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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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Evidence for an evolutionarily conserved nematode operon. (A) The structure of the cpt-2-nuaf-3 genomic regions from a range of nematode species mapped onto the nematode phylogeny. Genes are represented by arrows, and the gray lines represent the intercistronic regions (ICRs). Numbers above the ICRs represent the distances, in base pairs, between the stop and start codons of the upstream and downstream genes, respectively. The C. elegans operon numbers are given where appropriate. Fractions below the T. spiralis and T. muris genes represent the proportion of cDNAs derived from those genes that begins with a spliced leader sequence. (B) Detecting polycistronic RNAs derived from the cpt-2∼nuaf-3 operon in T. spiralis. The exon–intron structures of the amplicons used to identify polycistronic RNAs are shown, with exons represented by boxes (shaded to identify the genes from which they are derived using the same color coding that was used in A. The region removed during operon processing is represented by cream-colored boxes. The positions of the SL trans-splice 3′ spliced sites are indicated.
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fig3: Evidence for an evolutionarily conserved nematode operon. (A) The structure of the cpt-2-nuaf-3 genomic regions from a range of nematode species mapped onto the nematode phylogeny. Genes are represented by arrows, and the gray lines represent the intercistronic regions (ICRs). Numbers above the ICRs represent the distances, in base pairs, between the stop and start codons of the upstream and downstream genes, respectively. The C. elegans operon numbers are given where appropriate. Fractions below the T. spiralis and T. muris genes represent the proportion of cDNAs derived from those genes that begins with a spliced leader sequence. (B) Detecting polycistronic RNAs derived from the cpt-2∼nuaf-3 operon in T. spiralis. The exon–intron structures of the amplicons used to identify polycistronic RNAs are shown, with exons represented by boxes (shaded to identify the genes from which they are derived using the same color coding that was used in A. The region removed during operon processing is represented by cream-colored boxes. The positions of the SL trans-splice 3′ spliced sites are indicated.

Mentions: The analysis of one of the two SL trans-spliced T. muris mRNAs (GenBank accession no. FF145866) led to the identification of a putative operon conserved between multiple nematodes (Figure 3A). The two genes contained in these putative operons have C. elegans homologs, cpt-2 and nuaf-3, respectively, which are in the same operon (CEOP4424) (Figure 3A), although there is an additional gene, prx-14, located between these genes in CEOP4424 that is not present in the putative homologous T. spiralis operon. Examination of the genomic organization of the homologous genes in a selection of nematode species confirmed the evolutionary conservation of the synteny of the cpt-2 and nuaf-3 homologs (Figure 3A). This analysis also showed that insertion of prx-14 into the cpt-2∼nuaf-3 operon was a relatively recent event, since it is present only in C. elegans and other closely related Caenorhabditis species. We also find, based on the head-to-tail organization and spacing between coding regions, that there is variation in the composition of both operons in different species, and these genes in R. culicivorax are not in operons.


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)

Evidence for an evolutionarily conserved nematode operon. (A) The structure of the cpt-2-nuaf-3 genomic regions from a range of nematode species mapped onto the nematode phylogeny. Genes are represented by arrows, and the gray lines represent the intercistronic regions (ICRs). Numbers above the ICRs represent the distances, in base pairs, between the stop and start codons of the upstream and downstream genes, respectively. The C. elegans operon numbers are given where appropriate. Fractions below the T. spiralis and T. muris genes represent the proportion of cDNAs derived from those genes that begins with a spliced leader sequence. (B) Detecting polycistronic RNAs derived from the cpt-2∼nuaf-3 operon in T. spiralis. The exon–intron structures of the amplicons used to identify polycistronic RNAs are shown, with exons represented by boxes (shaded to identify the genes from which they are derived using the same color coding that was used in A. The region removed during operon processing is represented by cream-colored boxes. The positions of the SL trans-splice 3′ spliced sites are indicated.
© Copyright Policy - open-access
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4125394&req=5

fig3: Evidence for an evolutionarily conserved nematode operon. (A) The structure of the cpt-2-nuaf-3 genomic regions from a range of nematode species mapped onto the nematode phylogeny. Genes are represented by arrows, and the gray lines represent the intercistronic regions (ICRs). Numbers above the ICRs represent the distances, in base pairs, between the stop and start codons of the upstream and downstream genes, respectively. The C. elegans operon numbers are given where appropriate. Fractions below the T. spiralis and T. muris genes represent the proportion of cDNAs derived from those genes that begins with a spliced leader sequence. (B) Detecting polycistronic RNAs derived from the cpt-2∼nuaf-3 operon in T. spiralis. The exon–intron structures of the amplicons used to identify polycistronic RNAs are shown, with exons represented by boxes (shaded to identify the genes from which they are derived using the same color coding that was used in A. The region removed during operon processing is represented by cream-colored boxes. The positions of the SL trans-splice 3′ spliced sites are indicated.
Mentions: The analysis of one of the two SL trans-spliced T. muris mRNAs (GenBank accession no. FF145866) led to the identification of a putative operon conserved between multiple nematodes (Figure 3A). The two genes contained in these putative operons have C. elegans homologs, cpt-2 and nuaf-3, respectively, which are in the same operon (CEOP4424) (Figure 3A), although there is an additional gene, prx-14, located between these genes in CEOP4424 that is not present in the putative homologous T. spiralis operon. Examination of the genomic organization of the homologous genes in a selection of nematode species confirmed the evolutionary conservation of the synteny of the cpt-2 and nuaf-3 homologs (Figure 3A). This analysis also showed that insertion of prx-14 into the cpt-2∼nuaf-3 operon was a relatively recent event, since it is present only in C. elegans and other closely related Caenorhabditis species. We also find, based on the head-to-tail organization and spacing between coding regions, that there is variation in the composition of both operons in different species, and these genes in R. culicivorax are not in operons.

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