Literature DB >> 27527588

The Need for Integrated Approaches in Metabolic Engineering.

Anna Lechner1,2, Elizabeth Brunk3, Jay D Keasling1,2,4.   

Abstract

This review highlights state-of-the-art procedures for heterologous small-molecule biosynthesis, the associated bottlenecks, and new strategies that have the potential to accelerate future accomplishments in metabolic engineering. We emphasize that a combination of different approaches over multiple time and size scales must be considered for successful pathway engineering in a heterologous host. We have classified these optimization procedures based on the "system" that is being manipulated: transcriptome, translatome, proteome, or reactome. By bridging multiple disciplines, including molecular biology, biochemistry, biophysics, and computational sciences, we can create an integral framework for the discovery and implementation of novel biosynthetic production routes.
Copyright © 2016 Cold Spring Harbor Laboratory Press; all rights reserved.

Mesh:

Year:  2016        PMID: 27527588      PMCID: PMC5088530          DOI: 10.1101/cshperspect.a023903

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


  116 in total

Review 1.  Improved biocatalysts by directed evolution and rational protein design.

Authors:  U T Bornscheuer; M Pohl
Journal:  Curr Opin Chem Biol       Date:  2001-04       Impact factor: 8.822

Review 2.  Manufacturing molecules through metabolic engineering.

Authors:  Jay D Keasling
Journal:  Science       Date:  2010-12-03       Impact factor: 47.728

3.  Causes and effects of N-terminal codon bias in bacterial genes.

Authors:  Daniel B Goodman; George M Church; Sriram Kosuri
Journal:  Science       Date:  2013-09-26       Impact factor: 47.728

4.  Multiplex metabolic pathway engineering using CRISPR/Cas9 in Saccharomyces cerevisiae.

Authors:  Tadas Jakočiūnas; Ida Bonde; Markus Herrgård; Scott J Harrison; Mette Kristensen; Lasse E Pedersen; Michael K Jensen; Jay D Keasling
Journal:  Metab Eng       Date:  2015-01-28       Impact factor: 9.783

5.  Discovery and analysis of novel metabolic pathways for the biosynthesis of industrial chemicals: 3-hydroxypropanoate.

Authors:  Christopher S Henry; Linda J Broadbelt; Vassily Hatzimanikatis
Journal:  Biotechnol Bioeng       Date:  2010-06-15       Impact factor: 4.530

6.  Generation of an atlas for commodity chemical production in Escherichia coli and a novel pathway prediction algorithm, GEM-Path.

Authors:  Miguel A Campodonico; Barbara A Andrews; Juan A Asenjo; Bernhard O Palsson; Adam M Feist
Journal:  Metab Eng       Date:  2014-07-28       Impact factor: 9.783

7.  Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling.

Authors:  Nicholas T Ingolia; Sina Ghaemmaghami; John R S Newman; Jonathan S Weissman
Journal:  Science       Date:  2009-02-12       Impact factor: 47.728

8.  Design, construction and characterization of a set of insulated bacterial promoters.

Authors:  Joseph H Davis; Adam J Rubin; Robert T Sauer
Journal:  Nucleic Acids Res       Date:  2010-09-15       Impact factor: 16.971

9.  Optimality and evolution of transcriptionally regulated gene expression.

Authors:  Frank J Poelwijk; Philip D Heyning; Marjon G J de Vos; Daniel J Kiviet; Sander J Tans
Journal:  BMC Syst Biol       Date:  2011-08-16

10.  mRNA-programmed translation pauses in the targeting of E. coli membrane proteins.

Authors:  Nir Fluman; Sivan Navon; Eitan Bibi; Yitzhak Pilpel
Journal:  Elife       Date:  2014-08-18       Impact factor: 8.140

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  13 in total

Review 1.  Alternative Watson-Crick Synthetic Genetic Systems.

Authors:  Steven A Benner; Nilesh B Karalkar; Shuichi Hoshika; Roberto Laos; Ryan W Shaw; Mariko Matsuura; Diego Fajardo; Patricia Moussatche
Journal:  Cold Spring Harb Perspect Biol       Date:  2016-11-01       Impact factor: 10.005

2.  Adaptive Strategies of the Candidate Probiotic E. coli Nissle in the Mammalian Gut.

Authors:  Nathan Crook; Aura Ferreiro; Andrew J Gasparrini; Mitchell W Pesesky; Molly K Gibson; Bin Wang; Xiaoqing Sun; Zevin Condiotte; Stephen Dobrowolski; Daniel Peterson; Gautam Dantas
Journal:  Cell Host Microbe       Date:  2019-03-26       Impact factor: 21.023

Review 3.  Gas fermentation: cellular engineering possibilities and scale up.

Authors:  Björn D Heijstra; Ching Leang; Alex Juminaga
Journal:  Microb Cell Fact       Date:  2017-04-12       Impact factor: 5.328

4.  A combinatorial approach to synthetic transcription factor-promoter combinations for yeast strain engineering.

Authors:  Zain Y Dossani; Amanda Reider Apel; Heather Szmidt-Middleton; Nathan J Hillson; Samuel Deutsch; Jay D Keasling; Aindrila Mukhopadhyay
Journal:  Yeast       Date:  2017-12-07       Impact factor: 3.239

5.  Spatially organizing biochemistry: choosing a strategy to translate synthetic biology to the factory.

Authors:  Christopher M Jakobson; Danielle Tullman-Ercek; Niall M Mangan
Journal:  Sci Rep       Date:  2018-05-29       Impact factor: 4.379

Review 6.  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

7.  Engineering Saccharomyces cerevisiae for geranylgeraniol overproduction by combinatorial design.

Authors:  Tian-Qing Song; Ming-Zhu Ding; Fang Zhai; Duo Liu; Hong Liu; Wen-Hai Xiao; Ying-Jin Yuan
Journal:  Sci Rep       Date:  2017-11-08       Impact factor: 4.379

8.  Microbial Platform for Terpenoid Production: Escherichia coli and Yeast.

Authors:  Chonglong Wang; Mudanguli Liwei; Ji-Bin Park; Seong-Hee Jeong; Gongyuan Wei; Yujun Wang; Seon-Won Kim
Journal:  Front Microbiol       Date:  2018-10-12       Impact factor: 5.640

Review 9.  An estimate is worth about a thousand experiments: using order-of-magnitude estimates to identify cellular engineering targets.

Authors:  Kevin James Metcalf; Marilyn F Slininger Lee; Christopher Matthew Jakobson; Danielle Tullman-Ercek
Journal:  Microb Cell Fact       Date:  2018-08-30       Impact factor: 5.328

Review 10.  Nature's Chemists: The Discovery and Engineering of Phytochemical Biosynthesis.

Authors:  Kaouthar Eljounaidi; Benjamin R Lichman
Journal:  Front Chem       Date:  2020-11-09       Impact factor: 5.221

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