Identification of transcriptional and phosphatase regulators as interaction partners of human ADA3, a component of histone acetyltransferase complexes

2013 ◽  
Vol 450 (2) ◽  
pp. 311-320 ◽  
Author(s):  
Sevil Zencir ◽  
Adam Sike ◽  
Melanie J. Dobson ◽  
Ferhan Ayaydin ◽  
Imre Boros ◽  
...  
Keyword(s):  
Gene Expression ◽  
Rna Polymerase Ii ◽  
Protein Phosphatase ◽  
Histone Acetyltransferase ◽  
Fluorescent Microscopy ◽  
Regulation Of Gene Expression ◽  
Hybrid Approach ◽  
Regulatory Subunit ◽  
Altered Expression ◽  
Regulatory Subunits

ADA (alteration/deficiency in activation) 3 is a conserved component of several transcriptional adaptor and HAT (histone acetyltransferase) complexes that regulate RNA polymerase II-mediated gene expression. Within the HAT complexes ADA3 is associated with ADA2 and the HAT GCN5 (general control non-repressed 5). ADA3 plays roles in diverse cellular processes and also in malignancies by modulating GCN5 catalytic activity and/or by interactions with other regulators. To gain a better understanding of ADA3 function, we used a yeast two-hybrid approach to screen a human fetal cDNA library for proteins that interacted with hADA3 (human ADA3). We identified three novel hADA3-interacting partners, a transcriptional regulator, AATF (apoptosis-antagonizing transcription factor), and regulatory subunits of the PP1 (protein phosphatase 1) and PP2A (protein phosphatase 2A) [PPP1R7 (PP1 regulatory subunit 7) and PPP2R5D (PP2A 56 kDa regulatory subunit δ isoform) respectively]. Analysis of truncated versions of hADA3 indicated that the C-terminal ADA2-interacting domain was not required for these interactions. Fluorescent microscopy analysis and co-immunoprecipitation provided support for the co-localization and interaction of hADA3 with these proteins in human cells. Expression of the interacting proteins altered expression of an hADA3-regulated reporter gene, suggesting functional consequences for the interactions. The detected interactions of hADA3 might extend the spectrum of mechanisms by which ADA3 can contribute to the regulation of gene expression and shed light on processes mediated by these newly identified ADA3 partners.

Transcriptional control by chromosome-associated protein phosphatase-1

2005 ◽  
Vol 33 (6) ◽  
pp. 1444-1446 ◽  
Author(s):  
D. Bennett
Keyword(s):  
Gene Expression ◽  
Protein Phosphatase ◽  
Transcriptional Control ◽  
Regulation Of Gene Expression ◽  
Polytene Chromosomes ◽  
Protein Phosphatase 1 ◽  
Environmental Cues ◽  
Spatial And Temporal Patterns ◽  
Regulatory Subunits ◽  
Chromosomal Loci

Tight regulation of gene expression is critical for cells to respond normally to physiological and environmental cues and to allow cell specialization. Reversible phosphorylation of key structural and regulatory proteins, from histones to the transcriptional machinery, is acknowledged to be an important mechanism of regulating spatial and temporal patterns of gene expression. PP1 (protein phosphatase-1), a major class of serine/threonine protein phosphatase, is found at many sites on Drosophila polytene chromosomes where it is involved in controlling gene expression and chromatin structure. PP1 is targeted to different chromosomal loci through interaction with a variety of different regulatory subunits, which modify PP1's activity towards specific substrates. This mini-review gives an overview of known chromosome-associated PP1 complexes, their role in transcriptional control and the prospects for future analysis.

scholarly journals TORC1 signaling modulates Cdk8-dependent GAL gene expression in Saccharomyces cerevisiae

Genetics ◽  
2021 ◽  
Author(s):  
Riley Horvath ◽  
Nicole Hawe ◽  
Cindy Lam ◽  
Konstantin Mestnikov ◽  
Mariam Eji-Lasisi ◽  
...  
Keyword(s):  
Gene Expression ◽  
Rna Polymerase Ii ◽  
Nuclear Localization ◽  
Protein Phosphatase ◽  
Regulatory Subunit ◽  
Gal Genes ◽  
Dependent Site ◽  
Insight Into

Abstract Cdk8 of the RNA Polymerase II mediator kinase complex regulates gene expression by phosphorylating sequence-specific transcription factors. This function is conserved amongst eukaryotes, but the signals and mechanisms regulating Cdk8 activity and phosphorylation of its substrates are unknown. Full induction of the GAL genes in yeast requires phosphorylation of the transcriptional activator Gal4 by Cdk8. We used a screen to identify regulators of the Cdk8-dependent phosphorylation on Gal4, from which we identified multiple mutants with defects in TORC1 signaling. One mutant, designated gal four throttle 1 (gft1) was identified as a recessive allele of hom3, encoding aspartokinase, and mutations in hom3 caused effects typical of inhibition of TORC1, including rapamycin sensitivity and enhanced nuclear localization of the TORC1-responsive transcription factor Gat1. Mutations in hom3 also inhibit phosphorylation of Gal4 in vivo at the Cdk8-dependent site on Gal4, as did mutations of tor1, but these mutations did not affect activity of Cdk8 assayed in vitro. Disruption of cdc55, encoding a regulatory subunit of the TORC1-regulated protein phosphatase PP2A, suppressed the effect of hom3 and tor1 mutations on GAL expression, and also restored phosphorylation of Gal4 at the Cdk8-dependent site in vivo. These observations demonstrate that TORC1 signaling regulates GAL induction through the activity of PP2A/Cdc55, and suggest that Cdk8-dependent phosphorylation of Gal4 is opposed by PP2A/Cdc55 dephosphorylation. These results provide insight into how induction of transcription by a specific inducer can be modulated by global nutritional signals through regulation of Cdk8-dependent phosphorylation.

scholarly journals Akt Phosphorylation of p300 at Ser-1834 Is Essential for Its Histone Acetyltransferase and Transcriptional Activity

2005 ◽  
Vol 25 (15) ◽  
pp. 6592-6602 ◽  
Author(s):  
Wei-Chien Huang ◽  
Ching-Chow Chen
Keyword(s):  
Gene Expression ◽  
Rna Polymerase Ii ◽  
Histone Acetyltransferase ◽  
Critical Role ◽  
Regulation Of Gene Expression ◽  
Necrosis Factor Alpha ◽  
Akt Phosphorylation ◽  
Basal Transcriptional Machinery

ABSTRACT The PI3K/Akt pathway plays a critical role in the regulation of gene expression induced by numerous stimuli. p300, a transcriptional coactivator, acts in concert with transcription factors to facilitate gene expression. Here, we show that Akt is activated and translocated to the nucleus in response to tumor necrosis factor alpha. Nuclear Akt associates with p300 and phosphorylates its Ser-1834 both in vivo and in vitro. The phosphorylation induces recruitment of p300 to the ICAM-1 promoter, leading to the acetylation of histones in chromatin and association with the basal transcriptional machinery RNA polymerase II. These two events facilitate ICAM-1 gene expression and are abolished by the p300 S1834A mutant, inhibitors of PI3K/Akt, or small interfering RNA of Akt. Histone acetylation is attributed to the Akt-enhanced intrinsic histone acetyltransferase (HAT) activity of p300 and its association with another HAT, p/CAF. Our study provides a new insight into the molecular mechanism by which Akt promotes the transcriptional potential of p300.

scholarly journals AKINβ1, a regulatory subunit of SnRK1, regulates organic acid metabolism and acts as a global regulator of genes involved in carbon, lipid and nitrogen metabolism

2019 ◽  
Author(s):  
You Wang ◽  
Liping Wang ◽  
Barry J Micallef ◽  
Ian J Tetlow ◽  
Robert T Mullen ◽  
...  
Keyword(s):  
Gene Expression ◽  
Protein Kinase ◽  
Subcellular Localization ◽  
Tca Cycle ◽  
Regulatory Subunit ◽  
Regulatory Function ◽  
Insertion Mutant ◽  
Altered Expression ◽  
Regulatory Subunits ◽  
Dna Insertion

Abstract The Sucrose Non-fermenting-1-Related Protein Kinase 1 (SnRK1) is a highly conserved heterotrimeric protein kinase in plants. It possesses a catalytic subunit (α) and two regulatory subunits (β and γ). The effects of altered expression of AKINβ1 on carbohydrate metabolism and gene expression in leaves were investigated in an Arabidopsis T-DNA insertion mutant. The contents of key intermediates in the tricarboxylic acid (TCA) cycle of the mutant leaves were markedly reduced throughout the diurnal cycle, coupled with a decrease in measurable respiration rate. Compared to wild-type, 2485 genes and 188 genes were expressed differentially in leaves of the akinβ1 mutant in response to light and darkness respectively. Among these, several genes exhibited very substantial decreases in expression. Notably, expression of particular isoforms of multigene families involved in malate and lipid metabolism, and nitrate uptake showed decreases of 40-240 fold during the light period, but not during darkness. The subcellular localization of AKINβ1 and the regulatory function of N-myristoylation on the subcellular localization of AKINβ1 were investigated, showing that AKINβ1 localizes to Golgi. A model is hypothesized to explain the effects of AKINβ1 on metabolism and gene expression in Arabidopsis.

Linking transcription, RNA polymerase II elongation and alternative splicing

2020 ◽  
Vol 477 (16) ◽  
pp. 3091-3104 ◽  
Author(s):  
Luciana E. Giono ◽  
Alberto R. Kornblihtt
Keyword(s):  
Gene Expression ◽  
Alternative Splicing ◽  
Rna Polymerase Ii ◽  
Environmental Changes ◽  
Transcription Elongation ◽  
Single Gene ◽  
Regulation Of Gene Expression ◽  
Regulation Of Transcription ◽  
Stepping Stones ◽  
Eukaryotic Transcription

Gene expression is an intricately regulated process that is at the basis of cell differentiation, the maintenance of cell identity and the cellular responses to environmental changes. Alternative splicing, the process by which multiple functionally distinct transcripts are generated from a single gene, is one of the main mechanisms that contribute to expand the coding capacity of genomes and help explain the level of complexity achieved by higher organisms. Eukaryotic transcription is subject to multiple layers of regulation both intrinsic — such as promoter structure — and dynamic, allowing the cell to respond to internal and external signals. Similarly, alternative splicing choices are affected by all of these aspects, mainly through the regulation of transcription elongation, making it a regulatory knob on a par with the regulation of gene expression levels. This review aims to recapitulate some of the history and stepping-stones that led to the paradigms held today about transcription and splicing regulation, with major focus on transcription elongation and its effect on alternative splicing.

scholarly journals Differential expression of protein phosphatase PPM1B and multiple protein phosphatase regulatory subunits in glioblastoma.

2020 ◽  
Author(s):  
Shahan Mamoor
Keyword(s):  
Gene Expression ◽  
Brain Tissue ◽  
Protein Phosphatase ◽  
Treatment Options ◽  
Normal Brain ◽  
Regulatory Subunits ◽  
Gene Expression Information ◽  
Multiple Protein ◽  
Substrate Phosphorylation ◽  
Public Dataset

Glioblastoma multiforme is an aggressive brain cancer with few treatment options and poor survival outcomes (1, 2). We used a public dataset (3) containing the gene expression information of tumors from 17 patients diagnosed with glioblastoma and compared it to the gene expression information from the non-cancerous, healthy brain tissue from 8 individuals as a reference control, to understand what is most different between the transcriptional behavior of glioblastoma tumors relative to the tissue it arises from. We found that protein phosphatase PPM1B and three protein phosphatase regulatory subunits were among the genes whose expression was most different between glioblastoma tumors and “normal” brain tissue. The fact that multiple phosphatase regulatory genes are expressed at significantly lower levels in glioblastoma tumors suggests that alteration of substrate phosphorylation might be an important event in glioblastoma formation, maintenance or progression.

scholarly journals The Role of Protein Phosphatase 2A Catalytic Subunit Cα in Embryogenesis: Evidence from Sequence Analysis and Localization Studies

1999 ◽  
Vol 380 (9) ◽  
pp. 1117-1120 ◽  
Author(s):  
Jürgen Götz ◽  
Wilfried Kues
Keyword(s):  
Protein Phosphatase ◽  
Genomic Organization ◽  
Protein Phosphatase 2A ◽  
Catalytic Subunit ◽  
Regulatory Subunit ◽  
Catalytic Subunits ◽  
Regulatory Subunits ◽  
Phosphatase 2A ◽  
The Brain

AbstractProtein phosphatase 2A (PP2A) constitutes one of the major families of protein serine/threonine phosphatases found in all eukaryotic cells. PP2A holoenzymes are composed of a catalytic subunit complexed with a structural regulatory subunit of 65 kDa. These core subunits associate with regulatory subunits of various sizes to form different heterotrimers which have been purified and evaluated with regard to substrate specificity. In fully differentiated tissues PP2A expression levels are highest in the brain, however, relatively little is known about expression in the developing embryo.In order to determine the composition of PP2A catalytic subunits in the mouse, cDNAs were cloned and the genomic organization of PP2A Cα was determined.By a gene targeting approach in the mouse, we have previously shown that the absence of the major catalytic subunit of PP2A, Cα, resulted in embryonic lethality around embryonic day E6.5. No mesoderm was formed which implied that PP2A plays a crucial role in gastrulation.Here, we extended our studies and analyzed wildtype embryos for Cα expression at subsequent stages of development. After gastrulation is completed, we find high expression of Cα restricted to the neural folds, which suggests that PP2A plays an additional pivotal role in neurulation.

scholarly journals Genome-scale mapping reveals complex regulatory activities of RpoN in Yersinia pseudotuberculosis

2020 ◽  
Author(s):  
F.A.K.M. Mahmud ◽  
K. Nilsson ◽  
A. Fahlgren ◽  
R. Navais ◽  
R. Choudhry ◽  
...  
Keyword(s):  
Gene Expression ◽  
Binding Sites ◽  
Sigma Factor ◽  
Biofilm Formation ◽  
Yersinia Pseudotuberculosis ◽  
Regulation Of Gene Expression ◽  
Binding Motif ◽  
Alternative Sigma Factor ◽  
Altered Expression ◽  
Sense Strand

ABSTRACTRpoN, an alternative sigma factor commonly known as sigma 54, is implicated in persistent stages of Yersinia pseudotuberculosis infections in which genes associated with this regulator are upregulated. We here combined phenotypic and genomic assays to provide insight into its role and function in this pathogen. RpoN was found essential for Y. pseudotuberculosis virulence in mice, and in vitro functional assays showed that it controls biofilm formation and motility. Mapping genome-wide associations of Y. pseudotuberculosis RpoN using chromatin immunoprecipitation coupled with next-generation sequencing identified an RpoN-binding motif located at 103 inter- and intragenic sites on both sense and anti-sense strands. Deletion of rpoN had a large impact on gene expression, including down-regulation of genes encoding proteins involved in flagellar assembly, chemotaxis, and quorum sensing. There were also clear indications of cross talk with other sigma factors, together with indirect effects due to altered expression of other regulators. Matching differential gene expression with locations of the binding sites implicated around 130 genes or operons potentially activated or repressed by RpoN. Mutagenesis of selected intergenic binding sites confirmed both positive and negative regulatory effects of RpoN binding. Corresponding mutations of intragenic sense sites had less impact on associated gene expression. Surprisingly, mutating intragenic sites on the anti-sense strand commonly reduced expression of genes encoded by the corresponding sense strand.IMPORTANCEThe alternative sigma factor, RpoN (σ 54), which is widely distributed in eubacteria have been implicated to control gene expression of importance for numerous functions including virulence. Proper responses to host environments are crucial for bacteria to establish infection and regulatory mechanisms involved are therefore of high interest for development of future therapeutics. Little is known about the function of RpoN in the intestinal pathogen Y. pseudotuberculosis and we therefore investigated its regulatory role in this pathogen. This regulator was indeed found to be critical for establishment of infection in mice, likely involving its requirement for motility and biofilm formation. The RpoN regulon involved both activating and suppressive effects on gene expression which could be confirmed with mutagenesis of identified binding sites. This is the first of its kind study of RpoN in Y. pseudotuberculosis revealing complex regulation of gene expression involving both productive and silent effects of its binding to DNA providing important information about RpoN regulation in enterobacteria.

scholarly journals Promoter Proximal Pausing Limits Tumorous Growth Induced by the Yki Transcription Factor in Drosophila

Genetics ◽  
2020 ◽  
Vol 216 (1) ◽  
pp. 67-77 ◽  
Author(s):  
Sanket Nagarkar ◽  
Ruchi Wasnik ◽  
Pravallika Govada ◽  
Stephen Cohen ◽  
L. S. Shashidhara
Keyword(s):  
Gene Expression ◽  
Rna Polymerase Ii ◽  
Gene Expression Regulation ◽  
Regulation Of Gene Expression ◽  
Elongation Factor ◽  
Imaginal Discs ◽  
Link Type ◽  
Genome Wide ◽  
Wing Imaginal Discs ◽  
Tumorous Growth

Promoter proximal pausing (PPP) of RNA polymerase II has emerged as a crucial rate-limiting step in the regulation of gene expression. Regulation of PPP is brought about by complexes 7SK snRNP, P-TEFb (Cdk9/cycT), and the negative elongation factor (NELF), which are highly conserved from Drosophila to humans. Here, we show that RNAi-mediated depletion of bin3 or Hexim of the 7SK snRNP complex or depletion of individual components of the NELF complex enhances Yki-driven growth, leading to neoplastic transformation of Drosophila wing imaginal discs. We also show that increased CDK9 expression cooperates with Yki in driving neoplastic growth. Interestingly, overexpression of CDK9 on its own or in the background of depletion of one of the components of 7SK snRNP or the NELF complex necessarily, and specifically, needed Yki overexpression to cause tumorous growth. Genome-wide gene expression analyses suggested that deregulation of protein homeostasis is associated with tumorous growth of wing imaginal discs. As both Fat/Hippo/Yki pathway and PPP are highly conserved, our observations may provide insights into mechanisms of oncogenic function of YAP—the ortholog of Yki in humans.

Stability of transcription complexes on class II genes

1989 ◽  
Vol 9 (1) ◽  
pp. 342-344
Author(s):  
M W Van Dyke ◽  
M Sawadogo ◽  
R G Roeder
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Reaction Pathway ◽  
Regulation Of Gene Expression ◽  
Class Ii ◽  
Tata Box ◽  
Promoter Complex ◽  
Transcription Complexes

Commitment of a TATA box-driven class II gene to transcription requires binding of only one transcription factor, TFIID. Additional factors (TFIIB, TFIIE, and RNA polymerase II) do not remain associated with the TFIID-promoter complex during the course of transcription. This indicates that there are two intermediates along the transcription reaction pathway which may be potential targets for the regulation of gene expression.

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