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TitleHydrolytic endonucleolytic ribozyme (HYER) is programmable for sequence-specific DNA cleavage.
Journal, issue, pagesScience, Vol. 383, Issue 6682, Page eadh4859, Year 2024
Publish dateFeb 2, 2024
AuthorsZi-Xian Liu / Shouyue Zhang / Han-Zhou Zhu / Zhi-Hang Chen / Yun Yang / Long-Qi Li / Yuan Lei / Yun Liu / Dan-Yuan Li / Ao Sun / Cheng-Ping Li / Shun-Qing Tan / Gao-Li Wang / Jie-Yi Shen / Shuai Jin / Caixia Gao / Jun-Jie Gogo Liu /
PubMed AbstractRibozymes are catalytic RNAs with diverse functions including self-splicing and polymerization. This work aims to discover natural ribozymes that behave as hydrolytic and sequence-specific DNA ...Ribozymes are catalytic RNAs with diverse functions including self-splicing and polymerization. This work aims to discover natural ribozymes that behave as hydrolytic and sequence-specific DNA endonucleases, which could be repurposed as DNA manipulation tools. Focused on bacterial group II-C introns, we found that many systems without intron-encoded protein propagate multiple copies in their resident genomes. These introns, named HYdrolytic Endonucleolytic Ribozymes (HYERs), cleaved RNA, single-stranded DNA, bubbled double-stranded DNA (dsDNA), and plasmids in vitro. HYER1 generated dsDNA breaks in the mammalian genome. Cryo-electron microscopy analysis revealed a homodimer structure for HYER1, where each monomer contains a Mg-dependent hydrolysis pocket and captures DNA complementary to the target recognition site (TRS). Rational designs including TRS extension, recruiting sequence insertion, and heterodimerization yielded engineered HYERs showing improved specificity and flexibility for DNA manipulation.
External linksScience / PubMed:38301022
MethodsEM (single particle)
Resolution2.58 - 3.41 Å
Structure data

36776

8k0p

EMDB-36776, PDB-8k0p:
The Anoxybacillus pushchinoensis ORF-less Group IIC Intron HYER1 at symmetric apo state
Method: EM (single particle) / Resolution: 2.99 Å

36777

8k0q

EMDB-36777: The Anoxybacillus pushchinoensis ORF-less Group IIC Intron DR1 at symmetric pre-cleavage state
PDB-8k0q: The Anoxybacillus pushchinoensis ORF-less Group IIC Intron HYER1 at symmetric pre-cleavage state
Method: EM (single particle) / Resolution: 3.14 Å

36778

8k0r

EMDB-36778, PDB-8k0r:
The Anoxybacillus pushchinoensis ORF-less Group IIC Intron HYER1 at symmetric post cleavge state
Method: EM (single particle) / Resolution: 2.65 Å

36779

8k0s

EMDB-36779, PDB-8k0s:
The Anoxybacillus pushchinoensis ORF-less Group IIC Intron HYER1 with 10-nt TRS at symmetric apo state
Method: EM (single particle) / Resolution: 3.41 Å

36786

8k15

EMDB-36786, PDB-8k15:
The Streptococcus azizii ORF-less Group IIC intron HYER2 at apo state
Method: EM (single particle) / Resolution: 2.58 Å

Chemicals

ChemComp-MG:
Unknown entry

Source
  • anoxybacillus pushchinoensis (bacteria)
  • streptococcus azizii (bacteria)
KeywordsRNA / ORF-less Group IIC intron / ribozymes

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