• Journal of Microbiology and Biotechnology
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• 제30권3호
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• pp.417-426
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• 2020

Bacillus amyloliquefaciens is an important plant disease-preventing and growth-promoting microorganism. B. amyloliquefaciens WS-8 can stimulate plant growth and has strong antifungal properties. In this study, we sequenced the complete genome of B. amyloliquefaciens WS-8 by Pacific Biosciences RSII (PacBio) Single Molecule Real-Time (SMRT) sequencing. The genome consists of one chromosome (3,929,787 bp) and no additional plasmids. The main bacteriostatic substances were determined by genome, transcriptome, and mass spectrometry data. We thereby laid a theoretical foundation for the utilization of the strain. By genomic analysis, we identified 19 putative biosynthetic gene clusters for secondary metabolites, most of which are potentially involved in the biosynthesis of numerous bioactive metabolites, including difficidin, fengycin, and surfactin. Furthermore, a potential class II lanthipeptide biosynthetic gene cluster and genes that are involved in auxin biosynthesis were found. Through the analysis of transcriptome data, we found that the key bacteriostatic genes, as predicted in the genome, exhibited different levels of mRNA expression. Through metabolite isolation, purification, and exposure experiments, we found that a variety of metabolites of WS-8 exert an inhibitory effect on the necrotrophic fungus Botrytis cinerea, which causes gray mold; by mass spectrometry, we found that the main substances are mainly iturins and fengycins. Therefore, this strain has the potential to be utilized as an antifungal agent in agriculture.

• Molecules and Cells
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• 제27권1호
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• pp.83-88
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• 2009

Amino acid homology analysis predicted that rbmD, a putative glycosyltransferase from Streptomyces ribosidificus ATCC 21294, has the highest homology with neoD in neomycin biosynthesis. S. fradiae BS1, in which the production of neomycin was abolished, was generated by disruption of the neoD gene in the neomycin producer S. fradiae. The restoration of neomycin by self complementation suggested that there was no polar effect in the mutant. In addition, S. fradiae BS6 was created with complementation by rbmD in S. fradiae BS1, and secondary metabolite analysis by ESI/MS, LC/MS and MS/MS showed the restoration of neomycin production in S. fradiae BS6. These gene inactivation and complementation studies suggested that, like neoD, rbmD functions as a 2-N-acetlyglucosaminyltransferase and demonstrated the potential for the generation of novel aminoglycoside antibiotics using glycosyltransferases in vivo.

• Mycobiology
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• 제50권4호
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• pp.254-257
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• 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.

• Journal of Microbiology and Biotechnology
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• 제31권4호
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• pp.601-609
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• 2021

Erythrobacter species are extensively studied marine bacteria that produce various carotenoids. Due to their photoheterotrophic ability, it has been suggested that they play a crucial role in marine ecosystems. It is essential to identify the genome sequence and the genes of the species to predict their role in the marine ecosystem. In this study, we report the complete genome sequence of the marine bacterium Erythrobacter sp. 3-20A1M. The genome size was 3.1 Mbp and its GC content was 64.8%. In total, 2998 genetic features were annotated, of which 2882 were annotated as functional coding genes. Using the genetic information of Erythrobacter sp. 3-20A1M, we performed pan-genome analysis with other Erythrobacter species. This revealed highly conserved secondary metabolite biosynthesis-related COG functions across Erythrobacter species. Through subsequent secondary metabolite biosynthetic gene cluster prediction and KEGG analysis, the carotenoid biosynthetic pathway was proven conserved in all Erythrobacter species, except for the spheroidene and spirilloxanthin pathways, which are only found in photosynthetic Erythrobacter species. The presence of virulence genes, especially the plant-algae cell wall degrading genes, revealed that Erythrobacter sp. 3-20A1M is a potential marine plant-algae scavenger.

• Journal of Applied Biological Chemistry
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• 제61권1호
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• pp.83-91
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• 2018

박테리아와 진균의 유전체 정보 탐색을 통하여 이차대사 생합성을 지정하는 다수의 잠재 유전자군을 찾을 수 있으며, 유전체 정보를 기반으로 특정 유전자의 발현을 활성화하여 잠재 유전자군의 생성물을 추론하고, 해당 물질의 생물학적 기능을 연구하는 것이 가능하다. 동아시아 지역에서 잘 알려진 식용 사상진균 홍국에 대하여 몇 몇 유전체 정보가 공개되어있으며, 본 연구에서는 Monascus purpureus ${\Delta}MpPKS5$ 균주에서 polyketide synthase-nonribosomal peptide synthase 유전자 Mpfus1 상단에 Aspergillus gpdA 프로모터를 삽입하는 방식으로 이 유전자의 발현을 활성화하였다. Mpfus1 유전자군은 2-pyrrolidone/conjugated polyene 구조를 갖는 물질의 생합성 유전자군들과 높은 유사성을 보이며, 이들 화합물 그룹에서 진균 독소인 fusarin이 잘 알려져 있다. ${\Delta}MpPKS5$ 균주는 홍국 azaphilone 색소 생산 능력이 소실된 균주이며 색소 및 자외선 흡수 특성을 보이는 화합물들의 동정에 적절한 균주이다. Mpfus1 활성화는 균사체가 노란색을 띠도록 유도하며, 균사체의 methanol 추출액은 365 nm에서 최대 흡광도를 보임을 확인할 수 있었다. 해당 추출액의 HPLC 분석을 통하여 다수의 화합물들이 포함되어 있음을 확인할 수 있었으며 이를 통하여 MpFus1 효소의 생성물이 대사적, 화학적으로 불안정함을 추론할 수 있다. Mpfus1 활성화 균주 추출물을 LC-MS로 분석하여 MpFus1 생성물의 구조를 유추하여 Mpfus1 유전자군이 fusarin의 탈메틸 유사체 생합성을 지정하는 것으로 제안할 수 있었다. 본 연구는 홍국 균주에서 유전체 기반-미지 화합물 발굴 연구의 예를 제시하고 홍국 균주에서 새로운 생리활성의 동정 가능성을 시사하여 준다.