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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.


Related in: MedlinePlus

Length distribution of nanochromosomes of three highly fragmented macronuclear genomes.X axis is the contig length (nucleotides), Y axis is the frequency of contigs with the indicated lengths. The histograms show normalized frequencies for 29,413 nanochromosomes of Euplotes octocarinatus, 15,085 nanochromosomes of Oxytricha trifallax and 16,029 nanochromosomes of Stylonychia lemnae.
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f1: Length distribution of nanochromosomes of three highly fragmented macronuclear genomes.X axis is the contig length (nucleotides), Y axis is the frequency of contigs with the indicated lengths. The histograms show normalized frequencies for 29,413 nanochromosomes of Euplotes octocarinatus, 15,085 nanochromosomes of Oxytricha trifallax and 16,029 nanochromosomes of Stylonychia lemnae.

Mentions: Based on the GC content results of all contigs (Fig. S3), we suspected that the initial assembly contained a mixture of target DNA, bacterial DNA (endosymbionts of E. octocarinatus) and mitochondrial DNA (some sub-peaks were located behind the major peak). Therefore, a series of filters was applied to exclude the contamination (see Methods), and 1,628 bacterial contigs and 72 mitochondrial contigs were removed from the initial assembly. Finally, a total of 41,980 contigs with an average length of 2,117 bp were used as the E. octocarinatus MAC genome assembly, and most (70.1%) of these contigs were capped with telomeres on both ends. The completeness of the genome was supported by the assessment results (see Methods). Subsequently, we compared two reported highly fragmented macronuclear genomes3031 with the E. octocarinatus assembly. Similar to Oxytricha and Stylonychia, few nanochromosomes were assembled at either extremities of the length distribution in Euplotes (Fig. 1). Only 283 were shorter than 500 bp and 15 were longer than 15 kb.


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

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

Length distribution of nanochromosomes of three highly fragmented macronuclear genomes.X axis is the contig length (nucleotides), Y axis is the frequency of contigs with the indicated lengths. The histograms show normalized frequencies for 29,413 nanochromosomes of Euplotes octocarinatus, 15,085 nanochromosomes of Oxytricha trifallax and 16,029 nanochromosomes of Stylonychia lemnae.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f1: Length distribution of nanochromosomes of three highly fragmented macronuclear genomes.X axis is the contig length (nucleotides), Y axis is the frequency of contigs with the indicated lengths. The histograms show normalized frequencies for 29,413 nanochromosomes of Euplotes octocarinatus, 15,085 nanochromosomes of Oxytricha trifallax and 16,029 nanochromosomes of Stylonychia lemnae.
Mentions: Based on the GC content results of all contigs (Fig. S3), we suspected that the initial assembly contained a mixture of target DNA, bacterial DNA (endosymbionts of E. octocarinatus) and mitochondrial DNA (some sub-peaks were located behind the major peak). Therefore, a series of filters was applied to exclude the contamination (see Methods), and 1,628 bacterial contigs and 72 mitochondrial contigs were removed from the initial assembly. Finally, a total of 41,980 contigs with an average length of 2,117 bp were used as the E. octocarinatus MAC genome assembly, and most (70.1%) of these contigs were capped with telomeres on both ends. The completeness of the genome was supported by the assessment results (see Methods). Subsequently, we compared two reported highly fragmented macronuclear genomes3031 with the E. octocarinatus assembly. Similar to Oxytricha and Stylonychia, few nanochromosomes were assembled at either extremities of the length distribution in Euplotes (Fig. 1). Only 283 were shorter than 500 bp and 15 were longer than 15 kb.

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.


Related in: MedlinePlus