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1.
Nat Struct Mol Biol ; 31(5): 810-816, 2024 May.
Artigo em Inglês | MEDLINE | ID: mdl-38538914

RESUMO

The frequency of errors upon decoding of messenger RNA by the bacterial ribosome is low, with one misreading event per 1 × 104 codons. In the universal genetic code, the AUN codon box specifies two amino acids, isoleucine and methionine. In bacteria and archaea, decoding specificity of the AUA and AUG codons relies on the wobble avoidance strategy that requires modification of C34 in the anticodon loop of isoleucine transfer RNAIleCAU (tRNAIleCAU). Bacterial tRNAIleCAU with 2-lysylcytidine (lysidine) at the wobble position deciphers AUA while avoiding AUG. Here we report cryo-electron microscopy structures of the Escherichia coli 70S ribosome complexed with elongation factor thermo unstable (EF-Tu) and isoleucine-tRNAIleLAU in the process of decoding AUA and AUG. Lysidine in tRNAIleLAU excludes AUG by promoting the formation of an unusual Hoogsteen purine-pyrimidine nucleobase geometry at the third position of the codon, weakening the interactions with the mRNA and destabilizing the EF-Tu ternary complex. Our findings elucidate the molecular mechanism by which tRNAIleLAU specifically decodes AUA over AUG.


Assuntos
Microscopia Crioeletrônica , Escherichia coli , Modelos Moleculares , Fator Tu de Elongação de Peptídeos , RNA de Transferência de Isoleucina , Ribossomos , Fator Tu de Elongação de Peptídeos/metabolismo , Fator Tu de Elongação de Peptídeos/química , Fator Tu de Elongação de Peptídeos/genética , Escherichia coli/metabolismo , Escherichia coli/genética , Ribossomos/metabolismo , Ribossomos/ultraestrutura , Ribossomos/química , RNA de Transferência de Isoleucina/metabolismo , RNA de Transferência de Isoleucina/química , RNA de Transferência de Isoleucina/genética , Códon/metabolismo , Códon/genética , Anticódon/química , Anticódon/metabolismo , Conformação de Ácido Nucleico , Isoleucina/metabolismo , Isoleucina/química , RNA Mensageiro/metabolismo , RNA Mensageiro/química , RNA Mensageiro/genética , Lisina/análogos & derivados , Nucleosídeos de Pirimidina
2.
Nat Struct Mol Biol ; 31(5): 817-825, 2024 May.
Artigo em Inglês | MEDLINE | ID: mdl-38538915

RESUMO

The anticodon modifications of transfer RNAs (tRNAs) finetune the codon recognition on the ribosome for accurate translation. Bacteria and archaea utilize the modified cytidines, lysidine (L) and agmatidine (agm2C), respectively, in the anticodon of tRNAIle to decipher AUA codon. L and agm2C contain long side chains with polar termini, but their functions remain elusive. Here we report the cryogenic electron microscopy structures of tRNAsIle recognizing the AUA codon on the ribosome. Both modifications interact with the third adenine of the codon via a unique C-A geometry. The side chains extend toward 3' direction of the mRNA, and the polar termini form hydrogen bonds with 2'-OH of the residue 3'-adjacent to the AUA codon. Biochemical analyses demonstrated that AUA decoding is facilitated by the additional interaction between the polar termini of the modified cytidines and 2'-OH of the fourth mRNA residue. We also visualized cyclic N6-threonylcarbamoyladenosine (ct6A), another tRNA modification, and revealed a molecular basis how ct6A contributes to efficient decoding.


Assuntos
Anticódon , Microscopia Crioeletrônica , RNA de Transferência de Isoleucina , RNA de Transferência de Isoleucina/química , RNA de Transferência de Isoleucina/metabolismo , RNA de Transferência de Isoleucina/genética , Anticódon/química , Anticódon/metabolismo , Ribossomos/metabolismo , Ribossomos/química , Conformação de Ácido Nucleico , Modelos Moleculares , Códon/genética , Lisina/metabolismo , Lisina/química , Lisina/análogos & derivados , Citidina/análogos & derivados , Citidina/química , Citidina/metabolismo , RNA de Transferência/metabolismo , RNA de Transferência/química , RNA de Transferência/genética , Biossíntese de Proteínas , Nucleosídeos de Pirimidina
3.
FEBS J ; 289(16): 4888-4900, 2022 08.
Artigo em Inglês | MEDLINE | ID: mdl-35122395

RESUMO

In almost all eubacteria, the AUA codon is translated by tRNAIle2 bearing lysidine at the wobble position. Lysidine is introduced by tRNAIle lysidine synthetase (TilS) via post-transcriptional modification of the cytidine of tRNAIle2 (CAU). Lactobacillus casei and Lactobacillus plantarum have tilS homologues and tRNAIle2 (CAU) genes. In addition, L. casei also has another tRNAIle2 gene with an UAU anticodon. L. plantarum has a tRNAIle (UAU)-like RNA. Here, we demonstrate that L. casei tRNAIle2 (UAU) is charged with isoleucine by L. casei isoleucyl-tRNA synthetase (IleRS) but not by L. plantarum IleRS, even though the amino acid identity of these two enzymes is over 60%. It has been reported that, in Mycoplasma mobile, which has its tRNAIle2 (UAU) but no tilS homologue, an Arg residue at position 865 of the IleRS is required for recognition of the UAU anticodon. This position is occupied by an Arg also in the IleRSs from both of the Lactobacillus species. Thus, other residues in L. casei, IleRS should also contribute to the recognition of tRNAIle2 (UAU). We found that a chimeric L. casei IleRS in which the N-terminal domain was replaced by the corresponding region of L. plantatarum IleRS has very low aminoacylation activity towards both tRNAIle2 (UAU) and tRNAIle1 (GAU). The A18G mutant had barely detectable aminoacylation activity towards either of the tRNAsIle . However, a double point mutant of A18G and G19N aminoacylated tRNAIle1 (GAU), but not tRNAIle2 (UAU). Our results suggest that, for L. casei IleRS, Ala18 and Gly19 also play a critical role in recognition of tRNAIle2 (UAU).


Assuntos
Anticódon , Lactobacillales , Anticódon/genética , Isoleucina/genética , Isoleucina-tRNA Ligase/química , Lactobacillales/genética , Lactobacillales/metabolismo , RNA de Transferência/química , RNA de Transferência/genética , RNA de Transferência de Isoleucina/química , RNA de Transferência de Isoleucina/genética , RNA de Transferência de Isoleucina/metabolismo
4.
Nucleic Acids Res ; 49(18): 10677-10688, 2021 10 11.
Artigo em Inglês | MEDLINE | ID: mdl-34551428

RESUMO

Aside from providing adaptive immunity, type I CRISPR-Cas was recently unearthed to employ a noncanonical RNA guide (CreA) to transcriptionally repress an RNA toxin (CreT). Here, we report that, for most archaeal and bacterial CreTA modules, the creA gene actually carries two flanking 'CRISPR repeats', which are, however, highly divergent and degenerated. By deep sequencing, we show that the two repeats give rise to an 8-nt 5' handle and a 22-nt 3' handle, respectively, i.e., the conserved elements of a canonical CRISPR RNA, indicating they both retained critical nucleotides for Cas6 processing during divergent degeneration. We also uncovered a minimal CreT toxin that sequesters the rare transfer RNA for isoleucine, tRNAIleCAU, with a six-codon open reading frame containing two consecutive AUA codons. To fully relieve its toxicity, both tRNAIleCAU overexpression and supply of extra agmatine (modifies the wobble base of tRNAIleCAU to decipher AUA codons) are required. By replacing AUA to AGA/AGG codons, we reprogrammed this toxin to sequester rare arginine tRNAs. These data provide essential information on CreTA origin and for future CreTA prediction, and enrich the knowledge of tRNA-sequestering small RNAs that are employed by CRISPR-Cas to get addictive to the host.


Assuntos
Toxinas Bacterianas/metabolismo , Sistemas CRISPR-Cas , Haloarcula/genética , Halobacterium/genética , Pequeno RNA não Traduzido/metabolismo , RNA de Transferência de Isoleucina/metabolismo , Toxinas Bacterianas/química , Toxinas Bacterianas/genética , Engenharia Celular , Genes Arqueais , Genes Bacterianos , Biossíntese de Proteínas , Pequeno RNA não Traduzido/química , Pequeno RNA não Traduzido/genética , RNA de Transferência de Arginina/metabolismo
5.
Nat Struct Mol Biol ; 26(12): 1114-1122, 2019 12.
Artigo em Inglês | MEDLINE | ID: mdl-31792448

RESUMO

T-box riboswitches are modular bacterial noncoding RNAs that sense and regulate amino acid availability through direct interactions with tRNAs. Between the 5' anticodon-binding stem I domain and the 3' amino acid sensing domains of most T-boxes lies the stem II domain of unknown structure and function. Here, we report a 2.8-Å cocrystal structure of the Nocardia farcinica ileS T-box in complex with its cognate tRNAIle. The structure reveals a perpendicularly arranged ultrashort stem I containing a K-turn and an elongated stem II bearing an S-turn. Both stems rest against a compact pseudoknot, dock via an extended ribose zipper and jointly create a binding groove specific to the anticodon of its cognate tRNA. Contrary to proposed distal contacts to the tRNA elbow region, stem II locally reinforces the codon-anticodon interactions between stem I and tRNA, achieving low-nanomolar affinity. This study illustrates how mRNA junctions can create specific binding sites for interacting RNAs of prescribed sequence and structure.


Assuntos
Proteínas de Bactérias/genética , Regulação Bacteriana da Expressão Gênica , Isoleucina-tRNA Ligase/genética , Nocardia/genética , Motivos de Nucleotídeos , RNA Bacteriano/química , RNA de Transferência de Isoleucina/química , Riboswitch/genética , Sítios de Ligação , Cristalografia por Raios X , Modelos Moleculares , RNA Bacteriano/metabolismo , RNA de Transferência de Isoleucina/metabolismo , Relação Estrutura-Atividade
6.
Nucleic Acids Res ; 46(15): 7873-7885, 2018 09 06.
Artigo em Inglês | MEDLINE | ID: mdl-29931259

RESUMO

Prokaryotic toxin-antitoxin (TA) modules are highly abundant and are involved in stress response and drug tolerance. The most common type II TA modules consist of two interacting proteins. The type II toxins are diverse enzymes targeting various essential intracellular targets. The antitoxin binds to cognate toxin and inhibits its function. Recently, TA modules whose toxins are GNAT-family acetyltransferases were described. For two such systems, the target of acetylation was shown to be aminoacyl-tRNA: the TacT toxin targets aminoacylated elongator tRNAs, while AtaT targets the amino acid moiety of initiating tRNAMet. We show that the itaRT gene pair from Escherichia coli encodes a TA module with acetyltransferase toxin ItaT that specifically and exclusively acetylates Ile-tRNAIle thereby blocking translation and inhibiting cell growth. ItaT forms a tight complex with the ItaR antitoxin, which represses the transcription of itaRT operon. A comprehensive bioinformatics survey of GNAT acetyltransferases reveals that enzymes encoded by validated or putative TA modules are common and form a distinct branch of the GNAT family tree. We speculate that further functional analysis of such TA modules will result in identification of enzymes capable of specifically targeting many, perhaps all, aminoacyl tRNAs.


Assuntos
Acetiltransferases/genética , Antitoxinas/genética , Toxinas Bacterianas/genética , Proteínas de Escherichia coli/genética , RNA de Transferência de Isoleucina/genética , Acetilação , Acetiltransferases/metabolismo , Antitoxinas/metabolismo , Toxinas Bacterianas/metabolismo , Proteínas de Escherichia coli/metabolismo , Biossíntese de Proteínas/genética , Processamento de Proteína Pós-Traducional , RNA de Transferência de Isoleucina/metabolismo , RNA de Transferência de Metionina/genética , RNA de Transferência de Metionina/metabolismo
7.
J Biochem ; 163(3): 233-241, 2018 Mar 01.
Artigo em Inglês | MEDLINE | ID: mdl-29092074

RESUMO

In most eubacteria, the minor AUA isoleucine codon is decoded by tRNAIle2, which has a lysidine (L) in the anticodon loop. The lysidine is introduced by tRNAIle-lysidine synthetase (TilS) through post-transcriptional modification of cytidine to yield an LAU anticodon. Some bacteria, Lactobacillus plantarum for example, possess two tRNAIle2(UAU) genes in addition to, two tRNAIle2(CAU) genes and the tilS gene. tRNA expression from all these genes would generate redundancy in a tRNA that decodes a rare AUA codon. In this study, we investigated the tRNA expression from these genes in L. plantarum and characterized the corresponding tRNAs. The tRNAIle2(CAU) gene products are modified by TilS to produce tRNAIle2(LAU), while tRNAIle2(UAU) lacks modification especially in the anticodon sequence. We found that tRNAIle2(LAU) is charged with isoleucine but tRNAIle2(UAU) is not. Our results suggest that the tRNAIle2 redundancy may be related to different roles of these tRNAs in the cell.


Assuntos
Anticódon/genética , Lactobacillus plantarum/genética , RNA de Transferência de Isoleucina/genética , Anticódon/metabolismo , Isoleucina/metabolismo , Lactobacillus plantarum/metabolismo , RNA de Transferência de Isoleucina/metabolismo , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz
8.
Mol Cell ; 63(1): 110-24, 2016 07 07.
Artigo em Inglês | MEDLINE | ID: mdl-27345152

RESUMO

The Lupus autoantigen La is an RNA-binding protein that stabilizes RNA polymerase III (Pol III) transcripts and supports RNA folding and has in addition been implicated in the mammalian microRNA (miRNA) pathway. Here, we have analyzed effects of La depletion on Argonaute (Ago)-bound small RNAs in human cells. We find that in the absence of La, distinct tRNA fragments are loaded into Ago proteins. Thus, La functions as gatekeeper ensuring correct tRNA maturation and protecting the miRNA pathway from potentially functional tRNA fragments. However, one specific isoleucin pre-tRNA produces both a functional tRNA and a miRNA even when La is present. We demonstrate that the fully complementary 5' leader and 3' trailer of the pre-tRNA-Ile form a double-stranded RNA molecule that has low affinity to La. Instead, Exportin-5 (Xpo5) recognizes it as miRNA precursor and transports it into the cytoplasm for Dicer processing and Ago loading.


Assuntos
Autoantígenos/metabolismo , MicroRNAs/metabolismo , Precursores de RNA/metabolismo , Processamento Pós-Transcricional do RNA , RNA de Transferência de Isoleucina/metabolismo , Ribonucleoproteínas/metabolismo , Células A549 , Proteínas Argonautas/metabolismo , Autoantígenos/genética , Sítios de Ligação , RNA Helicases DEAD-box/metabolismo , Células HEK293 , Células HeLa , Células Hep G2 , Herpesvirus Humano 4/genética , Herpesvirus Humano 4/metabolismo , Humanos , Carioferinas/metabolismo , Células MCF-7 , MicroRNAs/genética , Conformação de Ácido Nucleico , Ligação Proteica , Interferência de RNA , RNA Polimerase III/metabolismo , Precursores de RNA/química , Precursores de RNA/genética , RNA de Transferência de Isoleucina/química , RNA de Transferência de Isoleucina/genética , RNA Viral/genética , RNA Viral/metabolismo , Ribonuclease III/metabolismo , Ribonucleoproteínas/genética , Relação Estrutura-Atividade , Transfecção , Antígeno SS-B
9.
PLoS One ; 11(4): e0154044, 2016.
Artigo em Inglês | MEDLINE | ID: mdl-27101286

RESUMO

In the current concept, tRNA maturation in vertebrate cells, including splicing of introns, trimming of 5' leader and 3' trailer, and adding of CCA, is thought to occur exclusively in the nucleus. Here we provide evidence to challenge this concept. Unspliced intron-containing precursor tRNAIle was identified in Human Immunodeficiency Virus type 1 (HIV-1) virions, which are synthesized in the cytoplasm. Northern blot, confocal microscopy and quantitative RT-PCR further verified enrichment of this unspliced tRNAIle within the cytoplasm in human cells. In addition to containing an intron, the cytoplasmic precursor tRNAIle also contains a short incompletely processed 5´ leader and a 3´ trailer, which abundance is around 1000 fold higher than the nuclear precursor tRNAIle with long 5' leader and long 3' trailer. In vitro data also suggest that the cytoplasmic unspliced end-immature precursor tRNAIle could be processed by short isoform of RNase Z, but not long isoform of RNase Z. These data suggest that precursor tRNAs could export from the nucleus to the cytoplasm in human cells, instead of be processed only in the nucleus.


Assuntos
Núcleo Celular/metabolismo , Citoplasma/metabolismo , Precursores de RNA/metabolismo , RNA de Transferência de Isoleucina/metabolismo , Transporte Biológico , Genes Virais , HIV-1/genética , Humanos , Íntrons , Processamento Pós-Transcricional do RNA , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Vírion/genética
10.
Plant Physiol ; 169(1): 627-46, 2015 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-26152711

RESUMO

Plastid gene expression is crucial for organelle function, but the factors that control it are still largely unclear. Members of the so-called mitochondrial transcription termination factor (mTERF) family are found in metazoans and plants and regulate organellar gene expression at different levels. Arabidopsis (Arabidopsis thaliana) mTERF6 is localized in chloroplasts and mitochondria, and its knockout perturbs plastid development and results in seedling lethality. In the leaky mterf6-1 mutant, a defect in photosynthesis is associated with reduced levels of photosystem subunits, although corresponding messenger RNA levels are unaffected, whereas translational capacity and maturation of chloroplast ribosomal RNAs (rRNAs) are perturbed in mterf6-1 mutants. Bacterial one-hybrid screening, electrophoretic mobility shift assays, and coimmunoprecipitation experiments reveal a specific interaction between mTERF6 and an RNA sequence in the chloroplast isoleucine transfer RNA gene (trnI.2) located in the rRNA operon. In vitro, recombinant mTERF6 bound to its plastid DNA target site can terminate transcription. At present, it is unclear whether disturbed rRNA maturation is a primary or secondary defect. However, it is clear that mTERF6 is required for the maturation of trnI.2. This points to an additional function of mTERFs.


Assuntos
Proteínas de Arabidopsis/metabolismo , Arabidopsis/metabolismo , Fatores de Transcrição de Zíper de Leucina Básica/metabolismo , Cloroplastos/metabolismo , Mitocôndrias/metabolismo , Proteínas Mitocondriais/metabolismo , RNA de Transferência de Isoleucina/metabolismo , Terminação da Transcrição Genética , Regiões 5' não Traduzidas/genética , Aminoacilação , Arabidopsis/genética , Proteínas de Arabidopsis/genética , Sequência de Bases , Fatores de Transcrição de Zíper de Leucina Básica/genética , DNA Bacteriano/genética , Regulação da Expressão Gênica de Plantas , Loci Gênicos , Proteínas Mitocondriais/genética , Dados de Sequência Molecular , Mutagênese Insercional/genética , Mutação , Fenótipo , Fotossíntese , Ligação Proteica , Transporte Proteico , Processamento Pós-Transcricional do RNA , RNA Ribossômico/genética , RNA de Transferência de Isoleucina/química , RNA de Transferência de Isoleucina/genética , Ribossomos/metabolismo , Plântula/metabolismo , Sementes/ultraestrutura
11.
FEBS Lett ; 589(16): 2124-30, 2015 Jul 22.
Artigo em Inglês | MEDLINE | ID: mdl-26143376

RESUMO

Protozoan mitochondrial tRNAs (mt-tRNAs) are repaired by a process known as 5'-editing. Mt-tRNA sequencing revealed organism-specific patterns of editing G-U base pairs, wherein some species remove G-U base pairs during 5'-editing, while others retain G-U pairs in the edited tRNA. We tested whether 3'-5' polymerases that catalyze the repair step of 5'-editing exhibit organism-specific preferences that explain the treatment of G-U base pairs. Biochemical and kinetic approaches revealed that a 3'-5' polymerase from Acanthamoeba castellanii tolerates G-U wobble pairs in editing substrates much more readily than several other enzymes, consistent with its biological pattern of editing.


Assuntos
Acanthamoeba castellanii/enzimologia , Mitocôndrias/enzimologia , Proteínas de Protozoários/metabolismo , Edição de RNA , RNA Nucleotidiltransferases/metabolismo , RNA de Protozoário/metabolismo , RNA de Transferência/metabolismo , Acanthamoeba castellanii/metabolismo , Dictyostelium/enzimologia , Dictyostelium/metabolismo , Eletroforese em Gel de Poliacrilamida , Isoenzimas/genética , Isoenzimas/metabolismo , Marcação por Isótopo , Cinética , Mitocôndrias/metabolismo , Modelos Moleculares , Radioisótopos de Fósforo , Proteínas de Protozoários/genética , RNA Nucleotidiltransferases/genética , RNA de Protozoário/química , RNA de Transferência/química , RNA de Transferência de Isoleucina/química , RNA de Transferência de Isoleucina/metabolismo , Proteínas Recombinantes/metabolismo , Especificidade da Espécie , Especificidade por Substrato
12.
Biochemistry ; 53(39): 6189-98, 2014 Oct 07.
Artigo em Inglês | MEDLINE | ID: mdl-25207837

RESUMO

The accurate expression of genetic information relies on the fidelity of amino acid-tRNA coupling by aminoacyl-tRNA synthetases (aaRS). When the specificity against structurally similar noncognate amino acids in the synthetic reaction does not support a threshold fidelity level for translation, the aaRS employ intrinsic hydrolytic editing to correct errors in aminoacylation. Escherichia coli isoleucyl-tRNA synthetase (EcIleRS) is a class I aaRS that is notable for its use of tRNA-dependent pretransfer editing to hydrolyze noncognate valyl-adenylate prior to aminoacyl-tRNA formation. On the basis of the finding that IleRS possessing an inactivated post-transfer editing domain is still capable of robust tRNA-dependent editing, we have recently proposed that the pretransfer editing activity resides within the synthetic site. Here we apply an improved methodology that allows quantitation of the AMP fraction that arises particularly from tRNA-dependent aa-AMP hydrolysis. By this approach, we demonstrate that tRNA-dependent pretransfer editing accounts for nearly one-third of the total proofreading by EcIleRS and that a highly conserved tyrosine within the synthetic site modulates both editing and aminoacylation. Therefore, synthesis of aminoacyl-tRNA and hydrolysis of aminoacyl-adenylates employ overlapping amino acid determinants. We suggest that this overlap hindered the evolution of synthetic site-based pretransfer editing as the predominant proofreading pathway, because that activity is difficult to accommodate in the context of efficient aminoacyl-tRNA synthesis. Instead, the acquisition of a spatially separate domain dedicated to post-transfer editing alone allowed for the development of a powerful deacylation machinery that effectively competes with dissociation of misacylated tRNAs.


Assuntos
Proteínas de Escherichia coli/metabolismo , Isoleucina-tRNA Ligase/metabolismo , Edição de RNA , RNA de Transferência/metabolismo , Sequência de Aminoácidos , Sítios de Ligação/genética , Vias Biossintéticas/genética , Escherichia coli/genética , Escherichia coli/metabolismo , Proteínas de Escherichia coli/química , Proteínas de Escherichia coli/genética , Hidrólise , Isoleucina-tRNA Ligase/química , Isoleucina-tRNA Ligase/genética , Cinética , Modelos Moleculares , Dados de Sequência Molecular , Ligação Proteica , Estrutura Terciária de Proteína , RNA de Transferência/química , RNA de Transferência/genética , RNA de Transferência de Isoleucina/química , RNA de Transferência de Isoleucina/genética , RNA de Transferência de Isoleucina/metabolismo , Homologia de Sequência de Aminoácidos , Aminoacilação de RNA de Transferência , Tirosina/genética , Tirosina/metabolismo
13.
BMC Med Genet ; 15: 84, 2014 Jul 23.
Artigo em Inglês | MEDLINE | ID: mdl-25056089

RESUMO

BACKGROUND: Hypertension is a very common cardiovascular disease influenced by multiple genetic and environmental factors. More recently, there are some studies showed that mutations in mitochondrial DNA have been involved in its pathogenesis. In this study we did further investigations on this relationship. METHODS: Epidemiological research found a Han Chinese family with probable maternally transmitted hypertension. Sequence analysis of the whole mitochondrial DNA was detected from all the family members. And evaluations of the clinical, genetic and molecular characterization were also performed. RESULTS: Matrilineal relatives within the family exhibited varying degrees of hypertension with an onset age of 48-55 years. Sequence analysis of this pedigree showed a novel homoplasmic 4329C > G mutation located at the 3' end of the tRNAIle and tRNAGln genes that was absent from 366 Chinese controls. The cytosine (C) at 4329 position was very important in the structural formation and stabilization of functional tRNAs, which was highly conserved in mitochondria of various organisms and also contributed to the high fidelity of the acceptor arm. Cells carrying this mutation were also shown to harbor mitochondrial dysfunctions. CONCLUSIONS: The C4329G point mutation in tRNAIle and tRNAGln was involved in the pathogenesis of hypertension, perhaps in association with other modifying factors.


Assuntos
Citosina/metabolismo , DNA Mitocondrial/genética , Guanina/metabolismo , Hipertensão/genética , RNA de Transferência de Glutamina/genética , RNA de Transferência de Isoleucina/genética , Povo Asiático/genética , Estudos de Casos e Controles , Feminino , Predisposição Genética para Doença , Variação Genética , Humanos , Hipertensão/epidemiologia , Masculino , Pessoa de Meia-Idade , Mitocôndrias/genética , Linhagem , Mutação Puntual , RNA de Transferência de Glutamina/metabolismo , RNA de Transferência de Isoleucina/metabolismo
14.
FEMS Microbiol Lett ; 351(2): 133-44, 2014 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-24433543

RESUMO

One of the major challenges in contemporary synthetic biology is to find a route to engineer synthetic organisms with altered chemical constitution. In terms of core reaction types, nature uses an astonishingly limited repertoire of chemistries when compared with the exceptionally rich and diverse methods of organic chemistry. In this context, the most promising route to change and expand the fundamental chemistry of life is the inclusion of amino acid building blocks beyond the canonical 20 (i.e. expanding the genetic code). This strategy would allow the transfer of numerous chemical functionalities and reactions from the synthetic laboratory into the cellular environment. Due to limitations in terms of both efficiency and practical applicability, state-of-the-art nonsense suppression- or frameshift suppression-based methods are less suitable for such engineering. Consequently, we set out to achieve this goal by sense codon emancipation, that is, liberation from its natural decoding function - a prerequisite for the reassignment of degenerate sense codons to a new 21st amino acid. We have achieved this by redesigning of several features of the post-transcriptional modification machinery which are directly involved in the decoding process. In particular, we report first steps towards the reassignment of 5797 AUA isoleucine codons in Escherichia coli using efficient tools for tRNA nucleotide modification pathway engineering.


Assuntos
Aminoácidos/genética , Códon , Código Genético , Engenharia Metabólica/métodos , Biossíntese de Proteínas , Escherichia coli/genética , Escherichia coli/metabolismo , RNA de Transferência de Isoleucina/genética , RNA de Transferência de Isoleucina/metabolismo
15.
RNA ; 20(2): 177-88, 2014 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-24344322

RESUMO

Most archaea and bacteria use a modified C in the anticodon wobble position of isoleucine tRNA to base pair with A but not with G of the mRNA. This allows the tRNA to read the isoleucine codon AUA without also reading the methionine codon AUG. To understand why a modified C, and not U or modified U, is used to base pair with A, we mutated the C34 in the anticodon of Haloarcula marismortui isoleucine tRNA (tRNA2(Ile)) to U, expressed the mutant tRNA in Haloferax volcanii, and purified and analyzed the tRNA. Ribosome binding experiments show that although the wild-type tRNA2(Ile) binds exclusively to the isoleucine codon AUA, the mutant tRNA binds not only to AUA but also to AUU, another isoleucine codon, and to AUG, a methionine codon. The G34 to U mutant in the anticodon of another H. marismortui isoleucine tRNA species showed similar codon binding properties. Binding of the mutant tRNA to AUG could lead to misreading of the AUG codon and insertion of isoleucine in place of methionine. This result would explain why most archaea and bacteria do not normally use U or a modified U in the anticodon wobble position of isoleucine tRNA for reading the codon AUA. Biochemical and mass spectrometric analyses of the mutant tRNAs have led to the discovery of a new modified nucleoside, 5-cyanomethyl U in the anticodon wobble position of the mutant tRNAs. 5-Cyanomethyl U is present in total tRNAs from euryarchaea but not in crenarchaea, eubacteria, or eukaryotes.


Assuntos
Anticódon/genética , Haloarcula marismortui/genética , RNA Arqueal/genética , RNA de Transferência de Isoleucina/genética , Uridina/análogos & derivados , Pareamento de Bases , Sequência de Bases , Códon/genética , Escherichia coli/genética , Haloferax/genética , Estrutura Molecular , Mutação Puntual , RNA Arqueal/química , RNA Arqueal/metabolismo , RNA Bacteriano/genética , RNA Fúngico/genética , RNA de Transferência de Isoleucina/química , RNA de Transferência de Isoleucina/metabolismo , Ribossomos/química , Saccharomyces cerevisiae/genética , Sulfolobus/genética , Aminoacilação de RNA de Transferência , Uridina/química , Uridina/genética
16.
Nucleic Acids Res ; 42(3): 1904-15, 2014 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-24194599

RESUMO

Translation of the isoleucine codon AUA in most prokaryotes requires a modified C (lysidine or agmatidine) at the wobble position of tRNA2(Ile) to base pair specifically with the A of the AUA codon but not with the G of AUG. Recently, a Bacillus subtilis strain was isolated in which the essential gene encoding tRNA(Ile)-lysidine synthetase was deleted for the first time. In such a strain, C34 at the wobble position of tRNA2(Ile) is expected to remain unmodified and cells depend on a mutant suppressor tRNA derived from tRNA1(Ile), in which G34 has been changed to U34. An important question, therefore, is how U34 base pairs with A without also base pairing with G. Here, we show (i) that unlike U34 at the wobble position of all B. subtilis tRNAs of known sequence, U34 in the mutant tRNA is not modified, and (ii) that the mutant tRNA binds strongly to the AUA codon on B. subtilis ribosomes but only weakly to AUG. These in vitro data explain why the suppressor strain displays only a low level of misreading AUG codons in vivo and, as shown here, grows at a rate comparable to that of the wild-type strain.


Assuntos
Bacillus subtilis/genética , Códon , Isoleucina/metabolismo , Biossíntese de Proteínas , RNA de Transferência de Isoleucina/química , RNA de Transferência de Isoleucina/metabolismo , Aminoacil-tRNA Sintetases/genética , Bacillus subtilis/crescimento & desenvolvimento , Deleção de Genes , Fenótipo , RNA de Transferência de Isoleucina/isolamento & purificação , Ribossomos/metabolismo , Aminoacilação de RNA de Transferência
17.
J Biol Chem ; 288(27): 19625-32, 2013 Jul 05.
Artigo em Inglês | MEDLINE | ID: mdl-23696642

RESUMO

Recognition strategies for tRNA aminoacylation are ancient and highly conserved, having been selected very early in the evolution of the genetic code. In most cases, the trinucleotide anticodons of tRNA are important identity determinants for aminoacylation by cognate aminoacyl-tRNA synthetases. However, a degree of ambiguity exists in the recognition of certain tRNA(Ile) isoacceptors that are initially transcribed with the methionine-specifying CAU anticodon. In most organisms, the C34 wobble position in these tRNA(Ile) precursors is rapidly modified to lysidine to prevent recognition by methionyl-tRNA synthetase (MRS) and production of a chimeric Met-tRNA(Ile) that would compromise translational fidelity. In certain bacteria, however, lysidine modification is not required for MRS rejection, indicating that this recognition strategy is not universally conserved and may be relatively recent. To explore the actual distribution of lysidine-dependent tRNA(Ile) rejection by MRS, we have investigated the ability of bacterial MRSs from different clades to differentiate cognate tRNACAU(Met) from near-cognate tRNACAU(Ile). Discrimination abilities vary greatly and appear unrelated to phylogenetic or structural features of the enzymes or sequence determinants of the tRNA. Our data indicate that tRNA(Ile) identity elements were established late and independently in different bacterial groups. We propose that the observed variation in MRS discrimination ability reflects differences in the evolution of genetic code machineries of emerging bacterial clades.


Assuntos
Anticódon , Bactérias , Proteínas de Bactérias , Evolução Molecular , Metionina tRNA Ligase , Aminoacil-RNA de Transferência , RNA de Transferência de Isoleucina , Anticódon/genética , Anticódon/metabolismo , Bactérias/enzimologia , Bactérias/genética , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Metionina tRNA Ligase/genética , Metionina tRNA Ligase/metabolismo , Aminoacil-RNA de Transferência/genética , Aminoacil-RNA de Transferência/metabolismo , RNA de Transferência de Isoleucina/genética , RNA de Transferência de Isoleucina/metabolismo
18.
Nat Struct Mol Biol ; 20(5): 641-3, 2013 May.
Artigo em Inglês | MEDLINE | ID: mdl-23542153

RESUMO

Decoding of the AUA isoleucine codon in bacteria and archaea requires modification of a C in the anticodon wobble position of the isoleucine tRNA. Here, we report the crystal structure of the archaeal tRNA2(Ile), which contains the modification agmatidine in its anticodon, in complex with the AUA codon on the 70S ribosome. The structure illustrates how agmatidine confers codon specificity for AUA over AUG.


Assuntos
Archaea/genética , Códon , Isoleucina/genética , Biossíntese de Proteínas , RNA de Transferência de Isoleucina/química , Ribossomos/química , Archaea/química , Archaea/metabolismo , Isoleucina/metabolismo , Modelos Moleculares , Conformação de Ácido Nucleico , RNA de Transferência de Isoleucina/metabolismo , Ribossomos/metabolismo
19.
Nucleic Acids Res ; 41(4): 2621-31, 2013 Feb 01.
Artigo em Inglês | MEDLINE | ID: mdl-23295668

RESUMO

Deciphering the genetic code is a fundamental process in all living organisms. In many bacteria, AUA codons are deciphered by tRNA(Ile2) bearing lysidine (L) at the wobble position. L is a modified cytidine introduced post-transcriptionally by tRNA(Ile)-lysidine synthetase (TilS). Some bacteria, including Mycoplasma mobile, do not carry the tilS gene, indicating that they have established a different system to decode AUA codons. In this study, tRNA(Ile2) has been isolated from M. mobile and was found to contain a UAU anticodon without any modification. Mycoplasma mobile isoleucyl-tRNA synthetase (IleRS) recognized the UAU anticodon, whereas Escherichia coli IleRS did not efficiently aminoacylate tRNA(Ile2)(UAU). In M. mobile IleRS, a single Arg residue at position 865 was critical for specificity for the UAU anticodon and, when the corresponding site (W905) in E. coli IleRS was substituted with Arg, the W905R mutant efficiently aminoacylated tRNA with UAU anticodon. Mycoplasma mobile tRNA(Ile2) cannot distinguish between AUA and AUG codon on E. coli ribosome. However, on M. mobile ribosome, M. mobile tRNA(Ile2)(UAU) specifically recognized AUA codon, and not AUG codon, suggesting M. mobile ribosome has a property that prevents misreading of AUG codon. These findings provide an insight into the evolutionary reorganization of the AUA decoding system.


Assuntos
Anticódon/química , Códon/química , Isoleucina-tRNA Ligase/química , Mycoplasma/genética , RNA de Transferência de Isoleucina/química , Sequência de Aminoácidos , Arginina/química , Isoleucina-tRNA Ligase/metabolismo , Cinética , Dados de Sequência Molecular , Mycoplasma/enzimologia , RNA de Transferência de Isoleucina/isolamento & purificação , RNA de Transferência de Isoleucina/metabolismo , Ribossomos/metabolismo , Alinhamento de Sequência
20.
Hum Mol Genet ; 21(1): 85-100, 2012 Jan 01.
Artigo em Inglês | MEDLINE | ID: mdl-21945886

RESUMO

The genetic and epigenetic factors underlying the variable penetrance of homoplasmic mitochondrial DNA mutations are poorly understood. We investigated a 16-year-old patient with hypertrophic cardiomyopathy harboring a homoplasmic m.4277T>C mutation in the mt-tRNA(Ile) (MTTI) gene. Skeletal muscle showed multiple respiratory chain enzyme abnormalities and a decreased steady-state level of the mutated mt-tRNA(Ile). Transmitochondrial cybrids grown on galactose medium demonstrated a functional effect of this mutation on cell viability, confirming pathogenicity. These findings were reproduced in transmitochondrial cybrids, harboring a previously described homoplasmic m.4300A>G MTTI mutation. The pathogenic role of the m.4277T>C mutation may be ascribed to misfolding of the mt-tRNA molecule, as demonstrated by the altered electrophoretic migration of the mutated mt-tRNA. Indeed, structure and sequence analyses suggest that thymidine at position 4277 of mt-tRNA(Ile) is involved in a conserved tertiary interaction with thymidine at position 4306. Interestingly, the mutation showed variable penetrance within family members, with skeletal muscle from the patient's clinically unaffected mother demonstrating normal muscle respiratory chain activities and steady-state levels of mt-tRNA(Ile), while homoplasmic for the m.4277T>C mutation. Analysis of mitochondrial isoleucyl-tRNA synthetase revealed significantly higher expression levels in skeletal muscle and fibroblasts of the unaffected mother when compared with the proband, while the transient over-expression of the IARS2 gene in patient transmitochondrial cybrids improved cell viability. This is the first observation that constitutively high levels of aminoacyl-tRNA synthetases (aaRSs) in human tissues prevent the phenotypic expression of a homoplasmic mt-tRNA point mutation. These findings extend previous observations on aaRSs therapeutic effects in yeast and human.


Assuntos
Cardiomiopatia Hipertrófica/enzimologia , Cardiomiopatia Hipertrófica/genética , Isoleucina-tRNA Ligase/metabolismo , Penetrância , Mutação Puntual , RNA de Transferência de Isoleucina/genética , Adolescente , Sequência de Bases , DNA Mitocondrial/genética , DNA Mitocondrial/metabolismo , Humanos , Isoleucina-tRNA Ligase/genética , Masculino , Mitocôndrias/genética , Mitocôndrias/metabolismo , Dados de Sequência Molecular , RNA de Transferência de Isoleucina/metabolismo
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