مفاهیم نوظهور در ساختار، بیوژنز و عملکرد ریبوزوم

__Emerging Concepts in Ribosome Structure, Biogenesis, and Function__ provides a synthesized overview on all parts in this process. The book begins with an introduction to the ribosome factory, its origin and its evolution of translation. Sections discuss subunits, RNA, protein components, and its emergence as a frontier research area for translational potential in cancer and other diseases. In addition, the book explores current developments in ribosome research, including the emergence of ribosomopathies, how deregulation of ribosome biogenesis can impact disease mechanisms and aging, and the discovery of specialized ribosomes. This book provides the emerging research on ribosomes, their biogenesis, and other important topics on structure and function. Therefore, it will serve as a resourceful introduction for both new researchers and those engaged in interdisciplinary ribosomal research. Front Cover Emerging Concepts in Ribosome Structure, Biogenesis, and Function Copyright Contents Contributors Chapter 1: Introduction to ribosome factory, origin, and evolution of translation What are ribosomes? Basic components and structure of the ribosome Functions of ribosome Ribosome biogenesis and assembly Ribosomal gene mutations and ribosomopathies Inhibition of ribosome biogenesis Summary and conclusions References Chapter 2: Ribosome structure Introduction Structure of prokaryotic ribosome Structure of eukaryotic ribosome Novel features of the 80S Ribosome’s structure Eukaryote-specific protein tails Expansion segments Intersubunit bridges Structure of mitochondrial ribosome Summary and conclusions References Chapter 3: rDNA gene structure, transcription, and its coregulation Introduction Organization and regulation of ribosomal RNA genes Processing and maturation of pre-rRNA Organization and regulation of RNA pol III promoter Summary and conclusions References Chapter 4: Ribosome proteins—Their balanced production Introduction Structure of ribosomes Ribosomal proteins Nomenclature of RPs The function of ribosomal proteins The 40S small subunit ribosomal proteins The 60S large subunit ribosomal proteins Eukaryotic mitochondrial ribosome or mitoribosomes Extra ribosomal functions of ribosomal proteins Balanced production of RPs At the transcription level At the translational level At the posttranslational level Summary and conclusions References Chapter 5: Ribosome diversity Introduction Variation in r-protein complement Paralogues of r-proteins R-protein posttranslational modifications Ribosome-associated factors Contribution of rRNA alternatives in ribosome diversity Modifications of rRNA contribute to ribosome diversity Special ribosomes of mitochondria Congenital anomalies and mutations of ribosomal proteins Summary and conclusions References Chapter 6: Ribosome cycle—Assembly, degradation, and recycling Introduction Ribosome assembly The pathways and steps of ribosome assembly Assembly of small subunit of ribosome (40S subunit) Assembly of large subunit of ribosome (60S subunit) Degradation of the ribosome and ribosomal proteins Ubiquitination—Selective degradation of ribosomal proteins Ribophagy—Selective degradation of ribosome Ribosome recycling Splitting of 80S ribosome ABCE1-dependent 80S ribosome splitting Initiation of translation by post-TCs Summary and conclusions References Chapter 7: Ribosomal biogenesis in eukaryotes Introduction Yeast as an eukaryotic model to study ribosome biogenesis Preinitiation complex formation Control of rDNA transcription Processing of pre-rRNA Coordination of folding and processing of pre-rRNA Roles of the ribosomal proteins Role of ribosome assembly factors Maturation of ribosomal subunits Maturation of the 40S subunit Maturation of the pre-60S subunit Modifications of pre-RNA snoRNPs and rRNA modifications Summary and conclusions References Further reading Chapter 8: Ribosome biogenesis in prokaryotes Introduction Escherichia coli as a model organism to study ribosome biogenesis r-RNA gene structure, transcription, and posttranscriptional processing Regulation of rrn expression Structure of the ribosomal protein-coding genes, the operons and regulation of expression Modification of RPs Assembly of ribosome Assembly of 30S subunit Assembly of 50S subunit Differences in protein composition of the ribosome from exponential and stationary bacterial growth phases Role of ions in ribosome assembly Proteins facilitating ribosome assembly RNA helicases Chaperones GTPases Association and dissociation of ribosomal subunits Ribosome degradation, modifications, and recycling Ribosomal rejuvenation Ribosomal quality control Rescue of stalled ribosomes on mRNAs with defective or no stop codon Ribosome biogenesis in archaebacteria Summary and conclusions References Chapter 9: Translation—Process and control The process of translation Translation initiation Recycling of ribosomes Formation of 43S complex Initiator aa-tRNA recognition Formation of the eIF2-GTP ternary complex Attachment of 43S complexes to mRNA Recognition of initiation codon Scanning model Ribosome scanning of mRNA 5 ′ UTRs Noncanonical translation initiation in eukaryotes Internal ribosome entry sites Cellular IRESs Ribosomal shunting Joining of subunits Reinitiation, initiation at non-AUG codons and leaky scanning Translation elongation Decoding of mRNA EF-Tu in translation elongation Peptide bond transfer and translocation The hybrid state models of translocation “ α -ε” model for translocation Termination of translation Control of translation Aminoacyl tRNA and translation elongation Modifications in tRNAs Codon usage bias and stability of transcripts Ribosome stalling Ribosome profiling Application of ribosome profiling Insights into mechanism of translation Insights into translation of noncoding RNAs, especially lncRNA Expansion of translatome Limitations of ribosome profiling References Chapter 10: Inhibitors of ribosome biogenesis in prokaryotes and eukaryotes Introduction Prokaryotic ribosome biogenesis and inhibitors Ribosome biosynthesis and assembly Inhibitors of ribosome biogenesis in prokaryotes Ribosome biogenesis can be the target of cold stress Lamotrigine is the most promising cold sensitive chemical compound Antibiotics that target ribosome biogenesis Eukaryotic ribosome biogenesis and inhibitors Ribosome biosynthesis Ribosome biogenesis inhibitors—Chemical probes Examples of inhibitors Rbin-1 Diazaborine Ribosome biogenesis inhibitors and cancer Ribosome biogenesis has a highly variable turnaround in cancer cells Conclusions References Chapter 11: Ribosomopathies—A tree of pathologies with many roots and branches! Introduction Diamond-Blackfan anemia Other ribosomopathies Suspected ribosomopathies Is cancer a ribosomopathy? Conclusions References Chapter 12: Ribosomal profiling—Diversity and applications Introduction Tools and techniques of ribosome profiling Sample preparation RNase protection assay Isolation of ribosome footprints High throughput sequencing Bioinformatics analysis Other critical parameters Quality control of mRNA Canonical decay of mRNA and connections to translation elongation Nonsense-mediated decay of mRNA No-go decay of mRNAs with disruptions within the ORF Nonstop decay of mRNAs Degradation of truncated mRNAs Understanding the mechanism and regulation of translation Ribosome profiling of initiating ribosomes Ribosome profiling of elongating ribosomes Ribosome profiling of translation termination Diversity and applications of ribosome profiling Effect of stress on translation Cell cycle and translation regulation Ribosome profiling during viral infections Ribosome profiling during parasitic infections Ribosome profiling in Escherichia coli Summary and conclusions References Index Back Cover Ribosome biogenesis is the process of making ribosomes which are responsible for mRNA translation into proteins. It is a tightly regulated process closely linked to nearly all biochemical and cellular processes, including cell division, growth, and development. Emerging Concepts in Ribosome Structure, Biogenesis, and Function provides a synthesized overview of all the parts engaged in this process. The book begins by providing an introduction to the ribosome factory, its origin, and its evolution of translation. It then goes on to describe ribosome structure including subunits, RNA, and protein components. Ribosome biogenesis and its emergence as a frontier research area for translational potential in cancer and other diseases are also discussed. In addition, the book explores current developments in ribosome research like the emergence of ribosomopathies, how deregulation of ribosome biogenesis can impact disease mechanisms and aging, and the discovery of specialized ribosomes that have specific functions that may translate differentially with consequences on normal and pathological processes. Emerging Concepts in Ribosome Structure, Biogenesis, and Function provides fundamental coverage and emerging research on ribosomes, biogenesis, and their structure and function and is a resourceful introduction for new researchers and those engaged in interdisciplinary ribosomal research. Provides an overview of ribosome biogenesis and examines its involvement in cell transformation and cancerous growth Covers disorders related to the ribosome (ribosomopathies) and explains the significance of ribosome dysfunction in human diseases Includes commonly used methods to study ribosomes, such as polysome preparation, RNA profiling and proteomics, CryoEM, and Cell-free assays along with proper illustrations