Pseudouridines on Trypanosoma brucei spliceosomal small nuclear RNAs and their implication for RNA and protein interactions

K. Shanmugha Rajan, Tirza Doniger, Smadar Cohen-Chalamish, Dana Chen, Oz Semo, Saurav Aryal, Efrat Glick Saar, Vaibhav Chikne, Doron Gerber, Ron Unger, Christian Tschudi, Shulamit Michaeli

Research output: Contribution to journalArticlepeer-review

32 Scopus citations

Abstract

The parasite Trypanosoma brucei, the causative agent of sleeping sickness, cycles between an insect and a mammalian host. Here, we investigated the presence of pseudouridines (s) on the spliceosomal small nuclear RNAs (snRNAs), which may enable growth at the very different temperatures characterizing the two hosts. To this end, we performed the first high-throughput mapping of spliceosomal snRNA s by small RNA-seq. The analysis revealed 42 s on T. brucei snRNAs, which is the highest number reported so far. We show that a trypanosome protein analogous to human protein WDR79, is essential for guiding on snRNAs but not on rRNAs. snoRNA species implicated in snRNA pseudouridylation were identified by a genome-wide approach based on ligation of RNAs following in vivo UV cross-linking. snRNA s are guided by single hairpin snoRNAs, also implicated in rRNA modification. Depletion of such guiding snoRNA by RNAi compromised the guided modification on snRNA and reduced parasite growth at elevated temperatures. We further demonstrate that strengthens U4/U6 RNA–RNA and U2B"/U2A’ proteins-U2 snRNA interaction at elevated temperatures. The existence of single hairpin RNAs that modify both the spliceosome and ribosome RNAs is unique for these parasites, and may be related to their ability to cycle between their two hosts that differ in temperature.

Original languageEnglish
Pages (from-to)7633-7647
Number of pages15
JournalNucleic Acids Research
Volume47
Issue number14
Early online date31 May 2019
DOIs
StatePublished - 22 Aug 2019

Bibliographical note

Publisher Copyright:
© The Author(s) 2019.

Funding

Israel–US Binational Science Foundation (BSF); Israel Science Foundation; NIH grant [RO1 AI 056333]. Funding for open access charge: Israel–US Binational Science Foundation (BSF); Israel Science Foundation; NIH grant [RO1 AI 056333]. Conflict of interest statement. None declared.

FundersFunder number
US Binational Science Foundation
National Institutes of HealthRO1 AI 056333
National Institute of Allergy and Infectious DiseasesR01AI110325
United States-Israel Binational Science Foundation
Israel Science Foundation

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