Regulation of primate lentiviral RNA dimerization by structural entrapment

Retrovirology

Volumn 5, Issue , 2008, Pages

  Baig, Tayyba T ^a   Strong, Christy L ^a   Lodmell, J Stephen ^a   Lanchy, Jean Marc ^a  

^a UNIVERSITY OF MONTANA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GAG PROTEIN; VIRUS RNA; ANTISENSE OLIGONUCLEOTIDE; SPLICED LEADER RNA;

ARTICLE; BASE PAIRING; CODON; DIMERIZATION; DOWN REGULATION; GENE SEQUENCE; GENETIC REGULATION; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS 2; LENTIVIRINAE; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PRIMATE; PROTEIN SECONDARY STRUCTURE; REVERSE TRANSCRIPTION; RNA CONFORMATION; RNA PURIFICATION; RNA SEQUENCE; RNA STABILITY; RNA STRUCTURE; RNA SYNTHESIS; SIGNAL PROCESSING; SIMIAN IMMUNODEFICIENCY VIRUS; VIRUS CAPSID; VIRUS PARTICLE; ANIMAL; CHEMISTRY; CLASSIFICATION; CONFORMATION; GENETICS; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS; KINETICS; METABOLISM; MOLECULAR GENETICS;

HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS 2; PRIMATES;

ANIMALS; BASE PAIRING; BASE SEQUENCE; DIMERIZATION; HIV-1; HIV-2; HUMANS; KINETICS; LENTIVIRUSES, PRIMATE; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; OLIGONUCLEOTIDES, ANTISENSE; RNA, SPLICED LEADER; RNA, VIRAL; SIMIAN IMMUNODEFICIENCY VIRUS;

EID: 48749084874     PISSN: None     EISSN: 17424690     Source Type: Journal    
DOI: 10.1186/1742-4690-5-65     Document Type: Article

References (54)

1. Berkhout B Structure and function of the human immunodeficiency virus leader RNA Prog Nucleic Acid Res Mol Biol 1996/01/01 1996, 54:1-34. 8768071
2. Paillart JC Shehu-Xhilaga M Marquet R Mak J Dimerization of retroviral RNA genomes: An inseparable pair Nat Rev Microbiol 2004, 2(6):461-472. 15152202
3. Ooms M Huthoff H Russell R Liang C Berkhout B A riboswitch regulates RNA dimerization and packaging in human immunodeficiency virus type 1 virions J Virol 2004, 78(19):10814-10819. 516375 15367648
4. Greatorex J Lever A Retroviral RNA dimer linkage J Gen Virol 1998. 79(Pt 12):2877-2882. 9880000
5. McCann EM Lever AM Location of cis-acting signals important for RNA encapsidation in the leader sequence of human immunodeficiency virus type 2 J Virol 1997/05/01 1997, 71(5):4133-4137. 191571 9094696
6. Lanchy JM Lodmell JS An extended stem-loop 1 is necessary for human immunodeficiency virus type 2 replication and affects genomic RNA encapsidation J Virol 2007/01/19 2007, 81(7):3285-3292. 1866085 17229705
7. L'Hernault A Greatorex JS Crowther A Lever AM Dimerisation of HIV-2 genomic RNA is linked to efficient RNA packaging, normal particle maturation and viral infectivity Retrovirology 2007/12/15 2007, 4(1):90. 2222663 18078509
8. Griffin SD Allen JF Lever AM The major human immunodeficiency virus type 2 (HIV-2) packaging signal is present on all HIV-2 RNA species: cotranslational RNA encapsidation and limitation of Gag protein confer specificity J Virol 2001/11/17 2001, 75(24):12058-12069. 116101 11711596
9. D'Souza V Summers MF Structural basis for packaging the dimeric genome of Moloney murine leukaemia virus Nature 2004/10/01 2004, 431(7008):586-590. 15457265
10. Bender W Davidson N Mapping of poly(A) sequences in the electron microscope reveals unusual structure of type C oncornavirus RNA molecules Cell 1976/04/01 1976, 7(4):595-607. 182376
11. Hoglund S Ohagen A Goncalves J Panganiban AT Gabuzda D Ultrastructure of HIV-1 genomic RNA Virology 1997/07/07 1997, 233(2):271-279. 9217051
12. Skripkin E Paillart JC Marquet R Ehresmann B Ehresmann C Identification of the primary site of the human immunodeficiency virus type 1 RNA dimerization in vitro Proc Natl Acad Sci U S A 1994/05/24 1994, 91(11):4945-4949. 43906 8197162
13. Muriaux D Girard PM Bonnet-Mathoniere B Paoletti J Dimerization of HIV-1Lai RNA at low ionic strength. An autocomplementary sequence in the 5′ leader region is evidenced by an antisense oligonucleotide J Biol Chem 1995/04/07 1995, 270(14):8209-8216. 7713927
14. Laughrea M Jette L A 19-nucleotide sequence upstream of the 5′ major splice donor is part of the dimerization domain of human immunodeficiency virus 1 genomic RNA Biochemistry 1994/11/15 1994, 33(45):13464-13474. 7947755
15. Russell RS Liang C Wainberg MA Is HIV-1 RNA dimerization a prerequisite for packaging? Yes, no, probably? Retrovirology 2004/09/04 2004, 1:23. 516451 15345057
16. Song R Kafaie J Yang L Laughrea M HIV-1 viral RNA is selected in the form of monomers that dimerize in a three-step protease-dependent process; the DIS of stem-loop 1 initiates viral RNA dimerization J Mol Biol 2007/06/30 2007, 371(4):1084-1098. 17599354
17. Abbink TE Berkhout B A novel long distance base-pairing interaction in human immunodeficiency virus type 1 RNA occludes the Gag start codon J Biol Chem 2002/11/30 2003, 278(13):11601-11611. 12458192
18. Abbink TE Ooms M Haasnoot PC Berkhout B The HIV-1 leader RNA conformational switch regulates RNA dimerization but does not regulate mRNA translation Biochemistry 2005/06/22 2005, 44(25):9058-9066. 15966729
19. Jossinet F Lodmell JS Ehresmann C Ehresmann B Marquet R Identification of the in vitro HIV-2/SIV RNA dimerization site reveals striking differences with HIV-1 J Biol Chem 2001, 276(8):5598-5604. 11092889
20. Lanchy JM Lodmell JS Alternate usage of two dimerization initiation sites in HIV-2 viral RNA in vitro J Mol Biol 2002/06/11 2002, 319(3):637-648. 12054860
21. Dirac AM Huthoff H Kjems J Berkhout B Regulated HIV-2 RNA dimerization by means of alternative RNA conformations Nucleic Acids Res 2002/06/13 2002, 30(12):2647-2655. 117293 12060681
22. Dirac AM Huthoff H Kjems J Berkhout B The dimer initiation site hairpin mediates dimerization of the human immunodeficiency virus, type 2 RNA genome J Biol Chem 2001/06/09 2001, 276(34):32345-32352. 11397802
23. Laughrea M Jette L Kissing-loop model of HIV-1 genome dimerization: HIV-1 RNAs can assume alternative dimeric forms, and all sequences upstream or downstream of hairpin 248-271 are dispensable for dimer formation Biochemistry 1996/02/06 1996, 35(5):1589-1598. 8634290
24. Muriaux D Fosse P Paoletti J A kissing complex together with a stable dimer is involved in the HIV-1Lai RNA dimerization process in vitro Biochemistry 1996/04/16 1996, 35(15):5075-5082. 8664300
25. Lanchy JM Rentz CA Ivanovitch JD Lodmell JS Elements located upstream and downstream of the major splice donor site influence the ability of HIV-2 leader RNA to dimerize in vitro Biochemistry 2003, 42(9):2634-2642. 1473984 12614158
26. Lanchy JM Ivanovitch JD Lodmell JS A structural linkage between the dimerization and encapsidation signals in HIV-2 leader RNA RNA 2003/07/ 19 2003, 9(8):1007-1018. 1370466 12869711
27. Baig TT Lanchy JM Lodmell JS HIV-2 RNA dimerization is regulated by intramolecular interactions in vitro RNA 2007/06/27 2007, 13(8):1341-1354. 1924897 17592043
28. Regier DA Desrosiers RC The complete nucleotide sequence of a pathogenic molecular clone of simian immunodeficiency virus AIDS Res Hum Retroviruses 1990/11/01 1990, 6(11):1221-1231. 2078405
29. Kestler H Kodama T Ringler D Marthas M Pedersen N Lackner A Regier D Sehgal P Daniel M King N Desrosiers RC Induction of AIDS in rhesus monkeys by molecularly cloned simian immunodeficiency virus Science 1990, 248(4959):1109-1112. 2160735
30. Gibbs JS Regier DA Desrosiers RC Construction and in vitro properties of HIV-1 mutants with deletions in "nonessential" genes AIDS Res Hum Retroviruses 1994/04/01 1994, 10(4):343-350. 8068414
31. Laughrea M Jette L HIV-1 genome dimerization: Kissing-loop hairpin dictates whether nucleotides downstream of the 5′ splice junction contribute to loose and tight dimerization of human immunodeficiency virus RNA Biochemistry 1997/08/05 1997, 36(31):9501-9508. 9235995
32. Marquet R Paillart JC Skripkin E Ehresmann C Ehresmann B Dimerization of human immunodeficiency virus type 1 RNA involves sequences located upstream of the splice donor site Nucleic Acids Res 1994/01/25 1994, 22(2):145-151. 307764 8121797
33. Shubsda MF McPike MP Goodisman J Dabrowiak JC Monomer-dimer equilibrium constants of RNA in the dimer initiation site of human immunodeficiency virus type 1 Biochemistry 1999/08/06 1999, 38(31):10147-10157. 10433723
34. Huthoff H Berkhout B Multiple secondary structure rearrangements during HIV-1 RNA dimerization Biochemistry 2002/08/14 2002, 41(33):10439-10445. 12173930
35. Berkhout B Ooms M Beerens N Huthoff H Southern E Verhoef K In vitro evidence that the untranslated leader of the HIV-1 genome is an RNA checkpoint that regulates multiple functions through conformational changes J Biol Chem 2002, 277(22):19967-19975. 11896057
36. Deer EL Douk B Lanchy JM Lodmell JS Elucidation and characterization of oligonucleotide-accessible sites on HIV-2 leader region RNA Antisense Nucleic Acid Drug Dev 2003/04/15 2003, 13(1):45-55. 1403296 12691535
37. Leitner T Foley B Hahn B Marx P McCutchan F Mellors J Wolinsky S Korber B HIV Sequence Compendium 2006/2007 Theoretical Biology and Biophysics Group, Los Alamos National Laboratory 2007 http://www.hiv.lanl.gov/content/sequence/HIV/COMPENDIUM/ 2006_7compendium.html
38. Mathews DH Sabina J Zuker M Turner DH Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure J Mol Biol 1999/05/18 1999, 288(5):911-940. 10329189
39. Zuker M Mfold web server for nucleic acid folding and hybridization prediction Nucleic Acids Res 2003/06/26 2003, 31(13):3406-3415. 169194 12824337
40. Strappe PM Hampton DW Brown D Cachon-Gonzalez B Caldwell M Fawcett JW Lever AM Identification of unique reciprocal and non reciprocal cross packaging relationships between HIV-1, HIV-2 and SIV reveals an efficient SIV/HIV-2 lentiviral vector system with highly favourable features for in vivo testing and clinical usage Retrovirology 2005, 2:55. 1253535 16168051
41. Damgaard CK Andersen ES Knudsen B Gorodkin J Kjems J RNA interactions in the 5′ region of the HIV-1 genome J Mol Biol 2004/02/06 2004, 336(2):369-379. 14757051
42. Kasprzak W Bindewald E Shapiro BA Structural polymorphism of the HIV-1 leader region explored by computational methods Nucleic Acids Res 2005/ 12/24 2005, 33(22):7151-7163. 1322270 16371347
43. Laughrea M Shen N Jette L Wainberg MA Variant effects of non-native kissing-loop hairpin palindromes on HIV replication and HIV RNA dimerization: Role of stem-loop B in HIV replication and HIV RNA dimerization Biochemistry 1999/01/16 1999, 38(1):226-234. 9890902
44. Shen N Jette L Liang C Wainberg MA Laughrea M Impact of human immunodeficiency virus type 1 RNA dimerization on viral infectivity and of stem-loop B on RNA dimerization and reverse transcription and dissociation of dimerization from packaging J Virol 2000, 74(12):5729-5735. 112063 10823883
45. Shen N Jette L Wainberg MA Laughrea M Role of stem B, loop B, and nucleotides next to the primer binding site and the kissing-loop domain in human immunodeficiency virus type 1 replication and genomic-RNA dimerization J Virol 2001/10/03 2001, 75(21):10543-10549. 114635 11581429
46. Clever JL Wong ML Parslow TG Requirements for kissing-loop-mediated dimerization of human immunodeficiency virus RNA J Virol 1996/09/01 1996, 70(9):5902-5908. 190608 8709210
47. Mujeeb A Ulyanov NB Georgantis S Smirnov I Chung J Parslow TG James TL Nucleocapsid protein-mediated maturation of dimer initiation complex of full-length SL1 stemloop of HIV-1: Sequence effects and mechanism of RNA refolding Nucleic Acids Res 2007/03/08 2007, 35(6):2026-2034. 1874624 17341460
48. Sun X Zhang Q Al-Hashimi HM Resolving fast and slow motions in the internal loop containing stem-loop 1 of HIV-1 that are modulated by Mg2+ binding: Role in the kissing-duplex structural transition Nucleic Acids Res 2007/02/22 2007, 35(5):1698-1713 1865058 17311812
49. Takahashi KI Baba S Chattopadhyay P Koyanagi Y Yamamoto N Takaku H Kawai G Structural requirement for the two-step dimerization of human immunodeficiency virus type 1 genome RNA 2000/02/11 2000, 6(1):96-102. 1369897 10668802
50. Whitney JB Wainberg MA Impaired RNA incorporation and dimerization in live attenuated leader-variants of SIVmac239 Retrovirology 2006/12/23 2006, 3:96. 1766366 17184529
51. Whitney JB Wainberg MA Recovery of fitness of a live attenuated simian immunodeficiency virus through compensation in both the coding and non-coding regions of the viral genome Retrovirology 2007/07/05 2007, 4:44. 1934378 17608929
52. Moore MD Fu W Nikolaitchik O Chen J Ptak RG Hu WS Dimer initiation signal of human immunodeficiency virus type 1: Its role in partner selection during RNA copackaging and its effects on recombination J Virol 2007/02/03 2007, 81(8):4002-4011. 1866129 17267488
53. Strappe PM Greatorex J Thomas J Biswas P McCann E Lever AM The packaging signal of simian immunodeficiency virus is upstream of the major splice donor at a distance from the RNA cap site similar to that of human immunodeficiency virus types 1 and 2 J Gen Virol 2003/08/15 2003, 84(Pt 9):2423-2430. 12917463
54. De Guzman RN Wu ZR Stalling CC Pappalardo L Borer PN Summers MF Structure of the HIV-1 nucleocapsid protein bound to the SL3 psi-RNA recognition element Science 1998, 279(5349):384-388. 9430589