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International Journal of Molecular... Feb 2024Several types of mood disorders lie along a continuum, with nebulous boundaries between them. Understanding the mechanisms that contribute to mood disorder complexity is...
Several types of mood disorders lie along a continuum, with nebulous boundaries between them. Understanding the mechanisms that contribute to mood disorder complexity is critical for effective treatment. However, present treatments are largely centered around neurotransmission and receptor-based hypotheses, which, given the high instance of treatment resistance, fail to adequately explain the complexities of mood disorders. In this opinion piece, based on our recent results, we propose a ribosome hypothesis of mood disorders. We suggest that any hypothesis seeking to explain the diverse nature of mood disorders must incorporate infrastructure diversity that results in a wide range of effects. Ribosomes, with their mobility across neurites and complex composition, have the potential to become specialized during stress; thus, ribosome diversity and dysregulation are well suited to explaining mood disorder complexity. Here, we first establish a framework connecting ribosomes to the current state of knowledge associated with mood disorders. Then, we describe the potential mechanisms through which ribosomes could homeostatically regulate systems to manifest diverse mood disorder phenotypes and discuss approaches for substantiating the ribosome hypothesis. Investigating these mechanisms as therapeutic targets holds promise for transdiagnostic avenues targeting mood disorders.
Topics: Humans; Ribosomes; Mood Disorders; Ribosomal Proteins
PubMed: 38474062
DOI: 10.3390/ijms25052815 -
FEMS Microbiology Reviews Jun 1999The translocation step of protein elongation entails a large-scale rearrangement of the tRNA-mRNA-ribosome complex. Recent years have seen major advances in unraveling... (Review)
Review
The translocation step of protein elongation entails a large-scale rearrangement of the tRNA-mRNA-ribosome complex. Recent years have seen major advances in unraveling the mechanism of the process on the molecular level. A number of intermediate states have been defined and, in part, characterized structurally. The article reviews the recent evidence that suggests a dynamic role of the ribosome and its ligands during translocation. The focus is on dynamic aspects of tRNA movement and on the role of elongation factor G and GTP hydrolysis in translocation catalysis. The significance of structural changes of the ribosome induced by elongation factor G as well the role of ribosomal RNA are addressed. A functional model of elongation factor G as a motor protein driven by GTP hydrolysis is discussed.
Topics: Guanosine Triphosphate; Peptide Elongation Factor G; Peptide Elongation Factors; Protein Biosynthesis; RNA, Ribosomal; RNA, Transfer; Ribosomes
PubMed: 10371036
DOI: 10.1111/j.1574-6976.1999.tb00402.x -
Antimicrobial Agents and Chemotherapy Feb 2021Zinc is an essential micronutrient for mycobacteria, and its depletion induces multiple adaptive changes in cellular physiology, the most remarkable of which are...
Zinc is an essential micronutrient for mycobacteria, and its depletion induces multiple adaptive changes in cellular physiology, the most remarkable of which are remodeling and hibernation of ribosomes. Ribosome remodeling, induced upon relatively moderate depletion of zinc, involves replacement of multiple ribosomal proteins containing the zinc-binding CXXC motif (called C+ r proteins) by their motif-free C- paralogs. Severe zinc depletion induces binding of mycobacterial protein Y (Mpy) to the 70S C- ribosome, thereby stabilizing the ribosome in an inactive state that is also resistant to kanamycin and streptomycin. Because the Mpy binding region on the ribosome is proximal to the binding pocket of spectinamides (Spa), the preclinical drug candidates for tuberculosis, we addressed the impact of remodeling and hibernation of ribosomes on Spa sensitivity. We report here that while Mpy binding has no significant effect on Spa sensitivity to the ribosome, replacement of S14 with its C- counterpart reduces the binding affinity of the drug by ∼2-fold, causing increased Spa tolerance in and cells harboring the C- ribosome. The altered interaction between Spa and ribosomes likely results from new contact points for D67 and R83 residues of S14 with U1138 and C1184 of 16S rRNA helix 34, respectively. Given that induces ribosome remodeling during progression from the acute to chronic phase of lung infection, our findings highlight new considerations in the development of Spa as effective drugs against tuberculosis.
Topics: Pharmaceutical Preparations; RNA, Ribosomal, 16S; Ribosomal Proteins; Ribosomes; Transcription Factors; Zinc
PubMed: 33361293
DOI: 10.1128/AAC.01833-20 -
Biomolecules Sep 2018RNA-RNA interaction slowly emerges as a critical component for the smooth functioning of gene expression processes, in particular in translation where the central actor... (Review)
Review
RNA-RNA interaction slowly emerges as a critical component for the smooth functioning of gene expression processes, in particular in translation where the central actor is an RNA powered molecular machine. Overall, ribosome dynamic results from sequential interactions between three main RNA species: ribosomal, transfer and messenger RNA (rRNA, tRNA and mRNA). In recent decades, special attention has been paid to the physical principles governing codon-anticodon pairing, whereas individual RNA positioning mostly relies on ribosomal RNA framework. Here, we provide a brief overview on the actual knowledge of RNA infrastructure throughout the process of translation in mammalian cells: where and how do these physical contacts occur? What are their potential roles and functions? Are they involved in disease development? What will be the main challenges ahead?
Topics: Anticodon; Binding Sites; Codon; Humans; Nucleic Acid Conformation; Protein Biosynthesis; RNA, Messenger; RNA, Ribosomal; RNA, Transfer; Ribosomes
PubMed: 30261607
DOI: 10.3390/biom8040100 -
Nucleic Acids Research Jun 2023The existence of naturally occurring ribosome heterogeneity is now a well-acknowledged phenomenon. However, whether this heterogeneity leads to functionally diverse...
The existence of naturally occurring ribosome heterogeneity is now a well-acknowledged phenomenon. However, whether this heterogeneity leads to functionally diverse 'specialized ribosomes' is still a controversial topic. Here, we explore the biological function of RPL3L (uL3L), a ribosomal protein (RP) paralogue of RPL3 (uL3) that is exclusively expressed in skeletal muscle and heart tissues, by generating a viable homozygous Rpl3l knockout mouse strain. We identify a rescue mechanism in which, upon RPL3L depletion, RPL3 becomes up-regulated, yielding RPL3-containing ribosomes instead of RPL3L-containing ribosomes that are typically found in cardiomyocytes. Using both ribosome profiling (Ribo-seq) and a novel orthogonal approach consisting of ribosome pulldown coupled to nanopore sequencing (Nano-TRAP), we find that RPL3L modulates neither translational efficiency nor ribosome affinity towards a specific subset of transcripts. In contrast, we show that depletion of RPL3L leads to increased ribosome-mitochondria interactions in cardiomyocytes, which is accompanied by a significant increase in ATP levels, potentially as a result of fine-tuning of mitochondrial activity. Our results demonstrate that the existence of tissue-specific RP paralogues does not necessarily lead to enhanced translation of specific transcripts or modulation of translational output. Instead, we reveal a complex cellular scenario in which RPL3L modulates the expression of RPL3, which in turn affects ribosomal subcellular localization and, ultimately, mitochondrial activity.
Topics: Animals; Mice; Heart; Mitochondria; Muscle, Skeletal; Protein Biosynthesis; Ribosomal Proteins; Ribosomes
PubMed: 36882085
DOI: 10.1093/nar/gkad121 -
ELife Jun 2024The protein translocon at the endoplasmic reticulum comprises the Sec61 translocation channel and numerous accessory factors that collectively facilitate the biogenesis...
The protein translocon at the endoplasmic reticulum comprises the Sec61 translocation channel and numerous accessory factors that collectively facilitate the biogenesis of secretory and membrane proteins. Here, we leveraged recent advances in cryo-electron microscopy (cryo-EM) and structure prediction to derive insights into several novel configurations of the ribosome-translocon complex. We show how a transmembrane domain (TMD) in a looped configuration passes through the Sec61 lateral gate during membrane insertion; how a nascent chain can bind and constrain the conformation of ribosomal protein uL22; and how the translocon-associated protein (TRAP) complex can adjust its position during different stages of protein biogenesis. Most unexpectedly, we find that a large proportion of translocon complexes contains RAMP4 intercalated into Sec61's lateral gate, widening Sec61's central pore and contributing to its hydrophilic interior. These structures lead to mechanistic hypotheses for translocon function and highlight a remarkably plastic machinery whose conformations and composition adjust dynamically to its diverse range of substrates.
Topics: Ribosomes; Cryoelectron Microscopy; SEC Translocation Channels; Endoplasmic Reticulum; Protein Conformation; Ribosomal Proteins; Humans; Models, Molecular; Protein Transport; Membrane Proteins
PubMed: 38896445
DOI: 10.7554/eLife.95814 -
BMC Molecular Biology Feb 2015Ribosomes and functional complexes of them have been analyzed at the atomic level. Far less is known about the dynamic assembly and degradation events that define the...
BACKGROUND
Ribosomes and functional complexes of them have been analyzed at the atomic level. Far less is known about the dynamic assembly and degradation events that define the half-life of ribosomes and guarantee their quality control.
RESULTS
We developed a system that allows visualization of intact ribosomal subunits and assembly intermediates (i.e. assembly landscapes) by convenient fluorescence-based analysis. To this end, we labeled the early assembly ribosomal proteins L1 and S15 with the fluorescent proteins mAzami green and mCherry, respectively, using chromosomal gene insertion. The reporter strain harbors fluorescently labeled ribosomal subunits that operate wild type-like, as shown by biochemical and growth assays. Using genetic and chemical perturbations by depleting genes encoding the ribosomal proteins L3 and S17, respectively, or using ribosome-targeting antibiotics, we provoked ribosomal subunit assembly defects. These defects were readily identified by fluorometric analysis after sucrose density centrifugation in unprecedented resolution.
CONCLUSION
This strategy is useful to monitor and characterize subunit specific assembly defects caused by ribosome-targeting drugs that are currently used and to characterize new molecules that affect ribosome assembly and thereby constitute new classes of antibacterial agents.
Topics: Anti-Bacterial Agents; Escherichia coli; Escherichia coli Proteins; Fluorometry; Gene Knockout Techniques; Green Fluorescent Proteins; Luminescent Proteins; Mutagenesis, Insertional; Protein Multimerization; Ribosomal Proteins; Ribosome Subunits, Large, Bacterial; Ribosome Subunits, Small, Bacterial; Ribosomes; Red Fluorescent Protein
PubMed: 25884162
DOI: 10.1186/s12867-015-0031-y -
Science Advances Jun 2017Bypassing is a recoding event that leads to the translation of two distal open reading frames into a single polypeptide chain. We present the structure of a translating...
Bypassing is a recoding event that leads to the translation of two distal open reading frames into a single polypeptide chain. We present the structure of a translating ribosome stalled at the bypassing take-off site of of bacteriophage T4. The nascent peptide in the exit tunnel anchors the P-site peptidyl-tRNA to the ribosome and locks an inactive conformation of the peptidyl transferase center (PTC). The mRNA forms a short dynamic hairpin in the decoding site. The ribosomal subunits adopt a rolling conformation in which the rotation of the small subunit around its long axis causes the opening of the A-site region. Together, PTC conformation and mRNA structure safeguard against premature termination and read-through of the stop codon and reconfigure the ribosome to a state poised for take-off and sliding along the noncoding mRNA gap.
Topics: Models, Molecular; Peptides; Protein Biosynthesis; Protein Conformation; RNA, Messenger; Ribosome Subunits, Small, Bacterial; Ribosomes; Structure-Activity Relationship
PubMed: 28630923
DOI: 10.1126/sciadv.1700147 -
International Journal of Molecular... Mar 2019The effects of RNA on in-cell NMR spectroscopy and ribosomes on the kinetic activity of several metabolic enzymes are reviewed. Quinary interactions between labelled... (Review)
Review
The effects of RNA on in-cell NMR spectroscopy and ribosomes on the kinetic activity of several metabolic enzymes are reviewed. Quinary interactions between labelled target proteins and RNA broaden in-cell NMR spectra yielding apparent megadalton molecular weights in-cell. The in-cell spectra can be resolved by using cross relaxation-induced polarization transfer (CRINEPT), heteronuclear multiple quantum coherence (HMQC), transverse relaxation-optimized, NMR spectroscopy (TROSY). The effect is reproduced in vitro by using reconstituted total cellular RNA and purified ribosome preparations. Furthermore, ribosomal binding antibiotics alter protein quinary structure through protein-ribosome and protein-mRNA-ribosome interactions. The quinary interactions of Adenylate kinase, Thymidylate synthase and Dihydrofolate reductase alter kinetic properties of the enzymes. The results demonstrate that ribosomes may specifically contribute to the regulation of biological activity.
Topics: Adenylate Kinase; Anti-Bacterial Agents; Catalytic Domain; Models, Molecular; Nuclear Magnetic Resonance, Biomolecular; Protein Binding; Protein Structure, Quaternary; Quantum Theory; RNA; Ribosomes; Tetrahydrofolate Dehydrogenase; Thymidylate Synthase
PubMed: 30875837
DOI: 10.3390/ijms20061297 -
Bioscience Reports Jul 2023Ribosome biogenesis is the complex and essential process that ultimately leads to the synthesis of cellular proteins. Understanding each step of this essential process... (Review)
Review
Ribosome biogenesis is the complex and essential process that ultimately leads to the synthesis of cellular proteins. Understanding each step of this essential process is imperative to increase our understanding of basic biology, but also more critically, to provide novel therapeutic avenues for genetic and developmental diseases such as ribosomopathies and cancers which can arise when this process is impaired. In recent years, significant advances in technology have made identifying and characterizing novel human regulators of ribosome biogenesis via high-content, high-throughput screens. Additionally, screening platforms have been used to discover novel therapeutics for cancer. These screens have uncovered a wealth of knowledge regarding novel proteins involved in human ribosome biogenesis, from the regulation of the transcription of the ribosomal RNA to global protein synthesis. Specifically, comparing the discovered proteins in these screens showed interesting connections between large ribosomal subunit (LSU) maturation factors and earlier steps in ribosome biogenesis, as well as overall nucleolar integrity. In this review, a discussion of the current standing of screens for human ribosome biogenesis factors through the lens of comparing the datasets and discussing the biological implications of the areas of overlap will be combined with a look toward other technologies and how they can be adapted to discover more factors involved in ribosome synthesis, and answer other outstanding questions in the field.
Topics: Humans; Ribosomes; Protein Biosynthesis; RNA, Ribosomal; Cell Nucleolus; Neoplasms; Ribosomal Proteins
PubMed: 37335083
DOI: 10.1042/BSR20230631