Cryptic Gene Clusters Flashcards
(18 cards)
Cryptic gene clusters
Fungal genomes contain cryptic SM gene clusters, requiring stimuli or genetic mutations to be activated.
Regulators of cryptic SM gene clusters
Regulated by cluster-specific transcription factors.
How can these gene clusters be activated through genetic manipulation?
- Overexpressing or deleting transcription pathways through CRISPR.
- Overexpressing or deleting global regulators such as lacA and VelA can broadly influence these gene clusters, but this is not specific.
Examples of genetically manipulated cryptic cluster activation.
- Overexpression of apdR in aspergillus nidulans causes the production of emericellamides.
- Overexpression of LacA in penicillium expansum revealed novel compounds.
Environmental stimuli of cryptic gene clusters
UV light, oxidative agents, nutrient deprivation and other stresses.
Example of environmental stimuli.
UV irradiation activated a silent polyketide synthase (PKS) in fusarium graminearum activated SM gene clusters.
Chemical stimuli of cryptic gene clusters.
- Histone acetylation and methylation in chromatin remodeling.
- Histone deacetylases like suberolyninide hydroximic acid.
- DNA methyltransferases like 5-azacytidine.
Example of chemical stimuli.
In aspergillus fumigatus, DNA methyltransferases were used to activate the cryptic non-ribosomal peptide synthetase cluster.
Co cultivation for cryptic SM gene clusters.
Co-operation of microbial communities often trigger activation of cryptic SM gene clusters.
Example of co cultivation.
Aspergillus nidulans and Strpetomyces rapamycinicus activate PKS-NRPS hybrid clusters when cultivated together due to transformed signaling molecules.
Heterologous expression of cryptic SM gene clusters.
Removing and cloning cryptic SM gene clusters and then transferring them into suitable hosts, such as E. coli. CRISPR is essential.
Example of heterologous expression.
Saccharomyces cerevisiae heterologous expression of the aspercryptin cluster from aspergillus oryzae for identification of peptides.
Promoter engineering for SM gene clusters.
By replacing native promoters of cryptic genes with constitutively active promoters can force expression.
Example of promoter engineering.
In Aspergillus terreus activated cryptic PKS gene cluster, which revealed novel compounds.
Omics technology
Transproteomics and meta-bolomics can identifying gene clusters, using tools such as NMR and LC-MS.
Example of Omics technologies for cryptic SM gene clusters.
RNA sequencing of penicllium chrysogenum identified cryptic clusters later linked to novel metabolite production.
Pathway refactoring for cryptic SM gene clusters.
Reconstruction of cryptic gene clusters modifies the assembly of genes and their regulators to optimize expression.
Example for pathway refactoring
Refactoring lovastatin pathways in E.coli revealed intermediates that were previously unknown.
