1
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Senn KA, Hoskins AA. Mechanisms and regulation of spliceosome-mediated pre-mRNA splicing in Saccharomyces cerevisiae. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1866. [PMID: 38972853 DOI: 10.1002/wrna.1866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 05/19/2024] [Accepted: 05/28/2024] [Indexed: 07/09/2024]
Abstract
Pre-mRNA splicing, the removal of introns and ligation of flanking exons, is a crucial step in eukaryotic gene expression. The spliceosome, a macromolecular complex made up of five small nuclear RNAs (snRNAs) and dozens of proteins, assembles on introns via a complex pathway before catalyzing the two transesterification reactions necessary for splicing. All of these steps have the potential to be highly regulated to ensure correct mRNA isoform production for proper cellular function. While Saccharomyces cerevisiae (yeast) has a limited set of intron-containing genes, many of these genes are highly expressed, resulting in a large number of transcripts in a cell being spliced. As a result, splicing regulation is of critical importance for yeast. Just as in humans, yeast splicing can be influenced by protein components of the splicing machinery, structures and properties of the pre-mRNA itself, or by the action of trans-acting factors. It is likely that further analysis of the mechanisms and pathways of splicing regulation in yeast can reveal general principles applicable to other eukaryotes. This article is categorized under: RNA Processing > Splicing Mechanisms RNA Processing > Splicing Regulation/Alternative Splicing.
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Affiliation(s)
- Katherine Anne Senn
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Aaron A Hoskins
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
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2
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Higdon AL, Won NH, Brar GA. Truncated protein isoforms generate diversity of protein localization and function in yeast. Cell Syst 2024; 15:388-408.e4. [PMID: 38636458 PMCID: PMC11075746 DOI: 10.1016/j.cels.2024.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 01/21/2024] [Accepted: 03/20/2024] [Indexed: 04/20/2024]
Abstract
Genome-wide measurement of ribosome occupancy on mRNAs has enabled empirical identification of translated regions, but high-confidence detection of coding regions that overlap annotated coding regions has remained challenging. Here, we report a sensitive and robust algorithm that revealed the translation of 388 N-terminally truncated proteins in budding yeast-more than 30-fold more than previously known. We extensively experimentally validated them and defined two classes. The first class lacks large portions of the annotated protein and tends to be produced from a truncated transcript. We show that two such cases, Yap5truncation and Pus1truncation, have condition-specific regulation and distinct functions from their respective annotated isoforms. The second class of truncated protein isoforms lacks only a small region of the annotated protein and is less likely to be produced from an alternative transcript isoform. Many display different subcellular localizations than their annotated counterpart, representing a common strategy for dual localization of otherwise functionally identical proteins. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Andrea L Higdon
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Center for Computational Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Nathan H Won
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Gloria A Brar
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Center for Computational Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
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3
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Čáp M, Palková Z. Non-Coding RNAs: Regulators of Stress, Ageing, and Developmental Decisions in Yeast? Cells 2024; 13:599. [PMID: 38607038 PMCID: PMC11012152 DOI: 10.3390/cells13070599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 03/19/2024] [Accepted: 03/27/2024] [Indexed: 04/13/2024] Open
Abstract
Cells must change their properties in order to adapt to a constantly changing environment. Most of the cellular sensing and regulatory mechanisms described so far are based on proteins that serve as sensors, signal transducers, and effectors of signalling pathways, resulting in altered cell physiology. In recent years, however, remarkable examples of the critical role of non-coding RNAs in some of these regulatory pathways have been described in various organisms. In this review, we focus on all classes of non-coding RNAs that play regulatory roles during stress response, starvation, and ageing in different yeast species as well as in structured yeast populations. Such regulation can occur, for example, by modulating the amount and functional state of tRNAs, rRNAs, or snRNAs that are directly involved in the processes of translation and splicing. In addition, long non-coding RNAs and microRNA-like molecules are bona fide regulators of the expression of their target genes. Non-coding RNAs thus represent an additional level of cellular regulation that is gradually being uncovered.
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Affiliation(s)
- Michal Čáp
- Department of Genetics and Microbiology, Faculty of Science, Charles University, BIOCEV, 128 00 Prague, Czech Republic
| | - Zdena Palková
- Department of Genetics and Microbiology, Faculty of Science, Charles University, BIOCEV, 128 00 Prague, Czech Republic
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4
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Higdon AL, Won NH, Brar GA. Truncated protein isoforms generate diversity of protein localization and function in yeast. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.13.548938. [PMID: 37503254 PMCID: PMC10369987 DOI: 10.1101/2023.07.13.548938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Genome-wide measurements of ribosome occupancy on mRNA transcripts have enabled global empirical identification of translated regions. These approaches have revealed an unexpected diversity of protein products, but high-confidence identification of new coding regions that entirely overlap annotated coding regions - including those that encode truncated protein isoforms - has remained challenging. Here, we develop a sensitive and robust algorithm focused on identifying N-terminally truncated proteins genome-wide, identifying 388 truncated protein isoforms, a more than 30-fold increase in the number known in budding yeast. We perform extensive experimental validation of these truncated proteins and define two general classes. The first set lack large portions of the annotated protein sequence and tend to be produced from a truncated transcript. We show two such cases, Yap5 truncation and Pus1 truncation , to have condition-specific regulation and functions that appear distinct from their respective annotated isoforms. The second set of N-terminally truncated proteins lack only a small region of the annotated protein and are less likely to be regulated by an alternative transcript isoform. Many localize to different subcellular compartments than their annotated counterpart, representing a common strategy for achieving dual localization of otherwise functionally identical proteins.
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5
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Challakkara MF, Chhabra R. snoRNAs in hematopoiesis and blood malignancies: A comprehensive review. J Cell Physiol 2023; 238:1207-1225. [PMID: 37183323 DOI: 10.1002/jcp.31032] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 03/29/2023] [Accepted: 04/04/2023] [Indexed: 05/16/2023]
Abstract
Small nucleolar RNAs (snoRNAs) are noncoding RNA molecules of highly variable size, usually ranging from 60 to 150 nucleotides. They are classified into H/ACA box snoRNAs, C/D box snoRNAs, and scaRNAs. Their functional profile includes biogenesis of ribosomes, processing of rRNAs, 2'-O-methylation and pseudouridylation of RNAs, alternative splicing and processing of mRNAs and the generation of small RNA molecules like miRNA. The snoRNAs have been observed to have an important role in hematopoiesis and malignant hematopoietic conditions including leukemia, lymphoma, and multiple myeloma. Blood malignancies arise in immune system cells or the bone marrow due to chromosome abnormalities. It has been estimated that annually over 1.25 million cases of blood cancer occur worldwide. The snoRNAs often show a differential expression profile in blood malignancies. Recent reports associate the abnormal expression of snoRNAs with the inhibition of apoptosis, uncontrolled cell proliferation, angiogenesis, and metastasis. This implies that targeting snoRNAs could be a potential way to treat hematologic malignancies. In this review, we describe the various functions of snoRNAs, their role in hematopoiesis, and the consequences of their dysregulation in blood malignancies. We also evaluate the potential of the dysregulated snoRNAs as biomarkers and therapeutic targets for blood malignancies.
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Affiliation(s)
- Mohamed Fahad Challakkara
- Department of Biochemistry, School of Basic Sciences, Central University of Punjab, Bathinda, Punjab, India
| | - Ravindresh Chhabra
- Department of Biochemistry, School of Basic Sciences, Central University of Punjab, Bathinda, Punjab, India
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6
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Cerneckis J, Cui Q, He C, Yi C, Shi Y. Decoding pseudouridine: an emerging target for therapeutic development. Trends Pharmacol Sci 2022; 43:522-535. [DOI: 10.1016/j.tips.2022.03.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 03/12/2022] [Accepted: 03/22/2022] [Indexed: 01/18/2023]
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7
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Beneventi G, Munita R, Cao Thi Ngoc P, Madej M, Cieśla M, Muthukumar S, Krogh N, Nielsen H, Swaminathan V, Bellodi C. The small Cajal body-specific RNA 15 (SCARNA15) directs p53 and redox homeostasis via selective splicing in cancer cells. NAR Cancer 2021; 3:zcab026. [PMID: 34316713 PMCID: PMC8271217 DOI: 10.1093/narcan/zcab026] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 05/19/2021] [Accepted: 06/18/2021] [Indexed: 01/05/2023] Open
Abstract
Small Cajal body-specific RNAs (scaRNAs) guide post-transcriptional modification of spliceosomal RNA and, while commonly altered in cancer, have poorly defined roles in tumorigenesis. Here, we uncover that SCARNA15 directs alternative splicing (AS) and stress adaptation in cancer cells. Specifically, we find that SCARNA15 guides critical pseudouridylation (Ψ) of U2 spliceosomal RNA to fine-tune AS of distinct transcripts enriched for chromatin and transcriptional regulators in malignant cells. This critically impacts the expression and function of the key tumor suppressors ATRX and p53. Significantly, SCARNA15 loss impairs p53-mediated redox homeostasis and hampers cancer cell survival, motility and anchorage-independent growth. In sum, these findings highlight an unanticipated role for SCARNA15 and Ψ in directing cancer-associated splicing programs.
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Affiliation(s)
- Giulia Beneventi
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, 22184, Lund, Sweden
| | - Roberto Munita
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, 22184, Lund, Sweden
| | - Phuong Cao Thi Ngoc
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, 22184, Lund, Sweden
| | - Magdalena Madej
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, 22184, Lund, Sweden
| | - Maciej Cieśla
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, 22184, Lund, Sweden
| | - Sowndarya Muthukumar
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, 22184, Lund, Sweden
| | - Nicolai Krogh
- Department of Cellular and Molecular Medicine, The Panum Institute, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Henrik Nielsen
- Department of Cellular and Molecular Medicine, The Panum Institute, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Vinay Swaminathan
- Division of Oncology, Department of Clinical Sciences, Lund University, 22184, Lund, Sweden
| | - Cristian Bellodi
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, 22184, Lund, Sweden
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8
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Morais P, Adachi H, Yu YT. Spliceosomal snRNA Epitranscriptomics. Front Genet 2021; 12:652129. [PMID: 33737950 PMCID: PMC7960923 DOI: 10.3389/fgene.2021.652129] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 02/08/2021] [Indexed: 12/15/2022] Open
Abstract
Small nuclear RNAs (snRNAs) are critical components of the spliceosome that catalyze the splicing of pre-mRNA. snRNAs are each complexed with many proteins to form RNA-protein complexes, termed as small nuclear ribonucleoproteins (snRNPs), in the cell nucleus. snRNPs participate in pre-mRNA splicing by recognizing the critical sequence elements present in the introns, thereby forming active spliceosomes. The recognition is achieved primarily by base-pairing interactions (or nucleotide-nucleotide contact) between snRNAs and pre-mRNA. Notably, snRNAs are extensively modified with different RNA modifications, which confer unique properties to the RNAs. Here, we review the current knowledge of the mechanisms and functions of snRNA modifications and their biological relevance in the splicing process.
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Affiliation(s)
| | - Hironori Adachi
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester Medical Center, Rochester, NY, United States
| | - Yi-Tao Yu
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester Medical Center, Rochester, NY, United States
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9
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Borchardt EK, Martinez NM, Gilbert WV. Regulation and Function of RNA Pseudouridylation in Human Cells. Annu Rev Genet 2020; 54:309-336. [PMID: 32870730 DOI: 10.1146/annurev-genet-112618-043830] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Recent advances in pseudouridine detection reveal a complex pseudouridine landscape that includes messenger RNA and diverse classes of noncoding RNA in human cells. The known molecular functions of pseudouridine, which include stabilizing RNA conformations and destabilizing interactions with varied RNA-binding proteins, suggest that RNA pseudouridylation could have widespread effects on RNA metabolism and gene expression. Here, we emphasize how much remains to be learned about the RNA targets of human pseudouridine synthases, their basis for recognizing distinct RNA sequences, and the mechanisms responsible for regulated RNA pseudouridylation. We also examine the roles of noncoding RNA pseudouridylation in splicing and translation and point out the potential effects of mRNA pseudouridylation on protein production, including in the context of therapeutic mRNAs.
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Affiliation(s)
- Erin K Borchardt
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, Yale University, New Haven, Connecticut 06520, USA; , ,
| | - Nicole M Martinez
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, Yale University, New Haven, Connecticut 06520, USA; , ,
| | - Wendy V Gilbert
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, Yale University, New Haven, Connecticut 06520, USA; , ,
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10
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Cooperative Analysis of Structural Dynamics in RNA-Protein Complexes by Single-Molecule Förster Resonance Energy Transfer Spectroscopy. Molecules 2020; 25:molecules25092057. [PMID: 32354083 PMCID: PMC7248720 DOI: 10.3390/molecules25092057] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 03/31/2020] [Accepted: 04/13/2020] [Indexed: 12/24/2022] Open
Abstract
RNA-protein complexes (RNPs) are essential components in a variety of cellular processes, and oftentimes exhibit complex structures and show mechanisms that are highly dynamic in conformation and structure. However, biochemical and structural biology approaches are mostly not able to fully elucidate the structurally and especially conformationally dynamic and heterogeneous nature of these RNPs, to which end single molecule Förster resonance energy transfer (smFRET) spectroscopy can be harnessed to fill this gap. Here we summarize the advantages of strategic smFRET studies to investigate RNP dynamics, complemented by structural and biochemical data. Focusing on recent smFRET studies of three essential biological systems, we demonstrate that investigation of RNPs on a single molecule level can answer important functional questions that remained elusive with structural or biochemical approaches alone: The complex structural rearrangements throughout the splicing cycle, unwinding dynamics of the G-quadruplex (G4) helicase RHAU, and aspects in telomere maintenance regulation and synthesis.
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11
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van der Feltz C, Hoskins AA. Structural and functional modularity of the U2 snRNP in pre-mRNA splicing. Crit Rev Biochem Mol Biol 2019; 54:443-465. [PMID: 31744343 DOI: 10.1080/10409238.2019.1691497] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The U2 small nuclear ribonucleoprotein (snRNP) is an essential component of the spliceosome, the cellular machine responsible for removing introns from precursor mRNAs (pre-mRNAs) in all eukaryotes. U2 is an extraordinarily dynamic splicing factor and the most frequently mutated in cancers. Cryo-electron microscopy (cryo-EM) has transformed our structural and functional understanding of the role of U2 in splicing. In this review, we synthesize these and other data with respect to a view of U2 as an assembly of interconnected functional modules. These modules are organized by the U2 small nuclear RNA (snRNA) for roles in spliceosome assembly, intron substrate recognition, and protein scaffolding. We describe new discoveries regarding the structure of U2 components and how the snRNP undergoes numerous conformational and compositional changes during splicing. We specifically highlight large scale movements of U2 modules as the spliceosome creates and rearranges its active site. U2 serves as a compelling example for how cellular machines can exploit the modular organization and structural plasticity of an RNP.
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Affiliation(s)
| | - Aaron A Hoskins
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
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12
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Bakshi A, Moin M, Madhav MS, Kirti PB. Target of rapamycin, a master regulator of multiple signalling pathways and a potential candidate gene for crop improvement. PLANT BIOLOGY (STUTTGART, GERMANY) 2019; 21:190-205. [PMID: 30411830 DOI: 10.1111/plb.12935] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 11/05/2018] [Indexed: 06/08/2023]
Abstract
The target of rapamycin (TOR) protein regulates growth and development in photosynthetic and non-photosynthetic eukaryotes. Although the TOR regulatory networks are involved in nutrient and energy signalling, and transcriptional and translational control of multiple signalling pathways, the molecular mechanism of TOR regulation of plant abiotic stress responses is still unclear. The TOR-mediated transcriptional regulation of genes encoding ribosomal proteins (RP) is a necessity under stress conditions for balanced growth and productivity in plants. The activation of SnRKs (sucrose non-fermenting-related kinases) and the inactivation of TOR signalling in abiotic stresses is in line with the accumulation of ABA and transcriptional activation of stress responsive genes. Autophagy is induced under abiotic stress conditions, which results in degradation of proteins and the release of amino acids, which might possibly induce phosphorylation of TOR and, hence, its activation. TOR signalling also has a role in regulating ABA biosynthesis for transcriptional regulation of stress-related genes. The switch between activation and inactivation of TOR by its phosphorylation and de-phosphorylation maintains balanced growth in response to stresses. In the present review, we discuss the important signalling pathways that are regulated by TOR and try to assess the relationship between TOR signalling and tolerance to abiotic stresses in plants. The review also discusses possible cross-talk between TOR and RP genes in response to abiotic stresses.
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Affiliation(s)
- A Bakshi
- Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - M Moin
- Department of Biotechnology, Indian Institute of Rice Research, Hyderabad, India
| | - M S Madhav
- Department of Biotechnology, Indian Institute of Rice Research, Hyderabad, India
| | - P B Kirti
- Department of Plant Sciences, University of Hyderabad, Hyderabad, India
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13
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Adachi H, De Zoysa MD, Yu YT. Post-transcriptional pseudouridylation in mRNA as well as in some major types of noncoding RNAs. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1862:230-239. [PMID: 30414851 DOI: 10.1016/j.bbagrm.2018.11.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 10/29/2018] [Accepted: 11/02/2018] [Indexed: 01/13/2023]
Abstract
Pseudouridylation is a post-transcriptional isomerization reaction that converts a uridine to a pseudouridine (Ψ) within an RNA chain. Ψ has chemical properties that are distinct from that of uridine and any other known nucleotides. Experimental data accumulated thus far have indicated that Ψ is present in many different types of RNAs, including coding and noncoding RNAs. Ψ is particularly concentrated in rRNA and spliceosomal snRNAs, and plays an important role in protein translation and pre-mRNA splicing, respectively. Ψ has also been found in mRNA, but its function there remains essentially unknown. In this review, we discuss the mechanisms and functions of RNA pseudouridylation, focusing on rRNA, snRNA and mRNA. We also discuss the methods, which have been developed to detect Ψs in RNAs. This article is part of a Special Issue entitled: mRNA modifications in gene expression control edited by Dr. Soller Matthias and Dr. Fray Rupert.
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Affiliation(s)
- Hironori Adachi
- University of Rochester Medical Center, Department of Biochemistry and Biophysics, Center for RNA Biology, 601 Elmwood Avenue, Rochester, NY 14642, USA
| | - Meemanage D De Zoysa
- University of Rochester Medical Center, Department of Biochemistry and Biophysics, Center for RNA Biology, 601 Elmwood Avenue, Rochester, NY 14642, USA
| | - Yi-Tao Yu
- University of Rochester Medical Center, Department of Biochemistry and Biophysics, Center for RNA Biology, 601 Elmwood Avenue, Rochester, NY 14642, USA.
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14
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Cao L, Weetall M, Trotta C, Cintron K, Ma J, Kim MJ, Furia B, Romfo C, Graci JD, Li W, Du J, Sheedy J, Hedrick J, Risher N, Yeh S, Qi H, Arasu T, Hwang S, Lennox W, Kong R, Petruska J, Moon YC, Babiak J, Davis TW, Jacobson A, Almstead NG, Branstrom A, Colacino JM, Peltz SW. Targeting of Hematologic Malignancies with PTC299, A Novel Potent Inhibitor of Dihydroorotate Dehydrogenase with Favorable Pharmaceutical Properties. Mol Cancer Ther 2018; 18:3-16. [PMID: 30352802 DOI: 10.1158/1535-7163.mct-18-0863] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 08/22/2018] [Accepted: 10/17/2018] [Indexed: 01/09/2023]
Abstract
PTC299 was identified as an inhibitor of VEGFA mRNA translation in a phenotypic screen and evaluated in the clinic for treatment of solid tumors. To guide precision cancer treatment, we performed extensive biological characterization of the activity of PTC299 and demonstrated that inhibition of VEGF production and cell proliferation by PTC299 is linked to a decrease in uridine nucleotides by targeting dihydroorotate dehydrogenase (DHODH), a rate-limiting enzyme for de novo pyrimidine nucleotide synthesis. Unlike previously reported DHODH inhibitors that were identified using in vitro enzyme assays, PTC299 is a more potent inhibitor of DHODH in isolated mitochondria suggesting that mitochondrial membrane lipid engagement in the DHODH conformation in situ is required for its optimal activity. PTC299 has broad and potent activity against hematologic cancer cells in preclinical models, reflecting a reduced pyrimidine nucleotide salvage pathway in leukemia cells. Archived serum samples from patients treated with PTC299 demonstrated increased levels of dihydroorotate, the substrate of DHODH, indicating target engagement in patients. PTC299 has advantages over previously reported DHODH inhibitors, including greater potency, good oral bioavailability, and lack of off-target kinase inhibition and myelosuppression, and thus may be useful for the targeted treatment of hematologic malignancies.
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Affiliation(s)
- Liangxian Cao
- PTC Therapeutics, Inc., South Plainfield, New Jersey.
| | - Marla Weetall
- PTC Therapeutics, Inc., South Plainfield, New Jersey
| | | | | | - Jiyuan Ma
- PTC Therapeutics, Inc., South Plainfield, New Jersey
| | - Min Jung Kim
- PTC Therapeutics, Inc., South Plainfield, New Jersey
| | - Bansri Furia
- PTC Therapeutics, Inc., South Plainfield, New Jersey
| | - Charles Romfo
- PTC Therapeutics, Inc., South Plainfield, New Jersey
| | - Jason D Graci
- PTC Therapeutics, Inc., South Plainfield, New Jersey
| | - Wencheng Li
- PTC Therapeutics, Inc., South Plainfield, New Jersey
| | - Joshua Du
- PTC Therapeutics, Inc., South Plainfield, New Jersey
| | | | - Jean Hedrick
- PTC Therapeutics, Inc., South Plainfield, New Jersey
| | - Nicole Risher
- PTC Therapeutics, Inc., South Plainfield, New Jersey
| | - Shirley Yeh
- PTC Therapeutics, Inc., South Plainfield, New Jersey
| | - Hongyan Qi
- PTC Therapeutics, Inc., South Plainfield, New Jersey
| | - Tamil Arasu
- PTC Therapeutics, Inc., South Plainfield, New Jersey
| | | | | | - Ronald Kong
- PTC Therapeutics, Inc., South Plainfield, New Jersey
| | | | | | - John Babiak
- PTC Therapeutics, Inc., South Plainfield, New Jersey
| | | | - Allan Jacobson
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts
| | | | - Art Branstrom
- PTC Therapeutics, Inc., South Plainfield, New Jersey
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15
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Zhao Y, Dunker W, Yu YT, Karijolich J. The Role of Noncoding RNA Pseudouridylation in Nuclear Gene Expression Events. Front Bioeng Biotechnol 2018; 6:8. [PMID: 29473035 PMCID: PMC5809436 DOI: 10.3389/fbioe.2018.00008] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 01/22/2018] [Indexed: 12/23/2022] Open
Abstract
Pseudouridine is the most abundant internal RNA modification in stable noncoding RNAs (ncRNAs). It can be catalyzed by both RNA-dependent and RNA-independent mechanisms. Pseudouridylation impacts both the biochemical and biophysical properties of RNAs and thus influences RNA-mediated cellular processes. The investigation of nuclear-ncRNA pseudouridylation has demonstrated that it is critical for the proper control of multiple stages of gene expression regulation. Here, we review how nuclear-ncRNA pseudouridylation contributes to transcriptional regulation and pre-mRNA splicing.
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Affiliation(s)
- Yang Zhao
- Department of Pathology, Microbiology, and Immunology, School of Medicine, Vanderbilt University, Nashville, TN, United States
| | - William Dunker
- Department of Pathology, Microbiology, and Immunology, School of Medicine, Vanderbilt University, Nashville, TN, United States
| | - Yi-Tao Yu
- Department of Biochemistry and Biophysics, Center for RNA Biology, School of Medicine and Dentistry, University of Rochester, Rochester, NY, United States
| | - John Karijolich
- Department of Pathology, Microbiology, and Immunology, School of Medicine, Vanderbilt University, Nashville, TN, United States.,Vanderbilt-Ingram Cancer Center, Nashville, TN, United States
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16
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van der Feltz C, DeHaven AC, Hoskins AA. Stress-induced Pseudouridylation Alters the Structural Equilibrium of Yeast U2 snRNA Stem II. J Mol Biol 2017; 430:524-536. [PMID: 29079482 DOI: 10.1016/j.jmb.2017.10.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 10/09/2017] [Accepted: 10/14/2017] [Indexed: 12/21/2022]
Abstract
In yeast, the U2 small nuclear ribonucleic acid (snRNA) component of the spliceosome is targeted for additional post-transcriptional modifications in response to cellular stress. Uridines 56 and 93 are both modified to pseudouridines (Ψ) during nutrient deprivation, while U56 is also pseudouridylated during heat shock. Both positions are located within stem II, which must toggle between two mutually exclusive structures during splicing. Stem IIa forms during spliceosome assembly, and stem IIc forms during the catalytic steps. We have studied how uridine 56 and 93 pseudouridylation impacts conformational switching of stem II. Using single-molecule Förster resonance energy transfer, we show that Ψ56 dampens conformational dynamics of stem II and stabilizes stem IIc. In contrast, Ψ93 increases dynamics of non-stem IIc conformations. Pseudouridylation impacts conformational switching of stem II by Mg2+ or the U2 protein Cus2; however, when Mg2+ and Cus2 are used in combination, the impacts of pseudouridylation can be suppressed. These results show that stress-induced post-transcriptional modification of U56 and U93 alters snRNA conformational dynamics by distinct mechanisms and that protein and metal cofactors of the spliceosome alter how snRNAs respond to these modifications.
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Affiliation(s)
- Clarisse van der Feltz
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Dr., Madison, WI 53706, USA
| | - Alexander C DeHaven
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Dr., Madison, WI 53706, USA
| | - Aaron A Hoskins
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Dr., Madison, WI 53706, USA.
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17
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van Delft P, Akay A, Huber SM, Bueschl C, Rudolph KLM, Di Domenico T, Schuhmacher R, Miska EA, Balasubramanian S. The Profile and Dynamics of RNA Modifications in Animals. Chembiochem 2017; 18:979-984. [PMID: 28449301 PMCID: PMC5784800 DOI: 10.1002/cbic.201700093] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Indexed: 12/28/2022]
Abstract
More than a hundred distinct modified nucleosides have been identified in RNA, but little is known about their distribution across different organisms, their dynamic nature and their response to cellular and environmental stress. Mass-spectrometry-based methods have been at the forefront of identifying and quantifying modified nucleosides. However, they often require synthetic reference standards, which do not exist in the case of many modified nucleosides, and this therefore impedes their analysis. Here we use a metabolic labelling approach to achieve rapid generation of bio-isotopologues of the complete Caenorhabditis elegans transcriptome and its modifications and use them as reference standards to characterise the RNA modification profile in this multicellular organism through an untargeted liquid-chromatography tandem high-resolution mass spectrometry (LC-HRMS) approach. We furthermore show that several of these RNA modifications have a dynamic response to environmental stress and that, in particular, changes in the tRNA wobble base modification 5-methoxycarbonylmethyl-2-thiouridine (mcm5 s2 U) lead to codon-biased gene-expression changes in starved animals.
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Affiliation(s)
- Pieter van Delft
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
| | - Alper Akay
- Gurdon InstituteUniversity of CambridgeTennis Court RoadCambridgeCB2 1QNUK
- Department of GeneticsUniversity of CambridgeDowning StreetCambridgeCB2 3EHUK
| | - Sabrina M. Huber
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
| | - Christoph Bueschl
- Center for Analytical ChemistryDepartment of AgrobiotechnologyUniversity of Natural Resources and Life SciencesViennaKonrad-Lorenz-Strasse 203430Tulln an der DonauAustria
| | - Konrad L. M. Rudolph
- Gurdon InstituteUniversity of CambridgeTennis Court RoadCambridgeCB2 1QNUK
- Department of GeneticsUniversity of CambridgeDowning StreetCambridgeCB2 3EHUK
- Wellcome Trust Sanger InstituteWellcome Trust Genome CampusCambridgeCB10 1SAUK
| | - Tomás Di Domenico
- Gurdon InstituteUniversity of CambridgeTennis Court RoadCambridgeCB2 1QNUK
- Department of GeneticsUniversity of CambridgeDowning StreetCambridgeCB2 3EHUK
- Wellcome Trust Sanger InstituteWellcome Trust Genome CampusCambridgeCB10 1SAUK
| | - Rainer Schuhmacher
- Center for Analytical ChemistryDepartment of AgrobiotechnologyUniversity of Natural Resources and Life SciencesViennaKonrad-Lorenz-Strasse 203430Tulln an der DonauAustria
| | - Eric A. Miska
- Gurdon InstituteUniversity of CambridgeTennis Court RoadCambridgeCB2 1QNUK
- Department of GeneticsUniversity of CambridgeDowning StreetCambridgeCB2 3EHUK
- Wellcome Trust Sanger InstituteWellcome Trust Genome CampusCambridgeCB10 1SAUK
| | - Shankar Balasubramanian
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
- Cancer Research UK Cambridge InstituteUniversity of CambridgeRobinson WayCambridgeCB2 0REUK
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18
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Rintala-Dempsey AC, Kothe U. Eukaryotic stand-alone pseudouridine synthases - RNA modifying enzymes and emerging regulators of gene expression? RNA Biol 2017; 14:1185-1196. [PMID: 28045575 PMCID: PMC5699540 DOI: 10.1080/15476286.2016.1276150] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
For a long time, eukaryotic stand-alone pseudouridine synthases (Pus enzymes) were neglected as non-essential enzymes adding seemingly simple modifications to tRNAs and small nuclear RNAs. Most studies were limited to the identification and initial characterization of the yeast Pus enzymes. However, recent transcriptome-wide mapping of pseudouridines in yeast and humans revealed pervasive modification of mRNAs and other non-coding RNAs by Pus enzymes which is dynamically regulated in response to cellular stress. Moreover, mutations in at least 2 genes encoding human Pus enzymes cause inherited diseases affecting muscle and brain function. Together, the recent findings suggest a broader-than-anticipated role of the Pus enzymes which are emerging as potential regulators of gene expression. In this review, we summarize the current knowledge on Pus enzymes, generate hypotheses regarding their cellular function and outline future areas of research of pseudouridine synthases.
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Affiliation(s)
- Anne C Rintala-Dempsey
- a Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry , University of Lethbridge , Lethbridge , AB , Canada
| | - Ute Kothe
- a Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry , University of Lethbridge , Lethbridge , AB , Canada
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