Structure and Biosynthesis of the Antibiotic Bottromycin D

Hou, Yunfei; Tianero, Ma. Diarey B.; Kwan, Jason C.; Wyche, Thomas P.; Michel, Cole; Ellis, Gregory A.; Vazquez-Rivera, Emmanuel; Braun, D. C.; Rose, Warren E.; Schmidt, Eric W.; Bugni, Tim S.

doi:10.1021/ol3022758

Cited by 81 publications

(86 citation statements)

References 19 publications

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“…The bacteriocins are an important group of RiPPs that can be classified as either modified or unmodified based on post-translational modifications to their core peptides. To date, a number of bacteriocins with diverse structures and bioactivities are generated by the action of various modification enzymes such as Ser/Thr dehydratases, methyltransferases, and macrocylases9101112.…”

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confidence: 99%

Genome mining unveils widespread natural product biosynthetic capacity in human oral microbe Streptococcus mutans

Liu

Hao

Xie

et al. 2016

Sci Rep

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Streptococcus mutans is a major pathogen causing human dental caries. As a Gram-positive bacterium with a small genome (about 2 Mb) it is considered a poor source of natural products. Due to a recent explosion in genomic data available for S. mutans strains, we were motivated to explore the natural product production potential of this organism. Bioinformatic characterization of 169 publically available genomes of S. mutans from human dental caries revealed a surprisingly rich source of natural product biosynthetic gene clusters. Anti-SMASH analysis identified one nonribosomal peptide synthetase (NRPS) gene cluster, seven polyketide synthase (PKS) gene clusters and 136 hybrid PKS/NRPS gene clusters. In addition, 211 ribosomally synthesized and post-translationally modified peptides (RiPPs) clusters and 615 bacteriocin precursors were identified by a combined analysis using BAGEL and anti-SMASH. S. mutans harbors a rich and diverse natural product genetic capacity, which underscores the importance of probing the human microbiome and revisiting species that have traditionally been overlooked as “poor” sources of natural products.

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confidence: 99%

Genome mining unveils widespread natural product biosynthetic capacity in human oral microbe Streptococcus mutans

Liu

Hao

Xie

et al. 2016

Sci Rep

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“…There has been widespread recent interest in both the biosynthesis [5][6][7][8] and biological activity [9,35] of bottromycin owing to its unusual structure and potent antimicrobial activity.I nt his study,w ehave harnessed untargeted metabolomics to elucidate the biosynthetic pathway to bottromycin Table S4). Our analysis identified aw ide array of metabolites related to bottromycin, and the untargeted metabolomic data matrix (Supporting Information, Table S5) indicates that there may be further, currently uncharacterized, metabolites produced by this pathway.T his study also reveals the first example of YcaO domain-catalyzed macrocyclization, which provides the foundation for detailed mechanistic investigations into this step.…”

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confidence: 99%

Dissecting Bottromycin Biosynthesis Using Comparative Untargeted Metabolomics

et al. 2016

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Bottromycin A 2 is astructurally unique ribosomally synthesized and post-translationally modified peptide (RiPP) that possesses potent antibacterial activity towards multidrugresistant bacteria. The structural noveltyofbottromycin stems from its unprecedented macrocyclic amidine and rare bmethylated amino acid residues.The N-terminus of aprecursor peptide (BtmD) is converted into bottromycin A 2 by tailoring enzymes encoded in the btm gene cluster.H owever,l ittle was knowna bout key transformations in this pathway,i ncluding the unprecedented macrocyclization. To understand the pathway in detail, an untargeted metabolomic approacht hat harnesses mass spectral networking was used to assess the metabolomes of aseries of pathway mutants.This analysis has yielded key information on the function of av ariety of previously uncharacterized biosynthetic enzymes,i ncluding aY caO domain protein and ap artner protein that together catalyze the macrocyclization.Ribosomally synthesized and post-translationally modified peptides (RiPPs) are natural products that are prevalent throughout nature, [1] and their biosynthetic pathways are capable of transforming simple proteinogenic amino acids into structurally complex compounds that have potent bioactivities. [2][3][4] However,e lucidating the biosynthesis of RiPPs can be hindered by the difficulty of isolating intermediates,asthe biosynthesis takes place on alarger precursor peptide,a nd intermediates may be rapidly proteolyzed. Therefore,i mproved methods for the identification of RiPP intermediates are desirable.Bottromycin A 2 (1,Scheme 1) [5][6][7][8] possesses potent antibacterial activity towards multidrugresistant bacteria, [9] and is structurally unique owing its unprecedented macrocyclic amidine,r are b-methylated amino acids residues,and aterminal thiazole.Nature employs av ariety of strategies for peptide macrocyclization, [10][11][12] but amidine formation has only been observed for bottromycin. Initial studies on bottromycin biosynthesis showed that its amino acids were b-methylated by radical SAM methyltransferases [5,7] (RSMTs), but the rest of the bottromycin pathway represented abiosynthetic black box, where little was known about key steps in the pathway,including the unprecedented macrocyclization. In this study,weemploy untargeted metabolomics and mass spectral networking to deduce the biosynthetic route to bottromycins in Streptomyces scabies.T his analysis identifies the enzymes responsible for macrocyclization, thiazole formation, and aspartate epimerization, thereby demonstrating the utility of an untargeted metabolomic approach for elucidating atargeted biosynthetic pathway.To assess the role of the putative tailoring genes in the bottromycin pathway (Supporting Information, Figure S1), we had previously generated S. scabies DbtmC, DbtmE, DbtmF, DbtmI,a nd DbtmJ,b ut were unable to identify bottromycin-like compounds in these mutants. [5] We therefore established that these deletions did not lead to deleterious polar effects on the pathway b...

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“…strain. 21 However, the radical SAM methyltransferase believed to be responsible for the methylation of proline is β-methylating it and so the product is 3-methylproline. 21 The diverse synthesis mechanisms reveal multiple strategies for the inclusion of the rare amino acids in the natural products produced by cyanobacteria and other organisms.…”

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4-Methylproline Guided Natural Product Discovery: Co-Occurrence of 4-Hydroxy- and 4-Methylprolines in Nostoweipeptins and Nostopeptolides

et al. 2014

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4-methylproline (4-mPro) is a rare nonproteinogenic amino acid produced by cyanobacteria through the action of a zinc-dependent long-chain dehydrogenase and a Δ(1)-pyrroline-5-carboxylic acid (P5C) reductase homologue. Here, we used the presence of 4-mPro biosynthetic genes to discover new bioactive compounds from cyanobacteria. Eight biosynthetic gene clusters containing the 4-mPro biosynthetic genes nosE and nosF were found from publicly available cyanobacteria genomes, showing that 4-mPro is a good marker to discover previously unknown nonribosomal peptides. A combination of polymerase chain reaction (PCR) and liquid chromatography-mass spectroscopy (LC-MS) methods was used to screen 116 cyanobacteria strains from 8 genera. The 4-mPro biosynthetic genes were detected in 30 of the 116 cyanobacteria strains, 12 which were confirmed to produce 4-mPro by amino acid analysis. Species from the genus Nostoc were responsible for 80% of the positive results. Altogether, 11 new nonribosomal cyclic peptides, nostoweipeptin W1-W7 and nostopeptolide L1-L4, were identified from Nostoc sp. XPORK 5A and Nostoc sp. UK2aImI, respectively, and their chemical structure was elucidated. Interestingly, screening with 4-mPro genes resulted in the detection of peptides that do not contain just one 4-mPro but also 4-hydroxylproline (nostopeptolides) and, in case of nostoweipeptins, two 4-mPros and two 4-hydroxyprolines. Peptides from both groups inhibit microcystin-induced apoptosis of hepatocytes HEK293. The cell experiments indicated that these cyclic peptides inhibit the uptake of microcystin by blocking the organic anion-transporters OATP1B1/B3. This study enriches the drug library of microcystin antitoxin.

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Structure and Biosynthesis of the Antibiotic Bottromycin D

Cited by 81 publications

References 19 publications

Genome mining unveils widespread natural product biosynthetic capacity in human oral microbe Streptococcus mutans

Genome mining unveils widespread natural product biosynthetic capacity in human oral microbe Streptococcus mutans

Dissecting Bottromycin Biosynthesis Using Comparative Untargeted Metabolomics

4-Methylproline Guided Natural Product Discovery: Co-Occurrence of 4-Hydroxy- and 4-Methylprolines in Nostoweipeptins and Nostopeptolides

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