Chapter 2: Trackable Multiplex Recombineering (TRMR) and Next-Generation Genome Design Technologies: Modifying Gene Expression in E. coli by Inserting Synthetic DNA Cassettes and Molecular Barcodes

Freed, Emily; Eckert, Carrie A; Pines, Gur; Gill, Ryan T.

doi:10.1002/9783527688104.ch2

Title: Chapter 2: Trackable Multiplex Recombineering (TRMR) and Next-Generation Genome Design Technologies: Modifying Gene Expression in E. coli by Inserting Synthetic DNA Cassettes and Molecular Barcodes

Book · Sat Mar 03 00:00:00 EST 2018

DOI:https://doi.org/10.1002/9783527688104.ch2· OSTI ID:1465638

Freed, Emily ^[1];

^[1]; Pines, Gur ^[2]; Gill, Ryan T. ^[2]

National Renewable Energy Laboratory (NREL), Golden, CO (United States)
University of Colorado

This chapter describes the trackable multiplex recombineering (TRMR) and tunable trackable multiplex recombineering (T2RMR) techniques, which not only make the multiplexing of recombineering possible in Escherichia coli but also provide the ability to track the engineered genetic changes accurately. TRMR and T2RMR have only been used for modifying the expression level of genes. Screening and selection of TRMR and T2RMR clones can be carried out using either liquid or solid media with any chemical compound that modifies growth or confers a phenotype that can be detected by a high-throughput assay. In order to engineer a genome using TRMR or T2RMR, a synthetic DNA (synDNA) cassette is created that encodes for a genetic feature and a molecular barcode that is used to track each feature. These synDNA cassettes are then introduced in parallel into cell populations via recombineering.

OSTI does not have a digital full text copy available. For more information, please see document availability, search WorldCat, or search Google Scholar.

Cite

Export

Save

Research Organization:: National Renewable Energy Laboratory (NREL), Golden, CO (United States)

Sponsoring Organization:: USDOE Office of Energy Efficiency and Renewable Energy (EERE)

DOE Contract Number:: AC36-08GO28308

OSTI ID:: 1465638

Report Number(s):: NREL/CH-2700-72219

Country of Publication:: United States

Language:: English

References (42)

Codon Compression Algorithms for Saturation Mutagenesis Pines, Gur; Pines, Assaf; Garst, Andrew D. ACS Synthetic Biology, Vol. 4, Issue 5, p. 604-614 https://doi.org/10.1021/sb500282v	journal	September 2014
Bacterial Recombineering: Genome Engineering via Phage-Based Homologous Recombination Pines, Gur; Freed, Emily F.; Winkler, James D. ACS Synthetic Biology, Vol. 4, Issue 11 https://doi.org/10.1021/acssynbio.5b00009	journal	April 2015
The beta protein of phage λ binds preferentially to an intermediate in DNA renaturation Karakousis, G.; Ye, N.; Li, Z. Journal of Molecular Biology, Vol. 276, Issue 4 https://doi.org/10.1006/jmbi.1997.1573	journal	March 1998
Single-stranded heteroduplex intermediates in λ Red homologous recombination Maresca, Marcello; Erler, Axel; Fu, Jun BMC Molecular Biology, Vol. 11, Article No. 54 https://doi.org/10.1186/1471-2199-11-54	journal	January 2010
A new logic for DNA engineering using recombination in Escherichia coli Zhang, Youming; Buchholz, Frank; Muyrers, Joep P. P. Nature Genetics, Vol. 20, Issue 2 https://doi.org/10.1038/2417	journal	October 1998
Parallel analysis of genetic selections using whole genome oligonucleotide arrays Cho, R. J.; Fromont-Racine, M.; Wodicka, L. Proceedings of the National Academy of Sciences, Vol. 95, Issue 7 https://doi.org/10.1073/pnas.95.7.3752	journal	March 1998
Multiplexed tracking of combinatorial genomic mutations in engineered cell populations Zeitoun, Ramsey I.; Garst, Andrew D.; Degen, George D. Nature Biotechnology, Vol. 33, Issue 6, p. 631-637 https://doi.org/10.1038/nbt.3177	journal	March 2015
A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity Jinek, M.; Chylinski, K.; Fonfara, I. Science, Vol. 337, Issue 6096, p. 816-821 https://doi.org/10.1126/science.1225829	journal	June 2012
The expanding scope of DNA sequencing Shendure, Jay; Aiden, Erez Lieberman Nature Biotechnology, Vol. 30, Issue 11 https://doi.org/10.1038/nbt.2421	journal	November 2012
Metabolic ensemble modeling for strain engineers Tan, Yikun; Liao, James C. Biotechnology Journal, Vol. 7, Issue 3 https://doi.org/10.1002/biot.201100186	journal	October 2011
Identification and analysis of recombineering functions from Gram-negative and Gram-positive bacteria and their phages Datta, S.; Costantino, N.; Zhou, X. Proceedings of the National Academy of Sciences, Vol. 105, Issue 5 https://doi.org/10.1073/pnas.0709089105	journal	January 2008
Strategy for directing combinatorial genome engineering in Escherichia coli Sandoval, N. R.; Kim, J. Y. H.; Glebes, T. Y. Proceedings of the National Academy of Sciences, Vol. 109, Issue 26, p. 10540-10545 https://doi.org/10.1073/pnas.1206299109	journal	June 2012
Refactoring the nitrogen fixation gene cluster from Klebsiella oxytoca Temme, K.; Zhao, D.; Voigt, C. A. Proceedings of the National Academy of Sciences, Vol. 109, Issue 18 https://doi.org/10.1073/pnas.1120788109	journal	April 2012
A set of recombineering plasmids for gram-negative bacteria Datta, Simanti; Costantino, Nina; Court, Donald L. Gene, Vol. 379, p. 109-115 https://doi.org/10.1016/j.gene.2006.04.018	journal	September 2006
Genome-Wide Tuning of Protein Expression Levels to Rapidly Engineer Microbial Traits Freed, Emily F.; Winkler, James D.; Weiss, Sophie J. ACS Synthetic Biology, Vol. 4, Issue 11 https://doi.org/10.1021/acssynbio.5b00133	journal	November 2015
Programming cells by multiplex genome engineering and accelerated evolution Wang, Harris H.; Isaacs, Farren J.; Carr, Peter A. Nature, Vol. 460, Issue 7257, p. 894-898 https://doi.org/10.1038/nature08187	journal	July 2009
Parallel Mapping of Antibiotic Resistance Alleles in Escherichia coli Weiss, Sophie J.; Mansell, Thomas J.; Mortazavi, Pooneh PLOS ONE, Vol. 11, Issue 1 https://doi.org/10.1371/journal.pone.0146916	journal	January 2016
Comparison of genome-wide selection strategies to identify furfural tolerance genes in Escherichia coli: Genome-Wide Mapping of Furfural Tolerance Alleles Glebes, Tirzah Y.; Sandoval, Nicholas R.; Gillis, Jacob H. Biotechnology and Bioengineering, Vol. 112, Issue 1, p. 129-140 https://doi.org/10.1002/bit.25325	journal	September 2014
Recombineering: a homologous recombination-based method of genetic engineering Sharan, Shyam K.; Thomason, Lynn C.; Kuznetsov, Sergey G. Nature Protocols, Vol. 4, Issue 2 https://doi.org/10.1038/nprot.2008.227	journal	January 2009
Coupling mutagenesis and parallel deep sequencing to probe essential residues in a genome or gene Robins, William P.; Faruque, Shah M.; Mekalanos, John J. Proceedings of the National Academy of Sciences, Vol. 110, Issue 9 https://doi.org/10.1073/pnas.1222538110	journal	February 2013
Lagging Strand-Biased Initiation of Red Recombination by Linear Double-Stranded DNAs Lim, Sung In; Min, Byung Eun; Jung, Gyoo Yeol Journal of Molecular Biology, Vol. 384, Issue 5 https://doi.org/10.1016/j.jmb.2008.10.047	journal	December 2008
Genetic interaction mapping with microfluidic-based single cell sequencing Haliburton, John R.; Shao, Wenjun; Deutschbauer, Adam PLOS ONE, Vol. 12, Issue 2 https://doi.org/10.1371/journal.pone.0171302	journal	February 2017
A unique and universal molecular barcode array Pierce, Sarah E.; Fung, Eula L.; Jaramillo, Daniel F. Nature Methods, Vol. 3, Issue 8 https://doi.org/10.1038/nmeth905	journal	July 2006
Network rigidity and metabolic engineering in metabolite overproduction Stephanopoulos, G.; Vallino, J. Science, Vol. 252, Issue 5013 https://doi.org/10.1126/science.1904627	journal	June 1991
An efficient recombination system for chromosome engineering in Escherichia coli Yu, D.; Ellis, H. M.; Lee, E-C. Proceedings of the National Academy of Sciences, Vol. 97, Issue 11, p. 5978-5983 https://doi.org/10.1073/pnas.100127597	journal	May 2000
Trackable Multiplex Recombineering for Gene-Trait Mapping in E. coli Mansell, Thomas J.; Warner, Joseph R.; Gill, Ryan T. Methods in Molecular Biology https://doi.org/10.1007/978-1-62703-299-5_12	book	January 2013
Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex Hamady, Micah; Walker, Jeffrey J.; Harris, J. Kirk Nature Methods, Vol. 5, Issue 3, p. 235-237 https://doi.org/10.1038/nmeth.1184	journal	February 2008
Minimalist Active-Site Redesign: Teaching Old Enzymes New Tricks Toscano, Miguel D.; Woycechowsky, Kenneth J.; Hilvert, Donald Angewandte Chemie International Edition, Vol. 46, Issue 18, p. 3212-3236 https://doi.org/10.1002/anie.200604205	journal	April 2007
Rapid profiling of a microbial genome using mixtures of barcoded oligonucleotides Warner, Joseph R.; Reeder, Philippa J.; Karimpour-Fard, Anis Nature Biotechnology, Vol. 28, Issue 8, p. 856-862 https://doi.org/10.1038/nbt.1653	journal	July 2010
CRISPR–Cas9-assisted recombineering in Lactobacillus reuteri Oh, Jee-Hwan; van Pijkeren, Jan-Peter Nucleic Acids Research, Vol. 42, Issue 17, p. e131-e131 https://doi.org/10.1093/nar/gku623	journal	July 2014
Quantitative Tracking of Combinatorially Engineered Populations with Multiplexed Binary Assemblies Zeitoun, Ramsey I.; Pines, Gur; Grau, Willliam C. ACS Synthetic Biology, Vol. 6, Issue 4 https://doi.org/10.1021/acssynbio.6b00376	journal	January 2017
Quantitative phenotypic analysis of yeast deletion mutants using a highly parallel molecular bar–coding strategy Shoemaker, Daniel D.; Lashkari, Deval A.; Morris, Don Nature Genetics, Vol. 14, Issue 4 https://doi.org/10.1038/ng1296-450	journal	December 1996
Lambda Red Recombineering in Escherichia coli Occurs Through a Fully Single-Stranded Intermediate Mosberg, J. A.; Lajoie, M. J.; Church, G. M. Genetics, Vol. 186, Issue 3 https://doi.org/10.1534/genetics.110.120782	journal	September 2010
A New Method for Rapidly Generating Gene-Targeting Vectors by Engineering BACs Through Homologous Recombination in Bacteria Cotta-de-Almeida, V. Genome Research, Vol. 13, Issue 9 https://doi.org/10.1101/gr.1356503	journal	September 2003
Metabolic modeling of microbial strains in silico Covert, Markus W.; Schilling, Christophe H.; Famili, Iman Trends in Biochemical Sciences, Vol. 26, Issue 3 https://doi.org/10.1016/S0968-0004(00)01754-0	journal	March 2001
Genome-wide mapping of mutations at single-nucleotide resolution for protein, metabolic and genome engineering Garst, Andrew D.; Bassalo, Marcelo C.; Pines, Gur Nature Biotechnology, Vol. 35, Issue 1, p. 48-55 https://doi.org/10.1038/nbt.3718	journal	December 2016
RNA-guided editing of bacterial genomes using CRISPR-Cas systems Jiang, Wenyan; Bikard, David; Cox, David Nature Biotechnology, Vol. 31, Issue 3, p. 233-239 https://doi.org/10.1038/nbt.2508	journal	January 2013
Lambda Gam protein inhibits the helicase and chi-stimulated recombination activities of Escherichia coli RecBCD enzyme. Murphy, K. C. Journal of Bacteriology, Vol. 173, Issue 18 https://doi.org/10.1128/jb.173.18.5808-5821.1991	journal	September 1991
High efficiency mutagenesis, repair, and engineering of chromosomal DNA using single-stranded oligonucleotides Ellis, H. M.; Yu, D.; DiTizio, T. Proceedings of the National Academy of Sciences, Vol. 98, Issue 12, p. 6742-6746 https://doi.org/10.1073/pnas.121164898	journal	May 2001
Precise and reliable gene expression via standard transcription and translation initiation elements Mutalik, Vivek K.; Guimaraes, Joao C.; Cambray, Guillaume Nature Methods, Vol. 10, Issue 4 https://doi.org/10.1038/nmeth.2404	journal	March 2013
Toward a science of metabolic engineering Bailey, J. E. Science, Vol. 252, Issue 5013, p. 1668-1675 https://doi.org/10.1126/science.2047876	journal	June 1991
Production of complex nucleic acid libraries using highly parallel in situ oligonucleotide synthesis Cleary, Michele A.; Kilian, Kristopher; Wang, Yanqun Nature Methods, Vol. 1, Issue 3 https://doi.org/10.1038/nmeth724	journal	November 2004

Similar Records

Dual-barcoded shotgun expression library sequencing for high-throughput characterization of functional traits in bacteria

Journal Article · Fri Jan 18 00:00:00 EST 2019 · Nature Communications · OSTI ID:1465638

Mutalik, Vivek K.; Novichkov, Pavel S.; Price, Morgan N.; +5 more

Multiplex growth rate phenotyping of synthetic mutants in selection to engineer glucose and xylose co‐utilization in Escherichia coli

Journal Article · Thu Dec 15 00:00:00 EST 2016 · Biotechnology and Bioengineering · OSTI ID:1465638

Groot, Joost; Cepress‐Mclean, Sidney C.; Robbins‐Pianka, Adam; +2 more

High-yield recombinant bacterial expression of ¹³C-, ¹⁵N-labeled, serine-16 phosphorylated, murine amelogenin using a modified third generation genetic code expansion protocol

Journal Article · Sat Dec 31 00:00:00 EST 2022 · Protein Science · OSTI ID:1465638

Buchko, Garry W.; Zhou, Mowei; Vesely, Cat H.; +4 more

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
E. coli
gene expression
genetic feature
molecular barcodes
next-generation genome design technologies
synthetic DNA cassette
tunable trackable multiplex recombineering

Title: Chapter 2: Trackable Multiplex Recombineering (TRMR) and Next-Generation Genome Design Technologies: Modifying Gene Expression in E. coli by Inserting Synthetic DNA Cassettes and Molecular Barcodes

Citation Formats

References (42)

Similar Records

Related Subjects