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Sharma V, Swaminathan K, Shukla R. The Ribosome Hypothesis: Decoding Mood Disorder Complexity. Int J Mol Sci 2024; 25:2815. [PMID: 38474062 PMCID: PMC10931790 DOI: 10.3390/ijms25052815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 02/26/2024] [Accepted: 02/26/2024] [Indexed: 03/14/2024] Open
Abstract
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.
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Affiliation(s)
- Vandana Sharma
- Department of Zoology and Physiology, University of Wyoming, Laramie, WY 82071, USA;
- Department of Neurosciences, University of Wyoming, Laramie, WY 82071, USA
| | - Karthik Swaminathan
- Department of Zoology and Physiology, University of Wyoming, Laramie, WY 82071, USA;
- Department of Neurosciences, University of Wyoming, Laramie, WY 82071, USA
| | - Rammohan Shukla
- Department of Zoology and Physiology, University of Wyoming, Laramie, WY 82071, USA;
- Department of Neurosciences, University of Wyoming, Laramie, WY 82071, USA
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Delorme-Hinoux V, Mbodj A, Brando S, De Bures A, Llauro C, Covato F, Garrigue J, Guisset C, Borrut J, Mirouze M, Reichheld JP, Sáez-Vásquez J. 45S rDNA Diversity In Natura as One Step towards Ribosomal Heterogeneity in Arabidopsis thaliana. Plants (Basel) 2023; 12:2722. [PMID: 37514338 PMCID: PMC10386311 DOI: 10.3390/plants12142722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023]
Abstract
The keystone of ribosome biogenesis is the transcription of 45S rDNA. The Arabidopsis thaliana genome contains hundreds of 45S rDNA units; however, they are not all transcribed. Notably, 45S rDNA units contain insertions/deletions revealing the existence of heterogeneous rRNA genes and, likely, heterogeneous ribosomes for rRNAs. In order to obtain an overall picture of 45S rDNA diversity sustaining the synthesis of rRNAs and, subsequently, of ribosomes in natura, we took advantage of 320 new occurrences of Arabidopsis thaliana as a metapopulation named At66, sampled from 0 to 1900 m of altitude in the eastern Pyrenees in France. We found that the 45S rDNA copy number is very dynamic in natura and identified new genotypes for both 5' and 3' External Transcribed Spacers (ETS). Interestingly, the highest 5'ETS genotype diversity is found in altitude while the highest 3'ETS genotype diversity is found at sea level. Structural analysis of 45S rDNA also shows conservation in natura of specific 5'ETS and 3'ETS sequences/features required to control rDNA expression and the processing of rRNAs. In conclusion, At66 is a worthwhile natural laboratory, and unraveled 45S rDNA diversity represents an interesting starting material to select subsets for rDNA transcription and alter the rRNA composition of ribosomes both intra- and inter-site.
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Affiliation(s)
- Valérie Delorme-Hinoux
- Université de Perpignan Via Domitia (UPVD), Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, 66860 Perpignan, France
- Centre National de la Recherche Scientifique, Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, 66860 Perpignan, France
- EMR LGDP/MANGO, Mechanisms of Adaptation and Genomics, IRD-CNRS-UPVD, 66860 Perpignan, France
- Association Charles Flahault, 66350 Toulouges, France
| | - Assane Mbodj
- Université de Perpignan Via Domitia (UPVD), Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, 66860 Perpignan, France
- Centre National de la Recherche Scientifique, Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, 66860 Perpignan, France
- EMR LGDP/MANGO, Mechanisms of Adaptation and Genomics, IRD-CNRS-UPVD, 66860 Perpignan, France
- Institut de Recherche pour le Développement (IRD), ECOBIO, 34000 Montpellier, France
| | - Sophie Brando
- Université de Perpignan Via Domitia (UPVD), Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, 66860 Perpignan, France
- Centre National de la Recherche Scientifique, Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, 66860 Perpignan, France
| | - Anne De Bures
- Université de Perpignan Via Domitia (UPVD), Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, 66860 Perpignan, France
- Centre National de la Recherche Scientifique, Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, 66860 Perpignan, France
| | - Christel Llauro
- Université de Perpignan Via Domitia (UPVD), Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, 66860 Perpignan, France
- Centre National de la Recherche Scientifique, Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, 66860 Perpignan, France
- EMR LGDP/MANGO, Mechanisms of Adaptation and Genomics, IRD-CNRS-UPVD, 66860 Perpignan, France
| | - Fabrice Covato
- FRNC, Fédération des Réserves Naturelles Catalanes, 66500 Prades, France
| | - Joseph Garrigue
- FRNC, Fédération des Réserves Naturelles Catalanes, 66500 Prades, France
| | - Claude Guisset
- Association Charles Flahault, 66350 Toulouges, France
- FRNC, Fédération des Réserves Naturelles Catalanes, 66500 Prades, France
| | | | - Marie Mirouze
- Université de Perpignan Via Domitia (UPVD), Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, 66860 Perpignan, France
- Centre National de la Recherche Scientifique, Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, 66860 Perpignan, France
- EMR LGDP/MANGO, Mechanisms of Adaptation and Genomics, IRD-CNRS-UPVD, 66860 Perpignan, France
- Institut de Recherche pour le Développement (IRD), ECOBIO, 34000 Montpellier, France
| | - Jean-Philippe Reichheld
- Université de Perpignan Via Domitia (UPVD), Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, 66860 Perpignan, France
- Centre National de la Recherche Scientifique, Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, 66860 Perpignan, France
| | - Julio Sáez-Vásquez
- Université de Perpignan Via Domitia (UPVD), Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, 66860 Perpignan, France
- Centre National de la Recherche Scientifique, Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, 66860 Perpignan, France
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Kochavi A, Lovecchio D, Faller WJ, Agami R. Proteome diversification by mRNA translation in cancer. Mol Cell 2023; 83:469-480. [PMID: 36521491 DOI: 10.1016/j.molcel.2022.11.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 11/14/2022] [Accepted: 11/16/2022] [Indexed: 12/15/2022]
Abstract
mRNA translation is a highly conserved and tightly controlled mechanism for protein synthesis and is well known to be altered by oncogenes to promote cancer development. This distorted mRNA translation is accompanied by the vulnerability of cancer to inhibitors of key mRNA translation components. Novel studies also suggest that these alternations could be utilized for immunotherapy. Ribosome heterogeneity and alternative responses to nutrient shortages, which aid cancer growth and spread, are proposed to elicit aberrant protein production but may also result in previously unidentified therapeutic targets, such as the presentation of cancer-specific peptides at the surface of cancer cells (neoepitopes). This review will assess the driving forces in tRNA and ribosome function that underlie proteome diversification due to alterations in mRNA translation in cancer cells.
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Affiliation(s)
- Adva Kochavi
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands; Oncode Institute, the Netherlands
| | - Domenica Lovecchio
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands; Oncode Institute, the Netherlands
| | - William James Faller
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands
| | - Reuven Agami
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands; Oncode Institute, the Netherlands; Erasmus MC, Rotterdam University, Rotterdam, the Netherlands.
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Babaian A, Rothe K, Girodat D, Minia I, Djondovic S, Milek M, Spencer Miko SE, Wieden HJ, Landthaler M, Morin GB, Mager DL. Loss of m 1acp 3Ψ Ribosomal RNA Modification Is a Major Feature of Cancer. Cell Rep 2020; 31:107611. [PMID: 32375039 DOI: 10.1016/j.celrep.2020.107611] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 02/03/2020] [Accepted: 04/14/2020] [Indexed: 12/22/2022] Open
Abstract
The ribosome is an RNA-protein complex that is essential for translation in all domains of life. The structural and catalytic core of the ribosome is its ribosomal RNA (rRNA). While mutations in ribosomal protein (RP) genes are known drivers of oncogenesis, oncogenic rRNA variants have remained elusive. We identify a cancer-specific single-nucleotide variation in 18S rRNA at nucleotide 1248.U in up to 45.9% of patients with colorectal carcinoma (CRC) and present across >22 cancer types. This is the site of a unique hyper-modified base, 1-methyl-3-α-amino-α-carboxyl-propyl pseudouridine (m1acp3Ψ), a >1-billion-years-conserved RNA modification at the peptidyl decoding site of the ribosome. A subset of CRC tumors we call hypo-m1acp3Ψ shows sub-stoichiometric m1acp3Ψ modification, unlike normal control tissues. An m1acp3Ψ knockout model and hypo-m1acp3Ψ patient tumors share a translational signature characterized by highly abundant ribosomal proteins. Thus, m1acp3Ψ-deficient rRNA forms an uncharacterized class of "onco-ribosome" which may serve as a chemotherapeutic target for treating cancer patients.
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Sarangdhar MA, Allam R. Angiogenin (ANG)-Ribonuclease Inhibitor (RNH1) System in Protein Synthesis and Disease. Int J Mol Sci 2021; 22:1287. [PMID: 33525475 DOI: 10.3390/ijms22031287] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/25/2021] [Accepted: 01/25/2021] [Indexed: 12/16/2022] Open
Abstract
Protein synthesis is a highly complex process executed by well-organized translation machinery. Ribosomes, tRNAs and mRNAs are the principal components of this machinery whereas RNA binding proteins and ribosome interacting partners act as accessory factors. Angiogenin (ANG)-Ribonuclease inhibitor (RNH1) system is one such accessory part of the translation machinery that came into focus afresh due to its unconventional role in the translation. ANG is conventionally known for its ability to induce blood vessel formation and RNH1 as a "sentry" to protect RNAs from extracellular RNases. However, recent studies suggest them to be important in translation regulation. During cell homeostasis, ANG in the nucleus promotes rRNA transcription. While under stress, ANG translocates to the cytosol and cleaves tRNA into fragments which inhibit ribosome biogenesis and protein synthesis. RNH1, which intimately interacts with ANG to inhibit its ribonucleolytic activity, can also bind to the 40S ribosomes and control translation by yet to be known mechanisms. Here, we review recent advancement in the knowledge of translation regulation by the ANG-RNH1 system. We also gather information about this system in cell homeostasis as well as in pathological conditions such as cancer and ribosomopathies. Additionally, we discuss the future research directions and therapeutic potential of this system.
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Abstract
Translation of mRNAs is the primary function of the ribosomal machinery. Although cells allow for a certain level of translational errors/mistranslation (which may well be a strategic need), maintenance of the fidelity of translation is vital for the cellular function and fitness. The P-site bound initiator tRNA selects the start codon in an mRNA and specifies the reading frame. A direct P-site binding of the initiator tRNA is a function of its special structural features, ribosomal elements, and the initiation factors. A highly conserved feature of the 3 consecutive G:C base pairs (3 GC pairs) in the anticodon stem of the initiator tRNAs is vital in directing it to the P-site. Mutations in the 3 GC pairs diminish/abolish initiation under normal physiological conditions. Using molecular genetics approaches, we have identified conditions that allow initiation with the mutant tRNAs in Escherichia coli. During our studies, we have uncovered a novel phenomenon of in vivo initiation by elongator tRNAs. Here, we recapitulate how the cellular abundance of the initiator tRNA, and nucleoside modifications in rRNA are connected with the tRNA selection in the P-site. We then discuss our recent finding of how a conserved feature in the mRNA, the Shine-Dalgarno sequence, influences tRNA selection in the P-site.
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Affiliation(s)
- Sunil Shetty
- a Department of Microbiology and Cell Biology; Indian Institute of Science ; Bangalore , India
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