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Fujinaga K, Huang F, Peterlin BM. P-TEFb: The master regulator of transcription elongation. Mol Cell 2023; 83:393-403. [PMID: 36599353 PMCID: PMC9898187 DOI: 10.1016/j.molcel.2022.12.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 11/10/2022] [Accepted: 12/08/2022] [Indexed: 01/05/2023]
Abstract
The positive transcription elongation factor b (P-TEFb) is composed of cyclins T1 or T2 and cyclin-dependent kinase 9 that regulate the elongation phase of transcription by RNA polymerase II. By antagonizing negative elongation factors and phosphorylating the C-terminal domain of RNA polymerase II, P-TEFb facilitates the elongation and co-transcriptional processing of nascent transcripts. This step is critical for the expression of most eukaryotic genes. In growing cells, P-TEFb is regulated negatively by its reversible associations with HEXIM1/2 in the 7SK snRNP and positively by a number of transcription factors, as well as the super elongation complex. In resting cells, P-TEFb falls apart, and cyclin T1 is degraded by the proteasome. This complex regulation of P-TEFb has evolved for the precise temporal and spatial regulation of gene expression in the organism. Its dysregulation contributes to inflammatory and neoplastic conditions.
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Affiliation(s)
- Koh Fujinaga
- Departments of Medicine, Microbiology and Immunology, University of California at San Francisco, San Francisco, CA 94143, USA.
| | - Fang Huang
- Departments of Medicine, Microbiology and Immunology, University of California at San Francisco, San Francisco, CA 94143, USA
| | - B Matija Peterlin
- Departments of Medicine, Microbiology and Immunology, University of California at San Francisco, San Francisco, CA 94143, USA.
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Huang F, Feng Y, Peterlin BM, Fujinaga K. P-TEFb is degraded by Siah1/2 in quiescent cells. Nucleic Acids Res 2022; 50:5000-5013. [PMID: 35524561 PMCID: PMC9122529 DOI: 10.1093/nar/gkac291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 04/05/2022] [Accepted: 04/12/2022] [Indexed: 11/12/2022] Open
Abstract
P-TEFb, composed of CycT1 and CDK9, regulates the elongation of transcription by RNA polymerase II. In proliferating cells, it is regulated by 7SK snRNA in the 7SK snRNP complex. In resting cells, P-TEFb is absent, because CycT1 is dephosphorylated, released from CDK9 and rapidly degraded. In this study, we identified the mechanism of this degradation. We mapped the ubiquitination and degradation of free CycT1 to its N-terminal region from positions 1 to 280. This region is ubiquitinated at six lysines, where E3 ligases Siah1 and Siah2 bind and degrade these sequences. Importantly, the inhibition of Siah1/2 rescued the expression of free CycT1 in proliferating as well as resting primary cells. We conclude that Siah1/2 are the E3 ligases that bind and degrade the dissociated CycT1 in resting, terminally differentiated, anergic and/or exhausted cells.
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Affiliation(s)
- Fang Huang
- Departments of Medicine, Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Yongmei Feng
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - B Matija Peterlin
- Departments of Medicine, Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Koh Fujinaga
- Departments of Medicine, Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
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Huang F, Nguyen TT, Echeverria I, Rakesh R, Cary DC, Paculova H, Sali A, Weiss A, Peterlin BM, Fujinaga K. Reversible phosphorylation of cyclin T1 promotes assembly and stability of P-TEFb. eLife 2021; 10:68473. [PMID: 34821217 PMCID: PMC8648303 DOI: 10.7554/elife.68473] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 11/19/2021] [Indexed: 01/06/2023] Open
Abstract
The positive transcription elongation factor b (P-TEFb) is a critical coactivator for transcription of most cellular and viral genes, including those of HIV. While P-TEFb is regulated by 7SK snRNA in proliferating cells, P-TEFb is absent due to diminished levels of CycT1 in quiescent and terminally differentiated cells, which has remained unexplored. In these cells, we found that CycT1 not bound to CDK9 is rapidly degraded. Moreover, productive CycT1:CDK9 interactions are increased by PKC-mediated phosphorylation of CycT1 in human cells. Conversely, dephosphorylation of CycT1 by PP1 reverses this process. Thus, PKC inhibitors or removal of PKC by chronic activation results in P-TEFb disassembly and CycT1 degradation. This finding not only recapitulates P-TEFb depletion in resting CD4+ T cells but also in anergic T cells. Importantly, our studies reveal mechanisms of P-TEFb inactivation underlying T cell quiescence, anergy, and exhaustion as well as proviral latency and terminally differentiated cells.
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Affiliation(s)
- Fang Huang
- Departments of Medicine, Microbiology and Immunology, University of California, San Francisco, San Francisco, United States.,Department of Medicine, San Francisco, United States
| | - Trang Tt Nguyen
- Departments of Medicine, Microbiology and Immunology, University of California, San Francisco, San Francisco, United States.,Department of Medicine, San Francisco, United States.,The Howard Hughes Medical Institute, San Francisco, United States
| | - Ignacia Echeverria
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States.,Departmentof Cellular Molecular Pharmacology, California Institute for Quantitative Biosciences (QBI), and Department of Bioengineering and Therapeutic Sciences, San Francisco, United States
| | - Ramachandran Rakesh
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States.,Departmentof Cellular Molecular Pharmacology, California Institute for Quantitative Biosciences (QBI), and Department of Bioengineering and Therapeutic Sciences, San Francisco, United States
| | - Daniele C Cary
- Departments of Medicine, Microbiology and Immunology, University of California, San Francisco, San Francisco, United States.,Department of Medicine, San Francisco, United States
| | - Hana Paculova
- Departments of Medicine, Microbiology and Immunology, University of California, San Francisco, San Francisco, United States
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States.,Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences (QBI), San Francisco, United States
| | - Arthur Weiss
- Departments of Medicine, Microbiology and Immunology, University of California, San Francisco, San Francisco, United States.,Department of Medicine, San Francisco, United States.,The Howard Hughes Medical Institute, San Francisco, United States
| | - Boris Matija Peterlin
- Departments of Medicine, Microbiology and Immunology, University of California, San Francisco, San Francisco, United States.,Department of Medicine, San Francisco, United States
| | - Koh Fujinaga
- Departments of Medicine, Microbiology and Immunology, University of California, San Francisco, San Francisco, United States.,Department of Medicine, San Francisco, United States
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Covino DA, Desimio MG, Doria M. Combinations of Histone Deacetylase Inhibitors with Distinct Latency Reversing Agents Variably Affect HIV Reactivation and Susceptibility to NK Cell-Mediated Killing of T Cells That Exit Viral Latency. Int J Mol Sci 2021; 22:ijms22136654. [PMID: 34206330 PMCID: PMC8267728 DOI: 10.3390/ijms22136654] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 06/19/2021] [Indexed: 01/23/2023] Open
Abstract
The ‘shock-and-kill’ strategy to purge the latent HIV reservoir relies on latency-reversing agents (LRAs) to reactivate the provirus and subsequent immune-mediated killing of HIV-expressing cells. Yet, clinical trials employing histone deacetylase inhibitors (HDACis; Vorinostat, Romidepsin, Panobinostat) as LRAs failed to reduce the HIV reservoir size, stressing the need for more effective latency reversal strategies, such as 2-LRA combinations, and enhancement of the immune responses. Interestingly, several LRAs are employed to treat cancer because they up-modulate ligands for the NKG2D NK-cell activating receptor on tumor cells. Therefore, using in vitro T cell models of HIV latency and NK cells, we investigated the capacity of HDACis, either alone or combined with a distinct LRA, to potentiate the NKG2D/NKG2D ligands axis. While Bortezomib proteasome inhibitor was toxic for both T and NK cells, the GS-9620 TLR-7 agonist antagonized HIV reactivation and NKG2D ligand expression by HDACis. Conversely, co-administration of the Prostratin PKC agonist attenuated HDACi toxicity and, when combined with Romidepsin, stimulated HIV reactivation and further up-modulated NKG2D ligands on HIV+ T cells and NKG2D on NK cells, ultimately boosting NKG2D-mediated viral suppression by NK cells. These findings disclose limitations of LRA candidates and provide evidence that NK cell suppression of reactivated HIV may be modulated by specific 2-LRA combinations.
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Fujinaga K, Cary DC. Experimental Systems for Measuring HIV Latency and Reactivation. Viruses 2020; 12:v12111279. [PMID: 33182414 PMCID: PMC7696534 DOI: 10.3390/v12111279] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 11/02/2020] [Accepted: 11/05/2020] [Indexed: 02/07/2023] Open
Abstract
The final obstacle to achieving a cure to HIV/AIDS is the presence of latent HIV reservoirs scattered throughout the body. Although antiretroviral therapy maintains plasma viral loads below the levels of detection, upon cessation of therapy, the latent reservoir immediately produces infectious progeny viruses. This results in elevated plasma viremia, which leads to clinical progression to AIDS. Thus, if a HIV cure is ever to become a reality, it will be necessary to target and eliminate the latent reservoir. To this end, tremendous effort has been dedicated to locate the viral reservoir, understand the mechanisms contributing to latency, find optimal methods to reactivate HIV, and specifically kill latently infected cells. Although we have not yet identified a therapeutic approach to completely eliminate HIV from patients, these efforts have provided many technological breakthroughs in understanding the underlying mechanisms that regulate HIV latency and reactivation in vitro. In this review, we summarize and compare experimental systems which are frequently used to study HIV latency. While none of these models are a perfect proxy for the complex systems at work in HIV+ patients, each aim to replicate HIV latency in vitro.
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Affiliation(s)
- Koh Fujinaga
- Division of Rheumatology, Department of Medicine, School of Medicine, University of California, San Francisco, CA 94143-0703, USA
- Correspondence: ; Tel.: +1-415-502-1908
| | - Daniele C. Cary
- Department of Medicine, Microbiology, and Immunology, School of Medicine, University of California, San Francisco, CA 94143-0703, USA;
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