Analysis of an Inactive Cyanobactin Biosynthetic Gene Cluster Leads to Discovery of New Natural Products from Strains of the Genus Microcystis

ABSTRACT Mark Walker studies the biosynthesis and engineering of bacterial natural products with the long-term goal of identifying new antibiotic compounds. In this mSphere of Influence, he reflects on how “Direct cloning and refactoring of a silent lipopeptide biosynthetic gene cluster yields the antibiotic taromycin A” by K. Yamanaka, K. A. Reynolds, R. D. Kersten, K. S. Ryan, et al. (Proc Natl Acad Sci USA 111:1957–1962, 2014, https://doi.org/10.1073/pnas.1319584111) impacted his thinking on using synthetic biology approaches to study natural product biosynthesis.

Download Full-text

Biosynthetic Potential of a Novel Antarctic Actinobacterium Marisediminicola antarctica ZS314T Revealed by Genomic Data Mining and Pigment Characterization

Marine Drugs ◽

10.3390/md17070388 ◽

2019 ◽

Vol 17 (7) ◽

pp. 388 ◽

Cited By ~ 5

Author(s):

Li Liao ◽

Shiyuan Su ◽

Bin Zhao ◽

Chengqi Fan ◽

Jin Zhang ◽

...

Keyword(s):

Data Mining ◽

Natural Products ◽

Gene Cluster ◽

Genomic Data ◽

Gene Clusters ◽

Biosynthetic Gene Cluster ◽

The Novel ◽

Biosynthetic Gene ◽

Base Pairs ◽

Peptide Synthetase

Rare actinobacterial species are considered as potential resources of new natural products. Marisediminicola antarctica ZS314T is the only type strain of the novel actinobacterial genus Marisediminicola isolated from intertidal sediments in East Antarctica. The strain ZS314T was able to produce reddish orange pigments at low temperatures, showing characteristics of carotenoids. To understand the biosynthetic potential of this strain, the genome was completely sequenced for data mining. The complete genome had 3,352,609 base pairs (bp), much smaller than most genomes of actinomycetes. Five biosynthetic gene clusters (BGCs) were predicted in the genome, including a gene cluster responsible for the biosynthesis of C50 carotenoid, and four additional BGCs of unknown oligosaccharide, salinixanthin, alkylresorcinol derivatives, and NRPS (non-ribosomal peptide synthetase) or amino acid-derived compounds. Further experimental characterization indicated that the strain may produce C.p.450-like carotenoids, supporting the genomic data analysis. A new xanthorhodopsin gene was discovered along with the analysis of the salinixanthin biosynthetic gene cluster. Since little is known about this genus, this work improves our understanding of its biosynthetic potential and provides opportunities for further investigation of natural products and strategies for adaptation to the extreme Antarctic environment.

Download Full-text

Discovery of the Pseudomonas Polyyne Protegencin by a Phylogeny-Guided Study of Polyyne Biosynthetic Gene Cluster Diversity

mBio ◽

10.1128/mbio.00715-21 ◽

2021 ◽

Author(s):

Alex J. Mullins ◽

Gordon Webster ◽

Hak Joong Kim ◽

Jinlian Zhao ◽

Yoana D. Petrova ◽

...

Keyword(s):

Biological Control ◽

Natural Products ◽

Gene Cluster ◽

Plant Pathogens ◽

Biological Activities ◽

Pathogenic Fungi ◽

Biosynthetic Gene Cluster ◽

Biosynthetic Gene ◽

Carbon Bond ◽

Ecological Roles

Natural products bearing alkyne (triple carbon bond) or polyyne (multiple alternating single and triple carbon bonds) moieties exhibit a broad range of important biological activities. Polyyne metabolites have been implicated in important ecological roles such as cepacin mediating biological control of plant pathogens and caryoynencin protecting Lagriinae beetle eggs against pathogenic fungi.

Download Full-text

Thioesterase from Cereulide Biosynthesis Is Responsible for Oligomerization and Macrocyclization of a Linear Tetradepsipeptide

10.26434/chemrxiv.11933232.v1 ◽

2020 ◽

Author(s):

Christopher Boddy ◽

Graham Heberlig

Keyword(s):

Natural Products ◽

Bacillus Cereus ◽

Gene Cluster ◽

Recent Work ◽

Biosynthetic Gene Cluster ◽

Alternative Mechanism ◽

Biosynthetic Gene ◽

Peptide Synthetases ◽

Canonical Activity

Cereulide is a cyclic depsidodecapeptide produced in Bacillus cereus by two non-ribosomal peptide synthetases, CesA and CesB. While highly similar in structure and with a homologous biosynthetic gene cluster to valinomycin, recent work suggests that cereulide is produced via a different mechanism, which relys on a non-canonical coupling of two didepsipeptide-PCP bound intermediates. Ultimately this alternative mechanism generates a tetradepsipeptide-PCP bound intermediate that is prosed to differ from the tetradepsipeptide predicted from canonical activity of CesA and CesB. To test this hypothesis, we chemically synthetize both tetradepsipeptides as N-acetyl cysteamine thioesters and probed the ability of the purified recombinant terminal CesB thioesterase (CesB TE) to oligomerize and macrocyclize each substrate. Only the canonical substrate is converted cereulide, ruling out this alternative mechanism. We also show that CesB TE can use related tertradepsipeptide substrates, such as the valinomycin tetradespipetide and a hybride cereulide-valinomycin tetradespispetide in conjunction with its native substrate to generate chimeric natural products. This work clarifies the biosynthetic origins of cereulide and provides a powerful biocatalyst to access analogs of these ionophoric forming natural products.

Download Full-text

Discovery of the Tyrobetaine Natural Products and Their Biosynthetic Gene Cluster via Metabologenomics

ACS Chemical Biology ◽

10.1021/acschembio.7b01089 ◽

2018 ◽

Vol 13 (4) ◽

pp. 1029-1037 ◽

Cited By ~ 15

Author(s):

Elizabeth I. Parkinson ◽

James H. Tryon ◽

Anthony W. Goering ◽

Kou-San Ju ◽

Ryan A. McClure ◽

...

Keyword(s):

Natural Products ◽

Gene Cluster ◽

Biosynthetic Gene Cluster ◽

Biosynthetic Gene

Download Full-text

Mutational Analysis of nocK and nocL in the Nocardicin A Producer Nocardia uniformis

Journal of Bacteriology ◽

10.1128/jb.187.2.739-746.2005 ◽

2005 ◽

Vol 187 (2) ◽

pp. 739-746 ◽

Cited By ~ 17

Author(s):

Wendy L. Kelly ◽

Craig A. Townsend

Keyword(s):

Natural Products ◽

Gene Cluster ◽

Mutational Analysis ◽

Biosynthetic Gene Cluster ◽

Biosynthetic Gene ◽

Wild Type ◽

Nocardicin A ◽

Lactam Ring ◽

Undetermined Function

ABSTRACT The nocardicins are a family of monocyclic β-lactam antibiotics produced by the actinomycete Nocardia uniformis subsp. tsuyamanensis ATCC 21806. The most potent of this series is nocardicin A, containing a syn-configured oxime moiety, an uncommon feature in natural products. The nocardicin A biosynthetic gene cluster was recently identified and found to encode proteins in keeping with nocardicin A production, including the nocardicin N-oxygenase, NocL, in addition to genes of undetermined function, such as nocK, which bears similarities to a broad family of esterases. The latter was hypothesized to be involved in the formation of the critical β-lactam ring. While previously shown to effect oxidation of the 2′-amine of nocardicin C to provide nocardicin A, it was uncertain whether NocL was the only N-oxidizing enzyme required for nocardicin A biosynthesis. To further detail the role of NocL in nocardicin production in N. uniformis, and to examine the function of nocK, a method for the transformation of N. uniformis protoplasts to inactivate both nocK and nocL was developed and applied. A reliable protocol is reported to achieve both insertional disruption and in trans complementation in this strain. While the nocK mutant still produced nocardicin A at levels near that seen for wild-type N. uniformis, and therefore has no obvious role in nocardicin biosynthesis, the nocL disruptant failed to generate the oxime-containing metabolite. Nocardicin A production was restored in the nocL mutant upon in trans expression of the gene. Furthermore, the nocL mutant accumulated the biosynthetic intermediate nocardicin C, confirming its role as the sole oxime-forming enzyme required for production of nocardicin A.

Download Full-text

Thioesterase from Cereulide Biosynthesis Is Responsible for Oligomerization and Macrocyclization of a Linear Tetradepsipeptide

10.26434/chemrxiv.11933232 ◽

2020 ◽

Author(s):

Christopher Boddy ◽

Graham Heberlig

Keyword(s):

Natural Products ◽

Bacillus Cereus ◽

Gene Cluster ◽

Recent Work ◽

Biosynthetic Gene Cluster ◽

Alternative Mechanism ◽

Biosynthetic Gene ◽

Peptide Synthetases ◽

Canonical Activity

Cereulide is a cyclic depsidodecapeptide produced in Bacillus cereus by two non-ribosomal peptide synthetases, CesA and CesB. While highly similar in structure and with a homologous biosynthetic gene cluster to valinomycin, recent work suggests that cereulide is produced via a different mechanism, which relys on a non-canonical coupling of two didepsipeptide-PCP bound intermediates. Ultimately this alternative mechanism generates a tetradepsipeptide-PCP bound intermediate that is prosed to differ from the tetradepsipeptide predicted from canonical activity of CesA and CesB. To test this hypothesis, we chemically synthetize both tetradepsipeptides as N-acetyl cysteamine thioesters and probed the ability of the purified recombinant terminal CesB thioesterase (CesB TE) to oligomerize and macrocyclize each substrate. Only the canonical substrate is converted cereulide, ruling out this alternative mechanism. We also show that CesB TE can use related tertradepsipeptide substrates, such as the valinomycin tetradespipetide and a hybride cereulide-valinomycin tetradespispetide in conjunction with its native substrate to generate chimeric natural products. This work clarifies the biosynthetic origins of cereulide and provides a powerful biocatalyst to access analogs of these ionophoric forming natural products.

Download Full-text

The expansive library of jadomycins

Canadian Journal of Chemistry ◽

10.1139/cjc-2017-0573 ◽

2018 ◽

Vol 96 (6) ◽

pp. 495-501 ◽

Cited By ~ 3

Author(s):

Jeanna M. MacLeod ◽

Stephanie M. Forget ◽

David L. Jakeman

Keyword(s):

Amino Acids ◽

Natural Products ◽

Amino Acid ◽

Heterologous Expression ◽

Gene Cluster ◽

Gene Deletion ◽

Biosynthetic Gene Cluster ◽

Biosynthetic Gene ◽

Synthetic Derivatives ◽

Subsequent Identification

The jadomycin family of natural products was discovered from Streptomyces venezuelae ISP5230 in the 1990s. Subsequent identification of the biosynthetic gene cluster along with synthetic efforts established that incorporation of an amino acid into the polyaromatic angucycline core occurs non-enzymatically. Over two decades, the precursor-directed biosynthetic potential of the jadomycins has been heavily exploited, generating a library exceeding 70 compounds. This review compiles the jadomycins that have been isolated and characterized to date; these include jadomycins incorporating proteinogenic and non-proteinogenic amino acids, semi-synthetic derivatives, biosynthetic shunt products, compounds isolated in structural gene deletion studies, and deoxysugar sugar variant jadomycins produced by deletion or heterologous expression of sugar biosynthetic genes.

Download Full-text

Discovery and Heterologous Production of Sarubicins and Quinazolinone C-Glycosides with Protecting Activity for Cardiomyocytes

Organic Chemistry Frontiers ◽

10.1039/d1qo00470k ◽

2021 ◽

Author(s):

Mingming Yu ◽

Jianying Luo ◽

Dan Luo ◽

Qiang He ◽

Yijun Yan ◽

...

Keyword(s):

Natural Products ◽

Gene Cluster ◽

Genome Mining ◽

Biosynthetic Gene Cluster ◽

Heterologous Production ◽

Biosynthetic Gene ◽

Pharmaceutical Agents

Glycosylated natural products and their derivatives are important pharmaceutical agents. Genome mining of C-glycosylated metabolites biosynthetic gene cluster (BGC) from a soil-derived Streptomyces led to the isolation of sarubicins A...

Download Full-text

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

10.26434/chemrxiv.5346739.v1 ◽

2017 ◽

Cited By ~ 1

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 Anabaena. 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 (1), from Sphaerospermopsis sp. LEGE 00249. The anacyclamide biosynthetic gene cluster (acy) encoding the novel macrocyclic prenylated cyanobactin, was sequenced. Heterologous expression of the acy gene cluster in Escherichia coli established the connection between genomic and mass spectrometric data. Unambiguous establishment of the type and site of prenylation required the full structural elucidation of 1 using Nuclear Magnetic Resonance (NMR), which demonstrated that a forward prenylation occurred on the tyrosine residue. Compound 1 was tested in pharmacologically or ecologically relevant biological assays and revealed moderate antimicrobial activity towards the fouling bacterium Halomonas aquamarina CECT 5000.

Download Full-text