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Zhang MM, Yuan B, Wang YT, Zhang FL, Liu CG, Zhao XQ. Differential Protein Expression in Set5p-Mediated Acetic Acid Stress Response and Novel Targets for Engineering Yeast Stress Tolerance. J Proteome Res 2024; 23:2986-2998. [PMID: 38396335 DOI: 10.1021/acs.jproteome.3c00617] [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: 02/25/2024]
Abstract
Acetic acid is a prevalent inhibitor in lignocellulosic hydrolysate, which represses microbial growth and bioproduction. Histone modification and chromatin remodeling have been revealed to be critical for regulating eukaryotic metabolism. However, related studies in chronic acetic acid stress responses remain unclear. Our previous studies revealed that overexpression of the histone H4 methyltransferase Set5p enhanced acetic acid stress tolerance of the budding yeast Saccharomyces cerevisiae. In this study, we examined the role of Set5p in acetic acid stress by analyzing global protein expression. Significant activation of intracellular protein expression under the stress was discovered, and the functions of the differential proteins were mainly involved in chromatin modification, signal transduction, and carbohydrate metabolism. Notably, a substantial increase of Set5p expression was observed in response to acetic acid stress. Functional studies demonstrated that the restriction of the telomere capping protein Rtc3p, as well as Ies3p and Taf14p, which are related to chromatin regulation, was critical for yeast stress response. This study enriches the understanding of the epigenetic regulatory mechanisms underlying yeast stress response mediated by histone-modifying enzymes. The results also benefit the development of robust yeast strains for lignocellulosic bioconversion.
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Affiliation(s)
- Ming-Ming Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Bing Yuan
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ya-Ting Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Feng-Li Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chen-Guang Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xin-Qing Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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2
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Deng L, Kumar J, Rose R, McIntyre W, Fabris D. Analyzing RNA posttranscriptional modifications to decipher the epitranscriptomic code. MASS SPECTROMETRY REVIEWS 2024; 43:5-38. [PMID: 36052666 DOI: 10.1002/mas.21798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 05/23/2022] [Accepted: 05/27/2022] [Indexed: 06/15/2023]
Abstract
The discovery of RNA silencing has revealed that non-protein-coding sequences (ncRNAs) can cover essential roles in regulatory networks and their malfunction may result in severe consequences on human health. These findings have prompted a general reassessment of the significance of RNA as a key player in cellular processes. This reassessment, however, will not be complete without a greater understanding of the distribution and function of the over 170 variants of the canonical ribonucleotides, which contribute to the breathtaking structural diversity of natural RNA. This review surveys the analytical approaches employed for the identification, characterization, and detection of RNA posttranscriptional modifications (rPTMs). The merits of analyzing individual units after exhaustive hydrolysis of the initial biopolymer are outlined together with those of identifying their position in the sequence of parent strands. Approaches based on next generation sequencing and mass spectrometry technologies are covered in depth to provide a comprehensive view of their respective merits. Deciphering the epitranscriptomic code will require not only mapping the location of rPTMs in the various classes of RNAs, but also assessing the variations of expression levels under different experimental conditions. The fact that no individual platform is currently capable of meeting all such demands implies that it will be essential to capitalize on complementary approaches to obtain the desired information. For this reason, the review strived to cover the broadest possible range of techniques to provide readers with the fundamental elements necessary to make informed choices and design the most effective possible strategy to accomplish the task at hand.
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Affiliation(s)
- L Deng
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
| | - J Kumar
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
| | - R Rose
- Department of Advanced Research Technologies, New York University Langone Health Center, New York, USA
| | - W McIntyre
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
| | - Daniele Fabris
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
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3
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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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4
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Petri BJ, Cave MC, Klinge CM. Changes in m6A in Steatotic Liver Disease. Genes (Basel) 2023; 14:1653. [PMID: 37628704 PMCID: PMC10454815 DOI: 10.3390/genes14081653] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/10/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
Fatty liver disease is one of the major causes of morbidity and mortality worldwide. Fatty liver includes non-alcoholic fatty liver disease (NAFLD) and non-alcoholic steatohepatitis (NASH), now replaced by a consensus group as metabolic dysfunction-associated steatotic liver disease (MASLD). While excess nutrition and obesity are major contributors to fatty liver, the underlying mechanisms remain largely unknown and therapeutic interventions are limited. Reversible chemical modifications in RNA are newly recognized critical regulators controlling post-transcriptional gene expression. Among these modifications, N6-methyladenosine (m6A) is the most abundant and regulates transcript abundance in fatty liver disease. Modulation of m6A by readers, writers, and erasers (RWE) impacts mRNA processing, translation, nuclear export, localization, and degradation. While many studies focus on m6A RWE expression in human liver pathologies, limitations of technology and bioinformatic methods to detect m6A present challenges in understanding the epitranscriptomic mechanisms driving fatty liver disease progression. In this review, we summarize the RWE of m6A and current methods of detecting m6A in specific genes associated with fatty liver disease.
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Affiliation(s)
- Belinda J. Petri
- Department of Biochemistry, University of Louisville School of Medicine, Louisville, KY 40292, USA;
| | - Matthew C. Cave
- Center for Integrative Environmental Health Sciences (CIEHS), University of Louisville, Louisville, KY 40292, USA;
- Hepatobiology and Toxicology Center, University of Louisville, Louisville, KY 40292, USA
- Division of Gastroenterology, Hepatology & Nutrition, Department of Medicine, University of Louisville School of Medicine, Louisville, KY 40292, USA
| | - Carolyn M. Klinge
- Department of Biochemistry, University of Louisville School of Medicine, Louisville, KY 40292, USA;
- Center for Integrative Environmental Health Sciences (CIEHS), University of Louisville, Louisville, KY 40292, USA;
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5
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Breznak SM, Peng Y, Deng L, Kotb NM, Flamholz Z, Rapisarda IT, Martin ET, LaBarge KA, Fabris D, Gavis ER, Rangan P. H/ACA snRNP-dependent ribosome biogenesis regulates translation of polyglutamine proteins. SCIENCE ADVANCES 2023; 9:eade5492. [PMID: 37343092 PMCID: PMC10284551 DOI: 10.1126/sciadv.ade5492] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 05/17/2023] [Indexed: 06/23/2023]
Abstract
Stem cells in many systems, including Drosophila germline stem cells (GSCs), increase ribosome biogenesis and translation during terminal differentiation. Here, we show that the H/ACA small nuclear ribonucleoprotein (snRNP) complex that promotes pseudouridylation of ribosomal RNA (rRNA) and ribosome biogenesis is required for oocyte specification. Reducing ribosome levels during differentiation decreased the translation of a subset of messenger RNAs that are enriched for CAG trinucleotide repeats and encode polyglutamine-containing proteins, including differentiation factors such as RNA-binding Fox protein 1. Moreover, ribosomes were enriched at CAG repeats within transcripts during oogenesis. Increasing target of rapamycin (TOR) activity to elevate ribosome levels in H/ACA snRNP complex-depleted germlines suppressed the GSC differentiation defects, whereas germlines treated with the TOR inhibitor rapamycin had reduced levels of polyglutamine-containing proteins. Thus, ribosome biogenesis and ribosome levels can control stem cell differentiation via selective translation of CAG repeat-containing transcripts.
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Affiliation(s)
- Shane M. Breznak
- Department of Biological Sciences, RNA Institute, University at Albany, 1400 Washington Avenue, LSRB 2033D, Albany, NY 12222, USA
| | - Yingshi Peng
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Limin Deng
- Department of Biological Sciences, RNA Institute, University at Albany, 1400 Washington Avenue, LSRB 2033D, Albany, NY 12222, USA
- Department of Chemistry, University of Connecticut, 55N Eagleville Rd, Storrs, CT 06269, USA
| | - Noor M. Kotb
- Department of Biological Sciences, RNA Institute, University at Albany, 1400 Washington Avenue, LSRB 2033D, Albany, NY 12222, USA
- Department of Biomedical Sciences, University at Albany School of Public Health, Albany, NY 12144, USA
| | - Zachary Flamholz
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Ian T. Rapisarda
- Department of Biological Sciences, RNA Institute, University at Albany, 1400 Washington Avenue, LSRB 2033D, Albany, NY 12222, USA
- Lake Erie College of Osteopathic Medicine, College of Medicine, 1858 W Grandview Blvd, Erie, PA 16509, USA
| | - Elliot T. Martin
- Department of Biological Sciences, RNA Institute, University at Albany, 1400 Washington Avenue, LSRB 2033D, Albany, NY 12222, USA
| | - Kara A. LaBarge
- Department of Biological Sciences, RNA Institute, University at Albany, 1400 Washington Avenue, LSRB 2033D, Albany, NY 12222, USA
| | - Dan Fabris
- Department of Biological Sciences, RNA Institute, University at Albany, 1400 Washington Avenue, LSRB 2033D, Albany, NY 12222, USA
- Department of Chemistry, University of Connecticut, 55N Eagleville Rd, Storrs, CT 06269, USA
| | - Elizabeth R. Gavis
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Prashanth Rangan
- Department of Biological Sciences, RNA Institute, University at Albany, 1400 Washington Avenue, LSRB 2033D, Albany, NY 12222, USA
- Black Family Stem Cell Institute, Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029, USA
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6
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Piell KM, Petri BJ, Head KZ, Wahlang B, Xu R, Zhang X, Pan J, Rai SN, de Silva K, Chariker JH, Rouchka EC, Tan M, Li Y, Cave MC, Klinge CM. Disruption of the mouse liver epitranscriptome by long-term aroclor 1260 exposure. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2023; 100:104138. [PMID: 37137421 PMCID: PMC10330322 DOI: 10.1016/j.etap.2023.104138] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 04/26/2023] [Accepted: 04/29/2023] [Indexed: 05/05/2023]
Abstract
Chronic environmental exposure to polychlorinated biphenyls (PCBs) is associated with non-alcoholic fatty liver disease (NAFLD) and exacerbated by a high fat diet (HFD). Here, chronic (34 wks.) exposure of low fat diet (LFD)-fed male mice to Aroclor 1260 (Ar1260), a non-dioxin-like (NDL) mixture of PCBs, resulted in steatohepatitis and NAFLD. Twelve hepatic RNA modifications were altered with Ar1260 exposure including reduced abundance of 2'-O-methyladenosine (Am) and N(6)-methyladenosine (m6A), in contrast to increased Am in the livers of HFD-fed, Ar1260-exposed mice reported previously. Differences in 13 RNA modifications between LFD- and HFD- fed mice, suggest that diet regulates the liver epitranscriptome. Integrated network analysis of epitranscriptomic modifications identified a NRF2 (Nfe2l2) pathway in the chronic, LFD, Ar1260-exposed livers and an NFATC4 (Nfatc4) pathway for LFD- vs. HFD-fed mice. Changes in protein abundance were validated. The results demonstrate that diet and Ar1260 exposure alter the liver epitranscriptome in pathways associated with NAFLD.
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Affiliation(s)
- Kellianne M Piell
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40292, USA
| | - Belinda J Petri
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40292, USA
| | - Kimberly Z Head
- University of Louisville Hepatobiology and Toxicology Center, USA
| | - Banrida Wahlang
- University of Louisville Hepatobiology and Toxicology Center, USA
| | - Raobo Xu
- University of Louisville Hepatobiology and Toxicology Center, USA; Department of Chemistry, University of Louisville College of Arts and Sciences, USA
| | - Xiang Zhang
- University of Louisville Hepatobiology and Toxicology Center, USA; Department of Chemistry, University of Louisville College of Arts and Sciences, USA; University of Louisville Center for Integrative Environmental Health Sciences (CIEHS), USA
| | - Jianmin Pan
- Division of Biostatistics and Bioinformatics, Department of Environmental and Public Health Sciences, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA; Cancer Data Science Center, Biostatistics and Informatics Shared Resource, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA
| | - Shesh N Rai
- Division of Biostatistics and Bioinformatics, Department of Environmental and Public Health Sciences, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA; Cancer Data Science Center, Biostatistics and Informatics Shared Resource, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA
| | - Kalpani de Silva
- KY INBRE Bioinformatics Core, University of Louisville, Louisville, KY 40292, USA; Department of Neuroscience Training, University of Louisville, Louisville, KY 40292, USA
| | - Julia H Chariker
- KY INBRE Bioinformatics Core, University of Louisville, Louisville, KY 40292, USA; Department of Neuroscience Training, University of Louisville, Louisville, KY 40292, USA
| | - Eric C Rouchka
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40292, USA; KY INBRE Bioinformatics Core, University of Louisville, Louisville, KY 40292, USA
| | - Min Tan
- Division of Surgical Oncology, Department of Surgery, University of Louisville School of Medicine, Louisville, KY 40292, USA
| | - Yan Li
- Division of Surgical Oncology, Department of Surgery, University of Louisville School of Medicine, Louisville, KY 40292, USA
| | - Matthew C Cave
- University of Louisville Hepatobiology and Toxicology Center, USA; University of Louisville Center for Integrative Environmental Health Sciences (CIEHS), USA; Division of Gastroenterology, Hepatology & Nutrition, Department of Medicine, University of Louisville School of Medicine, Louisville, KY 40292, USA; The University of Louisville Superfund Research Center, USA
| | - Carolyn M Klinge
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40292, USA; University of Louisville Center for Integrative Environmental Health Sciences (CIEHS), USA.
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7
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Janssen KA, Xie Y, Kramer MC, Gregory BD, Garcia BA. Data-Independent Acquisition for the Detection of Mononucleoside RNA Modifications by Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:885-893. [PMID: 35357823 PMCID: PMC9425428 DOI: 10.1021/jasms.2c00065] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
RNA is dynamically modified in cells by a plethora of chemical moieties to modulate molecular functions and processes. Over 140 modifications have been identified across species and RNA types, with the highest density and diversity of modifications found in tRNA (tRNA). The methods used to identify and quantify these modifications have developed over recent years and continue to advance, primarily in the fields of next-generation sequencing (NGS) and mass spectrometry (MS). Most current NGS methods are limited to antibody-recognized or chemically derivatized modifications and have limitations in identifying multiple modifications simultaneously. Mass spectrometry can overcome both of these issues, accurately identifying a large number of modifications in a single run. Here, we present advances in MS data acquisition for the purpose of RNA modification identification and quantitation. Using this approach, we identified multiple tRNA wobble position modifications in Arabidopsis thaliana that are upregulated in salt-stressed growth conditions and may stabilize translation of salt stress induced proteins. This work presents improvements in methods for studying RNA modifications and introduces a possible regulatory role of wobble position modifications in A. thaliana translation.
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Affiliation(s)
- Kevin A. Janssen
- Center for Mitochondrial and Epigenomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Yixuan Xie
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | | | - Brian D. Gregory
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Benjamin A. Garcia
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Corresponding Author: Correspondence to: Benjamin A. Garcia;
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8
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Evke S, Lin Q, Melendez JA, Begley TJ. Epitranscriptomic Reprogramming Is Required to Prevent Stress and Damage from Acetaminophen. Genes (Basel) 2022; 13:genes13030421. [PMID: 35327975 PMCID: PMC8955276 DOI: 10.3390/genes13030421] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/13/2022] [Accepted: 02/16/2022] [Indexed: 02/06/2023] Open
Abstract
Epitranscriptomic marks, in the form of enzyme catalyzed RNA modifications, play important gene regulatory roles in response to environmental and physiological conditions. However, little is known with respect to how acute toxic doses of pharmaceuticals influence the epitranscriptome. Here we define how acetaminophen (APAP) induces epitranscriptomic reprogramming and how the writer Alkylation Repair Homolog 8 (Alkbh8) plays a key gene regulatory role in the response. Alkbh8 modifies tRNA selenocysteine (tRNASec) to translationally regulate the production of glutathione peroxidases (Gpx’s) and other selenoproteins, with Gpx enzymes known to play protective roles during APAP toxicity. We demonstrate that APAP increases toxicity and markers of damage, and decreases selenoprotein levels in Alkbh8 deficient mouse livers, when compared to wildtype. APAP also promotes large scale reprogramming of many RNA marks comprising the liver tRNA epitranscriptome including: 5-methoxycarbonylmethyluridine (mcm5U), isopentenyladenosine (i6A), pseudouridine (Ψ), and 1-methyladenosine (m1A) modifications linked to tRNASec and many other tRNA’s. Alkbh8 deficiency also leads to wide-spread epitranscriptomic dysregulation in response to APAP, demonstrating that a single writer defect can promote downstream changes to a large spectrum of RNA modifications. Our study highlights the importance of RNA modifications and translational responses to APAP, identifies writers as key modulators of stress responses in vivo and supports the idea that the epitranscriptome may play important roles in responses to pharmaceuticals.
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Affiliation(s)
- Sara Evke
- Nanobioscience Constellation, College of Nanoscale Science and Engineering, SUNY Polytechnic Institute, Albany, NY 12203, USA; (S.E.); (J.A.M.)
- The RNA Institute, University at Albany, Albany, NY 12222, USA;
| | - Qishan Lin
- The RNA Institute, University at Albany, Albany, NY 12222, USA;
- Department of Biological Sciences, University at Albany, Albany, NY 12222, USA
- RNA Epitranscriptomics and Proteomics Resource, University at Albany, Albany, NY 12222, USA
| | - Juan Andres Melendez
- Nanobioscience Constellation, College of Nanoscale Science and Engineering, SUNY Polytechnic Institute, Albany, NY 12203, USA; (S.E.); (J.A.M.)
- The RNA Institute, University at Albany, Albany, NY 12222, USA;
| | - Thomas John Begley
- The RNA Institute, University at Albany, Albany, NY 12222, USA;
- Department of Biological Sciences, University at Albany, Albany, NY 12222, USA
- RNA Epitranscriptomics and Proteomics Resource, University at Albany, Albany, NY 12222, USA
- Correspondence:
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9
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Dannfald A, Favory JJ, Deragon JM. Variations in transfer and ribosomal RNA epitranscriptomic status can adapt eukaryote translation to changing physiological and environmental conditions. RNA Biol 2021; 18:4-18. [PMID: 34159889 PMCID: PMC8677040 DOI: 10.1080/15476286.2021.1931756] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/07/2021] [Accepted: 05/13/2021] [Indexed: 01/27/2023] Open
Abstract
The timely reprogramming of gene expression in response to internal and external cues is essential to eukaryote development and acclimation to changing environments. Chemically modifying molecular receptors and transducers of these signals is one way to efficiently induce proper physiological responses. Post-translation modifications, regulating protein biological activities, are central to many well-known signal-responding pathways. Recently, messenger RNA (mRNA) chemical (i.e. epitranscriptomic) modifications were also shown to play a key role in these processes. In contrast, transfer RNA (tRNA) and ribosomal RNA (rRNA) chemical modifications, although critical for optimal function of the translation apparatus, and much more diverse and quantitatively important compared to mRNA modifications, were until recently considered as mainly static chemical decorations. We present here recent observations that are challenging this view and supporting the hypothesis that tRNA and rRNA modifications dynamically respond to various cell and environmental conditions and contribute to adapt translation to these conditions.
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Affiliation(s)
- Arnaud Dannfald
- CNRS LGDP-UMR5096, Pepignan, France
- Université de Perpignan via Domitia, Perpignan, France
| | - Jean-Jacques Favory
- CNRS LGDP-UMR5096, Pepignan, France
- Université de Perpignan via Domitia, Perpignan, France
| | - Jean-Marc Deragon
- CNRS LGDP-UMR5096, Pepignan, France
- Université de Perpignan via Domitia, Perpignan, France
- Institut Universitaire de France, Paris, France
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10
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McIntyre WD, Nemati R, Salehi M, Aldrich CC, FitzGibbon M, Deng L, Pazos MA, Rose RE, Toro B, Netzband RE, Pager CT, Robinson IP, Bialosuknia SM, Ciota AT, Fabris D. Agnostic Framework for the Classification/Identification of Organisms Based on RNA Post-Transcriptional Modifications. Anal Chem 2021; 93:7860-7869. [PMID: 34043326 PMCID: PMC8351319 DOI: 10.1021/acs.analchem.1c00359] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We propose a novel approach for building a classification/identification framework based on the full complement of RNA post-transcriptional modifications (rPTMs) expressed by an organism at basal conditions. The approach relies on advanced mass spectrometry techniques to characterize the products of exonuclease digestion of total RNA extracts. Sample profiles comprising identities and relative abundances of all detected rPTM were used to train and test the capabilities of different machine learning (ML) algorithms. Each algorithm proved capable of identifying rigorous decision rules for differentiating closely related classes and correctly assigning unlabeled samples. The ML classifiers resolved different members of the Enterobacteriaceae family, alternative Escherichia coli serotypes, a series of Saccharomyces cerevisiae knockout mutants, and primary cells of the Homo sapiens central nervous system, which shared very similar genetic backgrounds. The excellent levels of accuracy and resolving power achieved by training on a limited number of classes were successfully replicated when the number of classes was significantly increased to escalate complexity. A dendrogram generated from ML-curated data exhibited a hierarchical organization that closely resembled those afforded by established taxonomic systems. Finer clustering patterns revealed the extensive effects induced by the deletion of a single pivotal gene. This information provided a putative roadmap for exploring the roles of rPTMs in their respective regulatory networks, which will be essential to decipher the epitranscriptomics code. The ubiquitous presence of RNA in virtually all living organisms promises to enable the broadest possible range of applications, with significant implications in the diagnosis of RNA-related diseases.
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Affiliation(s)
| | - Reza Nemati
- Dept. of Chemistry, University at Albany (SUNY), Albany, NY 12222, USA
| | - Mehraveh Salehi
- Dept. of Electrical Engineering, Yale University, New Haven, CT 06520, USA
| | - Colin C. Aldrich
- Dept. of Chemistry, University at Albany (SUNY), Albany, NY 12222, USA
| | - Molly FitzGibbon
- Dept. of Biological Sciences, University at Albany, Albany, NY 12222, USA
| | - Limin Deng
- Dept. of Chemistry, University of Connecticut, Storrs, CT 06269, USA
| | - Manuel A. Pazos
- Dept. of Biological Sciences, University at Albany, Albany, NY 12222, USA
| | - Rebecca E. Rose
- Dept. of Chemistry, University at Albany (SUNY), Albany, NY 12222, USA
| | - Botros Toro
- Dept. of Biological Sciences, University at Albany, Albany, NY 12222, USA
| | - Rachel E. Netzband
- Dept. of Biological Sciences, University at Albany, Albany, NY 12222, USA
| | - Cara T. Pager
- Dept. of Biological Sciences, University at Albany, Albany, NY 12222, USA
- RNA Institute, University at Albany, Albany, NY 12222, USA
| | - Ingrid P. Robinson
- Dept. of Biological Sciences, University at Albany, Albany, NY 12222, USA
| | | | | | - Daniele Fabris
- Dept. of Chemistry, University of Connecticut, Storrs, CT 06269, USA
- RNA Institute, University at Albany, Albany, NY 12222, USA
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11
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Sarkar A, Gasperi W, Begley U, Nevins S, Huber SM, Dedon PC, Begley TJ. Detecting the epitranscriptome. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 12:e1663. [PMID: 33987958 DOI: 10.1002/wrna.1663] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 04/15/2021] [Accepted: 04/16/2021] [Indexed: 11/09/2022]
Abstract
RNA modifications and their corresponding epitranscriptomic writer and eraser enzymes regulate gene expression. Altered RNA modification levels, dysregulated writers, and sequence changes that disrupt epitranscriptomic marks have been linked to mitochondrial and neurological diseases, cancer, and multifactorial disorders. The detection of epitranscriptomics marks is challenging, but different next generation sequencing (NGS)-based and mass spectrometry-based approaches have been used to identify and quantitate the levels of individual and groups of RNA modifications. NGS and mass spectrometry-based approaches have been coupled with chemical, antibody or enzymatic methodologies to identify modifications in most RNA species, mapped sequence contexts and demonstrated the dynamics of specific RNA modifications, as well as the collective epitranscriptome. While epitranscriptomic analysis is currently limited to basic research applications, specific approaches for the detection of individual RNA modifications and the epitranscriptome have potential biomarker applications in detecting human conditions and diseases. This article is categorized under: RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems RNA Processing > tRNA Processing RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Anwesha Sarkar
- Department of Biological Sciences, University at Albany, Albany, New York, USA.,The RNA Institute, University at Albany, Albany, New York, USA
| | - William Gasperi
- Department of Biological Sciences, University at Albany, Albany, New York, USA.,The RNA Institute, University at Albany, Albany, New York, USA
| | - Ulrike Begley
- Department of Biological Sciences, University at Albany, Albany, New York, USA.,The RNA Institute, University at Albany, Albany, New York, USA
| | - Steven Nevins
- Nanoscale Science Constellation, SUNY Polytechnic Institute, Albany, New York, USA
| | | | - Peter C Dedon
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore
| | - Thomas J Begley
- Department of Biological Sciences, University at Albany, Albany, New York, USA.,The RNA Institute, University at Albany, Albany, New York, USA
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12
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Netzband R, Pager CT. Viral Epitranscriptomics. Virology 2021. [DOI: 10.1002/9781119818526.ch4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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13
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Waldern JM, Smith D, Piazza CL, Bailey EJ, Schiraldi NJ, Nemati R, Fabris D, Belfort M, Novikova O. Methylation of rRNA as a host defense against rampant group II intron retrotransposition. Mob DNA 2021; 12:9. [PMID: 33678171 PMCID: PMC7938551 DOI: 10.1186/s13100-021-00237-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 02/22/2021] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Group II introns are mobile retroelements, capable of invading new sites in DNA. They are self-splicing ribozymes that complex with an intron-encoded protein to form a ribonucleoprotein that targets DNA after splicing. These molecules can invade DNA site-specifically, through a process known as retrohoming, or can invade ectopic sites through retrotransposition. Retrotransposition, in particular, can be strongly influenced by both environmental and cellular factors. RESULTS To investigate host factors that influence retrotransposition, we performed random insertional mutagenesis using the ISS1 transposon to generate a library of over 1000 mutants in Lactococcus lactis, the native host of the Ll.LtrB group II intron. By screening this library, we identified 92 mutants with increased retrotransposition frequencies (RTP-ups). We found that mutations in amino acid transport and metabolism tended to have increased retrotransposition frequencies. We further explored a subset of these RTP-up mutants, the most striking of which is a mutant in the ribosomal RNA methyltransferase rlmH, which exhibited a reproducible 20-fold increase in retrotransposition frequency. In vitro and in vivo experiments revealed that ribosomes in the rlmH mutant were defective in the m3Ψ modification and exhibited reduced binding to the intron RNA. CONCLUSIONS Taken together, our results reinforce the importance of the native host organism in regulating group II intron retrotransposition. In particular, the evidence from the rlmH mutant suggests a role for ribosome modification in limiting rampant retrotransposition.
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Affiliation(s)
- Justin M. Waldern
- Department of Biological Sciences and RNA Institute, University at Albany, 1400 Washington Avenue, Albany, NY 12222 USA
- Current address: Department of Biology, University of North Carolina, 270 Bell Tower Drive, Chapel Hill, NC 27599 USA
| | - Dorie Smith
- Department of Biological Sciences and RNA Institute, University at Albany, 1400 Washington Avenue, Albany, NY 12222 USA
| | - Carol Lyn Piazza
- Department of Biological Sciences and RNA Institute, University at Albany, 1400 Washington Avenue, Albany, NY 12222 USA
| | - E. Jake Bailey
- Department of Biological Sciences and RNA Institute, University at Albany, 1400 Washington Avenue, Albany, NY 12222 USA
| | - Nicholas J. Schiraldi
- Academic and Research Computing Center, Information Technology Services, University at Albany, 1400 Washington Avenue, Albany, NY 12222 USA
| | - Reza Nemati
- Department of Chemistry, University at Albany, 1400 Washington Avenue, Albany, NY 12222 USA
- Current address: Biogen, 125 Broadway, Cambridge, MA 02142 USA
| | - Dan Fabris
- Department of Biological Sciences and RNA Institute, University at Albany, 1400 Washington Avenue, Albany, NY 12222 USA
- Department of Chemistry, University at Albany, 1400 Washington Avenue, Albany, NY 12222 USA
- Current address: Department of Chemistry, University of Connecticut, 55 N. Eagleville Road, Storrs, CT 06268 USA
| | - Marlene Belfort
- Department of Biological Sciences and RNA Institute, University at Albany, 1400 Washington Avenue, Albany, NY 12222 USA
- Department of Biomedical Sciences, School of Public Health, University at Albany, 1400 Washington Avenue, Albany, NY 12222 USA
| | - Olga Novikova
- Department of Biological Sciences and RNA Institute, University at Albany, 1400 Washington Avenue, Albany, NY 12222 USA
- Current address: Biology Department, SUNY Buffalo State College, 1300 Elmwood Avenue, Buffalo, NY 14222 USA
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14
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Galvanin A, Vogt LM, Grober A, Freund I, Ayadi L, Bourguignon-Igel V, Bessler L, Jacob D, Eigenbrod T, Marchand V, Dalpke A, Helm M, Motorin Y. Bacterial tRNA 2'-O-methylation is dynamically regulated under stress conditions and modulates innate immune response. Nucleic Acids Res 2020; 48:12833-12844. [PMID: 33275131 PMCID: PMC7736821 DOI: 10.1093/nar/gkaa1123] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 11/03/2020] [Indexed: 12/23/2022] Open
Abstract
RNA modifications are a well-recognized way of gene expression regulation at the post-transcriptional level. Despite the importance of this level of regulation, current knowledge on modulation of tRNA modification status in response to stress conditions is far from being complete. While it is widely accepted that tRNA modifications are rather dynamic, such variations are mostly assessed in terms of total tRNA, with only a few instances where changes could be traced to single isoacceptor species. Using Escherichia coli as a model system, we explored stress-induced modulation of 2'-O-methylations in tRNAs by RiboMethSeq. This analysis and orthogonal analytical measurements by LC-MS show substantial, but not uniform, increase of the Gm18 level in selected tRNAs under mild bacteriostatic antibiotic stress, while other Nm modifications remain relatively constant. The absence of Gm18 modification in tRNAs leads to moderate alterations in E. coli mRNA transcriptome, but does not affect polysomal association of mRNAs. Interestingly, the subset of motility/chemiotaxis genes is significantly overexpressed in ΔTrmH mutant, this corroborates with increased swarming motility of the mutant strain. The stress-induced increase of tRNA Gm18 level, in turn, reduced immunostimulation properties of bacterial tRNAs, which is concordant with the previous observation that Gm18 is a suppressor of Toll-like receptor 7 (TLR7)-mediated interferon release. This documents an effect of stress induced modulation of tRNA modification that acts outside protein translation.
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Affiliation(s)
- Adeline Galvanin
- Université de Lorraine, CNRS, IMoPA (UMR7365), F54000 Nancy, France
| | - Lea-Marie Vogt
- Institute of Pharmaceutical and Biomedical Science, Johannes Gutenberg-University Mainz, 55128 Mainz, Germany
| | - Antonia Grober
- Institute of Medical Microbiology and Hygiene, Technische Universität Dresden, 01307 Dresden, Germany
| | - Isabel Freund
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Ruprecht-Karls University Heidelberg, 69117 Heidelberg, Germany
| | - Lilia Ayadi
- Université de Lorraine, CNRS, IMoPA (UMR7365), F54000 Nancy, France
- Université de Lorraine, CNRS, INSERM, IBSLor (UMS2008/US40), Epitranscriptomics and RNA Sequencing Core Facility, F54000 Nancy, France
| | - Valerie Bourguignon-Igel
- Université de Lorraine, CNRS, IMoPA (UMR7365), F54000 Nancy, France
- Université de Lorraine, CNRS, INSERM, IBSLor (UMS2008/US40), Epitranscriptomics and RNA Sequencing Core Facility, F54000 Nancy, France
| | - Larissa Bessler
- Institute of Pharmaceutical and Biomedical Science, Johannes Gutenberg-University Mainz, 55128 Mainz, Germany
| | - Dominik Jacob
- Institute of Pharmaceutical and Biomedical Science, Johannes Gutenberg-University Mainz, 55128 Mainz, Germany
| | - Tatjana Eigenbrod
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Ruprecht-Karls University Heidelberg, 69117 Heidelberg, Germany
| | - Virginie Marchand
- Université de Lorraine, CNRS, INSERM, IBSLor (UMS2008/US40), Epitranscriptomics and RNA Sequencing Core Facility, F54000 Nancy, France
| | - Alexander Dalpke
- Institute of Medical Microbiology and Hygiene, Technische Universität Dresden, 01307 Dresden, Germany
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Science, Johannes Gutenberg-University Mainz, 55128 Mainz, Germany
| | - Yuri Motorin
- Université de Lorraine, CNRS, IMoPA (UMR7365), F54000 Nancy, France
- Université de Lorraine, CNRS, INSERM, IBSLor (UMS2008/US40), Epitranscriptomics and RNA Sequencing Core Facility, F54000 Nancy, France
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15
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2'-O-ribose methylation of transfer RNA promotes recovery from oxidative stress in Saccharomyces cerevisiae. PLoS One 2020; 15:e0229103. [PMID: 32053677 PMCID: PMC7018073 DOI: 10.1371/journal.pone.0229103] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 01/29/2020] [Indexed: 11/19/2022] Open
Abstract
Chemical modifications that regulate protein expression at the translational level are emerging as vital components of the cellular stress response. Transfer RNAs (tRNAs) are significant targets for methyl-based modifications, which are catalyzed by tRNA methyltransferases (Trms). Here, Saccharomyces cerevisiae served as a model eukaryote system to investigate the role of 2'-O-ribose tRNA methylation in the cell's response to oxidative stress. Using 2'-O-ribose deletion mutants for trms 3, 7, 13, and 44, in acute and chronic exposure settings, we demonstrate a broad cell sensitivity to oxidative stress-inducing toxicants (i.e., hydrogen peroxide, rotenone, and acetic acid). A global analysis of hydrogen peroxide-induced tRNA modifications shows a complex profile of decreased, or undetectable, 2'-O-ribose modification events in 2’-O-ribose trm mutant strains, providing a critical link between this type of modification event and Trm status post-exposure. Based on the pronounced oxidative stress sensitivity observed for trm7 mutants, we used a bioinformatic tool to identify transcripts as candidates for regulation by Trm7-catalyzed modifications (i.e., enriched in UUC codons decoded by tRNAPheGmAA). This screen identified transcripts linked to diverse biological processes that promote cellular recovery after oxidative stress exposure, including DNA repair, chromatin remodeling, and nutrient acquisition (i.e., CRT10, HIR3, HXT2, and GNP1); moreover, these mutants were also oxidative stress-sensitive. Together, these results solidify a role for TRM3, 7, 13, and 44, in the cellular response to oxidative stress, and implicate 2'-O-ribose tRNA modification as an epitranscriptomic strategy for oxidative stress recovery.
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16
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Kenderdine T, Nemati R, Baker A, Palmer M, Ujma J, FitzGibbon M, Deng L, Royzen M, Langridge J, Fabris D. High-resolution ion mobility spectrometry-mass spectrometry of isomeric/isobaric ribonucleotide variants. JOURNAL OF MASS SPECTROMETRY : JMS 2020; 55:e4465. [PMID: 31697854 PMCID: PMC8363168 DOI: 10.1002/jms.4465] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 09/13/2019] [Accepted: 10/22/2019] [Indexed: 06/01/2023]
Abstract
In this report, we explored the benefits of cyclic ion mobility (cIM) mass spectrometry in the analysis of isomeric post-transcriptional modifications of RNA. Standard methyl-cytidine samples were initially utilized to test the ability to correctly distinguish different structures sharing the same elemental composition and thus molecular mass. Analyzed individually, the analytes displayed characteristic arrival times (tD ) determined by the different positions of the modifying methyl groups onto the common cytidine scaffold. Analyzed in mixture, the widths of the respective signals resulted in significant overlap that initially prevented their resolution on the tD scale. The separation of the four isomers was achieved by increasing the number of passes through the cIM device, which enabled to fully differentiate the characteristic ion mobility behaviors associated with very subtle structural variations. The placement of the cIM device between the mass-selective quadrupole and the time-of-flight analyzer allowed us to perform gas-phase activation of each of these ion populations, which had been first isolated according to a common mass-to-charge ratio and then separated on the basis of different ion mobility behaviors. The observed fragmentation patterns confirmed the structures of the various isomers thus substantiating the benefits of complementing unique tD information with specific fragmentation data to reach more stringent analyte identification. These capabilities were further tested by analyzing natural mono-nucleotide mixtures obtained by exonuclease digestion of total RNA extracts. In particular, the combination of cIM separation and post-mobility dissociation allowed us to establish the composition of methyl-cytidine and methyl-adenine components present in the entire transcriptome of HeLa cells. For this reason, we expect that this technique will benefit not only epitranscriptomic studies requiring the determination of identity and expression levels of RNA modifications, but also metabolomics investigations involving the analysis of natural extracts that may possibly contain subsets of isomeric/isobaric species.
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Affiliation(s)
| | | | - A. Baker
- Waters Corporation, Wilmslow SK9 4AX, UK
| | - M. Palmer
- Waters Corporation, Wilmslow SK9 4AX, UK
| | - J. Ujma
- Waters Corporation, Wilmslow SK9 4AX, UK
| | - M FitzGibbon
- University at Albany, Albany, NY 12222
- University of California San Diego, La Jolla, CA 92093
| | - L. Deng
- University at Albany, Albany, NY 12222
| | - M. Royzen
- University at Albany, Albany, NY 12222
| | | | - D. Fabris
- University at Albany, Albany, NY 12222
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17
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McIntyre W, Netzband R, Bonenfant G, Biegel JM, Miller C, Fuchs G, Henderson E, Arra M, Canki M, Fabris D, Pager CT. Positive-sense RNA viruses reveal the complexity and dynamics of the cellular and viral epitranscriptomes during infection. Nucleic Acids Res 2019; 46:5776-5791. [PMID: 29373715 PMCID: PMC6009648 DOI: 10.1093/nar/gky029] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 01/15/2018] [Indexed: 12/26/2022] Open
Abstract
More than 140 post-transcriptional modifications (PTMs) are known to decorate cellular RNAs, but their incidence, identity and significance in viral RNA are still largely unknown. We have developed an agnostic analytical approach to comprehensively survey PTMs on viral and cellular RNAs. Specifically, we used mass spectrometry to analyze PTMs on total RNA isolated from cells infected with Zika virus, Dengue virus, hepatitis C virus (HCV), poliovirus and human immunodeficiency virus type 1. All five RNA viruses significantly altered global PTM landscapes. Examination of PTM profiles of individual viral genomes isolated by affinity capture revealed a plethora of PTMs on viral RNAs, which far exceeds the handful of well-characterized modifications. Direct comparison of viral epitranscriptomes identified common and virus-specific PTMs. In particular, specific dimethylcytosine modifications were only present in total RNA from virus-infected cells, and in intracellular HCV RNA, and viral RNA from Zika and HCV virions. Moreover, dimethylcytosine abundance during viral infection was modulated by the cellular DEAD-box RNA helicase DDX6. By opening the Pandora's box on viral PTMs, this report presents numerous questions and hypotheses on PTM function and strongly supports PTMs as a new tier of regulation by which RNA viruses subvert the host and evade cellular surveillance systems.
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Affiliation(s)
- Will McIntyre
- The RNA Institute, University at Albany-SUNY, Albany, NY 12222, USA
| | - Rachel Netzband
- The RNA Institute, University at Albany-SUNY, Albany, NY 12222, USA
| | - Gaston Bonenfant
- The RNA Institute, University at Albany-SUNY, Albany, NY 12222, USA
| | - Jason M Biegel
- The RNA Institute, University at Albany-SUNY, Albany, NY 12222, USA
| | - Clare Miller
- The RNA Institute, University at Albany-SUNY, Albany, NY 12222, USA
| | - Gabriele Fuchs
- The RNA Institute, University at Albany-SUNY, Albany, NY 12222, USA
| | - Eric Henderson
- The RNA Institute, University at Albany-SUNY, Albany, NY 12222, USA
| | - Manoj Arra
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, NY 12208, USA
| | - Mario Canki
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, NY 12208, USA
| | - Daniele Fabris
- The RNA Institute, University at Albany-SUNY, Albany, NY 12222, USA
| | - Cara T Pager
- The RNA Institute, University at Albany-SUNY, Albany, NY 12222, USA
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18
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The Versatile Roles of the tRNA Epitranscriptome during Cellular Responses to Toxic Exposures and Environmental Stress. TOXICS 2019; 7:toxics7010017. [PMID: 30934574 PMCID: PMC6468425 DOI: 10.3390/toxics7010017] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 03/19/2019] [Accepted: 03/21/2019] [Indexed: 12/11/2022]
Abstract
Living organisms respond to environmental changes and xenobiotic exposures by regulating gene expression. While heat shock, unfolded protein, and DNA damage stress responses are well-studied at the levels of the transcriptome and proteome, tRNA-mediated mechanisms are only recently emerging as important modulators of cellular stress responses. Regulation of the stress response by tRNA shows a high functional diversity, ranging from the control of tRNA maturation and translation initiation, to translational enhancement through modification-mediated codon-biased translation of mRNAs encoding stress response proteins, and translational repression by stress-induced tRNA fragments. tRNAs need to be heavily modified post-transcriptionally for full activity, and it is becoming increasingly clear that many aspects of tRNA metabolism and function are regulated through the dynamic introduction and removal of modifications. This review will discuss the many ways that nucleoside modifications confer high functional diversity to tRNAs, with a focus on tRNA modification-mediated regulation of the eukaryotic response to environmental stress and toxicant exposures. Additionally, the potential applications of tRNA modification biology in the development of early biomarkers of pathology will be highlighted.
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19
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Chan C, Pham P, Dedon PC, Begley TJ. Lifestyle modifications: coordinating the tRNA epitranscriptome with codon bias to adapt translation during stress responses. Genome Biol 2018; 19:228. [PMID: 30587213 PMCID: PMC6307160 DOI: 10.1186/s13059-018-1611-1] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Cells adapt to stress by altering gene expression at multiple levels. Here, we propose a new mechanism regulating stress-dependent gene expression at the level of translation, with coordinated interplay between the tRNA epitranscriptome and biased codon usage in families of stress-response genes. In this model, auxiliary genetic information contained in synonymous codon usage enables regulation of codon-biased and functionally related transcripts by dynamic changes in the tRNA epitranscriptome. This model partly explains the association between synchronous stress-dependent epitranscriptomic marks and significant multi-codon usage skewing in families of translationally regulated transcripts. The model also predicts translational adaptation during viral infections.
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Affiliation(s)
- Cheryl Chan
- Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, 138602, Singapore
| | - Phuong Pham
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Peter C Dedon
- Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, 138602, Singapore. .,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - Thomas J Begley
- The RNA Institute, College of Arts and Science, University at Albany, SUNY, Albany, NY, 12222, USA.
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20
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van Delft P, Akay A, Huber SM, Bueschl C, Rudolph KLM, Di Domenico T, Schuhmacher R, Miska EA, Balasubramanian S. The Profile and Dynamics of RNA Modifications in Animals. Chembiochem 2017; 18:979-984. [PMID: 28449301 PMCID: PMC5784800 DOI: 10.1002/cbic.201700093] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Indexed: 12/28/2022]
Abstract
More than a hundred distinct modified nucleosides have been identified in RNA, but little is known about their distribution across different organisms, their dynamic nature and their response to cellular and environmental stress. Mass-spectrometry-based methods have been at the forefront of identifying and quantifying modified nucleosides. However, they often require synthetic reference standards, which do not exist in the case of many modified nucleosides, and this therefore impedes their analysis. Here we use a metabolic labelling approach to achieve rapid generation of bio-isotopologues of the complete Caenorhabditis elegans transcriptome and its modifications and use them as reference standards to characterise the RNA modification profile in this multicellular organism through an untargeted liquid-chromatography tandem high-resolution mass spectrometry (LC-HRMS) approach. We furthermore show that several of these RNA modifications have a dynamic response to environmental stress and that, in particular, changes in the tRNA wobble base modification 5-methoxycarbonylmethyl-2-thiouridine (mcm5 s2 U) lead to codon-biased gene-expression changes in starved animals.
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Affiliation(s)
- Pieter van Delft
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
| | - Alper Akay
- Gurdon InstituteUniversity of CambridgeTennis Court RoadCambridgeCB2 1QNUK
- Department of GeneticsUniversity of CambridgeDowning StreetCambridgeCB2 3EHUK
| | - Sabrina M. Huber
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
| | - Christoph Bueschl
- Center for Analytical ChemistryDepartment of AgrobiotechnologyUniversity of Natural Resources and Life SciencesViennaKonrad-Lorenz-Strasse 203430Tulln an der DonauAustria
| | - Konrad L. M. Rudolph
- Gurdon InstituteUniversity of CambridgeTennis Court RoadCambridgeCB2 1QNUK
- Department of GeneticsUniversity of CambridgeDowning StreetCambridgeCB2 3EHUK
- Wellcome Trust Sanger InstituteWellcome Trust Genome CampusCambridgeCB10 1SAUK
| | - Tomás Di Domenico
- Gurdon InstituteUniversity of CambridgeTennis Court RoadCambridgeCB2 1QNUK
- Department of GeneticsUniversity of CambridgeDowning StreetCambridgeCB2 3EHUK
- Wellcome Trust Sanger InstituteWellcome Trust Genome CampusCambridgeCB10 1SAUK
| | - Rainer Schuhmacher
- Center for Analytical ChemistryDepartment of AgrobiotechnologyUniversity of Natural Resources and Life SciencesViennaKonrad-Lorenz-Strasse 203430Tulln an der DonauAustria
| | - Eric A. Miska
- Gurdon InstituteUniversity of CambridgeTennis Court RoadCambridgeCB2 1QNUK
- Department of GeneticsUniversity of CambridgeDowning StreetCambridgeCB2 3EHUK
- Wellcome Trust Sanger InstituteWellcome Trust Genome CampusCambridgeCB10 1SAUK
| | - Shankar Balasubramanian
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
- Cancer Research UK Cambridge InstituteUniversity of CambridgeRobinson WayCambridgeCB2 0REUK
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21
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Mihailovic MK, Chen A, Gonzalez-Rivera JC, Contreras LM. Defective Ribonucleoproteins, Mistakes in RNA Processing, and Diseases. Biochemistry 2017; 56:1367-1382. [PMID: 28206738 DOI: 10.1021/acs.biochem.6b01134] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Ribonucleoproteins (RNPs) are vital to many cellular events. To this end, many neurodegenerative diseases and cancers have been linked to RNP malfunction, particularly as this relates to defective processing of cellular RNA. The connection of RNPs and diseases has also propagated a shift of focus onto RNA targeting from traditional protein targeting treatments. However, therapeutic development in this area has been limited by incomplete molecular insight into the specific contributions of RNPs to disease. This review outlines the role of several RNPs in diseases, focusing on molecular defects in processes that affect proper RNA handling in the cell. This work also evaluates the contributions of recently developed methods to understanding RNP association and function. We review progress in this area by focusing on molecular malfunctions of RNPs associated with the onset and progression of several neurodegenerative diseases and cancer and conclude with a brief discussion of RNA-based therapeutic efforts.
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Affiliation(s)
- Mia K Mihailovic
- McKetta Department of Chemical Engineering, University of Texas at Austin , 200 East. Dean Keeton Street, Stop C0400, Austin, Texas 78712, United States
| | - Angela Chen
- McKetta Department of Chemical Engineering, University of Texas at Austin , 200 East. Dean Keeton Street, Stop C0400, Austin, Texas 78712, United States
| | - Juan C Gonzalez-Rivera
- McKetta Department of Chemical Engineering, University of Texas at Austin , 200 East. Dean Keeton Street, Stop C0400, Austin, Texas 78712, United States
| | - Lydia M Contreras
- McKetta Department of Chemical Engineering, University of Texas at Austin , 200 East. Dean Keeton Street, Stop C0400, Austin, Texas 78712, United States
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