Download or read book RNA Polymerase II Carboxy terminal Domain Phosphatase written by and published by . This book was released on 2001 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
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.
Download or read book RNA Polymerase II Carboxy terminal Domain Phosphatase microform written by Michael S. (Michael Steffen) Kobor and published by National Library of Canada = Bibliothèque nationale du Canada. This book was released on 2001 with total page 712 pages. Available in PDF, EPUB and Kindle. Book excerpt:
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 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
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:
Download or read book Computation Finite and Infinite Machines written by Marvin Lee Minsky and published by Prentice Hall. This book was released on 1967 with total page 344 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Methods in Yeast Genetics written by David C. Amberg and published by CSHL Press. This book was released on 2005 with total page 250 pages. Available in PDF, EPUB and Kindle. Book excerpt: "Methods in Yeast Genetics" is a course that has been offered annually at Cold Spring Harbor for the last 30 years. This provides a set of teaching experiments along with the protocols and recipes for the standard techniques and reagents used in the study of yeast biology.
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.
Download or read book Dynamic Changes in Phosphorylation of RNA Polymerase II Carboxy terminal Domain During Transcription Cycle written by E. J. Cho and published by . This book was released on 2002 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Mechanisms of Recruitment of the CTD Phosphatase Rtr1 to RNA Polymerase II written by Michael J. Berna (Sr.) and published by . This book was released on 2012 with total page 166 pages. Available in PDF, EPUB and Kindle. Book excerpt: The C-terminal domain (CTD) of the RNA polymerase II (RNAPII) subunit Rpb1 must exist in a hypophosphorylated state prior to forming a competent transcription initiation complex. However, during transcription, specific kinases and phosphatases act on the RNAPII CTD to regulate its phosphorylation state, which serves to recruit sequence-specific and general transcription factors at the appropriate stage of transcription. A key phosphatase involved in this process, Rtr1 (Regulator of Transcription 1), was shown to regulate a key step important for transcription elongation and termination. Although the role that Rtr1 plays in regulating RNAPII transcription has been described, the mechanism involved in the recruitment of Rtr1 to RNAPII during transcription has not been elucidated in yeast. Consequently, the present work utilized both affinity purification schemes in Saccharomyces cerevisiae and mass spectrometry to identify key Rtr1-interacting proteins and post-translational modifications that potentially play a role in recruiting Rtr1 to RNAPII. In addition to RNAPII subunits, which were the most consistently enriched Rtr1-interacting proteins, seven proteins were identified that are potentially involved in Rtr1 recruitment. These included PAF complex subunits (Cdc73, Ctr9, Leo1), the heat shock protein Hsc82, the GTPase Npa3, the ATPase Rpt6, and Spn1. Indirect evidence was also uncovered that implicates that the CTDK-I complex, a kinase involved in RNAPII CTD phosphorylation, is important in facilitating interactions between Rtr1, RNAPII, and select transcription factors. Additionally, a putative phosphorylation site was identified on Ser217 of Rtr1 that may also play a role in its recruitment to RNAPII during transcription.
Download or read book Advancements of Mass Spectrometry in Biomedical Research written by Alisa G. Woods and published by Springer. This book was released on 2014-06-20 with total page 601 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume explores the use of mass spectrometry for biomedical applications. Chapters focus on specific therapeutic areas such as oncology, infectious disease and psychiatry. Additional chapters focus on methodology as well as new technologies and instrumentation. This volume provides readers with a comprehensive and informative manual that will allow them to appreciate mass spectrometry and proteomic research but also to initiate and improve their own work. Thus the book acts as a technical guide but also a conceptual guide to the newest information in this exciting field. Mass spectrometry is the central tool used in proteomic research today and is rapidly becoming indispensable to the biomedical scientist. With the completion of the human genome project and the genomic revolution, the proteomic revolution has followed closely behind. Understanding the human proteome has become critical to basic and clinical biomedical research and holds the promise of providing comprehensive understanding of human physiological processes. In addition, proteomics and mass spectrometry are bringing unprecedented biomarker discovery and are helping to personalize medicine.
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.
Download or read book RNA Exosome written by Torben Heick Jensen and published by Springer Science & Business Media. This book was released on 2011-06-29 with total page 161 pages. Available in PDF, EPUB and Kindle. Book excerpt: The diversity of RNAs inside living cells is amazing. We have known of the more “classic” RNA species: mRNA, tRNA, rRNA, snRNA and snoRNA for some time now, but in a steady stream new types of molecules are being described as it is becoming clear that most of the genomic information of cells ends up in RNA. To deal with the enormous load of resulting RNA processing and degradation reactions, cells need adequate and efficient molecular machines. The RNA exosome is arising as a major facilitator to this effect. Structural and functional data gathered over the last decade have illustrated the biochemical importance of this multimeric complex and its many co-factors, revealing its enormous regulatory power. By gathering some of the most prominent researchers in the exosome field, it is the aim of this volume to introduce this fascinating protein complex as well as to give a timely and rich account of its many functions. The exosome was discovered more than a decade ago by Phil Mitchell and David Tollervey by its ability to trim the 3’end of yeast, S. cerevisiae, 5. 8S rRNA. In a historic account they laid out the events surrounding this identification and the subsequent birth of the research field. In the chapter by Kurt Januszyk and Christopher Lima the structural organization of eukaryotic exosomes and their evolutionary counterparts in bacteria and archaea are discussed in large part through presentation of structures.
Download or read book The Role of the CTD Phosphatase Rtr1 and Post translational Modifications in Regulation of RNA Polymerase II written by Mary L. Cox and published by . This book was released on 2013 with total page 186 pages. Available in PDF, EPUB and Kindle. Book excerpt: RNA polymerase II (RNAPII) is regulated by multiple modifications to the C-terminal domain (CTD) of the largest subunit, Rpb1. This study has focused on the relationship between hyperphosphorylation of the CTD and RNAPII turnover and proteolytic degradation as well as post-translational modifications of the globular core of RNAPII. Following tandem affinity purification, western blot analysis showed that MG132 treated RTR1 ERG6 deletion yeast cells have accumulation of total RNAPII and in particular, the hyperphosphorylated form of the protein complex. In addition, proteomic studies using MuDPIT have revealed increased interaction between proteins of the ubiquitin-proteasome degradation system in the mutant MG132 treated yeast cells as well as potential ubiquitin and phosphorylation sites in RNAPII subunits, Rpb6 and Rpb1, respectively. A novel Rpb1 phosphorylation site, T1471-P, is located in the linker region between the CTD and globular domain of Rpb1 and will be the focus of future studies to determine biological significance of this post-translational modification.
Download or read book The Functional Significance of the Carboxyl terminal Domain of RNA Polymerase IIa o written by Paul James Laybourn and published by . This book was released on 1989 with total page 360 pages. Available in PDF, EPUB and Kindle. Book excerpt:
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.
