Guanidine Riboswitch-Regulated Efflux Transporters Protect Bacteria against Ionic Liquid Toxicity
Abstract
Plant cell walls contain a renewable, nearly limitless supply of sugar that could be used to support microbial production of commodity chemicals and biofuels. Imidazolium ionic liquid (IIL) solvents are among the best reagents for gaining access to the sugars in this otherwise recalcitrant biomass. However, the sugars from IIL-treated biomass are inevitably contaminated with residual IILs that inhibit growth in bacteria and yeast, blocking biochemical production by these organisms. IIL toxicity is, therefore, a critical roadblock in many industrial biosynthetic pathways. Although several IIL-tolerant (IILT) bacterial and yeast isolates have been identified in nature, few genetic mechanisms have been identified. In this study, we identified two IILT Bacillus isolates as well as a spontaneous IILT Escherichia coli lab strain that are tolerant to high levels of two widely used IILs. We demonstrate that all three IILT strains contain one or more pumps of the small multidrug resistance (SMR) family, and two of these strains contain mutations that affect an adjacent regulatory guanidine riboswitch. Furthermore, we show that the regulation of E. coli sugE by the guanidine II riboswitch can be exploited to promote IIL tolerance by the simple addition of guanidine to the medium. Our results demonstrate the criticalmore »
- Authors:
-
[3];
[1]
- Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
- Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Sandia National Lab. (SNL-CA), Livermore, CA (United States)
- Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
- Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Publication Date:
- Research Org.:
- Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
- Sponsoring Org.:
- USDOE National Nuclear Security Administration (NNSA)
- OSTI Identifier:
- 1544473
- Report Number(s):
- LLNL-JRNL-767148
Journal ID: ISSN 0021-9193; 957444
- Grant/Contract Number:
- AC52-07NA27344
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Journal of Bacteriology
- Additional Journal Information:
- Journal Volume: 201; Journal Issue: 13; Journal ID: ISSN 0021-9193
- Publisher:
- American Society for Microbiology
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 09 BIOMASS FUELS
Citation Formats
Higgins, Douglas A., Gladden, John M., Kimbrel, Jeff A., Simmons, Blake A., Singer, Steven W., and Thelen, Michael P.. Guanidine Riboswitch-Regulated Efflux Transporters Protect Bacteria against Ionic Liquid Toxicity. United States: N. p., 2019.
Web. doi:10.1128/JB.00069-19.
Higgins, Douglas A., Gladden, John M., Kimbrel, Jeff A., Simmons, Blake A., Singer, Steven W., & Thelen, Michael P.. Guanidine Riboswitch-Regulated Efflux Transporters Protect Bacteria against Ionic Liquid Toxicity. United States. https://doi.org/10.1128/JB.00069-19
Higgins, Douglas A., Gladden, John M., Kimbrel, Jeff A., Simmons, Blake A., Singer, Steven W., and Thelen, Michael P.. Mon .
"Guanidine Riboswitch-Regulated Efflux Transporters Protect Bacteria against Ionic Liquid Toxicity". United States. https://doi.org/10.1128/JB.00069-19. https://www.osti.gov/servlets/purl/1544473.
@article{osti_1544473,
title = {Guanidine Riboswitch-Regulated Efflux Transporters Protect Bacteria against Ionic Liquid Toxicity},
author = {Higgins, Douglas A. and Gladden, John M. and Kimbrel, Jeff A. and Simmons, Blake A. and Singer, Steven W. and Thelen, Michael P.},
abstractNote = {Plant cell walls contain a renewable, nearly limitless supply of sugar that could be used to support microbial production of commodity chemicals and biofuels. Imidazolium ionic liquid (IIL) solvents are among the best reagents for gaining access to the sugars in this otherwise recalcitrant biomass. However, the sugars from IIL-treated biomass are inevitably contaminated with residual IILs that inhibit growth in bacteria and yeast, blocking biochemical production by these organisms. IIL toxicity is, therefore, a critical roadblock in many industrial biosynthetic pathways. Although several IIL-tolerant (IILT) bacterial and yeast isolates have been identified in nature, few genetic mechanisms have been identified. In this study, we identified two IILT Bacillus isolates as well as a spontaneous IILT Escherichia coli lab strain that are tolerant to high levels of two widely used IILs. We demonstrate that all three IILT strains contain one or more pumps of the small multidrug resistance (SMR) family, and two of these strains contain mutations that affect an adjacent regulatory guanidine riboswitch. Furthermore, we show that the regulation of E. coli sugE by the guanidine II riboswitch can be exploited to promote IIL tolerance by the simple addition of guanidine to the medium. Our results demonstrate the critical role that transporter genes play in IIL tolerance in their native bacterial hosts. The study presented here is another step in engineering IIL tolerance into industrial strains toward overcoming this key gap in biofuels and industrial biochemical production processes.},
doi = {10.1128/JB.00069-19},
journal = {Journal of Bacteriology},
number = 13,
volume = 201,
place = {United States},
year = {2019},
month = {6}
}
Free Publicly Available Full Text
Publisher's Version of Record
Other availability
Search WorldCat to find libraries that may hold this journal
Cited by: 13 works
Citation information provided by
Web of Science
Web of Science
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.
Works referenced in this record:
Designing tailored microbial and enzymatic response in ionic liquids for lignocellulosic biorefineries
journal, April 2018
- Singh, Seema
- Biophysical Reviews, Vol. 10, Issue 3
Comparison of enzymatic reactivity of corn stover solids prepared by dilute acid, AFEX™, and ionic liquid pretreatments
journal, January 2014
- Gao, Xiadi; Kumar, Rajeev; Singh, Seema
- Biotechnology for Biofuels, Vol. 7, Issue 1
Visualization of biomass solubilization and cellulose regeneration during ionic liquid pretreatment of switchgrass
journal, September 2009
- Singh, Seema; Simmons, Blake A.; Vogel, Kenneth P.
- Biotechnology and Bioengineering, Vol. 104, Issue 1, p. 68-75
Comparison of dilute acid and ionic liquid pretreatment of switchgrass: Biomass recalcitrance, delignification and enzymatic saccharification
journal, July 2010
- Li, Chenlin; Knierim, Bernhard; Manisseri, Chithra
- Bioresource Technology, Vol. 101, Issue 13
Lignin Depletion Enhances the Digestibility of Cellulose in Cultured Xylem Cells
journal, July 2013
- Lacayo, Catherine I.; Hwang, Mona S.; Ding, Shi-You
- PLoS ONE, Vol. 8, Issue 7
Biomass deconstruction to sugars
journal, August 2011
- Blanch, Harvey W.; Simmons, Blake A.; Klein-Marcuschamer, Daniel
- Biotechnology Journal, Vol. 6, Issue 9
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
Emergence of resistance to antibacterial agents: the role of quaternary ammonium compounds—a critical review
journal, May 2012
- Buffet-Bataillon, Sylvie; Tattevin, Pierre; Bonnaure-Mallet, Martine
- International Journal of Antimicrobial Agents, Vol. 39, Issue 5
Complete genome sequence of “Enterobacter lignolyticus” SCF1
journal, September 2011
- DeAngelis, Kristen M.; D’Haeseleer, Patrik; Chivian, Dylan
- Standards in Genomic Sciences, Vol. 5, Issue 1
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
Isolation and Characterisation of 1-Alkyl-3-Methylimidazolium Chloride Ionic Liquid-Tolerant and Biodegrading Marine Bacteria
journal, April 2013
- Megaw, Julianne; Busetti, Alessandro; Gilmore, Brendan F.
- PLoS ONE, Vol. 8, Issue 4
Draft Genome Sequence of the Ionic Liquid-Tolerant Bacterium Bacillus amyloliquefaciens CMW1
journal, September 2014
- Kurata, A.; Hirose, Y.; Misawa, N.
- Genome Announcements, Vol. 2, Issue 5
Bacillus coagulans tolerance to 1-ethyl-3-methylimidazolium-based ionic liquids in aqueous and solid-state thermophilic culture
journal, January 2014
- Simmons, Christopher W.; Reddy, Amitha P.; VanderGheynst, Jean S.
- Biotechnology Progress, Vol. 30, Issue 2
Enrichment, isolation and characterization of fungi tolerant to 1-ethyl-3-methylimidazolium acetate: Ionic liquid-tolerant fungi
journal, February 2011
- Singer, S. W.; Reddy, A. P.; Gladden, J. M.
- Journal of Applied Microbiology, Vol. 110, Issue 4
Yeast tolerance to the ionic liquid 1-ethyl-3-methylimidazolium acetate
journal, November 2014
- Sitepu, Irnayuli R.; Shi, Shuang; Simmons, Blake A.
- FEMS Yeast Research, Vol. 14, Issue 8
Natural Variation in the Multidrug Efflux Pump SGE1 Underlies Ionic Liquid Tolerance in Yeast
journal, July 2018
- Higgins, Douglas A.; Young, Megan K. M.; Tremaine, Mary
- Genetics, Vol. 210, Issue 1
An auto-inducible mechanism for ionic liquid resistance in microbial biofuel production
journal, March 2014
- Ruegg, Thomas L.; Kim, Eun-Mi; Simmons, Blake A.
- Nature Communications, Vol. 5, Issue 1
The Saccharomyces cerevisiae SGE1 gene product: a novel drug-resistance protein within the major facilitator superfamily
journal, January 1994
- Ehrenhofer-Murray, AnnE.; W�rgler, FriedrichE.; Sengstag, Christian
- MGG Molecular & General Genetics, Vol. 244, Issue 3
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
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
- Eng, Thomas; Demling, Philipp; Herbert, Robin A.
- Microbial Cell Factories, Vol. 17, Issue 1
Metabolism of Free Guanidine in Bacteria Is Regulated by a Widespread Riboswitch Class
journal, January 2017
- Nelson, James W.; Atilho, Ruben M.; Sherlock, Madeline E.
- Molecular Cell, Vol. 65, Issue 2
Biochemical Validation of a Second Guanidine Riboswitch Class in Bacteria
journal, January 2017
- Sherlock, Madeline E.; Malkowski, Sarah N.; Breaker, Ronald R.
- Biochemistry, Vol. 56, Issue 2
Overexpression of the Escherichia coli sugE Gene Confers Resistance to a Narrow Range of Quaternary Ammonium Compounds
journal, May 2002
- Chung, Y. J.; Saier, M. H.
- Journal of Bacteriology, Vol. 184, Issue 9
A Broad-Specificity Multidrug Efflux Pump Requiring a Pair of Homologous SMR-Type Proteins
journal, April 2000
- Jack, D. L.; Storms, M. L.; Tchieu, J. H.
- Journal of Bacteriology, Vol. 182, Issue 8
Routine Markerless Gene Replacement in Bacillus anthracis
journal, February 2006
- Janes, B. K.; Stibitz, S.
- Infection and Immunity, Vol. 74, Issue 3
Construction of cloning vectors for Bacillus thuringiensis
journal, December 1991
- Arantes, Olivia; Lereclus, Didier
- Gene, Vol. 108, Issue 1
New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control
journal, April 2004
- Barrick, J. E.; Corbino, K. A.; Winkler, W. C.
- Proceedings of the National Academy of Sciences, Vol. 101, Issue 17
Challenges of ligand identification for riboswitch candidates
journal, January 2011
- Meyer, Michelle M.; Hammond, Ming C.; Salinas, Yasmmyn
- RNA Biology, Vol. 8, Issue 1
Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline
journal, July 2007
- Weinberg, Zasha; Barrick, Jeffrey E.; Yao, Zizhen
- Nucleic Acids Research, Vol. 35, Issue 14
Structural basis for guanidine sensing by the ykkC family of riboswitches
journal, January 2017
- Battaglia, Robert A.; Price, Ian R.; Ke, Ailong
- RNA, Vol. 23, Issue 4
Suite of novel vectors for ectopic insertion of GFP, CFP and IYFP transcriptional fusions in single copy at the amyE and bglS loci in Bacillus subtilis
journal, November 2010
- Bisicchia, Paola; Botella, Eric; Devine, Kevin M.
- Plasmid, Vol. 64, Issue 3
Discovery of two novel β-glucosidases from an Amazon soil metagenomic library
journal, December 2013
- Bergmann, Jessica C.; Costa, Ohana Yonara A.; Gladden, John M.
- FEMS Microbiology Letters, Vol. 351, Issue 2
EmrE, an Escherichia coli 12-kDa Multidrug Transporter, Exchanges Toxic Cations and H + and Is Soluble in Organic Solvents
journal, March 1995
- Yerushalmi, Hagit; Lebendiker, Mario; Schuldiner, Shimon
- Journal of Biological Chemistry, Vol. 270, Issue 12
The Structure of the Guanidine-II Riboswitch
journal, June 2017
- Huang, Lin; Wang, Jia; Lilley, David M. J.
- Cell Chemical Biology, Vol. 24, Issue 6
Structural basis for ligand binding to the guanidine-II riboswitch
journal, June 2017
- Reiss, Caroline W.; Strobel, Scott A.
- RNA, Vol. 23, Issue 9
The methyl viologen-resistance-encoding gene smvA of Salmonella typhimurium
journal, October 1994
- Etsuko, Hongo; Mitsuoki, Morimyo; Kazuei, Mita
- Gene, Vol. 148, Issue 1
Recombinant Bacillus subtilis That Grows on Untreated Plant Biomass
journal, November 2012
- Anderson, Timothy D.; Miller, J. Izaak; Fierobe, Henri-Pierre
- Applied and Environmental Microbiology, Vol. 79, Issue 3
Developing Bacillus spp. as a cell factory for production of microbial enzymes and industrially important biochemicals in the context of systems and synthetic biology
journal, June 2013
- Liu, Long; Liu, Yanfeng; Shin, Hyun-dong
- Applied Microbiology and Biotechnology, Vol. 97, Issue 14
One-step production of biocommodities from lignocellulosic biomass by recombinant cellulolytic Bacillus subtilis: Opportunities and challenges
journal, August 2010
- Zhang, Xiao-Zhou; Zhang, Yi-Heng P.
- Engineering in Life Sciences, Vol. 10, Issue 5
Small multidrug resistance proteins: A multidrug transporter family that continues to grow
journal, September 2008
- Bay, Denice C.; Rommens, Kenton L.; Turner, Raymond J.
- Biochimica et Biophysica Acta (BBA) - Biomembranes, Vol. 1778, Issue 9
Guanidinium export is the primal function of SMR family transporters
journal, March 2018
- Kermani, Ali A.; Macdonald, Christian B.; Gundepudi, Roja
- Proceedings of the National Academy of Sciences, Vol. 115, Issue 12
Presence of disinfectant resistance genes in Escherichia coli isolated from retail meats in the USA
journal, June 2014
- Zou, Likou; Meng, Jianghong; McDermott, Patrick F.
- Journal of Antimicrobial Chemotherapy, Vol. 69, Issue 10
Distribution of a transposon-like element carrying blaCMY-2 among Salmonella and other Enterobacteriaceae
journal, January 2006
- Su, Lin-Hui; Chen, Hsiu-Ling; Chia, Ju-Hsin
- Journal of Antimicrobial Chemotherapy, Vol. 57, Issue 3
CMY-2 β-lactamase-carrying community-acquired urinary tract Escherichia coli: genetic correlation with Salmonella enterica serotypes Choleraesuis and Typhimurium
journal, April 2007
- Wu, Tsu-Lan; Chia, Ju-Hsin; Su, Lin-Hui
- International Journal of Antimicrobial Agents, Vol. 29, Issue 4
Glycoside Hydrolase Activities of Thermophilic Bacterial Consortia Adapted to Switchgrass
journal, July 2011
- Gladden, John M.; Allgaier, Martin; Miller, Christopher S.
- Applied and Environmental Microbiology, Vol. 77, Issue 16, p. 5804-5812
BglBrick vectors and datasheets: A synthetic biology platform for gene expression
journal, January 2011
- Lee, Taek; Krupa, Rachel A.; Zhang, Fuzhong
- Journal of Biological Engineering, Vol. 5, Issue 1
Full expression of the cryIIIA toxin gene of Bacillus thuringiensis requires a distant upstream DNA sequence affecting transcription.
journal, May 1993
- de Souza, M. T.; Lecadet, M. M.; Lereclus, D.
- Journal of Bacteriology, Vol. 175, Issue 10
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
One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products
journal, May 2000
- Datsenko, K. A.; Wanner, B. L.
- Proceedings of the National Academy of Sciences, Vol. 97, Issue 12, p. 6640-6645
Identification and Characterization of a Novel FosA7 Member from Fosfomycin-Resistant Escherichia coli Clinical Isolates from Canadian Hospitals
journal, December 2020
- Milner, Kieran A.; Bay, Denice C.; Alexander, David
- Antimicrobial Agents and Chemotherapy, Vol. 65, Issue 1
Restoration of biofuel production levels and increased tolerance under ionic liquid stress is enabled by a mutation in the essential Escherichia coli gene cydC
text, January 2018
- Eng, Thomas; Demling, Philipp; Herbert, Robin A.
- RWTH Aachen University
Works referencing / citing this record:
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