R2D ligase: Unveiling a novel DNA ligase with surprising DNA-to-RNA ligation activity.
biocatalysis
biochemistry
molecular biotechnology
next‐generation sequencing
Journal
Biotechnology journal
ISSN: 1860-7314
Titre abrégé: Biotechnol J
Pays: Germany
ID NLM: 101265833
Informations de publication
Date de publication:
Mar 2024
Mar 2024
Historique:
revised:
14
02
2024
received:
18
12
2023
accepted:
16
02
2024
medline:
26
3
2024
pubmed:
26
3
2024
entrez:
26
3
2024
Statut:
ppublish
Résumé
DNA ligases catalyze bond formation in the backbone of nucleic acids via the formation of a phosphodiester bond between adjacent 5' phosphates and 3' hydroxyl groups on one strand of the duplex. While DNA ligases preferentially ligate single breaks in double-stranded DNA (dsDNA), they are capable of ligating a multitude of other nucleic acid substrates like blunt-ended dsDNA, TA overhangs, short overhangs and various DNA-RNA hybrids. Here we report a novel DNA ligase from Cronobacter phage CR 9 (R2D Ligase) with an unexpected DNA-to-RNA ligation activity. The R2D ligase shows excellent efficiency when ligating DNA to either end of RNA molecules using a DNA template. Furthermore, we show that DNA can be ligated simultaneously to both the 5' and 3' ends of microRNA-like molecules in a single reaction mixture. Abortive adenylated side product formation is suppressed at lower ATP concentrations and the ligase reaction reaches near completion when ligating RNA-to-DNA or DNA-to-RNA. The ligation of a DNA strand to the 5'-PO
Identifiants
pubmed: 38528369
doi: 10.1002/biot.202300711
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
e2300711Informations de copyright
© 2024 The Authors. Biotechnology Journal published by Wiley‐VCH GmbH.
Références
Lohman, G. J. S., Chen, L., & Evans, T. C., Jr (2011). Kinetic characterization of single strand break ligation in duplex DNA by T4 DNA ligase. The Journal of biological chemistry, 286(51), 44187–44196. https://doi.org/10.1074/jbc.M111.284992
Shuman, S. (2009). DNA ligases: Progress and prospect. The Journal of Biological Chemistry, 284(26), 17365–17369. https://doi.org/10.1074/jbc.R900017200
Williamson, A., & Leiros, H. S. (2020). Structural insight into DNA joining: From conserved mechanisms to diverse scaffolds. Nucleic acids research, 48(15), 8225–8242. https://doi.org/10.1093/nar/gkaa307
Gibson, D. G., Young, L., Chuang, R. Y., Venter, J. C., Hutchison, C. A., 3rd, & Smith, H. O. (2009). Enzymatic assembly of DNA molecules up to several hundred kilobases. Nature Methods, 6(5), 343–345. https://doi.org/10.1038/nmeth.1318
Hughes, R. A., & Ellington, A. D. (2017). Synthetic DNA synthesis and assembly: Putting the synthetic in synthetic biology. Cold Spring Harbor Perspectives in Biology, 9(1), a023812. https://doi.org/10.1101/cshperspect.a023812
Reuter, J. A., Spacek, D. V., & Snyder, M. P. (2015). High‐throughput sequencing technologies. Molecular Cell, 58(4), 586–597. https://doi.org/10.1016/j.molcel.2015.05.004
Lohman, G. J. S., Tabor, S., & Nichols, N. M. (2011). DNA ligases. Current Protocols in Molecular Biology, 94(1), 3.14.1–3.14.7. https://doi.org/10.1002/0471142727.mb0314s94
Rossi, R. (1997). Functional characterization of the T4 DNA ligase: A new insight into the mechanism of action. Nucleic acids research, 25(11), 2106–2113. https://doi.org/10.1093/nar/25.11.2106
Shi, K., Bohl, T. E., Park, J., Zasada, A., Malik, S., Banerjee, S., Tran, V., Li, N., Yin, Z., Kurniawan, F., Orellana, K., & Aihara, H. (2018). T4 DNA ligase structure reveals a prototypical ATP‐dependent ligase with a unique mode of sliding clamp interaction. Nucleic acids research, 46(19), 10474–10488. https://doi.org/10.1093/nar/gky776
Bullard, D. R., & Bowater, R. P. (2006). Direct comparison of nick‐joining activity of the nucleic acid ligases from bacteriophage T4. Biochemical Journal, 398(1), 135–144. https://doi.org/10.1042/BJ20060313
Nair, P. A., Nandakumar, J., Smith, P., Odell, M., Lima, C. D., & Shuman, S. (2007). Structural basis for nick recognition by a minimal pluripotent DNA ligase. Nature Structural & Molecular Biology, 14(8), 770–778. https://doi.org/10.1038/nsmb1266
Lohman, G. J., Zhang, Y., Zhelkovsky, A. M., Cantor, E. J., & Evans, T. C., Jr (2014). Efficient DNA ligation in DNA–RNA hybrid helices by Chlorella virus DNA ligase. Nucleic Acids Research, 42(3), 1831–1844. https://doi.org/10.1093/nar/gkt1032
Kim, J. H., Lee, K. K., Sun, Y., Seo, G. J., Cho, S. S., Kwon, S. H., & Kwon, S. T. (2013). Broad nucleotide cofactor specificity of DNA ligase from the hyperthermophilic crenarchaeon Hyperthermus butylicus and its evolutionary significance. Extremophiles : life under extreme conditions, 17(3), 515–522. https://doi.org/10.1007/s00792‐013‐0536‐6
Taylor, M. R. (2014). the role of divalent metal ions in enzymatic DNA ligation, Doctoral dissertation, University of Michigan.
Chan, S. H., Whipple, J. M., Dai, N., Kelley, T. M., Withers, K., Tzertzinis, G., Corrêa, I. R., Jr, & Robb, G. B. (2022). RNase H‐based analysis of synthetic mRNA 5′ cap incorporation. RNA (New York, N.Y.), 28(8), 1144–1155. https://doi.org/10.1261/rna.079173.122