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Structural Basis Of Rna Polymerase Ii C Terminal Domain Kinase And Phosphatase Specificity And Their Impact On Transcriptional Regulation
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Book Synopsis Structural Basis of RNA Polymerase II C-terminal Domain Kinase and Phosphatase Specificity and Their Impact on Transcriptional Regulation by : Nathaniel Tate Burkholder
Download or read book Structural Basis of RNA Polymerase II C-terminal Domain Kinase and Phosphatase Specificity and Their Impact on Transcriptional Regulation written by Nathaniel Tate Burkholder and published by . This book was released on 2019 with total page 292 pages. Available in PDF, EPUB and Kindle. Book excerpt: Transcription from a most basic perspective is the process of generating strands of RNA from DNA templates. However, in order to control when, where, and how much of specific RNAs are made, cells have evolved vast arrays of transcriptional regulatory mechanisms that allow for extensive differentiation and formation of complex traits. One of the unique and most important mechanisms of transcriptional regulation in eukaryotic cells is the reversible phosphorylation of the RNA polymerase II C-terminal domain (RNAPII CTD). The CTD contains heptad repeats composed of the consensus sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7 and all of the non-proline sites are phosphorylated in cells. The human CTD contains 52 repeats where the first 26 proximal heptads are mostly consensus sequence whereas the last 26 distal heptads contain several variations primarily at the Ser7 position. In Chapter 2, I describe how these variations and their modifications alter the phosphorylation of Tyr1 sites by using a combination of biochemical assays and mass spectrometry. Data presented in this chapter reveal how a conserved positively charged pocket in tyrosine kinases likely mediates the interaction residues in the Ser7 position and can potentially affect in vivo Tyr1 phospho-patterning. Futhermore, in Chapter 3 I describe the methodology behind synthesis and testing of cis/trans-locked Ser-Pro CTD peptides for understanding the role of prolyl isomerization on CTD regulation. We used these tools to determine the specificity of several CTD phosphatases, which revealed how the Ser5 phosphatase SSU72 structurally prefers the cis- over the trans-configuration of the phosphorylated Ser5-Pro6 motif. Among the phosphatases discovered to dephosphorylate the CTD, the family of SCP phosphatases seem to be more involved in regulating transcription through dephosphorylation of a different protein called the RE-1 silencing transcription factor (REST). REST is a major silencer of neuronal gene expression in non-neuronal cells which helps prevent development of improper neuronal phenotypes. Abnormally high protein levels of REST have been found in subsets of glioblastoma isolates which likely contributes to their oncogenesis and resistance of chemotherapeutics. SCP1 upregulates REST protein levels through dephosphorylating two degron sites that normally promote rapid turnover of REST, making it a potential drug target for glioblastomas in future studies. In Chapter 4, we show structurally how SCP1 recognizes these REST phosphorylation sites through complex x-ray crystallography. Data presented in this chapter reveal SCP1 specificity for each REST site and how SCP1 activity towards both of them promote REST gene silencing function
Book Synopsis Phosphatases and Prolyl-isomerase in the Regulation of the C-terminal Domain of Eukaryotic RNA Polymerase II by : Mengmeng Zhang
Download or read book Phosphatases and Prolyl-isomerase in the Regulation of the C-terminal Domain of Eukaryotic RNA Polymerase II written by Mengmeng Zhang and published by . This book was released on 2012 with total page 428 pages. Available in PDF, EPUB and Kindle. Book excerpt: In eukaryotes, the first step of interpreting the genetic information is the transcription of DNA into RNA. For protein-coding genes, such transcription is carried out by RNA polymerase II. A special domain of RNA polymerase II, called the C-terminal domain (CTD), functions as a master controller for the transcription process by providing a platform to recruit regulatory proteins to nascent mRNA (Chapter 1-2). The modifications and conformational states of the CTD, termed the 'CTD code', represent a critical regulatory checkpoint for transcription. The CTD, found only in eukaryotes, consists of 26--52 tandem heptapeptide repeats with the consensus sequence, Tyr1Ser2Pro3Thr4Ser5Pro6Ser--. Phosphorylation of the serines and prolyl isomerization of the prolines represent two major regulatory mechanisms of the CTD. Interestingly, the phosphorylation sites are typically close to prolines, thus the conformation of the adjacent proline could impact the specificity of the corresponding kinases and phosphatases. Understanding how those modifying enzymes recognize and regulate the CTD is important for expanding our knowledge on the transcription regulation and deciphering the 'CTD code'. During my PhD study, I studied the function of CTD phosphatases and prolyl isomerase in the CTD regulation using Scp1, Ssu72 and Pin1 as model regulators. Scp1 and Ssu72 are both Ser5 phosphatases. However, Ssu72 is an essential protein and regulates the global transcription while Scp1 epigenetically silences the expression of specific neuronal genes. Pin1 is a highly conserved phosphorylation-specific prolyl isomerase that recognizes the phospho-Ser/Thr-Pro motif within the CTD as one of its primary substrates in vivo. Among these enzymes, Scp1 is the focal point of this dissertation, as it was studied from different angles, such as enzymatic mechanism (Chapter 3 describes the capture of phospho-aspartyl intermediate of Scp1 as a direct evidence for the proposed two-step mechanism), specific inhibition (Chapter 4 describes the identification and characterization of the first specific inhibitor of Scp1), and its non-active-site contact with the CTD (Chapter 5 describes the structural basis of this contact). These studies are of great importance towards understanding the molecular mechanism of the dephosphorylation process of the CTD by Scp1.
Book Synopsis Structural Heterogeneity in the RNA Polymerase II C-Terminal Domain by : Bede Portz
Download or read book Structural Heterogeneity in the RNA Polymerase II C-Terminal Domain written by Bede Portz and published by . This book was released on 2017 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: RNA polymerase II contains a repetitive and intrinsically disordered C-Terminal Domain (CTD) composed of heptad repeats of the consensus sequence YSPTSPS. The CTD can be heavily phosphorylated and serves as a scaffold, interacting with factors involved in transcription initiation, elongation, termination, RNA processing and chromatin modification. Despite its role as a nexus of eukaryotic gene regulation, the structure of the CTD and the structural implications of CTD phosphorylation, are poorly understood. Additionally, there is an increasing awareness of the importance of intrinsically disordered proteins (IDPs) that function without adopting a stably folded structure. Here I present a biophysical and biochemical interrogation of the structure of the full-length CTD of D. melanogaster, which I conclude is a compact random coil. I find that the repetitive CTD is structurally heterogeneous as evidenced by a discontinuous pattern of cutting in limited proteolysis assays. Small Angle X-Ray scattering (SAXS) is a method ideally suited for the structural interrogation of large IDPs and can be employed to measure the size of a protein and to monitor structural changes in response to post-translational modification. Using SAXS I determined that phosphorylation by the kinase P-TEFb caused an increase in CTD radius and stiffness. Limited proteolysis of the phosphorylated CTD showed these gross structural changes are accompanied by increased protease accessibility and an alteration in relative protease accessibility across the length of the CTD.Additionally, we show that the human CTD is also structurally heterogeneous and able to substitute for the Drosophila melanogaster CTD in supporting the development of flies to adulthood. These finding implicate conserved structural organization, not a precise array of heptad motifs, as important to CTD function.The CTD is attached to the catalytic core of Pol II via a linker. I show that this linker is more compact than the CTD repeats and serves as an independent structural unit. The phosphorylated linker-CTD remains flexible relative to the phosphorylated CTD alone. Together, these results support a mechanism by which phosphorylation reduces the conformational entropy of the CTD, generating a more binding competent dock for CTD:protein interactions, with the linker region maintaining the ability of CTD bound factors to sample the 3-dimensional space which may be required for RNA processing and histone modification.The data described herein represent the most thorough structural characterization to date of the full length CTD on the global and local scales, examining both the overall size and local structural organization of the CTD. These studies establish the Drosophila CTD as an attractive model for the biophysical, biochemical and genetic interrogation of the structure and function of the CTD from a developmentally complex organism.
Book Synopsis Cyclin Dependent Kinase 5 (Cdk5) by : Nancy Y. Ip
Download or read book Cyclin Dependent Kinase 5 (Cdk5) written by Nancy Y. Ip and published by Springer Science & Business Media. This book was released on 2009-02-28 with total page 326 pages. Available in PDF, EPUB and Kindle. Book excerpt: Cyclin Dependent Kinase 5 provides a comprehensive and up-to-date collection of reviews on the discovery, signaling mechanisms and functions of Cdk5, as well as the potential implication of Cdk5 in the treatment of neurodegenerative diseases. Since the identification of this unique member of the Cdk family, Cdk5 has emerged as one of the most important signal transduction mediators in the development, maintenance and fine-tuning of neuronal functions and networking. Further studies have revealed that Cdk5 is also associated with the regulation of neuronal survival during both developmental stages and in neurodegenerative diseases. These observations indicate that precise control of Cdk5 is essential for the regulation of neuronal survival. The pivotal role Cdk5 appears to play in both the regulation of neuronal survival and synaptic functions thus raises the interesting possibility that Cdk5 inhibitors may serve as therapeutic treatment for a number of neurodegenerative diseases.
Book Synopsis The Role of RNA Polymerase II Phosphorylation in the Early Stages of Transcription by : Jonathan Donald Chesnut
Download or read book The Role of RNA Polymerase II Phosphorylation in the Early Stages of Transcription written by Jonathan Donald Chesnut and published by . This book was released on 1994 with total page 280 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis RNA Polymerase III Transcription by : Robert J. White
Download or read book RNA Polymerase III Transcription written by Robert J. White and published by Springer Science & Business Media. This book was released on 2013-11-11 with total page 274 pages. Available in PDF, EPUB and Kindle. Book excerpt: This monograph reviews and summarizes the substantial body of work that has been published on the transcription by polymerase III over the past 5 years. Progress in this field has been very rapid since 1993, and this new edition incorporates all the recent developments and offers the reader a highly detailed analysis of the current state of research on this largest and most complex of the eukaryotic RNA polymerases.
Book Synopsis Protein Phosphorylation in Human Health by : Cai Huang
Download or read book Protein Phosphorylation in Human Health written by Cai Huang and published by BoD – Books on Demand. This book was released on 2012-09-06 with total page 482 pages. Available in PDF, EPUB and Kindle. Book excerpt: 15 chapters on protein phosphorylation and human health written by expert scientists. Covers most important research hot points, such as Akt, AMPK and mTOR. Bridges the basic protein phosphorylation pathways with human health and diseases. Detailed and comprehensive text with excellent figure illustration.
Book Synopsis Protein Conformational Dynamics by : Ke-li Han
Download or read book Protein Conformational Dynamics written by Ke-li Han and published by Springer Science & Business Media. This book was released on 2014-01-20 with total page 488 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book discusses how biological molecules exert their function and regulate biological processes, with a clear focus on how conformational dynamics of proteins are critical in this respect. In the last decade, the advancements in computational biology, nuclear magnetic resonance including paramagnetic relaxation enhancement, and fluorescence-based ensemble/single-molecule techniques have shown that biological molecules (proteins, DNAs and RNAs) fluctuate under equilibrium conditions. The conformational and energetic spaces that these fluctuations explore likely contain active conformations that are critical for their function. More interestingly, these fluctuations can respond actively to external cues, which introduces layers of tight regulation on the biological processes that they dictate. A growing number of studies have suggested that conformational dynamics of proteins govern their role in regulating biological functions, examples of this regulation can be found in signal transduction, molecular recognition, apoptosis, protein / ion / other molecules translocation and gene expression. On the experimental side, the technical advances have offered deep insights into the conformational motions of a number of proteins. These studies greatly enrich our knowledge of the interplay between structure and function. On the theoretical side, novel approaches and detailed computational simulations have provided powerful tools in the study of enzyme catalysis, protein / drug design, protein / ion / other molecule translocation and protein folding/aggregation, to name but a few. This work contains detailed information, not only on the conformational motions of biological systems, but also on the potential governing forces of conformational dynamics (transient interactions, chemical and physical origins, thermodynamic properties). New developments in computational simulations will greatly enhance our understanding of how these molecules function in various biological events.
Book Synopsis Structural Basis of Initiation and Elongation by RNA Polymerase II by : Kenneth Dale Westover
Download or read book Structural Basis of Initiation and Elongation by RNA Polymerase II written by Kenneth Dale Westover and published by . This book was released on 2005 with total page 222 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis RNA Polymerase II Carboxy-terminal Domain Phosphatase by : Michael S. Kobor
Download or read book RNA Polymerase II Carboxy-terminal Domain Phosphatase written by Michael S. Kobor and published by . This book was released on 2001 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: The form of RNA polymerase II (RNAPII) that binds preferentially to promoters is not extensively phosphorylated on the carboxy-terminal heptapeptide repeat domain (CTD) of its largest subunit. The CTD becomes phosphorylated during or shortly after initiation and elongating RNAPII generally has a phosphorylated CTD. Prior to or following transcriptional termination, dephosphorylation of the CTD presumably must occur to regenerate the hypophosphorylated form of RNAPII that is capable of reinitiating transcription. This thesis examines the function of the CTD phosphatase Fcp1p in the yeast 'Saccharomyces cerevisiae'. In chapter 2, it is shown that Fcp1 is an unusual eukaryotic protein phosphatase that is required for dephosphorylation of the CTD 'in vivo ' and for transcription by RNAPII 'in vivo'. These results suggest that Fcp1p is the founding member of a new class of protein phosphatases and acts as a general transcription factor 'in vivo'. In chapter 3, affinity chromatography is used to study the binding of Fcp1p to TFIIB and the RAP74 subunit of TFIIF. Fcp1p binds in a similar way to both of these factors. RAP74 and TFIIB have a short region of homology and amino acid changes in this region affect the binding to Fcp1p. The genes encoding RAP74 and Fcp1p interact 'in vivo'. Fcp1p can activate transcription when artificially tethered to a promoter and this effect is largely dependent on binding to RAP74. In chapter 4, it is shown that yeast strains with mutations in ' fcp1' grow much worse when the gene encoding the major CTD kinase Kin28p is also mutated. In contrast, inactivation of another CTD kinase encoded by the 'SRB10' gene suppresses the temperature-sensitivity and the sensitivity to certain cell cycle checkpoint inducing drugs of ' fcp1' mutant strains. These results therefore suggest that Fcp1p and Srb10p have opposing roles 'in vivo'. In chapter 5, analysis of the phosphorylation state of the CTD reveals that reduced Fcp1p activity results in a increased amount of the largest subunit of RNAPII but this subunit is not incorporated into functional enzyme and is largely degraded at a higher temperature.
Book Synopsis RNA Polymerase II Controls Transcription Dynamics by :
Download or read book RNA Polymerase II Controls Transcription Dynamics written by and published by . This book was released on 2013 with total page 261 pages. Available in PDF, EPUB and Kindle. Book excerpt: The C-terminal domain (CTD) of RNA polymerase II (Pol II) consists of conserved heptapeptide repeats that are subject to sequential waves of posttranslational modifications during specific stages of the transcription cycle. These patterned modifications have led to the postulation of the CTD code hypothesis, where stage-specific patterns define a spatiotemporal code that is recognized by the appropriate interacting partners. This thesis summarizes our efforts to define the CTD code, identify the writers and erasers, and explore the function of the code during transcription. We examined the genome-wide distributions of the phospho-serine modifications. We found unique profile clusters for the "early" serine 5 phosphorylation (Ser5-P), the "mid" serine 7 phosphorylation (Ser7-P), and the "late" serine 2 phosphorylation (Ser2-P). We also identified gene class-specific patterns and find widespread co-occurrence of the CTD marks. These phosphorylation marks are placed by an array of phospho-serine kinases. We identified Kin28 (CDK7) as a Ser7-P kinase, and specific inhibition of Kin28 caused a significant decrease in Ser7-P levels at promoters. However, the promoter-distal Ser7-P marks are not remnants of early phosphorylation by Kin28. Instead, we find that Bur1 (CDK9) is positioned to phosphorylate Ser7 within the coding regions. Next, we investigated the phosphatases that erase the CTD code. The importance of these enzymes is emphasized by our observation that an inability to remove Ser7-P marks is lethal. We identified Ssu72 as a Ser7-P phosphatase, and inactivation of Ssu72 triggers a drastic remodeling of Ser7-P distributions across protein-coding and non-coding genes. Furthermore, we report that removal of all phospho-CTD marks during transcription termination is mechanistically coupled. An inability to remove these marks prevents Pol II from terminating efficiently at both gene classes and also impedes proper transcription initiation. Interestingly, Ssu72 seems to be enriched within introns, peaking at the 3' splice site. Interestingly, we do not find polymerase pausing at the 3' splice site or at the terminal exons, as has been previously reported. Instead, we believe Ssu72 may be involved in facilitating the cotranscriptional recruitment of splicing factors by establishing a chromatin state accommodating to splicing.
Book Synopsis Fundamentals of Molecular Structural Biology by : Subrata Pal
Download or read book Fundamentals of Molecular Structural Biology written by Subrata Pal and published by Academic Press. This book was released on 2019-09-02 with total page 518 pages. Available in PDF, EPUB and Kindle. Book excerpt: Fundamentals of Molecular Structural Biology reviews the mathematical and physical foundations of molecular structural biology. Based on these fundamental concepts, it then describes molecular structure and explains basic genetic mechanisms. Given the increasingly interdisciplinary nature of research, early career researchers and those shifting into an adjacent field often require a "fundamentals" book to get them up-to-speed on the foundations of a particular field. This book fills that niche. Provides a current and easily digestible resource on molecular structural biology, discussing both foundations and the latest advances Addresses critical issues surrounding macromolecular structures, such as structure-based drug discovery, single-particle analysis, computational molecular biology/molecular dynamic simulation, cell signaling and immune response, macromolecular assemblies, and systems biology Presents discussions that ultimately lead the reader toward a more detailed understanding of the basis and origin of disease
Book Synopsis Encyclopedia of Signaling Molecules by : Sangdun Choi
Download or read book Encyclopedia of Signaling Molecules written by Sangdun Choi and published by Springer. This book was released on 2017-12-15 with total page 6330 pages. Available in PDF, EPUB and Kindle. Book excerpt: The second edition of this encyclopedia presents over 400 biologically important signaling molecules and the content is built on the core concepts of their functions along with early findings written by some of the world’s foremost experts. The molecules are described by recognized leaders in each molecule. The interactions of these single molecules in signal transduction networks will also be explored. This encyclopedia marks a new era in overview of current cellular signaling molecules for the specialist and the interested non-specialist alike. Currently, there are more than 30,000 genes in human genome. However, not all the proteins encoded by these genes work equally in order to maintain homeostasis. Understanding the important signaling molecules as completely as possible will significantly improve our research-based teaching and scientific capabilities.
Author :Errol C. Friedberg Publisher :American Society for Microbiology Press ISBN 13 :1555813194 Total Pages :2587 pages Book Rating :4.5/5 (558 download)
Book Synopsis DNA Repair and Mutagenesis by : Errol C. Friedberg
Download or read book DNA Repair and Mutagenesis written by Errol C. Friedberg and published by American Society for Microbiology Press. This book was released on 2005-11-22 with total page 2587 pages. Available in PDF, EPUB and Kindle. Book excerpt: An essential resource for all scientists researching cellular responses to DNA damage. • Introduces important new material reflective of the major changes and developments that have occurred in the field over the last decade. • Discussed the field within a strong historical framework, and all aspects of biological responses to DNA damage are detailed. • Provides information on covering sources and consequences of DNA damage; correcting altered bases in DNA: DNA repair; DNA damage tolerance and mutagenesis; regulatory responses to DNA damage in eukaryotes; and disease states associated with defective biological responses to DNA damage.
Book Synopsis Centromeres and Kinetochores by : Ben E. Black
Download or read book Centromeres and Kinetochores written by Ben E. Black and published by Springer. This book was released on 2017-08-23 with total page 552 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents the latest advances concerning the regulation of chromosome segregation during cell division by means of centromeres and kinetochores. The authors cover both state-of-the-art techniques and a range of species and model systems, shedding new light on the molecular mechanisms controlling the transmission of genetic material between cell divisions and from parent to offspring. The chapters cover five major areas related to the current study of centromeres and kinetochores: 1) their genetic and epigenetic features, 2) key breakthroughs at the molecular, proteomic, imaging and biochemical level, 3) the constitutive centromere proteins, 4) the role of centromere proteins in the physical process of chromosome segregation and its careful orchestration through elaborate regulation, and 5) intersections with reproductive biology, human health and disease, as well as chromosome evolution. The book offers an informative and provocative guide for newcomers as well as those already acquainted with the field.
Book Synopsis Regulation of RNA Polymerase II CTD Phosphatase in S. Cerevisiae by : Susanne Jutta Hoheisel
Download or read book Regulation of RNA Polymerase II CTD Phosphatase in S. Cerevisiae written by Susanne Jutta Hoheisel and published by . This book was released on 2005 with total page 328 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book HIV-1 Latency written by Guido Silvestri and published by Springer. This book was released on 2018-10-11 with total page 253 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume summarizes recent advances in understanding the mechanisms of HIV-1 latency, in characterizing residual viral reservoirs, and in developing targeted interventions to reduce HIV-1 persistence during antiretroviral therapy. Specific chapters address the molecular mechanisms that govern and regulate HIV-1 transcription and latency; assays and technical approaches to quantify viral reservoirs in humans and animal models; the complex interchange between viral reservoirs and the host immune system; computational strategies to model viral reservoir dynamics; and the development of therapeutic approaches that target viral reservoir cells. With contributions from an interdisciplinary group of investigators that cover a broad spectrum of subjects, from molecular virology to proof-of-principle clinical trials, this book is a valuable resource for basic scientists, translational investigators, infectious-disease physicians, individuals living with HIV/AIDS and the general public.
