An auto-inducible mechanism for ionic liquid resistance in microbial biofuel production

Nature Communications

Volumn 5, Issue , 2014, Pages

  Ruegg, Thomas L ^a,b,c   Kim, Eun Mi ^a,d   Simmons, Blake A ^a,e   Keasling, Jay D ^a,d,f   Singer, Steven W ^a,d   Soon Lee, Taek ^a,d   Thelen, Michael P ^a,c  

^a JOINT BIOENERGY INSTITUTE   (United States)

^b UNIVERSITY OF BASEL   (Switzerland)

^c LAWRENCE LIVERMORE NATIONAL LABORATORY   (United States)

^d LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^e SANDIA NATIONAL LABORATORIES   (United States)

^f University of California at Berkeley   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

IMIDAZOLE DERIVATIVE; IONIC LIQUID; LIGNOCELLULOSE; TERPENE; BACTERIAL PROTEIN; BIOFUEL; SOLVENT;

BACTERIUM; BIOFUEL; BIOMASS; CELLULOSE; ION; LIGNIN; MICROBIAL ACTIVITY; RAINFOREST; SOIL MICROORGANISM; SOLVENT;

ARTICLE; AUTOREGULATION; BACTERIAL GROWTH; BIOFUEL PRODUCTION; BIOMASS; CONTROLLED STUDY; ENTEROBACTER; ENTEROBACTER LIGNOLYTICUS; ESCHERICHIA COLI; GENE EXPRESSION; GROWTH INHIBITION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHENOTYPE; PROMOTER REGION; TRANSCRIPTOMICS; ANTIBIOTIC RESISTANCE; DRUG EFFECTS; GENETICS; PHYSIOLOGY;

BACTERIAL PROTEINS; BIOFUELS; BIOMASS; DRUG RESISTANCE, BACTERIAL; ENTEROBACTER; ESCHERICHIA COLI; IMIDAZOLES; IONIC LIQUIDS; SOLVENTS;

EID: 84897092506     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms4490     Document Type: Article

References (33)

1. Rabinovitch-Deere, C. A., Oliver, J. W. K., Rodriguez, G. M. & Atsumi, S. Synthetic biology and metabolic engineering approaches to produce biofuels. Chem. Rev. 113, 4611-4632 (2013).
2. Wen, M., Bond-Watts, B. B. & Chang, M. C. Production of advanced biofuels in engineered E. coli. Curr. Opin. Chem. Biol. 17, 472-479 (2013).
3. Liu, T. G. & Khosla, C. Genetic engineering of Escherichia coli for biofuel production. Annu. Rev. Genet. 44, 53-69 (2010).
4. de Jong, B., Siewers, V. & Nielsen, J. Systems biology of yeast: enabling technology for development of cell factories for production of advanced biofuels. Curr. Opin. Biotechnol. 23, 624-630 (2012).
5. Bokinsky, G. et al. Synthesis of three advanced biofuels from ionic liquidpretreated switchgrass using engineered Escherichia coli. Proc. Natl Acad. Sci. USA 108, 19949-19954 (2011).
6. Mora-Pale, M., Meli, L., Doherty, T. V., Linhardt, R. J. & Dordick, J. S. Room temperature ionic liquids as emerging solvents for the pretreatment of lignocellulosic biomass. Biotechnol. Bioeng. 108, 1229-1245 (2011).
7. Liu, C. Z., Wang, F., Stiles, A. R. & Guo, C. Ionic liquids for biofuel production: opportunities and challenges. Appl. Energ. 92, 406-414 (2012).
8. Blanch, H. W., Simmons, B. A. & Klein-Marcuschamer, D. Biomass deconstruction to sugars. Biotechnol. J. 6, 1086-1102 (2011).
9. Li, C. L. et al. Comparison of dilute acid and ionic liquid pretreatment of switchgrass: biomass recalcitrance, delignification and enzymatic saccharification. Bioresour. Technol. 101, 4900-4906 (2010).
10. Ouellet, M. et al. Impact of ionic liquid pretreated plant biomass on Saccharomyces cerevisiae growth and biofuel production. Green Chem. 13, 2743-2749 (2011).
11. Park, J. I. et al. A thermophilic ionic liquid-tolerant cellulase cocktail for the production of cellulosic biofuels. PLoS One 7, e37010 (2012).
12. Nancharaiah, Y. V. & Francis, A. J. Alkyl-methylimidazolium ionic liquids affect the growth and fermentative metabolism of Clostridium sp. Bioresour. Technol. 102, 6573-6578 (2011).
13. Klein-Marcuschamer, D., Simmons, B. A. & Blanch, H. W. Techno-economic analysis of a lignocellulosic ethanol biorefinery with ionic liquid pre-treatment. Biofuel Bioprod. Bior. 5, 562-569 (2011).
14. Deangelis, K. M. et al. Complete genome sequence of "Enterobacter lignolyticus" SCF1. Stand. Genomic Sci. 5, 69-85 (2011).
15. Khudyakov, J. I. et al. Global transcriptome response to ionic liquid by a tropical rain forest soil bacterium, Enterobacter lignolyticus. Proc. Natl Acad. Sci. USA 109, E2173-E2182 (2012).
16. Fluman, N. & Bibi, E. Bacterial multidrug transport through the lens of the major facilitator superfamily. Biochim. Biophys. Acta 1794, 738-747 (2009).
17. Paulsen, I. T., Brown, M. H. & Skurray, R. A. Proton-dependent multidrug efflux systems. Microbiol. Rev. 60, 575-608 (1996).
18. Saier, M. H. & Paulsen, I. T. Phylogeny of multidrug transporters. Semin. Cell Dev. Biol. 12, 205-213 (2001).
19. Ogawa, W., Koterasawa, M., Kuroda, T. & Tsuchiya, T. KmrA multidrug efflux pump from Klebsiella pneumoniae. Biol. Pharm. Bull. 29, 550-553 (2006).
20. Santiviago, C. A. et al. The Salmonella enterica sv. Typhimurium smvA, yddG and ompD (porin) genes are required for the efficient efflux of methyl viologen. Mol. Microbiol. 46, 687-698 (2002).
21. Wade, H. MD recognition by MDR gene regulators. Curr. Opin. Struc. Biol. 20, 489-496 (2010).
22. Ramos, J. L. et al. The TetR family of transcriptional repressors. Microbiol. Mol. Biol. Rev. 69, 326-356 (2005).
23. Cho, Y. H. et al. The pqrAB operon is responsible for paraquat resistance in Streptomyces coelicolor. J. Bacteriol. 185, 6756-6763 (2003).
24. Wagner, S. et al. Consequences of membrane protein overexpression in Escherichia coli. Mol. Cell. Proteomics 6, 1527-1550 (2007).
25. Dunlop, M. J. et al. Engineering microbial biofuel tolerance and export using efflux pumps. Mol. Syst. Biol. 7, 487 (2011).
26. Peralta-Yahya, P. P. et al. Identification and microbial production of a terpenebased advanced biofuel. Nat. Commun. 2, 483 (2011).
27. Klinke, H. B., Thomsen, A. B. & Ahring, B. K. Inhibition of ethanol-producing yeast and bacteria by degradation products produced during pre-treatment of biomass. Appl. Microbiol. Biotechnol. 66, 10-26 (2004).
28. Wilson, K. Preparation of Genomic DNA from Bacteria. Curr. Protoc. Mol. Biol. Chapter 2, Unit 2.4 (2001).
29. Lee, T. S. et al. BglBrick vectors and datasheets: A synthetic biology platform for gene expression. J. Biol. Eng. 5, 12 (2011).
30. Quan, J. & Tian, J. Circular polymerase extension cloning of complex gene libraries and pathways. PLoS One 4, e6441 (2009).
31. Pedelacq, J. D., Cabantous, S., Tran, T., Terwilliger, T. C. & Waldo, G. S. Engineering and characterization of a superfolder green fluorescent protein. Nat. Biotechnol. 24, 79-88 (2006).
32. Baranyi, J. & Roberts, T. A. A dynamic approach to predicting bacterial growth in food. Int. J. Food Microbiol. 23, 277-294 (1994).
33. Stepnowski, P. et al. Reversed-phase liquid chromatographic method for the determination of selected room-temperature ionic liquid cations. J. Chromatogr. A 993, 173-178 (2003).