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Author : Yiling Yvonne Koh
Publisher :
ISBN 13 :
Total Pages : 166 pages
Book Rating : 4.:/5 (794 download)
Download or read book RNA Recognition by the PUF Protein Family written by Yiling Yvonne Koh and published by . This book was released on 2011 with total page 166 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : Laura J. Opperman
Publisher :
ISBN 13 :
Total Pages : 216 pages
Book Rating : 4.:/5 (891 download)
Download or read book PUF Proteins written by Laura J. Opperman and published by . This book was released on 2008 with total page 216 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : Douglas F. Porter
Publisher :
ISBN 13 :
Total Pages : 0 pages
Book Rating : 4.:/5 (988 download)
Download or read book Target Selection by Natural and Redesigned PUF Proteins written by Douglas F. Porter and published by . This book was released on 2015 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: RNA-binding proteins define extensive, subtle networks of regulation in Eukaryotes. RNA-binding proteins control the amount of protein produced from mRNA, the location of translation and the protein isoform produced. Pumilio/PUF proteins are a family of RNA-binding protein families present in humans, as well as Eukaryotes in general, one of a limited number of such families. Pumilio/PUF proteins bind specific sequences in single-stranded RNA. The modular nature of the PUF-RNA interaction has led to the use of Pumilio/PUF proteins in reengineering RNA-binding proteins to recognize new RNA motifs. S. cerevisiae possesses a Pumilio/PUF protein representing a special subfamily we term the Puf2p family. The Puf2p family recognizes the unusual cognate motif of UAAU in RNA. We identify the RNA-binding map of S. cerevisiae Puf2p, determining that Puf2p binds roughly a fifth of the yeast genome and binds through clusters of UAAU motifs in 3'UTRs. In addition, we find that regions outside the PUF domain affect binding. Next, we reengineered Puf2p to recognize a UAAG site, and identified that the reengineered Puf2p binds its novel site in RNA with the same specificity as wild-type or greater. We evaluate the prediction of the RNA-binding map of a redesigned protein, and find that PUF-RNA interactions involve many factors beyond the binding site. We find that Puf2p is a repressor, and that reengineered Puf2p represses a novel RNA network. Our results suggest that direct RNA-binding by PUF proteins has small effects on many RNAs and large effects on a few RNAs. We find that, when redesigned to a new specificity, redesigned PUF proteins conserve targets, partly by finding new sites in the same mRNAs. Next, we identified the RNA binding specificity of the conserved stem cell regulator and PUF protein FBF in C. elegans. We find that FBF binds predominantly in mRNA 3'UTRs at its cognate motif, but that it also binds an alternative 7-mer site in the cell and that many FBF interaction sites are 'secondary' interactions near a stronger, primary interaction. Our results suggest a method for improving our understanding of RNA-protein interactions.
Author :
Publisher :
ISBN 13 :
Total Pages : 0 pages
Book Rating : 4.:/5 (935 download)
Download or read book Specificity and Manipulation of PUF-RNA Interactions written by and published by . This book was released on 2015 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Post-transcriptional control is essential for biological processes. RNA-binding factors are critical for eliciting mRNA-specific control. The Pumilio and Fem-3 binding factor (PUF) family of proteins is a single-stranded RNA-binding family conserved throughout eukaryotes. PUF proteins bind mRNAs with high specificity in order to control their translation, localization and stability. PUF regulation is dependent upon specific RNA recognition through protein-RNA contacts within the PUF RNA-binding domain (RBD). In these studies, we have elucidated mechanisms governing PUF-RNA interactions and determined binding properties of manipulated PUF scaffolds. We performed structure-based mutational analyses of PUF binding to RNA across several PUF scaffolds. This work led to the identification of critical PUF-RNA interactions and uncovered a binding pattern applicable across PUF proteins. We discovered a mechanism that determines alternate RNA base-flipping patterns observed in Saccharomyces cerevisiae Puf4p and Caenorhabditis elegans FBF-2 crystal structures, and we determined overlapping in vivo regulatory targets of S. cerevisiae Puf4p and Puf5p. Modularity of PUF RBDs allows for their engineered specificity. Three important amino acids, termed the tripartite recognition motif (TRM), impart RNA base specificity for each PUF repeat. We showed the generality of a TRM recognition code across PUF RBD scaffolds and PUF repeats, demonstrating the use of specific TRM combinations to target desired RNA sequences. We also found that additional PUF-RNA contacts do not substantially increase binding affinity or specificity by testing RNA-binding of extended PUF RBDs. Together, these data have furthered our knowledge of how PUF proteins recognize target mRNAs, uncovered details of in vivo PUF regulation, and further developed the PUF RBD as a scaffold for engineered RNA-targeting.
Author : Brad A. Hook
Publisher :
ISBN 13 :
Total Pages : 276 pages
Book Rating : 4.:/5 (89 download)
Download or read book PUF Proteins written by Brad A. Hook and published by . This book was released on 2006 with total page 276 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : Kiyoshi Nagai
Publisher : Oxford University Press, USA
ISBN 13 :
Total Pages : 302 pages
Book Rating : 4.3/5 (91 download)
Download or read book RNA-protein Interactions written by Kiyoshi Nagai and published by Oxford University Press, USA. This book was released on 1994 with total page 302 pages. Available in PDF, EPUB and Kindle. Book excerpt: The study of RNA-protein interactions is crucial to understanding the mechanisms and control of gene expression and protein synthesis. The realization that RNAs are often far more biologically active than was previously appreciated has stimulated a great deal of new research in this field. Uniquely, in this book, the world's leading researchers have collaborated to produce a comprehensive and current review of RNA-protein interactions for all scientists working in this area. Timely, comprehensive, and authoritative, this new Frontiers title will be invaluable for all researchers in molecular biology, biochemistry and structural biology.
Author : Muhammad Fazril Mohamad Razif
Publisher :
ISBN 13 :
Total Pages : 286 pages
Book Rating : 4.:/5 (93 download)
Download or read book Engineering RNA-binding Proteins written by Muhammad Fazril Mohamad Razif and published by . This book was released on 2012 with total page 286 pages. Available in PDF, EPUB and Kindle. Book excerpt: RNA-protein interactions have key roles in the regulation of gene expression and are vital for many cellular processes and complex developmental programs in eukaryotes. Proteins that have the ability to bind RNAs tend to do so in various modes that are often difficult to predict, limiting the ability to engineer these RNA-binding proteins for medical and biotechnological use. Hence, engineering proteins that can bind a specific RNA sequence has many potential applications, analogous to that of siRNAs and miRNAs, with even more potential benefits. The ability to fuse RNA-binding proteins to any desired effector domain, in turn enabling the manipulation of any aspect of the target RNA's metabolism makes engineering these proteins highly appealing. Here, the recognition of PUF repeats beyond adenine, guanine and uracil has been achieved through directed evolution, enabling them to specifically bind cytosine. With this code, PUF domains capable of selectively binding RNA targets of diverse sequence and structure can be designed. Unlike the PUFs, the basis for nucleotide RNA recognition by pentatricopeptide repeat (PPR) proteins, another RNA-binding protein, remains ambiguous. Here, computational methods have been used to create a stable, highly reduced PPR architecture for the study of RNA-binding specificity and the design of specific tools to manipulate RNA metabolism. We used these synthetic PPRs to examine the amino acid codes for nucleotide recognition by PPRs, which also revealed that PPRs have a modular recognition mechanism similar to that of PUFs. These findings provide a significant step towards predicting native binding sites of the vast number of PPR proteins found in nature. It also highlights the possibility of a PPR scaffold to be engineered for new functions and sequence specificities.
Author : Alessia Galgano
Publisher :
ISBN 13 :
Total Pages : 251 pages
Book Rating : 4.:/5 (73 download)
Download or read book Comparative Analysis of MRNA Targets for Human PUF-family RNA-binding Proteins written by Alessia Galgano and published by . This book was released on 2010 with total page 251 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book RNA Regulatory Networks Diversified Through Curvature of the PUF Protein Scaffold written by and published by . This book was released on 2015 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Proteins bind and control mRNAs, directing their localization, translation and stability. Members of the PUF family of RNA-binding proteins control multiple mRNAs in a single cell, and play key roles in development, stem cell maintenance and memory formation. Here we identified the mRNA targets of a S. cerevisiae PUF protein, Puf5p, by ultraviolet-crosslinking-affinity purification and high-throughput sequencing (HITS-CLIP). The binding sites recognized by Puf5p are diverse, with variable spacer lengths between two specific sequences. Each length of site correlates with a distinct biological function. Crystal structures of Puf5p-RNA complexes reveal that the protein scaffold presents an exceptionally flat and extended interaction surface relative to other PUF proteins. In complexes with RNAs of different lengths, the protein is unchanged. A single PUF protein repeat is sufficient to induce broadening of specificity. Changes in protein architecture, such as alterations in curvature, may lead to evolution of mRNA regulatory networks.
Author :
Publisher :
ISBN 13 :
Total Pages : 0 pages
Book Rating : 4.:/5 (939 download)
Download or read book Evolution of RNA-PUF Protein Networks written by and published by . This book was released on 2015 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Proteins bind and control mRNAs, directing their localization, translation, and stability. Members of the PUF family of RNA-binding proteins control multiple mRNAs in a single cell, and play key roles in development, stem cell maintenance and memory formation. Here we demonstrate the conservation of PUF regulatory networks by bioinformatic analysis. We identified the mRNA targets of two Saccharomyces cerevisiae PUF proteins, Puf3p and Puf5p, and two Neurospora crassa PUF proteins, PUF3 and PUF5, by UV-crosslinking-affinity purification and high-throughput sequencing (HITS-CLIP). Taken together these data allowed us to elucidate a rewiring of a nulcear-endcoded circuit of mitochondrial related mRNAs. S. cerevisiae Puf5p associates with ~1,000 RNAs, suggesting that it is a broad spectrum regulator. The binding sites recognized by both Puf5 proteins are diverse, with variable spacer lengths between two specific sequences. S. cerevisiae Puf3p binds a group of RNAs significantly enriched for nuclear encoded RNAs that code for mitochondrial proteins. Many of these orthologous RNAs are bound by N. crassa PUF5. This constitutes a switch, from Puf3p to Puf5, regulation, when comparing S. cerevisiae and N. crassa PUF regulatory networks. Crystal structures of S. cerevisiae Puf5p-RNA complexes reveal that the protein scaffold presents an exceptionally flat and extended interaction surface relative to other PUF proteins. A single PUF protein repeat is sufficient to induce broadening of specificity. Changes in protein architecture, such as alterations in curvature, may have led to evolution of mRNA regulatory networks which we observe.
Author :
Publisher : Academic Press
ISBN 13 : 0128019360
Total Pages : 675 pages
Book Rating : 4.1/5 (28 download)
Download or read book Structures of Large RNA Molecules and Their Complexes written by and published by Academic Press. This book was released on 2015-06-06 with total page 675 pages. Available in PDF, EPUB and Kindle. Book excerpt: This new volume of Methods in Enzymology continues the legacy of this premier serial with quality chapters authored by leaders in the field. This volume covers research methods in RNA folding and dynamics, RNA-protein interactions and large RNPs. Continues the legacy of this premier serial with quality chapters on structures of large RNA molecules and their complexes
Author : Victor A. Bloomfield
Publisher : Sterling Publishing Company
ISBN 13 : 9780935702491
Total Pages : 854 pages
Book Rating : 4.7/5 (24 download)
Download or read book Nucleic Acids written by Victor A. Bloomfield and published by Sterling Publishing Company. This book was released on 2000-04-17 with total page 854 pages. Available in PDF, EPUB and Kindle. Book excerpt: Providing a comprehensive account of the structures and physical chemistry properties of nucleic acids, with special emphasis on biological function, this text has been organized to meet the needs of those who have only a basic understanding of physical chemistry and molecular biology.
Author : Randi J. Ulbricht
Publisher :
ISBN 13 :
Total Pages : 78 pages
Book Rating : 4.:/5 (566 download)
Download or read book Identification of New MRNA Targets of Puf Protein-mediated Decay in Yeast written by Randi J. Ulbricht and published by . This book was released on 2005 with total page 78 pages. Available in PDF, EPUB and Kindle. Book excerpt: Precise regulation of gene expression is accomplished at many levels. Puf proteins are a widely conserved family of RNA binding proteins that regulate gene expression by influencing the stability of their target mRNA transcripts. Puf family members have been characterized as transcript-specific repressors in Drosophila, Dictyostelium, mouse, C. elegans, and Xenopus. In S. cerevisiae, there are 5 conserved Puf family members. Two of them, Puf3p and Puf5p, are known to destabilize their mRNA targets, down-regulating gene expression. The remaining yeast Pufs, Puf1p, Puf2p and Puf4p, are homologous to Puf3p and Puf5p, suggesting that they too have regulatory roles not yet observed. In this work, I attempt to identify new mRNA targets of Puf mediated decay in yeast. In particular, I am interested in targets of the uncharacterized yeast Pufs. The ability of a Puf protein to regulate its target transcript is dependent on Puf binding to a conserved element in the 3'UTR of the target mRNA. A search for similar 3'UTR elements and previous microarray data helped to identify numerous potential mRNA targets of Puf-mediated decay. In this work, experimental analysis of the candidate mRNAs positively identified three new targets of Puf mediated mRNA decay. Two of the targets, HXK1 and TIF1, are destabilized in vivo by Puf1p and Puf5p, respectively. The third target, YHB1, is actually stabilized by Puf2p. Interestingly, while the TIF1 and HXK1 3'UTRs are sufficient for Puf mediated decay as expected, the YHB1 3'UTR is not sufficient to confer Puf2p mediated decay onto the MFA2 coding region. In addition to these functional studies, I also demonstrate Puf interaction with conserved sequence elements in each 3'UTR. Together, my work provides evidence that all yeast Puf proteins selectively regulate mRNA decay, and in some cases, Puf proteins may up-regulate gene expression.
Author :
Publisher :
ISBN 13 :
Total Pages : 6 pages
Book Rating : 4.:/5 (986 download)
Download or read book A Divergent Pumilio Repeat Protein Family for Pre-rRNA Processing and MRNA Localization written by and published by . This book was released on 2014 with total page 6 pages. Available in PDF, EPUB and Kindle. Book excerpt: Pumilio/feminization of XX and XO animals (fem)-3 mRNA-binding factor (PUF) proteins bind sequence specifically to mRNA targets using a single-stranded RNA-binding domain comprising eight Pumilio (PUM) repeats. PUM repeats have now been identified in proteins that function in pre-rRNA processing, including human Puf-A and yeast Puf6. This is a role not previously ascribed to PUF proteins. In this paper we present crystal structures of human Puf-A that reveal a class of nucleic acid-binding proteins with 11 PUM repeats arranged in an "L"--Like shape. In contrast to classical PUF proteins, Puf-A forms sequence-independent interactions with DNA or RNA, mediated by conserved basic residues. We demonstrate that equivalent basic residues in yeast Puf6 are important for RNA binding, pre-rRNA processing, and mRNA localization. Finally, PUM repeats can be assembled into alternative folds that bind to structured nucleic acids in addition to forming canonical eight-repeat crescent-shaped RNA-binding domains found in classical PUF proteins.
Author :
Publisher : Academic Press
ISBN 13 : 0128168323
Total Pages : 468 pages
Book Rating : 4.1/5 (281 download)
Download or read book RNA Recognition written by and published by Academic Press. This book was released on 2019-06-23 with total page 468 pages. Available in PDF, EPUB and Kindle. Book excerpt: RNA Recognition, Volume 623, the latest volume in the Methods in Enzymology series, continues the legacy of this premier serial with quality chapters authored by leaders in the field. This updated volume covers a variety of topics, including The Preparation of cooperative RNA recognition complexes for crystallographic structural studies, Methods for thermal denaturation studies of fluorogenic aptamers, Dynamic combinatorial chemistry as a rapid, fragment-based approach to RNA-targeted compound discovery, Using a click chemistry assay to identify natural product ligands for pre-microRNAs, Lessons from exploration of chemical and structural small molecule:RNA space, Using ligand-observed NMR to study RNA-small molecule interactions, and much more. Provides the authority and expertise of leading contributors from an international board of authors Presents the latest release in the Methods in Enzymology series Includes the latest information on RNA Recognition
Author : Sean Thomas Saxton
Publisher :
ISBN 13 :
Total Pages : 68 pages
Book Rating : 4.:/5 (262 download)
Download or read book Studying the Basis for Sequence Specific RNA Recognition by a New Class of RNA Binding Proteins written by Sean Thomas Saxton and published by . This book was released on 2008 with total page 68 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : Olivier Binda
Publisher : Academic Press
ISBN 13 : 012802609X
Total Pages : 468 pages
Book Rating : 4.1/5 (28 download)
Download or read book Chromatin Signaling and Diseases written by Olivier Binda and published by Academic Press. This book was released on 2016-08-06 with total page 468 pages. Available in PDF, EPUB and Kindle. Book excerpt: Chromatin Signaling and Diseases covers the molecular mechanisms that regulate gene expression, which govern everything from embryonic development, growth, and human pathologies associated with aging, such as cancer. This book helps researchers learn about or keep up with the quickly expanding field of chromatin signaling. After reading this book, clinicians will be more capable of explaining the mechanisms of gene expression regulation to their patients to reassure them about new drug developments that target chromatin signaling mechanisms. For example, several epigenetic drugs that act on chromatin signaling factors are in clinical trials or even approved for usage in cancer treatments, Alzheimer's, and Huntington's diseases. Other epigenetic drugs are in development to regulate various class of chromatin signaling factors. To keep up with this changing landscape, clinicians and doctors will need to stay familiar with genetic advances that translate to clinical practice, such as chromatin signaling. Although sequencing of the human genome was completed over a decade ago and its structure investigated for nearly half a century, molecular mechanisms that regulate gene expression remain largely misunderstood. An emerging concept called chromatin signaling proposes that small protein domains recognize chemical modifications on the genome scaffolding histone proteins, facilitating the nucleation of enzymatic complexes at specific loci that then open up or shut down the access to genetic information, thereby regulating gene expression. The addition and removal of chemical modifications on histones, as well as the proteins that specifically recognize these, is reviewed in Chromatin Signaling and Diseases. Finally, the impact of gene expression defects associated with malfunctioning chromatin signaling is also explored. Explains molecular mechanisms that regulate gene expression, which governs everything from embryonic development, growth, and human pathologies associated with aging Educates clinicians and researchers about chromatin signaling, a molecular mechanism that is changing our understanding of human pathology Explores the addition and removal of chemical modifications on histones, the proteins that specifically recognize these, and the impact of gene expression defects associated with malfunctioning chromatin signaling Helps researchers learn about the quickly expanding field of chromatin signaling
