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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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A putative extended HH structure in Dolichopoda cave crickets. The sequence is the same as for the previously suggested dHH sensu Rojas et al (2000), but here the structure consists of one sequence folding into a HH structure with an extended stem I, as opposed to the dHH that consists of two sequences hybridizing with each other. The color code is as in Figure 1.
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Figure 3: A putative extended HH structure in Dolichopoda cave crickets. The sequence is the same as for the previously suggested dHH sensu Rojas et al (2000), but here the structure consists of one sequence folding into a HH structure with an extended stem I, as opposed to the dHH that consists of two sequences hybridizing with each other. The color code is as in Figure 1.

Mentions: The biological role of HH ribozymes that have been uncovered to date can be divided in two groups. One is related to the viroid and viroid-like HH ribozymes which play a role in RNA replication through rolling circle amplification [17,18,44]. The second is the role of the HH ribozymes found in eukaryotic organisms which remains speculative [39]. For example, the newt HH ribozyme, which is embedded in the Satellite 2 family (sat2), has been associated with a ribonucleoprotein (RNP) in the ovaries [45]; an RNA binding protein (NORA) has been characterized as a promising candidate as a constituent of this complex [19]. The function of this complex is unclear; however, it has been associated with trans cleavage of an RNA target [45]. The sat2 with its HH ribozyme has been found in nine different species representing four families of amphibians [46]. There are striking similarities between the HH ribozyme in amphibians and Dolichopoda as they are both found in satellite DNA transcripts and are conserved between large numbers of species. In addition, the Dolichopoda HH also has the potential to form an extended HH structure (Figure 3) as previously described for the amphibian HH ribozyme [46,47]. Whether the HH ribozyme in the pDo500 satDNA from Dolichopoda is involved in a similar RNP complex as in amphibians needs to be investigated. Neither the well-characterized HH ribozyme from S. mansoni, which is also derived from satDNA transcripts, nor the HH ribozyme from A. thaliana, have been linked to a function. On the other hand, the split HH ribozyme found in mRNA from rodents has been implicated in regulation of gene expression [22].


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)

A putative extended HH structure in Dolichopoda cave crickets. The sequence is the same as for the previously suggested dHH sensu Rojas et al (2000), but here the structure consists of one sequence folding into a HH structure with an extended stem I, as opposed to the dHH that consists of two sequences hybridizing with each other. The color code is as in Figure 1.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: A putative extended HH structure in Dolichopoda cave crickets. The sequence is the same as for the previously suggested dHH sensu Rojas et al (2000), but here the structure consists of one sequence folding into a HH structure with an extended stem I, as opposed to the dHH that consists of two sequences hybridizing with each other. The color code is as in Figure 1.
Mentions: The biological role of HH ribozymes that have been uncovered to date can be divided in two groups. One is related to the viroid and viroid-like HH ribozymes which play a role in RNA replication through rolling circle amplification [17,18,44]. The second is the role of the HH ribozymes found in eukaryotic organisms which remains speculative [39]. For example, the newt HH ribozyme, which is embedded in the Satellite 2 family (sat2), has been associated with a ribonucleoprotein (RNP) in the ovaries [45]; an RNA binding protein (NORA) has been characterized as a promising candidate as a constituent of this complex [19]. The function of this complex is unclear; however, it has been associated with trans cleavage of an RNA target [45]. The sat2 with its HH ribozyme has been found in nine different species representing four families of amphibians [46]. There are striking similarities between the HH ribozyme in amphibians and Dolichopoda as they are both found in satellite DNA transcripts and are conserved between large numbers of species. In addition, the Dolichopoda HH also has the potential to form an extended HH structure (Figure 3) as previously described for the amphibian HH ribozyme [46,47]. Whether the HH ribozyme in the pDo500 satDNA from Dolichopoda is involved in a similar RNP complex as in amphibians needs to be investigated. Neither the well-characterized HH ribozyme from S. mansoni, which is also derived from satDNA transcripts, nor the HH ribozyme from A. thaliana, have been linked to a function. On the other hand, the split HH ribozyme found in mRNA from rodents has been implicated in regulation of gene expression [22].

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