Citation: Xiao-Meng Tang, Tian-Tian Ye, Xue-Jiao You, Xiao-Ming Yin, Jiang-Hui Ding, Wen-Xuan Shao, Meng-Yuan Chen, Bi-Feng Yuan, Yu-Qi Feng. Mass spectrometry profiling analysis enables the identification of new modifications in ribosomal RNA[J]. Chinese Chemical Letters, ;2023, 34(3): 107531. doi: 10.1016/j.cclet.2022.05.045 shu

Mass spectrometry profiling analysis enables the identification of new modifications in ribosomal RNA

a.
Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China
b.
School of Public Health, Wuhan University, Wuhan 430071, China

bfyuan@whu.edu.cn

Received Date: 7 March 2022
Revised Date: 5 May 2022
Accepted Date: 13 May 2022
Available Online: 17 May 2022

Figures(4)

Ribosomal RNAs (rRNAs) provide the structural framework of ribosomes and play critical roles in protein translation. In ribosome biogenesis, rRNAs acquire various modifications that can influence the structure and catalytic activity of ribosomes. However, rRNA modifications in plants have yet to be fully defined. Herein, we proposed a method to purify rRNAs by a successive isolation with different strategies, including polyA-based mRNA depletion and agarose gel electrophoresis-based purification, with which highly pure rRNAs could be obtained. In addition, we developed a liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS) method to systematically profile and characterize modifications from the isolated highly pure plant 18S rRNA and 25S rRNA. LC-ESI-MS/MS analysis showed that 10 and 12 kinds of modifications were present in plant 18S rRNA and 25S rRNA, respectively. Notably, among these identified modifications, 2 kinds of modifications of N²,N²-dimethylguanosine (m^2,2G) and N⁶,N⁶-dimethyladenosine (m^6,6A) in 18S rRNA, and 4 kinds of modifications of m^2,2G, m^6,6A, N7-methylguanosine (m⁷G) and 3-methyluridin (m³U) in 25S rRNA, were first reported to be present in plants. Moreover, exposure of Arabidopsis thaliana to cadmium (Cd) led to significant changes of modifications in both 18S rRNA and 25S rRNA of plants, indicating that rRNA modifications play important roles in response to environmental stress. The discovery of new modifications in plant rRNAs improves the spectra of plant rRNA modifications and may promote the investigation of the functional roles of plant ribosomes in regulating gene expression.
- Ribosomal RNA,
- RNA modification,
- Plant,
- Arabidopsis thaliana,
- Profiling,
- Mass spectrometry
1. [1]
  P. Boccaletto, F. Stefaniak, A. Ray, et al., Nucleic Acids Res. 50 (2022) D231–D235. doi: 10.1093/nar/gkab1083
2. [2]
  Y. Dai, C.B. Qi, Y. Feng, et al., Anal. Chem. 93 (2021) 6938–6946. doi: 10.1021/acs.analchem.0c04630
3. [3]
  M.Y. Cheng, X.J. You, J.H. Ding, et al., Chem. Sci. 12 (2021) 8149–8156. doi: 10.1039/D1SC01972D
4. [4]
  M.Y. Chen, C.B. Qi, X.M. Tang, et al., Chin. Chem. Lett. 33 (2022) 3772–3776. doi: 10.1016/j.cclet.2021.12.008
5. [5]
  M. Frye, B.T. Harada, M. Behm, C. He, Science 361 (2018) 1346–1349. doi: 10.1126/science.aau1646
6. [6]
  I. Barbieri, T. Kouzarides, Nat. Rev. Cancer 20 (2020) 303–322. doi: 10.1038/s41568-020-0253-2
7. [7]
  J.C. Bowman, A.S. Petrov, M. Frenkel-Pinter, P.I. Penev, L.D. Williams, Chem. Rev. 120 (2020) 4848–4878. doi: 10.1021/acs.chemrev.9b00742
8. [8]
  J. Jiang, H. Seo, C.S. Chow, Acc. Chem. Res. 49 (2016) 893–901. doi: 10.1021/acs.accounts.6b00014
9. [9]
  S.K. Natchiar, A.G. Myasnikov, H. Kratzat, I. Hazemann, B.P. Klaholz, Nature 551 (2017) 472–477. doi: 10.1038/nature24482
10. [10]
  O. Sergeeva, A. Bogdanov, P. Sergiev, Biochimie 117 (2015) 110–118. doi: 10.1016/j.biochi.2014.11.019
11. [11]
  H.C. Duan, L.H. Wei, C. Zhang, et al., Plant Cell 29 (2017) 2995–3011. doi: 10.1105/tpc.16.00912
12. [12]
  X. Cui, Z. Liang, L. Shen, et al., Mol. Plant 10 (2017) 1387–1399. doi: 10.1016/j.molp.2017.09.013
13. [13]
  J. Azevedo-Favory, C. Gaspin, L. Ayadi, et al., RNA Biol. 18 (2021) 1760–1777. doi: 10.1080/15476286.2020.1869892
14. [14]
  L. Sun, Y. Xu, S. Bai, et al., J. Exp. Bot. 70 (2019) 5089–5600. doi: 10.1093/jxb/erz273
15. [15]
  C. Enroth, L.D. Poulsen, S. Iversen, et al., Nucleic Acids Res. 47 (2019) e126. doi: 10.1093/nar/gkz736
16. [16]
  A.L. Burgess, R. David, I.R. Searle, BMC Plant Biol. 15 (2015) 199. doi: 10.1186/s12870-015-0580-8
17. [17]
  D. Palm, D. Streit, T. Shanmugam, et al., Nucleic Acids Res. 47 (2019) 1880–1895. doi: 10.1093/nar/gky1261
18. [18]
  C.B. Qi, J.H. Ding, B.F. Yuan, Y.Q. Feng, Chin. Chem. Lett. 30 (2019) 1618–1626. doi: 10.1016/j.cclet.2019.02.005
19. [19]
  M.D. Lan, B.F. Yuan, Y.Q. Feng, Chin. Chem. Lett. 30 (2019) 1–6. doi: 10.1016/j.cclet.2018.04.021
20. [20]
  M. Helm, Y. Motorin, Nat. Rev. Genet. 18 (2017) 275–291. doi: 10.1038/nrg.2016.169
21. [21]
  H. Grosjean, G. Keith, L. Droogmans, Methods Mol. Biol. 265 (2004) 357–391. doi: 10.1385/1-59259-775-0:357
22. [22]
  L. Shen, Z. Liang, H. Yu, Bio. Protoc. 7 (2017) e2095.
23. [23]
  B. Chen, B.F. Yuan, Y.Q. Feng, Anal. Chem. 91 (2019) 743–756. doi: 10.1021/acs.analchem.8b04078
24. [24]
  M.Y. Chen, Z. Gui, K.K. Chen, et al., Chin. Chem. Lett. 33 (2022) 2086–2090. doi: 10.1016/j.cclet.2021.08.094
25. [25]
  C.B. Qi, H.P. Jiang, J. Xiong, B.F. Yuan, Y.Q. Feng, Chin. Chem. Lett. 30 (2019) 553–557. doi: 10.1016/j.cclet.2018.11.029
26. [26]
  X.J. You, L. Li, T.T. Ji, et al., Chin. Chem. Lett. 34 (2023) 107181. doi: 10.1016/j.cclet.2022.01.074
27. [27]
  Y.J. Feng, X.J. You, J.H. Ding, et al., Anal. Chem. 94 (2022) 4747–4755. doi: 10.1021/acs.analchem.1c05292
28. [28]
  F.L. Liu, T.T. Ye, J.H. Ding, et al., Anal. Chem. 93 (2021) 6848–6856. doi: 10.1021/acs.analchem.1c00915
29. [29]
  Q.Y. Cheng, J. Xiong, C.J. Ma, et al., Chem. Sci. 11 (2020) 1878–1891. doi: 10.1039/C9SC05094A
30. [30]
  X.J. You, T. Liu, C.J. Ma, et al., Anal. Chem. 91 (2019) 10477–10483. doi: 10.1021/acs.analchem.9b01318
31. [31]
  M. Sakurai, T. Yano, H. Kawabata, H. Ueda, T. Suzuki, Nat. Chem. Biol. 6 (2010) 733–740. doi: 10.1038/nchembio.434
32. [32]
  K.D. Meyer, Y. Saletore, P. Zumbo, et al., Cell 149 (2012) 1635–1646. doi: 10.1016/j.cell.2012.05.003
33. [33]
  Z. Zhang, L.Q. Chen, Y.L. Zhao, et al., Sci. Adv. 5 (2019) eaax0250. doi: 10.1126/sciadv.aax0250
34. [34]
  A.J. Westermann, S.A. Gorski, J. Vogel, Nat. Rev. Microbiol. 10 (2012) 618–630. doi: 10.1038/nrmicro2852
35. [35]
  C.T. Chan, M. Dyavaiah, M.S. DeMott, et al., PLoS Genet. 6 (2010) e1001247. doi: 10.1371/journal.pgen.1001247
36. [36]
  J.M. Chu, T.T. Ye, C.J. Ma, et al., ACS Chem. Biol. 13 (2018) 3243–3250. doi: 10.1021/acschembio.7b00906
37. [37]
  Q. Gu, Z. Chen, W. Cui, et al., Ecotoxicol. Environ. Saf. 147 (2018) 861–871. doi: 10.1016/j.ecoenv.2017.09.054
38. [38]
  B. Hussain, M.N. Ashraf, S.U. Rahman, et al., Sci. Total Environ. 754 (2021) 142188. doi: 10.1016/j.scitotenv.2020.142188
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沈阳化工大学材料科学与工程学院沈阳 110142