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Alalam H, Zepeda-Martínez JA, Sunnerhagen P. Global SLAM-seq for accurate mRNA decay determination and identification of NMD targets. RNA (NEW YORK, N.Y.) 2022; 28:905-915. [PMID: 35296539 PMCID: PMC9074897 DOI: 10.1261/rna.079077.121] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 03/02/2022] [Indexed: 06/14/2023]
Abstract
Gene expression analysis requires accurate measurements of global RNA degradation rates, earlier problematic with methods disruptive to cell physiology. Recently, metabolic RNA labeling emerged as an efficient and minimally invasive technique applied in mammalian cells. Here, we have adapted SH-linked alkylation for the metabolic sequencing of RNA (SLAM-seq) for a global mRNA stability study in yeast using 4-thiouracil pulse-chase labeling. We assign high-confidence half-life estimates for 67.5% of expressed ORFs, and measure a median half-life of 9.4 min. For mRNAs where half-life estimates exist in the literature, their ranking order was in good agreement with previous data, indicating that SLAM-seq efficiently classifies stable and unstable transcripts. We then leveraged our yeast protocol to identify targets of the nonsense-mediated decay (NMD) pathway by measuring the change in RNA half-lives, instead of steady-state RNA level changes. With SLAM-seq, we assign 580 transcripts as putative NMD targets, based on their measured half-lives in wild-type and upf3Δ mutants. We find 225 novel targets, and observe a strong agreement with previous reports of NMD targets, 61.2% of our candidates being identified in previous studies. This indicates that SLAM-seq is a simpler and more economic method for global quantification of mRNA half-lives. Our adaptation for yeast yielded global quantitative measures of the NMD effect on transcript half-lives, high correlation with RNA half-lives measured previously with more technically challenging protocols, and identification of novel NMD regulated transcripts that escaped prior detection.
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Affiliation(s)
- Hanna Alalam
- Department of Chemistry and Molecular Biology, Lundberg Laboratory, University of Gothenburg, S-405 30 Göteborg, Sweden
| | | | - Per Sunnerhagen
- Department of Chemistry and Molecular Biology, Lundberg Laboratory, University of Gothenburg, S-405 30 Göteborg, Sweden
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2
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Gameiro PA, Encheva V, Dos Santos MS, MacRae JI, Ule J. Metabolic turnover and dynamics of modified ribonucleosides by 13C labeling. J Biol Chem 2021; 297:101294. [PMID: 34634303 PMCID: PMC8567201 DOI: 10.1016/j.jbc.2021.101294] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/21/2021] [Accepted: 09/22/2021] [Indexed: 01/27/2023] Open
Abstract
Tandem mass spectrometry (MS/MS) is an accurate tool to assess modified ribonucleosides and their dynamics in mammalian cells. However, MS/MS quantification of lowly abundant modifications in non-ribosomal RNAs is unreliable, and the dynamic features of various modifications are poorly understood. Here, we developed a 13C labeling approach, called 13C-dynamods, to quantify the turnover of base modifications in newly transcribed RNA. This turnover-based approach helped to resolve mRNA from ncRNA modifications in purified RNA or free ribonucleoside samples and showed the distinct kinetics of the N6-methyladenosine (m6A) versus 7-methylguanosine (m7G) modification in polyA+-purified RNA. We uncovered that N6,N6-dimethyladenosine (m62A) exhibits distinct turnover in small RNAs and free ribonucleosides when compared to known m62A-modified large rRNAs. Finally, combined measurements of turnover and abundance of these modifications informed on the transcriptional versus posttranscriptional sensitivity of modified ncRNAs and mRNAs, respectively, to stress conditions. Thus, 13C-dynamods enables studies of the origin of modified RNAs at steady-state and subsequent dynamics under nonstationary conditions. These results open new directions to probe the presence and biological regulation of modifications in particular RNAs.
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Affiliation(s)
- Paulo A Gameiro
- RNA Networks Laboratory, Francis Crick Institute, London, UK; Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK.
| | - Vesela Encheva
- Mass Spectrometry Science Technology Platform, Francis Crick Institute, London, UK
| | | | - James I MacRae
- Mass Spectrometry Science Technology Platform, Francis Crick Institute, London, UK
| | - Jernej Ule
- RNA Networks Laboratory, Francis Crick Institute, London, UK; Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
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3
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Gasser C, Delazer I, Neuner E, Pascher K, Brillet K, Klotz S, Trixl L, Himmelstoß M, Ennifar E, Rieder D, Lusser A, Micura R. Thioguanosine Conversion Enables mRNA‐Lifetime Evaluation by RNA Sequencing Using Double Metabolic Labeling (TUC‐seq DUAL). Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201916272] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Catherina Gasser
- Institute of Organic Chemistry and Center for Molecular BiosciencesLeopold-Franzens University Innrain 80 6020 Innsbruck Austria
| | - Isabel Delazer
- Institute of Molecular BiologyBiocenterMedical University of Innsbruck Innrain 82 6020 Innsbruck Austria
| | - Eva Neuner
- Institute of Organic Chemistry and Center for Molecular BiosciencesLeopold-Franzens University Innrain 80 6020 Innsbruck Austria
| | - Katharina Pascher
- Institute of Molecular BiologyBiocenterMedical University of Innsbruck Innrain 82 6020 Innsbruck Austria
| | - Karl Brillet
- Université de StrasbourgArchitecture et Réactivité de l'ARN—CNRS UPR 9002Institut de Biologie Moléculaire et Cellulaire 67000 Strasbourg France
| | - Sarah Klotz
- Institute of Organic Chemistry and Center for Molecular BiosciencesLeopold-Franzens University Innrain 80 6020 Innsbruck Austria
| | - Lukas Trixl
- Institute of Molecular BiologyBiocenterMedical University of Innsbruck Innrain 82 6020 Innsbruck Austria
| | - Maximilian Himmelstoß
- Institute of Organic Chemistry and Center for Molecular BiosciencesLeopold-Franzens University Innrain 80 6020 Innsbruck Austria
| | - Eric Ennifar
- Université de StrasbourgArchitecture et Réactivité de l'ARN—CNRS UPR 9002Institut de Biologie Moléculaire et Cellulaire 67000 Strasbourg France
| | - Dietmar Rieder
- Institute of BioinformaticsBiocenterMedical University of Innsbruck Innrain 82 6020 Innsbruck Austria
| | - Alexandra Lusser
- Institute of Molecular BiologyBiocenterMedical University of Innsbruck Innrain 82 6020 Innsbruck Austria
| | - Ronald Micura
- Institute of Organic Chemistry and Center for Molecular BiosciencesLeopold-Franzens University Innrain 80 6020 Innsbruck Austria
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4
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Gasser C, Delazer I, Neuner E, Pascher K, Brillet K, Klotz S, Trixl L, Himmelstoß M, Ennifar E, Rieder D, Lusser A, Micura R. Thioguanosine Conversion Enables mRNA-Lifetime Evaluation by RNA Sequencing Using Double Metabolic Labeling (TUC-seq DUAL). Angew Chem Int Ed Engl 2020; 59:6881-6886. [PMID: 31999864 PMCID: PMC7186826 DOI: 10.1002/anie.201916272] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Indexed: 12/24/2022]
Abstract
Temporal information about cellular RNA populations is essential to understand the functional roles of RNA. We have developed the hydrazine/NH4 Cl/OsO4 -based conversion of 6-thioguanosine (6sG) into A', where A' constitutes a 6-hydrazino purine derivative. A' retains the Watson-Crick base-pair mode and is efficiently decoded as adenosine in primer extension assays and in RNA sequencing. Because 6sG is applicable to metabolic labeling of freshly synthesized RNA and because the conversion chemistry is fully compatible with the conversion of the frequently used metabolic label 4-thiouridine (4sU) into C, the combination of both modified nucleosides in dual-labeling setups enables high accuracy measurements of RNA decay. This approach, termed TUC-seq DUAL, uses the two modified nucleosides in subsequent pulses and their simultaneous detection, enabling mRNA-lifetime evaluation with unprecedented precision.
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Affiliation(s)
- Catherina Gasser
- Institute of Organic Chemistry and Center for Molecular Biosciences, Leopold-Franzens University, Innrain 80, 6020, Innsbruck, Austria
| | - Isabel Delazer
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Innrain 82, 6020, Innsbruck, Austria
| | - Eva Neuner
- Institute of Organic Chemistry and Center for Molecular Biosciences, Leopold-Franzens University, Innrain 80, 6020, Innsbruck, Austria
| | - Katharina Pascher
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Innrain 82, 6020, Innsbruck, Austria
| | - Karl Brillet
- Université de Strasbourg, Architecture et Réactivité de l'ARN-CNRS UPR 9002, Institut de Biologie Moléculaire et Cellulaire, 67000, Strasbourg, France
| | - Sarah Klotz
- Institute of Organic Chemistry and Center for Molecular Biosciences, Leopold-Franzens University, Innrain 80, 6020, Innsbruck, Austria
| | - Lukas Trixl
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Innrain 82, 6020, Innsbruck, Austria
| | - Maximilian Himmelstoß
- Institute of Organic Chemistry and Center for Molecular Biosciences, Leopold-Franzens University, Innrain 80, 6020, Innsbruck, Austria
| | - Eric Ennifar
- Université de Strasbourg, Architecture et Réactivité de l'ARN-CNRS UPR 9002, Institut de Biologie Moléculaire et Cellulaire, 67000, Strasbourg, France
| | - Dietmar Rieder
- Institute of Bioinformatics, Biocenter, Medical University of Innsbruck, Innrain 82, 6020, Innsbruck, Austria
| | - Alexandra Lusser
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Innrain 82, 6020, Innsbruck, Austria
| | - Ronald Micura
- Institute of Organic Chemistry and Center for Molecular Biosciences, Leopold-Franzens University, Innrain 80, 6020, Innsbruck, Austria
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5
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Rodrigues DF, Costa VM, Silvestre R, Bastos ML, Carvalho F. Methods for the analysis of transcriptome dynamics. Toxicol Res (Camb) 2019; 8:597-612. [PMID: 31588338 PMCID: PMC6764467 DOI: 10.1039/c9tx00088g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 07/18/2019] [Indexed: 12/13/2022] Open
Abstract
The transcriptome is the complete set of transcripts in a cell or tissue and includes ribosomal RNA (rRNA), messenger RNA (mRNA), transfer RNA (tRNA), and regulatory noncoding RNA. At steady-state, the transcriptome results from a compensatory variation of the transcription and decay rate to maintain the RNA concentration constant. RNA transcription constitutes the first stage in gene expression, and thus is a major and primary mode of gene expression control. Nevertheless, regulation of RNA decay is also a key factor in gene expression control, involving either selective RNA stabilization or enhanced degradation. Transcriptome analysis allows the identification of gene expression alterations, providing new insights regarding the pathways and mechanisms involved in physiological and pathological processes. Upon perturbation of cell homeostasis, rapid changes in gene expression are required to adapt to new conditions. Thus, to better understand the regulatory mechanisms associated with gene expression alterations, it is vital to acknowledge the relative contribution of RNA synthesis and decay to the transcriptome. To the toxicology field, the study of gene expression regulation mechanisms can help identify the early and mechanistic relevant cellular events associated with a particular response. This review aims to provide a critical comparison of the available methods used to analyze the contribution of RNA transcription and decay to gene expression dynamics. Notwithstanding, an integration of the data obtained is necessary to understand the entire repercussions of gene transcription changes at a system-level. Thus, a brief overview of the methods available for the integration and analysis of the data obtained from transcriptome analysis will also be provided.
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Affiliation(s)
- Daniela F Rodrigues
- UCIBIO , REQUIMTE , Laboratory of Toxicology , Faculty of Pharmacy , University of Porto , Rua Jorge Viterbo Ferreira , 228 , 4050-313 , Porto , Portugal . ;
| | - Vera M Costa
- UCIBIO , REQUIMTE , Laboratory of Toxicology , Faculty of Pharmacy , University of Porto , Rua Jorge Viterbo Ferreira , 228 , 4050-313 , Porto , Portugal . ;
| | - Ricardo Silvestre
- Life and Health Sciences Research Institute (ICVS) , School of Medicine , University of Minho , Campus de Gualtar , 4710-057 , Braga , Portugal
- ICVS/3B's-PT Government Associate Laboratory , Braga/Guimarães , Campus de Gualtar , 4710-057 , Braga , Portugal
| | - Maria L Bastos
- UCIBIO , REQUIMTE , Laboratory of Toxicology , Faculty of Pharmacy , University of Porto , Rua Jorge Viterbo Ferreira , 228 , 4050-313 , Porto , Portugal . ;
| | - Félix Carvalho
- UCIBIO , REQUIMTE , Laboratory of Toxicology , Faculty of Pharmacy , University of Porto , Rua Jorge Viterbo Ferreira , 228 , 4050-313 , Porto , Portugal . ;
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6
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Global analysis of RNA metabolism using bio-orthogonal labeling coupled with next-generation RNA sequencing. Methods 2018; 155:88-103. [PMID: 30529548 DOI: 10.1016/j.ymeth.2018.12.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 11/30/2018] [Accepted: 12/03/2018] [Indexed: 11/21/2022] Open
Abstract
Many open questions in RNA biology relate to the kinetics of gene expression and the impact of RNA binding regulatory factors on processing or decay rates of particular transcripts. Steady state measurements of RNA abundance obtained from RNA-seq approaches are not able to separate the effects of transcription from those of RNA decay in the overall abundance of any given transcript, instead only giving information on the (presumed steady-state) abundances of transcripts. Through the combination of metabolic labeling and high-throughput sequencing, several groups have been able to measure both transcription rates and decay rates of the entire transcriptome of an organism in a single experiment. This review focuses on the methodology used to specifically measure RNA decay at a global level. By comparing and contrasting approaches and describing the experimental protocols in a modular manner, we intend to provide both experienced and new researchers to the field the ability to combine aspects of various protocols to fit the unique needs of biological questions not addressed by current methods.
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7
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Neymotin B, Athanasiadou R, Gresham D. Determination of in vivo RNA kinetics using RATE-seq. RNA (NEW YORK, N.Y.) 2014; 20:1645-52. [PMID: 25161313 PMCID: PMC4174445 DOI: 10.1261/rna.045104.114] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Accepted: 07/07/2014] [Indexed: 05/24/2023]
Abstract
The abundance of a transcript is determined by its rate of synthesis and its rate of degradation; however, global methods for quantifying RNA abundance cannot distinguish variation in these two processes. Here, we introduce RNA approach to equilibrium sequencing (RATE-seq), which uses in vivo metabolic labeling of RNA and approach to equilibrium kinetics, to determine absolute RNA degradation and synthesis rates. RATE-seq does not disturb cellular physiology, uses straightforward normalization with exogenous spike-ins, and can be readily adapted for studies in most organisms. We demonstrate the use of RATE-seq to estimate genome-wide kinetic parameters for coding and noncoding transcripts in Saccharomyces cerevisiae.
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Affiliation(s)
- Benjamin Neymotin
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003, USA
| | - Rodoniki Athanasiadou
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003, USA
| | - David Gresham
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003, USA
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8
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Kosturko LD, Maggipinto MJ, Korza G, Lee JW, Carson JH, Barbarese E. Heterogeneous nuclear ribonucleoprotein (hnRNP) E1 binds to hnRNP A2 and inhibits translation of A2 response element mRNAs. Mol Biol Cell 2006; 17:3521-33. [PMID: 16775011 PMCID: PMC1525244 DOI: 10.1091/mbc.e05-10-0946] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Heterogeneous nuclear ribonucleoprotein (hnRNP) A2 is a trans-acting RNA-binding protein that mediates trafficking of RNAs containing the cis-acting A2 response element (A2RE). Previous work has shown that A2RE RNAs are transported to myelin in oligodendrocytes and to dendrites in neurons. hnRNP E1 is an RNA-binding protein that regulates translation of specific mRNAs. Here, we show by yeast two-hybrid analysis, in vivo and in vitro coimmunoprecipitation, in vitro cross-linking, and fluorescence correlation spectroscopy that hnRNP E1 binds to hnRNP A2 and is recruited to A2RE RNA in an hnRNP A2-dependent manner. hnRNP E1 is colocalized with hnRNP A2 and A2RE mRNA in granules in dendrites of oligodendrocytes. Overexpression of hnRNP E1 or microinjection of exogenous hnRNP E1 in neural cells inhibits translation of A2RE mRNA, but not of non-A2RE RNA. Excess hnRNP E1 added to an in vitro translation system reduces translation efficiency of A2RE mRNA, but not of nonA2RE RNA, in an hnRNP A2-dependent manner. These results are consistent with a model where hnRNP E1 recruited to A2RE RNA granules by binding to hnRNP A2 inhibits translation of A2RE RNA during granule transport.
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Affiliation(s)
| | | | - George Korza
- Molecular, Microbial, and Structural Biology, and
| | - Joo Won Lee
- Biomedical Science Graduate Program, University of Connecticut Health Center, Farmington, CT 06030
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9
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Pels Rijcken WR, Overdijk B, van den Eijnden DH, Ferwerda W. Pyrimidine nucleotide metabolism in rat hepatocytes: evidence for compartmentation of nucleotide pools. Biochem J 1993; 293 ( Pt 1):207-13. [PMID: 8328961 PMCID: PMC1134341 DOI: 10.1042/bj2930207] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Pyrimidine nucleotide metabolism in rat hepatocytes was studied by measurement of the labelling kinetics of the various intermediates after double labelling with [14C]orotic acid and [3H]cytidine, the precursors for the de novo and the salvage pathways respectively. For the uridine nucleotides, differences were found for the 14C/3H ratios in the UDP-sugars, in UMP (of RNA) and in their precursor UTP, suggesting the existence of separated flows of the radioactive precursors through the de novo and the salvage pathways. Higher ratios in the UDP-sugars, which are synthesized in the cytoplasm, and a lower ratio in UMP (of RNA) relative to the 14C/3H ratio in UTP indicated that UTP derived from orotic acid is preferentially used for the cytoplasmic biosynthesis of the UDP-sugars. Uridine, derived from cytidine, is preferentially used for the nuclear-localized synthesis of RNA. In contrast to these findings, the 14C/3H ratios in the cytidine derivatives CMP-NeuAc and CMP (of RNA), and in the liponucleotides CDP-choline and CDP-ethanolamine, were all lower than that in the precursor CTP. This indicates a preferential utilization of the salvage-derived CTP for the synthesis of the liponucleotides as well as for RNA and CMP-NeuAc. Similar conclusions could be drawn from experiments in which the intracellular amounts of several uridine- and cytidine-nucleotide-containing derivatives were increased by preincubating the hepatocytes with unlabelled pyrimidine nucleotides or ethanolamine. Based on these data, we propose a refined model for the intracellular compartmentation of pyrimidine nucleotide biosynthesis in which three pools of UTP are distinguished: a pool of de novo-derived molecules and a pool of salvage-derived molecules, both of which are channelled to the site of utilization; in addition an 'overflow' pool exists, consisting of molecules having escaped from channelling. An overflow pool could also be distinguished for CTP, but no discrimination between de novo and salvage-derived molecules could be made.
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Affiliation(s)
- W R Pels Rijcken
- Department of Medical Chemistry, Vrije Universiteit, Amsterdam, The Netherlands
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10
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Karnahl U, Wasternack C. Half-life of cytoplasmic rRNA and tRNA, of plastid rRNA and of uridine nucleotides in heterotrophically and photoorganotrophically grown cells of Euglena gracilis and its apoplastic mutant W3BUL. THE INTERNATIONAL JOURNAL OF BIOCHEMISTRY 1992; 24:493-7. [PMID: 1551462 DOI: 10.1016/0020-711x(92)90044-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
1. For Euglena gracilis half-life data were calculated according to Greenberg's equation (Nature 240, 102-104, 1972) using steady-state specific radioactivities determined for cyt-rRNA, cyt-tRNA and pl-rRNA. 2. For all RNAs equal half-lives were found of 45 and 38 hr, respectively, in heterotrophically and photoorganotrophically grown cells. 3. Using the decay analysis equal half-lives were found for cyt-rRNA, cyt-tRNA and pl-rRNA being 79, 43 and 60 hr, respectively, in heterotrophically and photoorganotrophically grown wild-type cells and the mutant W3BUL. 4. As suggested by the specific radioactivity of intracellular [3H]UMP compared to that of [3H]uracil fed, the remarkable differences between RNA half-lives determined for heterotrophically and photoorganotrophically grown wild-type cells, seem to be caused by a different extent of the de novo synthesis of UMP. 5. Reutilization of RNA breakdown products suggested by increased half-lives of RNAs in the decay analysis compared to those determined by Greenberg's equation seems to occur mainly in heterotrophically grown cells.
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Affiliation(s)
- U Karnahl
- Institut für Biologie, Fachbereich Biochemie/Biotechnologie, Pflanzenbiochemische Abteilung, Halle/Saale, Fed. Rep. Germany
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van Lancker JL. Molecular events in liver regeneration and repair. CURRENT TOPICS IN PATHOLOGY. ERGEBNISSE DER PATHOLOGIE 1989; 79:205-54. [PMID: 2644085 DOI: 10.1007/978-3-642-73855-5_9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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12
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Andersson M, Lewan L, Stenram U. Compartmentation of purine and pyrimidine nucleotides in animal cells. THE INTERNATIONAL JOURNAL OF BIOCHEMISTRY 1988; 20:1039-50. [PMID: 3073978 DOI: 10.1016/0020-711x(88)90248-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- M Andersson
- Department of Pathology, University Hospital, Lund, Sweden
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13
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Andersson M, Christensson PI, Lewan L, Stenram U. Isotachophoretic and HPLC determination of nucleotides in rat liver cell nuclei isolated by non-aqueous technique. THE INTERNATIONAL JOURNAL OF BIOCHEMISTRY 1987; 19:641-7. [PMID: 2442044 DOI: 10.1016/0020-711x(87)90231-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Rat liver whole cells and cell nuclei were prepared by a non-aqueous technique (glycerol). The nuclear preparations were of different purity as determined by RNA/DNA ratios (0.17-1.60) and accordingly were divided into 3 subgroups (mean values 0.29, 1.04 and 1.48). RNA nucleotides were separated by isotachophoresis and HPLC and calculated per mg DNA. Two of the nuclear subgroups (RNA/DNA = 1.04 and 1.48) had significantly elevated nucleotide values in relation to RNA/DNA. UDP-N-acetylhexosamine/DNA, on the contrary, was reduced in conformity with RNA in the preparations. Our findings may indicate different nucleotide concentrations in different parts of the cell.
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14
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Nikolov EN, Dineva BB, Dabeva MD, Nikolov TK. Turnover of ribosomal proteins in regenerating rat liver after partial hepatectomy. THE INTERNATIONAL JOURNAL OF BIOCHEMISTRY 1987; 19:159-63. [PMID: 3569644 DOI: 10.1016/0020-711x(87)90326-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The rates of synthesis and degradation of ribosomal proteins, prelabelled with [14C]bicarbonate, were determined as an index of the rate of ribosome turnover in regenerating rat liver. The half-life of ribosomes is about 178 and 75 hr in regenerating and normal liver, respectively. The comparison of turnover rates of ribosomal proteins with the corrected values of rRNA, based on re-utilization of nucleotides, suggests that ribosomes are metabolized as a unit in vivo. There is at least 70% overestimation for ribosome half-life when orotate-labelled RNA is used for turnover determinations. The absolute rate of synthesis is estimated as 3925 and 1081 ribosomes/min per cell in 24 hr regenerating and normal rat liver, respectively.
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