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The Gypsy Database (GyDB) of mobile genetic elements.

Lloréns C, Futami R, Bezemer D, Moya A - Nucleic Acids Res. (2007)

Bottom Line: In this first version, we contemplate eukaryotic Ty3/Gypsy and Retroviridae long terminal repeats (LTR) retroelements.Phylogenetic analyses based on the gag-pro-pol internal region commonly presented by these two groups strongly support a certain number of previously described Ty3/Gypsy lineages originally reported from reverse-transcriptase (RT) analyses.Vertebrate retroviruses (Retroviridae) are also constituted in several monophyletic groups consistent with genera proposed by the ICTV nomenclature, as well as with the current tendency to classify both endogenous and exogenous retroviruses by three major classes (I, II and III).

View Article: PubMed Central - PubMed

Affiliation: Biotech Vana, Valencia, Institut Cavanilles de Biodiversitat i Biología Evolutiva Universitat de València, Spain.

ABSTRACT
In this article, we introduce the Gypsy Database (GyDB) of mobile genetic elements, an in-progress database devoted to the non-redundant analysis and evolutionary-based classification of mobile genetic elements. In this first version, we contemplate eukaryotic Ty3/Gypsy and Retroviridae long terminal repeats (LTR) retroelements. Phylogenetic analyses based on the gag-pro-pol internal region commonly presented by these two groups strongly support a certain number of previously described Ty3/Gypsy lineages originally reported from reverse-transcriptase (RT) analyses. Vertebrate retroviruses (Retroviridae) are also constituted in several monophyletic groups consistent with genera proposed by the ICTV nomenclature, as well as with the current tendency to classify both endogenous and exogenous retroviruses by three major classes (I, II and III). Our inference indicates that all protein domains codified by the gag-pro-pol internal region of these two groups agree in a collective presentation of a particular evolutionary history, which may be used as a main criterion to differentiate their molecular diversity in a comprehensive collection of phylogenies and non-redundant molecular profiles useful in the identification of new Ty3/Gypsy and Retroviridae species. The GyDB project is available at http://gydb.uv.es.

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(a) Pairwise alignment between the ORFX MRC sequence and the PyERV–ORF X. (b) Multiple alignment.
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Figure 4: (a) Pairwise alignment between the ORFX MRC sequence and the PyERV–ORF X. (b) Multiple alignment.

Mentions: In an attempt to provide an empirical example of the possibilities of our database, in this section we analyze the recently described Python molurus retrovirus (PyERV), an endogenous retrovirus whose classification is unclear (55). According to the authors of this study, PyERV is a possible true recombinant related to B- and D-type retroviruses. From both viral taxonomy and morphology, it is now known that betaretroviruses may be divided into B- and D-type retroviruses (40). Also, it should be noted that although B- and D-type betaretroviruses are closely similar in the entire gag-pro-pol internal region, they differ in the env region. In this regard, it is well known that primates’ D-type betaretroviruses present a common surface receptor also utilized by baboon and cat endogenous C-type gammaretroviruses (56,57). This evidence seems to be related to the high similarity displayed between env polyproteins encoded by gammaretroviruses and D-type betaretroviruses, where it is usually assumed that D-type betaretroviruses might be recombinant hybrids between C-type gammaretroviruses and primates’ B-type betaretroviruses (40,58). With this, our profile database provides two independent HMM profiles independently describing the env polyproteins of B- and D-type betaretroviruses. Regarding PyERV, this retrovirus contains intact ORFs for the gag, pro, pol and env genes characteristic of retroviruses, and also an additional ORF of unknown function. Several comparisons were established against the HMM server using all protein domains encoded by PyERV as query examples (Genbank accession AF500296). Except in the case of the env polyprotein, where PyERV is slightly closer to gammaretroviruses than to D-type betaretroviruses (Table 2), all gag-pro-pol comparisons revealed that PyERV is clearly similar to betaretroviruses in general (Table 2). On the other hand, PyERV encodes for a dUTPase (DUT) domain, which is characteristic of betaretroviruses, non-primate lentiviruses and ERV-L elements (59). However, as it is also observed in betaretroviruses, PyERV-DUT is found in frame and N-terminal to the PR domain, while lentiviruses and ERV-L elements present this gene between or downstream to the RNAseH and INT domains. Analyses did not detect similarity between the unknown ORF described by the authors of PyERV study. However, immediately downstream to the same frame, PyERV codify for an amino acid stretch significantly similar to the putative ORF-X protein of betaretroviruses (Figure 4a). This is probably a frameshifting of the uncharacterized ORF described in PyERV by Huder et al. (55). ORF-X was originally described in the Jaagsiekte Sheep Retrovirus (JSRV) and other endogenous sheep betaretroviruses as a putative accessory gene that codifies for a protein similar to a portion of the mammalian adenosine receptor subtype 3 (60). It is still unclear if this ORF is functional (it shows several stop codons in other betaretroviruses), but it is well preserved in both endogenous and exogenous JRSV isolates (61), and we have also found this ORF to be present in other betaretroviruses characteristic of humans, primates and mice, as shown in Figure 4b. We therefore confirm that ORF-X is at least a feature specific of almost all betaretroviruses (another question is if this ORF is functional indeed). With this and based on the significant degree of sequence similarity displayed by PyERV to betaretroviruses, as well as on their identical gag-dut/pro-pol-env plus ORF-X organization, we may definitively conclude that PyERV is pure and exclusively a betaretrovirus and likely a D-type betaretrovirus. However, a very interesting point arises from this analysis because if PyERV is a true recombinant, then the simplest hypothesis to explain the emergence of D-type betaretroviruses is that the recombination event between gammaretroviruses and B-type betaretroviruses is more ancient than previously thought. The debate is open.Table 2.


The Gypsy Database (GyDB) of mobile genetic elements.

Lloréns C, Futami R, Bezemer D, Moya A - Nucleic Acids Res. (2007)

(a) Pairwise alignment between the ORFX MRC sequence and the PyERV–ORF X. (b) Multiple alignment.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238898&req=5

Figure 4: (a) Pairwise alignment between the ORFX MRC sequence and the PyERV–ORF X. (b) Multiple alignment.
Mentions: In an attempt to provide an empirical example of the possibilities of our database, in this section we analyze the recently described Python molurus retrovirus (PyERV), an endogenous retrovirus whose classification is unclear (55). According to the authors of this study, PyERV is a possible true recombinant related to B- and D-type retroviruses. From both viral taxonomy and morphology, it is now known that betaretroviruses may be divided into B- and D-type retroviruses (40). Also, it should be noted that although B- and D-type betaretroviruses are closely similar in the entire gag-pro-pol internal region, they differ in the env region. In this regard, it is well known that primates’ D-type betaretroviruses present a common surface receptor also utilized by baboon and cat endogenous C-type gammaretroviruses (56,57). This evidence seems to be related to the high similarity displayed between env polyproteins encoded by gammaretroviruses and D-type betaretroviruses, where it is usually assumed that D-type betaretroviruses might be recombinant hybrids between C-type gammaretroviruses and primates’ B-type betaretroviruses (40,58). With this, our profile database provides two independent HMM profiles independently describing the env polyproteins of B- and D-type betaretroviruses. Regarding PyERV, this retrovirus contains intact ORFs for the gag, pro, pol and env genes characteristic of retroviruses, and also an additional ORF of unknown function. Several comparisons were established against the HMM server using all protein domains encoded by PyERV as query examples (Genbank accession AF500296). Except in the case of the env polyprotein, where PyERV is slightly closer to gammaretroviruses than to D-type betaretroviruses (Table 2), all gag-pro-pol comparisons revealed that PyERV is clearly similar to betaretroviruses in general (Table 2). On the other hand, PyERV encodes for a dUTPase (DUT) domain, which is characteristic of betaretroviruses, non-primate lentiviruses and ERV-L elements (59). However, as it is also observed in betaretroviruses, PyERV-DUT is found in frame and N-terminal to the PR domain, while lentiviruses and ERV-L elements present this gene between or downstream to the RNAseH and INT domains. Analyses did not detect similarity between the unknown ORF described by the authors of PyERV study. However, immediately downstream to the same frame, PyERV codify for an amino acid stretch significantly similar to the putative ORF-X protein of betaretroviruses (Figure 4a). This is probably a frameshifting of the uncharacterized ORF described in PyERV by Huder et al. (55). ORF-X was originally described in the Jaagsiekte Sheep Retrovirus (JSRV) and other endogenous sheep betaretroviruses as a putative accessory gene that codifies for a protein similar to a portion of the mammalian adenosine receptor subtype 3 (60). It is still unclear if this ORF is functional (it shows several stop codons in other betaretroviruses), but it is well preserved in both endogenous and exogenous JRSV isolates (61), and we have also found this ORF to be present in other betaretroviruses characteristic of humans, primates and mice, as shown in Figure 4b. We therefore confirm that ORF-X is at least a feature specific of almost all betaretroviruses (another question is if this ORF is functional indeed). With this and based on the significant degree of sequence similarity displayed by PyERV to betaretroviruses, as well as on their identical gag-dut/pro-pol-env plus ORF-X organization, we may definitively conclude that PyERV is pure and exclusively a betaretrovirus and likely a D-type betaretrovirus. However, a very interesting point arises from this analysis because if PyERV is a true recombinant, then the simplest hypothesis to explain the emergence of D-type betaretroviruses is that the recombination event between gammaretroviruses and B-type betaretroviruses is more ancient than previously thought. The debate is open.Table 2.

Bottom Line: In this first version, we contemplate eukaryotic Ty3/Gypsy and Retroviridae long terminal repeats (LTR) retroelements.Phylogenetic analyses based on the gag-pro-pol internal region commonly presented by these two groups strongly support a certain number of previously described Ty3/Gypsy lineages originally reported from reverse-transcriptase (RT) analyses.Vertebrate retroviruses (Retroviridae) are also constituted in several monophyletic groups consistent with genera proposed by the ICTV nomenclature, as well as with the current tendency to classify both endogenous and exogenous retroviruses by three major classes (I, II and III).

View Article: PubMed Central - PubMed

Affiliation: Biotech Vana, Valencia, Institut Cavanilles de Biodiversitat i Biología Evolutiva Universitat de València, Spain.

ABSTRACT
In this article, we introduce the Gypsy Database (GyDB) of mobile genetic elements, an in-progress database devoted to the non-redundant analysis and evolutionary-based classification of mobile genetic elements. In this first version, we contemplate eukaryotic Ty3/Gypsy and Retroviridae long terminal repeats (LTR) retroelements. Phylogenetic analyses based on the gag-pro-pol internal region commonly presented by these two groups strongly support a certain number of previously described Ty3/Gypsy lineages originally reported from reverse-transcriptase (RT) analyses. Vertebrate retroviruses (Retroviridae) are also constituted in several monophyletic groups consistent with genera proposed by the ICTV nomenclature, as well as with the current tendency to classify both endogenous and exogenous retroviruses by three major classes (I, II and III). Our inference indicates that all protein domains codified by the gag-pro-pol internal region of these two groups agree in a collective presentation of a particular evolutionary history, which may be used as a main criterion to differentiate their molecular diversity in a comprehensive collection of phylogenies and non-redundant molecular profiles useful in the identification of new Ty3/Gypsy and Retroviridae species. The GyDB project is available at http://gydb.uv.es.

Show MeSH