Frequency in Arabidopsis (http://tinyurl.com/9abt23p)

Variance-Controlling Genes in Arabidopsis (http://tinyurl.com/9jgawu5)

Acquisition of Pluripotency from Cultured Arabidopsis Tissues (http://tinyurl.com/9vkafkg)

Genetic Basis of Pollinator Adaptation (http://tinyurl.com/9v7af98)


Via Mary Williams
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PLoS Genetics: The Aspergillus nidulans MAPK Module AnSte11-Ste50-Ste7-Fus3 Controls Development and Secondary Metabolism

PLoS Genetics: The Aspergillus nidulans MAPK Module AnSte11-Ste50-Ste7-Fus3 Controls Development and Secondary Metabolism | The Mycology | Scoop.it

Mitogen activated protein (MAP) kinase cascades are conserved from yeast to man to transmit an external signal to the nucleus and induce an appropriate cellular response. The yeast Fus3 MAP kinase module represents a textbook paradigm for signal transduction. The pathway is activated by external sexual hormones triggering several kinases that transmit the signal at the plasma membrane to Fus3. Phosphorylated Fus3 is released from the membrane-associated module, crosses the cytoplasm, and enters the nucleus to activate transcription factors for sexual development. We describe here the Fus3 MAPK pathway of a filamentous fungus that controls sexual development as well as secondary metabolism, which are coordinated processes in filamentous fungi. Aspergillus nidulans is able to release Fus3 as a complex from the membrane. Complexes of Fus3 can include two additional kinases and an adaptor protein, and these complexes can migrate from the membrane to the nuclear envelope where only A. nidulans Fus3 can enter the nucleus to control nuclear regulators. Revealing specific functions of cellular Aspergillus Fus3 complexes in signal transduction to control fungal development and secondary metabolism will be a fascinating future task.

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BMC Genomics | Abstract | Oomycete transcriptomics database: A resource for oomycete transcriptomes

Oomycete pathogens have attracted significant attention in recent years due to their economic impact. With improving sequencing technologies, large amounts of oomycete transcriptomics data are now available which have great biological utility. A known bottleneck with next generation sequencing data however lies with their analysis, interpretation, organization, storage and visualization. A number of efforts have been made in this respect resulting in development of a myriad of resources. Most of the existing NGS browsers work as standalone applications that need processed data to be uploaded to the browser locally for visualization. At the same time, several oomycete EST databases such as PFGD, ESTAP and SPC, are not available anymore, so there is an immediate need for a database resource that can store and disseminate this legacy information in addition to NGS data. Description Oomycetes Transcriptomics Database is an integrated transcriptome and EST data resource for oomycete pathogens. The database currently stores processed ABI SOLiD transcript sequences from Phytophthora sojae and its host soybean (P. sojae mycelia, healthy soybean and P. sojae-infected soybean) as well as Illumina transcript sequences from five Hyaloperonospora arabidopsidis libraries. In addition to those resources, it has also a complete set of Sanger EST sequences from P. sojae, P. infestans and H. arabidopsidis grown under various conditions. A web-based transcriptome browser was created for visualization of assembled transcripts, their mapping to the reference genome, expression profiling and depth of read coverage for particular locations on the genome. The transcriptome browser merges EST-derived contigs with NGS-derived assembled transcripts on the fly and displays the consensus. OTD possesses strong query features and the database interacts with the VBI Microbial Database as well as the Phytophthora Transcriptomics Database.
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ScienceDirect.com - Mycological Research - A higher-level phylogenetic classification of the Fungi

ScienceDirect.com - Mycological Research - A higher-level phylogenetic classification of the Fungi | The Mycology | Scoop.it

A comprehensive phylogenetic classification of the kingdom Fungi is proposed, with reference to recent molecular phylogenetic analyses, and with input from diverse members of the fungal taxonomic community. The classification includes 195 taxa, down to the level of order, of which 16 are described or validated here: Dikarya subkingdom nov.; Chytridiomycota, Neocallimastigomycota phyla nov.; Monoblepharidomycetes, Neocallimastigomycetes class. nov.; Eurotiomycetidae, Lecanoromycetidae, Mycocaliciomycetidae subclass. nov.; Acarosporales, Corticiales, Baeomycetales, Candelariales, Gloeophyllales, Melanosporales, Trechisporales, Umbilicariales ords. nov. The clade containing Ascomycota and Basidiomycota is classified as subkingdom Dikarya, reflecting the putative synapomorphy of dikaryotic hyphae. The most dramatic shifts in the classification relative to previous works concern the groups that have traditionally been included in the Chytridiomycota and Zygomycota. The Chytridiomycota is retained in a restricted sense, with Blastocladiomycota and Neocallimastigomycota representing segregate phyla of flagellated Fungi. Taxa traditionally placed in Zygomycota are distributed among Glomeromycota and several subphyla incertae sedis, including Mucoromycotina, Entomophthoromycotina, Kickxellomycotina, and Zoopagomycotina. Microsporidia are included in the Fungi, but no further subdivision of the group is proposed. Several genera of ‘basal’ Fungi of uncertain position are not placed in any higher taxa, including Basidiobolus, Caulochytrium, Olpidium, and Rozella.

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Molecular Cell - A Structurally Unique E2-Binding Domain Activates Ubiquitination by the ERAD E2, Ubc7p, through Multiple Mechanisms

Cue1p is an integral component of yeast endoplasmic reticulum (ER)-associated degradation (ERAD) ubiquitin ligase (E3) complexes. It tethers the ERAD ubiquitin-conjugating enzyme (E2), Ubc7p, to the ER and prevents its degradation, and also activates Ubc7p via unknown mechanisms. We have now determined the crystal structure of the Ubc7p-binding region (U7BR) of Cue1p with Ubc7p. The U7BR is a unique E2-binding domain that includes three α-helices that interact extensively with the “backside” of Ubc7p. Residues essential for E2 binding are also required for activation of Ubc7p and for ERAD. We establish that the U7BR stimulates both RING-independent and RING-dependent ubiquitin transfer from Ubc7p. Moreover, the U7BR enhances ubiquitin-activating enzyme (E1)-mediated charging of Ubc7p with ubiquitin. This demonstrates that an essential component of E3 complexes can simultaneously bind to E2 and enhance its loading with ubiquitin. These findings provide mechanistic insights into how ubiquitination can be stimulated.

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27th Fungal Genetics Conference, March 12-17, 2013, Asilomar, California

27th Fungal Genetics Conference, March 12-17, 2013, Asilomar, California | The Mycology | Scoop.it

The Fungal Genetics Policy Committee invites you to attend the 27th Fungal Genetics Conference, sponsored by the Genetics Society of America. The meeting is held every two years at the Asilomar Conference Grounds, Pacific Grove, California (near Monterey, California). The conference will open on Tuesday evening, March 12 with an Opening Mixer from 7:30 pm – 10:30 pm and end on Sunday, March 17. Regine Kahmann will present the Perkins/Metzenberg Lecture on Saturday, March 16 at 6:30 pm, followed by the banquet and closing party. 


Via Kamoun Lab @ TSL
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PLOS Pathogens: Antifungal Drug Discovery: Something Old and Something New

PLOS Pathogens: Antifungal Drug Discovery: Something Old and Something New | The Mycology | Scoop.it

An interesting theme shared by the new antifungal targets described above is that many target proteins with orthologs in human cells. Since the targets of most current antifungal drugs are unique to fungi, this represents a significant conceptual evolution that seeks to exploit the sometimes subtle differences in protein structure between host and pathogen to identify molecules with selectivity for the fungal protein and, thereby, acceptable toxicity toward the host. The viability of this approach is due to powerful recent advances in structural biology and medicinal chemistry. Finally, it is important to emphasize that new developments in drug discovery should not replace older approaches but be additive and, thus, be used to expand the tool box of methods available for application to an increasingly important research problem.

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PLoS Genetics: Reversal of PCNA Ubiquitylation by Ubp10 in Saccharomyces cerevisiae

PLoS Genetics: Reversal of PCNA Ubiquitylation by Ubp10 in Saccharomyces cerevisiae | The Mycology | Scoop.it

DNA damage is a major source of genome instability and cancer. A universal mechanism of DNA damage tolerance is based on translesion synthesis (TLS) by specialized low-fidelity DNA polymerases capable of replicating over DNA lesions during replication. Translesion synthesis requires the switch between replicative and TLS DNA polymerases, and this switching is controlled through the ubiquitylation of the proliferating-cell nuclear antigen (PCNA), a processivity factor for DNA synthesis. It is thought that DNA polymerase switching is a reversible process that has a favorable outcome for cells in the prevention of irreversible DNA replication forks collapse. However, the low-fidelity nature of TLS polymerases has unfavorable consequences like the increased risk of mutations opposite to DNA lesions. Here we identify Ubp10 as an enzyme controlling PCNA deubiquitylation in the model yeast S. cerevisiae. The identification of Ubp10 is a first step that will allow us to understand its biological significance and its potential role as part of a safeguard mechanism limiting the residence time of TLS DNA polymerases on replicating chromatin in eukaryotes.

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The distinct wiring between cell cycle regulation and the widely conserved Morphogenesis-Related (MOR) pathway in the fungus Ustilago maydis determines the morphological outcome

The MOR (Morphogenesis-related NDR kinase) pathway regulates morphogenesis in fungi. In spite of the high conservation of its components, impairing their functions results in highly divergent cellular responses depending on the fungal species. The reasons for such differences are unclear. Here we propose that the species-specific connections between the cell cycle regulation and the MOR pathway could be in part responsible for these divergences. We based our conclusion on the characterization of the MOR pathway in the fungus Ustilago maydis. Each gene that encodes proteins of this pathway in U. maydis was deleted. All mutants exhibited a constitutive hyperpolarized growth contrasting with the loss of polarity observed in other fungi. Using a conditional allele of the central NDR kinase Ukc1, we found that impairing MOR function resulted in an elongated G2 phase. This cell cycle delay appears to be the consequence of an increase in Cdk1 inhibitory phosphorylation. Strikingly, abrogation of the inhibitory Cdk1 phosphorylation prevents the hyperpolarized growth associated with MOR pathway depletion. We found that enlarged G2 phase resulted in higher levels of expression of crk1, a conserved kinase that promotes polar growth in U. maydis. Deletion of crk1 also abolished the dramatic activation of polar growth in cells lacking MOR pathway. Taken together, our results suggest that Cdk1 inhibitory phosphorylation may act as an integrator of signaling cascades regulating fungal morphogenesis and that the distinct morphological response observed in U. maydis upon impairment of the MOR pathway could be due to a cell cycle deregulation.

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Exploring pathogenic mechanisms of Botrytis cinerea secretome under different ambient pH based on comparative proteomic analysis - Journal of Proteome Research (ACS Publications)

Botrytis cinerea causes gray mould rot on over 200 plant species worldwide, resulting in great economic loss every year. Cooperation of proteins secreted by B. cinerea plays an important role in its successful infection to host plants. The ambient pH, as one of the most important environmental parameters, can regulate expression of secreted proteins in various fungal pathogens. In the present study, we mainly investigated the effect of ambient pH on secretome of B. cinerea strain B05.10 with a comparative proteomic method based on 2-DE. Distinct differences in secretome of B. cinerea were found between pH 4 and 6 treatments, and 47 differential spots, corresponding to 21 unique proteins, were identified using MALDI-TOF/TOF. At pH 4, more proteins related to proteolysis were induced, whereas, most of up-accumulated proteins were cell wall degrading enzymes at pH 6. Analysis of gene expression using quantitative real-time PCR suggests that production of most of these proteins was regulated at the level of transcription. These findings indicate that B. cinerea can adjust protein profile of secretome responding to different ambient pH values, and which provide evidence to deeply understand the complicated infecting mechanisms of B. cinerea on a wide range of plant hosts.

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PLoS Genetics: Gene Conversion Occurs within the Mating-Type Locus of Cryptococcus neoformans during Sexual Reproduction

PLoS Genetics: Gene Conversion Occurs within the Mating-Type Locus of Cryptococcus neoformans during Sexual Reproduction | The Mycology | Scoop.it
PLoS Genetics is an open-access...
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