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Title: Generation of ionic liquid tolerant Pseudomonas putida KT2440 strains via adaptive laboratory evolution

Abstract

Although the use of ionic liquids (ILs) for the pretreatment of lignocellulosic biomass has been limited due to high costs, recent efforts to develop low-cost protic ILs show promise for achieving cost-effectiveness for biorefineries. However, an additional challenge remains in that ILs present in biomass hydrolysates are toxic to most microbial hosts, resulting in poor growth phenotypes. To address this issue, we applied an adaptive laboratory evolution (ALE) approach for tolerizing Pseudomonas putida KT2440, an industrially relevant bacterial host, to two low-cost ILs (triethanolammonium acetate [TEOH][OAc] and triethylammonium hydrogen sulfate [TEA][HS]). After continuous cultivations with gradually increased IL levels, we obtained evolved strains showing significant improvements in their growth performance under high concentrations of the ILs (maximum 4% [TEOH][OAc] and 8% [TEA][HS], in w/v) at which the wild-type strain cannot grow. Sequencing of evolved strains revealed multiple regions where mutations were associated with improved performance in minimal media conditions (relA, gacS, oprB/PP_1446, fleQ, tktA, and uvrY/PP_4100) and in IL-specific conditions (PP_5350, PP_4929/emrE, oprD, and PP_5324). We further validated the causality of the PP_5350 and emrE genes for improved IL tolerance via reverse engineering and transcriptomic analysis. Here, a common mutation in the PP_5350 gene, encoding a RpiR family transcriptional regulator,more » was shown to significantly upregulate the glyoxylate cycle for efficient acetate catabolism. In addition, it was suggested that the emrE gene encodes an efflux pump which can export [TEA][HS]. Finally, the cultivation of two of the best performing evolved strains with IL-treated biomass hydrolysates demonstrated their considerable potential to be used as platform strains. Taken as a whole, this work provides strains for utilization of IL-treated biomass and a mechanistic understanding that could be further leveraged to develop efficient microbial bioprocesses.« less

Authors:
ORCiD logo [1];  [2];  [3]; ORCiD logo [4]; ORCiD logo [2];  [3];  [3];  [5]; ORCiD logo [6]; ORCiD logo [2]; ORCiD logo [2];  [2]; ORCiD logo [7]
+ Show Author Affiliations
  1. Univ. of California, San Diego, La Jolla, CA (United States); Joint BioEnergy Institute (JBEI), Emeryville, CA (United States)
  2. Joint BioEnergy Institute (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  3. Univ. of California, San Diego, La Jolla, CA (United States)
  4. Joint BioEnergy Institute (JBEI), Emeryville, CA (United States); Sandia National Lab. (SNL-CA), Livermore, CA (United States)
  5. Univ. of California, San Diego, La Jolla, CA (United States); Joint BioEnergy Institute (JBEI), Emeryville, CA (United States); Technical Univ. of Denmark, Lyngby (Denmark); Univ. of California, San Diego, CA (United States)
  6. Joint BioEnergy Institute (JBEI), Emeryville, CA (United States); Agile BioFoundry, Emeryville, CA (United States); Sandia National Lab. (SNL-CA), Livermore, CA (United States)
  7. Univ. of California, San Diego, La Jolla, CA (United States); Joint BioEnergy Institute (JBEI), Emeryville, CA (United States); Technical Univ. of Denmark, Lyngby (Denmark)
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Joint BioEnergy Institute (JBEI), Emeryville, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1782190
Alternate Identifier(s):
OSTI ID: 1646932
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Green Chemistry
Additional Journal Information:
Journal Volume: 22; Journal Issue: 17; Journal ID: ISSN 1463-9262
Publisher:
Royal Society of Chemistry
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY

Citation Formats

Lim, Hyun Gyu, Fong, Bonnie, Alarcon, Geovanni, Magurudeniya, Harsha D., Eng, Thomas, Szubin, Richard, Olson, Connor A., Palsson, Bernhard O., Gladden, John M., Simmons, Blake A., Mukhopadhyay, Aindrila, Singer, Steven W., and Feist, Adam M. Generation of ionic liquid tolerant Pseudomonas putida KT2440 strains via adaptive laboratory evolution. United States: N. p., 2020. Web. doi:10.1039/d0gc01663b.
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Lim, Hyun Gyu, Fong, Bonnie, Alarcon, Geovanni, Magurudeniya, Harsha D., Eng, Thomas, Szubin, Richard, Olson, Connor A., Palsson, Bernhard O., Gladden, John M., Simmons, Blake A., Mukhopadhyay, Aindrila, Singer, Steven W., & Feist, Adam M. Generation of ionic liquid tolerant Pseudomonas putida KT2440 strains via adaptive laboratory evolution. United States. https://doi.org/10.1039/d0gc01663b
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Lim, Hyun Gyu, Fong, Bonnie, Alarcon, Geovanni, Magurudeniya, Harsha D., Eng, Thomas, Szubin, Richard, Olson, Connor A., Palsson, Bernhard O., Gladden, John M., Simmons, Blake A., Mukhopadhyay, Aindrila, Singer, Steven W., and Feist, Adam M. Tue . "Generation of ionic liquid tolerant Pseudomonas putida KT2440 strains via adaptive laboratory evolution". United States. https://doi.org/10.1039/d0gc01663b. https://www.osti.gov/servlets/purl/1782190.
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@article{osti_1782190,
title = {Generation of ionic liquid tolerant Pseudomonas putida KT2440 strains via adaptive laboratory evolution},
author = {Lim, Hyun Gyu and Fong, Bonnie and Alarcon, Geovanni and Magurudeniya, Harsha D. and Eng, Thomas and Szubin, Richard and Olson, Connor A. and Palsson, Bernhard O. and Gladden, John M. and Simmons, Blake A. and Mukhopadhyay, Aindrila and Singer, Steven W. and Feist, Adam M.},
abstractNote = {Although the use of ionic liquids (ILs) for the pretreatment of lignocellulosic biomass has been limited due to high costs, recent efforts to develop low-cost protic ILs show promise for achieving cost-effectiveness for biorefineries. However, an additional challenge remains in that ILs present in biomass hydrolysates are toxic to most microbial hosts, resulting in poor growth phenotypes. To address this issue, we applied an adaptive laboratory evolution (ALE) approach for tolerizing Pseudomonas putida KT2440, an industrially relevant bacterial host, to two low-cost ILs (triethanolammonium acetate [TEOH][OAc] and triethylammonium hydrogen sulfate [TEA][HS]). After continuous cultivations with gradually increased IL levels, we obtained evolved strains showing significant improvements in their growth performance under high concentrations of the ILs (maximum 4% [TEOH][OAc] and 8% [TEA][HS], in w/v) at which the wild-type strain cannot grow. Sequencing of evolved strains revealed multiple regions where mutations were associated with improved performance in minimal media conditions (relA, gacS, oprB/PP_1446, fleQ, tktA, and uvrY/PP_4100) and in IL-specific conditions (PP_5350, PP_4929/emrE, oprD, and PP_5324). We further validated the causality of the PP_5350 and emrE genes for improved IL tolerance via reverse engineering and transcriptomic analysis. Here, a common mutation in the PP_5350 gene, encoding a RpiR family transcriptional regulator, was shown to significantly upregulate the glyoxylate cycle for efficient acetate catabolism. In addition, it was suggested that the emrE gene encodes an efflux pump which can export [TEA][HS]. Finally, the cultivation of two of the best performing evolved strains with IL-treated biomass hydrolysates demonstrated their considerable potential to be used as platform strains. Taken as a whole, this work provides strains for utilization of IL-treated biomass and a mechanistic understanding that could be further leveraged to develop efficient microbial bioprocesses.},
doi = {10.1039/d0gc01663b},
journal = {Green Chemistry},
number = 17,
volume = 22,
place = {United States},
year = {Tue Aug 04 00:00:00 EDT 2020},
month = {Tue Aug 04 00:00:00 EDT 2020}
}
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https://doi.org/10.1039/d0gc01663b
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Works referenced in this record:

Rediscovering Acetate Metabolism: Its Potential Sources and Utilization for Biobased Transformation into Value-Added Chemicals
journal, April 2018

  • Lim, Hyun Gyu; Lee, Ji Hoon; Noh, Myung Hyun
  • Journal of Agricultural and Food Chemistry, Vol. 66, Issue 16
  • DOI: 10.1021/acs.jafc.8b00458

Catalytic Transformation of Lignocellulose into Chemicals and Fuel Products in Ionic Liquids
journal, November 2016

Enzyme promiscuity shapes adaptation to novel growth substrates
journal, April 2019

  • Guzmán, Gabriela I.; Sandberg, Troy E.; LaCroix, Ryan A.
  • Molecular Systems Biology, Vol. 15, Issue 4
  • DOI: 10.15252/msb.20188462

Front Cover: Chemoenzymatic Halocyclization of γ,δ‐Unsaturated Carboxylic Acids and Alcohols (ChemSusChem 1/2020)
journal, December 2019

  • Younes, Sabry H. H.; Tieves, Florian; Lan, Dongming
  • ChemSusChem, Vol. 13, Issue 1
  • DOI: 10.1002/cssc.201903373

Improving ionic liquid tolerance in Saccharomyces cerevisiae through heterologous expression and directed evolution of an ILT1 homolog from Yarrowia lipolytica
journal, August 2019

  • Reed, Kevin B.; Wagner, James M.; d’Oelsnitz, Simon
  • Journal of Industrial Microbiology & Biotechnology, Vol. 46, Issue 12
  • DOI: 10.1007/s10295-019-02228-9

Physiological and transcriptomic characterization of a fliA mutant of Pseudomonas putida KT2440: Physiological and transcriptiomic characterization of KT2440
journal, October 2009

  • Rodríguez-Herva, José Juan; Duque, Estrella; Molina-Henares, María Antonia
  • Environmental Microbiology Reports, Vol. 2, Issue 3
  • DOI: 10.1111/j.1758-2229.2009.00084.x

Membrane transporter engineering in industrial biotechnology and whole cell biocatalysis
journal, April 2015

Negative Regulation of the Pseudomonas aeruginosa Outer Membrane Porin OprD Selective for Imipenem and Basic Amino Acids
journal, May 1999

  • Ochs, Martina M.; McCusker, Matthew P.; Bains, Manjeet
  • Antimicrobial Agents and Chemotherapy, Vol. 43, Issue 5
  • DOI: 10.1128/AAC.43.5.1085

Room temperature ionic liquids as emerging solvents for the pretreatment of lignocellulosic biomass
journal, April 2011

  • Mora-Pale, Mauricio; Meli, Luciana; Doherty, Thomas V.
  • Biotechnology and Bioengineering, Vol. 108, Issue 6
  • DOI: 10.1002/bit.23108

Ensiled Wet Storage Accelerates Pretreatment for Bioconversion of Corn Stover
journal, December 2018

Role of RpoS and MutS in phase variation of Pseudomonas sp. PCL1171
journal, May 2005

  • van den Broek, Daan; Chin-A-Woeng, Thomas F. C.; Bloemberg, Guido V.
  • Microbiology, Vol. 151, Issue 5
  • DOI: 10.1099/mic.0.27777-0

Design of low-cost ionic liquids for lignocellulosic biomass pretreatment
journal, January 2015

  • George, Anthe; Brandt, Agnieszka; Tran, Kim
  • Green Chemistry, Vol. 17, Issue 3
  • DOI: 10.1039/C4GC01208A

Outer membrane vesicles catabolize lignin-derived aromatic compounds in Pseudomonas putida KT2440
journal, April 2020

  • Salvachúa, Davinia; Werner, Allison Z.; Pardo, Isabel
  • Proceedings of the National Academy of Sciences, Vol. 117, Issue 17
  • DOI: 10.1073/pnas.1921073117

Comparison of dilute acid and ionic liquid pretreatment of switchgrass: Biomass recalcitrance, delignification and enzymatic saccharification
journal, July 2010

Efficient biomass pretreatment using ionic liquids derived from lignin and hemicellulose
journal, August 2014

  • Socha, A. M.; Parthasarathi, R.; Shi, J.
  • Proceedings of the National Academy of Sciences, Vol. 111, Issue 35
  • DOI: 10.1073/pnas.1405685111

Progress on the pre-treatment of lignocellulosic biomass employing ionic liquids
journal, May 2019

  • Halder, Pobitra; Kundu, Sazal; Patel, Savankumar
  • Renewable and Sustainable Energy Reviews, Vol. 105
  • DOI: 10.1016/j.rser.2019.01.052

Revisiting the stringent response, ppGpp and starvation signaling
journal, April 2001

Functional Genomics of Stress Response in Pseudomonas putida KT2440
journal, May 2006

  • Reva, O. N.; Weinel, C.; Weinel, M.
  • Journal of Bacteriology, Vol. 188, Issue 11
  • DOI: 10.1128/JB.00101-06

Efficient Conversion of Acetate to 3-Hydroxypropionic Acid by Engineered Escherichia coli
journal, November 2018

Ionic liquids: Promising green solvents for lignocellulosic biomass utilization
journal, June 2017

  • Yoo, Chang Geun; Pu, Yunqiao; Ragauskas, Arthur J.
  • Current Opinion in Green and Sustainable Chemistry, Vol. 5
  • DOI: 10.1016/j.cogsc.2017.03.003

Cumulative Number of Cell Divisions as a Meaningful Timescale for Adaptive Laboratory Evolution of Escherichia coli
journal, October 2011

Use of Adaptive Laboratory Evolution To Discover Key Mutations Enabling Rapid Growth of Escherichia coli K-12 MG1655 on Glucose Minimal Medium
journal, October 2014

  • LaCroix, Ryan A.; Sandberg, Troy E.; O'Brien, Edward J.
  • Applied and Environmental Microbiology, Vol. 81, Issue 1
  • DOI: 10.1128/AEM.02246-14

STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets
journal, November 2018

  • Szklarczyk, Damian; Gable, Annika L.; Lyon, David
  • Nucleic Acids Research, Vol. 47, Issue D1
  • DOI: 10.1093/nar/gky1131

Global transcriptome response to ionic liquid by a tropical rain forest soil bacterium, Enterobacter lignolyticus
journal, May 2012

  • Khudyakov, J. I.; D'haeseleer, P.; Borglin, S. E.
  • Proceedings of the National Academy of Sciences, Vol. 109, Issue 32, p. E2173-E2182
  • DOI: 10.1073/pnas.1112750109

Development of 3-hydroxypropionic-acid-tolerant strain of Escherichia coli W and role of minor global regulator yieP
journal, May 2019

Identification of reciprocal adhesion genes in pathogenic and non-pathogenic Pseudomonas: Microbes:surface interaction
journal, March 2012

Synthesis of three advanced biofuels from ionic liquid-pretreated switchgrass using engineered Escherichia coli
journal, November 2011

  • Bokinsky, G.; Peralta-Yahya, P. P.; George, A.
  • Proceedings of the National Academy of Sciences, Vol. 108, Issue 50, p. 19949-19954
  • DOI: 10.1073/pnas.1106958108

Lignocellulosic Biomass: Understanding Recalcitrance and Predicting Hydrolysis
journal, December 2019

Structure, function and regulation of Pseudomonas aeruginosa porins
journal, July 2017

  • Chevalier, Sylvie; Bouffartigues, Emeline; Bodilis, Josselin
  • FEMS Microbiology Reviews, Vol. 41, Issue 5
  • DOI: 10.1093/femsre/fux020

A bacterium that degrades and assimilates poly(ethylene terephthalate)
journal, March 2016

Production of itaconic acid from acetate by engineering acid-tolerant Escherichia coli W
journal, December 2017

  • Noh, Myung Hyun; Lim, Hyun Gyu; Woo, Sung Hwa
  • Biotechnology and Bioengineering, Vol. 115, Issue 3
  • DOI: 10.1002/bit.26508

New insights on the reorganization of gene transcription in Pseudomonas putida KT2440 at elevated pressure
journal, January 2013

  • Follonier, Stéphanie; Escapa, Isabel F.; Fonseca, Pilar M.
  • Microbial Cell Factories, Vol. 12, Issue 1
  • DOI: 10.1186/1475-2859-12-30

Optimization of Ionic Liquid Pretreatment of Mixed Softwood by Response Surface Methodology and Reutilization of Ionic Liquid from Hydrolysate
journal, March 2018

  • Trinh, Ly Thi Phi; Lee, Young-Ju; Lee, Jae-Won
  • Biotechnology and Bioprocess Engineering, Vol. 23, Issue 2
  • DOI: 10.1007/s12257-017-0209-x

Genomic analysis of the aromatic catabolic pathways from Pseudomonas putida KT2440
journal, December 2002

Structure and function of the LysR-type transcriptional regulator (LTTR) family proteins
journal, December 2008

Engineering glucose metabolism for enhanced muconic acid production in Pseudomonas putida KT2440
journal, May 2020

Recent trends in ionic liquid (IL) tolerant enzymes and microorganisms for biomass conversion
journal, October 2013

Guanidine Riboswitch-Regulated Efflux Transporters Protect Bacteria against Ionic Liquid Toxicity
journal, April 2019

  • Higgins, Douglas A.; Gladden, John M.; Kimbrel, Jeff A.
  • Journal of Bacteriology, Vol. 201, Issue 13
  • DOI: 10.1128/JB.00069-19

Tuning Escherichia coli for membrane protein overexpression
journal, September 2008

  • Wagner, S.; Klepsch, M. M.; Schlegel, S.
  • Proceedings of the National Academy of Sciences, Vol. 105, Issue 38
  • DOI: 10.1073/pnas.0804090105

Reducing ppGpp Level Rescues an Extreme Growth Defect Caused by Mutant EF-Tu
journal, February 2014

Ethanol production in switchgrass hydrolysate by ionic liquid-tolerant yeasts
journal, September 2019

Inexpensive ionic liquids: [HSO 4 ] − -based solvent production at bulk scale
journal, January 2014

  • Chen, Long; Sharifzadeh, Mahdi; Mac Dowell, Niall
  • Green Chem., Vol. 16, Issue 6
  • DOI: 10.1039/C4GC00016A

Metabolic effects of furaldehydes and impacts on biotechnological processes
journal, January 2009

  • Almeida, João R. M.; Bertilsson, Magnus; Gorwa-Grauslund, Marie F.
  • Applied Microbiology and Biotechnology, Vol. 82, Issue 4
  • DOI: 10.1007/s00253-009-1875-1

Lignin Extraction from Straw by Ionic Liquids and Enzymatic Hydrolysis of the Cellulosic Residues
journal, March 2010

  • Fu, Dongbao; Mazza, Giuseppe; Tamaki, Yukihiro
  • Journal of Agricultural and Food Chemistry, Vol. 58, Issue 5
  • DOI: 10.1021/jf903616y

Transcriptional regulation of central carbon metabolism in Pseudomonas aeruginosa
journal, January 2020

  • Dolan, Stephen K.; Pereira, Greicy; Silva‐Rocha, Rafael
  • Microbial Biotechnology, Vol. 13, Issue 1
  • DOI: 10.1111/1751-7915.13423

Ionic liquid-tolerant microorganisms and microbial communities for lignocellulose conversion to bioproducts
journal, November 2016

  • Yu, Chaowei; Simmons, Blake A.; Singer, Steven W.
  • Applied Microbiology and Biotechnology, Vol. 100, Issue 24
  • DOI: 10.1007/s00253-016-7955-0

Generation of a platform strain for ionic liquid tolerance using adaptive laboratory evolution
journal, November 2017

  • Mohamed, Elsayed T.; Wang, Shizeng; Lennen, Rebecca M.
  • Microbial Cell Factories, Vol. 16, Issue 1
  • DOI: 10.1186/s12934-017-0819-1

An economically viable ionic liquid for the fractionation of lignocellulosic biomass
journal, January 2017

  • Brandt-Talbot, Agnieszka; Gschwend, Florence J. V.; Fennell, Paul S.
  • Green Chemistry, Vol. 19, Issue 13
  • DOI: 10.1039/C7GC00705A

Fast gapped-read alignment with Bowtie 2
journal, March 2012

  • Langmead, Ben; Salzberg, Steven L.
  • Nature Methods, Vol. 9, Issue 4
  • DOI: 10.1038/nmeth.1923

Development of an E. coli strain for one-pot biofuel production from ionic liquid pretreated cellulose and switchgrass
journal, January 2016

  • Frederix, Marijke; Mingardon, Florence; Hu, Matthew
  • Green Chemistry, Vol. 18, Issue 15
  • DOI: 10.1039/C6GC00642F

Generation of an E. coli platform strain for improved sucrose utilization using adaptive laboratory evolution
journal, June 2019

  • Mohamed, Elsayed T.; Mundhada, Hemanshu; Landberg, Jenny
  • Microbial Cell Factories, Vol. 18, Issue 1
  • DOI: 10.1186/s12934-019-1165-2

Precise tuning of the glyoxylate cycle in Escherichia coli for efficient tyrosine production from acetate
journal, March 2019

Some physico-chemical properties of ethanolamine ionic liquids: Behavior in different solvents
journal, March 2013

  • Simijonović, Dušica; Petrović, Zorica D.; Petrović, Vladimir P.
  • Journal of Molecular Liquids, Vol. 179
  • DOI: 10.1016/j.molliq.2012.12.020

Understanding cost drivers and economic potential of two variants of ionic liquid pretreatment for cellulosic biofuel production
journal, January 2014

  • Konda, Nvsn; Shi, Jian; Singh, Seema
  • Biotechnology for Biofuels, Vol. 7, Issue 1
  • DOI: 10.1186/1754-6834-7-86

Pseudomonas putida as a functional chassis for industrial biocatalysis: From native biochemistry to trans-metabolism
journal, November 2018

Adaptive laboratory evolution – principles and applications for biotechnology
journal, January 2013

Lignocellulosic biomass: a sustainable platform for the production of bio-based chemicals and polymers
journal, January 2015

  • Isikgor, Furkan H.; Becer, C. Remzi
  • Polymer Chemistry, Vol. 6, Issue 25
  • DOI: 10.1039/C5PY00263J

Identification of Mutations in Laboratory-Evolved Microbes from Next-Generation Sequencing Data Using breseq
book, January 2014

Restoration of biofuel production levels and increased tolerance under ionic liquid stress is enabled by a mutation in the essential Escherichia coli gene cydC
journal, October 2018

Pretreatment of bagasse with a minimum amount of cholinium ionic liquid for subsequent saccharification at high loading and co-fermentation for ethanol production
journal, February 2018

  • Ninomiya, Kazuaki; Utami, Amaliyah Rohsari Indah; Tsuge, Yota
  • Chemical Engineering Journal, Vol. 334
  • DOI: 10.1016/j.cej.2017.10.113

Thermophilic enrichment of microbial communities in the presence of the ionic liquid 1-ethyl-3-methylimidazolium acetate
journal, October 2012

  • Reddy, A. P.; Simmons, C. W.; Claypool, J.
  • Journal of Applied Microbiology, Vol. 113, Issue 6
  • DOI: 10.1111/jam.12002

Tolerance engineering in bacteria for the production of advanced biofuels and chemicals
journal, August 2015

One-pot integrated biofuel production using low-cost biocompatible protic ionic liquids
journal, January 2017

  • Sun, Jian; Konda, N. V. S. N. Murthy; Parthasarathi, Ramakrishnan
  • Green Chemistry, Vol. 19, Issue 13
  • DOI: 10.1039/C7GC01179B

Effect of CO partial pressure on cell-recycled continuous CO fermentation by Eubacterium limosum KIST612
journal, December 2001

The emergence of adaptive laboratory evolution as an efficient tool for biological discovery and industrial biotechnology
journal, December 2019

ALEdb 1.0: a database of mutations from adaptive laboratory evolution experimentation
journal, October 2018

  • Phaneuf, Patrick V.; Gosting, Dennis; Palsson, Bernhard O.
  • Nucleic Acids Research, Vol. 47, Issue D1
  • DOI: 10.1093/nar/gky983

Fermentation of lignocellulosic hydrolysates. II: inhibitors and mechanisms of inhibition
journal, August 2000

Life-Cycle Greenhouse Gas and Water Intensity of Cellulosic Biofuel Production Using Cholinium Lysinate Ionic Liquid Pretreatment
journal, September 2017

  • Neupane, Binod; Konda, N. V. S. N. Murthy; Singh, Seema
  • ACS Sustainable Chemistry & Engineering, Vol. 5, Issue 11
  • DOI: 10.1021/acssuschemeng.7b02116

A Model for Designing Adaptive Laboratory Evolution Experiments
journal, February 2017

  • LaCroix, Ryan A.; Palsson, Bernhard O.; Feist, Adam M.
  • Applied and Environmental Microbiology, Vol. 83, Issue 8
  • DOI: 10.1128/AEM.03115-16

Improving membrane protein expression and function using genomic edits
journal, October 2017

Roles of Cyclic Di-GMP and the Gac System in Transcriptional Control of the Genes Coding for the Pseudomonas putida Adhesins LapA and LapF
journal, January 2014

  • Martinez-Gil, M.; Ramos-Gonzalez, M. I.; Espinosa-Urgel, M.
  • Journal of Bacteriology, Vol. 196, Issue 8
  • DOI: 10.1128/JB.01287-13

Development and evaluation of consolidated bioprocessing yeast for ethanol production from ionic liquid-pretreated bagasse
journal, December 2017

Software for Computing and Annotating Genomic Ranges
journal, August 2013

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
journal, December 2014

Ensiling and hydrothermal pretreatment of grass: consequences for enzymatic biomass conversion and total monosaccharide yields
journal, January 2014

  • Ambye-Jensen, Morten; Johansen, Katja S.; Didion, Thomas
  • Biotechnology for Biofuels, Vol. 7, Issue 1
  • DOI: 10.1186/1754-6834-7-95

Structural features affecting the enzymatic digestibility of pine wood pretreated with ionic liquids: Understanding Digestibility of IL Pretreated Pine
journal, September 2015

  • Torr, Kirk M.; Love, Karen T.; Simmons, Blake A.
  • Biotechnology and Bioengineering, Vol. 113, Issue 3
  • DOI: 10.1002/bit.25831

A survey of tools for variant analysis of next-generation genome sequencing data
journal, January 2013

  • Pabinger, S.; Dander, A.; Fischer, M.
  • Briefings in Bioinformatics, Vol. 15, Issue 2
  • DOI: 10.1093/bib/bbs086

High‐quality genome‐scale metabolic modelling of Pseudomonas putida highlights its broad metabolic capabilities
journal, November 2019

  • Nogales, Juan; Mueller, Joshua; Gudmundsson, Steinn
  • Environmental Microbiology, Vol. 22, Issue 1
  • DOI: 10.1111/1462-2920.14843
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