Structure-guided discovery of ancestral CRISPR-Cas13 ribonucleases

被引：10

作者：

Yoon, Peter H. ^{[1
,2
,3
]}

Zhang, Zeyuan ^{[2
,3
,4
,5
]}

Loi, Kenneth J. ^{[1
,2
]}

Adler, Benjamin A. ^{[2
,3
,5
]}

Lahiri, Arushi ^{[1
,2
]}

Vohra, Kamakshi ^{[2
,5
]}

Shi, Honglue ^{[2
,3
]}

Rabelo, Daniel Bellieny ^{[2
,5
]}

Trinidad, Marena ^{[2
,3
]}

Boger, Ron S. ^{[2
,3
,4
]}

Al-Shimary, Muntathar J. ^{[1
,2
,3
]}

Doudna, Jennifer A. ^{[1
,2
,3
,5
,6
,7
,8
,9
]}

机构：

[1] Univ Calif Berkeley, Dept Mol & Cell Biol, Berkeley, CA 94720 USA

[2] Univ Calif Berkeley, Innovat Genom Inst, Berkeley, CA 94720 USA

[3] Univ Calif Berkeley, Howard Hughes Med Inst, Berkeley, CA 94720 USA

[4] Univ Calif Berkeley, Biophys Grad Grp, Berkeley, CA USA

[5] Univ Calif Berkeley, Calif Inst Quantitat Biosci, Berkeley, CA 94720 USA

[6] Gladstone Inst, San Francisco, CA 94158 USA

[7] Gladstone UCSF Inst Genom Immunol, San Francisco, CA 94115 USA

[8] Lawrence Berkeley Natl Lab, Mol Biophys & Integrated Bioimaging Div, Berkeley, CA 94720 USA

[9] Univ Calif Berkeley, Dept Chem, Berkeley, CA 94720 USA

来源：

SCIENCE | 2024年 / 385卷 / 6708期

基金：

美国国家科学基金会;

关键词：

PROTEIN-STRUCTURE; RNA; ALGORITHM; CLEAVAGE; CAS13B;

D O I：

10.1126/science.adq0553

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

The RNA-guided ribonuclease CRISPR-Cas13 enables adaptive immunity in bacteria and programmable RNA manipulation in heterologous systems. Cas13s share limited sequence similarity, hindering discovery of related or ancestral systems. To address this, we developed an automated structural-search pipeline to identify an ancestral clade of Cas13 (Cas13an) and further trace Cas13 origins to defense-associated ribonucleases. Despite being one-third the size of other Cas13s, Cas13an mediates robust programmable RNA depletion and defense against diverse bacteriophages. However, unlike its larger counterparts, Cas13an uses a single active site for both CRISPR RNA processing and RNA-guided cleavage, revealing that the ancestral nuclease domain has two modes of activity. Discovery of Cas13an deepens our understanding of CRISPR-Cas evolution and expands opportunities for precision RNA editing, showcasing the promise of structure-guided genome mining.

引用

页码：538 / 543

页数：6

共 54 条

[1] RNA targeting with CRISPR-Cas13 [J].

Abudayyeh, Omar O. ;

Gootenberg, Jonathan S. ;

Essletzbichler, Patrick ;

Han, Shuo ;

Joung, Julia ;

Belanto, Joseph J. ;

Verdine, Vanessa ;

Cox, David B. T. ;

Kellner, Max J. ;

Regev, Aviv ;

Lander, Eric S. ;

Voytas, Daniel F. ;

Ting, Alice Y. ;

Zhang, Feng .

NATURE, 2017, 550 (7675) :280-+

[2] C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector [J].

Abudayyeh, Omar O. ;

Gootenberg, Jonathan S. ;

Konermann, Silvana ;

Joung, Julia ;

Slaymaker, Ian M. ;

Cox, David B. T. ;

Shmakov, Sergey ;

Makarova, Kira S. ;

Semenova, Ekaterina ;

Minakhin, Leonid ;

Severinov, Konstantin ;

Regev, Aviv ;

Lander, Eric S. ;

Koonin, Eugene V. ;

Zhang, Feng .

SCIENCE, 2016, 353 (6299)

[3] Broad-spectrum CRISPR-Cas13a enables efficient phage genome editing [J].

Adler, Benjamin A. ;

Hessler, Tomas ;

Cress, Brady F. ;

Lahiri, Arushi ;

Mutalik, Vivek K. ;

Barrangou, Rodolphe ;

Banfield, Jillian ;

Doudna, Jennifer A. .

NATURE MICROBIOLOGY, 2022, 7 (12) :1967-+

[4] The widespread IS200/IS605 transposon family encodes diverse programmable RNA-guided endonucleases [J].

Altae-Tran, Han ;

Kannan, Soumya ;

Demircioglu, F. Esra ;

Oshiro, Rachel ;

Nety, Suchita P. ;

McKay, Luke J. ;

Dlakic, Mensur ;

Inskeep, William P. ;

Makarova, Kira S. ;

Macrae, Rhiannon K. ;

Koonin, Eugene, V ;

Zhang, Feng .

SCIENCE, 2021, 374 (6563) :57-+

[5] Gapped BLAST and PSI-BLAST: a new generation of protein database search programs [J].

Altschul, SF ;

Madden, TL ;

Schaffer, AA ;

Zhang, JH ;

Zhang, Z ;

Miller, W ;

Lipman, DJ .

NUCLEIC ACIDS RESEARCH, 1997, 25 (17) :3389-3402

[6] Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and RNA processing [J].

Anantharaman, Vivek ;

Makarova, Kira S. ;

Burroughs, A. Maxwell ;

Koonin, Eugene V. ;

Aravind, L. .

BIOLOGY DIRECT, 2013, 8

[7] Clustering predicted structures at the scale of the known protein universe [J].

Barrio-Hernandez, Inigo ;

Yeo, Jingi ;

Janes, Jurgen ;

Mirdita, Milot ;

Gilchrist, Cameron L. M. ;

Wein, Tanita ;

Varadi, Mihaly ;

Velankar, Sameer ;

Beltrao, Pedro ;

Steinegger, Martin .

NATURE, 2023, 622 (7983) :637-+

[8]

Bellieny D., 2024, Zenodo, DOI [10.5281/zenodo.12615632, DOI 10.5281/ZENODO.12615632]

[9] CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats [J].

Bland, Charles ;

Ramsey, Teresa L. ;

Sabree, Fareedah ;

Lowe, Micheal ;

Brown, Kyndall ;

Kyrpides, Nikos C. ;

Hugenholtz, Philip .

BMC BIOINFORMATICS, 2007, 8 (1)

[10]

Boger R., 2023, ICML WORKSH COMP BIO

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