1
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Schultz SK, Katanski CD, Halucha M, Peña N, Fahlman RP, Pan T, Kothe U. Modifications in the T arm of tRNA globally determine tRNA maturation, function, and cellular fitness. Proc Natl Acad Sci U S A 2024; 121:e2401154121. [PMID: 38889150 DOI: 10.1073/pnas.2401154121] [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: 01/18/2024] [Accepted: 05/22/2024] [Indexed: 06/20/2024] Open
Abstract
Almost all elongator tRNAs (Transfer RNAs) harbor 5-methyluridine 54 and pseudouridine 55 in the T arm, generated by the enzymes TrmA and TruB, respectively, in Escherichia coli. TrmA and TruB both act as tRNA chaperones, and strains lacking trmA or truB are outcompeted by wild type. Here, we investigate how TrmA and TruB contribute to cellular fitness. Deletion of trmA and truB in E. coli causes a global decrease in aminoacylation and alters other tRNA modifications such as acp3U47. While overall protein synthesis is not affected in ΔtrmA and ΔtruB strains, the translation of a subset of codons is significantly impaired. As a consequence, we observe translationally reduced expression of many specific proteins, that are either encoded with a high frequency of these codons or that are large proteins. The resulting proteome changes are not related to a specific growth phenotype, but overall cellular fitness is impaired upon deleting trmA and truB in accordance with a general protein synthesis impact. In conclusion, we demonstrate that universal modifications of the tRNA T arm are critical for global tRNA function by enhancing tRNA maturation, tRNA aminoacylation, and translation, thereby improving cellular fitness irrespective of the growth conditions which explains the conservation of trmA and truB.
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Affiliation(s)
- Sarah K Schultz
- Department of Chemistry, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
| | - Christopher D Katanski
- Department of Biochemistry & Molecular Biology, University of Chicago, Chicago, IL 60637
| | - Mateusz Halucha
- Department of Biochemistry & Molecular Biology, University of Chicago, Chicago, IL 60637
| | - Noah Peña
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637
| | - Richard P Fahlman
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Tao Pan
- Department of Biochemistry & Molecular Biology, University of Chicago, Chicago, IL 60637
| | - Ute Kothe
- Department of Chemistry, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
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2
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Yared MJ, Marcelot A, Barraud P. Beyond the Anticodon: tRNA Core Modifications and Their Impact on Structure, Translation and Stress Adaptation. Genes (Basel) 2024; 15:374. [PMID: 38540433 PMCID: PMC10969862 DOI: 10.3390/genes15030374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 06/14/2024] Open
Abstract
Transfer RNAs (tRNAs) are heavily decorated with post-transcriptional chemical modifications. Approximately 100 different modifications have been identified in tRNAs, and each tRNA typically contains 5-15 modifications that are incorporated at specific sites along the tRNA sequence. These modifications may be classified into two groups according to their position in the three-dimensional tRNA structure, i.e., modifications in the tRNA core and modifications in the anticodon-loop (ACL) region. Since many modified nucleotides in the tRNA core are involved in the formation of tertiary interactions implicated in tRNA folding, these modifications are key to tRNA stability and resistance to RNA decay pathways. In comparison to the extensively studied ACL modifications, tRNA core modifications have generally received less attention, although they have been shown to play important roles beyond tRNA stability. Here, we review and place in perspective selected data on tRNA core modifications. We present their impact on tRNA structure and stability and report how these changes manifest themselves at the functional level in translation, fitness and stress adaptation.
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Affiliation(s)
| | | | - Pierre Barraud
- Expression Génétique Microbienne, Université Paris Cité, CNRS, Institut de Biologie Physico-Chimique, F-75005 Paris, France; (M.-J.Y.); (A.M.)
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3
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Chen H, Zhao S. Research progress of RNA pseudouridine modification in nervous system. Int J Neurosci 2024:1-11. [PMID: 38407188 DOI: 10.1080/00207454.2024.2315483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 02/02/2024] [Indexed: 02/27/2024]
Abstract
Recent advances of pseudouridine (Ψ, 5-ribosyluracil) modification highlight its crucial role as a post-transcriptional regulator in gene expression and its impact on various RNA processes. Ψ synthase (PUS), a category of RNA-modifying enzymes, orchestrates the pseudouridylation reaction. It can specifically recognize conserved sequences or structural motifs within substrates, thereby regulating the biological function of various RNA molecules accurately. Our comprehensive review underscored the close association of PUS1, PUS3, PUS7, PUS10, and dyskerin PUS1 with various nervous system disorders, including neurodevelopmental disorders, nervous system tumors, mitochondrial myopathy, lactic acidosis and sideroblastic anaemia (MLASA) syndrome, peripheral nervous system disorders, and type II myotonic dystrophy. In light of these findings, this study elucidated how Ψ strengthened RNA structures and contributed to RNA function, thereby providing valuable insights into the intricate molecular mechanisms underlying nervous system diseases. However, the detailed effects and mechanisms of PUS on neuron remain elusive. This lack of mechanistic understanding poses a substantial obstacle to the development of therapeutic approaches for various neurological disorders based on Ψ modification.
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Affiliation(s)
- Hui Chen
- School of Basic Medical Sciences, Youjiang Medical University for Nationalities, Baise, Guangxi, China
| | - Shuang Zhao
- School of Basic Medical Sciences, Youjiang Medical University for Nationalities, Baise, Guangxi, China
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4
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Dhingra Y, Gupta S, Gupta V, Agarwal M, Katiyar-Agarwal S. The emerging role of epitranscriptome in shaping stress responses in plants. PLANT CELL REPORTS 2023; 42:1531-1555. [PMID: 37481775 DOI: 10.1007/s00299-023-03046-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 07/03/2023] [Indexed: 07/25/2023]
Abstract
KEY MESSAGE RNA modifications and editing changes constitute 'epitranscriptome' and are crucial in regulating the development and stress response in plants. Exploration of the epitranscriptome and associated machinery would facilitate the engineering of stress tolerance in crops. RNA editing and modifications post-transcriptionally decorate almost all classes of cellular RNAs, including tRNAs, rRNAs, snRNAs, lncRNAs and mRNAs, with more than 170 known modifications, among which m6A, Ψ, m5C, 8-OHG and C-to-U editing are the most abundant. Together, these modifications constitute the "epitranscriptome", and contribute to changes in several RNA attributes, thus providing an additional structural and functional diversification to the "cellular messages" and adding another layer of gene regulation in organisms, including plants. Numerous evidences suggest that RNA modifications have a widespread impact on plant development as well as in regulating the response of plants to abiotic and biotic stresses. High-throughput sequencing studies demonstrate that the landscapes of m6A, m5C, Am, Cm, C-to-U, U-to-G, and A-to-I editing are remarkably dynamic during stress conditions in plants. GO analysis of transcripts enriched in Ψ, m6A and m5C modifications have identified bonafide components of stress regulatory pathways. Furthermore, significant alterations in the expression pattern of genes encoding writers, readers, and erasers of certain modifications have been documented when plants are grown in challenging environments. Notably, manipulating the expression levels of a few components of RNA editing machinery markedly influenced the stress tolerance in plants. We provide updated information on the current understanding on the contribution of RNA modifications in shaping the stress responses in plants. Unraveling of the epitranscriptome has opened new avenues for designing crops with enhanced productivity and stress resilience in view of global climate change.
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Affiliation(s)
- Yashika Dhingra
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Shitij Gupta
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, Bern, Switzerland
| | - Vaishali Gupta
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Manu Agarwal
- Department of Botany, University of Delhi North Campus, Delhi, 110007, India
| | - Surekha Katiyar-Agarwal
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India.
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5
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Schultz SK, Kothe U. Fluorescent labeling of tRNA for rapid kinetic interaction studies with tRNA-binding proteins. Methods Enzymol 2023; 692:103-126. [PMID: 37925176 DOI: 10.1016/bs.mie.2023.05.007] [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] [Indexed: 11/06/2023]
Abstract
Transfer RNA (tRNA) plays a critical role during translation and interacts with numerous proteins during its biogenesis, functional cycle and degradation. In particular, tRNA is extensively post-transcriptionally modified by various tRNA modifying enzymes which each target a specific nucleotide at different positions within tRNAs to introduce different chemical modifications. Fluorescent assays can be used to study the interaction between a protein and tRNA. Moreover, rapid mixing fluorescence stopped-flow assays provide insights into the kinetics of the tRNA-protein interaction in order to elucidate the tRNA binding mechanism for the given protein. A prerequisite for these studies is a fluorescently labeled molecule, such as fluorescent tRNA, wherein a change in fluorescence occurs upon protein binding. In this chapter, we discuss the utilization of tRNA modifications in order to introduce fluorophores at particular positions within tRNAs. Particularly, we focus on in vitro thiolation of a uridine at position 8 within tRNAs using the tRNA modification enzyme ThiI, followed by labeling of the thiol group with fluorescein. As such, this fluorescently labeled tRNA is primarily unmodified, with the exception of the thiolation modification to which the fluorophore is attached, and can be used as a substrate to study the binding of different tRNA-interacting factors. Herein, we discuss the example of studying the tRNA binding mechanism of the tRNA modifying enzymes TrmB and DusA using internally fluorescein-labeled tRNA.
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Affiliation(s)
- Sarah K Schultz
- Alberta RNA Research and Training Institute (ARRTI), Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, Canada; Department of Chemistry, University of Manitoba, Winnipeg, MB, Canada
| | - Ute Kothe
- Alberta RNA Research and Training Institute (ARRTI), Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, Canada; Department of Chemistry, University of Manitoba, Winnipeg, MB, Canada.
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6
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Jürgenstein K, Tagel M, Ilves H, Leppik M, Kivisaar M, Remme J. Variance in translational fidelity of different bacterial species is affected by pseudouridines in the tRNA anticodon stem-loop. RNA Biol 2022; 19:1050-1058. [PMID: 36093925 PMCID: PMC9481147 DOI: 10.1080/15476286.2022.2121447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Delicate variances in the translational machinery affect how efficiently different organisms approach protein synthesis. Determining the scale of this effect, however, requires knowledge on the differences of mistranslation levels. Here, we used a dual-luciferase reporter assay cloned into a broad host range plasmid to reveal the translational fidelity profiles of Pseudomonas putida, Pseudomonas aeruginosa and Escherichia coli. We observed that these profiles are surprisingly different, whereas species more prone to translational frameshifting are not necessarily more prone to stop codon readthrough. As tRNA modifications are among the factors that have been implicated to affect translation accuracy, we also show that translational fidelity is context-specifically influenced by pseudouridines in the anticodon stem-loop of tRNA, but the effect is not uniform between species.
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Affiliation(s)
- Karl Jürgenstein
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Mari Tagel
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Heili Ilves
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Margus Leppik
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Maia Kivisaar
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Jaanus Remme
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
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7
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Lahry K, Gopal A, Kumar Sahu A, Nora Marbaniang C, Ahmad Shah R, Mehta A, Varshney U. An alternative role of RluD in the fidelity of translation initiation in Escherichia coli. J Mol Biol 2022; 434:167588. [DOI: 10.1016/j.jmb.2022.167588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/21/2022] [Accepted: 04/10/2022] [Indexed: 10/18/2022]
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8
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Genome-Wide Identification and Expression Analysis of Pseudouridine Synthase Family in Arabidopsis and Maize. Int J Mol Sci 2022; 23:ijms23052680. [PMID: 35269820 PMCID: PMC8910892 DOI: 10.3390/ijms23052680] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 02/25/2022] [Accepted: 02/25/2022] [Indexed: 02/04/2023] Open
Abstract
Pseudouridine (Ψ), the isomer of uridine (U), is the most abundant type of RNA modification, which is crucial for gene regulation in various cellular processes. Pseudouridine synthases (PUSs) are the key enzymes for the U-to-Ψ conversion. However, little is known about the genome-wide features and biological function of plant PUSs. In this study, we identified 20 AtPUSs and 22 ZmPUSs from Arabidopsis and maize (Zea mays), respectively. Our phylogenetic analysis indicated that both AtPUSs and ZmPUSs could be clustered into six known subfamilies: RluA, RsuA, TruA, TruB, PUS10, and TruD. RluA subfamily is the largest subfamily in both Arabidopsis and maize. It's noteworthy that except the canonical XXHRLD-type RluAs, another three conserved RluA variants, including XXNRLD-, XXHQID-, and XXHRLG-type were also identified in those key nodes of vascular plants. Subcellular localization analysis of representative AtPUSs and ZmPUSs in each subfamily revealed that PUS proteins were localized in different organelles including nucleus, cytoplasm and chloroplasts. Transcriptional expression analysis indicated that AtPUSs and ZmPUSs were differentially expressed in various tissues and diversely responsive to abiotic stresses, especially suggesting their potential roles in response to heat and salt stresses. All these results would facilitate the functional identification of these pseudouridylation in the future.
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9
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Purchal MK, Eyler DE, Tardu M, Franco MK, Korn MM, Khan T, McNassor R, Giles R, Lev K, Sharma H, Monroe J, Mallik L, Koutmos M, Koutmou KS. Pseudouridine synthase 7 is an opportunistic enzyme that binds and modifies substrates with diverse sequences and structures. Proc Natl Acad Sci U S A 2022; 119:e2109708119. [PMID: 35058356 PMCID: PMC8794802 DOI: 10.1073/pnas.2109708119] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 11/17/2021] [Indexed: 12/13/2022] Open
Abstract
Pseudouridine (Ψ) is a ubiquitous RNA modification incorporated by pseudouridine synthase (Pus) enzymes into hundreds of noncoding and protein-coding RNA substrates. Here, we determined the contributions of substrate structure and protein sequence to binding and catalysis by pseudouridine synthase 7 (Pus7), one of the principal messenger RNA (mRNA) modifying enzymes. Pus7 is distinct among the eukaryotic Pus proteins because it modifies a wider variety of substrates and shares limited homology with other Pus family members. We solved the crystal structure of Saccharomyces cerevisiae Pus7, detailing the architecture of the eukaryotic-specific insertions thought to be responsible for the expanded substrate scope of Pus7. Additionally, we identified an insertion domain in the protein that fine-tunes Pus7 activity both in vitro and in cells. These data demonstrate that Pus7 preferentially binds substrates possessing the previously identified UGUAR (R = purine) consensus sequence and that RNA secondary structure is not a strong requirement for Pus7-binding. In contrast, the rate constants and extent of Ψ incorporation are more influenced by RNA structure, with Pus7 modifying UGUAR sequences in less-structured contexts more efficiently both in vitro and in cells. Although less-structured substrates were preferred, Pus7 fully modified every transfer RNA, mRNA, and nonnatural RNA containing the consensus recognition sequence that we tested. Our findings suggest that Pus7 is a promiscuous enzyme and lead us to propose that factors beyond inherent enzyme properties (e.g., enzyme localization, RNA structure, and competition with other RNA-binding proteins) largely dictate Pus7 substrate selection.
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Affiliation(s)
- Meredith K Purchal
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109
| | - Daniel E Eyler
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109
| | - Mehmet Tardu
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109
| | - Monika K Franco
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109
| | - Megan M Korn
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109
| | - Taslima Khan
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109
| | - Ryan McNassor
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109
| | - Rachel Giles
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109
| | - Katherine Lev
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109
| | - Hari Sharma
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109
| | - Jeremy Monroe
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109
| | - Leena Mallik
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48109
| | - Markos Koutmos
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109;
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48109
| | - Kristin S Koutmou
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109;
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109
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10
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Garus A, Autexier C. Dyskerin: an essential pseudouridine synthase with multifaceted roles in ribosome biogenesis, splicing, and telomere maintenance. RNA (NEW YORK, N.Y.) 2021; 27:1441-1458. [PMID: 34556550 PMCID: PMC8594475 DOI: 10.1261/rna.078953.121] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Dyskerin and its homologs are ancient and conserved enzymes that catalyze the most common post-transcriptional modification found in cells, pseudouridylation. The resulting pseudouridines provide stability to RNA molecules and regulate ribosome biogenesis and splicing events. Dyskerin does not act independently-it is the core component of a protein heterotetramer, which associates with RNAs that contain the H/ACA motif. The variety of H/ACA RNAs that guide the function of this ribonucleoprotein (RNP) complex highlights the diversity of cellular processes in which dyskerin participates. When associated with small nucleolar (sno) RNAs, it regulates ribosomal (r) RNAs and ribosome biogenesis. By interacting with small Cajal body (sca) RNAs, it targets small nuclear (sn) RNAs to regulate pre-mRNA splicing. As a component of the telomerase holoenzyme, dyskerin binds to the telomerase RNA to modulate telomere maintenance. In a disease context, dyskerin malfunction can result in multiple detrimental phenotypes. Mutations in DKC1, the gene that encodes dyskerin, cause the premature aging syndrome X-linked dyskeratosis congenita (X-DC), a still incurable disorder that typically leads to bone marrow failure. In this review, we present the classical and most recent findings on this essential protein, discussing the evolutionary, structural, and functional aspects of dyskerin and the H/ACA RNP. The latest research underscores the role that dyskerin plays in the regulation of gene expression, translation efficiency, and telomere maintenance, along with the impacts that defective dyskerin has on aging, cell proliferation, haematopoietic potential, and cancer.
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Affiliation(s)
- Alexandre Garus
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, H3A 0C7, Canada
- Jewish General Hospital, Lady Davis Institute, Montreal, Quebec, H3T 1E2, Canada
| | - Chantal Autexier
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, H3A 0C7, Canada
- Jewish General Hospital, Lady Davis Institute, Montreal, Quebec, H3T 1E2, Canada
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11
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Georgeson J, Schwartz S. The ribosome epitranscriptome: inert-or a platform for functional plasticity? RNA (NEW YORK, N.Y.) 2021; 27:1293-1301. [PMID: 34312287 PMCID: PMC8522695 DOI: 10.1261/rna.078859.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
A universal property of all rRNAs explored to date is the prevalence of post-transcriptional ("epitranscriptional") modifications, which expand the chemical and topological properties of the four standard nucleosides. Are these modifications an inert, constitutive part of the ribosome? Or could they, in part, also regulate the structure or function of the ribosome? In this review, we summarize emerging evidence that rRNA modifications are more heterogeneous than previously thought, and that they can also vary from one condition to another, such as in the context of a cellular response or a developmental trajectory. We discuss the implications of these results and key open questions on the path toward connecting such heterogeneity with function.
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Affiliation(s)
- Joseph Georgeson
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Schraga Schwartz
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
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12
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Garcia DM, Campbell EA, Jakobson CM, Tsuchiya M, Shaw EA, DiNardo AL, Kaeberlein M, Jarosz DF. A prion accelerates proliferation at the expense of lifespan. eLife 2021; 10:e60917. [PMID: 34545808 PMCID: PMC8455135 DOI: 10.7554/elife.60917] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 08/12/2021] [Indexed: 12/23/2022] Open
Abstract
In fluctuating environments, switching between different growth strategies, such as those affecting cell size and proliferation, can be advantageous to an organism. Trade-offs arise, however. Mechanisms that aberrantly increase cell size or proliferation-such as mutations or chemicals that interfere with growth regulatory pathways-can also shorten lifespan. Here we report a natural example of how the interplay between growth and lifespan can be epigenetically controlled. We find that a highly conserved RNA-modifying enzyme, the pseudouridine synthase Pus4/TruB, can act as a prion, endowing yeast with greater proliferation rates at the cost of a shortened lifespan. Cells harboring the prion grow larger and exhibit altered protein synthesis. This epigenetic state, [BIG+] (better in growth), allows cells to heritably yet reversibly alter their translational program, leading to the differential synthesis of dozens of proteins, including many that regulate proliferation and aging. Our data reveal a new role for prion-based control of an RNA-modifying enzyme in driving heritable epigenetic states that transform cell growth and survival.
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Affiliation(s)
- David M Garcia
- Department of Chemical & Systems Biology, Stanford University School of Medicine, Stanford, United States
- Institute of Molecular Biology, Department of Biology, University of Oregon, Eugene, United States
| | - Edgar A Campbell
- Department of Chemical & Systems Biology, Stanford University School of Medicine, Stanford, United States
| | - Christopher M Jakobson
- Department of Chemical & Systems Biology, Stanford University School of Medicine, Stanford, United States
| | - Mitsuhiro Tsuchiya
- Department of Pathology, University of Washington, Seattle, United States
| | - Ethan A Shaw
- Institute of Molecular Biology, Department of Biology, University of Oregon, Eugene, United States
| | - Acadia L DiNardo
- Institute of Molecular Biology, Department of Biology, University of Oregon, Eugene, United States
| | - Matt Kaeberlein
- Department of Pathology, University of Washington, Seattle, United States
| | - Daniel F Jarosz
- Department of Chemical & Systems Biology, Stanford University School of Medicine, Stanford, United States
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, United States
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13
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Porat J, Kothe U, Bayfield MA. Revisiting tRNA chaperones: New players in an ancient game. RNA (NEW YORK, N.Y.) 2021; 27:rna.078428.120. [PMID: 33593999 PMCID: PMC8051267 DOI: 10.1261/rna.078428.120] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 02/10/2021] [Indexed: 05/03/2023]
Abstract
tRNAs undergo an extensive maturation process including post-transcriptional modifications that influence secondary and tertiary interactions. Precursor and mature tRNAs lacking key modifications are often recognized as aberrant and subsequently targeted for decay, illustrating the importance of modifications in promoting structural integrity. tRNAs also rely on tRNA chaperones to promote the folding of misfolded substrates into functional conformations. The best characterized tRNA chaperone is the La protein, which interacts with nascent RNA polymerase III transcripts to promote folding and offers protection from exonucleases. More recently, certain tRNA modification enzymes have also been demonstrated to possess tRNA folding activity distinct from their catalytic activity, suggesting that they may act as tRNA chaperones. In this review, we will discuss pioneering studies relating post-transcriptional modification to tRNA stability and decay pathways, present recent advances into the mechanism by which the RNA chaperone La assists pre-tRNA maturation, and summarize emerging research directions aimed at characterizing modification enzymes as tRNA chaperones. Together, these findings shed light on the importance of tRNA folding and how tRNA chaperones, in particular, increase the fraction of nascent pre-tRNAs that adopt a folded, functional conformation.
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14
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Tagel M, Ilves H, Leppik M, Jürgenstein K, Remme J, Kivisaar M. Pseudouridines of tRNA Anticodon Stem-Loop Have Unexpected Role in Mutagenesis in Pseudomonas sp. Microorganisms 2020; 9:microorganisms9010025. [PMID: 33374637 PMCID: PMC7822408 DOI: 10.3390/microorganisms9010025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 12/17/2020] [Accepted: 12/21/2020] [Indexed: 02/06/2023] Open
Abstract
Pseudouridines are known to be important for optimal translation. In this study we demonstrate an unexpected link between pseudouridylation of tRNA and mutation frequency in Pseudomonas species. We observed that the lack of pseudouridylation activity of pseudouridine synthases TruA or RluA elevates the mutation frequency in Pseudomonas putida 3 to 5-fold. The absence of TruA but not RluA elevates mutation frequency also in Pseudomonas aeruginosa. Based on the results of genetic studies and analysis of proteome data, the mutagenic effect of the pseudouridylation deficiency cannot be ascribed to the involvement of error-prone DNA polymerases or malfunctioning of DNA repair pathways. In addition, although the deficiency in TruA-dependent pseudouridylation made P. putida cells more sensitive to antimicrobial compounds that may cause oxidative stress and DNA damage, cultivation of bacteria in the presence of reactive oxygen species (ROS)-scavenging compounds did not eliminate the mutator phenotype. Thus, the elevated mutation frequency in the absence of tRNA pseudouridylation could be the result of a more specific response or, alternatively, of a cumulative effect of several small effects disturbing distinct cellular functions, which remain undetected when studied independently. This work suggests that pseudouridines link the translation machinery to mutation frequency.
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Affiliation(s)
- Mari Tagel
- Correspondence: (M.T.); (J.R.); (M.K.); Tel.: +372-737-5036 (M.K.)
| | | | | | | | - Jaanus Remme
- Correspondence: (M.T.); (J.R.); (M.K.); Tel.: +372-737-5036 (M.K.)
| | - Maia Kivisaar
- Correspondence: (M.T.); (J.R.); (M.K.); Tel.: +372-737-5036 (M.K.)
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15
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Abstract
Following its transcription, RNA can be modified by >170 chemically distinct types of modifications - the epitranscriptome. In recent years, there have been substantial efforts to uncover and characterize the modifications present on mRNA, motivated by the potential of such modifications to regulate mRNA fate and by discoveries and advances in our understanding of N 6-methyladenosine (m6A). Here, we review our knowledge regarding the detection, distribution, abundance, biogenesis, functions and possible mechanisms of action of six of these modifications - pseudouridine (Ψ), 5-methylcytidine (m5C), N 1-methyladenosine (m1A), N 4-acetylcytidine (ac4C), ribose methylations (Nm) and N 7-methylguanosine (m7G). We discuss the technical and analytical aspects that have led to inconsistent conclusions and controversies regarding the abundance and distribution of some of these modifications. We further highlight shared commonalities and important ways in which these modifications differ with respect to m6A, based on which we speculate on their origin and their ability to acquire functions over evolutionary timescales.
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16
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Kurimoto R, Chiba T, Ito Y, Matsushima T, Yano Y, Miyata K, Yashiro Y, Suzuki T, Tomita K, Asahara H. The tRNA pseudouridine synthase TruB1 regulates the maturation of let-7 miRNA. EMBO J 2020; 39:e104708. [PMID: 32926445 PMCID: PMC7560213 DOI: 10.15252/embj.2020104708] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 08/07/2020] [Accepted: 08/08/2020] [Indexed: 12/14/2022] Open
Abstract
Let-7 is an evolutionary conserved microRNA that mediates post-transcriptional gene silencing to regulate a wide range of biological processes, including development, differentiation, and tumor suppression. Let-7 biogenesis is tightly regulated by several RNA-binding proteins, including Lin28A/B, which represses let-7 maturation. To identify new regulators of let-7, we devised a cell-based functional screen of RNA-binding proteins using a let-7 sensor luciferase reporter and identified the tRNA pseudouridine synthase, TruB1. TruB1 enhanced maturation specifically of let-7 family members. Rather than inducing pseudouridylation of the miRNAs, high-throughput sequencing crosslinking immunoprecipitation (HITS-CLIP) and biochemical analyses revealed direct binding between endogenous TruB1 and the stem-loop structure of pri-let-7, which also binds Lin28A/B. TruB1 selectively enhanced the interaction between pri-let-7 and the microprocessor DGCR8, which mediates miRNA maturation. Finally, TruB1 suppressed cell proliferation, which was mediated in part by let-7. Altogether, we reveal an unexpected function for TruB1 in promoting let-7 maturation.
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Affiliation(s)
- Ryota Kurimoto
- Department of Systems BioMedicineGraduate School of Medical and Dental SciencesTokyo Medical and Dental University (TMDU)TokyoJapan
| | - Tomoki Chiba
- Department of Systems BioMedicineGraduate School of Medical and Dental SciencesTokyo Medical and Dental University (TMDU)TokyoJapan
| | - Yoshiaki Ito
- Department of Systems BioMedicineGraduate School of Medical and Dental SciencesTokyo Medical and Dental University (TMDU)TokyoJapan
- Research CoreResearch Facility ClusterInstitute of ResearchTokyo Medical and Dental University (TMDU)TokyoJapan
| | - Takahide Matsushima
- Department of Systems BioMedicineGraduate School of Medical and Dental SciencesTokyo Medical and Dental University (TMDU)TokyoJapan
| | - Yuki Yano
- Department of Systems BioMedicineGraduate School of Medical and Dental SciencesTokyo Medical and Dental University (TMDU)TokyoJapan
| | - Kohei Miyata
- Department Obstetrics and GynecologyFaculty of MedicineFukuoka UniversityFukuokaJapan
| | - Yuka Yashiro
- Department of Computational Biology and Medical SciencesGraduate School of Frontier SciencesThe University of TokyoKashiwaChibaJapan
| | - Tsutomu Suzuki
- Department of Chemistry and BiotechnologyGraduate School of EngineeringUniversity of TokyoTokyoJapan
| | - Kozo Tomita
- Department of Computational Biology and Medical SciencesGraduate School of Frontier SciencesThe University of TokyoKashiwaChibaJapan
| | - Hiroshi Asahara
- Department of Systems BioMedicineGraduate School of Medical and Dental SciencesTokyo Medical and Dental University (TMDU)TokyoJapan
- Department of Molecular and Experimental MedicineThe Scripps Research InstituteSan DiegoCAUSA
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17
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Keffer-Wilkes LC, Soon EF, Kothe U. The methyltransferase TrmA facilitates tRNA folding through interaction with its RNA-binding domain. Nucleic Acids Res 2020; 48:7981-7990. [PMID: 32597953 PMCID: PMC7641329 DOI: 10.1093/nar/gkaa548] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 05/29/2020] [Accepted: 06/17/2020] [Indexed: 11/12/2022] Open
Abstract
tRNAs are the most highly modified RNAs in all cells, and formation of 5-methyluridine (m5U) at position 54 in the T arm is a common RNA modification found in all tRNAs. The m5U modification is generated by the methyltransferase TrmA. Here, we test and prove the hypothesis that Escherichia coli TrmA has dual functions, acting both as a methyltransferase and as a tRNA chaperone. We identify two conserved residues, F106 and H125, in the RNA-binding domain of TrmA, which interact with the tRNA elbow and are critical for tRNA binding. Co-culture competition assays reveal that the catalytic activity of TrmA is important for cellular fitness, and that substitutions of F106 or H125 impair cellular fitness. We directly show that TrmA enhances tRNA folding in vitro independent of its catalytic activity. In conclusion, our study suggests that F106 and H125 in the RNA-binding domain of TrmA act as a wedge disrupting tertiary interactions between tRNA’s D arm and T arm; this tRNA unfolding is the mechanistic basis for TrmA’s tRNA chaperone activity. TrmA is the second tRNA modifying enzyme next to the pseudouridine synthase TruB shown to act as a tRNA chaperone supporting a functional link between RNA modification and folding.
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Affiliation(s)
- Laura Carole Keffer-Wilkes
- University of Lethbridge, Alberta RNA Research and Training Institute (ARRTI), Department of Chemistry and Biochemistry, Lethbridge, AB T1K 3M4, Canada
| | - Emily F Soon
- University of Lethbridge, Alberta RNA Research and Training Institute (ARRTI), Department of Chemistry and Biochemistry, Lethbridge, AB T1K 3M4, Canada
| | - Ute Kothe
- University of Lethbridge, Alberta RNA Research and Training Institute (ARRTI), Department of Chemistry and Biochemistry, Lethbridge, AB T1K 3M4, Canada
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18
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Vargas-Blanco DA, Shell SS. Regulation of mRNA Stability During Bacterial Stress Responses. Front Microbiol 2020; 11:2111. [PMID: 33013770 PMCID: PMC7509114 DOI: 10.3389/fmicb.2020.02111] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 08/11/2020] [Indexed: 12/12/2022] Open
Abstract
Bacteria have a remarkable ability to sense environmental changes, swiftly regulating their transcriptional and posttranscriptional machinery as a response. Under conditions that cause growth to slow or stop, bacteria typically stabilize their transcriptomes in what has been shown to be a conserved stress response. In recent years, diverse studies have elucidated many of the mechanisms underlying mRNA degradation, yet an understanding of the regulation of mRNA degradation under stress conditions remains elusive. In this review we discuss the diverse mechanisms that have been shown to affect mRNA stability in bacteria. While many of these mechanisms are transcript-specific, they provide insight into possible mechanisms of global mRNA stabilization. To that end, we have compiled information on how mRNA fate is affected by RNA secondary structures; interaction with ribosomes, RNA binding proteins, and small RNAs; RNA base modifications; the chemical nature of 5' ends; activity and concentration of RNases and other degradation proteins; mRNA and RNase localization; and the stringent response. We also provide an analysis of reported relationships between mRNA abundance and mRNA stability, and discuss the importance of stress-associated mRNA stabilization as a potential target for therapeutic development.
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Affiliation(s)
- Diego A Vargas-Blanco
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA, United States
| | - Scarlet S Shell
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA, United States.,Program in Bioinformatics and Computational Biology, Worcester Polytechnic Institute, Worcester, MA, United States
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19
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Jayalath K, Frisbie S, To M, Abeysirigunawardena S. Pseudouridine Synthase RsuA Captures an Assembly Intermediate that Is Stabilized by Ribosomal Protein S17. Biomolecules 2020; 10:biom10060841. [PMID: 32486254 PMCID: PMC7356742 DOI: 10.3390/biom10060841] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 05/28/2020] [Accepted: 05/28/2020] [Indexed: 01/03/2023] Open
Abstract
The ribosome is a large ribonucleoprotein complex that synthesizes protein in all living organisms. Ribosome biogenesis is a complex process that requires synchronization of various cellular events, including ribosomal RNA (rRNA) transcription, ribosome assembly, and processing and post-transcriptional modification of rRNA. Ribosome biogenesis is fine-tuned with various assembly factors, possibly including nucleotide modification enzymes. Ribosomal small subunit pseudouridine synthase A (RsuA) pseudouridylates U516 of 16S helix 18. Protein RsuA is a multi-domain protein that contains the N-terminal peripheral domain, which is structurally similar to the ribosomal protein S4. Our study shows RsuA preferably binds and pseudouridylates an assembly intermediate that is stabilized by ribosomal protein S17 over the native-like complex. In addition, the N-terminal domain truncated RsuA showed that the presence of the S4-like domain is important for RsuA substrate recognition.
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20
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Chloroplast development at low temperature requires the pseudouridine synthase gene TCD3 in rice. Sci Rep 2020; 10:8518. [PMID: 32444695 PMCID: PMC7244722 DOI: 10.1038/s41598-020-65467-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 04/08/2020] [Indexed: 12/04/2022] Open
Abstract
Low temperature affects a broad spectrum of cellular components in plants, such as chloroplasts, as well as plant metabolism. On the other hand, pseudouridine (Ψ) synthases are required for the most abundant post-transcriptional modification of RNA in Escherichia coli. However, the role of rice Ψ synthases in regulating chloroplast development at low temperature remains elusive. In this study, we identified the rice thermo-sensitive chlorophyll-deficient (tcd3) mutant, which displays an albino phenotype before the 4-leaf stage and ultimately dies when grown at 20 °C, but can grow normally at 32 °C. Genetic analysis showed that the mutant trait is controlled by a single recessive nuclear gene (tcd3). Map-based cloning, complementation and knockout tests revealed that TCD3 encodes a chloroplast-localized Ψ synthase. TCD3 is a cold-induced gene that is mainly expressed in leaves. The disruption of TCD3 severely affected the transcript levels of various chloroplast-associated genes, as well as ribosomal genes involved in chloroplast rRNA assembly at low temperature (20 °C), whereas the transcript levels of these genes were normal at high temperature (32 °C). These results provide a first glimpse into the importance of rice Ψ synthase gene in chloroplast development at low temperatures.
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21
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Defining the Environmental Adaptations of Genus Devosia: Insights into its Expansive Short Peptide Transport System and Positively Selected Genes. Sci Rep 2020; 10:1151. [PMID: 31980727 PMCID: PMC6981132 DOI: 10.1038/s41598-020-58163-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 12/19/2019] [Indexed: 12/21/2022] Open
Abstract
Devosia are well known for their dominance in soil habitats contaminated with various toxins and are best characterized for their bioremediation potential. In this study, we compared the genomes of 27 strains of Devosia with aim to understand their metabolic abilities. The analysis revealed their adaptive gene repertoire which was bared from 52% unique pan-gene content. A striking feature of all genomes was the abundance of oligo- and di-peptide permeases (oppABCDF and dppABCDF) with each genome harboring an average of 60.7 ± 19.1 and 36.5 ± 10.6 operon associated genes respectively. Apart from their primary role in nutrition, these permeases may help Devosia to sense environmental signals and in chemotaxis at stressed habitats. Through sequence similarity network analyses, we identified 29 Opp and 19 Dpp sequences that shared very little homology with any other sequence suggesting an expansive short peptidic transport system within Devosia. The substrate determining components of these permeases viz. OppA and DppA further displayed a large diversity that separated into 12 and 9 homologous clusters respectively in addition to large number of isolated nodes. We also dissected the genome scale positive evolution and found genes associated with growth (exopolyphosphatase, HesB_IscA_SufA family protein), detoxification (moeB, nifU-like domain protein, alpha/beta hydrolase), chemotaxis (cheB, luxR) and stress response (phoQ, uspA, luxR, sufE) were positively selected. The study highlights the genomic plasticity of the Devosia spp. for conferring adaptation, bioremediation and the potential to utilize a wide range of substrates. The widespread toxin-antitoxin loci and ‘open’ state of the pangenome provided evidence of plastic genomes and a much larger genetic repertoire of the genus which is yet uncovered.
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22
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Song J, Zhuang Y, Zhu C, Meng H, Lu B, Xie B, Peng J, Li M, Yi C. Differential roles of human PUS10 in miRNA processing and tRNA pseudouridylation. Nat Chem Biol 2019; 16:160-169. [PMID: 31819270 DOI: 10.1038/s41589-019-0420-5] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 10/27/2019] [Indexed: 11/09/2022]
Abstract
Pseudouridine synthases (PUSs) are responsible for installation of pseudouridine (Ψ) modification in RNA. However, the activity and function of the PUS enzymes remain largely unexplored. Here we focus on human PUS10 and find that it co-expresses with the microprocessor (DROSHA-DGCR8 complex). Depletion of PUS10 results in a marked reduction of the expression level of a large number of mature miRNAs and concomitant accumulation of unprocessed primary microRNAs (pri-miRNAs) in multiple human cells. Mechanistically, PUS10 directly binds to pri-miRNAs and interacts with the microprocessor to promote miRNA biogenesis. Unexpectedly, this process is independent of the catalytic activity of PUS10. Additionally, we develop a sequencing method to profile Ψ in the tRNAome and report PUS10-dependent Ψ sites in tRNA. Collectively, our findings reveal differential functions of PUS10 in nuclear miRNA processing and in cytoplasmic tRNA pseudouridylation.
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Affiliation(s)
- Jinghui Song
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Yuan Zhuang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Chenxu Zhu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.,Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Haowei Meng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Bo Lu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Bingteng Xie
- Center for Reproductive Medicine, Peking University Third Hospital, Beijing, China
| | - Jinying Peng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Mo Li
- Center for Reproductive Medicine, Peking University Third Hospital, Beijing, China.
| | - Chengqi Yi
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China. .,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China. .,Department of Chemical Biology and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
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23
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Boccitto M, Wolin SL. Ro60 and Y RNAs: structure, functions, and roles in autoimmunity. Crit Rev Biochem Mol Biol 2019; 54:133-152. [PMID: 31084369 DOI: 10.1080/10409238.2019.1608902] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Ro60, also known as SS-A or TROVE2, is an evolutionarily conserved RNA-binding protein that is found in most animal cells, approximately 5% of sequenced prokaryotic genomes and some archaea. Ro60 is present in cells as both a free protein and as a component of a ribonucleoprotein complex, where its best-known partners are members of a class of noncoding RNAs called Y RNAs. Structural and biochemical analyses have revealed that Ro60 is a ring-shaped protein that binds Y RNAs on its outer surface. In addition to Y RNAs, Ro60 binds misfolded and aberrant noncoding RNAs in some animal cell nuclei. Although the fate of these defective Ro60-bound noncoding RNAs in animal cells is not well-defined, a bacterial Ro60 ortholog functions with 3' to 5' exoribonucleases to assist structured RNA degradation. Studies of Y RNAs have revealed that these RNAs regulate the subcellular localization of Ro60, tether Ro60 to effector proteins and regulate the access of other RNAs to its central cavity. As both mammalian cells and bacteria lacking Ro60 are sensitized to ultraviolet irradiation, Ro60 function may be important during exposure to some environmental stressors. Here we summarize the current knowledge regarding the functions of Ro60 and Y RNAs in animal cells and bacteria. Because the Ro60 RNP is a clinically important target of autoantibodies in patients with rheumatic diseases such as Sjogren's syndrome, systemic lupus erythematosus, and neonatal lupus, we also discuss potential roles for Ro60 RNPs in the initiation and pathogenesis of systemic autoimmune rheumatic disease.
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Affiliation(s)
- Marco Boccitto
- a RNA Biology Laboratory, Center for Cancer Research , National Cancer Institute , Frederick , MD , USA
| | - Sandra L Wolin
- a RNA Biology Laboratory, Center for Cancer Research , National Cancer Institute , Frederick , MD , USA
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24
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Hori H, Kawamura T, Awai T, Ochi A, Yamagami R, Tomikawa C, Hirata A. Transfer RNA Modification Enzymes from Thermophiles and Their Modified Nucleosides in tRNA. Microorganisms 2018; 6:E110. [PMID: 30347855 PMCID: PMC6313347 DOI: 10.3390/microorganisms6040110] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 10/17/2018] [Accepted: 10/17/2018] [Indexed: 12/11/2022] Open
Abstract
To date, numerous modified nucleosides in tRNA as well as tRNA modification enzymes have been identified not only in thermophiles but also in mesophiles. Because most modified nucleosides in tRNA from thermophiles are common to those in tRNA from mesophiles, they are considered to work essentially in steps of protein synthesis at high temperatures. At high temperatures, the structure of unmodified tRNA will be disrupted. Therefore, thermophiles must possess strategies to stabilize tRNA structures. To this end, several thermophile-specific modified nucleosides in tRNA have been identified. Other factors such as RNA-binding proteins and polyamines contribute to the stability of tRNA at high temperatures. Thermus thermophilus, which is an extreme-thermophilic eubacterium, can adapt its protein synthesis system in response to temperature changes via the network of modified nucleosides in tRNA and tRNA modification enzymes. Notably, tRNA modification enzymes from thermophiles are very stable. Therefore, they have been utilized for biochemical and structural studies. In the future, thermostable tRNA modification enzymes may be useful as biotechnology tools and may be utilized for medical science.
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Affiliation(s)
- Hiroyuki Hori
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Japan.
| | - Takuya Kawamura
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Japan.
| | - Takako Awai
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Japan.
| | - Anna Ochi
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Japan.
| | - Ryota Yamagami
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Japan.
| | - Chie Tomikawa
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Japan.
| | - Akira Hirata
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Japan.
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25
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Fujikane R, Behm-Ansmant I, Tillault AS, Loegler C, Igel-Bourguignon V, Marguet E, Forterre P, Branlant C, Motorin Y, Charpentier B. Contribution of protein Gar1 to the RNA-guided and RNA-independent rRNA:Ψ-synthase activities of the archaeal Cbf5 protein. Sci Rep 2018; 8:13815. [PMID: 30218085 PMCID: PMC6138745 DOI: 10.1038/s41598-018-32164-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 08/29/2018] [Indexed: 01/09/2023] Open
Abstract
Archaeal RNA:pseudouridine-synthase (PUS) Cbf5 in complex with proteins L7Ae, Nop10 and Gar1, and guide box H/ACA sRNAs forms ribonucleoprotein (RNP) catalysts that insure the conversion of uridines into pseudouridines (Ψs) in ribosomal RNAs (rRNAs). Nonetheless, in the absence of guide RNA, Cbf5 catalyzes the in vitro formation of Ψ2603 in Pyrococcus abyssi 23S rRNA and of Ψ55 in tRNAs. Using gene-disrupted strains of the hyperthermophilic archaeon Thermococcus kodakarensis, we studied the in vivo contribution of proteins Nop10 and Gar1 to the dual RNA guide-dependent and RNA-independent activities of Cbf5 on 23S rRNA. The single-null mutants of the cbf5, nop10, and gar1 genes are viable, but display a thermosensitive slow growth phenotype. We also generated a single-null mutant of the gene encoding Pus10, which has redundant activity with Cbf5 for in vitro formation of Ψ55 in tRNA. Analysis of the presence of Ψs within the rRNA peptidyl transferase center (PTC) of the mutants demonstrated that Cbf5 but not Pus10 is required for rRNA modification. Our data reveal that, in contrast to Nop10, Gar1 is crucial for in vivo and in vitro RNA guide-independent formation of Ψ2607 (Ψ2603 in P. abyssi) by Cbf5. Furthermore, our data indicate that pseudouridylation at orphan position 2589 (2585 in P. abyssi), for which no PUS or guide sRNA has been identified so far, relies on RNA- and Gar1-dependent activity of Cbf5.
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Affiliation(s)
- Ryosuke Fujikane
- Université de Lorraine, CNRS, UMR 7365 Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), F-54500, Nancy, France
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, F-91198, Gif-sur-Yvette cedex, France
- Fukuoka Dental College, Department of Physiological Sciences and Molecular Biology, Section of Cellular and Molecular Regulation, 2-15-1 Tamura, Sawara-ku, Fukuoka, 814-0193, Japan
| | - Isabelle Behm-Ansmant
- Université de Lorraine, CNRS, UMR 7365 Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), F-54500, Nancy, France
| | - Anne-Sophie Tillault
- Université de Lorraine, CNRS, UMR 7365 Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), F-54500, Nancy, France
- Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Christine Loegler
- Université de Lorraine, CNRS, UMR 7365 Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), F-54500, Nancy, France
| | - Valérie Igel-Bourguignon
- Université de Lorraine, CNRS, UMR 7365 Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), F-54500, Nancy, France
| | - Evelyne Marguet
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, F-91198, Gif-sur-Yvette cedex, France
| | - Patrick Forterre
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, F-91198, Gif-sur-Yvette cedex, France
- Institut Pasteur, Département de Microbiologie, 25 rue du Dr Roux, F-7505, Paris, France
| | - Christiane Branlant
- Université de Lorraine, CNRS, UMR 7365 Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), F-54500, Nancy, France
| | - Yuri Motorin
- Université de Lorraine, CNRS, UMR 7365 Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), F-54500, Nancy, France
- Université de Lorraine, CNRS, INSERM, UMS2008 IBSLor, F-54500, Nancy, France
| | - Bruno Charpentier
- Université de Lorraine, CNRS, UMR 7365 Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), F-54500, Nancy, France.
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26
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Identification of Fitness Determinants during Energy-Limited Growth Arrest in Pseudomonas aeruginosa. mBio 2017; 8:mBio.01170-17. [PMID: 29184024 PMCID: PMC5705914 DOI: 10.1128/mbio.01170-17] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microbial growth arrest can be triggered by diverse factors, one of which is energy limitation due to scarcity of electron donors or acceptors. Genes that govern fitness during energy-limited growth arrest and the extent to which they overlap between different types of energy limitation are poorly defined. In this study, we exploited the fact that Pseudomonas aeruginosa can remain viable over several weeks when limited for organic carbon (pyruvate) as an electron donor or oxygen as an electron acceptor. ATP values were reduced under both types of limitation, yet more severely in the absence of oxygen. Using transposon-insertion sequencing (Tn-seq), we identified fitness determinants in these two energy-limited states. Multiple genes encoding general functions like transcriptional regulation and energy generation were required for fitness during carbon or oxygen limitation, yet many specific genes, and thus specific activities, differed in their relevance between these states. For instance, the global regulator RpoS was required during both types of energy limitation, while other global regulators such as DksA and LasR were required only during carbon or oxygen limitation, respectively. Similarly, certain ribosomal and tRNA modifications were specifically required during oxygen limitation. We validated fitness defects during energy limitation using independently generated mutants of genes detected in our screen. Mutants in distinct functional categories exhibited different fitness dynamics: regulatory genes generally manifested a phenotype early, whereas genes involved in cell wall metabolism were required later. Together, these results provide a new window into how P. aeruginosa survives growth arrest. Growth-arrested bacteria are ubiquitous in nature and disease yet understudied at the molecular level. For example, growth-arrested cells constitute a major subpopulation of mature biofilms, serving as an antibiotic-tolerant reservoir in chronic infections. Identification of the genes required for survival of growth arrest (encompassing entry, maintenance, and exit) is an important first step toward understanding the physiology of bacteria in this state. Using Tn-seq, we identified and validated genes required for fitness of Pseudomonas aeruginosa when energy limited for organic carbon or oxygen, which represent two common causes of growth arrest for P. aeruginosa in diverse habitats. This unbiased, genome-wide survey is the first to reveal essential activities for a pathogen experiencing different types of energy limitation, finding both shared and divergent activities that are relevant at different survival stages. Future efforts can now be directed toward understanding how the biomolecules responsible for these activities contribute to fitness under these conditions.
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27
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Lorenz C, Lünse CE, Mörl M. tRNA Modifications: Impact on Structure and Thermal Adaptation. Biomolecules 2017; 7:E35. [PMID: 28375166 PMCID: PMC5485724 DOI: 10.3390/biom7020035] [Citation(s) in RCA: 191] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Revised: 03/27/2017] [Accepted: 03/28/2017] [Indexed: 12/27/2022] Open
Abstract
Transfer RNAs (tRNAs) are central players in translation, functioning as adapter molecules between the informational level of nucleic acids and the functional level of proteins. They show a highly conserved secondary and tertiary structure and the highest density of post-transcriptional modifications among all RNAs. These modifications concentrate in two hotspots-the anticodon loop and the tRNA core region, where the D- and T-loop interact with each other, stabilizing the overall structure of the molecule. These modifications can cause large rearrangements as well as local fine-tuning in the 3D structure of a tRNA. The highly conserved tRNA shape is crucial for the interaction with a variety of proteins and other RNA molecules, but also needs a certain flexibility for a correct interplay. In this context, it was shown that tRNA modifications are important for temperature adaptation in thermophilic as well as psychrophilic organisms, as they modulate rigidity and flexibility of the transcripts, respectively. Here, we give an overview on the impact of modifications on tRNA structure and their importance in thermal adaptation.
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Affiliation(s)
- Christian Lorenz
- Institute of Biochemistry, Leipzig University, Brüderstraße 34, 04103 Leipzig, Germany.
| | - Christina E Lünse
- Institute of Biochemistry, Leipzig University, Brüderstraße 34, 04103 Leipzig, Germany.
| | - Mario Mörl
- Institute of Biochemistry, Leipzig University, Brüderstraße 34, 04103 Leipzig, Germany.
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Schmid K, Adobes-Vidal M, Helm M. Alkyne-Functionalized Coumarin Compound for Analytic and Preparative 4-Thiouridine Labeling. Bioconjug Chem 2017; 28:1123-1134. [PMID: 28263563 DOI: 10.1021/acs.bioconjchem.7b00035] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Bioconjugation of RNA is a dynamic field recently reinvigorated by a surge in research on post-transcriptional modification. This work focuses on the bioconjugation of 4-thiouridine, a nucleoside that occurs as a post-transcriptional modification in bacterial RNA and is used as a metabolic label and for cross-linking purposes in eukaryotic RNA. A newly designed coumarin compound named 4-bromomethyl-7-propargyloxycoumarin (PBC) is introduced, which exhibits remarkable selectivity for 4-thiouridine. Bearing a terminal alkyne group, it is conductive to secondary bioconjugation via "click chemistry", thereby offering a wide range of preparative and analytical options. We applied PBC to quantitatively monitor the metabolic incorporation of s4U as a label into RNA and for site-specific introduction of a fluorophore into bacterial tRNA at position 8, allowing the determination of its binding constant to an RNA-modification enzyme.
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Affiliation(s)
- Katharina Schmid
- Institute of Pharmacy and Biochemistry, Johannes-Gutenberg University Mainz , Staudingerweg 5, D-55128 Mainz, Germany
| | - Maria Adobes-Vidal
- Electrochemistry & Interfaces Group, Department of Chemistry, University of Warwick , Coventry, CV4 7AL United Kingdom
| | - Mark Helm
- Institute of Pharmacy and Biochemistry, Johannes-Gutenberg University Mainz , Staudingerweg 5, D-55128 Mainz, Germany
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29
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Two for the price of one: RNA modification enzymes as chaperones. Proc Natl Acad Sci U S A 2016; 113:14176-14178. [PMID: 27911836 DOI: 10.1073/pnas.1617402113] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
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30
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Abstract
Cellular RNAs are chemically modified by many RNA modification enzymes; however, often the functions of modifications remain unclear, such as for pseudouridine formation in the tRNA TΨC arm by the bacterial tRNA pseudouridine synthase TruB. Here we test the hypothesis that RNA modification enzymes also act as RNA chaperones. Using TruB as a model, we demonstrate that TruB folds tRNA independent of its catalytic activity, thus increasing the fraction of tRNA that can be aminoacylated. By rapid kinetic stopped-flow analysis, we identified the molecular mechanism of TruB's RNA chaperone activity: TruB binds and unfolds both misfolded and folded tRNAs thereby providing misfolded tRNAs a second chance at folding. Previously, it has been shown that a catalytically inactive TruB variant has no phenotype when expressed in an Escherichia coli truB KO strain [Gutgsell N, et al. (2000) RNA 6(12):1870-1881]. However, here we uncover that E. coli strains expressing a TruB variant impaired in tRNA binding and in in vitro tRNA folding cannot compete with WT E. coli. Consequently, the tRNA chaperone activity of TruB is critical for bacterial fitness. In conclusion, we prove the tRNA chaperone activity of the pseudouridine synthase TruB, reveal its molecular mechanism, and demonstrate its importance for cellular fitness. We discuss the likelihood that other RNA modification enzymes are also RNA chaperones.
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31
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Addepalli B, Limbach PA. Pseudouridine in the Anticodon of Escherichia coli tRNATyr(QΨA) Is Catalyzed by the Dual Specificity Enzyme RluF. J Biol Chem 2016; 291:22327-22337. [PMID: 27551044 DOI: 10.1074/jbc.m116.747865] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Indexed: 02/02/2023] Open
Abstract
Pseudouridine is found in almost all cellular ribonucleic acids (RNAs). Of the multiple characteristics attributed to pseudouridine, making messenger RNAs (mRNAs) highly translatable and non-immunogenic is one such feature that directly implicates this modification in protein synthesis. We report the existence of pseudouridine in the anticodon of Escherichia coli tyrosine transfer RNAs (tRNAs) at position 35. Pseudouridine was verified by multiple detection methods, which include pseudouridine-specific chemical derivatization and gas phase dissociation of RNA during liquid chromatography tandem mass spectrometry (LC-MS/MS). Analysis of total tRNA isolated from E. coli pseudouridine synthase knock-out mutants identified RluF as the enzyme responsible for this modification. Furthermore, the absence of this modification compromises the translational ability of a luciferase reporter gene coding sequence when it is preceded by multiple tyrosine codons. This effect has implications for the translation of mRNAs that are rich in tyrosine codons in bacterial expression systems.
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Affiliation(s)
- Balasubrahmanyam Addepalli
- From the Department of Chemistry, Rieveschl Laboratories for Mass Spectrometry, University of Cincinnati, Cincinnati, Ohio 45221
| | - Patrick A Limbach
- From the Department of Chemistry, Rieveschl Laboratories for Mass Spectrometry, University of Cincinnati, Cincinnati, Ohio 45221
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32
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Scoma A, Barbato M, Hernandez-Sanabria E, Mapelli F, Daffonchio D, Borin S, Boon N. Microbial oil-degradation under mild hydrostatic pressure (10 MPa): which pathways are impacted in piezosensitive hydrocarbonoclastic bacteria? Sci Rep 2016; 6:23526. [PMID: 27020120 PMCID: PMC4810429 DOI: 10.1038/srep23526] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 03/08/2016] [Indexed: 01/19/2023] Open
Abstract
Oil spills represent an overwhelming carbon input to the marine environment that immediately impacts the sea surface ecosystem. Microbial communities degrading the oil fraction that eventually sinks to the seafloor must also deal with hydrostatic pressure, which linearly increases with depth. Piezosensitive hydrocarbonoclastic bacteria are ideal candidates to elucidate impaired pathways following oil spills at low depth. In the present paper, we tested two strains of the ubiquitous Alcanivorax genus, namely A. jadensis KS_339 and A. dieselolei KS_293, which is known to rapidly grow after oil spills. Strains were subjected to atmospheric and mild pressure (0.1, 5 and 10 MPa, corresponding to a depth of 0, 500 and 1000 m, respectively) providing n-dodecane as sole carbon source. Pressures equal to 5 and 10 MPa significantly lowered growth yields of both strains. However, in strain KS_293 grown at 10 MPa CO2 production per cell was not affected, cell integrity was preserved and PO4(3-) uptake increased. Analysis of its transcriptome revealed that 95% of its genes were downregulated. Increased transcription involved protein synthesis, energy generation and respiration pathways. Interplay between these factors may play a key role in shaping the structure of microbial communities developed after oil spills at low depth and limit their bioremediation potential.
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Affiliation(s)
- Alberto Scoma
- Laboratory of Microbial Ecology and Technology (LabMET), University of Gent, Coupure Links 653, B 9000 Gent, Belgium
| | - Marta Barbato
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milano, Via Celoria 2, 20133, Milano, Italy
| | - Emma Hernandez-Sanabria
- Laboratory of Microbial Ecology and Technology (LabMET), University of Gent, Coupure Links 653, B 9000 Gent, Belgium
| | - Francesca Mapelli
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milano, Via Celoria 2, 20133, Milano, Italy
| | - Daniele Daffonchio
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division, Thuwal 23955-6900, Kingdom of Saudi Arabia.,Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milano, Via Celoria 2, 20133, Milano, Italy
| | - Sara Borin
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milano, Via Celoria 2, 20133, Milano, Italy
| | - Nico Boon
- Laboratory of Microbial Ecology and Technology (LabMET), University of Gent, Coupure Links 653, B 9000 Gent, Belgium
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Abstract
The modified nucleosides of RNA are chemically altered versions of the standard A, G, U, and C nucleosides. This review reviews the nature and location of the modified nucleosides of Escherichia coli rRNA, the enzymes that form them, and their known and/or putative functional role. There are seven Ψ (pseudouridines) synthases to make the 11 pseudouridines in rRNA. There is disparity in numbers because RluC and RluD each make 3 pseudouridines. Crystal structures have shown that the Ψ synthase domain is a conserved fold found only in all five families of Ψ synthases. The conversion of uridine to Ψ has no precedent in known metabolic reactions. Other enzymes are known to cleave the glycosyl bond but none carry out rotation of the base and rejoining to the ribose while still enzyme bound. Ten methyltransferases (MTs) are needed to make all the methylated nucleosides in 16S RNA, and 14 are needed for 23S RNA. Biochemical studies indicate that the modes of substrate recognition are idiosyncratic for each Ψ synthase since no common mode of recognition has been detected in studies of the seven synthases. Eight of the 24 expected MTs have been identified, and six crystal structures have been determined. Seven of the MTs and five of the structures are class I MTs with the appropriate protein fold plus unique appendages for the Ψ synthases. The remaining MT, RlmB, has the class IV trefoil knot fold.
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Abstract
Transfer RNA (tRNA) from all organisms on this planet contains modified nucleosides, which are derivatives of the four major nucleosides. tRNA from Escherichia coli/Salmonella enterica contains 31 different modified nucleosides, which are all, except for one (Queuosine[Q]), synthesized on an oligonucleotide precursor, which through specific enzymes later matures into tRNA. The corresponding structural genes for these enzymes are found in mono- and polycistronic operons, the latter of which have a complex transcription and translation pattern. The syntheses of some of them (e.g.,several methylated derivatives) are catalyzed by one enzyme, which is position and base specific, but synthesis of some have a very complex biosynthetic pathway involving several enzymes (e.g., 2-thiouridines, N6-threonyladenosine [t6A],and Q). Several of the modified nucleosides are essential for viability (e.g.,lysidin, t6A, 1-methylguanosine), whereas deficiency in others induces severe growth defects. However, some have no or only a small effect on growth at laboratory conditions. Modified nucleosides that are present in the anticodon loop or stem have a fundamental influence on the efficiency of charging the tRNA, reading cognate codons, and preventing missense and frameshift errors. Those, which are present in the body of the tRNA, have a primarily stabilizing effect on the tRNA. Thus, the ubiquitouspresence of these modified nucleosides plays a pivotal role in the function of the tRNA by their influence on the stability and activity of the tRNA.
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35
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Abstract
Cellular RNAs can be chemically modified over a hundred different ways. These modifications were once thought to be static, discrete, and utilized to fine-tune RNA structure and function. However, recent studies have revealed that some modifications, like mRNA methylation, can be reversed, and these reversible modifications may play active roles in regulating diverse biological processes. In this perspective, we summarize examples of dynamic RNA modifications that affect biological functions. We further propose that reversible modifications might occur on tRNA, rRNA, and other noncoding RNAs to regulate gene expression analogous to the reversible mRNA methylation.
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36
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Chen X, Sim S, Wurtmann EJ, Feke A, Wolin SL. Bacterial noncoding Y RNAs are widespread and mimic tRNAs. RNA (NEW YORK, N.Y.) 2014; 20:1715-1724. [PMID: 25232022 PMCID: PMC4201824 DOI: 10.1261/rna.047241.114] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 07/30/2014] [Indexed: 05/30/2023]
Abstract
Many bacteria encode an ortholog of the Ro60 autoantigen, a ring-shaped protein that is bound in animal cells to noncoding RNAs (ncRNAs) called Y RNAs. Studies in Deinococcus radiodurans revealed that Y RNA tethers Ro60 to polynucleotide phosphorylase, specializing this exoribonuclease for structured RNA degradation. Although Ro60 orthologs are present in a wide range of bacteria, Y RNAs have been detected in only two species, making it unclear whether these ncRNAs are common Ro60 partners in bacteria. In this study, we report that likely Y RNAs are encoded near Ro60 in >250 bacterial and phage species. By comparing conserved features, we discovered that at least one Y RNA in each species contains a domain resembling tRNA. We show that these RNAs contain nucleotide modifications characteristic of tRNA and are substrates for several enzymes that recognize tRNAs. Our studies confirm the importance of Y RNAs in bacterial physiology and identify a new class of ncRNAs that mimic tRNA.
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Affiliation(s)
- Xinguo Chen
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06510, USA
| | - Soyeong Sim
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06510, USA
| | - Elisabeth J Wurtmann
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06510, USA
| | - Ann Feke
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06510, USA
| | - Sandra L Wolin
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06510, USA Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06510, USA
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37
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Björk GR, Hagervall TG. Transfer RNA Modification: Presence, Synthesis, and Function. EcoSal Plus 2014; 6. [PMID: 26442937 DOI: 10.1128/ecosalplus.esp-0007-2013] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Indexed: 06/05/2023]
Abstract
Transfer RNA (tRNA) from all organisms on this planet contains modified nucleosides, which are derivatives of the four major nucleosides. tRNA from Escherichia coli/Salmonella enterica serovar Typhimurium contains 33 different modified nucleosides, which are all, except one (Queuosine [Q]), synthesized on an oligonucleotide precursor, which by specific enzymes later matures into tRNA. The structural genes for these enzymes are found in mono- and polycistronic operons, the latter of which have a complex transcription and translation pattern. The synthesis of the tRNA-modifying enzymes is not regulated similarly, and it is not coordinated to that of their substrate, the tRNA. The synthesis of some of them (e.g., several methylated derivatives) is catalyzed by one enzyme, which is position and base specific, whereas synthesis of some has a very complex biosynthetic pathway involving several enzymes (e.g., 2-thiouridines, N 6-cyclicthreonyladenosine [ct6A], and Q). Several of the modified nucleosides are essential for viability (e.g., lysidin, ct6A, 1-methylguanosine), whereas the deficiency of others induces severe growth defects. However, some have no or only a small effect on growth at laboratory conditions. Modified nucleosides that are present in the anticodon loop or stem have a fundamental influence on the efficiency of charging the tRNA, reading cognate codons, and preventing missense and frameshift errors. Those that are present in the body of the tRNA primarily have a stabilizing effect on the tRNA. Thus, the ubiquitous presence of these modified nucleosides plays a pivotal role in the function of the tRNA by their influence on the stability and activity of the tRNA.
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Affiliation(s)
- Glenn R Björk
- Department of Molecular Biology, Umeå University, S-90187 Umeå, Sweden
| | - Tord G Hagervall
- Department of Molecular Biology, Umeå University, S-90187 Umeå, Sweden
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38
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Chatterjee K, Blaby IK, Thiaville PC, Majumder M, Grosjean H, Yuan YA, Gupta R, de Crécy-Lagard V. The archaeal COG1901/DUF358 SPOUT-methyltransferase members, together with pseudouridine synthase Pus10, catalyze the formation of 1-methylpseudouridine at position 54 of tRNA. RNA (NEW YORK, N.Y.) 2012; 18:421-33. [PMID: 22274953 PMCID: PMC3285931 DOI: 10.1261/rna.030841.111] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
The methylation of pseudouridine (Ψ) at position 54 of tRNA, producing m(1)Ψ, is a hallmark of many archaeal species, but the specific methylase involved in the formation of this modification had yet to be characterized. A comparative genomics analysis had previously identified COG1901 (DUF358), part of the SPOUT superfamily, as a candidate for this missing methylase family. To test this prediction, the COG1901 encoding gene, HVO_1989, was deleted from the Haloferax volcanii genome. Analyses of modified base contents indicated that while m(1)Ψ was present in tRNA extracted from the wild-type strain, it was absent from tRNA extracted from the mutant strain. Expression of the gene encoding COG1901 from Halobacterium sp. NRC-1, VNG1980C, complemented the m(1)Ψ minus phenotype of the ΔHVO_1989 strain. This in vivo validation was extended with in vitro tests. Using the COG1901 recombinant enzyme from Methanocaldococcus jannaschii (Mj1640), purified enzyme Pus10 from M. jannaschii and full-size tRNA transcripts or TΨ-arm (17-mer) fragments as substrates, the sequential pathway of m(1)Ψ54 formation in Archaea was reconstituted. The methylation reaction is AdoMet dependent. The efficiency of the methylase reaction depended on the identity of the residue at position 55 of the TΨ-loop. The presence of Ψ55 allowed the efficient conversion of Ψ54 to m(1)Ψ54, whereas in the presence of C55, the reaction was rather inefficient and no methylation reaction occurred if a purine was present at this position. These results led to renaming the Archaeal COG1901 members as TrmY proteins.
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Affiliation(s)
- Kunal Chatterjee
- Department of Biochemistry and Molecular Biology, Southern Illinois University, Carbondale, Illinois 62901-4413, USA
| | - Ian K. Blaby
- Department of Microbiology & Cell Science, University of Florida, Gainesville, Florida 32611-0700, USA
| | - Patrick C. Thiaville
- Department of Microbiology & Cell Science, University of Florida, Gainesville, Florida 32611-0700, USA
| | - Mrinmoyee Majumder
- Department of Biochemistry and Molecular Biology, Southern Illinois University, Carbondale, Illinois 62901-4413, USA
| | - Henri Grosjean
- Université Paris11, IGM, CNRS, UMR 8621, Orsay, F 91405, France
| | - Y. Adam Yuan
- Department of Biological Sciences and Temasek Life Sciences Laboratory, National University of Singapore, Singapore, 117543
| | - Ramesh Gupta
- Department of Biochemistry and Molecular Biology, Southern Illinois University, Carbondale, Illinois 62901-4413, USA
- Corresponding authors.E-mail .E-mail .
| | - Valérie de Crécy-Lagard
- Department of Microbiology & Cell Science, University of Florida, Gainesville, Florida 32611-0700, USA
- Corresponding authors.E-mail .E-mail .
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39
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Wright JR, Keffer-Wilkes LC, Dobing SR, Kothe U. Pre-steady-state kinetic analysis of the three Escherichia coli pseudouridine synthases TruB, TruA, and RluA reveals uniformly slow catalysis. RNA (NEW YORK, N.Y.) 2011; 17:2074-84. [PMID: 21998096 PMCID: PMC3222121 DOI: 10.1261/rna.2905811] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2011] [Accepted: 08/29/2011] [Indexed: 05/20/2023]
Abstract
Pseudouridine synthases catalyze formation of the most abundant modification of functional RNAs by site-specifically isomerizing uridines to pseudouridines. While the structure and substrate specificity of these enzymes have been studied in detail, the kinetic and the catalytic mechanism of pseudouridine synthases remain unknown. Here, the first pre-steady-state kinetic analysis of three Escherichia coli pseudouridine synthases is presented. A novel stopped-flow absorbance assay revealed that substrate tRNA binding by TruB takes place in two steps with an overall rate of 6 sec(-1). In order to observe catalysis of pseudouridine formation directly, the traditional tritium release assay was adapted for the quench-flow technique, allowing, for the first time, observation of a single round of pseudouridine formation. Thereby, the single-round rate constant of pseudouridylation (k(Ψ)) by TruB was determined to be 0.5 sec(-1). This rate constant is similar to the k(cat) obtained under multiple-turnover conditions in steady-state experiments, indicating that catalysis is the rate-limiting step for TruB. In order to investigate if pseudouridine synthases are characterized by slow catalysis in general, the rapid kinetic quench-flow analysis was also performed with two other E. coli enzymes, RluA and TruA, which displayed rate constants of pseudouridine formation of 0.7 and 0.35 sec(-1), respectively. Hence, uniformly slow catalysis might be a general feature of pseudouridine synthases that share a conserved catalytic domain and supposedly use the same catalytic mechanism.
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Affiliation(s)
- Jaden R. Wright
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada T1K 3M4
| | - Laura C. Keffer-Wilkes
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada T1K 3M4
| | - Selina R. Dobing
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada T1K 3M4
| | - Ute Kothe
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada T1K 3M4
- Corresponding author.E-mail .
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40
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Sasarman F, Antonicka H, Horvath R, Shoubridge EA. The 2-thiouridylase function of the human MTU1 (TRMU) enzyme is dispensable for mitochondrial translation. Hum Mol Genet 2011; 20:4634-43. [PMID: 21890497 DOI: 10.1093/hmg/ddr397] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
MTU1 (TRMU) is a mitochondrial enzyme responsible for the 2-thiolation of the wobble U in tRNA(Lys), tRNA(Glu) and tRNA(Gln), a post-transcriptional modification believed to be important for accurate and efficient synthesis of the 13 respiratory chain subunits encoded by mtDNA. Mutations in MTU1 are associated with acute infantile liver failure, and this has been ascribed to a transient lack of cysteine, the sulfur donor for the thiouridylation reaction, resulting in a mitochondrial translation defect during early development. A mutation in tRNA(Lys) that causes myoclonic epilepsy with ragged-red fibers (MERRF) is also reported to prevent modification of the wobble U. Here we show that mitochondrial translation is unaffected in fibroblasts from an MTU1 patient, in which MTU1 is undetectable by immunoblotting, despite the severe reduction in the 2-thiolation of mitochondrial tRNA(Lys), tRNA(Glu) and tRNA(Gln). The only respiratory chain abnormality that we could observe in these cells was an accumulation of a Complex II assembly intermediate, which, however, did not affect the level of the fully assembled enzyme. The identical phenotype was observed by siRNA-mediated knockdown of MTU1 in HEK 293 cells. Further, the mitochondrial translation deficiencies present in myoblasts from mitochondrial encephalomyopathy, lactic acidosis and stroke-like episode and MERRF patients, which are associated with defects in post-transcriptional modification of mitochondrial tRNAs, did not worsen following knockdown of MTU1 in these cells. This study demonstrates that MTU1 is not required for mitochondrial translation at normal steady-state levels of tRNAs, and that it may possess an as yet uncharacterized function in another sulfur-trafficking pathway.
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Affiliation(s)
- Florin Sasarman
- Montreal Neurological Institute, McGill University, Montreal H3A 2B4, Canada
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41
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Blaby IK, Majumder M, Chatterjee K, Jana S, Grosjean H, de Crécy-Lagard V, Gupta R. Pseudouridine formation in archaeal RNAs: The case of Haloferax volcanii. RNA (NEW YORK, N.Y.) 2011; 17:1367-80. [PMID: 21628430 PMCID: PMC3138572 DOI: 10.1261/rna.2712811] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Pseudouridine (Ψ), the isomer of uridine, is commonly found at various positions of noncoding RNAs of all organisms. Ψ residues are formed by a number of single- or multisite specific Ψ synthases, which generally act as stand-alone proteins. In addition, in Eukarya and Archaea, specific ribonucleoprotein complexes, each containing a distinct box H/ACA guide RNA and four core proteins, can produce Ψ at many sites of different cellular RNAs. Cbf5 is the core Ψ synthase in these complexes. Using Haloferax volcanii as an archaeal model organism, we show that, contrary to eukaryotes, the Cbf5 homolog (HVO_2493) is not essential in this archaeon. The Cbf5-deleted strain of H. volcanii completely lacks Ψ at positions 1940, 1942, 2605, and 2591 (Escherichia coli positions 1915, 1917, 2572, and 2586) of its 23S rRNA, and contains reduced steady-state levels of some box H/ACA RNAs. Archaeal Cbf5 is known to have tRNA Ψ55 synthase activity in vitro but we could not confirm this activity in vivo in H. volcanii. Conversely, the Pus10 (previously PsuX) homolog (HVO_1979), which can produce tRNA Ψ55, as well as Ψ54 in vitro, is shown here to be essential in H. volcanii, whereas the corresponding tRNA Ψ55 synthases, Pus4 and TruB, are not essential in yeast and E. coli, respectively. Finally, we demonstrate that HVO_1852, the TruA/Pus3 homolog, is responsible for the pseudouridylation of position 39 in H. volcanii tRNAs and that the corresponding gene is not essential.
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Affiliation(s)
- Ian K. Blaby
- Department of Microbiology & Cell Science, University of Florida, Gainesville, Florida 32611-0700, USA
| | - Mrinmoyee Majumder
- Department of Biochemistry and Molecular Biology, Southern Illinois University, Carbondale, Illinois 62901-4413, USA
| | - Kunal Chatterjee
- Department of Biochemistry and Molecular Biology, Southern Illinois University, Carbondale, Illinois 62901-4413, USA
| | - Sujata Jana
- Department of Biochemistry and Molecular Biology, Southern Illinois University, Carbondale, Illinois 62901-4413, USA
| | - Henri Grosjean
- Université Paris 11, IGM, CNRS, UMR 8621, Orsay, F 91405, France
| | - Valérie de Crécy-Lagard
- Department of Microbiology & Cell Science, University of Florida, Gainesville, Florida 32611-0700, USA
- Corresponding authors.E-mail .E-mail .
| | - Ramesh Gupta
- Department of Biochemistry and Molecular Biology, Southern Illinois University, Carbondale, Illinois 62901-4413, USA
- Corresponding authors.E-mail .E-mail .
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42
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Ishida K, Kunibayashi T, Tomikawa C, Ochi A, Kanai T, Hirata A, Iwashita C, Hori H. Pseudouridine at position 55 in tRNA controls the contents of other modified nucleotides for low-temperature adaptation in the extreme-thermophilic eubacterium Thermus thermophilus. Nucleic Acids Res 2011; 39:2304-18. [PMID: 21097467 PMCID: PMC3064792 DOI: 10.1093/nar/gkq1180] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2010] [Revised: 11/02/2010] [Accepted: 11/02/2010] [Indexed: 11/13/2022] Open
Abstract
Pseudouridine at position 55 (Ψ55) in eubacterial tRNA is produced by TruB. To clarify the role of the Ψ55 modification, we constructed a truB gene disruptant (ΔtruB) strain of Thermus thermophilus which is an extreme-thermophilic eubacterium. Unexpectedly, the ΔtruB strain exhibited severe growth retardation at 50 °C. We assumed that these phenomena might be caused by lack of RNA chaperone activity of TruB, which was previously hypothetically proposed by others. To confirm this idea, we replaced the truB gene in the genome with mutant genes, which express TruB proteins with very weak or no enzymatic activity. However the growth retardation at 50 °C was not rescued by these mutant proteins. Nucleoside analysis revealed that Gm18, m(5)s(2)U54 and m(1)A58 in tRNA from the ΔtruB strain were abnormally increased. An in vitro assay using purified tRNA modification enzymes demonstrated that the Ψ55 modification has a negative effect on Gm18 formation by TrmH. These experimental results show that the Ψ55 modification is required for low-temperature adaptation to control other modified. (35)S-Met incorporation analysis showed that the protein synthesis activity of the ΔtruB strain was inferior to that of the wild-type strain and that the cold-shock proteins were absence in the ΔtruB cells at 50°C.
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Affiliation(s)
- Kazuo Ishida
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto, Kyoto 615-8510, Venture Business Laboratory, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577 and RIKEN SPring-8 Center, Kouto 1-1-1, Sayo-cho, Sayo-gun, Hyougo 679-5148, Japan
| | - Takashi Kunibayashi
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto, Kyoto 615-8510, Venture Business Laboratory, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577 and RIKEN SPring-8 Center, Kouto 1-1-1, Sayo-cho, Sayo-gun, Hyougo 679-5148, Japan
| | - Chie Tomikawa
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto, Kyoto 615-8510, Venture Business Laboratory, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577 and RIKEN SPring-8 Center, Kouto 1-1-1, Sayo-cho, Sayo-gun, Hyougo 679-5148, Japan
| | - Anna Ochi
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto, Kyoto 615-8510, Venture Business Laboratory, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577 and RIKEN SPring-8 Center, Kouto 1-1-1, Sayo-cho, Sayo-gun, Hyougo 679-5148, Japan
| | - Tamotsu Kanai
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto, Kyoto 615-8510, Venture Business Laboratory, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577 and RIKEN SPring-8 Center, Kouto 1-1-1, Sayo-cho, Sayo-gun, Hyougo 679-5148, Japan
| | - Akira Hirata
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto, Kyoto 615-8510, Venture Business Laboratory, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577 and RIKEN SPring-8 Center, Kouto 1-1-1, Sayo-cho, Sayo-gun, Hyougo 679-5148, Japan
| | - Chikako Iwashita
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto, Kyoto 615-8510, Venture Business Laboratory, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577 and RIKEN SPring-8 Center, Kouto 1-1-1, Sayo-cho, Sayo-gun, Hyougo 679-5148, Japan
| | - Hiroyuki Hori
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto, Kyoto 615-8510, Venture Business Laboratory, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577 and RIKEN SPring-8 Center, Kouto 1-1-1, Sayo-cho, Sayo-gun, Hyougo 679-5148, Japan
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O'Connor M, Gregory ST. Inactivation of the RluD pseudouridine synthase has minimal effects on growth and ribosome function in wild-type Escherichia coli and Salmonella enterica. J Bacteriol 2011; 193:154-62. [PMID: 21037010 PMCID: PMC3019933 DOI: 10.1128/jb.00970-10] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Accepted: 10/18/2010] [Indexed: 11/20/2022] Open
Abstract
The Escherichia coli rluD gene encodes a pseudouridine synthase responsible for the pseudouridine (Ψ) modifications at positions 1911, 1915, and 1917 in helix 69 of 23S rRNA. It has been reported that deletion of rluD in K-12 strains of E. coli is associated with extremely slow growth, increased readthrough of stop codons, and defects in 50S ribosomal subunit assembly and 30S-50S subunit association. Suppressor mutations in the prfB and prfC genes encoding release factor 2 (RF2) and RF3 that restore the wild type-growth rate and also correct the ribosomal defects have now been isolated. These suppressors link helix 69 Ψ residues with the termination phase of protein synthesis. However, further genetic analysis reported here also reveals that the slow growth and other defects associated with inactivation of rluD in E. coli K-12 strains are due to a defective RF2 protein, with a threonine at position 246, which is present in all K-12 strains. This is in contrast to the more typical alanine found at this position in most bacterial RF2s, including those of other E. coli strains. Inactivation of rluD in E. coli strains containing the prfB allele from E. coli B or in Salmonella enterica, both carrying an RF2 with Ala246, has negligible effects on growth, termination, or ribosome function. The results indicate that, in contrast to those in wild bacteria, termination functions in E. coli K-12 strains carrying a partially defective RF2 protein are especially susceptible to perturbation of ribosome-RF interactions, such as that caused by loss of h69 Ψ modifications.
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Affiliation(s)
- Michael O'Connor
- School of Biological Sciences, University of Missouri-Kansas City, 5007 Rockhill Rd, Kansas City, Missouri 64110, USA.
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Benítez-Páez A, Villarroya M, Douthwaite S, Gabaldón T, Armengod ME. YibK is the 2'-O-methyltransferase TrmL that modifies the wobble nucleotide in Escherichia coli tRNA(Leu) isoacceptors. RNA (NEW YORK, N.Y.) 2010; 16:2131-43. [PMID: 20855540 PMCID: PMC2957053 DOI: 10.1261/rna.2245910] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2010] [Accepted: 08/18/2010] [Indexed: 05/25/2023]
Abstract
Transfer RNAs are the most densely modified nucleic acid molecules in living cells. In Escherichia coli, more than 30 nucleoside modifications have been characterized, ranging from methylations and pseudouridylations to more complex additions that require multiple enzymatic steps. Most of the modifying enzymes have been identified, although a few notable exceptions include the 2'-O-methyltransferase(s) that methylate the ribose at the nucleotide 34 wobble position in the two leucyl isoacceptors tRNA(Leu)(CmAA) and tRNA(Leu)(cmnm5UmAA). Here, we have used a comparative genomics approach to uncover candidate E. coli genes for the missing enzyme(s). Transfer RNAs from null mutants for candidate genes were analyzed by mass spectrometry and revealed that inactivation of yibK leads to loss of 2'-O-methylation at position 34 in both tRNA(Leu)(CmAA) and tRNA(Leu)(cmnm5UmAA). Loss of YibK methylation reduces the efficiency of codon-wobble base interaction, as demonstrated in an amber suppressor supP system. Inactivation of yibK had no detectable effect on steady-state growth rate, although a distinct disadvantage was noted in multiple-round, mixed-population growth experiments, suggesting that the ability to recover from the stationary phase was impaired. Methylation is restored in vivo by complementing with a recombinant copy of yibK. Despite being one of the smallest characterized α/β knot proteins, YibK independently catalyzes the methyl transfer from S-adenosyl-L-methionine to the 2'-OH of the wobble nucleotide; YibK recognition of this target requires a pyridine at position 34 and N⁶-(isopentenyl)-2-methylthioadenosine at position 37. YibK is one of the last remaining E. coli tRNA modification enzymes to be identified and is now renamed TrmL.
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Affiliation(s)
- Alfonso Benítez-Páez
- Laboratorio de Genética Molecular, Centro de Investigación Príncipe Felipe, 46012 Valencia, Spain
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Purta E, O'Connor M, Bujnicki JM, Douthwaite S. YgdE is the 2'-O-ribose methyltransferase RlmM specific for nucleotide C2498 in bacterial 23S rRNA. Mol Microbiol 2009; 72:1147-58. [PMID: 19400805 DOI: 10.1111/j.1365-2958.2009.06709.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The rRNAs of Escherichia coli contain four 2'-O-methylated nucleotides. Similar to other bacterial species and in contrast with Archaea and Eukaryota, the E. coli rRNA modifications are catalysed by specific methyltransferases that find their nucleotide targets without being guided by small complementary RNAs. We show here that the ygdE gene encodes the methyltransferase that catalyses 2'-O-methylation at nucleotide C2498 in the peptidyl transferase loop of E. coli 23S rRNA. Analyses of rRNAs using MALDI mass spectrometry showed that inactivation of the ygdE gene leads to loss of methylation at nucleotide C2498. The loss of ygdE function causes a slight reduction in bacterial fitness. Methylation at C2498 was restored by complementing the knock-out strain with a recombinant copy of ygdE. The recombinant YgdE methyltransferase modifies C2498 in naked 23S rRNA, but not in assembled 50S subunits or ribosomes. Nucleotide C2498 is situated within a highly conserved and heavily modified rRNA sequence, and YgdE's activity is influenced by other modification enzymes that target this region. Phylogenetically, YgdE is placed in the cluster of orthologous groups COG2933 together with S-adenosylmethionine-dependent, Rossmann-fold methyltransferases such as the archaeal and eukaryotic RNA-guided fibrillarins. The ygdE gene has been redesignated rlmM for rRNA large subunit methyltransferase M.
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Affiliation(s)
- Elzbieta Purta
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
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46
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A pseudouridine synthase homologue is critical to cellular differentiation in Toxoplasma gondii. EUKARYOTIC CELL 2009; 8:398-409. [PMID: 19124578 DOI: 10.1128/ec.00329-08] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Toxoplasma gondii is a haploid protozoan parasite infecting about one in seven people in the United States. Key to the worldwide prevalence of T. gondii is its ability to establish a lifelong, chronic infection by evading the immune system, and central to this is the developmental switch between the two asexual forms, tachyzoites and bradyzoites. A library of mutants defective in tachyzoite-to-bradyzoite differentiation (Tbd(-)) was created through insertional mutagenesis. This library contains mutants that, compared to the wild type, are between 20% and 74% as efficient at stage conversion. Two mutants, TBD5 and TBD8, with disruptions in a gene encoding a putative pseudouridine synthase, PUS1, were identified. The disruption in TBD8 is in the 5' end of the PUS1 gene and appears to produce a null allele with a 50% defect in differentiation. This is about the same switch efficiency as obtained with an engineered pus1 deletion mutant (Deltapus1). The insertion in TBD5 is within the PUS1 coding region, and this appears to result in a more extreme phenotype of only approximately 10% switch efficiency. Complementation of TBD8 with the genomic PUS1 allele restored wild-type differentiation efficiency. Infection of mice with pus1 mutant strains results in increased mortality during the acute phase and higher cyst burdens during the chronic infection, demonstrating an aberrant differentiation phenotype in vivo due to PUS1 disruption. Our results suggest a surprising and important role for RNA modification in this biological process.
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Purta E, Kaminska KH, Kasprzak JM, Bujnicki JM, Douthwaite S. YbeA is the m3Psi methyltransferase RlmH that targets nucleotide 1915 in 23S rRNA. RNA (NEW YORK, N.Y.) 2008; 14:2234-44. [PMID: 18755835 PMCID: PMC2553730 DOI: 10.1261/rna.1198108] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2008] [Accepted: 07/09/2008] [Indexed: 05/26/2023]
Abstract
Pseudouridines in the stable RNAs of Bacteria are seldom subjected to further modification. There are 11 pseudouridine (Psi) sites in Escherichia coli rRNA, and further modification is found only at Psi1915 in 23S rRNA, where the N-3 position of the base becomes methylated. Here, we report the identity of the E. coli methyltransferase that specifically catalyzes methyl group addition to form m(3)Psi1915. Analyses of E. coli rRNAs using MALDI mass spectrometry showed that inactivation of the ybeA gene leads to loss of methylation at nucleotide Psi1915. Methylation is restored by complementing the knockout strain with a plasmid-encoded copy of ybeA. Homologs of the ybeA gene, and thus presumably the ensuing methylation at nucleotide m(3)Psi1915, are present in most bacterial lineages but are essentially absent in the Archaea and Eukaryota. Loss of ybeA function in E. coli causes a slight slowing of the growth rate. Phylogenetically, ybeA and its homologs are grouped with other putative S-adenosylmethionine-dependent, SPOUT methyltransferase genes in the Cluster of Orthologous Genes COG1576; ybeA is the first member to be functionally characterized. The YbeA methyltransferase is active as a homodimer and docks comfortably into the ribosomal A site without encroaching into the P site. YbeA makes extensive interface contacts with both the 30S and 50S subunits to align its active site cofactor adjacent to nucleotide Psi1915. Methylation by YbeA (redesignated RlmH for rRNA large subunit methyltransferase H) possibly functions as a stamp of approval signifying that the 50S subunit has engaged in translational initiation.
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Affiliation(s)
- Elzbieta Purta
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark
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48
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YccW is the m5C methyltransferase specific for 23S rRNA nucleotide 1962. J Mol Biol 2008; 383:641-51. [PMID: 18786544 DOI: 10.1016/j.jmb.2008.08.061] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2008] [Revised: 08/13/2008] [Accepted: 08/21/2008] [Indexed: 11/20/2022]
Abstract
Methylation at the 5-position of cytosine [m(5)C (5-methylcytidine)] occurs at three RNA nucleotides in Escherichia coli. All these modifications are at highly conserved nucleotides in the rRNAs, and each is catalyzed by its own m(5)C methyltransferase enzyme. Two of the enzymes, RsmB and RsmF, are already known and methylate 16S rRNA at nucleotides C967 and C1407, respectively. Here, we report the identity of the third E. coli m(5)C methyltransferase. Analysis of rRNAs by matrix-assisted laser desorption/ionization mass spectrometry showed that inactivation of the yccW gene leads to loss of m(5)C methylation at nucleotide 1962 in E. coli 23S rRNA. This methylation is restored by complementing the knockout strain with a plasmid-encoded copy of the yccW gene. Purified recombinant YccW protein retains its specificity for C1962 in vitro and methylates naked 23S rRNA isolated from the yccW knockout strain. However, YccW does not methylate assembled 50S subunits, and this is somewhat surprising as the published crystal structures show nucleotide C1962 to be fully accessible at the subunit interface. YccW-directed methylation at nucleotide C1962 is conserved in bacteria, and loss of this methylation in E. coli marginally reduces its growth rate. YccW had previously eluded identification because it displays only limited sequence similarity to the m(5)C methyltransferases RsmB and RsmF and is in fact more similar to known m(5)U (5-methyluridine) RNA methyltransferases. In keeping with the previously proposed nomenclature system for bacterial rRNA methyltransferases, yccW is now designated as the rRNA large subunit methyltransferase gene rlmI.
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Durairaj A, Limbach PA. Mass spectrometry of the fifth nucleoside: a review of the identification of pseudouridine in nucleic acids. Anal Chim Acta 2008; 623:117-25. [PMID: 18620915 PMCID: PMC2597214 DOI: 10.1016/j.aca.2008.06.027] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2008] [Revised: 06/17/2008] [Accepted: 06/18/2008] [Indexed: 10/21/2022]
Abstract
Pseudouridine, the so-called fifth nucleoside due to its ubiquitous presence in ribonucleic acids (RNAs), remains among the most challenging modified nucleosides to characterize. As an isomer of the major nucleoside uridine, pseudouridine cannot be detected by standard reverse-transcriptase-based DNA sequencing or RNase mapping approaches. Thus, over the past 15 years, investigators have focused on the unique structural properties of pseudouridine to develop selective derivatization or fragmentation strategies for its determination. While the N-cyclohexyl-N'-beta-(4-methylmorpholinium)ethylcarbodiimide p-tosylate (CMCT)-reverse transcriptase assay remains both a popular and powerful approach to screen for pseudouridine in larger RNAs, mass-spectrometry-based approaches are poised to play an increasingly important role in either confirming the findings of the CMCT-reverse transcriptase assay or in characterizing pseudouridine sequence placement and abundance in smaller RNAs. This review includes a brief discussion of pseudouridine including a summary of its biosynthesis and known importance within various RNAs. The review then focuses on chemical derivatization approaches that can be used to selectively modify pseudouridine to improve its detection, and the development of mass-spectrometry-based assays for the identification and sequencing of pseudouridine in various RNAs.
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Affiliation(s)
- Anita Durairaj
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, PO Box 210172, University of Cincinnati, Cincinnati, OH 45221-0172, United States
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Characterization of chromosomal regions conserved in Yersinia pseudotuberculosis and lost by Yersinia pestis. Infect Immun 2008; 76:4592-9. [PMID: 18678673 DOI: 10.1128/iai.00568-08] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The transformation of the enteropathogenic bacterium Yersinia pseudotuberculosis into the plague bacillus, Yersinia pestis, has been accompanied by extensive genetic loss. This study focused on chromosomal regions conserved in Y. pseudotuberculosis and lost during its transformation into Y. pestis. An extensive PCR screening of 78 strains of the two species identified five regions (R1 to R5) and four open reading frames (ORFs; orf1 to orf4) that were conserved in Y. pseudotuberculosis and absent from Y. pestis. Their conservation in Y. pseudotuberculosis suggests a positive selective pressure and a role during the life cycle of this species. Attempts to delete two ORFs (orf3 and orf4) from the chromosome of strain IP32953 were unsuccessful, indicating that they are essential for its viability. The seven remaining loci were individually deleted from the IP32953 chromosome, and the ability of each mutant to grow in vitro and to kill mice upon intragastric infection was evaluated. Four loci (orf1, R2, R4, and R5) were not required for optimal growth or virulence of Y. pseudotuberculosis. In contrast, orf2, encoding a putative pseudouridylate synthase involved in RNA stability, was necessary for the optimal growth of IP32953 at 37 degrees C in a chemically defined medium (M63S). Deletion of R1, a region predicted to encode the methionine salvage pathway, altered the mutant pathogenicity, suggesting that the availability of free methionine is severely restricted in vivo. R3, a region composed mostly of genes of unknown functions, was necessary for both optimal growth of Y. pseudotuberculosis at 37 degrees C in M63S and for virulence. Therefore, despite their loss in Y. pestis, five of the nine Y. pseudotuberculosis-specific chromosomal loci studied play a role in the survival, growth, or virulence of this species.
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