antiSMASH 7.0: new and improved predictions for detection, regulation, chemical structures and visualisation

Blin, Kai; Shaw, Simon J.; Augustijn, Hannah E.; Reitz, Zachary L.; Biermann, Friederike; Alanjary, Mohammad; Fetter, Artem; Terlouw, Barbara R.; Metcalf, William W.; Helfrich, Eric J. N.; Wezel, Gilles P. van; Medema, Marnix H.; Weber, Tilmann

doi:10.1093/nar/gkad344

Cited by 375 publications

(297 citation statements)

References 40 publications

(42 reference statements)

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“…It has been previously reported that variation in culture pH can affect metabolite production. , In an attempt to activate silent BGCs, the ROS-forming strain S. indonesiensis DSM41759, which harbors 51 BGCs based on antiSMASH analysis of the genome sequence (NCBI accession no. JAGSHY000000000), was grown in R5A-rich media at four different pH (pH 5.4, 6.4, 7.4, and 8.4).…”

Section: Results and Discussionmentioning

confidence: 99%

Acidonemycins A–C, Glycosylated Angucyclines with Antivirulence Activity Produced by the Acidic Culture of Streptomyces indonesiensis

Kim,

et al. 2023

J. Nat. Prod.

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The genome of Streptomyces indonesiensis is highly enriched with cryptic biosynthetic gene clusters (BGCs). The majority of these cryptic BGCs are transcriptionally silent in normal laboratory culture conditions as determined by transcriptome analysis. When cultured in acidic pH (pH 5.4), this strain has been shown to produce a set of new metabolites that were not observed in cultures of neutral pH (pH 7.4). The organic extract of the acidic culture displayed an antivirulence activity against methicillin-resistant Staphylococcus aureus (MRSA). Here, we report the structures of new glycosylated aromatic polyketides, named acidonemycins A−C (1−3), belonging to the family of angucyclines. Type II polyketide synthase BGC responsible for the production of 1−3 was identified by a transcriptome comparison between acidic (pH 5.4) and neutral (pH 7.4) cultures and further confirmed by heterologous expression in Streptomyces albus J1074. Of the three new compounds, acidonemycins A and B (1 and 2) displayed antivirulence activity against MRSA. The simultaneous identification of both antivirulent compounds and their BGC provides a starting point for the future effort of combinatorial biosynthesis.

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Section: Results and Discussionmentioning

confidence: 99%

Acidonemycins A–C, Glycosylated Angucyclines with Antivirulence Activity Produced by the Acidic Culture of Streptomyces indonesiensis

Kim,

et al. 2023

J. Nat. Prod.

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“…The genomic signature sequences of the RAST-annotated strain GXMU-J15 T and its closely related strains were analysed for comparative homology by the OrthoVenn2 [46] online tool. The secondary metabolite biosynthesis gene clusters (smBGCs) in the bacterial genomes were evaluated using the anti-SMASH 7.0 [47]. The average nucleotide identity (ANI) values of this strain and its closely related strains were computed by pairwise calculations using the ANI- blast (ANIb) and ANI-MUMmer (ANIm) algorithms [48] on the JSpecies Web Server [49], respectively.…”

Section: Methodsmentioning

confidence: 99%

Streptomyces fuscus sp. nov., a brown-black pigment producing actinomycete isolated from dry mudflat sand

Xie,

Zhang,

et al. 2023

International Journal of Systematic and Evolutionary Microbiology

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A novel Gram-stain-positive, aerobic actinobacterial strain, designated GXMU-J15T, was isolated from dry mudflat sand. A polyphasic approach was employed for its taxonomic characterization. The strain developed extensively branched yellowish white to light yellow substrate mycelia and white aerial mycelia, and produced smooth cylindrical spores in a loose straight spore chain on International Streptomyces Project 2–7 agar media. Strain GXMU-J15T grew at 20–50 °C (optimum, 35 °C), at pH 5.0–8.0 (optimum, pH 7.0) and in the presence of 0–8 % (w/v) NaCl. Analysis of 16S rRNA gene sequences indicated that strain GXMU-J15T represents a member of the genus Streptomyces . Strain GXMU-J15T showed the highest 16S rRNA gene sequence similarity to Streptomyces lusitanus CGMCC 4.1745T (99.1 %) and Streptomyces thermocarboxydus CGMCC 4.1883T (98.8 %). Phylogenetic tree analysis based on multilocus sequence analysis (MLSA) and whole genome sequence construction revealed that strain GXMU-J15T was most closely related to Streptomyces cupreus PSKA01T, Streptomyces cinnabarinus DSM 40467T and Streptomyces davaonensis JCM 4913T. The MLSA and genome-to-genome distances between strain GXMU-J15T and its relatives were 0.0418, 0.0443 and 0.0485 and 0.1237, 0.1188 and 0.1179, respectively. The results of orthologous average nucleotide identity and digital DNA–DNA hybridization analysis corroborated the results of the MLSA and whole genome sequence evolution analysis, indicating that the novel isolate represents a distinct species of the genus Streptomyces . The whole-cell sugars of strain GXMU-J15T were xylose, glucose and galactose. The characteristic diamino acid in the cell-wall hydrolysate was ll-diaminopimelic acid. The lipids contained diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine, phosphatidylinositol, phosphatidylglycerol, phosphatidylglycerides, phosphatidylcholine, two phospholipids of an unknown structure containing glucosamine, one unknown phospholipid and two unknown lipids. The major cellular fatty acid components were iso-C15 : 0, anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. The main respiratory quinone types were MK-9(H6) and MK-9(H8). The whole genome size of strain GXMU-J15T was 8.68 Mbp, with 71.23 mol% G+C content. Genomic analysis indicated that strain GXMU-J15T has the potential to synthesize polyketides, terpenes and a series of important antibiotics besides the gene cluster for melanin synthesis. Based on these genotypic and phenotypic data, strain GXMU-J15T is proposed to represent a new species of the genus Streptomyces named Streptomyces fuscus sp. nov. The type strain is GXMU-J15T (=MCCC 1K08211T=JCM 35917T).

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“…The draft genome was explicated using Rapid Annotation using Subsystem Technology ( rast ) [38] and the NCBI PGAP. The genes involved in the secondary metabolism were predicted using antiSMASH 7.0 [39]. The comparison of the orthologous clusters (OCs) among strains chi3 T and sf7 T , as well as the closely related members of Alteromonas and Erythrobacter , was conducted using the Ortho Venn2 online tool [40].…”

Section: Methodsmentioning

confidence: 99%

Alteromonas gilva sp. nov. and Erythrobacter fulvus sp. nov., isolated from a tidal mudflat

Park,

Kim,

Chhetri

et al. 2023

International Journal of Systematic and Evolutionary Microbiology

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Strains chi3T and sf7T were collected from a tidal mudflat around Dongmak beach in Ganghwa, Republic of Korea. Both strains were Gram-stain-negative, aerobic or facultatively anaerobic, and rod-shaped. Results of phylogenetic tree analysis based on 16S rRNA and whole-genome sequences suggested that strains chi3T and sf7T belong to the genera Alteromonas and Erythrobacter , respectively. The cells of strain chi3T were non-motile and grew at 15–45 °C (optimum, 38 °C), at pH 6.0–10.0 (optimum, pH 8.0) and in the presence of 0–9.0 % (w/v) NaCl (optimum, 2.0 %). The cells of strain sf7T were motile as they had flagella and grew at 20–48 °C (optimum, 38 °C), at pH 6.0–10.0 (optimum, pH 9.0) and in the presence of 0–5.0 % (w/v) NaCl (optimum, 1.0 %). Strains chi3T and sf7T have average nucleotide identity values (70.0–70.4% and 78.9–81.7 %) and digital DNA–DNA hybridization values (21.8–22.3% and 21.0–25.6 %) with reference strains in the genera Alteromonas and Erythrobacter , respectively. Data from digital DNA–DNA hybridization, as well as phylogenetic, biochemical and physiological analyses, indicated the distinction of the two strains from the genera Alteromonas and Erythrobacter , respectively, and we thus propose the names Alteromonas gilva sp. nov. (type strain chi3T=KACC 22866T=TBRC 16612T) and Erythrobacter fulvus sp. nov. (type strain sf7T=KACC 22865T=TBRC 16611T).

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antiSMASH 7.0: new and improved predictions for detection, regulation, chemical structures and visualisation

Cited by 375 publications

References 40 publications

Acidonemycins A–C, Glycosylated Angucyclines with Antivirulence Activity Produced by the Acidic Culture of Streptomyces indonesiensis

Acidonemycins A–C, Glycosylated Angucyclines with Antivirulence Activity Produced by the Acidic Culture of Streptomyces indonesiensis

Streptomyces fuscus sp. nov., a brown-black pigment producing actinomycete isolated from dry mudflat sand

Alteromonas gilva sp. nov. and Erythrobacter fulvus sp. nov., isolated from a tidal mudflat

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