Abstract
We describe a new way to trigger mRNA degradation in Saccharomyces cerevisiae synthetic gene circuits. Our method demands to modify either the 5′- or the 3′-UTR that flanks a target gene with elements from the pre-crRNA of type V Cas12a proteins and expresses a DNase-deficient Cas12a (dCas12a). dCas12a recognizes and cleaves the pre-crRNA motifs on mRNA sequences. Our tool does not require complex engineering operations and permits an efficient control of protein expression via mRNA degradation.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Parker R, Song H (2004) The enzymes and control of eukaryotic mRNA turnover. Nat Struct Mol Biol 11(2):121–127. https://doi.org/10.1038/nsmb724
Isaacs FJ, Dwyer DJ, Collins JJ (2006) RNA synthetic biology. Nat Biotechnol 24(5):545–554. https://doi.org/10.1038/nbt1208
Wang Y, Wang Z, Tanaka Hall TM (2013) Engineered proteins with Pumilio/fem-3 mRNA binding factor scaffold to manipulate RNA metabolism. FEBS J 280(16):3755–3767. https://doi.org/10.1111/febs.12367
Ahringer J, Kimble J (1991) Control of the sperm–oocyte switch in Caenorhabditis elegans hermaphrodites by the fem-3 3′ untranslated region. Nature 349(6307):346–348. https://doi.org/10.1038/349346a0
Ohrt T, Merkle D, Birkenfeld K, Echeverri CJ, Schwille P (2006) In situ fluorescence analysis demonstrates active siRNA exclusion from the nucleus by Exportin 5. Nucleic Acids Res 34(5):1369–1380. https://doi.org/10.1093/nar/gkl001
He L, Hannon GJ (2004) MicroRNAs: small RNAs with a big role in gene regulation. Nat Rev Genet 5(7):522–531. https://doi.org/10.1038/nrg1379
Ge H, Marchisio MA (2021) Aptamers, riboswitches, and ribozymes in S. cerevisiae synthetic biology. Life (Basel) 11(3). https://doi.org/10.3390/life11030248
Qi L, Haurwitz RE, Shao W, Doudna JA, Arkin AP (2012) RNA processing enables predictable programming of gene expression. Nat Biotechnol 30(10):1002–1006. https://doi.org/10.1038/nbt.2355
Borchardt EK, Vandoros LA, Huang M, Lackey PE, Marzluff WF, Asokan A (2015) Controlling mRNA stability and translation with the CRISPR endoribonuclease Csy4. RNA 21(11):1921–1930. https://doi.org/10.1261/rna.051227.115
Tang X, Zheng X, Qi Y, Zhang D, Cheng Y, Tang A, Voytas DF, Zhang Y (2016) A single transcript CRISPR-Cas9 system for efficient genome editing in plants. Mol Plant 9(7):1088–1091. https://doi.org/10.1016/j.molp.2016.05.001
Fonfara I, Richter H, Bratovic M, Le Rhun A, Charpentier E (2016) The CRISPR-associated DNA-cleaving enzyme Cpf1 also processes precursor CRISPR RNA. Nature 532(7600):517–521. https://doi.org/10.1038/nature17945
Yu L, Marchisio MA (2021) Saccharomyces cerevisiae synthetic transcriptional networks harnessing dCas12a and type V-A anti-CRISPR proteins. ACS Synth Biol 10(4):870–883. https://doi.org/10.1021/acssynbio.1c00006
Campa CC, Weisbach NR, Santinha AJ, Incarnato D, Platt RJ (2019) Multiplexed genome engineering by Cas12a and CRISPR arrays encoded on single transcripts. Nat Methods 16(9):887–893. https://doi.org/10.1038/s41592-019-0508-6
Kempton HR, Goudy LE, Love KS, Qi LS (2020) Multiple input sensing and signal integration using a split Cas12a system. Mol Cell. https://doi.org/10.1016/j.molcel.2020.01.016
Kleinstiver BP, Sousa AA, Walton RT, Tak YE, Hsu JY, Clement K, Welch MM, Horng JE, Malagon-Lopez J, Scarfò I, Maus MV, Pinello L, Aryee MJ, Joung JK (2019) Engineered CRISPR-Cas12a variants with increased activities and improved targeting ranges for gene, epigenetic and base editing. Nat Biotechnol 37(3):276–282. https://doi.org/10.1038/s41587-018-0011-0
Yu L, Marchisio MA (2023) CRISPR-associated type V proteins as a tool for controlling mRNA stability in S. cerevisiae synthetic gene circuits. Nucleic Acids Res. https://doi.org/10.1093/nar/gkac1270
Chee MK, Haase SB (2012) New and redesigned pRS plasmid shuttle vectors for genetic manipulation of Saccharomyces cerevisiae. G3 (Bethesda, Md) 2(5):515–526. https://doi.org/10.1534/g3.111.001917
Hahn S, Hoar ET, Guarente L (1985) Each of three “TATA elements” specifies a subset of the transcription initiation sites at the CYC-1 promoter of Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 82(24):8562–8566. https://doi.org/10.1073/pnas.82.24.8562
Sheff MA, Thorn KS (2004) Optimized cassettes for fluorescent protein tagging in Saccharomyces cerevisiae. Yeast 21(8):661–670. https://doi.org/10.1002/yea.1130
Sambrook MRGJ (2018) Molecular cloning, 4th edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor
Gietz RD, Woods RA (2002) Transformation of yeast by lithium acetate/single-stranded carrier DNA/polyethylene glycol method. Methods Enzymol 350:87–96. https://doi.org/10.1016/s0076-6879(02)50957-5
Yu L, Zhang Y, Marchisio MA (2022) Gene digital circuits based on CRISPR-Cas systems and anti-CRISPR proteins. J Vis Exp (188). https://doi.org/10.3791/64539
Wang X, Tian X, Marchisio MA (2023) Logic circuits based on 2A peptide sequences in the yeast Saccharomyces cerevisiae. ACS Synth Biol 12(1):224–237. https://doi.org/10.1021/acssynbio.2c00506
Asemoloye MD, Marchisio MA (2022) Synthetic Saccharomyces cerevisiae tolerate and degrade highly pollutant complex hydrocarbon mixture. Ecotoxicol Environ Saf 241:113768. https://doi.org/10.1016/j.ecoenv.2022.113768
Lorenz R, Bernhart SH, Siederdissen CHZ, Tafer H, Flamm C, Stadler PF, Hofacker IL (2011) ViennaRNA Package 2.0. Algorithms Mol Biol 6:26. https://doi.org/10.1186/1748-7188-6-26
Bae S, Park J, Kim JS (2014) Cas-OFFinder: a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases. Bioinformatics (Oxford, England) 30(10):1473–1475. https://doi.org/10.1093/bioinformatics/btu048
Acknowledgments
We are grateful to the students of the Synthetic Biology lab for their help. We want to thank Xiangyang Zhang and Zhi Li for their assistance in the FACS experiments.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2024 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
Yu, L., Marchisio, M.A. (2024). dCas12a:Pre-crRNA: A New Tool to Induce mRNA Degradation in Saccharomyces cerevisiae Synthetic Gene Circuits. In: Braman, J.C. (eds) Synthetic Biology. Methods in Molecular Biology, vol 2760. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3658-9_6
Download citation
DOI: https://doi.org/10.1007/978-1-0716-3658-9_6
Published:
Publisher Name: Humana, New York, NY
Print ISBN: 978-1-0716-3657-2
Online ISBN: 978-1-0716-3658-9
eBook Packages: Springer Protocols