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Mart Krupovic - One of the best experts on this subject based on the ideXlab platform.
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ICTV Virus Taxonomy Profile: Metaviridae.
The Journal of general virology, 2020Co-Authors: Carlos Llorens, Beatriz Soriano, Mart KrupovicAbstract:Metaviridae is a family of retrotransposons and reverse-transcribing viruses with long terminal repeats belonging to the order Ortervirales. Members of the genera Errantivirus and Metavirus include, respectively, Saccharomyces cerevisiae Ty3 virus and its Gypsy-like relatives in drosophilids. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Metaviridae, which is available at ictv.global/report/Metaviridae.
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Reverse-transcribing viruses of the families Belpaoviridae, Metaviridae and Pseudoviridae (order Ortervirales)
Reference Module in Life Sciences, 2020Co-Authors: Carlos Llorens, Beatriz Soriano, María A. Navarrete-muñoz, Ahmed Ibrahem Hafez, Vicente Arnau, José Miguel Benito, Toni Gabaldón, Norma Rallón, Jaume Pérez-sánchez, Mart KrupovicAbstract:Abstract The Metaviridae, Pseudoviridae, and Belpaoviridae are the three families of eukaryotic reverse-transcribing viruses with Long Terminal Repeats (LTRs), popularly known as Ty3/Gypsy, Ty1/Copia, and Bel/Pao LTR retrotransposons, respectively. The three families are unified into the order Ortervirales together with members of the families Retroviridae and Caulimoviridae which infect vertebrates and plants, respectively. Here, we review the molecular biology and diversity of metaviruses, pseudoviruses and belpaoviruses. We explore the similarities and evolutionary relationships among them as well as with other members of the Ortervirales based on life cycle, sequence, architecture of genes and other features. Their host range and impact on the biology and evolution of eukaryotes is also discussed.
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Homologous Capsid Proteins Testify to the Common Ancestry of Retroviruses, Caulimoviruses, Pseudoviruses, and Metaviruses
Journal of Virology, 2017Co-Authors: Mart Krupovic, Eugene KooninAbstract:Reverse-transcribing viruses are classified into 5 different families, Retroviridae, Metaviridae, Pseudoviridae, Caulimoviridae, and Hepadnaviridae (1). Retroviruses, hepadnaviruses, and caulimoviruses are full-fledged viruses, whereas metaviruses and pseudoviruses are more often referred to as retrotransposons. Nevertheless [...]
Carlos Llorens - One of the best experts on this subject based on the ideXlab platform.
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ICTV Virus Taxonomy Profile: Metaviridae.
The Journal of general virology, 2020Co-Authors: Carlos Llorens, Beatriz Soriano, Mart KrupovicAbstract:Metaviridae is a family of retrotransposons and reverse-transcribing viruses with long terminal repeats belonging to the order Ortervirales. Members of the genera Errantivirus and Metavirus include, respectively, Saccharomyces cerevisiae Ty3 virus and its Gypsy-like relatives in drosophilids. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Metaviridae, which is available at ictv.global/report/Metaviridae.
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Reverse-transcribing viruses of the families Belpaoviridae, Metaviridae and Pseudoviridae (order Ortervirales)
Reference Module in Life Sciences, 2020Co-Authors: Carlos Llorens, Beatriz Soriano, María A. Navarrete-muñoz, Ahmed Ibrahem Hafez, Vicente Arnau, José Miguel Benito, Toni Gabaldón, Norma Rallón, Jaume Pérez-sánchez, Mart KrupovicAbstract:Abstract The Metaviridae, Pseudoviridae, and Belpaoviridae are the three families of eukaryotic reverse-transcribing viruses with Long Terminal Repeats (LTRs), popularly known as Ty3/Gypsy, Ty1/Copia, and Bel/Pao LTR retrotransposons, respectively. The three families are unified into the order Ortervirales together with members of the families Retroviridae and Caulimoviridae which infect vertebrates and plants, respectively. Here, we review the molecular biology and diversity of metaviruses, pseudoviruses and belpaoviruses. We explore the similarities and evolutionary relationships among them as well as with other members of the Ortervirales based on life cycle, sequence, architecture of genes and other features. Their host range and impact on the biology and evolution of eukaryotes is also discussed.
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Ty3/Gypsy Retrotransposons: Description of New Arabidopsis thaliana Elements and Evolutionary Perspectives Derived from Comparative Genomic Data
Molecular biology and evolution, 2000Co-Authors: Ignacio Marín, Carlos LlorensAbstract:We performed a comprehensive analysis of the evolution of the Ty3/GYPSY: group of long-terminal-repeat retrotransposons (also known as Metaviridae:). Exhaustive database searches allowed us to detect novel elements of this group. In particular, the Arabidopsis thaliana and Drosophila melanogaster genome sequencing projects have recently disclosed a large number of new Ty3/GYPSY: sequences. So far, elements of three different Ty3/GYPSY: lineages had been described for A. thaliana. Here, we describe six new lineages, which we have called Tit-for-tat1, Tit-for-tat2, Gimli, Gloin, Legolas, and Little Athila. We confirm that plant Ty3/GYPSY: elements form two main monophyletic groups. Moreover, our results suggest that at least four independent ancestral lineages existed before the monocot-dicot split, about 200 MYA. Twelve sequences from D. melanogaster that may correspond to new elements are also described. Some of these sequences are similar to those of OSVALDO: and Ulysses, two elements of the OSVALDO: clade that had never before been described for D. melanogaster. Comparative analyses of multiple organisms, some of them with completely sequenced genomes, show that the number of lineages of Ty3/GYPSY: elements is very variable. Thus, while only 1 lineage is present in Saccharomyces cerevisiae, at least 6 exist in Caenorhabditis elegans, at least 9 are present in the A. thaliana, and perhaps 20 are present in D. melanogaster. Finally, we suggest that the presence of a chromodomain-containing integrase, a feature of some closely related Ty3/GYPSY: elements of fungi, plants, and animals, may be used to define a new Metaviridae: genus.
Vini Pereira - One of the best experts on this subject based on the ideXlab platform.
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insertion bias and purifying selection of retrotransposons in the arabidopsis thaliana genome
Genome Biology, 2004Co-Authors: Vini PereiraAbstract:Background: Genome evolution and size variation in multicellular organisms are profoundly influenced by the activity of retrotransposons. In higher eukaryotes with compact genomes retrotransposons are found in lower copy numbers than in larger genomes, which could be due to either suppression of transposition or to elimination of insertions, and are non-randomly distributed along the chromosomes. The evolutionary mechanisms constraining retrotransposon copy number and chromosomal distribution are still poorly understood. Results: I investigated the evolutionary dynamics of long terminal repeat (LTR)-retrotransposons in the compact Arabidopsis thaliana genome, using an automated method for obtaining genomewide, age and physical distribution profiles for different groups of elements, and then comparing the distributions of young and old insertions. Elements of the Pseudoviridae family insert randomly along the chromosomes and have been recently active, but insertions tend to be lost from euchromatic regions where they are less likely to fix, with a half-life estimated at approximately 470,000 years. In contrast, members of the Metaviridae (particularly Athila) preferentially target heterochromatin, and were more active in the past. Conclusion: Diverse evolutionary mechanisms have constrained both the copy number and chromosomal distribution of retrotransposons within a single genome. In A. thaliana, their nonrandom genomic distribution is due to both selection against insertions in euchromatin and preferential targeting of heterochromatin. Constant turnover of euchromatic insertions and a decline in activity for the elements that target heterochromatin have both limited the contribution of retrotransposon DNA to genome size expansion in A. thaliana.
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Insertion bias and purifying selection of retrotransposons in the Arabidopsis thalianagenome
Genome Biology, 2004Co-Authors: Vini PereiraAbstract:Background Genome evolution and size variation in multicellular organisms are profoundly influenced by the activity of retrotransposons. In higher eukaryotes with compact genomes retrotransposons are found in lower copy numbers than in larger genomes, which could be due to either suppression of transposition or to elimination of insertions, and are non-randomly distributed along the chromosomes. The evolutionary mechanisms constraining retrotransposon copy number and chromosomal distribution are still poorly understood. Results I investigated the evolutionary dynamics of long terminal repeat (LTR)-retrotransposons in the compact Arabidopsis thaliana genome, using an automated method for obtaining genome-wide, age and physical distribution profiles for different groups of elements, and then comparing the distributions of young and old insertions. Elements of the Pseudoviridae family insert randomly along the chromosomes and have been recently active, but insertions tend to be lost from euchromatic regions where they are less likely to fix, with a half-life estimated at approximately 470,000 years. In contrast, members of the Metaviridae (particularly Athila ) preferentially target heterochromatin, and were more active in the past. Conclusion Diverse evolutionary mechanisms have constrained both the copy number and chromosomal distribution of retrotransposons within a single genome. In A. thaliana , their non-random genomic distribution is due to both selection against insertions in euchromatin and preferential targeting of heterochromatin. Constant turnover of euchromatic insertions and a decline in activity for the elements that target heterochromatin have both limited the contribution of retrotransposon DNA to genome size expansion in A. thaliana .
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Insertion bias and purifying selection of retrotransposons in the Arabidopsis thaliana genome.
Genome biology, 2004Co-Authors: Vini PereiraAbstract:Genome evolution and size variation in multicellular organisms are profoundly influenced by the activity of retrotransposons. In higher eukaryotes with compact genomes retrotransposons are found in lower copy numbers than in larger genomes, which could be due to either suppression of transposition or to elimination of insertions, and are non-randomly distributed along the chromosomes. The evolutionary mechanisms constraining retrotransposon copy number and chromosomal distribution are still poorly understood. I investigated the evolutionary dynamics of long terminal repeat (LTR)-retrotransposons in the compact Arabidopsis thaliana genome, using an automated method for obtaining genome-wide, age and physical distribution profiles for different groups of elements, and then comparing the distributions of young and old insertions. Elements of the Pseudoviridae family insert randomly along the chromosomes and have been recently active, but insertions tend to be lost from euchromatic regions where they are less likely to fix, with a half-life estimated at approximately 470,000 years. In contrast, members of the Metaviridae (particularly Athila) preferentially target heterochromatin, and were more active in the past. Diverse evolutionary mechanisms have constrained both the copy number and chromosomal distribution of retrotransposons within a single genome. In A. thaliana, their non-random genomic distribution is due to both selection against insertions in euchromatin and preferential targeting of heterochromatin. Constant turnover of euchromatic insertions and a decline in activity for the elements that target heterochromatin have both limited the contribution of retrotransposon DNA to genome size expansion in A. thaliana.
Daniel F. Voytas - One of the best experts on this subject based on the ideXlab platform.
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Chromosomal distribution of LTRs for the Metaviridae and Pseudoviridae families in
2011Co-Authors: Brooke D. Peterson-burch, Dan Nettleton, Daniel F. VoytasAbstract:Copyright information:Taken from "Genomic neighborhoods for retrotransposons: a role for targeted integration in the distribution of the Metaviridae"Genome Biology 2004;5(10):R78-R78.Published online 29 Sep 2004PMCID:PMC545598.Copyright © 2004 Peterson-Burch et al.; licensee BioMed Central Ltd. Chromosomes are displayed as in Figure 3. In addition, solo LTRs are drawn as open triangles. The upper chromosome depicts the distribution of Pseudoviridae, the lower the distribution of Metaviridae. In contrast to Figure 3, shading is not used to distinguish between the families
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Genomic neighborhoods for Arabidopsisretrotransposons: a role for targeted integration in the distribution of the Metaviridae
Genome Biology, 2004Co-Authors: Brooke D. Peterson-burch, Dan Nettleton, Daniel F. VoytasAbstract:Background Retrotransposons are an abundant component of eukaryotic genomes. The high quality of the Arabidopsis thaliana genome sequence makes it possible to comprehensively characterize retroelement populations and explore factors that contribute to their genomic distribution. Results We identified the full complement of A. thaliana long terminal repeat (LTR) retroelements using RetroMap, a software tool that iteratively searches genome sequences for reverse transcriptases and then defines retroelement insertions. Relative ages of full-length elements were estimated by assessing sequence divergence between LTRs: the Pseudoviridae were significantly younger than the Metaviridae. All retroelement insertions were mapped onto the genome sequence and their distribution was distinctly non-uniform. Although both Pseudoviridae and Metaviridae tend to cluster within pericentromeric heterochromatin, this association is significantly more pronounced for all three Metaviridae sublineages ( Metavirus , Tat and Athila ). Among these, Tat and Athila are strictly associated with pericentromeric heterochromatin. Conclusions The non-uniform genomic distribution of the Pseudoviridae and the Metaviridae can be explained by a variety of factors including target-site bias, selection against integration into euchromatin and pericentromeric accumulation of elements as a result of suppression of recombination. However, comparisons based on the age of elements and their chromosomal location indicate that integration-site specificity is likely to be the primary factor determining distribution of the Athila and Tat sublineages of the Metaviridae. We predict that, like retroelements in yeast, the Athila and Tat elements target integration to pericentromeric regions by recognizing a specific feature of pericentromeric heterochromatin.
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Genomic neighborhoods for Arabidopsis retrotransposons: a role for targeted integration in the distribution of the Metaviridae
Genome biology, 2004Co-Authors: Brooke D. Peterson-burch, Dan Nettleton, Daniel F. VoytasAbstract:Background Retrotransposons are an abundant component of eukaryotic genomes. The high quality of the Arabidopsis thaliana genome sequence makes it possible to comprehensively characterize retroelement populations and explore factors that contribute to their genomic distribution.
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athila4 of arabidopsis and calypso of soybean define a lineage of endogenous plant retroviruses
Genome Research, 2002Co-Authors: David A Wright, Daniel F. VoytasAbstract:Retrotransposons and retroviruses (collectively referred to as retroelements) replicate by a common mechanism of reverse transcription (for review, see Coffin et al. 1997). Retroelement genomes are delimited by direct long terminal repeats (LTRs), and they encode gag and pol genes, whose products form a particulate replication intermediate wherein reverse transcription takes place. The primary distinguishing feature between the retrotransposons and retroviruses is that the latter have a third gene called envelope (env). env encodes a transmembrane protein that associates with the cell membrane. The replication intermediate buds from the cell as a membrane-bound virion, and Env extends from the virion surface and interacts with cellular receptors to mediate infection. Phylogenetic relationships based on reverse transcriptase amino acid sequences identify six distinct lineages of retroelements (Xiong and Eickbush 1990; Malik 2000). One of these—the vertebrate retroviruses—encodes env genes and is infectious. The five remaining groups are comprised mostly of retrotransposons and include the well-studied Ty1-copia (Pseudoviridae) and Ty3-gypsy (Metaviridae) elements (van Regenmortel et al. 2000), the so-called DIRS1 and BEL groups, and the caulimoviruses (Malik et al. 2000). With the exception of the caulimoviruses and the sparsely populated DIRS1 group, some members of each lineage encode open reading frames (ORFs) with env-like features—most notably transmembrane domains. These include a large number of invertebrate Ty3-gypsy elements (e.g., gypsy, 17.6, 297, and ZAM from Drosophila melanogaster; TOM from Drosophila ananassae; TED from Trichoplusia ni; Yoyo from Ceratitis capitata; for review, see Lerat and Capy 1999), two Ty1-copia elements from plants (i.e., SIRE-1 from Glycine max [soybean] and Endovir from A. thaliana; Laten et al. 1998; Kapitonov and Jurka 1999; Peterson-Burch et al. 2000), and several BEL group elements (e.g., Tas from Ascaris lumbricoides and Cer7 from Caenorhabditis elegans; Felder et al. 1994; Bowen and McDonald 1999). Analyses of env-like genes from the various retroelement groups suggests that env was independently acquired from viruses multiple times during evolution. The env-like ORFs of several insect Ty3-gypsy elements are closely related to env of the bacculoviruses, and for some Cer elements, the env-like gene is related to env of the phleboviruses (Malik et al. 2000). Despite the widespread presence of env-like ORFs and their similarity to known viral env genes, gypsy of D. melanogaster is the only known retroelement outside of the retroviruses for which Env is known to play a role in infection (Kim et al. 1994; Song et al. 1994). In our analysis of the A. thaliana genome sequence, we determined that Athila—a degenerate, centromere-associated retroelement (Pelissier et al. 1995, 1996; Copenhaver et al. 1999)—is a Ty3-gypsy group retrotransposon with an env-like ORF (Wright and Voytas 1998). A related element was also described in Pisum sativum (pea) called Cyclops-2 (Chavanne et al. 1998). Because Cyclops-2 was less degenerate than Athila and prevalent in related legumes, we sought potential functional homologs in soybean. The soybean elements, called Calypso, encode an env-like gene that shares 29% amino acid identity to the corresponding gene of Cyclops-2 (Peterson-Burch et al. 2000). This suggests that the env-like ORF has evolved under functional constraint and likely plays a role in the life cycle of these elements. For simplicity, we refer to Athila and related retroelements as endogenous retroviruses, with the understanding that the biological role of their env-like genes remains to be determined. The sequence degeneracy of the endogenous plant retroviruses described to date has frustrated attempts to define their structural features. However, further characterization of the soybean Calypso elements and completion of the A. thaliana genome sequence has enabled us to construct consensus elements that likely approximate functional elements. Here we report a detailed description of these endogenous retroviruses and provide evidence of their widespread distribution in higher plants.
Vivien Measday - One of the best experts on this subject based on the ideXlab platform.
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Retrotransposon targeting to RNA polymerase III-transcribed genes
Mobile DNA, 2018Co-Authors: Stephanie Cheung, Savrina Manhas, Vivien MeasdayAbstract:Retrotransposons are genetic elements that are similar in structure and life cycle to retroviruses by replicating via an RNA intermediate and inserting into a host genome. The Saccharomyces cerevisiae ( S. cerevisiae ) Ty1–5 elements are long terminal repeat (LTR) retrotransposons that are members of the Ty1- copia ( Pseudoviridae ) or Ty3- gypsy ( Metaviridae ) families. Four of the five S. cerevisiae Ty elements are inserted into the genome upstream of RNA Polymerase (Pol) III-transcribed genes such as transfer RNA (tRNA) genes. This particular genomic locus provides a safe environment for Ty element insertion without disruption of the host genome and is a targeting strategy used by retrotransposons that insert into compact genomes of hosts such as S. cerevisiae and the social amoeba Dictyostelium . The mechanism by which Ty1 targeting is achieved has been recently solved due to the discovery of an interaction between Ty1 Integrase (IN) and RNA Pol III subunits. We describe the methods used to identify the Ty1-IN interaction with Pol III and the Ty1 targeting consequences if the interaction is perturbed. The details of Ty1 targeting are just beginning to emerge and many unexplored areas remain including consideration of the 3-dimensional shape of genome. We present a variety of other retrotransposon families that insert adjacent to Pol III-transcribed genes and the mechanism by which the host machinery has been hijacked to accomplish this targeting strategy. Finally, we discuss why retrotransposons selected Pol III-transcribed genes as a target during evolution and how retrotransposons have shaped genome architecture.