Current State and Future Directions of Genetics and Genomics of Endophytic Fungi for Bioprospecting Efforts

Abstract

The bioprospecting of secondary metabolites from endophytic fungi received great attention in the 1990s and 2000s, when the controversy around taxol production from Taxus spp. endophytes was at its height. Since then, hundreds of reports have described the isolation and characterization of putative secondary metabolites from endophytic fungi. However, only very few studies also report the genetic basis for these phenotypic observations. With low sequencing cost and fast sample turnaround, genetics- and genomics-based approaches have risen to become comprehensive approaches to study natural products from a wide-range of organisms, especially to elucidate underlying biosynthetic pathways. However, in the field of fungal endophyte biology, elucidation of biosynthetic pathways is still a major challenge. As a relatively poorly investigated group of microorganisms, even in the light of recent efforts to sequence more fungal genomes, such as the 1000 Fungal Genomes Project at the Joint Genome Institute (JGI), the basis for bioprospecting of enzymes and pathways from endophytic fungi is still rather slim. In this review we want to discuss the current approaches and tools used to associate phenotype and genotype to elucidate biosynthetic pathways of secondary metabolites in endophytic fungi through the lens of bioprospecting. This review will point out the reported successes and shortcomings, and discuss future directions in sampling, and genetics and genomics of endophytic fungi. Identifying responsible biosynthetic genes for the numerous secondary metabolites isolated from endophytic fungi opens the opportunity to explore the genetic potential of producer strains to discover novel secondary metabolites and enhance secondary metabolite production by metabolic engineering resulting in novel and more affordable medicines and food additives.

Root Morphogenesis of Arabidopsis thaliana Tuned by Plant Growth-Promoting Streptomyces Isolated From Root-Associated Soil of Artemisia annua

“…On the other hand, the domination of Streptomyces spp. in roots reduced the alpha diversity, which may have risks to break the ecological balance of endophytic community even though negative effect to root growth and development was not observed in this study (Sagita et al, 2021). The changes in endophytic microbial diversity which cause by alien microbial inoculation should be considered during PGPR strategic design, which could be optimized in the proper inoculating dosage or synthetic consortium.…”

Bioengineering of fungal endophytes through the CRISPR/Cas9 system

“…Cas9/guide RNA complexes are in vivo generated by delivering the Cas9 gene and guide DNA in expression cassettes. A DNA shuttle, selective markers, and promoter and terminator sequences that are compatible with the native host are required for this method, which is often unavailable for new isolates ( Sagita et al, 2021 ). To overcome this problem, it is now possible to prepare Cas9-gRNA ribonucleoprotein complex in vitro and transform them into fungal protoplasts.…”

Potentials of Endophytic Fungi in the Biosynthesis of Versatile Secondary Metabolites and Enzymes

“…The major restrictions regarding this issue have been attributed to possible difficulties in microbial isolation/characterization and also BGC identification, the existence of cryptic BGCs, low stability or instability of fungal secondary metabolites expressed and/or the possible isolation of already known BGCs [130] (Figure 3). Depending on each situation, several methods could be used to solve issues and speed-up the discovery process, to decipher novel secondary metabolites contributing to the advancement of numerous vital fields [131,132]. Reportedly, numerous scientists have demonstrated the crucial role of advanced genetic, proteomic, metabolomic, bioinformatic and mass spectrometry tools to predict, understand and manipulate the biosynthetic pathways of natural products [133][134][135][136].…”