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Current Opinion in Cell Biology Feb 2009Ribosomes and spliceosomes are ribonucleoprotein nanomachines that catalyze translation of mRNA to synthesize proteins and splicing of introns from pre-mRNAs,... (Review)
Review
Ribosomes and spliceosomes are ribonucleoprotein nanomachines that catalyze translation of mRNA to synthesize proteins and splicing of introns from pre-mRNAs, respectively. Assembly of ribosomes involves more than 300 proteins and RNAs, and that of spliceosomes over 100 proteins and RNAs. Construction of these enormous ribonucleoprotein particles (RNPs) is a dynamic process, in which the nascent RNPs undergo numerous ordered rearrangements of RNA-RNA, RNA-protein, and protein-protein interactions. Here we outline similar principles that have emerged from studies of ribosome and spliceosome assembly. Constituents of both RNPs form subassembly complexes, which can simplify the task of assembly and segregate functions of assembly factors. Reorganization of RNP topology, and proofreading of proper assembly, are catalyzed by protein- or RNA-dependent ATPases or GTPases. Dynamics of intermolecular interactions may be facilitated or regulated by cycles of post-translational modifications. Despite this repertoire of tools, mistakes occur in RNP assembly or in processing of RNA substrates. Quality control mechanisms recognize and turnover misassembled RNPs and reject improper substrates.
Topics: Animals; Humans; RNA, Ribosomal; Ribonucleoproteins; Ribonucleoproteins, Small Nuclear; Ribosomes; Spliceosomes
PubMed: 19167202
DOI: 10.1016/j.ceb.2009.01.003 -
IUBMB Life Jun 2012One of the hallmarks of life is the widespread use of certain essential ribozymes. The ubiquitous ribonuclease P (RNase P) and eukaryotic RNase MRP are essential... (Review)
Review
One of the hallmarks of life is the widespread use of certain essential ribozymes. The ubiquitous ribonuclease P (RNase P) and eukaryotic RNase MRP are essential complexes where a structured, noncoding RNA acts in catalysis. Recent discoveries have elucidated the three-dimensional structure of the ancestral ribonucleoprotein complex, suggested the possibility of a protein-only composition in organelles, and even noted the absence of RNase P in a non-free-living organism. With respect to these last two findings, import mechanisms for RNases P/MRP into mitochondria have been demonstrated, and RNase P is present in organisms with some of the smallest known genomes. Together, these results have led to an ongoing debate regarding the precise definition of how "essential" these ribozymes truly are.
Topics: Animals; Catalytic Domain; Endoribonucleases; Evolution, Molecular; Humans; Nucleic Acid Conformation; RNA; Ribonuclease P; Ribonucleoproteins
PubMed: 22605678
DOI: 10.1002/iub.1052 -
Wiley Interdisciplinary Reviews. RNA Jul 2017Investigating the interactions of RNA-binding proteins (RBPs) with RNAs is a complex task for molecular and computational biologists. The molecular biology techniques... (Review)
Review
Investigating the interactions of RNA-binding proteins (RBPs) with RNAs is a complex task for molecular and computational biologists. The molecular biology techniques and the computational approaches to understand RBP-RNA (or ribonucleoprotein, RNP) interactions have advanced considerably over the past few years and numerous and diverse software tools have been developed to analyze these data. Accordingly, laboratories interested in RNP biology face the challenge of choosing adequately among the available software tools those that best address the biological problem they are studying. Here, we focus on state-of-the-art molecular biology techniques that employ crosslinking and immunoprecipitation (CLIP) of an RBP to study and map RNP interactions. We review the different software tools and databases available to analyze the most widely used CLIP methods, HITS-CLIP, PAR-CLIP, and iCLIP. WIREs RNA 2017, 8:e1404. doi: 10.1002/wrna.1404 For further resources related to this article, please visit the WIREs website.
Topics: Animals; Computational Biology; Cross-Linking Reagents; Humans; Immunoprecipitation; Ribonucleoproteins; Software; Statistics as Topic
PubMed: 28008714
DOI: 10.1002/wrna.1404 -
Molecular Cell May 2014The proper processing, export, localization, translation, and degradation of mRNAs are necessary for regulation of gene expression. These processes are controlled by... (Review)
Review
The proper processing, export, localization, translation, and degradation of mRNAs are necessary for regulation of gene expression. These processes are controlled by mRNA-specific regulatory proteins, noncoding RNAs, and core machineries common to most mRNAs. These factors bind the mRNA in large complexes known as messenger ribonucleoprotein particles (mRNPs). Herein, we review the components of mRNPs, how they assemble and rearrange, and how mRNP composition differentially affects mRNA biogenesis, function, and degradation. We also describe how properties of the mRNP "interactome" lead to emergent principles affecting the control of gene expression.
Topics: Active Transport, Cell Nucleus; Cell Nucleus; Eukaryotic Cells; Gene Expression Regulation; Models, Genetic; RNA, Messenger; RNA, Untranslated; RNA-Binding Proteins; Ribonucleoproteins
PubMed: 24856220
DOI: 10.1016/j.molcel.2014.04.033 -
RNA Biology Sep 2019From biogenesis to degradation, mRNA goes through diverse types of regulation and interaction with other biomolecules. Uneven distribution of mRNA transcripts and the... (Review)
Review
From biogenesis to degradation, mRNA goes through diverse types of regulation and interaction with other biomolecules. Uneven distribution of mRNA transcripts and the diverse isoforms and modifications of mRNA make us wonder how cells manage the complexity and keep the functional integrity for the normal development of cells and organisms. Single-molecule microscopy tools have expanded the scope of RNA research with unprecedented spatiotemporal resolution. In this review, we highlight the recent progress in the methods for labeling mRNA targets and analyzing the quantitative information from fluorescence images of single mRNA molecules. In particular, the MS2 system and its various applications are the main focus of this article. We also review how recent studies have addressed biological questions related to the significance of mRNA localization . Efforts to visualize the dynamics of single mRNA molecules in live cells will push forward our knowledge on the nature of heterogeneity in RNA sequence, structure, and distribution as well as their molecular function and coordinated interaction with RNA binding proteins.
Topics: Multiprotein Complexes; RNA, Messenger; RNA-Binding Proteins; Ribonucleoproteins; Single Molecule Imaging
PubMed: 30336727
DOI: 10.1080/15476286.2018.1536592 -
Current Biology : CB May 2009
Topics: Animals; Cell Line; Cytoplasmic Granules; Humans; Ribonucleoproteins; Stress, Physiological
PubMed: 19467203
DOI: 10.1016/j.cub.2009.03.013 -
Cold Spring Harbor Perspectives in... Feb 2019Eukaryotic cells contain a large number of RNA-protein assemblies, generically referred to as ribonucleoprotein (RNP) granules. Such RNP granules include stress granules... (Review)
Review
Eukaryotic cells contain a large number of RNA-protein assemblies, generically referred to as ribonucleoprotein (RNP) granules. Such RNP granules include stress granules and P-bodies in the cytosol and the nucleolus, Cajal bodies, and paraspeckles in the nucleus. A variety of imaging approaches have been used to reveal different components, structural features, and dynamics of RNP granules. In this review, we discuss imaging approaches that have been used to study stress granules and the insights gained from these experiments. A general theme is that these approaches can be transferred to other RNP granules to examine similar aspects of their composition, ultrastructure, dynamics and control.
Topics: Cytoplasm; Cytoplasmic Granules; Eukaryotic Cells; Ribonucleoproteins; Stress, Physiological
PubMed: 30709880
DOI: 10.1101/cshperspect.a033068 -
RNA Biology 2014Localization and the associated translational control of mRNA is a well established mechanism for segregating cellular protein expression. Drosophila has been... (Review)
Review
Localization and the associated translational control of mRNA is a well established mechanism for segregating cellular protein expression. Drosophila has been instrumental in deciphering the prevailing mechanisms of mRNA localization and regulation. This review will discuss the diverse roles of mRNA localization in the Drosophila germline, the cis-elements and cellular components regulating localization and the superimposition of translational regulatory mechanisms. Despite a history of discovery, there are still many fundamental questions regarding mRNA localization that remain unanswered. Take home messages, outstanding questions and future approaches that will likely lead to resolving these unknowns in the future are summarized at the end.
Topics: Animals; Animals, Genetically Modified; Drosophila melanogaster; Gene Expression Regulation, Developmental; Germ Cells; Oocytes; RNA, Messenger; Ribonucleoproteins
PubMed: 25482896
DOI: 10.4161/rna.36097 -
Reviews in Medical Virology Nov 2010The influenza A virus genome consists of eight segmented, single-stranded, negative-sense RNAs. Each viral RNA (vRNA) segment forms a ribonucleoprotein (RNP) complex... (Review)
Review
The influenza A virus genome consists of eight segmented, single-stranded, negative-sense RNAs. Each viral RNA (vRNA) segment forms a ribonucleoprotein (RNP) complex together with NPs and a polymerase complex, which is a fundamental unit for transcription and replication of the viral genome. Although the exact structure of the intact RNP remains poorly understood, recent electron microscopic studies have revealed certain structural characteristics of the RNP. This review focuses on the findings of these various electron microscopic analyses of RNPs extracted from virions and RNPs inside virions. Based on the morphological and structural observations, we present the architecture of RNPs within a virion and discuss the genome packaging mechanism by which the vRNA segments are incorporated into virions.
Topics: Influenza A virus; Microscopy, Electron; Models, Biological; Ribonucleoproteins; Virion; Virus Assembly
PubMed: 20853340
DOI: 10.1002/rmv.666 -
Analytical Chemistry Jan 2022Advances in gene-editing technology enable efficient, targeted engineering of different cell types, which offer a potential therapeutic platform for most challenging...
Advances in gene-editing technology enable efficient, targeted engineering of different cell types, which offer a potential therapeutic platform for most challenging disease areas. CRISPR-Cas9 is a widely used gene-editing tool in therapeutic applications. The quality of gene-editing reagents (i.e., Cas9 nuclease, single guide (sg)RNA) is associated with the final cellular product quality as they can impact the gene-editing accuracy and efficiency. To assess the impact of the quality of Cas9 protein and sgRNA in the formation of a Cas9 ribonucleoprotein (RNP) complex, stability, and functional activities, we developed a size exclusion chromatography method that utilizes multiple detectors and an DNA cleavage assay using anion-exchange chromatography. Using these methods, we characterized the formation and stability of Cas9 RNP complexes associated with Cas9 and sgRNA characteristics as well as their functional activities. Multi-angle light scattering characterization showed different types and levels of aggregates in different source sgRNA materials, which contribute to form different Cas9 RNP complexes. The aggregations irreversibly dissociated at high temperatures. When the Cas9 RNP complexes derived from non-heated and heated sgRNAs were characterized, the data showed that specific RNP peaks were impacted. The Cas9 RNP complexes derived from the heated sgRNA retained their biological function and cleaved the double-strand target DNA at a higher rate. This work provides new tools to characterize the Cas9 RNP complex formation, stability, and functional activity and provides insights into sgRNA properties and handling procedures to better control the Cas9 RNP complex formation.
Topics: CRISPR-Associated Protein 9; CRISPR-Cas Systems; Gene Editing; RNA, Guide, CRISPR-Cas Systems; Ribonucleoproteins
PubMed: 34958212
DOI: 10.1021/acs.analchem.1c04795