1
|
Fatica T, Naas T, Liwak U, Slaa H, Souaid M, Frangione B, Kattini R, Gaudreau-Lapierre A, Trinkle-Mulcahy L, Chakraborty P, Holcik M. TRNT-1 Deficiency Is Associated with Loss of tRNA Integrity and Imbalance of Distinct Proteins. Genes (Basel) 2023; 14:genes14051043. [PMID: 37239403 DOI: 10.3390/genes14051043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/01/2023] [Accepted: 05/04/2023] [Indexed: 05/28/2023] Open
Abstract
Mitochondrial diseases are a group of heterogeneous disorders caused by dysfunctional mitochondria. Interestingly, a large proportion of mitochondrial diseases are caused by defects in genes associated with tRNA metabolism. We recently discovered that partial loss-of-function mutations in tRNA Nucleotidyl Transferase 1 (TRNT1), the nuclear gene encoding the CCA-adding enzyme essential for modifying both nuclear and mitochondrial tRNAs, causes a multisystemic and clinically heterogenous disease termed SIFD (sideroblastic anemia with B-cell immunodeficiency, periodic fevers, and developmental delay; SIFD). However, it is not clear how mutations in a general and essential protein like TRNT1 cause disease with such clinically broad but unique symptomatology and tissue involvement. Using biochemical, cell, and mass spectrometry approaches, we demonstrate that TRNT1 deficiency is associated with sensitivity to oxidative stress, which is due to exacerbated, angiogenin-dependent cleavage of tRNAs. Furthermore, reduced levels of TRNT1 lead to phosphorylation of Eukaryotic Translation Initiation Factor 2 Subunit Alpha (eIF2α), increased reactive oxygen species (ROS) production, and changes in the abundance of distinct proteins. Our data suggest that the observed variable SIFD phenotypes are likely due to dysregulation of tRNA maturation and abundance, which in turn negatively affects the translation of distinct proteins.
Collapse
Affiliation(s)
- Thet Fatica
- Department of Health Sciences, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Turaya Naas
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON K1H 8L1, Canada
| | - Urszula Liwak
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON K1H 8L1, Canada
| | - Hannah Slaa
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON K1H 8L1, Canada
| | - Maryam Souaid
- Department of Health Sciences, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Brianna Frangione
- Department of Health Sciences, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Ribal Kattini
- Department of Health Sciences, Carleton University, Ottawa, ON K1S 5B6, Canada
| | | | - Laura Trinkle-Mulcahy
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Pranesh Chakraborty
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON K1H 8L1, Canada
| | - Martin Holcik
- Department of Health Sciences, Carleton University, Ottawa, ON K1S 5B6, Canada
| |
Collapse
|
2
|
Single-base resolution mapping of 2′-O-methylation sites by an exoribonuclease-enriched chemical method. SCIENCE CHINA LIFE SCIENCES 2022; 66:800-818. [PMID: 36323972 DOI: 10.1007/s11427-022-2210-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 09/21/2022] [Indexed: 11/06/2022]
Abstract
2'-O-methylation (Nm) is one of the most abundant RNA epigenetic modifications and plays a vital role in the post-transcriptional regulation of gene expression. Current Nm mapping approaches are normally limited to highly abundant RNAs and have significant technical hurdles in mRNAs or relatively rare non-coding RNAs (ncRNAs). Here, we developed a new method for enriching Nm sites by using RNA exoribonuclease and periodate oxidation reactivity to eliminate 2'-hydroxylated (2'-OH) nucleosides, coupled with sequencing (Nm-REP-seq). We revealed several novel classes of Nm-containing ncRNAs as well as mRNAs in humans, mice, and drosophila. We found that some novel Nm sites are present at fixed positions in different tRNAs and are potential substrates of fibrillarin (FBL) methyltransferase mediated by snoRNAs. Importantly, we discovered, for the first time, that Nm located at the 3'-end of various types of ncRNAs and fragments derived from them. Our approach precisely redefines the genome-wide distribution of Nm and provides new technologies for functional studies of Nm-mediated gene regulation.
Collapse
|
3
|
Role of the Ribonuclease ONCONASE in miRNA Biogenesis and tRNA Processing: Focus on Cancer and Viral Infections. Int J Mol Sci 2022; 23:ijms23126556. [PMID: 35742999 PMCID: PMC9223570 DOI: 10.3390/ijms23126556] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/25/2022] [Accepted: 06/09/2022] [Indexed: 12/23/2022] Open
Abstract
The majority of transcribed RNAs do not codify for proteins, nevertheless they display crucial regulatory functions by affecting the cellular protein expression profile. MicroRNAs (miRNAs) and transfer RNA-derived small RNAs (tsRNAs) are effectors of interfering mechanisms, so that their biogenesis is a tightly regulated process. Onconase (ONC) is an amphibian ribonuclease known for cytotoxicity against tumors and antiviral activity. Additionally, ONC administration in patients resulted in clinical effectiveness and in a well-tolerated feature, at least for lung carcinoma and malignant mesothelioma. Moreover, the ONC therapeutic effects are actually potentiated by cotreatment with many conventional antitumor drugs. This review not only aims to describe the ONC activity occurring either in different tumors or in viral infections but also to analyze the molecular mechanisms underlying ONC pleiotropic and cellular-specific effects. In cancer, data suggest that ONC affects malignant phenotypes by generating tRNA fragments and miRNAs able to downregulate oncogenes expression and upregulate tumor-suppressor proteins. In cells infected by viruses, ONC hampers viral spread by digesting the primer tRNAs necessary for viral DNA replication. In this scenario, new therapeutic tools might be developed by exploiting the action of ONC-elicited RNA derivatives.
Collapse
|
4
|
Genome Sequencing of Hericium coralloides by a Combination of PacBio RS II and Next-Generation Sequencing Platforms. Int J Genomics 2022; 2022:4017654. [PMID: 35141329 PMCID: PMC8820905 DOI: 10.1155/2022/4017654] [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] [Received: 08/27/2021] [Revised: 12/07/2021] [Accepted: 01/09/2022] [Indexed: 11/17/2022] Open
Abstract
The fruiting bodies or mycelia of Hericium coralloides (H. coralloides) contain many physiologically active compounds that are used to treat various diseases, including cardiovascular disorders and cancers. However, the genome of H. coralloides has not been sequenced, which hinders further investigations into aspects, such as bioactivity or evolutionary events. The present study is aimed at (i) performing de novo sequencing of the assembled genome; (ii) mapping the reads from PE400 DNA into the assembled genome; (iii) identifying the full length of all the repeated sequences; and (iv) annotating protein-coding genes using GO, eggNOG, and KEGG databases. The assembled genome comprised 5,59,05,675 bp, including 307 contigs. The mapping rate of reads obtained from PE400 DNA in the assembled genome was 92.46%. We identified 2,525 repeated sequences of 14,23,274 bp length. We predicted ncRNAs of 48,895 bp and 11,736 genes encoding proteins that were annotated in the GO, eggNOG, and KEGG databases. We are the first to sequence the entire H. coralloides genome (NCBI; Assembly: ASM367540v1), which will serve as a reference for studying the evolutionary diversification of edible and medicinal mushrooms and facilitate the application of bioactivity in H. coralloides.
Collapse
|
5
|
Lyu X, Yang Q, Li L, Dang Y, Zhou Z, Chen S, Liu Y. Adaptation of codon usage to tRNA I34 modification controls translation kinetics and proteome landscape. PLoS Genet 2020; 16:e1008836. [PMID: 32479508 PMCID: PMC7289440 DOI: 10.1371/journal.pgen.1008836] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 06/11/2020] [Accepted: 05/06/2020] [Indexed: 02/07/2023] Open
Abstract
Codon usage bias is a universal feature of all genomes and plays an important role in regulating protein expression levels. Modification of adenosine to inosine at the tRNA anticodon wobble position (I34) by adenosine deaminases (ADATs) is observed in all eukaryotes and has been proposed to explain the correlation between codon usage and tRNA pool. However, how the tRNA pool is affected by I34 modification to influence codon usage-dependent gene expression is unclear. Using Neurospora crassa as a model system, by combining molecular, biochemical and bioinformatics analyses, we show that silencing of adat2 expression severely impaired the I34 modification levels for the ADAT-related tRNAs, resulting in major ADAT-related tRNA profile changes and reprogramming of translation elongation kinetics on ADAT-related codons. adat2 silencing also caused genome-wide codon usage-biased ribosome pausing on mRNAs and proteome landscape changes, leading to selective translational repression or induction of different mRNAs. The induced expression of CPC-1, the Neurospora ortholog of yeast GCN4p, mediates the transcriptional response after adat2 silencing and amino acid starvation. Together, our results demonstrate that the tRNA I34 modification by ADAT plays a major role in driving codon usage-biased translation to shape proteome landscape. Modification of transfer RNA (tRNA) can have profound impacts on gene expression by shaping cellular tRNA pool. How codon usage bias and tRNA profiles synergistically regulate gene expression is unclear. By combining molecular, biochemical and bioinformatics analyses, we showed that the correlation between genome codon usage and tRNA I34 (inosine 34) modification modulates translation elongation kinetics and proteome landscape. Inhibition of tRNA I34 modification causes codon usage-dependent ribosome pausing on mRNAs during translation and changes cellular protein contents in a codon usage biased manner. Together, our results demonstrate that the tRNA I34 modification plays a major role in driving codon usage-dependent translation to determine proteome landscape in a eukaryotic organism.
Collapse
Affiliation(s)
- Xueliang Lyu
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
- Department of Physiology, The University of Texas Southwestern Medical Center,Harry Hines Blvd., Dallas, Texas, United States of America
| | - Qian Yang
- Department of Physiology, The University of Texas Southwestern Medical Center,Harry Hines Blvd., Dallas, Texas, United States of America
| | - Lin Li
- National Institute of Biological Sciences, Changping District, Beijing, China
| | - Yunkun Dang
- State Key Laboratory for Conservation and Utilization of Bio-Resources and Center for Life Science, School of Life Sciences, Yunnan University, Kunming, China
| | - Zhipeng Zhou
- Department of Physiology, The University of Texas Southwestern Medical Center,Harry Hines Blvd., Dallas, Texas, United States of America
- College of Life Sciences and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - She Chen
- Department of Physiology, The University of Texas Southwestern Medical Center,Harry Hines Blvd., Dallas, Texas, United States of America
| | - Yi Liu
- Department of Physiology, The University of Texas Southwestern Medical Center,Harry Hines Blvd., Dallas, Texas, United States of America
- * E-mail:
| |
Collapse
|
6
|
Costa OY, Zerillo MM, Zühlke D, Kielak AM, Pijl A, Riedel K, Kuramae EE. Responses of Acidobacteria Granulicella sp. WH15 to High Carbon Revealed by Integrated Omics Analyses. Microorganisms 2020; 8:E244. [PMID: 32059463 PMCID: PMC7074687 DOI: 10.3390/microorganisms8020244] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 02/08/2020] [Accepted: 02/10/2020] [Indexed: 01/18/2023] Open
Abstract
The phylum Acidobacteria is widely distributed in soils, but few representatives have been cultured. In general, Acidobacteria are oligotrophs and exhibit slow growth under laboratory conditions. We sequenced the genome of Granulicella sp. WH15, a strain obtained from decaying wood, and determined the bacterial transcriptome and proteome under growth in poor medium with a low or high concentration of sugar. We detected the presence of 217 carbohydrate-associated enzymes in the genome of strain WH15. Integrated analysis of the transcriptomic and proteomic profiles showed that high sugar triggered a stress response. As part of this response, transcripts related to cell wall stress, such as sigma factor σW and toxin-antitoxin (TA) systems, were upregulated, as were several proteins involved in detoxification and repair, including MdtA and OprM. KEGG metabolic pathway analysis indicated the repression of carbon metabolism (especially the pentose phosphate pathway) and the reduction of protein synthesis, carbohydrate metabolism, and cell division, suggesting the arrest of cell activity and growth. In summary, the stress response of Granulicella sp. WH15 induced by the presence of a high sugar concentration in the medium resulted in the intensification of secretion functions to eliminate toxic compounds and the reallocation of resources to cell maintenance instead of growth.
Collapse
Affiliation(s)
- Ohana Y.A. Costa
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands (M.M.Z.); (A.M.K.); (A.P.)
| | - Marcelo M. Zerillo
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands (M.M.Z.); (A.M.K.); (A.P.)
| | - Daniela Zühlke
- Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Strasse 8, 17487 Greifswald, Germany; (D.Z.); (K.R.)
| | - Anna M. Kielak
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands (M.M.Z.); (A.M.K.); (A.P.)
| | - Agata Pijl
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands (M.M.Z.); (A.M.K.); (A.P.)
| | - Katharina Riedel
- Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Strasse 8, 17487 Greifswald, Germany; (D.Z.); (K.R.)
| | - Eiko E. Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands (M.M.Z.); (A.M.K.); (A.P.)
| |
Collapse
|
7
|
Zheng LL, Xu WL, Liu S, Sun WJ, Li JH, Wu J, Yang JH, Qu LH. tRF2Cancer: A web server to detect tRNA-derived small RNA fragments (tRFs) and their expression in multiple cancers. Nucleic Acids Res 2016; 44:W185-93. [PMID: 27179031 PMCID: PMC4987945 DOI: 10.1093/nar/gkw414] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Accepted: 05/04/2016] [Indexed: 12/31/2022] Open
Abstract
tRNA-derived small RNA fragments (tRFs) are one class of small non-coding RNAs derived from transfer RNAs (tRNAs). tRFs play important roles in cellular processes and are involved in multiple cancers. High-throughput small RNA (sRNA) sequencing experiments can detect all the cellular expressed sRNAs, including tRFs. However, distinguishing genuine tRFs from RNA fragments generated by random degradation remains a major challenge. In this study, we developed an integrated web-based computing system, tRF2Cancer, to accurately identify tRFs from sRNA deep-sequencing data and evaluate their expression in multiple cancers. The binomial test was introduced to evaluate whether reads from a small RNA-seq data set represent tRFs or degraded fragments. A classification method was then used to annotate the types of tRFs based on their sites of origin in pre-tRNA or mature tRNA. We applied the pipeline to analyze 10 991 data sets from 32 types of cancers and identified thousands of expressed tRFs. A tool called ‘tRFinCancer’ was developed to facilitate the users to inspect the expression of tRFs across different types of cancers. Another tool called ‘tRFBrowser’ shows both the sites of origin and the distribution of chemical modification sites in tRFs on their source tRNA. The tRF2Cancer web server is available at http://rna.sysu.edu.cn/tRFfinder/.
Collapse
Affiliation(s)
- Ling-Ling Zheng
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P. R. China
| | - Wei-Lin Xu
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P. R. China
| | - Shun Liu
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P. R. China
| | - Wen-Ju Sun
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P. R. China
| | - Jun-Hao Li
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P. R. China
| | - Jie Wu
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P. R. China
| | - Jian-Hua Yang
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P. R. China
| | - Liang-Hu Qu
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P. R. China
| |
Collapse
|
8
|
Dégut C, Monod A, Brachet F, Crépin T, Tisné C. In Vitro/In Vivo Production of tRNA for X-Ray Studies. Methods Mol Biol 2016; 1320:37-57. [PMID: 26227036 DOI: 10.1007/978-1-4939-2763-0_4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
tRNAs occupy a central role in the cellular life, and they are involved in a broad range of biological processes that relies on their interaction with proteins and RNA. Crystallization and structure resolution of tRNA or/and tRNA/partner complexes can yield in valuable information on structural organizations of key elements of cellular machinery. However, crystallization of RNA, is often challenging. Here we review two methods to produce and purify tRNA in quantity and quality to perform X-ray studies.
Collapse
Affiliation(s)
- Clément Dégut
- Laboratoire de Cristallographie et RMN Biologiques, CNRS, Paris Sorbonne Cité, 4 avenue de l'Observatoire, Paris, 75006, France
| | | | | | | | | |
Collapse
|
9
|
Dhahbi JM. Circulating small noncoding RNAs as biomarkers of aging. Ageing Res Rev 2014; 17:86-98. [PMID: 24607831 DOI: 10.1016/j.arr.2014.02.005] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Revised: 02/17/2014] [Accepted: 02/24/2014] [Indexed: 12/31/2022]
Abstract
Small noncoding RNAs (sncRNAs) mediate a variety of cellular functions in animals and plants. Deep sequencing has made it possible to obtain highly detailed information on the types and abundance of sncRNAs in biological specimens, leading to the discovery that sncRNAs circulate in the blood of humans and mammals. The most abundant types of circulating sncRNAs are microRNAs (miRNAs), 5' transfer RNA (tRNA) halves, and YRNA fragments, with minute amounts of other types that may nevertheless be significant. Of the more abundant circulating sncRNAs only miRNAs have well described functions, but characteristics of the others suggest specific processing and secretion as complexes that protect the RNA from degradation. The properties of circulating sncRNAs are consistent with their serving as signaling molecules, and investigations of circulating miRNAs support the view that they can enter cells and regulate cellular functions. The serum levels of specific sncRNAs change markedly with age, and these changes can be mitigated by calorie restriction (CR), indicating that levels are under physiologic control. The ability of circulating sncRNAs to transmit functions between cells and to regulate a broad spectrum of cellular functions, and the changes in their levels with age, implicate them in the manifestations of aging. Our understanding of the functions of circulating sncRNA, particularly in relation to aging, is currently at a very early stage; results to date suggest that more extensive investigation will yield important insights into mechanisms of aging.
Collapse
Affiliation(s)
- Joseph M Dhahbi
- Department of Biochemistry, University of California at Riverside, Riverside, CA 92521, USA; Center for Genetics, Children's Hospital Oakland Research Institute, Oakland, CA 94609, USA.
| |
Collapse
|
10
|
Vojtech L, Woo S, Hughes S, Levy C, Ballweber L, Sauteraud RP, Strobl J, Westerberg K, Gottardo R, Tewari M, Hladik F. Exosomes in human semen carry a distinctive repertoire of small non-coding RNAs with potential regulatory functions. Nucleic Acids Res 2014; 42:7290-304. [PMID: 24838567 PMCID: PMC4066774 DOI: 10.1093/nar/gku347] [Citation(s) in RCA: 413] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 04/01/2014] [Accepted: 04/11/2014] [Indexed: 12/21/2022] Open
Abstract
Semen contains relatively ill-defined regulatory components that likely aid fertilization, but which could also interfere with defense against infection. Each ejaculate contains trillions of exosomes, membrane-enclosed subcellular microvesicles, which have immunosuppressive effects on cells important in the genital mucosa. Exosomes in general are believed to mediate inter-cellular communication, possibly by transferring small RNA molecules. We found that seminal exosome (SE) preparations contain a substantial amount of RNA from 20 to 100 nucleotides (nts) in length. We sequenced 20-40 and 40-100 nt fractions of SE RNA separately from six semen donors. We found various classes of small non-coding RNA, including microRNA (21.7% of the RNA in the 20-40 nt fraction) as well as abundant Y RNAs and tRNAs present in both fractions. Specific RNAs were consistently present in all donors. For example, 10 (of ∼2600 known) microRNAs constituted over 40% of mature microRNA in SE. Additionally, tRNA fragments were strongly enriched for 5'-ends of 18-19 or 30-34 nts in length; such tRNA fragments repress translation. Thus, SE could potentially deliver regulatory signals to the recipient mucosa via transfer of small RNA molecules.
Collapse
Affiliation(s)
- Lucia Vojtech
- Department of Obstetrics and Gynecology, University of Washington, Seattle, USA
| | - Sangsoon Woo
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, USA
| | - Sean Hughes
- Department of Obstetrics and Gynecology, University of Washington, Seattle, USA
| | - Claire Levy
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, USA
| | - Lamar Ballweber
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, USA
| | - Renan P Sauteraud
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, USA
| | - Johanna Strobl
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, USA
| | - Katharine Westerberg
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, USA
| | - Raphael Gottardo
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, USA Department of Medicine, University of Washington, Seattle, USA
| | - Muneesh Tewari
- Department of Medicine, University of Washington, Seattle, USA Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, USA
| | - Florian Hladik
- Department of Obstetrics and Gynecology, University of Washington, Seattle, USA Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, USA Department of Medicine, University of Washington, Seattle, USA
| |
Collapse
|
11
|
Abstract
Post-transcriptional cleavage of RNA molecules to generate smaller fragments is a widespread mechanism that enlarges the structural and functional complexity of cellular RNomes. Substrates for such RNA fragmentations are coding as well as non-protein-coding RNAs. In particular, fragments derived from both precursor and mature tRNAs represent one of the rapidly growing classes of post-transcriptional RNA pieces. Importantly, these tRNA fragments possess distinct expression patterns, abundance, cellular localizations, or biological roles compared with their parental tRNA molecules. Here we review recent reports on tRNA cleavage and attempt to categorize tRNA pieces according to their origin and cellular function. The biological scope of tRNA-derived fragments ranges from translation control, over RNA silencing, to regulating apoptosis, and thus clearly enlarges the functional repertoire of ncRNA biology.
Collapse
Affiliation(s)
- Jennifer Gebetsberger
- Department of Chemistry and Biochemistry; University of Bern; Bern, Switzerland; Graduate School for Cellular and Biomedical Sciences; University of Bern; Bern, Switzerland
| | - Norbert Polacek
- Department of Chemistry and Biochemistry; University of Bern; Bern, Switzerland; Division of Genomics and RNomics; Medical University Innsbruck; Innsbruck, Austria
| |
Collapse
|
12
|
Extracellular vesicles shed by Trypanosoma cruzi are linked to small RNA pathways, life cycle regulation, and susceptibility to infection of mammalian cells. Parasitol Res 2013; 113:285-304. [DOI: 10.1007/s00436-013-3655-1] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Accepted: 10/14/2013] [Indexed: 10/26/2022]
|
13
|
Nowacka M, Strozycki PM, Jackowiak P, Hojka-Osinska A, Szymanski M, Figlerowicz M. Identification of stable, high copy number, medium-sized RNA degradation intermediates that accumulate in plants under non-stress conditions. PLANT MOLECULAR BIOLOGY 2013; 83:191-204. [PMID: 23708952 PMCID: PMC3777163 DOI: 10.1007/s11103-013-0079-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Accepted: 05/15/2013] [Indexed: 05/22/2023]
Abstract
It is becoming increasingly evident that the RNA degradome is a crucial component of the total cellular RNA pool. Here, we present an analysis of the medium-sized RNAs (midi RNAs) that form in Arabidopsis thaliana. Our analyses revealed that the midi RNA fraction contained mostly 20-70-nt-long fragments derived from various RNA species, including tRNA, rRNA, mRNA and snRNA. The majority of these fragments could be classified as stable RNA degradation intermediates (RNA degradants). Using two dimensional polyacrylamide gel electrophoresis, we demonstrated that high copy number RNA (hcn RNA) degradants appear in plant cells not only during stress, as it was earlier suggested. They are continuously produced also under physiological conditions. The data collected indicated that the accumulation pattern of the hcn RNA degradants is organ-specific and can be affected by various endogenous and exogenous factors. In addition, we demonstrated that selected degradants efficiently inhibit translation in vitro. Thus, the results of our studies suggest that hcn RNA degradants are likely to be involved in the regulation of gene expression in plants.
Collapse
Affiliation(s)
- Martyna Nowacka
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
- Present Address: Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Trojdena 4, 02-109 Warsaw, Poland
| | - Pawel M. Strozycki
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Paulina Jackowiak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Anna Hojka-Osinska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Maciej Szymanski
- Computational Genomics Laboratory, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
- Institute of Computing Science, Poznan University of Technology, Piotrowo 3A, 60-965 Poznan, Poland
| |
Collapse
|
14
|
Rogers TE, Ataide SF, Dare K, Katz A, Seveau S, Roy H, Ibba M. A pseudo-tRNA modulates antibiotic resistance in Bacillus cereus. PLoS One 2012; 7:e41248. [PMID: 22815980 PMCID: PMC3399842 DOI: 10.1371/journal.pone.0041248] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Accepted: 06/19/2012] [Indexed: 01/18/2023] Open
Abstract
Bacterial genomic islands are often flanked by tRNA genes, which act as sites for the integration of foreign DNA into the host chromosome. For example, Bacillus cereus ATCC14579 contains a pathogenicity island flanked by a predicted pseudo-tRNA, tRNAOther, which does not function in translation. Deletion of tRNAOther led to significant changes in cell wall morphology and antibiotic resistance and was accompanied by changes in the expression of numerous genes involved in oxidative stress responses, several of which contain significant complementarities to sequences surrounding tRNAOther. This suggested that tRNAOther might be expressed as part of a larger RNA, and RACE analysis subsequently confirmed the existence of several RNA species that significantly extend both the 3′ and 5′-ends of tRNAOther. tRNAOther expression levels were found to be responsive to changes in extracellular iron concentration, consistent with the presence of three putative ferric uptake regulator (Fur) binding sites in the 5′ leader region of one of these larger RNAs. Taken together with previous data, this study now suggests that tRNAOther may function by providing a tRNA-like structural element within a larger regulatory RNA. These findings illustrate that while integration of genomic islands often leaves tRNA genes intact and functional, in other instances inactivation may generate tRNA-like elements that are then recruited to other functions in the cell.
Collapse
Affiliation(s)
- Theresa E. Rogers
- Department of Microbiology, Ohio State University, Columbus, Ohio, United States of America
| | - Sandro F. Ataide
- Department of Microbiology, Ohio State University, Columbus, Ohio, United States of America
| | - Kiley Dare
- Department of Microbiology, Ohio State University, Columbus, Ohio, United States of America
| | - Assaf Katz
- Department of Microbiology, Ohio State University, Columbus, Ohio, United States of America
| | - Stephanie Seveau
- Department of Microbiology, Ohio State University, Columbus, Ohio, United States of America
| | - Hervé Roy
- Department of Microbiology, Ohio State University, Columbus, Ohio, United States of America
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida, United States of America
| | - Michael Ibba
- Department of Microbiology, Ohio State University, Columbus, Ohio, United States of America
- Ohio State Biochemistry Program, Ohio State University, Columbus, Ohio, United States of America
- Center for RNA Biology, Ohio State University, Columbus, Ohio, United States of America
- * E-mail:
| |
Collapse
|
15
|
Pastore C, Topalidou I, Forouhar F, Yan AC, Levy M, Hunt JF. Crystal structure and RNA binding properties of the RNA recognition motif (RRM) and AlkB domains in human AlkB homolog 8 (ABH8), an enzyme catalyzing tRNA hypermodification. J Biol Chem 2011; 287:2130-43. [PMID: 22065580 DOI: 10.1074/jbc.m111.286187] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Humans express nine paralogs of the bacterial DNA repair enzyme AlkB, an iron/2-oxoglutarate-dependent dioxygenase that reverses alkylation damage to nucleobases. The biochemical and physiological roles of these paralogs remain largely uncharacterized, hampering insight into the evolutionary expansion of the AlkB family. However, AlkB homolog 8 (ABH8), which contains RNA recognition motif (RRM) and methyltransferase domains flanking its AlkB domain, recently was demonstrated to hypermodify the anticodon loops in some tRNAs. To deepen understanding of this activity, we performed physiological and biophysical studies of ABH8. Using GFP fusions, we demonstrate that expression of the Caenorhabditis elegans ABH8 ortholog is widespread in larvae but restricted to a small number of neurons in adults, suggesting that its function becomes more specialized during development. In vitro RNA binding studies on several human ABH8 constructs indicate that binding affinity is enhanced by a basic α-helix at the N terminus of the RRM domain. The 3.0-Å-resolution crystal structure of a construct comprising the RRM and AlkB domains shows disordered loops flanking the active site in the AlkB domain and a unique structural Zn(II)-binding site at its C terminus. Although the catalytic iron center is exposed to solvent, the 2-oxoglutarate co-substrate likely adopts an inactive conformation in the absence of tRNA substrate, which probably inhibits uncoupled free radical generation. A conformational change in the active site coupled to a disorder-to-order transition in the flanking protein segments likely controls ABH8 catalytic activity and tRNA binding specificity. These results provide insight into the functional and structural adaptations underlying evolutionary diversification of AlkB domains.
Collapse
Affiliation(s)
- Chiara Pastore
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | | | | | | | | | | |
Collapse
|
16
|
Heinemann IU, Nakamura A, O'Donoghue P, Eiler D, Söll D. tRNAHis-guanylyltransferase establishes tRNAHis identity. Nucleic Acids Res 2011; 40:333-44. [PMID: 21890903 PMCID: PMC3245924 DOI: 10.1093/nar/gkr696] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Histidine transfer RNA (tRNA) is unique among tRNA species as it carries an additional nucleotide at its 5' terminus. This unusual G(-1) residue is the major tRNA(His) identity element, and essential for recognition by the cognate histidyl-tRNA synthetase to allow efficient His-tRNA(His) formation. In many organisms G(-1) is added post-transcriptionally as part of the tRNA maturation process. tRNA(His) guanylyltransferase (Thg1) specifically adds the guanylyate residue by recognizing the tRNA(His) anticodon. Thg1 homologs from all three domains of life have been the subject of exciting research that gave rise to a detailed biochemical, structural and phylogenetic enzyme characterization. Thg1 homologs are phylogenetically classified into eukaryal- and archaeal-type enzymes differing characteristically in their cofactor requirements and specificity. Yeast Thg1 displays a unique but limited ability to add 2-3 G or C residues to mutant tRNA substrates, thus catalyzing a 3' → 5' RNA polymerization. Archaeal-type Thg1, which has been horizontally transferred to certain bacteria and few eukarya, displays a more relaxed substrate range and may play additional roles in tRNA editing and repair. The crystal structure of human Thg1 revealed a fascinating structural similarity to 5' → 3' polymerases, indicating that Thg1 derives from classical polymerases and evolved to assume its specific function in tRNA(His) processing.
Collapse
Affiliation(s)
- Ilka U Heinemann
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA
| | | | | | | | | |
Collapse
|
17
|
Jackowiak P, Nowacka M, Strozycki PM, Figlerowicz M. RNA degradome--its biogenesis and functions. Nucleic Acids Res 2011; 39:7361-70. [PMID: 21653558 PMCID: PMC3177198 DOI: 10.1093/nar/gkr450] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
RNA degradation is among the most fundamental processes that occur in living cells. The continuous decay of RNA molecules is associated not only with nucleotide turnover, but also with transcript maturation and quality control. The efficiency of RNA decay is ensured by a broad spectrum of both specific and non-specific ribonucleases. Some of these ribonucleases participate mainly in processing primary transcripts and in RNA quality control. Others preferentially digest mature, functional RNAs to yield a variety of molecules that together constitute the RNA degradome. Recently, it has become increasingly clear that the composition of the cellular RNA degradome can be modulated by numerous endogenous and exogenous factors (e.g. by stress). In addition, instead of being hydrolyzed to single nucleotides, some intermediates of RNA degradation can accumulate and function as signalling molecules or participate in mechanisms that control gene expression. Thus, RNA degradation appears to be not only a process that contributes to the maintenance of cellular homeostasis but also an underestimated source of regulatory molecules.
Collapse
Affiliation(s)
- Paulina Jackowiak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań and Institute of Computing Science, Poznan University of Technology, Piotrowo 3A, 60-965 Poznań, Poland
| | - Martyna Nowacka
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań and Institute of Computing Science, Poznan University of Technology, Piotrowo 3A, 60-965 Poznań, Poland
| | - Pawel M. Strozycki
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań and Institute of Computing Science, Poznan University of Technology, Piotrowo 3A, 60-965 Poznań, Poland
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań and Institute of Computing Science, Poznan University of Technology, Piotrowo 3A, 60-965 Poznań, Poland
- *To whom correspondence should be addressed. Tel: 48 61 8528503; Fax: 48 61 8520532;
| |
Collapse
|
18
|
Focused on Frontier Sciences and Dedicated to Academic Exchanges-<I>Science China: Life Sciences</I> in 2009 at a New Beginning. PROG BIOCHEM BIOPHYS 2011. [DOI: 10.3724/sp.j.1206.2010.00555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
19
|
The Recent Progress of Non-coding RNA and RNomics. PROG BIOCHEM BIOPHYS 2010. [DOI: 10.3724/sp.j.1206.2010.00475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
20
|
Research frontiers highlighted in Science China Life Sciences in 2009. CHINESE SCIENCE BULLETIN-CHINESE 2010. [DOI: 10.1007/s11434-010-4229-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
21
|
Placido A, Sieber F, Gobert A, Gallerani R, Giegé P, Maréchal-Drouard L. Plant mitochondria use two pathways for the biogenesis of tRNAHis. Nucleic Acids Res 2010; 38:7711-7. [PMID: 20660484 PMCID: PMC2995067 DOI: 10.1093/nar/gkq646] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
All tRNAHis possess an essential extra G–1 guanosine residue at their 5′ end. In eukaryotes after standard processing by RNase P, G–1 is added by a tRNAHis guanylyl transferase. In prokaryotes, G–1 is genome-encoded and retained during maturation. In plant mitochondria, although trnH genes possess a G–1 we find here that both maturation pathways can be used. Indeed, tRNAHis with or without a G–1 are found in a plant mitochondrial tRNA fraction. Furthermore, a recombinant Arabidopsis mitochondrial RNase P can cleave tRNAHis precursors at both positions G+1 and G–1. The G–1 is essential for recognition by plant mitochondrial histidyl-tRNA synthetase. Whether, as shown in prokaryotes and eukaryotes, the presence of uncharged tRNAHis without G–1 has a function or not in plant mitochondrial gene regulation is an open question. We find that when a mutated version of a plant mitochondrial trnH gene containing no encoded extra G is introduced and expressed into isolated potato mitochondria, mature tRNAHis with a G–1 are recovered. This shows that a previously unreported tRNAHis guanylyltransferase activity is present in plant mitochondria.
Collapse
Affiliation(s)
- Antonio Placido
- Dipartimento di Biochimica e Biologia Molecolare Ernesto Quagliariello, Universita' degli Studi di Bari Aldo Moro, Via Orabona 4, 70126 Bari, Italy
| | | | | | | | | | | |
Collapse
|
22
|
Garcia-Silva MR, Frugier M, Tosar JP, Correa-Dominguez A, Ronalte-Alves L, Parodi-Talice A, Rovira C, Robello C, Goldenberg S, Cayota A. A population of tRNA-derived small RNAs is actively produced in Trypanosoma cruzi and recruited to specific cytoplasmic granules. Mol Biochem Parasitol 2010; 171:64-73. [PMID: 20156490 DOI: 10.1016/j.molbiopara.2010.02.003] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2009] [Revised: 02/04/2010] [Accepted: 02/05/2010] [Indexed: 11/30/2022]
Abstract
Over the last years an expanding family of small RNAs (i.e. microRNAs, siRNAs and piRNAs) was recognized as key players in diverse forms of gene silencing and chromatin organization. Effectors functions of these small RNAs are achieved through ribonucleoprotein (RNP) complexes containing at their center an Argonaute/Piwi protein. Although these proteins and their small RNA-associated machinery can be traced back to the common ancestor of eukaryotes, this machinery seems to be entirely lost or extensively simplified in some unicellular organisms including Trypanosoma cruzi, which are unable to trigger RNAi related phenomena. Speculating about the presence of alternate small RNA-mediated pathways in these organisms, we constructed and analyzed a size-fractionated cDNA library (20-35 nt) from epimastigotes forms of T. cruzi. Our results showed the production of an abundant class of tRNA-derived small RNAs preferentially restricted to specific isoacceptors and whose production was more accentuated under nutritional stress. These small tRNAs derived preferentially from the 5' halves of mature tRNAs and were recruited to distinctive cytoplasmic granules. Our data favor the idea that tRNA cleavage is unlikely to be the consequence of non-specific degradation but a controlled process, whose biological significance remains to be elucidated.
Collapse
Affiliation(s)
- Maria Rosa Garcia-Silva
- Functional Genomics Unit, Institut Pasteur de Montevideo, Mataojo 2020, CP11400 Montevideo, Uruguay
| | | | | | | | | | | | | | | | | | | |
Collapse
|