ABSTRACT
Gene translation depends on accurate decoding of mRNA, the structural mechanism of which remains poorly understood. Ribosomes decode mRNA codons by selecting cognate aminoacyl-tRNAs delivered by elongation factor Tu (EF-Tu). Here we present high-resolution structural ensembles of ribosomes with cognate or near-cognate aminoacyl-tRNAs delivered by EF-Tu. Both cognate and near-cognate tRNA anticodons explore the aminoacyl-tRNA-binding site (A site) of an open 30S subunit, while inactive EF-Tu is separated from the 50S subunit. A transient conformation of decoding-centre nucleotide G530 stabilizes the cognate codon-anticodon helix, initiating step-wise 'latching' of the decoding centre. The resulting closure of the 30S subunit docks EF-Tu at the sarcin-ricin loop of the 50S subunit, activating EF-Tu for GTP hydrolysis and enabling accommodation of the aminoacyl-tRNA. By contrast, near-cognate complexes fail to induce the G530 latch, thus favouring open 30S pre-accommodation intermediates with inactive EF-Tu. This work reveals long-sought structural differences between the pre-accommodation of cognate and near-cognate tRNAs that elucidate the mechanism of accurate decoding.
Subject(s)
Cryoelectron Microscopy , Protein Biosynthesis , Ribosomes/metabolism , Ribosomes/ultrastructure , Anticodon/chemistry , Anticodon/genetics , Anticodon/ultrastructure , Codon/chemistry , Codon/genetics , Codon/ultrastructure , Escherichia coli/chemistry , Escherichia coli/genetics , Escherichia coli/ultrastructure , GTP Phosphohydrolases/metabolism , GTP Phosphohydrolases/ultrastructure , Guanosine Triphosphate/metabolism , Hydrolysis , Models, Molecular , Peptide Elongation Factor Tu/metabolism , Peptide Elongation Factor Tu/ultrastructure , Protein Domains , RNA, Ribosomal, 16S/genetics , RNA, Ribosomal, 16S/metabolism , RNA, Ribosomal, 16S/ultrastructure , RNA, Transfer, Amino Acyl/genetics , RNA, Transfer, Amino Acyl/metabolism , RNA, Transfer, Amino Acyl/ultrastructure , Ribosome Subunits/chemistry , Ribosome Subunits/metabolism , Ribosome Subunits/ultrastructure , Ribosomes/chemistryABSTRACT
It has been shown that the distribution of genes in eukaryotic genomes is not random; however, formerly reported relations between gene function and genomic organization were relatively weak. Previous studies have demonstrated that codon usage bias is related to all stages of gene expression and to protein function. Here we apply a novel tool for assessing functional relatedness, codon usage frequency similarity (CUFS), which measures similarity between genes in terms of codon and amino acid usage. By analyzing chromosome conformation capture data, describing the three-dimensional (3D) conformation of the DNA, we show that the functional similarity between genes captured by CUFS is directly and very strongly correlated with their 3D distance in Saccharomyces cerevisiae, Schizosaccharomyces pombe, Arabidopsis thaliana, mouse and human. This emphasizes the importance of three-dimensional genomic localization in eukaryotes and indicates that codon usage is tightly linked to genome architecture.
Subject(s)
Codon/chemistry , Codon/ultrastructure , DNA/chemistry , Genome , Software , Animals , Arabidopsis/genetics , DNA/ultrastructure , Gene Expression , Genetic Code , Humans , Mice , Models, Genetic , Nucleic Acid Conformation , Saccharomyces cerevisiae/genetics , Schizosaccharomyces/geneticsABSTRACT
Introducción. La neoplasia endocrina múltiple tipo 2B (NEM2B) es un síndrome con carácter dominante hereditario que se caracteriza por el desarrollo de diversas neoplasias de origen neuroendocrino en distintos órganos, tales como carcinoma medular de tiroides (CMT), feocromocitomas, neuromas mucosales, ganglioneuromas del aparato gastrointestinal, también se observan anormalidades esqueléticas y oftálmicas. En más de 95 por ciento de los casos, este padecimiento se asocia con una mutación puntual específica en el dominio tirosina cinasa del proto-oncogen ret, en el codón 918 (METÕTHR), la cual surge de novo en 50 por ciento de los pacientes. Material y métodos. El probando fue un paciente masculino de 19 años de edad sin antecedentes de importancia para la enfermedad y que inició su padecimiento a los 5 años con neuromas submucosos en lengua y labios, así como habitus marfanoide que se acentuó a los 19 años. Determinándose la presencia de la mutación mencionada anteriormente en el DNA de leucocitos de sangre periférica y de carcinoma medular de tiroides de este paciente afectado por NEM2B y se realizó la búsqueda de la misma en leucocitos de sus familiares. Resultados. Los elevados niveles séricos de calcitonina basal (600 pg/mL) sugirieron, además del aspecto clínico y evolución, que el paciente era portador de NEM2B. El estudio histopatológico de tiroides reveló la presencia de CTM clásico. Al estudio del DNA de células de sangre periférica se observó una banda extra sugiriendo que contenía una mutación. Se confirmó la presencia de la mutación ATGÕACG en el codón 918. Conclusión. Al no encontrarse la mutación en los familiares del paciente sugiere que ésta surgió de novo en etapas tempranas del desarrollo embrionario.
Subject(s)
Humans , Male , Adult , DNA Mutational Analysis/methods , Multiple Endocrine Neoplasia/diagnosis , Codon/ultrastructure , Carcinoma, Medullary/diagnosis , NeuromaSubject(s)
Codon/ultrastructure , Gene Expression Regulation , Genes , RNA, Messenger/ultrastructure , Animals , Base Composition , DNA/ultrastructure , HumansABSTRACT
Adaptor properties of linear hairpin helices have been examined. The analysis suggests that neither right nor left handed hairpin helices can simultaneously read a comma free messenger and align aminoacyl residues for peptide condensation. Comparison of these studies with the model of the present day peptidyl transfer intermediate suggests that the "L" shaped folding of the present day tRNAs may be a prerequisite for adaptor function. Therefore, the three-dimensional organization of the ancestral adaptor molecule must have had structural features similar to its present day counterpart.
