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The FEBS Journal Oct 2023How nucleic acids interact with proteins, and how they affect protein folding, aggregation, and misfolding is a still-evolving area of research. Considerable effort is... (Review)
Review
How nucleic acids interact with proteins, and how they affect protein folding, aggregation, and misfolding is a still-evolving area of research. Considerable effort is now focusing on a particular structure of RNA and DNA, G-quadruplexes, and their role in protein homeostasis and disease. In this state-of-the-art review, we track recent reports on how G-quadruplexes influence protein aggregation, proteolysis, phase separation, and protein misfolding diseases, and pose currently unanswered questions in the advance of this scientific field.
Topics: G-Quadruplexes; Proteostasis; DNA; Proteins; RNA
PubMed: 36017725
DOI: 10.1111/febs.16608 -
The Journal of Biological Chemistry Nov 2023Positive-strand RNA viruses use long open reading frames to express large polyproteins that are processed into individual proteins by viral proteases. Polyprotein...
Positive-strand RNA viruses use long open reading frames to express large polyproteins that are processed into individual proteins by viral proteases. Polyprotein processing is highly regulated and yields intermediate species with different functions than the fully processed proteins, increasing the biochemical diversity of the compact viral genome while also presenting challenges in that proteins must remain stably folded in multiple contexts. We have used circular dichroism spectroscopy and single molecule microscopy to examine the solution structure and self-association of the poliovirus P3 region protein composed of membrane binding 3A, RNA priming 3B (VPg), 3C protease, and 3D RNA-dependent RNA polymerase proteins. Our data indicate that co-folding interactions within the 3ABC segment stabilize the conformational state of the 3C protease region, and this stabilization requires the full-length 3A and 3B proteins. Enzymatic activity assays show that 3ABC is also an active protease, and it cleaves peptide substrates at rates comparable to 3C. The cleavage of a larger polyprotein substrate is stimulated by the addition of RNA, and 3ABC becomes 20-fold more active than 3C in the presence of stoichiometric amounts of viral cre RNA. The data suggest that co-folding within the 3ABC region results in a protease that can be highly activated toward certain cleavage sites by localization to specific RNA elements within the viral replication center, providing a mechanism for regulating viral polyprotein processing.
Topics: Peptide Hydrolases; Poliovirus; Polyproteins; RNA, Viral; Viral Proteins; Protein Folding; Circular Dichroism; Protein Stability; Enzyme Activation; Protein Structure, Secondary; Amino Acid Sequence
PubMed: 37717698
DOI: 10.1016/j.jbc.2023.105258 -
Annual Review of Biochemistry May 2024During the last ten years, developments in cryo-electron microscopy have transformed our understanding of eukaryotic ribosome assembly. As a result, the field has... (Review)
Review
During the last ten years, developments in cryo-electron microscopy have transformed our understanding of eukaryotic ribosome assembly. As a result, the field has advanced from a list of the vast array of ribosome assembly factors toward an emerging molecular movie in which individual frames are represented by structures of stable ribosome assembly intermediates with complementary biochemical and genetic data. In this review, we discuss the mechanisms driving the assembly of yeast and human small and large ribosomal subunits. A particular emphasis is placed on the most recent findings that illustrate key concepts of ribosome assembly, such as folding of preribosomal RNA, the enforced chronology of assembly, enzyme-mediated irreversible transitions, and proofreading of preribosomal particles.
PubMed: 38768392
DOI: 10.1146/annurev-biochem-030222-113611 -
Nature Nanotechnology Jul 2023RNA origami is a method for designing RNA nanostructures that can self-assemble through co-transcriptional folding with applications in nanomedicine and synthetic...
RNA origami is a method for designing RNA nanostructures that can self-assemble through co-transcriptional folding with applications in nanomedicine and synthetic biology. However, to advance the method further, an improved understanding of RNA structural properties and folding principles is required. Here we use cryogenic electron microscopy to study RNA origami sheets and bundles at sub-nanometre resolution revealing structural parameters of kissing-loop and crossover motifs, which are used to improve designs. In RNA bundle designs, we discover a kinetic folding trap that forms during folding and is only released after 10 h. Exploration of the conformational landscape of several RNA designs reveal the flexibility of helices and structural motifs. Finally, sheets and bundles are combined to construct a multidomain satellite shape, which is characterized by individual-particle cryo-electron tomography to reveal the domain flexibility. Together, the study provides a structural basis for future improvements to the design cycle of genetically encoded RNA nanodevices.
Topics: RNA; Nanotechnology; Nanostructures; Molecular Conformation; Nanomedicine; Nucleic Acid Conformation
PubMed: 36849548
DOI: 10.1038/s41565-023-01321-6 -
FEBS Letters Nov 2023This graphical review provides a mechanistic overview of different molecular processes that are tightly coupled and cooperate to achieve efficient and spatial-temporally... (Review)
Review
This graphical review provides a mechanistic overview of different molecular processes that are tightly coupled and cooperate to achieve efficient and spatial-temporally regulated co-transcriptional protein-RNA complex assembly, including co-transcriptional RNA folding, processing, modification and the assembly in context of biomolecular condensates.
Topics: RNA Folding; RNA
PubMed: 37877427
DOI: 10.1002/1873-3468.14758 -
Microbiology and Molecular Biology... Dec 2023SUMMARYNegative and ambisense RNA viruses are the causative agents of important human diseases such as influenza, measles, Lassa fever, and Ebola hemorrhagic fever. The... (Review)
Review
SUMMARYNegative and ambisense RNA viruses are the causative agents of important human diseases such as influenza, measles, Lassa fever, and Ebola hemorrhagic fever. The viral genome of these RNA viruses consists of one or more single-stranded RNA molecules that are encapsidated by viral nucleocapsid proteins to form a ribonucleoprotein complex (RNP). This RNP acts as protection, as a scaffold for RNA folding, and as the context for viral replication and transcription by a viral RNA polymerase. However, the roles of the viral nucleoproteins extend beyond these functions during the viral infection cycle. Recent advances in structural biology techniques and analysis methods have provided new insights into the formation, function, dynamics, and evolution of negative sense virus nucleocapsid proteins, as well as the role that they play in host innate immune responses against viral infection. In this review, we discuss the various roles of nucleocapsid proteins, both in the context of RNPs and in RNA-free states, as well as the open questions that remain.
Topics: Humans; RNA Viruses; Ribonucleoproteins; RNA, Viral; Virus Replication; Nucleocapsid Proteins; Virus Diseases
PubMed: 37750733
DOI: 10.1128/mmbr.00082-23 -
Trends in Cell Biology Nov 2023The endoplasmic reticulum (ER) is central to the processing of luminal, transmembrane, and secretory proteins, and maintaining a functional ER is essential for... (Review)
Review
The endoplasmic reticulum (ER) is central to the processing of luminal, transmembrane, and secretory proteins, and maintaining a functional ER is essential for organismal physiology and health. Increased protein-folding load on the ER causes ER stress, which activates quality control mechanisms to restore ER function and protein homeostasis. Beyond protein quality control, mRNA decay pathways have emerged as potent ER fidelity regulators, but their mechanistic roles in ER quality control and their interrelationships remain incompletely understood. Herein, we review ER-associated RNA decay pathways - including regulated inositol-requiring enzyme 1α (IRE1α)-dependent mRNA decay (RIDD), nonsense-mediated mRNA decay (NMD), and Argonaute-dependent RNA silencing - in ER homeostasis, and highlight the intricate coordination of ER-targeted RNA and protein decay mechanisms and their association with antiviral defense.
PubMed: 38008608
DOI: 10.1016/j.tcb.2023.11.003 -
Interdisciplinary Sciences,... Sep 2023RNA folding prediction is very meaningful and challenging. The molecular dynamics simulation (MDS) of all atoms (AA) is limited to the folding of small RNA molecules. At...
RNA folding prediction is very meaningful and challenging. The molecular dynamics simulation (MDS) of all atoms (AA) is limited to the folding of small RNA molecules. At present, most of the practical models are coarse grained (CG) model, and the coarse-grained force field (CGFF) parameters usually depend on known RNA structures. However, the limitation of the CGFF is obvious that it is difficult to study the modified RNA. Based on the 3 beads model (AIMS_RNA_B3), we proposed the AIMS_RNA_B5 model with three beads representing a base and two beads representing the main chain (sugar group and phosphate group). We first run the all atom molecular dynamic simulation (AAMDS), and fit the CGFF parameter with the AA trajectory. Then perform the coarse-grained molecular dynamic simulation (CGMDS). AAMDS is the foundation of CGMDS. CGMDS is mainly to carry out the conformation sampling based on the current AAMDS state and improve the folding speed. We simulated the folding of three RNAs, which belong to hairpin, pseudoknot and tRNA respectively. Compared to the AIMS_RNA_B3 model, the AIMS_RNA_B5 model is more reasonable and performs better.
Topics: RNA Folding; Molecular Dynamics Simulation; RNA
PubMed: 37115389
DOI: 10.1007/s12539-023-00561-3 -
Genome Research Dec 2023Mammalian sperm show an unusual and heavily compacted genomic packaging state. In addition to its role in organizing the compact and hydrodynamic sperm head, it has been...
Mammalian sperm show an unusual and heavily compacted genomic packaging state. In addition to its role in organizing the compact and hydrodynamic sperm head, it has been proposed that sperm chromatin architecture helps to program gene expression in the early embryo. Scores of genome-wide surveys in sperm have reported patterns of chromatin accessibility, nucleosome localization, histone modification, and chromosome folding. Here, we revisit these studies in light of recent reports that sperm obtained from the mouse epididymis are contaminated with low levels of cell-free chromatin. In the absence of proper sperm lysis, we readily recapitulate multiple prominent genome-wide surveys of sperm chromatin, suggesting that these profiles primarily reflect contaminating cell-free chromatin. Removal of cell-free DNA, and appropriate lysis conditions, are together required to reveal a sperm chromatin state distinct from most previous reports. Using ATAC-seq to explore relatively accessible genomic loci, we identify a landscape of open loci associated with early development and transcriptional control. Histone modification and chromosome folding profiles also strongly support the hypothesis that prior studies suffer from contamination, but technical challenges associated with reliably preserving the architecture of the compacted sperm head prevent us from confidently assaying true localization patterns for these epigenetic marks. Together, our studies show that our knowledge of chromosome packaging in mammalian sperm remains largely incomplete, and motivate future efforts to more accurately characterize genome organization in mature sperm.
PubMed: 38129076
DOI: 10.1101/gr.277845.123 -
Current Opinion in Genetics &... Apr 2024It is long known that an RNA polymerase transcribing through a nucleosome can generate subnucleosomal particles called hexasomes. These particles lack an H2A-H2B dimer,... (Review)
Review
It is long known that an RNA polymerase transcribing through a nucleosome can generate subnucleosomal particles called hexasomes. These particles lack an H2A-H2B dimer, breaking the symmetry of a nucleosome and revealing new interfaces. Whether hexasomes are simply a consequence of RNA polymerase action or they also have a regulatory impact remains an open question. Recent biochemical and structural studies of RNA polymerases and chromatin remodelers with hexasomes motivated us to revisit this question. Here, we build on previous models to discuss how formation of hexasomes can allow sophisticated regulation of transcription and also significantly impact chromatin folding. We anticipate that further cellular and biochemical analysis of these subnucleosomal particles will uncover additional regulatory roles.
Topics: Nucleosomes; Chromatin; DNA-Directed RNA Polymerases
PubMed: 38412564
DOI: 10.1016/j.gde.2024.102163