Overexpression of the Lactobacillus plantarum peptidoglycan biosynthesis murA2 gene increases the tolerance of Escherichia coli to alcohols and enhances ethanol produc

详细信息    查看全文

• 作者：Yongbo Yuan ; Changhao Bi ; Sergios A. Nicolaou…
• 关键词：Alcohol tolerance ; Lactobacillus plantarum ; Small noncoding RNA ; E. coli ; Overexpression ; Genomic integration
• 刊名：Applied Microbiology and Biotechnology
• 出版年：2014
• 出版时间：October 2014
• 年：2014
• 卷：98
• 期：19
• 页码：8399-8411
• 全文大小：1,366 KB
• 参考文献：1. Alper H, Moxley J, Nevoigt E, Fink GR, Stephanopoulos G (2006) Engineering yeast transcription machinery for improved ethanol tolerance and production. Science 314:1565-568. doi:10.1126/science.1131969 CrossRef
  2. Block KF, Puerta-Fernandez E, Wallace JG, Breaker RR (2011) Association of OLE RNA with bacterial membranes via an RNA-protein interaction. Mol Microbiol 79:21-4. doi:10.1111/j.1365-2958.2010.07439.x CrossRef
  3. Borden JR, Jones SW, Indurthi D, Chen Y, Papoutsakis ET (2010) A genomic-library based discovery of a novel, possibly synthetic, acid-tolerance mechanism in / Clostridium acetobutylicum involving non-coding RNAs and ribosomal RNA processing. Metab Eng 12:268-81. doi:10.1016/j.ymben.2009.12.004 CrossRef
  4. Cho SH, Lei R, Henninger TD, Contreras LM (2014) Discovery of ethanol responsive small RNAs in / Zymomonas mobilis. Appl Environ Microbiol. doi:10.1128/aem.00429-14
  5. Couto JA, Pina C, Hogg T (1997) Enhancement of apparent resistance to ethanol in / Lactobacillus hilgardii. Biotechnol Lett 19:487-90 CrossRef
  6. Datsenko KA, Wanner BL (2000) One-step inactivation of chromosomal genes in / Escherichia coli K-12 using PCR products. Proc Natl Acad Sci U S A 97:6640-645. doi:10.1073/pnas.120163297 CrossRef
  7. Du W, Brown JR, Sylvester DR, Huang J, Chalker AF, So CY, Holmes DJ, Payne DJ, Wallis NG (2000) Two active forms of UDP- / N-acetylglucosamine enolpyruvyl transferase in gram-positive bacteria. J Bacteriol 182:4146-152 CrossRef
  8. Dunlop MJ (2011) Engineering microbes for tolerance to next-generation biofuels. Biotechnol Biofuels 4:32. doi:10.1186/1754-6834-4-32 CrossRef
  9. Fernandes P, Ferreira BS, Cabral JMS (2003) Solvent tolerance in bacteria: role of efflux pumps and cross-resistance with antibiotics. Int J Antimicrob Agents 22:211-16 CrossRef
  10. Gaida SM, Al-Hinai MA, Indurthi DC, Nicolaou SA, Papoutsakis ET (2013) Synthetic tolerance: three noncoding small RNAs, DsrA, ArcZ and RprA, acting supra-additively against acid stress. Nucleic Acids Res 41:8726-737. doi:10.1093/nar/gkt651 CrossRef
  11. G-Alegria E, Lopez I, Ruiz JI, Saenz J, Fernandez E, Zarazaga M, Dizy M, Torres C, Ruiz-Larrea F (2004) High tolerance of wild / Lactobacillus plantarum and / Oenococcus oeni strains to lyophilisation and stress environmental conditions of acid pH and ethanol. FEMS Microbiol Lett 230:53-1 CrossRef
  12. Gautam A, Rishi P, Tewari R (2011) UDP- / N-acetylglucosamine enolpyruvyl transferase as a potential target for antibacterial chemotherapy: recent developments. Appl Microbiol Biotechnol 92:211-25. doi:10.1007/s00253-011-3512-z CrossRef
  13. Gold RS, Meagher MM, Hutkins R, Conway T (1992) Ethanol tolerance and carbohydrate-metabolism in / Lactobacilli. J Ind Microbiol 10:45-4 CrossRef
  14. Goodarzi H, Bennett BD, Amini S, Reaves ML, Hottes AK, Rabinowitz JD, Tavazoie S (2010) Regulatory and metabolic rewiring during laboratory evolution of ethanol tolerance in / E. coli. Mol Syst Biol 6:378 CrossRef
  15. Gupta A, Singh R, Khare SK, Gupta MN (2006) A solvent tolerant isolate of / Enterobacter aerogenes. Bioresour Technol 97:99-03 CrossRef
  16. Hosokawa K, Park NH, Inaoka T, Itoh Y, Ochi K (2002) Streptomycin-resistant ( / rpsL) or rifampicin-resistant ( / rpoB) mutation in / Pseudomonas putida KH146-2 confers enhanced tolerance to organic chemicals. Environ Microbiol 4:703-12
  17. Kameyama Y, Kawabe Y, Ito A, Kamihira M (2010) An accumulative site-specific gene integration system using cre recombinase-mediated cassette exchange. Biotechnol Bioeng 105:1106-114. doi:10.1002/bit.22619
  18. Kleerebezem M, Boekhorst J, van Kranenburg R, Molenaar D, Kuipers OP, Leer R, Tarchini R, Peters SA, Sandbrink HM, Fiers MWEJ, Stiekema W, Lankhorst RMK, Bron PA, Hoffer SM, Groot MNN, Kerkhoven R, de Vries M, Ursing B, de Vos WM, Siezen RJ (2003) Complete genome sequence of / Lactobacillus plantarum WCFS1. Proc NatI Acad Sci U S A 100:1990-995 CrossRef
  19. Knoshaug EP, Zhang M (2009) Butanol tolerance in a selection of microorganisms. Appl Biochem Biotechnol 153:13-0 CrossRef
  20. Marquardt JL, Siegele DA, Kolter R, Walsh CT (1992) Cloning and sequencing of / Escherichia coli murZ and purification of its product, a UDP- / N-acetylglucosamine enolpyruvyl transferase. J Bacteriol 174:5748-752
  21. 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 12:307-31. doi:10.1016/j.ymben.2010.03.004 CrossRef
  22. 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. doi:10.1093/nar/gkr817 CrossRef
  23. Nicolaou SA, Gaida SM, Papoutsakis ET (2012) Exploring the combinatorial genomic space in / Escherichia coli for ethanol tolerance. Biotechnol J 7:1337-345. doi:10.1002/biot.201200227 CrossRef
  24. Ohta K, Beall DS, Mejia JP, Shanmugam KT, Ingram LO (1991) Genetic improvement of / Escherichia coli for ethanol production: chromosomal integration of / Zymomonas mobilis genes encoding pyruvate decarboxylase and alcohol dehydrogenase II. Appl Environ Microbiol 57:893-00
  25. Papoutsakis ET, Bi C, Nicolaou S (2011) Engineering complex microbial phenotypes with successive integrations of exogenous DNA (Siedna). USA Patent US2011300553-A1; WO2011153342-A2; WO2011153342-A3,
  26. Santos PM, Benndorf D, Sa-Correia I (2004) Insights into / Pseudomonas putida KT2440 response to phenol-induced stress by quantitative proteomics. Proteomics 4:2640-652 CrossRef
  27. Venkataramanan KP, Jones SW, McCormick KP, Kunjeti SG, Ralston MT, Meyers BC, Papoutsakis ET (2013) The Clostridium small RNome that responds to stress: the paradigm and importance of toxic metabolite stress in / C. acetobutylicum. BMC Genomics. 14 doi:10.1186/1471-2164-14-849
  28. Vollmer W, Blanot D, de Pedro MA (2008) Peptidoglycan structure and architecture. FEMS Microbiol Rev 32:149-67. doi:10.1111/j.1574-6976.2007.00094.x CrossRef
  29. Wilkins BM, Pritchard RH (1987) / Escherichia coli and / Salmonella typhimurium—cellular and molecular biology, Vol 1- - Neidhardt, Fc. Nature 330:707-08
  30. Woodruff LBA, Pandhal J, Ow SY, Karimpour-Fard A, Weiss SJ, Wright PC, Gill RT (2013) Genome-scale identification and characterization of ethanol tolerance genes in / Escherichia coli. Metab Eng 15:124-33. doi:10.1016/j.ymben.2012.10.007 CrossRef
  31. Zhou K, Zhou L, Lim Q, Zou R, Stephanopoulos G, Too HP (2011) Novel reference genes for quantifying transcriptional responses of / Escherichia coli to protein overexpression by quantitative PCR. BMC Mol Biol 12:18. doi:10.1186/1471-2199-12-18 CrossRef
  32. Zingaro KA, Papoutsakis ET (2012) Toward a semisynthetic stress response system to engineer microbial solvent tolerance. Mbio 3(5) doi:10.1128/mBio.00308-12
  33. Zingaro KA, Papoutsakis ET (2013) 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 15:196-05. doi:10.1016/j.ymben.2012.07.009
  34. Zingaro KA, Nicolaou SA, Papoutsakis ET (2013) Dissecting the assays to assess microbial tolerance to toxic chemicals in bioprocessing. Trends Biotechnol 31:643-53. doi:10.1016/j.tibtech.2013.08.005 CrossRef
  35. Zingaro KA, Nicolaou SA, Yuan Y, Papoutsakis ET (2014) Exploring the heterologous genomic space for building, stepwise, complex, multicomponent tolerance to toxic chemicals. ACS Synth Biol 3:476-86. doi:10.1021/sb400156v CrossRef
  
• 作者单位：Yongbo Yuan (1)
  Changhao Bi (1) (2)
  Sergios A. Nicolaou (1)
  Kyle A. Zingaro (1)
  Matthew Ralston (1)
  Eleftherios T. Papoutsakis (1)
  
  1. Department of Chemical Engineering & Delaware Biotechnology Institute, University of Delaware, 15 Innovation Way, Newark, DE, 19711, USA
  2. Tianjin Institute of Biotechnology, Chinese Academy of Sciences, Tianjin, China
  
• ISSN：1432-0614

文摘

A major challenge in producing chemicals and biofuels is to increase the tolerance of the host organism to toxic products or byproducts. An Escherichia coli strain with superior ethanol and more generally alcohol tolerance was identified by screening a library constructed by randomly integrating Lactobacillus plantarum genomic DNA fragments into the E. coli chromosome via Cre-lox recombination. Sequencing identified the inserted DNA fragment as the murA2 gene and its upstream intergenic 973-bp sequence, both coded on the negative genomic DNA strand. Overexpression of this murA2 gene and its upstream 973-bp sequence significantly enhanced ethanol tolerance in both E. coli EC100 and wild type E. coli MG1655 strains by 4.1-fold and 2.0-fold compared to control strains, respectively. Tolerance to n-butanol and i-butanol in E. coli MG1655 was increased by 1.85-fold and 1.91-fold, respectively. We show that the intergenic 973-bp sequence contains a native promoter for the murA2 gene along with a long 5-UTR (286?nt) on the negative strand, while a noncoding, small RNA, named MurA2S, is expressed off the positive strand. MurA2S is expressed in E. coli and may interact with murA2, but it does not affect murA2’s ability to enhance alcohol tolerance in E. coli. Overexpression of murA2 with its upstream region in the ethanologenic E. coli KO11 strain significantly improved ethanol production in cultures that simulate the industrial Melle-Boinot fermentation process.