OptSSeq: High-Throughput Sequencing Readout of Growth Enrichment Defines Optimal Gene Expression Elements for Homoethanologenesis

Ghosh, Indro Neil; Landick, Robert

doi:10.1021/acssynbio.6b00121

Title: OptSSeq: High-Throughput Sequencing Readout of Growth Enrichment Defines Optimal Gene Expression Elements for Homoethanologenesis

Journal Article · 01 August 2016 · ACS Synthetic Biology

DOI: https://doi.org/10.1021/acssynbio.6b00121 · OSTI ID:1294691

Ghosh, Indro Neil ^[1]; Landick, Robert ^[1]

DOE Great Lakes Bioenergy Research Center, University of Wisconsin—Madison, Madison, Wisconsin 53726, United States

Not Available

View Journal Article

Cite

Export

Save

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: FC02-07ER64494

OSTI ID:: 1294691

Journal Information:: ACS Synthetic Biology, Journal Name: ACS Synthetic Biology Journal Issue: 12 Vol. 5; ISSN 2161-5063

Publisher:: American Chemical SocietyCopyright Statement

Country of Publication:: United States

Language:: English

References (107)

E. coli Genome Manipulation by P1 Transduction Thomason, Lynn C.; Costantino, Nina; Court, Donald L. Current Protocols in Molecular Biology, Vol. 79, Issue 1 https://doi.org/10.1002/0471142727.mb0117s79	journal	May 2014
Optknock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization Burgard, Anthony P.; Pharkya, Priti; Maranas, Costas D. Biotechnology and Bioengineering, Vol. 84, Issue 6 https://doi.org/10.1002/bit.10803	journal	October 2003
Towards a metabolic engineering strain “commons”: An Escherichia coli platform strain for ethanol production Woodruff, Lauren B. A.; May, Brian L.; Warner, Joseph R. Biotechnology and Bioengineering, Vol. 110, Issue 5 https://doi.org/10.1002/bit.24840	journal	January 2013
Central metabolic responses to the overproduction of fatty acids in Escherichia coli based on ¹³ C-metabolic flux analysis He, Lian; Xiao, Yi; Gebreselassie, Nikodimos Biotechnology and Bioengineering, Vol. 111, Issue 3 https://doi.org/10.1002/bit.25124	journal	October 2013
Transport and intracellular accumulation of acetaldehyde insaccharomyces cerevisiae Stanley, G. A.; Pamment, N. B. Biotechnology and Bioengineering, Vol. 42, Issue 1 https://doi.org/10.1002/bit.260420104	journal	June 1993
Bioprocess optimization using design-of-experiments methodology Mandenius, Carl-Fredrik; Brundin, Anders Biotechnology Progress, Vol. 24, Issue 6 https://doi.org/10.1002/btpr.67	journal	November 2008
Promoters of Escherichia coli: a hierarchy of in vivo strength indicates alternate structures. Deuschle, U.; Kammerer, W.; Gentz, R. The EMBO Journal, Vol. 5, Issue 11 https://doi.org/10.1002/j.1460-2075.1986.tb04596.x	journal	November 1986
Repression oflacPromoter as a Function of Distance, Phase and Quality of an AuxiliarylacOperator Müller, Johannes; Oehler, Stefan; Müller-Hill, Benno Journal of Molecular Biology, Vol. 257, Issue 1 https://doi.org/10.1006/jmbi.1996.0143	journal	March 1996
Redistribution of Metabolic Fluxes inEscherichia coliwith Fermentative Lactate Dehydrogenase Overexpression and Deletion Yang, Yea-Tyng; San, Ka-Yiu; Bennett, George N. Metabolic Engineering, Vol. 1, Issue 2 https://doi.org/10.1006/mben.1998.0111	journal	April 1999
Roles of alcohol dehydrogenases of Zymomonas mobilis (ZADH): characterization of a ZADH-2-negative mutant O'Mullan, P. J.; Buchholz, S. E.; Chase, T. Applied Microbiology and Biotechnology, Vol. 43, Issue 4 https://doi.org/10.1007/BF00164772	journal	September 1995
Pentose metabolism in Zymomonas mobilis wild-type and recombinant strains Feldmann, SigrunD.; Sahm, Hermann; Sprenger, GeorgA. Applied Microbiology and Biotechnology, Vol. 38, Issue 3 https://doi.org/10.1007/BF00170086	journal	December 1992
Purification of two alcohol dehydrogenases from Zymomonas mobilis and their properties Kinoshita, Shinichi; Kakizono, Toshihide; Kadota, Keiichi Applied Microbiology and Biotechnology, Vol. 22, Issue 4 https://doi.org/10.1007/BF00252025	journal	August 1985
Evidence against transcription termination within the E. coli lac operon Lim, Louis W.; Kennell, David Molecular and General Genetics MGG, Vol. 133, Issue 4 https://doi.org/10.1007/BF00332713	journal	December 1974
Purification and kinetic characteristics of pyruvate decarboxylase and ethanol dehydrogenase from Zymomonas mobilis in relation to ethanol production Hoppner, Toni C.; Doelle, Horst W. European Journal of Applied Microbiology and Biotechnology, Vol. 17, Issue 3 https://doi.org/10.1007/BF00505880	journal	January 1983
Elucidating and reprogramming Escherichia coli metabolisms for obligate anaerobic n-butanol and isobutanol production Trinh, Cong T. Applied Microbiology and Biotechnology, Vol. 95, Issue 4 https://doi.org/10.1007/s00253-012-4197-7	journal	June 2012
Growth rate of a non-fermentative Escherichia coli strain is influenced by NAD+ regeneration Vázquez-Limón, Consuelo; Vega-Badillo, Joel; Martínez, Alfredo Biotechnology Letters, Vol. 29, Issue 12 https://doi.org/10.1007/s10529-007-9481-8	journal	October 2007
Re-engineering Escherichia coli for ethanol production Yomano, L. P.; York, S. W.; Zhou, S. Biotechnology Letters, Vol. 30, Issue 12 https://doi.org/10.1007/s10529-008-9821-3	journal	September 2008
Improved cellobiose utilization in E. coli by including both hydrolysis and phosphorolysis mechanisms Rutter, Charles; Chen, Rachel Biotechnology Letters, Vol. 36, Issue 2 https://doi.org/10.1007/s10529-013-1355-7	journal	October 2013
Gene disruption in Escherichia coli: TcR and KmR cassettes with the option of Flp-catalyzed excision of the antibiotic-resistance determinant Cherepanov, Peter P.; Wackernagel, Wilfried Gene, Vol. 158, Issue 1 https://doi.org/10.1016/0378-1119(95)00193-A	journal	January 1995
Four new derivatives of the broad-host-range cloning vector pBBR1MCS, carrying different antibiotic-resistance cassettes Kovach, Michael E.; Elzer, Philip H.; Steven Hill, D. Gene, Vol. 166, Issue 1 https://doi.org/10.1016/0378-1119(95)00584-1	journal	December 1995
Metabolic load and heterologous gene expression Glick, Bernard R. Biotechnology Advances, Vol. 13, Issue 2 https://doi.org/10.1016/0734-9750(95)00004-A	journal	January 1995
The Ribosome Binding Site Calculator Salis, Howard M. Methods in Enzymology https://doi.org/10.1016/B978-0-12-385120-8.00002-4	book	May 2011
Spacing of the -10 and -35 regions in the tac promoter. Effect on its in vivo activity. Brosius, J.; Erfle, M.; Storella, J. Journal of Biological Chemistry, Vol. 260, Issue 6 https://doi.org/10.1016/S0021-9258(19)83655-4	journal	March 1985
Physiology of Zymomonas mobilis: Some Unanswered Questions Kalnenieks, Uldis Advances in Microbial Physiology Volume 51 https://doi.org/10.1016/S0065-2911(06)51002-1	book	September 2006
Differential contributions of two elements of rho-independent terminator to transcription termination and mRNA stabilization Abe, H.; Aiba, H. Biochimie, Vol. 78, Issue 11-12 https://doi.org/10.1016/S0300-9084(97)86727-2	journal	January 1996
Quantitative characterization of gene regulation by Rho dependent transcription termination Hussein, Razika; Lee, Tiffany Y.; Lim, Han N. Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, Vol. 1849, Issue 8 https://doi.org/10.1016/j.bbagrm.2015.05.003	journal	August 2015
Covalently linking the Escherichia coli global anaerobic regulator FNR in tandem allows it to function as an oxygen stable dimer Shan, Yue; Pan, Qing; Liu, Junyan Biochemical and Biophysical Research Communications, Vol. 419, Issue 1 https://doi.org/10.1016/j.bbrc.2012.01.121	journal	March 2012
Isocost Lines Describe the Cellular Economy of Genetic Circuits Gyorgy, Andras; Jiménez, José I.; Yazbek, John Biophysical Journal, Vol. 109, Issue 3 https://doi.org/10.1016/j.bpj.2015.06.034	journal	August 2015
rRNA Promoter Regulation by Nonoptimal Binding of σ Region 1.2: An Additional Recognition Element for RNA Polymerase Haugen, Shanil P.; Berkmen, Melanie B.; Ross, Wilma Cell, Vol. 125, Issue 6 https://doi.org/10.1016/j.cell.2006.04.034	journal	June 2006
Engineering Static and Dynamic Control of Synthetic Pathways Holtz, William J.; Keasling, Jay D. Cell, Vol. 140, Issue 1 https://doi.org/10.1016/j.cell.2009.12.029	journal	January 2010
Quantifying Absolute Protein Synthesis Rates Reveals Principles Underlying Allocation of Cellular Resources Li, Gene-Wei; Burkhardt, David; Gross, Carol Cell, Vol. 157, Issue 3 https://doi.org/10.1016/j.cell.2014.02.033	journal	April 2014
Respiratory behaviour of a Zymomonas mobilis adhB::kan ^r mutant supports the hypothesis of two alcohol dehydrogenase isoenzymes catalysing opposite reactions Kalnenieks, U.; Galinina, N.; Toma, M. M. FEBS Letters, Vol. 580, Issue 21 https://doi.org/10.1016/j.febslet.2006.08.034	journal	August 2006
Construction and optimization of synthetic pathways in metabolic engineering Na, Dokyun; Kim, Tae Yong; Lee, Sang Yup Current Opinion in Microbiology, Vol. 13, Issue 3 https://doi.org/10.1016/j.mib.2010.02.004	journal	June 2010
Balancing a heterologous mevalonate pathway for improved isoprenoid production in Escherichia coli Pitera, Douglas J.; Paddon, Chris J.; Newman, Jack D. Metabolic Engineering, Vol. 9, Issue 2 https://doi.org/10.1016/j.ymben.2006.11.002	journal	March 2007
Combinatorial pathway analysis for improved L-tyrosine production in Escherichia coli: Identification of enzymatic bottlenecks by systematic gene overexpression Lütke-Eversloh, Tina; Stephanopoulos, Gregory Metabolic Engineering, Vol. 10, Issue 2, p. 69-77 https://doi.org/10.1016/j.ymben.2007.12.001	journal	March 2008
Combinatorial optimization of cyanobacterial 2,3-butanediol production Oliver, John W. K.; Machado, Iara M. P.; Yoneda, Hisanari Metabolic Engineering, Vol. 22 https://doi.org/10.1016/j.ymben.2014.01.001	journal	March 2014
Rational design of a synthetic Entner–Doudoroff pathway for improved and controllable NADPH regeneration Ng, Chiam Yu; Farasat, Iman; Maranas, Costas D. Metabolic Engineering, Vol. 29 https://doi.org/10.1016/j.ymben.2015.03.001	journal	May 2015
A Minimal Model of Ribosome Allocation Dynamics Captures Trade-offs in Expression between Endogenous and Synthetic Genes Gorochowski, Thomas E.; Avcilar-Kucukgoze, Irem; Bovenberg, Roel A. L. ACS Synthetic Biology, Vol. 5, Issue 7 https://doi.org/10.1021/acssynbio.6b00040	journal	April 2016
Biosynthetic Burden and Plasmid Burden Limit Expression of Chromosomally Integrated Heterologous Genes (pdc, adhB) in Escherichia coli Martinez, A.; York, S. W.; Yomano, L. P. Biotechnology Progress, Vol. 15, Issue 5 https://doi.org/10.1021/bp990103p	journal	October 1999
Transcription Factor-Based Screens and Synthetic Selections for Microbial Small-Molecule Biosynthesis Dietrich, Jeffrey A.; Shis, David L.; Alikhani, Azadeh ACS Synthetic Biology, Vol. 2, Issue 1 https://doi.org/10.1021/sb300091d	journal	September 2012
Quantifying Translational Coupling in E. coli Synthetic Operons Using RBS Modulation and Fluorescent Reporters Levin-Karp, Ayelet; Barenholz, Uri; Bareia, Tasneem ACS Synthetic Biology, Vol. 2, Issue 6 https://doi.org/10.1021/sb400002n	journal	March 2013
Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants the Keio collection Baba, Tomoya; Ara, Takeshi; Hasegawa, Miki Molecular Systems Biology, Vol. 2, Article No. 2006.0008 https://doi.org/10.1038/msb4100050	journal	February 2006
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
Design of a dynamic sensor-regulator system for production of chemicals and fuels derived from fatty acids Zhang, Fuzhong; Carothers, James M.; Keasling, Jay D. Nature Biotechnology, Vol. 30, Issue 4 https://doi.org/10.1038/nbt.2149	journal	March 2012
Functional optimization of gene clusters by combinatorial design and assembly Smanski, Michael J.; Bhatia, Swapnil; Zhao, Dehua Nature Biotechnology, Vol. 32, Issue 12, p. 1241-1249 https://doi.org/10.1038/nbt.3063	journal	November 2014
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
Engineering and characterization of a superfolder green fluorescent protein Pédelacq, Jean-Denis; Cabantous, Stéphanie; Tran, Timothy Nature Biotechnology, Vol. 24, Issue 1, p. 79-88 https://doi.org/10.1038/nbt1172	journal	December 2005
Combinatorial engineering of intergenic regions in operons tunes expression of multiple genes Pfleger, Brian F.; Pitera, Douglas J.; Smolke, Christina D. Nature Biotechnology, Vol. 24, Issue 8 https://doi.org/10.1038/nbt1226	journal	July 2006
Enzymatic assembly of DNA molecules up to several hundred kilobases Gibson, Daniel G.; Young, Lei; Chuang, Ray-Yuan Nature Methods, Vol. 6, Issue 5, p. 343-345 https://doi.org/10.1038/nmeth.1318	journal	April 2009
Characterization of 582 natural and synthetic terminators and quantification of their design constraints Chen, Ying-Ja; Liu, Peng; Nielsen, Alec A. K. Nature Methods, Vol. 10, Issue 7 https://doi.org/10.1038/nmeth.2515	journal	June 2013
Quantifying cellular capacity identifies gene expression designs with reduced burden Ceroni, Francesca; Algar, Rhys; Stan, Guy-Bart Nature Methods, Vol. 12, Issue 5 https://doi.org/10.1038/nmeth.3339	journal	April 2015
Insights into transcriptional regulation and competition from an equilibrium model of RNA polymerase binding to DNA Grigorova, I. L.; Phleger, N. J.; Mutalik, V. K. Proceedings of the National Academy of Sciences, Vol. 103, Issue 14 https://doi.org/10.1073/pnas.0600828103	journal	March 2006
A monomeric red fluorescent protein Campbell, R. E.; Tour, O.; Palmer, A. E. Proceedings of the National Academy of Sciences, Vol. 99, Issue 12, p. 7877-7882 https://doi.org/10.1073/pnas.082243699	journal	June 2002
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
Glycolytic strategy as a tradeoff between energy yield and protein cost Flamholz, A.; Noor, E.; Bar-Even, A. Proceedings of the National Academy of Sciences, Vol. 110, Issue 24 https://doi.org/10.1073/pnas.1215283110	journal	April 2013
Evolution-guided optimization of biosynthetic pathways Raman, Srivatsan; Rogers, Jameson K.; Taylor, Noah D. Proceedings of the National Academy of Sciences, Vol. 111, Issue 50, p. 17803-17808 https://doi.org/10.1073/pnas.1409523111	journal	December 2014
Mechanistic links between cellular trade-offs, gene expression, and growth Weiße, Andrea Y.; Oyarzún, Diego A.; Danos, Vincent Proceedings of the National Academy of Sciences, Vol. 112, Issue 9 https://doi.org/10.1073/pnas.1416533112	journal	February 2015
Dissecting enzyme function with microfluidic-based deep mutational scanning Romero, Philip A.; Tran, Tuan M.; Abate, Adam R. Proceedings of the National Academy of Sciences, Vol. 112, Issue 23 https://doi.org/10.1073/pnas.1422285112	journal	May 2015
Multiplexed barcoded CRISPR-Cas9 screening enabled by CombiGEM Wong, Alan S. L.; Choi, Gigi C. G.; Cui, Cheryl H. Proceedings of the National Academy of Sciences, Vol. 113, Issue 9 https://doi.org/10.1073/pnas.1517883113	journal	February 2016
Characterization of individual polynucleotide molecules using a membrane channel Kasianowicz, J. J.; Brandin, E.; Branton, D. Proceedings of the National Academy of Sciences, Vol. 93, Issue 24 https://doi.org/10.1073/pnas.93.24.13770	journal	November 1996
Evolution of the adhE Gene Product of Escherichia coli from a Functional Reductase to a Dehydrogenase: GENETIC AND BIOCHEMICAL STUDIES OF THE MUTANT PROTEINS Membrillo-Hernández, Jorge; Echave, Pedro; Cabiscol, Elisa Journal of Biological Chemistry, Vol. 275, Issue 43 https://doi.org/10.1074/jbc.M005464200	journal	August 2000
Compilation and analysis of Escherichia coli promoter DNA sequences Hawley, Diane K.; McClure, William R. Nucleic Acids Research, Vol. 11, Issue 8, p. 2237-2255 https://doi.org/10.1093/nar/11.8.2237	journal	January 1983
Analysis of E.Coli Pormoter sequences Harley, Calvin B.; Reynolds, Robert P. Nucleic Acids Research, Vol. 15, Issue 5 https://doi.org/10.1093/nar/15.5.2343	journal	January 1987
Defining the consensus sequences of E.coli promoter elements by random selectio Oliphant, Arnold R.; Struhl, Kevin Nucleic Acids Research, Vol. 16, Issue 15 https://doi.org/10.1093/nar/16.15.7673	journal	January 1988
DNAWorks: an automated method for designing oligonucleotides for PCR-based gene synthesis Hoover, D. M. Nucleic Acids Research, Vol. 30, Issue 10 https://doi.org/10.1093/nar/30.10.e43	journal	May 2002
Studies on the selectivity of DNA precipitation by spermine Hoopes, Barbara C.; McClure, William R. Nucleic Acids Research, Vol. 9, Issue 20 https://doi.org/10.1093/nar/9.20.5493	journal	January 1981
Design, construction and characterization of a set of insulated bacterial promoters Davis, J. H.; Rubin, A. J.; Sauer, R. T. Nucleic Acids Research, Vol. 39, Issue 3, p. 1131-1141 https://doi.org/10.1093/nar/gkq810	journal	September 2010
Enhanced multiplex genome engineering through co-operative oligonucleotide co-selection Carr, Peter A.; Wang, Harris H.; Sterling, Bram Nucleic Acids Research, Vol. 40, Issue 17 https://doi.org/10.1093/nar/gks455	journal	May 2012
Spanning high-dimensional expression space using ribosome-binding site combinatorics Zelcbuch, Lior; Antonovsky, Niv; Bar-Even, Arren Nucleic Acids Research, Vol. 41, Issue 9 https://doi.org/10.1093/nar/gkt151	journal	March 2013
The activity of the Escherichia coli transcription factor FNR is regulated by a change in oligomeric state. Lazazzera, B. A.; Bates, D. M.; Kiley, P. J. Genes & Development, Vol. 7, Issue 10 https://doi.org/10.1101/gad.7.10.1993	journal	October 1993
Selective repression by Fis and H-NS at the Escherichia coli dps promoter Grainger, David C.; Goldberg, Martin D.; Lee, David J. Molecular Microbiology, Vol. 68, Issue 6 https://doi.org/10.1111/j.1365-2958.2008.06253.x	journal	June 2008
The two alcohol dehydrogenases of Zymomonas mobilis. Purification by differential dye ligand chromatography, molecular characterisation and physiological roles Neale, Alan D.; Scopes, Robert K.; Kelly, Janice M. European Journal of Biochemistry, Vol. 154, Issue 1 https://doi.org/10.1111/j.1432-1033.1986.tb09366.x	journal	January 1986
Real-Time DNA Sequencing from Single Polymerase Molecules Eid, John; Fehr, Adrian; Gray, Jeremy Science, Vol. 323, Issue 5910, p. 133-138 https://doi.org/10.1126/science.1162986	journal	January 2009
Isoprenoid Pathway Optimization for Taxol Precursor Overproduction in Escherichia coli Ajikumar, P. K.; Xiao, W.-H.; Tyo, K. E. J. Science, Vol. 330, Issue 6000, p. 70-74 https://doi.org/10.1126/science.1191652	journal	September 2010
Interdependence of Cell Growth and Gene Expression: Origins and Consequences Scott, M.; Gunderson, C. W.; Mateescu, E. M. Science, Vol. 330, Issue 6007 https://doi.org/10.1126/science.1192588	journal	November 2010
The Complete Genome Sequence of Escherichia coli K-12 Blattner, F. R. Science, Vol. 277, Issue 5331 https://doi.org/10.1126/science.277.5331.1453	journal	September 1997
Determination of intrinsic transcription termination efficiency by RNA polymerase elongation rate McDowell, J.; Roberts, J.; Jin, D. Science, Vol. 266, Issue 5186 https://doi.org/10.1126/science.7526463	journal	November 1994
Requirement of the Type II Secretion System for Utilization of Cellulosic Substrates by Cellvibrio japonicus Gardner, J. G.; Keating, D. H. Applied and Environmental Microbiology, Vol. 76, Issue 15 https://doi.org/10.1128/AEM.00454-10	journal	June 2010
Flavin Mononucleotide-Based Fluorescent Reporter Proteins Outperform Green Fluorescent Protein-Like Proteins as Quantitative In Vivo Real-Time Reporters Drepper, Thomas; Huber, Robert; Heck, Achim Applied and Environmental Microbiology, Vol. 76, Issue 17 https://doi.org/10.1128/AEM.00701-10	journal	September 2010
Driving Forces Enable High-Titer Anaerobic 1-Butanol Synthesis in Escherichia coli Shen, Claire R.; Lan, Ethan I.; Dekishima, Yasumasa Applied and Environmental Microbiology, Vol. 77, Issue 9, p. 2905-2915 https://doi.org/10.1128/AEM.03034-10	journal	March 2011
Coproduction of Acetaldehyde and Hydrogen during Glucose Fermentation by Escherichia coli Zhu, Huilin; Gonzalez, Ramon; Bobik, Thomas A. Applied and Environmental Microbiology, Vol. 77, Issue 18 https://doi.org/10.1128/AEM.05358-11	journal	July 2011
Modular Engineering of l-Tyrosine Production in Escherichia coli Juminaga, Darmawi; Baidoo, Edward E. K.; Redding-Johanson, Alyssa M. Applied and Environmental Microbiology, Vol. 78, Issue 1, p. 89-98 https://doi.org/10.1128/AEM.06017-11	journal	October 2011
Complex Physiology and Compound Stress Responses during Fermentation of Alkali-Pretreated Corn Stover Hydrolysate by an Escherichia coli Ethanologen Schwalbach, Michael S.; Keating, David H.; Tremaine, Mary Applied and Environmental Microbiology, Vol. 78, Issue 9, p. 3442-3457 https://doi.org/10.1128/AEM.07329-11	journal	March 2012
Newly Identified Genetic Variations in Common Escherichia coli MG1655 Stock Cultures Freddolino, Peter L.; Amini, Sasan; Tavazoie, Saeed Journal of Bacteriology, Vol. 194, Issue 2 https://doi.org/10.1128/JB.06087-11	journal	January 2012
Transposon Tn21, Flagship of the Floating Genome Liebert, Cynthia A.; Hall, Ruth M.; Summers, Anne O. Microbiology and Molecular Biology Reviews, Vol. 63, Issue 3 https://doi.org/10.1128/MMBR.63.3.507-522.1999	journal	January 1999
Genetic engineering of ethanol production in Escherichia coli. Ingram, L. O.; Conway, T.; Clark, D. P. Applied and Environmental Microbiology, Vol. 53, Issue 10 https://doi.org/10.1128/aem.53.10.2420-2425.1987	journal	January 1987
Production of Acetaldehyde by Zymomonas mobilis Wecker, Matt S. A.; Zall, Robert R. Applied and Environmental Microbiology, Vol. 53, Issue 12 https://doi.org/10.1128/aem.53.12.2815-2820.1987	journal	January 1987
Genetic improvement of Escherichia coli for ethanol production: chromosomal integration of Zymomonas mobilis genes encoding pyruvate decarboxylase and alcohol dehydrogenase II. Ohta, K.; Beall, D. S.; Mejia, J. P. Applied and Environmental Microbiology, Vol. 57, Issue 4 https://doi.org/10.1128/aem.57.4.893-900.1991	journal	January 1991
Culture Medium for Enterobacteria Neidhardt, Frederick C.; Bloch, Philip L.; Smith, David F. Journal of Bacteriology, Vol. 119, Issue 3 https://doi.org/10.1128/jb.119.3.736-747.1974	journal	January 1974
DNA sequence fine-structure analysis of ilvG (IlvG+) mutations of Escherichia coli K-12. Lawther, R. P.; Calhoun, D. H.; Gray, J. Journal of Bacteriology, Vol. 149, Issue 1 https://doi.org/10.1128/jb.149.1.294-298.1982	journal	January 1982
Pyruvate decarboxylase of Zymomonas mobilis: isolation, properties, and genetic expression in Escherichia coli. Neale, A. D.; Scopes, R. K.; Wettenhall, R. E. Journal of Bacteriology, Vol. 169, Issue 3 https://doi.org/10.1128/jb.169.3.1024-1028.1987	journal	January 1987
The Escherichia coli K-12 "wild types" W3110 and MG1655 have an rph frameshift mutation that leads to pyrimidine starvation due to low pyrE expression levels. Jensen, K. F. Journal of Bacteriology, Vol. 175, Issue 11 https://doi.org/10.1128/jb.175.11.3401-3407.1993	journal	June 1993
Anaerobic regulation of the adhE gene, encoding the fermentative alcohol dehydrogenase of Escherichia coli. Leonardo, M. R.; Cunningham, P. R.; Clark, D. P. Journal of Bacteriology, Vol. 175, Issue 3 https://doi.org/10.1128/jb.175.3.870-878.1993	journal	January 1993
Predicting the Operon Structure of Bacillus Subtilis Using Operon Length, Intergene Distance, and gene Expression Information De Hoon, M. J. L.; Imoto, S.; Kobayashi, K. Proceedings of the Pacific Symposium, Biocomputing 2004 https://doi.org/10.1142/9789812704856_0027	conference	November 2011
Evolution combined with genomic study elucidates genetic bases of isobutanol tolerance in Escherichia coli Minty, Jeremy J.; Lesnefsky, Ann A.; Lin, Fengming Microbial Cell Factories, Vol. 10, Issue 1 https://doi.org/10.1186/1475-2859-10-18	journal	January 2011
In silico profiling of Escherichia coli and Saccharomyces cerevisiae as terpenoid factories Gruchattka, Evamaria; Hädicke, Oliver; Klamt, Steffen Microbial Cell Factories, Vol. 12, Issue 1 https://doi.org/10.1186/1475-2859-12-84	journal	January 2013
OptORF: Optimal metabolic and regulatory perturbations for metabolic engineering of microbial strains Kim, Joonhoon; Reed, Jennifer L. BMC Systems Biology, Vol. 4, Issue 1, Article No. 53 https://doi.org/10.1186/1752-0509-4-53	journal	January 2010
Inhibition of growth of Zymomonas mobilis by model compounds found in lignocellulosic hydrolysates Franden, Mary Ann; Pilath, Heidi M.; Mohagheghi, Ali Biotechnology for Biofuels, Vol. 6, Issue 1 https://doi.org/10.1186/1754-6834-6-99	journal	January 2013
An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR) Reed, Jennifer L.; Vo, Thuy D.; Schilling, Christophe H. Genome Biology, Vol. 4, Issue 9, p. R54 https://doi.org/10.1186/gb-2003-4-9-r54	journal	August 2003
Tuning Promoter Strength through RNA Polymerase Binding Site Design in Escherichia coli Brewster, Robert C.; Jones, Daniel L.; Phillips, Rob PLoS Computational Biology, Vol. 8, Issue 12 https://doi.org/10.1371/journal.pcbi.1002811	journal	December 2012
Multiparameter RNA and Codon Optimization: A Standardized Tool to Assess and Enhance Autologous Mammalian Gene Expression Fath, Stephan; Bauer, Asli Petra; Liss, Michael PLoS ONE, Vol. 6, Issue 3 https://doi.org/10.1371/journal.pone.0017596	journal	March 2011
Adaptive Evolution of Synthetic Cooperating Communities Improves Growth Performance Zhang, Xiaolin; Reed, Jennifer L. PLoS ONE, Vol. 9, Issue 10 https://doi.org/10.1371/journal.pone.0108297	journal	October 2014
Programmed Evolution for Optimization of Orthogonal Metabolic Output in Bacteria Eckdahl, Todd T.; Campbell, A. Malcolm; Heyer, Laurie J. PLOS ONE, Vol. 10, Issue 2 https://doi.org/10.1371/journal.pone.0118322	journal	February 2015
Efficient search, mapping, and optimization of multi-protein genetic systems in diverse bacteria Farasat, I.; Kushwaha, M.; Collens, J. Molecular Systems Biology, Vol. 10, Issue 6, p. 731-731 https://doi.org/10.15252/msb.20134955	journal	June 2014
Enhancing DNA electrotransformation efficiency in Escherichia coli DH10B electrocompetent cells Wu, Ning; Matand, Kanyand; Kebede, Bizuayehu Electronic Journal of Biotechnology, Vol. 13, Issue 5 https://doi.org/10.2225/vol13-issue5-fulltext-11	journal	September 2010
Carbohydrate Metabolism in Zymomonas Viikari, Liisa; Berry, David R. Critical Reviews in Biotechnology, Vol. 7, Issue 3 https://doi.org/10.3109/07388558809146603	journal	January 1988
Rapid Protocol for Preparation of Electrocompetent Escherichia coli and Vibrio cholerae Gonzales, Miguel F.; Brooks, Teresa; Pukatzki, Stefan U. Journal of Visualized Experiments, Issue 80 https://doi.org/10.3791/50684	journal	January 2013

Similar Records

High throughput methods for gene cloning and expression.

Journal Article · 2002 · Protein Expr. Purif. · OSTI ID:949430

Dieckman, L; Gu, M; Stols, L; +2 more

Express primer tool for high-throughput gene cloning and expression.

Journal Article · 2002 · Biotech. · OSTI ID:949669

Yoon, J R; Laible, P D; Gu, M; +2 more

An expanded maize gene expression atlas based on RNA sequencing and its use to explore root development

Journal Article · 2015 · The Plant Genome · OSTI ID:1363961

Stelpflug, Scott C.; Sekhon, Rajandeep S.; Vaillancourt, Brieanne; +4 more

Title: OptSSeq: High-Throughput Sequencing Readout of Growth Enrichment Defines Optimal Gene Expression Elements for Homoethanologenesis

Citation Formats

References (107)

Similar Records

Related Subjects