Optimization of a yeast RNA interference system for controlling gene expression and enabling rapid metabolic engineering

ACS Synthetic Biology

Volumn 3, Issue 5, 2014, Pages 307-313

  Crook, Nathan C ^a   Schmitz, Alexander C ^a   Alper, Hal S ^a,b  

^a The University of Texas at Austin   (United States)

^b UNIVERSITY OF TEXAS AT AUSTIN   (United States)

Author keywords

gene knockdown; itaconic acid; metabolic engineering; RNA interference; yeast

Indexed keywords

ACONITIC ACID; ARGONAUTE PROTEIN; COMPLEMENTARY RNA; DICER; DOUBLE STRANDED RNA; ITACONIC ACID; SHORT HAIRPIN RNA; SMALL INTERFERING RNA; YELLOW FLUORESCENT PROTEIN; SUCCINIC ACID DERIVATIVE;

ARTICLE; AUXOTROPHY; CONTROLLED STUDY; DOWN REGULATION; FUNGAL GENE; FUNGAL STRAIN; FUNGUS GROWTH; GENE SILENCING; GROWTH RATE; HETEROLOGOUS EXPRESSION; METABOLIC ENGINEERING; MOLECULAR CLONING; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN EXPRESSION; PROTEIN SECONDARY STRUCTURE; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA INTERFERENCE; SACCHAROMYCES CEREVISIAE; CHEMISTRY; CONFORMATION; ESCHERICHIA COLI; GENE EXPRESSION; GENETICS; METABOLISM; PROCEDURES; SYNTHETIC BIOLOGY;

ESCHERICHIA COLI; GENE EXPRESSION; GENE KNOCKDOWN TECHNIQUES; METABOLIC ENGINEERING; NUCLEIC ACID CONFORMATION; RNA INTERFERENCE; RNA, SMALL INTERFERING; SACCHAROMYCES CEREVISIAE; SUCCINATES; SYNTHETIC BIOLOGY;

EID: 84900873278     PISSN: None     EISSN: 21615063     Source Type: Journal    
DOI: 10.1021/sb4001432     Document Type: Article

References (28)

1. Curran, K. A., Leavitt, J. M., Karim, A. S., and Alper, H. S. (2013) Metabolic engineering of muconic acid production in Saccharomyces cerevisiae Metab. Eng. 15, 55-66
2. Alper, H., Miyaoku, K., and Stephanopoulos, G. (2005) Construction of lycopene-overproducing E. coli strains by combining systematic and combinatorial gene knockout targets Nat. Biotechnol. 23, 612-616
3. Yim, H., Haselbeck, R., Niu, W., Pujol-Baxley, C., Burgard, A., Boldt, J., Khandurina, J., Trawick, J. D., Osterhout, R. E., Stephen, R., Estadilla, J., Teisan, S., Schreyer, H. B., Andrae, S., Yang, T. H., Lee, S. Y., Burk, M. J., and Van Dien, S. (2011) Metabolic engineering of Escherichia coli for direct production of 1,4-butanediol Nat. Chem. Biol. 7, 445-452
4. Atsumi, S., Cann, A. F., Connor, M. R., Shen, C. R., Smith, K. M., Brynildsen, M. P., Chou, K. J., Hanai, T., and Liao, J. C. (2008) Metabolic engineering of Escherichia coli for 1-butanol production Metab. Eng. 10, 305-311
5. Liu, L., Redden, H., and Alper, H. S. (2013) Frontiers of yeast metabolic engineering: diversifying beyond ethanol and Saccharomyces Curr. Opin. Biotechnol. 24, 1023-1030
6. Westfall, P. J., Pitera, D. J., Lenihan, J. R., Eng, D., Woolard, F. X., Regentin, R., Horning, T., Tsuruta, H., Melis, D. J., Owens, A., Fickes, S., Diola, D., Benjamin, K. R., Keasling, J. D., Leavell, M. D., McPhee, D. J., Renninger, N. S., Newman, J. D., and Paddon, C. J. (2012) Production of amorphadiene in yeast, and its conversion to dihydroartemisinic acid, precursor to the antimalarial agent artemisinin Proc. Natl. Acad. Sci. U. S. A. 10.1073/pnas.1110740109
7. Na, D., Yoo, S. M., Chung, H., Park, H., Park, J. H., and Lee, S. Y. (2013) Metabolic engineering of Escherichia coli using synthetic small regulatory RNAs Nat. Biotechnol. 31, 170-174
8. Tomari, Y. and Zamore, P. D. (2005) Perspective: machines for RNAi Genes Dev. 19, 517-529
9. Soutschek, J., Akinc, A., Bramlage, B., Charisse, K., Constien, R., Donoghue, M., Elbashir, S., Geick, A., Hadwiger, P., Harborth, J., John, M., Kesavan, V., Lavine, G., Pandey, R. K., Racie, T., Rajeev, K. G., Rohl, I., Toudjarska, I., Wang, G., Wuschko, S., Bumcrot, D., Koteliansky, V., Limmer, S., Manoharan, M., and Vornlocher, H. P. (2004) Therapeutic silencing of an endogenous gene by systemic administration of modified siRNAs Nature 432, 173-178
10. Dietzl, G., Chen, D., Schnorrer, F., Su, K. C., Barinova, Y., Fellner, M., Gasser, B., Kinsey, K., Oppel, S., Scheiblauer, S., Couto, A., Marra, V., Keleman, K., and Dickson, B. J. (2007) A genome-wide transgenic RNAi library for conditional gene inactivation in Drosophila Nature 448, 151-U151
11. Kamath, R. S., Fraser, A. G., Dong, Y., Poulin, G., Durbin, R., Gotta, M., Kanapin, A., Le Bot, N., Moreno, S., Sohrmann, M., Welchman, D. P., Zipperlen, P., and Ahringer, J. (2003) Systematic functional analysis of the Caenorhabditis elegans genome using RNAi Nature 421, 231-237
12. Chuang, C. F. and Meyerowitz, E. M. (2000) Specific and heritable genetic interference by double-stranded RNA in Arabidopsis thaliana Proc. Natl. Acad. Sci. U. S. A. 97, 4985-4990
13. Mansoor, S., Amin, I., Hussain, M., Zafar, Y., and Briddon, R. W. (2006) Engineering novel traits in plants through RNA interference Trends Plant Sci. 11, 559-565
14. Drinnenberg, I. A., Weinberg, D. E., Xie, K. T., Mower, J. P., Wolfe, K. H., Fink, G. R., and Bartel, D. P. (2009) RNAi in budding yeast Science 326, 544-550
15. Werpy, T. and Peterson, G. (2004) Top Value Added Chemicals from Biomass, U.S. Department of Energy, Washington D.C.
16. Hegemann, J. H. and Heick, S. B. (2011) Delete and repeat: a comprehensive toolkit for sequential gene knockout in the budding yeast Saccharomyces cerevisiae Methods Mol. Biol. 765, 189-206
17. Hooshangi, S., Thiberge, S., and Weiss, R. (2005) Ultrasensitivity and noise propagation in a synthetic transcriptional cascade Proc. Natl. Acad. Sci. U. S. A. 102, 3581-3586
18. Friedland, A. E., Lu, T. K., Wang, X., Shi, D., Church, G., and Collins, J. J. (2009) Synthetic gene networks that count Science 324, 1199-1202
19. Shirane, D., Sugao, K., Namiki, S., Tanabe, M., Iino, M., and Hirose, K. (2004) Enzymatic production of RNAi libraries from cDNAs Nat. Genet. 36, 190-196
20. Johnson, E. and Srivastava, R. (2013) Volatility in mRNA secondary structure as a design principle for antisense Nucleic Acids Res. 41, e43
21. Sledz, C. A., Holko, M., de Veer, M. J., Silverman, R. H., and Williams, B. R. G. (2003) Activation of the interferon system by short-interfering RNAs Nat. Cell Biol. 5, 834-839
22. Huang, L., Jin, J., Deighan, P., Kiner, E., McReynolds, L., and Lieberman, J. (2013) Efficient and specific gene knockdown by small interfering RNAs produced in bacteria Nat. Biotechnol. 31, 350-356
23. Voineagu, I., Narayanan, V., Lobachev, K. S., and Mirkin, S. M. (2008) Replication stalling at unstable inverted repeats: Interplay between DNA hairpins and fork stabilizing proteins Proc. Natl. Acad. Sci. U. S. A. 105, 9936-9941
24. Yoshimatsu, T. and Nagawa, F. (1989) Control of gene expression by artificial introns in Saccharomyces cerevisiae Science 244, 1346-1348
25. Blazeck, J., Miller, J., Pan, A., Gengler, J., Holden, C., Jamoussi, M., and Alper, H. S. (2013) Metabolic engineering of Saccharomyces cerevisiae for itaconic acid production. In Revision, Biotechnology and Bioengineering.
26. Elowitz, M. B. and Leibler, S. (2000) A synthetic oscillatory network of transcriptional regulators Nature 403, 335-338
27. Sambrook, J. and Russell, D. W. (2001) Molecular Cloning: A Laboratory Manual, 3 rd ed., Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.
28. Shao, Z., Zhao, H., and Zhao, H. (2009) DNA assembler, an in vivo genetic method for rapid construction of biochemical pathways Nucleic Acids Res. 37, e16