Literature DB >> 27503995

Synthetic Biology of Natural Products.

Rainer Breitling1, Eriko Takano1.   

Abstract

The diversity and natural modularity of their biosynthetic pathways has turned natural products into attractive, but challenging, targets for synthetic biology approaches. Here, we discuss the current state of the field, highlighting recent advances and remaining bottlenecks. Global genomic assessments of natural product biosynthetic capacities across large parts of microbial diversity provide a first survey of the available natural parts libraries and identify evolutionary design rules for further engineering. Methods for compound and pathway detection and characterization are developed increasingly on the basis of synthetic biology tools, contributing to an accelerated translation of genomic information into usable building blocks for pathway assembly. A wide range of methods is also becoming available for accessing ever larger parts of chemical space by rational diversification of natural products, guided by rapid progress in our understanding of the underlying biochemistry and enzymatic mechanisms. Enhanced genome assembly and editing tools, adapted to the needs of natural products research, facilitate the realization of ambitious engineering strategies, ranging from combinatorial library generation to high-throughput optimization of product titers. Together, these tools and concepts contribute to the emergence of a new generation of revitalized natural product research.
Copyright © 2016 Cold Spring Harbor Laboratory Press; all rights reserved.

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Year:  2016        PMID: 27503995      PMCID: PMC5046697          DOI: 10.1101/cshperspect.a023994

Source DB:  PubMed          Journal:  Cold Spring Harb Perspect Biol        ISSN: 1943-0264            Impact factor:   10.005


  77 in total

Review 1.  Computational tools for the synthetic design of biochemical pathways.

Authors:  Marnix H Medema; Renske van Raaphorst; Eriko Takano; Rainer Breitling
Journal:  Nat Rev Microbiol       Date:  2012-01-23       Impact factor: 60.633

2.  Integration of high-content screening and untargeted metabolomics for comprehensive functional annotation of natural product libraries.

Authors:  Kenji L Kurita; Emerson Glassey; Roger G Linington
Journal:  Proc Natl Acad Sci U S A       Date:  2015-09-14       Impact factor: 11.205

3.  Rapid one-step inactivation of single or multiple genes in Escherichia coli.

Authors:  Chan Woo Song; Sang Yup Lee
Journal:  Biotechnol J       Date:  2013-06-21       Impact factor: 4.677

Review 4.  DNA assembly for synthetic biology: from parts to pathways and beyond.

Authors:  Tom Ellis; Tom Adie; Geoff S Baldwin
Journal:  Integr Biol (Camb)       Date:  2011-01-19       Impact factor: 2.192

Review 5.  Recent advances in natural product discovery.

Authors:  Yunzi Luo; Ryan E Cobb; Huimin Zhao
Journal:  Curr Opin Biotechnol       Date:  2014-09-26       Impact factor: 9.740

6.  CRISPR-Cas9 Based Engineering of Actinomycetal Genomes.

Authors:  Yaojun Tong; Pep Charusanti; Lixin Zhang; Tilmann Weber; Sang Yup Lee
Journal:  ACS Synth Biol       Date:  2015-04-07       Impact factor: 5.110

Review 7.  Old obstacles and new horizons for microbial chemical production.

Authors:  Danilo Porro; Paola Branduardi; Michael Sauer; Diethard Mattanovich
Journal:  Curr Opin Biotechnol       Date:  2014-07-05       Impact factor: 9.740

Review 8.  In silico tools for the analysis of antibiotic biosynthetic pathways.

Authors:  Tilmann Weber
Journal:  Int J Med Microbiol       Date:  2014-02-19       Impact factor: 3.473

Review 9.  Advancing secondary metabolite biosynthesis in yeast with synthetic biology tools.

Authors:  Michael S Siddiqui; Kate Thodey; Isis Trenchard; Christina D Smolke
Journal:  FEMS Yeast Res       Date:  2012-01-11       Impact factor: 2.796

10.  antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences.

Authors:  Marnix H Medema; Kai Blin; Peter Cimermancic; Victor de Jager; Piotr Zakrzewski; Michael A Fischbach; Tilmann Weber; Eriko Takano; Rainer Breitling
Journal:  Nucleic Acids Res       Date:  2011-06-14       Impact factor: 16.971

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  8 in total

1.  Output ordering and prioritisation system (OOPS): ranking biosynthetic gene clusters to enhance bioactive metabolite discovery.

Authors:  Alejandro Peña; Francesco Del Carratore; Matthew Cummings; Eriko Takano; Rainer Breitling
Journal:  J Ind Microbiol Biotechnol       Date:  2017-12-18       Impact factor: 3.346

Review 2.  Recent advances in understanding Streptomyces.

Authors:  Keith F Chater
Journal:  F1000Res       Date:  2016-11-30

3.  Chimeric Leader Peptides for the Generation of Non-Natural Hybrid RiPP Products.

Authors:  Brandon J Burkhart; Nidhi Kakkar; Graham A Hudson; Wilfred A van der Donk; Douglas A Mitchell
Journal:  ACS Cent Sci       Date:  2017-06-06       Impact factor: 14.553

Review 4.  Engineering actinomycetes for biosynthesis of macrolactone polyketides.

Authors:  Dipesh Dhakal; Jae Kyung Sohng; Ramesh Prasad Pandey
Journal:  Microb Cell Fact       Date:  2019-08-13       Impact factor: 5.328

Review 5.  Unraveling Plant Natural Chemical Diversity for Drug Discovery Purposes.

Authors:  Emmanuelle Lautié; Olivier Russo; Pierre Ducrot; Jean A Boutin
Journal:  Front Pharmacol       Date:  2020-04-07       Impact factor: 5.810

6.  Mixing and matching genes of marine and terrestrial origin in the biosynthesis of the mupirocin antibiotics.

Authors:  Luoyi Wang; Zhongshu Song; Paul R Race; James Spencer; Thomas J Simpson; Matthew P Crump; Christine L Willis
Journal:  Chem Sci       Date:  2020-05-09       Impact factor: 9.825

Review 7.  Metabolic reprogramming during the Trypanosoma brucei life cycle.

Authors:  Terry K Smith; Frédéric Bringaud; Derek P Nolan; Luisa M Figueiredo
Journal:  F1000Res       Date:  2017-05-16

8.  Diversity and Antimicrobial Activity of Vietnamese Sponge-Associated Bacteria.

Authors:  Ton That Huu Dat; Nguyen Thi Kim Cuc; Pham Viet Cuong; Hauke Smidt; Detmer Sipkema
Journal:  Mar Drugs       Date:  2021-06-22       Impact factor: 5.118

  8 in total

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