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1.
Nucleic Acids Res ; 50(16): 9368-9381, 2022 09 09.
Artigo em Inglês | MEDLINE | ID: mdl-36018806

RESUMO

Pseudouridine (Ψ) at position 55 in tRNAs plays an important role in their structure and function. This modification is catalyzed by TruB/Pus4/Cbf5 family of pseudouridine synthases in bacteria and yeast. However, the mechanism of TRUB family underlying the formation of Ψ55 in the mammalian tRNAs is largely unknown. In this report, the CMC/reverse transcription assays demonstrated the presence of Ψ55 in the human mitochondrial tRNAAsn, tRNAGln, tRNAGlu, tRNAPro, tRNAMet, tRNALeu(UUR) and tRNASer(UCN). TRUB1 knockout (KO) cell lines generated by CRISPR/Cas9 technology exhibited the loss of Ψ55 modification in mitochondrial tRNAAsn, tRNAGln, tRNAGlu and tRNAPro but did not affect other 18 mitochondrial tRNAs. An in vitro assay revealed that recombinant TRUB1 protein can catalyze the efficient formation of Ψ55 in tRNAAsn and tRNAGln, but not in tRNAMet and tRNAArg. Notably, the overexpression of TRUB1 cDNA reversed the deficient Ψ55 modifications in these tRNAs in TRUB1KO HeLa cells. TRUB1 deficiency affected the base-pairing (18A/G-Ψ55), conformation and stability but not aminoacylation capacity of these tRNAs. Furthermore, TRUB1 deficiency impacted mitochondrial translation and biogenesis of oxidative phosphorylation system. Our findings demonstrated that human TRUB1 is a highly conserved mitochondrial pseudouridine synthase responsible for the Ψ55 modification in the mitochondrial tRNAAsn, tRNAGln, tRNAGlu and tRNAPro.


Assuntos
Transferases Intramoleculares , RNA de Transferência de Ácido Glutâmico , Animais , Humanos , RNA de Transferência de Glutamina , RNA de Transferência de Prolina , RNA de Transferência de Asparagina , RNA de Transferência de Metionina , Células HeLa , Transferases Intramoleculares/genética , Transferases Intramoleculares/metabolismo , Pseudouridina/genética , Pseudouridina/metabolismo , RNA de Transferência/metabolismo , Mamíferos/genética
2.
Proteins ; 88(9): 1133-1142, 2020 09.
Artigo em Inglês | MEDLINE | ID: mdl-32067260

RESUMO

The nondiscriminating aspartyl-tRNA synthetase (ND-AspRS), found in many archaea and bacteria, covalently attaches aspartic acid to tRNAAsp and tRNAAsn generating a correctly charged Asp-tRNAAsp and an erroneous Asp-tRNAAsn . This relaxed tRNA specificity is governed by interactions between the tRNA and the enzyme. In an effort to assess the contributions of the anticodon-binding domain to tRNA specificity, we constructed two chimeric enzymes, Chimera-D and Chimera-N, by replacing the native anticodon-binding domain in the Helicobacter pylori ND-AspRS with that of a discriminating AspRS (Chimera-D) and an asparaginyl-tRNA synthetase (AsnRS, Chimera-N), both from Escherichia coli. Both chimeric enzymes showed similar secondary structure compared to wild-type (WT) ND-AspRS and maintained the ability to form dimeric complexes in solution. Although less catalytically active than WT, Chimera-D was more discriminating as it aspartylated tRNAAsp over tRNAAsn with a specificity ratio of 7.0 compared to 2.9 for the WT enzyme. In contrast, Chimera-N exhibited low catalytic activity toward tRNAAsp and was unable to aspartylate tRNAAsn . The observed catalytic activities for the two chimeras correlate with their heterologous toxicity when expressed in E. coli. Molecular dynamics simulations show a reduced hydrogen bond network at the interface between the anticodon-binding domain and the catalytic domain in Chimera-N compared to Chimera-D or WT, explaining its lower stability and catalytic activity.


Assuntos
Anticódon , Aspartato-tRNA Ligase/metabolismo , Escherichia coli/enzimologia , Helicobacter pylori/enzimologia , Aminoacil-RNA de Transferência/metabolismo , RNA de Transferência de Asparagina/metabolismo , RNA de Transferência de Ácido Aspártico/metabolismo , Sequência de Aminoácidos , Aspartato-tRNA Ligase/química , Aspartato-tRNA Ligase/genética , Sítios de Ligação , Biocatálise , Clonagem Molecular , Cristalografia por Raios X , Escherichia coli/genética , Expressão Gênica , Vetores Genéticos/química , Vetores Genéticos/metabolismo , Helicobacter pylori/genética , Simulação de Dinâmica Molecular , Mutação , Ligação Proteica , Conformação Proteica em alfa-Hélice , Conformação Proteica em Folha beta , Domínios e Motivos de Interação entre Proteínas , Aminoacil-RNA de Transferência/química , Aminoacil-RNA de Transferência/genética , RNA de Transferência de Asparagina/química , RNA de Transferência de Ácido Aspártico/química , Proteínas Recombinantes de Fusão/química , Proteínas Recombinantes de Fusão/genética , Proteínas Recombinantes de Fusão/metabolismo , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Alinhamento de Sequência , Homologia de Sequência de Aminoácidos , Especificidade por Substrato
3.
Neuromuscul Disord ; 29(5): 358-367, 2019 05.
Artigo em Inglês | MEDLINE | ID: mdl-30962064

RESUMO

Chronic progressive external ophthalmoplegia (CPEO) is a frequent clinical manifestation of disorders caused by pathogenic mitochondrial DNA mutations. However, for diagnostic purposes skeletal muscle tissue is used, since extraocular muscle tissue is usually not available for work-up. In the present study we aimed to identify causative factors that are responsible for extraocular muscle to be primarily affected in CPEO. We performed comparative histochemical and molecular genetic analyses of extraocular muscle and skeletal muscle single fibers in a case of isolated CPEO caused by the heteroplasmic m.5667G>A mutation in the mitochondrial tRNAAsn gene (MT-TN). Histochemical analyses revealed higher proportion of cytochrome c oxidase deficient fibers in extraocular muscle (41%) compared to skeletal muscle (10%). However, genetic analyses of single fibers revealed no significant difference either in the mutation loads between extraocular muscle and skeletal muscle cytochrome c oxidase deficient single fibers (extraocular muscle 86% ±â€¯4.6%; skeletal muscle 87.8 %±â€¯5.7%, p = 0.246) nor in the mutation threshold (extraocular muscle 74% ±â€¯3%; skeletal muscle 74% ±â€¯4%). We hypothesize that higher proportion of cytochrome c oxidase deficient fibers in extraocular muscle compared to skeletal muscle might be due to facilitated segregation of the m.5667G>A mutation into extraocular muscle, which may explain the preferential ocular manifestation and clinically isolated CPEO.


Assuntos
Complexo IV da Cadeia de Transporte de Elétrons/metabolismo , Fibras Musculares Esqueléticas/metabolismo , Músculos Oculomotores/metabolismo , Oftalmoplegia Externa Progressiva Crônica/genética , Músculo Quadríceps/metabolismo , RNA de Transferência de Asparagina/genética , Adolescente , Deficiência de Citocromo-c Oxidase , Complexo de Proteínas da Cadeia de Transporte de Elétrons/metabolismo , Humanos , Imuno-Histoquímica , Masculino , Fibras Musculares Esqueléticas/patologia , Músculo Esquelético , Músculos Oculomotores/patologia , Oftalmoplegia Externa Progressiva Crônica/metabolismo , Oftalmoplegia Externa Progressiva Crônica/patologia , Músculo Quadríceps/patologia
4.
Genes (Basel) ; 10(4)2019 04 01.
Artigo em Inglês | MEDLINE | ID: mdl-30939863

RESUMO

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.


Assuntos
Aspartato-tRNA Ligase/genética , Glutamato-tRNA Ligase/genética , RNA de Transferência de Asparagina/genética , RNA de Transferência de Ácido Aspártico/genética , Sequência de Aminoácidos/genética , Asparagina/química , Asparagina/genética , Aspartato-tRNA Ligase/química , Código Genético/genética , Glutamato-tRNA Ligase/química , Mycobacterium smegmatis/química , Mycobacterium smegmatis/genética , Conformação Proteica , Proteoma/química , Proteoma/genética , Aminoacil-RNA de Transferência/genética , RNA de Transferência de Asparagina/química , RNA de Transferência de Ácido Aspártico/química , Homologia de Sequência de Aminoácidos
5.
Mitochondrion ; 47: 139-140, 2019 07.
Artigo em Inglês | MEDLINE | ID: mdl-31026515

RESUMO

We report here on a patient who presented with myasthenia gravis type symptoms (fatigable ptosis, increased jitter on single fiber EMG, and a thymic mass) who was subsequently diagnosed with a mitochondrial myopathy. Sequencing of the mitochondrial genome (mtDNA) identified a transition variant in the tRNA asparagine gene (MT-TN) (m.5728T>C) at in 41% of mtDNA molecules in muscle tissue. The variant was not detectable in blood. The m.5728T>C variant has been reported previously in a ten year old male with global developmental delays, failure to thrive, ataxia, weakness, cognitive regression, seizures, and glomerulosclerosis. The variant was seen in 97% of mtDNA molecules in muscle and 50% in blood. This case report supports the pathogenicity of the m.5728T>C and helps to establish the phenotypic spectrum of this condition at a lower heteroplasmy.


Assuntos
DNA Mitocondrial/genética , Mitocôndrias Musculares/genética , Miastenia Gravis/genética , Mutação Puntual , RNA Mitocondrial/genética , RNA de Transferência de Asparagina/genética , Criança , Feminino , Humanos
7.
SLAS Discov ; 23(3): 294-301, 2018 03.
Artigo em Inglês | MEDLINE | ID: mdl-29186665

RESUMO

Pseudomonas aeruginosa, an opportunistic pathogen, is highly susceptible to developing resistance to multiple antibiotics. The gene encoding aspartyl-tRNA synthetase (AspRS) from P. aeruginosa was cloned and the resulting protein characterized. AspRS was kinetically evaluated, and the KM values for aspartic acid, ATP, and tRNA were 170, 495, and 0.5 µM, respectively. AspRS was developed into a screening platform using scintillation proximity assay (SPA) technology and used to screen 1690 chemical compounds, resulting in the identification of two inhibitory compounds, BT02A02 and BT02C05. The minimum inhibitory concentrations (MICs) were determined against nine clinically relevant bacterial strains, including efflux pump mutant and hypersensitive strains of P. aeruginosa. The compounds displayed broad-spectrum antibacterial activity and inhibited growth of the efflux and hypersensitive strains with MICs of 16 µg/mL. Growth of wild-type strains were unaffected, indicating that efflux was likely responsible for this lack of activity. BT02A02 did not inhibit growth of human cell cultures at any concentration. However, BT02C05 did inhibit human cell cultures with a cytotoxicity concentration (CC50) of 61.6 µg/mL. The compounds did not compete with either aspartic acid or ATP for binding AspRS, indicating that the mechanism of action of the compound occurs outside the active site of aminoacylation.


Assuntos
Antibacterianos/farmacologia , Aspartato-tRNA Ligase/genética , Pseudomonas aeruginosa/efeitos dos fármacos , RNA de Transferência de Asparagina/genética , RNA de Transferência/genética , Proteínas de Bactérias/genética , Domínio Catalítico/efeitos dos fármacos , Linhagem Celular , Proliferação de Células/efeitos dos fármacos , Citotoxinas/farmacologia , Células HEK293 , Humanos , Concentração Inibidora 50 , Testes de Sensibilidade Microbiana/métodos , Pseudomonas aeruginosa/genética
8.
Acta Crystallogr F Struct Biol Commun ; 73(Pt 2): 62-69, 2017 02 01.
Artigo em Inglês | MEDLINE | ID: mdl-28177315

RESUMO

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.


Assuntos
Anticódon/química , Aspartato-tRNA Ligase/química , Proteínas de Bactérias/química , Helicobacter pylori/química , RNA de Transferência de Asparagina/química , RNA de Transferência de Ácido Aspártico/química , Sequência de Aminoácidos , Anticódon/metabolismo , Apoproteínas/química , Apoproteínas/genética , Apoproteínas/metabolismo , Aspartato-tRNA Ligase/genética , Aspartato-tRNA Ligase/metabolismo , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Sítios de Ligação , Clonagem Molecular , Cristalografia por Raios X , Escherichia coli/enzimologia , Escherichia coli/genética , Expressão Gênica , Helicobacter pylori/enzimologia , Modelos Moleculares , Plasmídeos/química , Plasmídeos/metabolismo , Ligação Proteica , Conformação Proteica em alfa-Hélice , Conformação Proteica em Folha beta , Domínios e Motivos de Interação entre Proteínas , Pseudomonas aeruginosa/enzimologia , Pseudomonas aeruginosa/genética , RNA de Transferência de Asparagina/genética , RNA de Transferência de Asparagina/metabolismo , RNA de Transferência de Ácido Aspártico/genética , RNA de Transferência de Ácido Aspártico/metabolismo , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Alinhamento de Sequência , Homologia Estrutural de Proteína
9.
J Mol Biol ; 428(3): 618-630, 2016 Feb 13.
Artigo em Inglês | MEDLINE | ID: mdl-26804570

RESUMO

Synthesis of asparaginyl-tRNA (Asn-tRNA(Asn)) in bacteria can be formed either by directly ligating Asn to tRNA(Asn) using an asparaginyl-tRNA synthetase (AsnRS) or by synthesizing Asn on the tRNA. In the latter two-step indirect pathway, a non-discriminating aspartyl-tRNA synthetase (ND-AspRS) attaches Asp to tRNA(Asn) and the amidotransferase GatCAB transamidates the Asp to Asn on the tRNA. GatCAB can be similarly used for Gln-tRNA(Gln) formation. Most bacteria are predicted to use only one route for Asn-tRNA(Asn) formation. Given that Bacillus halodurans and Bacillus subtilis encode AsnRS for Asn-tRNA(Asn) formation and Asn synthetases to synthesize Asn and GatCAB for Gln-tRNA(Gln) synthesis, their AspRS enzymes were thought to be specific for tRNA(Asp). However, we demonstrate that the AspRSs are non-discriminating and can be used with GatCAB to synthesize Asn. The results explain why B. subtilis with its Asn synthetase genes knocked out is still an Asn prototroph. Our phylogenetic analysis suggests that this may be common among Firmicutes and 30% of all bacteria. In addition, the phylogeny revealed that discrimination toward tRNA(Asp) by AspRS has evolved independently multiple times. The retention of the indirect pathway in B. subtilis and B. halodurans likely reflects the ancient link between Asn biosynthesis and its use in translation that enabled Asn to be added to the genetic code.


Assuntos
Asparagina/metabolismo , Aspartato-tRNA Ligase/metabolismo , Bacillus/enzimologia , Aminoacil-RNA de Transferência/metabolismo , RNA de Transferência de Asparagina/metabolismo , Bacillus/metabolismo , Bacillus subtilis/enzimologia , Bacillus subtilis/metabolismo , Especificidade por Substrato
10.
Artigo em Inglês | MEDLINE | ID: mdl-24960567

RESUMO

The complete mitochondrial genome of the whitetip reef shark Triaenodon obesus is determined in this study. It is 16,700 bp in length, with the typical gene composition, arrangement and transcriptional orientation in vertebrates. The overall base composition is 31.4% A, 25.8% C, 13.2% G and 29.7% T. Two start codons and two stop codons are found in the protein-coding genes. The 22 tRNA genes ranged from 67 to 75 nucleotides. The tRNA-Ser2 lost the DHU arm and could not be folded to the typical cloverleaf secondary structure. The origin of L-strand replication (OL) sequence was identified between tRNA-Asn and tRNA-Cys genes. The high A+T content of control region is due to a lot of poly A and poly T.


Assuntos
Elasmobrânquios/genética , Genoma Mitocondrial/genética , Tubarões/genética , Animais , Composição de Bases/genética , Códon de Iniciação/genética , Códon de Terminação/genética , RNA de Transferência de Asparagina/genética , Análise de Sequência de DNA/métodos
11.
Proc Natl Acad Sci U S A ; 112(2): 382-7, 2015 Jan 13.
Artigo em Inglês | MEDLINE | ID: mdl-25548166

RESUMO

Many prokaryotes lack a tRNA synthetase to attach asparagine to its cognate tRNA(Asn), and instead synthesize asparagine from tRNA(Asn)-bound aspartate. This conversion involves two enzymes: a nondiscriminating aspartyl-tRNA synthetase (ND-AspRS) that forms Asp-tRNA(Asn), and a heterotrimeric amidotransferase GatCAB that amidates Asp-tRNA(Asn) to form Asn-tRNA(Asn) for use in protein synthesis. ND-AspRS, GatCAB, and tRNA(Asn) may assemble in an ∼400-kDa complex, known as the Asn-transamidosome, which couples the two steps of asparagine biosynthesis in space and time to yield Asn-tRNA(Asn). We report the 3.7-Šresolution crystal structure of the Pseudomonas aeruginosa Asn-transamidosome, which represents the most common machinery for asparagine biosynthesis in bacteria. We show that, in contrast to a previously described archaeal-type transamidosome, a bacteria-specific GAD domain of ND-AspRS provokes a principally new architecture of the complex. Both tRNA(Asn) molecules in the transamidosome simultaneously serve as substrates and scaffolds for the complex assembly. This architecture rationalizes an elevated dynamic and a greater turnover of ND-AspRS within bacterial-type transamidosomes, and possibly may explain a different evolutionary pathway of GatCAB in organisms with bacterial-type vs. archaeal-type Asn-transamidosomes. Importantly, because the two-step pathway for Asn-tRNA(Asn) formation evolutionarily preceded the direct attachment of Asn to tRNA(Asn), our structure also may reflect the mechanism by which asparagine was initially added to the genetic code.


Assuntos
Asparagina/biossíntese , Pseudomonas aeruginosa/metabolismo , RNA de Transferência de Asparagina/metabolismo , Sequência de Aminoácidos , Aspartato-tRNA Ligase/química , Aspartato-tRNA Ligase/genética , Aspartato-tRNA Ligase/metabolismo , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Domínio Catalítico , Cristalografia por Raios X , Evolução Molecular , Modelos Moleculares , Dados de Sequência Molecular , Filogenia , Conformação Proteica , Estrutura Terciária de Proteína , Pseudomonas aeruginosa/genética , RNA de Transferência de Asparagina/genética , Homologia de Sequência de Aminoácidos , Thermus thermophilus/genética , Thermus thermophilus/metabolismo , Aminoacilação de RNA de Transferência/genética
12.
PLoS One ; 9(10): e110842, 2014.
Artigo em Inglês | MEDLINE | ID: mdl-25338061

RESUMO

The predatory bacterium Bdellovibrio bacteriovorus preys on other Gram-negative bacteria and was predicted to be an asparagine auxotroph. However, despite encoding asparaginyl-tRNA synthetase and glutaminyl-tRNA synthetase, B. bacteriovorus also contains the amidotransferase GatCAB. Deinococcus radiodurans, and Thermus thermophilus also encode both of these aminoacyl-tRNA synthetases with GatCAB. Both also code for a second aspartyl-tRNA synthetase and use the additional aspartyl-tRNA synthetase with GatCAB to synthesize asparagine on tRNAAsn. Unlike those two bacteria, B. bacteriovorus encodes only one aspartyl-tRNA synthetase. Here we demonstrate the lone B. bacteriovorus aspartyl-tRNA synthetase catalyzes aspartyl-tRNAAsn formation that GatCAB can then amidate to asparaginyl-tRNAAsn. This non-discriminating aspartyl-tRNA synthetase with GatCAB thus provides B. bacteriovorus a second route for Asn-tRNAAsn formation with the asparagine synthesized in a tRNA-dependent manner. Thus, in contrast to a previous prediction, B. bacteriovorus codes for a biosynthetic route for asparagine. Analysis of bacterial genomes suggests a significant number of other bacteria may also code for both routes for Asn-tRNAAsn synthesis with only a limited number encoding a second aspartyl-tRNA synthetase.


Assuntos
Aspartato-tRNA Ligase/química , Proteínas de Bactérias/química , Bdellovibrio/enzimologia , RNA de Transferência de Asparagina/química , Vias Biossintéticas , Escherichia coli , Teste de Complementação Genética , Cinética , Especificidade por Substrato , Aminoacilação de RNA de Transferência
13.
FEBS Lett ; 588(9): 1808-12, 2014 May 02.
Artigo em Inglês | MEDLINE | ID: mdl-24685427

RESUMO

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.


Assuntos
Asparagina/biossíntese , Aspartato-tRNA Ligase/química , RNA de Transferência de Asparagina/química , RNA de Transferência de Ácido Aspártico/química , Staphylococcus aureus/enzimologia , Sequência de Aminoácidos , Aminoacilação , Escherichia coli/genética , Escherichia coli/crescimento & desenvolvimento , Cinética , Dados de Sequência Molecular , RNA Bacteriano/química , RNA Bacteriano/genética , RNA de Transferência de Asparagina/genética , RNA de Transferência de Ácido Aspártico/genética , Especificidade por Substrato
14.
J Biol Chem ; 288(51): 36361-71, 2013 Dec 20.
Artigo em Inglês | MEDLINE | ID: mdl-24196969

RESUMO

Genome sequencing revealed an extreme AT-rich genome and a profusion of asparagine repeats associated with low complexity regions (LCRs) in proteins of the malarial parasite Plasmodium falciparum. Despite their abundance, the function of these LCRs remains unclear. Because they occur in almost all families of plasmodial proteins, the occurrence of LCRs cannot be associated with any specific metabolic pathway; yet their accumulation must have given selective advantages to the parasite. Translation of these asparagine-rich LCRs demands extraordinarily high amounts of asparaginylated tRNA(Asn). However, unlike other organisms, Plasmodium codon bias is not correlated to tRNA gene copy number. Here, we studied tRNA(Asn) accumulation as well as the catalytic capacities of the asparaginyl-tRNA synthetase of the parasite in vitro. We observed that asparaginylation in this parasite can be considered standard, which is expected to limit the availability of asparaginylated tRNA(Asn) in the cell and, in turn, slow down the ribosomal translation rate when decoding asparagine repeats. This observation strengthens our earlier hypothesis considering that asparagine rich sequences act as "tRNA sponges" and help cotranslational folding of parasite proteins. However, it also raises many questions about the mechanistic aspects of the synthesis of asparagine repeats and about their implications in the global control of protein expression throughout Plasmodium life cycle.


Assuntos
Plasmodium falciparum/metabolismo , RNA de Transferência de Asparagina/metabolismo , Aminoacilação de RNA de Transferência , Sequência de Aminoácidos , Aminoacil-tRNA Sintetases/metabolismo , Asparagina/química , Asparagina/metabolismo , Proteínas de Bactérias/química , Proteínas de Bactérias/metabolismo , Humanos , Cinética , Dados de Sequência Molecular , Plasmodium falciparum/enzimologia , Proteínas de Protozoários/biossíntese , Proteínas de Protozoários/química , Proteínas de Protozoários/metabolismo , Pyrococcus abyssi/enzimologia , RNA de Transferência de Asparagina/biossíntese , Sequências Repetitivas de Aminoácidos
15.
Proc Natl Acad Sci U S A ; 110(31): 12756-61, 2013 Jul 30.
Artigo em Inglês | MEDLINE | ID: mdl-23858450

RESUMO

T-box riboswitches control transcription of downstream genes through the tRNA-binding formation of terminator or antiterminator structures. Previously reported T-boxes were described as single-specificity riboswitches that can bind specific tRNA anticodons through codon-anticodon interactions with the nucleotide triplet of their specifier loop (SL). However, the possibility that T-boxes might exhibit specificity beyond a single tRNA had been overlooked. In Clostridium acetobutylicum, the T-box that regulates the operon for the essential tRNA-dependent transamidation pathway harbors a SL with two potential overlapping codon positions for tRNA(Asn) and tRNA(Glu). To test its specificity, we performed extensive mutagenic, biochemical, and chemical probing analyses. Surprisingly, both tRNAs can efficiently bind the SL in vitro and in vivo. The dual specificity of the T-box is allowed by a single base shift on the SL from one overlapping codon to the next. This feature allows the riboswitch to sense two tRNAs and balance the biosynthesis of two amino acids. Detailed genomic comparisons support our observations and suggest that "flexible" T-box riboswitches are widespread among bacteria, and, moreover, their specificity is dictated by the metabolic interconnection of the pathways under control. Taken together, our results support the notion of a genome-dependent codon ambiguity of the SLs. Furthermore, the existence of two overlapping codons imposes a unique example of tRNA-dependent regulation at the transcriptional level.


Assuntos
Anticódon/metabolismo , Clostridium acetobutylicum/metabolismo , RNA Bacteriano/metabolismo , RNA de Transferência de Asparagina/metabolismo , RNA de Transferência de Ácido Glutâmico/metabolismo , Riboswitch/fisiologia , Anticódon/química , Anticódon/genética , Asparagina/biossíntese , Asparagina/genética , Clostridium acetobutylicum/química , Clostridium acetobutylicum/genética , Ácido Glutâmico/biossíntese , Ácido Glutâmico/genética , RNA Bacteriano/química , RNA Bacteriano/genética , RNA de Transferência de Asparagina/química , RNA de Transferência de Asparagina/genética , RNA de Transferência de Ácido Glutâmico/química , RNA de Transferência de Ácido Glutâmico/genética
16.
Neuromuscul Disord ; 23(4): 330-6, 2013 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-23375258

RESUMO

We report a heteroplasmic novel mutation m.5658T>C in the mt-tRNA(Asn) gene in a patient who initially presented myopathy, bilateral ptosis and ophthalmoparesis and several years later developed a non-nephrotic proteinuria. The muscle biopsy showed cytochrome c oxidase (COX) negative and ragged red fibers and in the kidney biopsy that was taken in order to identify the causes of non-nephrotic proteinuria, a focal segmental glomerulosclerosis was observed. Using laser capture microdissection we isolated COX negative fibers and COX positive fibers from the muscle of the patient and determined that there was a clear increase in the mutation load in the COX negative muscle fibers. However, the low degree of mutation load found in the renal biopsy of the patient does not allow us to conclude that the m.5658T>C mutation is responsible for focal glomerulosclerosis. Additionally, we hypothesize that the mutated m.5658T nucleotide might be structurally relevant, as it is one of the fifteen nucleotides conserved in all the species analyzed and is situated contiguously to the discriminator base in the 3'end of the mt-tRNA, where the tRNase Z cleaves the 3' trailer sequence during mt-tRNA maturation.


Assuntos
Genes Mitocondriais/genética , Glomerulosclerose Segmentar e Focal/genética , Miopatias Mitocondriais/genética , Oftalmoplegia/genética , RNA de Transferência de Asparagina/genética , Adulto , Blefaroptose/complicações , Blefaroptose/genética , Glomerulosclerose Segmentar e Focal/complicações , Humanos , Masculino , Miopatias Mitocondriais/complicações , Mutação , Oftalmoplegia/complicações
17.
BMC Genomics ; 13: 690, 2012 Dec 10.
Artigo em Inglês | MEDLINE | ID: mdl-23227809

RESUMO

BACKGROUND: The bacterium Pelobacter carbinolicus is able to grow by fermentation, syntrophic hydrogen/formate transfer, or electron transfer to sulfur from short-chain alcohols, hydrogen or formate; it does not oxidize acetate and is not known to ferment any sugars or grow autotrophically. The genome of P. carbinolicus was sequenced in order to understand its metabolic capabilities and physiological features in comparison with its relatives, acetate-oxidizing Geobacter species. RESULTS: Pathways were predicted for catabolism of known substrates: 2,3-butanediol, acetoin, glycerol, 1,2-ethanediol, ethanolamine, choline and ethanol. Multiple isozymes of 2,3-butanediol dehydrogenase, ATP synthase and [FeFe]-hydrogenase were differentiated and assigned roles according to their structural properties and genomic contexts. The absence of asparagine synthetase and the presence of a mutant tRNA for asparagine encoded among RNA-active enzymes suggest that P. carbinolicus may make asparaginyl-tRNA in a novel way. Catabolic glutamate dehydrogenases were discovered, implying that the tricarboxylic acid (TCA) cycle can function catabolically. A phosphotransferase system for uptake of sugars was discovered, along with enzymes that function in 2,3-butanediol production. Pyruvate:ferredoxin/flavodoxin oxidoreductase was identified as a potential bottleneck in both the supply of oxaloacetate for oxidation of acetate by the TCA cycle and the connection of glycolysis to production of ethanol. The P. carbinolicus genome was found to encode autotransporters and various appendages, including three proteins with similarity to the geopilin of electroconductive nanowires. CONCLUSIONS: Several surprising metabolic capabilities and physiological features were predicted from the genome of P. carbinolicus, suggesting that it is more versatile than anticipated.


Assuntos
Butileno Glicóis/metabolismo , Deltaproteobacteria/genética , Genoma Bacteriano/genética , Redes e Vias Metabólicas/genética , Pareamento de Bases , Sequência de Bases , Colina/metabolismo , Deltaproteobacteria/metabolismo , Etanolamina/metabolismo , Etilenoglicol/metabolismo , Glicerol/metabolismo , Anotação de Sequência Molecular , Dados de Sequência Molecular , Mutação/genética , Oxirredução , Oxirredutases/genética , Propilenoglicóis/metabolismo , RNA de Transferência de Asparagina/genética , Análise de Sequência de DNA
18.
Nucleic Acids Res ; 40(11): 4965-76, 2012 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-22362756

RESUMO

Helicobacter pylori catalyzes Asn-tRNA(Asn) formation by use of the indirect pathway that involves charging of Asp onto tRNA(Asn) by a non-discriminating aspartyl-tRNA synthetase (ND-AspRS), followed by conversion of the mischarged Asp into Asn by the GatCAB amidotransferase. We show that the partners of asparaginylation assemble into a dynamic Asn-transamidosome, which uses a different strategy than the Gln-transamidosome to prevent the release of the mischarged aminoacyl-tRNA intermediate. The complex is described by gel-filtration, dynamic light scattering and kinetic measurements. Two strategies for asparaginylation are shown: (i) tRNA(Asn) binds GatCAB first, allowing aminoacylation and immediate transamidation once ND-AspRS joins the complex; (ii) tRNA(Asn) is bound by ND-AspRS which releases the Asp-tRNA(Asn) product much slower than the cognate Asp-tRNA(Asp); this kinetic peculiarity allows GatCAB to bind and transamidate Asp-tRNA(Asn) before its release by the ND-AspRS. These results are discussed in the context of the interrelation between the Asn and Gln-transamidosomes which use the same GatCAB in H. pylori, and shed light on a kinetic mechanism that ensures faithful codon reassignment for Asn.


Assuntos
Aspartato-tRNA Ligase/metabolismo , Helicobacter pylori/enzimologia , Transferases de Grupos Nitrogenados/metabolismo , RNA de Transferência de Asparagina/metabolismo , Aminoacilação de RNA de Transferência , Asparagina/metabolismo , Ácido Aspártico/metabolismo , Código Genético , Cinética , RNA de Transferência de Ácido Aspártico/metabolismo
19.
Eur J Hum Genet ; 20(3): 357-60, 2012 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-22189266

RESUMO

Although mutations in mitochondrial tRNAs constitute the most common mtDNA defect, the presence of pathological variants in mitochondrial tRNA(Asn) is extremely rare. We were able to identify a novel mtDNA tRNA(Asn) gene pathogenic mutation associated with a myopathic phenotype and a previously unreported respiratory impairment. Our proband is an adult woman with ophthalmoparesis and respiratory impairment. Her muscle biopsy presented several cytochrome c oxidase-negative (COX-) fibres and signs of mitochondrial proliferation (ragged red fibres). Sequence analysis of the muscle-derived mtDNA revealed an m.5709T>C substitution, affecting mitochondrial tRNA(Asn) gene. Restriction-fragment length polymorphism analysis of the mutation in isolated muscle fibres showed that a threshold of at least 91.9% mutated mtDNA results in the COX deficiency phenotype. The new phenotype further increases the clinical spectrum of mitochondrial diseases caused by mutations in the tRNA(Asn) gene.


Assuntos
Mutação , Oftalmoplegia/genética , RNA de Transferência de Asparagina/genética , RNA/genética , Sequência de Bases , Complexo IV da Cadeia de Transporte de Elétrons/genética , Feminino , Humanos , Pessoa de Meia-Idade , Miopatias Mitocondriais/diagnóstico , Miopatias Mitocondriais/genética , Fibras Musculares Esqueléticas/enzimologia , Oftalmoplegia/diagnóstico , Fenótipo , RNA Mitocondrial , Alinhamento de Sequência
20.
Biochem Biophys Res Commun ; 412(4): 518-21, 2011 Sep 09.
Artigo em Inglês | MEDLINE | ID: mdl-21741368

RESUMO

We report an 11-year-old boy with exercise-related myopathy, and a novel mutation m.5669G>A in the mitochondrial tRNA Asparagine gene (mt-tRNA(Asn), MTTN). Muscle biopsy studies showed COX-negative, SDH-positive fibers at histochemistry and biochemical defects of oxidative metabolism. The m.5669G>A mutation was present only in patient's muscle resulting in the first muscle-specific MTTN mutation. Mt-tRNA(Asn) steady-state levels and in silico predictions supported the pathogenicity of this mutation. A mitochondrial myopathy should be considered in the differential diagnosis of exercise intolerance in children.


Assuntos
DNA Mitocondrial/genética , Mitocôndrias Musculares/genética , Miopatias Mitocondriais/genética , Músculo Esquelético/metabolismo , RNA de Transferência de Asparagina/genética , RNA/genética , Sequência de Bases , Criança , Tolerância ao Exercício/genética , Humanos , Masculino , Miopatias Mitocondriais/patologia , Miopatias Mitocondriais/fisiopatologia , Dados de Sequência Molecular , Debilidade Muscular/genética , Debilidade Muscular/patologia , Músculo Esquelético/patologia , Conformação de Ácido Nucleico , RNA/química , RNA Mitocondrial , RNA de Transferência de Asparagina/química
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