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Cited by 351CRISPR and Genetic EngineeringRNA regulation and diseaseRNA Interference and Gene Delivery

Programmable RNA editing with compact CRISPR–Cas13 systems from uncultivated microbes

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Xu, Chunlong, Zhou, Yingsi, Xiao, Qingquan, He, Bingbing, Geng, Guannan, Wang, Zikang, Cao, Birong, Dong, Xue +8 more·2021·Nature Methods
DOI 10.1038/s41592-021-01124-4

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Abstract

Competitive coevolution between microbes and viruses has led to the diversification of CRISPR-Cas defense systems against infectious agents. By analyzing metagenomic terabase datasets, we identified two compact families (775 to 803 amino acids (aa)) of CRISPR-Cas ribonucleases from hypersaline samples, named Cas13X and Cas13Y. We engineered Cas13X.1 (775 aa) for RNA interference experiments in mammalian cell lines. We found Cas13X.1 could tolerate single-nucleotide mismatches in RNA recognition, facilitating prophylactic RNA virus inhibition. Moreover, a minimal RNA base editor, composed of engineered deaminase (385 aa) and truncated Cas13X.1 (445 aa), exhibited robust editing efficiency and high specificity to induce RNA base conversions. Our results suggest that there exist untapped bacterial defense systems in natural microbes that can function efficiently in mammalian cells, and thus potentially are useful for RNA-editing-based research.

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  • Hypercompact Cas13bt3 (Cas13X) enzymes range at 775 amino acids.

    “More recently, hypercompact Cas13bt3 (also reported as Cas13X) enzymes were described, ranging even smaller at 775 amino acids (11, 12).”

    From Characterization of RNA editing and gene therapy with a compact CRISPR-Cas13 in the retina (2024) · cites this paper as [11]

    The Main Text (page unavailable) reports exceptionally small Cas13 proteins ranging from 775 to 803 amino acids. It identifies them as Cas13e and Cas13f, however, and does not establish that Cas13bt3 (Cas13X) is 775 amino acids long. (LLM, conf=0.83)

    Experimental — accuracy not yet measured

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Research works printed but not linked: 34

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Authors
Xu, C., Zhou, Y., Xiao, Q., He, B., Geng, G., Wang, Z., Cao, B., Dong, X., Bai, W., Wang, Y., Wang, X., Zhou, D., Yuan, T., Huo, X., Lai, J., & Yang, H.
Affiliations
  • Chinese Academy of Sciences (CN)
  • Fudan University (CN)
  • Agricultural Genomics Institute at Shenzhen (CN)
  • China Agricultural University (CN)
Corresponding author
  • Zhou, Yingsi
  • Lai, Jinsheng
  • Yang, Hui
ORCID
Venue
Nature Methods
Publisher
Springer Science and Business Media LLC
Published
2021-05
Volume
18
Issue
5
Pages
499-506
ISSN
  • 1548-7091 (ISSN-L)
  • 1548-7105
DOI
10.1038/s41592-021-01124-4
OpenAlex
W3158499862
Cited by
351
References
4
Citations by year
2026: 39 · 2025: 67 · 2024: 91 · 2023: 73 · 2022: 58 · 2021: 22 · 2020: 1
FWCI
19.62
Type
journal article
Language
en
Update notices
correction (2022-01-02)
Open access
Licence
Locations
  • Nature Methods (publishedVersion)
  • Research Square (acceptedVersion, cc-by)
  • PubMed (publishedVersion)
Funders
  • National Natural Science Foundation of China (XDB32060000, 31925016, 82021001, 2017YFC1001300, 2018SHZDZX05, 31871502, 31901047, 91957122, 2018YFC2000100)
  • Chinese Academy of Sciences (31925016, XDB32060000, 82021001, ZDBS-LY-SM001, 153D31KYSB20170059, 2018SHZDZX05, 2018YFC2000100)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA regulation and disease
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Interference and Gene Delivery
Keywords
CRISPR-Cas13, RNA editing, RNA interference, hypersaline environments, SARS-CoV-2, H1N1, bacterial defense mechanisms
MeSH terms
Animals, Bacterial Proteins, Cell Line, Cloning, Molecular, Dogs, Humans, RNA, Bacterial, RNA Editing, Databases, Nucleic Acid, RNA Interference, Mice, CRISPR-Cas Systems

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