Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Search research articles

Related Experiment Video

Updated: May 19, 2026

From a Natural Product to Its Biosynthetic Gene Cluster: A Demonstration Using Polyketomycin from Streptomyces diastatochromogenes Tü6028

From a Natural Product to Its Biosynthetic Gene Cluster: A Demonstration Using Polyketomycin from Streptomyces diastatochromogenes Tü6028

Published on: January 13, 2017

PKMiner: a database for exploring type II polyketide synthases.

Jinki Kim¹, Gwan-Su Yi

¹Department of Information and Communications Engineering, KAIST, Daejeon, 305-701, South Korea.

BMC Microbiology

|August 9, 2012

Summary

This summary is machine-generated.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

GPCRact: a hierarchical framework for predicting ligand-induced GPCR activity via allosteric communication modeling.

Briefings in bioinformatics·2026

Same author

Comparative plastome evaluation, phylogenomic analysis, and DNA signatures of medicinally important malvaceous genera and their adulterants.

Scientific reports·2025

Same author

Astrocytic NHERF-1 Increases Seizure Susceptibility by Inhibiting Surface Expression of TREK-1.

Glia·2024

Same author

BASE: a web service for providing compound-protein binding affinity prediction datasets with reduced similarity bias.

BMC bioinformatics·2024

Same author

Characterization of the complete plastome sequence of Korean endemic, <i>Cardamine glechomifolia</i> H.Lév. (Brassicaceae, Brassicales).

Mitochondrial DNA. Part B, Resources·2024

Same author

Connectivity and network burst properties of in-vitro neuronal networks induced by a clustered structure with alginate hydrogel patterning.

Biomedical engineering letters·2023

Same journal

Genome-to-function integrated exploration of polyethylene biodegradation by Rhodococcus opacus R7.

BMC microbiology·2026

Same journal

Overcoming the bottleneck in Treponema pallidum quantification: a novel flow cytometric assay for rapid, precise, and cost-effective detection.

BMC microbiology·2026

Same journal

Synergistic anti-Helicobacter pylori efficacy of a molecularly identified Limosilactobacillus fermentum isolate in combination with multiple antibiotics.

BMC microbiology·2026

Same journal

Unraveling a new Klebsiella phage KP47 against Klebsiella spp.

BMC microbiology·2026

Same journal

High burden of bla<sub>KPC-2</sub>-positive carbapenem-resistant Klebsiella pneumoniae among inpatients in a Tertiary Care Hospital in Kathmandu.

BMC microbiology·2026

Same journal

Proline protects Wickerhamomyces anomalus against ethanol‑induced damage during logarithmic growth: integrated physiological, transcriptomic, and metabolomic analyses.

BMC microbiology·2026

See all related articles

This study identifies novel bacterial aromatic polyketides by analyzing type II polyketide synthases (PKSs) in actinobacteria genomes. The findings pinpoint specific actinomycete taxa for efficient polyketide discovery and synthesis.

Area of Science:

Microbiology
Biochemistry
Genomics

Background:

Bacterial aromatic polyketides are crucial natural products synthesized by type II polyketide synthases (PKSs).
Discovering novel polyketides is challenging due to limited knowledge of prolific taxa and difficulties in microbial isolation and optimization.
Computational analysis of type II PKSs and prediction of chemotypes can facilitate novel polyketide discovery.

Purpose of the Study:

To perform a comprehensive computational analysis of type II PKSs in actinobacterial genomes.
To develop accurate domain classifiers and prediction rules for aromatic polyketide chemotypes.
To identify prolific actinobacterial taxa for polyketide synthesis and facilitate the discovery of novel compounds.

Main Methods:

Computational analysis of type II PKSs and their gene clusters in 319 actinobacterial genomes.

More Related Videos

Mass Spectrometry-Guided Genome Mining as a Tool to Uncover Novel Natural Products

Mass Spectrometry-Guided Genome Mining as a Tool to Uncover Novel Natural Products

Published on: March 12, 2020

Related Experiment Videos

Last Updated: May 19, 2026

From a Natural Product to Its Biosynthetic Gene Cluster: A Demonstration Using Polyketomycin from Streptomyces diastatochromogenes Tü6028

From a Natural Product to Its Biosynthetic Gene Cluster: A Demonstration Using Polyketomycin from Streptomyces diastatochromogenes Tü6028

Published on: January 13, 2017

Mass Spectrometry-Guided Genome Mining as a Tool to Uncover Novel Natural Products

Mass Spectrometry-Guided Genome Mining as a Tool to Uncover Novel Natural Products

Published on: March 12, 2020

Identification of type II PKS subclasses and development of domain classifiers.

Prediction of aromatic polyketide chemotypes based on PKS domain combinations.

Main Results:

Predicted 231 type II PKSs and 40 PKS gene clusters in 25 actinobacterial genomes.
Identified polyketide chemotypes for 22 novel PKS gene clusters in 16 genomes.
Showed that aromatic polyketide production is concentrated in specific Actinomycetales suborders (e.g., Catenulisporineae, Frankineae).

Conclusions:

Novel type II PKS gene clusters and their polyketide chemotypes were identified in actinobacterial genomes.
Specific actinomycete suborders are identified as prolific taxa for polyketide synthesis.
The developed chemotype-prediction rules and the PKMiner database aid in discovering and engineering novel bacterial aromatic polyketides.