Genomics-directed activation of cryptic natural product pathways deciphers codes for biosynthesis and molecular function

Abstract

Natural products, which can be isolated from living organisms worldwide, have played a pivotal role in drug discovery since ancient times. However, it has become more challenging to identify a structurally novel molecule with promising biological activity for pharmaceutical development, mainly due to the limited methodologies for their acquisition. In this review, we summarize our recent studies that activate the biosynthetic potential of filamentous fungi by genetic engineering to harness the metabolic flow for the efficient production of unprecedented natural products. The recent revolution in genome sequencing technology enables the accumulation of vast amounts of information on biosynthetic genes, the blueprint of the molecular construction. Utilizing the established heterologous expression system, activation of the pathway-specific transcription factor coupled with a knockout strategy, and manipulating the global regulatory gene, the biosynthetic genes were exploited to activate biosynthetic pathways and decipher the encoded enzyme functions. We show that this methodology was beneficial for acquiring fungal treasures for drug discovery. These studies also enabled the investigation of the molecular function of natural products in fungal development.

Genomic Analysis of Stropharia rugosoannulata Reveals Its Nutritional Strategy and Application Potential in Bioremediation

“…It has been confirmed that CC1G_04210 (cpf1) Siderophores are generally synthesized by two pathways: An NRPS-dependent pathway and an NRPS-independent pathway. It has been confirmed that CC1G_04210 (cpf1) encodes a siderophore synthetase and this NPRS cluster is responsible for the production of coprinoferrin, which is necessary for extracellular iron acquisition and is crucial for the growth and maturation of C. cinerea [46]. Homologous comparison and transcriptome analysis revealed that the NRPS cluster (cluster 6 in Figure S9) in S. rugosoannulata might be responsible for the production of coprinoferrin-related compounds.…”

“…Homologous comparison and transcriptome analysis revealed that the NRPS cluster (cluster 6 in Figure S9) in S. rugosoannulata might be responsible for the production of coprinoferrin-related compounds. These NPRS siderophore synthetases are widespread in mushrooms and evolved from a common ancestor of basidiomycetes [46]. Moreover, two other siderophore clusters (clusters 4 and 7 in Figure S9) were predicted by Antismash in the genome of S. rugosoannulata.…”

“…Transcriptome analysis showed that all of the genes in the two siderophore clusters were expressed in the mycelia. It was recently confirmed that the NRPS gene cluster is responsible for produci coprinoferrin in the Basidiomycete C. cinerea [46]. This gene cluster includes 17 genes the genome of C. cinerea, and it was found that the 15 genes of the NRPS cluster (cluste in Figure S9) in S. rugosoannulata shared a sequence similarity of over 40% to 80% w those of C. cinerea (Figure 5C and Table S17) and H. sublateritium, respectively, and the fore might be responsible for the production of coprinoferrin-related compounds.…”

“…Phylogenetic analysis showed that the known psi cybin biosynthesis enzymes were grouped as a cluster with high support values, and related proteins of S. rugosoannulata are grouped into different clusters with PsiD, Ps and PsiM, which were confirmed to encode for psilocybin biosynthesis enzymes (Figu 6). This suggests that the gene cluster for psilocybin biosynthesis is absent in It was recently confirmed that the NRPS gene cluster is responsible for producing coprinoferrin in the Basidiomycete C. cinerea [46]. This gene cluster includes 17 genes in the genome of C. cinerea, and it was found that the 15 genes of the NRPS cluster (cluster 6 in Figure S9) in S. rugosoannulata shared a sequence similarity of over 40% to 80% with those of C. cinerea (Figure 5C and Table S17) and H. sublateritium, respectively, and therefore might be responsible for the production of coprinoferrin-related compounds.…”

Presence, Mode of Action, and Application of Pathway Specific Transcription Factors in Aspergillus Biosynthetic Gene Clusters

“…The growing interest in fungal SMs is to discover new drugs and to take control of their production. Therefore, novel solutions of activating/regulating "cryptic" BGCs must be developed [13,14]. Hence, an important goal in mining fungal SMs is to characterize the molecular mechanisms of their production [15].…”