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It has been shown that SL1 may provide a secondary [[binding site]] for the viral Rev protein. <ref name="pmid12851400">{{cite journal | author = Gallego J | title = Rev binds specifically to a purine loop in the SL1 region of the HIV-1 leader RNA | journal = J. Biol. Chem. | volume = 278 | issue = 41 | pages = 40385–91 | year = 2003 | pmid = 12851400 | doi = 10.1074/jbc.M301041200 | author-separator = , | author2 = Greatorex J | author3 = Zhang H | display-authors = 3 | last4 = Yang | first4 = B | last5 = Arunachalam | first5 = S | last6 = Fang | first6 = J | last7 = Seamons | first7 = J | last8 = Lea | first8 = S | last9 = Pomerantz | first9 = RJ}}</ref> The Rev protein is an essential HIV regulatory protein which increases the stability and transport of the unspliced viral RNA.<ref name="pmid2784208">{{Cite pmid|2784208}}</ref>
It has been shown that SL1 may provide a secondary [[binding site]] for the viral Rev protein. <ref name="pmid12851400">{{cite journal | author = Gallego J | title = Rev binds specifically to a purine loop in the SL1 region of the HIV-1 leader RNA | journal = J. Biol. Chem. | volume = 278 | issue = 41 | pages = 40385–91 | year = 2003 | pmid = 12851400 | doi = 10.1074/jbc.M301041200 | author-separator = , | author2 = Greatorex J | author3 = Zhang H | display-authors = 3 | last4 = Yang | first4 = B | last5 = Arunachalam | first5 = S | last6 = Fang | first6 = J | last7 = Seamons | first7 = J | last8 = Lea | first8 = S | last9 = Pomerantz | first9 = RJ}}</ref> The Rev protein is an essential HIV regulatory protein which increases the stability and transport of the unspliced viral RNA.<ref name="pmid2784208">{{Cite pmid|2784208}}</ref>

{{Rfam_box|acc=HIV-1_SD|description=Human immunodeficiency virus type 1 major splice donor|abbreviation=HIV-1_SD|type=Cis-reg;|avg_length=19|avg_identity=00|ss=Published; {{PMID|18160437}}|se={{PMID|18160437}}|type=Cis-reg;}}

The '''Human immunodeficiency virus type 1 major splice donor (HIV-1 SD)''' is an [[RNA structure]] that is shown to modulate splicing efficiency of [[HIV-1]] mRNAs.

The HIV-1 SD structure consists of a highly conserved 19 nt stem-loop which was predicted within the HIV-1 5' untranslated leader and confirmed by mutagenesis.<ref>{{cite journal| last1= Abbink| first1= TE| last2= Berkhout| first2= B| title= RNA Structure Modulates Splicing Efficiency at the Human Immunodeficiency Virus Type 1 Major Splice Donor| journal= Journal of virology| volume= 82| issue= 6| pages= 3090–8| year= 2008 | pmid = 18160437| pmc= 2258995| doi= 10.1128/JVI.01479-07}}</ref>
The [[Rfam]] structure is based on a covariation model.

This element forms part of a larger [[Retroviral Psi packaging element]] in the [[HIV]] genome.

==See also==
[[Retroviral Psi packaging element]]

==References==
{{reflist|1}}

==External links==
* {{Rfam|id=HIV-1_SD|name=Human immunodeficiency virus type 1 major splice donor}}

{{DEFAULTSORT:Human Immunodeficiency Virus Type 1 Major Splice Donor}}
[[Category:Cis-regulatory RNA elements]]


{{molecular-cell-biology-stub}}


==References==
==References==

Revision as of 15:57, 31 October 2011


Human immunodeficiency virus type 1 dimerisation initiation site
Predicted secondary structure and sequence conservation of HIV-1_DIS
Identifiers
SymbolHIV-1_DIS
Alt. SymbolsRetroviral_psi
RfamRF00175
Other data
RNA type Cis-reg
Domain(s)Viruses
SOSO:0000233
PDB structuresPDBe
A 3D representation that includes the retroviral psi packaging element. This is a solution RNA structure model of the HIV-1 dimerization initiation site in the kissing-loop dimer.[1]

Retroviral Psi packaging element is a cis-acting RNA element identified in the genomes of the retroviruses Human immunodeficiency virus (HIV) [2] and Simian immunodeficiency virus (SIV). [3] It is involved in regulating the essential process of packaging the retroviral RNA genome into the viral capsid during replication.[4][5] [6][7] The final virion contains a dimer of two identical unspliced copies of the viral genome.

In HIV, the Psi element is ∼80–150 nucleotides in length, and located at the 5' end of the genome just upstream of the gag initiaion codon.[8] It has a known secondary structure composed of four hairpins called SL1 to SL4 (SL is for Stem-loop) which are connected by relatively short linkers. All four stem loops are important for genome packaging and each of the stem loops SL1 [8] , SL2 [9],SL3 [10][11] and SL4 [12] has been independently expressed and structurally characterised.

Stem-loop SL1 (also refered to as HIV-1_DIS) consists of a conserved hairpin structure with a palindromic loop sequence which was predicted and confirmed by mutagenesis.[13] This palindromic loop is known as the primary dimer initiation site (DIS) as it is believed to promote dimerization of the viral genome through formation of a “kissing dimer” intermediate. [14] The Rfam structure shown is based on a covariation model.

It has been shown that SL1 may provide a secondary binding site for the viral Rev protein. [15] The Rev protein is an essential HIV regulatory protein which increases the stability and transport of the unspliced viral RNA.[16]

Retroviral psi packaging element
Identifiers
Other data
PDB structuresPDBe

The Human immunodeficiency virus type 1 major splice donor (HIV-1 SD) is an RNA structure that is shown to modulate splicing efficiency of HIV-1 mRNAs.

The HIV-1 SD structure consists of a highly conserved 19 nt stem-loop which was predicted within the HIV-1 5' untranslated leader and confirmed by mutagenesis.[17] The Rfam structure is based on a covariation model.

This element forms part of a larger Retroviral Psi packaging element in the HIV genome.

See also

Retroviral Psi packaging element

References

  1. ^ Baba S, Takahashi K, Noguchi S, Takaku H, Koyanagi Y, Yamamoto N, Kawai G (2005). "Solution RNA structures of the HIV-1 dimerization initiation site in the kissing-loop and extended-duplex dimers". J Biochem. 138 (5): 583–92. doi:10.1093/jb/mvi158. PMID 16272570.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  2. ^ Lever A, Gottlinger H, Haseltine W, Sodroski J (1989). "Identification of a sequence required for efficient packaging of human immunodeficiency virus type 1 RNA into virions". J Virol. 63 (9): 4085–7. PMC 251012. PMID 2760989.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  3. ^ Strappe PM, Greatorex J, Thomas J, Biswas P, McCann E, Lever AM (2003). "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. 84 (9): 2423–30. doi:10.1099/vir.0.19185-0.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  4. ^ McBride MS, Panganiban AT (1997). "Position dependence of functional hairpins important for human immunodeficiency virus type 1 RNA encapsidation in vivo". J. Virol. 71 (3): 2050–8. PMC 191293. PMID 9032337.
  5. ^ McBride MS, Schwartz MD, Panganiban AT (1997). "Efficient encapsidation of human immunodeficiency virus type 1 vectors and further characterization of cis elements required for encapsidation". J. Virol. 71 (6): 4544–54. PMC 191676. PMID 9151848.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  6. ^ McBride MS, Panganiban AT (1996). "The human immunodeficiency virus type 1 encapsidation site is a multipartite RNA element composed of functional hairpin structures". J. Virol. 70 (5): 2963–73. PMC 190155. PMID 8627772.
  7. ^ Lever AM (2007). "HIV-1 RNA packaging". Adv. Pharmacol. Advances in Pharmacology. 55: 1–32. doi:10.1016/S1054-3589(07)55001-5. ISBN 9780123736109. PMID 17586311.
  8. ^ a b Lawrence DC, Stover CC, Noznitsky J, Wu Z, Summers MF (2003). "Structure of the intact stem and bulge of HIV-1 Psi-RNA stem-loop SL1". J. Mol. Biol. 326 (2): 529–42. doi:10.1016/S0022-2836(02)01305-0. PMID 12559920.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  9. ^ Amarasinghe GK, De Guzman RN, Turner RB, Chancellor KJ, Wu ZR, Summers MF (2000). "NMR structure of the HIV-1 nucleocapsid protein bound to stem-loop SL2 of the psi-RNA packaging signal. Implications for genome recognition". J. Mol. Biol. 301 (2): 491–511. doi:10.1006/jmbi.2000.3979. PMID 10926523.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  10. ^ Zeffman A, Hassard S, Varani G, Lever A (2000). "The major HIV-1 packaging signal is an extended bulged stem loop whose structure is altered on interaction with the Gag polyprotein". J Mol Biol. 297 (4): 877–93. doi:10.1006/jmbi.2000.3611. PMID 10736224.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  11. ^ Pappalardo L, Kerwood DJ, Pelczer I, Borer PN (1998). "Three-dimensional folding of an RNA hairpin required for packaging HIV-1". J. Mol. Biol. 282 (4): 801–18. doi:10.1006/jmbi.1998.2046. PMID 9743628.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  12. ^ Kerwood DJ, Cavaluzzi MJ, Borer PN (2001). "Structure of SL4 RNA from the HIV-1 packaging signal". Biochemistry. 40 (48): 14518–29. doi:10.1021/bi0111909. PMID 11724565.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  13. ^ Berkhout, B; Van Wamel, JL (1996). "Role of the DIS hairpin in replication of human immunodeficiency virus type 1". Journal of virology. 70 (10): 6723–32. PMC 190715. PMID 8794309.
  14. ^ Attention: This template ({{cite pmid}}) is deprecated. To cite the publication identified by PMID 8197162, please use {{cite journal}} with |pmid=8197162 instead.
  15. ^ Gallego J; Greatorex J; Zhang H; et al. (2003). "Rev binds specifically to a purine loop in the SL1 region of the HIV-1 leader RNA". J. Biol. Chem. 278 (41): 40385–91. doi:10.1074/jbc.M301041200. PMID 12851400. {{cite journal}}: Unknown parameter |author-separator= ignored (help)CS1 maint: unflagged free DOI (link)
  16. ^ Attention: This template ({{cite pmid}}) is deprecated. To cite the publication identified by PMID 2784208, please use {{cite journal}} with |pmid=2784208 instead.
  17. ^ Abbink, TE; Berkhout, B (2008). "RNA Structure Modulates Splicing Efficiency at the Human Immunodeficiency Virus Type 1 Major Splice Donor". Journal of virology. 82 (6): 3090–8. doi:10.1128/JVI.01479-07. PMC 2258995. PMID 18160437.


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References

See also

Human immunodeficiency virus type 1 major splice donor

Human immunodeficiency virus type 1 stem-loop 3 Psi packaging signal

Human immunodeficiency virus type 1 stem-loop 4 packaging signal

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