Analysis of the Sorangicin Gene Cluster Reinforces the Utility of a Combined Phylogenetic/Retrobiosynthetic Analysis for Deciphering Natural Product Assembly by trans-AT PKS

ChemBioChem ◽  
2010 ◽  
Vol 11 (13) ◽  
pp. 1840-1849 ◽  
Author(s):  
Herbert Irschik ◽  
Maren Kopp ◽  
Kira J. Weissman ◽  
Kathrin Buntin ◽  
Jörn Piel ◽  
...  
Keyword(s):  
Natural Product ◽  
Gene Cluster ◽  
Product Assembly

Unzipping Natural Products: Improved Natural Product Structure Predictions by Ensemble Modeling and Fingerprint Matching

2018 ◽  
Author(s):  
William A. Shirley ◽  
Brian P. Kelley ◽  
Yohann Potier ◽  
John H. Koschwanez ◽  
Robert Bruccoleri ◽  
...  
Keyword(s):  
Natural Products ◽  
Open Source ◽  
Natural Product ◽  
Gene Cluster ◽  
Public Domain ◽  
Product Structure ◽  
Fingerprint Matching ◽  
Ensemble Modeling ◽  
Chemical Structures ◽  
Source Gene

This pre-print explores ensemble modeling of natural product targets to match chemical structures to precursors found in large open-source gene cluster repository antiSMASH. Commentary on method, effectiveness, and limitations are enclosed. All structures are public domain molecules and have been reviewed for release.

scholarly journals New Insights into the Genetic Organization of the FK228 Biosynthetic Gene Cluster inChromobacterium violaceumNo. 968

2010 ◽  
Vol 77 (4) ◽  
pp. 1508-1511 ◽  
Author(s):  
Vishwakanth Y. Potharla ◽  
Shane R. Wesener ◽  
Yi-Qiang Cheng
Keyword(s):  
Natural Product ◽  
Gene Cluster ◽  
Gene Deletion ◽  
Regulatory Gene ◽  
Biosynthetic Gene Cluster ◽  
Transcriptional Analysis ◽  
Biosynthetic Gene ◽  
Genetic Organization

ABSTRACTThe biosynthetic gene cluster of FK228, an FDA-approved anticancer natural product, was identified and sequenced previously. The genetic organization of this gene cluster has now been delineated through systematic gene deletion and transcriptional analysis. As a result, the gene cluster is redefined to contain 12 genes:depAthroughdepJ,depM, and a newly identified pathway regulatory gene,depR.

scholarly journals Discovery of Amidotemplated Natural Product Assembly

Biochemistry ◽  
2019 ◽  
Vol 58 (46) ◽  
pp. 4583-4584
Author(s):  
Evelyn M. Molloy ◽  
Maria Dell ◽  
Christian Hertweck
Keyword(s):  
Natural Product ◽  
Product Assembly

scholarly journals mSphere of Influence: Synthetic Biology of Natural Product Biosynthesis

mSphere ◽  
2020 ◽  
Vol 5 (1) ◽  
Author(s):  
Mark C. Walker
Keyword(s):  
Natural Products ◽  
Synthetic Biology ◽  
Natural Product ◽  
Gene Cluster ◽  
Biosynthetic Gene Cluster ◽  
Biosynthetic Gene ◽  
Natural Product Biosynthesis ◽  
Antibiotic Compounds ◽  
Approaches To Study

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.

Heterologous Expression and Structural Characterisation of a Pyrazinone Natural Product Assembly Line

ChemBioChem ◽  
2012 ◽  
Vol 13 (16) ◽  
pp. 2408-2415 ◽  
Author(s):  
Morgan A. Wyatt ◽  
M. C. Y. Mok ◽  
Murray Junop ◽  
Nathan A. Magarvey
Keyword(s):  
Heterologous Expression ◽  
Natural Product ◽  
Assembly Line ◽  
Structural Characterisation ◽  
Product Assembly

scholarly journals Elucidating the Rimosamide-Detoxin Natural Product Families and Their Biosynthesis Using Metabolite/Gene Cluster Correlations

2016 ◽  
Vol 11 (12) ◽  
pp. 3452-3460 ◽  
Author(s):  
Ryan A. McClure ◽  
Anthony W. Goering ◽  
Kou-San Ju ◽  
Joshua A. Baccile ◽  
Frank C. Schroeder ◽  
...  
Keyword(s):  
Natural Product ◽  
Gene Cluster ◽  
Product Families

New Natural Product Families from an Environmental DNA (eDNA) Gene Cluster

2002 ◽  
Vol 124 (34) ◽  
pp. 9968-9969 ◽  
Author(s):  
Sean F. Brady ◽  
Carol J. Chao ◽  
Jon Clardy
Keyword(s):  
Natural Product ◽  
Gene Cluster ◽  
Environmental Dna ◽  
Product Families

scholarly journals Biosynthesis of a Complex Yersiniabactin-Like Natural Product via themicLocus in Phytopathogen Ralstonia solanacearum

2011 ◽  
Vol 77 (17) ◽  
pp. 6117-6124 ◽  
Author(s):  
Martin F. Kreutzer ◽  
Hirokazu Kage ◽  
Peter Gebhardt ◽  
Barbara Wackler ◽  
Hans P. Saluz ◽  
...  
Keyword(s):  
Natural Product ◽  
Gene Cluster ◽  
Ralstonia Solanacearum ◽  
Insertional Mutagenesis ◽  
Polyketide Synthase ◽  
Genome Mining ◽  
Content Type ◽  
A Genome ◽  
Iron Deficient ◽  
Peptide Synthetase

ABSTRACTA genome mining study in the plant pathogenic bacteriumRalstonia solanacearumGMI1000 unveiled a polyketide synthase/nonribosomal peptide synthetase gene cluster putatively involved in siderophore biosynthesis. Insertional mutagenesis confirmed the respective locus to be operational under iron-deficient conditions and spurred the isolation of the associated natural product. Bioinformatic analyses of the gene cluster facilitated the structural characterization of this compound, which was subsequently identified as the antimycoplasma agent micacocidin. The metal-chelating properties of micacocidin were evaluated in competition experiments, and the cellular uptake of gallium-micacocidin complexes was demonstrated inR. solanacearumGMI1000, indicating a possible siderophore role. Comparative genomics revealed a conservation of the micacocidin gene cluster in defined, but globally dispersed phylotypes ofR. solanacearum.

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