Reference
[1] Bracher, J. M., de Hulster, E., Koster, C. C., van den Broek, M., Daran, J. G., van Maris, A. J. A., & Pronk, J. T. (2017). Laboratory Evolution of a Biotin-Requiring Saccharomyces cerevisiae Strain for Full Biotin Prototrophy and Identification of Causal Mutations. Appl Environ Microbiol , 83, AEM.00892-17.
[2] Wang, M., Li, S., & Zhao, H. (2016). Design and engineering of intracellular-metabolite-sensing/regulation gene circuits in Saccharomyces cerevisiae. Biotechnol Bioeng , 113 , 206-215.
[3] Reyes, L. H., Gomez, J. M., & Kao, K. C. (2014). Improving carotenoids production in yeast via adaptive laboratory evolution.Metab Eng , 21 , 26-33.
[4] Kim, S. R., Skerker, J. M., Kang, W., Lesmana, A., Wei, N., Arkin, A. P., & Jin, Y. S. (2013). Rational and evolutionary engineering approaches uncover a small set of genetic changes efficient for rapid xylose fermentation in Saccharomyces cerevisiae. PLoS One , 8 , e57048.
[5] Patzschke, A., Steiger, M. G., Holz, C., Lang, C., Mattanovich, D., & Sauer, M. (2015). Enhanced glutathione production by evolutionary engineering of Saccharomyces cerevisiae strains. Biotechnol J ,10 , 1719-1726.
[6] Wang, G., Li, Q., Zhang, Z., Yin, X., Wang, B., & Yang, X. (2023). Recent progress in adaptive laboratory evolution of industrial microorganisms. J Ind Microbiol Biotechnol , 50 .
[7] Hashimoto, S., Ogura, M., Aritomi, K., Hoshida, H., Nishizawa, Y., & Akada, R. (2005). Isolation of auxotrophic mutants of diploid industrial yeast strains after UV mutagenesis. Appl Environ Microbiol , 71 , 312-319.
[8] Patnaik, R. (2008). Engineering complex phenotypes in industrial strains. Biotechnology Progress , 24 , 38-47.
[9] Jiang, G., Yang, Z., Wang, Y., Yao, M., Chen, Y., Xiao, W., & Yuan, Y. (2020). Enhanced astaxanthin production in yeast via combined mutagenesis and evolution. Biochemical Engineering Journal ,156, 107519.
[10] Roy, K. R., Smith, J. D., Vonesch, S. C., Lin, G., Tu, C. S., Lederer, A. R., Chu, A., Suresh, S., Nguyen, M., Horecka, J., Tripathi, A., Burnett, W. T., Morgan, M. A., Schulz, J., Orsley, K. M., Wei, W., Aiyar, R. S., Davis, R. W., Bankaitis, V. A., Haber, J. E., Salit, M. L., St Onge, R. P., & Steinmetz, L. M. (2018). Multiplexed precision genome editing with trackable genomic barcodes in yeast. Nat Biotechnol , 36 , 512-520.
[11] Bao, Z., HamediRad, M., Xue, P., Xiao, H., Tasan, I., Chao, R., Liang, J., & Zhao, H. (2018). Genome-scale engineering of Saccharomyces cerevisiae with single-nucleotide precision. Nat Biotechnol ,36 , 505-508.
[12] Froehlich, J. J., Uyar, B., Herzog, M., Theil, K., Glazar, P., Akalin, A., & Rajewsky, N. (2021). Parallel genetics of regulatory sequences using scalable genome editing in vivo. Cell Rep ,35 , 108988.
[13] Neggers, J. E., Jacquemyn, M., Dierckx, T., Kleinstiver, B. P., Thibaut, H. J., & Daelemans, D. (2021). enAsCas12a Enables CRISPR-Directed Evolution to Screen for Functional Drug Resistance Mutations in Sequences Inaccessible to SpCas9. Mol Ther ,29 , 208-224.
[14] Tou, C. J., Schaffer, D. V., & Dueber, J. E. (2020). Targeted Diversification in the S. cerevisiae Genome with CRISPR-Guided DNA Polymerase I. ACS Synth Biol , 9 , 1911-1916.
[15] Hess, G. T., Fresard, L., Han, K., Lee, C. H., Li, A., Cimprich, K. A., Montgomery, S. B., & Bassik, M. C. (2016). Directed evolution using dCas9-targeted somatic hypermutation in mammalian cells.Nat Methods , 13 , 1036-1042.
[16] Nishida, K., Arazoe, T., Yachie, N., Banno, S., Kakimoto, M., Tabata, M., Mochizuki, M., Miyabe, A., Araki, M., Hara, K. Y., Shimatani, Z., & Kondo, A. (2016). Targeted nucleotide editing using hybrid prokaryotic and vertebrate adaptive immune systems.Science , 353 .
[17] Despres, P. C., Dube, A. K., Nielly-Thibault, L., Yachie, N., & Landry, C. R. (2018). Double Selection Enhances the Efficiency of Target-AID and Cas9-Based Genome Editing in Yeast. G3 (Bethesda) ,8 , 3163-3171.
[18] Halperin, S. O., Tou, C. J., Wong, E. B., Modavi, C., Schaffer, D. V., & Dueber, J. E. (2018). CRISPR-guided DNA polymerases enable diversification of all nucleotides in a tunable window. Nature ,560 , 248-252.
[19] Feng, S., Liang, L., Shen, C., Lin, D., Li, J., Lyu, L., Liang, W., Zhong, L. L., Cook, G. M., Doi, Y., Chen, C., & Tian, G. B. (2022). A CRISPR-guided mutagenic DNA polymerase strategy for the detection of antibiotic-resistant mutations in M. tuberculosis. Mol Ther Nucleic Acids , 29 , 354-367.
[20] Hao, W., Cui, W., Suo, F., Han, L., Cheng, Z., & Zhou, Z. (2022). Construction and application of an efficient dual-base editing platform for Bacillus subtilis evolution employing programmable base conversion. Chem Sci , 13 , 14395-14409.
[21] Chen, H., Liu, S., Padula, S., Lesman, D., Griswold, K., Lin, A., Zhao, T., Marshall, J. L., & Chen, F. (2020). Efficient, continuous mutagenesis in human cells using a pseudo-random DNA editor. Nat Biotechnol , 38 , 165-168.
[22] Park, H., & Kim, S. (2021). Gene-specific mutagenesis enables rapid continuous evolution of enzymes in vivo. Nucleic Acids Res ,49 , e32.
[23] Cravens, A., Jamil, O. K., Kong, D., Sockolosky, J. T., & Smolke, C. D. (2021). Polymerase-guided base editing enables in vivo mutagenesis and rapid protein engineering. Nat Commun , 12 , 1579.
[24] Moore, C. L., Papa, L. J., & Shoulders, M. D. (2018). A Processive Protein Chimera Introduces Mutations across Defined DNA Regions In Vivo. J Am Chem Soc , 140 , 11560-11564.
[25] Mengiste, A. A., Wilson, R. H., Weissman, R. F., Papa Iii, L. J., Hendel, S. J., Moore, C. L., Butty, V. L., & Shoulders, M. D. (2023). Expanded MutaT7 toolkit efficiently and simultaneously accesses all possible transition mutations in bacteria. Nucleic Acids Res .
[26] Velazquez, E., Alvarez, B., Fernandez, L. A., & de Lorenzo, V. (2022). Hypermutation of specific genomic loci of Pseudomonas putida for continuous evolution of target genes. Microb Biotechnol ,15 , 2309-2323.
[27] Butt, H., Ramirez, J. L. M., & Mahfouz, M. (2022). Synthetic evolution of herbicide resistance using a T7 RNAP-based random DNA base editor. Life Sci Alliance , 5 .
[28] Liu, M., & Schatz, D. G. (2009). Balancing AID and DNA repair during somatic hypermutation. Trends Immunol , 30 , 173-181.
[29] Muramatsu, M., Kinoshita, K., Fagarasan, S., Yamada, S., Shinkai, Y., & Honjo, T. (2000). Class switch recombination and hypermutation require activation-induced cytidine deaminase (AID), a potential RNA editing enzyme. Cell , 102 , 553-563.
[30] Komor, A. C., Kim, Y. B., Packer, M. S., Zuris, J. A., & Liu, D. R. (2016). Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature , 533 , 420-424.
[31] Kurt, I. C., Zhou, R., Iyer, S., Garcia, S. P., Miller, B. R., Langner, L. M., Grunewald, J., & Joung, J. K. (2021). CRISPR C-to-G base editors for inducing targeted DNA transversions in human cells.Nat Biotechnol , 39 , 41-46.
[32] Zhao, D., Li, J., Li, S., Xin, X., Hu, M., Price, M. A., Rosser, S. J., Bi, C., & Zhang, X. (2021). Glycosylase base editors enable C-to-A and C-to-G base changes. Nat Biotechnol , 39 , 35-40.
[33] Zafra, M. P., Schatoff, E. M., Katti, A., Foronda, M., Breinig, M., Schweitzer, A. Y., Simon, A., Han, T., Goswami, S., Montgomery, E., Thibado, J., Kastenhuber, E. R., Sanchez-Rivera, F. J., Shi, J., Vakoc, C. R., Lowe, S. W., Tschaharganeh, D. F., & Dow, L. E. (2018). Optimized base editors enable efficient editing in cells, organoids and mice. Nat Biotechnol , 36 , 888-893.
[34] Wallace, S. S. (2014). Base excision repair: a critical player in many games. DNA Repair (Amst) , 19 , 14-26.
[35] Chatterjee, N., & Walker, G. C. (2017). Mechanisms of DNA damage, repair, and mutagenesis. Environ Mol Mutagen , 58 , 235-263.
[36] Tkach, J. M., Yimit, A., Lee, A. Y., Riffle, M., Costanzo, M., Jaschob, D., Hendry, J. A., Ou, J., Moffat, J., Boone, C., Davis, T. N., Nislow, C., & Brown, G. W. (2012). Dissecting DNA damage response pathways by analysing protein localization and abundance changes during DNA replication stress. Nat Cell Biol , 14 , 966-976.
[37] Admiraal, S. J., Eyler, D. E., Baldwin, M. R., Brines, E. M., Lohans, C. T., Schofield, C. J., & O’Brien, P. J. (2019). Expansion of base excision repair compensates for a lack of DNA repair by oxidative dealkylation in budding yeast. J Biol Chem , 294 , 13629-13637.
[38] Finney-Manchester, S. P., & Maheshri, N. (2013). Harnessing mutagenic homologous recombination for targeted mutagenesis in vivo by TaGTEAM. Nucleic Acids Res , 41 , e99.
[39] Boiteux, S., & Guillet, M. (2004). Abasic sites in DNA: repair and biological consequences in Saccharomyces cerevisiae. DNA Repair (Amst) , 3 , 1-12.
[40] Swartzlander, D. B., Griffiths, L. M., Lee, J., Degtyareva, N. P., Doetsch, P. W., & Corbett, A. H. (2010). Regulation of base excision repair: Ntg1 nuclear and mitochondrial dynamic localization in response to genotoxic stress. Nucleic Acids Res , 38 , 3963-3974.
[41] Zan, H., White, C. A., Thomas, L. M., Mai, T., Li, G., Xu, Z., Zhang, J., & Casali, P. (2012). Rev1 recruits ung to switch regions and enhances du glycosylation for immunoglobulin class switch DNA recombination. Cell Rep , 2 , 1220-1232.
[42] Clairmont, C. S., & D’Andrea, A. D. (2021). REV7 directs DNA repair pathway choice. Trends Cell Biol , 31 , 965-978.
[43] Tran, P. T., Erdeniz, N., Dudley, S., & Liskay, R. M. (2002). Characterization of nuclease-dependent functions of Exo1p in Saccharomyces cerevisiae. DNA Repair , 1 , 895-912.
[44] Sakamoto, A. N., Stone, J. E., Kissling, G. E., McCulloch, S. D., Pavlov, Y. I., & Kunkel, T. A. (2007). Mutator alleles of yeast DNA polymerase zeta. DNA Repair (Amst) , 6 , 1829-1838.
[45] Sertic, S., Quadri, R., Lazzaro, F., & Muzi-Falconi, M. (2020). EXO1: A tightly regulated nuclease. DNA Repair (Amst) ,93 , 102929.
[46] Memisoglu, A., & Samson, L. (2000). Base excision repair in yeast and mammals. Mutation Research-Fundamental and Molecular Mechanisms of Mutagenesis , 451 , 39-51.