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1.
RNA ; 25(5): 645-655, 2019 05.
Artigo em Inglês | MEDLINE | ID: mdl-30803999

RESUMO

External guide sequences (EGSs) signify the short RNAs that induce ribonuclease P (RNase P), an enzyme responsible for processing the 5' termini of tRNA, to specifically cleave a target mRNA by forming a precursor tRNA-like complex. Hence, the EGS technology may serve as a potential strategy for gene-targeting therapy. Our previous studies have revealed that engineered EGS variants induced RNase P to efficiently hydrolyze target mRNAs. In the present research, an EGS variant was designed to be complementary to the mRNA coding for human cytomegalovirus (HCMV) major capsid protein (MCP), which is vital to form the viral capsid. In vitro, the EGS variant was about 80-fold more efficient in inducing human RNase P-mediated cleavage of the target mRNA than a natural tRNA-derived EGS. Moreover, the expressed variant and natural tRNA-originated EGSs led to a decrease of MCP expression by 98% and 73%-74% and a decrease of viral growth by about 10,000- and 200-fold in cells infected with HCMV, respectively. These results reveal direct evidence that the engineered EGS variant has higher efficiency in blocking the expression of HCMV genes and viral growth than the natural tRNA-originated EGS. Therefore, our findings imply that the EGS variant can be a potent candidate agent for the treatment of infections caused by HCMV.


Assuntos
Proteínas do Capsídeo/genética , Citomegalovirus/genética , RNA Guia de Cinetoplastídeos/genética , RNA Mensageiro/genética , RNA de Transferência de Serina/genética , RNA Viral/genética , Ribonuclease P/metabolismo , Pareamento de Bases , Proteínas do Capsídeo/biossíntese , Linhagem Celular Transformada , Linhagem Celular Tumoral , Citomegalovirus/metabolismo , Fibroblastos/metabolismo , Fibroblastos/virologia , Regulação Viral da Expressão Gênica , Marcação de Genes/métodos , Engenharia Genética/métodos , Interações Hospedeiro-Patógeno/genética , Humanos , Terapia de Alvo Molecular , Neuroglia/metabolismo , Neuroglia/virologia , Conformação de Ácido Nucleico , Cultura Primária de Células , Clivagem do RNA , RNA Guia de Cinetoplastídeos/química , RNA Guia de Cinetoplastídeos/metabolismo , RNA Mensageiro/química , RNA Mensageiro/metabolismo , RNA de Transferência de Serina/química , RNA de Transferência de Serina/metabolismo , RNA Viral/química , RNA Viral/metabolismo , Ribonuclease P/química , Ribonuclease P/genética , Replicação Viral/fisiologia
2.
RNA ; 23(11): 1685-1699, 2017 11.
Artigo em Inglês | MEDLINE | ID: mdl-28808125

RESUMO

Seryl-tRNA synthetase (SerRS) attaches L-serine to the cognate serine tRNA (tRNASer) and the noncognate selenocysteine tRNA (tRNASec). The latter activity initiates the anabolic cycle of selenocysteine (Sec), proper decoding of an in-frame Sec UGA codon, and synthesis of selenoproteins across all domains of life. While the accuracy of SerRS is important for overall proteome integrity, it is its substrate promiscuity that is vital for the integrity of the selenoproteome. This raises a question as to what elements in the two tRNA species, harboring different anticodon sequences and adopting distinct folds, facilitate aminoacylation by a common aminoacyl-tRNA synthetase. We sought to answer this question by analyzing the ability of human cytosolic SerRS to bind and act on tRNASer, tRNASec, and 10 mutant and chimeric constructs in which elements of tRNASer were transposed onto tRNASec We show that human SerRS only subtly prefers tRNASer to tRNASec, and that discrimination occurs at the level of the serylation reaction. Surprisingly, the tRNA mutants predicted to adopt either the 7/5 or 8/5 fold are poor SerRS substrates. In contrast, shortening of the acceptor arm of tRNASec by a single base pair yields an improved SerRS substrate that adopts an 8/4 fold. We suggest that an optimal tertiary arrangement of structural elements within tRNASec and tRNASer dictate their utility for serylation. We also speculate that the extended acceptor-TΨC arm of tRNASec evolved as a compromise for productive binding to SerRS while remaining the major recognition element for other enzymes involved in Sec and selenoprotein synthesis.


Assuntos
RNA de Transferência Aminoácido-Específico/metabolismo , RNA de Transferência de Serina/metabolismo , Serina-tRNA Ligase/metabolismo , Sequência de Bases , Sítios de Ligação , Citosol/enzimologia , Humanos , Cinética , Modelos Moleculares , Mutagênese , Conformação de Ácido Nucleico , Dobramento de RNA , RNA de Transferência Aminoácido-Específico/química , RNA de Transferência Aminoácido-Específico/genética , RNA de Transferência de Serina/química , RNA de Transferência de Serina/genética , Especificidade por Substrato
3.
RNA ; 23(3): 406-419, 2017 03.
Artigo em Inglês | MEDLINE | ID: mdl-28003514

RESUMO

The 3-methylcytidine (m3C) modification is ubiquitous in eukaryotic tRNA, widely found at C32 in the anticodon loop of tRNAThr, tRNASer, and some tRNAArg species, as well as in the variable loop (V-loop) of certain tRNASer species. In the yeast Saccharomyces cerevisiae, formation of m3C32 requires Trm140 for six tRNA substrates, including three tRNAThr species and three tRNASer species, whereas in Schizosaccharomyces pombe, two Trm140 homologs are used, one for tRNAThr and one for tRNASer The occurrence of a single Trm140 homolog is conserved broadly among Ascomycota, whereas multiple Trm140-related homologs are found in metazoans and other fungi. We investigate here how S. cerevisiae Trm140 protein recognizes its six tRNA substrates. We show that Trm140 has two modes of tRNA substrate recognition. Trm140 recognizes G35-U36-t6A37 of the anticodon loop of tRNAThr substrates, and this sequence is an identity element because it can be used to direct m3C modification of tRNAPhe However, Trm140 recognition of tRNASer substrates is different, since their anticodons do not share G35-U36 and do not have any nucleotides in common. Rather, specificity of Trm140 for tRNASer is achieved by seryl-tRNA synthetase and the distinctive tRNASer V-loop, as well as by t6A37 and i6A37 We provide evidence that all of these components are important in vivo and that seryl-tRNA synthetase greatly stimulates m3C modification of tRNASer(CGA) and tRNASer(UGA) in vitro. In addition, our results show that Trm140 binding is a significant driving force for tRNA modification and suggest separate contributions from each recognition element for the modification.


Assuntos
Anticódon/química , Citidina/análogos & derivados , Proteínas dos Microfilamentos/metabolismo , RNA de Transferência de Serina/química , Proteínas de Saccharomyces cerevisiae/metabolismo , Saccharomyces cerevisiae/metabolismo , tRNA Metiltransferases/metabolismo , Anticódon/metabolismo , Sequência de Bases , Sítios de Ligação , Clonagem Molecular , Citidina/genética , Citidina/metabolismo , Escherichia coli/genética , Escherichia coli/metabolismo , Expressão Gênica , Proteínas dos Microfilamentos/genética , Conformação de Ácido Nucleico , Ligação Proteica , Biossíntese de Proteínas , Domínios Proteicos , RNA de Transferência de Fenilalanina/química , RNA de Transferência de Fenilalanina/genética , RNA de Transferência de Fenilalanina/metabolismo , RNA de Transferência de Serina/genética , RNA de Transferência de Serina/metabolismo , RNA de Transferência de Treonina/química , RNA de Transferência de Treonina/genética , RNA de Transferência de Treonina/metabolismo , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/genética , Especificidade por Substrato , tRNA Metiltransferases/genética
4.
Nature ; 500(7460): 107-10, 2013 Aug 01.
Artigo em Inglês | MEDLINE | ID: mdl-23812587

RESUMO

During normal translation, the binding of a release factor to one of the three stop codons (UGA, UAA or UAG) results in the termination of protein synthesis. However, modification of the initial uridine to a pseudouridine (Ψ) allows efficient recognition and read-through of these stop codons by a transfer RNA (tRNA), although it requires the formation of two normally forbidden purine-purine base pairs. Here we determined the crystal structure at 3.1 Å resolution of the 30S ribosomal subunit in complex with the anticodon stem loop of tRNA(Ser) bound to the ΨAG stop codon in the A site. The ΨA base pair at the first position is accompanied by the formation of purine-purine base pairs at the second and third positions of the codon, which show an unusual Watson-Crick/Hoogsteen geometry. The structure shows a previously unsuspected ability of the ribosomal decoding centre to accommodate non-canonical base pairs.


Assuntos
Pareamento de Bases , Códon de Terminação/genética , Códon de Terminação/metabolismo , Ribossomos/química , Ribossomos/metabolismo , Anticódon/química , Anticódon/genética , Anticódon/metabolismo , Sequência de Bases , Códon de Terminação/química , Cristalografia por Raios X , Modelos Moleculares , Conformação de Ácido Nucleico , Conformação Proteica , Pseudouridina/química , Pseudouridina/genética , Pseudouridina/metabolismo , RNA de Transferência de Serina/química , RNA de Transferência de Serina/genética , RNA de Transferência de Serina/metabolismo , Subunidades Ribossômicas Menores de Bactérias/química , Subunidades Ribossômicas Menores de Bactérias/genética , Subunidades Ribossômicas Menores de Bactérias/metabolismo , Ribossomos/genética
5.
J Biol Chem ; 291(7): 3613-25, 2016 Feb 12.
Artigo em Inglês | MEDLINE | ID: mdl-26677220

RESUMO

Leucyl-tRNA synthetase (LeuRS) is a multidomain enzyme that catalyzes Leu-tRNA(Leu) formation and is classified into bacterial and archaeal/eukaryotic types with significant diversity in the C-terminal domain (CTD). CTDs of both bacterial and archaeal LeuRSs have been reported to recognize tRNA(Leu) through different modes of interaction. In the human pathogen Candida albicans, the cytoplasmic LeuRS (CaLeuRS) is distinguished by its capacity to recognize a uniquely evolved chimeric tRNA(Ser) (CatRNA(Ser)(CAG)) in addition to its cognate CatRNA(Leu), leading to CUG codon reassignment. Our previous study showed that eukaryotic but not archaeal LeuRSs recognize this peculiar tRNA(Ser), suggesting the significance of their highly divergent CTDs in tRNA(Ser) recognition. The results of this study provided the first evidence of the indispensable function of the CTD of eukaryotic LeuRS in recognizing non-cognate CatRNA(Ser) and cognate CatRNA(Leu). Three lysine residues were identified as involved in mediating enzyme-tRNA interaction in the leucylation process: mutation of all three sites totally ablated the leucylation activity. The importance of the three lysine residues was further verified by gel mobility shift assays and complementation of a yeast leuS gene knock-out strain.


Assuntos
Candida albicans/enzimologia , Proteínas Fúngicas/metabolismo , Leucina-tRNA Ligase/metabolismo , Modelos Moleculares , RNA Fúngico/metabolismo , RNA de Transferência de Leucina/metabolismo , RNA de Transferência de Serina/metabolismo , Sequência de Aminoácidos , Substituição de Aminoácidos , Sítios de Ligação , Candida albicans/metabolismo , Sequência Conservada , Proteínas Fúngicas/química , Proteínas Fúngicas/genética , Técnicas de Inativação de Genes , Leucina-tRNA Ligase/química , Leucina-tRNA Ligase/genética , Lisina/química , Proteínas Mutantes/química , Proteínas Mutantes/metabolismo , Conformação de Ácido Nucleico , Filogenia , Conformação Proteica , Domínios e Motivos de Interação entre Proteínas , RNA Fúngico/química , RNA de Transferência de Leucina/química , RNA de Transferência de Serina/química , Proteínas Recombinantes de Fusão/química , Proteínas Recombinantes de Fusão/metabolismo , Proteínas Recombinantes/química , Proteínas Recombinantes/metabolismo , Alinhamento de Sequência , Especificidade por Substrato
6.
Zhonghua Yi Xue Yi Chuan Xue Za Zhi ; 34(1): 128-132, 2017 Feb 10.
Artigo em Zh | MEDLINE | ID: mdl-28186612

RESUMO

Mitochondrial tRNASer(UCN) gene mutation is closely related to acoustic nerve deafness. Some mutations can affect the structure and transcriptional processing of tRNASer(UCN), for instance m.7444G>A mutation in tRNASer(UCN) precursor 3' side, m.7472 insC as well as m.7511T>C mutations in the stem and ring of tRNASer(UCN), may influence tRNASer(UCN) stability, thus affect the synthesis of mitochondrial peptides, reduce the production of ATP and cause deafness. This article focuses on mitochondrial tRNASer(UCN) gene mutations as well as the mechanism underlying hearing loss.


Assuntos
Perda Auditiva/genética , Mutação , RNA de Transferência de Serina/genética , RNA/genética , Sequência de Aminoácidos , Sequência de Bases , Predisposição Genética para Doença/genética , Humanos , Proteínas Mitocondriais/biossíntese , Proteínas Mitocondriais/genética , Conformação de Ácido Nucleico , RNA/química , RNA Mitocondrial , RNA de Transferência de Serina/química
7.
Nucleic Acids Res ; 40(5): 2107-18, 2012 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-22102571

RESUMO

Pseudouridine synthase 1 (Pus1p) is an unusual site-specific modification enzyme in that it can modify a number of positions in tRNAs and can recognize several other types of RNA. No consensus recognition sequence or structure has been identified for Pus1p. Human Pus1p was used to determine which structural or sequence elements of human tRNA(Ser) are necessary for pseudouridine (Ψ) formation at position 28 in the anticodon stem-loop (ASL). Some point mutations in the ASL stem of tRNA(Ser) had significant effects on the levels of modification and compensatory mutation, to reform the base pair, restored a wild-type level of Ψ formation. Deletion analysis showed that the tRNA(Ser) TΨC stem-loop was a determinant for modification in the ASL. A mini-substrate composed of the ASL and TΨC stem-loop exhibited significant Ψ formation at position 28 and a number of mutants were tested. Substantial base pairing in the ASL stem (3 out of 5 bp) is required, but the sequence of the TΨC loop is not required for modification. When all nucleotides in the ASL stem other than U28 were changed in a single mutant, but base pairing was retained, a near wild-type level of modification was observed.


Assuntos
Hidroliases/metabolismo , RNA de Transferência de Serina/química , Pareamento de Bases , Sequência de Bases , Humanos , Mutagênese Sítio-Dirigida , Conformação de Ácido Nucleico , Pseudouridina/metabolismo , RNA de Transferência de Serina/metabolismo
8.
Nucleic Acids Res ; 39(11): 4728-42, 2011 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-21317186

RESUMO

We used a genetic screen based on tRNA-mediated suppression (TMS) in a Schizosaccharomyces pombe La protein (Sla1p) mutant. Suppressor pre-tRNA(Ser)UCA-C47:6U with a debilitating substitution in its variable arm fails to produce tRNA in a sla1-rrm mutant deficient for RNA chaperone-like activity. The parent strain and spontaneous mutant were analyzed using Solexa sequencing. One synonymous single-nucleotide polymorphism (SNP), unrelated to the phenotype, was identified. Further sequence analyses found a duplication of the tRNA(Ser)UCA-C47:6U gene, which was shown to cause the phenotype. Ninety percent of 28 isolated mutants contain duplicated tRNA(Ser)UCA-C47:6U genes. The tRNA gene duplication led to a disproportionately large increase in tRNA(Ser)UCA-C47:6U levels in sla1-rrm but not sla1-null cells, consistent with non-specific low-affinity interactions contributing to the RNA chaperone-like activity of La, similar to other RNA chaperones. Our analysis also identified 24 SNPs between ours and S. pombe 972h- strain yFS101 that was recently sequenced using Solexa. By including mitochondrial (mt) DNA in our analysis, overall coverage increased from 52% to 96%. mtDNA from our strain and yFS101 shared 14 mtSNPs relative to a 'reference' mtDNA, providing the first identification of these S. pombe mtDNA discrepancies. Thus, strain-specific and spontaneous phenotypic mutations can be mapped in S. pombe by Solexa sequencing.


Assuntos
Duplicação Gênica , Polimorfismo de Nucleotídeo Único , RNA de Transferência de Serina/genética , Proteínas de Ligação a RNA/genética , Proteínas de Schizosaccharomyces pombe/genética , Schizosaccharomyces/genética , Alelos , Sequência de Bases , Núcleo Celular/genética , DNA Mitocondrial/química , Genes Fúngicos , Genoma Fúngico , Dados de Sequência Molecular , Mutação , Fenótipo , RNA de Transferência de Serina/química , RNA de Transferência de Serina/metabolismo , Análise de Sequência de DNA , Supressão Genética
9.
Biochem Biophys Res Commun ; 427(1): 148-53, 2012 Oct 12.
Artigo em Inglês | MEDLINE | ID: mdl-22989754

RESUMO

A hallmark of cancer cells is their ability to continuously divide; and rapid proliferation requires increased protein translation. Elevating levels of misfolded proteins can elicit growth arrest due to ER stress and decreased global translation. Failure to correct prolonged ER stress eventually results in cell death via apoptosis. tRNA(Ser)(AAU) is an engineered human tRNA(Ser) with an anticodon coding for isoleucine. Here we test the possibility that tRNA(Ser)(AAU) can be an effective killing agent of breast cancer cells and can effectively inhibit tumor-formation in mice. We found that tRNA(Ser)(AAU) exert strong effects on breast cancer translation activity, cell viability, and tumor formation. Translation is strongly inhibited by tRNA(Ser)(AAU) in both tumorigenic and non-tumorigenic cells. tRNA(Ser)(AAU) significantly decreased the number of viable cells over time. A short time treatment with tRNA(Ser)(AAU) was sufficient to eliminate breast tumor formation in a xenograft mouse model. Our results indicate that tRNA(Ser)(AAU) can inhibit breast cancer metabolism, growth and tumor formation. This RNA has strong anti-cancer effects and presents an opportunity for its development into an anti-tumor agent. Because tRNA(Ser)(AAU) corrupts the protein synthesis mechanism that is an integral component of the cell, it would be extremely difficult for tumor cells to evolve and develop resistance against this anti-tumor agent.


Assuntos
Neoplasias da Mama/terapia , RNA de Transferência de Serina/uso terapêutico , Animais , Apoptose , Linhagem Celular Tumoral , Células HeLa , Humanos , Camundongos , Camundongos Nus , Plasmídeos/química , Plasmídeos/uso terapêutico , Biossíntese de Proteínas/genética , RNA de Transferência de Serina/química , Transfecção
10.
Nucleic Acids Res ; 38(5): e30, 2010 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-20007146

RESUMO

Misfolded proteins are caused by genomic mutations, aberrant splicing events, translation errors or environmental factors. The accumulation of misfolded proteins is a phenomenon connected to several human disorders, and is managed by stress responses specific to the cellular compartments being affected. In wild-type cells these mechanisms of stress response can be experimentally induced by expressing recombinant misfolded proteins or by incubating cells with large concentrations of amino acid analogues. Here, we report a novel approach for the induction of stress responses to protein aggregation. Our method is based on engineered transfer RNAs that can be expressed in cells or tissues, where they actively integrate in the translation machinery causing general proteome substitutions. This strategy allows for the introduction of mutations of increasing severity randomly in the proteome, without exposing cells to unnatural compounds. Here, we show that this approach can be used for the differential activation of the stress response in the Endoplasmic Reticulum (ER). As an example of the applications of this method, we have applied it to the identification of human microRNAs activated or repressed during unfolded protein stress.


Assuntos
Proteoma/genética , RNA de Transferência de Serina/química , Resposta a Proteínas não Dobradas/genética , Animais , Processos de Crescimento Celular , Linhagem Celular , Sobrevivência Celular , Embrião de Galinha , Interpretação Estatística de Dados , Humanos , MicroRNAs/classificação , MicroRNAs/metabolismo , Mutagênese Sítio-Dirigida , Mutação , Biossíntese de Proteínas , RNA de Transferência de Serina/metabolismo
11.
Nat Commun ; 13(1): 209, 2022 01 11.
Artigo em Inglês | MEDLINE | ID: mdl-35017528

RESUMO

Modified nucleotides in tRNAs are important determinants of folding, structure and function. Here we identify METTL8 as a mitochondrial matrix protein and active RNA methyltransferase responsible for installing m3C32 in the human mitochondrial (mt-)tRNAThr and mt-tRNASer(UCN). METTL8 crosslinks to the anticodon stem loop (ASL) of many mt-tRNAs in cells, raising the question of how methylation target specificity is achieved. Dissection of mt-tRNA recognition elements revealed U34G35 and t6A37/(ms2)i6A37, present concomitantly only in the ASLs of the two substrate mt-tRNAs, as key determinants for METTL8-mediated methylation of C32. Several lines of evidence demonstrate the influence of U34, G35, and the m3C32 and t6A37/(ms2)i6A37 modifications in mt-tRNAThr/Ser(UCN) on the structure of these mt-tRNAs. Although mt-tRNAThr/Ser(UCN) lacking METTL8-mediated m3C32 are efficiently aminoacylated and associate with mitochondrial ribosomes, mitochondrial translation is mildly impaired by lack of METTL8. Together these results define the cellular targets of METTL8 and shed new light on the role of m3C32 within mt-tRNAs.


Assuntos
Anticódon/química , Metiltransferases/genética , Mitocôndrias/genética , RNA Mitocondrial/química , RNA de Transferência de Serina/química , RNA de Transferência de Treonina/química , Anticódon/metabolismo , Pareamento de Bases , Citosina/metabolismo , Regulação da Expressão Gênica , Células HEK293 , Humanos , Metilação , Metiltransferases/metabolismo , Mitocôndrias/metabolismo , Conformação de Ácido Nucleico , Ligação Proteica , Biossíntese de Proteínas , RNA Mitocondrial/genética , RNA Mitocondrial/metabolismo , RNA de Transferência de Serina/genética , RNA de Transferência de Serina/metabolismo , RNA de Transferência de Treonina/genética , RNA de Transferência de Treonina/metabolismo , Transdução de Sinais
12.
Biochem Biophys Res Commun ; 412(4): 532-6, 2011 Sep 09.
Artigo em Inglês | MEDLINE | ID: mdl-21787751

RESUMO

tRNAs are aminoacylated by the aminoacyl-tRNA synthetases. There are at least 20 natural amino acids, but due to the redundancy of the genetic code, 64 codons on the mRNA. Therefore, there exist tRNA isoacceptors that are aminoacylated with the same amino acid, but differ in their sequence and in the anticodon. tRNA identity elements, which are sequence or structure motifs, assure the amino acid specificity. The Seryl-tRNA synthetase is an enzyme that depends on rather few and simple identity elements in tRNA(Ser). The Seryl-tRNA-synthetase interacts with the tRNA(Ser) acceptor stem, which makes this part of the tRNA a valuable structural element for investigating motifs of the protein-RNA complex. We solved the high resolution crystal structures of two tRNA(Ser) acceptor stem microhelices and investigated their interaction with the Seryl-tRNA-synthetase by superposition experiments. The results presented here show that the amino acid side chains Ser151 and Ser156 of the synthetase are interacting in a very similar way with the RNA backbone of the microhelix and that the involved water molecules have almost identical positions within the tRNA/synthetase interface.


Assuntos
RNA de Transferência de Serina/química , Serina-tRNA Ligase/química , Água/química , Sítios de Ligação , Cristalografia por Raios X , Conformação de Ácido Nucleico , Conformação Proteica
13.
J Theor Biol ; 269(1): 287-96, 2011 Jan 21.
Artigo em Inglês | MEDLINE | ID: mdl-21073883

RESUMO

Pathogenic mutations in mitochondrial tRNAs are 6.5 times more frequent than in other mitochondrial genes. This suggests that tRNA mutations perturb more than one function. A potential additional tRNA gene function is that of templating for antisense tRNAs. Pathogenic mutations weaken cloverleaf secondary structures of sense tRNAs. Analyses here show similar effects for most antisense tRNAs, especially after adjusting for associations between sense and antisense cloverleaf stabilities. These results imply translational activity by antisense tRNAs. For sense tRNAs Ala and Ser UCN, pathogenicity associates as much with sense as with antisense cloverleaf formation. For tRNA Pro, pathogenicity seems associated only with antisense, not sense tRNA cloverleaf formation. Translational activity by antisense tRNAs is expected for the 11 antisense tRNAs processed by regular sense RNA maturation, those recognized by their cognate amino acid's tRNA synthetase, and those forming relatively stable cloverleaves as compared to their sense counterpart. Most antisense tRNAs probably function routinely in translation and extend the tRNA pool (extension hypothesis); others do not (avoidance hypothesis). The greater the expected translational activity of an antisense tRNA, the more pathogenic mutations weaken its cloverleaf secondary structure. Some evidence for RNA interference, a more classical role for antisense tRNAs, exists only for tRNA Ser UCN. Mutation pathogenicity probably frequently results from a mixture of effects due to sense and antisense tRNA translational activity for many mitochondrial tRNAs. Genomic studies should routinely explore for translational activity by antisense tRNAs.


Assuntos
Mutação/genética , RNA Antissenso/genética , RNA de Transferência/genética , RNA/genética , Anticódon/química , Anticódon/genética , Sequência de Bases , Distribuição de Qui-Quadrado , Genoma Mitocondrial/genética , Humanos , Conformação de Ácido Nucleico , RNA Antissenso/química , RNA Mitocondrial , RNA de Transferência/química , RNA de Transferência de Serina/química , RNA de Transferência de Serina/genética , Análise de Regressão
14.
Mitochondrion ; 57: 1-8, 2021 03.
Artigo em Inglês | MEDLINE | ID: mdl-33279600

RESUMO

BACKGROUND: Mitochondrial disorders are a group of heterogeneous diseases characterized by biochemical disturbances in oxidative phosphorylation (OXPHOS). Mutations in mitochondrial transfer RNA (mt-tRNA) genes are the most frequently in mitochondrial disease. However, few studies have detailed the molecular mechanisms behind these mutations. METHODS: We performed clinical evaluation, genetic analysis, muscle histochemistry, and molecular and biochemical investigations in muscle tissue and proband-derived cybrid cell lines. RESULTS: We found a mitochondrial tRNASer(UCN) mutation (m.7453G>A) in a 15-year-old patient with severe mitochondrial myopathy. We demonstrated that this mutation caused impairment of mitochondrial translation, respiratory deficiency, overproduction of reactive oxygen species (ROS), and decreased mitochondrial membrane potential (MMP), which ultimately led to severe mitochondrial myopathy. CONCLUSION: Our findings offer valuable new insights into the tRNASer(UCN) m.7453G>A mutation for both the pathogenic mechanism and functional consequences.


Assuntos
Miopatias Mitocondriais/genética , Polimorfismo de Nucleotídeo Único , RNA de Transferência de Serina/genética , Análise de Sequência de DNA/métodos , Adolescente , Linhagem Celular , Feminino , Genoma Mitocondrial , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Potencial da Membrana Mitocondrial , Miopatias Mitocondriais/metabolismo , Modelos Moleculares , Conformação de Ácido Nucleico , Biossíntese de Proteínas , RNA de Transferência de Serina/química , Espécies Reativas de Oxigênio/metabolismo
15.
Biochem Biophys Res Commun ; 395(3): 291-5, 2010 May 07.
Artigo em Inglês | MEDLINE | ID: mdl-20361934

RESUMO

We solved the X-ray structures of two Escherichia coli tRNA(Ser) acceptor stem microhelices. As both tRNAs are aminoacylated by the same seryl-tRNA-synthetase, we performed a comparative structure analysis of both duplexes to investigate the helical conformation, the hydration patterns and magnesium binding sites. It is well accepted, that the hydration of RNA plays an important role in RNA-protein interactions and that the extensive solvent content of the minor groove has a special function in RNA. The detailed comparison of both tRNA(Ser) microhelices provides insights into the structural arrangement of the isoacceptor tRNA aminoacyl stems with respect to the surrounding water molecules and may eventually help us to understand their biological function at atomic resolution.


Assuntos
Escherichia coli/metabolismo , RNA de Transferência de Serina/química , Sequência de Bases , Sítios de Ligação , Cristalografia por Raios X , Magnésio/química , Conformação de Ácido Nucleico
16.
Nucleic Acids Res ; 36(17): 5472-81, 2008 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-18718926

RESUMO

Secondary and tertiary structures of tRNAs are remarkably preserved from bacteria to humans, the notable exception being the mitochondrial (m) tRNAs of metazoans, which often deviate substantially from the canonical cloverleaf (secondary) or 'L'-shaped (tertiary) structure. Many metazoan mtRNAs lack either the TpsiC (T) or dihydrouridine (D) loops of the canonical cloverleaf, which are known to confer structural rigidity to the folded structure. Thus, the absence of canonical TpsiC-D interactions likely results in greater dispersion of anticodon-acceptor interstem angle than for canonical tRNAs. To test this hypothesis, we have assessed the dispersion of the anticodon-acceptor angle for bovine mtRNA(Ser)(AGY), which lacks the canonical D arm and is thus incapable of forming stabilizing interarm interactions. Using the method of transient electric birefringence (TEB), and by changing the helical torsion angle between a core mtRNA bend and a second bend of known angle/rigidity, we have demonstrated that the core of mtRNA(Ser)(AGY) has substantially greater flexibility than its well-characterized canonical counterpart, yeast cytoplasmic tRNA(Phe). These results suggest that increased flexibility, in addition to a more open interstem angle, would allow both noncanonical and canonical mtRNAs to utilize the same protein synthetic apparatus.


Assuntos
RNA de Transferência/química , RNA/química , Animais , Sequência de Bases , Bovinos , Eletroforese em Gel de Poliacrilamida , Magnésio/química , Dados de Sequência Molecular , Conformação de Ácido Nucleico , RNA Fúngico/química , RNA Mitocondrial , RNA de Transferência de Fenilalanina/química , RNA de Transferência de Serina/química , Deleção de Sequência , Temperatura
17.
Nucleic Acids Res ; 36(6): 1871-80, 2008 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-18267971

RESUMO

Selenocysteine (Sec) biosynthesis in archaea and eukaryotes requires three steps: serylation of tRNA(Sec) by seryl-tRNA synthetase (SerRS), phosphorylation of Ser-tRNA(Sec) by O-phosphoseryl-tRNA(Sec) kinase (PSTK), and conversion of O-phosphoseryl-tRNA(Sec) (Sep-tRNA(Sec)) by Sep-tRNA:Sec-tRNA synthase (SepSecS) to Sec-tRNA(Sec). Although SerRS recognizes both tRNA(Sec) and tRNA(Ser) species, PSTK must discriminate Ser-tRNA(Sec) from Ser-tRNA(Ser). Based on a comparison of the sequences and secondary structures of archaeal tRNA(Sec) and tRNA(Ser), we introduced mutations into Methanococcus maripaludis tRNA(Sec) to investigate how Methanocaldococcus jannaschii PSTK distinguishes tRNA(Sec) from tRNA(Ser). Unlike eukaryotic PSTK, the archaeal enzyme was found to recognize the acceptor stem rather than the length and secondary structure of the D-stem. While the D-arm and T-loop provide minor identity elements, the acceptor stem base pairs G2-C71 and C3-G70 in tRNA(Sec) were crucial for discrimination from tRNA(Ser). Furthermore, the A5-U68 base pair in tRNA(Ser) has some antideterminant properties for PSTK. Transplantation of these identity elements into the tRNA(Ser)(UGA) scaffold resulted in phosphorylation of the chimeric Ser-tRNA. The chimera was able to stimulate the ATPase activity of PSTK albeit at a lower level than tRNA(Sec), whereas tRNA(Ser) did not. Additionally, the seryl moiety of Ser-tRNA(Sec) is not required for enzyme recognition, as PSTK efficiently phosphorylated Thr-tRNA(Sec).


Assuntos
Proteínas Arqueais/metabolismo , Methanococcales/enzimologia , Mathanococcus/genética , Fosfotransferases (Aceptor do Grupo Álcool)/metabolismo , RNA de Transferência Aminoácido-Específico/química , RNA de Transferência de Serina/química , Adenosina Trifosfatases/metabolismo , Animais , Anticódon/química , Bactérias/genética , Pareamento de Bases , Sequência de Bases , Humanos , Dados de Sequência Molecular , Fosforilação , Aminoacil-RNA de Transferência/metabolismo , Especificidade por Substrato
18.
Yi Chuan ; 32(9): 951-60, 2010 Sep.
Artigo em Zh | MEDLINE | ID: mdl-20870617

RESUMO

The complete mitochondrial genome of a China endemic bird, Podoces hendersoni, was sequenced using La-PCR and conserved primer walking approaches. The mtDNA seqnence is 16 867 bp in length and deposited in GenBank with accession number GU592504. The mitochondrial genomic organization of P. hendersoni is the same with that in chicken, which contains 13 protein coding genes (PCGs), 22 tRNA, 2 rRNA, and a control region. Except for COI gene, which uses GTG as the initiation codon, all other 12 PCGs of the P. hendersoni mtDNA start with the typical ATG codon. Codons TAA, AGG, and AGA were used in 11 PCGs as usual termination codons; however, the COIII and ND4 had incomplete termination codon T. The secondary structures of 20 tRNAs formed typical cloverleaf, except for tRNASer (AGY) that had an absence of the DHU arm and tRNALeu (CUN) in which anticodon-loop consisted of 9 bases, rather than the standard 7 bases. The secondary structures of rRNA were predicted. There are 4 domains, 43 helices structures in 12S rRNA, and 6 domains, 55 helices structures in 16S rRNA. Besides, F-box, D-box, C-box, B-box, Bird similarity-box and CSB1-box, which were found in the control region of other birds, also existed in the P. hendersoni.


Assuntos
DNA Mitocondrial/análise , Genoma Mitocondrial/genética , Passeriformes/genética , RNA Ribossômico/química , Animais , Sequência de Bases , China , Códon , Dados de Sequência Molecular , Conformação de Ácido Nucleico , Filogenia , RNA de Transferência/análise , RNA de Transferência de Serina/química , RNA de Transferência de Serina/genética
19.
Biochem Biophys Res Commun ; 386(2): 368-73, 2009 Aug 21.
Artigo em Inglês | MEDLINE | ID: mdl-19527687

RESUMO

tRNA identity elements assure the correct aminoacylation of tRNAs by the cognate aminoacyl-tRNA synthetases. tRNA(Ser) belongs to the so-called class II system, in which the identity elements are rather simple and are mostly located in the acceptor stem region, in contrast to 'class I', where tRNA determinants are more complex and are located within different regions of the tRNA. The structure of an Escherichia coli tRNA(Ser) acceptor stem microhelix was solved by high resolution X-ray structure analysis. The RNA crystallizes in the space group C2, with one molecule per asymmetric unit and with the cell constants a=35.79, b=39.13, c=31.37A, and beta=111.1 degrees . A defined hydration pattern of 97 water molecules surrounds the tRNA(Ser) acceptor stem microhelix. Additionally, two magnesium binding sites were detected in the tRNA(Ser) aminoacyl stem.


Assuntos
Escherichia coli/metabolismo , Magnésio/química , RNA de Transferência de Serina/química , Sequência de Bases , Sítios de Ligação , Cristalografia por Raios X , Conformação de Ácido Nucleico
20.
Artigo em Inglês | MEDLINE | ID: mdl-19652346

RESUMO

Modified nucleic acids are of great interest with respect to their nuclease resistance and enhanced thermostability. In therapeutical and diagnostic applications, such molecules can substitute for labile natural nucleic acids that are targeted against particular diseases or applied in gene therapy. The so-called 'locked nucleic acids' contain modified sugar moieties such as 2'-O,4'-C-methylene-bridged beta-D-ribofuranose and are known to be very stable nucleic acid derivatives. The structure of locked nucleic acids in single or multiple LNA-substituted natural nucleic acids and in LNA-DNA or LNA-RNA heteroduplexes has been well investigated, but the X-ray structure of an ;all-locked' nucleic acid double helix has not been described to date. Here, the crystallization and X-ray diffraction data analysis of an 'all-locked' nucleic acid helix, which was designed as an LNA originating from a tRNA(Ser) microhelix RNA structure, is presented. The crystals belonged to space group C2, with unit-cell parameters a = 77.91, b = 40.74, c = 30.06 A, beta = 91.02 degrees . A high-resolution and a low-resolution data set were recorded, with the high-resolution data showing diffraction to 1.9 A resolution. The crystals contained two double helices per asymmetric unit, with a Matthews coefficient of 2.48 A(3) Da(-1) and a solvent content of 66.49% for the merged data.


Assuntos
Conformação de Ácido Nucleico , Ácidos Nucleicos/química , RNA de Transferência de Serina/química , Cristalização , Cristalografia por Raios X , Modelos Moleculares
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