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Bose R, Saleem I, Mustoe AM. Causes, functions, and therapeutic possibilities of RNA secondary structure ensembles and alternative states. Cell Chem Biol 2024; 31:17-35. [PMID: 38199037 PMCID: PMC10842484 DOI: 10.1016/j.chembiol.2023.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/21/2023] [Accepted: 12/12/2023] [Indexed: 01/12/2024]
Abstract
RNA secondary structure plays essential roles in encoding RNA regulatory fate and function. Most RNAs populate ensembles of alternatively paired states and are continually unfolded and refolded by cellular processes. Measuring these structural ensembles and their contributions to cellular function has traditionally posed major challenges, but new methods and conceptual frameworks are beginning to fill this void. In this review, we provide a mechanism- and function-centric compendium of the roles of RNA secondary structural ensembles and minority states in regulating the RNA life cycle, from transcription to degradation. We further explore how dysregulation of RNA structural ensembles contributes to human disease and discuss the potential of drugging alternative RNA states to therapeutically modulate RNA activity. The emerging paradigm of RNA structural ensembles as central to RNA function provides a foundation for a deeper understanding of RNA biology and new therapeutic possibilities.
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Affiliation(s)
- Ritwika Bose
- Therapeutic Innovation Center (THINC), Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Irfana Saleem
- Therapeutic Innovation Center (THINC), Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Anthony M Mustoe
- Therapeutic Innovation Center (THINC), Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
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2
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Elkholi IE, Boulais J, Thibault MP, Phan HD, Robert A, Lai LB, Faubert D, Smith MJ, Gopalan V, Côté JF. Mapping the MOB proteins' proximity network reveals a unique interaction between human MOB3C and the RNase P complex. J Biol Chem 2023; 299:105123. [PMID: 37536630 PMCID: PMC10480535 DOI: 10.1016/j.jbc.2023.105123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 07/20/2023] [Accepted: 07/23/2023] [Indexed: 08/05/2023] Open
Abstract
Distinct functions mediated by members of the monopolar spindle-one-binder (MOB) family of proteins remain elusive beyond the evolutionarily conserved and well-established roles of MOB1 (MOB1A/B) in regulating tissue homeostasis within the Hippo pathway. Since MOB proteins are adaptors, understanding how they engage in protein-protein interactions and help assemble complexes is essential to define the full scope of their biological functions. To address this, we undertook a proximity-dependent biotin identification approach to define the interactomes of all seven human MOB proteins in HeLa and human embryonic kidney 293 cell lines. We uncovered >200 interactions, of which at least 70% are unreported on BioGrid. The generated dataset reliably recalled the bona fide interactors of the well-studied MOBs. We further defined the common and differential interactome between different MOBs on a subfamily and an individual level. We discovered a unique association between MOB3C and 7 of 10 protein subunits of the RNase P complex, an endonuclease that catalyzes tRNA 5' maturation. As a proof of principle for the robustness of the generated dataset, we validated the specific interaction of MOB3C with catalytically active RNase P by using affinity purification-mass spectrometry and pre-tRNA cleavage assays of MOB3C pulldowns. In summary, our data provide novel insights into the biology of MOB proteins and reveal the first interactors of MOB3C, components of the RNase P complex, and hence an exciting nexus with RNA biology.
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Affiliation(s)
- Islam E Elkholi
- Montreal Clinical Research Institute (IRCM), Montreal, Quebec, Canada; Molecular Biology Programs, Université de Montréal, Montreal, Quebec, Canada; Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada.
| | - Jonathan Boulais
- Montreal Clinical Research Institute (IRCM), Montreal, Quebec, Canada
| | | | - Hong-Duc Phan
- Department of Chemistry & Biochemistry, Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
| | - Amélie Robert
- Montreal Clinical Research Institute (IRCM), Montreal, Quebec, Canada
| | - Lien B Lai
- Department of Chemistry & Biochemistry, Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
| | - Denis Faubert
- Montreal Clinical Research Institute (IRCM), Montreal, Quebec, Canada
| | - Matthew J Smith
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Quebec, Canada
| | - Venkat Gopalan
- Department of Chemistry & Biochemistry, Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
| | - Jean-Franҫois Côté
- Montreal Clinical Research Institute (IRCM), Montreal, Quebec, Canada; Molecular Biology Programs, Université de Montréal, Montreal, Quebec, Canada; Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada; Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, Quebec, Canada.
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3
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Biela A, Hammermeister A, Kaczmarczyk I, Walczak M, Koziej L, Lin TY, Glatt S. The diverse structural modes of tRNA binding and recognition. J Biol Chem 2023; 299:104966. [PMID: 37380076 PMCID: PMC10424219 DOI: 10.1016/j.jbc.2023.104966] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 06/20/2023] [Accepted: 06/22/2023] [Indexed: 06/30/2023] Open
Abstract
tRNAs are short noncoding RNAs responsible for decoding mRNA codon triplets, delivering correct amino acids to the ribosome, and mediating polypeptide chain formation. Due to their key roles during translation, tRNAs have a highly conserved shape and large sets of tRNAs are present in all living organisms. Regardless of sequence variability, all tRNAs fold into a relatively rigid three-dimensional L-shaped structure. The conserved tertiary organization of canonical tRNA arises through the formation of two orthogonal helices, consisting of the acceptor and anticodon domains. Both elements fold independently to stabilize the overall structure of tRNAs through intramolecular interactions between the D- and T-arm. During tRNA maturation, different modifying enzymes posttranscriptionally attach chemical groups to specific nucleotides, which not only affect translation elongation rates but also restrict local folding processes and confer local flexibility when required. The characteristic structural features of tRNAs are also employed by various maturation factors and modification enzymes to assure the selection, recognition, and positioning of specific sites within the substrate tRNAs. The cellular functional repertoire of tRNAs continues to extend well beyond their role in translation, partly, due to the expanding pool of tRNA-derived fragments. Here, we aim to summarize the most recent developments in the field to understand how three-dimensional structure affects the canonical and noncanonical functions of tRNA.
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Affiliation(s)
- Anna Biela
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | | | - Igor Kaczmarczyk
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland; Doctoral School of Exact and Natural Sciences, Jagiellonian University, Krakow, Poland
| | - Marta Walczak
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland; Doctoral School of Exact and Natural Sciences, Jagiellonian University, Krakow, Poland
| | - Lukasz Koziej
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Ting-Yu Lin
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.
| | - Sebastian Glatt
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.
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Westhof E, Thornlow B, Chan PP, Lowe TM. Eukaryotic tRNA sequences present conserved and amino acid-specific structural signatures. Nucleic Acids Res 2022; 50:4100-4112. [PMID: 35380696 PMCID: PMC9023262 DOI: 10.1093/nar/gkac222] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 03/16/2022] [Accepted: 03/22/2022] [Indexed: 11/18/2022] Open
Abstract
Metazoan organisms have many tRNA genes responsible for decoding amino acids. The set of all tRNA genes can be grouped in sets of common amino acids and isoacceptor tRNAs that are aminoacylated by corresponding aminoacyl-tRNA synthetases. Analysis of tRNA alignments shows that, despite the high number of tRNA genes, specific tRNA sequence motifs are highly conserved across multicellular eukaryotes. The conservation often extends throughout the isoacceptors and isodecoders with, in some cases, two sets of conserved isodecoders. This study is focused on non-Watson–Crick base pairs in the helical stems, especially GoU pairs. Each of the four helical stems may contain one or more conserved GoU pairs. Some are amino acid specific and could represent identity elements for the cognate aminoacyl tRNA synthetases. Other GoU pairs are found in more than a single amino acid and could be critical for native folding of the tRNAs. Interestingly, some GoU pairs are anticodon-specific, and others are found in phylogenetically-specific clades. Although the distribution of conservation likely reflects a balance between accommodating isotype-specific functions as well as those shared by all tRNAs essential for ribosomal translation, such conservations may indicate the existence of specialized tRNAs for specific translation targets, cellular conditions, or alternative functions.
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Affiliation(s)
- Eric Westhof
- Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire, Architecture et Réactivité de l'ARN, CNRS UPR 9002, 2, allée Konrad Roentgen, F-67084 Strasbourg, France
| | - Bryan Thornlow
- Department of Biomolecular Engineering, Baskin School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA.,UCSC Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Patricia P Chan
- Department of Biomolecular Engineering, Baskin School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA.,UCSC Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Todd M Lowe
- Department of Biomolecular Engineering, Baskin School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA.,UCSC Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
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