Potential multiple endonuclease functions and a ribonuclease H encoded in retroposon genomes

Virology

Volumn 296, Issue 1, 2002, Pages 147-158

  McClure, Marcella A ^a   Donaldson, Eric ^a   Corro, Seanna ^a  

^a MONTANA STATE UNIVERSITY   (United States)

Author keywords

Bioinformatics; Endonuclease; Multiple alignment; Retroid agent; Retroposon; Ribonuclease H

Indexed keywords

AMINO ACID; ENDONUCLEASE; RIBONUCLEASE H;

AMINO ACID SEQUENCE; ARTICLE; CONTROLLED STUDY; ENZYME ACTIVITY; GENOME; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RETROPOSON; TRYPANOSOMA BRUCEI;

BACTERIA (MICROORGANISMS); TRYPANOSOMA; TRYPANOSOMA BRUCEI;

EID: 0036343346     PISSN: 00426822     EISSN: None     Source Type: Journal    
DOI: 10.1006/viro.2002.1392     Document Type: Article

References (57)

1. Basic local alignment search tool
2. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
3. Structural implications of spectroscopic characterization of a putative zinc-finger peptide from HIV-1 integrase
4. Domains of the integrase protein of human immunodeficiency virus type 1 responsible for polynucleotidyl transfer and zinc binding
5. Solution structure of the N-terminal zinc binding domain of HIV-1 integrase
6. Quasispecies in retrotransposons: A role for sequence variability in Tnt1 evolution
7. Sequence variability within the tobacco retrotransposon Tnt1 population
8. Target specificity of the endonuclease from the Xenopus laevis non-long terminal repeat retrotransposon, Tx1L
9. Crystal structure of the ribonuclease H domain of HIV-1 reverse transcriptase
10. A model of evolutionary change in proteins
11. RNA virus mutations and fitness for survival
12. Origins and evolutionary relationships of retroviruses
13. Crystal structure of the catalytic domain of HIV-1 integrase: Similarity to other polynucleotidyl transferases
14. R1 and R2 retrotransposable elements of drosophila evolve at rates similar to those of nuclear genes
15. Functional similarities between retroviruses and the IS3 family of bacterial insertion sequences
16. Progressive sequence alignment as a prerequisite to correct phylognetic trees
17. Human L1 retrotransposons encode a conserved endonuclease required for retrotransposition
18. Replication infidelity during a single cycle of Ty1 retrotransposition
19. A rapidly rearranging retrotransposon within the miniexon gene locus of Crithidia fasciculata
20. Recoding: Dynamic reprogramming of translation
21. Incorporating motif information into pairwise alignment
22. Self-splicing group I and group II introns encode homologous (putative) DNA endonucleases of a new family
23. Retroviral DNA integration
24. Computer analysis of retroviral pol genes: Assignment of enzymatic functions
25. Protein secondary structure prediction based on position-specific scoring matrices
26. Identification of the amino acid residues involved in an active site of Escherichia
27. Three-dimensional structure of ribonuclease H from E. coli
28. Crystal structure at 3.5 A resolution of HIV-1 reverse transcriptase complexed with an inhibitor
29. The Ty1-copia group of retrotransposons in plants: Genomic organization, evolution, and use as molecular markers
30. Characterization of a non-Long terminal repeat retrotransposon cDNA (L1Tc) from Trypanosoma cruzi: Homology of the first ORF with the ape family of DNA repair enzymes
31. Evolution of retroposons by acquisition or deletion of retrovirus-like genes
32. The retroid agents: Disease function and evolution
33. The complexities of genome analysis, the retroid agent perspective
34. Comparative analysis of multiple protein-sequence alignment methods
35. Evolutionary relationships among group II intron-encoded proteins and identification of a conserved domain that may be related to maturease function
36. The open reading frame 1 of the L1Tc retrotransposon of Trypanosoma cruzi codes for a protein with apurinic-apyrimidinic nuclease activity
37. The L1Tc, long interspersed nucleotide element from Trypanosoma cruzi, encodes a protein with 3′-phosphatase and 3′-phosphodiesterase enzymatic activities
38. Petunia vein-cleaning virus: A plant pararetrovirus with core sequences for an integrase function
39. Point mutations in conserved amino acid residues within the C-terminal domain of HIV-1 reverse transcriptase specifically repress RNase H function
40. Amino acid sequence motif of group I intron endonucleases is conserved in open reading frames of group II introns
41. LINE-1: A human transposable element
42. Domain structure of the Moloney murine leukemia virus reverse transcriptase: Mutational analysis and separate expression of the DNA polymerase and RNAase H activities
43. Reverse transcription in the eukaryotic genome: Retroviruses, pararetroviruses, retrotransposons, and retrotranscripts
44. Retrons in bacteria
45. Analysis of the role of the pseudoknot component in the SRV-1 gag-pro ribosomal frameshift signal: Loop lengths and stability of the stem regions
46. Equilibrium unfolding pathway of an H-type RNA pseudoknot which promotes programmed-1 ribo-somal frameshifting
47. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
48. A new member of a family of site-specific retrotransposons is present in the spliced leader RNA genes of Trypanosoma cruzi
49. Non-LTR retrotransposons encoding a restriction enzyme-like endonuclease in vertebrates
50. Tdd-4, a DNA transposon of Dictyostelium that encodes proteins similar to LTR retroelement integrases
51. Functional expression of a sequence-specific endonuclease encoded by the retrotransposon R2BM
52. Identification of the endonuclease domain encoded by R2 and other site-specific, non-long terminal repeat retrotransposable elements
53. Protein sequence similarity searches using patterns as seeds