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== '''Introduction''' ==
Retroelements with long terminal repeats (LTRs) represent one of the four major groups of retrotranscribing mobile genetic elements. This system includes the broad range of LTR retrotransposons and retroviruses present in animals, plants and fungi (for more information in this topic, see[[Retroelements| Retroelements]]), and other non-autonomous retroelements evolved from LTR retroelements. We additionally consider caulimoviruses of plants within the system of autonomous LTR retroelements because of their common evolutionary relationship with them based on the gag-pol region.

== '''Autonomous LTR retroelements''' ==
These are composed of an internal coding region bounded by LTRs of variable size. The LTRs usually end in short inverted repeats, they do not encode for any known protein but contain promoters and features associated with the element transcription ([[Literature:40507|Kumar and Bennetzen 1999]]). LTR retroelements have a Primer Binding Site (PBS) as well as a Polypurine Tract (PPT) downstream to the 5´LTR and upstream to the 3´LTR, respectively (for more information, see[[LTRs| LTRs]]). The internal region contains the characteristics gag and pol (and env in the case of retroviruses) ORFs, which encode for the different protein products required for the replication cycle and transposition of LTR retroelements ([[Literature:88885|Eickbush and Jamburuthugoda 2008]]). The replication cycle of LTR retrotransposons includes both nuclear and cytoplasmic stages. Inserted LTR retroelements are transcribed into mRNAs which are then exported to the cytoplasm to form virus-like particles (VLPs) and retrotranscribed cDNA copies that go back to the nucleus for integration in the host's DNA genome. Based on sequence similarity and other features LTR retroelements can be classified into four major families called ''Ty1/Copia'', ''Ty3/Gypsy'', ''Bel/Pao'' and ''Retroviridae''.
=== ''Ty1/Copia'' ===
''Ty1/Copia'' elements are abundant in species ranging from single-cell algae to superior plants and animals. The Ty1/Copia internal region encodes for the typical gag and pol polyproteins but differ from other LTR retrotransposons in the ORF position of integrase (INT), which maps after to protease (PR). The classification of this family is in continous progress. According to the ICTV, the ''Ty1/Copia'' family (taxonomically the ''Pseudoviridae'') was originally divided into three genera: Pseudovirus, Hemivirus and Sirevirus (for more details, see [[Literature:100591| Boeke ''et al''. 2005]]). However, a recent study ([[Literature:100596|Llorens ''et al''. 2009]]) shows that the diversity of ''Ty1/Copia'' LTR retroelements is greater than this original classification. On the other hand, genomic studies have revealed the presence of an ''env''-like ORF in some ''Ty1/Copia'' species belonging to the genus Sirevirus ([[Literature:41869|Laten ''et al''. 1998]]; [[Literature:29886|Havecker ''et al''. 2005]]). Also, some ''Ty1/Copia'' elements (called ''CoDi-A'') described in diatoms encode for integrases (INTs) carrying a putative chromodomain similar to that found in the INTs coded by ''Ty3/Gypsy'' chromoviruses (for more information about this family, see [[Ty1/Copia| ''Ty1/Copia'']] family).

=== ''Ty3/Gypsy'' ===
''Ty3/Gypsy'' LTR retroelements also spread in animal, plant and fungal organisms. In almost (but not all) ''Ty3/Gypsy'' LTR retroelements ''int'' maps after to the Ribonuclease H (RH) in the pol polyprotein ([[Literature:88885|Eickbush and Jamburuthugoda 2008]]). The exception is the ''Ty3/Gypsy'' lineage called ''Gmr1'' ([[Literature:26669|Goodwin and Poulter 2002]]) which show an ORF organization identical to that of ''Ty1/Copia'' elements. The classification of ''Ty3/Gypsy'' LTR retroelements is also an in-progress matter. ICTV originally classified this family into two major genera, namely Metavirus and Errantivirus, based on the presence or absence of a third ORF ''env'' (''Metaviridae'' group, [[Literature:100590|Eickbush ''et al''. 2005]]). However, increasing evidences have revealed that these two genera include retroviruses and retrotransposons (for more details, see [[Ty3/Gypsy|''Ty3/Gypsy'']] family).

=== ''Bel/Pao'' ===
''Bel/Pao'' LTR retroelements have been only described in metazoan genomes. This family includes both LTR retrotransposons and retroviruses, as it is now known that some ''Bel/Pao'' species encode for putative ''env''-like genes ([[Literature:8238|Bowen and McDonald 1999]]; [[Literature:29887|Havecker ''et al''. 2004]]; [[Literature:88885|Eickbush and Jamburuthugoda 2008]]). These LTR retroelements show the same genomic ORF organization than ''Ty3/Gypsy'' family and are taxonomically known as semotiviruses (according to the ICTV, [[Literature:100590|Eickbush ''et al''. 2005]]). For more information, see[[Bel/Pao| ''Bel/Pao'']] family.

=== ''Retroviridae'' ===
''Retroviridae'' constitute a family of retroviruses which specifically inhabit or circulate in the genomes of vertebrates. The gag-pol-env genome ORF organization of the ''Retroviridae'' is similar to that of ''Ty3/Gypsy'' and ''Bel/Pao'' simple retroviruses. In most cases the multiple distinct ''Retroviridae'' species are complex retroviruses that incorporate in their genomes some additional accessory genes which are necessary for the replication cycle and transmission from a host into another. According to the ICTV ([[Literature:100589|Fauquet ''et al''. 2005]]), the ''Retroviridae'' can be divided into seven genera namely ''Alpha-'', ''Beta-'', ''Gamma-'', ''Delta-'', ''Epsilon-'', ''Spumaretroviridae'' and ''Lentiviridae'' (for further information, see [[Retroviridae |''Retroviridae'']] family).

<center>[[File:auton_LTRs.jpg]]</center>

===Caulimoviruses===
Plant caulimoviruses (''Caulimoviridae'') are double-stranded DNA unenveloped pararetroviruses that do not regularly integrate into the host genome for replication. Caulimoviral particles could be either bacilliform or isometric. According to ICTV, this family comprises six genera: ''Caulimovirus'', ''Soymovirus'', ''Cavemovirus'', ''Tungrovirus'', ''Badnavirus'' and ''Petuvirus'' ([[Literature:100592|Hull ''et al''. 2005]]). These replicate in plants via a RNA intermediate evolved from LTR retroelements ([[Literature:86892|Bousalem ''et al''. 2008]]). Despite caulimoviruses are not LTR retroelements and have not LTRs, they show a gag-PR-RT-RH genomic architecture similar to that of LTR retroelements. Additionally, caulimoviruses encode for other proteins required in their replication cycle and transmission (see the figure below, which represents the genome structure of the ''Cauliflower mosaic virus'' (CaMV) ([[Literature:100593|Franck ''et al'' 1980]]; [[Literature:100594|Stavolone ''et al''. 2005]])).
That is, the distinct caulimoviruses species show particular ORFs encoding for both structural and non structural proteins - movement protein, proteases, reverse transcriptase, RNase H and transactivator protein - as well as some proteins which function is unknown yet.
<center>[[File:Caulimovirus.jpg]]</center>

== '''Non-autonomous LTR retroelements''' ==
This is a family of retrotransposons showing LTRs, PBS and PPT sequences characteristics of autonomous LTR retrotransposons but usually lacking of coding capacity. Two classes of non-autonomous LTR retrotransposons have been described: the LArge Retrotransposons Derivatives ('''LARDs''') and the Terminal-repeat Retrotransposons In Miniature ('''TRIMs'''). These elements probably need the help of mobility-related proteins encoded by other functional (autonomous) retrotransposons. To date, non-autonomous LTR retroelements have been only described in plants. As there is no intermediate sequences described between TRIMs and LARDs, these appear to follow different replicational or life-cycle strategies and probably have distinct histories ([[Literature:35840|Kalendar ''et al''. 2004]]).

==='''LARDs'''===
LARDs range from 5.5 kb to 8.5 kb and have large-conserved-no coding internal domains of 3.5 kb flanked by long LTRs (4.5 kb). Although LARD elements have been found throughout the ''Triticeae'' tribe (they have been primarily described from barley and related grasses and called ''Sukkula''-like elements) they have also been detected in grass species outside the ''Triticeae'' and in rice ([[Literature:100595|Jiang ''et al''. 2002a]]; [[Literature:34872|2002b]]). It has been suggested that LARDs evolve from ''Ty3/Gypsy'' LTR retroelements as they apparently use (for replication and integration) distinct protein products encoded by their putative ''Ty3/Gypsy'' LTR retroelements partners ([[Literature:35840|Kalendar ''et al''. 2004]]).
==='''TRIMs'''===
TRIMs elements are less than 540 bp in size. They show a small non-coding central domain of 100–300 bp which contains PBS and PPT motifs and that is flanked by small LTRs of 100–250 bp in size. The complete lack of coding capacity makes it impossible to classify TRIMs elements conventionally into ''Ty1/Copia'' or ''Ty3/Gypsy'' families ([[Literature:83212|Witte ''et al''. 2001]]). These elements have been described in both monocotyledonous and dicotyledonous plant species and seem to be involved actively in the restructuring of plant genomes ([[Literature:83212|Witte ''et al''. 2001]]).

<center>[[File:non-auton_LTRs.jpg]]</center>

[[Category:Retroelements]]

LTR Retroelements - Revision history

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