Biosynthetic Pathway and Gene Cluster Analysis of Curacin A, an Antitubulin Natural Product from the Tropical Marine CyanobacteriumLyngbyamajuscula†

2004 ◽  
Vol 67 (8) ◽  
pp. 1356-1367 ◽  
Author(s):  
Zunxue Chang ◽  
Namthip Sitachitta ◽  
James V. Rossi ◽  
Mary Ann Roberts ◽  
Patricia M. Flatt ◽  
...  
Keyword(s):  
Cluster Analysis ◽  
Natural Product ◽  
Gene Cluster ◽  
Biosynthetic Pathway ◽  
Curacin A

scholarly journals Cloning and Characterization of the Biosynthetic Gene Cluster for Tomaymycin, an SJG-136 Monomeric Analog

2009 ◽  
Vol 75 (9) ◽  
pp. 2958-2963 ◽  
Author(s):  
Wei Li ◽  
ShenChieh Chou ◽  
Ankush Khullar ◽  
Barbara Gerratana
Keyword(s):  
Cluster Analysis ◽  
Gene Cluster ◽  
Biosynthetic Pathway ◽  
Biosynthetic Gene Cluster ◽  
Gene Replacement ◽  
Biosynthetic Gene

ABSTRACT Tomaymycin produced by Streptomyces achromogenes is a naturally produced pyrrolobenzodiazepine (PBD). The biosynthetic gene cluster for tomaymycin was identified and sequenced. The gene cluster analysis reveals a novel biosynthetic pathway for the anthranilate moiety of PBDs. Gene replacement and chemical complementation studies were used to confirm the proposed biosynthetic pathway.

scholarly journals A Single Biosynthetic Gene Cluster Is Responsible for the Production of Bagremycin Antibiotics and Ferroverdin Iron Chelators

mBio ◽  
2019 ◽  
Vol 10 (4) ◽  
Author(s):  
Loïc Martinet ◽  
Aymeric Naômé ◽  
Benoit Deflandre ◽  
Marta Maciejewska ◽  
Déborah Tellatin ◽  
...  
Keyword(s):  
Natural Product ◽  
Gene Cluster ◽  
Biosynthetic Pathway ◽  
Genome Mining ◽  
Gene Clusters ◽  
Bioactive Molecules ◽  
Bioactive Metabolites ◽  
Biosynthetic Gene ◽  
Single Family ◽  
Biosynthetic Gene Clusters

ABSTRACT Biosynthetic gene clusters (BGCs) are organized groups of genes involved in the production of specialized metabolites. Typically, one BGC is responsible for the production of one or several similar compounds with bioactivities that usually only vary in terms of strength and/or specificity. Here we show that the previously described ferroverdins and bagremycins, which are families of metabolites with different bioactivities, are produced from the same BGC, whereby the fate of the biosynthetic pathway depends on iron availability. Under conditions of iron depletion, the monomeric bagremycins are formed, representing amino-aromatic antibiotics resulting from the condensation of 3-amino-4-hydroxybenzoic acid with p-vinylphenol. Conversely, when iron is abundantly available, the biosynthetic pathway additionally produces a molecule based on p-vinylphenyl-3-nitroso-4-hydroxybenzoate, which complexes iron to form the trimeric ferroverdins that have anticholesterol activity. Thus, our work shows a unique exception to the concept that BGCs should only produce a single family of molecules with one type of bioactivity and that in fact different bioactive molecules may be produced depending on the environmental conditions. IMPORTANCE Access to whole-genome sequences has exposed the general incidence of the so-called cryptic biosynthetic gene clusters (BGCs), thereby renewing their interest for natural product discovery. As a consequence, genome mining is the often first approach implemented to assess the potential of a microorganism for producing novel bioactive metabolites. By revealing a new level of complexity of natural product biosynthesis, we further illustrate the difficulty of estimation of the panel of molecules associated with a BGC based on genomic information alone. Indeed, we found that the same gene cluster is responsible for the production of compounds which differ in terms of structure and bioactivity. The production of these different compounds responds to different environmental triggers, which suggests that multiplication of culture conditions is essential for revealing the entire panel of molecules made by a single BGC.

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 Gene Cluster Analysis Method Identifies Horizontally Transferred Genes with High Reliability and Indicates that They Provide the Main Mechanism of Operon Gain in 8 Species of γ-Proteobacteria

2006 ◽  
Vol 24 (3) ◽  
pp. 805-813 ◽  
Author(s):  
Keiichi Homma ◽  
Satoshi Fukuchi ◽  
Yoji Nakamura ◽  
Takashi Gojobori ◽  
Ken Nishikawa
Keyword(s):  
Cluster Analysis ◽  
Gene Cluster ◽  
High Reliability ◽  
Main Mechanism ◽  
Analysis Method ◽  
Cluster Analysis Method

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.

Sa1825 The Clinical Utility of Blood Derived Gene Cluster Analysis of Neuroendocrine Tumors Using Neoplasia Hallmark Criteria

2015 ◽  
Vol 148 (4) ◽  
pp. S-342
Author(s):  
Mark Kidd ◽  
Ignat Drozdov ◽  
Irvin M. Modlin
Keyword(s):  
Cluster Analysis ◽  
Gene Cluster ◽  
Neuroendocrine Tumors ◽  
Clinical Utility

scholarly journals The Tripod for Bacterial Natural Product Discovery: Genome Mining, Silent Pathway Induction, and Mass Spectrometry-Based Molecular Networking

mSystems ◽  
2018 ◽  
Vol 3 (2) ◽  
Author(s):  
Daniela B. B. Trivella ◽  
Rafael de Felicio
Keyword(s):  
Mass Spectrometry ◽  
Natural Products ◽  
Natural Product ◽  
Biosynthetic Pathway ◽  
Genome Mining ◽  
Chemical Compounds ◽  
Gene Clusters ◽  
Tandem Mass ◽  
Molecular Networking ◽  
Natural Product Discovery

ABSTRACT Natural products are the richest source of chemical compounds for drug discovery. Particularly, bacterial secondary metabolites are in the spotlight due to advances in genome sequencing and mining, as well as for the potential of biosynthetic pathway manipulation to awake silent (cryptic) gene clusters under laboratory cultivation. Further progress in compound detection, such as the development of the tandem mass spectrometry (MS/MS) molecular networking approach, has contributed to the discovery of novel bacterial natural products. The latter can be applied directly to bacterial crude extracts for identifying and dereplicating known compounds, therefore assisting the prioritization of extracts containing novel natural products, for example. In our opinion, these three approaches—genome mining, silent pathway induction, and MS-based molecular networking—compose the tripod for modern bacterial natural product discovery and will be discussed in this perspective.

Structural revision of natural cyclic depsipeptide MA026 established by total synthesis and biosynthetic gene cluster analysis

2021 ◽  
Author(s):  
Chihiro Uchiyama ◽  
Akane Fukuda ◽  
Minagi Mukaiyama ◽  
Yoshiki Nakazawa ◽  
Yuka Kuramochi ◽  
...  
Keyword(s):  
Cluster Analysis ◽  
Total Synthesis ◽  
Gene Cluster ◽  
Biosynthetic Gene Cluster ◽  
Biosynthetic Gene ◽  
Structural Revision ◽  
Cyclic Depsipeptide

scholarly journals A Gene Cluster Containing Two Fungal Polyketide Synthases Encodes the Biosynthetic Pathway for a Polyketide, Asperfuranone, inAspergillus nidulans

2009 ◽  
Vol 131 (8) ◽  
pp. 2965-2970 ◽  
Author(s):  
Yi-Ming Chiang ◽  
Edyta Szewczyk ◽  
Ashley D. Davidson ◽  
Nancy Keller ◽  
Berl R. Oakley ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Biosynthetic Pathway ◽  
Polyketide Synthases
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