Easy efficient HDR-based targeted knock-in in Saccharomyces cerevisiae genome using CRISPR-Cas9 system

References

• Hong KK, Nielsen J. Metabolic engineering of S. cerevisiae: a key cell factory platform for future biorefineries. Cell Mol Life Sci. 2012;69:2671–2690.
   PubMed Web of Science ®Google Scholar
• Buchholz K, Collins J. The roots—a short history of industrial microbiology and biotechnology. Appl Microbiol Biotechnol. 2013;97(2013):3747–3762.
   PubMedGoogle Scholar
• Štafa A, Žunar B, Pranklin A, et al. Novel approach in the construction of bioethanol-producing S. cerevisiae hybrids. Food Technol Biotechnol. 2019;57:5–16.
   PubMed Web of Science ®Google Scholar
• Zunar B, Stafa A, Zandona A, et al. Novel approach in developing S. cerevisiae hybrid bioethanol producers by mating of natural isolates having desirable traits. J Biotechnol. 2018;280:S89.
   Web of Science ®Google Scholar
• Narendranath NV, Thomas KC, Ingledew WM. Effects of acetic acid and lactic acid on the growth of S. cerevisiae in a minimal medium. J Ind Microbiol Biotechnol. 2001;26:171–177.
   PubMed Web of Science ®Google Scholar
• Ro DK, Paradise EM, Ouellet M, et al. Production of the antimalarial drug precursor artemisinic acid in engineered yeast. Nature. 2006;440:940–943.
   PubMed Web of Science ®Google Scholar
• Singh R, Chandel S, Ghosh A, et al. Application of CRISPR/cas system in the metabolic engineering of small molecules. Mol Biotechnol. 2021;63:459–476.
   PubMed Web of Science ®Google Scholar
• Parapouli M, Vasileiadis A, Afendra AS, et al. S. cerevisiae and its industrial applications. AIMS Microbial. 2020;6:1.
   PubMed Web of Science ®Google Scholar
• Uddin F, Rudin CM, Sen T. CRISPR gene therapy: applications, limitations, and implications for the future. FRONT ONCOL. 2020;10:1387.
   PubMed Web of Science ®Google Scholar
• Doudna JA, Charpentier E. The new frontier of genome engineering with CRISPR-Cas9. Sci. 2014;346:6213.
   Web of Science ®Google Scholar
• Hsu PD, Lander ES, Zhang F. Development and applications of CRISPR-Cas9 for genome engineering. Cell. 2014;157:1262–1278.
   PubMed Web of Science ®Google Scholar
• DiCarlo JE, Norville JE, Mali P, et al. Genome engineering in S. cerevisiae using CRISPR-Cas systems. Nucleic Acids Res. 2013;41:4336–4343.
   PubMed Web of Science ®Google Scholar
• Bahmed K, Seth A, Nitiss KC, et al. End-processing during non-homologous end-joining: a role for exonuclease 1. Nucleic Acids Res. 2011;39:970–978.
   PubMed Web of Science ®Google Scholar
• Hegde V, Klein H. Requirement for the SRS2 DNA helicase gene in non-homologous end joining in yeast. Nucleic Acids Res. 2000;28:2779–2783.
   PubMed Web of Science ®Google Scholar
• Herrmann G, Lindahl T, Schär P. S. cerevisiae LIF1: a function involved in DNA double‐strand break repair related to mammalian XRCC4. EMBO Rep. 1998;17:4188–4198.
   Google Scholar
• Bao Z, Xiao H, Liang J, et al. Homology-integrated CRISPR–Cas (HI-CRISPR) system for one-step multigene disruption in S. cerevisiae. ACS Synth Biol. 2015;4:585–594.
   PubMed Web of Science ®Google Scholar
• Horwitz AA, Walter JM, Schubert MG, et al. Efficient multiplexed integration of synergistic alleles and metabolic pathways in yeasts via CRISPR-Cas. Cell Syst. 2015;1:88–96.
   PubMed Web of Science ®Google Scholar
• Jakočiūnas T, Bonde I, Herrgård M, et al. Multiplex metabolic pathway engineering using CRISPR/Cas9 in S. cerevisiae. Metab Eng. 2015;28:213–222.
   PubMed Web of Science ®Google Scholar
• Ryan OW, Skerker JM, Maurer MJ, et al. Selection of chromosomal DNA libraries using a multiplex CRISPR system. Elife. 2014;3:e03703.
   PubMed Web of Science ®Google Scholar
• Laughery MF, Wyrick JJ. Simple CRISPR‐Cas9 genome editing in S. cerevisiae. Curr Protoc Mol Biol. 2019;129:e110.
   PubMedGoogle Scholar
• Laughery MF, Hunter T, Brown A, et al. New vectors for simple and streamlined CRISPR–Cas9 genome editing in S. cerevisiae. yeast. 2015;32:711–720.
   PubMed Web of Science ®Google Scholar
• Liu JJ, Kong II, Zhang GC, et al. C.V.Metabolic engineering of probiotic S. boulardii. Appl Environ Microbiol. 2016;82:2280–2287.
   PubMed Web of Science ®Google Scholar
• Lõoke M, Kristjuhan K, Kristjuhan A. Extraction of genomic DNA from yeasts for PCR-based applications. Biotechniques. 2011;50:325–328.
   PubMed Web of Science ®Google Scholar
• Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30(15):2114–2120.
   PubMed Web of Science ®Google Scholar
• Bağcı C, Patz S, Huson DH. DIAMOND+ MEGAN: fast and easy taxonomic and functional analysis of short and long microbiome sequences. Curr Protoc. 2021;1(3):e59.
   PubMedGoogle Scholar
• Huson DH, Beier S, Flade I, et al. MEGAN community edition-interactive exploration and analysis of large-scale microbiome sequencing data. PLoS Comput Biol. 2016;12(6):e1004957.
   PubMed Web of Science ®Google Scholar
• Buchfink B, Xie C, Huson DH. Fast and sensitive protein alignment using DIAMOND. Nat Methods. 2015;12(1):59–60.
   PubMed Web of Science ®Google Scholar
• Huson DH, Auch AF, Qi J, et al. MEGAN analysis of metagenomic data. Genome Res. 2007;17(3):377–386.
   PubMed Web of Science ®Google Scholar
• Gautam A, Felderhoff H, Bağci C, et al. Using annotree to get more assignments, faster, in DIAMOND+MEGAN microbiome analysis. mSystems. 2022;7(1):e01408–21.
   PubMed Web of Science ®Google Scholar
• Prjibelski A, Antipov D, Meleshko D, et al. Using SPAdes de novo assembler. Curr Protoc Bioinformatics. 2020;70(1):e102.
   PubMedGoogle Scholar
• Gurevich A, Saveliev V, Vyahhi N, et al. QUAST: quality assessment tool for genome assemblies. Bioinformatics. 2013;29(8):1072–1075.
   PubMed Web of Science ®Google Scholar
• Alonge M, Lebeigle L, Kirsche M, et al. Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing. Genome Biol. 2022;23:258. DOI:10.1186/s13059-022-02823-7
   Google Scholar
• Hommel U, Eberhard M, Kirschner K. Phosphoribosyl anthranilate isomerase catalyzes a reversible amadori reaction. Biochemistry. 1995;34:5429–5439.
   PubMed Web of Science ®Google Scholar
• Hampsey M. A review of phenotypes in S. cerevisiae. yeast. 1997;13:1099–1133.
   PubMed Web of Science ®Google Scholar
• Raschmanová H, Weninger A, Glieder A, et al. Implementing CRISPR-Cas technologies in conventional and non-conventional yeasts: current state and future prospects. Biotechnol Adv. 2018;36(2018):641–665.
   PubMedGoogle Scholar
• Cai P, Gao J, Zhou Y. CRISPR-mediated genome editing in non-conventional yeasts for biotechnological applications. Microb Cell Factories. 2019;18:1–12.
   PubMed Web of Science ®Google Scholar
• Komor AC, Badran AH, Liu DR. CRISPR-based technologies for the manipulation of eukaryotic genomes. Cell. 2017;168:20–36.
   PubMed Web of Science ®Google Scholar
• Ronda C, Maury J, Jakociunas T, et al. CrEdit: CRISPR mediated multi-loci gene integration in S. cerevisiae. Microb Cell Factories. 2015;14:, pp.1–11.
   PubMed Web of Science ®Google Scholar
• Vogl T, Gebbie L, Palfreyman RW, et al. Effect of plasmid design and type of integration event on recombinant protein expression in Pichia pastoris. Appl Environ Microbiol. 2018;84:e02712–17.
   PubMed Web of Science ®Google Scholar
• Souza-Moreira TM, Navarrete C, Chen X, et al. Screening of 2A peptides for polycistronic gene expression in yeast. FEMS Yeast Res. 2018;18:foy036.
   Web of Science ®Google Scholar
• Minskaia E, Nicholson J, Ryan MD. Optimisation of the foot-and-mouth disease virus 2A co-expression system for biomedical applications. BMC Biotechnol. 2013;13: 1–11.
   PubMed Web of Science ®Google Scholar
• Minskaia E, Luke GA. 2A-the” go-to” technology for transgene co-expression. Single Cell Biol. 2015.
   Google Scholar
• Unkles SE, Valiante V, Mattern DJ, et al. Synthetic biology tools for bioprospecting of natural products in eukaryotes. Chem Biol. 2014;21(2014):502–508.
   PubMedGoogle Scholar
• Kavšček M, Stražar M, Curk T, et al. yeast as a cell factory: current state and perspectives. Microb Cell Factories. 2015;14:1–10.
   PubMed Web of Science ®Google Scholar
• de Jong B, Siewers V, Nielsen J. Systems biology of yeast: enabling technology for development of cell factories for production of advanced biofuels. Curr Opin Biotechnol. 2012;23:624–630.
   PubMed Web of Science ®Google Scholar
• Zhou YJ, Kerkhoven EJ, Nielsen J. Barriers and opportunities in bio-based production of hydrocarbons. Nat Energy. 2018;3:925–935.
   Web of Science ®Google Scholar
• Braus GH. Aromatic amino acid biosynthesis in the yeast S. cerevisiae: a model system for the regulation of a eukaryotic biosynthetic pathway. Microbiol Rev. 1991;55:349–370.
   PubMedGoogle Scholar
• Leng G, Song K, Jamieson D. Watch out for your TRP1 marker: the effect of TRP1 gene on the growth at high and low temperatures in budding yeast. FEMS Microbiol Lett. 2016;363. DOI:10.1093/femsle/fnw093
   PubMed Web of Science ®Google Scholar
• Hamedi H, Misaghi A, Modarressi MH, et al. Generation of a uracil auxotroph strain of the probiotic yeast S. boulardii as a host for the recombinant protein production. Avicenna J Med Biotechnol. 2013;5:29.
   PubMedGoogle Scholar
• Hudson LE, Fasken MB, McDermott CD, et al. Functional heterologous protein expression by genetically engineered probiotic yeast S. boulardii. PloS one. 2014;9:e112660.
   PubMed Web of Science ®Google Scholar
• Fu Y, Foden JA, Khayter C, et al. High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells. Nat Biotechnol. 2013;31:822–826.
   PubMed Web of Science ®Google Scholar
• Ran FA, Hsu PD, Lin CY, et al. Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity. Cell. 2013;154:1380–1389.
   PubMed Web of Science ®Google Scholar
• Gibson DG, Benders GA, Andrews-Pfannkoch C, et al. Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome. Sci. 2008;319:1215–1220.
   PubMed Web of Science ®Google Scholar
• Shao Z, Zhao H, Zhao H. DNA assembler, an in vivo genetic method for rapid construction of biochemical pathways. Nucleic Acids Res. 2009;37:e16–e16.
   PubMed Web of Science ®Google Scholar
• Shao Z, Zhao H. Construction and engineering of large biochemical pathways via DNA assembler. Methods Mol Biol. 2013;1073:85–106. DOI:10.1007/978-1-62703-625-2_9
   Google Scholar
• Eckert‐Boulet N, Pedersen ML, Krogh BO, et al. Optimization of ordered plasmid assembly by gap repair in S. cerevisiae. yeast. 2012;29:323–334.
   PubMed Web of Science ®Google Scholar
• Zhang Z, Moo-Young M, Chisti Y. Plasmid stability in recombinant S. cerevisiae. Biotechnol Adv. 1996;14:401–435.
   PubMed Web of Science ®Google Scholar
• Özaydın B, Burd H, Lee TS, et al. Carotenoid-based phenotypic screen of the yeast deletion collection reveals new genes with roles in isoprenoid production. Metab Eng. 2013;15:174–183.
   PubMed Web of Science ®Google Scholar
• Storici F, Lewis LK, Resnick MA. In vivo site-directed mutagenesis using oligonucleotides. Nat Biotechnol. 2001;19:773–776.
   PubMed Web of Science ®Google Scholar
• Storici F, Durham CL, Gordenin DA, et al. Chromosomal site-specific double-strand breaks are efficiently targeted for repair by oligonucleotides in yeast. Pnas. 2003;100:14994–14999.
   PubMed Web of Science ®Google Scholar
• Malcı K, Walls LE, Rios-Solis L. Multiplex genome engineering methods for yeast cell factory development. Front Bioeng Biotechnol. 2020;8:1264.
   Web of Science ®Google Scholar
• Hayden MS, Byers B. Minimal extent of homology required for completion of meiotic recombination in S. cerevisiae. Dev Genet. 1992;13:498–514.
   PubMedGoogle Scholar
• Guo X, Wang Y, Wu M, et al. Gene insertion in Saccharomyces cerevisiae using the CRISPR/Cas9 system. 3 Biotech. 2021; 11:90. DOI:10.1007/s13205-021-02648-4
   PubMedGoogle Scholar
• Hou S, Qin Q, Dai J. Wicket: a versatile tool for the integration and optimization of exogenous pathways in Saccharomyces cerevisiae. ACS Synth Biol. 2018;7(3):782–788.
   PubMed Web of Science ®Google Scholar
• Hayashi A, Tanaka K. Short-homology-mediated CRISPR/Cas9-based method for genome editing in fission yeast. G3: genes. Genomes, Genetics. 2019;9:1153–1163.
   Web of Science ®Google Scholar
• Rubnitz J, Subramani S. The minimum amount of homology required for homologous recombination in mammalian cells. Mol Cell Biol. 1984;4:2253–2258.
   PubMed Web of Science ®Google Scholar
• Meng J, Qiu Y, Shi S. CRISPR/Cas9 systems for the development of S. cerevisiae cell factories. Front Bioeng Biotechnol. 2020;8. DOI:10.3389/fbioe.2020.594347
   Web of Science ®Google Scholar
• Ryan MD, King AM, Thomas GP. Cleavage of foot-and-mouth disease virus polyprotein is mediated by residues located within a 19 amino acid sequence. J Gen Virol. 1991;72:2727–2732.
   PubMed Web of Science ®Google Scholar
• Ryan MD, Drew J. Foot‐and‐mouth disease virus 2A oligopeptide mediated cleavage of an artificial polyprotein. EMBO Rep. 1994;13:928–933.
   Google Scholar
• Ryan MD, Donnelly M, Lewis A, et al. A model for nonstoichiometric, cotranslational protein scission in eukaryotic ribosomes. Bioorg Chem. 1999;27:55–79.
   Web of Science ®Google Scholar
• Provost E, Rhee J, Leach SD. Viral 2A peptides allow expression of multiple proteins from a single ORF in transgenic zebrafish embryos. Gen. 2007;45:625–629.
   Google Scholar
• Halpin C, Cooke SE, Barakate A, et al. Self‐processing 2A‐polyproteins–a system for co‐ordinate expression of multiple proteins in transgenic plants. Plant J. 1999;17:453–459.
   PubMed Web of Science ®Google Scholar
• Doronina VA, Wu C, de Felipe P, et al. Site-specific release of nascent chains from ribosomes at a sense codon. Mol Cell Biol. 2008;28:4227–4239.
   PubMed Web of Science ®Google Scholar
• Luke GA, de Felipe P, Lukashev A, et al. Occurrence, function and evolutionary origins of ‘2A-like’sequences in virus genomes. J Gen Virol. 2008;89:1036.
   PubMed Web of Science ®Google Scholar
• Kim JH, Lee SR, Li LH, et al. High cleavage efficiency of a 2A peptide derived from porcine teschovirus-1 in human cell lines, zebrafish and mice. PloS one. 2011;6:e18556.
   PubMed Web of Science ®Google Scholar
• Gao SY, Jack MM, O’Neill C. Towards optimising the production of and expression from polycistronic vectors in embryonic stem cells. PloS one. 2012;7:e48668.
   PubMed Web of Science ®Google Scholar
• Sharma P, Yan F, Doronina VA, et al. 2A peptides provide distinct solutions to driving stop-carry on translational recoding. Nucleic Acids Res. 2012;40(2012):3143–3151.
   PubMedGoogle Scholar
• Odon V, Luke GA, Roulston C, et al. APE-type non-LTR retrotransposons of multicellular organisms encode virus-like 2A oligopeptide sequences, which mediate translational recoding during protein synthesis. Mol Biol Evol. 2013;30(2013):1955–1965.
   PubMedGoogle Scholar
• Daniels RW, Rossano AJ, Macleod GT, et al. Expression of multiple transgenes from a single construct using viral 2A peptides in Drosophila. PloS one. 2014;9(2014):e100637.
   PubMedGoogle Scholar
• Geier M, Fauland P, Vogl T, et al. Compact multi-enzyme pathways in P. pastoris. ChemComm. 2015;51:1643–1646.
   PubMed Web of Science ®Google Scholar
• Roulston C, Luke GA, de Felipe P, et al. ‘2A‐Like’Signal sequences mediating translational recoding: a novel form of dual protein targeting. Traffic. 2016;17:923–939.
   PubMed Web of Science ®Google Scholar