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...

We found that loss of integrity of the ribosome by removal of a putative ribosome maturation factor or a ribosomal protein conferred salt tolerance on Escherichia coli cells. Some protein synthesis inhibitors including kasugamycin and chloramphenicol also had a similar effect, although kasugamycin affected neither 16S rRNA maturation nor subunit association into a 70S ribosome. Thus, salt toler...