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1.
Nucleic Acids Res ; 51(8): 3918-3933, 2023 05 08.
Artículo en Inglés | MEDLINE | ID: mdl-37026483

RESUMEN

DNA modifications are critical in fine-tuning the biological processes in model organisms. However, the presence of cytosine methylation (5mC) and the function of the putative DNA methyltransferase, PfDNMT2, in the human malaria pathogen, Plasmodium falciparum, remain controversial. Here, we revisited the 5mC in the parasite genome and the function of PfDNMT2. Low levels of genomic 5mC (0.1-0.2%) during asexual development were identified using a sensitive mass spectrometry procedure. Native PfDNMT2 displayed substantial DNA methylation activities, and disruption or overexpression of PfDNMT2 resulted in reduced or elevated genomic 5mC levels, respectively. PfDNMT2 disruption led to an increased proliferation phenotype, with the parasites having an extended schizont stage and producing a higher number of progenies. Consistent with PfDNMT2's interaction with an AP2 domain-containing transcription factor, transcriptomic analyses revealed that PfDNMT2 disruption led to a drastic alteration in the expression of many genes, some of which provided the molecular basis of enhanced proliferation after PfDNMT2 disruption. Furthermore, levels of tRNAAsp and its methylation rate at position C38, and the translation of a reporter containing an aspartate repeat were significantly reduced after PfDNMT2 disruption, while the levels of tRNAAsp and its C38 methylation were restored after complementation of PfDNMT2. Our study sheds new light on the dual function of PfDNMT2 during P. falciparum asexual development.


Asunto(s)
Metiltransferasas , Plasmodium falciparum , Proteínas Protozoarias , ADN/genética , Metilación de ADN , Metiltransferasas/genética , Plasmodium falciparum/genética , Proteínas Protozoarias/genética , Proteínas Protozoarias/metabolismo , ARN de Transferencia de Aspártico/genética
2.
Nucleic Acids Res ; 49(22): 13045-13061, 2021 12 16.
Artículo en Inglés | MEDLINE | ID: mdl-34871455

RESUMEN

Dnmt2, a member of the DNA methyltransferase superfamily, catalyzes the formation of 5-methylcytosine at position 38 in the anticodon loop of tRNAs. Dnmt2 regulates many cellular biological processes, especially the production of tRNA-derived fragments and intergenerational transmission of paternal metabolic disorders to offspring. Moreover, Dnmt2 is closely related to human cancers. The tRNA substrates of mammalian Dnmt2s are mainly detected using bisulfite sequencing; however, we lack supporting biochemical data concerning their substrate specificity or recognition mechanism. Here, we deciphered the tRNA substrates of human DNMT2 (hDNMT2) as tRNAAsp(GUC), tRNAGly(GCC) and tRNAVal(AAC). Intriguingly, for tRNAAsp(GUC) and tRNAGly(GCC), G34 is the discriminator element; whereas for tRNAVal(AAC), the inosine modification at position 34 (I34), which is formed by the ADAT2/3 complex, is the prerequisite for hDNMT2 recognition. We showed that the C32U33(G/I)34N35 (C/U)36A37C38 motif in the anticodon loop, U11:A24 in the D stem, and the correct size of the variable loop are required for Dnmt2 recognition of substrate tRNAs. Furthermore, mammalian Dnmt2s possess a conserved tRNA recognition mechanism.


Asunto(s)
5-Metilcitosina/metabolismo , Anticodón/metabolismo , ADN (Citosina-5-)-Metiltransferasas/metabolismo , ARN de Transferencia/metabolismo , Adenosina Desaminasa/genética , Adenosina Desaminasa/metabolismo , Animales , Anticodón/genética , Secuencia de Bases , ADN (Citosina-5-)-Metiltransferasas/química , ADN (Citosina-5-)-Metiltransferasas/genética , Células HEK293 , Células HeLa , Humanos , Inosina/metabolismo , Ratones , Modelos Moleculares , Células 3T3 NIH , Conformación de Ácido Nucleico , Unión Proteica , ARN de Transferencia/química , ARN de Transferencia/genética , ARN de Transferencia de Aspártico/química , ARN de Transferencia de Aspártico/genética , ARN de Transferencia de Aspártico/metabolismo , ARN de Transferencia de Glicerina/química , ARN de Transferencia de Glicerina/genética , ARN de Transferencia de Glicerina/metabolismo , ARN de Transferencia de Valina/química , ARN de Transferencia de Valina/genética , ARN de Transferencia de Valina/metabolismo , Proteínas de Unión al ARN/genética , Proteínas de Unión al ARN/metabolismo , Especificidad por Sustrato
3.
Genes (Basel) ; 10(4)2019 04 01.
Artículo en Inglés | MEDLINE | ID: mdl-30939863

RESUMEN

The aminoacyl-tRNA synthetases (aaRSs) are well established as the translators of the genetic code, because their products, the aminoacyl-tRNAs, read codons to translate messenger RNAs into proteins. Consequently, deleterious errors by the aaRSs can be transferred into the proteome via misacylated tRNAs. Nevertheless, many microorganisms use an indirect pathway to produce Asn-tRNAAsn via Asp-tRNAAsn. This intermediate is produced by a non-discriminating aspartyl-tRNA synthetase (ND-AspRS) that has retained its ability to also generate Asp-tRNAAsp. Here we report the discovery that ND-AspRS and its discriminating counterpart, AspRS, are also capable of specifically producing Glu-tRNAGlu, without producing misacylated tRNAs like Glu-tRNAAsn, Glu-tRNAAsp, or Asp-tRNAGlu, thus maintaining the fidelity of the genetic code. Consequently, bacterial AspRSs have glutamyl-tRNA synthetase-like activity that does not contaminate the proteome via amino acid misincorporation.


Asunto(s)
Aspartato-ARNt Ligasa/genética , Glutamato-ARNt Ligasa/genética , ARN de Transferencia de Asparagina/genética , ARN de Transferencia de Aspártico/genética , Secuencia de Aminoácidos/genética , Asparagina/química , Asparagina/genética , Aspartato-ARNt Ligasa/química , Código Genético/genética , Glutamato-ARNt Ligasa/química , Mycobacterium smegmatis/química , Mycobacterium smegmatis/genética , Conformación Proteica , Proteoma/química , Proteoma/genética , Aminoacil-ARN de Transferencia/genética , ARN de Transferencia de Asparagina/química , ARN de Transferencia de Aspártico/química , Homología de Secuencia de Aminoácido
4.
EMBO J ; 37(18)2018 09 14.
Artículo en Inglés | MEDLINE | ID: mdl-30093495

RESUMEN

Global protein translation as well as translation at the codon level can be regulated by tRNA modifications. In eukaryotes, levels of tRNA queuosinylation reflect the bioavailability of the precursor queuine, which is salvaged from the diet and gut microbiota. We show here that nutritionally determined Q-tRNA levels promote Dnmt2-mediated methylation of tRNA Asp and control translational speed of Q-decoded codons as well as at near-cognate codons. Deregulation of translation upon queuine depletion results in unfolded proteins that trigger endoplasmic reticulum stress and activation of the unfolded protein response, both in cultured human cell lines and in germ-free mice fed with a queuosine-deficient diet. Taken together, our findings comprehensively resolve the role of this anticodon tRNA modification in the context of native protein translation and describe a novel mechanism that links nutritionally determined modification levels to effective polypeptide synthesis and cellular homeostasis.


Asunto(s)
Estrés del Retículo Endoplásmico , Alimentos Formulados , Nucleósido Q/metabolismo , Procesamiento Postranscripcional del ARN , ARN de Transferencia de Aspártico/metabolismo , Respuesta de Proteína Desplegada , Animales , ADN (Citosina-5-)-Metiltransferasas/genética , ADN (Citosina-5-)-Metiltransferasas/metabolismo , Células HCT116 , Células HeLa , Humanos , Ratones , Nucleósido Q/genética , ARN de Transferencia de Aspártico/genética
5.
Biochim Biophys Acta Gene Regul Mech ; 1860(10): 1047-1057, 2017 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-28847733

RESUMEN

In eukaryotes, cytosine methylation regulates diverse biological processes such as gene expression, development and maintenance of genomic integrity. However, cytosine methylation and its functions in pathogenic apicomplexan protozoans remain enigmatic. To address this, here we investigated the presence of cytosine methylation in the nucleic acids of the protozoan Plasmodium falciparum. Interestingly, P. falciparum has TRDMT1, a conserved homologue of DNA methyltransferase DNMT2. However, we found that TRDMT1 did not methylate DNA, in vitro. We demonstrate that TRDMT1 methylates cytosine in the endogenous aspartic acid tRNA of P. falciparum. Through RNA bisulfite sequencing, we mapped the position of 5-methyl cytosine in aspartic acid tRNA and found methylation only at C38 position. P. falciparum proteome has significantly higher aspartic acid content and a higher proportion of proteins with poly aspartic acid repeats than other apicomplexan pathogenic protozoans. Proteins with such repeats are functionally important, with significant roles in host-pathogen interactions. Therefore, TRDMT1 mediated C38 methylation of aspartic acid tRNA might play a critical role by translational regulation of important proteins and modulate the pathogenicity of the malarial parasite.


Asunto(s)
ADN (Citosina-5-)-Metiltransferasas/química , Plasmodium falciparum/enzimología , ARN Protozoario/química , ARN de Transferencia de Aspártico/química , ADN (Citosina-5-)-Metiltransferasas/genética , ADN (Citosina-5-)-Metiltransferasas/metabolismo , Metilación , ARN Protozoario/genética , ARN Protozoario/metabolismo , ARN de Transferencia de Aspártico/genética , ARN de Transferencia de Aspártico/metabolismo
6.
Nucleic Acids Res ; 45(15): 9108-9120, 2017 Sep 06.
Artículo en Inglés | MEDLINE | ID: mdl-28645172

RESUMEN

Transfer RNAs (tRNAs) function in translational machinery and further serves as a source of short non-coding RNAs (ncRNAs). tRNA-derived ncRNAs show differential expression profiles and play roles in many biological processes beyond translation. Molecular mechanisms that shape and regulate their expression profiles are largely unknown. Here, we report the mechanism of biogenesis for tRNA-derived Piwi-interacting RNAs (td-piRNAs) expressed in Bombyx BmN4 cells. In the cells, two cytoplasmic tRNA species, tRNAAspGUC and tRNAHisGUG, served as major sources for td-piRNAs, which were derived from the 5'-part of the respective tRNAs. cP-RNA-seq identified the two tRNAs as major substrates for the 5'-tRNA halves as well, suggesting a previously uncharacterized link between 5'-tRNA halves and td-piRNAs. An increase in levels of the 5'-tRNA halves, induced by BmNSun2 knockdown, enhanced the td-piRNA expression levels without quantitative change in mature tRNAs, indicating that 5'-tRNA halves, not mature tRNAs, are the direct precursors for td-piRNAs. For the generation of tRNAHisGUG-derived piRNAs, BmThg1l-mediated nucleotide addition to -1 position of tRNAHisGUG was required, revealing an important function of BmThg1l in piRNA biogenesis. Our study advances the understanding of biogenesis mechanisms and the genesis of specific expression profiles for tRNA-derived ncRNAs.


Asunto(s)
Proteínas Argonautas/genética , Bombyx/genética , Proteínas de Insectos/genética , ARN Interferente Pequeño/genética , ARN de Transferencia de Aspártico/genética , ARN de Transferencia de Histidina/genética , Animales , Proteínas Argonautas/metabolismo , Secuencia de Bases , Bombyx/crecimiento & desarrollo , Bombyx/metabolismo , Regulación del Desarrollo de la Expresión Génica , Células Germinativas/crecimiento & desarrollo , Células Germinativas/metabolismo , Proteínas de Insectos/metabolismo , Conformación de Ácido Nucleico , ARN Interferente Pequeño/metabolismo , ARN de Transferencia de Aspártico/metabolismo , ARN de Transferencia de Histidina/metabolismo
7.
Nucleic Acids Res ; 45(12): 7441-7454, 2017 Jul 07.
Artículo en Inglés | MEDLINE | ID: mdl-28499021

RESUMEN

The RNase P family comprises structurally diverse endoribonucleases ranging from complex ribonucleoproteins to single polypeptides. We show that the organellar (AtPRORP1) and the two nuclear (AtPRORP2,3) single-polypeptide RNase P isoenzymes from Arabidopsis thaliana confer viability to Escherichia coli cells with a lethal knockdown of its endogenous RNA-based RNase P. RNA-Seq revealed that AtPRORP1, compared with bacterial RNase P or AtPRORP3, cleaves several precursor tRNAs (pre-tRNAs) aberrantly in E. coli. Aberrant cleavage by AtPRORP1 was mainly observed for pre-tRNAs that can form short acceptor-stem extensions involving G:C base pairs, including tRNAAsp(GUC), tRNASer(CGA) and tRNAHis. However, both AtPRORP1 and 3 were defective in processing of E. coli pre-tRNASec carrying an acceptor stem expanded by three G:C base pairs. Instead, pre-tRNASec was degraded, suggesting that tRNASec is dispensable for E. coli under laboratory conditions. AtPRORP1, 2 and 3 are also essentially unable to process the primary transcript of 4.5S RNA, a hairpin-like non-tRNA substrate processed by E. coli RNase P, indicating that PRORP enzymes have a narrower, more tRNA-centric substrate spectrum than bacterial RNA-based RNase P enzymes. The cells' viability also suggests that the essential function of the signal recognition particle can be maintained with a 5΄-extended 4.5S RNA.


Asunto(s)
Proteínas de Escherichia coli/genética , Escherichia coli/genética , Regulación Bacteriana de la Expresión Génica , Precursores del ARN/genética , Ribonucleasa P/genética , Arabidopsis/genética , Arabidopsis/metabolismo , Proteínas de Arabidopsis/genética , Proteínas de Arabidopsis/metabolismo , Emparejamiento Base , Secuencia de Bases , Escherichia coli/metabolismo , Proteínas de Escherichia coli/metabolismo , Prueba de Complementación Genética , Viabilidad Microbiana , Conformación de Ácido Nucleico , Precursores del ARN/metabolismo , ARN Bacteriano/genética , ARN Bacteriano/metabolismo , ARN de Transferencia de Aspártico/genética , ARN de Transferencia de Aspártico/metabolismo , ARN de Transferencia de Histidina/genética , ARN de Transferencia de Histidina/metabolismo , ARN de Transferencia de Serina/genética , ARN de Transferencia de Serina/metabolismo , Ribonucleasa P/deficiencia , Ribonucleasa P/metabolismo , Transgenes
8.
Acta Crystallogr F Struct Biol Commun ; 73(Pt 2): 62-69, 2017 02 01.
Artículo en Inglés | MEDLINE | ID: mdl-28177315

RESUMEN

The N-terminal anticodon-binding domain of the nondiscriminating aspartyl-tRNA synthetase (ND-AspRS) plays a crucial role in the recognition of both tRNAAsp and tRNAAsn. Here, the first X-ray crystal structure of the N-terminal domain of this enzyme (ND-AspRS1-104) from the human-pathogenic bacterium Helicobacter pylori is reported at 2.0 Šresolution. The apo form of H. pylori ND-AspRS1-104 shares high structural similarity with the N-terminal anticodon-binding domains of the discriminating aspartyl-tRNA synthetase (D-AspRS) from Escherichia coli and ND-AspRS from Pseudomonas aeruginosa, allowing recognition elements to be proposed for tRNAAsp and tRNAAsn. It is proposed that a long loop (Arg77-Lys90) in this H. pylori domain influences its relaxed tRNA specificity, such that it is classified as nondiscriminating. A structural comparison between D-AspRS from E. coli and ND-AspRS from P. aeruginosa suggests that turns E and F (78GAGL81 and 83NPKL86) in H. pylori ND-AspRS play a crucial role in anticodon recognition. Accordingly, the conserved Pro84 in turn F facilitates the recognition of the anticodons of tRNAAsp (34GUC36) and tRNAAsn (34GUU36). The absence of the amide H atom allows both C and U bases to be accommodated in the tRNA-recognition site.


Asunto(s)
Anticodón/química , Aspartato-ARNt Ligasa/química , Proteínas Bacterianas/química , Helicobacter pylori/química , ARN de Transferencia de Asparagina/química , ARN de Transferencia de Aspártico/química , Secuencia de Aminoácidos , Anticodón/metabolismo , Apoproteínas/química , Apoproteínas/genética , Apoproteínas/metabolismo , Aspartato-ARNt Ligasa/genética , Aspartato-ARNt Ligasa/metabolismo , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Sitios de Unión , Clonación Molecular , Cristalografía por Rayos X , Escherichia coli/enzimología , Escherichia coli/genética , Expresión Génica , Helicobacter pylori/enzimología , Modelos Moleculares , Plásmidos/química , Plásmidos/metabolismo , Unión Proteica , Conformación Proteica en Hélice alfa , Conformación Proteica en Lámina beta , Dominios y Motivos de Interacción de Proteínas , Pseudomonas aeruginosa/enzimología , Pseudomonas aeruginosa/genética , ARN de Transferencia de Asparagina/genética , ARN de Transferencia de Asparagina/metabolismo , ARN de Transferencia de Aspártico/genética , ARN de Transferencia de Aspártico/metabolismo , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Alineación de Secuencia , Homología Estructural de Proteína
9.
RNA ; 23(4): 483-492, 2017 04.
Artículo en Inglés | MEDLINE | ID: mdl-28115596

RESUMEN

Structured RNAs have a central role in cellular function. The capability of structured RNAs to adopt fixed architectural structures or undergo dynamic conformational changes contributes to their diverse role in the regulation of gene expression. Although numerous biophysical and biochemical tools have been developed to study structured RNAs, there is a continuing need for the development of new methods for the investigation of RNA structures, especially methods that allow RNA structure to be studied in solution close to its native cellular conditions. Here we use osmium tetroxide (OsO4) as a chemical probe of RNA structure. In this method, we have used fluorescence-based sequencing technologies to detect OsO4 modified RNA. We characterized the requirements for OsO4 modification of RNA by investigating three known structured RNAs: the M-box, glycine riboswitch RNAs, and tRNAasp Our results show that OsO4 predominantly modifies RNA at uracils that are conformationally exposed on the surface of the RNA. We also show that changes in OsO4 reactivity at flexible positions in the RNA correlate with ligand-driven conformational changes in the RNA structure. Osmium tetroxide modification of RNA will provide insights into the structural features of RNAs that are relevant to their underlying biological functions.


Asunto(s)
Sondas Moleculares/química , Tetróxido de Osmio/química , ARN de Transferencia de Aspártico/química , Riboswitch/genética , Secuencia de Bases , Conformación de Ácido Nucleico , ARN de Transferencia de Aspártico/genética , Coloración y Etiquetado/métodos , Uracilo/química
10.
Nucleic Acids Res ; 45(5): 2571-2584, 2017 03 17.
Artículo en Inglés | MEDLINE | ID: mdl-27956500

RESUMEN

Conflicts between replication and transcription challenge chromosome duplication. Escherichia coli replisome movement along transcribed DNA is promoted by Rep and UvrD accessory helicases with Δrep ΔuvrD cells being inviable under rapid growth conditions. We have discovered that mutations in a tRNA gene, aspT, in an aminoacyl tRNA synthetase, AspRS, and in a translation factor needed for efficient proline-proline bond formation, EF-P, suppress Δrep ΔuvrD lethality. Thus replication-transcription conflicts can be alleviated by the partial sacrifice of a mechanism that reduces replicative barriers, namely translating ribosomes that reduce RNA polymerase backtracking. Suppression depends on RelA-directed synthesis of (p)ppGpp, a signalling molecule that reduces replication-transcription conflicts, with RelA activation requiring ribosomal pausing. Levels of (p)ppGpp in these suppressors also correlate inversely with the need for Rho activity, an RNA translocase that can bind to emerging transcripts and displace transcription complexes. These data illustrate the fine balance between different mechanisms in facilitating gene expression and genome duplication and demonstrate that accessory helicases are a major determinant of this balance. This balance is also critical for other aspects of bacterial survival: the mutations identified here increase persistence indicating that similar mutations could arise in naturally occurring bacterial populations facing antibiotic challenge.


Asunto(s)
Replicación del ADN , Escherichia coli/genética , Genoma Bacteriano , Extensión de la Cadena Peptídica de Translación , ADN Helicasas/genética , Escherichia coli/enzimología , Escherichia coli/crecimiento & desarrollo , Proteínas de Escherichia coli/genética , Proteínas de Escherichia coli/metabolismo , Mutación , ARN de Transferencia de Aspártico/genética , Supresión Genética , Aminoacilación de ARN de Transferencia
11.
Nucleic Acids Res ; 44(22): 10974-10985, 2016 12 15.
Artículo en Inglés | MEDLINE | ID: mdl-27536005

RESUMEN

In this report, we investigated the pathogenic mechanism underlying the deafness-associated mitochondrial(mt) tRNAAsp 7551A > G mutation. The m.7551A > G mutation is localized at a highly conserved nucleotide(A37), adjacent (3') to the anticodon, which is important for the fidelity of codon recognition and stabilization in functional tRNAs. It was anticipated that the m.7551A > G mutation altered the structure and function of mt-tRNAAsp The primer extension assay demonstrated that the m.7551A > G mutation created the m1G37 modification of mt-tRNAAsp Using cybrid cell lines generated by transferring mitochondria from lymphoblastoid cell lines derived from a Chinese family into mitochondrial DNA(mtDNA)-less (ρo) cells, we demonstrated the significant decreases in the efficiency of aminoacylation and steady-state level of mt-tRNAAsp in mutant cybrids, compared with control cybrids. A failure in metabolism of mt-tRNAAsp caused the variable reductions in mtDNA-encoded polypeptides in mutant cybrids. Impaired mitochondrial translation led to the respiratory phenotype in mutant cybrids. The respiratory deficiency lowed mitochondrial adenosine triphosphate production and increased the production of oxidative reactive species in mutant cybrids. Our data demonstrated that mitochondrial dysfunctions caused by the m.7551A > G mutation are associated with deafness. Our findings may provide new insights into the pathophysiology of maternally transmitted deafness that was manifested by altered nucleotide modification of mitochondrial tRNA.


Asunto(s)
Sordera/genética , Mitocondrias/genética , ARN de Transferencia de Aspártico/genética , Línea Celular , Estudios de Asociación Genética , Humanos , Masculino , Potencial de la Membrana Mitocondrial , Linaje , Mutación Puntual , Estabilidad del ARN , Especies Reactivas de Oxígeno/metabolismo , Adulto Joven
12.
Biochimie ; 112: 66-72, 2015 May.
Artículo en Inglés | MEDLINE | ID: mdl-25747896

RESUMEN

Methylation of tRNA is an important post-transcriptional modification and aberrations in tRNA modification has been implicated in cancer. The DNMT2 protein methylates C38 of tRNA-Asp and it has a role in cellular physiology and stress response and its expression levels are altered in cancer tissues. Here we studied whether DNMT2 somatic mutations found in cancer tissues affect the activity of the enzyme. We have generated 13 DNMT2 variants and purified the corresponding proteins. All proteins were properly folded as determined by circular dichroism spectroscopy. We tested their RNA methylation activity using in vitro generated tRNA-Asp. One of the mutations (E63K) caused a twofold increase in activity, while two of them led to a strong (over fourfold) decrease in activity (G155S and L257V). Two additional mutant proteins were almost inactive (R371H and G155V). The strong effect of some of the somatic cancer mutations on DNMT2 activity suggests that these mutations have a functional role in tumorigenesis.


Asunto(s)
ADN (Citosina-5-)-Metiltransferasas/química , Mutación Missense , Proteínas de Neoplasias/química , Neoplasias/enzimología , Procesamiento Postranscripcional del ARN , ARN de Transferencia de Aspártico/química , Sustitución de Aminoácidos , Animales , Catálisis , ADN (Citosina-5-)-Metiltransferasas/genética , ADN (Citosina-5-)-Metiltransferasas/metabolismo , Humanos , Metilación , Ratones , Proteínas de Neoplasias/genética , Proteínas de Neoplasias/metabolismo , Neoplasias/genética , ARN de Transferencia de Aspártico/genética , ARN de Transferencia de Aspártico/metabolismo
13.
Neuromuscul Disord ; 25(1): 81-4, 2015 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-25447692

RESUMEN

Mitochondrial transfer RNA (mt-tRNA) mutations are the commonest sub-type of mitochondrial (mtDNA) mutations associated with human disease. We report a patient with multisytemic disease characterised by myopathy, spinal ataxia, sensorineural hearing loss, cataract and cognitive impairment in whom a novel m.7539C>T mt-tRNA(Asp) transition was identified. Muscle biopsy revealed extensive histopathological findings including cytochrome c oxidase (COX)-deficient fibres. Pyrosequencing confirmed mtDNA heteroplasmy for the mutation whilst single muscle fibre segregation studies revealed statistically significant higher mutation loads in COX-deficient fibres than in COX-positive fibres. Absence from control databases, hierarchical mt-tRNA mutation segregation within tissues, and occurrence at conserved sequence positions, further confirm this novel mt-tRNA mutation to be pathogenic. To date only three mt-tRNA(Asp) gene mutations have been described with clear evidence of pathogenicity. The novel m.7539C>T mt-tRNA(Asp) gene mutation extends the spectrum of pathogenic mutations in this gene, further supporting the notion that mt-tRNA(Asp) gene mutations are associated with multisystemic disease presentations.


Asunto(s)
ADN Mitocondrial/genética , Enfermedades Mitocondriales/diagnóstico , Enfermedades Mitocondriales/genética , Mutación Puntual , ARN de Transferencia de Aspártico/genética , ARN/genética , Encéfalo/patología , Complejo IV de Transporte de Electrones/metabolismo , Femenino , Humanos , Persona de Mediana Edad , Mitocondrias/metabolismo , Músculo Esquelético/enzimología , Músculo Esquelético/patología , ARN Mitocondrial
14.
FEBS Lett ; 588(9): 1808-12, 2014 May 02.
Artículo en Inglés | MEDLINE | ID: mdl-24685427

RESUMEN

The human pathogen Staphylococcus aureus is an asparagine prototroph despite its genome not encoding an asparagine synthetase. S. aureus does use an asparaginyl-tRNA synthetase (AsnRS) to directly ligate asparagine to tRNA(Asn). The S. aureus genome also codes for one aspartyl-tRNA synthetase (AspRS). Here we demonstrate the lone S. aureus aspartyl-tRNA synthetase has relaxed tRNA specificity and can be used with the amidotransferase GatCAB to synthesize asparagine on tRNA(Asn). S. aureus thus encodes both the direct and indirect routes for Asn-tRNA(Asn) formation while encoding only one aspartyl-tRNA synthetase. The presence of the indirect pathway explains how S. aureus synthesizes asparagine without either asparagine synthetase.


Asunto(s)
Asparagina/biosíntesis , Aspartato-ARNt Ligasa/química , ARN de Transferencia de Asparagina/química , ARN de Transferencia de Aspártico/química , Staphylococcus aureus/enzimología , Secuencia de Aminoácidos , Aminoacilación , Escherichia coli/genética , Escherichia coli/crecimiento & desarrollo , Cinética , Datos de Secuencia Molecular , ARN Bacteriano/química , ARN Bacteriano/genética , ARN de Transferencia de Asparagina/genética , ARN de Transferencia de Aspártico/genética , Especificidad por Sustrato
15.
Biochimie ; 95(2): 195-203, 2013 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-23023194

RESUMEN

Nucleotides of 28S rRNA involved in binding of the human 80S ribosome with acceptor ends of the A site and the P site tRNAs were determined using two complementary approaches, namely, cross-linking with application of tRNA(Asp) analogues substituted with 4-thiouridine in position 75 or 76 and hydroxyl radical footprinting with the use of the full sized tRNA and the tRNA deprived of the 3'-terminal trinucleotide CCA. In general, these 28S rRNA nucleotides are located in ribosomal regions homologous to the A, P and E sites of the prokaryotic 50S subunit. However, none of the approaches used discovered interactions of the apex of the large rRNA helix 80 with the acceptor end of the P site tRNA typical with prokaryotic ribosomes. Application of the results obtained to available atomic models of 50S and 60S subunits led us to a conclusion that the A site tRNA is actually present in both A/A and A/P states and the P site tRNA in the P/P and P/E states. Thus, the present study gives a biochemical confirmation of the data on the structure and dynamics of the mammalian ribosomal pretranslocation complex obtained with application of cryo-electron microscopy and single-molecule FRET [Budkevich et al., 2011]. Moreover, in our study, particular sets of 28S rRNA nucleotides involved in oscillations of tRNAs CCA-termini between their alternative locations in the mammalian 80S ribosome are revealed.


Asunto(s)
Biosíntesis de Proteínas , ARN de Transferencia de Aspártico/química , Ribosomas/química , Tiouridina/química , Animales , Emparejamiento Base , Sitios de Unión , Reactivos de Enlaces Cruzados , Microscopía por Crioelectrón , Transferencia Resonante de Energía de Fluorescencia , Humanos , Secuencias Invertidas Repetidas/genética , Modelos Moleculares , Mutación , Conformación de Ácido Nucleico , ARN Ribosómico 28S , ARN de Transferencia de Aspártico/genética , ARN de Transferencia de Aspártico/metabolismo , Ribosomas/genética , Ribosomas/metabolismo , Tiouridina/metabolismo
16.
Artículo en Chino | MEDLINE | ID: mdl-24506995

RESUMEN

OBJECTIVE: We reported here the clinical and genetic evaluations as well as mutational analysis of mitochondrial DNA(mtDNA) in a Chinese family with maternally transmitted non-syndromic hearing loss and investigated the influence of the mitochondrial tRNA(Asp) A7551G mutation to the phenotypic manifestation of the deafness. METHODS: One Chinese Han pedigrees of maternally transmitted nonsyndromic hearing loss were collected. The proband and family members underwent clinical, genetic, and molecular evaluations, such as audiological examinations, mutational analysis of mitochondrial genome and mutational analysis of GJB2 gene. RESULTS: Six people of this pedigree suffered from hearing loss, including four matrilineal members, and others did not have significant clinical abnormalities. Sequence analysis of the complete mitochondrial genome in the proband showed that there were 28 mtDNA polymorphisms belonging to East -Asian haplogroup A4.In addition to the A7551G homogeneity mutation, there were no other functionally significant variants found in this family. The A7551G mutation located immediately at the three prime end to the anticodon, corresponding with the conventional position 37 of tRNA(Asp), and its' CI value was 100% compared with other 15 primate species. The A7551G mutation was absent in other Chinese controls. The mutations on GJB2 were detected by direct sequence analysis,GJB2 235delC and 299delAT which was associated with hearing loss were found in the genomic DNA of the proband and some matrilineal members. Clinical evaluation showed a variable phenotype of severity, age-at-onset and audiometric configuration of hearing loss in the matrilineal relatives in these families. CONCLUSIONS: The A7551G mutation may modify the secondary structure of the tRNA, and affect the stabilization of tRNA(Asp), produce non-normal functional tRNA(Asp) ultimately. And it may cause the phenotypic manifestation of the deafness that associated with A7551G mutation. Therefore, the mitochondrial tRNA(Asp) A7551G mutation may be a new mitochondrial mutation for hearing loss.


Asunto(s)
ADN Mitocondrial/genética , Mutación , ARN de Transferencia de Aspártico/genética , Adulto , Estudios de Casos y Controles , Preescolar , Conexina 26 , Conexinas/genética , Análisis Mutacional de ADN , Sordera/genética , Femenino , Humanos , Masculino , Persona de Mediana Edad , Linaje , Fenotipo , ARN Ribosómico/genética
17.
Biochimie ; 94(5): 1090-7, 2012 May.
Artículo en Inglés | MEDLINE | ID: mdl-22402012

RESUMEN

Many mammalian mitochondrial aminoacyl-tRNA synthetases are of bacterial-type and share structural domains with homologous bacterial enzymes of the same specificity. Despite this high similarity, synthetases from bacteria are known for their inability to aminoacylate mitochondrial tRNAs, while mitochondrial enzymes do aminoacylate bacterial tRNAs. Here, the reasons for non-aminoacylation by a bacterial enzyme of a mitochondrial tRNA have been explored. A mutagenic analysis performed on in vitro transcribed human mitochondrial tRNA(Asp) variants tested for their ability to become aspartylated by Escherichia coli aspartyl-tRNA synthetase, reveals that full conversion cannot be achieved on the basis of the currently established tRNA/synthetase recognition rules. Integration of the full set of aspartylation identity elements and stabilization of the structural tRNA scaffold by restoration of D- and T-loop interactions, enable only a partial gain in aspartylation efficiency. The sequence context and high structural instability of the mitochondrial tRNA are additional features hindering optimal adaptation of the tRNA to the bacterial enzyme. Our data support the hypothesis that non-aminoacylation of mitochondrial tRNAs by bacterial synthetases is linked to the large sequence and structural relaxation of the organelle encoded tRNAs, itself a consequence of the high rate of mitochondrial genome divergence.


Asunto(s)
Aspartato-ARNt Ligasa/metabolismo , Mitocondrias/metabolismo , Aminoacilación/genética , Aminoacilación/fisiología , Aspartato-ARNt Ligasa/genética , Escherichia coli/genética , Escherichia coli/metabolismo , Humanos , Conformación de Ácido Nucleico , Estabilidad del ARN , ARN de Transferencia de Aspártico/genética , ARN de Transferencia de Aspártico/metabolismo
18.
Proc Natl Acad Sci U S A ; 108(40): E794-802, 2011 Oct 04.
Artículo en Inglés | MEDLINE | ID: mdl-21896722

RESUMEN

Several classes of small noncoding RNAs are key players in cellular metabolism including mRNA decoding, RNA processing, and mRNA stability. Here we show that a tRNA(Asp) isodecoder, corresponding to a human tRNA-derived sequence, binds to an embedded Alu RNA element contained in the 3' UTR of the human aspartyl-tRNA synthetase mRNA. This interaction between two well-known classes of RNA molecules, tRNA and Alu RNA, is driven by an unexpected structural motif and induces a global rearrangement of the 3' UTR. Besides, this 3' UTR contains two functional polyadenylation signals. We propose a model where the tRNA/Alu interaction would modulate the accessibility of the two alternative polyadenylation sites and regulate the stability of the mRNA. This unique regulation mechanism would link gene expression to RNA polymerase III transcription and may have implications in a primate-specific signal pathway.


Asunto(s)
Regiones no Traducidas 3'/genética , Elementos Alu/fisiología , Aspartato-ARNt Ligasa/metabolismo , Modelos Biológicos , Conformación Proteica , Pliegue del ARN/fisiología , Procesamiento Postranscripcional del ARN/fisiología , ARN de Transferencia de Aspártico/metabolismo , Elementos Alu/genética , Aspartato-ARNt Ligasa/genética , Secuencia de Bases , Northern Blotting , Cartilla de ADN/genética , Ensayo de Cambio de Movilidad Electroforética , Células HeLa , Humanos , Datos de Secuencia Molecular , Reacción en Cadena de la Polimerasa , Procesamiento Postranscripcional del ARN/genética , ARN de Transferencia de Aspártico/genética , Transfección
19.
RNA ; 15(8): 1462-8, 2009 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-19535463

RESUMEN

More than 130 mutations in human mitochondrial tRNA (mt-tRNA) genes have been correlated with a variety of neurodegenerative and neuromuscular disorders. Their molecular impacts are of mosaic type, affecting various stages of tRNA biogenesis, structure, and/or functions in mt-translation. Knowledge of mammalian mt-tRNA structures per se remains scarce however. Primary and secondary structures deviate from classical tRNAs, while rules for three-dimensional (3D) folding are almost unknown. Here, we take advantage of a myopathy-related mutation A7526G (A9G) in mt-tRNA(Asp) to investigate both the primary molecular impact underlying the pathology and the role of nucleotide 9 in the network of 3D tertiary interactions. Experimental evidence is presented for existence of a 9-12-23 triple in human mt-tRNA(Asp) with a strongly conserved interaction scheme in mammalian mt-tRNAs. Mutation A7526G disrupts the triple interaction and in turn reduces aspartylation efficiency.


Asunto(s)
ARN de Transferencia de Aspártico/química , ARN de Transferencia de Aspártico/genética , ARN/química , ARN/genética , Sitios de Unión/genética , Humanos , Cinética , Miopatías Mitocondriales/genética , Miopatías Mitocondriales/metabolismo , Miopatías Mitocondriales/patología , Modelos Moleculares , Mutación Missense , Conformación de Ácido Nucleico , ARN/metabolismo , ARN Mitocondrial , ARN de Transferencia de Aspártico/metabolismo , Aminoacilación de ARN de Transferencia/genética
20.
J Am Chem Soc ; 131(7): 2541-6, 2009 Feb 25.
Artículo en Inglés | MEDLINE | ID: mdl-19193004

RESUMEN

The difficulty of analyzing higher order RNA structure, especially for folding intermediates and for RNAs whose functions require domains that are conformationally flexible, emphasizes the need for new approaches for modeling RNA tertiary structure accurately. Here, we report a concise approach that makes use of facile RNA structure probing experiments that are then interpreted using a computational algorithm, carefully tailored to optimize both the resolution and refinement speed for the resulting structures, without requiring user intervention. The RNA secondary structure is first established using SHAPE chemistry. We then use a sequence-directed cleavage agent, which can be placed arbitrarily in many helical motifs, to obtain high quality inter-residue distances. We interpret this in-solution chemical information using a fast, coarse grained, discrete molecular dynamics engine in which each RNA nucleotide is represented by pseudoatoms for the phosphate, ribose, and nucleobase groups. By this approach, we refine base paired positions in yeast tRNA(Asp) to 4 A rmsd without any preexisting information or assumptions about secondary or tertiary structures. This blended experimental and computational approach has the potential to yield native-like models for the diverse universe of functionally important RNAs whose structures cannot be characterized by conventional structural methods.


Asunto(s)
ARN/química , Secuencia de Bases , Ácido Edético/análogos & derivados , Ácido Edético/química , Compuestos Férricos/química , Compuestos Ferrosos/química , Modelos Moleculares , Datos de Secuencia Molecular , Conformación de Ácido Nucleico , ARN/genética , ARN de Transferencia de Aspártico/química , ARN de Transferencia de Aspártico/genética
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