Phylogenetic analysis of ribonuclease H domains suggests a late, chimeric origin of LTR retrotransposable elements and retroviruses.

PubWeight™: 1.78‹?› | Rank: Top 3%

🔗 View Article (PMID 11435400)

Published in Genome Res on July 01, 2001

Authors

H S Malik1, T H Eickbush

Author Affiliations

1: Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA. hsmalik@fhcrc.org

Articles citing this

The ancient Virus World and evolution of cells. Biol Direct (2006) 3.06

The take and give between retrotransposable elements and their hosts. Annu Rev Genet (2008) 1.86

Murine endogenous retroviruses. Cell Mol Life Sci (2008) 1.85

The Gypsy Database (GyDB) of mobile genetic elements: release 2.0. Nucleic Acids Res (2010) 1.58

The diversity of retrotransposons and the properties of their reverse transcriptases. Virus Res (2008) 1.51

Overlapping genes produce proteins with unusual sequence properties and offer insight into de novo protein creation. J Virol (2009) 1.42

Recruitment of host functions suggests a repair pathway for late steps in group II intron retrohoming. Genes Dev (2005) 1.41

Mapping the LINE1 ORF1 protein interactome reveals associated inhibitors of human retrotransposition. Nucleic Acids Res (2013) 1.31

Transposon telomeres are widely distributed in the Drosophila genus: TART elements in the virilis group. Proc Natl Acad Sci U S A (2003) 1.30

Network dynamics of eukaryotic LTR retroelements beyond phylogenetic trees. Biol Direct (2009) 1.27

Virus world as an evolutionary network of viruses and capsidless selfish elements. Microbiol Mol Biol Rev (2014) 1.26

SVA retrotransposons: Evolution and genetic instability. Semin Cancer Biol (2010) 1.20

An infectious progenitor for the murine IAP retrotransposon: emergence of an intracellular genetic parasite from an ancient retrovirus. Genome Res (2008) 1.17

MOV10 RNA helicase is a potent inhibitor of retrotransposition in cells. PLoS Genet (2012) 1.17

Significant expansion of Vicia pannonica genome size mediated by amplification of a single type of giant retroelement. Genetics (2006) 1.14

Phylogenetic profiles reveal evolutionary relationships within the "twilight zone" of sequence similarity. Proc Natl Acad Sci U S A (2008) 1.11

DNA-directed DNA polymerase and strand displacement activity of the reverse transcriptase encoded by the R2 retrotransposon. J Mol Biol (2007) 1.11

Genomic evolution of the long terminal repeat retrotransposons in hemiascomycetous yeasts. Genome Res (2002) 1.11

Saci-1, -2, and -3 and Perere, four novel retrotransposons with high transcriptional activities from the human parasite Schistosoma mansoni. J Virol (2004) 1.09

Expression and site-directed mutagenesis of the lactococcal abortive phage infection protein AbiK. J Bacteriol (2005) 1.09

Centromeric retrotransposon lineages predate the maize/rice divergence and differ in abundance and activity. Mol Genet Genomics (2007) 1.08

The GATE retrotransposon in Drosophila melanogaster: mobility in heterochromatin and aspects of its expression in germline tissues. Mol Genet Genomics (2003) 1.08

Adaptive evolution involving gene duplication and insertion of a novel Ty1/copia-like retrotransposon in soybean. J Mol Evol (2009) 1.07

Eukaryotic translational coupling in UAAUG stop-start codons for the bicistronic RNA translation of the non-long terminal repeat retrotransposon SART1. Mol Cell Biol (2005) 1.05

Relationships of gag-pol diversity between Ty3/Gypsy and Retroviridae LTR retroelements and the three kings hypothesis. BMC Evol Biol (2008) 1.04

Murine endogenous retrovirus MuERV-L is the progenitor of the "orphan" epsilon viruslike particles of the early mouse embryo. J Virol (2007) 1.02

Evolution of ribonuclease H genes in prokaryotes to avoid inheritance of redundant genes. BMC Evol Biol (2007) 1.01

Sustained retrotransposition is mediated by nucleotide deletions and interelement recombinations. Proc Natl Acad Sci U S A (2008) 1.00

Ty3 reverse transcriptase complexed with an RNA-DNA hybrid shows structural and functional asymmetry. Nat Struct Mol Biol (2014) 1.00

Structure of a membrane-attack complex/perforin (MACPF) family protein from the human gut symbiont Bacteroides thetaiotaomicron. Acta Crystallogr Sect F Struct Biol Cryst Commun (2010) 0.98

A deep-branching clade of retrovirus-like retrotransposons in bdelloid rotifers. Gene (2006) 0.97

The Broad-Spectrum Antiviral Protein ZAP Restricts Human Retrotransposition. PLoS Genet (2015) 0.97

A highly conserved, small LTR retrotransposon that preferentially targets genes in grass genomes. PLoS One (2012) 0.93

Phylogeny of Banana Streak Virus reveals recent and repetitive endogenization in the genome of its banana host (Musa sp.). J Mol Evol (2009) 0.93

Roles for retrotransposon insertions in human disease. Mob DNA (2016) 0.92

Non-LTR retrotransposons in fungi. Funct Integr Genomics (2008) 0.91

An extraordinary retrotransposon family encoding dual endonucleases. Genome Res (2005) 0.90

Boudicca, a retrovirus-like long terminal repeat retrotransposon from the genome of the human blood fluke Schistosoma mansoni. J Virol (2003) 0.89

LTR retroelements in the genome of Daphnia pulex. BMC Genomics (2010) 0.88

DIRS retroelements in arthropods: identification of the recently active TcDirs1 element in the red flour beetle Tribolium castaneum. Mol Genet Genomics (2004) 0.87

A sequence similar to tRNA 3 Lys gene is embedded in HIV-1 U3-R and promotes minus-strand transfer. Nat Struct Mol Biol (2009) 0.87

Identification of RNA binding motifs in the R2 retrotransposon-encoded reverse transcriptase. Nucleic Acids Res (2014) 0.85

Conserved structure and inferred evolutionary history of long terminal repeats (LTRs). Mob DNA (2013) 0.85

The GLN family of murine endogenous retroviruses contains an element competent for infectious viral particle formation. J Virol (2008) 0.84

OVEX1, a novel chicken endogenous retrovirus with sex-specific and left-right asymmetrical expression in gonads. Retrovirology (2009) 0.84

Radiation of the Tnt1 retrotransposon superfamily in three Solanaceae genera. BMC Evol Biol (2007) 0.84

kangaroo, a mobile element from Volvox carteri, is a member of a newly recognized third class of retrotransposons. Genetics (2002) 0.83

Acquisition of an Archaea-like ribonuclease H domain by plant L1 retrotransposons supports modular evolution. Proc Natl Acad Sci U S A (2013) 0.82

PwRn1, a novel Ty3/gypsy-like retrotransposon of Paragonimus westermani: molecular characters and its differentially preserved mobile potential according to host chromosomal polyploidy. BMC Genomics (2008) 0.82

Evolution of diverse mechanisms for protecting chromosome ends by Drosophila TART telomere retrotransposons. Proc Natl Acad Sci U S A (2010) 0.82

Evolution of endogenous sequences of banana streak virus: what can we learn from banana (Musa sp.) evolution? J Virol (2010) 0.81

Functional roles of carboxylate residues comprising the DNA polymerase active site triad of Ty3 reverse transcriptase. Nucleic Acids Res (2005) 0.81

GalEa retrotransposons from galatheid squat lobsters (Decapoda, Anomura) define a new clade of Ty1/copia-like elements restricted to aquatic species. Mol Genet Genomics (2007) 0.81

Hellbender genome sequences shed light on genomic expansion at the base of crown salamanders. Genome Biol Evol (2014) 0.80

Mn2+ suppressor mutations and biochemical communication between Ty1 reverse transcriptase and RNase H domains. J Virol (2007) 0.80

Restricting retrotransposons: a review. Mob DNA (2016) 0.79

Divergent long-terminal-repeat retrotransposon families in the genome of Paragonimus westermani. Korean J Parasitol (2003) 0.79

Envelope-like retrotransposons in the plant kingdom: evidence of their presence in gymnosperms (Pinus pinaster). J Mol Evol (2008) 0.79

Deep sequencing reveals the complete genome and evidence for transcriptional activity of the first virus-like sequences identified in Aristotelia chilensis (Maqui Berry). Viruses (2015) 0.78

Evolutionary course of CsRn1 long-terminal-repeat retrotransposon and its heterogeneous integrations into the genome of the liver fluke, Clonorchis sinensis. Korean J Parasitol (2003) 0.78

Structure and properties of the esterase from non-LTR retrotransposons suggest a role for lipids in retrotransposition. Nucleic Acids Res (2013) 0.78

Convergent evolution of tRNA gene targeting preferences in compact genomes. Mob DNA (2016) 0.77

Drosophila errantiviruses. Mob Genet Elements (2012) 0.77

The Tnt1 family member Retrosol copy number and structure disclose retrotransposon diversification in different Solanum species. Mol Genet Genomics (2008) 0.76

Convergent evolution of ribonuclease h in LTR retrotransposons and retroviruses. Mol Biol Evol (2015) 0.76

Arm-specific cleavage and mutation during reverse transcription of 2΄,5΄-branched RNA by Moloney murine leukemia virus reverse transcriptase. Nucleic Acids Res (2017) 0.75

Protein-Coding Genes' Retrocopies and Their Functions. Viruses (2017) 0.75

Convergence of retrotransposons in oomycetes and plants. Mob DNA (2017) 0.75

Integration, Regulation, and Long-Term Stability of R2 Retrotransposons. Microbiol Spectr (2015) 0.75

Reverse Transcription in the Saccharomyces cerevisiae Long-Terminal Repeat Retrotransposon Ty3. Viruses (2017) 0.75

A copia-like retrotransposon gene encoding gypsy-like integrase in a red alga, Porphyra yezoensis. J Mol Evol (2007) 0.75

RNase H As Gene Modifier, Driver of Evolution and Antiviral Defense. Front Microbiol (2017) 0.75

Articles by these authors

Origin and evolution of retroelements based upon their reverse transcriptase sequences. EMBO J (1990) 9.93

Reverse transcription of R2Bm RNA is primed by a nick at the chromosomal target site: a mechanism for non-LTR retrotransposition. Cell (1993) 8.99

The age and evolution of non-LTR retrotransposable elements. Mol Biol Evol (1999) 4.38

Similarity of reverse transcriptase-like sequences of viruses, transposable elements, and mitochondrial introns. Mol Biol Evol (1988) 3.96

The histone core complex: an octamer assembled by two sets of protein-protein interactions. Biochemistry (1978) 2.78

RNA template requirements for target DNA-primed reverse transcription by the R2 retrotransposable element. Mol Cell Biol (1995) 2.62

Functional expression of a sequence-specific endonuclease encoded by the retrotransposon R2Bm. Cell (1988) 2.61

Isolation of multigene families and determination of homologies by filter hybridization methods. Methods Enzymol (1983) 2.44

The compaction of DNA helices into either continuous supercoils or folded-fiber rods and toroids. Cell (1978) 2.29

The site-specific ribosomal DNA insertion element R1Bm belongs to a class of non-long-terminal-repeat retrotransposons. Mol Cell Biol (1988) 2.22

Type I (R1) and type II (R2) ribosomal DNA insertions of Drosophila melanogaster are retrotransposable elements closely related to those of Bombyx mori. J Mol Biol (1990) 2.18

Modular evolution of the integrase domain in the Ty3/Gypsy class of LTR retrotransposons. J Virol (1999) 2.14

Retrotransposable elements R1 and R2 interrupt the rRNA genes of most insects. Proc Natl Acad Sci U S A (1991) 2.08

Poised for contagion: evolutionary origins of the infectious abilities of invertebrate retroviruses. Genome Res (2000) 2.01

The site-specific ribosomal insertion element type II of Bombyx mori (R2Bm) contains the coding sequence for a reverse transcriptase-like enzyme. Mol Cell Biol (1987) 1.87

Identification of the endonuclease domain encoded by R2 and other site-specific, non-long terminal repeat retrotransposable elements. Proc Natl Acad Sci U S A (1999) 1.79

Secondary structure model of the RNA recognized by the reverse transcriptase from the R2 retrotransposable element. RNA (1997) 1.68

The domain structure and retrotransposition mechanism of R2 elements are conserved throughout arthropods. Mol Biol Evol (1999) 1.58

Turnover of R1 (type I) and R2 (type II) retrotransposable elements in the ribosomal DNA of Drosophila melanogaster. Genetics (1992) 1.55

The RTE class of non-LTR retrotransposons is widely distributed in animals and is the origin of many SINEs. Mol Biol Evol (1998) 1.49

A walk in the chorion locus of Bombyx mori. Cell (1982) 1.46

Are retrotransposons long-term hitchhikers? Nature (1998) 1.44

Vertical transmission of the retrotransposable elements R1 and R2 during the evolution of the Drosophila melanogaster species subgroup. Genetics (1995) 1.44

Evolutionary specialization of the nuclear targeting apparatus. Proc Natl Acad Sci U S A (1997) 1.44

A highly reiterated family of transcribed oligo(A)-terminated, interspersed DNA elements in the genome of Bombyx mori. J Mol Biol (1986) 1.39

Sequence relationship of retrotransposable elements R1 and R2 within and between divergent insect species. Mol Biol Evol (1993) 1.38

Bombyx mori 28S ribosomal genes contain insertion elements similar to the Type I and II elements of Drosophila melanogaster. EMBO J (1985) 1.37

A "selfish" B chromosome that enhances its transmission by eliminating the paternal genome. Science (1988) 1.37

Dynamics of R1 and R2 elements in the rDNA locus of Drosophila simulans. Genetics (2001) 1.33

Ribosomal DNA insertion elements R1Bm and R2Bm can transpose in a sequence specific manner to locations outside the 28S genes. Nucleic Acids Res (1988) 1.33

Analysis of the 5' junctions of R2 insertions with the 28S gene: implications for non-LTR retrotransposition. Genetics (1996) 1.33

R4, a non-LTR retrotransposon specific to the large subunit rRNA genes of nematodes. Nucleic Acids Res (1995) 1.23

A single lineage of r2 retrotransposable elements is an active, evolutionarily stable component of the Drosophila rDNA locus. Mol Biol Evol (1997) 1.21

Integration of Bombyx mori R2 sequences into the 28S ribosomal RNA genes of Drosophila melanogaster. Mol Cell Biol (2000) 1.19

Downstream 28S gene sequences on the RNA template affect the choice of primer and the accuracy of initiation by the R2 reverse transcriptase. Mol Cell Biol (1996) 1.16

Multiple lineages of R1 retrotransposable elements can coexist in the rDNA loci of Drosophila. Mol Biol Evol (2001) 1.15

NeSL-1, an ancient lineage of site-specific non-LTR retrotransposons from Caenorhabditis elegans. Genetics (2000) 1.14

Conserved features at the 5 end of Drosophila R2 retrotransposable elements: implications for transcription and translation. Insect Mol Biol (1999) 1.14

The silkmoth late chorion locus. II. Gradients of gene conversion in two paired multigene families. J Mol Biol (1986) 1.12

Pao, a highly divergent retrotransposable element from Bombyx mori containing long terminal repeats with tandem copies of the putative R region. Nucleic Acids Res (1993) 1.10

Dong, a non-long terminal repeat (non-LTR) retrotransposable element from Bombyx mori. Nucleic Acids Res (1993) 1.09

R1 and R2 retrotransposable elements of Drosophila evolve at rates similar to those of nuclear genes. Genetics (1995) 1.08

Sequence identity in an early chorion multigene family is the result of localized gene conversion. Genetics (1991) 1.06

A chromatin-bound proteolytic activity with unique specificity for histone H2A. Cell (1976) 1.04

RNA-induced changes in the activity of the endonuclease encoded by the R2 retrotransposable element. Mol Cell Biol (1998) 1.03

Putative telomerase catalytic subunits from Giardia lamblia and Caenorhabditis elegans. Gene (2000) 1.02

Novel B family sequence from an early chorion cDNA library of Bombyx mori. Proc Natl Acad Sci U S A (1983) 1.01

Reversible association of calf thymus histones to form the symmetrical octamer (H2AH2BH3H4)2: a case of a mixed-associating system. Biochemistry (1980) 1.01

Ribosomal DNA genes of Bombyx mori: a minor fraction of the repeating units contain insertions. Nucleic Acids Res (1984) 1.00

Evolutionary stability of the R1 retrotransposable element in the genus Drosophila. Mol Biol Evol (1995) 0.96

Retrotransposable elements R1 and R2 in the rDNA units of Drosophila mercatorum: abnormal abdomen revisited. Genetics (1999) 0.95

Evolution of the silk moth chorion gene superfamily: gene families CA and CB. Proc Natl Acad Sci U S A (1986) 0.91

Diversity in a chorion multigene family created by tandem duplications and a putative gene-conversion event. J Mol Evol (1984) 0.90

A complex set of early chorion DNA sequences from Bombyx mori. Dev Biol (1985) 0.89

Maintenance of multiple lineages of R1 and R2 retrotransposable elements in the ribosomal RNA gene loci of Nasonia. Insect Mol Biol (2010) 0.89

Silkmoth chorion gene families contain patchwork patterns of sequence homology. Proc Natl Acad Sci U S A (1985) 0.88

Gene conversions can generate sequence variants in the late chorion multigene families of Bombyx mori. Genetics (1988) 0.86

Molecular biology. Introns gain ground. Nature (2000) 0.86

Molecular characterization of repetitive DNA sequences from a B chromosome. Chromosoma (1992) 0.84

Organization and expression of three genes from the silkmoth early chorion locus. Dev Biol (1988) 0.80

The silkmoth late chorion locus. I. Variation within two paired multigene families. J Mol Biol (1986) 0.80

Gene evolution and regulation in the chorion complex of Bombyx mori. Hybridization and sequence analysis of multiple developmentally middle A/B chorion gene pairs. J Mol Biol (1989) 0.78

A mechanism for the entrapment of DNA at an air-water interface. Biophys J (1977) 0.77

Ten-kilodalton domain in Ty3 Gag3-Pol3p between PR and RT is dispensable for Ty3 transposition. J Virol (2001) 0.75

Competition between R1 and R2 transposable elements in the 28S rRNA genes of insects. Cytogenet Genome Res (2005) 0.75