High frequency of +1 programmed ribosomal frameshifting in Euplotes octocarinatus

Scientific Reports
Ruanlin WangA Liang

Abstract

Programmed -1 ribosomal frameshifting (-1 PRF) has been identified as a mechanism to regulate the expression of many viral genes and some cellular genes. The slippery site of -1 PRF has been well characterized, whereas the +1 PRF signal and the mechanism involved in +1 PRF remain poorly understood. Previous study confirmed that +1 PRF is required for the synthesis of protein products in several genes of ciliates from the genus Euplotes. To accurately assess the frequency of genes requiring frameshift in Euplotes, the macronuclear genome and transcriptome of Euplotes octocarinatus were analyzed in this study. A total of 3,700 +1 PRF candidate genes were identified from 32,353 transcripts, and the gene products of these putative +1 PRFs were mainly identified as protein kinases. Furthermore, we reported a putative suppressor tRNA of UAA which may provide new insights into the mechanism of +1 PRF in euplotids. For the first time, our transcriptome-wide survey of +1 PRF in E. octocarinatus provided a dataset which serves as a valuable resource for the future understanding of the mechanism underlying +1 PRF.

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Citations

Nov 22, 2016·Nature Structural & Molecular Biology·Alexei V LobanovVadim N Gladyshev
Dec 8, 2016·Nucleic Acids Research·Dmitry E AndreevIvan N Shatsky
Jan 21, 2018·BMC Genomics·Ruan-Lin WangAi-Hua Liang
Feb 13, 2019·Life·Christian J Michel
Aug 17, 2019·The Journal of Eukaryotic Microbiology·Ruanlin WangAihua Liang
Jan 9, 2020·Science Advances·Junhong ChoiJoseph D Puglisi
Dec 10, 2016·Science·Boris Zinshteyn, Rachel Green
Aug 14, 2020·Genome Biology and Evolution·Yi FengLaura F Landweber
Jul 15, 2021·Computational and Structural Biotechnology Journal·Kai-Chun Chang, Jin-Der Wen
Aug 29, 2021·Journal of Genetics and Genomics = Yi Chuan Xue Bao·Chao LiYing Yan

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Datasets Mentioned

BETA
PRJNA294366
SRX1267944
SRX1270715
SRX1270740

Methods Mentioned

BETA
RNA-seq
RNA Assay

Software Mentioned

- Toolkit
fastq
LASTZ
TBLASTN
EMBOSS package
HMMER3
Mira
BLASTP
custom Perl
Pfamscan

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