imported>Fmaumus at 12:02, 29 October 2012

2012-10-29T12:02:10Z

New page

==Introduction==
The ''Ty1/Copia'' depicts one of the most important and representative families of LTR retroelements in eukaryotes (see also, [[Literature:20028|Eickbush and Malik 2002]]). The abundant representation of ''Ty1/Copia'' LTR retroelements in the genomes of plants, fungi, animals, algae and several protists suggests that the ancestors of this family probably co-existed with the ancestors of ''Ty3/Gypsy'' LTR retroelements before the split between plants and unikonts (see, [[Literature:100596|Llorens ''et al.'' 2009]] and references therein). Although the LTR retrotransposon form is what predominates in the ''Ty1/Copia'' family it is now known that several ''Ty1/Copia'' elements described in plants (those belonging to ''Sire'' clade) are carriers of a third ORF ''env'' which confer them the status of potential retrovirus ([[Literature:29886|Havecker ''et al''. 2005]]). To date, there is no evidence about retrovirus-like ''Ty1/Copia'' representatives in fungal and metazoan organisms.

== Genomic structure: ==
''Ty1/Copia'' LTR retroelements show identical functions and similar genome organization than other LTR retroelements. That usually is:
*A 5' long terminal repeat (LTR) of 100-1300 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 100-1300 nt

However, ''Ty1/Copia'' elements differ from other other LTR retroelements in the position of integrase (INT) domain within pol polyprotein. While ''Bel/Pao'', ''Retroviridae'' and almost but not all ''Ty3/Gypsy'' LTR retroelements show the INT at the C-terminus of pol (after RNase H), ''Ty1/Copia'' elements present INT N-terminal to the reverse transcriptase (after the protease domain) (for a review, see [[Literature:88885 |Eickbush and Jamburuthugoda 2008]]; see also [[LTR retroelements|LTR retroelements]]).

<center>[[File:INT_domain.jpg]]</center>
<center>(figure not to scale. Violet and blue arrows indicate respectively the INT domain position within the ''Ty1/Copia'' and ''Ty3/Gypsy'' – ''Bel/Pao'' pol polyproteins)</center>

==Evolutionary history and in-progress taxonomy==
The classification of ''Ty1/Copia'' family is work in progress. According to the International Committee on the Taxonomy of Viruses (ICTV) the ''Ty1/Copia'' family is called ''Pseudoviridae'' and was originary divided into three genera namely, ''Pseudovirus'' (type species ''Saccharomyces cerevisiae Ty1'' element, SceTy1V), ''Hemivirus'' (type species ''Drosophila melanogaster'' Copia element, DmeCV) and ''Sirevirus'' (type species ''Glycine max'' SIRE-1 virus, GmaSIRE-1V) ([[Literature:100591|Boeke ''et al.'' 2005]]). Pseudoviruses and hemiviruses are normally distinguished by the primer used for reverse transcription (a full tRNA or a half tRNA, respectively) while sireviruses derive from plant hosts and make up a distinct cluster according to their RT amino-acid sequences ([[Literature:29887 |Havecker ''et al''. 2004]]).

The ICTV classification is important for understanding the original ''Ty1/Copia'' family but it is not conclusive to date for managing the currently available diversity of this family. According to ([[Literature:100596|Llorens ''et al'' 2009]]), an update of the phylogeny of ''Ty1/Copia'' LTR retroelements based on pol reveals two major branches 1 and 2. Branch 1 collects ''Pseudovirus'' genus (see [[Literature:29887 |Havecker ''et al''. 2004]]) together with a clade called ''GalEA'' ([[Literature:98385|Terrat ''et al.'' 2008]]), found in marine bilaterians, and all ''CoDi''-like LTR retrotransposons found in diatom genomes ([[Literature:86909|Bowler ''et al''. 2008]]; [[Literature:100685|Maumus ''et al.'' 2009]]). According to [[Literature:100596|Llorens ''et al.'' 2009]], the wide variety of ''CoDi''-like elements splits into four clades that we simply name I, II (or A and B), C and D. One of the most exciting aspects of ''CoDi''-like elements is that the different elements belonging to clade A encode INTs carrying a putative chromodomain at their C-terminus ([[Literature:100596|Llorens ''et al.'' 2009]]). The second ''Ty1/Copia'' branch encompasses the remaining lineages of LTR retroelements, including the previously described ''Copia''-like hemiviruses and sireviruses. A description follows in the table and discussion below.

{| cellpadding="4" cellspacing="0" align="center" style="border:1px solid #000000"
|- class="tableHeader"
!Branch
!Host Phyla
!Genus
!Clade
!Env
!Chromodomain
|-
|Branch 1
|Fungi
|Pseudovirus ''(Pseudoviridae)''
|[[#Ty (Pseudovirus)|''Ty (Pseudovirus)'']]
|no
|<center> no</center>
|-
|Branch 1
|Diatoms ''(Heterokontophyta)''
|
|[[#CoDi|''CoDi-I'' or ''CoDi-A'']]
|no
|<center> yes</center>
|-
|Branch 1
|Diatoms ''(Heterokontophyta)''
|
|[[#CoDi|''CoDi-II'' or ''CoDi-B'']]
|no
|<center> no</center>
|-
|Branch 1
|Diatoms ''(Heterokontophyta)''
|
|[[#CoDi|''CoDi-C'']]
|no
|<center> no</center>
|-
|Branch 1
|Diatoms ''(Heterokontophyta)''
|
|[[#CoDi|''CoDi-D'']]
|no
|<center> no</center>
|-
|Branch 1
|Marine Arthropoda
|
|[[#GalEA|''GalEA'']]
|no
|<center> no</center>
|-
|Branch 2
|Fungi
|
|[[#p-Cretro|''p-Cretro'']]
|no
|<center> no</center>
|-
|Branch 2
|Land plants ''(Viridiplantae)''
|Sirevirus ''(Pseudoviridae)''
|[[#Sire|''Sire'']]
|yes
|<center> no</center>
|-
|Branch 2
|Land plants ''(Viridiplantae)''
|Sirevirus ''(Pseudoviridae)''
|[[#Oryco|''Oryco'']]
|no
|<center> no</center>
|-
|Branch 2
|Land plants ''(Viridiplantae)''
|
|[[#Retrofit|''Retrofit'']]
|no
|<center> no</center>
|-
|Branch 2
|Land plants ''(Viridiplantae)''
|
|[[#Tork|''Tork'']]
|no
|<center> no</center>
|-
|Branch 2
|Green algae ''(Viridiplantae)''
|
|[[#Osser|''Osser'']]
|no
|<center> no</center>
|-
|Branch 2
|Red algae ''(Rhodophyta)''
|
|[[#PyRE1G1|''PyRE1G1'']]
|no
|<center> no</center>
|-
|Branch 2
|Cnidaria ''(Metazoa)''
|
|[[#Hydra|''Hydra'']]
|no
|<center> no</center>
|-
|Branch 2
|Arthropoda
|Hemivirus ''(Pseudoviridae)''
|[[#Copia|''Copia'']]
|no
|<center> no</center>
|-
|Branch 2
|Arthropoda
|
|[[#1731|''1731'']]
|no
|<center> no</center>
|-
|Branch 2
|Arthropoda
|
|[[#Tricopia|''Tricopia'']]
|no
|<center> no</center>
|-
|Branch 2
|Arthropoda
|
|[[#Mtanga|''Mtanga'']]
|no
|<center> no</center>
|-
|Branch 2
|Arthropoda
|
|[[#Humnum|''Humnum'']]
|no
|<center> no</center>
|}

<center>Taxonomical table summarizing phylogenetic results reported by both [[Phylogeny:GAGPOL_Ty1/Copia|gag-pol]] and [[Phylogeny:POL_Ty1/Copia|pol]] ''Ty1/Copia'' inferred trees</center>

===Branch 1===
The first branch, which we call Branch 1, encompasses the original ''Pseudovirus'' genus together with a ''GalEA'' clade called, a lineage specifically found in marine bilaterians, and all ''CoDi''-like LTR retrotransposons described in diatoms. The variety of ''CoDi''-like elements splits into four clades that we simply name A, B, (or I and II), C and D ([[Literature:100596|Llorens ''et al''. 2009]]).

====''Ty (Pseudovirus)''====
Pseudovirus elements are ''Ty1/Copia'' LTR retrotransposons normally found in fungi ([[Literature:29887 |Havecker ''et al''. 2004]]). The members of this clade usually have a genome of 5.6-6.8 Kb in size, which show an internal gag-pol region flanked by LTRs of 0.3-0.4 Kb and showing the typical Primer Bindind Site (PBS) and one or two Polypurine Tracts (PPT) downstream and upstream to the 5´and 3´LTRs, respectively ([[Literature:48474|Mattews ''et al.'' 1997]]; [[Literature:23281|Friant ''et al.'' 1996]]; [[Literature:30799|Heyman ''et al.'' 2003]]; [[Literature:54327|Neuvéglise ''et al.'' 2002]]). Among ''Ty'' retrotransposons only ''Ty4'' elements contain the ''gag''-associated RNA-binding motif (CCHC). This motif has not been identified in the ''gags'' of the other members belonging to this clade ([[Literature:59075|Peterson-Burch and Voytas 2002]]; [[Literature:54327|Neuvéglise ''et al.'' 2002]]).

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

====''CoDi-I'' ====
The elements belonging to clade ''CoDi-I'' ([[Literature:100685|Maumus ''et al.'' 2009]]) also called CoDi-A ([[Literature:100596|Llorens ''et al''. 2009]]) have been described in the genomes of the marine pennate diatom ''Phaeodactylum tricornutum'' and the marine algae phytoplankton ''Thalassiosira pseudonana'' ([[Literature:100685|Maumus ''et al.'' 2009]]; [[Literature:86909|Bowler ''et al.'' 2008]]). The genome of these ''Ty1/Copia''-like LTR retroelements is about of 5.9-7.4 Kb in size, including LTRs of 0.15-0.69 Kb long that flank a single long ORF. The ORF contains the ''gag'' and ''pol'' typical ''Ty1/Copia'' domains structure (gag, protease, integrase, reverse transcriptase and ribonuclease H). The conserved integrase motif has not been clearly identified in the genome of these elements, a well as the gag-associated zinc finger motif. Interestingly, ''CoDi-I'' represents the first described set of ''Ty1/Copia'' retroelements carrying a putative chromodomain at the C-terminus of their pol-INT domain ([[Literature:100596|Llorens ''et al''. 2009]]) similarly to ''Ty3/Gypsy'' chromoviruses ([[Literature:47259|Marin and Llorens 2000]]), which use this feature for chromatin integration ([[Literature:89590|Gao ''et al.'' 2008]]).

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

====''CoDi-II''====
''CoDi-II'' ''Ty1/Copia''-like LTR retroelements ([[Literature:100685|Maumus ''et al.'' 2009]]), also called CoDi-B ([[Literature:100596|Llorens ''et al''. 2009]]), have been described in the genomes of the marine pennate diatom ''Phaeodactylum tricornutum'' and the marine algae phytoplankton ''Thalassiosira pseudonana'' ([[Literature:100685|Maumus ''et al.'' 2009]]; [[Literature:86909|Bowler ''et al.'' 2008]]). These display a genome of about 5.2-6.1 Kb in size, including LTRs of 0.16-0.30 Kb long that bound one or two overlapping ORFs. The translated regions contain both gag and pol ''Ty1/Copia''-like polyproteins domains (gag, protease, integrase, reverse transcriptase and ribonuclease H). The conserved integrase motif has not been clearly identified in the genome of ''CoDi-II'' retroelements.

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

====''CoDi-C''====
''CoDi-C'' clade is the term used by Llorens ''et al.'' ([[Literature:100596|2009)]] to differentiate the two clades constituted by the ''CoDi-6''-like elements described by Maumus et al. ([[Literature:100685|2009]]) in the genomes of the marine pennate diatom ''Phaeodactylum tricornutum'' and the marine algae phytoplankton ''Thalassiosira pseudonana'' (see also [[Literature:86909|Bowler ''et al.'' 2008]]). The genome of ''CoDi-C'' elements, of about of 6.6-8 Kb in size, includes 0.27-0.49 Kb LTRs long flanking one or two overlapping ORFs that show both gag and pol ''Ty1/Copia''-like polyproteins domains (gag, protease, integrase, reverse transcriptase and ribonuclease H). ''CoDi-6''-like elements are the most divergent ''CoDi''-like, their position in the ''Ty1/Copia'' phylogeny is still under study as depending on the protein domain evaluated they may fall together with other ''CoDi''-like clades within Branch 1 or close to other ''Ty1/Copia'' elements of protostomes (for more details, see the collection of trees provided at
[[Phylogeny:POL_LTR_retroelements|GyDB]], or ([[Literature:100596|Llorens ''et al''. 2009]]; [[Literature:100685|Maumus ''et al.'' 2009]]).

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

====''CoDi-D''====
The term ''CoDi-D'' ([[Literature:100596|Llorens ''et al''. 2009]]) is used to differentiate the two clades constituted by the ''CoDi-6''-like elements described by Maumus ''et al.'' ([[Literature:100685|2009]]) in the genomes of the marine pennate diatom ''Phaeodactylum tricornutum'' and the marine algae phytoplankton ''Thalassiosira pseudonana'' (see also [[Literature:86909|Bowler ''et al.'' 2008]]). ''CoDi-D'' retroelements display a genome of about 5.1-5.3 Kb in size including LTRs of 0.16-0.41 Kb long. The LTRs flanked internal region encodes for a single long ORF that contains both gag and pol ''Ty1/Copia''-like polyproteins domains (gag, protease, integrase, reverse transcriptase and ribonuclease H). In the gag-nucleocapsid domain of ''CoDi-D'' elements have been identified two zinc finger motifs. ''CoDi-6''-like elements are the most divergent ''CoDi''-like, their position in the ''Ty1/Copia'' phylogeny is still under study as depending on the protein domain evaluated they may fall together with other ''CoDi''-like clades within Branch 1 or close to other ''Ty1/Copia'' elements of protostomes (for more details, see the collection of trees provided at [[Phylogeny:POL_LTR_retroelements|GyDB]], or ([[Literature:100596|Llorens ''et al''. 2009]]; [[Literature:100685|Maumus ''et al.'' 2009]]).

<center>[[File:CoDi-02.png]]</center>
<center>(''figure not to scale'')</center>

====''GalEA''====
This is a lineage of LTR retrotransposons, which seems to be restricted to aquatic species (they have been identified in crustaceans, fishes and urochordates). Its name derives from ''Galatheids Eumunida annulosa'' retrotransposons. The distinct members of this clade usually show an internal region of 3.9-4.4 kb in size delimited by LTRs of 0.12 – 0.32 kb, that includes a single large ORF containing gag and pol regions ([[Literature:98385|Terrat ''et al''. 2008]]).

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

=== Branch 2 ===
The second ''Ty1/Copia'' branch encompasses the remaining lineages of LTR retrotransposons and potential retroviruses, including ''Copia''-like hemiviruses and sireviruses.
====''pCretro''====
The elements belonging to this clade have been described in the genome of lignin-degrading basidiomycete ''Phanerochaete chrysosporium'' ([[Literature:41746|Larrondo ''et al''. 2007]]). The full-lenght consensus of known to date ''pCretro'' elements is about of 5 kb in size, contains 5' and 3' LTRs 0.36-0.4 kb long, and shows an internal region that codes for the gag and pol polyproteins characteristic of ''Ty1/Copia'' LTR retrotransposons.

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

====''Sireviruses'' ====
These ([[Literature:29887|Havecker ''et al''. 2004]]; [[Literature:29886|Havecker ''et al''. 2005]]) constitute a cluster of LTR retrotransposons and retroviruses described in plants and can be divided in two phylogenetically related lineages "Sire" and "Oryco" (according to [[Literature:100596|Llorens ''et al.'' 2009]]). These two differ in that the elements belonging to ''Sire'' clade usually (but not always) code for an additional putative ''env'' gene and are considered as potential retroviruses, while ''Oryco''-like elements are small LTR retrotransposons.
=====''Sire''=====
<blockquote>
''Sire'' elements are large LTR retroelements showing genomes of 9.3-9.8 kb in size flanked by LTRs of 0.5-1.2kb. Additionally to the typical gag and pol ORFs ''Sire''-like elements show a third ''env''-like ORF downstream to RNase H domain (and are thus considered potential retroviruses, [[Literature:29887|Havecker ''et al''. 2004]]; [[Literature:29886|Havecker ''et al''. 2005]]) and encode for a significantly large gag polyprotein, which may has two or three zinc finger arrays at its C-terminus ([[Literature:29886 |Havecker ''et al''. 2005]]). The most representative example of ''Sire''-like element encoding for a putative ENV is ''SIRE-1'', an element originally identified in the soybean ''Glycine max'' ([[Literature:41869 |Laten ''et al''. 1998]]; [[Literature:41868|Laten 1999]]). ''SIRE1''-like elements are widespread among plant species, both in monocots (rice, maize, sorghum) and dicots (Arabidopsis, lotus, medicago, citrus) ([[Literature:29886 |Havecker ''et al''. 2005]]).
</blockquote>

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

===== ''Oryco'' =====
<blockquote>
These LTR retrotransposons have been found in the genome of some plant species: ''Vitis vinifera'', ''Arabidopsis thaliana'', ''Popolus tricocarpa'' and ''Oryza sativa'' ([[Literature:100596|Llorens ''et al''. 2009]]). Their small genome is about of 4.2-4.9 Kb in size included LTRs of 0.16-0.44 Kb long. The internal coding region displays the ''gag-pol'' domain order of ''Ty1/Copia'' retrotransposons. No ''env''-gene has been detected in their genome.
</blockquote>

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

====''Retrofit''====
The plant LTR retrotransposons that constitute ''Retrofit'' clade have a genome of about 4.7-4.9 Kb, included small LTRs of 0.12-0.3 kb long, encoding for both gag-pol polyprotein which domain organization is the tipical of ''Ty1/Copia'' LTR retrotransposons ([[Literature:58027|Pastuglia ''et al''. 1997]]; [[Literature:100617|Song ''et al.'' 1997]]; [[Literature:82569|White ''et al.'' 1994]]; [[Literature:100596|Llorens ''et al''. 2009]]; [[Literature:59507|Piegu ''et al.'' 2006]]).

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

====''Tork''====
''Tork'' clade belong LTR retrotransposons described in the genome of different plant species: ''Zea mays'', ''Solanum lycopersicum'', ''Vitis vinifera'', ''Nicotiana tabacum'' and ''Vigna radiata'' ([[Literature: 66255|SanMiguel ''et al''. 1996]]; [[Literature:100596|Llorens ''et al''. 2009]]; [[Literature:47253|Marillonnet and Wessler 1998]]; [[Literature:27170|Grandbastien ''et al.'' 1989]]; [[Literature:31156|Hirochika ''et al.'' 1996]]; [[Literature:83886|Xiao ''et al.'' 2007]]). The members of this clade show very different size in both LTRs and coding regions being respectively of 0.12-1.2 Kb and 4.1-6.7 Kb long.

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

====''Osser''====
''Osser'' is the first complete ''Ty1/copia''-like retrotransposon described in the colonial green alga ''Volvox carteri''. Its genome is 4.875 bp in size and bordered by two identical LTRs of 197 bp in length. ''Osser'' internal region is characterized by a large central domain with the typical gag-pol organization of retrotransposons belonging to the ''Tyl/copia'' family ([[Literature:44101|Lindauer ''et al.'' 1993]]) (for more details see the file of [[Element:Osser|Osser]] element).

====''PyRE1G1''====
''PyRE1G1'' is a ''Ty1/copia''-like retrotransposon constituting a single clade that was characterized in the genome of the red alga ''Porphyra yezoensis''. Its genome is 4807 bp in size including two LTRs of 204 bp. The internal region of this element presents an ORF of 1401 residues that codes for a single gag-pol polyprotein ([[Literature:95611|Peddigari ''et al.'' 2008]]) (for more details see the file of [[Element:PyRE1G1|PyRE1G1]] element).

====''Hydra''====
''Hydra'' clade collect at least two elements - ''Hydra1-1'' and Hydra ''1-2'' - both described in the genome of the freshwater animal ''Hydra magnipapillata'' and in that of the zebra fish ''Danio rerio'' ([[Literature:100596|Llorens ''et al''. 2009]]). The genome of these elements is about of 4.1-4.3 Kb and reveals a single long ORF that, although is broken by stop codons, contains the typical ''Ty1/Copia'' ''gag-pol'' domains structure. LTRs of 163 bp in size have been described for ''Hydra1-1'', while information about the LTRs of ''Hydra1-2'' is not yet available.

<center>[[File:Hydra-02.png]]</center>
<center>(''figure not to scale'')</center>

====''Copia''====
The elements of ''Copia'' clade constitute a clade of LTR retrotransposons described in Insecta ([[Literature:59075|Peterson-Burch and Voytas 2002]]; [[Literature:55859|Ohbayashi ''et al.'' 1998]]; [[Literature:85100|Yoshioka ''et al.'' 1992]]). Their genome, about of 4.7-5.2Kb in size, includes LTRs of 0.18-0.27 kb bounding an internal region constituted by one or two overlapping ORFs which domain organization is the typical of ''Ty1/Copia'' retroelements.

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

====''1731''====
''1731'' clade is a lineage of diptera LTR retrotransposons, which usually are 4.5-4.6 kb in size and show an internal gag-pol coding region flanked by LTRs of 0.2-0.3 kb long ([[Literature:22874|Fourcade-Peronnet ''et al.'' 1988]]).

<center>[[File:1731-01.png]]</center>
<center>(''figure not to scale'')</center>

====''Tricopia''====
''Tricopia'' represents a small clade of LTR retrotransposons described in the genome of the red flour beetle ''Tribolium castaneum'' ([[Literature:100596|Llorens ''et al''. 2009]]) and shows the typical ''Ty1/Copia'' genome structure: a translated region containing the ''gag-pol'' domains flanked by 0.25-0.26-bp LTRs. The ''Tricopia'' full-length genome is 4541 bp long (for more details see the file of [[Element:Tricopia|Tricopia]] element).

====''Mtanga''====
''Mtanga'' represents a clade of ''Ty1/Copia'' LTR retrotransposons described from the African malaria vector, ''Anopheles gambiae''. As they are specific to the Y chromosome of this mosquito they are designated as mtanga-Y elements. The genome of these elements normally is 4.284 bp and reveals two overlapping ''gag'' and ''pol'' genes bounded by LTRs of 119 bp in size ([[Literature:64155|Rohr ''et al.'' 2002]]) (for more details see the file of [[Element:Mtanga|Mtanga]] element).

====''Humnum'' ====
''Humnum'' is a ''Ty1/copia''-like retrotransposon found in the genome of the Lepidoptera ''Heliconius numata'' ([[Literature:100596|Llorens ''et al''. 2009]]). ''Humnum'' genome, of about of 4.4 Kb in size, includes 139-bp LTRs flanking a single long polyprotein. The encoded polyprotein contains both ''gag'' and ''pol'' ''Ty1/Copia'' associated domains (for more details see the file of [[Element:Humnum|Humnum ]] element).

[[Category:Retroelements]]

Ty1/Copia - Revision history

imported>Fmaumus at 12:02, 29 October 2012