Strategies for Natural Product Discovery by Unlocking Cryptic Biosynthetic Gene Clusters in Fungi

Hur, Jae Young; Jeong, Eunju; Kim, Young Chan; Lee, Seoung Rak

doi:10.3390/separations10060333

Cited by 13 publications

(3 citation statements)

References 126 publications

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“…Even with the immense genetic similarity, not all genes and gene clusters evaluated are expressive, and they may be inactive (Onaka 2017;Hur et al 2023). In total, 882 putative proteins identified through protein prediction tools indicated the presence of new gene clusters, some of which remain dormant or unexpressed.…”

Section: Discussionmentioning

confidence: 99%

Bioinformatic insights into the xenobiotic degradation potential gene clusters of fish-associated novel Bacillus velezensis SNR14-4

Madhavan,

Dinesh,

Muhammed

et al. 2024

EEB

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Bacillus velezensis is a member of the genus Bacillus, which harbours useful, novel, and efficient secondary metabolites that can be utilized in the disruption of xenobiotics. Although a few strains of B. velezensis and related species are reported every year as having xenobiotic metabolism potential, several novel gene clusters are still unexplored, which could be more potent than those already discovered. The current B. velezensis strain was isolated from gills of healthy Oreochromis niloticus and the novelty of the strain was assessed through whole genome sequence analysis. Prokka, DFAST, BAKTA, and RASTtk were computational tools utilized for genome elucidation following the genome assembly. Protein and protein pathway prediction was achieved through the PATRIC database. Additionally, the resistance genes against microorganisms were examined through CARD (via Proksee), bacteriocin, and RiPPs using BAGEL4, and forecast of virulence factors using VFDB in PATRIC. The analysis led to identification of indicator genes for xenobiotic breakdown. The results were compared to pre-existing strains of B. velezensis and it was compelling to conclude the high biotechnological potential and the candidacy of the strain in xenobiotic degradation.

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Section: Discussionmentioning

confidence: 99%

Bioinformatic insights into the xenobiotic degradation potential gene clusters of fish-associated novel Bacillus velezensis SNR14-4

Madhavan,

Dinesh,

Muhammed

et al. 2024

EEB

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“…This is an unusual sesquiterpene alcohol synthesized by a sesquiterpene cyclase from Trichoderma sp. [70]. In region 95.1, one NRPS was found to be accountable for the biosynthesis of ilicicolin H. This compound is a broad-spectrum antifungal agent that acts…”

Section: The Secondary Metabolism In the Dc2mentioning

confidence: 99%

Genome Characteristics of the Endophytic Fungus Talaromyces sp. DC2 Isolated from Catharanthus roseus (L.) G. Don

Quan,

Nguyen,

Giang

et al. 2024

JoF

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Talaromyces sp. DC2 is an endophytic fungus that was isolated from the stem of Catharanthus roseus (L.) G. Don in Hanoi, Vietnam and is capable of producing vinca alkaloids. This study utilizes the PacBio Sequel technology to completely sequence the whole genome of Talaromyces sp. DC2The genome study revealed that DC2 contains a total of 34.58 Mb spanned by 156 contigs, with a GC content of 46.5%. The identification and prediction of functional protein-coding genes, tRNA, and rRNA were comprehensively predicted and highly annotated using various BLAST databases, including non-redundant (Nr) protein sequence, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Clusters of Orthologous Groups (COG), and Carbohydrate-Active Enzymes (CAZy) databases. The genome of DC2 has a total of 149, 227, 65, 153, 53, and 6 genes responsible for cellulose, hemicellulose, lignin, pectin, chitin, starch, and inulin degradation, respectively. The Antibiotics and Secondary Metabolites Analysis Shell (AntiSMASH) analyses revealed that strain DC2 possesses 20 biosynthetic gene clusters responsible for producing secondary metabolites. The strain DC2 has also been found to harbor the DDC gene encoding aromatic L-amino acid decarboxylase enzyme. Conclusively, this study has provided a comprehensive understanding of the processes involved in secondary metabolites and the ability of the Talaromyces sp. DC2 strain to degrade plant cell walls.

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“…In many cases, these limitations arise from the difficulty in isolating pure active substances from endophytes and the low yields of the resultant compounds—issues that are further complicated by the fact that some of the compounds are synthesized only during a limited phase of the endophytes’ life cycle [ 28 , 29 , 30 ]. Therefore, it is important to identify biosynthetic gene clusters for biologically active secondary metabolites of endophytes [ 31 ]. With such identification, it would be possible to dissect the biosynthesis pathway of a given secondary metabolite and the main genes encoding the enzymes responsible for the biosynthesis.…”

Section: Introductionmentioning

confidence: 99%

Antimicrobial Action Mechanisms of Natural Compounds Isolated from Endophytic Microorganisms

Eshboev,

Mamadalieva,

Nazarov

et al. 2024

Antibiotics

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Infectious diseases are a significant challenge to global healthcare, especially in the face of increasing antibiotic resistance. This urgent issue requires the continuous exploration and development of new antimicrobial drugs. In this regard, the secondary metabolites derived from endophytic microorganisms stand out as promising sources for finding antimicrobials. Endophytic microorganisms, residing within the internal tissues of plants, have demonstrated the capacity to produce diverse bioactive compounds with substantial pharmacological potential. Therefore, numerous new antimicrobial compounds have been isolated from endophytes, particularly from endophytic fungi and actinomycetes. However, only a limited number of these compounds have been subjected to comprehensive studies regarding their mechanisms of action against bacterial cells. Furthermore, the investigation of their effects on antibiotic-resistant bacteria and the identification of biosynthetic gene clusters responsible for synthesizing these secondary metabolites have been conducted for only a subset of these promising compounds. Through a comprehensive analysis of current research findings, this review describes the mechanisms of action of antimicrobial drugs and secondary metabolites isolated from endophytes, antibacterial activities of the natural compounds derived from endophytes against antibiotic-resistant bacteria, and biosynthetic gene clusters of endophytic fungi responsible for the synthesis of bioactive secondary metabolites.

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Strategies for Natural Product Discovery by Unlocking Cryptic Biosynthetic Gene Clusters in Fungi

Cited by 13 publications

References 126 publications

Bioinformatic insights into the xenobiotic degradation potential gene clusters of fish-associated novel Bacillus velezensis SNR14-4

Bioinformatic insights into the xenobiotic degradation potential gene clusters of fish-associated novel Bacillus velezensis SNR14-4

Genome Characteristics of the Endophytic Fungus Talaromyces sp. DC2 Isolated from Catharanthus roseus (L.) G. Don

Antimicrobial Action Mechanisms of Natural Compounds Isolated from Endophytic Microorganisms

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