Chemical structure metagenomics of microbial natural products: surveying nonribosomal peptides and beyond

• Thomas Ma and
• John Chu

Beilstein J. Org. Chem. 2024, 20, 3050–3060, doi:10.3762/bjoc.20.253

• Thomas Ma John Chu Department of Chemistry, National Taiwan University, Taipei City 10617, Taiwan 10.3762/bjoc.20.253 Abstract Bioactivity-guided fractionation (BGF) has historically been a fruitful natural product discovery workflow. However, it is plagued by increasing rediscovery rates in

• ; natural products; natural product discovery; nonribosomal peptides; Introduction Natural products present diverse structures to elicit a wide range of biological activities and are of paramount importance to both translational science and basic research. Despite not knowing the underlying active

• the power of this viewpoint. It complements existing approaches to facilitate a broader and more efficient survey of the vast natural product chemical space that awaits our exploration. In BGF for microbial natural product discovery, the culture extract is fractionated using chromatographic methods

Young investigators in natural products chemistry, biosynthesis, and enzymology

• Jeffrey D. Rudolf,
• Lena Barra and
• Takayoshi Awakawa

Beilstein J. Org. Chem. 2024, 20, 2720–2721, doi:10.3762/bjoc.20.229

• present this collection of 19 Full Research Papers, three Letters, and nine Review articles from our colleagues around the world. Topics covered include natural product discovery efforts from a variety of organisms, genome and transcriptome mining and bioinformatics of natural products, biosynthetic gene

Polymer degrading marine Microbulbifer bacteria: an un(der)utilized source of chemical and biocatalytic novelty

• Weimao Zhong and
• Vinayak Agarwal

Beilstein J. Org. Chem. 2024, 20, 1635–1651, doi:10.3762/bjoc.20.146

• commonly detected in the commensal marine microbiomes. These bacteria have been recognized for their ability to degrade polysaccharides and other polymeric materials. Increasingly, Microbulbifer genomes indicate these bacteria to be an untapped reservoir for novel natural product discovery and biosynthetic

• barriers to natural product discovery; high rediscovery rates, reliance on largely serendipitous response in bioactivity assays, and the resources and expertise required for their structure determination being the primary impediments [1][2]. With this background, accessing biological sources that have not

• yet been extensively mined for natural product discovery is a promising route, one which, at the very least, promises to ameliorate the problem of continued rediscovery of known natural products. This review outlines the recent progress that has been realized using bacteria of the genus Microbulbifer

A myo-inositol dehydrogenase involved in aminocyclitol biosynthesis of hygromycin A

• Michael O. Akintubosun and
• Melanie A. Higgins

Beilstein J. Org. Chem. 2024, 20, 589–596, doi:10.3762/bjoc.20.51

• family containing Hyg17 and discuss genome mining strategies that target this protein family to identify biosynthetic clusters for natural product discovery. Keywords: aminocyclitol; biosynthesis; hygromycin A; inositol dehydrogenase; myo-inositol; Introduction Hygromycin A is a natural product that

• (PF13536) sequences. Together, this suggests that PF01408 sequences may be found in a significant number of uncharacterized biosynthetic gene clusters. However, a more detailed analysis of the genomic neighborhoods is needed to assess their promising potential in natural product discovery. Conclusion

Navigating and expanding the roadmap of natural product genome mining tools

• Friederike Biermann,
• Sebastian L. Wenski and
• Eric J. N. Helfrich

Beilstein J. Org. Chem. 2022, 18, 1656–1671, doi:10.3762/bjoc.18.178

• sequencing technology has resulted in the introduction of an alternative approach towards novel natural product scaffolds: Genome mining. Genome mining is an in-silico natural product discovery strategy in which sequenced genomes are analyzed for the potential of the associated organism to produce natural

New azodyrecins identified by a genome mining-directed reactivity-based screening

• Atina Rizkiya Choirunnisa,
• Kuga Arima,
• Yo Abe,
• Noritaka Kagaya,
• Kei Kudo,
• Hikaru Suenaga,
• Junko Hashimoto,
• Manabu Fujie,
• Noriyuki Satoh,
• Kazuo Shin-ya,
• Kenichi Matsuda and
• Toshiyuki Wakimoto

Beilstein J. Org. Chem. 2022, 18, 1017–1025, doi:10.3762/bjoc.18.102

• N2H4-detecting reactivity-based screening led to the identification of four new analogs and two types of biosynthetic gene clusters of azodyrecins, demonstrating its utility in natural product discovery and deorphanization of biosynthetic gene clusters. Evaluation of cytotoxicities of azodyrecins A

Herpetopanone, a diterpene from Herpetosiphon aurantiacus discovered by isotope labeling

• Xinli Pan,
• Nicole Domin,
• Sebastian Schieferdecker,
• Hirokazu Kage,
• Martin Roth and
• Markus Nett

Beilstein J. Org. Chem. 2017, 13, 2458–2465, doi:10.3762/bjoc.13.242

• natural product discovery. By comparing the ion chromatograms of cultures that were grown in the presence or absence of singly labeled glucose, it might be possible to identify terpenoid natural products in a complex metabolic background. To validate the feasibility of this approach, we chose the