RNA structural probing of guanine and uracil nucleotides in yeast.
Journal
PloS one
ISSN: 1932-6203
Titre abrégé: PLoS One
Pays: United States
ID NLM: 101285081
Informations de publication
Date de publication:
2023
2023
Historique:
received:
16
03
2023
accepted:
17
06
2023
medline:
10
7
2023
pubmed:
7
7
2023
entrez:
7
7
2023
Statut:
epublish
Résumé
RNA structure can be essential for its cellular function. Therefore, methods to investigate the structure of RNA in vivo are of great importance for understanding the role of cellular RNAs. RNA structure probing is an indirect method to asess the three-dimensional structure of RNA by analyzing the reactivity of different nucleotides to chemical modifications. Dimethyl sulfate (DMS) is a well-established compound that reports on base pairing context of adenine (A) and cytidine (C) in-vitro and in-vivo, but is not reactive to guanine (G) or uracil (U). Recently, new compounds were used to modify Gs and Us in plant, bacteria, and human cells. To complement the scope of RNA structural probing by chemical modifications in the model organism yeast, we analyze the effectiveness of guanine modification by the glyoxal family in Saccharomyces cerevisiae and Candida albicans. We show that within glyoxal family of compounds, phenylglyoxal (PGO) is the best guanine probe for structural probing in S. cerevisiae and C. albicans. Further, we show that PGO treatment does not affect the processing of different RNA species in the cell and is not toxic for the cells under the conditions we have established for RNA structural probing. We also explore the effectiveness of uracil modification by Cyclohexyl-3-(2-Morpholinoethyl) Carbodiimide metho-p-Toluenesulfonate (CMCT) in vivo and demonstrate that uracils can be modified by CMCT in S. cerevisiae in vivo. Our results provide the conditions for in vivo probing the reactivity of guanine and uracil nucleotides in RNA structures in yeast and offer a valuable tool for studying RNA structure and function in two widely used yeast model systems.
Identifiants
pubmed: 37418367
doi: 10.1371/journal.pone.0288070
pii: PONE-D-23-07908
pmc: PMC10328344
doi:
Substances chimiques
RNA
63231-63-0
Guanine
5Z93L87A1R
1-cyclohexyl-3-(2-(4-morpholinyl)ethyl)carbodiimide
15580-20-8
Uracil Nucleotides
0
Glyoxal
50NP6JJ975
Carbodiimides
0
Uracil
56HH86ZVCT
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
e0288070Subventions
Organisme : NIGMS NIH HHS
ID : R35 GM138123
Pays : United States
Informations de copyright
Copyright: © 2023 Xiao et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Déclaration de conflit d'intérêts
The authors have declared that no competing interests exist.
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