scholarly journals Genome Mining and Metabolomics Uncover a Rare d-Capreomycidine Containing Natural Product and Its Biosynthetic Gene Cluster

2020 ◽  
Vol 15 (11) ◽  
pp. 3013-3020
Author(s):  
James H. Tryon ◽  
Jennifer C. Rote ◽  
Li Chen ◽  
Matthew T. Robey ◽  
Marvin M. Vega ◽  
...  
Keyword(s):  
Natural Product ◽  
Gene Cluster ◽  
Genome Mining ◽  
Biosynthetic Gene Cluster ◽  
Biosynthetic Gene

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.

Discovery of a Potential Liver Fibrosis Inhibitor from a Mushroom Endophytic Fungus by Genome Mining of a Silent Biosynthetic Gene Cluster

2021 ◽  
Vol 69 (38) ◽  
pp. 11303-11310
Author(s):  
Jin-Tao Cheng ◽  
Han-Min Wang ◽  
Jia-Hui Yu ◽  
Chen-Fan Sun ◽  
Fei Cao ◽  
...  
Keyword(s):  
Liver Fibrosis ◽  
Gene Cluster ◽  
Endophytic Fungus ◽  
Genome Mining ◽  
Biosynthetic Gene Cluster ◽  
Biosynthetic Gene

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.

scholarly journals Bioactivity-Guided Genome Mining Reveals the Lomaiviticin Biosynthetic Gene Cluster inSalinispora tropica

ChemBioChem ◽  
2013 ◽  
Vol 14 (8) ◽  
pp. 955-962 ◽  
Author(s):  
Roland D. Kersten ◽  
Amy L. Lane ◽  
Markus Nett ◽  
Taylor K. S. Richter ◽  
Brendan M. Duggan ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Genome Mining ◽  
Biosynthetic Gene Cluster ◽  
Biosynthetic Gene

scholarly journals Correction: Genome mining and molecular characterization of the biosynthetic gene cluster of a diterpenic meroterpenoid, 15-deoxyoxalicine B, in Penicillium canescens

2016 ◽  
Vol 7 (3) ◽  
pp. 2440-2440 ◽  
Author(s):  
Junko Yaegashi ◽  
Jillian Romsdahl ◽  
Yi-Ming Chiang ◽  
Clay C. C. Wang
Keyword(s):  
Gene Cluster ◽  
Molecular Characterization ◽  
Genome Mining ◽  
Biosynthetic Gene Cluster ◽  
Biosynthetic Gene ◽  
Penicillium Canescens

Correction for ‘Genome mining and molecular characterization of the biosynthetic gene cluster of a diterpenic meroterpenoid, 15-deoxyoxalicine B, in Penicillium canescens’ by Junko Yaegashi et al., Chem. Sci., 2015, 6, 6537–6544.

Genome Mining-Directed Activation of a Silent Angucycline Biosynthetic Gene Cluster inStreptomyces chattanoogensis

ChemBioChem ◽  
2014 ◽  
Vol 16 (3) ◽  
pp. 496-502 ◽  
Author(s):  
Zhenxing Zhou ◽  
Qingqing Xu ◽  
Qingting Bu ◽  
Yuanyang Guo ◽  
Shuiping Liu ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Genome Mining ◽  
Biosynthetic Gene Cluster ◽  
Biosynthetic Gene

scholarly journals Comparative transcriptomics as a guide to natural product discovery and biosynthetic gene cluster functionality

2017 ◽  
Vol 114 (52) ◽  
pp. E11121-E11130 ◽  
Author(s):  
Gregory C. A. Amos ◽  
Takayoshi Awakawa ◽  
Robert N. Tuttle ◽  
Anne-Catrin Letzel ◽  
Min Cheol Kim ◽  
...  
Keyword(s):  
Natural Product ◽  
Gene Cluster ◽  
Genetic Manipulation ◽  
Expression Profiles ◽  
Genome Mining ◽  
Gene Clusters ◽  
Comparative Transcriptomics ◽  
Regulatory Control ◽  
Biosynthetic Gene ◽  
Metabolomics Data

Bacterial natural products remain an important source of new medicines. DNA sequencing has revealed that a majority of natural product biosynthetic gene clusters (BGCs) maintained in bacterial genomes have yet to be linked to the small molecules whose biosynthesis they encode. Efforts to discover the products of these orphan BGCs are driving the development of genome mining techniques based on the premise that many are transcriptionally silent during normal laboratory cultivation. Here, we employ comparative transcriptomics to assess BGC expression among four closely related strains of marine bacteria belonging to the genusSalinispora. The results reveal that slightly more than half of the BGCs are expressed at levels that should facilitate product detection. By comparing the expression profiles of similar gene clusters in different strains, we identified regulatory genes whose inactivation appears linked to cluster silencing. The significance of these subtle differences between expressed and silent BGCs could not have been predicted a priori and was only revealed by comparative transcriptomics. Evidence for the conservation of silent clusters among a larger number of strains for which genome sequences are available suggests they may be under different regulatory control from the expressed forms or that silencing may represent an underappreciated mechanism of gene cluster evolution. Coupling gene expression and metabolomics data established a bioinformatic link between the salinipostins and their associated BGC, while genetic manipulation established the genetic basis for this series of compounds, which were previously unknown fromSalinispora pacifica.

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