Recombination machinery engineering for precise genome editing in methylotrophic yeast Ogataea polymorpha

iScience - Tập 24 - Trang 102168 - 2021
Jiaoqi Gao1,2,3, Ning Gao1,3, Xiaoxin Zhai1,3, Yongjin J. Zhou1,2,3
1Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, PR China
2CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, PR China
3Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, CAS, 457 Zhongshan Road, Dalian, 116023, PR China

Tài liệu tham khảo

Aird, 2018, Increasing Cas9-mediated homology-directed repair efficiency through covalent tethering of DNA repair template, Commun. Biol., 1, 54, 10.1038/s42003-018-0054-2

Arjun, 2010, Enhancement of gene targeting in human cells by intranuclear permeation of the Saccharomyces cerevisiae Rad52 protein, Nucleic Acids Res., 38, e149, 10.1093/nar/gkq486

Cao, 2017, Centromeric DNA facilitates nonconventional yeast genetic engineering, ACS Synth. Biol., 6, 1545, 10.1021/acssynbio.7b00046

Ceccaldi, 2016, Repair pathway choices and consequences at the double-strand break, Trends Cell Biol., 26, 52, 10.1016/j.tcb.2015.07.009

Chang, 2017, Non-homologous DNA end joining and alternative pathways to double-strand break repair, Nat. Rev. Mol. Cell Bio, 18, 495, 10.1038/nrm.2017.48

Charpentier, 2018, CtIP fusion to Cas9 enhances transgene integration by homology-dependent repair, Nat. Commun., 9, 1133, 10.1038/s41467-018-03475-7

Clomburg, 2017, Industrial biomanufacturing: the future of chemical production, Science, 355, aag0804, 10.1126/science.aag0804

Cohen-Fix, 1996, Anaphase initiation in Saccharomyces cerevisiae is controlled by the APC-dependent degradation of the anaphase inhibitor Pds1p, Gene Dev., 10, 3081, 10.1101/gad.10.24.3081

Cordova, 2020, Direct production of fatty alcohols from glucose using engineered strains of Yarrowia lipolytica, Metab. Eng. Comm., 10, e00105, 10.1016/j.mec.2019.e00105

D’Espaux, 2017, Engineering high-level production of fatty alcohols by Saccharomyces cerevisiae from lignocellulosic feedstocks, Metab. Eng., 42, 115, 10.1016/j.ymben.2017.06.004

Di, 2005, Potentiation of gene targeting in human cells by expression of Saccharomyces cerevisiae Rad52, Nucleic Acids Res., 33, 4639, 10.1093/nar/gki778

Gutschner, 2016, Post-translational regulation of Cas9 during G1 enhances homology-directed repair, Cell Rep., 14, 1555, 10.1016/j.celrep.2016.01.019

Heyer, 2010, Regulation of homologous recombination in eukaryotes, Annu. Rev. Genet., 44, 113, 10.1146/annurev-genet-051710-150955

Jayathilaka, 2008, A chemical compound that stimulates the human homologous recombination protein RAD51, Proc. Natl. Acad. Sci. U S A, 105, 15848, 10.1073/pnas.0808046105

Johnson, 1996, Elevated levels of recombinational DNA repair in human somatic cells expressing the Saccharomyces cerevisiae RAD52 gene, Mutat. Res./DNA Repair, 363, 179, 10.1016/0921-8777(96)00007-9

Juergens, 2018, Genome editing in Kluyveromyces and Ogataea yeasts using a broad-host-range Cas9/gRNA co-expression plasmid, FEMS Yeast Res., 18, foy012, 10.1093/femsyr/foy012

Krejci, 2012, Homologous recombination and its regulation, Nucleic Acids Res., 40, 5795, 10.1093/nar/gks270

Liachko, 2014, An autonomously replicating sequence for use in a wide range of budding yeasts, FEMS Yeast Res., 14, 364, 10.1111/1567-1364.12123

Liu, 2020, Exploiting nonionic surfactants to enhance fatty alcohol production in Rhodosporidium toruloides, Biotechnol. Bioeng., 117, 1418, 10.1002/bit.27285

Manfrão-Netto, 2019, Advances in using Hansenula polymorpha as chassis for recombinant protein production, Front. Bioeng. Biotech., 7, 94, 10.3389/fbioe.2019.00094

McGinn, 2018, Molecular mechanisms of CRISPR-Cas spacer acquisition, Nat. Rev. Microbiol., 17, 7, 10.1038/s41579-018-0071-7

Mcneil, 2017, Optimization of C16 and C18 fatty alcohol production by an engineered strain of Lipomyces starkeyi, J. Ind. Microbiol. Biotechnol., 45, 1, 10.1007/s10295-017-1985-1

Mimitou, 2008, Sae2, Exo1 and Sgs1 collaborate in DNA double-strand break processing, Nature, 455, 770, 10.1038/nature07312

Nambu-Nishida, 2017, Development of a comprehensive set of tools for genome engineering in a cold-and thermo-tolerant Kluyveromyces marxianus yeast strain, Sci. Rep., 7, 1, 10.1038/s41598-017-08356-5

O'Driscoll, 2006, The role of double-strand break repair-insights from human genetics, Nat. Rev. Genet., 7, 45, 10.1038/nrg1746

Olson, 2015, Ethanol production by engineered thermophiles, Curr. Opin. Biotechnol., 33, 130, 10.1016/j.copbio.2015.02.006

Phithakrotchanakoon, 2018, CRISPR-Cas9 enabled targeted mutagenesis in the thermotolerant methylotrophic yeast Ogataea thermomethanolica, FEMS Microbiol. Lett., 365, fny105, 10.1093/femsle/fny105

Saraya, 2012, Novel genetic tools for Hansenula polymorpha, FEMS Yeast Res., 12, 271, 10.1111/j.1567-1364.2011.00772.x

Schwartz, 2017, CRISPRi repression of nonhomologous end-joining for enhanced genome engineering via homologous recombination in Yarrowia lipolytica, Biotechnol. Bioeng., 114, 2896, 10.1002/bit.26404

Schwartz, 2015, Synthetic RNA polymerase III promoters facilitate high-efficiency CRISPR-Cas9-mediated genome editing in Yarrowia lipolytica, ACS Synth. Biol., 5, 356, 10.1021/acssynbio.5b00162

Shao, 2008, DNA assembler, an in vivo genetic method for rapid construction of biochemical pathways, Nucleic Acids Res., 37, e16, 10.1093/nar/gkn991

Vispé, 1998, Overexpression of Rad51 protein stimulates homologous recombination and increases resistance of mammalian cells to ionizing radiation, Nucleic Acids Res., 26, 2859, 10.1093/nar/26.12.2859

Voronovsky, 2009, Development of strains of the thermotolerant yeast Hansenula polymorpha capable of alcoholic fermentation of starch and xylan, Metab. Eng., 11, 234, 10.1016/j.ymben.2009.04.001

Wang, 2018, Efficient CRISPR–Cas9 mediated multiplex genome editing in yeasts, Biotechnol. Biofuels, 11, 277, 10.1186/s13068-018-1271-0

Weninger, 2018, Expanding the CRISPR/Cas9 toolkit for Pichia pastoris with efficient donor integration and alternative resistance markers, J. Cell. Biochem., 119, 3183, 10.1002/jcb.26474

Yáñez, 1999, Gene targeting is enhanced in human cells overexpressing hRAD51, Gene Ther., 6, 1282, 10.1038/sj.gt.3300945

Yang, 2016, Enrichment of G2/M cell cycle phase in human pluripotent stem cells enhances HDR-mediated gene repair with customizable endonucleases, Sci. Rep., 6, 21264, 10.1038/srep21264

Yu, 2018, Reprogramming yeast metabolism from alcoholic fermentation to lipogenesis, Cell, 174, 1549, 10.1016/j.cell.2018.07.013

Zhou, 2016, Harnessing yeast peroxisomes for biosynthesis of fatty-acid-derived biofuels and chemicals with relieved side-pathway competition, J. Am. Chem. Soc., 138, 15368, 10.1021/jacs.6b07394

Zhou, 2016, Production of fatty acid-derived oleochemicals and biofuels by synthetic yeast cell factories, Nat. Commun., 7, 11709, 10.1038/ncomms11709

Zhou, 2012, Modular pathway engineering of diterpenoid synthases and the mevalonic acid pathway for miltiradiene production, J. Am. Chem. Soc., 134, 3234, 10.1021/ja2114486

Zhou, 2018, Barriers and opportunities in bio-based production of hydrocarbons, Nat. Energy, 3, 925, 10.1038/s41560-018-0197-x