Genome-scale biological models for industrial microbial systems

Applied Microbiology and Biotechnology
Nan XuLiming Liu

Abstract

The primary aims and challenges associated with microbial fermentation include achieving faster cell growth, higher productivity, and more robust production processes. Genome-scale biological models, predicting the formation of an interaction among genetic materials, enzymes, and metabolites, constitute a systematic and comprehensive platform to analyze and optimize the microbial growth and production of biological products. Genome-scale biological models can help optimize microbial growth-associated traits by simulating biomass formation, predicting growth rates, and identifying the requirements for cell growth. With regard to microbial product biosynthesis, genome-scale biological models can be used to design product biosynthetic pathways, accelerate production efficiency, and reduce metabolic side effects, leading to improved production performance. The present review discusses the development of microbial genome-scale biological models since their emergence and emphasizes their pertinent application in improving industrial microbial fermentation of biological products.

References

Jul 28, 1995·Science·R D FleischmannJ M Merrick
Jul 22, 1998·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·D ThieffryJ Collado-Vides
Mar 9, 1999·Bioinformatics·M TomitaC A Hutchison
Dec 2, 2000·Nature Biotechnology·B SchwikowskiS Fields
Jun 14, 2001·Methods : a Companion to Methods in Enzymology·O PuigB Séraphin
Jan 31, 2002·Proceedings of the National Academy of Sciences of the United States of America·David C Krakauer, Joshua B Plotkin
Mar 2, 2002·Science·Eric H DavidsonHamid Bolouri
Oct 26, 2002·Science·Tong Ihn LeeRichard A Young
Nov 5, 2002·Trends in Biotechnology·Paul BrazhnikPedro Mendes
Nov 5, 2002·Proceedings of the National Academy of Sciences of the United States of America·Daniel SegrèGeorge M Church
Feb 5, 2003·Genome Research·Jochen FörsterJens Nielsen
May 9, 2003·Nature·Loren L LoogerHomme W Hellinga
Aug 9, 2003·Nature Reviews. Drug Discovery·Jeremy K Nicholson, Ian D Wilson
Nov 3, 2004·Nature Reviews. Genetics·Hiroaki Kitano
Feb 24, 2006·Nature Reviews. Molecular Cell Biology·Andrew R Joyce, Bernhard Ø Palsson
May 3, 2006·Current Opinion in Structural Biology·Mikhail S Gelfand
Apr 28, 2007·Proceedings of the National Academy of Sciences of the United States of America·Jin Hwan ParkSang Yup Lee
Jun 3, 2008·Nature Methods·Ali MortazaviBarbara Wold
Oct 11, 2008·Journal of Industrial Microbiology & Biotechnology·Dong-jian ShiKui-ming Wang
Nov 1, 2008·Nucleic Acids Research·Ren Zhang, Yan Lin
Mar 17, 2009·Briefings in Bioinformatics·Karthik Raman, Nagasuma Chandra
Jun 17, 2009·Proceedings of the National Academy of Sciences of the United States of America·Jesse D Bloom, Frances H Arnold
Jun 27, 2009·Genome Biology·Christopher S HenryRick L Stevens
Aug 20, 2009·Molecular Systems Biology·Patrick F SuthersCostas D Maranas
Nov 6, 2009·Molecular Systems Biology·Matthew A OberhardtJason A Papin
Nov 6, 2009·Biotechnology and Bioengineering·José Manuel Otero, Jens Nielsen
Jan 9, 2010·Nature Protocols·Ines Thiele, Bernhard Ø Palsson
Jul 1, 2010·PLoS Computational Biology·Javier De Las Rivas, Celia Fontanillo
Aug 31, 2010·Nature Biotechnology·Christopher S HenryRick L Stevens
Nov 10, 2010·PLoS Computational Biology·Dipak BaruaJennifer L Reed
Apr 5, 2011·The American Naturalist·Oskar FranklinAndreas Richter
Jun 7, 2011·Applied and Environmental Microbiology·Cong T TrinhDouglas S Clark
Sep 3, 2011·Nature Protocols·Jan SchellenbergerBernhard Ø Palsson
Sep 29, 2011·Metabolic Engineering·Hanson LeeJohn E Dueber
Nov 8, 2011·Current Opinion in Biotechnology·Tae Yong KimSang Yup Lee

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Citations

Jul 26, 2018·Marine Drugs·Stefano RomanoAlan D W Dobson
Jun 28, 2019·Essays in Biochemistry·Sophie LandonClaire Grierson
Sep 3, 2021·Computational and Structural Biotechnology Journal·Ankur SahuNadine Töpfer

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Methods Mentioned

BETA
two-hybrid
tandem affinity purification

Software Mentioned

PRO
R
Path
COBRA
ModelSEED
Python
OptStrain
MATLAB
GEM

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