Env-like Gene Research Articles

Convergent evolution of ribonuclease h in LTR retrotransposons and retroviruses.

Ty3/Gypsy long terminals repeat (LTR) retrotransposons are structurally and phylogenetically close to retroviruses. Two notable structural differences between these groups of genetic elements are 1) the presence in retroviruses of an additional envelope gene, env, which mediates infection, and 2) a specific dual ribonuclease H (RNH) domain encoded by the retroviral pol gene. However, similar to retroviruses, many Ty3/Gypsy LTR retrotransposons harbor additional env-like genes, promoting concepts of the infective mode of these retrotransposons. Here, we provide a further line of evidence of similarity between retroviruses and some Ty3/Gypsy LTR retrotransposons. We identify that, together with their additional genes, plant Ty3/Gypsy LTR retrotransposons of the Tat group have a second RNH, as do retroviruses. Most importantly, we show that the resulting dual RNHs of Tat LTR retrotransposons and retroviruses emerged independently, providing strong evidence for their convergent evolution. The convergent resemblance of Tat LTR retrotransposons and retroviruses may indicate similar selection pressures acting on these diverse groups of elements and reveal potential evolutionary constraints on their structure. We speculate that dual RNH is required to accelerate retrotransposon evolution through increased rates of strand transfer events and subsequent recombination events.

Sequence heterogeneity of theenvelope-like domain in cultivated allotetraploidGossypium species and their diploid progenitors

Retroviral envelope (env)-like sequences in 2 cultivated allotetraploid cottons and their diploid progenitors have been identified and characterized in this study. DNA sequence analysis reveals that these sequences are heterogeneous. The observed sequence diversity, however, seems to preserve coding information. This is evidenced by the detection of the transmembrane domain (TM), which is the most conserved feature of the divergent retroviral env genes. The high ratio of synonymous to nonsynonymous changes suggests that these sequences are evolving under purifying selection. Phylogenetic analysis shows that Gossypium sequences closely cluster with a lineage of plant endogenous retroviruses that have an env-like gene. These results provide evidence for the antiquity and the wide diversity of env-like sequences in the Gossypium genome.

Envelope-Like Retrotransposons in the Plant Kingdom: Evidence of Their Presence in Gymnosperms (Pinus pinaster)

Retroviruses differ from retrotransposons due to their infective capacity, which depends critically on the encoded envelope. Some plant retroelements contain domains reminiscent of the env of animal retroviruses but the number of such elements described to date is restricted to angiosperms. We show here the first evidence of the presence of putative env-like gene sequences in a gymnosperm species, Pinus pinaster (maritime pine). Using a degenerate primer approach for conserved domains of RNaseH gene, three clones from putative envelope-like retrotransposons (PpRT2, PpRT3, and PpRT4) were identified. The env-like sequences of P. pinaster clones are predicted to encode proteins with transmembrane domains. These sequences showed identity scores of up to 30% with env-like sequences belonging to different organisms. A phylogenetic analysis based on protein alignment of deduced aminoacid sequences revealed that these clones clustered with env-containing plant retrotransposons, as well as with retrotransposons from invertebrate organisms. The differences found among the sequences of maritime pine clones isolated here suggest the existence of different putative classes of env-like retroelements. The identification for the first time of env-like genes in a gymnosperm species may support the ancestrality of retroviruses among plants shedding light on their role in plant evolution.

Analysis of the Drosophila gypsy endogenous retrovirus envelope glycoprotein.

gypsy is the only endogenous retrovirus of Drosophila whose infectious properties have been reported. Previous studies have shown an unexpected relationship between the gene encoding the putative envelope glycoprotein (Env) of gypsy and genes encoding the fusion protein of several baculoviruses. The fact that fusion proteins mediate membrane fusion suggests that Env of insect retroviruses might also have fusogenic properties. The results reported here indicate that gypsy Env mediates cell-to-cell fusion. Cleavage of the Env precursor was also studied; it is shown that this polypeptide is cleaved at a furin-like cleavage site. This is the first report that the env-like gene of insect retroviruses encodes a fusion protein.

SIRE1, an endogenous retrovirus family from Glycine max, is highly homogeneous and evolutionarily young.

SIRE1 is unusual among Ty1-copia retrotransposons in that it has an additional open reading frame with structural features similar to retroviral envelope proteins between pol and the 3' LTR. Here we report the characterization and comparison of eight different SIRE1 elements derived from a soybean genomic library, as well as SIRE1 reverse transcriptases from Glycine soja. The DNA sequences of the eight SIRE1 elements are highly homogeneous and share greater than 95% nucleotide identity. Partial sequences obtained from BAC ends are similarly conserved. Phylogenetic analyses resolve two closely related SIRE1 lineages, and nucleotide changes within and between SIRE1 lineages have occurred to preserve function. Both the gag and the env-like genes are evolving under similar levels of functional constraint. Considerable sequence heterogeneity in the form of short duplications was found within the LTRs and in the region between the envelope-like ORF and the 3' LTR. These duplications are suggestive of slippage by reverse transcriptase during replication. Sequence identity between LTRs of individual insertions suggests that they transposed within the past 70,000 years. Two of 10 SIRE1 insertions examined abut Ty3-gypsy retroelements. Since the soybean genome harbors more than 1,000 SIRE1 insertions, the collective data suggest that SIRE1 has undergone a very recent and robust amplification in soybean.

The soybean retroelement SIRE1 uses stop codon suppression to express its envelope-like protein.

The soybean SIRE1 family of Ty1/copia retrotransposons encodes an envelope-like gene (env-like). We analysed the DNA sequences of nine SIRE1 insertions and observed that the gag/pol and env-like genes are in the same reading frame and separated by a single UAG stop codon. The six nucleotides immediately downstream of the stop codon conform to a degenerate nucleotide motif, CARYYA, which is sufficient to facilitate stop codon suppression in tobacco mosaic virus. In vivo stop codon suppression assays indicate that SIRE1 sequences confer leakiness to the UAG stop codon at an efficiency of 5%. These data suggest that SIRE1 retro-elements use translational suppression to express their envelope-like protein; this is in contrast with all characterized retroviruses, which express the envelope protein from a spliced genomic messenger RNA.

Genes of the Pseudoviridae (Ty1/copia retrotransposons).

A comprehensive survey of the Pseudoviridae (Ty1/copia) retroelement family was conducted using the GenBank sequence database and completed genome sequences of several model organisms. Plant genomes were the most abundant sources of Pseudoviridae, with the Arabidopsis thaliana genome having 276 distinct elements. A reverse transcriptase amino acid sequence phylogeny indicated that the Pseudoviridae comprises highly divergent members. Coding sequences for a representative subset of elements were analyzed to identify conserved domains and differences that may underlie functional divergence. With the exception of some fungal elements (e.g., Ty1), most Pseudoviridae encode Gag and Pol on a single open reading frame. In addition to the nearly ubiquitous RNA-binding motif of nucleocapsid, three new conserved domains were identified in Gag. pol-encoded aspartic protease was similar to the retroviral enzyme and could be mapped onto the HIV-1 structure. Pol was highly conserved throughout the family. The greatest divergence among Pol sequences was seen in the C-terminus of integrase (IN). We defined a large motif (GKGY) after the IN catalytic domain that is unique to the Pseudoviridae. Additionally, the extreme C-terminus of IN is rich in simple sequence motifs. A distinct lineage of Pseudoviridae in plants have envlike genes. This lineage has undergone a large expansion of Gag characterized by an alpha-helix-rich domain containing coiled-coil motifs. In several elements, this domain is flanked on both sides by RNA-binding domains. We propose that this monophyletic lineage defines a new Pseudoviridae genus, herein referred to as the AGROVIRUS:

Poised for contagion: evolutionary origins of the infectious abilities of invertebrate retroviruses.

Phylogenetic analyses suggest that long-terminal repeat (LTR) bearing retrotransposable elements can acquire additional open-reading frames that can enable them to mediate infection. Whereas this process is best documented in the origin of the vertebrate retroviruses and their acquisition of an envelope (env) gene, similar independent events may have occurred in insects, nematodes, and plants. The origins of env-like genes are unclear, and are often masked by the antiquity of the original acquisitions and by their rapid rate of evolution. In this report, we present evidence that in three other possible transitions of LTR retrotransposons to retroviruses, an envelope-like gene was acquired from a viral source. First, the gypsy and related LTR retrotransposable elements (the insect errantiviruses) have acquired their envelope-like gene from a class of insect baculoviruses (double-stranded DNA viruses with no RNA stage). Second, the Cer retroviruses in the Caenorhabditis elegans genome acquired their envelope gene from a Phleboviral (single ambisense-stranded RNA viruses) source. Third, the Tas retroviral envelope (Ascaris lumricoides) may have been obtained from Herpesviridae (double-stranded DNA viruses, no RNA stage). These represent the only cases in which the env gene of a retrovirus has been traced back to its original source. This has implications for the evolutionary history of retroviruses as well as for the potential ability of all LTR-retrotransposable elements to become infectious agents.

Phylogenetic evidence for Ty1-copia-like endogenous retroviruses in plant genomes.

SIRE-1 is a multi-copy, Ty1-copia-like retroelement family found in the genome of Glycine max. A sequenced SIRE-1 genomic copy has an uninterrupted ORF that can be translated into a gag-pol polyprotein, followed by an unprecedented second ORF whose conceptual translation yielded a theoretical protein predicted to possess many of the same secondary structural elements found in mammalian retroviral envelope proteins. Similar, but clearly pseudogenic, envelope-like sequences were recovered from conceptual translations of 10 Arabidopsis GenBank accessions. All were associated with identifiable Ty1-copia-like retroelements. Phylogenetic analysis of the adjacent ribonuclease H regions from these sequences and three similarly endowed elements, two from maize and one from tomato, indicate that the 14 elements constitute a monophyletic group distinct from several closely related plant Ty1-copia-like elements in which pol is immediately followed by a downstream LTR. The conservation of identifiable env-like gene features suggests that these plant elements are endogenous retroviruses whose ancestors were acquired from animal vectors. The finding that the env and env-less retroelements identified in this study form distinct lineages does not support the hypothesis that horizontal transmission of retrotransposons is sponsored by ancestral infectious retroviruses that subsequently lost all traces of env genes.

Endogenous retroviruses and multiple sclerosis. II. HERV-7q

The search for new endogenous retroviral sequences, on the basis of sequence homologies with the pol gene of the recently reported multiple sclerosis associated retrovirus (MSRV), allowed us to identify a full length endogenous retrovirus sequence located on the long arm of human chromosome 7. This retrovirus, HERV-7q, includes in its env region, within a single 1 620 bp open reading frame, a 664 bp domain almost identical to a 3′ non-coding region of the rab7 gene. Transcripts encompassing both the env and the 3′ LTR regions of HERV-7q have already been identified as expressed sequence tags, suggesting that this env-like gene might code for a 538 amino acid long deduced protein.

Molecular structure of a gypsy element of Drosophila subobscura (gypsyDs) constituting a degenerate form of insect retroviruses.

We have determined the nucleotide sequence of a 7.5 kb full-size gypsy element from Drosophila subobscura strain H-271. Comparative analyses were carried out on the sequence and molecular structure of gypsy elements of D.subobscura (gypsyDs), D.melanogaster (gypsyDm) and D.virilis (gypsyDv). The three elements show a structure that maintains a common mechanism of expression. ORF1 and ORF2 show typical motifs of gag and pol genes respectively in the three gypsy elements and could encode functional proteins necessary for intracellular expansion. In the three ORF1 proteins an arginine-rich region was found which could constitute a RNA binding motif. The main differences among the gypsy elements are found in ORF3 (env-like gene); gypsyDm encodes functional env proteins, whereas gypsyDs and gypsyDv ORF3s lack some motifs essential for functionality of this protein. On the basis of these results, while gypsyDm is the first insect retrovirus described, gypsyDs and gypsyDv could constitute degenerate forms of these retroviruses. In this context, we have found some evidence that gypsyDm could have recently infected some D.subobscura strains. Comparative analyses of divergence and phylogenetic relationships of gypsy elements indicate that the gypsy elements belonging to species of different subgenera (gypsyDs and gypsyDv) are closer than gypsy elements of species belonging to the same subgenus (gypsyDs and gypsyDm). These data are congruent with horizontal transfer of gypsy elements among different Drosophila spp.