Toward a semisynthetic stress response system to engineer microbial solvent tolerance

mBio

Volumn 3, Issue 5, 2012, Pages

  Zingaro, Kyle A ^a   Papoutsakis, Eleftherios Terry ^a  

^a University of Delaware   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84868351277     PISSN: 21612129     EISSN: 21507511     Source Type: Journal    
DOI: 10.1128/mBio.00308-12     Document Type: Article

References (45)

1. Dunlop MJ. 2011. Engineering microbes for tolerance to next-generation biofuels. Biotechnol. Biofuels 4: 32. http://dx.doi.org/10.1186/1754-6834 -4-32.
2. Nicolaou SA, Gaida SM, Papoutsakis ET. 2010. A comparative view of metabolite and substrate stress and tolerance in microbial bioprocessing: from biofuels and chemicals, to biocatalysis and bioremediation. Metab. Eng. 12:307-331.
3. Papoutsakis ET. 2008. Engineering solventogenic clostridia. Curr. Opin. Biotechnol. 19:420-429.
4. Jarboe LR, et al. 2010. Metabolic engineering for production of biore-newable fuels and chemicals: contributions of synthetic biology. J. Biomed. Biotechnol. 2010:761042.
5. Onofrei T, Hurduc N, Arsene C, Ionescu D. 2000. Sorption of Cu(II), Co(II) and Ni(II) on 1(4=-azobenzylcellulose)-2-naphthol. Thermogravi-metric characterization. Cellulose Chem. Technol. 34:261-268.
6. Goloubinoff P, Mogk A, Ben Zvi AP, Tomoyasu T, Bukau B. 1999. Sequential mechanism of solubilization and refolding of stable protein aggregates by a bichaperone network. Proc. Natl. Acad. Sci. U. S. A. 96: 13732-13737.
7. Schröder H, Langer T, Hartl FU, Bukau B. 1993. Dnak, Dnaj and Grpe form a cellular chaperone machinery capable of repairing heat-induced protein damage. EMBO J. 12:4137-4144.
8. Wu B, Wawrzynow A, Zylicz M, Georgopoulos C. 1996. Structure-function analysis of the Escherichia coli GrpE heat shock protein. EMBO J. 15:4806-4816.
9. Haslberger T, Bukau B, Mogk A. 2010. Towards a unifying mechanism for ClpB/Hsp104-mediated protein disaggregation and prion propagation. Biochem. Cell Biol. 88:63-75.
10. Alsaker KV, Paredes C, Papoutsakis ET. 2010. Metabolite stress and tolerance in the production of biofuels and chemicals: gene-expression-based systems analysis of butanol, butyrate, and acetate stresses in the anaerobe Clostridium acetobutylicum. Biotechnol. Bioeng. 105: 1131-1147.
11. Alsaker KV, Spitzer TR, Papoutsakis ET. 2004. Transcriptional analysis of spo0A overexpression in Clostridium acetobutylicum and its effect on the cell's response to butanol stress. J. Bacteriol. 186: 1959 -1971.
12. Tomas CA, Beamish J, Papoutsakis ET. 2004. Transcriptional analysis of butanol stress and tolerance in Clostridium acetobutylicum. J. Bacteriol. 186:2006-2018.
13. Winkler J, Kao KC. 2011. Transcriptional analysis of Lactobacillus brevis to N-butanol and ferulic acid stress responses. PLoS One 6: e21438. http: //dx.doi.org/10.1371/journal.pone.0021438.
14. Tomas CA, Welker NE, Papoutsakis ET. 2003. Overexpression of groESL in Clostridium acetobutylicum results in increased solvent production and tolerance, prolonged metabolism, and changes in the cell's transcriptional program. Appl. Environ. Microbiol. 69:4951-4965.
15. Borden JR, Papoutsakis ET. 2007. Dynamics of genomic-library enrichment and identification of solvent tolerance genes for Clostridium aceto-butylicum. Appl. Environ. Microbiol. 73:3061-3068.
16. Nicolaou SA, Gaida SM, Papoutsakis ET. 2011. Coexisting/Coexpressing Genomic Libraries (CoGeL) identify interactions among distantly located genetic loci for developing complex microbial phenotypes. Nucleic Acids Res. 39:e152. http://dx.doi.org/10.1093/nar/gkq1027.
17. Goodarzi H, et al. 2010. Regulatory and metabolic rewiring during laboratory evolution of ethanol tolerance in E. coli. Mol. Syst. Biol. 6:378. http://dx.doi.org/10.1038/msb.2010.33.
18. Reyes LH, Almario MP, Kao KC. 2011. Genomic library screens for genes involved in N-butanol tolerance in Escherichia coli. PLoS One 6:e17678. http://dx.doi.org/10.1371/journal.pone.0017678.
19. Brynildsen MP, Liao JC. 2009. An integrated network approach identifies the isobutanol response network of Escherichia coli. Mol. Syst. Biol. 5:277. http://dx.doi.org/10.1038/msb.2009.34.
20. Kang HJ, et al. 2007. Functional characterization of Hsp33 protein from Bacillus psychrosaccharolyticus; additional functionofHSP33 onresistance to solvent stress. Biochem. Biophys. Res. Commun. 358:743-750.
21. Okochi M, Kanie K, Kurimoto M, Yohda M, Honda H. 2008. Overex-pression of prefoldin from the hyperthermophilic archaeum Pyrococcus horikoshii OT3 endowed Escherichia coli with organic solvent tolerance. Appl. Microbiol. Biotechnol. 79:443-449.
22. de Marco A. 2007. Protocol for preparing proteins with improved solu-bility by co-expressing with molecular chaperones in Escherichia coli. Nat. Protoc. 2: 2632-2639.
23. de Marco D, Zona G. 2007. Complex formation equilibria between Ag(I) and thioureas in n-propanol. Thermochim. Acta 452:82-84.
24. de Marco A, Deuerling E, Mogk A, Tomoyasu T, Bukau B. 2007. Chaperone-based procedure to increase yields of soluble recombinant proteins produced in E. coli. BMC Biotechnol. 7:32. http://dx.doi.org/10.1186/1472-6750-7-32.
25. Wang JD, Herman C, Tipton KA, Gross CA, Weissman JS. 2002. Directed evolution of substrate-optimized GroEL/S chaperonins. Cell 111:1027-1039.
26. Zingaro KA, Papoutsakis ET. GroESL overexpression imparts Escherichia coli tolerance to i-, n-, and 2-butanol, 1,2,4-butanetriol and ethanol with complex and unpredictable patterns. Metab. Eng., in press.
27. Sambrook JF, Fritsch EF, Maniatis T. 1989. Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.
28. Lutz R, Bujard H. 1997. Independent and tight regulation of transcrip-tional units in Escherichia coli via the LacR/O, the TetR/O and AraC/I1-I2 regulatory elements. Nucleic Acids Res. 25:1203-1210.
29. Blum P, Ory J, Bauernfeind J, Krska J. 1992. Physiological consequences of Dnak and Dnaj overproduction in Escherichia coli. J. Bacteriol. 174: 7436-7444.
30. Rutherford BJ, et al. 2010. Functional genomic study of exogenous n-butanol stress in Escherichia coli. Appl. Environ. Microbiol. 76: 1935-1945.
31. Guisbert E, Herman C, Lu CZ, Gross CA. 2004. A chaperone network controls the heat shock response in E. coli. Genes Dev. 18:2812-2821.
32. Muffler A, Barth M, Marschall C, HenggeAronis R. 1997. Heat shock regulation of sigma(S) turnover: a role for DnaK and relationship between stress responses mediated by sigma(S) and sigma(32) in Escherichia coli. J. Bacteriol. 179: 445- 452.
33. Yura T, et al. 2007. Analysis of sigma(32) mutants defective in chaperone-mediated feedback control reveals unexpected complexity of the heat shock response. Proc. Natl. Acad. Sci. U. S. A. 104:17638-17643.
34. Mogk A, Deuerling E, Vorderwülbecke S, Vierling E, Bukau B. 2003. Small heat shock proteins, ClpB and the DnaK system form a functional triade in reversing protein aggregation. Mol. Microbiol. 50:585-595.
35. Viitanen PV, Gatenby AA, Lorimer GH. 1992. Purified chaperonin 60 (Groel) interacts with the nonnative states of a multitude of Escherichia coli proteins. Protein Sci. 1:363-369.
36. Tomoyasu T, Mogk A, Langen H, Goloubinoff P, Bukau B. 2001. Genetic dissection of the roles of chaperones and proteases in protein folding and degradation in the Escherichia coli cytosol. Mol. Microbiol. 40:397-413.
37. Silva F, Queiroz JA, Domingues FC. 2012. Evaluating metabolic stress and plasmid stability in plasmid DNA production by Escherichia coli. Bio-technol. Adv. 30:691-708.
38. Alper H, Stephanopoulos G. 2007. Global transcription machinery engineering: a new approach for improving cellular phenotype. Metab. Eng. 9:258-267.
39. Atsumi S, et al. 2010. Evolution, genomic analysis, and reconstruction of isobutanol tolerance in Escherichia coli. Mol. Syst. Biol. 6:449. http://dx.doi.org/10.1038/msb.2010.98.
40. Dunlop MJ, et al. 2011. Engineering microbial biofuel tolerance and export using efflux pumps. Mol. Syst. Biol. 7:487. http://dx.doi.org/10.1038/msb.2011.21.
41. Pfleger BF, Pitera DJ, Smolke CD, Keasling JD. 2006. Combinatorial engineering of intergenic regions in operons tunes expression of multiple genes. Nat. Biotechnol. 24:1027-1032.
42. Wang HH, et al. 2009. Programming cells by multiplex genome engineering and accelerated evolution. Nature 460:894-898.
43. Borden JR, Jones SW, Indurthi D, Chen Y, Papoutsakis ET. 2010. A genomic-library based discovery of a novel, possibly synthetic, acid-tolerance mechanism inClostridium acetobutylicum involving non-coding RNAs and ribosomal RNA processing. Metab. Eng. 12:268-281.
44. Zhou K, et al. 2011. Novel reference genes for quantifying transcriptional responses of Escherichia coli to protein overexpression by quantitative PCR. BMC Mol. Biol. 12:18. http://dx.doi.org/10.1186/1471-2199-12-18.
45. Barnett ME, Zolkiewska A, Zolkiewski M. 2000. Structure and activity of ClpB from Escherichia coli - Role of the amino- and carboxyl-terminal domains. J. of Biol. Chem. 275:37565-37571.