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High frequency of +1 programmed ribosomal frameshifting in Euplotes octocarinatus.

Wang R, Xiong J, Wang W, Miao W, Liang A - Sci Rep (2016)

Bottom Line: Previous study confirmed that +1 PRF is required for the synthesis of protein products in several genes of ciliates from the genus Euplotes.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.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China.

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.

No MeSH data available.


WebLogo displaying conserved sequences associated with frameshift sites.Sizes of letters denote information content, or sequence conservation, at each position. The analysis is based on the alignment of 30 bp preceding and following the frameshift motif from 4,545 predicted slippery sites.
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f4: WebLogo displaying conserved sequences associated with frameshift sites.Sizes of letters denote information content, or sequence conservation, at each position. The analysis is based on the alignment of 30 bp preceding and following the frameshift motif from 4,545 predicted slippery sites.

Mentions: With sufficient samples of +1 PRF genes, the conserved sequence elements which might facilitate frameshifting were checked. To search the potential conserved sequence elements, 30 bp upstream and downstream of the conserved slippery sequence motif from 4,545 predicted slippery sites were extracted and analysed using WebLogo36. Consistent with a previous report, no conserved sequence element was found except the slippery site sequence 5′-WWW TAR-3′ (W=A or T, Fig. 4), suggesting that frameshifting does not depend on other sequence motifs.


High frequency of +1 programmed ribosomal frameshifting in Euplotes octocarinatus.

Wang R, Xiong J, Wang W, Miao W, Liang A - Sci Rep (2016)

WebLogo displaying conserved sequences associated with frameshift sites.Sizes of letters denote information content, or sequence conservation, at each position. The analysis is based on the alignment of 30 bp preceding and following the frameshift motif from 4,545 predicted slippery sites.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4759687&req=5

f4: WebLogo displaying conserved sequences associated with frameshift sites.Sizes of letters denote information content, or sequence conservation, at each position. The analysis is based on the alignment of 30 bp preceding and following the frameshift motif from 4,545 predicted slippery sites.
Mentions: With sufficient samples of +1 PRF genes, the conserved sequence elements which might facilitate frameshifting were checked. To search the potential conserved sequence elements, 30 bp upstream and downstream of the conserved slippery sequence motif from 4,545 predicted slippery sites were extracted and analysed using WebLogo36. Consistent with a previous report, no conserved sequence element was found except the slippery site sequence 5′-WWW TAR-3′ (W=A or T, Fig. 4), suggesting that frameshifting does not depend on other sequence motifs.

Bottom Line: Previous study confirmed that +1 PRF is required for the synthesis of protein products in several genes of ciliates from the genus Euplotes.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.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China.

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.

No MeSH data available.