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The Eukaryotic RNA Exosome

Author: John LaCava

Publisher: Springer Nature

Published: 2019-11-25

Total Pages: 513

ISBN-13: 1493998226

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This volume provides a cross-section of RNA exosome research protocols, applied to a diversity of model organisms. Chapters guide readers through methods that e.g. delineate eukaryotic exosomes’ origins in prokaryotes, probe its RNA substrates, adapter complexes and macromolecular interaction of networks, and establish critical structural-function relationships. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, The Eukaryotic RNA Exosome: Methods and Protocols aims to ensure successful results in the further study of this vital field.

Book Synopsis The Eukaryotic RNA Exosome by : John LaCava

Download or read book The Eukaryotic RNA Exosome written by John LaCava and published by Springer Nature. This book was released on 2019-11-25 with total page 513 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume provides a cross-section of RNA exosome research protocols, applied to a diversity of model organisms. Chapters guide readers through methods that e.g. delineate eukaryotic exosomes’ origins in prokaryotes, probe its RNA substrates, adapter complexes and macromolecular interaction of networks, and establish critical structural-function relationships. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, The Eukaryotic RNA Exosome: Methods and Protocols aims to ensure successful results in the further study of this vital field.

RNA Exosome

Author: Torben Heick Jensen

Publisher: Springer Science & Business Media

Published: 2011-06-29

Total Pages: 161

ISBN-13: 1441978410

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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.

Book Synopsis RNA Exosome by : Torben Heick Jensen

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.

Structure and Biochemistry of the Eukaryotic RNA Exosome

Author: Jaclyn Caye Greimann

Publisher:

Published: 2009

Total Pages: 210

ISBN-13:

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Book Synopsis Structure and Biochemistry of the Eukaryotic RNA Exosome by : Jaclyn Caye Greimann

Download or read book Structure and Biochemistry of the Eukaryotic RNA Exosome written by Jaclyn Caye Greimann and published by . This book was released on 2009 with total page 210 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Biochemical Studies of the Eukaryotic RNA Exosome

Author: Matthew Alan Bratkowski

Publisher:

Published: 2012

Total Pages: 209

ISBN-13:

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The RNA exosome is a multi-subunit protein complex involved in RNA maturation, surveillance, and turnover of cellular RNA. It is composed of a nine subunit core that contains an RNA binding central channel and associates with the additional subunit Rrp44. Rrp44 contains a 3' to 5' processive exoribonuclease activity and an endoribonuclease activity in its N-terminal PIN domain. The exosome is present in both the nucleus and cytoplasm. In the nucleus, the exosome associates with a second nuclease, Rrp6, which is a distributive 3' to 5' exoribonuclease. Although a wealth of studies have helped to characterize the exosome, it is still not entirely clear how the exosome core functions in concert with these two nucleases to degrade RNA. In this dissertation, I present structural and biochemical studies of both the Rrp44 and Rrp6 bound exosome. In particular, I have attempted to crystallize a sub-complex of Rrp44 bound to the exosome, and present data that suggest that structured RNA can access Rrp44 without being first channeled through the exosome. Despite this conclusion, the exosome core still appears to down-regulate both the exonuclease and endonuclease activities of Rrp44, possibly by causing the protein to assume a conformation that prohibits it from promiscuous RNA degradation. Work on the Rrp6 containing exosme was conducted in attempts of obtaining an EM reconstruction of this complex. Crystallization of an RNA and Rrp6 binding exosome associated iii protein, Rrp47, was also attempted alone and in complex with Rrp6. Overall, the results that I present here will help to further characterize the function of the exosome in RNA mediated degradation. iv.

Book Synopsis Biochemical Studies of the Eukaryotic RNA Exosome by : Matthew Alan Bratkowski

Download or read book Biochemical Studies of the Eukaryotic RNA Exosome written by Matthew Alan Bratkowski and published by . This book was released on 2012 with total page 209 pages. Available in PDF, EPUB and Kindle. Book excerpt: The RNA exosome is a multi-subunit protein complex involved in RNA maturation, surveillance, and turnover of cellular RNA. It is composed of a nine subunit core that contains an RNA binding central channel and associates with the additional subunit Rrp44. Rrp44 contains a 3' to 5' processive exoribonuclease activity and an endoribonuclease activity in its N-terminal PIN domain. The exosome is present in both the nucleus and cytoplasm. In the nucleus, the exosome associates with a second nuclease, Rrp6, which is a distributive 3' to 5' exoribonuclease. Although a wealth of studies have helped to characterize the exosome, it is still not entirely clear how the exosome core functions in concert with these two nucleases to degrade RNA. In this dissertation, I present structural and biochemical studies of both the Rrp44 and Rrp6 bound exosome. In particular, I have attempted to crystallize a sub-complex of Rrp44 bound to the exosome, and present data that suggest that structured RNA can access Rrp44 without being first channeled through the exosome. Despite this conclusion, the exosome core still appears to down-regulate both the exonuclease and endonuclease activities of Rrp44, possibly by causing the protein to assume a conformation that prohibits it from promiscuous RNA degradation. Work on the Rrp6 containing exosme was conducted in attempts of obtaining an EM reconstruction of this complex. Crystallization of an RNA and Rrp6 binding exosome associated iii protein, Rrp47, was also attempted alone and in complex with Rrp6. Overall, the results that I present here will help to further characterize the function of the exosome in RNA mediated degradation. iv.

Eukaryotic RNases and Their Partners in RNA Degradation and Biogenesis

Author: Guillaume F. Chanfreau

Publisher: Academic Press

Published: 2012

Total Pages: 295

ISBN-13: 0124047408

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Book Synopsis Eukaryotic RNases and Their Partners in RNA Degradation and Biogenesis by : Guillaume F. Chanfreau

Download or read book Eukaryotic RNases and Their Partners in RNA Degradation and Biogenesis written by Guillaume F. Chanfreau and published by Academic Press. This book was released on 2012 with total page 295 pages. Available in PDF, EPUB and Kindle. Book excerpt:

The Phosphorolytic Activity of the Exosome Core Complex Contributes to RRNA Maturation in Arabidopsis Thaliana

Author: Natalia Sikorska

Publisher:

Published: 2016

Total Pages: 0

ISBN-13:

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The eukaryotic RNA exosome complex is the main 3'-5' degradation machinery that plays an essential role in RNA decay, quality control and maturation. The exosome core complex (EXO9) is catalytically inert in yeast and humans, and therefore relies on the catalytic activity of associated RNases, Rrp6 and Rrp44. In this study I demonstrated that EXO9 is catalytically active in Arabidopsis. EXO9's activity is phosphate-dependent, releases nucleoside diphosphates and is reversible, meeting all criteria of a phosphorolytic activity. Importantly, EXO9's in vivo substrates include the archetypical exosome substrates, rRNA maturation by-products and 5.8S rRNA precursors. My data show that AtRRP44, EXO9 and AtRRP6L2 sequentially cooperate for the processing of 5.8S rRNA. This work sets a basis for studies aiming at further understanding the biological functions of EXO9's phosphorolytic activity in a eukaryotic organism.

Book Synopsis The Phosphorolytic Activity of the Exosome Core Complex Contributes to RRNA Maturation in Arabidopsis Thaliana by : Natalia Sikorska

Download or read book The Phosphorolytic Activity of the Exosome Core Complex Contributes to RRNA Maturation in Arabidopsis Thaliana written by Natalia Sikorska and published by . This book was released on 2016 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: The eukaryotic RNA exosome complex is the main 3'-5' degradation machinery that plays an essential role in RNA decay, quality control and maturation. The exosome core complex (EXO9) is catalytically inert in yeast and humans, and therefore relies on the catalytic activity of associated RNases, Rrp6 and Rrp44. In this study I demonstrated that EXO9 is catalytically active in Arabidopsis. EXO9's activity is phosphate-dependent, releases nucleoside diphosphates and is reversible, meeting all criteria of a phosphorolytic activity. Importantly, EXO9's in vivo substrates include the archetypical exosome substrates, rRNA maturation by-products and 5.8S rRNA precursors. My data show that AtRRP44, EXO9 and AtRRP6L2 sequentially cooperate for the processing of 5.8S rRNA. This work sets a basis for studies aiming at further understanding the biological functions of EXO9's phosphorolytic activity in a eukaryotic organism.

RNA Metabolism and Gene Expression in Archaea

Author: Béatrice Clouet-d'Orval

Publisher: Springer

Published: 2017-10-28

Total Pages: 269

ISBN-13: 331965795X

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This book focuses on the regulation of transcription and translation in Archaea and arising insights into the evolution of RNA processing pathways. From synthesis to degradation and the implications of gene expression, it presents the current state of knowledge on archaeal RNA biology in 13 chapters. Topics covered include the modification and maturation of RNAs, the function of small non-coding RNAs and the CRISPR-Cas defense system. While Archaea have long been considered exotic microbial extremophiles, they are now increasingly being recognized as important model microorganisms for the study of molecular mechanisms conserved across the three domains of life, and with regard to the relevance of similarities and differences to eukaryotes and bacteria. This unique book offers a valuable resource for all readers interested in the regulation of gene expression in Archaea and RNA metabolism in general.

Book Synopsis RNA Metabolism and Gene Expression in Archaea by : Béatrice Clouet-d'Orval

Download or read book RNA Metabolism and Gene Expression in Archaea written by Béatrice Clouet-d'Orval and published by Springer. This book was released on 2017-10-28 with total page 269 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book focuses on the regulation of transcription and translation in Archaea and arising insights into the evolution of RNA processing pathways. From synthesis to degradation and the implications of gene expression, it presents the current state of knowledge on archaeal RNA biology in 13 chapters. Topics covered include the modification and maturation of RNAs, the function of small non-coding RNAs and the CRISPR-Cas defense system. While Archaea have long been considered exotic microbial extremophiles, they are now increasingly being recognized as important model microorganisms for the study of molecular mechanisms conserved across the three domains of life, and with regard to the relevance of similarities and differences to eukaryotes and bacteria. This unique book offers a valuable resource for all readers interested in the regulation of gene expression in Archaea and RNA metabolism in general.

Eukaryotic RNases and their Partners in RNA Degradation and Biogenesis

Author:

Publisher: Academic Press

Published: 2012-11-27

Total Pages: 0

ISBN-13: 9780124047419

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This special volume of The Enzymes is targeted towards researchers in biochemistry, molecular and cell biology, pharmacology, and cancer. This thematic volume discusses Eukaryotic RNases and their partners in RNA degradation and biogenesis.

Book Synopsis Eukaryotic RNases and their Partners in RNA Degradation and Biogenesis by :

Download or read book Eukaryotic RNases and their Partners in RNA Degradation and Biogenesis written by and published by Academic Press. This book was released on 2012-11-27 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This special volume of The Enzymes is targeted towards researchers in biochemistry, molecular and cell biology, pharmacology, and cancer. This thematic volume discusses Eukaryotic RNases and their partners in RNA degradation and biogenesis.

RNA Turnover in Eukaryotes: Nucleases, Pathways and Analysis of mRNA Decay

Author: Lynne E. Maquat

Publisher: Academic Press

Published: 2009-01-30

Total Pages: 656

ISBN-13: 9780080922072

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Specific complexes of protein and RNA carry out many essential biological functions, including RNA processing, RNA turnover, RNA folding, as well as the translation of genetic information from mRNA into protein sequences. Messenger RNA (mRNA) decay is now emerging as an important control point and a major contributor to gene expression. Continuing identification of the protein factors and cofactors, and mRNA instability elements responsible for mRNA decay allow researchers to build a comprehensive picture of the highly orchestrated processes involved in mRNA decay and its regulation. Covers the nonsense-mediated mRNA decay (NMD) or mRNA surveillance pathway Expert researchers introduce the most advanced technologies and techniques to identify mRNA processing, transport, localization and turnover, which are central to the process of gene expression Offers step-by-step lab instructions, including necessary equipment and reagents

Book Synopsis RNA Turnover in Eukaryotes: Nucleases, Pathways and Analysis of mRNA Decay by : Lynne E. Maquat

Download or read book RNA Turnover in Eukaryotes: Nucleases, Pathways and Analysis of mRNA Decay written by Lynne E. Maquat and published by Academic Press. This book was released on 2009-01-30 with total page 656 pages. Available in PDF, EPUB and Kindle. Book excerpt: Specific complexes of protein and RNA carry out many essential biological functions, including RNA processing, RNA turnover, RNA folding, as well as the translation of genetic information from mRNA into protein sequences. Messenger RNA (mRNA) decay is now emerging as an important control point and a major contributor to gene expression. Continuing identification of the protein factors and cofactors, and mRNA instability elements responsible for mRNA decay allow researchers to build a comprehensive picture of the highly orchestrated processes involved in mRNA decay and its regulation. Covers the nonsense-mediated mRNA decay (NMD) or mRNA surveillance pathway Expert researchers introduce the most advanced technologies and techniques to identify mRNA processing, transport, localization and turnover, which are central to the process of gene expression Offers step-by-step lab instructions, including necessary equipment and reagents

Fungal Extracellular Vesicles

Author: Marcio Rodrigues

Publisher: Springer Nature

Published: 2022-01-01

Total Pages: 193

ISBN-13: 3030833917

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This book provides an in-depth overview on the manifold functions of fungal extracellular vesicles (EV) which span from cell-to-cell communication, pathogenicity and stimulation of host’s immunity to export of hundreds of biomolecules. The book summarizes the present knowledge on the impact of extracellular vesicles on fungal biology. Extracellular vesicles participate in fundamental biological processes in all living cells but only during the last 15 years the production and functions of EVs were identified and studied in fungal species too. Up to date more than 50 independent studies have shown that extracellular vesicles are produced by at least 20 fungal species. The book addresses researchers and advanced students in Microbiology, Mycology and Biotechnology.

Book Synopsis Fungal Extracellular Vesicles by : Marcio Rodrigues

Download or read book Fungal Extracellular Vesicles written by Marcio Rodrigues and published by Springer Nature. This book was released on 2022-01-01 with total page 193 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides an in-depth overview on the manifold functions of fungal extracellular vesicles (EV) which span from cell-to-cell communication, pathogenicity and stimulation of host’s immunity to export of hundreds of biomolecules. The book summarizes the present knowledge on the impact of extracellular vesicles on fungal biology. Extracellular vesicles participate in fundamental biological processes in all living cells but only during the last 15 years the production and functions of EVs were identified and studied in fungal species too. Up to date more than 50 independent studies have shown that extracellular vesicles are produced by at least 20 fungal species. The book addresses researchers and advanced students in Microbiology, Mycology and Biotechnology.