imported>Lcovelli: /* Tas */

2010-05-25T07:24:13Z

Tas

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== Introduction: ==
''Bel/Pao'' LTR retroelements ([[Literature:46548|Malik ''et al''. 2000]]) constitute a family of LTR retrotransposons and retroviruses described to date only in metazoan genomes ([[Literature:14755|Copeland ''et al''. 2005]]). This family was originally characterized with the discovery of element sequences such as ''Pao'' ([[Literature:83961|Xiong ''et al''. 1993]]), ''Bel'' ([[Literature:100598|Davis and Judd 1995]]), and ''Tas'' ([[Literature:100599|Aeby ''et al''. 1986]]) and the various ''Cer''-like sequences described in ''Caenorhabditis elegans'' ([[Literature:8238|Bowen and McDonald 1999]]). At present and according with the International Committee on the Taxonomy of Viruses (ICTV), the multiple distinct members of the ''Bel/Pao'' family are called semotiviruses (for a review, see [[Literature:88885|Eickbush and Jamburuthugoda 2008]]).

== Genomic structure: ==
Similarly to the ''[[Ty3/Gypsy]]'' and the ''[[Retroviridae]]'', ''Bel/Pao'' LTR retroelements normally show a ''gag-pol'' genome (GAG-PR-RT-RH-INT) plus ''env'' (in the case of retroviruses) of variable size (between 4 and 10 Kb), flanked by LTRs and structured (in its inserted genomic form) as follows:

*A 5' long terminal repeat (LTR) of 100-900 nt
*A non-coding region of variable size that corresponds to the first portion of the retrotranscribed genome.
*A Primer Binding Site (PBS) of 18 nt, complementary to a specific zone of the 3' end of a tRNA, normally provided by the host cell in order to start the retrotranscription.
*Open Reading Frames (ORFs) for ''gag, pol'', (and ''env'' in retroviruses) genes.
*A small region of ~10 A/G "Polypurine Tract" (PPT), responsible for starting the synthesis of the proviral DNA strand.
*A 3' long terminal repeat (LTR) of 100-900 nt

<center> [[File:bel_pao.png]]</center>
<center>(''figure not to scale'')</center>

== Evolutionary history and in-progress taxonomy: ==
The ''Bel/Pao'' family can be divided into five lineages called ''Pao'', ''Sinbad'', ''Bel'', ''Tas'' and ''Suzu'' ([[Literature:14755|Copeland ''et al''. 2005]]). Phylogenetic approaches based on ''pol'' ([[Literature:100596|Llorens ''et al.'' 2009]]) show that these five can be divided into three branches namely as 1, 2 and 3. The first includes the two clades ''Tas'' and ''Bel'', the second collects ''Pao'' and ''Sinbad'' clades, and the last consists of a single clade called ''Suzu''.

{| cellpadding="4" cellspacing="0" align="center" style="border:1px solid #000000"
|- class="tableHeader"
!Branch
!Host Phyla
!Genus
!Clade
!Env
|-
|Branch 1
|''Metazoa'' (Nematoda and Cnidaria)
|''Semotivirus''
|[[#Tas|''Tas'']]
|<center> some elements</center>
|-
|Branch 1
|''Metazoa'' (Insecta)
|''Semotivirus''
|[[Bel|''Bel'']]
|<center> one element</center>
|-
|Branch 2
|''Metazoa'' (Insecta and Vertebrata)
|''Semotivirus''
|[[#Pao|''Pao'']]
|<center> no</center>
|-
|Branch 2
|''Metazoa'' (Invertebrata)
|''Semotivirus''
|[[#Sinbad|''Sinbad'']]
|<center> no</center>
|-
|Branch 3
|''Metazoa'' (Echinodermata and Vertebrata)
|''Semotivirus''
|[[#Suzu|''Suzu'']]
|<center> no</center>
|-
|}

<center>Taxonomical table summarizing phylogenetic results reported by both [[Phylogeny:GAGPOL_Bel/Pao|gag-pol]] and [[Phylogeny:POL_Bel/Pao|pol]] ''Bel/Pao'' inferred trees</center>

=== Branch 1 ===
Branch 1 encompasses two clades of LTR retrotransposons and potential retroviruses called ''Tas'' and ''Bel'' found in the genomes of cnidarians and protostomes.
====''Tas''====
''Tas'' clade ([[Literature:14755|Copeland ''et al''. 2005]]) is constituted by diverse ''Bel/Pao''-like LTR retrotransposons and retroviruses described in nematodes and cnidarians ([[Literature:8238|Bowen and McDonald 1999]]; [[Literature:21668|Felder ''et al.'' 1994]]; [[Literature:100596|Llorens ''et al.'' 2009]]). Their genome is about of 5.4-10 Kb in size including, in almost (but not all) retroelements, LTRs of 0.23-0.81 Kb long. The internal coding region is respectively flanked by a Primer Binding Site (PBS) and a Polypurine Tract (PPT) and, although is usually disrupted by several stop codons and frameshiftings, it displays the distinct ''gag'' and ''pol'' domains typical of ''Bel/Pao'' LTR retrotransposons. In some elements of this clade, it has also been identified an ''env''-like gene located at their C-terminal translated regions ([[Literature:21668|Felder ''et al.'' 1994]]; [[Literature:8238|Bowen and McDonald 1999]]). (The figure below shows an idealized consensus of ''Tas'' elements genome organization).

<center>[[File:Tas_2-01.png]]</center>
<center>(''figure not to scale'')</center>

====''Bel''====
''Bel'' ([[Literature:14755|Copeland ''et al.'' 2005]]) is a lineage of insect LTR retrotransposons which usually are 4.6-9.0 Kb in size and show an internal region flanked by LTRs of 0.2-0.4 kb long. The members of this clade may encode for one, two or three ORFs displaying the typical gag-pol domains. Interestingly, our analyses reveal that the env coded by ''Roo'' (the ''Bel''-like element represented in the figure below) is more similar to those coded by ''Ty3/Gypsy'' errantiviruses than to those coded by other ''Bel/Pao'' potential retroviruses. This suggests that several ''Bel/Pao'' elements might have evolved from the chimeric recombination between a ''Ty3/Gypsy'' retrovirus and a ''Bel/Pao'' retrotransposon.

<center>[[File:Bel-01.png]]</center>
<center>(''figure not to scale'')</center>

=== Branch 2 ===
Branch 2 includes the ''Pao'' and ''Sinbad'' clades of LTR retrotransposons described in protostomes and deuterostomes.
====''Pao''====
''Pao'' is a lineage of LTR retrotransposons ([[Literature:14755|Copeland ''et al.'' 2005]]) widely distributed in the genomes of several protostomes and deuterostomes. ''Pao'' elements usually have a size of 4.7-8.3 Kb (including LTRs of 0.3-1.3 Kb), their internal region is characterized by the usual presence of a PBS, ''gag-pol'' coding region and PPT.

<center>[[File:Pao-01.png]]</center>
<center>(''figure not to scale'')</center>

==== ''Sinbad'' ====
''Sinbad'' clade ([[Literature:14755|Copeland ''et al.'' 2005]]) collects several LTR retrotransposons described in both protostome (Platyhelminthes) and deuterostome (Hemichordates) worms. ''Sinbad'' elements normally display genomes of 4.2-7.4 Kb in size, including flanking LTRs of 0.08-0.86 Kb and are characterized by an internal gag-pol region plus flanking PBS and PPT as is typical in ''Bel/Pao'' LTR retrotransposons.

<center>[[File:Sinbad-01.png]]</center>
<center>(''figure not to scale'')</center>

=== Branch 3 ===
Branch 3 consists of a single clade called ''Suzu'', which includes LTR retrotransposons that have so far been described exclusively in vertebrates.

====''Suzu'' ====
''Suzu'' clade ([[Literature:14755|Copeland ''et al.'' 2005]]) is constituted by diverse deuterostome LTR retrotrasposons (described in echinoderms and vertebrates). ''Suzu''-like elements usually are about 7-7.6 Kb in size including LTRs of 0.4-0.7 kb long and code for the typical gag and pol protein domains.

<center>[[File:Suzu-01.png]]</center>
<center>(''figure not to scale'')</center>

[[Category:Retroelements]]

Bel/Pao - Revision history

imported>Lcovelli: /* Tas */