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Kazimierczyk M, Fedoruk-Wyszomirska A, Gurda-Woźna D, Wyszko E, Swiatkowska A, Wrzesinski J. The expression profiles of piRNAs and their interacting Piwi proteins in cellular model of renal development: Focus on Piwil1 in mitosis. Eur J Cell Biol 2024; 103:151444. [PMID: 39024988 DOI: 10.1016/j.ejcb.2024.151444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 07/03/2024] [Accepted: 07/12/2024] [Indexed: 07/20/2024] Open
Abstract
Piwi proteins and Piwi interacting RNAs, piRNAs, presented in germline cells play a role in transposon silencing during germline development. In contrast, the role of somatic Piwi proteins and piRNAs still remains obscure. Here, we characterize the expression pattern and distribution of piRNAs in human renal cells in terms of their potential role in kidney development. Further, we show that all PIWI genes are expressed at the RNA level, however, only PIWIL1 gene is detected at the protein level by western blotting in healthy and cancerous renal cells. So far, the expression of human Piwil1 protein has only been shown in testes and cancer cells, but not in healthy somatic cell lines. Since we observe only Piwil1 protein, the regulation of other PIWI genes is probably more intricated, and depends on environmental conditions. Next, we demonstrate that downregulation of Piwil1 protein results in a decrease in the rate of cell proliferation, while no change in the level of apoptotic cells is observed. Confocal microscopy analysis reveals that Piwil1 protein is located in both cellular compartments, cytoplasm and nucleus in renal cells. Interestingly, in nucleus region Piwil1 is observed close to the spindle during all phases of mitosis in all tested cell lines. It strongly indicates that Piwil1 protein plays an essential role in proliferation of somatic cells. Moreover, involvement of Piwil1 in cell division could, at least partly, explain invasion and metastasis of many types of cancer cells with upregulation of PIWIL1 gene expression. It also makes Piwil1 protein as a potential target in the anticancer therapy.
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Affiliation(s)
- Marek Kazimierczyk
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, Poznan 61-704, Poland
| | | | - Dorota Gurda-Woźna
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, Poznan 61-704, Poland
| | - Eliza Wyszko
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, Poznan 61-704, Poland
| | - Agata Swiatkowska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, Poznan 61-704, Poland.
| | - Jan Wrzesinski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, Poznan 61-704, Poland.
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2
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Castellano LA, McNamara RJ, Pallarés HM, Gamarnik AV, Alvarez DE, Bazzini AA. Dengue virus preferentially uses human and mosquito non-optimal codons. Mol Syst Biol 2024:10.1038/s44320-024-00052-7. [PMID: 39039212 DOI: 10.1038/s44320-024-00052-7] [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: 01/29/2024] [Revised: 06/25/2024] [Accepted: 06/26/2024] [Indexed: 07/24/2024] Open
Abstract
Codon optimality refers to the effect that codon composition has on messenger RNA (mRNA) stability and translation level and implies that synonymous codons are not silent from a regulatory point of view. Here, we investigated the adaptation of virus genomes to the host optimality code using mosquito-borne dengue virus (DENV) as a model. We demonstrated that codon optimality exists in mosquito cells and showed that DENV preferentially uses nonoptimal (destabilizing) codons and avoids codons that are defined as optimal (stabilizing) in either human or mosquito cells. Human genes enriched in the codons preferentially and frequently used by DENV are upregulated during infection, and so is the tRNA decoding the nonoptimal and DENV preferentially used codon for arginine. We found that adaptation during single-host passaging in human or mosquito cells results in the selection of synonymous mutations towards DENV's preferred nonoptimal codons that increase virus fitness. Finally, our analyses revealed that hundreds of viruses preferentially use nonoptimal codons, with those infecting a single host displaying an even stronger bias, suggesting that host-pathogen interaction shapes virus-synonymous codon choice.
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Affiliation(s)
- Luciana A Castellano
- Stowers Institute for Medical Research, 1000 E 50th Street, Kansas City, MO, 64110, USA
| | - Ryan J McNamara
- Stowers Institute for Medical Research, 1000 E 50th Street, Kansas City, MO, 64110, USA
| | - Horacio M Pallarés
- Stowers Institute for Medical Research, 1000 E 50th Street, Kansas City, MO, 64110, USA
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires IIBBA-CONICET, Ciudad Autónoma de Buenos Aires, Argentina
| | - Andrea V Gamarnik
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires IIBBA-CONICET, Ciudad Autónoma de Buenos Aires, Argentina
| | - Diego E Alvarez
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín-CONICET, San Martín B1650, Argentina
| | - Ariel A Bazzini
- Stowers Institute for Medical Research, 1000 E 50th Street, Kansas City, MO, 64110, USA.
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City, KS, 66160, USA.
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3
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Elder JJH, Papadopoulos R, Hayne CK, Stanley RE. The making and breaking of tRNAs by ribonucleases. Trends Genet 2024; 40:511-525. [PMID: 38641471 PMCID: PMC11152995 DOI: 10.1016/j.tig.2024.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 03/21/2024] [Accepted: 03/21/2024] [Indexed: 04/21/2024]
Abstract
Ribonucleases (RNases) play important roles in supporting canonical and non-canonical roles of tRNAs by catalyzing the cleavage of the tRNA phosphodiester backbone. Here, we highlight how recent advances in cryo-electron microscopy (cryo-EM), protein structure prediction, reconstitution experiments, tRNA sequencing, and other studies have revealed new insight into the nucleases that process tRNA. This represents a very diverse group of nucleases that utilize distinct mechanisms to recognize and cleave tRNA during different stages of a tRNA's life cycle including biogenesis, fragmentation, surveillance, and decay. In this review, we provide a synthesis of the structure, mechanism, regulation, and modes of tRNA recognition by tRNA nucleases, along with open questions for future investigation.
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Affiliation(s)
- Jessica J H Elder
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Ry Papadopoulos
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA; Department of Chemistry, University of Chicago, Chicago, IL, USA
| | - Cassandra K Hayne
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA.
| | - Robin E Stanley
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA.
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4
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Chamberlain AR, Huynh L, Huang W, Taylor DJ, Harris ME. The specificity landscape of bacterial ribonuclease P. J Biol Chem 2024; 300:105498. [PMID: 38013087 PMCID: PMC10731613 DOI: 10.1016/j.jbc.2023.105498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 11/14/2023] [Accepted: 11/17/2023] [Indexed: 11/29/2023] Open
Abstract
Developing quantitative models of substrate specificity for RNA processing enzymes is a key step toward understanding their biology and guiding applications in biotechnology and biomedicine. Optimally, models to predict relative rate constants for alternative substrates should integrate an understanding of structures of the enzyme bound to "fast" and "slow" substrates, large datasets of rate constants for alternative substrates, and transcriptomic data identifying in vivo processing sites. Such data are either available or emerging for bacterial ribonucleoprotein RNase P a widespread and essential tRNA 5' processing endonuclease, thus making it a valuable model system for investigating principles of biological specificity. Indeed, the well-established structure and kinetics of bacterial RNase P enabled the development of high throughput measurements of rate constants for tRNA variants and provided the necessary framework for quantitative specificity modeling. Several studies document the importance of conformational changes in the precursor tRNA substrate as well as the RNA and protein subunits of bacterial RNase P during binding, although the functional roles and dynamics are still being resolved. Recently, results from cryo-EM studies of E. coli RNase P with alternative precursor tRNAs are revealing prospective mechanistic relationships between conformational changes and substrate specificity. Yet, extensive uncharted territory remains, including leveraging these advances for drug discovery, achieving a complete accounting of RNase P substrates, and understanding how the cellular context contributes to RNA processing specificity in vivo.
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Affiliation(s)
| | - Loc Huynh
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
| | - Wei Huang
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Derek J Taylor
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Michael E Harris
- Department of Chemistry, University of Florida, Gainesville, Florida, USA.
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5
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Arrivé M, Bruggeman M, Skaltsogiannis V, Coudray L, Quan YF, Schelcher C, Cognat V, Hammann P, Chicher J, Wolff P, Gobert A, Giegé P. A tRNA-modifying enzyme facilitates RNase P activity in Arabidopsis nuclei. NATURE PLANTS 2023; 9:2031-2041. [PMID: 37945696 DOI: 10.1038/s41477-023-01564-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 10/09/2023] [Indexed: 11/12/2023]
Abstract
RNase P is the essential activity that performs the 5' maturation of transfer RNA (tRNA) precursors. Beyond the ancestral form of RNase P containing a ribozyme, protein-only RNase P enzymes termed PRORP were identified in eukaryotes. In human mitochondria, PRORP forms a complex with two protein partners to become functional. In plants, although PRORP enzymes are active alone, we investigate their interaction network to identify potential tRNA maturation complexes. Here we investigate functional interactions involving the Arabidopsis nuclear RNase P PRORP2. We show, using an immuno-affinity strategy, that PRORP2 occurs in a complex with the tRNA methyl transferases TRM1A and TRM1B in vivo. Beyond RNase P, these enzymes can also interact with RNase Z. We show that TRM1A/TRM1B localize in the nucleus and find that their double knockout mutation results in a severe macroscopic phenotype. Using a combination of immuno-detections, mass spectrometry and a transcriptome-wide tRNA sequencing approach, we observe that TRM1A/TRM1B are responsible for the m22G26 modification of 70% of cytosolic tRNAs in vivo. We use the transcriptome wide tRNAseq approach as well as RNA blot hybridizations to show that RNase P activity is impaired in TRM1A/TRM1B mutants for specific tRNAs, in particular, tRNAs containing a m22G modification at position 26 that are strongly downregulated in TRM1A/TRM1B mutants. Altogether, results indicate that the m22G-adding enzymes TRM1A/TRM1B functionally cooperate with nuclear RNase P in vivo for the early steps of cytosolic tRNA biogenesis.
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Affiliation(s)
- Mathilde Arrivé
- Institut de biologie moléculaire des plantes, UPR2357 du CNRS, Université de Strasbourg, Strasbourg, France
| | - Mathieu Bruggeman
- Institut de biologie moléculaire des plantes, UPR2357 du CNRS, Université de Strasbourg, Strasbourg, France
| | - Vasileios Skaltsogiannis
- Institut de biologie moléculaire des plantes, UPR2357 du CNRS, Université de Strasbourg, Strasbourg, France
| | - Léna Coudray
- Institut de biologie moléculaire des plantes, UPR2357 du CNRS, Université de Strasbourg, Strasbourg, France
| | - Yi-Fat Quan
- Institut de biologie moléculaire des plantes, UPR2357 du CNRS, Université de Strasbourg, Strasbourg, France
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
| | - Cédric Schelcher
- Institut de biologie moléculaire des plantes, UPR2357 du CNRS, Université de Strasbourg, Strasbourg, France
| | - Valérie Cognat
- Institut de biologie moléculaire des plantes, UPR2357 du CNRS, Université de Strasbourg, Strasbourg, France
| | - Philippe Hammann
- Plateforme protéomique Strasbourg Esplanade, FR1589 du CNRS, Strasbourg, France
| | - Johana Chicher
- Plateforme protéomique Strasbourg Esplanade, FR1589 du CNRS, Strasbourg, France
| | - Philippe Wolff
- Plateforme protéomique Strasbourg Esplanade, FR1589 du CNRS, Strasbourg, France
- Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, Strasbourg, France
| | - Anthony Gobert
- Institut de biologie moléculaire des plantes, UPR2357 du CNRS, Université de Strasbourg, Strasbourg, France
| | - Philippe Giegé
- Institut de biologie moléculaire des plantes, UPR2357 du CNRS, Université de Strasbourg, Strasbourg, France.
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6
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Błaszczyk E, Płociński P, Lechowicz E, Brzostek A, Dziadek B, Korycka-Machała M, Słomka M, Dziadek J. Depletion of tRNA CCA-adding enzyme in Mycobacterium tuberculosis leads to polyadenylation of transcripts and precursor tRNAs. Sci Rep 2023; 13:20717. [PMID: 38001315 PMCID: PMC10673834 DOI: 10.1038/s41598-023-47944-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 11/20/2023] [Indexed: 11/26/2023] Open
Abstract
In reference to gene annotation, more than half of the tRNA species synthesized by Mycobacterium tuberculosis require the enzymatic addition of the cytosine-cytosine-adenine (CCA) tail, which is indispensable for amino acid charging and tRNA functionality. It makes the mycobacterial CCA-adding enzyme essential for survival of the bacterium and a potential target for novel pipelines in drug discovery avenues. Here, we described the rv3907c gene product, originally annotated as poly(A)polymerase (rv3907c, PcnA) as a functional CCA-adding enzyme (CCAMtb) essential for viability of M. tuberculosis. The depletion of the enzyme affected tRNAs maturation, inhibited bacilli growth, and resulted in abundant accumulation of polyadenylated RNAs. We determined the enzymatic activities displayed by the mycobacterial CCAMtb in vitro and studied the effects of inhibiting of its transcription in bacterial cells. We are the first to properly confirm the existence of RNA polyadenylation in mycobacteria, a previously controversial phenomenon, which we found promoted upon CCA-adding enzyme downexpression.
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Affiliation(s)
- Ewelina Błaszczyk
- Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, 93-232, Łódź, Poland
| | - Przemysław Płociński
- Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, 93-232, Łódź, Poland
- Department of Immunology and Infectious Biology, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 12/16, 90-237, Łódź, Poland
| | - Ewelina Lechowicz
- Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, 93-232, Łódź, Poland
| | - Anna Brzostek
- Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, 93-232, Łódź, Poland
| | - Bożena Dziadek
- Department of Molecular Microbiology, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 12/16, 90-237, Łódź, Poland
| | | | - Marcin Słomka
- Biobank Lab, Department of Oncobiology and Epigenetics, Faculty of Biology and Environmental Protection, University of Łódź, Pomorska 139, 90-235, Łódź, Poland
| | - Jarosław Dziadek
- Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, 93-232, Łódź, Poland.
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7
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Abstract
The study of eukaryotic tRNA processing has given rise to an explosion of new information and insights in the last several years. We now have unprecedented knowledge of each step in the tRNA processing pathway, revealing unexpected twists in biochemical pathways, multiple new connections with regulatory pathways, and numerous biological effects of defects in processing steps that have profound consequences throughout eukaryotes, leading to growth phenotypes in the yeast Saccharomyces cerevisiae and to neurological and other disorders in humans. This review highlights seminal new results within the pathways that comprise the life of a tRNA, from its birth after transcription until its death by decay. We focus on new findings and revelations in each step of the pathway including the end-processing and splicing steps, many of the numerous modifications throughout the main body and anticodon loop of tRNA that are so crucial for tRNA function, the intricate tRNA trafficking pathways, and the quality control decay pathways, as well as the biogenesis and biology of tRNA-derived fragments. We also describe the many interactions of these pathways with signaling and other pathways in the cell.
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Affiliation(s)
- Eric M Phizicky
- Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester School of Medicine, Rochester, New York 14642, USA
| | - Anita K Hopper
- Department of Molecular Genetics and Center for RNA Biology, Ohio State University, Columbus, Ohio 43235, USA
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8
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Raval PK, Ngan WY, Gallie J, Agashe D. The layered costs and benefits of translational redundancy. eLife 2023; 12:81005. [PMID: 36862572 PMCID: PMC9981150 DOI: 10.7554/elife.81005] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 01/25/2023] [Indexed: 03/03/2023] Open
Abstract
The rate and accuracy of translation hinges upon multiple components - including transfer RNA (tRNA) pools, tRNA modifying enzymes, and rRNA molecules - many of which are redundant in terms of gene copy number or function. It has been hypothesized that the redundancy evolves under selection, driven by its impacts on growth rate. However, we lack empirical measurements of the fitness costs and benefits of redundancy, and we have poor a understanding of how this redundancy is organized across components. We manipulated redundancy in multiple translation components of Escherichia coli by deleting 28 tRNA genes, 3 tRNA modifying systems, and 4 rRNA operons in various combinations. We find that redundancy in tRNA pools is beneficial when nutrients are plentiful and costly under nutrient limitation. This nutrient-dependent cost of redundant tRNA genes stems from upper limits to translation capacity and growth rate, and therefore varies as a function of the maximum growth rate attainable in a given nutrient niche. The loss of redundancy in rRNA genes and tRNA modifying enzymes had similar nutrient-dependent fitness consequences. Importantly, these effects are also contingent upon interactions across translation components, indicating a layered hierarchy from copy number of tRNA and rRNA genes to their expression and downstream processing. Overall, our results indicate both positive and negative selection on redundancy in translation components, depending on a species' evolutionary history with feasts and famines.
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Affiliation(s)
- Parth K Raval
- National Centre for Biological Sciences (NCBS-TIFR)BengaluruIndia
| | - Wing Yui Ngan
- Max Plank Institute for Evolutionary BiologyPlönGermany
| | - Jenna Gallie
- Max Plank Institute for Evolutionary BiologyPlönGermany
| | - Deepa Agashe
- National Centre for Biological Sciences (NCBS-TIFR)BengaluruIndia
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9
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Gast M, Nageswaran V, Kuss AW, Tzvetkova A, Wang X, Mochmann LH, Rad PR, Weiss S, Simm S, Zeller T, Voelzke H, Hoffmann W, Völker U, Felix SB, Dörr M, Beling A, Skurk C, Leistner DM, Rauch BH, Hirose T, Heidecker B, Klingel K, Nakagawa S, Poller WC, Swirski FK, Haghikia A, Poller W. tRNA-like Transcripts from the NEAT1-MALAT1 Genomic Region Critically Influence Human Innate Immunity and Macrophage Functions. Cells 2022; 11:cells11243970. [PMID: 36552736 PMCID: PMC9777231 DOI: 10.3390/cells11243970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 11/23/2022] [Accepted: 11/26/2022] [Indexed: 12/13/2022] Open
Abstract
The evolutionary conserved NEAT1-MALAT1 gene cluster generates large noncoding transcripts remaining nuclear, while tRNA-like transcripts (mascRNA, menRNA) enzymatically generated from these precursors translocate to the cytosol. Whereas functions have been assigned to the nuclear transcripts, data on biological functions of the small cytosolic transcripts are sparse. We previously found NEAT1-/- and MALAT1-/- mice to display massive atherosclerosis and vascular inflammation. Here, employing selective targeted disruption of menRNA or mascRNA, we investigate the tRNA-like molecules as critical components of innate immunity. CRISPR-generated human ΔmascRNA and ΔmenRNA monocytes/macrophages display defective innate immune sensing, loss of cytokine control, imbalance of growth/angiogenic factor expression impacting upon angiogenesis, and altered cell-cell interaction systems. Antiviral response, foam cell formation/oxLDL uptake, and M1/M2 polarization are defective in ΔmascRNA/ΔmenRNA macrophages, defining first biological functions of menRNA and describing new functions of mascRNA. menRNA and mascRNA represent novel components of innate immunity arising from the noncoding genome. They appear as prototypes of a new class of noncoding RNAs distinct from others (miRNAs, siRNAs) by biosynthetic pathway and intracellular kinetics. Their NEAT1-MALAT1 region of origin appears as archetype of a functionally highly integrated RNA processing system.
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Affiliation(s)
- Martina Gast
- Department of Cardiology, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 12200 Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Site Berlin, 12200 Berlin, Germany
| | - Vanasa Nageswaran
- Department of Cardiology, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 12200 Berlin, Germany
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, 12200 Berlin, Germany
| | - Andreas W Kuss
- Department of Functional Genomics, Interfaculty Institute of Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Ana Tzvetkova
- Department of Functional Genomics, Interfaculty Institute of Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany
- Institute of Bioinformatics, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Xiaomin Wang
- Department of Cardiology, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 12200 Berlin, Germany
| | - Liliana H Mochmann
- Department of Cardiology, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 12200 Berlin, Germany
| | - Pegah Ramezani Rad
- Department of Cardiology, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 12200 Berlin, Germany
| | - Stefan Weiss
- Department of Functional Genomics, Interfaculty Institute of Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany
- German Center for Cardiovascular Research (DZHK), Site Greifswald, 17487 Greifswald, Germany
| | - Stefan Simm
- Institute of Bioinformatics, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Tanja Zeller
- University Center of Cardiovascular Science, University Heart and Vascular Center, 20246 Hamburg, Germany
- German Center for Cardiovascular Research (DZHK), Site Hamburg/Lübeck/Kiel, 20246 Hamburg, Germany
| | - Henry Voelzke
- German Center for Cardiovascular Research (DZHK), Site Greifswald, 17487 Greifswald, Germany
- Institute for Community Medicine, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Wolfgang Hoffmann
- German Center for Cardiovascular Research (DZHK), Site Greifswald, 17487 Greifswald, Germany
- Institute for Community Medicine, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Uwe Völker
- Department of Functional Genomics, Interfaculty Institute of Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany
- German Center for Cardiovascular Research (DZHK), Site Greifswald, 17487 Greifswald, Germany
| | - Stefan B Felix
- German Center for Cardiovascular Research (DZHK), Site Greifswald, 17487 Greifswald, Germany
- Department of Cardiology, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Marcus Dörr
- German Center for Cardiovascular Research (DZHK), Site Greifswald, 17487 Greifswald, Germany
- Department of Cardiology, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Antje Beling
- German Center for Cardiovascular Research (DZHK), Site Berlin, 12200 Berlin, Germany
- Institute for Biochemistry, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 10178 Berlin, Germany
- Berlin Institute of Health (BIH), 10178 Berlin, Germany
| | - Carsten Skurk
- Department of Cardiology, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 12200 Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Site Berlin, 12200 Berlin, Germany
| | - David-Manuel Leistner
- Department of Cardiology, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 12200 Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Site Berlin, 12200 Berlin, Germany
- Berlin Institute of Health (BIH), 10178 Berlin, Germany
| | - Bernhard H Rauch
- German Center for Cardiovascular Research (DZHK), Site Greifswald, 17487 Greifswald, Germany
- Institute for Pharmacology, University Medicine Greifswald, 17487 Greifswald, Germany
- Department Human Medicine, Section Pharmacology and Toxicology, Carl von Ossietzky Universität, 26129 Oldenburg, Germany
| | - Tetsuro Hirose
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita 565-0871, Japan
| | - Bettina Heidecker
- Department of Cardiology, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 12200 Berlin, Germany
| | - Karin Klingel
- Institute for Pathology and Neuropathology, Department of Pathology, University Hospital Tübingen, 72076 Tübingen, Germany
| | - Shinichi Nakagawa
- RNA Biology Laboratory, RIKEN Advanced Research Institute, Wako, Saitama 351-0198, Japan
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Wolfram C Poller
- Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Filip K Swirski
- Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Arash Haghikia
- Department of Cardiology, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 12200 Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Site Berlin, 12200 Berlin, Germany
- Berlin Institute of Health (BIH), 10178 Berlin, Germany
| | - Wolfgang Poller
- Department of Cardiology, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 12200 Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Site Berlin, 12200 Berlin, Germany
- Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 13353 Berlin, Germany
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10
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Jiang Q, Ma Y, Zhao Y, Yao MD, Zhu Y, Zhang QY, Yan B. tRNA-derived fragment tRF-1001: A novel anti-angiogenic factor in pathological ocular angiogenesis. MOLECULAR THERAPY - NUCLEIC ACIDS 2022; 30:407-420. [DOI: 10.1016/j.omtn.2022.10.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 10/27/2022] [Indexed: 11/13/2022]
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11
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Hayne CK, Lewis TA, Stanley RE. Recent insights into the structure, function, and regulation of the eukaryotic transfer RNA splicing endonuclease complex. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1717. [PMID: 35156311 PMCID: PMC9465713 DOI: 10.1002/wrna.1717] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 01/12/2022] [Accepted: 01/13/2022] [Indexed: 04/30/2023]
Abstract
The splicing of transfer RNA (tRNA) introns is a critical step of tRNA maturation, for intron-containing tRNAs. In eukaryotes, tRNA splicing is a multi-step process that relies on several RNA processing enzymes to facilitate intron removal and exon ligation. Splicing is initiated by the tRNA splicing endonuclease (TSEN) complex which catalyzes the excision of the intron through its two nuclease subunits. Mutations in all four subunits of the TSEN complex are linked to a family of neurodegenerative and neurodevelopmental diseases known as pontocerebellar hypoplasia (PCH). Recent studies provide molecular insights into the structure, function, and regulation of the eukaryotic TSEN complex and are beginning to illuminate how mutations in the TSEN complex lead to neurodegenerative disease. Using new advancements in the prediction of protein structure, we created a three-dimensional model of the human TSEN complex. We review functions of the TSEN complex beyond tRNA splicing by highlighting recently identified substrates of the eukaryotic TSEN complex and discuss mechanisms for the regulation of tRNA splicing, by enzymes that modify cleaved tRNA exons and introns. Finally, we review recent biochemical and animal models that have worked to address the mechanisms that drive PCH and synthesize these studies with previous studies to try to better understand PCH pathogenesis. This article is categorized under: RNA Processing > tRNA Processing RNA in Disease and Development > RNA in Disease RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition.
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Affiliation(s)
- Cassandra K Hayne
- Department of Health and Human Services, Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA
| | - Tanae A Lewis
- Department of Chemistry, North Carolina Agricultural and Technical State University, Greensboro, North Carolina, USA
| | - Robin E Stanley
- Department of Health and Human Services, Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA
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12
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Proteome allocations change linearly with the specific growth rate of Saccharomyces cerevisiae under glucose limitation. Nat Commun 2022; 13:2819. [PMID: 35595797 PMCID: PMC9122918 DOI: 10.1038/s41467-022-30513-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 04/28/2022] [Indexed: 01/21/2023] Open
Abstract
Saccharomyces cerevisiae is a widely used cell factory; therefore, it is important to understand how it organizes key functional parts when cultured under different conditions. Here, we perform a multiomics analysis of S. cerevisiae by culturing the strain with a wide range of specific growth rates using glucose as the sole limiting nutrient. Under these different conditions, we measure the absolute transcriptome, the absolute proteome, the phosphoproteome, and the metabolome. Most functional protein groups show a linear dependence on the specific growth rate. Proteins engaged in translation show a perfect linear increase with the specific growth rate, while glycolysis and chaperone proteins show a linear decrease under respiratory conditions. Glycolytic enzymes and chaperones, however, show decreased phosphorylation with increasing specific growth rates; at the same time, an overall increased flux through these pathways is observed. Further analysis show that even though mRNA levels do not correlate with protein levels for all individual genes, the transcriptome level of functional groups correlates very well with its corresponding proteome. Finally, using enzyme-constrained genome-scale modeling, we find that enzyme usage plays an important role in controlling flux in amino acid biosynthesis. Understanding how yeast organizes its functional proteome is a fundamental task in systems biology. Here, the authors conduct a multiomics analysis on yeast cells cultured with different growth rates, identifying a linear dependence of the functional proteome on the growth rate.
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13
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Goldkamp AK, Li Y, Rivera RM, Hagen DE. Characterization of tRNA expression profiles in large offspring syndrome. BMC Genomics 2022; 23:273. [PMID: 35392796 PMCID: PMC8988405 DOI: 10.1186/s12864-022-08496-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 03/23/2022] [Indexed: 11/10/2022] Open
Abstract
Background Assisted Reproductive Technologies (ART) use can increase the risk of congenital overgrowth syndromes, such as large offspring syndrome (LOS) in ruminants. Epigenetic variations are known to influence gene expression and differentially methylated regions (DMRs) were previously determined to be associated with LOS in cattle. We observed DMRs overlapping tRNA clusters which could affect tRNA abundance and be associated with tissue specificity or overgrowth. Variations in tRNA expression have been identified in several disease pathways suggesting an important role in the regulation of biological processes. Understanding the role of tRNA expression in cattle offers an opportunity to reveal mechanisms of regulation at the translational level. We analyzed tRNA expression in the skeletal muscle and liver tissues of day 105 artificial insemination-conceived, ART-conceived with a normal body weight, and ART-conceived bovine fetuses with a body weight above the 97th percentile compared to Control-AI. Results Despite the centrality of tRNAs to translation, in silico predictions have revealed dramatic differences in the number of tRNA genes between humans and cattle (597 vs 1,659). Consistent with reports in human, only a fraction of predicted tRNA genes are expressed. We detected the expression of 474 and 487 bovine tRNA genes in the muscle and liver with the remainder being unexpressed. 193 and 198 unique tRNA sequences were expressed in all treatment groups within muscle and liver respectively. In addition, an average of 193 tRNA sequences were expressed within the same treatment group in different tissues. Some tRNA isodecoders were differentially expressed between treatment groups. In the skeletal muscle and liver, we categorized 11 tRNA isoacceptors with undetected expression as well as an isodecoder that was unexpressed in the liver (SerGGA). Our results identified variation in the proportion of tRNA gene copies expressed between tissues and differences in the highest contributing tRNA anticodon within an amino acid family due to treatment and tissue type. Out of all amino acid families, roughly half of the most highly expressed tRNA isoacceptors correlated to their most frequent codon in the bovine genome. Conclusion Although the number of bovine tRNA genes is nearly triple of that of the tRNA genes in human, there is a shared occurrence of transcriptionally inactive tRNA genes in both species. We detected differential expression of tRNA genes as well as tissue- and treatment- specific tRNA transcripts with unique sequence variations that could modulate translation during protein homeostasis or cellular stress, and give rise to regulatory products targeting genes related to overgrowth in the skeletal muscle and/or tumor development in the liver of LOS individuals. While the absence of certain isodecoders may be relieved by wobble base pairing, missing tRNA species could increase the likelihood of mistranslation or mRNA degradation. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08496-7.
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Affiliation(s)
- Anna K Goldkamp
- Department of Animal and Food Sciences, Oklahoma State University, Stillwater, OK, USA
| | - Yahan Li
- Division of Animal Sciences, University of Missouri, Columbia, MO, USA
| | - Rocio M Rivera
- Division of Animal Sciences, University of Missouri, Columbia, MO, USA
| | - Darren E Hagen
- Department of Animal and Food Sciences, Oklahoma State University, Stillwater, OK, USA.
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14
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Canpolat N, Liu D, Atayar E, Saygili S, Kara NS, Westfall TA, Ding Q, Brown BJ, Braun TA, Slusarski D, Oguz KK, Ozluk Y, Tuysuz B, Ozturk TT, Sever L, Sezerman OU, Topaloglu R, Caliskan S, Attanasio M, Ozaltin F. A splice site mutation in the TSEN2 causes a new syndrome with craniofacial and central nervous system malformations, and atypical hemolytic uremic syndrome. Clin Genet 2022; 101:346-358. [PMID: 34964109 PMCID: PMC10357464 DOI: 10.1111/cge.14105] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/19/2021] [Accepted: 12/26/2021] [Indexed: 07/22/2023]
Abstract
Recessive mutations in the genes encoding the four subunits of the tRNA splicing endonuclease complex (TSEN54, TSEN34, TSEN15, and TSEN2) cause various forms of pontocerebellar hypoplasia, a disorder characterized by hypoplasia of the cerebellum and the pons, microcephaly, dysmorphisms, and other variable clinical features. Here, we report an intronic recessive founder variant in the gene TSEN2 that results in abnormal splicing of the mRNA of this gene, in six individuals from four consanguineous families affected with microcephaly, multiple craniofacial malformations, radiological abnormalities of the central nervous system, and cognitive retardation of variable severity. Remarkably, unlike patients with previously described mutations in the components of the TSEN complex, all the individuals that we report developed atypical hemolytic uremic syndrome (aHUS) with thrombotic microangiopathy, microangiopathic hemolytic anemia, thrombocytopenia, proteinuria, severe hypertension, and end-stage kidney disease (ESKD) early in life. Bulk RNA sequencing of peripheral blood cells of four affected individuals revealed abnormal tRNA transcripts, indicating an alteration of the tRNA biogenesis. Morpholino-mediated skipping of exon 10 of tsen2 in zebrafish produced phenotypes similar to human patients. Thus, we have identified a novel syndrome accompanied by aHUS suggesting the existence of a link between tRNA biology and vascular endothelium homeostasis, which we propose to name with the acronym TRACK syndrome (TSEN2 Related Atypical hemolytic uremic syndrome, Craniofacial malformations, Kidney failure).
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Affiliation(s)
- Nur Canpolat
- Department of Pediatric Nephrology, Istanbul University-Cerrahpasa, Cerrahpasa Faculty of Medicine, Istanbul, Turkey
| | - Dingxiao Liu
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
- Department of Vascular Surgery, Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Emine Atayar
- Nephrogenetics Laboratory, Department of Pediatric Nephrology, Hacettepe University, Faculty of Medicine, Ankara, Turkey
| | - Seha Saygili
- Department of Pediatric Nephrology, Istanbul University-Cerrahpasa, Cerrahpasa Faculty of Medicine, Istanbul, Turkey
| | - Nazli Sila Kara
- Biostatistics and Medical Informatics Program, Faculty of Medicine, Graduate School of Health Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | | | - Qiong Ding
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Bartley J. Brown
- Center for Bioinformatics and Computational Biology, University of Iowa, Iowa City, Iowa, USA
| | - Terry A. Braun
- Center for Bioinformatics and Computational Biology, University of Iowa, Iowa City, Iowa, USA
| | - Diane Slusarski
- Center for Bioinformatics and Computational Biology, University of Iowa, Iowa City, Iowa, USA
| | - Kader Karli Oguz
- Department of Radiology, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Yasemin Ozluk
- Department of Pathology, Istanbul University Faculty of Medicine, Istanbul, Turkey
| | - Beyhan Tuysuz
- Department of Pediatric Genetics, Istanbul University-Cerrahpasa, Cerrahpasa Faculty of Medicine, Istanbul, Turkey
| | - Tugba Tastemel Ozturk
- Department of Pediatric Nephrology, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Lale Sever
- Department of Pediatric Nephrology, Istanbul University-Cerrahpasa, Cerrahpasa Faculty of Medicine, Istanbul, Turkey
| | - Osman Ugur Sezerman
- Biostatistics and Medical Informatics Program, Faculty of Medicine, Graduate School of Health Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Rezan Topaloglu
- Department of Pediatric Nephrology, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Salim Caliskan
- Department of Pediatric Nephrology, Istanbul University-Cerrahpasa, Cerrahpasa Faculty of Medicine, Istanbul, Turkey
| | - Massimo Attanasio
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Fatih Ozaltin
- Nephrogenetics Laboratory, Department of Pediatric Nephrology, Hacettepe University, Faculty of Medicine, Ankara, Turkey
- Department of Pediatric Nephrology, Hacettepe University Faculty of Medicine, Ankara, Turkey
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15
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Caba L, Florea L, Gug C, Dimitriu DC, Gorduza EV. Circular RNA-Is the Circle Perfect? Biomolecules 2021; 11:biom11121755. [PMID: 34944400 PMCID: PMC8698871 DOI: 10.3390/biom11121755] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 11/18/2021] [Accepted: 11/22/2021] [Indexed: 12/13/2022] Open
Abstract
Circular RNA (circRNA) is a distinct class of non-coding RNA produced, in principle, using a back-splicing mechanism, conserved during evolution, with increased stability and a tissue-dependent expression. Circular RNA represents a functional molecule with roles in the regulation of transcription and splicing, microRNA sponge, and the modulation of protein–protein interaction. CircRNAs are involved in essential processes of life such as apoptosis, cell cycle, and proliferation. Due to the regulatory role (upregulation/downregulation) in pathogenic mechanisms of some diseases (including cancer), its potential roles as a biomarker or therapeutic target in these diseases were studied. This review focuses on the importance of circular RNA in cancer.
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Affiliation(s)
- Lavinia Caba
- Department of Medical Genetics, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania;
- Correspondence:
| | - Laura Florea
- Department of Nephrology-Internal Medicine, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania;
| | - Cristina Gug
- Microscopic Morphology Department, “Victor Babes” University of Medicine and Pharmacy, 300041 Timișoara, Romania;
| | - Daniela Cristina Dimitriu
- Department of Morpho-Functional Sciences II, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania;
| | - Eusebiu Vlad Gorduza
- Department of Medical Genetics, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania;
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16
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Yan B, Tzertzinis G, Schildkraut I, Ettwiller L. Comprehensive determination of transcription start sites derived from all RNA polymerases using ReCappable-seq. Genome Res 2021; 32:162-174. [PMID: 34815308 PMCID: PMC8744680 DOI: 10.1101/gr.275784.121] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 11/19/2021] [Indexed: 11/24/2022]
Abstract
Determination of eukaryotic transcription start sites (TSSs) has been based on methods that require the cap structure at the 5' end of transcripts derived from Pol II RNA polymerase. Consequently, these methods do not reveal TSSs derived from the other RNA polymerases that also play critical roles in various cell functions. To address this limitation, we developed ReCappable-seq, which comprehensively identifies TSS for both Pol II and non-Pol II transcripts at single-nucleotide resolution. The method relies on specific enzymatic exchange of 5' m7G caps and 5' triphosphates with a selectable tag. When applied to human transcriptomes, ReCappable-seq identifies Pol II TSSs that are in agreement with orthogonal methods such as CAGE. Additionally, ReCappable-seq reveals a rich landscape of TSSs associated with Pol III transcripts that have not previously been amenable to study at genome-wide scale. Novel TSS from non-Pol II transcription can be located in the nuclear and mitochondrial genomes. ReCappable-seq interrogates the regulatory landscape of coding and noncoding RNA concurrently and enables the classification of epigenetic profiles associated with Pol II and non-Pol II TSS.
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Affiliation(s)
- Bo Yan
- New England Biolabs Incorporated, Ipswich, Massachusetts 01938, USA
| | | | - Ira Schildkraut
- New England Biolabs Incorporated, Ipswich, Massachusetts 01938, USA
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17
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Zhao YH, Zhou T, Wang JX, Li Y, Fang MF, Liu JN, Li ZH. Evolution and structural variations in chloroplast tRNAs in gymnosperms. BMC Genomics 2021; 22:750. [PMID: 34663228 PMCID: PMC8524817 DOI: 10.1186/s12864-021-08058-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 10/06/2021] [Indexed: 11/22/2022] Open
Abstract
Background Chloroplast transfer RNAs (tRNAs) can participate in various vital processes. Gymnosperms have important ecological and economic value, and they are the dominant species in forest ecosystems in the Northern Hemisphere. However, the evolution and structural changes in chloroplast tRNAs in gymnosperms remain largely unclear. Results In this study, we determined the nucleotide evolution, phylogenetic relationships, and structural variations in 1779 chloroplast tRNAs in gymnosperms. The numbers and types of tRNA genes present in the chloroplast genomes of different gymnosperms did not differ greatly, where the average number of tRNAs was 33 and the frequencies of occurrence for various types of tRNAs were generally consistent. Nearly half of the anticodons were absent. Molecular sequence variation analysis identified the conserved secondary structures of tRNAs. About a quarter of the tRNA genes were found to contain precoded 3′ CCA tails. A few tRNAs have undergone novel structural changes that are closely related to their minimum free energy, and these structural changes affect the stability of the tRNAs. Phylogenetic analysis showed that tRNAs have evolved from multiple common ancestors. The transition rate was higher than the transversion rate in gymnosperm chloroplast tRNAs. More loss events than duplication events have occurred in gymnosperm chloroplast tRNAs during their evolutionary process. Conclusions These findings provide novel insights into the molecular evolution and biological characteristics of chloroplast tRNAs in gymnosperms. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08058-3.
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Affiliation(s)
- Yu-He Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Tong Zhou
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Jiu-Xia Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Yan Li
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Min-Feng Fang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Jian-Ni Liu
- State Key Laboratory of Continental Dynamics, Department of Geology, Early Life Institute, Northwest University, Xi'an, 710069, China
| | - Zhong-Hu Li
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, 710069, China.
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18
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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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19
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Sekulovski S, Devant P, Panizza S, Gogakos T, Pitiriciu A, Heitmeier K, Ramsay EP, Barth M, Schmidt C, Tuschl T, Baas F, Weitzer S, Martinez J, Trowitzsch S. Assembly defects of human tRNA splicing endonuclease contribute to impaired pre-tRNA processing in pontocerebellar hypoplasia. Nat Commun 2021; 12:5610. [PMID: 34584079 PMCID: PMC8479045 DOI: 10.1038/s41467-021-25870-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 09/03/2021] [Indexed: 02/07/2023] Open
Abstract
Introns of human transfer RNA precursors (pre-tRNAs) are excised by the tRNA splicing endonuclease TSEN in complex with the RNA kinase CLP1. Mutations in TSEN/CLP1 occur in patients with pontocerebellar hypoplasia (PCH), however, their role in the disease is unclear. Here, we show that intron excision is catalyzed by tetrameric TSEN assembled from inactive heterodimers independently of CLP1. Splice site recognition involves the mature domain and the anticodon-intron base pair of pre-tRNAs. The 2.1-Å resolution X-ray crystal structure of a TSEN15–34 heterodimer and differential scanning fluorimetry analyses show that PCH mutations cause thermal destabilization. While endonuclease activity in recombinant mutant TSEN is unaltered, we observe assembly defects and reduced pre-tRNA cleavage activity resulting in an imbalanced pre-tRNA pool in PCH patient-derived fibroblasts. Our work defines the molecular principles of intron excision in humans and provides evidence that modulation of TSEN stability may contribute to PCH phenotypes. Mutations within subunits of the tRNA splicing endonuclease complex (TSEN) are associated with pontocerebellar hypoplasia (PCH). Here the authors show that tRNA intron excision is catalyzed by tetrameric TSEN assembled from inactive heterodimers, and provide evidence that modulation of TSEN stability may contribute to PCH phenotypes.
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Affiliation(s)
- Samoil Sekulovski
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt/Main, Germany
| | - Pascal Devant
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt/Main, Germany.,Ph.D. Program in Virology, Harvard Medical School, Boston, MA, USA.,Harvard Medical School and Division of Gastroenterology, Boston Children's Hospital, Boston, MA, USA
| | - Silvia Panizza
- Max Perutz Labs, Medical University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Tasos Gogakos
- Laboratory for RNA Molecular Biology, The Rockefeller University, New York, NY, USA
| | - Anda Pitiriciu
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt/Main, Germany
| | - Katharina Heitmeier
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt/Main, Germany
| | | | - Marie Barth
- Interdisciplinary research center HALOmem, Charles Tanford Protein Center, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Carla Schmidt
- Interdisciplinary research center HALOmem, Charles Tanford Protein Center, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Thomas Tuschl
- Laboratory for RNA Molecular Biology, The Rockefeller University, New York, NY, USA
| | - Frank Baas
- Department of Clinical Genetics, Leiden University, Leiden, Netherlands
| | - Stefan Weitzer
- Max Perutz Labs, Medical University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Javier Martinez
- Max Perutz Labs, Medical University of Vienna, Vienna Biocenter (VBC), Vienna, Austria.
| | - Simon Trowitzsch
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt/Main, Germany.
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20
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Wang Y, Zhang Y, Kong L, Song C, Chen X, Fang X, Zhang C. tRNA-derived RNA fragments in the exosomes of bovine milk and colostrum. J Food Compost Anal 2021. [DOI: 10.1016/j.jfca.2021.103948] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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21
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Novel Structural Variation and Evolutionary Characteristics of Chloroplast tRNA in Gossypium Plants. Genes (Basel) 2021; 12:genes12060822. [PMID: 34071968 PMCID: PMC8228828 DOI: 10.3390/genes12060822] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/16/2021] [Accepted: 05/24/2021] [Indexed: 11/16/2022] Open
Abstract
Cotton is one of the most important fiber and oil crops in the world. Chloroplast genomes harbor their own genetic materials and are considered to be highly conserved. Transfer RNAs (tRNAs) act as "bridges" in protein synthesis by carrying amino acids. Currently, the variation and evolutionary characteristics of tRNAs in the cotton chloroplast genome are poorly understood. Here, we analyzed the structural variation and evolution of chloroplast tRNA (cp tRNA) based on eight diploid and two allotetraploid cotton species. We also investigated the nucleotide evolution of chloroplast genomes in cotton species. We found that cp tRNAs in cotton encoded 36 or 37 tRNAs, and 28 or 29 anti-codon types with lengths ranging from 60 to 93 nucleotides. Cotton chloroplast tRNA sequences possessed specific conservation and, in particular, the Ψ-loop contained the conserved U-U-C-X3-U. The cp tRNAs of Gossypium L. contained introns, and cp tRNAIle contained the anti-codon (C-A-U), which was generally the anti-codon of tRNAMet. The transition and transversion analyses showed that cp tRNAs in cotton species were iso-acceptor specific and had undergone unequal rates of evolution. The intergenic region was more variable than coding regions, and non-synonymous mutations have been fixed in cotton cp genomes. On the other hand, phylogeny analyses indicated that cp tRNAs of cotton were derived from several inferred ancestors with greater gene duplications. This study provides new insights into the structural variation and evolution of chloroplast tRNAs in cotton plants. Our findings could contribute to understanding the detailed characteristics and evolutionary variation of the tRNA family.
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22
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Torres AG, Martí E. Toward an Understanding of Extracellular tRNA Biology. Front Mol Biosci 2021; 8:662620. [PMID: 33937338 PMCID: PMC8082309 DOI: 10.3389/fmolb.2021.662620] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 03/22/2021] [Indexed: 12/18/2022] Open
Abstract
Extracellular RNAs (exRNAs) including abundant full length tRNAs and tRNA fragments (tRFs) have recently garnered attention as a promising source of biomarkers and a novel mediator in cell-to-cell communication in eukaryotes. Depending on the physiological state of cells, tRNAs/tRFs are released to the extracellular space either contained in extracellular vesicles (EVs) or free, through a mechanism that is largely unknown. In this perspective article, we propose that extracellular tRNAs (ex-tRNAs) and/or extracellular tRFs (ex-tRFs) are relevant paracrine signaling molecules whose activity depends on the mechanisms of release by source cells and capture by recipient cells. We speculate on how ex-tRNA/ex-tRFs orchestrate the effects in target cells, depending on the type of sequence and the mechanisms of uptake. We further propose that tRNA modifications may be playing important roles in ex-tRNA biology.
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Affiliation(s)
- Adrian Gabriel Torres
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Eulàlia Martí
- Departament de Biomedicina, Facultat de Medicina i Ciències de la Salut, Institut de Neurociències, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red sobre Epidemiología y Salud Pública, Madrid, Spain
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23
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Zhong Q, Fu X, Zhang T, Zhou T, Yue M, Liu J, Li Z. Phylogeny and evolution of chloroplast tRNAs in Adoxaceae. Ecol Evol 2021; 11:1294-1309. [PMID: 33598131 PMCID: PMC7863635 DOI: 10.1002/ece3.7133] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 11/14/2020] [Accepted: 11/23/2020] [Indexed: 12/24/2022] Open
Abstract
Chloroplasts are semiautonomous organelles found in photosynthetic plants. The major functions of chloroplasts include photosynthesis and carbon fixation, which are mainly regulated by its circular genomes. In the highly conserved chloroplast genome, the chloroplast transfer RNA genes (cp tRNA) play important roles in protein translation within chloroplasts. However, the evolution of cp tRNAs remains unclear. Thus, in the present study, we investigated the evolutionary characteristics of chloroplast tRNAs in five Adoxaceae species using 185 tRNA gene sequences. In total, 37 tRNAs encoding 28 anticodons are found in the chloroplast genome in Adoxaceae species. Some consensus sequences are found within the Ψ-stem and anticodon loop of the tRNAs. Some putative novel structures were also identified, including a new stem located in the variable region of tRNATyr in a similar manner to the anticodon stem. Furthermore, phylogenetic and evolutionary analyses indicated that synonymous tRNAs may have evolved from multiple ancestors and frequent tRNA duplications during the evolutionary process may have been primarily caused by positive selection and adaptive evolution. The transition and transversion rates are uneven among different tRNA isotypes. For all tRNAs, the transition rate is greater with a transition/transversion bias of 3.13. Phylogenetic analysis of cp tRNA suggested that the type I introns in different taxa (including eukaryote organisms and cyanobacteria) share the conserved sequences "U-U-x2-C" and "U-x-G-x2-T," thereby indicating the diverse cyanobacterial origins of organelles. This detailed study of cp tRNAs in Adoxaceae may facilitate further investigations of the evolution, phylogeny, structure, and related functions of chloroplast tRNAs.
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Affiliation(s)
- Qiu‐Yi Zhong
- Shaanxi Key Laboratory for Animal ConservationKey Laboratory of Resource Biology and Biotechnology in Western ChinaMinistry of EducationCollege of Life SciencesNorthwest UniversityXi'anChina
- Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of BotanyChinese Academy of SciencesKunmingChina
| | - Xiao‐Gang Fu
- Shaanxi Key Laboratory for Animal ConservationKey Laboratory of Resource Biology and Biotechnology in Western ChinaMinistry of EducationCollege of Life SciencesNorthwest UniversityXi'anChina
| | - Ting‐Ting Zhang
- Shaanxi Key Laboratory for Animal ConservationKey Laboratory of Resource Biology and Biotechnology in Western ChinaMinistry of EducationCollege of Life SciencesNorthwest UniversityXi'anChina
| | - Tong Zhou
- Shaanxi Key Laboratory for Animal ConservationKey Laboratory of Resource Biology and Biotechnology in Western ChinaMinistry of EducationCollege of Life SciencesNorthwest UniversityXi'anChina
| | - Ming Yue
- Shaanxi Key Laboratory for Animal ConservationKey Laboratory of Resource Biology and Biotechnology in Western ChinaMinistry of EducationCollege of Life SciencesNorthwest UniversityXi'anChina
| | - Jian‐Ni Liu
- Department of GeologyState Key Laboratory of Continental DynamicsEarly Life InstituteNorthwest UniversityXi'anChina
| | - Zhong‐Hu Li
- Shaanxi Key Laboratory for Animal ConservationKey Laboratory of Resource Biology and Biotechnology in Western ChinaMinistry of EducationCollege of Life SciencesNorthwest UniversityXi'anChina
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24
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Non-Redundant tRNA Reference Sequences for Deep Sequencing Analysis of tRNA Abundance and Epitranscriptomic RNA Modifications. Genes (Basel) 2021; 12:genes12010081. [PMID: 33435213 PMCID: PMC7827920 DOI: 10.3390/genes12010081] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/04/2021] [Accepted: 01/07/2021] [Indexed: 12/29/2022] Open
Abstract
Analysis of RNA by deep-sequencing approaches has found widespread application in modern biology. In addition to measurements of RNA abundance under various physiological conditions, such techniques are now widely used for mapping and quantification of RNA modifications. Transfer RNA (tRNA) molecules are among the frequent targets of such investigation, since they contain multiple modified residues. However, the major challenge in tRNA examination is related to a large number of duplicated and point-mutated genes encoding those RNA molecules. Moreover, the existence of multiple isoacceptors/isodecoders complicates both the analysis and read mapping. Existing databases for tRNA sequencing provide near exhaustive listings of tRNA genes, but the use of such highly redundant reference sequences in RNA-seq analyses leads to a large number of ambiguously mapped sequencing reads. Here we describe a relatively simple computational strategy for semi-automatic collapsing of highly redundant tRNA datasets into a non-redundant collection of reference tRNA sequences. The relevance of the approach was validated by analysis of experimentally obtained tRNA-sequencing datasets for different prokaryotic and eukaryotic model organisms. The data demonstrate that non-redundant tRNA reference sequences allow improving unambiguous mapping of deep sequencing data.
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25
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Warren JM, Salinas-Giegé T, Hummel G, Coots NL, Svendsen JM, Brown KC, Drouard L, Sloan DB. Combining tRNA sequencing methods to characterize plant tRNA expression and post-transcriptional modification. RNA Biol 2021; 18:64-78. [PMID: 32715941 PMCID: PMC7834048 DOI: 10.1080/15476286.2020.1792089] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 06/18/2020] [Accepted: 06/30/2020] [Indexed: 12/27/2022] Open
Abstract
Differences in tRNA expression have been implicated in a remarkable number of biological processes. There is growing evidence that tRNA genes can play dramatically different roles depending on both expression and post-transcriptional modification, yet sequencing tRNAs to measure abundance and detect modifications remains challenging. Their secondary structure and extensive post-transcriptional modifications interfere with RNA-seq library preparation methods and have limited the utility of high-throughput sequencing technologies. Here, we combine two modifications to standard RNA-seq methods by treating with the demethylating enzyme AlkB and ligating with tRNA-specific adapters in order to sequence tRNAs from four species of flowering plants, a group that has been shown to have some of the most extensive rates of post-transcriptional tRNA modifications. This protocol has the advantage of detecting full-length tRNAs and sequence variants that can be used to infer many post-transcriptional modifications. We used the resulting data to produce a modification index of almost all unique reference tRNAs in Arabidopsis thaliana, which exhibited many anciently conserved similarities with humans but also positions that appear to be 'hot spots' for modifications in angiosperm tRNAs. We also found evidence based on northern blot analysis and droplet digital PCR that, even after demethylation treatment, tRNA-seq can produce highly biased estimates of absolute expression levels most likely due to biased reverse transcription. Nevertheless, the generation of full-length tRNA sequences with modification data is still promising for assessing differences in relative tRNA expression across treatments, tissues or subcellular fractions and help elucidate the functional roles of tRNA modifications.
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Affiliation(s)
- Jessica M. Warren
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Thalia Salinas-Giegé
- Institut De Biologie Moléculaire Des plantes-CNRS, Université De Strasbourg, Strasbourg, France
| | - Guillaume Hummel
- Institut De Biologie Moléculaire Des plantes-CNRS, Université De Strasbourg, Strasbourg, France
| | - Nicole L. Coots
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | | | - Kristen C. Brown
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Laurence Drouard
- Department of Biology, Colorado State University, Fort Collins, CO, USA
- Institut De Biologie Moléculaire Des plantes-CNRS, Université De Strasbourg, Strasbourg, France
| | - Daniel B. Sloan
- Department of Biology, Colorado State University, Fort Collins, CO, USA
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26
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Zhang TT, Hou YK, Yang T, Zhang SY, Yue M, Liu J, Li Z. Evolutionary analysis of chloroplast tRNA of Gymnosperm revealed the novel structural variation and evolutionary aspect. PeerJ 2020; 8:e10312. [PMID: 33304650 PMCID: PMC7698693 DOI: 10.7717/peerj.10312] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 10/15/2020] [Indexed: 12/27/2022] Open
Abstract
Gymnosperms such as ginkgo, conifers, cycads, and gnetophytes are vital components of land ecosystems, and they have significant economic and ecologic value, as well as important roles as forest vegetation. In this study, we investigated the structural variation and evolution of chloroplast transfer RNAs (tRNAs) in gymnosperms. Chloroplasts are important organelles in photosynthetic plants. tRNAs are key participants in translation where they act as adapter molecules between the information level of nucleic acids and functional level of proteins. The basic structures of gymnosperm chloroplast tRNAs were found to have family-specific conserved sequences. The tRNAΨ -loop was observed to contain a conforming sequence, i.e., U-U-C-N-A-N2. In gymnosperms, tRNAIle was found to encode a "CAU" anticodon, which is usually encoded by tRNAMet. Phylogenetic analysis suggested that plastid tRNAs have a common polyphyletic evolutionary pattern, i.e., rooted in abundant common ancestors. Analyses of duplication and loss events in chloroplast tRNAs showed that gymnosperm tRNAs have experienced little more gene loss than gene duplication. Transition and transversion analysis showed that the tRNAs are iso-acceptor specific and they have experienced unequal evolutionary rates. These results provide new insights into the structural variation and evolution of gymnosperm chloroplast tRNAs, which may improve our comprehensive understanding of the biological characteristics of the tRNA family.
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Affiliation(s)
- Ting-Ting Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, China
| | - Yi-Kun Hou
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, China
| | - Ting Yang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, China
| | - Shu-Ya Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, China
| | - Ming Yue
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, China
| | - Jianni Liu
- Early Life Institute, State Key Laboratory of Continental Dynamics, Department of Geology, Northwest University, Xi’an, China
| | - Zhonghu Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, China
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27
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Wicke L, Ponath F, Coppens L, Gerovac M, Lavigne R, Vogel J. Introducing differential RNA-seq mapping to track the early infection phase for Pseudomonas phage ɸKZ. RNA Biol 2020; 18:1099-1110. [PMID: 33103565 PMCID: PMC8244752 DOI: 10.1080/15476286.2020.1827785] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
As part of the ongoing renaissance of phage biology, more phage genomes are becoming available through DNA sequencing. However, our understanding of the transcriptome architecture that allows these genomes to be expressed during host infection is generally poor. Transcription start sites (TSSs) and operons have been mapped for very few phages, and an annotated global RNA map of a phage – alone or together with its infected host – is not available at all. Here, we applied differential RNA-seq (dRNA-seq) to study the early, host takeover phase of infection by assessing the transcriptome structure of Pseudomonas aeruginosa jumbo phage ɸKZ, a model phage for viral genetics and structural research. This map substantially expands the number of early expressed viral genes, defining TSSs that are active ten minutes after ɸKZ infection. Simultaneously, we record gene expression changes in the host transcriptome during this critical metabolism conversion. In addition to previously reported upregulation of genes associated with amino acid metabolism, we observe strong activation of genes with functions in biofilm formation (cdrAB) and iron storage (bfrB), as well as an activation of the antitoxin ParD. Conversely, ɸKZ infection rapidly down-regulates complexes IV and V of oxidative phosphorylation (atpCDGHF and cyoABCDE). Taken together, our data provide new insights into the transcriptional organization and infection process of the giant bacteriophage ɸKZ and adds a framework for the genome-wide transcriptomic analysis of phage–host interactions.
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Affiliation(s)
- Laura Wicke
- Institute for Molecular Infection Biology (IMIB), Medical Faculty, University of Würzburg, Würzburg, Germany.,Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Falk Ponath
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Lucas Coppens
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Milan Gerovac
- Institute for Molecular Infection Biology (IMIB), Medical Faculty, University of Würzburg, Würzburg, Germany
| | - Rob Lavigne
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Jörg Vogel
- Institute for Molecular Infection Biology (IMIB), Medical Faculty, University of Würzburg, Würzburg, Germany.,Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
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28
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Contribution of miRNAs, tRNAs and tRFs to Aberrant Signaling and Translation Deregulation in Lung Cancer. Cancers (Basel) 2020; 12:cancers12103056. [PMID: 33092114 PMCID: PMC7593945 DOI: 10.3390/cancers12103056] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/09/2020] [Accepted: 10/16/2020] [Indexed: 12/25/2022] Open
Abstract
Simple Summary The profiles of miRNAs, tRNA-derived fragments and tRNAs from lung cancer biopsy specimens indicate involvement of gene networks that modulate signaling and translation initiation. The current study highlights the important role of several regulatory small non-coding RNAs in aberrant signaling and translation deregulation in lung cancer. Abstract Transcriptomics profiles of miRNAs, tRNAs or tRFs are used as biomarkers, after separate examination of several cancer cell lines, blood samples or biopsies. However, the possible contribution of all three profiles on oncogenic signaling and translation as a net regulatory effect, is under investigation. The present analysis of miRNAs and tRFs from lung cancer biopsies indicated putative targets, which belong to gene networks involved in cell proliferation, transcription and translation regulation. In addition, we observed differential expression of specific tRNAs along with several tRNA-related genes with possible involvement in carcinogenesis. Transfection of lung adenocarcinoma cells with two identified tRFs and subsequent NGS analysis indicated gene targets that mediate signaling and translation regulation. Broader analysis of all major signaling and translation factors in several biopsy specimens revealed a crosstalk between the PI3K/AKT and MAPK pathways and downstream activation of eIF4E and eEF2. Subsequent polysome profile analysis and 48S pre-initiation reconstitution experiments showed increased global translation rates and indicated that aberrant expression patterns of translation initiation factors could contribute to elevated protein synthesis. Overall, our results outline the modulatory effects that possibly correlate the expression of important regulatory non-coding RNAs with aberrant signaling and translation deregulation in lung cancer.
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29
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Tosar JP, Cayota A. Extracellular tRNAs and tRNA-derived fragments. RNA Biol 2020; 17:1149-1167. [PMID: 32070197 PMCID: PMC7549618 DOI: 10.1080/15476286.2020.1729584] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 02/05/2020] [Accepted: 02/10/2020] [Indexed: 01/08/2023] Open
Abstract
Fragmentation of tRNAs generates a family of small RNAs collectively known as tRNA-derived fragments. These fragments vary in sequence and size but have been shown to regulate many processes involved in cell homoeostasis and adaptations to stress. Additionally, the field of extracellular RNAs (exRNAs) is rapidly growing because exRNAs are a promising source of biomarkers in liquid biopsies, and because exRNAs seem to play key roles in intercellular and interspecies communication. Herein, we review recent descriptions of tRNA-derived fragments in the extracellular space in all domains of life, both in biofluids and in cell culture. The purpose of this review is to find consensus on which tRNA-derived fragments are more prominent in each extracellular fraction (including extracellular vesicles, lipoproteins and ribonucleoprotein complexes). We highlight what is becoming clear and what is still controversial in this field, in order to stimulate future hypothesis-driven studies which could clarify the role of full-length tRNAs and tRNA-derived fragments in the extracellular space.
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Affiliation(s)
- Juan Pablo Tosar
- Analytical Biochemistry Unit, Nuclear Research Center, Faculty of Science, Universidad de la República, Montevideo, Uruguay
- Functional Genomics Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Alfonso Cayota
- Functional Genomics Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Department of Medicine, University Hospital, Universidad de la República, Montevideo, Uruguay
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30
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Roy G, Reier J, Garcia A, Martin T, Rice M, Wang J, Prophet M, Christie R, Dall’Acqua W, Ahuja S, Bowen MA, Marelli M. Development of a high yielding expression platform for the introduction of non-natural amino acids in protein sequences. MAbs 2020; 12:1684749. [PMID: 31775561 PMCID: PMC6927762 DOI: 10.1080/19420862.2019.1684749] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 10/14/2019] [Accepted: 10/18/2019] [Indexed: 12/11/2022] Open
Abstract
The ability to genetically encode non-natural amino acids (nnAAs) into proteins offers an expanded tool set for protein engineering. nnAAs containing unique functional moieties have enabled the study of post-translational modifications, protein interactions, and protein folding. In addition, nnAAs have been developed that enable a variety of biorthogonal conjugation chemistries that allow precise and efficient protein conjugations. These are being studied to create the next generation of antibody-drug conjugates with improved efficacy, potency, and stability for the treatment of cancer. However, the efficiency of nnAA incorporation, and the productive yields of cell-based expression systems, have limited the utility and widespread use of this technology. We developed a process to isolate stable cell lines expressing a pyrrolysyl-tRNA synthetase/tRNApyl pair capable of efficient nnAA incorporation. Two different platform cell lines generated by these methods were used to produce IgG-expressing cell lines with normalized antibody titers of 3 g/L using continuous perfusion. We show that the antibodies produced by these platform cells contain the nnAA functionality that enables facile conjugations. Characterization of these highly active and robust platform hosts identified key parameters that affect nnAA incorporation efficiency. These highly efficient host platforms may help overcome the expression challenges that have impeded the developability of this technology for manufacturing proteins with nnAAs and represents an important step in expanding its utility.
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Affiliation(s)
- Gargi Roy
- Antibody Discovery and Protein Engineering, AstraZeneca, Gaithersburg, Maryland, USA
| | - Jason Reier
- Cell Culture and Fermentation Sciences, AstraZeneca, Gaithersburg, Maryland, USA
| | - Andrew Garcia
- Antibody Discovery and Protein Engineering, AstraZeneca, Gaithersburg, Maryland, USA
| | - Tom Martin
- Antibody Discovery and Protein Engineering, AstraZeneca, Gaithersburg, Maryland, USA
| | - Megan Rice
- Antibody Discovery and Protein Engineering, AstraZeneca, Gaithersburg, Maryland, USA
| | - Jihong Wang
- Analytical Sciences, AstraZeneca, Gaithersburg, Maryland, USA
| | - Meagan Prophet
- Analytical Sciences, AstraZeneca, Gaithersburg, Maryland, USA
| | - Ronald Christie
- Antibody Discovery and Protein Engineering, AstraZeneca, Gaithersburg, Maryland, USA
| | - William Dall’Acqua
- Antibody Discovery and Protein Engineering, AstraZeneca, Gaithersburg, Maryland, USA
| | - Sanjeev Ahuja
- Cell Culture and Fermentation Sciences, AstraZeneca, Gaithersburg, Maryland, USA
| | - Michael A Bowen
- Antibody Discovery and Protein Engineering, AstraZeneca, Gaithersburg, Maryland, USA
| | - Marcello Marelli
- Antibody Discovery and Protein Engineering, AstraZeneca, Gaithersburg, Maryland, USA
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31
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T Magalhães B, Lourenço A, Azevedo NF. Computational resources and strategies to assess single-molecule dynamics of the translation process in S. cerevisiae. Brief Bioinform 2019; 22:219-231. [PMID: 31879749 DOI: 10.1093/bib/bbz149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 10/16/2019] [Accepted: 10/30/2019] [Indexed: 11/13/2022] Open
Abstract
This work provides a systematic and comprehensive overview of available resources for the molecular-scale modelling of the translation process through agent-based modelling. The case study is the translation in Saccharomyces cerevisiae, one of the most studied yeasts. The data curation workflow encompassed structural information about the yeast (i.e. the simulation environment), and the proteins, ribonucleic acids and other types of molecules involved in the process (i.e. the agents). Moreover, it covers the main process events, such as diffusion (i.e. motion of molecules in the environment) and collision efficiency (i.e. interaction between molecules). Data previously determined by wet-lab techniques were preferred, resorting to computational predictions/extrapolations only when strictly necessary. The computational modelling of the translation processes is of added industrial interest, since it may bring forward knowledge on how to control such phenomena and enhance the production of proteins of interest in a faster and more efficient manner.
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Affiliation(s)
| | - Anália Lourenço
- Department of Computer Science, University of Vigo, Spain, Centre of Biological Engineering, University of Minho, Portugal
| | - Nuno F Azevedo
- Department of Chemical Engineering, Faculty of Engineering of the University of Porto, Portugal
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32
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UV Laser-Induced, Time-Resolved Transcriptome Responses of Saccharomyces cerevisiae. G3-GENES GENOMES GENETICS 2019; 9:2549-2560. [PMID: 31213515 PMCID: PMC6686910 DOI: 10.1534/g3.119.400291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
We determined the effect on gene transcription of laser-mediated, long-wavelength UV-irradiation of Saccharomyces cerevisiae by RNAseq analysis at times T15, T30, and T60 min after recovery in growth medium. Laser-irradiated cells were viable, and the transcriptional response was transient, with over 400 genes differentially expressed at T15 or T30, returning to basal level transcription by T60. Identification of transcripts exhibiting enhanced differential expression that were unique to UV laser-irradiation were identified by imposing a stringent significance cut-off (P < 0.05, log2 difference >2) then filtering out genes known as environmental stress response (ESR) genes. Using these rigorous criteria, 56 genes were differentially expressed at T15; at T30 differential expression was observed for 57 genes, some of which persisted from T15. Among the highly up-regulated genes were those supporting amino acid metabolic processes sulfur amino acids, methionine, aspartate, cysteine, serine), sulfur regulation (hydrogen sulfite metabolic processes, sulfate assimilation, sulfate reduction), proteasome components, amino acid transporters, and the iron regulon. At T30, the expression profile shifted to expression of transcripts related to catabolic processes (oxidoreductase activity, peptidase activity). Transcripts common to both T15 and T30 suggested an up-regulation of catabolic events, including UV damage response genes, and protein catabolism via proteasome and peptidase activity. Specific genes encoding tRNAs were among the down-regulated genes adding to the suggestion that control of protein biosynthesis was a major response to long-wave UV laser irradiation. These transcriptional responses highlight the remarkable ability of the yeast cell to respond to a UV-induced environmental insult.
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33
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Kovanich D, Saisawang C, Sittipaisankul P, Ramphan S, Kalpongnukul N, Somparn P, Pisitkun T, Smith DR. Analysis of the Zika and Japanese Encephalitis Virus NS5 Interactomes. J Proteome Res 2019; 18:3203-3218. [PMID: 31199156 DOI: 10.1021/acs.jproteome.9b00318] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Mosquito-borne flaviviruses, including dengue virus (DENV), Japanese encephalitis virus (JEV), and Zika virus (ZIKV), are major human pathogens. Among the flaviviral proteins, the nonstructural protein 5 (NS5) is the largest, most conserved, and major enzymatic component of the viral replication complex. Disruption of the common key NS5-host protein-protein interactions critical for viral replication could aid in the development of broad-spectrum antiflaviviral therapeutics. Hundreds of NS5 interactors have been identified, but these are mostly DENV-NS5 interactors. To this end, we sought to investigate the JEV- and ZIKV-NS5 interactomes using EGFP immunoprecipitation with label-free quantitative mass spectrometry analysis. We report here a total of 137 NS5 interactors with a significant enrichment of spliceosomal and spliceosomal-associated proteins. The transcription complex Paf1C and phosphatase 6 were identified as common NS5-associated complexes. PAF1 was shown to play opposite roles in JEV and ZIKV infections. Additionally, we validated several NS5 targets and proposed their possible roles in infection. These include lipid-shuttling proteins OSBPL9 and OSBPL11, component of RNAP3 transcription factor TFIIIC, minichromosome maintenance, and cochaperone PAQosome. Mining this data set, our study expands the current interaction landscape of NS5 and uncovers several NS5 targets that are new to flavivirus biology.
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Affiliation(s)
- Duangnapa Kovanich
- Institute of Molecular Biosciences, Mahidol University , Nakhon Pathom , Thailand
| | - Chonticha Saisawang
- Institute of Molecular Biosciences, Mahidol University , Nakhon Pathom , Thailand
| | | | - Suwipa Ramphan
- Institute of Molecular Biosciences, Mahidol University , Nakhon Pathom , Thailand
| | - Nuttiya Kalpongnukul
- Center of Excellence in Systems Biology, Research affairs, Faculty of Medicine , Chulalongkorn University , Bangkok , Thailand
| | - Poorichaya Somparn
- Center of Excellence in Systems Biology, Research affairs, Faculty of Medicine , Chulalongkorn University , Bangkok , Thailand
| | - Trairak Pisitkun
- Center of Excellence in Systems Biology, Research affairs, Faculty of Medicine , Chulalongkorn University , Bangkok , Thailand
| | - Duncan R Smith
- Institute of Molecular Biosciences, Mahidol University , Nakhon Pathom , Thailand
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34
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Hummel G, Warren J, Drouard L. The multi-faceted regulation of nuclear tRNA gene transcription. IUBMB Life 2019; 71:1099-1108. [PMID: 31241827 DOI: 10.1002/iub.2097] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 05/16/2019] [Indexed: 12/31/2022]
Abstract
Transfer RNAs are among the most ancient molecules of life on earth. Beyond their crucial role in protein synthesis as carriers of amino acids, they are also important players in a plethora of other biological processes. Many debates in term of biogenesis, regulation and function persist around these fascinating non-coding RNAs. Our review focuses on the first step of their biogenesis in eukaryotes, i.e. their transcription from nuclear genes. Numerous and complementary ways have emerged during evolution to regulate transfer RNA gene transcription. Here, we will summarize the different actors implicated in this process: cis-elements, trans-factors, genomic contexts, epigenetic environments and finally three-dimensional organization of nuclear genomes. © 2019 IUBMB Life, 2019 © 2019 IUBMB Life, 71(8):1099-1108, 2019.
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Affiliation(s)
- Guillaume Hummel
- Institut de biologie moléculaire des plantes-CNRS, Université de Strasbourg, 12 rue du Général Zimmer, F-67084 Strasbourg, France
| | - Jessica Warren
- Department of biology, Colorado State University, Fort Collins, Colorado, 80523, USA
| | - Laurence Drouard
- Institut de biologie moléculaire des plantes-CNRS, Université de Strasbourg, 12 rue du Général Zimmer, F-67084 Strasbourg, France
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35
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Wellner K, Pöhler MT, Betat H, Mörl M. Dual expression of CCA-adding enzyme and RNase T in Escherichia coli generates a distinct cca growth phenotype with diverse applications. Nucleic Acids Res 2019; 47:3631-3639. [PMID: 30828718 PMCID: PMC6468291 DOI: 10.1093/nar/gkz133] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 02/14/2019] [Accepted: 02/18/2019] [Indexed: 11/22/2022] Open
Abstract
Correct synthesis and maintenance of functional tRNA 3′-CCA-ends is a crucial prerequisite for aminoacylation and must be achieved by the phylogenetically diverse group of tRNA nucleotidyltransferases. While numerous reports on the in vitro characterization exist, robust analysis under in vivo conditions is lacking. Here, we utilize Escherichia coli RNase T, a tRNA-processing enzyme responsible for the tRNA-CCA-end turnover, to generate an in vivo system for the evaluation of A-adding activity. Expression of RNase T results in a prominent growth phenotype that renders the presence of a CCA- or A-adding enzyme essential for cell survival in an E. coli Δcca background. The distinct growth fitness allows for both complementation and selection of enzyme variants in a natural environment. We demonstrate the potential of our system via detection of altered catalytic efficiency and temperature sensitivity. Furthermore, we select functional enzyme variants out of a sequence pool carrying a randomized codon for a highly conserved position essential for catalysis. The presented E. coli-based approach opens up a wide field of future studies including the investigation of tRNA nucleotidyltransferases from all domains of life and the biological relevance of in vitro data concerning their functionality and mode of operation.
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Affiliation(s)
- Karolin Wellner
- Institute for Biochemistry, Leipzig University, Brüderstr. 34, 04103 Leipzig, Germany
| | - Marie-Theres Pöhler
- Institute for Biochemistry, Leipzig University, Brüderstr. 34, 04103 Leipzig, Germany
| | - Heike Betat
- Institute for Biochemistry, Leipzig University, Brüderstr. 34, 04103 Leipzig, Germany
| | - Mario Mörl
- Institute for Biochemistry, Leipzig University, Brüderstr. 34, 04103 Leipzig, Germany
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36
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Abstract
The eukaryotic translation pathway has been studied for more than four decades, but the molecular mechanisms that regulate each stage of the pathway are not completely defined. This is in part because we have very little understanding of the kinetic framework for the assembly and disassembly of pathway intermediates. Steps of the pathway are thought to occur in the subsecond to second time frame, but most assays to monitor these events require minutes to hours to complete. Understanding translational control in sufficient detail will therefore require the development of assays that can precisely monitor the kinetics of the translation pathway in real time. Here, we describe the translation pathway from the perspective of its kinetic parameters, discuss advances that are helping us move toward the goal of a rigorous kinetic understanding, and highlight some of the challenges that remain.
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Lant JT, Berg MD, Heinemann IU, Brandl CJ, O'Donoghue P. Pathways to disease from natural variations in human cytoplasmic tRNAs. J Biol Chem 2019; 294:5294-5308. [PMID: 30643023 DOI: 10.1074/jbc.rev118.002982] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Perfectly accurate translation of mRNA into protein is not a prerequisite for life. Resulting from errors in protein synthesis, mistranslation occurs in all cells, including human cells. The human genome encodes >600 tRNA genes, providing both the raw material for genetic variation and a buffer to ensure that resulting translation errors occur at tolerable levels. On the basis of data from the 1000 Genomes Project, we highlight the unanticipated prevalence of mistranslating tRNA variants in the human population and review studies on synthetic and natural tRNA mutations that cause mistranslation or de-regulate protein synthesis. Although mitochondrial tRNA variants are well known to drive human diseases, including developmental disorders, few studies have revealed a role for human cytoplasmic tRNA mutants in disease. In the context of the unexpectedly large number of tRNA variants in the human population, the emerging literature suggests that human diseases may be affected by natural tRNA variants that cause mistranslation or de-regulate tRNA expression and nucleotide modification. This review highlights examples relevant to genetic disorders, cancer, and neurodegeneration in which cytoplasmic tRNA variants directly cause or exacerbate disease and disease-linked phenotypes in cells, animal models, and humans. In the near future, tRNAs may be recognized as useful genetic markers to predict the onset or severity of human disease.
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Affiliation(s)
| | | | | | | | - Patrick O'Donoghue
- From the Departments of Biochemistry and .,Chemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
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38
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Grafanaki K, Anastasakis D, Kyriakopoulos G, Skeparnias I, Georgiou S, Stathopoulos C. Translation regulation in skin cancer from a tRNA point of view. Epigenomics 2018; 11:215-245. [PMID: 30565492 DOI: 10.2217/epi-2018-0176] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Protein synthesis is a central and dynamic process, frequently deregulated in cancer through aberrant activation or expression of translation initiation factors and tRNAs. The discovery of tRNA-derived fragments, a new class of abundant and, in some cases stress-induced, small Noncoding RNAs has perplexed the epigenomics landscape and highlights the emerging regulatory role of tRNAs in translation and beyond. Skin is the biggest organ in human body, which maintains homeostasis of its multilayers through regulatory networks that induce translational reprogramming, and modulate tRNA transcription, modification and fragmentation, in response to various stress signals, like UV irradiation. In this review, we summarize recent knowledge on the role of translation regulation and tRNA biology in the alarming prevalence of skin cancer.
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Affiliation(s)
- Katerina Grafanaki
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece.,Department of Dermatology, School of Medicine, University of Patras, 26504 Patras, Greece
| | - Dimitrios Anastasakis
- National Institute of Musculoskeletal & Arthritis & Skin, NIH, 50 South Drive, Room 1152, Bethesda, MD 20892, USA
| | - George Kyriakopoulos
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece
| | - Ilias Skeparnias
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece
| | - Sophia Georgiou
- Department of Dermatology, School of Medicine, University of Patras, 26504 Patras, Greece
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Bennink S, von Bohl A, Ngwa CJ, Henschel L, Kuehn A, Pilch N, Weißbach T, Rosinski AN, Scheuermayer M, Repnik U, Przyborski JM, Minns AM, Orchard LM, Griffiths G, Lindner SE, Llinás M, Pradel G. A seven-helix protein constitutes stress granules crucial for regulating translation during human-to-mosquito transmission of Plasmodium falciparum. PLoS Pathog 2018; 14:e1007249. [PMID: 30133543 PMCID: PMC6122839 DOI: 10.1371/journal.ppat.1007249] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 09/04/2018] [Accepted: 07/29/2018] [Indexed: 12/16/2022] Open
Abstract
The complex life-cycle of the human malaria parasite Plasmodium falciparum requires a high degree of tight coordination allowing the parasite to adapt to changing environments. One of the major challenges for the parasite is the human-to-mosquito transmission, which starts with the differentiation of blood stage parasites into the transmissible gametocytes, followed by the rapid conversion of the gametocytes into gametes, once they are taken up by the blood-feeding Anopheles vector. In order to pre-adapt to this change of host, the gametocytes store transcripts in stress granules that encode proteins needed for parasite development in the mosquito. Here we report on a novel stress granule component, the seven-helix protein 7-Helix-1. The protein, a homolog of the human stress response regulator LanC-like 2, accumulates in stress granules of female gametocytes and interacts with ribonucleoproteins, such as CITH, DOZI, and PABP1. Malaria parasites lacking 7-Helix-1 are significantly impaired in female gametogenesis and thus transmission to the mosquito. Lack of 7-Helix-1 further leads to a deregulation of components required for protein synthesis. Consistently, inhibitors of translation could mimic the 7-Helix-1 loss-of-function phenotype. 7-Helix-1 forms a complex with the RNA-binding protein Puf2, a translational regulator of the female-specific antigen Pfs25, as well as with pfs25-coding mRNA. In accord, gametocytes deficient of 7-Helix-1 exhibit impaired Pfs25 synthesis. Our data demonstrate that 7-Helix-1 constitutes stress granules crucial for regulating the synthesis of proteins needed for life-cycle progression of Plasmodium in the mosquito vector.
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Affiliation(s)
- Sandra Bennink
- Division of Cellular and Applied Infection Biology, RWTH Aachen University, Aachen, Germany
| | - Andreas von Bohl
- Division of Cellular and Applied Infection Biology, RWTH Aachen University, Aachen, Germany
| | - Che J. Ngwa
- Division of Cellular and Applied Infection Biology, RWTH Aachen University, Aachen, Germany
| | - Leonie Henschel
- Division of Cellular and Applied Infection Biology, RWTH Aachen University, Aachen, Germany
| | - Andrea Kuehn
- Research Center for Infectious Diseases, University of Würzburg, Würzburg, Germany
| | - Nicole Pilch
- Division of Cellular and Applied Infection Biology, RWTH Aachen University, Aachen, Germany
| | - Tim Weißbach
- Division of Cellular and Applied Infection Biology, RWTH Aachen University, Aachen, Germany
| | - Alina N. Rosinski
- Division of Cellular and Applied Infection Biology, RWTH Aachen University, Aachen, Germany
| | | | - Urska Repnik
- Department of Biosciences, University of Oslo, Oslo, Norway
| | | | - Allen M. Minns
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States of America
| | - Lindsey M. Orchard
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States of America
| | | | - Scott E. Lindner
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States of America
| | - Manuel Llinás
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States of America
- Department of Chemistry & Huck Center for Malaria Research, The Pennsylvania State University, University Park, PA, United States of America
| | - Gabriele Pradel
- Division of Cellular and Applied Infection Biology, RWTH Aachen University, Aachen, Germany
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Boivin V, Deschamps-Francoeur G, Couture S, Nottingham RM, Bouchard-Bourelle P, Lambowitz AM, Scott MS, Abou-Elela S. Simultaneous sequencing of coding and noncoding RNA reveals a human transcriptome dominated by a small number of highly expressed noncoding genes. RNA (NEW YORK, N.Y.) 2018; 24:950-965. [PMID: 29703781 PMCID: PMC6004057 DOI: 10.1261/rna.064493.117] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 04/24/2018] [Indexed: 06/01/2023]
Abstract
Comparing the abundance of one RNA molecule to another is crucial for understanding cellular functions but most sequencing techniques can target only specific subsets of RNA. In this study, we used a new fragmented ribodepleted TGIRT sequencing method that uses a thermostable group II intron reverse transcriptase (TGIRT) to generate a portrait of the human transcriptome depicting the quantitative relationship of all classes of nonribosomal RNA longer than 60 nt. Comparison between different sequencing methods indicated that FRT is more accurate in ranking both mRNA and noncoding RNA than viral reverse transcriptase-based sequencing methods, even those that specifically target these species. Measurements of RNA abundance in different cell lines using this method correlate with biochemical estimates, confirming tRNA as the most abundant nonribosomal RNA biotype. However, the single most abundant transcript is 7SL RNA, a component of the signal recognition particle. Structured noncoding RNAs (sncRNAs) associated with the same biological process are expressed at similar levels, with the exception of RNAs with multiple functions like U1 snRNA. In general, sncRNAs forming RNPs are hundreds to thousands of times more abundant than their mRNA counterparts. Surprisingly, only 50 sncRNA genes produce half of the non-rRNA transcripts detected in two different cell lines. Together the results indicate that the human transcriptome is dominated by a small number of highly expressed sncRNAs specializing in functions related to translation and splicing.
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Affiliation(s)
- Vincent Boivin
- Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Gabrielle Deschamps-Francoeur
- Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Sonia Couture
- Département de microbiologie et d'infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Ryan M Nottingham
- Institute for Cellular and Molecular Biology and Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA
| | - Philia Bouchard-Bourelle
- Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Alan M Lambowitz
- Institute for Cellular and Molecular Biology and Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA
| | - Michelle S Scott
- Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Sherif Abou-Elela
- Département de microbiologie et d'infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
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Vito D, Smales CM. The Long Non-Coding RNA Transcriptome Landscape in CHO Cells Under Batch and Fed-Batch Conditions. Biotechnol J 2018; 13:e1800122. [PMID: 29781203 DOI: 10.1002/biot.201800122] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 04/16/2018] [Indexed: 12/18/2022]
Abstract
The role of non-coding RNAs in determining growth, productivity, and recombinant product quality attributes in Chinese hamster ovary (CHO) cells has received much attention in recent years, exemplified by studies into microRNAs in particular. However, other classes of non-coding RNAs have received less attention. One such class are the non-coding RNAs known collectively as long non-coding RNAs (lncRNAs). The authors have undertaken the first landscape analysis of the lncRNA transcriptome in CHO using a mouse based microarray that also provided for the surveillance of the coding transcriptome. The authors report on those lncRNAs present in a model host CHO cell line under batch and fed-batch conditions on two different days and relate the expression of different lncRNAs to each other. The authors demonstrate that the mouse microarray is suitable for the detection and analysis of thousands of CHO lncRNAs and validated a number of these by qRT-PCR. The authors then further analyzed the data to identify those lncRNAs whose expression changed the most between growth and stationary phases of culture or between batch and fed-batch culture to identify potential lncRNA targets for further functional studies with regard to their role in controlling growth of CHO cells. The authors discuss the implications for the publication of this rich dataset and how this may be used by the community.
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Affiliation(s)
- Davide Vito
- Industrial Biotechnology Centre and School of Biosciences, University of Kent, Canterbury, CT2 7NJ, Kent, UK
| | - Christopher Mark Smales
- Industrial Biotechnology Centre and School of Biosciences, University of Kent, Canterbury, CT2 7NJ, Kent, UK
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Angelova MT, Dimitrova DG, Dinges N, Lence T, Worpenberg L, Carré C, Roignant JY. The Emerging Field of Epitranscriptomics in Neurodevelopmental and Neuronal Disorders. Front Bioeng Biotechnol 2018; 6:46. [PMID: 29707539 PMCID: PMC5908907 DOI: 10.3389/fbioe.2018.00046] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 03/29/2018] [Indexed: 01/19/2023] Open
Abstract
Analogous to DNA methylation and histone modifications, RNA modifications represent a novel layer of regulation of gene expression. The dynamic nature and increasing number of RNA modifications offer new possibilities to rapidly alter gene expression upon specific environmental changes. Recent lines of evidence indicate that modified RNA molecules and associated complexes regulating and “reading” RNA modifications play key roles in the nervous system of several organisms, controlling both, its development and function. Mutations in several human genes that modify transfer RNA (tRNA) have been linked to neurological disorders, in particular to intellectual disability. Loss of RNA modifications alters the stability of tRNA, resulting in reduced translation efficiency and generation of tRNA fragments, which can interfere with neuronal functions. Modifications present on messenger RNAs (mRNAs) also play important roles during brain development. They contribute to neuronal growth and regeneration as well as to the local regulation of synaptic functions. Hence, potential combinatorial effects of RNA modifications on different classes of RNA may represent a novel code to dynamically fine tune gene expression during brain function. Here we discuss the recent findings demonstrating the impact of modified RNAs on neuronal processes and disorders.
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Affiliation(s)
- Margarita T Angelova
- Drosophila Genetics and Epigenetics, Sorbonne Université, Centre National de la Recherche Scientifique, Biologie du Développement-Institut de Biologie Paris Seine, Paris, France
| | - Dilyana G Dimitrova
- Drosophila Genetics and Epigenetics, Sorbonne Université, Centre National de la Recherche Scientifique, Biologie du Développement-Institut de Biologie Paris Seine, Paris, France
| | - Nadja Dinges
- Laboratory of RNA Epigenetics, Institute of Molecular Biology, Mainz, Germany
| | - Tina Lence
- Laboratory of RNA Epigenetics, Institute of Molecular Biology, Mainz, Germany
| | - Lina Worpenberg
- Laboratory of RNA Epigenetics, Institute of Molecular Biology, Mainz, Germany
| | - Clément Carré
- Drosophila Genetics and Epigenetics, Sorbonne Université, Centre National de la Recherche Scientifique, Biologie du Développement-Institut de Biologie Paris Seine, Paris, France
| | - Jean-Yves Roignant
- Laboratory of RNA Epigenetics, Institute of Molecular Biology, Mainz, Germany
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A tRNA's fate is decided at its 3' end: Collaborative actions of CCA-adding enzyme and RNases involved in tRNA processing and degradation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1861:433-441. [PMID: 29374586 DOI: 10.1016/j.bbagrm.2018.01.012] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 01/15/2018] [Accepted: 01/19/2018] [Indexed: 02/07/2023]
Abstract
tRNAs are key players in translation and are additionally involved in a wide range of distinct cellular processes. The vital importance of tRNAs becomes evident in numerous diseases that are linked to defective tRNA molecules. It is therefore not surprising that the structural intactness of tRNAs is continuously scrutinized and defective tRNAs are eliminated. In this process, erroneous tRNAs are tagged with single-stranded RNA sequences that are recognized by degrading exonucleases. Recent discoveries have revealed that the CCA-adding enzyme - actually responsible for the de novo synthesis of the 3'-CCA end - plays an indispensable role in tRNA quality control by incorporating a second CCA triplet that is recognized as a degradation tag. In this review, we give an update on the latest findings regarding tRNA quality control that turns out to represent an interplay of the CCA-adding enzyme and RNases involved in tRNA degradation and maturation. In particular, the RNase-induced turnover of the CCA end is now recognized as a trigger for the CCA-adding enzyme to repeatedly scrutinize the structural intactness of a tRNA. This article is part of a Special Issue entitled: SI: Regulation of tRNA synthesis and modification in physiological conditions and disease edited by Dr. Boguta Magdalena.
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45
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Mohanta TK, Syed AS, Ameen F, Bae H. Novel Genomic and Evolutionary Perspective of Cyanobacterial tRNAs. Front Genet 2017; 8:200. [PMID: 29321793 PMCID: PMC5733544 DOI: 10.3389/fgene.2017.00200] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 11/21/2017] [Indexed: 11/30/2022] Open
Abstract
Transfer RNA (tRNA) plays a central role in protein synthesis and acts as an adaptor molecule between an mRNA and an amino acid. A tRNA has an L-shaped clover leaf-like structure and contains an acceptor arm, D-arm, D-loop, anti-codon arm, anti-codon loop, variable loop, Ψ-arm and Ψ-loop. All of these arms and loops are important in protein translation. Here, we aimed to delineate the genomic architecture of these arms and loops in cyanobacterial tRNA. Studies from tRNA sequences from 61 cyanobacterial species showed that, except for few tRNAs (tRNAAsn, tRNALeu, tRNAGln, and tRNAMet), all contained a G nucleotide at the 1st position in the acceptor arm. tRNALeu and tRNAMet did not contain any conserved nucleotides at the 1st position whereas tRNAAsn and tRNAGln contained a conserved U1 nucleotide. In several tRNA families, the variable region also contained conserved nucleotides. Except for tRNAMet and tRNAGlu, all other tRNAs contained a conserved A nucleotide at the 1st position in the D-loop. The Ψ-loop contained a conserved U1-U2-C3-x-A5-x-U7 sequence, except for tRNAGly, tRNAAla, tRNAVal, tRNAPhe, tRNAThr, and tRNAGln in which the U7 nucleotide was not conserved. However, in tRNAAsp, the U7 nucleotide was substituted with a C7 nucleotide. Additionally, tRNAArg, tRNAGly, and tRNALys of cyanobacteria contained a group I intron within the anti-codon loop region. Maximum composite likelihood study on the transition/transversion of cyanobacterial tRNA revealed that the rate of transition was higher than the rate of transversion. An evolutionary tree was constructed to understand the evolution of cyanobacterial tRNA and analyses revealed that cyanobacterial tRNA may have evolved polyphyletically with high rate of gene loss.
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Affiliation(s)
- Tapan K Mohanta
- School of Biotechnology, Yeungnam University, Gyeongsan, South Korea
| | - Asad S Syed
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Fuad Ameen
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Hanhong Bae
- School of Biotechnology, Yeungnam University, Gyeongsan, South Korea
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46
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Differentially Expressed tRNA-Derived Small RNAs Co-Sediment Primarily with Non-Polysomal Fractions in Drosophila. Genes (Basel) 2017; 8:genes8110333. [PMID: 29156628 PMCID: PMC5704246 DOI: 10.3390/genes8110333] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 11/15/2017] [Accepted: 11/16/2017] [Indexed: 12/17/2022] Open
Abstract
Recent studies point to the existence of poorly characterized small regulatory RNAs generated from mRNAs, rRNAs and tRNAs. To explore the subcellular location of tRNA-derived small RNAs, 0–1 and 7–8 h Drosophila embryos were fractionated on sucrose density gradients. Analysis of 12,553,921 deep-sequencing reads from unfractionated and fractionated Drosophila embryos has revealed that tRFs, which are detected mainly from the 5’ends of tRNAs, co-sediment with the non-polysomal fractions. Interestingly, the expression levels of a subset of tRFs change temporally following the maternal-to-zygotic transition in embryos. We detected non-polysomal association of tRFs in S2 cells as well. Differential tRF expression pattern points to developmental significance at the organismal level. These results suggest that tRFs are associated primarily with the non-polysomal complexes in Drosophila embryos and S2 cells.
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47
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Svenningsen SL, Kongstad M, Stenum TS, Muñoz-Gómez AJ, Sørensen MA. Transfer RNA is highly unstable during early amino acid starvation in Escherichia coli. Nucleic Acids Res 2017; 45:793-804. [PMID: 27903898 PMCID: PMC5314770 DOI: 10.1093/nar/gkw1169] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 11/02/2016] [Accepted: 11/09/2016] [Indexed: 11/17/2022] Open
Abstract
Due to its long half-life compared to messenger RNA, bacterial transfer RNA is known as stable RNA. Here, we show that tRNAs become highly unstable as part of Escherichia coli's response to amino acid starvation. Degradation of the majority of cellular tRNA occurs within twenty minutes of the onset of starvation for each of several amino acids. Both the non-cognate and cognate tRNA for the amino acid that the cell is starving for are degraded, and both charged and uncharged tRNA species are affected. The alarmone ppGpp orchestrates the stringent response to amino acid starvation. However, tRNA degradation occurs in a ppGpp-independent manner, as it occurs with similar kinetics in a relaxed mutant. Further, we also observe rapid tRNA degradation in response to rifampicin treatment, which does not induce the stringent response. We propose a unifying model for these observations, in which the surplus tRNA is degraded whenever the demand for protein synthesis is reduced. Thus, the tRNA pool is a highly regulated, dynamic entity. We propose that degradation of surplus tRNA could function to reduce mistranslation in the stressed cell, because it would reduce competition between cognate and near-cognate charged tRNAs at the ribosomal A-site.
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Affiliation(s)
| | - Mette Kongstad
- Department of Biology, University of Copenhagen, 2200 Copenhagen N, Denmark
| | | | - Ana J Muñoz-Gómez
- Department of Biology, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Michael A Sørensen
- Department of Biology, University of Copenhagen, 2200 Copenhagen N, Denmark
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48
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Foretek D, Nuc P, Żywicki M, Karlowski WM, Kudla G, Boguta M. Maf1-mediated regulation of yeast RNA polymerase III is correlated with CCA addition at the 3' end of tRNA precursors. Gene 2016; 612:12-18. [PMID: 27575455 PMCID: PMC5390780 DOI: 10.1016/j.gene.2016.08.033] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 08/18/2016] [Accepted: 08/20/2016] [Indexed: 11/30/2022]
Abstract
In eukaryotic cells tRNA synthesis is negatively regulated by the protein Maf1, conserved from yeast to humans. Maf1 from yeast Saccharomyces cerevisiae mediates repression of trna transcription when cells are transferred from medium with glucose to medium with glycerol, a non-fermentable carbon source. The strain with deleted gene encoding Maf1 (maf1Δ) is viable but accumulates tRNA precursors. In this study tRNA precursors were analysed by RNA-Seq and Northern hybridization in wild type strain and maf1Δ mutant grown in glucose medium or upon shift to repressive conditions. A negative effect of maf1Δ mutant on the addition of the auxiliary CCA nucleotides to the 3′ end of pre-tRNAs was observed in cells shifted to unfavourable growth conditions. This effect was reduced by overexpression of the yeast CCA1 gene encoding ATP(CTP):tRNA nucleotidyltransferase. The CCA sequence at the 3′ end is important for export of tRNA precursors from the nucleus and essential for tRNA charging with amino acids. Data presented here indicate that CCA-addition to intron-containing end-processed tRNA precursors is a limiting step in tRNA maturation when there is no Maf1 mediated RNA polymerase III (Pol III) repression. The correlation between CCA synthesis and Pol III regulation by Maf1 could be important in coordination of tRNA transcription, processing and regulation of translation. Effect of Maf1 on maturation of tRNA precursors was analysed in yeast cells. CCA addition to the 3′ end of pre-tRNA was down-regulated in maf1Δ mutant under stress. Effect of inactivation and overproduction of Cca1 enzyme in maf1Δ cells was examined. Link between CCA synthesis and RNA polymerase III regulation is discussed.
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Affiliation(s)
- Dominika Foretek
- Department of Genetics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Przemysław Nuc
- Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, 61-614 Poznan, Poland
| | - Marek Żywicki
- Department of Computational Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland
| | - Wojciech M Karlowski
- Department of Computational Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland
| | - Grzegorz Kudla
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, Scotland, UK
| | - Magdalena Boguta
- Department of Genetics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland.
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van Hemert F, van der Kuyl AC, Berkhout B. Impact of the biased nucleotide composition of viral RNA genomes on RNA structure and codon usage. J Gen Virol 2016; 97:2608-2619. [PMID: 27519195 DOI: 10.1099/jgv.0.000579] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We are interested in the influence of nucleotide composition on the fundamental characteristics of the virus RNA genome. Most RNA viruses have genomes with a distinct nucleotide composition, e.g. ranging from minimally 12.9 % to maximally 40.3 % (C- and U-count, respectively, in coronavirus HKU). We present a global analysis of diverse virus types, including plus-strand, minus-strand and double-strand RNA viruses, for the impact of this nucleotide preference on the predicted structure of the RNA genome that is packaged in virion particles and on the codon usage in the viral open reading frames. Several virus-specific features will be described, but also some general conclusions were drawn. Without exception, the virus-specific nucleotide bias was enriched in the unpaired, single-stranded regions of the RNA genome, thus creating an even more striking virus-specific signature. We present a simple mechanism that is based on elementary aspects of RNA structure folding to explain this general trend. In general, the nucleotide bias was the major determinant of the virus-specific codon usages, thus limiting a role for codon selection and translational control. We will discuss molecular and evolutionary scenarios that may be responsible for the diverse nucleotide biases of RNA viruses.
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Affiliation(s)
- Formijn van Hemert
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam 1105 AZ, The Netherlands
| | - Antoinette C van der Kuyl
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam 1105 AZ, The Netherlands
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam 1105 AZ, The Netherlands
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Duechler M, Leszczyńska G, Sochacka E, Nawrot B. Nucleoside modifications in the regulation of gene expression: focus on tRNA. Cell Mol Life Sci 2016; 73:3075-95. [PMID: 27094388 PMCID: PMC4951516 DOI: 10.1007/s00018-016-2217-y] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 03/25/2016] [Accepted: 04/04/2016] [Indexed: 01/10/2023]
Abstract
Both, DNA and RNA nucleoside modifications contribute to the complex multi-level regulation of gene expression. Modified bases in tRNAs modulate protein translation rates in a highly dynamic manner. Synonymous codons, which differ by the third nucleoside in the triplet but code for the same amino acid, may be utilized at different rates according to codon-anticodon affinity. Nucleoside modifications in the tRNA anticodon loop can favor the interaction with selected codons by stabilizing specific base pairs. Similarly, weakening of base pairing can discriminate against binding to near-cognate codons. mRNAs enriched in favored codons are translated in higher rates constituting a fine-tuning mechanism for protein synthesis. This so-called codon bias establishes a basic protein level, but sometimes it is necessary to further adjust the production rate of a particular protein to actual requirements, brought by, e.g., stages in circadian rhythms, cell cycle progression or exposure to stress. Such an adjustment is realized by the dynamic change of tRNA modifications resulting in the preferential translation of mRNAs coding for example for stress proteins to facilitate cell survival. Furthermore, tRNAs contribute in an entirely different way to another, less specific stress response consisting in modification-dependent tRNA cleavage that contributes to the general down-regulation of protein synthesis. In this review, we summarize control functions of nucleoside modifications in gene regulation with a focus on recent findings on protein synthesis control by tRNA base modifications.
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Affiliation(s)
- Markus Duechler
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363, Lodz, Poland.
| | - Grażyna Leszczyńska
- Institute of Organic Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924, Lodz, Poland
| | - Elzbieta Sochacka
- Institute of Organic Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924, Lodz, Poland
| | - Barbara Nawrot
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363, Lodz, Poland
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