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Phylogenetic footprinting of non-coding RNA: hammerhead ribozyme sequences in a satellite DNA family of Dolichopoda cave crickets (Orthoptera, Rhaphidophoridae).

Martinsen L, Johnsen A, Venanzetti F, Bachmann L - BMC Evol. Biol. (2010)

Bottom Line: The HH region was significantly more conserved than the non-hammerhead (NHH) region of the pDo500 repeat.RNA folding of the HH sequences revealed that a potentially active HH ribozyme can be found in most of the Dolichopoda populations and species.Future studies need to demonstrate how the observed nucleotide changes and evolutionary constraint have affected the catalytic efficiency of the hammerhead.

View Article: PubMed Central - HTML - PubMed

Affiliation: Natural History Museum, Department for Research and Collections, University of Oslo, 0318 Oslo, Norway.

ABSTRACT

Background: The great variety in sequence, length, complexity, and abundance of satellite DNA has made it difficult to ascribe any function to this genome component. Recent studies have shown that satellite DNA can be transcribed and be involved in regulation of chromatin structure and gene expression. Some satellite DNAs, such as the pDo500 sequence family in Dolichopoda cave crickets, have a catalytic hammerhead (HH) ribozyme structure and activity embedded within each repeat.

Results: We assessed the phylogenetic footprints of the HH ribozyme within the pDo500 sequences from 38 different populations representing 12 species of Dolichopoda. The HH region was significantly more conserved than the non-hammerhead (NHH) region of the pDo500 repeat. In addition, stems were more conserved than loops. In stems, several compensatory mutations were detected that maintain base pairing. The core region of the HH ribozyme was affected by very few nucleotide substitutions and the cleavage position was altered only once among 198 sequences. RNA folding of the HH sequences revealed that a potentially active HH ribozyme can be found in most of the Dolichopoda populations and species.

Conclusions: The phylogenetic footprints suggest that the HH region of the pDo500 sequence family is selected for function in Dolichopoda cave crickets. However, the functional role of HH ribozymes in eukaryotic organisms is unclear. The possible functions have been related to trans cleavage of an RNA target by a ribonucleoprotein and regulation of gene expression. Whether the HH ribozyme in Dolichopoda is involved in similar functions remains to be investigated. Future studies need to demonstrate how the observed nucleotide changes and evolutionary constraint have affected the catalytic efficiency of the hammerhead.

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The dHH structure and the consensus alignment of the sHH (49 bp) and dHH (68 bp) regions from the pDo500 satDNA in Dolichopoda. The sHH and dHH regions of the pDo500 consensus sequences as derived for each population by Martinsen et al., in press [33]. The colors represent: pink = stem 0 green = stem I, yellow (light) = stem II, blue = stem III, yellow (deep) = cleavage site, magenta = invariable core residues, turquoise = compensatory mutations. A dHH structure - as suggested by Rojas et al. (2000) - is made up of two extended sHH sequences (49 bp + 19 bp) that hybridize. Stem I-III are found in both the sHH (see Figure 1) and the dHH structure. For the dHH stem III is folded exactly the same way as in the sHH - i.e. two areas (blue) from the same sequence pair with each other - while pairing of stem I and II requires two different sequences. The figure of the dHH is adopted from Rojas et al. (2000) and edited further to illustrate the alignment of the pDo500 consensus sequences. In cpr the D denotes A, T, or G, and in crq the ? denotes C, T, or gap.
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Figure 2: The dHH structure and the consensus alignment of the sHH (49 bp) and dHH (68 bp) regions from the pDo500 satDNA in Dolichopoda. The sHH and dHH regions of the pDo500 consensus sequences as derived for each population by Martinsen et al., in press [33]. The colors represent: pink = stem 0 green = stem I, yellow (light) = stem II, blue = stem III, yellow (deep) = cleavage site, magenta = invariable core residues, turquoise = compensatory mutations. A dHH structure - as suggested by Rojas et al. (2000) - is made up of two extended sHH sequences (49 bp + 19 bp) that hybridize. Stem I-III are found in both the sHH (see Figure 1) and the dHH structure. For the dHH stem III is folded exactly the same way as in the sHH - i.e. two areas (blue) from the same sequence pair with each other - while pairing of stem I and II requires two different sequences. The figure of the dHH is adopted from Rojas et al. (2000) and edited further to illustrate the alignment of the pDo500 consensus sequences. In cpr the D denotes A, T, or G, and in crq the ? denotes C, T, or gap.

Mentions: We analyzed 198 pDo500 satDNA sequences from several populations of 12 Dolichopoda species, each represented with 3-9 sequences. The molecular characteristics of these sequences were described in detail elsewhere [33]. The HH region sensu Rojas et al. [15] was present in all sequences except in sequence vat3 from D. geniculata which contains an extended deletion of 308 bp. The pDo500 sequences in the data set ranged from 463 bp to 505 bp out of which 49 bp relate to the regular sHH region (Figure 1) and 68 bp to the dHH region. The 68 bp region is a 19 bp extension of the 49 bp region (Figure 2).


Phylogenetic footprinting of non-coding RNA: hammerhead ribozyme sequences in a satellite DNA family of Dolichopoda cave crickets (Orthoptera, Rhaphidophoridae).

Martinsen L, Johnsen A, Venanzetti F, Bachmann L - BMC Evol. Biol. (2010)

The dHH structure and the consensus alignment of the sHH (49 bp) and dHH (68 bp) regions from the pDo500 satDNA in Dolichopoda. The sHH and dHH regions of the pDo500 consensus sequences as derived for each population by Martinsen et al., in press [33]. The colors represent: pink = stem 0 green = stem I, yellow (light) = stem II, blue = stem III, yellow (deep) = cleavage site, magenta = invariable core residues, turquoise = compensatory mutations. A dHH structure - as suggested by Rojas et al. (2000) - is made up of two extended sHH sequences (49 bp + 19 bp) that hybridize. Stem I-III are found in both the sHH (see Figure 1) and the dHH structure. For the dHH stem III is folded exactly the same way as in the sHH - i.e. two areas (blue) from the same sequence pair with each other - while pairing of stem I and II requires two different sequences. The figure of the dHH is adopted from Rojas et al. (2000) and edited further to illustrate the alignment of the pDo500 consensus sequences. In cpr the D denotes A, T, or G, and in crq the ? denotes C, T, or gap.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2837043&req=5

Figure 2: The dHH structure and the consensus alignment of the sHH (49 bp) and dHH (68 bp) regions from the pDo500 satDNA in Dolichopoda. The sHH and dHH regions of the pDo500 consensus sequences as derived for each population by Martinsen et al., in press [33]. The colors represent: pink = stem 0 green = stem I, yellow (light) = stem II, blue = stem III, yellow (deep) = cleavage site, magenta = invariable core residues, turquoise = compensatory mutations. A dHH structure - as suggested by Rojas et al. (2000) - is made up of two extended sHH sequences (49 bp + 19 bp) that hybridize. Stem I-III are found in both the sHH (see Figure 1) and the dHH structure. For the dHH stem III is folded exactly the same way as in the sHH - i.e. two areas (blue) from the same sequence pair with each other - while pairing of stem I and II requires two different sequences. The figure of the dHH is adopted from Rojas et al. (2000) and edited further to illustrate the alignment of the pDo500 consensus sequences. In cpr the D denotes A, T, or G, and in crq the ? denotes C, T, or gap.
Mentions: We analyzed 198 pDo500 satDNA sequences from several populations of 12 Dolichopoda species, each represented with 3-9 sequences. The molecular characteristics of these sequences were described in detail elsewhere [33]. The HH region sensu Rojas et al. [15] was present in all sequences except in sequence vat3 from D. geniculata which contains an extended deletion of 308 bp. The pDo500 sequences in the data set ranged from 463 bp to 505 bp out of which 49 bp relate to the regular sHH region (Figure 1) and 68 bp to the dHH region. The 68 bp region is a 19 bp extension of the 49 bp region (Figure 2).

Bottom Line: The HH region was significantly more conserved than the non-hammerhead (NHH) region of the pDo500 repeat.RNA folding of the HH sequences revealed that a potentially active HH ribozyme can be found in most of the Dolichopoda populations and species.Future studies need to demonstrate how the observed nucleotide changes and evolutionary constraint have affected the catalytic efficiency of the hammerhead.

View Article: PubMed Central - HTML - PubMed

Affiliation: Natural History Museum, Department for Research and Collections, University of Oslo, 0318 Oslo, Norway.

ABSTRACT

Background: The great variety in sequence, length, complexity, and abundance of satellite DNA has made it difficult to ascribe any function to this genome component. Recent studies have shown that satellite DNA can be transcribed and be involved in regulation of chromatin structure and gene expression. Some satellite DNAs, such as the pDo500 sequence family in Dolichopoda cave crickets, have a catalytic hammerhead (HH) ribozyme structure and activity embedded within each repeat.

Results: We assessed the phylogenetic footprints of the HH ribozyme within the pDo500 sequences from 38 different populations representing 12 species of Dolichopoda. The HH region was significantly more conserved than the non-hammerhead (NHH) region of the pDo500 repeat. In addition, stems were more conserved than loops. In stems, several compensatory mutations were detected that maintain base pairing. The core region of the HH ribozyme was affected by very few nucleotide substitutions and the cleavage position was altered only once among 198 sequences. RNA folding of the HH sequences revealed that a potentially active HH ribozyme can be found in most of the Dolichopoda populations and species.

Conclusions: The phylogenetic footprints suggest that the HH region of the pDo500 sequence family is selected for function in Dolichopoda cave crickets. However, the functional role of HH ribozymes in eukaryotic organisms is unclear. The possible functions have been related to trans cleavage of an RNA target by a ribonucleoprotein and regulation of gene expression. Whether the HH ribozyme in Dolichopoda is involved in similar functions remains to be investigated. Future studies need to demonstrate how the observed nucleotide changes and evolutionary constraint have affected the catalytic efficiency of the hammerhead.

Show MeSH
Related in: MedlinePlus