The protein kinase TOR (target of rapamycin) controls several steps of ribosome biogenesis, including gene expression of rRNA and ribosomal proteins, and processing of the 35S rRNA precursor, in the budding yeast Saccharomyces cerevisiae. Here we show that TOR also regulates late stages of ribosome maturation in the nucleoplasm via the nuclear GTP-binding protein Nog1. Nog1 formed a complex tha...

To study the function of Rli1/ABCE1 in vivo, we used ribosome profiling and biochemistry to characterize its contribution to ribosome recycling. When Rli1 levels were diminished, 80S ribosomes accumulated both at stop codons and in the adjoining 3'UTRs of most mRNAs. Frequently, these ribosomes reinitiated translation without the need for a canonical start codon, as small peptide products predi...

Ribosome profiling (Ribo-seq), a promising technology for exploring ribosome decoding rates, is characterized by the presence of infrequent high peaks in ribosome footprint density and by long alignment gaps. Here, to reduce the impact of data heterogeneity we introduce a simple normalization method, Ribo-seq Unit Step Transformation (RUST). RUST is robust and outperforms other normalization te...

By translating genetically encoded information to synthesize proteins, the ribosome has a central and fundamental role in the molecular biology of the cell. Virtually every molecule made in every cell was made either directly by the ribosome or by enzymes made by the ribosome. Although the ribosome was discovered half a century ago, progress in the field of translation has been revolutionized b...

Abstract Ribosome biogenesis requires auxiliary factors to promote folding and assembly of ribosomal proteins RNA. Particularly, maturation the peptidyl transferase center (PTC) is mediated by conserved GTPases, but molecular basis poorly understood. Here, we define mechanism GTPase-driven human mitochondrial large subunit (mtLSU) using endogenous complex purification, in vitro reconstitution c...

The movement of a ribosome along the mRNA was assessed by the following experimental strategy. mRNAs were synthesized which contained a short coding sequence with at least four codons and a 32P label at one end and an oligo(C) sequence at the other end. When these mRNAs were fixed on the ribosome with tRNAs specific for the defined codons, the oligo(C) stretches were partially outside of the ri...

It is becoming increasingly evident that a high degree of regulation is involved in the protein synthesis machinery entailing more interacting regulatory factors. A multitude of proteins have been identified recently which show regulatory function upon binding to the ribosome. Here, we identify tight association of a metabolic protein aldehyde-alcohol dehydrogenase E (AdhE) with the E. coli 70S...

Helix 38 (H38) of the large ribosomal subunit, with a length of 110 A, reaches the small subunit through intersubunit bridge B1a. Previous cryo-EM studies revealed that the tip of H38 moves by more than 10 A from the non-ratcheted to the ratcheted state of the ribosome while mutational studies implicated a key role of flexible H38 in attenuation of translocation and in dynamical signaling betwe...

Recent analysis by means of a direct chemical assay has shown that the numbers of aminoacyl-tRNA synthetase molecules per bacterial cell vary with the growth rate [ 1,2] . This type of control (‘metabolic regulation’) is responsible for the fact that under different rates of unrestricted growth the ratio of aminoacyl-tRNA synthetases relative to other components of the protein synthesis apparat...

In the fission yeast Schizosaccharomyces pombe, Wee1-dependent inhibitory phosphorylation of the highly conserved Cdc2/Cdk1 kinase determines the mitotic onset when cells have reached a defined size. The receptor of activated C kinase (RACK1) is a scaffolding protein strongly conserved among eukaryotes which binds to other proteins to regulate multiple processes in mammalian cells, including th...