Journal: Natural Product Reports

Abbreviation

Nat. prod. rep. (Print)

Publisher

Royal Society of Chemistry

Journal Volumes

ISSN

0265-0568
0265-0568
1460-4752

Description

Filters

Reset filters

Search Results

Publications1 - 10 of 13
  • New developments in RiPP discovery, enzymology and engineering
    Item type: Journal Article
    Montalbán-López, Manuel; Scott, Thomas A.; Ramesh, Sangeetha; et al. (2021)
    Natural Product Reports
    Covering: up to June 2020Ribosomally-synthesized and post-translationally modified peptides (RiPPs) are a large group of natural products. A community-driven review in 2013 described the emerging commonalities in the biosynthesis of RiPPs and the opportunities they offered for bioengineering and genome mining. Since then, the field has seen tremendous advances in understanding of the mechanisms by which nature assembles these compounds, in engineering their biosynthetic machinery for a wide range of applications, and in the discovery of entirely new RiPP families using bioinformatic tools developed specifically for this compound class. The First International Conference on RiPPs was held in 2019, and the meeting participants assembled the current review describing new developments since 2013. The review discusses the new classes of RiPPs that have been discovered, the advances in our understanding of the installation of both primary and secondary post-translational modifications, and the mechanisms by which the enzymes recognize the leader peptides in their substrates. In addition, genome mining tools used for RiPP discovery are discussed as well as various strategies for RiPP engineering. An outlook section presents directions for future research.
  • Biosynthesis of polyketides by trans-AT polyketide synthases
    Item type: Journal Article
    Helfrich, Eric J.N.; Piel, Jörn (2016)
    Natural Product Reports
  • Synthesis and biological evaluation of amphotericin B derivatives
    Item type: Review Article
    Volmer, Astrid A.; Szpilman, Alex M.; Carreira, Erick M. (2010)
    Natural Product Reports
  • Natural product isolation
    Item type: Journal Article
    Sticher, Otto (2008)
    Natural Product Reports
  • Anticancer drugs from nature
    Item type: Review Article
    Altmann, Karl-Heinz; Gertsch, Jürg (2007)
    Natural Product Reports
  • A roadmap for metagenomic enzyme discovery
    Item type: Journal Article
    Robinson, Serina; Piel, Jörn; Sunagawa, Shinichi (2021)
    Natural Product Reports
    Metagenomics has yielded massive amounts of sequencing data offering a glimpse into the biosynthetic potential of the uncultivated microbial majority. While genome-resolved information about microbial communities from nearly every environment on earth is now available, the ability to accurately predict biocatalytic functions directly from sequencing data remains challenging. Compared to primary metabolic pathways, enzymes involved in secondary metabolism often catalyze specialized reactions with diverse substrates, making these pathways rich resources for the discovery of new enzymology. To date, functional insights gained from studies on environmental DNA (eDNA) have largely relied on PCR- or activity-based screening of eDNA fragments cloned in fosmid or cosmid libraries. As an alternative, shotgun metagenomics holds underexplored potential for the discovery of new enzymes directly from eDNA by avoiding common biases introduced through PCR- or activity-guided functional metagenomics workflows. However, inferring new enzyme functions directly from eDNA is similar to searching for a ‘needle in a haystack’ without direct links between genotype and phenotype. The goal of this review is to provide a roadmap to navigate shotgun metagenomic sequencing data and identify new candidate biosynthetic enzymes. We cover both computational and experimental strategies to mine metagenomes and explore protein sequence space with a spotlight on natural product biosynthesis. Specifically, we compare in silico methods for enzyme discovery including phylogenetics, sequence similarity networks, genomic context, 3D structure-based approaches, and machine learning techniques. We also discuss various experimental strategies to test computational predictions including heterologous expression and screening. Finally, we provide an outlook for future directions in the field with an emphasis on meta-omics, single-cell genomics, cell-free expression systems, and sequence-independent methods.
  • En route to terpene natural products utilizing supramolecular cyclase mimetics
    Item type: Journal Article
    Zhang, Qi; Catti, Lorenzo; Syntrivanis, Leonidas-Dimitrios; et al. (2019)
    Natural Product Reports
    Terpenes are a class of natural products characterized by remarkable structural diversity. Much of this diversity arises biosynthetically from a handful of linear precursors through the so-called tail-to-head terpene cyclization reaction. This reaction is one of the most complex observed in nature, and historically attempts to replicate it with non-enzymatic means have met with little success. In recent years, however, the development of manmade binding pockets that allow such reactions to take place has been reported. This Highlight provides an overview of this nascent field, and outlines the challenges that need to be overcome moving forward.
  • Cyanophycin and its biosynthesis: not hot but very cool
    Item type: Review Article
    Sharon, Itai; Hilvert, Donald; Schmeing, T. Martin (2023)
    Natural Product Reports
    Covering: 1878 to early 2023 Cyanophycin is a biopolymer consisting of a poly-aspartate backbone with arginines linked to each Asp sidechain through isopeptide bonds. Cyanophycin is made by cyanophycin synthetase 1 or 2 through ATP-dependent polymerization of Asp and Arg, or beta-Asp-Arg, respectively. It is degraded into dipeptides by exo-cyanophycinases, and these dipeptides are hydrolyzed into free amino acids by general or dedicated isodipeptidase enzymes. When synthesized, chains of cyanophycin coalesce into large, inert, membrane-less granules. Although discovered in cyanobacteria, cyanophycin is made by species throughout the bacterial kingdom, and cyanophycin metabolism provides advantages for toxic bloom forming algae and some human pathogens. Some bacteria have developed dedicated schemes for cyanophycin accumulation and use, which include fine temporal and spatial regulation. Cyanophycin has also been heterologously produced in a variety of host organisms to a remarkable level, over 50% of the host's dry mass, and has potential for a variety of green industrial applications. In this review, we summarize the progression of cyanophycin research, with an emphasis on recent structural studies of enzymes in the cyanophycin biosynthetic pathway. These include several unexpected revelations that show cyanophycin synthetase to be a very cool, multi-functional macromolecular machine.
  • Efficient synthesis strategies by application of transition metal-catalyzed carbene/nitrene insertions into C-H bonds
    Item type: Journal Article
    Egger, Julian; Carreira, Erick M. (2014)
    Natural Product Reports
  • Ribosomally synthesized and post-translationally modified peptide natural products: Overview and recommendations for a universal nomenclature
    Item type: Review Article
    Arnison, Paul G.; Bibb, Mervyn J.; Bierbaum, Gabriele; et al. (2013)
    Natural Product Reports
Publications1 - 10 of 13