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Operons are a conserved feature of nematode genomes.

Pettitt J, Philippe L, Sarkar D, Johnston C, Gothe HJ, Massie D, Connolly B, Müller B - Genetics (2014)

Bottom Line: The organization of genes into operons, clusters of genes that are co-transcribed to produce polycistronic pre-mRNAs, is a trait found in a wide range of eukaryotic groups, including multiple animal phyla.We have nevertheless identified putative operons conserved between Enoplea and Chromadorea.Our data suggest that operons and "spliced leader" (SL) trans-splicing predate the radiation of the nematode phylum, an inference which is supported by the phylogenetic profile of proteins known to be involved in nematode SL trans-splicing.

View Article: PubMed Central - PubMed

Affiliation: School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, United Kingdom j.pettitt@abdn.ac.uk.

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T. muris SL sequences and SL RNA structure. (A) Tmu-SL1–13 genes were identified using a combination of cDNA sequencing and bioinformatics tools as described in Materials and Methods. Tmu-SL12 was found by 5′ RACE trans-spliced to nuaf-3 mRNA, and Tmu-SL13 was found trans-spliced to aph-1 mRNA. In the alignment, only the SL sequences are shown. T. muris SL sequences were manually aligned and conserved groups are countershaded. C. elegans SL1 and SL2 and the previously identified P. punctatus SL sequences were included for comparison. (B) The intron of Tmu-SL2 was experimentally identified and also found in the genome sequence. The proposed secondary structure was produced using M-fold (Zuker 2003). The SL sequence is shown in outline font and the putative Sm sequence motif is countershaded.
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fig2: T. muris SL sequences and SL RNA structure. (A) Tmu-SL1–13 genes were identified using a combination of cDNA sequencing and bioinformatics tools as described in Materials and Methods. Tmu-SL12 was found by 5′ RACE trans-spliced to nuaf-3 mRNA, and Tmu-SL13 was found trans-spliced to aph-1 mRNA. In the alignment, only the SL sequences are shown. T. muris SL sequences were manually aligned and conserved groups are countershaded. C. elegans SL1 and SL2 and the previously identified P. punctatus SL sequences were included for comparison. (B) The intron of Tmu-SL2 was experimentally identified and also found in the genome sequence. The proposed secondary structure was produced using M-fold (Zuker 2003). The SL sequence is shown in outline font and the putative Sm sequence motif is countershaded.

Mentions: As part of this analysis, we identified spliced leaders in T. muris, leading to the discovery of 13 Tmu-SLs (Figure 2; Table S2). Previous studies have shown that the primary sequences of spliced leaders in T. spiralis are much more variable than those found in the Chromadorea (Pettitt et al. 2008), and many lack the conserved motifs that characterize spliced leaders from these latter nematodes. In contrast, those of P. punctatus do not show the same diversity and display a greater degree of sequence similarity to the Chromadorid spliced leaders (Harrison et al. 2010). Analysis of the 13 distinct T. muris spliced leaders, designated Tmu-SL1–13, support this view, since the T. muris spliced leaders possess the same 5′ GGUWW and central CCC motifs that are highly conserved in the P. punctatus spliced leaders and Chromadorid SL1 and SL2 families, but missing in most of the T. spiralis spliced leaders. The presence of canonical nematode spliced leaders in T. muris and P. punctatus, despite the fact that the former nematode is more closely related to T. spiralis, supports the inference that the T. spiralis spliced leaders are derived features.


Operons are a conserved feature of nematode genomes.

Pettitt J, Philippe L, Sarkar D, Johnston C, Gothe HJ, Massie D, Connolly B, Müller B - Genetics (2014)

T. muris SL sequences and SL RNA structure. (A) Tmu-SL1–13 genes were identified using a combination of cDNA sequencing and bioinformatics tools as described in Materials and Methods. Tmu-SL12 was found by 5′ RACE trans-spliced to nuaf-3 mRNA, and Tmu-SL13 was found trans-spliced to aph-1 mRNA. In the alignment, only the SL sequences are shown. T. muris SL sequences were manually aligned and conserved groups are countershaded. C. elegans SL1 and SL2 and the previously identified P. punctatus SL sequences were included for comparison. (B) The intron of Tmu-SL2 was experimentally identified and also found in the genome sequence. The proposed secondary structure was produced using M-fold (Zuker 2003). The SL sequence is shown in outline font and the putative Sm sequence motif is countershaded.
© Copyright Policy - open-access
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4125394&req=5

fig2: T. muris SL sequences and SL RNA structure. (A) Tmu-SL1–13 genes were identified using a combination of cDNA sequencing and bioinformatics tools as described in Materials and Methods. Tmu-SL12 was found by 5′ RACE trans-spliced to nuaf-3 mRNA, and Tmu-SL13 was found trans-spliced to aph-1 mRNA. In the alignment, only the SL sequences are shown. T. muris SL sequences were manually aligned and conserved groups are countershaded. C. elegans SL1 and SL2 and the previously identified P. punctatus SL sequences were included for comparison. (B) The intron of Tmu-SL2 was experimentally identified and also found in the genome sequence. The proposed secondary structure was produced using M-fold (Zuker 2003). The SL sequence is shown in outline font and the putative Sm sequence motif is countershaded.
Mentions: As part of this analysis, we identified spliced leaders in T. muris, leading to the discovery of 13 Tmu-SLs (Figure 2; Table S2). Previous studies have shown that the primary sequences of spliced leaders in T. spiralis are much more variable than those found in the Chromadorea (Pettitt et al. 2008), and many lack the conserved motifs that characterize spliced leaders from these latter nematodes. In contrast, those of P. punctatus do not show the same diversity and display a greater degree of sequence similarity to the Chromadorid spliced leaders (Harrison et al. 2010). Analysis of the 13 distinct T. muris spliced leaders, designated Tmu-SL1–13, support this view, since the T. muris spliced leaders possess the same 5′ GGUWW and central CCC motifs that are highly conserved in the P. punctatus spliced leaders and Chromadorid SL1 and SL2 families, but missing in most of the T. spiralis spliced leaders. The presence of canonical nematode spliced leaders in T. muris and P. punctatus, despite the fact that the former nematode is more closely related to T. spiralis, supports the inference that the T. spiralis spliced leaders are derived features.

Bottom Line: The organization of genes into operons, clusters of genes that are co-transcribed to produce polycistronic pre-mRNAs, is a trait found in a wide range of eukaryotic groups, including multiple animal phyla.We have nevertheless identified putative operons conserved between Enoplea and Chromadorea.Our data suggest that operons and "spliced leader" (SL) trans-splicing predate the radiation of the nematode phylum, an inference which is supported by the phylogenetic profile of proteins known to be involved in nematode SL trans-splicing.

View Article: PubMed Central - PubMed

Affiliation: School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, United Kingdom j.pettitt@abdn.ac.uk.

Show MeSH
Related in: MedlinePlus