• Microbiology and Biotechnology Letters
• /
• v.37 no.1
• /
• pp.10-16
• /
• 2009

Polymerase chain reactin (PCR) could be a simple way to screen new microbial strains producing useful secondary metabolites if their biosynthetic genes are known and candidate strains to be screened are available. In this study, we have screened two myxobacterial strains, KYC3047 and KYC3076, carrying genes appeared to be biosynthetic genes of soraphen A, a potent antifungal substance, out of 50 cellulose degrading myxobacteria using PCR. The two strains were identified as Sorangium cellulosum based on morphological, physiological, and molecular biological characteristics. Both of the strains produced substances having strong antifungal activities as expected against Candida albicans, a causative agent of candidiasis, and Colletotrichum acutatum, a causative agent of anthracnose on pepper.

• The Plant Pathology Journal
• /
• v.36 no.5
• /
• pp.491-496
• /
• 2020

An understanding of the contribution of secondary metabolites (SMs) to the antagonistic and biocontrol activities of bacterial biocontrol agents serves to improve biocontrol potential of the strain. In this study, to evaluate the contribution of each SM produced by Pseudomonas fluorescens NBC275 (Pf275) to its antifungal and biocontrol activity, we combined in silico analysis of the genome with our previous study of transposon (Tn) mutants. Thirteen Tn mutants, which belonged to 6 biosynthetic gene clusters (BGCs) of a total 14 BGCs predicted by the antiSMASH tool were identified by the reduction of antifungal activity. The biocontrol performance of Pf275 was significantly dependent on 2,4-diacetylphloroglucinol and pyoverdine. The clusters that encode for arylpolyene and an unidentified small linear lipopeptide influenced antifungal and biocontrol activities. To our knowledge, our study identified the contribution of SMs, such as a small linear lipopeptide and arylpolyene, to biocontrol efficacy for the first time.

• Journal of Microbiology and Biotechnology
• /
• v.17 no.5
• /
• pp.830-839
• /
• 2007

Pradimicins are potent antifungal antibiotics having an unusual dihydrobenzo[$\alpha$]naphthacenequinone aglycone substituted with D-alanine and sugars. Pradimicins are polyketide antibiotics produced by Actinomadura hibisca P157-2. The gene cluster involved in the biosynthesis of pradimicins was cloned and sequenced. The pradimicin gene cluster was localized to a 39-kb DNA segment and its involvement in the biosynthesis of pradimicin was proven by gene inactivation of prmA and prmB(ketosynthases $\alpha\;and\;\beta$). The pradimicin gene cluster consists of 28 open reading frames(ORFs), encoding a type II polyketide synthase(PKS), the enzymes involved in sugar biosynthesis and tailoring enzymes as well as two resistance proteins. The deduced proteins showed strong similarities to the previously validated gene clusters of angucyclic polyketides such as rubromycin, griseorhodin, and fredericamycin. From the pradimicin gene cluster, prmP3 encoding a component of the acetyl-CoA carboxylase complex was disrupted. The production levels of pradimicins of the resulting mutants decreased to 62% of the level produced by the wild-type strain, which indicate that the acetyl-CoA carboxylase gene would have a significant role in the production of pradimicins through supplying the extender unit precursor, malonyl-CoA.

• Journal of Microbiology and Biotechnology
• /
• v.18 no.8
• /
• pp.1416-1422
• /
• 2008

Epothilone and its analogs are a potent new class of anticancer compounds produced by myxobacteria. Thus, in an effort to identify new myxobacterial strains producing epothilone and its analogs, cellulose-degrading myxobacteria were isolated from Korean soils, and 13 strains carrying epothilone biosynthetic gene homologs were screened using a polymerase chain reaction. A migration assay revealed that Sorangium cellulosum KYC3013, 3016, 3017, and 3018 all produced microtubule-stabilizing compounds, and an LC-MS/MS analysis showed that S. cellulosum KYC3013 synthesized epothilone A.

• Mycobiology
• /
• v.50 no.4
• /
• pp.254-257
• /
• 2022

Wolfiporia cocos is a wood-decay brown rot fungus belonging to the family Polyporaceae. While the fungus grows, the sclerotium body of the strain, dubbed Bokryeong in Korean, is formed around the roots of conifer trees. The dried sclerotium has been widely used as a key component of many medicinal recipes in East Asia. Wolfiporia cocos strain KMCC03342 is the reference strain registered and maintained by the Korea Seed and Variety Service for commercial uses. Here, we present the first draft genome sequence of W. cocos KMCC03342 using a hybrid assembly technique combining both short- and long-read sequences. The genome has a total length of 55.5 Mb comprised of 343 contigs with N50 of 332 kb and 95.8% BUSCO completeness. The GC ratio was 52.2%. We predicted 14,296 protein-coding gene models based on ab initio gene prediction and evidence-based annotation procedure using RNAseq data. The annotated genome was predicted to have 19 terpene biosynthesis gene clusters, which was the same number as the previously sequenced W. cocos strain MD-104 genome but higher than Chinese W. cocos strains. The genome sequence and the predicted gene clusters allow us to study biosynthetic pathways for the active ingredients of W. cocos.

• Korean Journal of Microbiology
• /
• v.55 no.3
• /
• pp.303-305
• /
• 2019

An actinobacterial strain designated Gordonia sp. MMS17-SY073 (=KCTC 49257) was isolated from a coastal soil of an island, and its complete genome was analyzed. A single contig consisting of 5,962,176 bp with the G + C content of 67.4% was obtained, and the annotation resulted in 5,201 protein-coding genes, 6 rRNA genes and 45 tRNA genes. Strain MMS17-SY073 was closest to the type strain of Gordonia soli based on the 16S rRNA gene sequence comparison, sharing 98.5% sequence similarity. A number of biosynthetic gene clusters for secondary metabolites, non-ribosomal peptide synthetase types in particular, could be identified from the genome.

• Journal of Microbiology and Biotechnology
• /
• v.25 no.10
• /
• pp.1648-1652
• /
• 2015

Azaphilone polyketides are synthesized by iterative non-reducing fungal polyketide synthases (NR-fPKSs) with a C-terminus reductive domain (-R). Several azaphilone biosynthetic gene clusters contain a putative serine hydrolase gene; the Monascus azaphilone pigment (MAzP) gene cluster harbors mppD. The MAzP productivity was significantly reduced by a knockout of mppD, and the MAzP NR-fPKS-R gene (MpPKS5) generated its product in yeast only when co-expressed with mppD. Site-directed mutations of mppD for conserved Ser/Asp/His residues abolished the product formation from the MpPKS5/mppD co-expression. MppD and its homologs are thus proposed as a new protein factor involved in the product formation of NR-fPKS-R.

• Microbiology and Biotechnology Letters
• /
• v.37 no.4
• /
• pp.316-321
• /
• 2009

We have isolated Chondromyces crocatus KYC2823 in pure culture and five other strains in mixed culture with companion bacteria from Korean soil samples. The strain KYC2823, which was isolated from the soil sample collected in Cheongdo-gun, Gyeongsangbuk-do, showed typical characteristics of C. crocatus, including the shape of fruiting bodies and production of a peculiar odor. In addition, the 16S rDNA sequence was 99.8% identical to that of the strain Cm c5, the proposed neotype strain of C. crocatus. Cloning and sequence analysis of the polyketide biosynthetic genes from KYC2823 by performing PCR have revealed that this strain has biosynthetic gene clusters for ajudazols (inhibitors of electron transport systems) and chondramides (substances affecting the function of the actin cytoskeleton), and biosynthetic genes for other polyketide compounds that have not been cloned yet.

• Journal of Applied Biological Chemistry
• /
• v.62 no.2
• /
• pp.157-165
• /
• 2019

Di- and tri-methylation of lysine 4 on histone H3 (H3K4me2 and H3K4me3, respectively) are epigenetic markers of active genes. Complex associated with Set1 (COMPASS) mediates these H3K4 methylations. The involvement of COMPASS activity in secondary metabolite (SM) biosynthesis was first demonstrated with an Aspergillus nidulans cclA knockout mutant. The cclA knockout induced the transcription of two cryptic SM biosynthetic gene clusters, leading to the production of the cognate SM. Monascus spp. are filamentous fungi that have been used for food fermentation in eastern Asia, and the pigment Monascus azaphione (MAz) is their main SM. Monascus highly produces MAz, implying that the cognate biosynthetic genes are highly active in transcription. In the present study, we examined how COMPASS activity modulates MAz biosynthesis by inactivating Monascus purpureus cclA (Mp-cclA) and swd1 (Mp-swd1). For both ${\Delta}Mp-cclA$ and ${\Delta}Mp-swd1$, a reduction in MAz production, accompanied by an abated cell growth, was observed. Suppression of MAz production was more effective in an agar culture than in the submerged liquid culture. The fidelity of the ${\Delta}Mp-swd1$ phenotypes was verified by restoring the WT-like phenotypes in a reversion recombinant mutant, namely, trpCp: Mp-swd1, that was generated from the ${\Delta}Mp-swd1$ mutant. Real-time quantitative Polymerase chain reaction analysis indicated that the transcription of MAz biosynthetic genes was repressed in the ${\Delta}Mp-swd1$ mutant. This study demonstrated that MAz biosynthesis is under the control of COMPASS activity and that the extent of this regulation is dependent on growth conditions.

• Microbiology and Biotechnology Letters
• /
• v.51 no.3
• /
• pp.325-327
• /
• 2023

This paper presents the complete genome sequence of a novel marine actinomycete, Streptomyces sp. MMBL 11-1. The genome of Streptomyces sp. MMBL 11-1 was obtained through next-generation sequencing using the PacBio Sequel system and Illumina platform provided by Macrogen, Korea. The assembled genome consists of five contigs, with a total length of 8,496,900 bp and a G+C content of 71.6%. The genome harbors multiple biosynthetic gene clusters (BGCs) associated with producing microbial natural products (MNPs). The comprehensive genomic information of this type of strain will serve as a valuable resource for identifying other marine actinomycetes strains.