JBC

HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS
QUICK SEARCH:   [advanced]


     

Originally published In Press as doi:10.1074/jbc.M102860200 on June 29, 2001

J. Biol. Chem., Vol. 276, Issue 39, 36482-36492, September 28, 2001
This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow All Versions of this Article:
276/39/36482    most recent
M102860200v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Right arrow Citation Map
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrow reprints & permissions
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Balakrishnan, M.
Right arrow Articles by Bambara, R. A.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Balakrishnan, M.
Right arrow Articles by Bambara, R. A.

The Kissing Hairpin Sequence Promotes Recombination within the HIV-I 5' Leader Region*

Mini BalakrishnanDagger , Philip J. FayDagger , and Robert A. BambaraDagger §

From the Dagger  Department of Biochemistry and Biophysics and § Cancer Center, University of Rochester Medical Center, Rochester, New York 14642

The role of RNA-RNA template interactions in facilitating recombination during reverse transcription of minus strand DNA has been examined. The tested hypothesis is that template switching by reverse transcriptase is promoted at sites where homologous regions of two RNAs are brought in close proximity via stable intertemplate interactions. Frequency and distribution of template switching between homologous donor and acceptor RNAs were examined within the human immunodeficiency virus type I (HIV-I) 5'-untranslated region (UTR) containing the dimer initiation sequence (DIS). Results were compared with control nondimerizing templates from the pol region. The dimerizing UTR templates displayed a 4-fold higher transfer efficiency than the control. A striking 53% of transfers in the UTR mapped near the DIS, of which two-thirds occurred immediately 5' to this sequence. In the UTR template, deletion of the DIS hairpin disrupted template dimerization and caused a 4-fold drop in transfer efficiency. Insertion of the DIS within the pol template increased both dimerization and transfer efficiency. Transfer distributions revealed that in both sets of templates, DIS-induced dimerization increased the efficiency of transfers across the whole template, with the transfers peaking around the dimerization site. Overall, these results suggest that template dimerization facilitated by the unique geometry of the DIS-promoted kissing interactions effectively promotes recombination within the HIV-I 5'-UTR.

* This work was supported by National Institutes of Health Grant GM 49573 (to R. A. B. and P. J. F.).The costs of publication of this article were defrayed in part by the payment of page charges. The article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

To whom correspondence should be addressed: Dept. of Biochemistry and Biophysics, Box 712, University of Rochester Medical Center, 601 Elmwood Ave., Rochester NY 14642. Tel.: 716-275-2764; Fax: 716-271-2683; E-mail: Robert_bambara@urmc.rochester.edu.

Copyright © 2001 by The American Society for Biochemistry and Molecular Biology, Inc.


This article has been cited by other articles:


Home page
 J. Biol. Chem.Home page
L. Gao, M. N. Hanson, M. Balakrishnan, P. L. Boyer, B. P. Roques, S. H. Hughes, B. Kim, and R. A. Bambara
Apparent Defects in Processive DNA Synthesis, Strand Transfer, and Primer Elongation of Met-184 Mutants of HIV-1 Reverse Transcriptase Derive Solely from a dNTP Utilization Defect
J. Biol. Chem., April 4, 2008; 283(14): 9196 - 9205.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
K. L. Jones, S. Sonza, and J. Mak
Primary T-lymphocytes rescue the replication of HIV-1 DIS RNA mutants in part by facilitating reverse transcription
Nucleic Acids Res., March 1, 2008; 36(5): 1578 - 1588.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
M. Song, V. P. Basu, M. N. Hanson, B. P. Roques, and R. A. Bambara
Proximity and Branch Migration Mechanisms in HIV-1 Minus Strand Strong Stop DNA Transfer
J. Biol. Chem., February 8, 2008; 283(6): 3141 - 3150.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
S. Bernacchi, S. Freisz, C. Maechling, B. Spiess, R. Marquet, P. Dumas, and E. Ennifar
Aminoglycoside binding to the HIV-1 RNA dimerization initiation site: thermodynamics and effect on the kissing-loop to duplex conversion
Nucleic Acids Res., December 18, 2007; 35(21): 7128 - 7139.
[Abstract] [Full Text] [PDF]

Home page
 RNAHome page
L. Sinck, D. Richer, J. Howard, M. Alexander, D. F.J. Purcell, R. Marquet, and J.-C. Paillart
In vitro dimerization of human immunodeficiency virus type 1 (HIV-1) spliced RNAs
RNA, December 1, 2007; 13(12): 2141 - 2150.
[Abstract] [Full Text] [PDF]

Home page
 J. Virol.Home page
N. Laham-Karam and E. Bacharach
Transduction of Human Immunodeficiency Virus Type 1 Vectors Lacking Encapsidation and Dimerization Signals
J. Virol., October 1, 2007; 81(19): 10687 - 10698.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
V. Purohit, B. P. Roques, B. Kim, and R. A. Bambara
Mechanisms That Prevent Template Inactivation by HIV-1 Reverse Transcriptase RNase H Cleavages
J. Biol. Chem., April 27, 2007; 282(17): 12598 - 12609.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
V. N. Minin, K. S. Dorman, F. Fang, and M. A. Suchard
Phylogenetic Mapping of Recombination Hotspots in Human Immunodeficiency Virus via Spatially Smoothed Change-Point Processes
Genetics, April 1, 2007; 175(4): 1773 - 1785.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
L. Gao, M. Balakrishnan, B. P. Roques, and R. A. Bambara
Insights into the Multiple Roles of Pausing in HIV-1 Reverse Transcriptase-promoted Strand Transfers
J. Biol. Chem., March 2, 2007; 282(9): 6222 - 6231.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
D. J. Operario, M. Balakrishnan, R. A. Bambara, and B. Kim
Reduced dNTP Interaction of Human Immunodeficiency Virus Type 1 Reverse Transcriptase Promotes Strand Transfer
J. Biol. Chem., October 27, 2006; 281(43): 32113 - 32121.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
H. A. Baird, R. Galetto, Y. Gao, E. Simon-Loriere, M. Abreha, J. Archer, J. Fan, D. L. Robertson, E. J. Arts, and M. Negroni
Sequence determinants of breakpoint location during HIV-1 intersubtype recombination
Nucleic Acids Res., October 6, 2006; (2006) gkl669v3.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
M. Song, M. Balakrishnan, Y. Chen, B. P. Roques, and R. A. Bambara
Stimulation of HIV-1 Minus Strand Strong Stop DNA Transfer by Genomic Sequences 3' of the Primer Binding Site
J. Biol. Chem., August 25, 2006; 281(34): 24227 - 24235.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
V. K. Jamburuthugoda, P. Chugh, and B. Kim
Modification of Human Immunodeficiency Virus Type 1 Reverse Transcriptase to Target Cells with Elevated Cellular dNTP Concentrations
J. Biol. Chem., May 12, 2006; 281(19): 13388 - 13395.
[Abstract] [Full Text] [PDF]

Home page
 J. Virol.Home page
C. Lanciault and J. J. Champoux
Pausing during Reverse Transcription Increases the Rate of Retroviral Recombination
J. Virol., March 1, 2006; 80(5): 2483 - 2494.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
R. Galetto, V. Giacomoni, M. Veron, and M. Negroni
Dissection of a Circumscribed Recombination Hot Spot in HIV-1 after a Single Infectious Cycle
J. Biol. Chem., February 3, 2006; 281(5): 2711 - 2720.
[Abstract] [Full Text] [PDF]

Home page
 J. Virol.Home page
P. Buxton, G. Tachedjian, and J. Mak
Analysis of the Contribution of Reverse Transcriptase and Integrase Proteins to Retroviral RNA Dimer Conformation
J. Virol., May 15, 2005; 79(10): 6338 - 6348.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
C. Lanciault and J. J. Champoux
Effects of Unpaired Nucleotides within HIV-1 Genomic Secondary Structures on Pausing and Strand Transfer
J. Biol. Chem., January 28, 2005; 280(4): 2413 - 2423.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
R. Galetto, A. Moumen, V. Giacomoni, M. Veron, P. Charneau, and M. Negroni
The Structure of HIV-1 Genomic RNA in the gp120 Gene Determines a Recombination Hot Spot in Vivo
J. Biol. Chem., August 27, 2004; 279(35): 36625 - 36632.
[Abstract] [Full Text] [PDF]

Home page
 J. Virol.Home page
R. Wierzchoslawski, A. Dzianott, and J. Bujarski
Dissecting the Requirement for Subgenomic Promoter Sequences by RNA Recombination of Brome Mosaic Virus In Vivo: Evidence for Functional Separation of Transcription and Recombination
J. Virol., August 15, 2004; 78(16): 8552 - 8564.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
J. G. Mikkelsen, S. V. Rasmussen, and F. S. Pedersen
Complementarity-directed RNA dimer-linkage promotes retroviral recombination in vivo
Nucleic Acids Res., January 9, 2004; 32(1): 102 - 114.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
R. H. Roda, M. Balakrishnan, M. N. Hanson, B. M. Wohrl, S. F. J. Le Grice, B. P. Roques, R. J. Gorelick, and R. A. Bambara
Role of the Reverse Transcriptase, Nucleocapsid Protein, and Template Structure in the Two-step Transfer Mechanism in Retroviral Recombination
J. Biol. Chem., August 22, 2003; 278(34): 31536 - 31546.
[Abstract] [Full Text] [PDF]

Home page
 J. Virol.Home page
R. Wierzchoslawski, A. Dzianott, S. Kunimalayan, and J. J. Bujarski
A Transcriptionally Active Subgenomic Promoter Supports Homologous Crossovers in a Plus-Strand RNA Virus
J. Virol., June 15, 2003; 77(12): 6769 - 6776.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
S. S. Derebail, M. J. Heath, and J. J. DeStefano
Evidence for the Differential Effects of Nucleocapsid Protein on Strand Transfer in Various Regions of the HIV Genome
J. Biol. Chem., April 25, 2003; 278(18): 15702 - 15712.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
A. Moumen, L. Polomack, T. Unge, M. Veron, H. Buc, and M. Negroni
Evidence for a Mechanism of Recombination during Reverse Transcription Dependent on the Structure of the Acceptor RNA
J. Biol. Chem., April 25, 2003; 278(18): 15973 - 15982.
[Abstract] [Full Text] [PDF]

Home page
 J. Virol.Home page
M. Balakrishnan, B. P. Roques, P. J. Fay, and R. A. Bambara
Template Dimerization Promotes an Acceptor Invasion-Induced Transfer Mechanism during Human Immunodeficiency Virus Type 1 Minus-Strand Synthesis
J. Virol., April 15, 2003; 77(8): 4710 - 4721.
[Abstract] [Full Text] [PDF]

Home page
 J. Virol.Home page
E. S. Andersen, R. E. Jeeninga, C. K. Damgaard, B. Berkhout, and J. Kjems
Dimerization and Template Switching in the 5' Untranslated Region between Various Subtypes of Human Immunodeficiency Virus Type 1
J. Virol., March 1, 2003; 77(5): 3020 - 3030.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
Y. Chen, M. Balakrishnan, B. P. Roques, P. J. Fay, and R. A. Bambara
Mechanism of Minus Strand Strong Stop Transfer in HIV-1 Reverse Transcription
J. Biol. Chem., February 28, 2003; 278(10): 8006 - 8017.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
E. Ennifar, J.-C. Paillart, R. Marquet, B. Ehresmann, C. Ehresmann, P. Dumas, and P. Walter
HIV-1 RNA Dimerization Initiation Site Is Structurally Similar to the Ribosomal A Site and Binds Aminoglycoside Antibiotics
J. Biol. Chem., January 17, 2003; 278(4): 2723 - 2730.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
R. H. Roda, M. Balakrishnan, J. K. Kim, B. P. Roques, P. J. Fay, and R. A. Bambara
Strand Transfer Occurs in Retroviruses by a Pause-initiated Two-step Mechanism
J. Biol. Chem., November 27, 2002; 277(49): 46900 - 46911.
[Abstract] [Full Text] [PDF]

Home page
 J. Virol.Home page
J. Zhuang, A. E. Jetzt, G. Sun, H. Yu, G. Klarmann, Y. Ron, B. D. Preston, and J. P. Dougherty
Human Immunodeficiency Virus Type 1 Recombination: Rate, Fidelity, and Putative Hot Spots
J. Virol., October 11, 2002; 76(22): 11273 - 11282.
[Abstract] [Full Text] [PDF]

Home page
 J. Gen. Virol.Home page
A. M. G. Dirac, H. Huthoff, J. Kjems, and B. Berkhout
Requirements for RNA heterodimerization of the human immunodeficiency virus type 1 (HIV-1) and HIV-2 genomes
J. Gen. Virol., October 1, 2002; 83(10): 2533 - 2542.
[Abstract] [Full Text] [PDF]

Home page
 J. Virol.Home page
J. B. Whitney, M. Oliveira, M. Detorio, Y. Guan, and M. A. Wainberg
The M184V Mutation in Reverse Transcriptase Can Delay Reversion of Attenuated Variants of Simian Immunodeficiency Virus
J. Virol., July 29, 2002; 76(17): 8958 - 8962.
[Abstract] [Full Text] [PDF]

Home page
 J. Virol.Home page
W. An and A. Telesnitsky
Effects of Varying Sequence Similarity on the Frequency of Repeat Deletion during Reverse Transcription of a Human Immunodeficiency Virus Type 1 Vector
J. Virol., June 27, 2002; 76(15): 7897 - 7902.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
B. Berkhout, M. Ooms, N. Beerens, H. Huthoff, E. Southern, and K. Verhoef
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., May 24, 2002; 277(22): 19967 - 19975.
[Abstract] [Full Text] [PDF]


HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS
 All ASBMB Journals   Molecular and Cellular Proteomics 
 Journal of Lipid Research   ASBMB Today 
Copyright © 2001 by the American Society for Biochemistry and Molecular Biology.