scholarly journals Motif-independent de novo detection of secondary metabolite gene clusters—toward identification from filamentous fungi

2015 ◽  
Vol 6 ◽  
Author(s):  
Myco Umemura ◽  
Hideaki Koike ◽  
Masayuki Machida
Keyword(s):  
Secondary Metabolite ◽  
Filamentous Fungi ◽  
De Novo ◽  
Gene Clusters

scholarly journals Accurate prediction of secondary metabolite gene clusters in filamentous fungi

2012 ◽  
Vol 110 (1) ◽  
pp. E99-E107 ◽  
Author(s):  
M. R. Andersen ◽  
J. B. Nielsen ◽  
A. Klitgaard ◽  
L. M. Petersen ◽  
M. Zachariasen ◽  
...  
Keyword(s):  
Secondary Metabolite ◽  
Filamentous Fungi ◽  
Gene Clusters ◽  
Accurate Prediction

scholarly journals De novo sequencing and detection of secondary metabolite gene clusters of Penicillium griseofulvum

2016 ◽  
pp. 157-162
Author(s):  
H. Banani ◽  
M. Marcet-Houben ◽  
A.-R. Ballester ◽  
P. Abbruscato ◽  
L. González-Candelas ◽  
...  
Keyword(s):  
Secondary Metabolite ◽  
De Novo ◽  
Gene Clusters ◽  
De Novo Sequencing ◽  
Penicillium Griseofulvum

scholarly journals MIDDAS-M: Motif-Independent De Novo Detection of Secondary Metabolite Gene Clusters through the Integration of Genome Sequencing and Transcriptome Data

PLoS ONE ◽  
2013 ◽  
Vol 8 (12) ◽  
pp. e84028 ◽  
Author(s):  
Myco Umemura ◽  
Hideaki Koike ◽  
Nozomi Nagano ◽  
Tomoko Ishii ◽  
Jin Kawano ◽  
...  
Keyword(s):  
Secondary Metabolite ◽  
Genome Sequencing ◽  
De Novo ◽  
Gene Clusters ◽  
Transcriptome Data

scholarly journals Applications of CRISPR/Cas9 in the Synthesis of Secondary Metabolites in Filamentous Fungi

2021 ◽  
Vol 12 ◽  
Author(s):  
Chunmiao Jiang ◽  
Gongbo Lv ◽  
Yayi Tu ◽  
Xiaojie Cheng ◽  
Yitian Duan ◽  
...  
Keyword(s):  
Secondary Metabolites ◽  
Genome Editing ◽  
Secondary Metabolite ◽  
Filamentous Fungi ◽  
Biological Activities ◽  
Genetic Research ◽  
Gene Clusters ◽  
Biologically Active ◽  
Future Application ◽  
Advanced Technique

Filamentous fungi possess the capacity to produce a wide array of secondary metabolites with diverse biological activities and structures, such as lovastatin and swainsonine. With the advent of the post-genomic era, increasing amounts of cryptic or uncharacterized secondary metabolite biosynthetic gene clusters are continually being discovered. However, owing to the longstanding lack of versatile, comparatively simple, and highly efficient genetic manipulation techniques, the broader exploration of industrially important secondary metabolites has been hampered thus far. With the emergence of CRISPR/Cas9-based genome editing technology, this dilemma may be alleviated, as this advanced technique has revolutionized genetic research and enabled the exploitation and discovery of new bioactive compounds from filamentous fungi. In this review, we introduce the CRISPR/Cas9 system in detail and summarize the latest applications of CRISPR/Cas9-mediated genome editing in filamentous fungi. We also briefly introduce the specific applications of the CRISPR/Cas9 system and CRISPRa in the improvement of secondary metabolite contents and discovery of novel biologically active compounds in filamentous fungi, with specific examples noted. Additionally, we highlight and discuss some of the challenges and deficiencies of using the CRISPR/Cas9-based genome editing technology in research on the biosynthesis of secondary metabolites as well as future application of CRISPR/Cas9 strategy in filamentous fungi are highlighted and discussed.

scholarly journals Genome Sequencing of Inonotus Obliquus Reveals Insights Into Candidate Genes Involved In Secondary Metabolite Biosynthesis

2021 ◽  
Author(s):  
Yingce Duan ◽  
Haiyan Han ◽  
Jianzhao Qi ◽  
Jin-ming Gao ◽  
Zhichao Xu ◽  
...  
Keyword(s):  
Secondary Metabolite ◽  
De Novo ◽  
Evolutionary Relationship ◽  
Gene Clusters ◽  
Inonotus Obliquus ◽  
Sequencing Platform ◽  
Oxford Nanopore ◽  
Secondary Metabolite Biosynthesis ◽  
Preclinical Trials ◽  
Genome Information

Abstract Background: Inonotus obliquus is an important edible and medicinal mushroom that was shown to have many pharmacological activities in preclinical trials, including anti-inflammatory, antitumor, immunomodulatory, and antioxidant effects. However, the biosynthesis of these pharmacological components has rarely been reported. The reason for this is that there have been no relevant reports on its genome information.Results: we report the genome of I. obliquus using a combined high-throughput Illumina NovaSeq with Oxford Nanopore PromethION sequencing platform. The de novo assembled 38.18 Mb I. obliquus genome was determined to harbor 12525 putative genes, with 81.83% of them having detectable sequence similarities to others available in public databases. Phylogenetic analysis revealed a close evolutionary relationship between I. obliquus and Fomitiporia mediterranea and Sanghuangporus baumii in the core Hymenochaetales clade. The I. obliquus genome was found to encode a repertoire of enzymes involved in carbohydrate metabolism, along with 135 cytochrome P450 proteins. Other annotated genes included those encoding key enzymes for secondary metabolite biosynthesis, such as those from polysaccharide, melanin, and triterpenoid pathways. Among them, the I. obliquus genome was particularly enriched in sesquiterpenoid biosynthesis genes and gene clusters.Conclusions: This study presents the first genome analysis of an important medical mushroom, I. obliquus, which can provide insights into the usefulness of this organism and its secondary metabolites in medicine.

scholarly journals Two Histone Deacetylases, FfHda1 and FfHda2, Are Important for Fusarium fujikuroi Secondary Metabolism and Virulence

2013 ◽  
Vol 79 (24) ◽  
pp. 7719-7734 ◽  
Author(s):  
L. Studt ◽  
F. J. Schmidt ◽  
L. Jahn ◽  
C. M. K. Sieber ◽  
L. R. Connolly ◽  
...  
Keyword(s):  
Secondary Metabolism ◽  
Secondary Metabolite ◽  
Filamentous Fungi ◽  
Histone Deacetylases ◽  
Control Plant ◽  
Gene Clusters ◽  
Phytopathogenic Fungus ◽  
Fusarium Fujikuroi ◽  
Content Type ◽  
Encoding Genes

ABSTRACTHistone modifications are crucial for the regulation of secondary metabolism in various filamentous fungi. Here we studied the involvement of histone deacetylases (HDACs) in secondary metabolism in the phytopathogenic fungusFusarium fujikuroi, a known producer of several secondary metabolites, including phytohormones, pigments, and mycotoxins. Deletion of three Zn2+-dependent HDAC-encoding genes,ffhda1,ffhda2, andffhda4, indicated that FfHda1 and FfHda2 regulate secondary metabolism, whereas FfHda4 is involved in developmental processes but is dispensable for secondary-metabolite production inF. fujikuroi. Single deletions offfhda1andffhda2resulted not only in an increase or decrease but also in derepression of metabolite biosynthesis under normally repressing conditions. Moreover, double deletion of both theffhda1andffhda2genes showed additive but also distinct phenotypes with regard to secondary-metabolite biosynthesis, and both genes are required for gibberellic acid (GA)-induced bakanae disease on the preferred host plant rice, as Δffhda1Δffhda2mutants resemble the uninfected control plant. Microarray analysis with a Δffhda1mutant that has lost the major HDAC revealed differential expression of secondary-metabolite gene clusters, which was subsequently verified by a combination of chemical and biological approaches. These results indicate that HDACs are involved not only in gene silencing but also in the activation of some genes. Chromatin immunoprecipitation with the Δffhda1mutant revealed significant alterations in the acetylation state of secondary-metabolite gene clusters compared to the wild type, thereby providing insights into the regulatory mechanism at the chromatin level. Altogether, manipulation of HDAC-encoding genes constitutes a powerful tool to control secondary metabolism in filamentous fungi.

scholarly journals Histone Deacetylase Activity Regulates Chemical Diversity in Aspergillus

2007 ◽  
Vol 6 (9) ◽  
pp. 1656-1664 ◽  
Author(s):  
E. Keats Shwab ◽  
Jin Woo Bok ◽  
Martin Tribus ◽  
Johannes Galehr ◽  
Stefan Graessle ◽  
...  
Keyword(s):  
Small Molecules ◽  
Aspergillus Nidulans ◽  
Histone Deacetylase ◽  
Secondary Metabolite ◽  
Filamentous Fungi ◽  
Small Molecule ◽  
Transcriptional Activation ◽  
Hdac Inhibitors ◽  
Gene Clusters ◽  
Chemical Diversity

ABSTRACT Bioactive small molecules are critical in Aspergillus species during their development and interaction with other organisms. Genes dedicated to their production are encoded in clusters that can be located throughout the genome. We show that deletion of hdaA, encoding an Aspergillus nidulans histone deacetylase (HDAC), causes transcriptional activation of two telomere-proximal gene clusters—and subsequent increased levels of the corresponding molecules (toxin and antibiotic)—but not of a telomere-distal cluster. Introduction of two additional HDAC mutant alleles in a ΔhdaA background had minimal effects on expression of the two HdaA-regulated clusters. Treatment of other fungal genera with HDAC inhibitors resulted in overproduction of several metabolites, suggesting a conserved mechanism of HDAC repression of some secondary-metabolite gene clusters. Chromatin regulation of small-molecule gene clusters may enable filamentous fungi to successfully exploit environmental resources by modifying chemical diversity.

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