1
|
D'Orso I. The HIV-1 Transcriptional Program: From Initiation to Elongation Control. J Mol Biol 2024:168690. [PMID: 38936695 DOI: 10.1016/j.jmb.2024.168690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 06/20/2024] [Accepted: 06/21/2024] [Indexed: 06/29/2024]
Abstract
A large body of work in the last four decades has revealed the key pillars of HIV-1 transcription control at the initiation and elongation steps. Here, I provide a recount of this collective knowledge starting with the genomic elements (DNA and nascent TAR RNA stem-loop) and transcription factors (cellular and the viral transactivator Tat), and later transitioning to the assembly and regulation of transcription initiation and elongation complexes, and the role of chromatin structure. Compelling evidence support a core HIV-1 transcriptional program regulated by the sequential and concerted action of cellular transcription factors and Tat to promote initiation and sustain elongation, highlighting the efficiency of a small virus to take over its host to produce the high levels of transcription required for viral replication. I summarize new advances including the use of CRISPR-Cas9, genetic tools for acute factor depletion, and imaging to study transcriptional dynamics, bursting and the progression through the multiple phases of the transcriptional cycle. Finally, I describe current challenges to future major advances and discuss areas that deserve more attention to both bolster our basic knowledge of the core HIV-1 transcriptional program and open up new therapeutic opportunities.
Collapse
Affiliation(s)
- Iván D'Orso
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| |
Collapse
|
2
|
Zhang Z, Xu J, Liu J, Wang J, Lei L. SEC: A core hub during cell fate alteration. FASEB J 2024; 38:e23680. [PMID: 38758186 DOI: 10.1096/fj.202400514r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 04/18/2024] [Accepted: 05/07/2024] [Indexed: 05/18/2024]
Abstract
Pol II pause release is a rate-limiting step in gene transcription, influencing various cell fate alterations. Numerous proteins orchestrate Pol II pause release, thereby playing pivotal roles in the intricate process of cellular fate modulation. Super elongation complex (SEC), a large assembly comprising diverse protein components, has garnered attention due to its emerging significance in orchestrating physiological and pathological cellular identity changes by regulating the transcription of crucial genes. Consequently, SEC emerges as a noteworthy functional complex capable of modulating cell fate alterations. Therefore, a comprehensive review is warranted to systematically summarize the core roles of SEC in different types of cell fate alterations. This review focuses on elucidating the current understanding of the structural and functional basis of SEC. Additionally, we discuss the intricate regulatory mechanisms governing SEC in various models of cell fate alteration, encompassing both physiological and pathological contexts. Furthermore, leveraging the existing knowledge of SEC, we propose some insightful directions for future research, aiming to enhance our mechanistic and functional comprehension of SEC within the diverse landscape of cell fate alterations.
Collapse
Affiliation(s)
- Zhijing Zhang
- College of Life Science, Northeast Agricultural University, Harbin, Heilongjiang Province, China
- Department of Histology and Embryology, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Jingyi Xu
- Department of Histology and Embryology, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Jiqiang Liu
- Department of Histology and Embryology, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Jiaqiang Wang
- College of Life Science, Northeast Agricultural University, Harbin, Heilongjiang Province, China
| | - Lei Lei
- Department of Histology and Embryology, Harbin Medical University, Harbin, Heilongjiang Province, China
| |
Collapse
|
3
|
Cisneros WJ, Walter M, Soliman SH, Simons LM, Cornish D, Halle AW, Kim EY, Wolinsky SM, Shilatifard A, Hultquist JF. Release of P-TEFb from the Super Elongation Complex promotes HIV-1 latency reversal. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.01.582881. [PMID: 38464055 PMCID: PMC10925308 DOI: 10.1101/2024.03.01.582881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
The persistence of HIV-1 in long-lived latent reservoirs during suppressive antiretroviral therapy (ART) remains one of the principal barriers to a functional cure. Blocks to transcriptional elongation play a central role in maintaining the latent state, and several latency reversal strategies focus on the release of positive transcription elongation factor b (P-TEFb) from sequestration by negative regulatory complexes, such as the 7SK complex and BRD4. Another major cellular reservoir of P-TEFb is in Super Elongation Complexes (SECs), which play broad regulatory roles in host gene expression. Still, it is unknown if the release of P-TEFb from SECs is a viable latency reversal strategy. Here, we demonstrate that the SEC is not required for HIV-1 replication in primary CD4+ T cells and that a small molecular inhibitor of the P-TEFb/SEC interaction (termed KL-2) increases viral transcription. KL-2 acts synergistically with other latency reversing agents (LRAs) to reactivate viral transcription in several cell line models of latency in a manner that is, at least in part, dependent on the viral Tat protein. Finally, we demonstrate that KL-2 enhances viral reactivation in peripheral blood mononuclear cells (PBMCs) from people living with HIV on suppressive ART, most notably in combination with inhibitor of apoptosis protein antagonists (IAPi). Taken together, these results suggest that the release of P-TEFb from cellular SECs may be a novel route for HIV-1 latency reactivation.
Collapse
Affiliation(s)
- William J. Cisneros
- Division of Infectious Diseases, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Havey Institute for Global Health, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Miriam Walter
- Division of Infectious Diseases, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Shimaa H.A. Soliman
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Lacy M. Simons
- Division of Infectious Diseases, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Havey Institute for Global Health, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Daphne Cornish
- Division of Infectious Diseases, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Havey Institute for Global Health, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Ariel W. Halle
- Division of Infectious Diseases, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Havey Institute for Global Health, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Eun-Young Kim
- Division of Infectious Diseases, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Steven M. Wolinsky
- Division of Infectious Diseases, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Ali Shilatifard
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Judd F. Hultquist
- Division of Infectious Diseases, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Havey Institute for Global Health, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| |
Collapse
|
4
|
Long Q, Xiang M, Xiao L, Wang J, Guan X, Liu J, Liao C. The Biological Significance of AFF4: Promoting Transcription Elongation, Osteogenic Differentiation and Tumor Progression. Comb Chem High Throughput Screen 2024; 27:1403-1412. [PMID: 37815186 DOI: 10.2174/0113862073241079230920082056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 06/23/2023] [Accepted: 07/27/2023] [Indexed: 10/11/2023]
Abstract
As a member of the AF4/FMR2 (AFF) family, AFF4 is a scaffold protein in the superelongation complex (SEC). In this mini-view, we discuss the role of AFF4 as a transcription elongation factor that mediates HIV activation and replication and stem cell osteogenic differentiation. AFF4 also promotes the progression of head and neck squamous cell carcinoma, leukemia, breast cancer, bladder cancer and other malignant tumors. The biological function of AFF4 is largely achieved through SEC assembly, regulates SRY-box transcription factor 2 (SOX2), MYC, estrogen receptor alpha (ESR1), inhibitor of differentiation 1 (ID1), c-Jun and noncanonical nuclear factor-κB (NF-κB) transcription and combines with fusion in sarcoma (FUS), unique regulatory cyclins (CycT1), or mixed lineage leukemia (MLL). We explore the prospects of using AFF4 as a therapeutic in Acquired immunodeficiency syndrome (AIDS) and malignant tumors and its potential as a stemness regulator.
Collapse
Affiliation(s)
- Qian Long
- Department of Orthodontics II, Affiliated Stomatological Hospital of Zunyi Medical University, Zunyi, 563000, China
- Oral Disease Research Key Laboratory of Guizhou Tertiary Institution, School of Stomatology, Zunyi Medical University, Zunyi, 563006, China
| | - Mingli Xiang
- Department of Orthodontics II, Affiliated Stomatological Hospital of Zunyi Medical University, Zunyi, 563000, China
- Oral Disease Research Key Laboratory of Guizhou Tertiary Institution, School of Stomatology, Zunyi Medical University, Zunyi, 563006, China
| | - Linlin Xiao
- Department of Orthodontics II, Affiliated Stomatological Hospital of Zunyi Medical University, Zunyi, 563000, China
- Oral Disease Research Key Laboratory of Guizhou Tertiary Institution, School of Stomatology, Zunyi Medical University, Zunyi, 563006, China
| | - Jiajia Wang
- Department of Orthodontics II, Affiliated Stomatological Hospital of Zunyi Medical University, Zunyi, 563000, China
- Oral Disease Research Key Laboratory of Guizhou Tertiary Institution, School of Stomatology, Zunyi Medical University, Zunyi, 563006, China
| | - Xiaoyan Guan
- Department of Orthodontics II, Affiliated Stomatological Hospital of Zunyi Medical University, Zunyi, 563000, China
- Oral Disease Research Key Laboratory of Guizhou Tertiary Institution, School of Stomatology, Zunyi Medical University, Zunyi, 563006, China
| | - Jianguo Liu
- Department of Orthodontics II, Affiliated Stomatological Hospital of Zunyi Medical University, Zunyi, 563000, China
- Oral Disease Research Key Laboratory of Guizhou Tertiary Institution, School of Stomatology, Zunyi Medical University, Zunyi, 563006, China
| | - Chengcheng Liao
- Department of Orthodontics II, Affiliated Stomatological Hospital of Zunyi Medical University, Zunyi, 563000, China
- Oral Disease Research Key Laboratory of Guizhou Tertiary Institution, School of Stomatology, Zunyi Medical University, Zunyi, 563006, China
| |
Collapse
|
5
|
Jin J, Bai H, Yan H, Deng T, Li T, Xiao R, Fan L, Bai X, Ning H, Liu Z, Zhang K, Wu X, Liang K, Ma P, Gao X, Hu D. PRMT2 promotes HIV-1 latency by preventing nucleolar exit and phase separation of Tat into the Super Elongation Complex. Nat Commun 2023; 14:7274. [PMID: 37949879 PMCID: PMC10638354 DOI: 10.1038/s41467-023-43060-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 10/30/2023] [Indexed: 11/12/2023] Open
Abstract
The HIV-1 Tat protein hijacks the Super Elongation Complex (SEC) to stimulate viral transcription and replication. However, the mechanisms underlying Tat activation and inactivation, which mediate HIV-1 productive and latent infection, respectively, remain incompletely understood. Here, through a targeted complementary DNA (cDNA) expression screening, we identify PRMT2 as a key suppressor of Tat activation, thus contributing to proviral latency in multiple cell line latency models and in HIV-1-infected patient CD4+ T cells. Our data reveal that the transcriptional activity of Tat is oppositely regulated by NPM1-mediated nucleolar retention and AFF4-induced phase separation in the nucleoplasm. PRMT2 preferentially methylates Tat arginine 52 (R52) to reinforce its nucleolar sequestration while simultaneously counteracting its incorporation into the SEC droplets, thereby leading to its functional inactivation to promote proviral latency. Thus, our studies unveil a central and unappreciated role for Tat methylation by PRMT2 in connecting its subnuclear distribution, liquid droplet formation, and transactivating function, which could be therapeutically targeted to eradicate latent viral reservoirs.
Collapse
Affiliation(s)
- Jiaxing Jin
- National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, State Key Laboratory of Experimental Hematology, Key Laboratory of Immune Microenvironment and Disease of Ministry of Education, Department of Cell Biology, School of Basic Medicine, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, 300070, Tianjin, China
| | - Hui Bai
- National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, State Key Laboratory of Experimental Hematology, Key Laboratory of Immune Microenvironment and Disease of Ministry of Education, Department of Cell Biology, School of Basic Medicine, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, 300070, Tianjin, China
| | - Han Yan
- National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, State Key Laboratory of Experimental Hematology, Key Laboratory of Immune Microenvironment and Disease of Ministry of Education, Department of Cell Biology, School of Basic Medicine, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, 300070, Tianjin, China
| | - Ting Deng
- Key Laboratory of Breast Cancer Prevention and Therapy of Ministry of Education, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, 300060, Tianjin, China
| | - Tianyu Li
- Department of Pathophysiology, School of Basic Medical Sciences, Wuhan University, 430071, Wuhan, China
| | - Ruijing Xiao
- Department of Pathophysiology, School of Basic Medical Sciences, Wuhan University, 430071, Wuhan, China
| | - Lina Fan
- Department of Infectious Diseases, Tianjin Second People's Hospital, Nankai University, 300192, Tianjin, China
| | - Xue Bai
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, 300070, Tianjin, China
| | - Hanhan Ning
- National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, State Key Laboratory of Experimental Hematology, Key Laboratory of Immune Microenvironment and Disease of Ministry of Education, Department of Cell Biology, School of Basic Medicine, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, 300070, Tianjin, China
| | - Zhe Liu
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, 300070, Tianjin, China
| | - Kai Zhang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, 300070, Tianjin, China
| | - Xudong Wu
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, 300070, Tianjin, China
| | - Kaiwei Liang
- Department of Pathophysiology, School of Basic Medical Sciences, Wuhan University, 430071, Wuhan, China
| | - Ping Ma
- Department of Infectious Diseases, Tianjin Second People's Hospital, Nankai University, 300192, Tianjin, China.
| | - Xin Gao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 300020, Tianjin, China.
- Tianjin Institutes of Health Science, 301600, Tianjin, China.
| | - Deqing Hu
- National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, State Key Laboratory of Experimental Hematology, Key Laboratory of Immune Microenvironment and Disease of Ministry of Education, Department of Cell Biology, School of Basic Medicine, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, 300070, Tianjin, China.
| |
Collapse
|
6
|
Ken ML, Roy R, Geng A, Ganser LR, Manghrani A, Cullen BR, Schulze-Gahmen U, Herschlag D, Al-Hashimi HM. RNA conformational propensities determine cellular activity. Nature 2023; 617:835-841. [PMID: 37198487 PMCID: PMC10429349 DOI: 10.1038/s41586-023-06080-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 04/12/2023] [Indexed: 05/19/2023]
Abstract
Cellular processes are the product of interactions between biomolecules, which associate to form biologically active complexes1. These interactions are mediated by intermolecular contacts, which if disrupted, lead to alterations in cell physiology. Nevertheless, the formation of intermolecular contacts nearly universally requires changes in the conformations of the interacting biomolecules. As a result, binding affinity and cellular activity crucially depend both on the strength of the contacts and on the inherent propensities to form binding-competent conformational states2,3. Thus, conformational penalties are ubiquitous in biology and must be known in order to quantitatively model binding energetics for protein and nucleic acid interactions4,5. However, conceptual and technological limitations have hindered our ability to dissect and quantitatively measure how conformational propensities affect cellular activity. Here we systematically altered and determined the propensities for forming the protein-bound conformation of HIV-1 TAR RNA. These propensities quantitatively predicted the binding affinities of TAR to the RNA-binding region of the Tat protein and predicted the extent of HIV-1 Tat-dependent transactivation in cells. Our results establish the role of ensemble-based conformational propensities in cellular activity and reveal an example of a cellular process driven by an exceptionally rare and short-lived RNA conformational state.
Collapse
Affiliation(s)
- Megan L Ken
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
| | - Rohit Roy
- Center for Genomic and Computational Biology, Duke University School of Medicine, Durham, NC, USA
| | - Ainan Geng
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
| | - Laura R Ganser
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA
| | - Akanksha Manghrani
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
| | - Bryan R Cullen
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
| | | | - Daniel Herschlag
- Department of Biochemistry, Stanford University, Stanford, CA, USA.
| | - Hashim M Al-Hashimi
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.
| |
Collapse
|
7
|
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.
Collapse
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.
| |
Collapse
|
8
|
Wu X, Xie Y, Zhao K, Lu J. Targeting the super elongation complex for oncogenic transcription driven tumor malignancies: Progress in structure, mechanisms and small molecular inhibitor discovery. Adv Cancer Res 2023; 158:387-421. [PMID: 36990537 DOI: 10.1016/bs.acr.2022.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Oncogenic transcription activation is associated with tumor development and resistance derived from chemotherapy or target therapy. The super elongation complex (SEC) is an important complex regulating gene transcription and expression in metazoans closely related to physiological activities. In normal transcriptional regulation, SEC can trigger promoter escape, limit proteolytic degradation of transcription elongation factors and increase the synthesis of RNA polymerase II (POL II), and regulate many normal human genes to stimulate RNA elongation. Dysregulation of SEC accompanied by multiple transcription factors in cancer promotes rapid transcription of oncogenes and induce cancer development. In this review, we summarized recent progress in understanding the mechanisms of SEC in regulating normal transcription, and importantly its roles in cancer development. We also highlighted the discovery of SEC complex target related inhibitors and their potential applications in cancer treatment.
Collapse
Affiliation(s)
- Xinyu Wu
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai, China; Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Yanqiu Xie
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai, China; Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Kehao Zhao
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai, China.
| | - Jing Lu
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai, China.
| |
Collapse
|
9
|
Tang D, Wang Y, Dong X, Yuan Y, Kang F, Tian W, Wang K, Li H, Qi S. Scramblases and virus infection. Bioessays 2022; 44:e2100261. [DOI: 10.1002/bies.202100261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 09/26/2022] [Accepted: 09/27/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Dan Tang
- Department of Urology Institute of Urology (Laboratory of Reconstructive Urology) State Key Laboratory of Oral Disease West China Hospital of Stomatology West China Hospital Sichuan University Chengdu Sichuan China
| | - Yichang Wang
- Department of Urology Institute of Urology (Laboratory of Reconstructive Urology) State Key Laboratory of Oral Disease West China Hospital of Stomatology West China Hospital Sichuan University Chengdu Sichuan China
| | - Xiuju Dong
- Department of Urology Institute of Urology (Laboratory of Reconstructive Urology) State Key Laboratory of Oral Disease West China Hospital of Stomatology West China Hospital Sichuan University Chengdu Sichuan China
| | - Yiqiong Yuan
- Department of Urology Institute of Urology (Laboratory of Reconstructive Urology) State Key Laboratory of Oral Disease West China Hospital of Stomatology West China Hospital Sichuan University Chengdu Sichuan China
| | - Fanchen Kang
- Department of Urology Institute of Urology (Laboratory of Reconstructive Urology) State Key Laboratory of Oral Disease West China Hospital of Stomatology West China Hospital Sichuan University Chengdu Sichuan China
| | - Weidong Tian
- Department of Urology Institute of Urology (Laboratory of Reconstructive Urology) State Key Laboratory of Oral Disease West China Hospital of Stomatology West China Hospital Sichuan University Chengdu Sichuan China
| | - Kunjie Wang
- Department of Urology Institute of Urology (Laboratory of Reconstructive Urology) State Key Laboratory of Oral Disease West China Hospital of Stomatology West China Hospital Sichuan University Chengdu Sichuan China
| | - Hong Li
- Department of Urology Institute of Urology (Laboratory of Reconstructive Urology) State Key Laboratory of Oral Disease West China Hospital of Stomatology West China Hospital Sichuan University Chengdu Sichuan China
| | - Shiqian Qi
- Department of Urology Institute of Urology (Laboratory of Reconstructive Urology) State Key Laboratory of Oral Disease West China Hospital of Stomatology West China Hospital Sichuan University Chengdu Sichuan China
| |
Collapse
|
10
|
Polyphenol Extracts from Grape Seeds and Apple Can Reactivate Latent HIV-1 Transcription through Promoting P-TEFb Release from 7SK snRNP. DISEASE MARKERS 2022; 2022:6055347. [PMID: 35178129 PMCID: PMC8843978 DOI: 10.1155/2022/6055347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 01/06/2022] [Indexed: 11/22/2022]
Abstract
The principal barrier for the eradication of HIV/AIDS is the virus latency. One of the effective strategies so called “shock and kill” is to use latency-reversing agents (LRAs) to activate the latent HIV reservoirs and then combine them with the highly active antiretroviral therapy (HAART) to eradicate the virus. However, most of the current LRAs are too toxic; therefore, they have not been used clinically. Our preliminary data indicated that polyphenols from grape seeds can activate HIV in latently infected Jurkat T cells. Owing to a lot of food containing polyphenols and based on a reasoning whether all of these kinds of polyphenols contain the latency-reversing function, in this study, we screened 22 fruits/vegetables to see whether polyphenols from these can reactivate latent HIV-1 transcription. We finally proved that the polyphenols from grape seeds, apple, pomegranate, and bilberry can reactivate latent HIV-1 transcription. The activation of which can be detected on the level of protein and mRNA. The activation of which is in a dose- and time-dependent manner, while the activated polyphenol extracts have the effects to stimulate Tat-independent HIV-1 transcription. The mechanism shows that polyphenol extracts from grape seeds and apple can stimulate P-TEFb's release from 7SK snRNP to induce HIV gene transcription. These results indicate that using a few food of high-content polyphenols as latent activators and combining HARRT may be of great use for the treatment of HIV/AIDS in the future.
Collapse
|
11
|
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.
Collapse
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
| |
Collapse
|
12
|
Wu F, Nie S, Yao Y, Huo T, Li X, Wu X, Zhao J, Lin YL, Zhang Y, Mo Q, Song Y. Small-molecule inhibitor of AF9/ENL-DOT1L/AF4/AFF4 interactions suppresses malignant gene expression and tumor growth. Theranostics 2021; 11:8172-8184. [PMID: 34373735 PMCID: PMC8344022 DOI: 10.7150/thno.56737] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 06/28/2021] [Indexed: 01/22/2023] Open
Abstract
Chromosome translocations involving mixed lineage leukemia (MLL) gene cause acute leukemia with a poor prognosis. MLL is frequently fused with transcription cofactors AF4 (~35%), AF9 (25%) or its paralog ENL (10%). The AHD domain of AF9/ENL binds to AF4, its paralog AFF4, or histone-H3 lysine-79 (H3K79) methyltransferase DOT1L. Formation of AF9/ENL/AF4/AFF4-containing super elongation complexes (SEC) and the catalytic activity of DOT1L are essential for MLL-rearranged leukemia. Protein-protein interactions (PPI) between AF9/ENL and DOT1L/AF4/AFF4 are therefore a potential drug target. Methods: Compound screening followed by medicinal chemistry was used to find inhibitors of such PPIs, which were examined for their biological activities against MLL-rearranged leukemia and other cancer cells. Results: Compound-1 was identified to be a novel small-molecule inhibitor of the AF9/ENL-DOT1L/AF4/AFF4 interaction with IC50s of 0.9-3.5 µM. Pharmacological inhibition of the PPIs significantly reduced SEC and DOT1L-mediated H3K79 methylation in the leukemia cells. Gene profiling shows compound-1 significantly suppressed the gene signatures related to onco-MLL, DOT1L, HoxA9 and Myc. It selectively inhibited proliferation of onco-MLL- or Myc-driven cancer cells and induced cell differentiation and apoptosis. Compound-1 exhibited strong antitumor activity in a mouse model of MLL-rearranged leukemia. Conclusions: The AF9/ENL-DOT1L/AF4/AFF4 interactions are validated to be an anticancer target and compound-1 is a useful in vivo probe for biological studies as well as a pharmacological lead for further drug development.
Collapse
|
13
|
Chen Y, Vos SM, Dienemann C, Ninov M, Urlaub H, Cramer P. Allosteric transcription stimulation by RNA polymerase II super elongation complex. Mol Cell 2021; 81:3386-3399.e10. [PMID: 34265249 DOI: 10.1016/j.molcel.2021.06.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 05/19/2021] [Accepted: 06/17/2021] [Indexed: 01/11/2023]
Abstract
The super elongation complex (SEC) contains the positive transcription elongation factor b (P-TEFb) and the subcomplex ELL2-EAF1, which stimulates RNA polymerase II (RNA Pol II) elongation. Here, we report the cryoelectron microscopy (cryo-EM) structure of ELL2-EAF1 bound to a RNA Pol II elongation complex at 2.8 Å resolution. The ELL2-EAF1 dimerization module directly binds the RNA Pol II lobe domain, explaining how SEC delivers P-TEFb to RNA Pol II. The same site on the lobe also binds the initiation factor TFIIF, consistent with SEC binding only after the transition from transcription initiation to elongation. Structure-guided functional analysis shows that the stimulation of RNA elongation requires the dimerization module and the ELL2 linker that tethers the module to the RNA Pol II protrusion. Our results show that SEC stimulates elongation allosterically and indicate that this stimulation involves stabilization of a closed conformation of the RNA Pol II active center cleft.
Collapse
Affiliation(s)
- Ying Chen
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany
| | - Seychelle M Vos
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany
| | - Christian Dienemann
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany
| | - Momchil Ninov
- Max Planck Institute for Biophysical Chemistry, Bioanalytical Mass Spectrometry, Am Fassberg 11, 37077 Göttingen, Germany; University Medical Center Göttingen, Institute of Clinical Chemistry, Bioanalytics Group, Robert-Koch-Straße 40, 37075 Göttingen, Germany
| | - Henning Urlaub
- Max Planck Institute for Biophysical Chemistry, Bioanalytical Mass Spectrometry, Am Fassberg 11, 37077 Göttingen, Germany; University Medical Center Göttingen, Institute of Clinical Chemistry, Bioanalytics Group, Robert-Koch-Straße 40, 37075 Göttingen, Germany
| | - Patrick Cramer
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany.
| |
Collapse
|
14
|
Liu C, Liu AS, Zhong D, Wang CG, Yu M, Zhang HW, Xiao H, Liu JH, Zhang J, Yin K. Circular RNA AFF4 modulates osteogenic differentiation in BM-MSCs by activating SMAD1/5 pathway through miR-135a-5p/FNDC5/Irisin axis. Cell Death Dis 2021; 12:631. [PMID: 34145212 PMCID: PMC8213698 DOI: 10.1038/s41419-021-03877-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 05/13/2021] [Accepted: 05/21/2021] [Indexed: 11/18/2022]
Abstract
Bone marrow-derived mesenchymal stem cells (BM-MSCs), the common progenitor cells of adipocytes and osteoblasts, have been recognized as the key mediator during bone formation. Herein, our study aim to investigate molecular mechanisms underlying circular RNA (circRNA) AFF4 (circ_AFF4)-regulated BM-MSCs osteogenesis. BM-MSCs were characterized by FACS, ARS, and ALP staining. Expression patterns of circ_AFF4, miR-135a-5p, FNDC5/Irisin, SMAD1/5, and osteogenesis markers, including ALP, BMP4, RUNX2, Spp1, and Colla1 were detected by qRT-PCR, western blot, or immunofluorescence staining, respectively. Interactions between circ_AFF4 and miR-135a-5p, FNDC5, and miR-135a-5p were analyzed using web tools including TargetScan, miRanda, and miRDB, and further confirmed by luciferase reporter assay and RNA pull-down. Complex formation between Irisin and Integrin αV was verified by Co-immunoprecipitation. To further verify the functional role of circ_AFF4 in vivo during bone formation, we conducted animal experiments harboring circ_AFF4 knockdown, and born samples were evaluated by immunohistochemistry, hematoxylin and eosin, and Masson staining. Circ_AFF4 was upregulated upon osteogenic differentiation induction in BM-MSCs, and miR-135a-5p expression declined as differentiation proceeds. Circ_AFF4 knockdown significantly inhibited osteogenesis potential in BM-MSCs. Circ_AFF4 stimulated FNDC5/Irisin expression through complementary binding to its downstream target molecule miR-135a-5p. Irisin formed an intermolecular complex with Integrin αV and activated the SMAD1/5 pathway during osteogenic differentiation. Our work revealed that circ_AFF4, acting as a sponge of miR-135a-5p, triggers the promotion of FNDC5/Irisin via activating the SMAD1/5 pathway to induce osteogenic differentiation in BM-MSCs. These findings gained a deeper insight into the circRNA-miRNA regulatory system in the bone marrow microenvironment and may improve our understanding of bone formation-related diseases at physiological and pathological levels.
Collapse
Affiliation(s)
- Chao Liu
- Department of Orthopedics, The First Affiliated Hospital of University of South China, Hengyang, 421001, Hunan Province, PR China
| | - An-Song Liu
- Department of Orthopedics, The First Affiliated Hospital of University of South China, Hengyang, 421001, Hunan Province, PR China
| | - Da Zhong
- Department of Orthopedics, Xiangya Hospital, Central South University, No. 87 Xiangya Road, Changsha, 410008, Hunan Province, PR China
| | - Cheng-Gong Wang
- Department of Orthopedics, Xiangya Hospital, Central South University, No. 87 Xiangya Road, Changsha, 410008, Hunan Province, PR China
| | - Mi Yu
- Medical College of University of South China, Hengyang, 421001, Hunan Province, PR China
| | - Hao-Wei Zhang
- Department of Orthopedics, The First Affiliated Hospital of University of South China, Hengyang, 421001, Hunan Province, PR China
| | - Han Xiao
- Department of Orthopedics, The First Affiliated Hospital of University of South China, Hengyang, 421001, Hunan Province, PR China
| | - Jian-Hua Liu
- Department of Hematology, The First Affiliated Hospital of University of South China, Hengyang, 421001, Hunan Province, PR China
| | - Jian Zhang
- Department of Orthopedics, The First Affiliated Hospital of University of South China, Hengyang, 421001, Hunan Province, PR China
| | - Ke Yin
- Department of Orthopedics, The First Affiliated Hospital of University of South China, Hengyang, 421001, Hunan Province, PR China.
| |
Collapse
|
15
|
Li X, Song Y. Structure, function and inhibition of critical protein-protein interactions involving mixed lineage leukemia 1 and its fusion oncoproteins. J Hematol Oncol 2021; 14:56. [PMID: 33823889 PMCID: PMC8022399 DOI: 10.1186/s13045-021-01057-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 03/05/2021] [Indexed: 12/13/2022] Open
Abstract
Mixed lineage leukemia 1 (MLL1, also known as MLL or KMT2A) is an important transcription factor and histone-H3 lysine-4 (H3K4) methyltransferase. It is a master regulator for transcription of important genes (e.g., Hox genes) for embryonic development and hematopoiesis. However, it is largely dispensable in matured cells. Dysregulation of MLL1 leads to overexpression of certain Hox genes and eventually leukemia initiation. Chromosome translocations involving MLL1 cause ~ 75% of acute leukemia in infants and 5–10% in children and adults with a poor prognosis. Targeted therapeutics against oncogenic fusion MLL1 (onco-MLL1) are therefore needed. Onco-MLL1 consists of the N-terminal DNA-interacting domains of MLL1 fused with one of > 70 fusion partners, among which transcription cofactors AF4, AF9 and its paralog ENL, and ELL are the most frequent. Wild-type (WT)- and onco-MLL1 involve numerous protein–protein interactions (PPI), which play critical roles in regulating gene expression in normal physiology and leukemia. Moreover, WT-MLL1 has been found to be essential for MLL1-rearranged (MLL1-r) leukemia. Rigorous studies of such PPIs have been performed and much progress has been achieved in understanding their structures, structure–function relationships and the mechanisms for activating gene transcription as well as leukemic transformation. Inhibition of several critical PPIs by peptides, peptidomimetic or small-molecule compounds has been explored as a therapeutic approach for MLL1-r leukemia. This review summarizes the biological functions, biochemistry, structure and inhibition of the critical PPIs involving MLL1 and its fusion partner proteins. In addition, challenges and perspectives of drug discovery targeting these PPIs for the treatment of MLL1-r leukemia are discussed.
Collapse
Affiliation(s)
- Xin Li
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Yongcheng Song
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA. .,Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.
| |
Collapse
|
16
|
Salamina M, Montefiore BC, Liu M, Wood DJ, Heath R, Ault JR, Wang LZ, Korolchuk S, Baslé A, Pastok MW, Reeks J, Tatum NJ, Sobott F, Arold ST, Pagano M, Noble ME, Endicott JA. Discriminative SKP2 Interactions with CDK-Cyclin Complexes Support a Cyclin A-Specific Role in p27KIP1 Degradation. J Mol Biol 2021; 433:166795. [PMID: 33422522 PMCID: PMC7895821 DOI: 10.1016/j.jmb.2020.166795] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/11/2020] [Accepted: 12/28/2020] [Indexed: 12/29/2022]
Abstract
The SCFSKP2 ubiquitin ligase relieves G1 checkpoint control of CDK-cyclin complexes by promoting p27KIP1 degradation. We describe reconstitution of stable complexes containing SKP1-SKP2 and CDK1-cyclin B or CDK2-cyclin A/E, mediated by the CDK regulatory subunit CKS1. We further show that a direct interaction between a SKP2 N-terminal motif and cyclin A can stabilize SKP1-SKP2-CDK2-cyclin A complexes in the absence of CKS1. We identify the SKP2 binding site on cyclin A and demonstrate the site is not present in cyclin B or cyclin E. This site is distinct from but overlapping with features that mediate binding of p27KIP1 and other G1 cyclin regulators to cyclin A. We propose that the capacity of SKP2 to engage with CDK2-cyclin A by more than one structural mechanism provides a way to fine tune the degradation of p27KIP1 and distinguishes cyclin A from other G1 cyclins to ensure orderly cell cycle progression.
Collapse
Affiliation(s)
- Marco Salamina
- Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Newcastle University, Paul O’Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Bailey C. Montefiore
- Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Newcastle University, Paul O’Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Mengxi Liu
- Department of Biochemistry and Molecular Pharmacology, Perlmutter NYU Cancer Center, New York University Grossman School of Medicine, and Howard Hughes Medical Institute, The Alexandria Center of Life Science, East Tower, 450 E, 29th Street, New York, NY 10016, USA
| | - Daniel J. Wood
- Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Newcastle University, Paul O’Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Richard Heath
- Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Newcastle University, Paul O’Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - James R. Ault
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Lan-Zhen Wang
- Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Newcastle University, Paul O’Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Svitlana Korolchuk
- Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Newcastle University, Paul O’Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Arnaud Baslé
- Biosciences Institute, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Martyna W. Pastok
- Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Newcastle University, Paul O’Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Judith Reeks
- Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Newcastle University, Paul O’Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Natalie J. Tatum
- Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Newcastle University, Paul O’Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Frank Sobott
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Stefan T. Arold
- Division of Biological and Environmental Sciences and Engineering (BESE), Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- Centre de Biochimie Structurale, CNRS, INSERM, Université de Montpellier, 34090 Montpellier, France
| | - Michele Pagano
- Department of Biochemistry and Molecular Pharmacology, Perlmutter NYU Cancer Center, New York University Grossman School of Medicine, and Howard Hughes Medical Institute, The Alexandria Center of Life Science, East Tower, 450 E, 29th Street, New York, NY 10016, USA
| | - Martin E.M. Noble
- Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Newcastle University, Paul O’Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Jane A. Endicott
- Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Newcastle University, Paul O’Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| |
Collapse
|
17
|
Katagi H, Takata N, Aoi Y, Zhang Y, Rendleman EJ, Blyth GT, Eckerdt FD, Tomita Y, Sasaki T, Saratsis AM, Kondo A, Goldman S, Becher OJ, Smith E, Zou L, Shilatifard A, Hashizume R. Therapeutic targeting of transcriptional elongation in diffuse intrinsic pontine glioma. Neuro Oncol 2021; 23:1348-1359. [PMID: 33471107 PMCID: PMC8328031 DOI: 10.1093/neuonc/noab009] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Diffuse intrinsic pontine glioma (DIPG) is associated with transcriptional dysregulation driven by H3K27 mutation. The super elongation complex (SEC) is required for transcriptional elongation through release of RNA polymerase II (Pol II). Inhibition of transcription elongation by SEC disruption can be an effective therapeutic strategy of H3K27M-mutant DIPG. Here, we tested the effect of pharmacological disruption of the SEC in H3K27M-mutant DIPG to advance understanding of the molecular mechanism and as a new therapeutic strategy for DIPG. METHODS Short hairpin RNAs (shRNAs) were used to suppress the expression of AF4/FMR2 4 (AFF4), a central SEC component, in H3K27M-mutant DIPG cells. A peptidomimetic lead compound KL-1 was used to disrupt a functional component of SEC. Cell viability assay, colony formation assay, and apoptosis assay were utilized to analyze the effects of KL-1 treatment. RNA- and ChIP-sequencing were used to determine the effects of KL-1 on gene expression and chromatin occupancy. We treated mice bearing H3K27M-mutant DIPG patient-derived xenografts (PDXs) with KL-1. Intracranial tumor growth was monitored by bioluminescence image and therapeutic response was evaluated by animal survival. RESULTS Depletion of AFF4 significantly reduced the cell growth of H3K27M-mutant DIPG. KL-1 increased genome-wide Pol II occupancy and suppressed transcription involving multiple cellular processes that promote cell proliferation and differentiation of DIPG. KL-1 treatment suppressed DIPG cell growth, increased apoptosis, and prolonged animal survival with H3K27M-mutant DIPG PDXs. CONCLUSIONS SEC disruption by KL-1 increased therapeutic benefit in vitro and in vivo, supporting a potential therapeutic activity of KL-1 in H3K27M-mutant DIPG.
Collapse
Affiliation(s)
- Hiroaki Katagi
- Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, Illinois,Department of Neurological Surgery, Juntendo University, Tokyo, Japan
| | - Nozomu Takata
- Center for Vascular and Developmental Biology, Feinberg Cardiovascular and Renal Research Institute (FCVRRI), Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Yuki Aoi
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Yongzhan Zhang
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Emily J Rendleman
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Gavin T Blyth
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, Illinois
| | - Frank D Eckerdt
- Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, Illinois,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, Illinois
| | - Yusuke Tomita
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois,Division of Hematology, Oncology, Neuro-Oncology and Stem Cell Transplantation, Ann and Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois
| | - Takahiro Sasaki
- Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Amanda M Saratsis
- Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, Illinois,Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, Illinois,Department of Surgery, Division of Pediatric Neurosurgery, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois
| | - Akihide Kondo
- Department of Neurological Surgery, Juntendo University, Tokyo, Japan
| | - Stewart Goldman
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, Illinois,Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois,Division of Hematology, Oncology, Neuro-Oncology and Stem Cell Transplantation, Ann and Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois
| | - Oren J Becher
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, Illinois,Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois,Division of Hematology, Oncology, Neuro-Oncology and Stem Cell Transplantation, Ann and Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois
| | - Edwin Smith
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, Illinois
| | - Lihua Zou
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, Illinois
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, Illinois
| | - Rintaro Hashizume
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, Illinois,Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois,Division of Hematology, Oncology, Neuro-Oncology and Stem Cell Transplantation, Ann and Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois,Corresponding Author: Rintaro Hashizume, MD, PhD, Department of Pediatrics, Northwestern University Feinberg School of Medicine, 303 East Superior Street, Simpson Querrey 4-514, Chicago, IL 60611, USA (, )
| |
Collapse
|
18
|
Zheng B, Aoi Y, Shah AP, Iwanaszko M, Das S, Rendleman EJ, Zha D, Khan N, Smith ER, Shilatifard A. Acute perturbation strategies in interrogating RNA polymerase II elongation factor function in gene expression. Genes Dev 2021; 35:273-285. [PMID: 33446572 PMCID: PMC7849361 DOI: 10.1101/gad.346106.120] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 12/03/2020] [Indexed: 12/20/2022]
Abstract
The regulation of gene expression catalyzed by RNA polymerase II (Pol II) requires a host of accessory factors to ensure cell growth, differentiation, and survival under environmental stress. Here, using the auxin-inducible degradation (AID) system to study transcriptional activities of the bromodomain and extraterminal domain (BET) and super elongation complex (SEC) families, we found that the CDK9-containing BRD4 complex is required for the release of Pol II from promoter-proximal pausing for most genes, while the CDK9-containing SEC is required for activated transcription in the heat shock response. By using both the proteolysis targeting chimera (PROTAC) dBET6 and the AID system, we found that dBET6 treatment results in two major effects: increased pausing due to BRD4 loss, and reduced enhancer activity attributable to BRD2 loss. In the heat shock response, while auxin-mediated depletion of the AFF4 subunit of the SEC has a more severe defect than AFF1 depletion, simultaneous depletion of AFF1 and AFF4 leads to a stronger attenuation of the heat shock response, similar to treatment with the SEC inhibitor KL-1, suggesting a possible redundancy among SEC family members. This study highlights the usefulness of orthogonal acute depletion/inhibition strategies to identify distinct and redundant biological functions among Pol II elongation factor paralogs.
Collapse
Affiliation(s)
- Bin Zheng
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Yuki Aoi
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Avani P Shah
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Marta Iwanaszko
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Siddhartha Das
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Emily J Rendleman
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Didi Zha
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Nabiha Khan
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Edwin R Smith
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Ali Shilatifard
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| |
Collapse
|
19
|
Depicting HIV-1 Transcriptional Mechanisms: A Summary of What We Know. Viruses 2020; 12:v12121385. [PMID: 33287435 PMCID: PMC7761857 DOI: 10.3390/v12121385] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 11/26/2020] [Accepted: 12/01/2020] [Indexed: 12/19/2022] Open
Abstract
Despite the introduction of combinatory antiretroviral therapy (cART), HIV-1 infection cannot be cured and is still one of the major health issues worldwide. Indeed, as soon as cART is interrupted, a rapid rebound of viremia is observed. The establishment of viral latency and the persistence of the virus in cellular reservoirs constitute the main barrier to HIV eradication. For this reason, new therapeutic approaches have emerged to purge or restrain the HIV-1 reservoirs in order to cure infected patients. However, the viral latency is a multifactorial process that depends on various cellular mechanisms. Since these new therapies mainly target viral transcription, their development requires a detailed and precise understanding of the regulatory mechanism underlying HIV-1 transcription. In this review, we discuss the complex molecular transcriptional network regulating HIV-1 gene expression by focusing on the involvement of host cell factors that could be used as potential drug targets to design new therapeutic strategies and, to a larger extent, to reach an HIV-1 functional cure.
Collapse
|
20
|
Tatum NJ, Endicott JA. Chatterboxes: the structural and functional diversity of cyclins. Semin Cell Dev Biol 2020; 107:4-20. [PMID: 32414682 DOI: 10.1016/j.semcdb.2020.04.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 04/28/2020] [Accepted: 04/29/2020] [Indexed: 12/16/2022]
Abstract
Proteins of the cyclin family have divergent sequences and execute diverse roles within the cell while sharing a common fold: the cyclin box domain. Structural studies of cyclins have played a key role in our characterization and understanding of cellular processes that they control, though to date only ten of the 29 CDK-activating cyclins have been structurally characterized by X-ray crystallography or cryo-electron microscopy with or without their cognate kinases. In this review, we survey the available structures of human cyclins, highlighting their molecular features in the context of their cellular roles. We pay particular attention to how cyclin activity is regulated through fine control of degradation motif recognition and ubiquitination. Finally, we discuss the emergent roles of cyclins independent of their roles as cyclin-dependent protein kinase activators, demonstrating the cyclin box domain to be a versatile and generalized scaffolding domain for protein-protein interactions across the cellular machinery.
Collapse
Affiliation(s)
- Natalie J Tatum
- Cancer Research UK Newcastle Drug Discovery Unit, Newcastle Centre for Cancer, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Jane A Endicott
- Cancer Research UK Newcastle Drug Discovery Unit, Newcastle Centre for Cancer, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom.
| |
Collapse
|
21
|
Walton SJ, Wang H, Quintero-Cadena P, Bateman A, Sternberg PW. Caenorhabditis elegans AF4/FMR2 Family Homolog affl-2 Regulates Heat-Shock-Induced Gene Expression. Genetics 2020; 215:1039-1054. [PMID: 32518061 PMCID: PMC7404228 DOI: 10.1534/genetics.120.302923] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 05/27/2020] [Indexed: 02/08/2023] Open
Abstract
To mitigate the deleterious effects of temperature increases on cellular organization and proteotoxicity, organisms have developed mechanisms to respond to heat stress. In eukaryotes, HSF1 is the master regulator of the heat shock transcriptional response, but the heat shock response pathway is not yet fully understood. From a forward genetic screen for suppressors of heat-shock-induced gene expression in Caenorhabditis elegans, we found a new allele of hsf-1 that alters its DNA-binding domain, and we found three additional alleles of sup-45, a previously molecularly uncharacterized genetic locus. We identified sup-45 as one of the two hitherto unknown C. elegans orthologs of the human AF4/FMR2 family proteins, which are involved in regulation of transcriptional elongation rate. We thus renamed sup-45 as affl-2 (AF4/FMR2-Like). Through RNA-seq, we demonstrated that affl-2 mutants are deficient in heat-shock-induced transcription. Additionally, affl-2 mutants have herniated intestines, while worms lacking its sole paralog (affl-1) appear wild type. AFFL-2 is a broadly expressed nuclear protein, and nuclear localization of AFFL-2 is necessary for its role in heat shock response. affl-2 and its paralog are not essential for proper HSF-1 expression and localization after heat shock, which suggests that affl-2 may function downstream of, or parallel to, hsf-1 Our characterization of affl-2 provides insights into the regulation of heat-shock-induced gene expression to protect against heat stress.
Collapse
Affiliation(s)
- Sophie J Walton
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125
| | - Han Wang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125
| | - Porfirio Quintero-Cadena
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125
| | - Alex Bateman
- European Molecular Biology Laboratory, European Bioinformatics Institute, (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Paul W Sternberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125
| |
Collapse
|
22
|
Ochsner SA, Pillich RT, McKenna NJ. Consensus transcriptional regulatory networks of coronavirus-infected human cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.04.24.059527. [PMID: 32511379 PMCID: PMC7263508 DOI: 10.1101/2020.04.24.059527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Establishing consensus around the transcriptional interface between coronavirus (CoV) infection and human cellular signaling pathways can catalyze the development of novel anti-CoV therapeutics. Here, we used publicly archived transcriptomic datasets to compute consensus regulatory signatures, or consensomes, that rank human genes based on their rates of differential expression in MERS-CoV (MERS), SARS-CoV-1 (SARS1) and SARS-CoV-2 (SARS2)-infected cells. Validating the CoV consensomes, we show that high confidence transcriptional targets (HCTs) of CoV infection intersect with HCTs of signaling pathway nodes with known roles in CoV infection. Among a series of novel use cases, we gather evidence for hypotheses that SARS2 infection efficiently represses E2F family target genes encoding key drivers of DNA replication and the cell cycle; that progesterone receptor signaling antagonizes SARS2-induced inflammatory signaling in the airway epithelium; and that SARS2 HCTs are enriched for genes involved in epithelial to mesenchymal transition. The CoV infection consensomes and HCT intersection analyses are freely accessible through the Signaling Pathways Project knowledgebase, and as Cytoscape-style networks in the Network Data Exchange repository.
Collapse
Affiliation(s)
- Scott A Ochsner
- The Signaling Pathways Project and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030
| | - Rudolf T Pillich
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Neil J McKenna
- The Signaling Pathways Project and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030
| |
Collapse
|
23
|
AFF4 regulates osteogenic differentiation of human dental follicle cells. Int J Oral Sci 2020; 12:20. [PMID: 32606293 PMCID: PMC7327054 DOI: 10.1038/s41368-020-0083-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 02/21/2020] [Accepted: 02/23/2020] [Indexed: 02/05/2023] Open
Abstract
As a member of the AFF (AF4/FMR2) family, AFF4 is a transcription elongation factor that is a component of the super elongation complex. AFF4 serves as a scaffolding protein that connects transcription factors and promotes gene transcription through elongation and chromatin remodelling. Here, we investigated the effect of AFF4 on human dental follicle cells (DFCs) in osteogenic differentiation. In this study, we found that small interfering RNA-mediated depletion of AFF4 resulted in decreased alkaline phosphatase (ALP) activity and impaired mineralization. In addition, the expression of osteogenic-related genes (DLX5, SP7, RUNX2 and BGLAP) was significantly downregulated. In contrast, lentivirus-mediated overexpression of AFF4 significantly enhanced the osteogenic potential of human DFCs. Mechanistically, we found that both the mRNA and protein levels of ALKBH1, a critical regulator of epigenetics, changed in accordance with AFF4 expression levels. Overexpression of ALKBH1 in AFF4-depleted DFCs partially rescued the impairment of osteogenic differentiation. Our data indicated that AFF4 promoted the osteogenic differentiation of DFCs by upregulating the transcription of ALKBH1.
Collapse
|
24
|
Basu S, Nandy A, Biswas D. Keeping RNA polymerase II on the run: Functions of MLL fusion partners in transcriptional regulation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194563. [PMID: 32348849 DOI: 10.1016/j.bbagrm.2020.194563] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 01/13/2020] [Accepted: 04/13/2020] [Indexed: 12/21/2022]
Abstract
Since the identification of key MLL fusion partners as transcription elongation factors regulating expression of HOX cluster genes during hematopoiesis, extensive work from the last decade has resulted in significant progress in our overall mechanistic understanding of role of MLL fusion partner proteins in transcriptional regulation of diverse set of genes beyond just the HOX cluster. In this review, we are going to detail overall understanding of role of MLL fusion partner proteins in transcriptional regulation and thus provide mechanistic insights into possible MLL fusion protein-mediated transcriptional misregulation leading to aberrant hematopoiesis and leukemogenesis.
Collapse
Affiliation(s)
- Subham Basu
- Laboratory of Transcription Biology, Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 32, India
| | - Arijit Nandy
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Debabrata Biswas
- Laboratory of Transcription Biology, Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 32, India.
| |
Collapse
|
25
|
Tang D, Chen C, Liao G, Liu J, Liao B, Huang Q, Chen Q, Zhao J, Jiang H, Duan J, Huang J, Wang K, Wang J, Zhou C, Chu W, Li W, Sun B, Li Z, Dai L, Fu X, Cheng W, Xue Y, Qi S. Structural and functional insight into the effect of AFF4 dimerization on activation of HIV-1 proviral transcription. Cell Discov 2020; 6:7. [PMID: 32128251 PMCID: PMC7026398 DOI: 10.1038/s41421-020-0142-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 12/23/2019] [Indexed: 02/05/2023] Open
Abstract
Super elongation complex (SEC) is a positive regulator of RNA polymerase II, which is required for HIV-1 proviral transcription. AFF1/4 is the scaffold protein that recruits other components of SEC and forms dimer depending on its THD domain (TPRL with Handle Region Dimerization Domain). Here we report the crystal structure of the human AFF4-THD at the resolution of 2.4 Å. The α4, α5, and α6 of one AFF4-THD mediate the formation of a dimer and pack tightly against the equivalent part of the second molecule in the dimer of AFF-THD. Mutagenesis analysis revealed that single mutations of either Phe1014 or Tyr1096 of AFF4 to alanine impair the formation of the AFF4 dimer. In addition, transactivation assay also indicated that Phe1014 and Tyr1096 of AFF4 are critical to the transactivation activity of AFF4. Interestingly, the corresponding residues Phe1063 and Tyr1145 in AFF1 have an effect on the transactivation of HIV-1 provirus. However, such mutations of AFF1/4 have no effect on the interaction of AFF1/4 with other subunits of the SEC. Together, our data demonstrated that the dimerization of AFF1/4 is essential to transactivation of HIV-1 provirus.
Collapse
Affiliation(s)
- Dan Tang
- Department of Urology, State Key Laboratory of Biotherapy, West China Hospital, College of Life Sciences, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041 China
| | - Chunjing Chen
- School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian 361102 China
| | - Ga Liao
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041 China
| | - Jiaming Liu
- Department of Urology, State Key Laboratory of Biotherapy, West China Hospital, College of Life Sciences, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041 China
| | - Banghua Liao
- Department of Urology, State Key Laboratory of Biotherapy, West China Hospital, College of Life Sciences, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041 China
| | - QingQing Huang
- School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian 361102 China
| | - Qianqian Chen
- Department of Urology, State Key Laboratory of Biotherapy, West China Hospital, College of Life Sciences, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041 China
| | - Jiahui Zhao
- Department of Urology, State Key Laboratory of Biotherapy, West China Hospital, College of Life Sciences, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041 China
| | - Hui Jiang
- Department of Urology, State Key Laboratory of Biotherapy, West China Hospital, College of Life Sciences, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041 China
| | - Jinsong Duan
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084 China
| | - Jin Huang
- Department of Urology, State Key Laboratory of Biotherapy, West China Hospital, College of Life Sciences, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041 China
| | - Kunjie Wang
- Department of Urology, State Key Laboratory of Biotherapy, West China Hospital, College of Life Sciences, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041 China
| | - Jiawei Wang
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084 China
| | - Cuiyan Zhou
- School of Biomedicine in Tsinghua University, National Protein Science Facility, Beijing, 100084 China
| | - Wendan Chu
- School of Biomedicine in Tsinghua University, National Protein Science Facility, Beijing, 100084 China
| | - Wenqi Li
- School of Biomedicine in Tsinghua University, National Protein Science Facility, Beijing, 100084 China
| | - Bo Sun
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201204 China
| | - Zhonghan Li
- Department of Urology, State Key Laboratory of Biotherapy, West China Hospital, College of Life Sciences, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041 China
| | - Lunzhi Dai
- Department of Urology, State Key Laboratory of Biotherapy, West China Hospital, College of Life Sciences, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041 China
| | - Xianghui Fu
- Department of Urology, State Key Laboratory of Biotherapy, West China Hospital, College of Life Sciences, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041 China
| | - Wei Cheng
- Department of Urology, State Key Laboratory of Biotherapy, West China Hospital, College of Life Sciences, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041 China
| | - Yuhua Xue
- School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian 361102 China
| | - Shiqian Qi
- Department of Urology, State Key Laboratory of Biotherapy, West China Hospital, College of Life Sciences, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041 China
| |
Collapse
|
26
|
AFF1 acetylation by p300 temporally inhibits transcription during genotoxic stress response. Proc Natl Acad Sci U S A 2019; 116:22140-22151. [PMID: 31611376 PMCID: PMC6823056 DOI: 10.1073/pnas.1907097116] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Mammalian cells are constantly exposed to genotoxic agents that can lead to DNA damage, genomic instability, and diseases, including cancers. Maintenance of genomic stability, a prerequisite for survival and proper functions of cells, is facilitated by the cellular DNA repair machinery. One of the earliest responses to DNA damage is a transient inhibition of transcription to avoid fatal collisions between the DNA repair and transcriptional machineries. However, the mechanisms underlying this early transcriptional inhibition are poorly understood. Our study establishes a critical role for AFF1, a key component of super elongation complex, in early transcription inhibition and cell survival upon DNA damage, as well as a mechanism involving p300-mediated acetylation of AFF1 and consequent inactivation of the super elongation complex. Soon after exposure to genotoxic reagents, mammalian cells inhibit transcription to prevent collisions with repair machinery and to mount a proper DNA damage response. However, mechanisms underlying early transcriptional inhibition are poorly understood. In this report, we show that site-specific acetylation of super elongation complex (SEC) subunit AFF1 by p300 reduces its interaction with other SEC components and impairs P-TEFb−mediated C-terminal domain phosphorylation of RNA polymerase II both in vitro and in vivo. Reexpression of wild-type AFF1, but not an acetylation mimic mutant, restores SEC component recruitment and target gene expression in AFF1 knockdown cells. Physiologically, we show that, upon genotoxic exposure, p300-mediated AFF1 acetylation is dynamic and strongly correlated with concomitant global down-regulation of transcription—and that this can be reversed by overexpression of an acetylation-defective AFF1 mutant. Therefore, we describe a mechanism of dynamic transcriptional regulation involving p300-mediated acetylation of a key elongation factor during genotoxic stress.
Collapse
|
27
|
Chen Y, Cramer P. Structure of the super-elongation complex subunit AFF4 C-terminal homology domain reveals requirements for AFF homo- and heterodimerization. J Biol Chem 2019; 294:10663-10673. [PMID: 31147444 PMCID: PMC6615702 DOI: 10.1074/jbc.ra119.008577] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 05/27/2019] [Indexed: 12/12/2022] Open
Abstract
AF4/FMR2 family member 4 (AFF4) is the scaffold protein of the multisubunit super-elongation complex, which plays key roles in the release of RNA polymerase II from promoter-proximal pausing and in the transactivation of HIV-1 transcription. AFF4 consists of an intrinsically disordered N-terminal region that interacts with other super-elongation complex subunits and a C-terminal homology domain (CHD) that is conserved among AF4/FMR2 family proteins, including AFF1, AFF2, AFF3, and AFF4. Here, we solved the X-ray crystal structure of the CHD in human AFF4 (AFF4-CHD) to 2.2 Å resolution and characterized its biochemical properties. The structure disclosed that AFF4-CHD folds into a novel domain that consists of eight helices and is distantly related to tetratrico peptide repeat motifs. Our analyses further revealed that AFF4-CHD mediates the formation of an AFF4 homodimer or an AFF1-AFF4 heterodimer. Results from fluorescence anisotropy experiments suggested that AFF4-CHD interacts with both RNA and DNA in vitro Furthermore, we identified a surface loop region in AFF4-CHD as a substrate for the P-TEFb kinase cyclin-dependent kinase 9, which triggers release of polymerase II from promoter-proximal pausing sites. In conclusion, the AFF-CHD structure and biochemical analyses reported here reveal the molecular basis for the homo- and heterodimerization of AFF proteins and implicate the AFF4-CHD in nucleic acid interactions. The high conservation of the CHD among several other proteins suggests that our results are also relevant for understanding other CHD-containing proteins and their dimerization behavior.
Collapse
Affiliation(s)
- Ying Chen
- From the Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Patrick Cramer
- From the Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| |
Collapse
|
28
|
Krasnopolsky S, Marom L, Victor RA, Kuzmina A, Schwartz JC, Fujinaga K, Taube R. Fused in sarcoma silences HIV gene transcription and maintains viral latency through suppressing AFF4 gene activation. Retrovirology 2019; 16:16. [PMID: 31238957 PMCID: PMC6593535 DOI: 10.1186/s12977-019-0478-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 06/11/2019] [Indexed: 12/12/2022] Open
Abstract
Background The human immunodeficiency virus (HIV) cell reservoir is currently a main obstacle towards complete eradication of the virus. This infected pool is refractory to anti-viral therapy and harbors integrated proviruses that are transcriptionally repressed but replication competent. As transcription silencing is key for establishing the HIV reservoir, significant efforts have been made to understand the mechanism that regulate HIV gene transcription, and the role of the elongation machinery in promoting this step. However, while the role of the super elongation complex (SEC) in enhancing transcription activation of HIV is well established, the function of SEC in modulating viral latency is less defined and its cell partners are yet to be identified. Results In this study we identify fused in sarcoma (FUS) as a partner of AFF4 in cells. FUS inhibits the activation of HIV transcription by AFF4 and ELL2, and silences overall HIV gene transcription. Concordantly, depletion of FUS elevates the occupancy of AFF4 and Cdk9 on the viral promoter and activates HIV gene transcription. Live cell imaging demonstrates that FUS co-localizes with AFF4 within nuclear punctuated condensates, which are disrupted upon treating cells with aliphatic alcohol. In HIV infected cells, knockout of FUS delays the gradual entry of HIV into latency, and similarly promotes viral activation in a T cell latency model that is treated with JQ1. Finally, effects of FUS on HIV gene transcription are also exhibited genome wide, where FUS mainly occupies gene promoters at transcription starting sites, while its knockdown leads to an increase in AFF4 and Cdk9 occupancy on gene promoters of FUS affected genes. Conclusions Towards eliminating the HIV infected reservoir, understanding the mechanisms by which the virus persists in the face of therapy is important. Our observations show that FUS regulates both HIV and global gene transcription and modulates viral latency, thus can potentially serve as a target for future therapy that sets to reactivate HIV from its latent state. Electronic supplementary material The online version of this article (10.1186/s12977-019-0478-x) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Simona Krasnopolsky
- The Shraga Segal Department of Microbiology Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, 84105, Beer Sheva, Israel
| | - Lital Marom
- The Shraga Segal Department of Microbiology Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, 84105, Beer Sheva, Israel
| | - Rachel A Victor
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, USA
| | - Alona Kuzmina
- The Shraga Segal Department of Microbiology Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, 84105, Beer Sheva, Israel
| | - Jacob C Schwartz
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, USA
| | - Koh Fujinaga
- Department of Medicine, University of California, San Francisco, CA, USA
| | - Ran Taube
- The Shraga Segal Department of Microbiology Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, 84105, Beer Sheva, Israel.
| |
Collapse
|
29
|
Wood DJ, Endicott JA. Structural insights into the functional diversity of the CDK-cyclin family. Open Biol 2019; 8:rsob.180112. [PMID: 30185601 PMCID: PMC6170502 DOI: 10.1098/rsob.180112] [Citation(s) in RCA: 141] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 08/10/2018] [Indexed: 12/17/2022] Open
Abstract
Since their characterization as conserved modules that regulate progression through the eukaryotic cell cycle, cyclin-dependent protein kinases (CDKs) in higher eukaryotic cells are now also emerging as significant regulators of transcription, metabolism and cell differentiation. The cyclins, though originally characterized as CDK partners, also have CDK-independent roles that include the regulation of DNA damage repair and transcriptional programmes that direct cell differentiation, apoptosis and metabolic flux. This review compares the structures of the members of the CDK and cyclin families determined by X-ray crystallography, and considers what mechanistic insights they provide to guide functional studies and distinguish CDK- and cyclin-specific activities. Aberrant CDK activity is a hallmark of a number of diseases, and structural studies can provide important insights to identify novel routes to therapy.
Collapse
Affiliation(s)
- Daniel J Wood
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Medical School, Newcastle University, Paul O'Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Jane A Endicott
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Medical School, Newcastle University, Paul O'Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| |
Collapse
|
30
|
Cat and Mouse: HIV Transcription in Latency, Immune Evasion and Cure/Remission Strategies. Viruses 2019; 11:v11030269. [PMID: 30889861 PMCID: PMC6466452 DOI: 10.3390/v11030269] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 03/04/2019] [Accepted: 03/13/2019] [Indexed: 12/13/2022] Open
Abstract
There is broad scientific and societal consensus that finding a cure for HIV infection must be pursued. The major barrier to achieving a cure for HIV/AIDS is the capacity of the HIV virus to avoid both immune surveillance and current antiretroviral therapy (ART) by rapidly establishing latently infected cell populations, termed latent reservoirs. Here, we provide an overview of the rapidly evolving field of HIV cure/remission research, highlighting recent progress and ongoing challenges in the understanding of HIV reservoirs, the role of HIV transcription in latency and immune evasion. We review the major approaches towards a cure that are currently being explored and further argue that small molecules that inhibit HIV transcription, and therefore uncouple HIV gene expression from signals sent by the host immune response, might be a particularly promising approach to attain a cure or remission. We emphasize that a better understanding of the game of "cat and mouse" between the host immune system and the HIV virus is a crucial knowledge gap to be filled in both cure and vaccine research.
Collapse
|
31
|
Structural mechanism for HIV-1 TAR loop recognition by Tat and the super elongation complex. Proc Natl Acad Sci U S A 2018; 115:12973-12978. [PMID: 30514815 DOI: 10.1073/pnas.1806438115] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Promoter-proximal pausing by RNA polymerase II (Pol II) is a key regulatory step in human immunodeficiency virus-1 (HIV-1) transcription and thus in the reversal of HIV latency. By binding to the nascent transactivating response region (TAR) RNA, HIV-1 Tat recruits the human super elongation complex (SEC) to the promoter and releases paused Pol II. Structural studies of TAR interactions have been largely focused on interactions between the TAR bulge and the arginine-rich motif (ARM) of Tat. Here, the crystal structure of the TAR loop in complex with Tat and the SEC core was determined at a 3.5-Å resolution. The bound TAR loop is stabilized by cross-loop hydrogen bonds. It makes structure-specific contacts with the side chains of the Cyclin T1 Tat-TAR recognition motif (TRM) and the zinc-coordinating loop of Tat. The TAR loop phosphate backbone forms electrostatic and VDW interactions with positively charged side chains of the CycT1 TRM. Mutational analysis showed that these interactions contribute importantly to binding affinity. The Tat ARM was present in the crystallized construct; however, it was not visualized in the electron density, and the TAR bulge was not formed in the RNA construct used in crystallization. Binding assays showed that TAR bulge-Tat ARM interactions contribute less to TAR binding affinity than TAR loop interactions with the CycT1 TRM and Tat core. Thus, the TAR loop evolved to make high-affinity interactions with the TRM while Tat has three roles: scaffolding and stabilizing the TRM, making specific interactions through its zinc-coordinating loop, and making electrostatic interactions through its ARM.
Collapse
|
32
|
Liang K, Smith ER, Aoi Y, Stoltz KL, Katagi H, Woodfin AR, Rendleman EJ, Marshall SA, Murray DC, Wang L, Ozark PA, Mishra RK, Hashizume R, Schiltz GE, Shilatifard A. Targeting Processive Transcription Elongation via SEC Disruption for MYC-Induced Cancer Therapy. Cell 2018; 175:766-779.e17. [PMID: 30340042 PMCID: PMC6422358 DOI: 10.1016/j.cell.2018.09.027] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 07/02/2018] [Accepted: 09/13/2018] [Indexed: 11/15/2022]
Abstract
The super elongation complex (SEC) is required for robust and productive transcription through release of RNA polymerase II (Pol II) with its P-TEFb module and promoting transcriptional processivity with its ELL2 subunit. Malfunction of SEC contributes to multiple human diseases including cancer. Here, we identify peptidomimetic lead compounds, KL-1 and its structural homolog KL-2, which disrupt the interaction between the SEC scaffolding protein AFF4 and P-TEFb, resulting in impaired release of Pol II from promoter-proximal pause sites and a reduced average rate of processive transcription elongation. SEC is required for induction of heat-shock genes and treating cells with KL-1 and KL-2 attenuates the heat-shock response from Drosophila to human. SEC inhibition downregulates MYC and MYC-dependent transcriptional programs in mammalian cells and delays tumor progression in a mouse xenograft model of MYC-driven cancer, indicating that small-molecule disruptors of SEC could be used for targeted therapy of MYC-induced cancer.
Collapse
Affiliation(s)
- Kaiwei Liang
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA,Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Edwin R. Smith
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA,Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA,Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, 303 E. Superior St., Chicago, IL 60611, USA
| | - Yuki Aoi
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA,Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Kristen L. Stoltz
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA,Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA,Center for Molecular Innovation and Drug Discovery, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Hiroaki Katagi
- Department of Neurosurgery, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Ashley R. Woodfin
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA,Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Emily J. Rendleman
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA,Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Stacy A. Marshall
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA,Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - David C. Murray
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA,Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Lu Wang
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA,Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Patrick A. Ozark
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA,Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Rama K. Mishra
- Center for Molecular Innovation and Drug Discovery, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA,Department of Pharmacology, Northwestern University Feinberg School of Medicine, 303 E. Superior St., Chicago, IL 60611, USA
| | - Rintaro Hashizume
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA,Department of Neurosurgery, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA,Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, 303 E. Superior St., Chicago, IL 60611, USA
| | - Gary E. Schiltz
- Center for Molecular Innovation and Drug Discovery, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA,Department of Pharmacology, Northwestern University Feinberg School of Medicine, 303 E. Superior St., Chicago, IL 60611, USA,Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, 303 E. Superior St., Chicago, IL 60611, USA
| | - Ali Shilatifard
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg, School of Medicine, 303 E. Superior Street, Chicago, IL 60611, USA.
| |
Collapse
|
33
|
Abstract
BACKGROUND The viral transactivator Tat protein is a key modulator of HIV-1 replication, as it regulates transcriptional elongation from the integrated proviral genome. Tat recruits the human transcription elongation factor b, and other host proteins, such as the super elongation complex, to activate the cellular RNA polymerase II, normally stalled shortly after transcription initiation at the HIV promoter. By means of a complex set of interactions with host cellular factors, Tat determines the fate of viral activity within the infected cell. The virus will either actively replicate to promote dissemination in blood and tissues, or become dormant mostly in memory CD4+ T cells, as part of a small but long-living latent reservoir, the main obstacle for HIV eradication. OBJECTIVE In this review, we summarize recent advances in the understanding of the multi-step mechanism that regulates Tat-mediated HIV-1 transcription and RNA polymerase II release, to promote viral transcription elongation. Early events of the human transcription elongation factor b release from the inhibitory 7SK small nuclear ribonucleoprotein complex and its recruitment to the HIV promoter will be discussed. Specific roles of the super elongation complex subunits during transcription elongation, and insight on recently identified cellular factors and mechanisms regulating HIV latency will be detailed. CONCLUSION Understanding the complexity of HIV transcriptional regulation by host factors may open the door for development of novel strategies to eradicate the resilient latent reservoir.
Collapse
Affiliation(s)
- Guillaume Mousseau
- The Scripps Research Institute, Department of Immunology and Microbiology, 130 Scripps Way, Jupiter, FL 33458. United States
| | - Susana T Valente
- The Scripps Research Institute, Department of Immunology and Microbiology, 130 Scripps Way, Jupiter, FL 33458. United States
| |
Collapse
|
34
|
Singh U, Chashoo G, Khan SU, Mahajan P, Nargotra A, Mahajan G, Singh A, Sharma A, Mintoo MJ, Guru SK, Aruri H, Thatikonda T, Sahu P, Chibber P, Kumar V, Mir SA, Bharate SS, Madishetti S, Nandi U, Singh G, Mondhe DM, Bhushan S, Malik F, Mignani S, Vishwakarma RA, Singh PP. Design of Novel 3-Pyrimidinylazaindole CDK2/9 Inhibitors with Potent In Vitro and In Vivo Antitumor Efficacy in a Triple-Negative Breast Cancer Model. J Med Chem 2017; 60:9470-9489. [DOI: 10.1021/acs.jmedchem.7b00663] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Umed Singh
- Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Academy of Scientific and Innovative Research, Canal Road, Jammu, Jammu & Kashmir-180001, India
| | - Gousia Chashoo
- Cancer Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Academy of Scientific and Innovative Research, Canal Road, Jammu, Jammu & Kashmir-180001, India
| | - Sameer U. Khan
- Cancer Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Academy of Scientific and Innovative Research, Canal Road, Jammu, Jammu & Kashmir-180001, India
| | - Priya Mahajan
- Discovery Informatics, CSIR-Indian Institute of Integrative Medicine, Academy of Scientific and Innovative Research, Canal Road, Jammu, Jammu & Kashmir-180001, India
| | - Amit Nargotra
- Discovery Informatics, CSIR-Indian Institute of Integrative Medicine, Academy of Scientific and Innovative Research, Canal Road, Jammu, Jammu & Kashmir-180001, India
| | - Girish Mahajan
- Cancer Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Academy of Scientific and Innovative Research, Canal Road, Jammu, Jammu & Kashmir-180001, India
| | - Amarinder Singh
- Pharmacokinetic & Pharmacodynamic Division, CSIR-Indian Institute of Integrative Medicine, Academy of Scientific and Innovative Research, Canal Road, Jammu, Jammu & Kashmir-180001, India
| | - Anjna Sharma
- Pharmacokinetic & Pharmacodynamic Division, CSIR-Indian Institute of Integrative Medicine, Academy of Scientific and Innovative Research, Canal Road, Jammu, Jammu & Kashmir-180001, India
| | - Mubashir J. Mintoo
- Cancer Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Academy of Scientific and Innovative Research, Canal Road, Jammu, Jammu & Kashmir-180001, India
| | - Santosh Kumar Guru
- Cancer Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Academy of Scientific and Innovative Research, Canal Road, Jammu, Jammu & Kashmir-180001, India
| | - Hariprasad Aruri
- Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Academy of Scientific and Innovative Research, Canal Road, Jammu, Jammu & Kashmir-180001, India
| | - Thanusha Thatikonda
- Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Academy of Scientific and Innovative Research, Canal Road, Jammu, Jammu & Kashmir-180001, India
| | - Promod Sahu
- Pharmacokinetic & Pharmacodynamic Division, CSIR-Indian Institute of Integrative Medicine, Academy of Scientific and Innovative Research, Canal Road, Jammu, Jammu & Kashmir-180001, India
| | - Pankaj Chibber
- Pharmacokinetic & Pharmacodynamic Division, CSIR-Indian Institute of Integrative Medicine, Academy of Scientific and Innovative Research, Canal Road, Jammu, Jammu & Kashmir-180001, India
| | - Vikas Kumar
- Preformulation Division, CSIR-Indian Institute of Integrative Medicine, Academy of Scientific and Innovative Research, Canal Road, Jammu, Jammu & Kashmir-180001, India
| | - Sameer A. Mir
- Cancer Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Academy of Scientific and Innovative Research, Canal Road, Jammu, Jammu & Kashmir-180001, India
| | - Sonali S. Bharate
- Preformulation Division, CSIR-Indian Institute of Integrative Medicine, Academy of Scientific and Innovative Research, Canal Road, Jammu, Jammu & Kashmir-180001, India
| | - Sreedhar Madishetti
- Pharmacokinetic & Pharmacodynamic Division, CSIR-Indian Institute of Integrative Medicine, Academy of Scientific and Innovative Research, Canal Road, Jammu, Jammu & Kashmir-180001, India
| | - Utpal Nandi
- Pharmacokinetic & Pharmacodynamic Division, CSIR-Indian Institute of Integrative Medicine, Academy of Scientific and Innovative Research, Canal Road, Jammu, Jammu & Kashmir-180001, India
| | - Gurdarshan Singh
- Pharmacokinetic & Pharmacodynamic Division, CSIR-Indian Institute of Integrative Medicine, Academy of Scientific and Innovative Research, Canal Road, Jammu, Jammu & Kashmir-180001, India
| | - Dilip Manikrao Mondhe
- Cancer Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Academy of Scientific and Innovative Research, Canal Road, Jammu, Jammu & Kashmir-180001, India
| | - Shashi Bhushan
- Cancer Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Academy of Scientific and Innovative Research, Canal Road, Jammu, Jammu & Kashmir-180001, India
- Indian Pharmacopoeia Commission, Sector-23, Raj Nagar, Ghaziabad-201002, India
| | - Fayaz Malik
- Cancer Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Academy of Scientific and Innovative Research, Canal Road, Jammu, Jammu & Kashmir-180001, India
| | - Serge Mignani
- Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Academy of Scientific and Innovative Research, Canal Road, Jammu, Jammu & Kashmir-180001, India
- PRES Sorbonne
Paris Cité, CNRS UMR 860, Laboratoire de Chimie et de Biochimie
Pharmacologiques et Toxicologique, Université Paris Descartes, 45,
rue des Saints Péres, 75006 Paris, France
| | - Ram A. Vishwakarma
- Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Academy of Scientific and Innovative Research, Canal Road, Jammu, Jammu & Kashmir-180001, India
| | - Parvinder Pal Singh
- Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Academy of Scientific and Innovative Research, Canal Road, Jammu, Jammu & Kashmir-180001, India
| |
Collapse
|
35
|
Stetz G, Tse A, Verkhivker GM. Ensemble-based modeling and rigidity decomposition of allosteric interaction networks and communication pathways in cyclin-dependent kinases: Differentiating kinase clients of the Hsp90-Cdc37 chaperone. PLoS One 2017; 12:e0186089. [PMID: 29095844 PMCID: PMC5667858 DOI: 10.1371/journal.pone.0186089] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 09/25/2017] [Indexed: 12/24/2022] Open
Abstract
The overarching goal of delineating molecular principles underlying differentiation of protein kinase clients and chaperone-based modulation of kinase activity is fundamental to understanding activity of many oncogenic kinases that require chaperoning of Hsp70 and Hsp90 systems to attain a functionally competent active form. Despite structural similarities and common activation mechanisms shared by cyclin-dependent kinase (CDK) proteins, members of this family can exhibit vastly different chaperone preferences. The molecular determinants underlying chaperone dependencies of protein kinases are not fully understood as structurally similar kinases may often elicit distinct regulatory responses to the chaperone. The regulatory divergences observed for members of CDK family are of particular interest as functional diversification among these kinases may be related to variations in chaperone dependencies and can be exploited in drug discovery of personalized therapeutic agents. In this work, we report the results of a computational investigation of several members of CDK family (CDK5, CDK6, CDK9) that represented a broad repertoire of chaperone dependencies—from nonclient CDK5, to weak client CDK6, and strong client CDK9. By using molecular simulations of multiple crystal structures we characterized conformational ensembles and collective dynamics of CDK proteins. We found that the elevated dynamics of CDK9 can trigger imbalances in cooperative collective motions and reduce stability of the active fold, thus creating a cascade of favorable conditions for chaperone intervention. The ensemble-based modeling of residue interaction networks and community analysis determined how differences in modularity of allosteric networks and topography of communication pathways can be linked with the client status of CDK proteins. This analysis unveiled depleted modularity of the allosteric network in CDK9 that alters distribution of communication pathways and leads to impaired signaling in the client kinase. According to our results, these network features may uniquely define chaperone dependencies of CDK clients. The perturbation response scanning and rigidity decomposition approaches identified regulatory hotspots that mediate differences in stability and cooperativity of allosteric interaction networks in the CDK structures. By combining these synergistic approaches, our study revealed dynamic and network signatures that can differentiate kinase clients and rationalize subtle divergences in the activation mechanisms of CDK family members. The therapeutic implications of these results are illustrated by identifying structural hotspots of pathogenic mutations that preferentially target regions of the increased flexibility to enable modulation of activation changes. Our study offers a network-based perspective on dynamic kinase mechanisms and drug design by unravelling relationships between protein kinase dynamics, allosteric communications and chaperone dependencies.
Collapse
Affiliation(s)
- Gabrielle Stetz
- Department of Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California, United States of America
| | - Amanda Tse
- Department of Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California, United States of America
| | - Gennady M. Verkhivker
- Department of Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California, United States of America
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, California, United States of America
- * E-mail:
| |
Collapse
|
36
|
Affiliation(s)
- Uri Mbonye
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106
| | - Jonathan Karn
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106
| |
Collapse
|
37
|
Paparidis NFDS, Durvale MC, Canduri F. The emerging picture of CDK9/P-TEFb: more than 20 years of advances since PITALRE. MOLECULAR BIOSYSTEMS 2017; 13:246-276. [PMID: 27833949 DOI: 10.1039/c6mb00387g] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
CDK9 is a prominent member of the transcriptional CDKs subfamily, a group of kinases whose function is to control the primary steps of mRNA synthesis and processing by eukaryotic RNA polymerase II. As a cyclin-dependent kinase, CDK9 activation in vivo depends upon its association with T-type cyclins to assemble the positive transcription elongation factor (P-TEFb). Although CDK9/P-TEFb phosphorylates the C-terminal domain of RNAP II in the same positions targeted by CDK7 (TFIIH) and CDK8 (Mediator), the former does not participate in the transcription initiation, but rather plays a unique role by driving the polymerase to productive elongation. In addition to RNAP II CTD, the negative transcription elongation factors DSIF and NELF also represent major CDK9 substrates, whose phosphorylation is required to overcome the proximal pause of the polymerase. CDK9 is recruited to specific genes through proteins that interact with both P-TEFb and distinct elements in DNA, RNA or chromatin, where it modulates the activity of individual RNAP II transcription complexes. The regulation of CDK9 function is an intricate network that includes post-translational modifications (phosphorylation/dephosphorylation and acetylation/deacetylation of key residues) as well as the association of P-TEFb with various proteins that can stimulate or inhibit its kinase activity. Several cases of CDK9 deregulation have been linked to important human diseases, including various types of cancer and also AIDS (due to its essential role in HIV replication). Not only HIV, but also many other human viruses have been shown to depend strongly on CDK9 activity to be transcribed within host cells. This review summarizes the main advances made on CDK9/P-TEFb field in more than 20 years, introducing the structural, functional and genetic aspects that have been elucidated ever since.
Collapse
Affiliation(s)
- Nikolas Ferreira Dos Santos Paparidis
- Department of Chemistry and Molecular Physics, Institute of Chemistry of Sao Carlos, Sao Paulo University, Av. Trabalhador Sãocarlense, 400, Zip Code 780, 13560-970, São Carlos-SP, Brazil.
| | - Maxwell Castro Durvale
- Department of Biochemistry, Institute of Chemistry, Sao Paulo University, Av. Prof. Lineu Prestes, 748, 05508-000, Butantã - São Paulo - SP, Brazil
| | - Fernanda Canduri
- Department of Chemistry and Molecular Physics, Institute of Chemistry of Sao Carlos, Sao Paulo University, Av. Trabalhador Sãocarlense, 400, Zip Code 780, 13560-970, São Carlos-SP, Brazil.
| |
Collapse
|
38
|
Liu K, Shen D, Shen J, Gao SM, Li B, Wong C, Feng W, Song Y. The Super Elongation Complex Drives Neural Stem Cell Fate Commitment. Dev Cell 2017; 40:537-551.e6. [PMID: 28350987 DOI: 10.1016/j.devcel.2017.02.022] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 01/13/2017] [Accepted: 02/26/2017] [Indexed: 10/19/2022]
Abstract
Asymmetric stem cell division establishes an initial difference between a stem cell and its differentiating sibling, critical for maintaining homeostasis and preventing carcinogenesis. Yet the mechanisms that consolidate and lock in such initial fate bias remain obscure. Here, we use Drosophila neuroblasts to demonstrate that the super elongation complex (SEC) acts as an intrinsic amplifier to drive cell fate commitment. SEC is highly expressed in neuroblasts, where it promotes self-renewal by physically associating with Notch transcription activation complex and enhancing HES (hairy and E(spl)) transcription. HES in turn upregulates SEC activity, forming an unexpected self-reinforcing feedback loop with SEC. SEC inactivation leads to neuroblast loss, whereas its forced activation results in neural progenitor dedifferentiation and tumorigenesis. Our studies unveil an SEC-mediated intracellular amplifier mechanism in ensuring robustness and precision in stem cell fate commitment and provide mechanistic explanation for the highly frequent association of SEC overactivation with human cancers.
Collapse
Affiliation(s)
- Kun Liu
- Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Dan Shen
- Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China
| | - Jingwen Shen
- Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China
| | - Shihong M Gao
- Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China
| | - Bo Li
- Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China
| | - Chouin Wong
- Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China
| | - Weidong Feng
- Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China
| | - Yan Song
- Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China.
| |
Collapse
|
39
|
Meyer NO, O'Donoghue AJ, Schulze-Gahmen U, Ravalin M, Moss SM, Winter MB, Knudsen GM, Craik CS. Multiplex Substrate Profiling by Mass Spectrometry for Kinases as a Method for Revealing Quantitative Substrate Motifs. Anal Chem 2017; 89:4550-4558. [PMID: 28322550 DOI: 10.1021/acs.analchem.6b05002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The more than 500 protein kinases comprising the human kinome catalyze hundreds of thousands of phosphorylation events to regulate a diversity of cellular functions; however, the extended substrate specificity is still unknown for many of these kinases. We report here a method for quantitatively describing kinase substrate specificity using an unbiased peptide library-based approach with direct measurement of phosphorylation by tandem liquid chromatography-tandem mass spectrometry (LC-MS/MS) peptide sequencing (multiplex substrate profiling by mass spectrometry, MSP-MS). This method can be deployed with as low as 10 nM enzyme to determine activity against S/T/Y-containing peptides; additionally, label-free quantitation is used to ascertain catalytic efficiency values for individual peptide substrates in the multiplex assay. Using this approach we developed quantitative motifs for a selection of kinases from each branch of the kinome, with and without known substrates, highlighting the applicability of the method. The sensitivity of this approach is evidenced by its ability to detect phosphorylation events from nanogram quantities of immunoprecipitated material, which allows for wider applicability of this method. To increase the information content of the quantitative kinase motifs, a sublibrary approach was used to expand the testable sequence space within a peptide library of approximately 100 members for CDK1, CDK7, and CDK9. Kinetic analysis of the HIV-1 Tat (transactivator of transcription)-positive transcription elongation factor b (P-TEFb) interaction allowed for localization of the P-TEFb phosphorylation site as well as characterization of the stimulatory effect of Tat on P-TEFb catalytic efficiency.
Collapse
Affiliation(s)
- Nicole O Meyer
- Department of Pharmaceutical Chemistry, University of California San Francisco , San Francisco, California 94158, United States
| | - Anthony J O'Donoghue
- Department of Pharmaceutical Chemistry, University of California San Francisco , San Francisco, California 94158, United States
| | - Ursula Schulze-Gahmen
- Department of Molecular and Cell Biology, University of California Berkeley , Berkeley, California 94720, United States
| | - Matthew Ravalin
- Department of Pharmaceutical Chemistry, University of California San Francisco , San Francisco, California 94158, United States
| | - Steven M Moss
- Department of Pharmaceutical Chemistry, University of California San Francisco , San Francisco, California 94158, United States
| | - Michael B Winter
- Department of Pharmaceutical Chemistry, University of California San Francisco , San Francisco, California 94158, United States
| | - Giselle M Knudsen
- Department of Pharmaceutical Chemistry, University of California San Francisco , San Francisco, California 94158, United States
| | - Charles S Craik
- Department of Pharmaceutical Chemistry, University of California San Francisco , San Francisco, California 94158, United States
| |
Collapse
|
40
|
Kuzmina A, Krasnopolsky S, Taube R. Super elongation complex promotes early HIV transcription and its function is modulated by P-TEFb. Transcription 2017; 8:133-149. [PMID: 28340332 DOI: 10.1080/21541264.2017.1295831] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Early work on the control of transcription of the human immunodeficiency virus (HIV) laid the foundation for our current knowledge of how RNA Polymerase II is released from promoter-proximal pausing sites and transcription elongation is enhanced. The viral Tat activator recruits Positive Transcription Elongation Factor b (P-TEFb) and Super Elongation Complex (SEC) that jointly drive transcription elongation. While substantial progress in understanding the role of SEC in HIV gene transcription elongation has been obtained, defining of the mechanisms that govern SEC functions is still limited, and the role of SEC in controlling HIV transcription in the absence of Tat is less clear. Here we revisit the contribution of SEC in early steps of HIV gene transcription. In the absence of Tat, the AF4/FMR2 Family member 4 (AFF4) of SEC efficiently activates HIV transcription, while gene activation by its homolog AFF1 is substantially lower. Differential recruitment to the HIV promoter and association with Human Polymerase-Associated Factor complex (PAFc) play key role in this functional distinction between AFF4 and AFF1. Moreover, while depletion of cyclin T1 expression has subtle effects on HIV gene transcription in the absence of Tat, knockout (KO) of AFF1, AFF4, or both proteins slightly repress this early step of viral transcription. Upon Tat expression, HIV transcription reaches optimal levels despite KO of AFF1 or AFF4 expression. However, double AFF1/AFF4 KO completely diminishes Tat trans-activation. Significantly, our results show that P-TEFb phosphorylates AFF4 and modulates SEC assembly, AFF1/4 dimerization and recruitment to the viral promoter. We conclude that SEC promotes both early steps of HIV transcription in the absence of Tat, as well as elongation of transcription, when Tat is expressed. Significantly, SEC functions are modulated by P-TEFb.
Collapse
Affiliation(s)
- Alona Kuzmina
- a The Shraga Segal Department of Microbiology Immunology and Genetics Faculty of Health Sciences , Ben-Gurion University of the Negev , Israel
| | - Simona Krasnopolsky
- a The Shraga Segal Department of Microbiology Immunology and Genetics Faculty of Health Sciences , Ben-Gurion University of the Negev , Israel
| | - Ran Taube
- a The Shraga Segal Department of Microbiology Immunology and Genetics Faculty of Health Sciences , Ben-Gurion University of the Negev , Israel
| |
Collapse
|
41
|
Structural basis for ELL2 and AFF4 activation of HIV-1 proviral transcription. Nat Commun 2017; 8:14076. [PMID: 28134250 PMCID: PMC5290273 DOI: 10.1038/ncomms14076] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 11/28/2016] [Indexed: 02/05/2023] Open
Abstract
The intrinsically disordered scaffold proteins AFF1/4 and the transcription elongation factors ELL1/2 are core components of the super elongation complex required for HIV-1 proviral transcription. Here we report the 2.0-Å resolution crystal structure of the human ELL2 C-terminal domain bound to its 50-residue binding site on AFF4, the ELLBow. The ELL2 domain has the same arch-shaped fold as the tight junction protein occludin. The ELLBow consists of an N-terminal helix followed by an extended hairpin that we refer to as the elbow joint, and occupies most of the concave surface of ELL2. This surface is important for the ability of ELL2 to promote HIV-1 Tat-mediated proviral transcription. The AFF4–ELL2 interface is imperfectly packed, leaving a cavity suggestive of a potential binding site for transcription-promoting small molecules. The host super elongation complex (SEC) is hijacked by HIV-1 for viral transcription. Here the authors present the structure of RNA polymerase elongation factor ELL2 bound to the intrinsically disordered scaffold protein AFF4, identifying an ELL2 surface important for HIV-1 transcription.
Collapse
|
42
|
Schulze-Gahmen U, Echeverria I, Stjepanovic G, Bai Y, Lu H, Schneidman-Duhovny D, Doudna JA, Zhou Q, Sali A, Hurley JH. Insights into HIV-1 proviral transcription from integrative structure and dynamics of the Tat:AFF4:P-TEFb:TAR complex. eLife 2016; 5. [PMID: 27731797 PMCID: PMC5072841 DOI: 10.7554/elife.15910] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 10/07/2016] [Indexed: 01/04/2023] Open
Abstract
HIV-1 Tat hijacks the human superelongation complex (SEC) to promote proviral transcription. Here we report the 5.9 Å structure of HIV-1 TAR in complex with HIV-1 Tat and human AFF4, CDK9, and CycT1. The TAR central loop contacts the CycT1 Tat-TAR recognition motif (TRM) and the second Tat Zn2+-binding loop. Hydrogen-deuterium exchange (HDX) shows that AFF4 helix 2 is stabilized in the TAR complex despite not touching the RNA, explaining how it enhances TAR binding to the SEC 50-fold. RNA SHAPE and SAXS data were used to help model the extended (Tat Arginine-Rich Motif) ARM, which enters the TAR major groove between the bulge and the central loop. The structure and functional assays collectively support an integrative structure and a bipartite binding model, wherein the TAR central loop engages the CycT1 TRM and compact core of Tat, while the TAR major groove interacts with the extended Tat ARM. DOI:http://dx.doi.org/10.7554/eLife.15910.001
Collapse
Affiliation(s)
- Ursula Schulze-Gahmen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,California Institute of Quantitative Biosciences, University of California, Berkeley, Berkeley, United States
| | - Ignacia Echeverria
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States.,Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States.,California Institute of Quantitative Biosciences, University of California San, Francisco, San Francisco, United States
| | - Goran Stjepanovic
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,California Institute of Quantitative Biosciences, University of California, Berkeley, Berkeley, United States.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Yun Bai
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,California Institute of Quantitative Biosciences, University of California, Berkeley, Berkeley, United States
| | - Huasong Lu
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,California Institute of Quantitative Biosciences, University of California, Berkeley, Berkeley, United States
| | - Dina Schneidman-Duhovny
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States.,Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States.,California Institute of Quantitative Biosciences, University of California San, Francisco, San Francisco, United States
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,California Institute of Quantitative Biosciences, University of California, Berkeley, Berkeley, United States.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States.,Department of Chemistry, University of California, Berkeley, Berkeley, United States
| | - Qiang Zhou
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,California Institute of Quantitative Biosciences, University of California, Berkeley, Berkeley, United States
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States.,Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States.,California Institute of Quantitative Biosciences, University of California San, Francisco, San Francisco, United States
| | - James H Hurley
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,California Institute of Quantitative Biosciences, University of California, Berkeley, Berkeley, United States.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States
| |
Collapse
|
43
|
Zhao Y, Karijolich J, Glaunsinger B, Zhou Q. Pseudouridylation of 7SK snRNA promotes 7SK snRNP formation to suppress HIV-1 transcription and escape from latency. EMBO Rep 2016; 17:1441-1451. [PMID: 27558685 DOI: 10.15252/embr.201642682] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 07/28/2016] [Indexed: 12/16/2022] Open
Abstract
The 7SK snRNA sequesters P-TEFb, a general transcription elongation factor and human co-factor for HIV-1 Tat protein, into the catalytically inactive 7SK snRNP Little is known about how 7SK RNA is regulated to perform this function. Here, we show that most of 7SK is pseudouridylated at position U250 by the predominant cellular pseudouridine synthase machinery, the DKC1-box H/ACA RNP Pseudouridylation is critical to stabilize 7SK snRNP, as its abolishment by either mutation at or around U250 or depletion of DKC1, the catalytic component of the box H/ACA RNP, disrupts 7SK snRNP and releases P-TEFb to form the super elongation complex (SEC) and the Brd4-P-TEFb complex. The SEC is then recruited by Tat to the HIV-1 promoter to stimulate viral transcription and escape from latency. Thus, although 7SK RNA levels remain mostly unchanged, its function is modulated by pseudouridylation, which in turn controls transcription of both HIV-1 and cellular genes.
Collapse
Affiliation(s)
- Yang Zhao
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - John Karijolich
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Britt Glaunsinger
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - Qiang Zhou
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| |
Collapse
|
44
|
Vos SM, Pöllmann D, Caizzi L, Hofmann KB, Rombaut P, Zimniak T, Herzog F, Cramer P. Architecture and RNA binding of the human negative elongation factor. eLife 2016; 5. [PMID: 27282391 PMCID: PMC4940160 DOI: 10.7554/elife.14981] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 06/09/2016] [Indexed: 11/30/2022] Open
Abstract
Transcription regulation in metazoans often involves promoter-proximal pausing of RNA polymerase (Pol) II, which requires the 4-subunit negative elongation factor (NELF). Here we discern the functional architecture of human NELF through X-ray crystallography, protein crosslinking, biochemical assays, and RNA crosslinking in cells. We identify a NELF core subcomplex formed by conserved regions in subunits NELF-A and NELF-C, and resolve its crystal structure. The NELF-AC subcomplex binds single-stranded nucleic acids in vitro, and NELF-C associates with RNA in vivo. A positively charged face of NELF-AC is involved in RNA binding, whereas the opposite face of the NELF-AC subcomplex binds NELF-B. NELF-B is predicted to form a HEAT repeat fold, also binds RNA in vivo, and anchors the subunit NELF-E, which is confirmed to bind RNA in vivo. These results reveal the three-dimensional architecture and three RNA-binding faces of NELF. DOI:http://dx.doi.org/10.7554/eLife.14981.001
Collapse
Affiliation(s)
- Seychelle M Vos
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - David Pöllmann
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Gene Center Munich, Ludwig-Maximilians-Universität München, Munich, Germany.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Livia Caizzi
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Katharina B Hofmann
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Pascaline Rombaut
- Gene Center Munich, Ludwig-Maximilians-Universität München, Munich, Germany.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Tomasz Zimniak
- Gene Center Munich, Ludwig-Maximilians-Universität München, Munich, Germany.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Franz Herzog
- Gene Center Munich, Ludwig-Maximilians-Universität München, Munich, Germany.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| |
Collapse
|
45
|
A Minor Subset of Super Elongation Complexes Plays a Predominant Role in Reversing HIV-1 Latency. Mol Cell Biol 2016; 36:1194-205. [PMID: 26830226 DOI: 10.1128/mcb.00994-15] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 01/21/2016] [Indexed: 11/20/2022] Open
Abstract
Promoter-proximal pausing by RNA polymerase II (Pol II) is a key rate-limiting step in HIV-1 transcription and latency reversal. The viral Tat protein recruits human super elongation complexes (SECs) to paused Pol II to overcome this restriction. Despite the recent progress in understanding the functions of different subsets of SECs in controlling cellular and Tat-activated HIV transcription, little is known about the SEC subtypes that help reverse viral latency in CD4(+) T cells. Here, we used the CRISPR-Cas9 genome-editing tool to knock out the gene encoding the SEC subunit ELL2, AFF1, or AFF4 in Jurkat/2D10 cells, a well-characterized HIV-1 latency model. Depletion of these proteins drastically reduced spontaneous and drug-induced latency reversal by suppressing HIV-1 transcriptional elongation. Surprisingly, a low-abundance subset of SECs containing ELL2 and AFF1 was found to play a predominant role in cooperating with Tat to reverse latency. By increasing the cellular level/activity of these Tat-friendly SECs, we could potently activate latent HIV-1 without using any drugs. These results implicate the ELL2/AFF1-SECs as an important target in the future design of a combinatorial therapeutic approach to purge latent HIV-1.
Collapse
|
46
|
Structural and Functional Analysis of the Cdk13/Cyclin K Complex. Cell Rep 2015; 14:320-31. [PMID: 26748711 DOI: 10.1016/j.celrep.2015.12.025] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 10/29/2015] [Accepted: 11/30/2015] [Indexed: 12/20/2022] Open
Abstract
Cyclin-dependent kinases regulate the cell cycle and transcription in higher eukaryotes. We have determined the crystal structure of the transcription kinase Cdk13 and its Cyclin K subunit at 2.0 Å resolution. Cdk13 contains a C-terminal extension helix composed of a polybasic cluster and a DCHEL motif that interacts with the bound ATP. Cdk13/CycK phosphorylates both Ser5 and Ser2 of the RNA polymerase II C-terminal domain (CTD) with a preference for Ser7 pre-phosphorylations at a C-terminal position. The peptidyl-prolyl isomerase Pin1 does not change the phosphorylation specificities of Cdk9, Cdk12, and Cdk13 but interacts with the phosphorylated CTD through its WW domain. Using recombinant proteins, we find that flavopiridol inhibits Cdk7 more potently than it does Cdk13. Gene expression changes after knockdown of Cdk13 or Cdk12 are markedly different, with enrichment of growth signaling pathways for Cdk13-dependent genes. Together, our results provide insights into the structure, function, and activity of human Cdk13/CycK.
Collapse
|
47
|
Discovery and SAR of novel pyrazolo[1,5-a]pyrimidines as inhibitors of CDK9. Bioorg Med Chem 2015; 23:6280-96. [DOI: 10.1016/j.bmc.2015.08.035] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 08/03/2015] [Accepted: 08/26/2015] [Indexed: 01/15/2023]
|
48
|
Scholz B, Kowarz E, Rössler T, Ahmad K, Steinhilber D, Marschalek R. AF4 and AF4N protein complexes: recruitment of P-TEFb kinase, their interactome and potential functions. AMERICAN JOURNAL OF BLOOD RESEARCH 2015; 5:10-24. [PMID: 26171280 PMCID: PMC4497493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 02/16/2015] [Indexed: 06/04/2023]
Abstract
AF4/AFF1 and AF5/AFF4 are the molecular backbone to assemble "super-elongation complexes" (SECs) that have two main functions: (1) control of transcriptional elongation by recruiting the positive transcription elongation factor b (P-TEFb = CyclinT1/CDK9) that is usually stored in inhibitory 7SK RNPs; (2) binding of different histone methyltransferases, like DOT1L, NSD1 and CARM1. This way, transcribed genes obtain specific histone signatures (e.g. H3K79me2/3, H3K36me2) to generate a transcriptional memory system. Here we addressed several questions: how is P-TEFb recruited into SEC, how is the AF4 interactome composed, and what is the function of the naturally occuring AF4N protein variant which exhibits only the first 360 amino acids of the AF4 full-length protein. Noteworthy, shorter protein variants are a specific feature of all AFF protein family members. Here, we demonstrate that full-length AF4 and AF4N are both catalyzing the transition of P-TEFb from 7SK RNP to their N-terminal domain. We have also mapped the protein-protein interaction network within both complexes. In addition, we have first evidence that the AF4N protein also recruits TFIIH and the tumor suppressor MEN1. This indicate that AF4N may have additional functions in transcriptional initiation and in MEN1-dependend transcriptional processes.
Collapse
Affiliation(s)
- Bastian Scholz
- Institute of Pharmaceutical Biology, Goethe-University of FrankfurtBiocenter, Max-von-Laue-Str. 9, D-60438 Frankfurt/Main, Germany
| | - Eric Kowarz
- Institute of Pharmaceutical Biology, Goethe-University of FrankfurtBiocenter, Max-von-Laue-Str. 9, D-60438 Frankfurt/Main, Germany
| | - Tanja Rössler
- Institute of Pharmaceutical Biology, Goethe-University of FrankfurtBiocenter, Max-von-Laue-Str. 9, D-60438 Frankfurt/Main, Germany
| | - Khalil Ahmad
- Institute of Pharmaceutical Chemistry, Goethe-University of FrankfurtBiocenter, Max-von-Laue-Str. 9, D-60438 Frankfurt/Main, Germany
| | - Dieter Steinhilber
- Institute of Pharmaceutical Chemistry, Goethe-University of FrankfurtBiocenter, Max-von-Laue-Str. 9, D-60438 Frankfurt/Main, Germany
| | - Rolf Marschalek
- Institute of Pharmaceutical Biology, Goethe-University of FrankfurtBiocenter, Max-von-Laue-Str. 9, D-60438 Frankfurt/Main, Germany
| |
Collapse
|
49
|
Lu H, Li Z, Zhang W, Schulze-Gahmen U, Xue Y, Zhou Q. Gene target specificity of the Super Elongation Complex (SEC) family: how HIV-1 Tat employs selected SEC members to activate viral transcription. Nucleic Acids Res 2015; 43:5868-79. [PMID: 26007649 PMCID: PMC4499153 DOI: 10.1093/nar/gkv541] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2015] [Accepted: 05/11/2015] [Indexed: 01/23/2023] Open
Abstract
The AF4/FMR2 proteins AFF1 and AFF4 act as a scaffold to assemble the Super Elongation Complex (SEC) that strongly activates transcriptional elongation of HIV-1 and cellular genes. Although they can dimerize, it is unclear whether the dimers exist and function within a SEC in vivo. Furthermore, it is unknown whether AFF1 and AFF4 function similarly in mediating SEC-dependent activation of diverse genes. Providing answers to these questions, our current study shows that AFF1 and AFF4 reside in separate SECs that display largely distinct gene target specificities. While the AFF1-SEC is more potent in supporting HIV-1 transactivation by the viral Tat protein, the AFF4-SEC is more important for HSP70 induction upon heat shock. The functional difference between AFF1 and AFF4 in Tat-transactivation has been traced to a single amino acid variation between the two proteins, which causes them to enhance the affinity of Tat for P-TEFb, a key SEC component, with different efficiency. Finally, genome-wide analysis confirms that the genes regulated by AFF1-SEC and AFF4-SEC are largely non-overlapping and perform distinct functions. Thus, the SEC represents a family of related complexes that exist to increase the regulatory diversity and gene control options during transactivation of diverse cellular and viral genes.
Collapse
Affiliation(s)
- Huasong Lu
- Innovation Center of Cell Signaling Network, School of Pharmaceutical Sciences, Xiamen University, Xiamen 361005, Fujian, China Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Zichong Li
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Wei Zhang
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Ursula Schulze-Gahmen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Yuhua Xue
- Innovation Center of Cell Signaling Network, School of Pharmaceutical Sciences, Xiamen University, Xiamen 361005, Fujian, China
| | - Qiang Zhou
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| |
Collapse
|
50
|
Jin HX, Go ML, Yin P, Qiu XT, Zhu P, Yan XJ. Determining the Functions of HIV-1 Tat and a Second Magnesium Ion in the CDK9/Cyclin T1 Complex: A Molecular Dynamics Simulation Study. PLoS One 2015; 10:e0124673. [PMID: 25909811 PMCID: PMC4409394 DOI: 10.1371/journal.pone.0124673] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 03/16/2015] [Indexed: 11/18/2022] Open
Abstract
The current paradigm of cyclin-dependent kinase (CDK) regulation based on the well-established CDK2 has been recently expanded. The determination of CDK9 crystal structures suggests the requirement of an additional regulatory protein, such as human immunodeficiency virus type 1 (HIV-1) Tat, to exert its physiological functions. In most kinases, the exact number and roles of the cofactor metal ions remain unappreciated, and the repertoire has thus gained increasing attention recently. Here, molecular dynamics (MD) simulations were implemented on CDK9 to explore the functional roles of HIV-1 Tat and the second Mg2+ ion at site 1 (Mg12+). The simulations unveiled that binding of HIV-1 Tat to CDK9 not only stabilized hydrogen bonds (H-bonds) between ATP and hinge residues Asp104 and Cys106, as well as between ATP and invariant Lys48, but also facilitated the salt bridge network pertaining to the phosphorylated Thr186 at the activation loop. By contrast, these H-bonds cannot be formed in CDK9 owing to the absence of HIV-1 Tat. MD simulations further revealed that the Mg12+ ion, coupled with the Mg22+ ion, anchored to the triphosphate moiety of ATP in its catalytic competent conformation. This observation indicates the requirement of the Mg12+ ion for CDK9 to realize its function. Overall, the introduction of HIV-1 Tat and Mg12+ ion resulted in the active site architectural characteristics of phosphorylated CDK9. These data highlighted the functional roles of HIV-1 Tat and Mg12+ ion in the regulation of CDK9 activity, which contributes an important complementary understanding of CDK molecular underpinnings.
Collapse
Affiliation(s)
- Hai-Xiao Jin
- Key Laboratory of Applied Marine Biotechnology Ministry of Education, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Mei-Lin Go
- Department of Pharmacy, National University of Singapore, Singapore, Singapore
| | - Peng Yin
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, China
| | - Xiao-Ting Qiu
- Key Laboratory of Applied Marine Biotechnology Ministry of Education, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Peng Zhu
- Key Laboratory of Applied Marine Biotechnology Ministry of Education, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Xiao-Jun Yan
- Key Laboratory of Applied Marine Biotechnology Ministry of Education, School of Marine Sciences, Ningbo University, Ningbo, China
- * E-mail:
| |
Collapse
|