Development of a CRISPR/Cas9-Based Tool for Gene Deletion in Issatchenkia orientalis

Tran, Vinh G.; Cao, Mingfeng; Fatma, Zia; Song, Xiaofei; Zhao, Huimin; Mitchell, ed., Aaron P.

doi:10.1128/mSphere.00345-19

Development of a CRISPR/Cas9-Based Tool for Gene Deletion in Issatchenkia orientalis

Journal Article · Wed Jun 26 00:00:00 EDT 2019 · mSphere

DOI:https://doi.org/10.1128/mSphere.00345-19· OSTI ID:1529164

Tran, Vinh G. ^[1]; Cao, Mingfeng ^[1]; Fatma, Zia ^[1]; Song, Xiaofei ^[2]; Zhao, Huimin ^[3]; Mitchell, ed., Aaron P.

Department of Chemical and Biomolecular Engineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
Department of Chemical and Biomolecular Engineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA, Department of Microbiology, Nankai University, Tianjin, China
Department of Chemical and Biomolecular Engineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA, Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA, Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA, Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA

Microbial production of fuels and chemicals from renewable and readily available biomass is a sustainable and economically attractive alternative to petroleum-based production. Because of its unusual tolerance to highly acidic conditions, I. orientalis is a promising potential candidate for the manufacture of valued organic acids. Nevertheless, reliable and efficient genetic engineering tools in I. orientalis are limited. The results outlined in this paper describe a stable episomal ARS-containing plasmid and the first CRISPR/Cas9-based system for gene disruptions in I. orientalis , paving the way for applying genome engineering and metabolic engineering strategies and tools in this microorganism for production of fuels and chemicals.

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Research Organization:: Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), Urbana, IL: (United States)

Sponsoring Organization:: USDOE; USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)

Grant/Contract Number:: SC0018420

OSTI ID:: 1529164

Alternate ID(s):: OSTI ID: 1542920

Journal Information:: mSphere, Journal Name: mSphere Journal Issue: 3 Vol. 4; ISSN 2379-5042

Publisher:: American Society for MicrobiologyCopyright Statement

Country of Publication:: United States

Language:: English

References (33)

Engineered CRISPR/Cas9 system for multiplex genome engineering of polyploid industrial yeast strains Lian, Jiazhang; Bao, Zehua; Hu, Sumeng Biotechnology and Bioengineering, Vol. 115, Issue 6 https://doi.org/10.1002/bit.26569	journal	March 2018
Low‐pH production of d ‐lactic acid using newly isolated acid tolerant yeast Pichia kudriavzevii NG7 Park, Hyun Joo; Bae, Jung‐Hoon; Ko, Hyeok‐Jin Biotechnology and Bioengineering, Vol. 115, Issue 9 https://doi.org/10.1002/bit.26745	journal	June 2018
Development of a CRISPR/Cas9 system for high efficiency multiplexed gene deletion in Rhodosporidium toruloides Schultz, J. Carl; Cao, Mingfeng; Zhao, Huimin Biotechnology and Bioengineering, Vol. 116, Issue 8 https://doi.org/10.1002/bit.27001	journal	May 2019
Only Centromeres Can Supply the Partition System Required for ARS Function in the Yeast Yarrowia lipolytica Vernis, Laurence; Poljak, Leonora; Chasles, Marion Journal of Molecular Biology, Vol. 305, Issue 2 https://doi.org/10.1006/jmbi.2000.4300	journal	January 2001
Multiplex gene editing of the Yarrowia lipolytica genome using the CRISPR-Cas9 system Gao, Shuliang; Tong, Yangyang; Wen, Zhiqiang Journal of Industrial Microbiology & Biotechnology, Vol. 43, Issue 8 https://doi.org/10.1007/s10295-016-1789-8	journal	June 2016
CRISPR-Based Technologies for the Manipulation of Eukaryotic Genomes Komor, Alexis C.; Badran, Ahmed H.; Liu, David R. Cell, Vol. 168, Issue 1-2 https://doi.org/10.1016/j.cell.2016.10.044	journal	January 2017
Time to Be Versatile: Regulation of the Replication Timing Program in Budding Yeast Yoshida, Kazumasa; Poveda, Ana; Pasero, Philippe Journal of Molecular Biology, Vol. 425, Issue 23 https://doi.org/10.1016/j.jmb.2013.09.020	journal	November 2013
Synthetic RNA Polymerase III Promoters Facilitate High-Efficiency CRISPR–Cas9-Mediated Genome Editing in Yarrowia lipolytica Schwartz, Cory M.; Hussain, Murtaza Shabbir; Blenner, Mark ACS Synthetic Biology, Vol. 5, Issue 4 https://doi.org/10.1021/acssynbio.5b00162	journal	January 2016
Centromeric DNA Facilitates Nonconventional Yeast Genetic Engineering Cao, Mingfeng; Gao, Meirong; Lopez-Garcia, Carmen Lorena ACS Synthetic Biology, Vol. 6, Issue 8 https://doi.org/10.1021/acssynbio.7b00046	journal	April 2017
Rapid Isolation of Centromeres from Scheffersomyces stipitis Cao, Mingfeng; Seetharam, Arun Somwarpet; Severin, Andrew Josef ACS Synthetic Biology, Vol. 6, Issue 11 https://doi.org/10.1021/acssynbio.7b00166	journal	August 2017
5S rRNA Promoter for Guide RNA Expression Enabled Highly Efficient CRISPR/Cas9 Genome Editing in Aspergillus niger Zheng, Xiaomei; Zheng, Ping; Zhang, Kun ACS Synthetic Biology, Vol. 8, Issue 7 https://doi.org/10.1021/acssynbio.7b00456	journal	April 2018
T7 Polymerase Expression of Guide RNAs in vivo Allows Exportable CRISPR-Cas9 Editing in Multiple Yeast Hosts Morse, Nicholas J.; Wagner, James M.; Reed, Kevin B. ACS Synthetic Biology, Vol. 7, Issue 4 https://doi.org/10.1021/acssynbio.7b00461	journal	March 2018
FairyTALE: A High-Throughput TAL Effector Synthesis Platform Liang, Jing; Chao, Ran; Abil, Zhanar ACS Synthetic Biology, Vol. 3, Issue 2 https://doi.org/10.1021/sb400109p	journal	September 2013
Homology-Integrated CRISPR–Cas (HI-CRISPR) System for One-Step Multigene Disruption in Saccharomyces cerevisiae Bao, Zehua; Xiao, Han; Liang, Jing ACS Synthetic Biology, Vol. 4, Issue 5 https://doi.org/10.1021/sb500255k	journal	September 2014
Off-target Effects in CRISPR/Cas9-mediated Genome Engineering Zhang, Xiao-Hui; Tee, Louis Y.; Wang, Xiao-Gang Molecular Therapy - Nucleic Acids, Vol. 4 https://doi.org/10.1038/mtna.2015.37	journal	January 2015
RNA-guided editing of bacterial genomes using CRISPR-Cas systems Jiang, Wenyan; Bikard, David; Cox, David Nature Biotechnology, Vol. 31, Issue 3, p. 233-239 https://doi.org/10.1038/nbt.2508	journal	January 2013
Genome-scale engineering of Saccharomyces cerevisiae with single-nucleotide precision Bao, Zehua; HamediRad, Mohammad; Xue, Pu Nature Biotechnology, Vol. 36, Issue 6 https://doi.org/10.1038/nbt.4132	journal	May 2018
Eukaryotic DNA replication origins: many choices for appropriate answers Méchali, Marcel Nature Reviews Molecular Cell Biology, Vol. 11, Issue 10 https://doi.org/10.1038/nrm2976	journal	September 2010
Combinatorial metabolic engineering using an orthogonal tri-functional CRISPR system Lian, Jiazhang; HamediRad, Mohammad; Hu, Sumeng Nature Communications, Vol. 8, Issue 1 https://doi.org/10.1038/s41467-017-01695-x	journal	November 2017
A gRNA-tRNA array for CRISPR-Cas9 based rapid multiplexed genome editing in Saccharomyces cerevisiae Zhang, Yueping; Wang, Juan; Wang, Zibai Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-09005-3	journal	March 2019
SgRNA Expression of CRIPSR-Cas9 System Based on MiRNA Polycistrons as a Versatile Tool to Manipulate Multiple and Tissue-Specific Genome Editing Xie, Chen; Chen, Yan-Lian; Wang, Dong-Fang Scientific Reports, Vol. 7, Issue 1 https://doi.org/10.1038/s41598-017-06216-w	journal	July 2017
CRISPR/Cas system for yeast genome engineering: advances and applications Stovicek, Vratislav; Holkenbrink, Carina; Borodina, Irina FEMS Yeast Research, Vol. 17, Issue 5 https://doi.org/10.1093/femsyr/fox030	journal	May 2017
The RNA polymerase III-dependent family of genes in hemiascomycetes: comparative RNomics, decoding strategies, transcription and evolutionary implications Marck, C. Nucleic Acids Research, Vol. 34, Issue 6 https://doi.org/10.1093/nar/gkl085	journal	March 2006
DNA assembler, an in vivo genetic method for rapid construction of biochemical pathways Shao, Zengyi; Zhao, Hua; Zhao, Huimin Nucleic Acids Research, Vol. 37, Issue 2 https://doi.org/10.1093/nar/gkn991	journal	December 2008
Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems DiCarlo, James E.; Norville, Julie E.; Mali, Prashant Nucleic Acids Research, Vol. 41, Issue 7, p. 4336-4343 https://doi.org/10.1093/nar/gkt135	journal	March 2013
Self‐processing of ribozyme‐flanked RNAs into guide RNAs in vitro and in vivo for CRISPR‐mediated genome editing Gao, Yangbin; Zhao, Yunde Journal of Integrative Plant Biology, Vol. 56, Issue 4 https://doi.org/10.1111/jipb.12152	journal	February 2014
RNA-Guided Human Genome Engineering via Cas9 Mali, P.; Yang, L.; Esvelt, K. M. Science, Vol. 339, Issue 6121, p. 823-826 https://doi.org/10.1126/science.1232033	journal	January 2013
Multiplex Real-Time PCR Targeting the RNase P RNA Gene for Detection and Identification of Candida Species in Blood Innings, A.; Ullberg, M.; Johansson, A. Journal of Clinical Microbiology, Vol. 45, Issue 3 https://doi.org/10.1128/JCM.01556-06	journal	January 2007
Exploiting Issatchenkia orientalis SD108 for succinic acid production Xiao, Han; Shao, Zengyi; Jiang, Yu Microbial Cell Factories, Vol. 13, Issue 1 https://doi.org/10.1186/s12934-014-0121-4	journal	August 2014
Centromere-Like Regions in the Budding Yeast Genome Lefrançois, Philippe; Auerbach, Raymond K.; Yellman, Christopher M. PLoS Genetics, Vol. 9, Issue 1 https://doi.org/10.1371/journal.pgen.1003209	journal	January 2013
Population genomics shows no distinction between pathogenic Candida krusei and environmental Pichia kudriavzevii: One species, four names Douglass, Alexander P.; Offei, Benjamin; Braun-Galleani, Stephanie PLOS Pathogens, Vol. 14, Issue 7 https://doi.org/10.1371/journal.ppat.1007138	journal	July 2018
Extraction of genomic DNA from yeasts for PCR-based applications Lõoke, Marko; Kristjuhan, Kersti; Kristjuhan, Arnold BioTechniques, Vol. 50, Issue 5 https://doi.org/10.2144/000113672	journal	May 2011
Isolation and Identification of a Novel Yeast Fermenting Ethanol under Acidic Conditions Hisamatsu, Makoto; Furubayashi, Takuya; Karita, Shuichi Journal of Applied Glycoscience, Vol. 53, Issue 2 https://doi.org/10.5458/jag.53.111	journal	January 2006

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