Secondary metabolism: Then, now and tomorrow

Keller, Nancy P.; Bennett, Joan W.; Turner, Geoff

doi:10.1016/j.fgb.2010.08.012

Cited by 6 publications

(5 citation statements)

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“…The discovery of these genes and the study of their evolution is a topic of increasing interest [30]. Several Penicillium species are sources of compounds or enzymatic activities that have important clinical or biotechnological applications [31].…”

Section: Resultsmentioning

confidence: 99%

Genome sequence of the necrotrophic fungus Penicillium digitatum, the main postharvest pathogen of citrus

et al. 2012

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BackgroundPenicillium digitatum is a fungal necrotroph causing a common citrus postharvest disease known as green mold. In order to gain insight into the genetic bases of its virulence mechanisms and its high degree of host-specificity, the genomes of two P. digitatum strains that differ in their antifungal resistance traits have been sequenced and compared with those of 28 other Pezizomycotina.ResultsThe two sequenced genomes are highly similar, but important differences between them include the presence of a unique gene cluster in the resistant strain, and mutations previously shown to confer fungicide resistance. The two strains, which were isolated in Spain, and another isolated in China have identical mitochondrial genome sequences suggesting a recent worldwide expansion of the species. Comparison with the closely-related but non-phytopathogenic P. chrysogenum reveals a much smaller gene content in P. digitatum, consistent with a more specialized lifestyle. We show that large regions of the P. chrysogenum genome, including entire supercontigs, are absent from P. digitatum, and that this is the result of large gene family expansions rather than acquisition through horizontal gene transfer. Our analysis of the P. digitatum genome is indicative of heterothallic sexual reproduction and reveals the molecular basis for the inability of this species to assimilate nitrate or produce the metabolites patulin and penicillin. Finally, we identify the predicted secretome, which provides a first approximation to the protein repertoire used during invasive growth.ConclusionsThe complete genome of P. digitatum, the first of a phytopathogenic Penicillium species, is a valuable tool for understanding the virulence mechanisms and host-specificity of this economically important pest.

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Section: Resultsmentioning

confidence: 99%

Genome sequence of the necrotrophic fungus Penicillium digitatum, the main postharvest pathogen of citrus

et al. 2012

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“…The secondary metabolism is an important characteristic of fungi and display a dichotomy within biological activities, some benefit the society by developing into medicines and agrochemicals, and some are pathogenic determinants of humans, animals and plants [57,58]. HXQ-H-1 secondary metabolites extractions such as nafuredin B showed cytotoxicity against a panel of human cancer cell lines, as well as varitatin A showed cytotoxicity against HCT-116 cell line (human colon cancer) and also inhibited the effects of protein tyrosine kinases [6,7].…”

Section: Functional Categorizationmentioning

confidence: 99%

Chromosome-Level Comprehensive Genome of Mangrove Sediment-Derived Fungus Penicillium variabile HXQ-H-1

Peng¹,

Li²,

Liu³

et al. 2019

JoF

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Penicillium is an ascomycetous genus widely distributed in the natural environment and is one of the dominant fungi involved in the decomposition of mangroves, which can produce a variety of antitumor compounds and bioactive substances. However, in mangrove ecosystems there is no complete genome in this genus. In this study, we isolated a fungus strain named Penicillium variabile HXQ-H-1 from coast mangrove (Fujian Province, China). We generated a chromosome-level genome with total size of 33.32 Mb, scaffold N50 of 5.23 Mb and contig N50 of 96.74 kb. Additionally, we anchored about 95.91% assembly sequences into the longest seven scaffolds, and predicted 10,622 protein-coding genes, in which 99.66% could be annotated by eight protein databases. The secondary metabolites analysis reveals the strain has various gene clusters involving polyketide synthase (PKS), non-ribosomal peptide synthetase (NRPS) and terpene synthase that may have a largely capacity of biotechnological potential. Comparison genome analysis between Penicillium variabile and Talaromyces islandicus reveals a small difference in the total number of genes, whereas HXQ-H-1 has a higher gene number with COG functional annotation. Evolutionary relationship of Penicillum based on genome-wide data was carried out for the first time, showing the strain HXQ-H-1 is closely related to Talaromyces islandicus. This genomic resource may provide a new resource for development of novel bioactive antibiotics, drug candidates and precursors in Penicillium variabile.

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“…Similar to their functions, these metabolites are chemically diverse. Based on their properties and the core enzymes and precursors involved in their biosynthesis, four major groups can be distinguished: polyketides, non-ribosomal peptides (NRPS), terpenoids and tryptophan derivatives [3]. The genes encoding most fungal secondary metabolites are located adjacent to each other (i.e., "clustered") in the genome [2,4].…”

Section: Introductionmentioning

confidence: 99%

“…Lichen polyketides are synthesized by Type I polyketide synthases (TI-PKS) [13], whose closest structural and functional analogue is the mammalian fatty acid synthase [14]. In the minimal configuration, the domain structure of TI-PKSs includes a ketoacyl synthase (KS), an acyltransferase (AT), and an acyl carrier protein (ACP), which are essential for polyketide synthesis [3]. This configuration can be supplemented by additional domains, such as starter unit-ACP transacylase (SAT), ketoreductase (KR), dehydratase (DH), enoyl reductase (ER), methyltransferase (CMeT), and thioesterase (TE) [3].…”

Section: Introductionmentioning

confidence: 99%

“…All three subgroups can be found in lichen-forming fungi, and their diversity has not gone unnoticed. Previous work suggests various ecological roles of polyketides in lichen-forming fungi ranging from light-screening and chemical weathering to allelopathic effects and herbivore defence [3,6,16,17]. More broadly, secondary metabolite profiles including polyketides are often characteristic for taxonomic groups and are thus extensively used to distinguish different lichen-forming fungi.…”

Section: Introductionmentioning

confidence: 99%

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High diversity of type I polyketide genes in Bacidia rubella as revealed by the comparative analysis of 23 lichen fungal genomes

Gerasimova¹,

Beck

Werth³

et al. 2022

Preprint

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Fungi involved in lichen symbioses produce a large array of different secondary metabolites. The high diversity of those substances has been known for decades and are often considered characteristic for taxonomical delimitation in lichen-forming fungi. Polyketides, the most common secondary metabolites, are synthesized by the Type I Polyketide synthases (TI-PKS) comprised of different enzymatic domains. We present a phylogenetic overview of Type I PKS genes recovered from the de-novo sequenced genome of Bacidia rubella in the context of additional twenty-one fungal genomes from the largest radiation of lichen-forming Ascomycetes (Lecanoromycetes) as well as the lichen-forming Eurotiomycete, Endocarpon pusillum. Using de-novo gene prediction and functional annotation combined with a phylogenetic analysis, we provide insights into the biosynthetic potential and PKS gene diversity of lichen-forming fungi. We discuss genes predicted in the lichen-forming fungal genomes in relation to previously characterized PKS genes from other fungi and bacteria. Our results reveal a high number of biosynthetic gene clusters and their gene domain composition. PKS gene content outnumbers known secondary substances produced by the lichen-forming fungi. We were able to assign putative functions to several of those PKS genes in silico, based on similarity to already characterized genes. In particular, we identified a putative PKS23 gene of Bacidia rubella, producing the common lichen substance atranorin. However, we also found that several lichen-forming fungi still possess homologs of different biosynthetic genes without producing the corresponding substances in detectable amounts. Although many PKSs remain without functional assignments in our analysis, our findings highlight that genes from lichen-forming fungi represent an untapped source of novel polyketide compounds. However, additional experimental approaches are necessary to link biosynthetic genes and secondary metabolites with confidence.

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Secondary metabolism: Then, now and tomorrow

Cited by 6 publications

References 0 publications

Genome sequence of the necrotrophic fungus Penicillium digitatum, the main postharvest pathogen of citrus

Genome sequence of the necrotrophic fungus Penicillium digitatum, the main postharvest pathogen of citrus

Chromosome-Level Comprehensive Genome of Mangrove Sediment-Derived Fungus Penicillium variabile HXQ-H-1

High diversity of type I polyketide genes in Bacidia rubella as revealed by the comparative analysis of 23 lichen fungal genomes

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