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PreprintCited by 240CRISPR and Genetic EngineeringRNA regulation and diseaseProtein Structure and Dynamics

The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.

Discovery of new deaminase functions by structure-based protein clustering

Open access
Huang, Jiaying, Lin, Qiupeng, Fei, Hongyuan, He, Zixin, Xu, Hu, Li, Yunjia, Qu, Kunli, Han, Peng, Gao, Qiang, Li, Boshu, Liu, Guanwen, Zhang, Lixiao, Hu, Jiacheng, Zhang, Rui, Zuo, Erwei, Luo, Yonglun, Ran, Yidong, Qiu, Jin-Long, Zhao, Kevin Tianmeng, Gao, Caixia·2023·Cell
DOI 10.1101/2023.05.21.541555

Preprint — published as 10.1016/j.cell.2023.05.041

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Abstract

Summary: The elucidation of protein function and its exploitation in bioengineering have greatly contributed to the development of the life sciences. Existing protein mining efforts generally rely on amino acid sequences rather than protein structures due to technical difficulties in structural elucidation. We describe here for the use of AlphaFold2 to predict and subsequently cluster an entire protein family based on predicted structure similarities. We selected the deaminase family of proteins to analyze and through this approach identified many previously unknown deaminase properties. We applied these new deaminases to the development of new cytosine base editors with distinct features. Although we found many new double-stranded DNA deaminases from the DddA-like protein clade, we were surprised to find that most of the proteins in this family were not actually double-stranded DNA cytidine deaminases. From this protein clade, we engineered the smallest single-strand specific cytidine deaminase, which facilitates the first efficient cytosine base editor to be packaged into a single AAV vector. Importantly, we also profiled a deaminase from this clade that edits robustly in soybean plants, which previously suffered from poor editing by cytosine base editors. These newly discovered deaminases based on AI-assisted structural predictions greatly expand the utility of base editors for therapeutic and agricultural applications.

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Research works printed but not linked: 61

  1. 10.1093/nar/gkab1207 · DOI
  2. 10.1038/s41579-019-0299-x · DOI · Paper page
  3. 10.1016/j.febslet.2010.04.043 · DOI
  4. 10.1093/nar/gkab1054 · DOI
  5. wwPDB consortium, 2019, Protein Data Bank: the single global archive for 3D macromolecular structure data, Nucleic Acids Res, 47, D520, 10.1093/nar/gky949 · DOI · Paper page
  6. 10.1093/nar/gkac1080 · DOI
  7. 10.1126/science.abj8754 · DOI · Paper page
  8. 10.1093/nar/gkab1061 · DOI · Paper page
  9. 10.1038/s41586-020-2477-4 · DOI
  10. 10.1038/nature01707 · DOI
  11. 10.1128/JB.00461-07 · DOI
  12. 10.1038/nature03238 · DOI
  13. 10.1038/nature17946 · DOI · Paper page
  14. 10.1126/science.aaf8729 · DOI · Paper page
  15. 10.1126/science.aaq0180 · DOI · Paper page
  16. 10.1016/S1097-2765(02)00742-6 · DOI
  17. 10.1038/nature24041 · DOI
  18. 10.1093/emboj/cdf362 · DOI
  19. 10.1093/nar/gkr691 · DOI
  20. 10.1073/pnas.1720897115 · DOI
  21. 10.1016/j.cell.2021.01.005 · DOI
  22. 10.1038/s41587-020-0561-9 · DOI · Paper page
  23. 10.1016/j.jgg.2021.05.001 · DOI
  24. 10.1007/s11427-020-1800-5 · DOI
  25. 10.1007/s11427-017-9021-5 · DOI
  26. 10.1038/nmeth.4027 · DOI
  27. 10.1038/nmeth.4038 · DOI
  28. 10.1038/s41467-020-15887-5 · DOI
  29. 10.1038/s41467-018-07709-6 · DOI
  30. 10.1038/s41551-019-0501-5 · DOI
  31. 10.1111/pbi.13386 · DOI
  32. 10.1038/s41592-022-01585-1 · DOI · Paper page
  33. 10.1038/nbt.3811 · DOI
  34. 10.1038/s41587-022-01256-8 · DOI
  35. 10.1038/nbt.4172 · DOI · Paper page
  36. 10.1038/nbt.4261 · DOI
  37. 10.1016/j.jgg.2021.04.003 · DOI
  38. Xiang, X. , Qu, K. , Liang, X. , Pan, X. , Wang, J. , Han, P. , Dong, Z. , Liu, L. , Zhong, J. , Ma, T. , Wang, Y. , et al. (2020). Massively parallel quantification of CRISPR editing in cells by TRAP-seq enables better design of Cas9, ABE, CBE gRNAs of high efficiency and accuracy. bioRxiv, https://doi.org/10.1101/2020.05.20.103614. · DOI
  39. 10.1126/science.aaw7166 · DOI · Paper page
  40. 10.1126/science.aav9973 · DOI · Paper page
  41. 10.1016/j.molcel.2020.07.005 · DOI · Paper page
  42. 10.1038/s41587-020-0414-6 · DOI · Paper page
  43. 10.1038/s41551-022-00911-4 · DOI
  44. 10.1038/s41467-022-32157-8 · DOI
  45. 10.1038/ncomms12642 · DOI
  46. 10.1016/j.molp.2020.03.002 · DOI
  47. 10.1038/s41477-021-00991-1 · DOI · Paper page
  48. 10.1002/ps.4744 · DOI
  49. 10.12688/f1000research.25097.1 · DOI
  50. 10.1038/s41586-019-1923-7 · DOI · Paper page
  51. 10.1038/nprot.2014.157 · DOI
  52. 10.1093/nar/gkn785 · DOI · Paper page
  53. 10.1093/nar/gkn201 · DOI
  54. 10.1093/nar/gkr367 · DOI · Paper page
  55. 10.1093/bioinformatics/bts565 · DOI · Paper page
  56. 10.1093/nar/gkh340 · DOI · Paper page
  57. 10.1093/molbev/msaa015 · DOI · Paper page
  58. 10.1038/s41596-022-00773-9 · DOI
  59. 10.1038/s41596-020-00423-y · DOI
  60. 10.1007/s00299-014-1669-5 · DOI
  61. 10.3389/fpls.2017.00246 · DOI

Metadata

Authors
Huang, J., Lin, Q., Fei, H., He, Z., Xu, H., Li, Y., Qu, K., Han, P., Gao, Q., Li, B., Liu, G., Zhang, L., Hu, J., Zhang, R., Zuo, E., Luo, Y., Ran, Y., Qiu, J.-L., Zhao, K. T., & Gao, C.
Affiliations
  • Chinese Academy of Sciences (CN)
  • BGI Group (China) (CN)
  • Agricultural Genomics Institute at Shenzhen (CN)
Corresponding author
  • Zhao, Kevin Tianmeng
  • Gao, Caixia
ORCID
Venue
Cell
Publisher
openRxiv
Published
2023-05-22
Volume
186
Issue
15
Pages
3182-3195.e14
ISSN
0092-8674 (ISSN-L)
DOI
10.1101/2023.05.21.541555
OpenAlex
W4382247824
Cited by
240
References
1
Citations by year
2026: 60 · 2025: 103 · 2024: 65 · 2023: 12
FWCI
21.32
Type
journal article
Language
en
Open access
Locations
  • Cell (publishedVersion)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
  • PubMed (publishedVersion)
Funders
  • National Natural Science Foundation of China (32388201)
  • Chinese Academy of Sciences (XDA24020102)
  • China Postdoctoral Science Foundation (2022M720163)
  • Youth Innovation Promotion Association of the Chinese Academy of Sciences (2022097)
  • Novo Nordisk Fonden (NNF21OC0068988, NNF21OC0072031)
  • National Postdoctoral Program for Innovative Talents (BX2021353)
  • National Key Research and Development Program of China (2022YFF1002802)
  • Steno Diabetes Center Aarhus
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 › Protein Structure and Dynamics
Keywords
AlphaFold2, cytidine deaminase, cytosine base editors, adeno-associated virus vectors
MeSH terms
Gene Editing, Cytidine Deaminase, Cytosine, DNA, Proteins, CRISPR-Cas Systems

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