This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
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 arrowReprints and Permissions
Right arrow Copyright Information
Right arrow Books from ASM Press
Right arrow MicrobeWorld
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Jeeninga, R. E.
Right arrow Articles by Berkhout, B.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Jeeninga, R. E.
Right arrow Articles by Berkhout, B.

 Previous Article  |  Next Article 

Journal of Virology, April 2000, p. 3740-3751, Vol. 74, No. 8
0022-538X/00/$04.00+0
Copyright © 2000, American Society for Microbiology. All rights reserved.

Functional Differences between the Long Terminal Repeat Transcriptional Promoters of Human Immunodeficiency Virus Type 1 Subtypes A through G

Rienk E. Jeeninga, Maarten Hoogenkamp, Mercedes Armand-Ugon, Michel de Baar, Koen Verhoef, and Ben Berkhout*

Department of Human Retrovirology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands

Received 24 September 1999/Accepted 25 January 2000

The current human immunodeficiency virus type 1 (HIV-1) shows an increasing number of distinct viral subtypes, as well as viruses that are recombinants of at least two subtypes. Although no biological differences have been described so far for viruses that belong to different subtypes, there is considerable sequence variation between the different HIV-1 subtypes. The HIV-1 long terminal repeat (LTR) encodes the transcriptional promoter, and the LTR of subtypes A through G was cloned and analyzed to test if there are subtype-specific differences in gene expression. Sequence analysis demonstrated a unique LTR enhancer-promoter configuration for each subtype. Transcription assays with luciferase reporter constructs showed that all subtype LTRs are functional promoters with a low basal transcriptional activity and a high activity in the presence of the viral Tat transcriptional activator protein. All subtype LTRs responded equally well to the Tat trans activator protein of subtype B. This result suggests that there are no major differences in the mechanism of Tat-mediated trans activation among the subtypes. Nevertheless, subtype-specific differences in the activity of the basal LTR promoter were measured in different cell types. Furthermore, we measured a differential response to tumor necrosis factor alpha treatment, and the induction level correlated with the number of NF-kappa B sites in the respective LTRs, which varies from one (subtype E) to three (subtype C). In general, subtype E was found to encode the most potent LTR, and we therefore inserted the core promoter elements of subtype E in the infectious molecular clone of the LAI isolate (subtype B). This recombinant LAI-E virus exhibited a profound replication advantage compared with the original LAI virus in the SupT1 T-cell line, indicating that subtle differences in LTR promoter activity can have a significant impact on viral replication kinetics. These results suggest that there may be considerable biological differences among the HIV-1 subtypes.

* Corresponding author. Mailing address: Department of Human Retrovirology, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands. Phone: (31-20) 566 4822. Fax: (31-20) 691 6531. E-mail: b.berkhout{at}amc.uva.nl.

Journal of Virology, April 2000, p. 3740-3751, Vol. 74, No. 8
0022-538X/00/$04.00+0
Copyright © 2000, American Society for Microbiology. All rights reserved.


This article has been cited by other articles:

  • Liu, Y. P., Gruber, J., Haasnoot, J., Konstantinova, P., Berkhout, B. (2009). RNAi-mediated inhibition of HIV-1 by targeting partially complementary viral sequences. Nucleic Acids Res 37: 6194-6204 [Abstract] [Full Text]  
  • Eggink, D., Langedijk, J. P. M., Bonvin, A. M. J. J., Deng, Y., Lu, M., Berkhout, B., Sanders, R. W. (2009). Detailed Mechanistic Insights into HIV-1 Sensitivity to Three Generations of Fusion Inhibitors. J. Biol. Chem. 284: 26941-26950 [Abstract] [Full Text]  
  • Abraha, A., Nankya, I. L., Gibson, R., Demers, K., Tebit, D. M., Johnston, E., Katzenstein, D., Siddiqui, A., Herrera, C., Fischetti, L., Shattock, R. J., Arts, E. J. (2009). CCR5- and CXCR4-Tropic Subtype C Human Immunodeficiency Virus Type 1 Isolates Have a Lower Level of Pathogenic Fitness than Other Dominant Group M Subtypes: Implications for the Epidemic. J. Virol. 83: 5592-5605 [Abstract] [Full Text]  
  • Dong, C., Kwas, C., Wu, L. (2009). Transcriptional Restriction of Human Immunodeficiency Virus Type 1 Gene Expression in Undifferentiated Primary Monocytes. J. Virol. 83: 3518-3527 [Abstract] [Full Text]  
  • Bontjer, I., Land, A., Eggink, D., Verkade, E., Tuin, K., Baldwin, C., Pollakis, G., Paxton, W. A., Braakman, I., Berkhout, B., Sanders, R. W. (2009). Optimization of Human Immunodeficiency Virus Type 1 Envelope Glycoproteins with V1/V2 Deleted, Using Virus Evolution. J. Virol. 83: 368-383 [Abstract] [Full Text]  
  • Waleria-Aleixo, A., Martins, A. N., Arruda, M. B., Brindeiro, R. M., Da-Silva, R. M., Nobre, F. F., Greco, D. B., Tanuri, A. (2008). Drug Resistance Mutation Profile and Accumulation Kinetics in Human Immunodeficiency Virus-Positive Individuals Infected with Subtypes B and F Failing Highly Active Antiretroviral Therapy Are Influenced by Different Viral Codon Usage Patterns. Antimicrob. Agents Chemother. 52: 4497-4502 [Abstract] [Full Text]  
  • Sanders, R. W., Hsu, S.-T. D., van Anken, E., Liscaljet, I. M., Dankers, M., Bontjer, I., Land, A., Braakman, I., Bonvin, A. M.J.J., Berkhout, B. (2008). Evolution Rescues Folding of Human Immunodeficiency Virus-1 Envelope Glycoprotein GP120 Lacking a Conserved Disulfide Bond. Mol. Biol. Cell 19: 4707-4716 [Abstract] [Full Text]  
  • van Anken, E., Sanders, R. W., Liscaljet, I. M., Land, A., Bontjer, I., Tillemans, S., Nabatov, A. A., Paxton, W. A., Berkhout, B., Braakman, I. (2008). Only Five of 10 Strictly Conserved Disulfide Bonds Are Essential for Folding and Eight for Function of the HIV-1 Envelope Glycoprotein. Mol. Biol. Cell 19: 4298-4309 [Abstract] [Full Text]  
  • Liu, Y. P., Haasnoot, J., ter Brake, O., Berkhout, B., Konstantinova, P. (2008). Inhibition of HIV-1 by multiple siRNAs expressed from a single microRNA polycistron. Nucleic Acids Res 36: 2811-2824 [Abstract] [Full Text]  
  • Mahlknecht, U., Dichamp, I., Varin, A., Van Lint, C., Herbein, G. (2008). NF-{kappa}B-dependent control of HIV-1 transcription by the second coding exon of Tat in T cells. J. Leukoc. Biol. 83: 718-727 [Abstract] [Full Text]  
  • Das, A. T., Klaver, B., Harwig, A., Vink, M., Ooms, M., Centlivre, M., Berkhout, B. (2007). Construction of a Doxycycline-Dependent Simian Immunodeficiency Virus Reveals a Nontranscriptional Function of Tat in Viral Replication. J. Virol. 81: 11159-11169 [Abstract] [Full Text]  
  • Liu, Y. P., Haasnoot, J., Berkhout, B. (2007). Design of extended short hairpin RNAs for HIV-1 inhibition. Nucleic Acids Res 35: 5683-5693 [Abstract] [Full Text]  
  • Das, A. T., Harwig, A., Vrolijk, M. M., Berkhout, B. (2007). The TAR Hairpin of Human Immunodeficiency Virus Type 1 Can Be Deleted When Not Required for Tat-Mediated Activation of Transcription. J. Virol. 81: 7742-7748 [Abstract] [Full Text]  
  • Oskarsson, T., Hreggvidsdottir, H. S., Agnarsdottir, G., Matthiasdottir, S., Ogmundsdottir, M. H., Jonsson, S. R., Georgsson, G., Ingvarsson, S., Andresson, O. S., Andresdottir, V. (2007). Duplicated Sequence Motif in the Long Terminal Repeat of Maedi-Visna Virus Extends Cell Tropism and Is Associated with Neurovirulence. J. Virol. 81: 4052-4057 [Abstract] [Full Text]  
  • Song, R. J., Chenine, A.-L., Rasmussen, R. A., Ruprecht, C. R., Mirshahidi, S., Grisson, R. D., Xu, W., Whitney, J. B., Goins, L. M., Ong, H., Li, P.-L., Shai-Kobiler, E., Wang, T., McCann, C. M., Zhang, H., Wood, C., Kankasa, C., Secor, W. E., McClure, H. M., Strobert, E., Else, J. G., Ruprecht, R. M. (2006). Molecularly Cloned SHIV-1157ipd3N4: a Highly Replication- Competent, Mucosally Transmissible R5 Simian-Human Immunodeficiency Virus Encoding HIV Clade C env.. J. Virol. 80: 8729-8738 [Abstract] [Full Text]  
  • van Opijnen, T., Boerlijst, M. C., Berkhout, B. (2006). Effects of random mutations in the human immunodeficiency virus type 1 transcriptional promoter on viral fitness in different host cell environments.. J. Virol. 80: 6678-6685 [Abstract] [Full Text]  
  • Hidalgo-Estevez, A. M., Gonzalez, E., Punzon, C., Fresno, M. (2006). Human immunodeficiency virus type 1 Tat increases cooperation between AP-1 and NFAT transcription factors in T cells. J. Gen. Virol. 87: 1603-1612 [Abstract] [Full Text]  
  • Imai, K., Okamoto, T. (2006). Transcriptional Repression of Human Immunodeficiency Virus Type 1 by AP-4. J. Biol. Chem. 281: 12495-12505 [Abstract] [Full Text]  
  • Eberhardy, S. R., Goncalves, J., Coelho, S., Segal, D. J., Berkhout, B., Barbas, C. F. III (2006). Inhibition of Human Immunodeficiency Virus Type 1 Replication with Artificial Transcription Factors Targeting the Highly Conserved Primer-Binding Site. J. Virol. 80: 2873-2883 [Abstract] [Full Text]  
  • Rizzi, C., Crippa, M. P., Jeeninga, R. E., Berkhout, B., Blasi, F., Poli, G., Alfano, M. (2006). Pertussis Toxin B-Oligomer Suppresses IL-6 Induced HIV-1 and Chemokine Expression in Chronically Infected U1 Cells via Inhibition of Activator Protein 1. J. Immunol. 176: 999-1006 [Abstract] [Full Text]  
  • Konstantinova, P., de Haan, P., Das, A. T., Berkhout, B. (2006). Hairpin-induced tRNA-mediated (HITME) recombination in HIV-1.. Nucleic Acids Res 34: 2206-2218 [Abstract] [Full Text]  
  • Ghaffari, G., Tuttle, D. L., Briggs, D., Burkhardt, B. R., Bhatt, D., Andiman, W. A., Sleasman, J. W., Goodenow, M. M. (2005). Complex Determinants in Human Immunodeficiency Virus Type 1 Envelope gp120 Mediate CXCR4-Dependent Infection of Macrophages. J. Virol. 79: 13250-13261 [Abstract] [Full Text]  
  • Desfosses, Y., Solis, M., Sun, Q., Grandvaux, N., Van Lint, C., Burny, A., Gatignol, A., Wainberg, M. A., Lin, R., Hiscott, J. (2005). Regulation of Human Immunodeficiency Virus Type 1 Gene Expression by Clade-Specific Tat Proteins. J. Virol. 79: 9180-9191 [Abstract] [Full Text]  
  • Chen, J., Malcolm, T., Estable, M. C., Roeder, R. G., Sadowski, I. (2005). TFII-I Regulates Induction of Chromosomally Integrated Human Immunodeficiency Virus Type 1 Long Terminal Repeat in Cooperation with USF. J. Virol. 79: 4396-4406 [Abstract] [Full Text]  
  • Lemieux, A.-M., Pare, M.-E., Audet, B., Legault, E., Lefort, S., Boucher, N., Landry, S., van Opijnen, T., Berkhout, B., Naghavi, M. H., Tremblay, M. J., Barbeau, B. (2004). T-cell Activation Leads to Poor Activation of the HIV-1 Clade E Long Terminal Repeat and Weak Association of Nuclear Factor-{kappa}B and NFAT with Its Enhancer Region. J. Biol. Chem. 279: 52949-52960 [Abstract] [Full Text]  
  • Grisson, R. D., Chenine, A.-L., Yeh, L.-Y., He, J., Wood, C., Bhat, G. J., Xu, W., Kankasa, C., Ruprecht, R. M. (2004). Infectious Molecular Clone of a Recently Transmitted Pediatric Human Immunodeficiency Virus Clade C Isolate from Africa: Evidence of Intraclade Recombination. J. Virol. 78: 14066-14069 [Abstract] [Full Text]  
  • van Opijnen, T., Kamoschinski, J., Jeeninga, R. E., Berkhout, B. (2004). The Human Immunodeficiency Virus Type 1 Promoter Contains a CATA Box Instead of a TATA Box for Optimal Transcription and Replication. J. Virol. 78: 6883-6890 [Abstract] [Full Text]  
  • Siddappa, N. B., Dash, P. K., Mahadevan, A., Jayasuryan, N., Hu, F., Dice, B., Keefe, R., Satish, K. S., Satish, B., Sreekanthan, K., Chatterjee, R., Venu, K., Satishchandra, P., Ravi, V., Shankar, S. K., Shankarappa, R., Ranga, U. (2004). Identification of Subtype C Human Immunodeficiency Virus Type 1 by Subtype-Specific PCR and Its Use in the Characterization of Viruses Circulating in the Southern Parts of India. J. Clin. Microbiol. 42: 2742-2751 [Abstract] [Full Text]  
  • van Opijnen, T., Jeeninga, R. E., Boerlijst, M. C., Pollakis, G. P., Zetterberg, V., Salminen, M., Berkhout, B. (2004). Human Immunodeficiency Virus Type 1 Subtypes Have a Distinct Long Terminal Repeat That Determines the Replication Rate in a Host-Cell-Specific Manner. J. Virol. 78: 3675-3683 [Abstract] [Full Text]  
  • Pollakis, G., Abebe, A., Kliphuis, A., Chalaby, M. I. M., Bakker, M., Mengistu, Y., Brouwer, M., Goudsmit, J., Schuitemaker, H., Paxton, W. A. (2004). Phenotypic and Genotypic Comparisons of CCR5- and CXCR4-Tropic Human Immunodeficiency Virus Type 1 Biological Clones Isolated from Subtype C-Infected Individuals. J. Virol. 78: 2841-2852 [Abstract] [Full Text]  
  • HUTHOFF, H., GIRARD, F., WIJMENGA, S. S., BERKHOUT, B. (2004). Evidence for a base triple in the free HIV-1 TAR RNA. RNA 10: 412-423 [Abstract] [Full Text]  
  • Rohr, O., Marban, C., Aunis, D., Schaeffer, E. (2003). Regulation of HIV-1 gene transcription: from lymphocytes to microglial cells. J. Leukoc. Biol. 74: 736-749 [Abstract] [Full Text]  
  • Kulinski, T., Olejniczak, M., Huthoff, H., Bielecki, L., Pachulska-Wieczorek, K., Das, A. T., Berkhout, B., Adamiak, R. W. (2003). The Apical Loop of the HIV-1 TAR RNA Hairpin Is Stabilized by a Cross-loop Base Pair. J. Biol. Chem. 278: 38892-38901 [Abstract] [Full Text]  
  • Wray, G. A., Hahn, M. W., Abouheif, E., Balhoff, J. P., Pizer, M., Rockman, M. V., Romano, L. A. (2003). The Evolution of Transcriptional Regulation in Eukaryotes. Mol Biol Evol 20: 1377-1419 [Abstract] [Full Text]  
  • Vidricaire, G., Tardif, M. R., Tremblay, M. J. (2003). The Low Viral Production in Trophoblastic Cells Is Due to a High Endocytic Internalization of the Human Immunodeficiency Virus Type 1 and Can Be Overcome by the Pro-inflammatory Cytokines Tumor Necrosis Factor-alpha and Interleukin-1. J. Biol. Chem. 278: 15832-15841 [Abstract] [Full Text]  
  • Tapia, N., Franco, S., Puig-Basagoiti, F., Menendez, C., Alonso, P. L., Mshinda, H., Clotet, B., Saiz, J. C., Martinez, M. A. (2003). Influence of human immunodeficiency virus type 1 subtype on mother-to-child transmission. J. Gen. Virol. 84: 607-613 [Abstract] [Full Text]  
  • Andersen, E. S., Jeeninga, R. E., Damgaard, C. K., Berkhout, B., Kjems, J. (2003). Dimerization and Template Switching in the 5' Untranslated Region between Various Subtypes of Human Immunodeficiency Virus Type 1. J. Virol. 77: 3020-3030 [Abstract] [Full Text]  
  • Spira, S., Wainberg, M. A., Loemba, H., Turner, D., Brenner, B. G. (2003). Impact of clade diversity on HIV-1 virulence, antiretroviral drug sensitivity and drug resistance. J Antimicrob Chemother 51: 229-240 [Abstract] [Full Text]  
  • Ball, S. C., Abraha, A., Collins, K. R., Marozsan, A. J., Baird, H., Quinones-Mateu, M. E., Penn-Nicholson, A., Murray, M., Richard, N., Lobritz, M., Zimmerman, P. A., Kawamura, T., Blauvelt, A., Arts, E. J. (2002). Comparing the Ex Vivo Fitness of CCR5-Tropic Human Immunodeficiency Virus Type 1 Isolates of Subtypes B and C. J. Virol. 77: 1021-1038 [Abstract] [Full Text]  
  • Quivy, V., Adam, E., Collette, Y., Demonte, D., Chariot, A., Vanhulle, C., Berkhout, B., Castellano, R., de Launoit, Y., Burny, A., Piette, J., Bours, V., Van Lint, C. (2002). Synergistic Activation of Human Immunodeficiency Virus Type 1 Promoter Activity by NF-{kappa}B and Inhibitors of Deacetylases: Potential Perspectives for the Development of Therapeutic Strategies. J. Virol. 76: 11091-11103 [Abstract] [Full Text]  
  • Marzio, G., Vink, M., Verhoef, K., de Ronde, A., Berkhout, B. (2002). Efficient Human Immunodeficiency Virus Replication Requires a Fine-Tuned Level of Transcription. J. Virol. 76: 3084-3088 [Abstract] [Full Text]  
  • Hudgens, M. G., Longini, I. M. Jr., Vanichseni, S., Hu, D. J., Kitayaporn, D., Mock, P. A., Halloran, M. E., Satten, G. A., Choopanya, K., Mastro, T. D. (2002). Subtype-specific Transmission Probabilities for Human Immunodeficiency Virus Type 1 among Injecting Drug Users in Bangkok, Thailand. Am J Epidemiol 155: 159-168 [Abstract] [Full Text]  
  • Ndung'u, T., Renjifo, B., Essex, M. (2001). Construction and Analysis of an Infectious Human Immunodeficiency Virus Type 1 Subtype C Molecular Clone. J. Virol. 75: 4964-4972 [Abstract] [Full Text]  
  • Naghavi, M. H., Estable, M. C., Schwartz, S., Roeder, R. G., Vahlne, A. (2001). Upstream stimulating factor affects human immunodeficiency virus type 1 (HIV-1) long terminal repeat-directed transcription in a cell-specific manner, independently of the HIV-1 subtype and the core-negative regulatory element. J. Gen. Virol. 82: 547-559 [Abstract] [Full Text]  
  • Alfano, M., Vallanti, G., Biswas, P., Bovolenta, C., Vicenzi, E., Mantelli, B., Pushkarsky, T., Rappuoli, R., Lazzarin, A., Bukrinsky, M., Poli, G. (2001). The Binding Subunit of Pertussis Toxin Inhibits HIV Replication in Human Macrophages and Virus Expression in Chronically Infected Promonocytic U1 Cells. J. Immunol. 166: 1863-1870 [Abstract] [Full Text]  
  • Verhoef, K., Marzio, G., Hillen, W., Bujard, H., Berkhout, B. (2001). Strict Control of Human Immunodeficiency Virus Type 1 Replication by a Genetic Switch: Tet for Tat. J. Virol. 75: 979-987 [Abstract] [Full Text]  
  • Alfano, M., Pushkarsky, T., Poli, G., Bukrinsky, M. (2000). The B-Oligomer of Pertussis Toxin Inhibits Human Immunodeficiency Virus Type 1 Replication at Multiple Stages. J. Virol. 74: 8767-8770 [Abstract] [Full Text]  
  • Marzio, G., Verhoef, K., Vink, M., Berkhout, B. (2001). In vitro evolution of a highly replicating, doxycycline-dependent HIV for applications in vaccine studies. Proc. Natl. Acad. Sci. USA 98: 6342-6347 [Abstract] [Full Text]  


Copyright © 2009 by the American Society for Microbiology.   For an alternate route to Journals.ASM.org, visit: http://intl-journals.asm.org | More Info»