Engineering robust microorganisms for organic acid production

Tran, Vinh G.; Zhao, Huimin

doi:10.1093/jimb/kuab067

Engineering robust microorganisms for organic acid production

Journal Article · Tue Sep 21 00:00:00 EDT 2021 · Journal of Industrial Microbiology and Biotechnology

DOI:https://doi.org/10.1093/jimb/kuab067· OSTI ID:1863114

Tran, Vinh G. ^[1]; Zhao, Huimin ^[2]

Department of Chemical and Biomolecular Engineering, U.S. Department of Energy Center for Bioenergy and Bioproducts Innovation (CABBI), Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
Department of Chemical and Biomolecular Engineering, U.S. Department of Energy Center for Bioenergy and Bioproducts Innovation (CABBI), Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA, Departments of Chemistry, Biochemistry, and Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA

Abstract

Organic acids are an important class of compounds that can be produced by microbial conversion of renewable feedstocks and have huge demands and broad applications in food, chemical, and pharmaceutical industries. An economically viable fermentation process for production of organic acids requires robust microbial cell factories with excellent tolerance to low pH conditions, high concentrations of organic acids, and lignocellulosic inhibitors. In this review, we summarize various strategies to engineer robust microorganisms for organic acid production and highlight their applications in a few recent examples.

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Sponsoring Organization:: USDOE

Grant/Contract Number:: SC0018420; SC0018260

OSTI ID:: 1863114

Alternate ID(s):: OSTI ID: 1822954
OSTI ID: 1834451

Journal Information:: Journal of Industrial Microbiology and Biotechnology, Journal Name: Journal of Industrial Microbiology and Biotechnology Journal Issue: 2 Vol. 49; ISSN 1367-5435

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: Germany

Language:: English

References (55)

Advancing Metabolic Engineering of Saccharomyces cerevisiae Using the CRISPR/Cas System Lian, Jiazhang; HamediRad, Mohammad; Zhao, Huimin Biotechnology Journal, Vol. 13, Issue 9 https://doi.org/10.1002/biot.201700601	journal	April 2018
Low‐pH production of d ‐lactic acid using newly isolated acid tolerant yeast Pichia kudriavzevii NG7 Park, Hyun Joo; Bae, Jung‐Hoon; Ko, Hyeok‐Jin Biotechnology and Bioengineering, Vol. 115, Issue 9 https://doi.org/10.1002/bit.26745	journal	June 2018
Impact of stress‐response related transcription factor overexpression on lignocellulosic inhibitor tolerance of Saccharomyces cerevisiae environmental isolates Mertens, Jeffrey A.; Skory, Christopher D.; Nichols, Nancy N. Biotechnology Progress, Vol. 37, Issue 2 https://doi.org/10.1002/btpr.3094	journal	October 2020
The role of high-throughput transcriptome analysis in metabolic engineering Jewett, Michael C.; Oliveira, Ana Paula; Patil, Kiran Raosaheb Biotechnology and Bioprocess Engineering, Vol. 10, Issue 5 https://doi.org/10.1007/BF02989821	journal	October 2005
Improving furfural tolerance of Zymomonas mobilis by rewiring a sigma factor RpoD protein Tan, Fu-Rong; Dai, Li-Chun; Wu, Bo Applied Microbiology and Biotechnology, Vol. 99, Issue 12 https://doi.org/10.1007/s00253-015-6577-2	journal	April 2015
Tolerance improvement of Corynebacterium glutamicum on lignocellulose derived inhibitors by adaptive evolution Wang, Xia; Khushk, Imrana; Xiao, Yanqiu Applied Microbiology and Biotechnology, Vol. 102, Issue 1 https://doi.org/10.1007/s00253-017-8627-4	journal	November 2017
HAA1 and PRS3 overexpression boosts yeast tolerance towards acetic acid improving xylose or glucose consumption: unravelling the underlying mechanisms Cunha, Joana T.; Costa, Carlos E.; Ferraz, Luís Applied Microbiology and Biotechnology, Vol. 102, Issue 10 https://doi.org/10.1007/s00253-018-8955-z	journal	April 2018
Microbial response to acid stress: mechanisms and applications Guan, Ningzi; Liu, Long Applied Microbiology and Biotechnology, Vol. 104, Issue 1 https://doi.org/10.1007/s00253-019-10226-1	journal	November 2019
Adaptive laboratory evolution of Yarrowia lipolytica improves ferulic acid tolerance Wang, Zedi; Zhou, Linlin; Lu, Minrui Applied Microbiology and Biotechnology, Vol. 105, Issue 4 https://doi.org/10.1007/s00253-021-11130-3	journal	February 2021
Genome shuffling improved acid-tolerance and succinic acid production of Actinobacillus succinogenes Hu, Shumeng; You, Ying; Xia, Feifei Food Science and Biotechnology, Vol. 28, Issue 3 https://doi.org/10.1007/s10068-018-0505-z	journal	November 2018
Engineering microbial factories for synthesis of value-added products Du, Jing; Shao, Zengyi; Zhao, Huimin Journal of Industrial Microbiology & Biotechnology, Vol. 38, Issue 8 https://doi.org/10.1007/s10295-011-0970-3	journal	April 2011
Inactivation of the transcription factor mig1 ( YGL035C ) in Saccharomyces cerevisiae improves tolerance towards monocarboxylic weak acids: acetic, formic and levulinic acid Balderas-Hernández, Victor E.; Correia, Kevin; Mahadevan, Radhakrishnan Journal of Industrial Microbiology and Biotechnology, Vol. 45, Issue 8 https://doi.org/10.1007/s10295-018-2053-1	journal	August 2018
Tolerance and transcriptional analysis of Corynebacterium glutamicum on biotransformation of toxic furaldehyde and benzaldehyde inhibitory compounds Zhou, Pingping; Khushk, Imrana; Gao, Qiuqiang Journal of Industrial Microbiology and Biotechnology, Vol. 46, Issue 7 https://doi.org/10.1007/s10295-019-02171-9	journal	July 2019
Understanding and engineering alcohol-tolerant bacteria using OMICS technology Horinouchi, Takaaki; Maeda, Tomoya; Furusawa, Chikara World Journal of Microbiology and Biotechnology, Vol. 34, Issue 11 https://doi.org/10.1007/s11274-018-2542-4	journal	October 2018
Protein and metabolic engineering for the production of organic acids Liu, Jingjing; Li, Jianghua; Shin, Hyun-dong Bioresource Technology, Vol. 239 https://doi.org/10.1016/j.biortech.2017.04.052	journal	September 2017
Deletion of acetate transporter gene ADY2 improved tolerance of Saccharomyces cerevisiae against multiple stresses and enhanced ethanol production in the presence of acetic acid Zhang, Mingming; Zhang, Keyu; Mehmood, Muhammad Aamer Bioresource Technology, Vol. 245 https://doi.org/10.1016/j.biortech.2017.05.191	journal	December 2017
Strategies for enhancing microbial tolerance to inhibitors for biofuel production: A review Wang, Shizeng; Sun, Xinxiao; Yuan, Qipeng Bioresource Technology, Vol. 258 https://doi.org/10.1016/j.biortech.2018.03.064	journal	June 2018
Rapid prototyping of microbial cell factories via genome-scale engineering Si, Tong; Xiao, Han; Zhao, Huimin Biotechnology Advances, Vol. 33, Issue 7 https://doi.org/10.1016/j.biotechadv.2014.11.007	journal	November 2015
Metabolic engineering in the biotechnological production of organic acids in the tricarboxylic acid cycle of microorganisms: Advances and prospects Yin, Xian; Li, Jianghua; Shin, Hyun-dong Biotechnology Advances, Vol. 33, Issue 6 https://doi.org/10.1016/j.biotechadv.2015.04.006	journal	November 2015
Mechanisms of acid tolerance in bacteria and prospects in biotechnology and bioremediation Liu, Yuping; Tang, Hongzhi; Lin, Zhanglin Biotechnology Advances, Vol. 33, Issue 7 https://doi.org/10.1016/j.biotechadv.2015.06.001	journal	November 2015
Metabolic engineering of yeast for lignocellulosic biofuel production Jin, Yong-Su; Cate, Jamie HD Current Opinion in Chemical Biology, Vol. 41 https://doi.org/10.1016/j.cbpa.2017.10.025	journal	December 2017
Unlocking nature’s biosynthetic potential by directed genome evolution Cao, Mingfeng; Tran, Vinh G.; Zhao, Huimin Current Opinion in Biotechnology, Vol. 66 https://doi.org/10.1016/j.copbio.2020.06.012	journal	December 2020
Identification of an acetate-tolerant strain of Saccharomyces cerevisiae and characterization by gene expression analysis Haitani, Yutaka; Tanaka, Koichi; Yamamoto, Mami Journal of Bioscience and Bioengineering, Vol. 114, Issue 6 https://doi.org/10.1016/j.jbiosc.2012.07.002	journal	December 2012
Transcriptional profiling reveals molecular basis and the role of arginine in response to low-pH stress in Pichia kudriavzevii Ji, Hao; Xu, Ke; Dong, Xiameng Journal of Bioscience and Bioengineering, Vol. 130, Issue 6 https://doi.org/10.1016/j.jbiosc.2020.07.014	journal	December 2020
Point mutation of H3/H4 histones affects acetic acid tolerance in Saccharomyces cerevisiae Liu, Xiangyong; Zhang, Xiaohua; Zhang, Zhaojie Journal of Biotechnology, Vol. 187 https://doi.org/10.1016/j.jbiotec.2014.07.445	journal	October 2014
Overexpression of RCK1 improves acetic acid tolerance in Saccharomyces cerevisiae Oh, Eun Joong; Wei, Na; Kwak, Suryang Journal of Biotechnology, Vol. 292 https://doi.org/10.1016/j.jbiotec.2018.12.013	journal	February 2019
Adaptive evolution improves acid tolerance and succinic acid production in Actinobacillus succinogenes Zhang, Wenming; Tao, Yuxuan; Wu, Min Process Biochemistry, Vol. 98 https://doi.org/10.1016/j.procbio.2020.08.003	journal	November 2020
Chaperone-dependent mechanisms for acid resistance in enteric bacteria Hong, Weizhe; Wu, Ye E.; Fu, Xinmiao Trends in Microbiology, Vol. 20, Issue 7 https://doi.org/10.1016/j.tim.2012.03.001	journal	July 2012
Evolution for exogenous octanoic acid tolerance improves carboxylic acid production and membrane integrity Royce, Liam A.; Yoon, Jong Moon; Chen, Yingxi Metabolic Engineering, Vol. 29 https://doi.org/10.1016/j.ymben.2015.03.014	journal	May 2015
Evolutionary engineering reveals divergent paths when yeast is adapted to different acidic environments Fletcher, Eugene; Feizi, Amir; Bisschops, Markus M. M. Metabolic Engineering, Vol. 39 https://doi.org/10.1016/j.ymben.2016.10.010	journal	January 2017
Recent advances in metabolic engineering of Saccharomyces cerevisiae: New tools and their applications Lian, Jiazhang; Mishra, Shekhar; Zhao, Huimin Metabolic Engineering, Vol. 50 https://doi.org/10.1016/j.ymben.2018.04.011	journal	November 2018
The emergence of adaptive laboratory evolution as an efficient tool for biological discovery and industrial biotechnology Sandberg, Troy E.; Salazar, Michael J.; Weng, Liam L. Metabolic Engineering, Vol. 56 https://doi.org/10.1016/j.ymben.2019.08.004	journal	December 2019
Adaptive laboratory evolution of tolerance to dicarboxylic acids in Saccharomyces cerevisiae Pereira, Rui; Wei, Yongjun; Mohamed, Elsayed Metabolic Engineering, Vol. 56 https://doi.org/10.1016/j.ymben.2019.09.008	journal	December 2019
A genetic toolbox for metabolic engineering of Issatchenkia orientalis Cao, Mingfeng; Fatma, Zia; Song, Xiaofei Metabolic Engineering, Vol. 59 https://doi.org/10.1016/j.ymben.2020.01.005	journal	May 2020
RNAi-Assisted Genome Evolution in Saccharomyces cerevisiae for Complex Phenotype Engineering Si, Tong; Luo, Yunzi; Bao, Zehua ACS Synthetic Biology, Vol. 4, Issue 3 https://doi.org/10.1021/sb500074a	journal	May 2014
Genome-scale engineering of Saccharomyces cerevisiae with single-nucleotide precision Bao, Zehua; HamediRad, Mohammad; Xue, Pu Nature Biotechnology, Vol. 36, Issue 6 https://doi.org/10.1038/nbt.4132	journal	May 2018
Automated multiplex genome-scale engineering in yeast Si, Tong; Chao, Ran; Min, Yuhao Nature Communications, Vol. 8, Issue 1 https://doi.org/10.1038/ncomms15187	journal	May 2017
Multi-functional genome-wide CRISPR system for high throughput genotype–phenotype mapping Lian, Jiazhang; Schultz, Carl; Cao, Mingfeng Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-13621-4	journal	December 2019
An acid-tolerance response system protecting exponentially growing Escherichia coli Xu, Ying; Zhao, Zhe; Tong, Wenhua Nature Communications, Vol. 11, Issue 1 https://doi.org/10.1038/s41467-020-15350-5	journal	March 2020
Elucidating aromatic acid tolerance at low pH in Saccharomyces cerevisiae using adaptive laboratory evolution Pereira, Rui; Mohamed, Elsayed T.; Radi, Mohammad S. Proceedings of the National Academy of Sciences, Vol. 117, Issue 45 https://doi.org/10.1073/pnas.2013044117	journal	October 2020
Programmable gene regulation for metabolic engineering using decoy transcription factor binding sites Wang, Tiebin; Tague, Nathan; Whelan, Stephen A. Nucleic Acids Research, Vol. 49, Issue 2 https://doi.org/10.1093/nar/gkaa1234	journal	December 2020
Adaptive laboratory evolution of Escherichia coli under acid stress Du, Bin; Olson, Connor A.; Sastry, Anand V. Microbiology, Vol. 166, Issue 2 https://doi.org/10.1099/mic.0.000867	journal	February 2020
Transport of carboxylic acids in yeasts Casal, Margarida; Paiva, Sandra; Queirós, Odília FEMS Microbiology Reviews, Vol. 32, Issue 6 https://doi.org/10.1111/j.1574-6976.2008.00128.x	journal	November 2008
Cg Cmk1 Activates Cg Rds2 To Resist Low-pH Stress in Candida glabrata Wu, Chengjin; Zhu, Guoxing; Ding, Qiang Applied and Environmental Microbiology, Vol. 86, Issue 11 https://doi.org/10.1128/AEM.00302-20	journal	May 2020
Silencing of NADPH-Dependent Oxidoreductase Genes (yqhD and dkgA) in Furfural-Resistant Ethanologenic Escherichia coli Miller, E. N.; Jarboe, L. R.; Yomano, L. P. Applied and Environmental Microbiology, Vol. 75, Issue 13, p. 4315-4323 https://doi.org/10.1128/AEM.00567-09	journal	May 2009
Roles of the Yap1 Transcription Factor and Antioxidants in Saccharomyces cerevisiae's Tolerance to Furfural and 5-Hydroxymethylfurfural, Which Function as Thiol-Reactive Electrophiles Generating Oxidative Stress Kim, D.; Hahn, J. -S. Applied and Environmental Microbiology, Vol. 79, Issue 16 https://doi.org/10.1128/AEM.00643-13	journal	June 2013
Molecular Basis of Bacterial Outer Membrane Permeability Revisited Nikaido, H. Microbiology and Molecular Biology Reviews, Vol. 67, Issue 4 https://doi.org/10.1128/MMBR.67.4.593-656.2003	journal	December 2003
Development of a CRISPR/Cas9-Based Tool for Gene Deletion in Issatchenkia orientalis Tran, Vinh G.; Cao, Mingfeng; Fatma, Zia mSphere, Vol. 4, Issue 3 https://doi.org/10.1128/mSphere.00345-19	journal	June 2019
Exploiting Issatchenkia orientalis SD108 for succinic acid production Xiao, Han; Shao, Zengyi; Jiang, Yu Microbial Cell Factories, Vol. 13, Issue 1 https://doi.org/10.1186/s12934-014-0121-4	journal	August 2014
Improvement of yeast tolerance to acetic acid through Haa1 transcription factor engineering: towards the underlying mechanisms Swinnen, Steve; Henriques, Sílvia F.; Shrestha, Ranjan Microbial Cell Factories, Vol. 16, Issue 1 https://doi.org/10.1186/s12934-016-0621-5	journal	January 2017
Profiling of Saccharomyces cerevisiae transcription factors for engineering the resistance of yeast to lignocellulose-derived inhibitors in biomass conversion Wu, Guochao; Xu, Zixiang; Jönsson, Leif J. Microbial Cell Factories, Vol. 16, Issue 1 https://doi.org/10.1186/s12934-017-0811-9	journal	November 2017
Engineering metabolite-responsive transcriptional factors to sense small molecules in eukaryotes: current state and perspectives Wan, Xia; Marsafari, Monireh; Xu, Peng Microbial Cell Factories, Vol. 18, Issue 1 https://doi.org/10.1186/s12934-019-1111-3	journal	March 2019
Enhanced acid-stress tolerance in Lactococcus lactis NZ9000 by overexpression of ABC transporters Zhu, Zhengming; Yang, Jinhua; Yang, Peishan Microbial Cell Factories, Vol. 18, Issue 1 https://doi.org/10.1186/s12934-019-1188-8	journal	August 2019
Identification and Characterization of a Novel Issatchenkia orientalis GPI-Anchored Protein, IoGas1, Required for Resistance to Low pH and Salt Stress Matsushika, Akinori; Negi, Kanako; Suzuki, Toshihiro PLOS ONE, Vol. 11, Issue 9 https://doi.org/10.1371/journal.pone.0161888	journal	September 2016
Development and Application of CRISPR/Cas in Microbial Biotechnology Ding, Wentao; Zhang, Yang; Shi, Shuobo Frontiers in Bioengineering and Biotechnology, Vol. 8 https://doi.org/10.3389/fbioe.2020.00711	journal	June 2020

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