scholarly journals Biosynthetic origin of butyrolactol A, an antifungal polyketide produced by a marine-derived Streptomyces

2017 ◽  
Vol 13 ◽  
pp. 441-450 ◽  
Author(s):  
Enjuro Harunari ◽  
Hisayuki Komaki ◽  
Yasuhiro Igarashi
Keyword(s):  
Natural Products ◽  
Analytical Data ◽  
Genomic Analysis ◽  
Butyl Group ◽  
Starter Unit ◽  
Labeling Pattern

Butyrolactol A is an antifungal polyketide of Streptomyces bearing an uncommon tert-butyl starter unit and a polyol system in which eight hydroxy/acyloxy carbons are contiguously connected. Except for its congener butyrolactol B, there exist no structurally related natural products to date. In this study, inspired by our previous genomic analysis, incorporation of 13C- and 2H-labeled precursors into butyrolactol A was investigated. Based on the labeling pattern and sequencing analytical data, we confirmed that the tert-butyl group is derived from valine and its C-methylation with methionine and the polyol carbons are derived from a glycolysis intermediate, possibly hydroxymalonyl-ACP.

scholarly journals Genome Reduction and Secondary Metabolism of the Marine Sponge-Associated Cyanobacterium Leptothoe

Marine Drugs ◽  
2021 ◽  
Vol 19 (6) ◽  
pp. 298
Author(s):  
Despoina Konstantinou ◽  
Rafael V. Popin ◽  
David P. Fewer ◽  
Kaarina Sivonen ◽  
Spyros Gkelis
Keyword(s):  
Natural Products ◽  
Microbial Communities ◽  
Genomic Analysis ◽  
Gene Clusters ◽  
Marine Sponges ◽  
Genome Reduction ◽  
Extracellular Polysaccharides ◽  
Comparative Genomic ◽  
Symbiotic Relationships ◽  
Genes Encoding

Sponges form symbiotic relationships with diverse and abundant microbial communities. Cyanobacteria are among the most important members of the microbial communities that are associated with sponges. Here, we performed a genus-wide comparative genomic analysis of the newly described marine benthic cyanobacterial genus Leptothoe (Synechococcales). We obtained draft genomes from Le. kymatousa TAU-MAC 1615 and Le. spongobia TAU-MAC 1115, isolated from marine sponges. We identified five additional Leptothoe genomes, host-associated or free-living, using a phylogenomic approach, and the comparison of all genomes showed that the sponge-associated strains display features of a symbiotic lifestyle. Le. kymatousa and Le. spongobia have undergone genome reduction; they harbored considerably fewer genes encoding for (i) cofactors, vitamins, prosthetic groups, pigments, proteins, and amino acid biosynthesis; (ii) DNA repair; (iii) antioxidant enzymes; and (iv) biosynthesis of capsular and extracellular polysaccharides. They have also lost several genes related to chemotaxis and motility. Eukaryotic-like proteins, such as ankyrin repeats, playing important roles in sponge-symbiont interactions, were identified in sponge-associated Leptothoe genomes. The sponge-associated Leptothoe stains harbored biosynthetic gene clusters encoding novel natural products despite genome reduction. Comparisons of the biosynthetic capacities of Leptothoe with chemically rich cyanobacteria revealed that Leptothoe is another promising marine cyanobacterium for the biosynthesis of novel natural products.

Use of 13C in biosynthetic studies. The labeling pattern in dihydrofusarubin enriched from [13C]- and [13C, 2H]acetate in cultures of Fusarium solani

1980 ◽  
Vol 58 (13) ◽  
pp. 1380-1385 ◽  
Author(s):  
Itsuo Kurobane ◽  
Leo C. Vining ◽  
A. Gavin McInnes ◽  
John A. Walter
Keyword(s):  
Fusarium Solani ◽  
Carrier Protein ◽  
Single Chain ◽  
Acetyl Coa ◽  
Biotin Carboxyl Carrier Protein ◽  
H Nmr ◽  
Malonyl Coa ◽  
Starter Unit ◽  
Biosynthetic Studies ◽  
Labeling Pattern

The pattern of 13C and 2H incorporation from [1-13C]-, [2-13C]-, [1-13C0;1;1,2-13C1;0;1]-, and [2-13C0;1,2-2H3;3]acetate into dihydrofusarubin 1, produced by cultures of Fusariumsolani, has been determined by 13C and 2H nmr of the derivatives anhydrofusarubin 3 and anhydrofusarubin diacetate 4. The results show that 1 is biosynthesized from seven uniformly-incorporated acetate units with C-3, C-11 originating from the "starter" unit. They strongly suggest that linear head-to-tail condensation of an acetate and six malonate units forms a single-chain heptaketide intermediate. The evidence also suggests that, during conversion of [13C, 2H]-labeled acetyl-CoA to malonyl-CoA, 2H is transferred to biotin carboxyl carrier protein where it does not exchange rapidly with the medium and is available for conversion of endogenous malonyl-CoA to [2H]-enriched acetyl-CoA.

scholarly journals Combining Mass Spectrometric Metabolic Profiling with Genomic Analysis: A Powerful Approach for Discovering Natural Products from Cyanobacteria

2015 ◽  
Vol 78 (7) ◽  
pp. 1671-1682 ◽  
Author(s):  
Karin Kleigrewe ◽  
Jehad Almaliti ◽  
Isaac Yuheng Tian ◽  
Robin B. Kinnel ◽  
Anton Korobeynikov ◽  
...  
Keyword(s):  
Natural Products ◽  
Metabolic Profiling ◽  
Genomic Analysis ◽  
Mass Spectrometric ◽  
Powerful Approach

scholarly journals Large-Scale Bioinformatics Analysis of Bacillus Genomes Uncovers Conserved Roles of Natural Products in Bacterial Physiology

mSystems ◽  
2017 ◽  
Vol 2 (6) ◽  
Author(s):  
Kirk J. Grubbs ◽  
Rachel M. Bleich ◽  
Kevin C. Santa Maria ◽  
Scott E. Allen ◽  
Sherif Farag ◽  
...  
Keyword(s):  
Natural Products ◽  
Large Scale ◽  
Genomic Analysis ◽  
Bacterial Group ◽  
Biological Functions ◽  
Metabolic Capacity ◽  
Full Spectrum ◽  
Bacterial Physiology ◽  
Specialized Metabolites ◽  
Biosynthetic Machinery

ABSTRACT Bacilli are capable of producing a diverse array of specialized metabolites, many of which have gained attention for their roles as signals that affect bacterial physiology and development. Up to this point, however, the Bacillus genus’s metabolic capacity has been underexplored. We undertook a deep genomic analysis of 1,566 Bacillus genomes to understand the full spectrum of metabolites that this bacterial group can make. We discovered that the majority of the specialized metabolites produced by Bacillus species are highly conserved, known compounds with important signaling roles in the physiology and development of this bacterium. Additionally, there is significant unique biosynthetic machinery distributed across the genus that might lead to new, unknown metabolites with diverse biological functions. Inspired by the findings of our genomic analysis, we speculate that the highly conserved alkylpyrones might have an important biological activity within this genus. We go on to validate this prediction by demonstrating that these natural products are developmental signals in Bacillus and act by inhibiting sporulation. Bacteria possess an amazing capacity to synthesize a diverse range of structurally complex, bioactive natural products known as specialized (or secondary) metabolites. Many of these specialized metabolites are used as clinical therapeutics, while others have important ecological roles in microbial communities. The biosynthetic gene clusters (BGCs) that generate these metabolites can be identified in bacterial genome sequences using their highly conserved genetic features. We analyzed an unprecedented 1,566 bacterial genomes from Bacillus species and identified nearly 20,000 BGCs. By comparing these BGCs to one another as well as a curated set of known specialized metabolite BGCs, we discovered that the majority of Bacillus natural products are comprised of a small set of highly conserved, well-distributed, known natural product compounds. Most of these metabolites have important roles influencing the physiology and development of Bacillus species. We identified, in addition to these characterized compounds, many unique, weakly conserved BGCs scattered across the genus that are predicted to encode unknown natural products. Many of these “singleton” BGCs appear to have been acquired via horizontal gene transfer. Based on this large-scale characterization of metabolite production in the Bacilli, we go on to connect the alkylpyrones, natural products that are highly conserved but previously biologically uncharacterized, to a role in Bacillus physiology: inhibiting spore development. IMPORTANCE Bacilli are capable of producing a diverse array of specialized metabolites, many of which have gained attention for their roles as signals that affect bacterial physiology and development. Up to this point, however, the Bacillus genus’s metabolic capacity has been underexplored. We undertook a deep genomic analysis of 1,566 Bacillus genomes to understand the full spectrum of metabolites that this bacterial group can make. We discovered that the majority of the specialized metabolites produced by Bacillus species are highly conserved, known compounds with important signaling roles in the physiology and development of this bacterium. Additionally, there is significant unique biosynthetic machinery distributed across the genus that might lead to new, unknown metabolites with diverse biological functions. Inspired by the findings of our genomic analysis, we speculate that the highly conserved alkylpyrones might have an important biological activity within this genus. We go on to validate this prediction by demonstrating that these natural products are developmental signals in Bacillus and act by inhibiting sporulation.

Mutasynthesis of Medicinally Significant Natural Products through the Manipulation of Gene Governing Starter Unit

2021 ◽  
Vol 25 ◽  
Author(s):  
Parul Grover ◽  
Deepak K Sharma ◽  
Anuj K. Chhalodia ◽  
Debaraj Mukherjee
Keyword(s):  
Natural Products ◽  
Literature Search ◽  
Culture Media ◽  
Biologically Active ◽  
Molecular Architecture ◽  
Diversity Oriented Synthesis ◽  
Chemically Modified ◽  
Starter Unit ◽  
Microbial Natural Products ◽  
Derivatives Of

: Most of the biologically active microbial natural products and their analogs bear a complex molecular architecture. The semisynthetic modifications and stereospecific diversity-oriented synthesis of these native natural products to generate analogs are difficult and time-consuming. Mutasynthesis is a powerful tool that utilizes the microorganism's genetic and metabolic engineering skills to produce derivatives of complex natural products of microbial origin. Mutasynthesis is based on the cellular uptake of chemically modified intermediates from the culture media and their addition to the secondary metabolism by mutant microorganisms. This review wouldf describe the importance of mutasynthesis in the generation of complex microbial secondary metabolites. We have covered a literature search on mutasynthesis over the last ten years (2011 - 2020) in this review.

scholarly journals Galactic Circos: User-friendly Circos plots within the Galaxy platform

GigaScience ◽  
2020 ◽  
Vol 9 (6) ◽  
Author(s):  
Helena Rasche ◽  
Saskia Hiltemann
Keyword(s):  
Analytical Data ◽  
Genomic Analysis ◽  
Scientific Data ◽  
Ease Of Use ◽  
Command Line ◽  
Web Browser ◽  
The Galaxy ◽  
Unix Command ◽  
User Friendly ◽  
High Degree

Abstract Background Circos is a popular, highly flexible software package for the circular visualization of complex datasets. While especially popular in the field of genomic analysis, Circos enables interactive graphing of any analytical data, including alternative scientific domain data and non-scientific data. This high degree of flexibility also comes with a high degree of complexity, which may present an obstacle for researchers not trained in programming or the UNIX command line. The Galaxy platform provides a user-friendly browser-based graphical interface incorporating a broad range of “wrapped” command line tools to facilitate accessibility. Findings We have developed a Galaxy wrapper for Circos, thus combining the power of Circos with the accessibility and ease of use of the Galaxy platform. The combination substantially simplifies the specification and configuration of Circos plots for end users while retaining the power to produce publication-quality visualizations of complex multidimensional datasets. Conclusions Galactic Circos enables the creation of publication-ready Circos plots using only a web browser, via the Galaxy platform. Users may download the full set of Circos configuration files of their plots for further manual customization. This version of Circos is available as an open-source installable application from the Galaxy ToolShed, with its use clarified in a training manual hosted by the Galaxy Training Network.

scholarly journals Total Synthesis of the Natural Products Ulmoside A and (2R,3R)-Taxifolin-6-C-β-d-glucopyranoside

Synlett ◽  
2020 ◽  
Vol 31 (11) ◽  
pp. 1097-1101
Author(s):  
Venkateswara Rao Batchu ◽  
Lingamurthy Macha ◽  
Aravind Reddy Dorigundla ◽  
Raju Gurrapu ◽  
Umamaheswara Sarma Vanka
Keyword(s):  
Natural Products ◽  
High Performance Liquid Chromatography ◽  
Liquid Chromatography ◽  
Total Synthesis ◽  
High Performance ◽  
Metabolic Disorders ◽  
Analytical Data ◽  
Reverse Phase ◽  
Diastereomeric Mixture ◽  
Absolute Stereochemistry

An efficient first total synthesis of highly polar ulmoside A and (2R,3R)-taxifolin-6-C-β-d-glucopyranoside, useful for the prevention of metabolic disorders, has been described. Key elements of the synthesis include a Sc(OTf)3-catalyzed regio- and stereoselective C-glycosidation on taxifolin in 35% yield with d-glucose and chiral semipreparative reverse-phase high-performance liquid chromatography (HPLC) for the separation of both taxifolins and the diastereomeric mixture of taxifolin-6-C-β-d-glucopyranosides. Correlation of the analytical data of synthetic ulmoside A and its diastereomer with a natural ulmoside A sample confirmed the assigned absolute stereochemistry of the natural products.

scholarly journals Dual activity of anthocyanidin reductase supports the dominant plant proanthocyanidin extension unit pathway

2021 ◽  
Vol 7 (20) ◽  
pp. eabg4682
Author(s):  
Ji Hyung Jun ◽  
Nan Lu ◽  
Maite Docampo-Palacios ◽  
Xiaoqiang Wang ◽  
Richard A. Dixon
Keyword(s):  
Natural Products ◽  
Human Health ◽  
Plant Species ◽  
In Planta ◽  
Anthocyanidin Reductase ◽  
Plant Natural Products ◽  
Starter Unit ◽  
Biochemical Analyses

Proanthocyanidins (PAs) are plant natural products important for agriculture and human health. They are polymers of flavan-3-ol subunits, commonly (−)-epicatechin and/or (+)-catechin, but the source of the in planta extension unit that comprises the bulk of the polymer remains unclear, as does how PA composition is determined in different plant species. Anthocyanidin reductase (ANR) can generate 2,3-cis-epicatechin as a PA starter unit from cyanidin, which itself arises from 2,3-trans-leucocyanidin, but ANR proteins from different species produce mixtures of flavan-3-ols with different stereochemistries in vitro. Genetic and biochemical analyses here show that ANR has dual activity and is involved not only in the production of (−)-epicatechin starter units but also in the formation of 2,3-cis-leucocyanidin to serve as (−)-epicatechin extension units. Differences in the product specificities of ANRs account for the presence/absence of PA polymerization and the compositions of PAs across plant species.

scholarly journals Draft Genome Sequence of Streptomyces canus ATCC 12647, a Producer of Telomycin

2016 ◽  
Vol 4 (2) ◽  
Author(s):  
Dennis Y. Liu ◽  
Yongchang Li ◽  
Nathan A. Magarvey
Keyword(s):  
Antibacterial Activity ◽  
Natural Products ◽  
Genome Sequence ◽  
Draft Genome ◽  
Genomic Analysis ◽  
Gene Clusters ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Bioinformatics Tool ◽  
Pharmacological Interest

We present here the genome sequence of Streptomyces canus ATCC 12647, a producer of the antibiotic telomycin, noted for its unique antibacterial activity against cardiolipin. Genomic analysis using the bioinformatics tool PRISM revealed the presence of multiple biosynthetic gene clusters, including those for telomycin and other natural products of potential pharmacological interest.

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