Chapter 28 : Newly Identified Retrotransposons of the Ty3/gypsy Class in Fungi, Plants, and Vertebrates

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Long terminal repeat (LTR)-containing retrotransposons (LTR-retrotransposons) are a large class of interspersed repeats that multiply by a process that includes reverse transcription. The sequence similarities of LTR-retroelements have allowed several laboratories to characterize the phylogenetic relationships. The most significant regions of homology are seven motifs in reverse transcriptase (RT). Extensive analysis of the sequences among LTR-elements revealed two principal classes of LTR-retrotransposons that are named for their founding members discovered in yeast and drosophila, Ty3/gypsy and Ty1/copia. The phylogenetic analyses also suggest that the Ty3/gypsy class of retrotransposons is more closely related to the retrovirus family than is the Ty1/copia group. The study of transposons in complex hosts such as plants reveals qualitative differences in the population of elements compared with those in single-cell organisms. The vertebrate transposons are a sister clade to several groups of Ty3/gypsy elements from fungal and plant hosts. This relationship may be due to a horizontal transmission event between either fungi or plants and an early species of vertebrate. An alternative model for the evolution of env genes in retroviruses, errantiviruses, and members of the copia and BEL families is that the third open reading frame (ORF) originated independently in each of these classes. It may be that much of the success of LTR-retroelements is that, early in their evolution, they developed a replication pathway and a structure that readily adapts to the introduction of env-like genes.

Citation: Levin H. 2002. Newly Identified Retrotransposons of the Ty3/gypsy Class in Fungi, Plants, and Vertebrates, p 684-702. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch28

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Image of Figure 1
Figure 1

The pathway of LTR-retrotransposition. The LTRs of retroelements are symbolized by triangles, and the unique sequences are represented by a rectangle. The process of transposition is initiated by integrated copies of the element. Fulllength transcripts of the transposon are translated and the protein is processed by PR into Gag, PR, RT, and IN. These proteins and copies of the mRNA assemble into VLPs. The RT reverse transcribes the mRNA into double-stranded cDNA that associates with IN in the preintegration complex. After transport into the nucleus, IN inserts the cDNA into a new position in the genome. The designations provirus and virus refer to analogous intermediates in the propagation of retroviruses.

Citation: Levin H. 2002. Newly Identified Retrotransposons of the Ty3/gypsy Class in Fungi, Plants, and Vertebrates, p 684-702. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch28
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Image of Figure 2
Figure 2

The general structure of elements in the Ty1/copia and Ty3/gypsy families. All three categories of elements contain PBS and polypurine tracts (PPT). The ORFs encoding Gag are generally separated from the sequences of Pol by a frameshift. The elements in the Ty1/copia class encode IN upstream of RT. This order is reversed in the Ty3/gypsy family. In some cases, Ty3/gypsy elements possess a third ORF that encodes an env-like protein. This ORF is encoded in a spliced mRNA that lacks the sequences of Pol.

Citation: Levin H. 2002. Newly Identified Retrotransposons of the Ty3/gypsy Class in Fungi, Plants, and Vertebrates, p 684-702. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch28
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Image of Figure 3
Figure 3

A genetic assay for Tf1 transposition activity. Transposition of Tf1 is induced from a plasmid that contains the URA3 gene and the nmt promoter fused to Tf1. Transposition is induced by activating the transcription of the element. The neo gene included in Tf1 causes cells to become resistant to G418. Once transposition is complete, cells are grown on medium containing 5-FOA to select for loss of the assay plasmid. Cells that receive transposed copies of Tf1-neo are detected on medium containing G418. A wild-type copy of Tf1 generates confluent growth on plates with G418 while mutations that block the expression of IN (IN fs) or RT and IN (PR fs) cause many fewer cells to become G418R.

Citation: Levin H. 2002. Newly Identified Retrotransposons of the Ty3/gypsy Class in Fungi, Plants, and Vertebrates, p 684-702. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch28
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Image of Figure 4
Figure 4

The self-priming mechanism of reverse transcription is required for Tf1 transposition. The first 11 nucleotides of the Tf1 mRNA anneal to the PBS and a nucleolytic cleavage between nucleotides 11 and 12 generates the primer (top). Single nucleotide substitutions in the PBS (5th base PBS, 7th base PBS) and in the first 11 nucleotides (5th base 5′end, 7th base 5′end) cause significant reductions in transposition (bottom). The combination of two of these mutations reestablishes complementarity and results in the rescue of the transposition defect.

Citation: Levin H. 2002. Newly Identified Retrotransposons of the Ty3/gypsy Class in Fungi, Plants, and Vertebrates, p 684-702. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch28
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Image of Figure 5
Figure 5

The conservation of priming structures. (Tf1) A large segment of the Tf1 mRNA near the 5′ end folds into an RNA structure that is required for the self-priming of reverse transcription. Single nucleotide substitutions in any of the four duplexes results in reduced cleavage of the mRNA. The arrow indicates the position of the nucleolytic cleavage. (RSV) The 5′ end of retrovirus mRNA folds into structures called the U5-IR and U5-leader stems. This structure is surprisingly similar to the selfpriming structure of Tf1. Mutations in the U5-IRand U5-leader stems cause significant defects in the initiation of reverse transcription.

Citation: Levin H. 2002. Newly Identified Retrotransposons of the Ty3/gypsy Class in Fungi, Plants, and Vertebrates, p 684-702. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch28
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Image of Figure 6
Figure 6

A phylogenetic tree of the Ty3/gypsy group of LTR-retrotransposons. Bootstrap values are derived from 100 replicate trees generated by neighbor-joining analysis of an alignment of amino acids that was produced by Clustal X. The sequences used were based on the seven domains of RT (70). This tree was rooted to four elements of the Ty1/copia family.

Citation: Levin H. 2002. Newly Identified Retrotransposons of the Ty3/gypsy Class in Fungi, Plants, and Vertebrates, p 684-702. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch28
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Table 1

Ty3/gypsy transposons

Citation: Levin H. 2002. Newly Identified Retrotransposons of the Ty3/gypsy Class in Fungi, Plants, and Vertebrates, p 684-702. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch28

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