Identification of HIV-1, X4, R5, and R5 subgroup genetic signatures in the viral promoter, Tat, and Vpr

2021 ◽  
Author(s):  
Benjamas Aiamkitsumrit
Keyword(s):  
Viral Promoter ◽  
Genetic Signatures ◽  
Hiv 1

scholarly journals A stronger transcription regulatory circuit of HIV-1C drives the rapid establishment of latency with implications for the direct involvement of Tat

2020 ◽  
Author(s):  
Sutanuka Chakraborty ◽  
Manisha Kabi ◽  
Udaykumar Ranga
Keyword(s):  
Transcription Factor ◽  
Viral Infection ◽  
Viral Vectors ◽  
Transcription Factor Binding ◽  
Jurkat Cells ◽  
Subtype C ◽  
Viral Promoter ◽  
Factor Binding ◽  
Transcriptional Silence ◽  
Hiv 1

AbstractThe magnitude of transcription factor binding site variation emerging in HIV-1C, especially the addition of NF-κB motifs by sequence duplication, makes the examination of transcriptional silence challenging. How can HIV-1 establish and maintain latency despite having a strong LTR? We constructed panels of sub-genomic reporter viral vectors with varying copy numbers of NF-κB motifs (0 to 4 copies) and examined the profile of latency establishment in Jurkat cells. We found surprisingly that the stronger the viral promoter, the faster the latency establishment. Importantly, at the time of commitment to latency and subsequent points, Tat levels in the cell were not limiting. Using highly sensitive strategies, we demonstrate the presence of Tat in the latent cell, recruited to the latent LTR. Our data allude, for the first time, to Tat establishing a negative feedback loop during the late phases of viral infection, leading to the rapid silencing of the viral promoter.ImportanceOver the past 10-15 years, HIV-1C has been evolving rapidly towards gaining stronger transcriptional activity by sequence duplication of major transcription factor binding sites. The duplication of NF-κB motifs is unique and exclusive for HIV-1C, a property not shared with any of the other eight HIV-1 genetic families. What mechanism(s) does HIV-1C employ to establish and maintain transcriptional silence despite the presence of a strong promoter and a concomitant strong, positive transcriptional feedback is the primary question we attempted to address in the present manuscript. The role Tat plays in latency reversal is well established. Our work with the most common HIV-1 subtype C (HIV-1C) offers crucial leads towards Tat possessing a dual-role in serving both as transcriptional activator and repressor at different phases of the viral infection of the cell. The leads we offer through the present work have significant implications for HIV-1 cure research.

scholarly journals The evolution of regulatory elements in the emerging promoter variant strains of HIV-1

2021 ◽  
Author(s):  
Disha Bhange ◽  
Nityanand Prasad ◽  
Swati Singh ◽  
Harshit Kumar Prajapati ◽  
Shesh Prakash Maurya ◽  
...  
Keyword(s):  
Viral Latency ◽  
Regulatory Elements ◽  
The Other ◽  
Clinical Samples ◽  
Latent Reservoir ◽  
Viral Gene ◽  
Viral Promoter ◽  
Reservoir Characteristics ◽  
Hiv 1

AbstractIn a multicentric, observational, investigator-blinded, and longitudinal clinical study of 764 ART-naïve subjects, we identified nine different promoter-variant strains of HIV-1 subtype C (HIV-1C) emerging in the Indian population, with some of these variants being reported for the first time. Unlike several previous studies, our work here focuses on the evolving viral regulatory elements, not coding sequences. The emerging viral strains contain additional copies of the existing transcription factor binding sites (TFBS), including TCF-1α/LEF-1, RBEIII, AP-1, and NF-κB, created by sequence duplication. The additional TFBS are genetically diverse and may blur the distinction between the modulatory region of the promoter and the viral enhancer. In a follow-up analysis, we found trends, but not significant associations between any specific variant promoter and prognostic markers, probably because the emerging viral strains might not have established mono infections yet. Illumina sequencing of four clinical samples containing a co-infection indicated the domination of one strain over the other and establishing a stable ratio with the second strain at the follow-up time-points. Since a single promoter regulates viral gene expression and constitutes the master regulatory circuit with Tat, the acquisition of additional and variant copies of the TFBS may significantly impact viral latency and latent reservoir characteristics. Further studies are urgently warranted to understand how the diverse TFBS profiles of the viral promoter may modulate the characteristics of the latent reservoir, especially following the initiation of antiretroviral therapy.Significance StatementA unique conglomeration of TFBS enables the HIV-1 promoter to accomplish two diametrically opposite functions – transcriptional activation and transcriptional silencing. The various phases of viral latency - establishment, maintenance, and reversal - collectively determine the replication fitness of individual viral strains. A profound variation in the TFBS composition of the viral promoter may significantly alter the viral latency properties and the latent reservoir characteristics. Although the duplication of certain TFBS remains a quality unique to HIV-1C, the high-level genetic recombination of HIV-1 may promote the transfer of such molecular properties to the other HIV-1 subtypes. The emergence of several promoter-variant viral strains may make the task of a ‘functional cure’ more challenging in HIV-1C.

Association of p65 and C/EBPβ with HIV-1 LTR modulates transcription of the viral promoter

2007 ◽  
Vol 100 (5) ◽  
pp. 1210-1216 ◽  
Author(s):  
Ruma Mukerjee ◽  
Bassel E. Sawaya ◽  
Kamel Khalili ◽  
Shohreh Amini
Keyword(s):  
Viral Promoter ◽  
Hiv 1

scholarly journals Functional Incompatibility between the Generic NF-κB Motif and a Subtype-Specific Sp1III Element Drives the Formation of the HIV-1 Subtype C Viral Promoter

2016 ◽  
Vol 90 (16) ◽  
pp. 7046-7065 ◽  
Author(s):  
Anjali Verma ◽  
Pavithra Rajagopalan ◽  
Rishikesh Lotke ◽  
Rebu Varghese ◽  
Deepak Selvam ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Binding Sites ◽  
Transcription Factor Binding Sites ◽  
Subtype C ◽  
Viral Promoter ◽  
Factor Binding ◽  
The Core ◽  
Immunodeficiency Virus ◽  
Hiv 1

ABSTRACTOf the various genetic subtypes of human immunodeficiency virus types 1 and 2 (HIV-1 and HIV-2) and simian immunodeficiency virus (SIV), only in subtype C of HIV-1 is a genetically variant NF-κB binding site found at the core of the viral promoter in association with a subtype-specific Sp1III motif. How the subtype-associated variations in the core transcription factor binding sites (TFBS) influence gene expression from the viral promoter has not been examined previously. Using panels of infectious viral molecular clones, we demonstrate that subtype-specific NF-κB and Sp1III motifs have evolved for optimal gene expression, and neither of the motifs can be replaced by a corresponding TFBS variant. The variant NF-κB motif binds NF-κB with an affinity 2-fold higher than that of the generic NF-κB site. Importantly, in the context of an infectious virus, the subtype-specific Sp1III motif demonstrates a profound loss of function in association with the generic NF-κB motif. An additional substitution of the Sp1III motif fully restores viral replication, suggesting that the subtype C-specific Sp1III has evolved to function with the variant, but not generic, NF-κB motif. A change of only two base pairs in the central NF-κB motif completely suppresses viral transcription from the provirus and converts the promoter into heterochromatin refractory to tumor necrosis factor alpha (TNF-α) induction. The present work represents the first demonstration of functional incompatibility between an otherwise functional NF-κB motif and a unique Sp1 site in the context of an HIV-1 promoter. Our work provides important leads as to the evolution of the HIV-1 subtype C viral promoter with relevance for gene expression regulation and viral latency.IMPORTANCESubtype-specific genetic variations provide a powerful tool to examine how these variations offer a replication advantage to specific viral subtypes, if any. Only in subtype C of HIV-1 are two genetically distinct transcription factor binding sites positioned at the most critical location of the viral promoter. Since a single promoter regulates viral gene expression, the promoter variations can play a critical role in determining the replication fitness of the viral strains. Our work for the first time provides a scientific explanation for the presence of a unique NF-κB binding motif in subtype C, a major HIV-1 genetic family responsible for half of the global HIV-1 infections. The results offer compelling evidence that the subtype C viral promoter not only is stronger but also is endowed with a qualitative gain-of-function advantage. The genetically variant NF-κB and the Sp1III motifs may be respond differently to specific cell signal pathways, and these mechanisms must be examined.

scholarly journals Defining Differential Genetic Signatures in CXCR4- and the CCR5-Utilizing HIV-1 Co-Linear Sequences

PLoS ONE ◽  
2014 ◽  
Vol 9 (9) ◽  
pp. e107389 ◽  
Author(s):  
Benjamas Aiamkitsumrit ◽  
Will Dampier ◽  
Julio Martin-Garcia ◽  
Michael R. Nonnemacher ◽  
Vanessa Pirrone ◽  
...  
Keyword(s):  
Genetic Signatures ◽  
Hiv 1

scholarly journals An emerging and variant viral promoter of HIV-1 subtype C exhibits low-level gene expression noise

Retrovirology ◽  
2021 ◽  
Vol 18 (1) ◽  
Author(s):  
Haider Ali ◽  
Disha Bhange ◽  
Kavita Mehta ◽  
Yuvrajsinh Gohil ◽  
Harshit Kumar Prajapati ◽  
...  
Keyword(s):  
Gene Expression ◽  
Binding Sites ◽  
High Throughput Screening ◽  
Cell Activation ◽  
Viral Gene ◽  
Viral Promoter ◽  
Gene Expression Noise ◽  
Low Level ◽  
Expression Noise ◽  
Hiv 1

Abstract Background We observe the emergence of several promoter-variant viral strains in India during recent years. The variant viral promoters contain additional copies of transcription factor binding sites present in the viral modulatory region or enhancer, including RBEIII, LEF-1, Ap-1 and/or NF-κB. These sites are crucial for governing viral gene expression and latency. Here, we infer that one variant viral promoter R2N3-LTR containing two copies of RBF-2 binding sites (an RBEIII site duplication) and three copies of NF-κB motifs may demonstrate low levels of gene expression noise as compared to the canonical RN3-LTR or a different variant R2N4-LTR (a duplication of an RBEIII site and an NF-κB motif). To demonstrate this, we constructed a panel of sub-genomic viral vectors of promoter-variant LTRs co-expressing two reporter proteins (mScarlet and Gaussia luciferase) under the dual-control of Tat and Rev. We established stable pools of CEM.NKR-CCR5 cells (CEM-CCR5RL reporter cells) and evaluated reporter gene expression under different conditions of cell activation. Results The R2N3-LTR established stringent latency that was highly resistant to reversal by potent cell activators such as TNF-α or PMA, or even to a cocktail of activators, compared to the canonical RN3- or the variant R2N4-LTR. The R2N3-LTR exhibited low-level basal gene expression in the absence of cell activation that enhanced marginally but significantly when activated. In the presence of Tat and Rev, trans-complemented in the form of an infectious virus, the R2N3-LTR demonstrated gene expression at levels comparable to the wild-type viral promoter. The R2N3-LTR is responsive to Tat and Rev factors derived from viral strains representing diverse genetic subtypes. Conclusion With extremely low-level transcriptional noise, the R2N3-LTR can serve as an excellent model to examine the establishment, maintenance, and reversal of HIV-1 latency. The R2N3-LTR would also be an ideal viral promoter to develop high-throughput screening assays to identify potent latency-reversing agents since the LTR is not affected by the usual background noise of the cell.

scholarly journals The HIV-1 Tat protein recruits a ubiquitin ligase to reorganize the 7SK snRNP for transcriptional activation

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Tyler B Faust ◽  
Yang Li ◽  
Curtis W Bacon ◽  
Gwendolyn M Jang ◽  
Amit Weiss ◽  
...  
Keyword(s):  
Rna Polymerase Ii ◽  
Ubiquitin Ligase ◽  
Transcriptional Activation ◽  
Transcriptional Activity ◽  
Kinase Inhibitor ◽  
Tat Protein ◽  
Viral Promoter ◽  
Rnap Ii ◽  
Elongation Control ◽  
Hiv 1

The HIV-1 Tat protein hijacks P-TEFb kinase to activate paused RNA polymerase II (RNAP II) at the viral promoter. Tat binds additional host factors, but it is unclear how they regulate RNAP II elongation. Here, we identify the cytoplasmic ubiquitin ligase UBE2O as critical for Tat transcriptional activity. Tat hijacks UBE2O to ubiquitinate the P-TEFb kinase inhibitor HEXIM1 of the 7SK snRNP, a fraction of which also resides in the cytoplasm bound to P-TEFb. HEXIM1 ubiquitination sequesters it in the cytoplasm and releases P-TEFb from the inhibitory 7SK complex. Free P-TEFb then becomes enriched in chromatin, a process that is also stimulated by treating cells with a CDK9 inhibitor. Finally, we demonstrate that UBE2O is critical for P-TEFb recruitment to the HIV-1 promoter. Together, the data support a unique model of elongation control where non-degradative ubiquitination of nuclear and cytoplasmic 7SK snRNP pools increases P-TEFb levels for transcriptional activation.

Sign in / Sign up

Export Citation Format

Share Document