Role of Long Range Interactions in Assembly of the Small Subunit of Escherichia Coli Ribosome PDF Download
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Author: Deepika S. Calidas
Publisher:
ISBN:
Category :
Languages : en
Pages : 136
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Book Description
"The function of the small subunit (SSU) of the ribosome of Escherichia coli is dependent on dynamic interactions at the intersection of its four domains; namely, the body, platform, head and penultimate stem. The in vitro assembly of each individual domain from its corresponding structural element in 16S ribosomal RNA (rRNA), i.e., the 5', central, 3' major and minor domains and associated ribosomal proteins (r-proteins) has been extensively researched. Less is understood of the long range interactions that occur during assembly as different domains co-assemble, both in vitro and in vivo. Our first approach was to use directed probing from the S8 r-protein as a monitor of SSU assembly. We found that assembly of the neck, a functionally significant region between the head and platform is dependent on assembly of the body. Furthermore, S8 binds two distinct binding sites in 16S rRNA separated by several hundred nucleotides, and the appropriate architecture of the later transcribed region is dependent upon incorporation of r-proteins to the earlier transcribed region. Elements of the body domain, including the 5' terminus do not assume their appropriate conformation except upon assembly of the entire domain. Also, we found that S12 could influence the architecture of the 5' terminus, leading us to examine the role of S12 in 30S subunit assembly, both in vitro and in vivo. S12 possesses a non-canonically structured extension that extends from the solvent surface to the intersubunit surface of the SSU, contacting multiple domains. An almost complete truncation of the extension was unable to support growth, while partial truncations of more than 6 amino acids exhibited growth defects. Truncation of half or all of the extension also resulted in reduced activity of SSUs assembled in vitro. The architecture of ribonucleoprotein complexes assembled with truncated proteins is also altered. The work presented in this thesis elucidates influence of widely separated elements of the SSU on each other during assembly"--Page v.
Author: Deepika S. Calidas
Publisher:
ISBN:
Category :
Languages : en
Pages : 136
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Book Description
"The function of the small subunit (SSU) of the ribosome of Escherichia coli is dependent on dynamic interactions at the intersection of its four domains; namely, the body, platform, head and penultimate stem. The in vitro assembly of each individual domain from its corresponding structural element in 16S ribosomal RNA (rRNA), i.e., the 5', central, 3' major and minor domains and associated ribosomal proteins (r-proteins) has been extensively researched. Less is understood of the long range interactions that occur during assembly as different domains co-assemble, both in vitro and in vivo. Our first approach was to use directed probing from the S8 r-protein as a monitor of SSU assembly. We found that assembly of the neck, a functionally significant region between the head and platform is dependent on assembly of the body. Furthermore, S8 binds two distinct binding sites in 16S rRNA separated by several hundred nucleotides, and the appropriate architecture of the later transcribed region is dependent upon incorporation of r-proteins to the earlier transcribed region. Elements of the body domain, including the 5' terminus do not assume their appropriate conformation except upon assembly of the entire domain. Also, we found that S12 could influence the architecture of the 5' terminus, leading us to examine the role of S12 in 30S subunit assembly, both in vitro and in vivo. S12 possesses a non-canonically structured extension that extends from the solvent surface to the intersubunit surface of the SSU, contacting multiple domains. An almost complete truncation of the extension was unable to support growth, while partial truncations of more than 6 amino acids exhibited growth defects. Truncation of half or all of the extension also resulted in reduced activity of SSUs assembled in vitro. The architecture of ribonucleoprotein complexes assembled with truncated proteins is also altered. The work presented in this thesis elucidates influence of widely separated elements of the SSU on each other during assembly"--Page v.
Author: Eleanor Spicer Ward
Publisher:
ISBN:
Category : Ribosomes
Languages : en
Pages : 468
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Book Description
Author: Marina V. Rodnina
Publisher: Springer Science & Business Media
ISBN: 3709102154
Category : Medical
Languages : en
Pages : 428
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Book Description
The ribosome is a macromolecular machine that synthesizes proteins with a high degree of speed and accuracy. Our present understanding of its structure, function and dynamics is the result of six decades of research. This book collects over 40 articles based on the talks presented at the 2010 Ribosome Meeting, held in Orvieto, Italy, covering all facets of the structure and function of the ribosome. New high-resolution crystal structures of functional ribosome complexes and cryo-EM structures of translating ribosomes are presented, while partial reactions of translation are examined in structural and mechanistic detail, featuring translocation as a most dynamic process. Mechanisms of initiation, both in bacterial and eukaryotic systems, translation termination, and novel details of the functions of the respective factors are described. Structure and interactions of the nascent peptide within, and emerging from, the ribosomal peptide exit tunnel are addressed in several articles. Structural and single-molecule studies reveal a picture of the ribosome exhibiting the energy landscape of a processive Brownian machine. The collection provides up-to-date reviews which will serve as a source of essential information for years to come.
Author: K Matsuno
Publisher: World Scientific
ISBN: 9814553549
Category :
Languages : en
Pages : 446
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Book Description
This volume examines the origin of eukaryotic cells both phylogenetically and morphogenetically. The evolutionary relationship between prokaryotic and eukaryotic organizations is emphasized. The difference of inferences from ribosomal RNA and protein phylogenetic trees suggests a new possibility of synthesizing an evolutionary origin of eukaryotic cells as integrating morphogenetic contributions.
Author: Richard D. Blake
Publisher: University Science Books
ISBN: 9781891389283
Category : Science
Languages : en
Pages : 812
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Book Description
This new text examines thebiophysics and biochemistry of nucleic acids and proteins, carving outthe dynamic interface between chemistry and molecular biology, and providing adetailed picture of nucleic acids and proteins, their structures, biologicalproperties, and origins and evolution.
Author:
Publisher:
ISBN:
Category : Medicine
Languages : en
Pages : 1860
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Book Description
Author: Heinz Bielka
Publisher: Walter de Gruyter GmbH & Co KG
ISBN: 3112729757
Category : Science
Languages : en
Pages : 340
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Book Description
No detailed description available for "The Eukaryotic Ribosome".
Author:
Publisher:
ISBN: 9780815332183
Category : Cells
Languages : en
Pages : 0
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Book Description
Author: Joshua James Black
Publisher:
ISBN:
Category :
Languages : en
Pages : 472
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Book Description
Ribosomes are the molecular machines that translate the genetic code into protein. They are assemblages of RNA and proteins, and they are divided into two functional halves called the large and small subunits. The intricate structures of the subunits are critical for faithful and efficient decoding and protein synthesis. In eukaryotes, the ribosomal subunits are made via an assembly line-like pathway involving the synthesis and processing of the ribosomal RNA, the binding of the ribosomal proteins, and the concerted actions of over 200 trans-acting assembly factors. These assembly factors drive the nascent subunits through a series of intermediate states to gradually shape them into their functional architecture. A conserved feature of the small subunit (SSU) is the central pseudoknot (CPK) which is formed by a long-range intramolecular RNA interaction. Importantly, the CPK organizes the overall architecture of the SSU, making its formation a critical event. However, a model that explains how the CPK forms is lacking. The earliest intermediate of SSU assembly is the SSU Processome. The Processome guides much of SSU assembly but holds the nascent subunit in a splayed-open architecture in which the CPK is unfolded. A major SSU Processome component is the U3 snoRNA which forms multiple duplexes with the RNA, including that of the CPK, to prevent improper SSU assembly. Consequentially, U3 removal is needed for CPK formation and continued SSU maturation. U3 is removed by the RNA helicase Dhr1, whose activity is linked to the assembly factors Utp14 and Bud23. However, how these factors coordinate the timing of Dhr1 unwinding U3 with CPK folding was not known. My dissertation explores the functions of Utp14 and Bud23 and provides significant insights into how these factors act within the SSU Processome to promote U3 release and CPK formation. From this, I propose a novel conceptual framework for understanding how the CPK of the eukaryotic SSU folds
Author: Ariel Amir
Publisher: Frontiers Media SA
ISBN: 2889631567
Category :
Languages : en
Pages : 246
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Book Description
The 1st volume of our Research Topic "The Bacterial Cell: Coupling between Growth, Nucleoid Replication, Cell Division and Shape” was published as an eBook in May 2016 (see: http://journal.frontiersin.org/researchtopic/2905/the-bacterial-cell-coupling-between-growth-nucleoid-replication-cell-division-and-shape). As a sign of growing interest to the topic, two workshops followed the same year: "Stochasticity in the Cell Cycle" in Jerusalem (Israel) by the Hebrew University’s Institute of Advanced Studies and EMBO's "Cell Size Regulation" in Joachimsthal (Germany). From the time of launching the first edition, several new groups have entered the field, and many established groups have made significant advances using state-of-the-art microscopy and microfluidics. Combining these approaches with the techniques pioneered by quantitative microbiologists decades ago, these approaches have provided remarkable amounts of numerical data. Most of these data needed yet to be put into a broader theoretical perspective. Moreover, the molecular mechanisms governing coordination and progression of the main bacterial cell cycle processes have remained largely unknown. These outstanding fundamental questions and the growing interest to the field motivated us to launch the next volume titled “The Bacterial Cell: Coupling between Growth, Nucleoid Replication, Cell Division, and Shape, Volume 2” shortly after completion of the first edition in October 2016. The issue contains 17 contributions from a diverse array of scientists whose field of study spans microbiology, biochemistry, genetics, experimental and theoretical biophysics. The specific questions addressed in the issue include: What triggers initiation of chromosome replication? How is cell division coordinated with replication both spatially and temporally? How is cell size controlled and linked to the rate of mass growth? What role plays physical organization of the chromosomes in their segregation and in regulation of cell division? The publications covering these questions are divided into three topical areas: 1) Cell Cycle Regulation, 2) Growth and Division, and 3) Nucleoid Structure and Replication. New ideas and techniques put forward in these articles bring us closer to understand these fundamental cellular processes, but the quest to resolve them is far from being complete. Plans for the next edition are under way along with further meetings and workshops, e.g., an EMBO Workshop on Bacterial cell biophysics: DNA replication, growth, division, size and shape in Ein Gedi (Israel), May 2020. We hope that via such interdisciplinary exchange of ideas we will come closer to answering the above-mentioned complex and multifaceted questions.
