Looking possible ltr

Added: Kelliann Lumley - Date: 28.09.2021 14:43 - Views: 32097 - Clicks: 7003

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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. Here, we discuss the current knowledge about these sense and antisense aORFs in plant LTR-retrotransposons, suggesting their possible origins, evolutionary relevance, and function. 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 internal region contains the primer binding site PBS and the polypurine tract PPTboth used during the retrotransposition process.

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The internal region also contains the gag and pol genes, which encode all the proteins necessary for the retrotranscription and integration processes not provided by the cell. Figure 1. Schematic representation of LTR-retrotransposons. C Arabidopis thaliana Athila Wright and Voytas, D Barley Bagy2 Vicient et al. G Silene latifolia Retand Kejnovsky et al. H Phaseolus vulgaris PvRetro13 Gao et al. I Botrytis cinerea Boty Zhao et al. As sequence data accumulate, the recognizing of sequences encoding for additional proteins aORFs in the internal region of plant LTR-retrotransposons seems to be more frequent Neumann et al.

Since retrotransposons have an intracellular retrotransposition cycle, it was initially thought that they do not need the ENV protein and, in fact, most do not have it. One of the conserved characteristics of the retroviral env domains is that they code for proteins with transmembrane domains, a characteristic that some of these aORFs-3S also have, which may suggest some functional similarity Vicient et al.

On the other hand, the retroviral mRNA is usually spliced to give rise to a message capable of expressing the envelope protein. Similar splicing events have been reported for some plant retrotransposons like barley Bagy2 Vicient et al. Together, the data suggest that aORFs-3S could encode proteins with functional similarities to retroviral ENV and therefore they are often called env-like domains Carvalho et al.

However, an ENV-like function in plants remains controversial because the plant cell wall may represent a barrier to the interaction of ENV with cellular receptors present in the plasma membrane. As a consequence, it has been proposed that ENV-like proteins in plants may have a different function than in retroviruses as, for example, to modify the molecular size exclusion limit of plasmodesmata Carrington et al. They are also present in non-plant species as, for example, in Boty from Botrytis cinerea and Sclerotinia sclerotiorum Zhao et al.

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 retrotransposon-encoded proteins, suggests that they may be important for the retrotransposition process Ohtsubo et al. Although a complete analysis of the presence, species distribution, and types of these aORF-3Rs is not yet available, the current data indicates that some of them are distributed in several species.

These homologies indicate an ancient origin, at least for some of the aORF-3R.

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Retroviruses have the potential to capture complete or parts of cellular genes in a process known as gene transduction. Gene transduction events have also been described in some Class I TEs. For example, human L1 retrotransposons can capture gene fragments by transduction Goodier et al.

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There are also some described examples in plants. Bs1, a maize LTR-retrotransposon, has transduced sequences from different host genes Elrouby and Bureau, A total of genes have been identified as transposon-captured genes in maize Schnable et al. However, retrotransposon-transduced gene sequences are usually in the same sense as the retrotransposon gag and pol genes. Another possible origin of the aORF is the insertion of a TE that, once inserted, became part of the element, losing part of its structure.

However, although nested insertions of TEs are relatively frequent in plant genomes SanMiguel and Bennetzen,the lack of similarity of the aORF sequences with that of other TEs or viruses does not support this hypothesis. In consequence, the origin of most of these aORFs remains unknown. No clear similarities with other proteins in databases have been described for any of the proteins encoded by aORFs-3R. These suggest that these proteins may fulfill some nuclear function. Moreover, the aORF-3R protein encoded by Retand ORF4 contains a transposase 28 domain pfamsuggesting a possible role in the retrotransposition process.

During retrotransposition, the pre-integration complex PIC produced in the cytoplasm must translocate to the nucleus McLane et al. In some retrotransposons, like the fission yeast Tf1, the nuclear localization al is provided by GAG Kim et al. Many retroviruses encode more ORFs in addition to gagpoland envcalled accessory factors. The Accessory factors encode for structural and enzymatic proteins essential for the regulation of transcription Tatthe transport of unspliced and partially spliced viral RNAs from the nucleus into the cytoplasm Revand others Vif, Vpr, Vpu, Vpx, and Nef Sauter and Kirchhoff, All these suggest that the proteins encoded by aORFs-3R in LTR-retrotransposons may play a role similar to some of the retroviral accessory proteins, regulating the retrotransposition process.

In maize Grande, the region corresponding to gene23 aORF-3R is ubiquitously transcribed in a relatively high level in antisense with respect to the gag - pol genes. Antisense promoters are not unusual in retrovirus. Antisense promoters have been also identified in other retrotransposons as, for example, the apple Mdoryco Wang et al. However, in the case of micropia, it transcribes two antisense RNAs of 1. In view of these last examples, we cannot rule out that, at least in some cases, the production of antisense mRNAs has itself some regulatory roles.

These two possible functions based on the generation of a protein or on the generation of dsRNA can be true simultaneously and represent a fine regulation of the LTR-retrotransposition mechanism. Sense aORFs show some functional and structural characteristics similar to the env genes in retroviruses, although their possible roles in retrotransposition remain unclear.

Antisense aORFs are also present in different retrotransposon families, but their functions are yet unknown. The nuclear localization identified in some cases and the comparison with the antisense genes of retroviruses suggest they may play a regulatory role in retrotransposition.

Antisense transcription may also play a regulatory role itself, through a dsRNA-mediated silencing mechanism.

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In conclusion, we believe that it is necessary to pay more attention to the presence of this type of additional ORFs in the annotations of the TEs. We also think that it is necessary to look at the possible presence of antisense and spliced transcripts. Finally, we think it would be interesting to carry out research efforts on the possible functions that the transcripts and the proteins they encode could perform. CV drafted the manuscript with contributions of JC.

Both CV and JC revised and approved the manuscript.

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The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. Barbeau, B. Viruses 3, — Carrington, J. Cell-to-cell and long-distance transport of viruses in plants. Plant Cell 8, — Carvalho, M. Presence of env-like sequences in Quercus suber retrotransposons. Danilevskaya, O. The two Drosophila telomeric transposable elements have very different patterns of transcription. Cell Biol. Dodonova, S. Druker, R.

Complex patterns of transcription at the insertion site of a retrotransposon in the mouse. Nucleic Acids Res. Elrouby, N. Bs1, a new chimeric gene formed by retrotransposon-mediated exon shuffling in maize. Plant Physiol. Gao, D. Annotation and sequence diversity of transposable elements in common bean Phaseolus vulgaris. Plant Sci. Integrase diversity and transcription of the maize retrotransposon Grande.

Genome 49, — Plant Mol. Goodier, J. Havecker, E. The diversity of LTR retrotransposons. Genome Biol. Jiang, S. Genome-wide survey and comparative analysis of LTR retrotransposons and their captured genes in rice and sorghum. PLoS One 8:e Kato, A. The antisense promoter of AtRE1, a retrotransposon in Arabidopsis thalianais activated in pollens and calluses. Google Scholar. Kejnovsky, E.

Retand: a novel family of gypsy-like retrotransposons harboring an amplified tandem repeat. Kim, M. The long terminal repeat-containing retrotransposon Tf1 possesses amino acids in gag that regulate nuclear localization and particle formation. Kogan, M. Retrovirology Kumar, A. Plant retrotransposons. PubMed Abstract Google Scholar. Lankenau, S. The Drosophila micropia retrotransposon encodes a testis-specific antisense RNA complementary to reverse transcriptase.

Laten, H. Grandbastien and J. Casacuberta Berlin: Springer, 89— Marchler-Bauer, A. CDD: a conserved domain database for the functional annotation of proteins. What makes Grande1 retrotransposon different? Genetica15— McLane, L. The Ty1 integrase protein can exploit the classical nuclear protein import machinery for entry into the nucleus. Neumann, P.

Systematic survey of plant LTR-retrotransposons elucidates phylogenetic relationships of their polyprotein domains and provides a reference for element classification. Nisole, S. Early steps of retrovirus replicative cycle. Retrovirology 1, 9— Ohtsubo, H. RIRE2, a novel gypsy-type retrotransposon from rice. Genes Genet. SanMiguel, P. Evidence that a recent increase in maize genome size was caused by the massive amplification of intergene retrotransposons. Sauter, D. Cytokine Growth Factor Rev. Schnable, P. The B73 maize genome: complexity, diversity, and dynamics.

Science— Song, S. An env-like protein encoded by a Drosophila retroelement: evidence that gypsy is an infectious retrovirus.

Looking possible ltr

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