scholarly journals Genome Wide Analysis Reveals the Role of VadA in Stress Response, Germination, and Sterigmatocystin Production in Aspergillus nidulans Conidia

2020 ◽  
Vol 8 (9) ◽  
pp. 1319 ◽  
Author(s):  
Ye-Eun Son ◽  
Hee-Soo Park
Keyword(s):  
Stress Response ◽  
Secondary Metabolism ◽  
Aspergillus Nidulans ◽  
Gene Clusters ◽  
Tube Formation ◽  
Spore Viability ◽  
Genetic Changes ◽  
Genome Wide ◽  
Trehalose Biosynthesis

In the Aspergillus species, conidia are asexual spores that are infectious particles responsible for propagation. Conidia contain various mycotoxins that can have detrimental effects in humans. Previous study demonstrated that VadA is required for fungal development and spore viability in the model fungus Aspergillus nidulans. In the present study, vadA transcriptomic analysis revealed that VadA affects the mRNA expression of a variety of genes in A. nidulans conidia. The genes that were primarily affected in conidia were associated with trehalose biosynthesis, cell-wall integrity, stress response, and secondary metabolism. Genetic changes caused by deletion of vadA were related to phenotypes of the vadA deletion mutant conidia. The deletion of vadA resulted in increased conidial sensitivity against ultraviolet stress and induced germ tube formation in the presence and absence of glucose. In addition, most genes in the secondary metabolism gene clusters of sterigmatocystin, asperfuranone, monodictyphenone, and asperthecin were upregulated in the mutant conidia with vadA deletion. The deletion of vadA led to an increase in the amount of sterigmatocystin in the conidia, suggesting that VadA is essential for the repression of sterigmatocystin production in conidia. These results suggest that VadA coordinates conidia maturation, stress response, and secondary metabolism in A. nidulans conidia.

scholarly journals The velvet Regulator VosA Governs Survival and Secondary Metabolism of Sexual Spores in Aspergillus nidulans

Genes ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 103 ◽  
Author(s):  
Min-Ju Kim ◽  
Mi-Kyung Lee ◽  
Huy Quang Pham ◽  
Myeong Ju Gu ◽  
Bohan Zhu ◽  
...  
Keyword(s):  
Aspergillus Nidulans ◽  
Gene Clusters ◽  
Primary Metabolism ◽  
Mrna Levels ◽  
Rna Seq ◽  
Spore Viability ◽  
Oxidative Stresses ◽  
Genome Wide ◽  
Elevated Expression ◽  
Trehalose Biosynthesis

The velvet regulator VosA plays a pivotal role in asexual sporulation in the model filamentous fungus Aspergillus nidulans. In the present study, we characterize the roles of VosA in sexual spores (ascospores) in A. nidulans. During ascospore maturation, the deletion of vosA causes a rapid decrease in spore viability. The absence of vosA also results in a lack of trehalose biogenesis and decreased tolerance of ascospores to thermal and oxidative stresses. RNA-seq-based genome-wide expression analysis demonstrated that the loss of vosA leads to elevated expression of sterigmatocystin (ST) biosynthetic genes and a slight increase in ST production in ascospores. Moreover, the deletion of vosA causes upregulation of additional gene clusters associated with the biosynthesis of other secondary metabolites, including asperthecin, microperfuranone, and monodictyphenone. On the other hand, the lack of vosA results in the downregulation of various genes involved in primary metabolism. In addition, vosA deletion alters mRNA levels of genes associated with the cell wall integrity and trehalose biosynthesis. Overall, these results demonstrate that the velvet regulator VosA plays a key role in the maturation and the cellular and metabolic integrity of sexual spores in A. nidulans.

scholarly journals HbxB Is a Key Regulator for Stress Response and β-Glucan Biogenesis in Aspergillus nidulans

2021 ◽  
Vol 9 (1) ◽  
pp. 144
Author(s):  
Sung-Hun Son ◽  
Mi-Kyung Lee ◽  
Ye-Eun Son ◽  
Hee-Soo Park
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Aspergillus Nidulans ◽  
Deletion Mutant ◽  
Phenotypic Analysis ◽  
Spore Viability ◽  
Fungal Development ◽  
Expression Of Genes ◽  
Trehalose Biosynthesis

Homeobox transcription factors are conserved in eukaryotes and act as multi-functional transcription factors in filamentous fungi. Previously, it was demonstrated that HbxB governs fungal development and spore viability in Aspergillus nidulans. Here, the role of HbxB in A. nidulans was further characterized. RNA-sequencing revealed that HbxB affects the transcriptomic levels of genes associated with trehalose biosynthesis and response to thermal, oxidative, and radiation stresses in asexual spores called conidia. A phenotypic analysis found that hbxB deletion mutant conidia were more sensitive to ultraviolet stress. The loss of hbxB increased the mRNA expression of genes associated with β-glucan degradation and decreased the amount of β-glucan in conidia. In addition, hbxB deletion affected the expression of the sterigmatocystin gene cluster and the amount of sterigmatocystin. Overall, these results indicated that HbxB is a key transcription factor regulating trehalose biosynthesis, stress tolerance, β-glucan degradation, and sterigmatocystin production in A.nidulans conidia.

scholarly journals Diversity of Secondary Metabolism in Aspergillus nidulans Clinical Isolates

mSphere ◽  
2020 ◽  
Vol 5 (2) ◽  
Author(s):  
M. T. Drott ◽  
R. W. Bastos ◽  
A. Rokas ◽  
L. N. A. Ries ◽  
T. Gabaldón ◽  
...  
Keyword(s):  
Secondary Metabolism ◽  
Aspergillus Nidulans ◽  
Reference Genome ◽  
Genetic Model ◽  
High Resolution Mass Spectrometry ◽  
Gene Clusters ◽  
Clinical Isolates ◽  
Biosynthetic Gene ◽  
Content Type ◽  
Natural Diversity

ABSTRACT The filamentous fungus Aspergillus nidulans has been a primary workhorse used to understand fungal genetics. Much of this work has focused on elucidating the genetics of biosynthetic gene clusters (BGCs) and the secondary metabolites (SMs) they produce. SMs are both niche defining in fungi and of great economic importance to humans. Despite the focus on A. nidulans, very little is known about the natural diversity in secondary metabolism within this species. We determined the BGC content and looked for evolutionary patterns in BGCs from whole-genome sequences of two clinical isolates and the A4 reference genome of A. nidulans. Differences in BGC content were used to explain SM profiles determined using liquid chromatography–high-resolution mass spectrometry. We found that in addition to genetic variation of BGCs contained by all isolates, nine BGCs varied by presence/absence. We discovered the viridicatumtoxin BGC in A. nidulans and suggest that this BGC has undergone a horizontal gene transfer from the Aspergillus section Nigri lineage into Penicillium sometime after the sections Nigri and Nidulantes diverged. We identified the production of viridicatumtoxin and several other compounds previously not known to be produced by A. nidulans. One isolate showed a lack of sterigmatocystin production even though it contained an apparently intact sterigmatocystin BGC, raising questions about other genes and processes known to regulate this BGC. Altogether, our work uncovers a large degree of intraspecies diversity in BGC and SM production in this genetic model species and offers new avenues to understand the evolution and regulation of secondary metabolism. IMPORTANCE Much of what we know about the genetics underlying secondary metabolite (SM) production and the function of SMs in the model fungus Aspergillus nidulans comes from a single reference genome. A growing body of research indicates the importance of biosynthetic gene cluster (BGC) and SM diversity within a species. However, there is no information about the natural diversity of secondary metabolism in A. nidulans. We discovered six novel clusters that contribute to the considerable variation in both BGC content and SM production within A. nidulans. We characterize a diverse set of mutations and emphasize how findings of single nucleotide polymorphisms (SNPs), deletions, and differences in evolutionary history encompass much of the variation observed in nonmodel systems. Our results emphasize that A. nidulans may also be a strong model to use within-species diversity to elucidate regulatory cross talk, fungal ecology, and drug discovery systems.

scholarly journals EvolClust: automated inference of evolutionary conserved gene clusters in eukaryotes

2019 ◽  
Author(s):  
Marina Marcet-Houben ◽  
Toni Gabaldón
Keyword(s):  
Secondary Metabolism ◽  
Computational Prediction ◽  
Gene Clusters ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Automated Inference ◽  
Or Gene ◽  
Conserved Gene ◽  
Genome Comparisons

Abstract Motivation The evolution and role of gene clusters in eukaryotes is poorly understood. Currently, most studies and computational prediction programs limit their focus to specific types of clusters, such as those involved in secondary metabolism. Results We present EvolClust, a python-based tool for the inference of evolutionary conserved gene clusters from genome comparisons, independently of the function or gene composition of the cluster. EvolClust predicts conserved gene clusters from pairwise genome comparisons and infers families of related clusters from multiple (all versus all) genome comparisons. Availability and implementation https://github.com/Gabaldonlab/EvolClust/. Supplementary information Supplementary data are available at Bioinformatics online.

Proteome analysis of the farnesol-induced stress response in Aspergillus nidulans—The role of a putative dehydrin

2012 ◽  
Vol 75 (13) ◽  
pp. 4038-4049 ◽  
Author(s):  
Dirk Wartenberg ◽  
Martin Vödisch ◽  
Olaf Kniemeyer ◽  
Daniela Albrecht-Eckardt ◽  
Kirstin Scherlach ◽  
...  
Keyword(s):  
Stress Response ◽  
Aspergillus Nidulans ◽  
Proteome Analysis ◽  
Induced Stress

scholarly journals Legionellashows a diverse secondary metabolism dependent on a broad spectrum Sfp-type phosphopantetheinyl transferase

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2720 ◽  
Author(s):  
Nicholas J. Tobias ◽  
Tilman Ahrendt ◽  
Ursula Schell ◽  
Melissa Miltenberger ◽  
Hubert Hilbi ◽  
...  
Keyword(s):  
Secondary Metabolism ◽  
Communication Systems ◽  
Fatty Acid Biosynthesis ◽  
Cell Communication ◽  
Gene Clusters ◽  
Phosphopantetheinyl Transferase ◽  
Biosynthetic Gene Clusters ◽  
Legionnaires Disease ◽  
Huge Variety

Several members of the genusLegionellacause Legionnaires’ disease, a potentially debilitating form of pneumonia. Studies frequently focus on the abundant number of virulence factors present in this genus. However, what is often overlooked is the role of secondary metabolites fromLegionella. Following whole genome sequencing, we assembled and annotated theLegionella parisiensisDSM 19216 genome. Together with 14 other members of theLegionella, we performed comparative genomics and analysed the secondary metabolite potential of each strain. We found thatLegionellacontains a huge variety of biosynthetic gene clusters (BGCs) that are potentially making a significant number of novel natural products with undefined function. Surprisingly, only a single Sfp-like phosphopantetheinyl transferase is found in allLegionellastrains analyzed that might be responsible for the activation of all carrier proteins in primary (fatty acid biosynthesis) and secondary metabolism (polyketide and non-ribosomal peptide synthesis). Using conserved active site motifs, we predict some novel compounds that are probably involved in cell-cell communication, differing to known communication systems. We identify several gene clusters, which may represent novel signaling mechanisms and demonstrate the natural product potential ofLegionella.

scholarly journals Evolclust: automated inference of evolutionary conserved gene clusters in eukaryotes

2019 ◽  
Author(s):  
Marina Marcet-Houben ◽  
Toni Gabaldón
Keyword(s):  
Secondary Metabolism ◽  
Computational Prediction ◽  
Gene Clusters ◽  
Link Type ◽  
Automated Inference ◽  
Or Gene ◽  
Conserved Gene ◽  
Genome Comparisons

AbstractMotivationThe evolution and role of gene clusters in eukaryotes is poorly understood. Currently, most studies and computational prediction programs limit their focus to specific types of clusters, such as those involved in secondary metabolism.ResultsWe present Evolclust, a python-based tool for the inference of evolutionary conserved gene clusters from genome comparisons, independently of the function or gene composition of the cluster. Evolclust predicts conserved gene clusters from pairwise genome comparisons and infers families of related clusters from multiple (all vs all) genome comparisons.Availabilityhttps://github.com/Gabaldonlab/EvolClust/[email protected]

scholarly journals Genome-wide identification and functional prediction of salt- stress related long non-coding RNAs (lncRNAs) in chickpea (Cicer arietinum L.)

2021 ◽  
Author(s):  
Neeraj Kumar ◽  
Chellapilla Bharadwaj ◽  
Sarika Sahu ◽  
Aalok Shiv ◽  
Abhishek Kumar Shrivastava ◽  
...  
Keyword(s):  
Salt Stress ◽  
Stress Response ◽  
Target Genes ◽  
Salt Stress Response ◽  
Rna Molecules ◽  
Transporter Family ◽  
Genome Wide ◽  
New Generation ◽  
In Cis

AbstractLncRNAs (long noncoding RNAs) are 200 bp length crucial RNA molecules, lacking coding potential and having important roles in regulating gene expression, particularly in response to abiotic stresses. In this study, we identified salt stress-induced lncRNAs in chickpea roots and predicted their intricate regulatory roles. A total of 3452 novel lncRNAs were identified to be distributed across all 08 chickpea chromosomes. On comparing salt-tolerant (ICCV 10, JG 11) and salt-sensitive cultivars (DCP 92–3, Pusa 256), 4446 differentially expressed lncRNAs were detected under various salt  treatments. We predicted 3373 lncRNAs to be regulating their target genes in cis regulating manner and 80 unique lncRNAs were observed as interacting with 136 different miRNAs, as eTMs (endogenous target mimic) targets of miRNAs and implicated them in the regulatory network of salt stress response. Functional analysis of these lncRNA revealed their association in targeting salt stress response-related genes like potassium transporter, transporter family genes, serine/threonine-protein kinase, aquaporins like TIP1-2, PIP2-5 and transcription factors like, AP2, NAC, bZIP, ERF, MYB and WRKY. Furthermore, about 614 lncRNA-SSRs (simple sequence repeats) were identified as a new generation of molecular markers with higher efficiency and specificity in chickpea. Overall, these findings will pave the understanding of comprehensive functional role of potential lncRNAs, which can help in providing insight into the molecular mechanism of salt tolerance in chickpea.

scholarly journals A novel fungal gene regulation system based on inducible VPR-dCas9 and nucleosome map-guided sgRNA positioning

2020 ◽  
Vol 104 (22) ◽  
pp. 9801-9822
Author(s):  
Andreas Schüller ◽  
Lisa Wolansky ◽  
Harald Berger ◽  
Lena Studt ◽  
Agnieszka Gacek-Matthews ◽  
...  
Keyword(s):  
Aspergillus Nidulans ◽  
Target Genes ◽  
Negative Impact ◽  
Constitutive Expression ◽  
Gene Clusters ◽  
Regulation System ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Genome Wide ◽  
A Genome

Abstract Programmable transcriptional regulation is a powerful tool to study gene functions. Current methods to selectively regulate target genes are mainly based on promoter exchange or on overexpressing transcriptional activators. To expand the discovery toolbox, we designed a dCas9-based RNA-guided synthetic transcription activation system for Aspergillus nidulans that uses enzymatically disabled “dead” Cas9 fused to three consecutive activation domains (VPR-dCas9). The dCas9-encoding gene is under the control of an estrogen-responsive promoter to allow induction timing and to avoid possible negative effects by strong constitutive expression of the highly active VPR domains. Especially in silent genomic regions, facultative heterochromatin and strictly positioned nucleosomes can constitute a relevant obstacle to the transcriptional machinery. To avoid this negative impact and to facilitate optimal positioning of RNA-guided VPR-dCas9 to targeted promoters, we have created a genome-wide nucleosome map from actively growing cells and stationary cultures to identify the cognate nucleosome-free regions (NFRs). Based on these maps, different single-guide RNAs (sgRNAs) were designed and tested for their targeting and activation potential. Our results demonstrate that the system can be used to regulate several genes in parallel and, depending on the VPR-dCas9 positioning, expression can be pushed to very high levels. We have used the system to turn on individual genes within two different biosynthetic gene clusters (BGCs) which are silent under normal growth conditions. This method also opens opportunities to stepwise activate individual genes in a cluster to decipher the correlated biosynthetic pathway. Keypoints • An inducible RNA-guided transcriptional regulator based on VPR-dCas9 was established in Aspergillus nidulans. • Genome-wide nucleosome positioning maps were created that facilitate sgRNA positioning. • The system was successfully applied to activate genes within two silent biosynthetic gene clusters.

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