Abstract
LTR-retrotransposons share a common genomic organization in which the 5′ long terminal repeat (LTR) is followed by the gag and pol genes and terminates with the 3′ LTR. Although GAG-POL-encoded proteins are considered sufficient to accomplish the LTR-retrotransposon transposition, a number of elements carrying additional open reading frames (aORF) have been described. In some cases, the presence of an aORF can be explained by a phenomenon similar to retrovirus gene transduction, but in these cases the aORFs are present in only one or a few copies. On the contrary, many elements contain aORFs, or derivatives, in all or most of their copies. These aORFs are more frequently located between pol and 3′ LTR, and they could be in sense or antisense orientation with respect to gag-pol. Sense aORFs include those encoding for ENV-like proteins, so called because they have some structural and functional similarities with retroviral ENV proteins. Antisense aORFs between pol and 3′ LTR are also relatively frequent and, for example, are present in some characterized LTR-retrotransposon families like maize Grande, rice RIRE2, or Silene Retand, although their possible roles have been not yet determined. Here, we discuss the current knowledge about these sense and antisense aORFs in plant LTR-retrotransposons, suggesting their possible origins, evolutionary relevance, and function.
Highlights
long terminal repeat (LTR)-retrotransposons are transposable elements (TEs) characterized by the presence of two long direct repeats flanking an internal region that contains the gag and pol genes encoding proteins required for transposition (Figures 1A,B)
Long terminal repeats provide the promoters and terminators associated with the transcription of the LTR-retrotransposon by RNA polymerase II (Kumar and Bennetzen, 1999)
Additional open reading frames located between the pol gene and the 3 LTR are present in some plant LTR-retrotransposon families
Summary
LTR-retrotransposons are transposable elements (TEs) characterized by the presence of two long direct repeats (long terminal repeats, LTRs) flanking an internal region that contains the gag and pol genes encoding proteins required for transposition (Figures 1A,B). The presence of coding domains in addition to the gag and pol genes between pol and 3 LTR in the same sense as gag and pol (aORFs-3S) have been described in some LTR-retrotransposons in insects (Song et al, 1994) and in plants (Vicient et al, 2001; Wright and Voytas, 2002; Laten and Gaston, 2012) They encode proteins with certain similarities to ENV, suggesting that they may exist in, at least, some LTR-retrotransposons (Figures 1C,D). They are present in non-plant species as, for example, in Boty from Botrytis cinerea and Sclerotinia sclerotiorum (Zhao et al, 2011; Figure 1I) The function of these aORF-3Rs is not known, but their presence in most of the copies of a family, with a degree of sequence conservation similar to that of other retrotransposonencoded proteins, suggests that they may be important for the retrotransposition process (Ohtsubo et al, 1999; Gómez-Orte et al, 2013). These homologies indicate an ancient origin, at least for some of the aORF-3R
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