scholarly journals Applications and Restrictions of Integrated Genomic and Metabolomic Screening: An Accelerator for Drug Discovery from Actinomycetes?

Molecules ◽  
2021 ◽  
Vol 26 (18) ◽  
pp. 5450
Author(s):  
Janina Krause
Keyword(s):  
Biosynthetic Gene Cluster ◽  
Biosynthetic Gene ◽  
Compound Identification ◽  
Bioactive Natural Products ◽  
Cluster Identification ◽  
Actinomyces Species ◽  
Bioinformatical Analysis ◽  
New Antibiotics ◽  
Bioactive Agents ◽  
New Procedures

Since the golden age of antibiotics in the 1950s and 1960s actinomycetes have been the most prolific source for bioactive natural products. However, the number of discoveries of new bioactive compounds decreases since decades. New procedures (e.g., activating strategies or innovative fermentation techniques) were developed to enhance the productivity of actinomycetes. Nevertheless, compound identification remains challenging among others due to high rediscovery rates. Rapid and cheap genome sequencing as well as the advent of bioinformatical analysis tools for biosynthetic gene cluster identification in combination with mass spectrometry-based molecular networking facilitated the tedious process of dereplication. In recent years several studies have been dedicated to accessing the biosynthetic potential of Actinomyces species, especially streptomycetes, by using integrated genomic and metabolomic screening in order to boost the discovery rate of new antibiotics. This review aims to present the various possible applications of this approach as well as the newly discovered molecules, covering studies between 2014 and 2021. Finally, the effectiveness of this approach with regard to find new bioactive agents from actinomycetes will be evaluated.

scholarly journals Further biochemical profiling of Hypholoma fasciculare metabolome reveals its chemogenetic diversity

2020 ◽  
Author(s):  
Suhad A.A. Al-Salihi ◽  
Ian Bull ◽  
Raghad A. Al-Salhi ◽  
Paul J. Gates ◽  
Kifah Salih ◽  
...  
Keyword(s):  
Natural Products ◽  
Chemical Properties ◽  
Structural Diversity ◽  
Gene Clusters ◽  
Biosynthetic Gene Cluster ◽  
Biosynthetic Gene ◽  
Microbial Drug Resistance ◽  
Bioactive Natural Products ◽  
Highly Active ◽  
Comprehensive Picture

AbstractThere is a desperate need in continuing the search for natural products with novel mechanism to battle the constant increase of microbial drug resistance. Previously mushroom forming fungi were neglected as a source of novel antibiotics, due to the difficulties associated with their culture preparation and genetic tractability. However, modern fungal molecular and synthetic biology tools, renewed the interest in exploring mushroom fungi for novel therapeutics. The aim of this study was to have a comprehensive picture of nine basidiomycetes secondary metabolites (SM), screen their biological and chemical properties to describe the genetic pathways associated with their production. H. fasciculare revealed to be highly active antagonistic species, with antimicrobial activity against three different microorganisms - Bacillus subtilis, Escherichia coli and Saccharomyces cerevisiae-. Extensive genomic comparison and chemical analysis using analytical chromatography, led to the characterisation of more than 15 variant biosynthetic gene clusters and the first identification of a potent antibacterial metabolite-3, 5-dichloromethoxy benzoic acid (3, 5-D)-in this species, for which a biosynthetic gene cluster was predicted. This work demonstrates the great potential of mushroom forming fungi as a reservoir of bioactive natural products which are currently unexplored, and that access to their genomic data and structural diversity natural products via utilizing modern computational analysis and efficient chemical methods, could accelerate the development and applications of such distinct molecules in both pharmaceutical and agrochemical industry.

scholarly journals Further Biochemical Profiling of Hypholoma fasciculare Metabolome Reveals Its Chemogenetic Diversity

2021 ◽  
Vol 9 ◽  
Author(s):  
Suhad A. A. Al-Salihi ◽  
Ian D. Bull ◽  
Raghad Al-Salhi ◽  
Paul J. Gates ◽  
Kifah S. M. Salih ◽  
...  
Keyword(s):  
Natural Products ◽  
Chemical Properties ◽  
Gene Clusters ◽  
Biosynthetic Gene Cluster ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Microbial Drug Resistance ◽  
Bioactive Natural Products ◽  
Highly Active ◽  
Hypholoma Fasciculare

Natural products with novel chemistry are urgently needed to battle the continued increase in microbial drug resistance. Mushroom-forming fungi are underutilized as a source of novel antibiotics in the literature due to their challenging culture preparation and genetic intractability. However, modern fungal molecular and synthetic biology tools have renewed interest in exploring mushroom fungi for novel therapeutic agents. The aims of this study were to investigate the secondary metabolites of nine basidiomycetes, screen their biological and chemical properties, and then investigate the genetic pathways associated with their production. Of the nine fungi selected, Hypholoma fasciculare was revealed to be a highly active antagonistic species, with antimicrobial activity against three different microorganisms: Bacillus subtilis, Escherichia coli, and Saccharomyces cerevisiae. Genomic comparisons and chromatographic studies were employed to characterize more than 15 biosynthetic gene clusters and resulted in the identification of 3,5-dichloromethoxy benzoic acid as a potential antibacterial compound. The biosynthetic gene cluster for this product is also predicted. This study reinforces the potential of mushroom-forming fungi as an underexplored reservoir of bioactive natural products. Access to genomic data, and chemical-based frameworks, will assist the development and application of novel molecules with applications in both the pharmaceutical and agrochemical industries.

scholarly journals Interplay between nucleoid-associated proteins and transcription factors in controlling specialized metabolism in Streptomyces

2021 ◽  
Author(s):  
Xiafei Zhang ◽  
Sara N. Andres ◽  
Marie A. Elliot
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Rna Polymerase ◽  
Antibiotic Production ◽  
Biosynthetic Gene Cluster ◽  
Regulatory Proteins ◽  
Biosynthetic Gene ◽  
Bioactive Natural Products ◽  
Associated Proteins ◽  
Insight Into

Lsr2 is a small nucleoid-associated protein found throughout the actinobacteria. Lsr2 functions similarly to the well-studied H-NS, in that it preferentially binds AT-rich sequences and represses gene expression. In Streptomyces venezuelae, Lsr2 represses the expression of many specialized metabolic clusters, including the chloramphenicol antibiotic biosynthetic gene cluster, and deleting lsr2 leads to significant upregulation of chloramphenicol cluster expression. We show here that Lsr2 likely exerts its repressive effects on the chloramphenicol cluster by polymerizing along the chromosome, and by bridging sites within and adjacent to the chloramphenicol cluster. CmlR is a known activator of the chloramphenicol cluster, but expression of its associated gene is not upregulated in an lsr2 mutant strain. We demonstrate that CmlR is essential for chloramphenicol production, and further reveal that CmlR functions to 'counter-silence' Lsr2's repressive effects by recruiting RNA polymerase and enhancing transcription, with RNA polymerase effectively clearing bound Lsr2 from the chloramphenicol cluster DNA. Our results provide insight into the interplay between opposing regulatory proteins that govern antibiotic production in S. venezuelae, which could be exploited to maximize the production of bioactive natural products in other systems.

scholarly journals Cytosine Base Editor-Mediated Multiplex Genome Editing to Accelerate Discovery of Novel Antibiotics in Bacillus subtilis and Paenibacillus polymyxa

2021 ◽  
Vol 12 ◽  
Author(s):  
Man Su Kim ◽  
Ha-Rim Kim ◽  
Da-Eun Jeong ◽  
Soo-Keun Choi
Keyword(s):  
Bacillus Subtilis ◽  
Genome Editing ◽  
Paenibacillus Polymyxa ◽  
Gene Clusters ◽  
Biosynthetic Gene Cluster ◽  
Antimicrobial Activities ◽  
Biosynthetic Gene ◽  
Single Nucleotide Variants ◽  
New Antibiotics ◽  
Bacteria And Fungi

Genome-based identification of new antibiotics is emerging as an alternative to traditional methods. However, uncovering hidden antibiotics under the background of known antibiotics remains a challenge. To over this problem using a quick and effective genetic approach, we developed a multiplex genome editing system using a cytosine base editor (CBE). The CBE system achieved simultaneous double, triple, quadruple, and quintuple gene editing with efficiencies of 100, 100, 83, and 75%, respectively, as well as the 100% editing efficiency of single targets in Bacillus subtilis. Whole-genome sequencing of the edited strains showed that they had an average of 8.5 off-target single-nucleotide variants at gRNA-independent positions. The CBE system was used to simultaneously knockout five known antibiotic biosynthetic gene clusters to leave only an uncharacterized polyketide biosynthetic gene cluster in Paenibacillus polymyxa E681. The polyketide showed antimicrobial activities against gram-positive bacteria, but not gram-negative bacteria and fungi. Therefore, our findings suggested that the CBE system might serve as a powerful tool for multiplex genome editing and greatly accelerating the unraveling of hidden antibiotics in Bacillus and Paenibacillus species.

scholarly journals ARTS 2.0: feature updates and expansion of the Antibiotic Resistant Target Seeker for comparative genome mining

2020 ◽  
Vol 48 (W1) ◽  
pp. W546-W552 ◽  
Author(s):  
Mehmet Direnç Mungan ◽  
Mohammad Alanjary ◽  
Kai Blin ◽  
Tilmann Weber ◽  
Marnix H Medema ◽  
...  
Keyword(s):  
Secondary Metabolites ◽  
Resistance Genes ◽  
Target Genes ◽  
Genome Mining ◽  
Biosynthetic Gene Cluster ◽  
Metagenomic Data ◽  
Drug Resistant ◽  
Biosynthetic Gene ◽  
Antibiotic Resistant ◽  
New Antibiotics

Abstract Multi-drug resistant pathogens have become a major threat to human health and new antibiotics are urgently needed. Most antibiotics are derived from secondary metabolites produced by bacteria. In order to avoid suicide, these bacteria usually encode resistance genes, in some cases within the biosynthetic gene cluster (BGC) of the respective antibiotic compound. Modern genome mining tools enable researchers to computationally detect and predict BGCs that encode the biosynthesis of secondary metabolites. The major challenge now is the prioritization of the most promising BGCs encoding antibiotics with novel modes of action. A recently developed target-directed genome mining approach allows researchers to predict the mode of action of the encoded compound of an uncharacterized BGC based on the presence of resistant target genes. In 2017, we introduced the ‘Antibiotic Resistant Target Seeker’ (ARTS). ARTS allows for specific and efficient genome mining for antibiotics with interesting and novel targets by rapidly linking housekeeping and known resistance genes to BGC proximity, duplication and horizontal gene transfer (HGT) events. Here, we present ARTS 2.0 available at http://arts.ziemertlab.com. ARTS 2.0 now includes options for automated target directed genome mining in all bacterial taxa as well as metagenomic data. Furthermore, it enables comparison of similar BGCs from different genomes and their putative resistance genes.

scholarly journals Biosynthetic gene cluster identification and biological activity of lucilactaene from Fusarium sp. RK97-94

2020 ◽  
Vol 84 (6) ◽  
pp. 1303-1307 ◽  
Author(s):  
Sho Kato ◽  
Takayuki Motoyama ◽  
Yushi Futamura ◽  
Masakazu Uramoto ◽  
Toshihiko Nogawa ◽  
...  
Keyword(s):  
Biological Activity ◽  
Gene Cluster ◽  
Biosynthetic Gene Cluster ◽  
Biosynthetic Gene ◽  
Cluster Identification ◽  
Fusarium Sp

Anacyclamide D8P, a prenylated cyanobactin from a Sphaerospermopsis sp. cyanobacterium

2017 ◽  
Author(s):  
Joana Martins ◽  
Niina Leikoski ◽  
Matti Wahlsten ◽  
Joana Azevedo ◽  
Jorge Antunes ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Cyclic Peptides ◽  
Biosynthetic Gene Cluster ◽  
The Novel ◽  
Tyrosine Residue ◽  
Biosynthetic Gene ◽  
Post Translational Modification ◽  
Biological Assays ◽  
Mass Spectrometric Data ◽  
Spectrometric Data

Cyanobactins are a family of linear and cyclic peptides produced through the post-translational modification of short precursor peptides. Anacyclamides are macrocyclic cyanobactins with a highly diverse sequence that are common in the genus <i>Anabaena</i>. A mass spectrometry-based screening of potential cyanobactin producers led to the discovery of a new prenylated member of this family of compounds, anacyclamide D8P (<b>1</b>), from <i>Sphaerospermopsis</i> sp. LEGE 00249. The anacyclamide biosynthetic gene cluster (<i>acy</i>) encoding the novel macrocyclic prenylated cyanobactin, was sequenced. Heterologous expression of the acy gene cluster in <i>Escherichia</i> <i>coli</i> established the connection between genomic and mass spectrometric data. Unambiguous establishment of the type and site of prenylation required the full structural elucidation of <b>1</b> using Nuclear Magnetic Resonance (NMR), which demonstrated that a forward prenylation occurred on the tyrosine residue. Compound <b>1</b> was tested in pharmacologically or ecologically relevant biological assays and revealed moderate antimicrobial activity towards the fouling bacterium <i>Halomonas aquamarina</i> CECT 5000.<br>

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