High-Throughput Functional Genomics for Energy Production
Abstract
Functional genomics remains a foundational field for establishing genotype-phenotype relationships that enable strain engineering. High-throughput (HTP) methods accelerate the Design-Build-Test-Learn cycle that currently drives synthetic biology towards a forward engineering future. Trackable mutagenesis techniques including transposon insertion sequencing and CRISPR-Cas-mediated genome editing allow for rapid fitness profiling of a collection, or library, of mutants to discover beneficial mutations. Due to the relative speed of these experiments compared to adaptive evolution experiments, iterative rounds of mutagenesis can be implemented for next-generation metabolic engineering efforts to design complex production and tolerance phenotypes. Further, the expansion of these mutagenesis techniques to novel bacteria are opening up industrial microbes that show promise for establishing a bio-based economy.
- Authors:
-
- Univ. of Colorado, Boulder, CO (United States)
- Univ. of Colorado, Boulder, CO (United States); National Renewable Energy Lab. (NREL), Golden, CO (United States)
- Publication Date:
- Research Org.:
- National Renewable Energy Lab. (NREL), Golden, CO (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1721731
- Alternate Identifier(s):
- OSTI ID: 1811078
- Report Number(s):
- NREL/JA-2700-77739
Journal ID: ISSN 0958-1669; MainId:30654;UUID:388cbc9c-c72d-475e-aefe-91faf80572c7;MainAdminID:18583
- Grant/Contract Number:
- AC36-08GO28308
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Current Opinion in Biotechnology
- Additional Journal Information:
- Journal Volume: 67; Journal ID: ISSN 0958-1669
- Publisher:
- Elsevier
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; high-throughput; genomic methods; microbial systems
Citation Formats
Fenster, Jacob A., and Eckert, Carrie A. High-Throughput Functional Genomics for Energy Production. United States: N. p., 2020.
Web. doi:10.1016/j.copbio.2020.09.010.
Fenster, Jacob A., & Eckert, Carrie A. High-Throughput Functional Genomics for Energy Production. United States. https://doi.org/10.1016/j.copbio.2020.09.010
Fenster, Jacob A., and Eckert, Carrie A. Mon .
"High-Throughput Functional Genomics for Energy Production". United States. https://doi.org/10.1016/j.copbio.2020.09.010. https://www.osti.gov/servlets/purl/1721731.
@article{osti_1721731,
title = {High-Throughput Functional Genomics for Energy Production},
author = {Fenster, Jacob A. and Eckert, Carrie A.},
abstractNote = {Functional genomics remains a foundational field for establishing genotype-phenotype relationships that enable strain engineering. High-throughput (HTP) methods accelerate the Design-Build-Test-Learn cycle that currently drives synthetic biology towards a forward engineering future. Trackable mutagenesis techniques including transposon insertion sequencing and CRISPR-Cas-mediated genome editing allow for rapid fitness profiling of a collection, or library, of mutants to discover beneficial mutations. Due to the relative speed of these experiments compared to adaptive evolution experiments, iterative rounds of mutagenesis can be implemented for next-generation metabolic engineering efforts to design complex production and tolerance phenotypes. Further, the expansion of these mutagenesis techniques to novel bacteria are opening up industrial microbes that show promise for establishing a bio-based economy.},
doi = {10.1016/j.copbio.2020.09.010},
journal = {Current Opinion in Biotechnology},
number = ,
volume = 67,
place = {United States},
year = {Mon Nov 02 00:00:00 EST 2020},
month = {Mon Nov 02 00:00:00 EST 2020}
}
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Works referenced in this record:
A history of genome editing in Saccharomyces cerevisiae
journal, January 2018
- Alexander, William G.
- Yeast, Vol. 35, Issue 5
Development of both type I–B and type II CRISPR/Cas genome editing systems in the cellulolytic bacterium Clostridium thermocellum
journal, June 2020
- Walker, Julie E.; Lanahan, Anthony A.; Zheng, Tianyong
- Metabolic Engineering Communications, Vol. 10
Functional profiling of the Saccharomyces cerevisiae genome
journal, July 2002
- Giaever, Guri; Chu, Angela M.; Ni, Li
- Nature, Vol. 418, Issue 6896
Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants the Keio collection
journal, February 2006
- Baba, Tomoya; Ara, Takeshi; Hasegawa, Miki
- Molecular Systems Biology, Vol. 2, Article No. 2006.0008
A genome-wide algal mutant library and functional screen identifies genes required for eukaryotic photosynthesis
journal, March 2019
- Li, Xiaobo; Patena, Weronika; Fauser, Friedrich
- Nature Genetics, Vol. 51, Issue 4
Analysis of a genome-wide set of gene deletions in the fission yeast Schizosaccharomyces pombe
journal, May 2010
- Kim, Dong-Uk; Hayles, Jacqueline; Kim, Dongsup
- Nature Biotechnology, Vol. 28, Issue 6
Quantitative phenotyping via deep barcode sequencing
journal, July 2009
- Smith, A. M.; Heisler, L. E.; Mellor, J.
- Genome Research, Vol. 19, Issue 10
Rapid Quantification of Mutant Fitness in Diverse Bacteria by Sequencing Randomly Bar-Coded Transposons
journal, May 2015
- Wetmore, Kelly M.; Price, Morgan N.; Waters, Robert J.
- mBio, Vol. 6, Issue 3, Article No. e00306-15
Genome-wide mapping of mutations at single-nucleotide resolution for protein, metabolic and genome engineering
journal, December 2016
- Garst, Andrew D.; Bassalo, Marcelo C.; Pines, Gur
- Nature Biotechnology, Vol. 35, Issue 1, p. 48-55
Genome-scale engineering of Saccharomyces cerevisiae with single-nucleotide precision
journal, May 2018
- Bao, Zehua; HamediRad, Mohammad; Xue, Pu
- Nature Biotechnology, Vol. 36, Issue 6
Enabling tools for high-throughput detection of metabolites: Metabolic engineering and directed evolution applications
journal, December 2017
- Lin, Jyun-Liang; Wagner, James M.; Alper, Hal S.
- Biotechnology Advances, Vol. 35, Issue 8
Approaches to querying bacterial genomes with transposon-insertion sequencing
journal, July 2013
- Barquist, Lars; Boinett, Christine J.; Cain, Amy K.
- RNA Biology, Vol. 10, Issue 7
Transposon insertion sequencing: a new tool for systems-level analysis of microorganisms
journal, May 2013
- van Opijnen, Tim; Camilli, Andrew
- Nature Reviews Microbiology, Vol. 11, Issue 7
The essential gene set of a photosynthetic organism
journal, October 2015
- Rubin, Benjamin E.; Wetmore, Kelly M.; Price, Morgan N.
- Proceedings of the National Academy of Sciences, Vol. 112, Issue 48
The Essential Genome of Escherichia coli K-12
journal, February 2018
- Goodall, Emily C. A.; Robinson, Ashley; Johnston, Iain G.
- mBio, Vol. 9, Issue 1
Genome-Wide Determination of Gene Essentiality by Transposon Insertion Sequencing in Yeast Pichia pastoris
journal, July 2018
- Zhu, Jinxiang; Gong, Ruiqing; Zhu, Qiaoyun
- Scientific Reports, Vol. 8, Issue 1
Functional mapping of yeast genomes by saturated transposition
journal, May 2017
- Michel, Agnès H.; Hatakeyama, Riko; Kimmig, Philipp
- eLife, Vol. 6
Genome-wide fitness assessment during diurnal growth reveals an expanded role of the cyanobacterial circadian clock protein KaiA
journal, July 2018
- Welkie, David G.; Rubin, Benjamin E.; Chang, Yong-Gang
- Proceedings of the National Academy of Sciences, Vol. 115, Issue 30
Functional genomics of lipid metabolism in the oleaginous yeast Rhodosporidium toruloides
journal, March 2018
- Coradetti, Samuel T.; Pinel, Dominic; Geiselman, Gina M.
- eLife, Vol. 7
Rapid, Parallel Identification of Catabolism Pathways of Lignin-Derived Aromatic Compounds in Novosphingobium aromaticivorans
journal, September 2018
- Cecil, Jacob H.; Garcia, David C.; Giannone, Richard J.
- Applied and Environmental Microbiology, Vol. 84, Issue 22
Identification, Characterization, and Application of a Highly Sensitive Lactam Biosensor from Pseudomonas putida
journal, December 2019
- Thompson, Mitchell G.; Pearson, Allison N.; Barajas, Jesus F.
- ACS Synthetic Biology, Vol. 9, Issue 1
Leveraging host metabolism for bisdemethoxycurcumin production in Pseudomonas putida
journal, June 2020
- Incha, Matthew R.; Thompson, Mitchell G.; Blake-Hedges, Jacquelyn M.
- Metabolic Engineering Communications, Vol. 10
Fatty Acid and Alcohol Metabolism in Pseudomonas putida: Functional Analysis Using Random Barcode Transposon Sequencing
journal, October 2020
- Thompson, Mitchell G.; Incha, Matthew R.; Pearson, Allison N.
- Applied and Environmental Microbiology, Vol. 86, Issue 21
Mutant phenotypes for thousands of bacterial genes of unknown function
journal, May 2018
- Price, Morgan N.; Wetmore, Kelly M.; Waters, R. Jordan
- Nature, Vol. 557, Issue 7706
Genetic-Metabolic Coupling for Targeted Metabolic Engineering
journal, August 2017
- Cardinale, Stefano; Tueros, Felipe Gonzalo; Sommer, Morten Otto Alexander
- Cell Reports, Vol. 20, Issue 5
Magic Pools: Parallel Assessment of Transposon Delivery Vectors in Bacteria
journal, January 2018
- Liu, Hualan; Price, Morgan N.; Waters, Robert Jordan
- mSystems, Vol. 3, Issue 1
A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity
journal, June 2012
- Jinek, M.; Chylinski, K.; Fonfara, I.
- Science, Vol. 337, Issue 6096, p. 816-821
RNA-guided editing of bacterial genomes using CRISPR-Cas systems
journal, January 2013
- Jiang, Wenyan; Bikard, David; Cox, David
- Nature Biotechnology, Vol. 31, Issue 3, p. 233-239
Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems
journal, March 2013
- DiCarlo, James E.; Norville, Julie E.; Mali, Prashant
- Nucleic Acids Research, Vol. 41, Issue 7, p. 4336-4343
Genome and metabolic engineering in non-conventional yeasts: Current advances and applications
journal, September 2017
- Löbs, Ann-Kathrin; Schwartz, Cory; Wheeldon, Ian
- Synthetic and Systems Biotechnology, Vol. 2, Issue 3
Strategies for Applying Nonhomologous End Joining-Mediated Genome Editing in Prokaryotes
journal, September 2019
- Cui, Yali; Dong, Huina; Ma, Yuanyuan
- ACS Synthetic Biology, Vol. 8, Issue 10
Nonhomologous End Joining in Yeast
journal, December 2005
- Daley, James M.; Palmbos, Phillip L.; Wu, Dongliang
- Annual Review of Genetics, Vol. 39, Issue 1
Bacterial DNA repair by non-homologous end joining
journal, November 2007
- Shuman, Stewart; Glickman, Michael S.
- Nature Reviews Microbiology, Vol. 5, Issue 11
Deep scanning lysine metabolism in Escherichia coli
journal, November 2018
- Bassalo, Marcelo C.; Garst, Andrew D.; Choudhury, Alaksh
- Molecular Systems Biology, Vol. 14, Issue 11
Large scale validation of an efficient CRISPR/Cas-based multi gene editing protocol in Escherichia coli
journal, April 2017
- Zerbini, Francesca; Zanella, Ilaria; Fraccascia, Davide
- Microbial Cell Factories, Vol. 16, Issue 1
Consequences of Cas9 cleavage in the chromosome of Escherichia coli
journal, April 2016
- Cui, Lun; Bikard, David
- Nucleic Acids Research, Vol. 44, Issue 9
Determinants for Efficient Editing with Cas9-Mediated Recombineering in Escherichia coli
journal, April 2020
- Choudhury, Alaksh; Fankhauser, Reilly G.; Freed, Emily F.
- ACS Synthetic Biology, Vol. 9, Issue 5
Improved sgRNA design in bacteria via genome-wide activity profiling
journal, June 2018
- Guo, Jiahui; Wang, Tianmin; Guan, Changge
- Nucleic Acids Research, Vol. 46, Issue 14
Validating genome-wide CRISPR-Cas9 function improves screening in the oleaginous yeast Yarrowia lipolytica
journal, September 2019
- Schwartz, Cory; Cheng, Jan-Fang; Evans, Robert
- Metabolic Engineering, Vol. 55
Genome engineering of E. coli for improved styrene production
journal, January 2020
- Liang, Liya; Liu, Rongming; Foster, Kyle E. O.
- Metabolic Engineering, Vol. 57
Beyond editing: repurposing CRISPR–Cas9 for precision genome regulation and interrogation
journal, December 2015
- Dominguez, Antonia A.; Lim, Wendell A.; Qi, Lei S.
- Nature Reviews Molecular Cell Biology, Vol. 17, Issue 1
CRISPR technologies for bacterial systems: Current achievements and future directions
journal, November 2016
- Choi, Kyeong Rok; Lee, Sang Yup
- Biotechnology Advances, Vol. 34, Issue 7
CRISPR /Cas‐based screening of a gene activation library in Saccharomyces cerevisiae identifies a crucial role of OLE 1 in thermotolerance
journal, November 2018
- Li, Pengsong; Fu, Xiaofen; Zhang, Lei
- Microbial Biotechnology, Vol. 12, Issue 6
Implementing CRISPR-Cas technologies in conventional and non-conventional yeasts: Current state and future prospects
journal, May 2018
- Raschmanová, Hana; Weninger, Astrid; Glieder, Anton
- Biotechnology Advances, Vol. 36, Issue 3
Multiplexed CRISPR Activation of Cryptic Sugar Metabolism Enables Yarrowia Lipolytica Growth on Cellobiose
journal, May 2018
- Schwartz, Cory; Curtis, Nicholas; Löbs, Ann-Kathrin
- Biotechnology Journal, Vol. 13, Issue 9
Engineered CRISPRa enables programmable eukaryote-like gene activation in bacteria
journal, August 2019
- Liu, Yang; Wan, Xinyi; Wang, Baojun
- Nature Communications, Vol. 10, Issue 1
Programmable CRISPR‐Cas transcriptional activation in bacteria
journal, July 2020
- Ho, Hsing‐I; Fang, Jennifer R.; Cheung, Jacky
- Molecular Systems Biology, Vol. 16, Issue 7
A Comprehensive, CRISPR-based Functional Analysis of Essential Genes in Bacteria
journal, June 2016
- Peters, Jason M.; Colavin, Alexandre; Shi, Handuo
- Cell, Vol. 165, Issue 6
Pooled CRISPRi screening of the cyanobacterium Synechocystis sp PCC 6803 for enhanced industrial phenotypes
journal, April 2020
- Yao, Lun; Shabestary, Kiyan; Björk, Sara M.
- Nature Communications, Vol. 11, Issue 1
Combinatorial metabolic engineering using an orthogonal tri-functional CRISPR system
journal, November 2017
- Lian, Jiazhang; HamediRad, Mohammad; Hu, Sumeng
- Nature Communications, Vol. 8, Issue 1
Multi-functional genome-wide CRISPR system for high throughput genotype–phenotype mapping
journal, December 2019
- Lian, Jiazhang; Schultz, Carl; Cao, Mingfeng
- Nature Communications, Vol. 10, Issue 1
Bioprocess development for muconic acid production from aromatic compounds and lignin
journal, January 2018
- Salvachúa, Davinia; Johnson, Christopher W.; Singer, Christine A.
- Green Chemistry, Vol. 20, Issue 21
Low pH d-xylonate production with Pichia kudriavzevii
journal, April 2013
- Toivari, Mervi; Vehkomäki, Maija-Leena; Nygård, Yvonne
- Bioresource Technology, Vol. 133
Low‐pH production of d ‐lactic acid using newly isolated acid tolerant yeast Pichia kudriavzevii NG7
journal, June 2018
- Park, Hyun Joo; Bae, Jung‐Hoon; Ko, Hyeok‐Jin
- Biotechnology and Bioengineering, Vol. 115, Issue 9
Next generation industrial biotechnology based on extremophilic bacteria
journal, April 2018
- Chen, Guo-Qiang; Jiang, Xiao-Ran
- Current Opinion in Biotechnology, Vol. 50
Local fitness landscape of the green fluorescent protein
journal, May 2016
- Sarkisyan, Karen S.; Bolotin, Dmitry A.; Meer, Margarita V.
- Nature, Vol. 533, Issue 7603
A global genetic interaction network maps a wiring diagram of cellular function
journal, September 2016
- Costanzo, M.; VanderSluis, B.; Koch, E. N.
- Science, Vol. 353, Issue 6306
CRISPR /Cas9 recombineering‐mediated deep mutational scanning of essential genes in Escherichia coli
journal, March 2020
- Choudhury, Alaksh; Fenster, Jacob A.; Fankhauser, Reilly G.
- Molecular Systems Biology, Vol. 16, Issue 3
Pooled CRISPR interference screening enables genome-scale functional genomics study in bacteria with superior performance
journal, June 2018
- Wang, Tianmin; Guan, Changge; Guo, Jiahui
- Nature Communications, Vol. 9, Issue 1
Genome-wide CRISPR-dCas9 screens in E. coli identify essential genes and phage host factors
journal, November 2018
- Rousset, François; Cui, Lun; Siouve, Elise
- PLOS Genetics, Vol. 14, Issue 11
A CRISPRi screen in E. coli reveals sequence-specific toxicity of dCas9
journal, May 2018
- Cui, Lun; Vigouroux, Antoine; Rousset, François
- Nature Communications, Vol. 9, Issue 1
Iterative screening methodology enables isolation of strains with improved properties for a FACS-based screen and increased L-DOPA production
journal, April 2019
- Savitskaya, Judy; Protzko, Ryan J.; Li, Francesca-Zhoufan
- Scientific Reports, Vol. 9, Issue 1
Omics-driven identification and elimination of valerolactam catabolism in Pseudomonas putida KT2440 for increased product titer
journal, December 2019
- Thompson, Mitchell G.; Valencia, Luis E.; Blake-Hedges, Jacquelyn M.
- Metabolic Engineering Communications, Vol. 9
Multiplex navigation of global regulatory networks (MINR) in yeast for improved ethanol tolerance and production
journal, January 2019
- Liu, Rongming; Liang, Liya; Choudhury, Alaksh
- Metabolic Engineering, Vol. 51
Directed combinatorial mutagenesis of Escherichia coli for complex phenotype engineering
journal, May 2018
- Liu, Rongming; Liang, Liya; Garst, Andrew D.
- Metabolic Engineering, Vol. 47