Ribonuclease H evolution in retrotransposable elements

@article{Malik2005RibonucleaseHE,
  title={Ribonuclease H evolution in retrotransposable elements},
  author={Harmit S. Malik},
  journal={Cytogenetic and Genome Research},
  year={2005},
  volume={110},
  pages={392 - 401}
}
Eukaryotic and prokaryotic genomes encode either Type I or Type II Ribonuclease H (RNH) which is important for processing RNA primers that prime DNA replication in almost all organisms. This review highlights the important role that Type I RNH plays in the life cycle of many retroelements, and its utility in tracing early events in retroelement evolution. Many retroelements utilize host genome-encoded RNH, but several lineages of retroelements, including some non-LTR retroposons and all LTR… 

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References

SHOWING 1-10 OF 63 REFERENCES
Phylogenetic analysis of ribonuclease H domains suggests a late, chimeric origin of LTR retrotransposable elements and retroviruses.
TLDR
A phylogenetic analysis of the Ribonuclease HI (RNH) domains present in Eubacteria, Eukarya, all long-term repeat (LTR)-bearing retrotransposons, and several late-branching clades of non-LTR retrotransposition provides surprising insights into the evolution of eukaryotic retro Transposons.
Origins and Evolution of Retrotransposons
TLDR
The authors have attempted to provide an overview of the diversity and mode of evolution of eukaryotic retrotransposable elements and to trace their origins back to prokaryotic sequences.
R2 and Related Site-Specific Non-Long Terminal Repeat Retrotransposons
R2 elements are unusual mobile elements because all copies insert into a specific site within the genome, the 28S rRNA genes. The target-primed reverse transcription (TPRT) reaction characterized for
Evolution of retroposons by acquisition or deletion of retrovirus-like genes.
TLDR
Protein-sequence alignment data demonstrate that subsets of the retroposons contain different assortments of retroviral-like genes and suggest that xenologous recombination and/or independent gene assortment have played a role in the evolution of the Retroposon lineage.
Potential multiple endonuclease functions and a ribonuclease H encoded in retroposon genomes.
TLDR
The results indicate that SLACS, CZAR, CRE1, CRE2, and some Trypanosoma brucei retroposon sequences encode multiple putative endonuclease functions.
Origin and evolution of retroelements based upon their reverse transcriptase sequences.
TLDR
The sequence similarity of these RNA polymerases to RT suggests that these two enzymes evolved from a common ancestor, and thus RNA polymerase can be used as an outgroup to root the RT tree.
Identification of the endonuclease domain encoded by R2 and other site-specific, non-long terminal repeat retrotransposable elements.
TLDR
Site-directed mutagenesis of the R2 protein was used to provide evidence that this motif is also part of the active site of the endonuclease encoded by this element, suggesting a scenario for the evolution of non-LTR elements.
Retroids in archaea: phylogeny and lateral origins.
TLDR
The discovery of retrointrons in Archaea as a consequence of LGT from Bacteria suggests that they did not originate in the progenote and parallels the "mitochondrial seed" theory of the origin of spliceosomes.
Ancient lineages of non-LTR retrotransposons in the primitive eukaryote, Giardia lamblia.
TLDR
Phylogenetic analysis indicates that the non-LTR retrotransposons present in one of the most primitive eukaryotes, the diplomonad Giardia lamblia, are among the oldest known lineages of non- LTR elements consistent with strict vertical descent.
Poised for contagion: evolutionary origins of the infectious abilities of invertebrate retroviruses.
TLDR
Evidence is presented that in three other possible transitions of LTR retrotransposons to retroviruses, an envelope-like gene was acquired from a viral source, representing the only cases in which the env gene of a retrovirus has been traced back to its original source.
...
1
2
3
4
5
...