An atlas of bacterial secondary metabolite biosynthesis gene clusters

Biosynthesis of mycotoxins involves transcriptional co-regulation of sets of clustered genes. We hypothesise that specific control of transcription of genes in these clusters by LaeA, a global regulator of secondary metabolite production and development in many filamentous fungi, results from its interaction with a Cys6Zn2 DNA-binding protein unique to the gene cluster.

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Diversified secondary metabolite biosynthesis gene repertoire revealed in symbiotic dinoflagellates

Scientific Reports ◽

10.1038/s41598-018-37792-0 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 8

Author(s):

Girish Beedessee ◽

Kanako Hisata ◽

Michael C. Roy ◽

Frances M. Van Dolah ◽

Noriyuki Satoh ◽

...

Keyword(s):

Secondary Metabolite ◽

Gene Repertoire ◽

Biosynthesis Gene ◽

Secondary Metabolite Biosynthesis ◽

Symbiotic Dinoflagellates

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Divergence of pigments in three phylogenetically close Monascus species (M. pilosus, M. ruber, and M. purpureus) based on secondary metabolite biosynthetic gene clusters

10.21203/rs.2.22197/v1 ◽

2020 ◽

Author(s):

YUKI HIGA ◽

Young-Soo Kim ◽

Md. Altaf-Ul-Amin ◽

Ming Huan ◽

Naoaki Ono ◽

...

Keyword(s):

Secondary Metabolite ◽

Food Industry ◽

Gene Clusters ◽

Illumina Miseq ◽

Biosynthetic Gene ◽

Asian Countries ◽

Biosynthetic Gene Clusters ◽

Natural Pigments ◽

Secondary Metabolite Biosynthesis ◽

Paired End Sequencing

Abstract Background: Species under the genus Monascus are considered as economically important and have been widely used in the production of yellow and red food colorants. In particular, three Monascus species, namely, M. pilosus , M. purpureus , and M. ruber , are used for food fermentation in the cuisine of East Asian countries such as China, Japan, and Korea. These species have also been utilized in the production of various kinds of natural pigments. Results: We examined the diversity of pigment-related biosynthetic pathways in three Monascus species ( M. pilosus , M. purpureus , and M. ruber ) at the metabolome and genome levels. Illumina MiSeq 300 bp paired-end sequencing generated 17 million high-quality short reads in each species, corresponding to 200 times the genome size. We measured the pigments and their related metabolites using potato dextrose liquid (PDL) media. The colors in the PDL media corresponding to the pigments and their related metabolites produced by the three species are very different from each other. The gene clusters for secondary metabolite biosynthesis of the three Monascus species also diverged, confirming that M. pilosus and M. purpureus are chemotaxonomically different. M. ruber has similar biosynthetic gene clusters for citrinin, monacolin K, and Monascus azaphilone pigments with M. pilosus and M. purpureus. The comparison of secondary metabolites produced also revealed divergence in the three species. Conclusions: Our findings are important for improving the utilization of Monascus species in the food industry and industrial field. However, in view of food safety, we need to determine if the toxins produced by some Monascus strains exist in the genome or in the metabolome.

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Transcriptome Comparison of Secondary Metabolite Biosynthesis Genes Expressed in Cultured and Lichenized Conditions of Cladonia rangiferina

Diversity ◽

10.3390/d13110529 ◽

2021 ◽

Vol 13 (11) ◽

pp. 529

Author(s):

Natalia Sveshnikova ◽

Michele D. Piercey-Normore

Keyword(s):

Secondary Metabolite ◽

Environmental Changes ◽

Gene Clusters ◽

Biosynthetic Gene Clusters ◽

Secondary Metabolite Biosynthesis ◽

Metabolite Synthesis ◽

Transcriptome Comparison ◽

Encoding Genes ◽

Cladonia Rangiferina ◽

Active Genes

Lichen secondary metabolites are natural products of high medicinal and industrial value, which are produced by the fungal symbiont (mycobiont) of lichens in response to environmental changes. It has been shown that the cultured mycobiont is capable of secondary metabolite production, specifically polyketides, and polyketide production is affected by the presence or absence of the algal or cyanobacterial symbiont (photobiont). Identification of polyketide synthases encoding genes is, in turn, key for understanding the regulation of secondary metabolite synthesis. Using a previously established method of resynthesis for Cladonia rangiferina as well as the sequenced and assembled genome of that species, we compared transcriptomes of C. rangiferina cultured alone and resynthesized with the photobiont (Asterochloris glomerata) to reveal transcriptionally active genes in secondary metabolic gene clusters, as well some of the neighbouring genes, induced by the presence of the photobiont and events of lichenization. The results identify potential candidates for PKS genes in C. rangiferina, identify potential neighbouring genes in the PKS cluster, and offer insights into further research. The study provides preliminary insights into the activity of several identified biosynthetic gene clusters (BGC) as well as interactions of genes within those clusters.

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Activation of a Silent Fungal Polyketide Biosynthesis Pathway through Regulatory Cross Talk with a Cryptic Nonribosomal Peptide Synthetase Gene Cluster

Applied and Environmental Microbiology ◽

10.1128/aem.00683-10 ◽

2010 ◽

Vol 76 (24) ◽

pp. 8143-8149 ◽

Cited By ~ 96

Author(s):

Sebastian Bergmann ◽

Alexander N. Funk ◽

Kirstin Scherlach ◽

Volker Schroeckh ◽

Ekaterina Shelest ◽

...

Keyword(s):

Natural Products ◽

Gene Cluster ◽

Secondary Metabolite ◽

Cross Talk ◽

Regulatory Gene ◽

Gene Clusters ◽

Nonribosomal Peptide Synthetase ◽

Nonribosomal Peptide ◽

Peptide Synthetase ◽

Biosynthesis Gene

ABSTRACT Filamentous fungi produce numerous natural products that constitute a consistent source of potential drug leads, yet it seems that the majority of natural products are overlooked since most biosynthesis gene clusters are silent under standard cultivation conditions. Screening secondary metabolite genes of the model fungus Aspergillus nidulans, we noted a silent gene cluster on chromosome II comprising two nonribosomal peptide synthetase (NRPS) genes, inpA and inpB, flanked by a regulatory gene that we named scpR for secondary metabolism cross-pathway regulator. The induced expression of the scpR gene using the promoter of the alcohol dehydrogenase AlcA led to the transcriptional activation of both the endogenous scpR gene and the NRPS genes. Surprisingly, metabolic profiling of the supernatant of mycelia overexpressing scpR revealed the production of the polyketide asperfuranone. Through transcriptome analysis we found that another silent secondary metabolite gene cluster located on chromosome VIII coding for asperfuranone biosynthesis was specifically induced. Quantitative reverse transcription-PCR proved the transcription not only of the corresponding polyketide synthase (PKS) biosynthesis genes, afoE and afoG, but also of their activator, afoA, under alcAp-scpR-inducing conditions. To exclude the possibility that the product of the inp cluster induced the asperfuranone gene cluster, a strain carrying a deletion of the NRPS gene inpB and, in addition, the alcAp-scpR overexpression cassette was generated. In this strain, under inducing conditions, transcripts of the biosynthesis genes of both the NRPS-containing gene cluster inp and the asperfuranone gene cluster except gene inpB were detected. Moreover, the existence of the polyketide product asperfuranone indicates that the transcription factor ScpR controls the expression of the asperfuranone biosynthesis gene cluster. This expression as well as the biosynthesis of asperfuranone was abolished after the deletion of the asperfuranone activator gene afoA, indicating that ScpR binds to the afoA promoter. To the best of our knowledge, this is the first report of regulatory cross talk between two biosynthesis gene clusters located on different chromosomes.

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Genome Sequencing of Inonotus Obliquus Reveals Insights Into Candidate Genes Involved In Secondary Metabolite Biosynthesis

10.21203/rs.3.rs-963591/v1 ◽

2021 ◽

Author(s):

Yingce Duan ◽

Haiyan Han ◽

Jianzhao Qi ◽

Jin-ming Gao ◽

Zhichao Xu ◽

...

Keyword(s):

Secondary Metabolite ◽

De Novo ◽

Evolutionary Relationship ◽

Gene Clusters ◽

Inonotus Obliquus ◽

Sequencing Platform ◽

Oxford Nanopore ◽

Secondary Metabolite Biosynthesis ◽

Preclinical Trials ◽

Genome Information

Abstract Background: Inonotus obliquus is an important edible and medicinal mushroom that was shown to have many pharmacological activities in preclinical trials, including anti-inflammatory, antitumor, immunomodulatory, and antioxidant effects. However, the biosynthesis of these pharmacological components has rarely been reported. The reason for this is that there have been no relevant reports on its genome information.Results: we report the genome of I. obliquus using a combined high-throughput Illumina NovaSeq with Oxford Nanopore PromethION sequencing platform. The de novo assembled 38.18 Mb I. obliquus genome was determined to harbor 12525 putative genes, with 81.83% of them having detectable sequence similarities to others available in public databases. Phylogenetic analysis revealed a close evolutionary relationship between I. obliquus and Fomitiporia mediterranea and Sanghuangporus baumii in the core Hymenochaetales clade. The I. obliquus genome was found to encode a repertoire of enzymes involved in carbohydrate metabolism, along with 135 cytochrome P450 proteins. Other annotated genes included those encoding key enzymes for secondary metabolite biosynthesis, such as those from polysaccharide, melanin, and triterpenoid pathways. Among them, the I. obliquus genome was particularly enriched in sesquiterpenoid biosynthesis genes and gene clusters.Conclusions: This study presents the first genome analysis of an important medical mushroom, I. obliquus, which can provide insights into the usefulness of this organism and its secondary metabolites in medicine.

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Identification of a Polyketide Synthase Gene Responsible for Ascochitine Biosynthesis in Ascochyta fabae and Its Abrogation in Sister Taxa

mSphere ◽

10.1128/msphere.00622-19 ◽

2019 ◽

Vol 4 (5) ◽

Cited By ~ 1

Author(s):

Wonyong Kim ◽

Judith Lichtenzveig ◽

Robert A. Syme ◽

Angela H. Williams ◽

Tobin L. Peever ◽

...

Keyword(s):

Gene Cluster ◽

Secondary Metabolite ◽

Polyketide Synthase ◽

Animal Health ◽

Gene Clusters ◽

Biosynthesis Gene Cluster ◽

Content Type ◽

Pathogenicity Factor ◽

Biosynthesis Gene ◽

Ascochyta Fabae

ABSTRACT The polyketide-derived secondary metabolite ascochitine is produced by species in the Didymellaceae family, including but not restricted to Ascochyta species pathogens of cool-season food legumes. Ascochitine is structurally similar to the well-known mycotoxin citrinin and exhibits broad-spectrum phytotoxicity and antimicrobial activities. Here, we identified a polyketide synthase (PKS) gene (denoted pksAC) responsible for ascochitine production in the filamentous fungus Ascochyta fabae. Deletion of the pksAC prevented production of ascochitine and its derivative ascochital in A. fabae. The putative ascochitine biosynthesis gene cluster comprises 11 genes that have undergone rearrangement and gain-and-loss events relative to the citrinin biosynthesis gene cluster in Monascus ruber. Interestingly, we also identified pksAC homologs in two recently diverged species, A. lentis and A. lentis var. lathyri, that are sister taxa closely related to ascochitine producers such as A. fabae and A. viciae-villosae. However, nonsense mutations have been independently introduced in coding sequences of the pksAC homologs of A. lentis and A. lentis var. lathyri that resulted in loss of ascochitine production. Despite its reported phytotoxicity, ascochitine was not a pathogenicity factor in A. fabae infection and colonization of faba bean (Vicia faba L.). Ascochitine was mainly produced from mature hyphae at the site of pycnidial formation, suggesting a possible protective role of the compound against other microbial competitors in nature. This report highlights the evolution of gene clusters harnessing the structural diversity of polyketides and a mechanism with the potential to alter secondary metabolite profiles via single nucleotide polymorphisms in closely related fungal species. IMPORTANCE Fungi produce a diverse array of secondary metabolites, many of which are of pharmacological importance whereas many others are noted for mycotoxins, such as aflatoxin and citrinin, that can threaten human and animal health. The polyketide-derived compound ascochitine, which is structurally similar to citrinin mycotoxin, has been considered to be important for pathogenicity of legume-associated Ascochyta species. Here, we identified the ascochitine polyketide synthase (PKS) gene in Ascochyta fabae and its neighboring genes that may be involved in ascochitine biosynthesis. Interestingly, the ascochitine PKS genes in other legume-associated Ascochyta species have been mutated, encoding truncated PKSs. This indicated that point mutations may have contributed to genetic diversity for secondary metabolite production in these fungi. We also demonstrated that ascochitine is not a pathogenicity factor in A. fabae. The antifungal activities and production of ascochitine during sporulation suggested that it may play a role in competition with other saprobic fungi in nature.

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Divergence of metabolites in three phylogenetically close Monascus species (M. pilosus, M. ruber, and M. purpureus) based on secondary metabolite biosynthetic gene clusters

BMC Genomics ◽

10.1186/s12864-020-06864-9 ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

Yuki Higa ◽

Young-Soo Kim ◽

Md. Altaf-Ul-Amin ◽

Ming Huang ◽

Naoaki Ono ◽

...

Keyword(s):

Secondary Metabolites ◽

Secondary Metabolite ◽

Genomic Analysis ◽

Gene Clusters ◽

Illumina Miseq ◽

Red Yeast Rice ◽

Biosynthetic Gene Clusters ◽

Secondary Metabolite Biosynthesis ◽

Genome Level ◽

Paired End Sequencing

Abstract Background Species of the genus Monascus are considered to be economically important and have been widely used in the production of yellow and red food colorants. In particular, three Monascus species, namely, M. pilosus, M. purpureus, and M. ruber, are used for food fermentation in the cuisine of East Asian countries such as China, Japan, and Korea. These species have also been utilized in the production of various kinds of natural pigments. However, there is a paucity of information on the genomes and secondary metabolites of these strains. Here, we report the genomic analysis and secondary metabolites produced by M. pilosus NBRC4520, M. purpureus NBRC4478 and M. ruber NBRC4483, which are NBRC standard strains. We believe that this report will lead to a better understanding of red yeast rice food. Results We examined the diversity of secondary metabolite production in three Monascus species (M. pilosus, M. purpureus, and M. ruber) at both the metabolome level by LCMS analysis and at the genome level. Specifically, M. pilosus NBRC4520, M. purpureus NBRC4478 and M. ruber NBRC4483 strains were used in this study. Illumina MiSeq 300 bp paired-end sequencing generated 17 million high-quality short reads in each species, corresponding to 200 times the genome size. We measured the pigments and their related metabolites using LCMS analysis. The colors in the liquid media corresponding to the pigments and their related metabolites produced by the three species were very different from each other. The gene clusters for secondary metabolite biosynthesis of the three Monascus species also diverged, confirming that M. pilosus and M. purpureus are chemotaxonomically different. M. ruber has similar biosynthetic and secondary metabolite gene clusters to M. pilosus. The comparison of secondary metabolites produced also revealed divergence in the three species. Conclusions Our findings are important for improving the utilization of Monascus species in the food industry and industrial field. However, in view of food safety, we need to determine if the toxins produced by some Monascus strains exist in the genome or in the metabolome.

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