Biochemical and structural insights into a 5’ to 3’ RNA ligase reveal a potential role in tRNA ligation
ATP-grasp superfamily enzymes contain a hand-like ATP-binding fold and catalyze a variety of reactions using a similar catalytic mechanism. More than 30 protein families are categorized in this superfamily, and they are involved in a plethora of cellular processes and human diseases. Here, we identify C12orf29 (RLIG1) as an atypical ATP-grasp enzyme that ligates RNA. Human RLIG1 and its homologs autoadenylate on an active site Lys residue as part of a reaction intermediate that specifically ligates RNA halves containing a 5’-phosphate and a 3’-hydroxyl. RLIG1 binds tRNA in cells and can ligate tRNA within the anticodon loop in vitro. Transcriptomic analyses of Rlig1 knockout mice revealed significant alterations in global tRNA levels in the brains of female mice, but not in those of male mice. Furthermore, crystal structures of a RLIG1 homolog from Yasminevirus bound to nucleotides revealed a minimal and atypical RNA ligase fold with a conserved active site architecture that participates in catalysis. Collectively, our results identify RLIG1 as an RNA ligase and suggest its involvement in tRNA biology.
Authors
- Alan M. Lambowitz (ORCID: https://orcid.org/0000-0001-6036-2423)
- Vincent S. Tagliabracci (ORCID: https://orcid.org/0000-0002-9735-4678)
- Benjamin T. Jones (ORCID: https://orcid.org/0000-0001-7782-628X)
- Diana R. Tomchick (ORCID: https://orcid.org/0000-0002-7529-4643)
- Bing Song (ORCID: https://orcid.org/0000-0002-5065-5182)
- Víctor López (ORCID: https://orcid.org/0000-0003-1618-5786)
- Joshua T. Mendell (ORCID: https://orcid.org/0000-0001-8479-2284)
- Masahiro Sakurai (ORCID: https://orcid.org/0000-0002-6376-0299)
- Kelly A. Servage (ORCID: https://orcid.org/0000-0001-7183-2865)
- Yingjie Hu (ORCID: https://orcid.org/0000-0003-3103-525X)
- Jun Wu (ORCID: https://orcid.org/0000-0001-9863-1668)
- Hengyi Xu (ORCID: https://orcid.org/0000-0001-9809-4882)
- Krzysztof Pawłowski (ORCID: https://orcid.org/0000-0002-5367-0935)
- Tao Wang (ORCID: https://orcid.org/0000-0002-0437-0557)
- James P. Pfister
Institutions
- Southwestern Medical Center (US)
- The University of Texas at Austin (US)
- The University of Texas Southwestern Medical Center (US)
Publication Details
- Journal
- Proceedings of the National Academy of Sciences
- Published
- 2024-10-10
- DOI
- https://doi.org/10.1073/pnas.2408249121
- Citations
- 7
- Primary Topic
- RNA modifications and cancer
- Type
- article
- Field-Weighted Citation Impact
- 1.64
Funders
- Foundation for the National Institutes of Health
- Howard Hughes Medical Institute
- Welch Foundation
- Cancer Prevention and Research Institute of Texas
- National Institutes of Health
- National Institute of General Medical Sciences