Generic placeholder image

Current Drug Targets


ISSN (Print): 1389-4501
ISSN (Online): 1873-5592

Review Article

Saccharomyces cerevisiae (Baker’s Yeast) as an Interfering RNA Expression and Delivery System

Author(s): Molly Duman-Scheel*

Volume 20 , Issue 9 , 2019

Page: [942 - 952] Pages: 11

DOI: 10.2174/1389450120666181126123538


The broad application of RNA interference for disease prevention is dependent upon the production of dsRNA in an economically feasible, scalable, and sustainable fashion, as well as the identification of safe and effective methods for RNA delivery. Current research has sparked interest in the use of Saccharomyces cerevisiae for these applications. This review examines the potential for commercial development of yeast interfering RNA expression and delivery systems. S. cerevisiae is a genetic model organism that lacks a functional RNA interference system, which may make it an ideal system for expression and accumulation of high levels of recombinant interfering RNA. Moreover, recent studies in a variety of eukaryotic species suggest that this microbe may be an excellent and safe system for interfering RNA delivery. Key areas for further research and development include optimization of interfering RNA expression in S. cerevisiae, industrial-sized scaling of recombinant yeast cultures in which interfering RNA molecules are expressed, the development of methods for largescale drying of yeast that preserve interfering RNA integrity, and identification of encapsulating agents that promote yeast stability in various environmental conditions. The genetic tractability of S. cerevisiae and a long history of using this microbe in both the food and pharmaceutical industry will facilitate further development of this promising new technology, which has many potential applications of medical importance.

Keywords: RNAi, shRNA, gene therapy, Aedes aegypti, Anopheles gambiae, mosquito, biopharmaceutical, bioengineering.

Graphical Abstract
Moazed D. Molecular biology. Rejoice--RNAi for yeast. Sci 2009; 326(5952): 533-4.
Roohvand F, Shokri M, Abdollahpour-Alitappeh M, Ehsani P. Biomedical applications of yeast- a patent view, part one: yeasts as workhorses for the production of therapeutics and vaccines. Expert Opin Ther Pat 2017; 27(8): 929-51.
Drinnenberg IA, Weinberg DE, Xie KT, et al. RNAi in budding yeast. Science 2009; 326(5952): 544-50.
Malone CD, Hannon GJ. Small RNAs as guardians of the genome. Cell 2009; 136(4): 656-68.
Tomari Y, Zamore PD. Perspective: machines for RNAi. Genes Dev 2005; 19(5): 517-29.
Bartel DP. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 2004; 116(2): 281-97.
Ghildiyal M, Zamore PD. Small silencing RNAs: an expanding universe. Nat Rev Genet 2009; 10(2): 94-108.
Tam C, Wong JH, Cheung RCF, Zuo T, Ng TB. Therapeutic potentials of short interfering RNAs. Appl Microbiol Biotechnol 2017; 101(19): 7091-111.
Hapairai LK, Mysore K, Chen Y, et al. Lure-and-kill yeast interfering RNA larvicides targeting neural genes in the human disease vector mosquito Aedes aegypti. Sci Rep 2017; 7(1): 13223.
Mysore K, Hapairai LK, Sun L, et al. Yeast interfering RNA larvicides targeting neural genes induce high rates of Anopheles larval mortality. Malar J 2017; 16(1): 461.
LaMattina J. Big pharma's turn on rnai shows that new technologies don't guarantee R & amp; D Success. Forbes 2014.
Tiemann K, Rossi JJ. RNAi-based therapeutics-current status, challenges and prospects. EMBO Mol Med 2009; 1(3): 142-51.
Zhang L, Zhang T, Wang L, et al. In vivo targeted delivery of CD40 shRNA to mouse intestinal dendritic cells by oral administration of recombinant Sacchromyces cerevisiae. Gene Ther 2014; 21(7): 709-14.
Murphy KA, Tabuloc CA, Cervantes KR, Chiu JC. Ingestion of genetically modified yeast symbiont reduces fitness of an insect pest via RNA interference. Sci Rep 2016; 6: 22587.
Crook NC, Schmitz AC, Alper HS. Optimization of a yeast RNA interference system for controlling gene expression and enabling rapid metabolic engineering. ACS Synth Biol 2014; 3(5): 307-13.
Si T, Luo Y, Bao Z, Zhao H. RNAi-assisted genome evolution in Saccharomyces cerevisiae for complex phenotype engineering. ACS Synth Biol 2015; 4(3): 283-91.
Crook N, Sun J, Morse N, Schmitz A, Alper HS. Identification of gene knockdown targets conferring enhanced isobutanol and 1-butanol tolerance to Saccharomyces cerevisiae using a tunable RNAi screening approach. Appl Microbiol Biotechnol 2016; 100(23): 10005-18.
Zhang J, Khan SA, Hasse C, et al. Pest control. Full crop protection from an insect pest by expression of long double-stranded RNAs in plastids. Sci 2015; 347(6225): 991-4.
Mewes HW, Albermann K, Bahr M, et al. Overview of the yeast genome. Nat 1997; 387(6632)(Suppl.): 7-65.
Wang G, Huang M, Nielsen J. Exploring the potential of Saccharomyces cerevisiae for biopharmaceutical protein production. Curr Opin Biotechnol 2017; 48: 77-84.
Meehl MA, Stadheim TA. Biopharmaceutical discovery and production in yeast. Curr Opin Biotechnol 2014; 30: 120-7.
Roeder A, Kirschning CJ, Rupec RA, Schaller M, Korting HC. Toll-like receptors and innate antifungal responses. Trends Microbiol 2004; 12(1): 44-9.
Banchereau J, Steinman RM. Dendritic cells and the control of immunity. Nat 1998; 392(6673): 245-52.
Palucka K, Banchereau J. Dendritic cells: A link between innate and adaptive immunity. J Clin Immunol 1999; 19(1): 12-25.
Qian C, Qian L, Yu Y, et al. Fas signal promotes the immunosuppressive function of regulatory dendritic cells via the ERK/beta-catenin pathway. J Biol Chem 2013; 288(39): 27825-35.
Blanquet S, Meunier JP, Minekus M, Marol-Bonnin S, Alric M. Recombinant Saccharomyces cerevisiae expressing P450 in artificial digestive systems: a model for biodetoxication in the human digestive environment. Appl Environ Microbiol 2003; 69(5): 2884-92.
Stubbs AC, Martin KS, Coeshott C, et al. Whole recombinant yeast vaccine activates dendritic cells and elicits protective cell-mediated immunity. Nat Med 2001; 7(5): 625-9.
Franzusoff A, Duke RC, King TH, Lu Y, Rodell TC. Yeasts encoding tumour antigens in cancer immunotherapy. Expert Opin Biol Ther 2005; 5(4): 565-75.
Howland SW, Tsuji T, Gnjatic S, et al. Inducing efficient crosspriming using antigen-coated yeast particles. J Immunother (Hagerstown, Md : 1997) 2008; 31(7): 607-19.
Walch B, Breinig T, Schmitt MJ, Breinig F. Delivery of functional DNA and messenger RNA to mammalian phagocytic cells by recombinant yeast. Gene Ther 2012; 19(3): 237-45.
Haller AA, Lauer GM, King TH, et al. Whole recombinant yeast-based immunotherapy induces potent T cell responses targeting HCV NS3 and core proteins. Vaccine 2007; 25(8): 1452-63.
Wansley EK, Chakraborty M, Hance KW, et al. Vaccination with a recombinant Saccharomyces cerevisiae expressing a tumor antigen breaks immune tolerance and elicits therapeutic antitumor responses. Clin Cancer Res 2008; 14(13): 4316-25.
Lutgens E, Daemen MJ. CD40-CD40L interactions in atherosclerosis. Trends Cardiovasc Med 2002; 12(1): 27-32.
Ma DY, Clark EA. The role of CD40 and CD154/CD40L in dendritic cells. Semin Immunol 2009; 21(5): 265-72.
Silva JM, Li MZ, Chang K, et al. Second-generation shRNA libraries covering the mouse and human genomes. Nat Genet 2005; 37(11): 1281-8.
Paddison PJ, Silva JM, Conklin DS, et al. A resource for large-scale RNA-interference-based screens in mammals. Nat 2004; 428(6981): 427-31.
Zeng Y, Wagner EJ, Cullen BR. Both natural and designed micro RNAs can inhibit the expression of cognate mRNAs when expressed in human cells. Mol Cell 2002; 9(6): 1327-33.
Xu K, Liu Z, Zhang L, Zhang T, Zhang Z. siRNA in vivo-targeted delivery to murine dendritic cells by oral administration of recombinant yeast. Methods Mol Biol 2016; 1364: 165-81.
WHO. World Malaria Report 2016. Geneva: World Health Organization 2016.
CDC. Surveillance and control of Aedes aegypti and Aedes albopictus. 2016: Available from: [Accessed January, 2016].
CDC. Zika virus. 2018: Available from: index.html [Accessed January 2018].
CDC. Dengue. 2018: Available from: index.html [Accessed January 2018].
WHO. Dengue guidelines for diagnosis, treatment, prevention and control: new edition. Geneva: World Health Organization 2009.
WHO. Larval source management: a supplementary measure for malaria vector control: an operational manual. Geneva: World Health Organization 2013.
Mysore K, Flannery EM, Tomchaney M, Severson DW, Duman-Scheel M. Disruption of Aedes aegypti olfactory system development through chitosan/siRNA nanoparticle targeting of semaphorin-1a. PLoS Negl Trop Dis 2013; 7(5): e2215.
Mysore K, Andrews E, Li P, Duman-Scheel M. Chitosan/siRNA nanoparticle targeting demonstrates a requirement for single-minded during larval and pupal olfactory system development of the vector mosquito Aedes aegypti. BMC Dev Biol 2014; 14: 9.
Mysore K, Flannery E, Leming MT, et al. Role of semaphorin-1a in the developing visual system of the disease vector mosquito Aedes aegypti. Dev Dyn 2014; 243(11): 1457-69.
Mysore K, Sun L, Tomchaney M, et al. siRNA-mediated silencing of doublesex during female development of the dengue vector mosquito Aedes aegypti. PLoS Negl Trop Dis 2015; 9(11): e0004213.
Mumberg D, Muller R, Funk M. Yeast vectors for the controlled expression of heterologous proteins in different genetic backgrounds. Gene 1995; 156(1): 119-22.
Fire A, Xu S, Montgomery MK, et al. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nat 1998; 391(6669): 806-11.
Timmons L, Court DL, Fire A. Ingestion of bacterially expressed dsRNAs can produce specific and potent genetic interference in Caenorhabditis elegans. Gene 2001; 263(1-2): 103-12.
Tenllado F, Martinez-Garcia B, Vargas M, Diaz-Ruiz JR. Crude extracts of bacterially expressed dsRNA can be used to protect plants against virus infections. BMC Biotechnol 2003; 3: 3.
Huang L, Jin J, Deighan P, et al. Efficient and specific gene knockdown by small interfering RNAs produced in bacteria. Nat Biotechnol 2013; 31(4): 350-6.
Huang L, Lieberman J. Production of highly potent recombinant siRNAs in Escherichia coli. Nat Protoc 2013; 8(12): 2325-36.
Kaur G, Cheung HC, Xu W, et al. Milligram scale production of potent recombinant small interfering RNAs in Escherichia coli. Biotechnol Bioeng 2018; 115(9): 2280-91.
Chanfreau G, Legrain P, Jacquier A. Yeast RNase III as a key processing enzyme in small nucleolar RNAs metabolism. J Mol Biol 1998; 284(4): 975-88.
Lamontagne B, Tremblay A, Abou Elela S. The N-terminal domain that distinguishes yeast from bacterial RNase III contains a dimerization signal required for efficient double-stranded RNA cleavage. Mol Cell Biol 2000; 20(4): 1104-15.
Gaudin C, Ghazal G, Yoshizawa S, Elela SA, Fourmy D. Structure of an AAGU tetraloop and its contribution to substrate selection by yeast RNase III. J Mol Biol 2006; 363(2): 322-31.
Lamontagne B, Hannoush RN, Damha MJ, Abou Elela S. Molecular requirements for duplex recognition and cleavage by eukaryotic RNase III: discovery of an RNA-dependent DNA cleavage activity of yeast Rnt1p. J Mol Biol 2004; 338(2): 401-18.
Sam M, Henras AK, Chanfreau G. A conserved major groove antideterminant for Saccharomyces cerevisiae RNase III recognition. Biochem 2005; 44(11): 4181-7.
Wu H, Henras A, Chanfreau G, Feigon J. Structural basis for recognition of the AGNN tetraloop RNA fold by the double-stranded RNA-binding domain of Rnt1p RNase III. Proc Natl Acad Sci USA 2004; 101(22): 8307-12.
Nielsen J. Production of biopharmaceutical proteins by yeast: advances through metabolic engineering. Bioengin 2013; 4(4): 207-11.
Ardiani A, Higgins JP, Hodge JW. Vaccines based on whole recombinant Saccharomyces cerevisiae cells. FEMS Yeast Res 2010; 10(8): 1060-9.
Chubukov V, Mukhopadhyay A, Petzold CJ, Keasling JD, Martin HG. Synthetic and systems biology for microbial production of commodity chemicals. NPJ Syst Biol Appl 2016; 2: 16009.
Baeshen NA, Baeshen MN, Sheikh A, et al. Cell factories for insulin production. Microb Cell Fact 2014; 13: 141.
Voineagu I, Narayanan V, Lobachev KS, Mirkin SM. Replication stalling at unstable inverted repeats: interplay between DNA hairpins and fork stabilizing proteins. Proc Natl Acad Sci USA 2008; 105(29): 9936-41.
Yoshimatsu T, Nagawa F. Control of gene expression by artificial introns in Saccharomyces cerevisiae. Sci 1989; 244(4910): 1346-8.
Kim H, Yoo SJ, Kang HA. Yeast synthetic biology for the production of recombinant therapeutic proteins. FEMS Yeast Res 2015; 15(1): 1-16.
Fang F, Salmon K, Shen MW, et al. A vector set for systematic metabolic engineering in Saccharomyces cerevisiae. Yeast (Chichester, England) 2011; 28(2): 123-36.
Papapetridis I, Goudriaan M, Vazquez Vitali M, et al. Optimizing anaerobic growth rate and fermentation kinetics in Saccharomyces cerevisiae strains expressing Calvin-cycle enzymes for improved ethanol yield. Biotechnol Biofuels 2018; 11: 17.
van den Brink J, Akeroyd M, van der Hoeven R, et al. Energetic limits to metabolic flexibility: responses of Saccharomyces cerevisiae to glucose-galactose transitions. Microbiology (Reading, England) 2009; 155(Pt 4): 1340-50.
Guadalupe-Medina V, Wisselink HW, Luttik MA, et al. Carbon dioxide fixation by Calvin-Cycle enzymes improves ethanol yield in yeast. Biotechnol Biofuels 2013; 6(1): 125.
Takors R. Scale-up of microbial processes: impacts, tools and open questions. J Biotechnol 2012; 160(1-2): 3-9.
Nicula AN, Nicula AT, Socaciu C, Du Breucq P. Application of advanced drying technologies for obtaining bioactive beer. Bulletin UASVM Agriculture 2009; 66(2): 581-90.
Bond C. Freeze drying of yeast cultures. Methods Mol Biol (Clifton, NJ) 2007; 368: 99-107.
Chandralekha A, Tavanandi AH, Amrutha N, et al. Encapsulation of yeast (Saccharomyces cereviciae) by spray drying for extension of shelf life. Dry Technol 2016; 34(11): 1307-18.
Sultana A, Miyamoto A, Hy QL, et al. Microencapsulation of flavors by spray drying using Saccharomyces cerevisiae. J Food Eng 2017; 199: 36-41.
Lakkis JM. Encapsulation and controlled release technologies in food systems. Oxford, U.K.: Blackwell Publishing 2007.
Ghorbani-Choboghlo H, Zahraei-Salehi T, Ashrafi-Helan J, et al. Microencapsulation of Saccharomyces cerevisiae and its evaluation to protect in simulated gastric conditions. Iran J Microbiol 2015; 7(6): 338-42.
Graff S, Hussain S, Chaumeil JC, Charrueau C. Increased intestinal delivery of viable Saccharomyces boulardii by encapsulation in microspheres. Pharm Res 2008; 25(6): 1290-6.
Song H, Yu W, Liu X, Ma X. Improved probiotic viability in stress environments with post-culture of alginate-chitosan microencapsulated low density cells. Carbohydr Polym 2014; 108: 10-6.
Zhang X, Zhang J, Zhu KY. Chitosan/double-stranded RNA nanoparticle-mediated RNA interference to silence chitin synthase genes through larval feeding in the African malaria mosquito (Anopheles gambiae). Insect Mol Biol 2010; 19(5): 683-93.
Zhang X, Mysore K, Flannery E, et al. Chitosan/interfering RNA nanoparticle mediated gene silencing in disease vector mosquito larvae. J Vis Exp 2015(97).
Jantzen M, Gopel A, Beermann C. Direct spray drying and microencapsulation of probiotic Lactobacillus reuteri from slurry fermentation with whey. J Appl Microbiol 2013; 115(4): 1029-36.

© 2022 Bentham Science Publishers | Privacy Policy