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Westhof E, Watson ZL, Zirbel CL, Cate JHD. Anionic G•U pairs in bacterial ribosomal rRNAs. RNA (NEW YORK, N.Y.) 2023; 29:1069-1076. [PMID: 37068913 DOI: 10.1261/rna.079583.123] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 04/05/2023] [Indexed: 06/18/2023]
Abstract
Wobble GU pairs (or G•U) occur frequently within double-stranded RNA helices interspersed between standard G=C and A-U Watson-Crick pairs. Another type of G•U pair interacting via their Watson-Crick edges has been observed in the A site of ribosome structures between a modified U34 in the tRNA anticodon triplet and G + 3 in the mRNA. In such pairs, the electronic structure of the U is changed with a negative charge on N3(U), resulting in two H-bonds between N1(G)…O4(U) and N2(G)…N3(U). Here, we report that such pairs occur in other highly conserved positions in ribosomal RNAs of bacteria in the absence of U modification. An anionic cis Watson-Crick G•G pair is also observed and well conserved in the small subunit. These pairs are observed in tightly folded regions.
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Affiliation(s)
- Eric Westhof
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de biologie moléculaire et cellulaire du CNRS, F-67084 Strasbourg, France
| | - Zoe L Watson
- Department of Chemistry, University of California, Berkeley, California 94720, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, USA
| | - Craig L Zirbel
- Department of Mathematics and Statistics, Bowling Green State University, Bowling Green, Ohio 43403, USA
| | - Jamie H D Cate
- Department of Chemistry, University of California, Berkeley, California 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, California 94720, USA
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2
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Hahm JY, Park J, Jang ES, Chi SW. 8-Oxoguanine: from oxidative damage to epigenetic and epitranscriptional modification. Exp Mol Med 2022; 54:1626-1642. [PMID: 36266447 PMCID: PMC9636213 DOI: 10.1038/s12276-022-00822-z] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 05/06/2022] [Accepted: 05/26/2022] [Indexed: 12/29/2022] Open
Abstract
In pathophysiology, reactive oxygen species control diverse cellular phenotypes by oxidizing biomolecules. Among these, the guanine base in nucleic acids is the most vulnerable to producing 8-oxoguanine, which can pair with adenine. Because of this feature, 8-oxoguanine in DNA (8-oxo-dG) induces a G > T (C > A) mutation in cancers, which can be deleterious and thus actively repaired by DNA repair pathways. 8-Oxoguanine in RNA (o8G) causes problems in aberrant quality and translational fidelity, thereby it is subjected to the RNA decay pathway. In addition to oxidative damage, 8-oxo-dG serves as an epigenetic modification that affects transcriptional regulatory elements and other epigenetic modifications. With the ability of o8G•A in base pairing, o8G alters structural and functional RNA-RNA interactions, enabling redirection of posttranscriptional regulation. Here, we address the production, regulation, and function of 8-oxo-dG and o8G under oxidative stress. Primarily, we focus on the epigenetic and epitranscriptional roles of 8-oxoguanine, which highlights the significance of oxidative modification in redox-mediated control of gene expression.
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Affiliation(s)
- Ja Young Hahm
- grid.222754.40000 0001 0840 2678Department of Life Sciences, Korea University, Seoul, 02481 Republic of Korea ,grid.222754.40000 0001 0840 2678Institute of Life Sciences and Biotechnology, Korea University, Seoul, 02481 Republic of Korea
| | - Jongyeun Park
- grid.222754.40000 0001 0840 2678Department of Life Sciences, Korea University, Seoul, 02481 Republic of Korea ,grid.222754.40000 0001 0840 2678Institute of Life Sciences and Biotechnology, Korea University, Seoul, 02481 Republic of Korea
| | - Eun-Sook Jang
- grid.222754.40000 0001 0840 2678Department of Life Sciences, Korea University, Seoul, 02481 Republic of Korea ,grid.222754.40000 0001 0840 2678Institute of Life Sciences and Biotechnology, Korea University, Seoul, 02481 Republic of Korea
| | - Sung Wook Chi
- grid.222754.40000 0001 0840 2678Department of Life Sciences, Korea University, Seoul, 02481 Republic of Korea ,grid.222754.40000 0001 0840 2678Institute of Life Sciences and Biotechnology, Korea University, Seoul, 02481 Republic of Korea ,grid.222754.40000 0001 0840 2678KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul, 02481 Republic of Korea
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3
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Affiliation(s)
- Marie Sissler
- ARNA - UMR5320 CNRS - U1212 INSERM, Université de Bordeaux, IECB, Pessac, France.
| | - Yaser Hashem
- ARNA - UMR5320 CNRS - U1212 INSERM, Université de Bordeaux, IECB, Pessac, France.
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Valach M, Gonzalez Alcazar JA, Sarrasin M, Lang BF, Gray MW, Burger G. An Unexpectedly Complex Mitoribosome in Andalucia godoyi, a Protist with the Most Bacteria-like Mitochondrial Genome. Mol Biol Evol 2021; 38:788-804. [PMID: 32886790 PMCID: PMC7947838 DOI: 10.1093/molbev/msaa223] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The mitoribosome, as known from studies in model organisms, deviates considerably from its ancestor, the bacterial ribosome. Deviations include substantial reduction of the mitochondrial ribosomal RNA (mt-rRNA) structure and acquisition of numerous mitochondrion-specific (M) mitoribosomal proteins (mtRPs). A broadly accepted view assumes that M-mtRPs compensate for structural destabilization of mt-rRNA resulting from its evolutionary remodeling. Since most experimental information on mitoribosome makeup comes from eukaryotes having derived mitochondrial genomes and mt-rRNAs, we tested this assumption by investigating the mitochondrial translation machinery of jakobids, a lineage of unicellular protists with the most bacteria-like mitochondrial genomes. We report here proteomics analyses of the Andalucia godoyi small mitoribosomal subunit and in silico transcriptomic and comparative genome analyses of four additional jakobids. Jakobids have mt-rRNA structures that minimally differ from their bacterial counterparts. Yet, with at least 31 small subunit and 44 large subunit mtRPs, the mitoriboproteome of Andalucia is essentially as complex as that in animals or fungi. Furthermore, the relatively high conservation of jakobid sequences has helped to clarify the identity of several mtRPs, previously considered to be lineage-specific, as divergent homologs of conserved M-mtRPs, notably mS22 and mL61. The coexistence of bacteria-like mt-rRNAs and a complex mitoriboproteome refutes the view that M-mtRPs were ancestrally recruited to stabilize deviations of mt-rRNA structural elements. We postulate instead that the numerous M-mtRPs acquired in the last eukaryotic common ancestor allowed mt-rRNAs to pursue a broad range of evolutionary trajectories across lineages: from dramatic reduction to acquisition of novel elements to structural conservatism.
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Affiliation(s)
- Matus Valach
- Department of Biochemistry and Molecular Medicine, Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, Quebec, Canada
| | - José Angel Gonzalez Alcazar
- Department of Biochemistry and Molecular Medicine, Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, Quebec, Canada
| | - Matt Sarrasin
- Department of Biochemistry and Molecular Medicine, Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, Quebec, Canada
| | - B Franz Lang
- Department of Biochemistry and Molecular Medicine, Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, Quebec, Canada
| | - Michael W Gray
- Department of Biochemistry and Molecular Biology, Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Gertraud Burger
- Department of Biochemistry and Molecular Medicine, Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, Quebec, Canada
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Baulin E, Metelev V, Bogdanov A. Base-intercalated and base-wedged stacking elements in 3D-structure of RNA and RNA-protein complexes. Nucleic Acids Res 2020; 48:8675-8685. [PMID: 32687167 PMCID: PMC7470943 DOI: 10.1093/nar/gkaa610] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 07/05/2020] [Accepted: 07/15/2020] [Indexed: 12/25/2022] Open
Abstract
Along with nucleobase pairing, base-base stacking interactions are one of the two main types of strong non-covalent interactions that define the unique secondary and tertiary structure of RNA. In this paper we studied two subfamilies of nucleobase-inserted stacking structures: (i) with any base intercalated between neighboring nucleotide residues (base-intercalated element, BIE, i + 1); (ii) with any base wedged into a hydrophobic cavity formed by heterocyclic bases of two nucleotides which are one nucleotide apart in sequence (base-wedged element, BWE, i + 2). We have exploited the growing database of natively folded RNA structures in Protein Data Bank to analyze the distribution and structural role of these motifs in RNA. We found that these structural elements initially found in yeast tRNAPhe are quite widespread among the tertiary structures of various RNAs. These motifs perform diverse roles in RNA 3D structure formation and its maintenance. They contribute to the folding of RNA bulges and loops and participate in long-range interactions of single-stranded stretches within RNA macromolecules. Furthermore, both base-intercalated and base-wedged motifs participate directly or indirectly in the formation of RNA functional centers, which interact with various ligands, antibiotics and proteins.
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Affiliation(s)
- Eugene Baulin
- Laboratory of Applied Mathematics, Institute of Mathematical Problems of Biology RAS - the Branch of Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
| | - Valeriy Metelev
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Alexey Bogdanov
- To whom correspondence should be addressed. Tel: +7 495 9393143; Fax: +7 495 9393181;
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Translesion synthesis by AMV, HIV, and MMLVreverse transcriptases using RNA templates containing inosine, guanosine, and their 8-oxo-7,8-dihydropurine derivatives. PLoS One 2020; 15:e0235102. [PMID: 32857764 PMCID: PMC7455023 DOI: 10.1371/journal.pone.0235102] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 08/07/2020] [Indexed: 12/31/2022] Open
Abstract
Inosine is ubiquitous and essential in many biological processes, including RNA-editing. In addition, oxidative stress on RNA has been a topic of increasing interest due, in part, to its potential role in the development/progression of disease. In this work we probed the ability of three reverse transcriptases (RTs) to catalyze the synthesis of cDNA in the presence of RNA templates containing inosine (I), 8-oxo-7,8-dihydroinosine (8oxo-I), guanosine (G), or 8-oxo-7,8-dihydroguanosine (8-oxoG), and explored the impact that these purine derivatives have as a function of position. To this end, we used 29-mers of RNA (as template) containing the modifications at position-18 and reverse transcribed DNA using 17-mers, 18-mers, or 19-mers (as primers). Generally reactivity of the viral RTs, AMV / HIV / MMLV, towards cDNA synthesis was similar for templates containing G or I as well as for those with 8-oxoG or 8-oxoI. Notable differences are: 1) the use of 18-mers of DNA (to explore cDNA synthesis past the lesion/modification) led to inhibition of DNA elongation in cases where a G:dA wobble pair was present, while the presence of I, 8-oxoI, or 8-oxoG led to full synthesis of the corresponding cDNA, with the latter two displaying a more efficient process; 2) HIV RT is more sensitive to modified base pairs in the vicinity of cDNA synthesis; and 3) the presence of a modification two positions away from transcription initiation has an adverse impact on the overall process. Steady-state kinetics were established using AMV RT to determine substrate specificities towards canonical dNTPs (N = G, C, T, A). Overall we found evidence that RNA templates containing inosine are likely to incorporate dC > dT > > dA, where reactivity in the presence of dA was found to be pH dependent (process abolished at pH 7.3); and that the absence of the C2-exocyclic amine, as displayed with templates containing 8-oxoI, leads to increased selectivity towards incorporation of dA over dC. The data will be useful in assessing the impact that the presence of inosine and/or oxidatively generated lesions have on viral processes and adds to previous reports where I codes exclusively like G. Similar results were obtained upon comparison of AMV and MMLV RTs.
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Current perspectives on the clinical implications of oxidative RNA damage in aging research: challenges and opportunities. GeroScience 2020; 43:487-505. [PMID: 32529593 PMCID: PMC8110629 DOI: 10.1007/s11357-020-00209-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 05/28/2020] [Indexed: 02/05/2023] Open
Abstract
Ribonucleic acid (RNA) molecules can be easily attacked by reactive oxygen species (ROS), which are produced during normal cellular metabolism and under various oxidative stress conditions. Numerous findings report that the amount of cellular 8-oxoG, the most abundant RNA damage biomarker, is a promising target for the sensitive measurement of oxidative stress and aging-associated diseases, including neuropsychiatric disorders. Most importantly, available data suggest that RNA oxidation has important implications for various signaling pathways and gene expression regulation in aging-related diseases, highlighting the necessity of using combinations of RNA oxidation adducts in both experimental studies and clinical trials. In this review, we primarily describe evidence for the effect of oxidative stress on RNA integrity modulation and possible quality control systems. Additionally, we discuss the profiles and clinical implications of RNA oxidation products that have been under intensive investigation in several aging-associated medical disorders.
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Shcherbik N, Pestov DG. The Impact of Oxidative Stress on Ribosomes: From Injury to Regulation. Cells 2019; 8:cells8111379. [PMID: 31684095 PMCID: PMC6912279 DOI: 10.3390/cells8111379] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 10/23/2019] [Accepted: 10/30/2019] [Indexed: 02/06/2023] Open
Abstract
The ribosome is a complex ribonucleoprotein-based molecular machine that orchestrates protein synthesis in the cell. Both ribosomal RNA and ribosomal proteins can be chemically modified by reactive oxygen species, which may alter the ribosome′s functions or cause a complete loss of functionality. The oxidative damage that ribosomes accumulate during their lifespan in a cell may lead to reduced or faulty translation and contribute to various pathologies. However, remarkably little is known about the biological consequences of oxidative damage to the ribosome. Here, we provide a concise summary of the known types of changes induced by reactive oxygen species in rRNA and ribosomal proteins and discuss the existing experimental evidence of how these modifications may affect ribosome dynamics and function. We emphasize the special role that redox-active transition metals, such as iron, play in ribosome homeostasis and stability. We also discuss the hypothesis that redox-mediated ribosome modifications may contribute to adaptive cellular responses to stress.
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Affiliation(s)
- Natalia Shcherbik
- Department of Cell Biology and Neuroscience, Rowan University School of Osteopathic Medicine, Stratford, NJ 08084, USA.
| | - Dimitri G Pestov
- Department of Cell Biology and Neuroscience, Rowan University School of Osteopathic Medicine, Stratford, NJ 08084, USA.
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Mammalian mitochondrial translation - revealing consequences of divergent evolution. Biochem Soc Trans 2019; 47:1429-1436. [PMID: 31551356 DOI: 10.1042/bst20190265] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 08/15/2019] [Accepted: 08/19/2019] [Indexed: 12/16/2022]
Abstract
Mitochondria are ubiquitous organelles present in the cytoplasm of all nucleated eukaryotic cells. These organelles are described as arising from a common ancestor but a comparison of numerous aspects of mitochondria between different organisms provides remarkable examples of divergent evolution. In humans, these organelles are of dual genetic origin, comprising ∼1500 nuclear-encoded proteins and thirteen that are encoded by the mitochondrial genome. Of the various functions that these organelles perform, it is only oxidative phosphorylation, which provides ATP as a source of chemical energy, that is dependent on synthesis of these thirteen mitochondrially encoded proteins. A prerequisite for this process of translation are the mitoribosomes. The recent revolution in cryo-electron microscopy has generated high-resolution mitoribosome structures and has undoubtedly revealed some of the most distinctive molecular aspects of the mitoribosomes from different organisms. However, we still lack a complete understanding of the mechanistic aspects of this process and many of the factors involved in post-transcriptional gene expression in mitochondria. This review reflects on the current knowledge and illustrates some of the striking differences that have been identified between mitochondria from a range of organisms.
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González-Serrano LE, Chihade JW, Sissler M. When a common biological role does not imply common disease outcomes: Disparate pathology linked to human mitochondrial aminoacyl-tRNA synthetases. J Biol Chem 2019; 294:5309-5320. [PMID: 30647134 PMCID: PMC6462531 DOI: 10.1074/jbc.rev118.002953] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Mitochondrial aminoacyl-tRNA synthetases (mt-aaRSs) are essential components of the mitochondrial translation machinery. The correlation of mitochondrial disorders with mutations in these enzymes has raised the interest of the scientific community over the past several years. Most surprising has been the wide-ranging presentation of clinical manifestations in patients with mt-aaRS mutations, despite the enzymes' common biochemical role. Even among cases where a common physiological system is affected, phenotypes, severity, and age of onset varies depending on which mt-aaRS is mutated. Here, we review work done thus far and propose a categorization of diseases based on tissue specificity that highlights emerging patterns. We further discuss multiple in vitro and in cellulo efforts to characterize the behavior of WT and mutant mt-aaRSs that have shaped hypotheses about the molecular causes of these pathologies. Much remains to do in order to complete our understanding of these proteins. We expect that futher work is likely to result in the discovery of new roles for the mt-aaRSs in addition to their fundamental function in mitochondrial translation, informing the development of treatment strategies and diagnoses.
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Affiliation(s)
- Ligia Elena González-Serrano
- From the Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, F-67000 Strasbourg, France and
| | - Joseph W Chihade
- the Department of Chemistry, Carleton College, Northfield, Minnesota 55057
| | - Marie Sissler
- From the Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, F-67000 Strasbourg, France and
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