Home LiteratureArticle Details
PMID: 1662367 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S.

Phylogenetic and physical analysis of the 5' leader RNA sequences of avian retroviruses.

Nucleic acids research ·Vol. 19 ·No. 24 ·1991-12-25 ·Pages 6929-34

Hackett PB, Dalton MW, Johnson DP, Petersen RB

Abstract

A study of the secondary structures of the 5'-leader RNA sequences of avian leukosis/sarcoma viruses was conducted using phylogenetic sequence alignment, theoretical structures calculated from base-pairing interactions involving the calculated minimal delta G values, and RNaseT1 sensitivity. The results suggest that all of the avian retroviral RNA leaders may be able to adopt similar conformations. Open reading frames in the leader RNAs may be positioned to facilitate viral activities such as translation and packaging of the genomic RNA into virus particles.

MeSH Terms
Avian Leukosis Virus/classification,genetics Avian Sarcoma Viruses/classification,genetics Base Composition Base Sequence Exoribonucleases/metabolism Gene Expression Regulation, Viral/genetics Molecular Sequence Data Nucleic Acid Conformation Open Reading Frames/genetics Phylogeny Protein Biosynthesis/genetics RNA, Viral/chemistry,genetics,metabolism Sequence Alignment Virus Replication/genetics
Chemicals
RNA, Viral Exoribonucleases exoribonuclease T
Authors & Affiliations
4 authors, click to expand affiliations / ORCID
Hackett P B
Department of Genetics and Cell Biology, University of Minnesota, St. Paul 55108-1095.
Dalton M W
Johnson D P
Petersen R B
References (38)
38 references, click to expand
  1. Regulation of expression of human immunodeficiency virus.
    New Biol. 1990 Jan;2(1):20-31 PMID: 2078551
  2. Methylmercury as a reversible denaturing agent for agarose gel electrophoresis.
    Anal Biochem. 1976 Jan;70(1):75-85 PMID: 1259158
  3. Role of the avian retrovirus mRNA leader in expression: evidence for novel translational control.
    Mol Cell Biol. 1986 Feb;6(2):372-9 PMID: 3023842
  4. Multiple upstream AUG codons mediate translational control of GCN4.
    Cell. 1986 Apr 25;45(2):201-7 PMID: 3516411
  5. Synthesis in vitro of a seven amino acid peptide encoded in the leader RNA of Rous sarcoma virus.
    J Mol Biol. 1986 Jul 5;190(1):45-57 PMID: 3023636
  6. Effects of alterations in the leader sequence of Rous sarcoma virus RNA on initiation of translation.
    J Virol. 1989 Nov;63(11):4986-90 PMID: 2552182
  7. Translational control of synthesis of simian virus 40 late proteins from polycistronic 19S late mRNA.
    J Virol. 1988 Sep;62(9):3182-92 PMID: 2841471
  8. Partial nucleotide sequence of the avian erythroblastosis virus (AEV ES4).
    Nucleic Acids Res. 1987 Nov 25;15(22):9612 PMID: 2825143
  9. Control of Rous sarcoma virus RNA translation and packaging by the 5' and 3' untranslated sequences.
    J Mol Biol. 1986 Jun 5;189(3):421-34 PMID: 3023627
  10. Nucleotide sequence of HBI, a novel recombinant MC29 derivative with altered pathogenic properties.
    J Virol. 1985 Dec;56(3):969-77 PMID: 2999450
  11. Characterization of ribosome binding on Rous sarcoma virus RNA in vitro.
    J Virol. 1985 Dec;56(3):683-90 PMID: 2999425
  12. Cap accessibility correlates with the initiation efficiency of alfalfa mosaic virus RNAs.
    Eur J Biochem. 1985 Mar 15;147(3):549-52 PMID: 2983983
  13. Nucleotide sequence of avian sarcoma virus UR2 and comparison of its transforming gene with other members of the tyrosine protein kinase oncogene family.
    J Virol. 1985 Mar;53(3):879-84 PMID: 2983097
  14. Phylogenetic comparative analysis and the secondary structure of ribonuclease P RNA--a review.
    Gene. 1989 Oct 15;82(1):65-75 PMID: 2479592
  15. Improved predictions of secondary structures for RNA.
    Proc Natl Acad Sci U S A. 1989 Oct;86(20):7706-10 PMID: 2479010
  16. On finding all suboptimal foldings of an RNA molecule.
    Science. 1989 Apr 7;244(4900):48-52 PMID: 2468181
  17. A retroviral RNA secondary structure required for efficient initiation of reverse transcription.
    J Virol. 1988 Oct;62(10):3622-30 PMID: 2458484
  18. RNA structure prediction.
    Annu Rev Biophys Biophys Chem. 1988;17:167-92 PMID: 2456074
  19. Characterization of ribosomal frameshifting in HIV-1 gag-pol expression.
    Nature. 1988 Jan 21;331(6153):280-3 PMID: 2447506
  20. A novel viral oncogene with structural similarity to phospholipase C.
    Nature. 1988 Mar 17;332(6161):272-5 PMID: 2450282
  21. Bacterial evolution.
    Microbiol Rev. 1987 Jun;51(2):221-71 PMID: 2439888
  22. A mutation in the short 5'-proximal open reading frame on Rous sarcoma virus RNA alters virus production.
    J Virol. 1989 Nov;63(11):4787-96 PMID: 2552153
  23. cis-trans models for post-transcriptional gene regulation.
    Science. 1989 Nov 17;246(4932):870-2 PMID: 2683086
  24. The scanning model for translation: an update.
    J Cell Biol. 1989 Feb;108(2):229-41 PMID: 2645293
  25. The involvement of mRNA secondary structure in protein synthesis.
    Biochem Cell Biol. 1987 Jun;65(6):576-81 PMID: 3322328
  26. Differential expression of alternative 5' untranslated regions in mRNAs encoding rat insulin-like growth factor I.
    Proc Natl Acad Sci U S A. 1987 Dec;84(24):8946-50 PMID: 3480521
  27. A multiple sequence alignment program.
    Nucleic Acids Res. 1986 Jan 10;14(1):363-74 PMID: 3753772
  28. Identification of a ribosome-binding site for a leader peptide encoded by Rous sarcoma virus RNA.
    J Virol. 1984 Sep;51(3):722-9 PMID: 6088795
  29. Secondary structure of mouse and rabbit alpha- and beta-globin mRNAs: differential accessibility of alpha and beta initiator AUG codons towards nucleases.
    Cell. 1980 Jan;19(1):91-102 PMID: 7357610
  30. Avian sarcoma virus Y73 genome sequence and structural similarity of its transforming gene product to that of Rous sarcoma virus.
    Nature. 1982 May 20;297(5863):205-8 PMID: 6281656
  31. Nucleotide sequence of noncoding regions in Rous-associated virus-2: comparisons delineate conserved regions important in replication and oncogenesis.
    J Virol. 1984 Feb;49(2):557-65 PMID: 6319755
  32. Nucleotide sequence of Rous sarcoma virus.
    Cell. 1983 Mar;32(3):853-69 PMID: 6299578
  33. Nucleotide sequence analysis of the proviral genome of avian myelocytomatosis virus (MC29).
    Proc Natl Acad Sci U S A. 1983 May;80(9):2500-4 PMID: 6302688
  34. Nucleotide sequence of the 5' noncoding region and part of the gag gene of Rous sarcoma virus.
    J Virol. 1982 Feb;41(2):535-41 PMID: 6281465
  35. The leader sequence of the subgenomic mRNA's of Rous sarcoma virus is approximately 390 nucleotides.
    J Virol. 1982 Feb;41(2):527-34 PMID: 6281464
  36. Sequence of the long terminal repeat and adjacent segments of the endogenous avian virus Rous-associated virus 0.
    J Virol. 1982 Jul;43(1):191-200 PMID: 6286997
  37. Nucleotide sequence of Fujinami sarcoma virus: evolutionary relationship of its transforming gene with transforming genes of other sarcoma viruses.
    Cell. 1982 Oct;30(3):787-95 PMID: 6291784
  38. Leader length and secondary structure modulate mRNA function under conditions of stress.
    Mol Cell Biol. 1988 Jul;8(7):2737-44 PMID: 3405216
Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
0305-1048
DOI
10.1093/nar/19.24.6929
Published
1991-12-25
Pages
6929-34
Language
English
Region
England
NLM ID
0411011
PMCID
PMC329330
Subset
IM
Grants
NCI NIH HHS · CA 43881 · United States
External Links
PubMed source DOI: 10.1093/nar/19.24.6929 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2