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Article ; Online: Transfer RNAs: diversity in form and function.

Berg, Matthew D / Brandl, Christopher J

2020 Volume 18, Issue 3, Page(s) 316–339

Abstract: As the adaptor that decodes mRNA sequence into protein, the basic aspects of tRNA structure and function are central to all studies of biology. Yet the complexities of their properties and cellular roles go beyond the view of tRNAs as static participants ...

Abstract	As the adaptor that decodes mRNA sequence into protein, the basic aspects of tRNA structure and function are central to all studies of biology. Yet the complexities of their properties and cellular roles go beyond the view of tRNAs as static participants in protein synthesis. Detailed analyses through more than 60 years of study have revealed tRNAs to be a fascinatingly diverse group of molecules in form and function, impacting cell biology, physiology, disease and synthetic biology. This review analyzes tRNA structure, biosynthesis and function, and includes topics that demonstrate their diversity and growing importance.
MeSH term(s)	Animals ; Evolution, Molecular ; Gene Expression Regulation ; Genetic Code ; Humans ; Nucleic Acid Conformation ; Protein Biosynthesis ; RNA Folding ; RNA Processing, Post-Transcriptional ; RNA Splicing ; RNA Transport ; RNA, Transfer/chemistry ; RNA, Transfer/genetics ; RNA, Transfer/metabolism ; Ribosomes/metabolism ; Structure-Activity Relationship ; Transcription, Genetic ; Transfer RNA Aminoacylation
Chemical Substances	RNA, Transfer (9014-25-9)
Language	English
Publishing date	2020-09-09
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2159587-2
ISSN	1555-8584 ; 1555-8584
ISSN (online)	1555-8584
ISSN	1555-8584
DOI	10.1080/15476286.2020.1809197
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Article ; Online: Evolutionary diversity of the control of the azole response by Tra1 across yeast species.

Librais, Gabriela Marsiglio Nunes / Jiang, Yuwei / Razzaq, Iqra / Brandl, Christopher J / Shapiro, Rebecca S / Lajoie, Patrick

G3 (Bethesda, Md.)

2023 Volume 14, Issue 2

Abstract: Tra1 is an essential coactivator protein of the yeast SAGA and NuA4 acetyltransferase complexes that regulate gene expression through multiple mechanisms including the acetylation of histone proteins. Tra1 is a pseudokinase of the PIKK family ... ...

Abstract	Tra1 is an essential coactivator protein of the yeast SAGA and NuA4 acetyltransferase complexes that regulate gene expression through multiple mechanisms including the acetylation of histone proteins. Tra1 is a pseudokinase of the PIKK family characterized by a C-terminal PI3K domain with no known kinase activity. However, mutations of specific arginine residues to glutamine in the PI3K domains (an allele termed tra1Q3) result in reduced growth and increased sensitivity to multiple stresses. In the opportunistic fungal pathogen Candida albicans, the tra1Q3 allele reduces pathogenicity and increases sensitivity to the echinocandin antifungal drug caspofungin, which disrupts the fungal cell wall. Here, we found that compromised Tra1 function, in contrast to what is seen with caspofungin, increases tolerance to the azole class of antifungal drugs, which inhibits ergosterol synthesis. In C. albicans, tra1Q3 increases the expression of genes linked to azole resistance, such as ERG11 and CDR1. CDR1 encodes a multidrug ABC transporter associated with efflux of multiple xenobiotics, including azoles. Consequently, cells carrying tra1Q3 show reduced intracellular accumulation of fluconazole. In contrast, a tra1Q3 Saccharomyces cerevisiae strain displayed opposite phenotypes: decreased tolerance to azole, decreased expression of the efflux pump PDR5, and increased intracellular accumulation of fluconazole. Therefore, our data provide evidence that Tra1 differentially regulates the antifungal response across yeast species.
MeSH term(s)	Saccharomyces cerevisiae/metabolism ; Antifungal Agents/pharmacology ; Antifungal Agents/metabolism ; Azoles/pharmacology ; Azoles/metabolism ; Fluconazole/pharmacology ; Fluconazole/metabolism ; Caspofungin ; Phylogeny ; Candida albicans/genetics ; Candida albicans/metabolism ; Phosphatidylinositol 3-Kinases/genetics ; Drug Resistance, Fungal/genetics ; Fungal Proteins/genetics ; Fungal Proteins/metabolism ; Microbial Sensitivity Tests ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism ; Histone Acetyltransferases/chemistry
Chemical Substances	Antifungal Agents ; Azoles ; Fluconazole (8VZV102JFY) ; Caspofungin (F0XDI6ZL63) ; Phosphatidylinositol 3-Kinases (EC 2.7.1.-) ; Fungal Proteins ; NuA4 protein, S cerevisiae (EC 2.3.1.48) ; Saccharomyces cerevisiae Proteins ; Histone Acetyltransferases (EC 2.3.1.48)
Language	English
Publishing date	2023-10-27
Publishing country	England
Document type	Journal Article
ZDB-ID	2629978-1
ISSN	2160-1836 ; 2160-1836
ISSN (online)	2160-1836
ISSN	2160-1836
DOI	10.1093/g3journal/jkad250
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Article ; Online: Tra1 controls the transcriptional landscape of the aging cell.

Bari, Khaleda Afrin / Berg, Matthew D / Genereaux, Julie / Brandl, Christopher J / Lajoie, Patrick

G3 (Bethesda, Md.)

2022 Volume 13, Issue 1

Abstract: Gene expression undergoes considerable changes during the aging process. The mechanisms regulating the transcriptional response to cellular aging remain poorly understood. Here, we employ the budding yeast Saccharomyces cerevisiae to better understand ... ...

Abstract	Gene expression undergoes considerable changes during the aging process. The mechanisms regulating the transcriptional response to cellular aging remain poorly understood. Here, we employ the budding yeast Saccharomyces cerevisiae to better understand how organisms adapt their transcriptome to promote longevity. Chronological lifespan assays in yeast measure the survival of nondividing cells at stationary phase over time, providing insights into the aging process of postmitotic cells. Tra1 is an essential component of both the yeast Spt-Ada-Gcn5 acetyltransferase/Spt-Ada-Gcn5 acetyltransferase-like and nucleosome acetyltransferase of H4 complexes, where it recruits these complexes to acetylate histones at targeted promoters. Importantly, Tra1 regulates the transcriptional response to multiple stresses. To evaluate the role of Tra1 in chronological aging, we took advantage of a previously characterized mutant allele that carries mutations in the TRA1 PI3K domain (tra1Q3). We found that loss of functions associated with tra1Q3 sensitizes cells to growth media acidification and shortens lifespan. Transcriptional profiling reveals that genes differentially regulated by Tra1 during the aging process are enriched for components of the response to stress. Notably, expression of catalases (CTA1, CTT1) involved in hydrogen peroxide detoxification decreases in chronologically aged tra1Q3 cells. Consequently, they display increased sensitivity to oxidative stress. tra1Q3 cells are unable to grow on glycerol indicating a defect in mitochondria function. Aged tra1Q3 cells also display reduced expression of peroxisomal genes, exhibit decreased numbers of peroxisomes, and cannot grow on media containing oleate. Thus, Tra1 emerges as an important regulator of longevity in yeast via multiple mechanisms.
MeSH term(s)	Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism ; Histone Acetyltransferases/metabolism ; Mutation ; Cellular Senescence
Chemical Substances	Saccharomyces cerevisiae Proteins ; Histone Acetyltransferases (EC 2.3.1.48) ; TRA1 protein, S cerevisiae
Language	English
Publishing date	2022-10-30
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2629978-1
ISSN	2160-1836 ; 2160-1836
ISSN (online)	2160-1836
ISSN	2160-1836
DOI	10.1093/g3journal/jkac287
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Article ; Online: Anticodon sequence determines the impact of mistranslating tRNA

Cozma, Ecaterina / Rao, Megha / Dusick, Madison / Genereaux, Julie / Rodriguez-Mias, Ricard A / Villén, Judit / Brandl, Christopher J / Berg, Matthew D

RNA biology

2023 Volume 20, Issue 1, Page(s) 791–804

Abstract: Transfer RNAs (tRNAs) maintain translation fidelity through accurate charging by their cognate aminoacyl-tRNA synthetase and codon:anticodon base pairing with the mRNA at the ribosome. Mistranslation occurs when an amino acid not specified by the genetic ...

Abstract	Transfer RNAs (tRNAs) maintain translation fidelity through accurate charging by their cognate aminoacyl-tRNA synthetase and codon:anticodon base pairing with the mRNA at the ribosome. Mistranslation occurs when an amino acid not specified by the genetic message is incorporated into proteins and has applications in biotechnology, therapeutics and is relevant to disease. Since the alanyl-tRNA synthetase uniquely recognizes a G3:U70 base pair in tRNA
MeSH term(s)	Anticodon/genetics ; RNA, Transfer, Ala/metabolism ; RNA, Transfer/metabolism ; Codon ; Alanine/genetics ; Alanine/metabolism ; Protein Biosynthesis
Chemical Substances	Anticodon ; RNA, Transfer, Ala ; RNA, Transfer (9014-25-9) ; Codon ; Alanine (OF5P57N2ZX)
Language	English
Publishing date	2023-09-30
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	2159587-2
ISSN	1555-8584 ; 1555-8584
ISSN (online)	1555-8584
ISSN	1555-8584
DOI	10.1080/15476286.2023.2257471
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Article ; Online: Mistranslating the genetic code with leucine in yeast and mammalian cells.

Davey-Young, Josephine / Hasan, Farah / Tennakoon, Rasangi / Rozik, Peter / Moore, Henry / Hall, Peter / Cozma, Ecaterina / Genereaux, Julie / Hoffman, Kyle S / Chan, Patricia P / Lowe, Todd M / Brandl, Christopher J / O'Donoghue, Patrick

RNA biology

2024 Volume 21, Issue 1, Page(s) 1–23

Abstract: Translation fidelity relies on accurate aminoacylation of transfer RNAs (tRNAs) by aminoacyl-tRNA synthetases (AARSs). AARSs specific for alanine (Ala), leucine (Leu), serine, and pyrrolysine do not recognize the anticodon bases. Single nucleotide ... ...

Abstract	Translation fidelity relies on accurate aminoacylation of transfer RNAs (tRNAs) by aminoacyl-tRNA synthetases (AARSs). AARSs specific for alanine (Ala), leucine (Leu), serine, and pyrrolysine do not recognize the anticodon bases. Single nucleotide anticodon variants in their cognate tRNAs can lead to mistranslation. Human genomes include both rare and more common mistranslating tRNA variants. We investigated three rare human tRNA
MeSH term(s)	Animals ; Humans ; Saccharomyces cerevisiae/genetics ; Anticodon/genetics ; Leucine/genetics ; RNA, Transfer, Leu/genetics ; Genetic Code ; Codon ; RNA, Transfer/genetics ; Amino Acyl-tRNA Synthetases/genetics ; Amino Acyl-tRNA Synthetases/metabolism ; Alanine/genetics ; Mammals/genetics
Chemical Substances	Anticodon ; Leucine (GMW67QNF9C) ; RNA, Transfer, Leu ; Codon ; RNA, Transfer (9014-25-9) ; Amino Acyl-tRNA Synthetases (EC 6.1.1.-) ; Alanine (OF5P57N2ZX)
Language	English
Publishing date	2024-04-17
Publishing country	United States
Document type	Journal Article
ZDB-ID	2159587-2
ISSN	1555-8584 ; 1555-8584
ISSN (online)	1555-8584
ISSN	1555-8584
DOI	10.1080/15476286.2024.2340297
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Article ; Online: A novel mistranslating tRNA model in Drosophila melanogaster has diverse, sexually dimorphic effects.

Isaacson, Joshua R / Berg, Matthew D / Charles, Brendan / Jagiello, Jessica / Villén, Judit / Brandl, Christopher J / Moehring, Amanda J

G3 (Bethesda, Md.)

2022 Volume 12, Issue 5

Abstract: Transfer RNAs (tRNAs) are the adaptor molecules required for reading the genetic code and producing proteins. Transfer RNA variants can lead to genome-wide mistranslation, the misincorporation of amino acids not specified by the standard genetic code ... ...

Abstract	Transfer RNAs (tRNAs) are the adaptor molecules required for reading the genetic code and producing proteins. Transfer RNA variants can lead to genome-wide mistranslation, the misincorporation of amino acids not specified by the standard genetic code into nascent proteins. While genome sequencing has identified putative mistranslating transfer RNA variants in human populations, little is known regarding how mistranslation affects multicellular organisms. Here, we create a multicellular model of mistranslation by integrating a serine transfer RNA variant that mistranslates serine for proline (tRNAUGG,G26ASer) into the Drosophila melanogaster genome. We confirm mistranslation via mass spectrometry and find that tRNAUGG,G26ASer misincorporates serine for proline at a frequency of ∼0.6% per codon. tRNAUGG,G26ASer extends development time and decreases the number of flies that reach adulthood. While both sexes of adult flies containing tRNAUGG,G26ASer present with morphological deformities and poor climbing performance, these effects are more pronounced in female flies and the impact on climbing performance is exacerbated by age. This model will enable studies into the synergistic effects of mistranslating transfer RNA variants and disease-causing alleles.
MeSH term(s)	Animals ; Drosophila melanogaster/genetics ; Drosophila melanogaster/metabolism ; Female ; Proline/genetics ; Proline/metabolism ; Protein Biosynthesis ; RNA, Transfer/genetics ; RNA, Transfer/metabolism ; Serine/metabolism
Chemical Substances	Serine (452VLY9402) ; RNA, Transfer (9014-25-9) ; Proline (9DLQ4CIU6V)
Language	English
Publishing date	2022-02-17
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2629978-1
ISSN	2160-1836 ; 2160-1836
ISSN (online)	2160-1836
ISSN	2160-1836
DOI	10.1093/g3journal/jkac035
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Article: Mistranslation: from adaptations to applications.

Hoffman, Kyle S / O'Donoghue, Patrick / Brandl, Christopher J

Biochimica et biophysica acta. General subjects

2017 Volume 1861, Issue 11 Pt B, Page(s) 3070–3080

Abstract: Background: The conservation of the genetic code indicates that there was a single origin, but like all genetic material, the cell's interpretation of the code is subject to evolutionary pressure. Single nucleotide variations in tRNA sequences can ... ...

Abstract	Background: The conservation of the genetic code indicates that there was a single origin, but like all genetic material, the cell's interpretation of the code is subject to evolutionary pressure. Single nucleotide variations in tRNA sequences can modulate codon assignments by altering codon-anticodon pairing or tRNA charging. Either can increase translation errors and even change the code. The frozen accident hypothesis argued that changes to the code would destabilize the proteome and reduce fitness. In studies of model organisms, mistranslation often acts as an adaptive response. These studies reveal evolutionary conserved mechanisms to maintain proteostasis even during high rates of mistranslation. Scope of review: This review discusses the evolutionary basis of altered genetic codes, how mistranslation is identified, and how deviations to the genetic code are exploited. We revisit early discoveries of genetic code deviations and provide examples of adaptive mistranslation events in nature. Lastly, we highlight innovations in synthetic biology to expand the genetic code. Major conclusions: The genetic code is still evolving. Mistranslation increases proteomic diversity that enables cells to survive stress conditions or suppress a deleterious allele. Genetic code variants have been identified by genome and metagenome sequence analyses, suppressor genetics, and biochemical characterization. General significance: Understanding the mechanisms of translation and genetic code deviations enables the design of new codes to produce novel proteins. Engineering the translation machinery and expanding the genetic code to incorporate non-canonical amino acids are valuable tools in synthetic biology that are impacting biomedical research. This article is part of a Special Issue entitled "Biochemistry of Synthetic Biology - Recent Developments" Guest Editor: Dr. Ilka Heinemann and Dr. Patrick O'Donoghue.
MeSH term(s)	Adaptation, Biological/genetics ; Animals ; Codon/genetics ; Evolution, Molecular ; Genetic Code ; Humans ; Mutation/physiology ; Polymorphism, Genetic/physiology ; Protein Biosynthesis/genetics ; Protein Engineering/methods ; Protein Engineering/trends
Chemical Substances	Codon
Language	English
Publishing date	2017-01-30
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	60-7
ISSN	1879-2596 ; 1879-260X ; 1872-8006 ; 1879-2642 ; 1879-2618 ; 1879-2650 ; 0304-4165 ; 0006-3002 ; 0005-2728 ; 0005-2736 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439 ; 1874-9399
ISSN (online)	1879-2596 ; 1879-260X ; 1872-8006 ; 1879-2642 ; 1879-2618 ; 1879-2650
ISSN	0304-4165 ; 0006-3002 ; 0005-2728 ; 0005-2736 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439 ; 1874-9399
DOI	10.1016/j.bbagen.2017.01.031
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Article ; Online: The Pseudokinase Domain of

Berg, Matthew D / Genereaux, Julie / Karagiannis, Jim / Brandl, Christopher J

G3 (Bethesda, Md.)

2018 Volume 8, Issue 6, Page(s) 1943–1957

Abstract: Tra1 is an essential component of the SAGA/SLIK and NuA4 complexes ... ...

Abstract	Tra1 is an essential component of the SAGA/SLIK and NuA4 complexes in
MeSH term(s)	Alleles ; Amino Acid Sequence ; Cell Nucleus/metabolism ; Genes, Suppressor ; Half-Life ; Histone Acetyltransferases/chemistry ; Histone Acetyltransferases/metabolism ; Models, Molecular ; Multiprotein Complexes/metabolism ; Phenotype ; Phosphatidylinositol 3-Kinases/chemistry ; Promoter Regions, Genetic/genetics ; Protein Binding ; Protein Domains ; Protein Transport ; Proteolysis ; Saccharomyces cerevisiae/growth & development ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/chemistry ; Saccharomyces cerevisiae Proteins/metabolism ; Stress, Physiological ; Synthetic Lethal Mutations ; Trans-Activators/metabolism ; Transcription, Genetic
Chemical Substances	Multiprotein Complexes ; SAGA complex, S cerevisiae ; Saccharomyces cerevisiae Proteins ; TRA1 protein, S cerevisiae ; Trans-Activators ; Histone Acetyltransferases (EC 2.3.1.48) ; NuA4 protein, S cerevisiae (EC 2.3.1.48)
Language	English
Publishing date	2018-05-31
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2629978-1
ISSN	2160-1836 ; 2160-1836
ISSN (online)	2160-1836
ISSN	2160-1836
DOI	10.1534/g3.118.200288
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Article ; Online: Regulating Expression of Mistranslating tRNAs by Readthrough RNA Polymerase II Transcription.

Berg, Matthew D / Isaacson, Joshua R / Cozma, Ecaterina / Genereaux, Julie / Lajoie, Patrick / Villén, Judit / Brandl, Christopher J

ACS synthetic biology

2021 Volume 10, Issue 11, Page(s) 3177–3189

Abstract: Transfer RNA (tRNA) variants that alter the genetic code increase protein diversity and have many applications in synthetic biology. Since the tRNA variants can cause a loss of proteostasis, regulating their expression is necessary to achieve high levels ...

Abstract	Transfer RNA (tRNA) variants that alter the genetic code increase protein diversity and have many applications in synthetic biology. Since the tRNA variants can cause a loss of proteostasis, regulating their expression is necessary to achieve high levels of novel protein. Mechanisms to positively regulate transcription with exogenous activator proteins like those often used to regulate RNA polymerase II (RNAP II)-transcribed genes are not applicable to tRNAs as their expression by RNA polymerase III requires elements internal to the tRNA. Here, we show that tRNA expression is repressed by overlapping transcription from an adjacent RNAP II promoter. Regulating the expression of the RNAP II promoter allows inverse regulation of the tRNA. Placing either Gal4- or TetR-VP16-activated promoters downstream of a mistranslating tRNA
MeSH term(s)	Codon/genetics ; Eukaryotic Cells/physiology ; G1 Phase/genetics ; Proline/genetics ; Promoter Regions, Genetic/genetics ; Protein Biosynthesis/genetics ; RNA Polymerase II/genetics ; RNA Polymerase III/genetics ; RNA, Transfer/genetics ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae Proteins/genetics ; Transcription, Genetic/genetics
Chemical Substances	Codon ; Saccharomyces cerevisiae Proteins ; RNA, Transfer (9014-25-9) ; Proline (9DLQ4CIU6V) ; RNA Polymerase II (EC 2.7.7.-) ; RNA Polymerase III (EC 2.7.7.6)
Language	English
Publishing date	2021-11-02
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ISSN	2161-5063
ISSN (online)	2161-5063
DOI	10.1021/acssynbio.1c00461
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Article ; Online: Pathways to disease from natural variations in human cytoplasmic tRNAs.

Lant, Jeremy T / Berg, Matthew D / Heinemann, Ilka U / Brandl, Christopher J / O'Donoghue, Patrick

The Journal of biological chemistry

2019 Volume 294, Issue 14, Page(s) 5294–5308

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 ... ...

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.
MeSH term(s)	Animals ; Cytoplasm/genetics ; Cytoplasm/metabolism ; Genetic Variation ; Genome, Human ; Humans ; Neoplasms/genetics ; Neoplasms/metabolism ; Neurodegenerative Diseases/genetics ; Neurodegenerative Diseases/metabolism ; Protein Biosynthesis ; RNA, Mitochondrial/genetics ; RNA, Mitochondrial/metabolism ; RNA, Neoplasm/genetics ; RNA, Neoplasm/metabolism ; RNA, Transfer/genetics ; RNA, Transfer/metabolism
Chemical Substances	RNA, Mitochondrial ; RNA, Neoplasm ; RNA, Transfer (9014-25-9)
Language	English
Publishing date	2019-01-14
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1074/jbc.REV118.002982
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