imported>Lcovelli: /* Tungrovirus */

2010-08-09T10:13:53Z

Tungrovirus

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==Introduction==
Caulimoviruses (''Caulimoviridae'') are DNA pararetroviruses that replicate in plants via a RNA intermediate evolved from LTR retroelements (for more details, see [[Literature:86892|Bousalem ''et al.'' 2008]]). "Pararetrovirus" is the term introduced by [[Literature:100600|Temin (1985)]] to define animal (''Hepadnaviridae'') and plant viruses (''Caulimoviridae'') that differ to retroviruses on the basis of their DNA genome and on their no regular integration into the host genome for replication. To date, it is known however that the genomic sequences of only a few plant pararetroviruses, thus as ''Petunia Vein Clearing Virus'' (PVCV) ([[Literature:63308|Richert-Pöggeler and Shepherd 1997]]) and ''Banana Streak badnavirus'' (BSV) ([[Literature:100608|Ndowora ''et al.'' 1999]]; [[Literature:100609|Harper ''et al.'' 2005]]), are integrated into their host genomes, and that the integrated elements can give rise to episomal virosis ([[Literature:100608|Ndowora ''et al.'' 1999]]). It is commonly assumed that these integrated sequences are relics of ancient infection events ([[Literature:100609|Harper ''et al.'' 2005]]) or representative sequence intermediates between caulimoviruses and LTR retrotransposons ([[Literature:86892|Bousalem ''et al.'' 2008]]; [[Literature:100596|Llorens ''et al.'' 2009]]).

==Virion morphology==
Caulimoviruses usually form unenveloped virus particles which can be either bacilliform or isometric. As shown in the figure below, these are approximately 35-50 nm in diameter and 900nm in length (for the bacilliforms) or 45-50 nm in diameter and icosahedral symmetry (for the isometrics). The genome of caulimoviruses is a semi circular double-stranded DNA of about 6-8 kb in size, which is flanked by direct terminal repeats reiterated internally in an inverted form (for more details see [[Literature:100589|Fauquet ''et al''. 2005]]). The caulimoviral genome also has an intergenic poly (A) region (which may also be absent), and single-stranded discontinuities or gaps at specific sites of both strands ([[Literature:29391|Harper ''et al.'' 2002]]).

<center>[[File:Caulimovirus.png]]</center>

==Genomic structure==
As noted in the section above, caulimoviruses have official taxonomical position within the viral nomenclature as pararetroviruses but although they are DNA viruses and do not have LTRs, they are evolutionarily related with eukaryotic LTR retroelements (particularly with those of the ''Ty3/Gypsy'' family, [[Literature:100596|Llorens ''et al.'' 2009]]) on the basis of a gag-pol ancestor (on this topic, see also [[Literature:39430|Koonin ''et al.'' 1991]]; [[Literature:86892|Bousalem ''et al.'' 2008]]; [[Literature:97845|Staginnus ''et al''. 2009]]).

<center>[[File:Ty3_caulimov.png]]</center>
<center>(relationship between the ''Ty3/Gypsy'' and an idealized ''Caulimoviridae'' consensus genome organization)</center>

Caulimoviruses commonly show other genes such as those coding for the Movement (MP or MOV) protein, the Aphid Transmission Factor (ATF), the Virus Associated Protein (VAP) and the Transactivator/viroplasmin protein or Inclusion Body Matrix Protein (TAV or IBMp) as well as diverse additional genes (that vary depending on the lineage), which are necessary for their viral life cycle and transmission (for more details see [[Literature:100589|Fauquet ''et al''. 2005]]). Upon this, prior trends relate caulimoviruses to other virus systems based on the common share of the movement protein ([[Literature:39430|Koonin ''et al.'' 1991]]), arguing that the most likely origin of caulimoviruses was chimeric (a hybrid between LTR retrotransposons and other RNA viruses).

==Replication==
Replication involves two phases: transcription of an RNA intermediate from the viral DNA in the nucleus and then reverse transcription of this RNA to rise dsDNA in the cytoplasm. The genome of pararetroviruses also contains a sequence complementary to a plant tRNAMet that corresponds to the initiation site of DNA replication. Usually this site is located inside or downstream of the large intergenic region (non-coding region) and is generally designated nucleotide 1 ([[Literature:100606|de Kochko ''et al.'' 1998]]). In contrast to retroviruses, plant pararetroviruses do not require their integration into the host genome for their replication, therefore their genome does not encode the integrase protein. Although this is a characteristic of pararetroviruses, sequences from certain ''Caulimoviridae'' species, termed Endogenous Pararetroviruses (EPRVs, [[Literature:97845|Staginnus ''et al''. 2009]]) show a putative integrase domain similar to those found in retroviruses and retrotransposons of the ''Ty3/Gypsy'' family ([[Literature:63308|Richert-Pöggeler and Shepherd 1997]]). In particular three viruses, BSV, PVCV and ''Tobacco vein clearing virus'' (TVCV) have been shown to have episomal infections associated with integrated sequences ([[Literature:29391|Harper ''et al.'' 2002]]).

==Biological distribution and host symptomatology==
The natural hosts of ''Caulimoviridae'' species belong to the Kingdom ''Plantae'' (Angiosperms of ''Dicotyledonae'' and ''Monocotyledonae'' classes).
Depending on the genera, the natural virus transmission could occurr via an insect vector (''Hemiptera'' insects of the families ''Aleyrodidae'' ''Aphididae'', ''Cicadellidae'', ''Pseudococcidae'') or by contact between plant hosts as well as by seeds or by pollen. Transmission can also be performed by techniques such as mechanical inoculation and grafting (for more details see [[Literature:100589|Fauquet ''et al''. 2005]]). The characteristic plant symptoms associated to caulimoviruses infection comprise: vein-clearing, banding mosaic, necrotic flecks, lines and chlorotic blotches, stunting, leaf curling, leaf malformation, twisting of leaflets, etc.

==Evolutionary history and viral taxonomy==
According to the ''International Committee on the Taxonomy of Viruses'' (ICTV, [[Literature:100589|Fauquet ''et al''. 2005]]), the ''Caulimoviridae'' can be taxonomically divided into six genera: ''Caulimovirus'', ''Soymovirus'', ''Cavemovirus'', ''Tungrovirus'', ''Badnavirus'' and ''Petuvirus''. Phylogenetic reconstruction analyses based on pol collect these six genera into four classes: Class 1 includes the genera ''Caulimovirus'' and ''Soymovirus''; Class 2 comprises Tungroviruses and Badnaviruses (the most abundant group of ''Caulimoviridae'' species); Class 3 represents the ''Cavemovirus'' genus; and finally Class 4 includes the ''Petunia Vein Clearing Virus'' (PVCV), which to date is the only known molecular species of ''Petuvirus'' genus ([[Literature:100596|Llorens ''et al.'' 2009]]).

{| cellpadding="4" cellspacing="0" align="center" style="border:1px solid #000000"
|- class="tableHeader"
!Class
!Host Phyla
!Genus
!Type species

|-
|Class 1
|Land plants (''Viridiplantae'')
|[[#Caulimovirus|''Caulimovirus'']]
|''Cauliflower mosaic virus'' (CaMV)
|-
|Class 1
|Land plants (''Viridiplantae'')
|[[#Soymovirus|''Soymovirus'']]
|''Soybean chlorotic mottle virus'' (SbCMV)
|-
|Class 2
|Land plants (''Viridiplantae'')
|[[#Badnavirus|''Badnavirus'']]
|''Commelina yellow mottle virus'' (CoYMV) or (ComYMV)
|-
|Class 2
|Land plants (''Viridiplantae'')
|[[#Tungrovirus|''Tungrovirus'']]
|''Rice tungro bacilliform virus'' (RTBV)
|-
|Class 3
|Land plants (''Viridiplantae'')
|[[#Cavemovirus|''Cavemovirus'']]
|''Cassava vein mosaic virus'' (CSVMV)
|-
|Class 4
|Land plants (''Viridiplantae'')
|[[#Petuvirus|''Petuvirus'']]
|''Petunia vein clearing virus'' (PVCV)
|}

<center>Taxonomical table summarizing phylogenetic results reported by both [[Phylogeny:COATPOL_Caulimovirus|coat-pol]] and [[Phylogeny:POL_Caulimovirus|pol]] ''Caulimoviridae'' inferred trees. </center>

=== Class 1 ===
Class 1 includes two genera – ''Caulimovirus'' and ''Soymovirus''.
====''Caulimovirus''====
The species belonging to this genus form isometric particles with a diameter between 35 and 50 nm. The viral genome contains a single molecule of circular double-stranded DNA of about 8000 bp long that codes for 6 or 7 ORFs usually in the order addressed in the figure below, which is an idealized full-lenght consensus (for more details see [[Literature:100589|Fauquet ''et al''. 2005]]). Usually, the genomes of ''Caulimovirus'' species contain two major transcriptional promoter sequences: one located in the 3′-terminus of ORF VI (TAV) and extending into the large intergenic region that transcribes whole genome of the virus (a full-length transcript equivalent to CaMV 35S transcript); while the second one, situated at the 3′-terminus of ORF V (Pol) and extending into the small intergenic region between ORF V and VI, transcribes only the ORF VI, (a sub-genomic transcript equivalent to CaMV 19S transcript) ([[Literature:100730|Bhattacharyya ''et al.'' 2002]]).
<center>[[File:Caulimov.png]]</center>
<center>(''figure not to scale, considering that the viral genomes are a semi circular dsDNAs, the ORFs order show in the figures below could change'')</center>

The natural plant hosts of the genus ''Caulimovirus'' are angiosperms of ''Dicotyledonae'' class. These viruses are usually transmitted in non- or semi-persistent manner by biological vectors, or via grafting, mechanical inoculation or by contact between hosts. The transmission vectors usually are insects of the order ''Hemiptera'' (''Aphididae'' family), in which the virus does not replicate.
Under experimental conditions, susceptible host species are found in the families ''Amaranthaceae'', ''Caryophyllaceae'', ''Chenopodiaceae'', ''Compositae'', ''Convolvulaceae'', ''Cruciferae'', ''Ericaceae'', ''Euphorbiaceae'', ''Leguminosae-Papilionoideae'', ''Nyctaginaceae'', ''Plantaginaceae'', ''Ranunculaceae'', ''Resedaceae'', ''Rosaceae'', ''Scrophulariaceae'', ''Solanaceae''. However some species of these families inoculated with virus do not show signs of susceptibility (i.e: ''Beta vulgaris, Brassica campestris Capsicum annuum, Chenopodium amaranticolor, Chenopodium quinoa, Cucumis sativus, Lycopersicon esculentum, Nicotiana benthamiana, Nicotiana clevelandii, Nicotiana tabacum, Petunia x hybrida, Phaseolus vulgaris, Pisum sativum, Spinacia oleracea, Vicia faba'', etc).

According to the ICTV ([[Literature:100589|Fauquet ''et al''. 2005]]) the ''Caulimovirus'' genus contains viral species as diverse as the ''Cauliflower mosaic virus'' (CaMV); ''Carnation etched ring virus'' (CERV); ''Figwort mosaic virus'' (FMV); ''Dahlia mosaic virus''(DMV); ''Strawberry vein banding virus'' (SVBV); ''Horseradish latent virus'' (HRLV); ''Mirabilis mosaic virus'' (MiMV); ''Thistle mottle virus'' (ThMoV); ''Aquilegia necrotic mosaic virus'' (ANMV, tentative species).

====''Soymovirus''====
Soymoviruses form round viral particles with icosahedral symmetry. The isometric capsid has a diameter of 42-50 nm and the viral genome contains a single molecule of double-stranded DNA of about 8200 bp long that forms an open circle (for more details see [[Literature:100589|Fauquet ''et al''. 2005]]). It contains 8 ORFs encoding for both structural and non-structural proteins (the figure below shows an idealized full-lenght consensus). ''Soymovirus'' genus differs from other caulimoviruses by the occurrence of three ORFs between ORF I and ORF IV instead of two (ORF II and III) that show little or no similarities to other caulimoviruses ORFs ([[Literature:100602|Hasegawa ''et al''. 1989]]; [[Literature:100603|Mushegian ''et al.'' 1995]]). ORF VII reveals sequence similarity to the typical protease domain, it is not clear if this sequence is a functionally active protease additional to that found in pol but the feature merits further attention as it is taxonomically preserved in almost (but not all) soymoviruses. Moreover this genus differs in the location of the putative primer-binding site (PBS) that in the other caulimoviruses is usually located in the intergenic region, while in soymoviruses has been found within ORF A (PSCV) or ORF Ia (SbCMV) or between ORF A and B (BRRV) ([[Literature:100603|Mushegian ''et al.'' 1995]]; [[Literature:100602|Hasegawa ''et al''. 1989]]; [[Literature:100686|Glasheen ''et al.'' 2002]]).
<center>[[File:Soymovirus.png]]</center>
<center>(''figure not to scale; AP is a putative aspartic protease additional to that codified by the Pol gene'')</center>

The natural plant hosts of soymoviruses are angiosperms of ''Dicotyledonae'' class. Under experimental conditions susceptible host species are found in the family ''Leguminosae''-''Papilionoideae''. Viruses are transmitted by mechanical inoculation, while they are not transmitted by seeds. According to the ICTV ([[Literature:100589|Fauquet ''et al''. 2005]]) the ''Soymovirus'' genus includes three species - ''Soybean chlorotic mottle virus'' (SbCMV), ''Peanut cholorotic streak virus'' (PCSV) and ''Blueberry red ringspot virus'' (BRRV) but although none tentative species has been yet reported, [[Literature:100693|Stavolone ''et al.'']](2003) describe the new pararetrovirus ''Cestrum yellow leaf curling virus'' (CmYLCV) closely related to SbCMV.

=== Class 2 ===
Class 2 consists of two other genera (''Tungrovirus'' and ''Badnavirus'') and it is the most abundant branch of ''Caulimoviridae'' elements.
====''Badnavirus''====
This genus is characterized by species with bacilliform virions that have a length of 95-130 nm, or 60-900 nm as well as a width of 24-35 nm (for more details see [[Literature:100589|Fauquet ''et al''. 2005]]). The genome of badnaviruses usually contains a single molecule of dsDNA of about 7200-7600 bp long that forms an open circle interrupted by site-specific discontinuities and that could contain an intergenic poly (A) region (i.e CoYMV, [[Literature:49349|Medberry ''et al''. 1990]]). The virus genome usually codes for 3 ORFs, but in some cases can present one or four additional ORFs which functions are already under study. The largest ORF III polyprotein product contains the movement protein, the virus coat (gag) protein, the aspartic protease, the reverse transcriptase and the ribonuclease H domains ([[Literature:49349|Medberry ''et al''. 1990]]; [[Literature:8054|Bouhida ''et al.'' 1993]]; [[Literature:100610|Briddon ''et al''. 1999]]). The COAT (gag) domain of badnaviral ORF III displays at the C-terminus a large region rich in zinc finger (CCHC) array duplications similarly to those of LTR retroelement nucleocapsids ([[Literature:8054|Bouhida ''et al.'' 1993]]; [[Literature:100596|Llorens ''et al.'' 2009]]). Additionally, some badnaviruses show an additional dUTPase domain upstream or downstream to the COAT domain within ORF III similar to that of several ''Retroviridae'' retroviruses ([[Literature:20174|Elder ''et al''. 1992]]) and several ''Ty3/Gypsy'' LTR retrotransposons ([[Literature:95064|Novikova and Blinov 2008]]). The figure below shows an idealized ''Badnavirus'' full-lenght genome consensus.
<center>[[File:Badnavirus.png]]</center>
<center>(''figure not to scale; some species contain additional ORFs downstream to the ORF III'') </center>

The plant hosts usually belong to the ''Dicotyledonae'' and ''Monocotyledonae'' classes. Depending on the ''Badnavirus'' species, the virus could be transmitted by mechanical inoculation, by grafting, by seeds or by pollen but not by contact between hosts. Badnaviruses can also be transmitted in a semi- or in a persistent manner via insect vectors of the order ''Hemiptera'' (''Aleyrodidae'', ''Aphididae'', ''Cicadellidae'' and ''Pseudococcidae'' families). In addition, ''Banana streak virus'' (BSV) infections can arise in healthy plants from integrated sequences (as a result of the process of ''in vitro'' propagation) during tissue culture ([[Literature:100608|Ndowora ''et al.'' 1999]];[[Literature:29391| Harper ''et al.'' 2002]]).
According to the ICTV ([[Literature:100589|Fauquet ''et al.'' 2005]]) the ''Badnavirus'' genus contains numerous species and tentative species, among which: ''Commelina yellow mottle virus'' (CoYMV or ComYMV) (type species in the genus), ''Aglaonema bacilliform virus'' (ABV), ''Banana streak virus'' (BSV), ''Cacao swollen shoot virus'' (CSSV), ''Citrus yellow mosaic virus'' (CMBV), ''Dioscorea alata bacilliform virus'' (DaBV), ''Kalanchoe top-spotting virus'' (KTSV), ''Sugarcane bacilliform virus'' (ScBV), have been described together with tentative species such as ''Pineapple bacilliform virus'' (PBV), ''Yucca bacilliform virus'' (YBV), ''Stilbocarpa mosaic bacilliform virus'' (SMBV).

====''Tungrovirus''====
Only one species has been referred to ''Tungrovirus'' genus: ''Rice tungro bacilliform virus'' (RTBV). The species consists of bacilliform particles long 110-400 nm and with a width of 30-35 nm that encapsidate a circular dsDNA of about 8000 bp long (for more details see [[Literature:100589|Fauquet ''et al''. 2005]]). The genome contains four ORFs that potentially encode for four proteins (P24, P12, P194, P46 respectively, [[Literature:100604|Hay ''et al.'' 1991]]). The largest ORF (III) encodes for a polyprotein containing the movement protein as well as the coat protein, the protease, the reverse transcriptase and RNase H domains characteristic of retroelements. The functions of the three other tungrovirus ORFs are unknown or not well yet demonstrated ([[Literature:100604|Hay ''et al.'' 1991]]; [[Literature:100605|Hull 1996]]), (figure show the genome organization of the type species ''Rice tungro bacilliform virus'', RTBV).
<center>[[File:Tungrovirus-new.png]]</center>
<center>(''figure not to scale'')</center>

The plant hosts of RTBV belong to the Angiosperms of ''Monocotyledonae'' class. The virus is transmitted by insect vectors of the order ''Hemiptera'', family ''Cicadellidae'' in a semi-persistent manner and requiring the presence of the ''Rice tungro spherical virus'' (RTSV) helper virus for transmission. RTBV and RTSV are both responsible for the "Rice tungro virus disease", one of the major causes to rice loss production in South and Southeast Asia ([[Literature:100605|Hull 1996]]).
Endogenous RTBV-like sequences (ERTBVs) have been found in the rice genome ([[Literature:100626|Kunii ''et al.'' 2004]]). Although they contain rearranged structures and no intact ORFs, the comparisons of their DNA and amino acid sequences suggested their closely relationship to RTBV and the possible role of these integrated sequences against the related viral disease ([[Literature:100626|Kunii ''et al.'' 2004]]).

=== Class 3 ===
Class 3 represents the genus ''Cavemovirus''.
====''Cavemovirus''====
This genus consists of two viral species - ''Cassava vein mosaic virus'' (CsVMV) and ''Tobacco vein clearing virus'' (TVCV) - according to the ICTV ([[Literature:100589|Fauquet ''et al''. 2005]]) and supported by phylogenetic analyses ([[Literature:100596|Llorens ''et al.'' 2009]]). These form round-to-elongated capsids with icosahedral symmetry and length and width of 95-130 nm (or 60-900 nm) and 24-35 nm, respectively (for more details see [[Literature:100589|Fauquet ''et al''. 2005]]). The viral genome usually consists of a single molecule of circular dsDNA of about 7.7-8.1 Kb long that encodes for 4 or 5 ORFs (the figure below shows an idealized consensus of the cavemoviruses genome organization).
<center>[[File:cavemovirus.png]]</center>
<center>(''figure not to scale'')</center>
Cavemoviruses differ from other ''Caulimoviridae'' genera, in the order of their coat and movement domains ([[Literature:100606|de Kochko ''et al.'' 1998]]; [[Literature:10456|Calvert ''et al.'' 1995]]; [[Literature:100607|Lockhart ''et al.'' 2000]]). In cavemoviruses, ''mov'' is downstream to coat. Additionally, CSVMV apparently codes for an extra protease domain, which is found within ORF I and upstream to the conventional pol protease domain. This feature is found in other ''Caulimoviridae'' species but not in TVCV. On the other hand, an interesting observation has been proposed by [[Literature:100607| Lockhart ''et al.'' (2000)]] who suggest that the episomal form of TVCV found into the infected hybrid tobacco species ''N. edwardsonii'' (''N. clevelandii'' x ''N. glutinosa'') probably arises from integrated pararetroviral sequences present in the host plant genome and that they are inherited from the male parent (''N. glutinosa'').

=== Class 4 ===
This class describes the genus ''Petuvirus'', which falls in the deepest position of the ''Caulimoviridae'' phylogeny .
====''Petuvirus''====
This is a genus to date composed only of a single sequence representative, the ''Petunia vein clearing virus'' (PVCV), which might constitute the most basal position in the ''Caulimoviridae'' phylogeny ([[Literature:86892|Bousalem ''et al.'' 2008]]; [[Literature:100596|Llorens ''et al.'' 2009]]). This viral species consists of unenveloped isometric particles of 43-46 nm in diameter (for more details see [[Literature:100589|Fauquet ''et al''. 2005]]). The genome is not segmented and consists of a molecule of circular dsDNA 7206 bp long, organized into a large ORF containing the movement protein typical of caulimoviruses, a putative [HHCC and DD(35)E] integrase similar to those coded by LTR retrotransposons, and the typical coat (gag) and pol (protease-reverse transcriptase-RNaseH) domains ([[Literature:63308|Richert-Pöggeler and Shepherd 1997]]; [[Literature:29391|Harper ''et al.'' 2002]]). The presence of a probable integrase function in the genome of this virus suggests that PVCV exists as a viral retroelement that may also has the potential to transpose in Petunia ([[Literature:63308|Richert-Pöggeler and Shepherd 1997]]).
<center>[[File:petuvirus.png]]</center>
<center>(''figure not to scale'')</center>

The plant hosts of PVCV belong to ''Solanaceae'' family (Angiosperms of ''Dicotyledonae'' class). The virus has been found in ''Petunia x hybrida'' (garden petunia) in which the characteristic symptoms are vein clearing and leaf malformation, and it is highly transmitted by seed and grafting but not by mechanical inoculation or by insect (aphid) vectors ([[Literature:29391|Harper ''et al.'' 2002]]).

[[Category:Retroelements]]

Caulimoviridae - Revision history

imported>Lcovelli: /* Tungrovirus */