Regulatory Nascent Polypeptides [electronic resource] /
Ito, Koreaki.editor.
This book highlights a new paradigm of translation control by regulatory nascent polypeptides, which is integrated into cellular regulatory systems. Translation lies in the hub of the central dogma of biology, in which the genetic information in the forms of 4-letter sentences is translated into 20-letter sentences: sequences of amino acids that constitute proteins, the functional molecules of life. The process involves a huge number of chemical reactions as well as physical movements of the ribosome along a messenger RNA and takes, on average, tens of seconds in prokaryotes and a few minutes in eukaryotes. Detailed knowledge about the progression of translation, called "elongation", only recently started to accumulate. Newly synthesized and growing polypeptides, called nascent polypeptides, can interact with the intra-ribosomal conduit, called the ribosomal exit tunnel, when they have some specific amino acid sequences, called "an arrest sequence". Such interaction leads to a halt in the elongation reaction. Resulting stalling of the ribosome on messenger RNA can affect the secondary structure and/or localization of the message in the cell, consequently leading to biological outputs such as elevation or reduction of a gene product. This book provides a first collection of knowledge focused on regulatory nascent polypeptides, which have been studied recently using diverse organisms including bacteria, plants, and animals. Readers will be impressed by a new paradigm showing that proteins can function even during the course of their biosynthesis and that the ribosome, the "factory" of protein production, interacts with and inspects its products to adjust the speed of completion of each product. Moreover, regulatory nascent polypeptides can sense or monitor physiological states of the cell and modulate its ability to arrest translation. Living organisms use such intricate control mechanisms of translational speed to regulate gene expression. This book will be a useful addition for established scientists while inspiring students and young scientists to gain deeper insights into the processes of expression of genetic information.
Description based upon print version of record.
Preface; Contents; Part I: Introduction; Chapter 1: Biological Significance of Nascent Polypeptides That Stall the Ribosome; 1.1 Overview; 1.1.1 Importance of Nascent Peptidyl-tRNA in the ``Translation Concert ́ ́; 1.1.2 Nascent Polypeptides Can Modulate Progression of Their Own Translation; 1.1.3 Nascent Polypeptide-Mediated Translation Modulation Responds to Environmental Changes; 1.1.4 Regulatory Nascent Polypeptides Monitor and Control Cellular Physiology; 1.2 Concepts Characteristically Associated with Regulatory Nascent Polypeptides
1.2.1 The Exit Tunnel Is Not Necessarily ``Teflon Like ́ ́1.2.2 Ribosomes Cannot Readily Synthesize Proteins Representing All the Possible Amino Acid Sequences; 1.2.3 The Use of a Posttranslational Determinant to Control Ongoing Translation; 1.2.4 Proteins Can Function Before They Are Completely Formed; 1.2.5 Nascent Polypeptides Can Direct the Subcellular Localization of mRNA; 1.2.6 Arrest Sequences Are Divergent in Their Primary Sequences; 1.2.7 Is Polypeptide-Directed Translational Pausing Ubiquitous?; 1.2.8 Arrest Control by the Dynamic Behavior of the Nascent Chain
1.2.9 Quality Control Systems and Regulatory Nascent PolypeptidesReferences; Part II: The Ribosome and the Exit Tunnel; Chapter 2: Recent Progress in Ribosome Structure Studies; 2.1 Introduction; 2.2 Structure of the Ribosome; 2.3 Mechanism of Translation; 2.3.1 Initiation of Translation; 2.3.2 The Elongation Cycle; 2.3.3 Mechanism of Decoding: Preliminary Binding; 2.3.4 Mechanism of Decoding: Proofreading; 2.3.5 The Peptide Bond Formation; 2.3.6 Translocation; 2.3.7 Termination and Recycling; 2.3.8 Polypeptide Exit Tunnel; References
Chapter 3: Structures of Nascent Polypeptide Chain-Dependent-Stalled Ribosome Complexes3.1 Introduction; 3.2 Cryo-EM Structure of the TnaC-SRC; 3.3 Cryo-EM Structure of the SecM-SRC; 3.4 Cryo-EM Structure of the CMV-SRC; 3.5 Cryo-EM Structure of the AAP-SRC; 3.6 Conclusions; References; Chapter 4: Tunnel Vision: Insights from Biochemical and Biophysical Studies; 4.1 Introduction; 4.2 The Physicochemical Properties of the Tunnel; 4.2.1 Tunnel Geometry; 4.2.2 Electrostatic Potentials in the Tunnel; 4.2.3 Effective Debye Length Along the Tunnel; 4.2.4 Water in the Tunnel; 4.2.5 pH in the Tunnel
4.2.6 Solvent-Accessible Volume4.3 The Peptide in the Tunnel; 4.3.1 Side-Chain Chemistry: A Couple of Questions; 4.3.2 Peptide Folding in the Tunnel; 4.3.2.1 Compaction in the Tunnel; 4.3.2.2 Tertiary Folding in the Tunnel; 4.3.2.3 A Folding Vestibule in the Tunnel; 4.3.3 Peptide Movement Along the Tunnel; 4.3.4 Rearrangements in the Tunnel: Regional Discrimination and Pathway; 4.4 Movement of Tunnel Wall Components; 4.5 Peptide-Tunnel Interactions: Relay Mechanisms; 4.6 A New View Going Forward; References
Chapter 5: Nascent Peptide-Induced Signaling from the Exit Tunnel to the Outside of the Ribosome
Includes bibliographical references at the end of each chapters and index.
This book highlights a new paradigm of translation control by regulatory nascent polypeptides, which is integrated into cellular regulatory systems. Translation lies in the hub of the central dogma of biology, in which the genetic information in the forms of 4-letter sentences is translated into 20-letter sentences: sequences of amino acids that constitute proteins, the functional molecules of life. The process involves a huge number of chemical reactions as well as physical movements of the ribosome along a messenger RNA and takes, on average, tens of seconds in prokaryotes and a few minutes in eukaryotes. Detailed knowledge about the progression of translation, called "elongation", only recently started to accumulate. Newly synthesized and growing polypeptides, called nascent polypeptides, can interact with the intra-ribosomal conduit, called the ribosomal exit tunnel, when they have some specific amino acid sequences, called "an arrest sequence". Such interaction leads to a halt in the elongation reaction. Resulting stalling of the ribosome on messenger RNA can affect the secondary structure and/or localization of the message in the cell, consequently leading to biological outputs such as elevation or reduction of a gene product. This book provides a first collection of knowledge focused on regulatory nascent polypeptides, which have been studied recently using diverse organisms including bacteria, plants, and animals. Readers will be impressed by a new paradigm showing that proteins can function even during the course of their biosynthesis and that the ribosome, the "factory" of protein production, interacts with and inspects its products to adjust the speed of completion of each product. Moreover, regulatory nascent polypeptides can sense or monitor physiological states of the cell and modulate its ability to arrest translation. Living organisms use such intricate control mechanisms of translational speed to regulate gene expression. This book will be a useful addition for established scientists while inspiring students and young scientists to gain deeper insights into the processes of expression of genetic information.
Biochemistry.
Cell biology.
Human genetics.
Gene expression.
Biochemistry, general.
Cell Biology.
Human Genetics.
Gene Expression.