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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.


Enriched GO terms of +1 PRF transcripts were analyzed with Bingo.Each circle represents a GO term, arrows indicate pairs of GO terms with a parent-child relationship. Colored circles are statistically significant overrepresented GO terms (functions); the deeper of the color, the smaller the corrected p-value (more significant). Overrepresented molecular functions (A) and biological processes (B).
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f3: Enriched GO terms of +1 PRF transcripts were analyzed with Bingo.Each circle represents a GO term, arrows indicate pairs of GO terms with a parent-child relationship. Colored circles are statistically significant overrepresented GO terms (functions); the deeper of the color, the smaller the corrected p-value (more significant). Overrepresented molecular functions (A) and biological processes (B).

Mentions: A GO enrichment analysis of putative +1 PRF genes was performed to investigate the functional enrichment of putative +1 PRF genes. Results showed that the identified putative +1 PRF genes were significantly overrepresented in the regulation of various biological processes such as dephosphorylation, protein amino acid phosphorylation, and ubiquitin-dependent protein catabolic process (Fig. 3).


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

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

Enriched GO terms of +1 PRF transcripts were analyzed with Bingo.Each circle represents a GO term, arrows indicate pairs of GO terms with a parent-child relationship. Colored circles are statistically significant overrepresented GO terms (functions); the deeper of the color, the smaller the corrected p-value (more significant). Overrepresented molecular functions (A) and biological processes (B).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f3: Enriched GO terms of +1 PRF transcripts were analyzed with Bingo.Each circle represents a GO term, arrows indicate pairs of GO terms with a parent-child relationship. Colored circles are statistically significant overrepresented GO terms (functions); the deeper of the color, the smaller the corrected p-value (more significant). Overrepresented molecular functions (A) and biological processes (B).
Mentions: A GO enrichment analysis of putative +1 PRF genes was performed to investigate the functional enrichment of putative +1 PRF genes. Results showed that the identified putative +1 PRF genes were significantly overrepresented in the regulation of various biological processes such as dephosphorylation, protein amino acid phosphorylation, and ubiquitin-dependent protein catabolic process (Fig. 3).

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.