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Chapter 49 : Origins and Evolution of Retrotransposons

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Abstract:

This chapter summarizes the similarities and differences of retrotransposons, as well as the phylogenetic relationships of the various elements that have been characterized from each of the two classes of retrotransposons. It discusses what can be inferred about the ages and origins of retroelements and their relationship to other cellular components. In the most unusual group of long terminal repeat (LTR), retrotransposons, complete elements have unusual inverted or split terminal repeats and do not encode an integrase. One of the most interesting aspects of the evolution of the LTR retrotransposons is their close relationship to retroviruses, caulimoviruses, and hepadnaviruses. The simplicity of the target-primed reverse transcription (TPRT) mechanism for inserting new copies appears to permit considerable structural flexibility in the evolution of different non-LTR retrotransposons. The authors suggest that it is more likely that the LTR retrotransposons evolved from the same lineages of eubacterial sequences as all other retroelements. They have attempted in this chapter to provide an overview of the diversity and mode of evolution of eukaryotic retrotransposable elements and to trace their origins back to prokaryotic sequences.

Citation: Eickbush T, Malik H. 2002. Origins and Evolution of Retrotransposons, p 1111-1144. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch49

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Group II Introns
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Circular Double-Stranded DNA
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Linear Double-Stranded DNA
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Figures

Image of Figure 1.
Figure 1.

Retrotransposition mechanism of retroviruses and most LTR retrotransposons. Only the basic steps of this reaction are shown for comparison to that of the non-LTR retrotransposition mechanism ( Fig. 7 ). Thick lines, flanking chromosomal sequences; thin lines, element sequences with long terminal repeats (LTRs) indicated as boxed triangles. The RNA template (wavy line) used for protein translation and reverse transcription begins and ends within the LTR sequences. The sequences within these terminal repeats that are used by the reverse transcriptase to template jump between ends are indicated with smaller boxed triangles. First-strand DNA synthesis is primed by a tRNA annealed near the 5′ terminal repeat of the RNA (clover leaf), while second-strand synthesis is primed by an RNase H-resistant RNA near the 3′ terminal repeat (not shown). After formation in the cytoplasm of a linear DNA intermediate, the element-encoded integrase binds to termini of the intermediate, migrates to the nucleus, cleaves a target site on chromosomal DNA, and inserts the DNA intermediate in a reaction similar to that of DNA transposons. Finally, DNA repair fills in the gaps that had been generated by the staggered cut in the chromosome, generating a target-site duplication of uniform length for each element (small open triangles).

Citation: Eickbush T, Malik H. 2002. Origins and Evolution of Retrotransposons, p 1111-1144. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch49
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Image of Figure 2.
Figure 2.

Phylogeny of the LTR retrotransposons and related viruses, based on their reverse transcriptase domain. The portion of the reverse transcriptase domain of each element used in this analysis (approximately 250 residues) includes the seven blocks of conserved residues found in the finger and palm regions of all retroelements ( ), as well as an eighth block corresponding to part of the thumb region ( ). The phylogram is a 50% consensus tree of the elements based on the neighbor joining distance algorithms ( ) and is rooted using non-LTR retrotransposon sequences (not shown). Numbers adjacent to branch points indicate bootstrap values (percentage from 1,000 trials). The name of each published element is shown at the right of each branch along with either the common name, well-known genus name, or complete species identification of the host in which the element was found. The names of the four major groups of LTR retrotransposons are shown to the right of the figure and correspond to one or more of the first elements identified in the group (see text). Several elements of the DIRS and BEL clade have been obtained directly from sequence databases and have not been named. The phylogeny does not include all available elements in each group; rather, it represents only the diversity of elements known to date. Accession numbers for each element sequence, as well as analyses involving more comprehensive sets of elements, can be found in several previous reports ( ).

Citation: Eickbush T, Malik H. 2002. Origins and Evolution of Retrotransposons, p 1111-1144. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch49
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Image of Figure 3.
Figure 3.

ORF structure of representative elements from each major group of LTR retrotransposons and of related viruses. The multiple ORFs of each element are indicated by the rectangular boxes, with boxes on different levels indicating ORFs in different reading frames or separated by termination codons. The three consensus ORFs found in all retroviruses () are shown, but additional small ORFs encoded by HIV are not indicated. Shaded regions indicate the enzymatic domains associated with the gene: RT, reverse transcriptase; RH, RNase H; IN, integrase; PR, protease. Vertical black bars within some or -like ORFs represent cysteine-histidine motifs believed to be associated with nucleic-acid binding domains. For the Ty3/copia, BEL, and Ty3/gypsy groups, two elements are shown, one with an -like ORF and one without an -like ORF.

Citation: Eickbush T, Malik H. 2002. Origins and Evolution of Retrotransposons, p 1111-1144. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch49
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Image of Figure 4.
Figure 4.

Phylogeny of the LTR retrotransposons and related viruses based on their RH domain. The RH domain of each element is approximately 140 residues in length ( ). The phylogram is based on the neighbor-joining distance algorithms and is rooted using cellular RH sequences of eubacteria. Seven eukaryotic and seven eubacterial sequences selected to represent the diversity in each kingdom were used in the analysis, but individual branches have not been shown to conserve space. Also to conserve space, only a subset of the LTR retrotransposons used in Fig. 2 is presented. The species used and accession numbers can be found in reference 91. Numbers adjacent to branch points indicate bootstrap values (percentage from 1,000 trials). Also included in the phylogram are the RH domains found in non-LTR retrotransposons of the I group ( Fig. 8 and 9 ). Only the name of each published element is shown at the right of each branch, since the host species can be found in either Fig. 2 or 9 .

Citation: Eickbush T, Malik H. 2002. Origins and Evolution of Retrotransposons, p 1111-1144. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch49
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Image of Figure 5.
Figure 5.

Comparison of the integrase (IN) domain of LTR retrotransposons. Representative elements were selected to show the diversity of structure in each group. Members of the DIRS, hepadnavirus, and caulimovirus groups of elements shown in Fig. 2 do not appear to contain an IN domain ( Fig. 3 ). The IN domain represents the end of the ORF in most elements; however, it is followed by the RT domain in theTy1/copia group and by an -like domain in Cer13. All IN domains contain a cysteine-histidine motif (HH-CC) at the N-terminal end and three conserved acidic residues (aspartic [D] or glutamic [E]), which form the active site of the catalytic domain. Spacing between these acidic residues is similar in retrovirus and gypsy/Ty3 groups but is different in the BEL and Ty1/copia groups. In the C-terminal direction from these common IN regions, the proteins differ between groups and even among elements of the same group. Regions with sequence identity between members of the same group are shaded gray. C-terminal protein regions that are poorly conserved within a group are not shaded. In the case of the Ty3/gypsy and retrovirus groups, sequence similarity between groups can also be detected. This similarity includes a short region found in all elements and a longer region (identified as GPY/F) found in only some elements of each group ( ). The C-terminal end of some members of the Ty3/gypsygroup contains a chromodomainor, in the case of Ty3, a modified chromodomain ( ).

Citation: Eickbush T, Malik H. 2002. Origins and Evolution of Retrotransposons, p 1111-1144. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch49
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Image of Figure 6.
Figure 6.

Schematic of LTR retrotransposon evolution showing the nine instances in which the lineage has given rise to viruses or potential viruses. The figure shows only a summary of the phylogenetic relationships derived from the reverse transcriptase sequences of the seven groups of elements (the detailed phylogeny is shown in Fig. 2 ). The length and height of each triangle represent, respectively, the presumed age (based on the diversity) and abundance of each group. The nine instances where an LTR-retrotransposon lineage (gray lines and triangles) can be proposed to have assumed viral-like properties are indicated in black. In only four instances (hepadnaviruses, caulimoviruses, retroviruses, and gypsy elements) have the elements directly been shown to be viruses. In the five other instances, the lineage is assumed to have viral-like properties because of the acquisition of an -like ORF. In four cases, the evolutionary origin of the protein that enables (or presumably enables) the element to leave a cell has been traced to the indicated viral source. Adapted from reference 95.

Citation: Eickbush T, Malik H. 2002. Origins and Evolution of Retrotransposons, p 1111-1144. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch49
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Image of Figure 7.
Figure 7.

Target-primed reverse transcription (TPRT) model for the integration of non-LTR retrotransposons. Most elements end in an A-rich or poly(A) 3′ end. Transcription is usually mediated by an internal promoter, which initiates RNA synthesis upstream of itself. However, some elements appear to be expressed as cotranscripts with host genes. Most of the information concerning the TPRT reaction is based on in vitro studies with the protein encoded by the R2 element ( ). This TPRT accounts for many of the integration properties of other non-LTR retrotransposons, but the degree to which this mechanism reflects that used by these different elements is not known. In the initial step of the integration reaction, an element encoded endonuclease cleaves the first (primer) strand of the target site and uses the released 3′ hydroxyl of the terminal nucleotide to prime reverse transcription starting within the poly(A) tail. Cleavage of the second (non-primer) strand occurs after reverse transcription. Thick lines, DNA target sequences; wavy lines, element RNA sequences; thin lines, element DNA sequences. The mechanism by which the 5′ end of the newly made cDNA is attached to the upstream target sequences is unclear, but it appears to be functionally equivalent to the reverse transcriptase simply jumping from the RNA template onto the DNA target. If this jump occurs before the reverse transcriptase reaches the end of the RNA template, a 5′ truncated copy is generated. The process of 5′ attachment generates considerable sequence variation at the junction of the element with the target site, even in the absence of 5′ truncations. The means by which the RNA is removed and the second strand of the element synthesized is not known. Non-LTR retrotransposons differ in whether they generate a target-site duplication and in whether that duplication is of a defined length.

Citation: Eickbush T, Malik H. 2002. Origins and Evolution of Retrotransposons, p 1111-1144. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch49
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Image of Figure 8.
Figure 8.

Diagram of the ORF structure of five non-LTR retrotransposons selected to represent the diversity of structures found in this class of elements. ORFs are represented by rectangular boxes, with boxes at different levels indicating ORFs in different reading frames or separated by termination codons. Shaded regions indicate identified enzymatic domains: RT, reverse transcriptase; RH, RNase H; APE, apurinic-apyrimidinic endonuclease; EN, endonuclease. Vertical black bars represent cysteine-histidine motifs believed to be associated with nucleic-acid binding domains. These elements represent the first element to be characterized from each of the five major groups of non-LTR retrotransposons identified in Fig. 9 and Table 1 .

Citation: Eickbush T, Malik H. 2002. Origins and Evolution of Retrotransposons, p 1111-1144. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch49
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Image of Figure 9.
Figure 9.

Phylogeny of the non-LTR retrotransposons based on their reverse transcriptase domain. This domain corresponds to approximately 440 amino acid residues as defined by Malik et al. ( ). The phylogeny is a 50% consensus tree of the elements using the neighbor-joining algorithms and is rooted with the reverse transcriptase sequences of the group II introns (not shown). Numbers at each node indicate bootstrap values (percentage of 1,000 trials). The name of each element and the host organism from which it was isolated are given to the right. The elements can be divided into distinct clades, with each clade named after one of the earliest elements described from that clade (intermediate size names to the right). The tree is similar to that previously reported ( ) except the addition of 13 new elements has defined three new clades. Individual, well-resolved clades or several clades containing elements with the same ORF structure have been placed into five groups (large names to the right). The elements within each group are delineated by the dotted horizontal lines. The basic structure of the elements in each group is shown in Fig. 8 .

Citation: Eickbush T, Malik H. 2002. Origins and Evolution of Retrotransposons, p 1111-1144. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch49
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Image of Figure 10.
Figure 10.

Alternative explanations as to why the phylogeny of a mobile element can violate the phylogeny of the host species. In scenario A, the mobile element lineage separates into two independent lineages (solid and broken lines) that are differentially maintained in the four extant species. Species A, C, and D each retain one lineage, while both lineages are lost in species B. The elements in species A and C represent an orthologous lineage, while the elements in species C and D represent paralogous lineages. In scenario B, a single lineage of the mobile element is lost from the ancestor of species A and B and retained in species C and D. A horizontal transfer of the element from species C introduces the elements into species A. Either series of events (panels A and B) can explain why the elements isolated from species C are more closely related to the elements from the distant species A, rather than to the elements from the related species D. The best means to differentiate between these two explanations is to estimate the rate of sequence evolution of the element and then to determine whether it is the divergence of elements in species A and D or the divergence of elements in species D and C that is most consistent with this rate of evolution.

Citation: Eickbush T, Malik H. 2002. Origins and Evolution of Retrotransposons, p 1111-1144. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch49
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Image of Figure 11.
Figure 11.

Plot of sequence divergence versus age estimates of non-LTR retrotransposons. Divergence calculations are based on the amino acid sequence of the RT domain. Circles, comparisons between arthropod elements; squares, comparisons between vertebrate elements. The clade from which each comparison is made ( Fig. 9 and Table 1 ) is shown immediately adjacent to each data point (J, Jockey clade). The curves are average rates of divergence in arthropods (solid line) based on data from the R1 and R2 clades and in vertebrates (dotted lines) based on data from the L1 clade ( ). Most divergences are based on the entire RT domain; however, in some cases the divergences are based on ∼50% of this domain corrected to the complete RT domain using several outgroup comparisons. Divergence time estimates are described in reference 91.

Citation: Eickbush T, Malik H. 2002. Origins and Evolution of Retrotransposons, p 1111-1144. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch49
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Image of Figure 12.
Figure 12.

Schematic diagram of the unrooted phylogenetic tree of eukaryotic and prokaryotic retroelements. The phylogram is derived from the amino acid sequence of their encoded reverse transcriptase domain. Each group of retroelements is represented by a triangle, with the length of that triangle related to the sequence diversity with the group. The phylogenetic analysis is similar to those used in previous reports ( ), except that the regions of conserved sequences were not forced into blocks and an additional conserved region (segment 2A, reference ) was included ( ). The extensive sequence changes have resulted in a long branch length leading to the LTR retrotransposon lineage, suggesting that its position on the phylogeny is in question (see text). The arrow indicates where the branch leading to the RNA-directed RNA polymerases would be located on this tree of retroelement sequences. As described in the text, utilization of these RNA polymerases only identifies the most divergent branch of the phylogeny (mid-point roots) and thus is of limited value.

Citation: Eickbush T, Malik H. 2002. Origins and Evolution of Retrotransposons, p 1111-1144. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch49
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Image of Figure 13.
Figure 13.

Mosaic origin of the LTR retrotransposons. All mobile elements in eukaryotes are assumed to have descended from bacterial elements. The structure and function of eukaryotic DNA transposons are virtually identical to those in bacteria ( ). Non-LTR retrotransposons are suggested to have descended from a bacterial retroelement, probably a mobile group II intron. The origin of the LTR retrotransposons is postulated to have resulted from the fusion of these two original classes of mobile elements. The reverse transcriptase, RNase H, and -like proteins were derived from a non-LTR retrotransposon, and the integrase was derived from a transposon. The only other protein component of LTR retrotransposons is a protease, presumably derived from the host genome. This model for the origin of the LTR retrotransposons suggests a change in the nomenclature. The originally termed non-LTR retrotransposons (or LINEs) are referred to simply as retroposons. This term faithfully reflects the original use of the term ( ) as elements which are simple reverse transcription products of an RNA. We suggest the originally termed LTR-retrotransposons continue to be referred to as posons. This term accurately reflects the mosaic nature of their structure and integration mechanism as part poson and part poson.

Citation: Eickbush T, Malik H. 2002. Origins and Evolution of Retrotransposons, p 1111-1144. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch49
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Tables

Generic image for table
Table 1.

Classification of non-LTR retrotransposons

Citation: Eickbush T, Malik H. 2002. Origins and Evolution of Retrotransposons, p 1111-1144. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch49

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