scholarly journals ClustScan : an integrated program package for the semi-automatic annotation of modular biosynthetic gene clusters and in silico prediction of novel chemical structures

2008 ◽  
Vol 36 (21) ◽  
pp. 6882-6892 ◽  
Author(s):  
Antonio Starcevic ◽  
Jurica Zucko ◽  
Jurica Simunkovic ◽  
Paul F. Long ◽  
John Cullum ◽  
...  
Keyword(s):  
In Silico ◽  
Gene Clusters ◽  
Program Package ◽  
Automatic Annotation ◽  
Biosynthetic Gene ◽  
In Silico Prediction ◽  
Biosynthetic Gene Clusters ◽  
Chemical Structures ◽  
Integrated Program

scholarly journals Recent development of antiSMASH and other computational approaches to mine secondary metabolite biosynthetic gene clusters

2017 ◽  
Vol 20 (4) ◽  
pp. 1103-1113 ◽  
Author(s):  
Kai Blin ◽  
Hyun Uk Kim ◽  
Marnix H Medema ◽  
Tilmann Weber
Keyword(s):  
Natural Products ◽  
Small Molecules ◽  
Sequence Similarity ◽  
Genome Mining ◽  
Gene Clusters ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Rule Based ◽  
Chemical Structures ◽  
Annotation Quality

Abstract Many drugs are derived from small molecules produced by microorganisms and plants, so-called natural products. Natural products have diverse chemical structures, but the biosynthetic pathways producing those compounds are often organized as biosynthetic gene clusters (BGCs) and follow a highly conserved biosynthetic logic. This allows for the identification of core biosynthetic enzymes using genome mining strategies that are based on the sequence similarity of the involved enzymes/genes. However, mining for a variety of BGCs quickly approaches a complexity level where manual analyses are no longer possible and require the use of automated genome mining pipelines, such as the antiSMASH software. In this review, we discuss the principles underlying the predictions of antiSMASH and other tools and provide practical advice for their application. Furthermore, we discuss important caveats such as rule-based BGC detection, sequence and annotation quality and cluster boundary prediction, which all have to be considered while planning for, performing and analyzing the results of genome mining studies.

scholarly journals In silico exploration of Red Sea Bacillus genomes for natural product biosynthetic gene clusters

BMC Genomics ◽  
2018 ◽  
Vol 19 (1) ◽  
Author(s):  
Ghofran Othoum ◽  
Salim Bougouffa ◽  
Rozaimi Razali ◽  
Ameerah Bokhari ◽  
Soha Alamoudi ◽  
...  
Keyword(s):  
Natural Product ◽  
Red Sea ◽  
In Silico ◽  
Gene Clusters ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters

scholarly journals Mining of Cyanobacterial Genomes Indicates That Plasmids Are Involved in the Production of Natural Products

2020 ◽  
Author(s):  
Rafael Popin ◽  
Danillo Alvarenga ◽  
Raquel Castelo-Branco ◽  
David Fewer ◽  
Kaarina Sivonen
Keyword(s):  
Natural Products ◽  
Natural Product ◽  
Biological Activities ◽  
Gene Clusters ◽  
Biosynthetic Pathways ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Chemical Structures ◽  
Wide Range ◽  
Genes Encoding

Abstract Background Microbial natural products have unique chemical structures and diverse biological activities. Cyanobacteria commonly possess a wide range of biosynthetic gene clusters to produce natural products. Several studies have mapped the distribution of natural product biosynthetic gene clusters in cyanobacterial genomes. However, little attention has been paid to natural product biosynthesis in plasmids. Some genes encoding cyanobacterial natural product biosynthetic pathways are believed to be dispersed by plasmids through horizontal gene transfer. Thus, we examined complete cyanobacterial genomes to assess if plasmids are involved in the production and dissemination of natural products by cyanobacteria.Results The 185 analyzed genomes possessed 1 to 42 gene clusters and an average of 10. In total, 1816 biosynthetic gene clusters were found. Approximately 95% of these clusters were present in chromosomes. The remaining 5% were present in plasmids, from which homologs of the biosynthetic pathways for aeruginosin, anabaenopeptin, ambiguine, cryptophycin, hassallidin, geosmin, and microcystin were manually curated. The cryptophycin pathway was previously described as active while the other gene cluster include all genes for biosynthesis. Approximately 12% of the 424 analyzed cyanobacterial plasmids contained homologs of genes involved in conjugation. Large plasmids, previously named as “chromids”, were also observed to be widespread in cyanobacteria. Sixteen cryptic natural product biosynthetic gene clusters and geosmin biosynthetic gene clusters were located in those mobile plasmids.Conclusion Homologues of genes involved in the production of toxins, protease inhibitors, odorous compounds, antimicrobials, antitumorals, and other unidentified natural products are located in cyanobacterial plasmids. Some of these plasmids are predicted to be conjugative. The present study provides in silico evidence that plasmids are involved in the distribution of natural product biosynthetic pathways in cyanobacteria.

scholarly journals Antimicrobial Activities of Lipopeptides and Polyketides of Bacillus velezensis for Agricultural Applications

Molecules ◽  
2020 ◽  
Vol 25 (21) ◽  
pp. 4973
Author(s):  
Muhammad Fazle Rabbee ◽  
Kwang-Hyun Baek
Keyword(s):  
Secondary Metabolites ◽  
Gene Clusters ◽  
Bioactive Metabolites ◽  
Bacillus Species ◽  
Biological Applications ◽  
Biosynthetic Gene ◽  
Bacillus Velezensis ◽  
Biosynthetic Gene Clusters ◽  
Chemical Structures ◽  
Plant Disease Management

Since the discovery of penicillin, bacteria are known to be major sources of secondary metabolites that can function as drugs or pesticides. Scientists worldwide attempted to isolate novel compounds from microorganisms; however, only less than 1% of all existing microorganisms have been successfully identified or characterized till now. Despite the limitations and gaps in knowledge, in recent years, many Bacillus velezensis isolates were identified to harbor a large number of biosynthetic gene clusters encoding gene products for the production of secondary metabolites. These chemically diverse bioactive metabolites could serve as a repository for novel drug discovery. More specifically, current projects on whole-genome sequencing of B. velezensis identified a large number of biosynthetic gene clusters that encode enzymes for the synthesis of numerous antimicrobial compounds, including lipopeptides and polyketides; nevertheless, their biological applications are yet to be identified or established. In this review, we discuss the recent research on synthesis of bioactive compounds by B. velezensis and related Bacillus species, their chemical structures, bioactive gene clusters of interest, as well as their biological applications for effective plant disease management.

scholarly journals Genome-Inspired Chemical Exploration of Marine Fungus Aspergillus fumigatus MF071

Marine Drugs ◽  
2020 ◽  
Vol 18 (7) ◽  
pp. 352
Author(s):  
Jianying Han ◽  
Miaomiao Liu ◽  
Ian D. Jenkins ◽  
Xueting Liu ◽  
Lixin Zhang ◽  
...  
Keyword(s):  
Minimum Inhibitory Concentration ◽  
Aspergillus Fumigatus ◽  
Inhibitory Concentration ◽  
Gene Clusters ◽  
2D Nmr ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Strong Activity ◽  
Chemical Structures ◽  
New Compounds

The marine-derived fungus Aspergillus fumigatus MF071, isolated from sediment collected from the Bohai Sea, China, yielded two new compounds 19S,20-epoxy-18-oxotryprostatin A (1) and 20-hydroxy-18-oxotryprostatin A (2), in addition to 28 known compounds (3–30). The chemical structures were established on the basis of 1D, 2D NMR and HRESIMS spectroscopic data. This is the first report on NMR data of monomethylsulochrin-4-sulphate (4) and pseurotin H (10) as naturally occurring compounds. Compounds 15, 16, 20, 23, and 30 displayed weak antibacterial activity (minimum inhibitory concentration: 100 μg/mL). Compounds 18 and 19 exhibited strong activity against S. aureus (minimum inhibitory concentration: 6.25 and 3.13 μg/mL, respectively) and E. coli (minimum inhibitory concentration: 6.25 and 3.13 μg/mL, respectively). A genomic data analysis revealed the putative biosynthetic gene clusters ftm for fumitremorgins, pso for pseurotins, fga for fumigaclavines, and hel for helvolinic acid. These putative biosynthetic gene clusters fundamentally underpinned the enzymatic and mechanistic function study for the biosynthesis of these compounds. The current study reported two new compounds and biosynthetic gene clusters of fumitremorgins, pseurotins, fumigaclavines and helvolinic acid from Aspergillus fumigatus MF071.

In silico genome mining of potential novel biosynthetic gene clusters for drug discovery from Burkholderia bacteria

2021 ◽  
pp. 105046
Author(s):  
Khorshed Alam ◽  
Md Mahmudul Islam ◽  
Kai Gong ◽  
Muhammad Nazeer Abbasi ◽  
Ruijuan Li ◽  
...  
Keyword(s):  
Drug Discovery ◽  
In Silico ◽  
Genome Mining ◽  
Gene Clusters ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters
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