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1.
Blood ; 137(21): 2947-2957, 2021 05 27.
Article in English | MEDLINE | ID: mdl-33259592

ABSTRACT

BH3 mimetics like venetoclax target prosurvival Bcl-2 family proteins and are important therapeutics in the treatment of hematological malignancies. We demonstrate that endogenous Bfl-1 expression can render preclinical lymphoma tumor models insensitive to Mcl-1 and Bcl-2 inhibitors. However, suppression of Bfl-1 alone was insufficient to fully induce apoptosis in Bfl-1-expressing lymphomas, highlighting the need for targeting additional prosurvival proteins in this context. Importantly, we demonstrated that cyclin-dependent kinase 9 (CDK9) inhibitors rapidly downregulate both Bfl-1 and Mcl-1, inducing apoptosis in BH3-mimetic-resistant lymphoma cell lines in vitro and driving in vivo tumor regressions in diffuse large B-cell lymphoma patient-derived xenograft models expressing Bfl-1. These data underscore the need to clinically develop CDK9 inhibitors, like AZD4573, for the treatment of lymphomas using Bfl-1 as a selection biomarker.


Subject(s)
Bridged Bicyclo Compounds, Heterocyclic/pharmacology , Cyclin-Dependent Kinase 9/antagonists & inhibitors , Drug Resistance, Neoplasm/drug effects , Lymphoma, Large B-Cell, Diffuse/drug therapy , Macrocyclic Compounds/pharmacology , Molecular Targeted Therapy , Neoplasm Proteins/antagonists & inhibitors , Proto-Oncogene Proteins c-bcl-2/antagonists & inhibitors , Sulfonamides/pharmacology , Animals , Antineoplastic Agents/pharmacology , Bridged Bicyclo Compounds, Heterocyclic/therapeutic use , Cell Line, Tumor , Cyclin-Dependent Kinase 9/physiology , Cycloheximide/pharmacology , Female , Gene Expression Regulation, Neoplastic/drug effects , Humans , Leupeptins/pharmacology , Macrocyclic Compounds/therapeutic use , Mice , Mice, Inbred NOD , Mice, SCID , Minor Histocompatibility Antigens/biosynthesis , Minor Histocompatibility Antigens/genetics , Myeloid Cell Leukemia Sequence 1 Protein/biosynthesis , Myeloid Cell Leukemia Sequence 1 Protein/genetics , Neoplasm Proteins/biosynthesis , Neoplasm Proteins/genetics , Peptide Fragments/antagonists & inhibitors , Piperazines/pharmacology , Proto-Oncogene Proteins/antagonists & inhibitors , Proto-Oncogene Proteins c-bcl-2/biosynthesis , Proto-Oncogene Proteins c-bcl-2/genetics , Pyridines/pharmacology , Sulfonamides/therapeutic use , Xenograft Model Antitumor Assays
2.
Sci Rep ; 9(1): 17369, 2019 11 22.
Article in English | MEDLINE | ID: mdl-31758083

ABSTRACT

Cyclin-dependent kinase 9 (CDK9), one crucial molecule in promoting the transition from transcription pausing to elongation, is a critical modulator of cell survival and death. However, the pathological function of CDK9 in bacterial inflammatory diseases has never been explored. CDK9 inhibition or knock-down attenuated Porphyromonas gingivalis-triggered inflammatory gene expression. Gene-expression microarray analysis of monocytes revealed that knock-down of CDK9 not only affected inflammatory responses, but also impacted cell death network, especially the receptor-interacting protein kinase 3 (RIPK3)-mixed lineage kinase domain-like (MLKL)-mediated necroptosis after P. gingivalis infection. Inhibition of CDK9 significantly decreased necroptosis with downregulation of both MLKL and phosphorylated MLKL. By regulating caspase-8 and cellular FLICE inhibitory protein (cFLIP), key molecules in regulating cell survival and death, CDK9 affected not only the classic RIPK1-RIPK3-mediated necroptosis, but also the alternate TIR-domain-containing adapter-inducing interferon-ß-RIPK3-mediated necroptosis. CDK9 inhibition dampened pro-inflammatory gene production in the acute infection process in the subcutaneous chamber model in vivo. Moreover, CDK9 inhibition contributed to the decreased periodontal bone loss and inflammatory response induced by P. gingivalis in the periodontal micro-environment. In conclusion, by modulating the RIPK3-MLKL-mediated necroptosis, CDK9 inhibition provided a novel mechanism to impact the progress of bacterial infection in the periodontal milieu.


Subject(s)
Cyclin-Dependent Kinase 9/physiology , Necroptosis/genetics , Periodontitis/genetics , Protein Kinases/physiology , Receptor-Interacting Protein Serine-Threonine Kinases/physiology , Adult , Animals , Bacteroidaceae Infections/complications , Bacteroidaceae Infections/genetics , Bacteroidaceae Infections/metabolism , Bacteroidaceae Infections/pathology , Case-Control Studies , Cyclin-Dependent Kinase 9/antagonists & inhibitors , Cyclin-Dependent Kinase 9/metabolism , Disease Progression , Enzyme Inhibitors/pharmacology , Female , Gene Expression Regulation/drug effects , Humans , Inflammation Mediators/metabolism , Male , Mice , Mice, Inbred C57BL , Middle Aged , Periodontitis/metabolism , Periodontitis/microbiology , Periodontitis/pathology , Porphyromonas gingivalis/physiology , Protein Kinases/genetics , Receptor-Interacting Protein Serine-Threonine Kinases/genetics , THP-1 Cells , Transcription Elongation, Genetic/drug effects
3.
Biochem Biophys Res Commun ; 513(4): 967-973, 2019 06 11.
Article in English | MEDLINE | ID: mdl-31005255

ABSTRACT

Circadian clock and cell cycle are vital cellular programs acting in a timely-regulated, cyclic manner. The two cellular oscillators are coupled in various ways to facilitate biological processes. Here we report CDK9, a kinase belongs to the CDK family in regulating cell cycle and RNA Pol II activity, can serve as a modulator for circadian clock. We identified CDK inhibitor LY2857785 potently blocked PER2:LUC expression in MEFs from a screen of 17 commonly-used CDK inhibitors. We further analyzed the possible targets of LY2857785 by siRNA approach, and confirmed CDK9 as the main effector. LY2857785 treatment, as well as Cdk9 knock-down, led to lowered expression of Bmal1 in accordance with elevated expression of Rev-Erbα. CDK9 associated with REV-ERBα thus attenuated REV-ERBα binding to the RORE for Bmal1 suppression. To conform the circadian-modulating activity of CDK9 in vivo, we knocked down CDK9 in mice at the anterior hypothalamus covering the central oscillator SCN, and found the respiratory exchange ratio, daily activity and circadian period were altered in the Cdk9-knockdown mice. Together, our finding designated CDK9 as a novel modulator in circadian clock. CDK9 may serve as a vital basis to understand circadian- and cell cycle-misregulated ailments such as cancer.


Subject(s)
Circadian Clocks , Cyclin-Dependent Kinase 9/physiology , Nuclear Receptor Subfamily 1, Group D, Member 1/metabolism , Animals , Cyclin-Dependent Kinase 9/antagonists & inhibitors , Cyclin-Dependent Kinase 9/genetics , Cyclohexylamines/pharmacology , Gene Knockdown Techniques , Humans , Indazoles/pharmacology , Mice , Poly(ADP-ribose) Polymerases/metabolism , Protein Binding
4.
Cell ; 175(1): 171-185.e25, 2018 09 20.
Article in English | MEDLINE | ID: mdl-30146162

ABSTRACT

CKIα ablation induces p53 activation, and CKIα degradation underlies the therapeutic effect of lenalidomide in a pre-leukemia syndrome. Here we describe the development of CKIα inhibitors, which co-target the transcriptional kinases CDK7 and CDK9, thereby augmenting CKIα-induced p53 activation and its anti-leukemic activity. Oncogene-driving super-enhancers (SEs) are highly sensitive to CDK7/9 inhibition. We identified multiple newly gained SEs in primary mouse acute myeloid leukemia (AML) cells and demonstrate that the inhibitors abolish many SEs and preferentially suppress the transcription elongation of SE-driven oncogenes. We show that blocking CKIα together with CDK7 and/or CDK9 synergistically stabilize p53, deprive leukemia cells of survival and proliferation-maintaining SE-driven oncogenes, and induce apoptosis. Leukemia progenitors are selectively eliminated by the inhibitors, explaining their therapeutic efficacy with preserved hematopoiesis and leukemia cure potential; they eradicate leukemia in MLL-AF9 and Tet2-/-;Flt3ITD AML mouse models and in several patient-derived AML xenograft models, supporting their potential efficacy in curing human leukemia.


Subject(s)
Casein Kinase Ialpha/antagonists & inhibitors , Leukemia, Myeloid, Acute/drug therapy , Animals , Apoptosis/drug effects , Casein Kinase Ialpha/physiology , Cell Proliferation/drug effects , Cyclin-Dependent Kinase 9/antagonists & inhibitors , Cyclin-Dependent Kinase 9/physiology , Cyclin-Dependent Kinases/antagonists & inhibitors , Cyclin-Dependent Kinases/physiology , DNA-Binding Proteins , Disease Models, Animal , Enhancer Elements, Genetic/genetics , Hematopoiesis , Humans , Mice , Mice, Inbred C57BL , Oncogene Proteins, Fusion/metabolism , Protein Serine-Threonine Kinases , Proto-Oncogene Proteins , Tumor Suppressor Protein p53/physiology , Xenograft Model Antitumor Assays
5.
Endocr Relat Cancer ; 23(12): T211-T226, 2016 12.
Article in English | MEDLINE | ID: mdl-27582311

ABSTRACT

Cyclin-dependent kinase 9 (CDK9) is a key transcriptional regulator and a lucrative target for cancer treatment. Targeting CDK9 can effectively confine the hyperactivity of androgen receptor and the constitutive expression of anti-apoptotic proteins; both being main causes of prostate cancer (PCa) development and progression. In castrate-resistant PCa, traditional therapies that only target androgen receptor (AR) have become obsolete due to reprograming in AR activity to make the cells independent of androgen. CDK9 inhibitors may provide a new and better therapeutic opportunity over traditional treatment options by targeting both androgen receptor activity and anti-apoptotic proteins, improving the chances of positive outcomes, especially in patients with the advanced disease. This review focuses on biological functions of CDK9, its involvement with AR and the potential for therapeutic opportunities in PCa treatment.


Subject(s)
Antineoplastic Agents/therapeutic use , Cyclin-Dependent Kinase 9/physiology , Molecular Targeted Therapy/methods , Prostatic Neoplasms/drug therapy , Animals , Cyclin-Dependent Kinase 9/antagonists & inhibitors , Humans , Male , Molecular Targeted Therapy/trends , Prostatic Neoplasms/genetics
6.
Mol Cell ; 46(5): 705-13, 2012 Jun 08.
Article in English | MEDLINE | ID: mdl-22681891

ABSTRACT

Extensive changes in posttranslational histone modifications accompany the rewiring of the transcriptional program during stem cell differentiation. However, the mechanisms controlling the changes in specific chromatin modifications and their function during differentiation remain only poorly understood. We show that histone H2B monoubiquitination (H2Bub1) significantly increases during differentiation of human mesenchymal stem cells (hMSCs) and various lineage-committed precursor cells and in diverse organisms. Furthermore, the H2B ubiquitin ligase RNF40 is required for the induction of differentiation markers and transcriptional reprogramming of hMSCs. This function is dependent upon CDK9 and the WAC adaptor protein, which are required for H2B monoubiquitination. Finally, we show that RNF40 is required for the resolution of the H3K4me3/H3K27me3 bivalent poised state on lineage-specific genes during the transition from an inactive to an active chromatin conformation. Thus, these data indicate that H2Bub1 is required for maintaining multipotency of hMSCs and plays a central role in controlling stem cell differentiation.


Subject(s)
Cell Differentiation/genetics , Histones/metabolism , Mesenchymal Stem Cells/cytology , Multipotent Stem Cells/cytology , Adaptor Proteins, Signal Transducing/genetics , Adaptor Proteins, Signal Transducing/physiology , Cell Line , Chromatin Assembly and Disassembly , Cyclin-Dependent Kinase 9/genetics , Cyclin-Dependent Kinase 9/physiology , Humans , Mesenchymal Stem Cells/metabolism , Multipotent Stem Cells/metabolism , Protein Processing, Post-Translational , Ubiquitin-Protein Ligases/genetics , Ubiquitin-Protein Ligases/metabolism , Ubiquitin-Protein Ligases/physiology , Ubiquitination
7.
Nucleic Acids Res ; 39(18): 7908-19, 2011 Oct.
Article in English | MEDLINE | ID: mdl-21724609

ABSTRACT

Autoimmune regulator (AIRE) is a transcription factor that induces the expression of a large subset of otherwise strictly tissue restricted antigens in medullary thymic epithelial cells, thereby enabling their presentation to developing T cells for negative selection. Mutations in AIRE lead to autoimmune-polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED), a rare monogenetic disease. Although it has been reported that AIRE interacts with proteins involved in nuclear transport, DNA-damage response, chromatin remodeling, transcription and pre-mRNA-splicing, the precise mechanism of AIRE-induced tissue restricted antigen expression has remained elusive. In this study, we investigated an APECED patient mutation that causes the loss of the extreme C-terminus of AIRE and found that this mutant protein is transcriptionaly inactive. When tethered heterologously to DNA, this domain could stimulate transcription and splicing by itself. Moreover, the loss of this C-terminus disrupted interactions with the positive transcription elongation factor b (P-TEFb). Via P-TEFb, AIRE increased levels of RNA polymerase II on and enhanced pre-mRNA splicing of heterologous and endogenous target genes. Indeed, the inhibition of CDK9, the kinase subunit of P-TEFb, inhibited AIRE-induced pre-mRNA splicing of these genes. Thus, AIRE requires P-TEFb to activate transcription elongation and co-transcriptional processing of target genes.


Subject(s)
Mutation , Polyendocrinopathies, Autoimmune/genetics , Positive Transcriptional Elongation Factor B/metabolism , RNA Splicing , Transcription Factors/genetics , Transcriptional Activation , Animals , Cell Line , Cyclin-Dependent Kinase 9/antagonists & inhibitors , Cyclin-Dependent Kinase 9/physiology , Humans , Mice , Phosphorylation , Protein Structure, Tertiary , RNA Precursors/metabolism , RNA, Messenger/metabolism , Transcription Factors/chemistry , Transcription Factors/metabolism , AIRE Protein
8.
Cell Cycle ; 10(1): 28-32, 2011 Jan 01.
Article in English | MEDLINE | ID: mdl-21200140

ABSTRACT

Cyclin-dependent kinase 9 (CDK9), with its cyclin T regulatory subunit, is a component of the positive transcription elongation factor b (P-TEFb) complex, which stimulates transcription elongation and also functions in co-transcriptional histone modification, mRNA processing, and mRNA export. CDK9 also binds to cyclin K but the function of this CDK9-cyclin K complex is less clear. We and others have recently shown that CDK9 functions directly in maintaining genome integrity. This activity is restricted to CDK9-cyclin K. Depletion of CDK9 or its cyclin K but not cyclin T regulatory subunit impairs cell cycle recovery in response to replication stress and induces spontaneous DNA damage in replicating cells. CDK9-cyclin K also interacts with ATR and other DNA damage response and DNA repair proteins. CDK9 accumulates on chromatin and limits the amount of single-stranded DNA in response to replication stress. Collectively, these data are consistent with a model in which CDK9 responds to replication stress by localizing to chromatin to reduce the breakdown of stalled replication forks and promote recovery from replication arrest. The direct role of CDK9-cyclin K in pathways that maintain genome integrity in response to replication stress appear to be evolutionarily conserved.


Subject(s)
Cyclin-Dependent Kinase 9/physiology , Cyclins/physiology , Genome, Human/genetics , Animals , Conserved Sequence , Cyclin-Dependent Kinase 9/genetics , Cyclins/genetics , Evolution, Molecular , Humans
9.
Curr Med Chem ; 18(3): 342-58, 2011.
Article in English | MEDLINE | ID: mdl-21143121

ABSTRACT

Cyclin Dependent Kinases (CDKs) are important regulators of cell cycle and gene expression. Since an up-to-date review about the pharmacological inhibitors of CDK family (CDK1-10) is not available; therefore in the present paper we briefly summarize the most relevant inhibitors and point out the low number of selective inhibitors. Among CDKs, CDK9 is a validated pathological target in HIV infection, inflammation and cardiac hypertrophy; however selective CDK9 inhibitors are still not available. We present a selective inhibitor family of CDK9 based on the 4-phenylamino-6- phenylpyrimidine nucleus. We show a convenient synthetic method to prepare a useful intermediate and its derivatisation resulting in novel compounds. The CDK9 inhibitory activity of the derivatives was measured in specific kinase assay and the CDK inhibitory profile of the best ones (IC(50) < 100 nM) was determined. The most selective compounds had high selectivity over CDK1, 2, 3, 5, 6, 7 and showed at least one order of magnitude higher inhibitory activity over CDK4 inhibition. The most selective molecules were examined in cytotoxicity assays and their ability to inhibit HIV-1 replication was determined in cellular assays.


Subject(s)
Anti-HIV Agents/chemistry , Cyclin-Dependent Kinase 9/antagonists & inhibitors , HIV Infections/drug therapy , Protein Kinase Inhibitors/chemistry , Anti-HIV Agents/therapeutic use , Anti-HIV Agents/toxicity , Binding Sites , Catalytic Domain , Cell Line , Computer Simulation , Cyclin-Dependent Kinase 2/antagonists & inhibitors , Cyclin-Dependent Kinase 2/metabolism , Cyclin-Dependent Kinase 2/physiology , Cyclin-Dependent Kinase 4/antagonists & inhibitors , Cyclin-Dependent Kinase 4/metabolism , Cyclin-Dependent Kinase 4/physiology , Cyclin-Dependent Kinase 9/metabolism , Cyclin-Dependent Kinase 9/physiology , HIV/drug effects , Humans , Protein Kinase Inhibitors/therapeutic use , Protein Kinase Inhibitors/toxicity , Pyrimidines/chemistry , Virus Replication/drug effects
10.
Cell Cycle ; 8(22): 3636-42, 2009 Nov 15.
Article in English | MEDLINE | ID: mdl-19844166

ABSTRACT

Cyclin-dependent kinase-9 (CDK9) was originally characterized as a transcription elongation factor which regulates RNA Polymerase II (RNAPII) activity following transcriptional initiation. However, recent evidence from a number of studies have shown that CDK9 plays an important role in regulating not only RNAPII activity but also co-transcriptional histone modification and mRNA processing events such as splicing and 3' end processing. Importantly, our previous work and the work presented here demonstrate that CDK9 functions to guide a complex network of chromatin modifications including histone H2B monoubiquitination (H2Bub1), H3 lysine 4 trimethylation (H3K4me3) and H3K36me3. This function appears to be dependent upon not only the phosphorylation of the RNA Polymerase II C-terminal domain but also upon other CDK9 targets such as the Suppressor of Ty Homolog-5 (SUPT5H), Negative Elongation Factor-E (NELF-E) and probably the human Rad6 homolog UBE2A. We provide a working model by which CDK9 may control co-transcriptional replication-dependent histone mRNA 3' end processing in an H2Bub1 and H3K4me3-dependent manner and uncover new and important differences between the functions of human CDK9 and its yeast counterparts Ctk1 and Bur1.


Subject(s)
Chromatin Assembly and Disassembly/physiology , Cyclin-Dependent Kinase 9/physiology , Histones/physiology , Models, Biological , RNA Polymerase II/metabolism , RNA Processing, Post-Transcriptional/physiology , Cyclin-Dependent Kinase 9/metabolism , Cyclin-Dependent Kinases/metabolism , Humans , Protein Kinases/metabolism , Saccharomyces cerevisiae Proteins/metabolism , Species Specificity
11.
EMBO Rep ; 10(8): 894-900, 2009 Aug.
Article in English | MEDLINE | ID: mdl-19575011

ABSTRACT

Post-translational histone modifications have essential roles in controlling nuclear processes; however, the specific mechanisms regulating these modifications and their combinatorial activities remain elusive. Cyclin-dependent kinase 9 (CDK9) regulates gene expression by phosphorylating transcriptional regulatory proteins, including the RNA polymerase II carboxy-terminal domain. Here, we show that CDK9 activity is essential for maintaining global and gene-associated levels of histone H2B monoubiquitination (H2Bub1). Furthermore, CDK9 activity and H2Bub1 help to maintain correct replication-dependent histone messenger RNA (mRNA) 3'-end processing. CDK9 knockdown consistently resulted in inefficient recognition of the correct mRNA 3'-end cleavage site and led to increased read-through of RNA polymerase II to an alternative downstream polyadenylation signal. Thus, CDK9 acts to integrate phosphorylation during transcription with chromatin modifications to control co-transcriptional histone mRNA processing.


Subject(s)
Cyclin-Dependent Kinase 9/physiology , Histones/metabolism , RNA, Messenger/metabolism , Animals , Blotting, Western , Cell Line , Cell Line, Tumor , Chromatin Immunoprecipitation , Cyclin-Dependent Kinase 9/antagonists & inhibitors , Cyclin-Dependent Kinase 9/metabolism , Dactinomycin/pharmacology , Dichlororibofuranosylbenzimidazole/pharmacology , Flavonoids/pharmacology , Humans , Mice , Nucleic Acid Synthesis Inhibitors/pharmacology , Piperidines/pharmacology , Transcription, Genetic/drug effects , Transcription, Genetic/physiology , Ubiquitin-Protein Ligases/genetics , Ubiquitin-Protein Ligases/physiology , Ubiquitination/genetics
12.
Blood ; 112(13): 4884-94, 2008 Dec 15.
Article in English | MEDLINE | ID: mdl-18780834

ABSTRACT

The transcription factor GATA-1 participates in programming the differentiation of multiple hematopoietic lineages. In megakaryopoiesis, loss of GATA-1 function produces complex developmental abnormalities and underlies the pathogenesis of megakaryocytic leukemia in Down syndrome. Its distinct functions in megakaryocyte and erythroid maturation remain incompletely understood. In this study, we identified functional and physical interaction of GATA-1 with components of the positive transcriptional elongation factor P-TEFb, a complex containing cyclin T1 and the cyclin-dependent kinase 9 (Cdk9). Megakaryocytic induction was associated with dynamic changes in endogenous P-TEFb composition, including recruitment of GATA-1 and dissociation of HEXIM1, a Cdk9 inhibitor. shRNA knockdowns and pharmacologic inhibition both confirmed contribution of Cdk9 activity to megakaryocytic differentiation. In mice with megakaryocytic GATA-1 deficiency, Cdk9 inhibition produced a fulminant but reversible megakaryoblastic disorder reminiscent of the transient myeloproliferative disorder of Down syndrome. P-TEFb has previously been implicated in promoting elongation of paused RNA polymerase II and in programming hypertrophic differentiation of cardiomyocytes. Our results offer evidence for P-TEFb cross-talk with GATA-1 in megakaryocytic differentiation, a program with parallels to cardiomyocyte hypertrophy.


Subject(s)
Cell Differentiation , Cyclin-Dependent Kinase 9/physiology , GATA1 Transcription Factor/metabolism , Megakaryocytes/cytology , Positive Transcriptional Elongation Factor B/metabolism , Receptor Cross-Talk , Animals , Cells, Cultured , Cyclin-Dependent Kinase 9/antagonists & inhibitors , Down Syndrome , GATA1 Transcription Factor/genetics , Humans , Mice , Mice, Knockout , Myeloproliferative Disorders
13.
Med Chem ; 4(3): 210-8, 2008 May.
Article in English | MEDLINE | ID: mdl-18473913

ABSTRACT

The family of Cyclin-Dependent Kinases (CDKs) can be subdivided into two major functional groups based on their roles in cell cycle and/or transcriptional control. CDK9 is the catalytic subunit of positive transcription elongation factor b (P-TEFb). CDK9 is the kinase of the TAK complex (Tat-associated kinase complex), and binds to Tat protein of HIV, suggesting a possible role for CDK9 in AIDS progression. CDK9 complexed with its regulatory partner cyclin T1, serves as a cellular mediator of the transactivation function of the HIV Tat protein. P-TEFb is responsible for the phosphorylation of the carboxyl-terminal domain of RNA Pol II, resulting in stimulation of transcription. Furthermore, the complexes containing CDK9 induce the differentiation in distinct tissue. The CDK9/cyclin T1 complex is expressed at higher level in more differentiated primary neuroectodermal and neuroblastoma tumors, showing a correlation between the kinase expression and tumor differentiation grade. This may have clinical and therapeutical implications for these tumor types. Among the CDK inhibitors two have shown to be effective against CDK9: Roscovitine and Flavopiridol. These two inhibitors prevented the replication of human immunodeficiency virus (HIV) type 1 by blocking Tat transactivation of the HIV type 1 promoter. These compounds inhibit CDKs by binding to the catalytic domain in place of ATP, preventing transfer of a phosphate group to the substrate. More sensitive therapeutic agents of CDK9 can be designed, and structural studies can add information in the understanding of this kinase. The major features related to CDK9 inhibition will be reviewed in this article.


Subject(s)
Cyclin-Dependent Kinase 9/antagonists & inhibitors , Cyclin-Dependent Kinase 9/chemistry , Amino Acid Sequence , Catalytic Domain , Cloning, Molecular , Cyclin-Dependent Kinase 9/physiology , Flavones/chemistry , Flavones/pharmacology , Humans , Models, Molecular , Molecular Sequence Data , Purines/chemistry , Purines/pharmacology , Pyrazoles/chemistry , Pyrazoles/pharmacology , Recombinant Proteins/antagonists & inhibitors , Recombinant Proteins/chemistry , Recombinant Proteins/isolation & purification , Sequence Alignment
14.
Mol Genet Genomics ; 277(2): 101-14, 2007 Feb.
Article in English | MEDLINE | ID: mdl-17001490

ABSTRACT

Phosphorylation of the large RNA Polymerase II subunit C-terminal domain (CTD) is believed to be important in promoter clearance and for recruiting protein factors that function in messenger RNA synthesis and processing. P-TEFb is a protein kinase that targets the (CTD). The goal of this study was to identify chromatin modifications and associations that require P-TEFb activity in vivo. We knocked down the catalytic subunit of P-TEFb, Cdk9, in Drosophila melanogaster using RNA interference. Cdk9 knockdown flies die during metamorphosis. Phosphorylation at serine 2 and serine 5 of the CTD heptad repeat were both dramatically reduced in knockdown larvae. Hsp 70 mRNA induction by heat shock was attenuated in Cdk9 knockdown larvae. Both mono- and trimethylation of histone H3 at lysine 4 were dramatically reduced, suggesting a link between CTD phosphorylation and histone methylation in transcribed chromatin in vivo. Levels of the chromo helicase protein CHD1 were reduced in Cdk9 knockdown chromosomes, suggesting that CHD1 is targeted to chromosomes through P-TEFb-dependent histone methylation. Dimethylation of histone H3 at lysine 36 was significantly reduced in knockdown larvae, implicating CTD phosphorylation in the regulation of this chromatin modification. Binding of the RNA Polymerase II elongation factor ELL was reduced in knockdown chromosomes, suggesting that ELL is recruited to active polymerase via CTD phosphorylation.


Subject(s)
Cyclin-Dependent Kinase 9/physiology , Drosophila melanogaster/enzymology , Heat-Shock Proteins/metabolism , Histones/metabolism , Protein Processing, Post-Translational , Transcriptional Elongation Factors/metabolism , Animals , Animals, Genetically Modified , Chromosomes/metabolism , Cyclin-Dependent Kinase 9/antagonists & inhibitors , DNA-Binding Proteins/metabolism , Drosophila Proteins/metabolism , Elongin , Heat-Shock Response , Methylation , RNA Interference , RNA Polymerase II/metabolism , Transcription Factors/metabolism
15.
Eur J Histochem ; 50(1): 19-23, 2006.
Article in English | MEDLINE | ID: mdl-16584981

ABSTRACT

Myocyte differentiation is due to transcription of genes that characterize the phenotypic and biochemical identity of differentiated muscle cells. These are the myogenic regulatory factors (MRFs) MyoD, Myf5, myogenin and MRF4. Overexpression of cdk/cyclins has been reported to inhibit the activity of MyoD and prevent myogenic differentiation by different modalities. Unlike other cdk/cyclin complexes, overexpression of cdk9/cyclin T2a, enhances MyoD function and promotes myogenic differentiation. In addition, cyclin T2a interacting with a novel partner, PKN alpha, is able to strongly enhance the expression of myogenic differentiation markers, such as myogenin and Myosin Heavy Chain. So, cyclin T2a could stimulate myogenic differentiation interacting with different kinase partners Cdk9 or PKN alpha in a synergistic or antagonistic way.


Subject(s)
Cell Differentiation/physiology , Cyclin-Dependent Kinases/physiology , Cyclins/physiology , Muscle Development/physiology , Muscles/physiology , Animals , Cyclin T , Cyclin-Dependent Kinase 9/physiology , Humans , Muscles/cytology , Myogenic Regulatory Factors/physiology
16.
J Virol ; 80(10): 4781-91, 2006 May.
Article in English | MEDLINE | ID: mdl-16641271

ABSTRACT

Human T-lymphotropic virus type 1 (HTLV-1) encodes a transcriptional activator, Tax, whose function is essential for viral transcription and replication. Tax transactivates the viral long-terminal repeat through a series of protein-protein interactions which facilitate CREB and CBP/p300 binding. In addition, Tax dissociates transcription repressor histone deacetylase 1 interaction with the CREB response element. The subsequent events through which Tax interacts and communicates with RNA polymerase II and cyclin-dependent kinases (CDKs) are not clearly understood. Here we present evidence that Tax recruits positive transcription elongation factor b (P-TEFb) (CDK9/cyclin T1) to the viral promoter. This recruitment likely involves protein-protein interactions since Tax associates with P-TEFb in vitro as demonstrated by glutathione S-transferase fusion protein pull-down assays and in vivo as shown by co-immunoprecipitation assays. Functionally, small interfering RNA directed toward CDK9 inhibited Tax transactivation in transient assays. Consistent with these findings, the depletion of CDK9 from nuclear extracts inhibited Tax transactivation in vitro. Reconstitution of the reaction with wild-type P-TEFb, but not a kinase-dead mutant, recovered HTLV-1 transcription. Moreover, the addition of the CDK9 inhibitor flavopiridol blocked Tax transactivation in vitro and in vivo. Interestingly, we found that Tax regulates CDK9 kinase activity through a novel autophosphorylation pathway.


Subject(s)
Gene Products, tax/metabolism , Human T-lymphotropic virus 1/genetics , Human T-lymphotropic virus 1/metabolism , Positive Transcriptional Elongation Factor B/metabolism , Transcriptional Activation/physiology , Cell Line , Cyclin-Dependent Kinase 9/antagonists & inhibitors , Cyclin-Dependent Kinase 9/physiology , HeLa Cells , Human T-lymphotropic virus 1/physiology , Humans , Phosphorylation , Positive Transcriptional Elongation Factor B/genetics , Positive Transcriptional Elongation Factor B/physiology , RNA, Viral/biosynthesis , Threonine/metabolism
17.
Mol Endocrinol ; 20(7): 1494-505, 2006 Jul.
Article in English | MEDLINE | ID: mdl-16484339

ABSTRACT

Positive transcription elongation factor b (P-TEFb) phosphorylates the C-terminal domain of RNA polymerase II, facilitating transcriptional elongation. In addition to its participation in general transcription, P-TEFb is recruited to specific promoters by some transcription factors such as c-Myc or MyoD. The P-TEFb complex is composed of a cyclin-dependent kinase (cdk9) subunit and a regulatory partner (cyclin T1, cyclin T2, or cyclin K). Because cdk9 has been shown to participate in differentiation processes, such as muscle cell differentiation, we studied a possible role of cdk9 in adipogenesis. In this study we show that the expression of the cdk9 p55 isoform is highly regulated during 3T3-L1 adipocyte differentiation at RNA and protein levels. Furthermore, cdk9, as well as cyclin T1 and cyclin T2, shows differences in nuclear localization at distinct stages of adipogenesis. Overexpression of cdk9 increases the adipogenic potential of 3T3-L1 cells, whereas inhibition of cdk9 by specific cdk inhibitors, and dominant-negative cdk9 mutant impairs adipogenesis. We show that the positive effects of cdk9 on the differentiation of 3T3-L1 cells are mediated by a direct interaction with and phosphorylation of peroxisome proliferator-activated receptor gamma (PPARgamma), which is the master regulator of this process, on the promoter of PPARgamma target genes. PPARgamma-cdk9 interaction results in increased transcriptional activity of PPARgamma and therefore increased adipogenesis.


Subject(s)
Adipogenesis , Gene Expression Regulation , PPAR gamma/metabolism , Positive Transcriptional Elongation Factor B/metabolism , 3T3 Cells , Adipogenesis/drug effects , Adipogenesis/physiology , Animals , CHO Cells , Cell Differentiation , Cell Division/drug effects , Cricetinae , Cyclin-Dependent Kinase 9/antagonists & inhibitors , Cyclin-Dependent Kinase 9/metabolism , Cyclin-Dependent Kinase 9/physiology , Dichlororibofuranosylbenzimidazole/pharmacology , Mice , Phosphorylation , Protein Binding
18.
EMBO J ; 24(23): 4154-65, 2005 Dec 07.
Article in English | MEDLINE | ID: mdl-16308568

ABSTRACT

Phosphorylation of Ser2 of the heptapeptide repeat of the CTD of mammalian pol II by P-TEFb is associated with productive elongation of transcription of protein-coding genes. Here, we show that the CTD of pol II transcribing the human U2 snRNA genes is phosphorylated on Ser2 in vivo and that both the CDK9 kinase and cyclin T components of P-TEFb are required for cotranscriptional recognition of the 3' box RNA 3' end processing signal. However, inhibitors of CDK9 do not affect transcription of the U2 genes, indicating that P-TEFb functions exclusively as an RNA processing factor in expression of these relatively short, intronless genes. We also show that inhibition of CDK9 does not adversely affect either transcription of an intron-less, replication-activated histone H2b gene or recognition of the histone gene-specific U7-dependent RNA 3' end formation signal. These results emphasize that the role of P-TEFb as an activator of transcription elongation can be separated from its role in RNA processing and that neither function is universally required for expression of mammalian pol II-dependent genes.


Subject(s)
Histones/genetics , Introns , Positive Transcriptional Elongation Factor B/physiology , RNA, Small Nuclear/genetics , Amino Acid Sequence , Cyclin-Dependent Kinase 9/physiology , DNA Polymerase II/genetics , DNA Polymerase II/metabolism , Enzyme Inhibitors/pharmacology , Histones/biosynthesis , Humans , Molecular Sequence Data , Mutation , Phosphorylation/drug effects , Protein Kinases/metabolism , Protein Structure, Tertiary , RNA Precursors/metabolism , RNA, Small Nuclear/biosynthesis , Serine/genetics , Serine/metabolism
19.
Circ Res ; 95(9): 867-76, 2004 Oct 29.
Article in English | MEDLINE | ID: mdl-15514168

ABSTRACT

Over the past decade and a half, the paradigm has emerged of cardiac hypertrophy and ensuing heart failure as fundamentally a problem in signal transduction, impinging on the altered expression or function of gene-specific transcription factors and their partners, which then execute the hypertrophic phenotype. Strikingly, RNA polymerase II (RNAPII) is itself a substrate for two protein kinases-the cyclin-dependent kinases Cdk7 and Cdk9--that are activated by hypertrophic cues. Phosphorylation of RNAPII in the carboxyl terminal domain (CTD) of its largest subunit controls a number of critical steps subsequent to transcription initiation, among them enabling RNAPII to overcome its stalling in the promoter-proximal region and to engage in efficient transcription elongation. Here, we summarize our current understanding of the RNAPII-directed protein kinases in cardiac hypertrophy. Cdk9 activation is essential in tissue culture for myocyte enlargement and sufficient in transgenic mice for hypertrophy to occur and yet is unrelated to the "fetal" gene program that is typical of pathophysiological heart growth. Although this trophic effect of Cdk9 appears benign superficially, pathophysiological levels of Cdk9 activity render myocardium remarkably susceptible to apoptotic stress. Cdk9 interacts adversely with Gq-dependent pathways for hypertrophy, impairing the expression of numerous genes for mitochondrial proteins, and, in particular, suppressing master regulators of mitochondrial biogenesis and function, perioxisome proliferator-activated receptor-gamma coactivator-1 (PGC-1), and nuclear respiratory factor-1 (NRF-1). Given the dual transcriptional roles of Cdk9 in hypertrophic growth and mitochondrial dysfunction, we suggest the potential usefulness of Cdk9 as a target in heart failure drug discovery.


Subject(s)
Cyclin-Dependent Kinase 9/physiology , Myocytes, Cardiac/enzymology , Amino Acid Sequence , Animals , Apoptosis , Cardiomegaly/enzymology , Cardiomegaly/genetics , Cardiomegaly/pathology , Cardiomegaly/prevention & control , Cell Size , Cells, Cultured/cytology , Cells, Cultured/enzymology , Cyclin T , Cyclin-Dependent Kinases/chemistry , Cyclins/physiology , Drug Design , Enzyme Activation , Humans , Mice , Mitochondria, Heart/enzymology , Molecular Sequence Data , Myocytes, Cardiac/cytology , Phosphorylation , Protein Processing, Post-Translational , RNA Polymerase II/metabolism , RNA, Small Nuclear/metabolism , Sequence Alignment , Sequence Homology, Amino Acid , Transcription Factors/metabolism , Transcription, Genetic/physiology
20.
AIDS Res Hum Retroviruses ; 19(9): 767-78, 2003 Sep.
Article in English | MEDLINE | ID: mdl-14585207

ABSTRACT

Tat-mediated trans-activation of the HIV-1 long terminal repeat (LTR) occurs through the phosphorylation of the carboxy-terminal domain of the RNA polymerase II. The kinase complex, pTEFb, composed of cyclin T1 (CycT1) and CDK9, mediates this process. The trans-activation response (TAR) RNA-binding protein 2 (TRBP2) increases HIV-1 LTR expression through TAR and protein kinase R (PKR) binding, but not through interactions with the Tat-CycT1-CDK9 complex. TRBP2 and the Tat-CycT1-CDK9 complex have overlapping binding sites on TAR RNA. TRBP2 and CycT1 increased Tat trans-activation in NIH 3T3 cells with additive effects. Upon transfection of HIV-1 pLAI, pNL4-3, pMAL, and pAD molecular clones, reverse transcriptase (RT) activity and p24 concentration were decreased 200- to 900-fold in NIH 3T3 cells compared with HeLa cells in both cells and supernatants. In murine cells, cotransfection of the HIV clones with CycT1 or TRBP2 increased modestly the expression of RT activity in cell extracts. The analysis of Gag expression in murine cells transfected with CycT1 compared with human cells showed a 20-fold decrease in expression and a strong processing defect. The expression of both CycT1 and TRBP2 had a more than additive activity on RT function in cell extracts and on viral particle production in supernatant of murine cells. These results suggest an activity of CycT1 and TRBP2 at different steps in HIV-1 expression and indicate the requirement for another posttranscriptional factor in murine cells for full HIV replication.


Subject(s)
Cyclins/pharmacology , HIV-1/drug effects , RNA-Binding Proteins/pharmacology , Transcriptional Activation , Animals , Cyclin T , Cyclin-Dependent Kinase 9/physiology , Drug Synergism , Gene Products, gag/metabolism , Gene Products, tat/pharmacology , HIV Long Terminal Repeat , HIV-1/physiology , HeLa Cells , Humans , Mice , NIH 3T3 Cells , Virus Replication/drug effects , tat Gene Products, Human Immunodeficiency Virus
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