In recent years, the Ribosome profiling technique (Ribo–seq) has emerged as a powerful method for globally monitoring translation process in vivo at single nucleotide resolution. Based on deep sequencing of mRNA fragments, Ribo–seq allows to obtain profiles that reflect time spent by ribosomes translating each part an open reading frame. Unfortunately, produced this can vary significantly diffe...

Ribosomal protein synthesis is a central process of the modern biological world. Because ribosome contains proteins itself, it very important to understand its precursor and evolution. Small ribozymes have demonstrated principle “RNA world” hypothesis, but free peptide ligase remains elusive. In this report, we identified two fragments in peptidyl transfer center that can synthesize 9-mer poly-...

In eukaryotes, newly synthesized proteins interact co-translationally with a multitude of different ribosome-bound factors and chaperones including the conserved heterodimeric nascent polypeptide-associated complex (NAC) and a Hsp40/70-based chaperone system. These factors are thought to play an important role in protein folding and targeting, yet their specific ribosomal localizations, which a...

The structure of the mammalian ribosome, reconstructed at 25 A resolution, has added a new dimension to our current knowledge, as it manifests the conservation and universality of the ribosome in respect to its primary tasks in protein biosynthesis. A combined approach to study of the ribosome, using X-ray crystallography and electron microscopy, may further improve our understanding of ribosom...

The intergenic region internal ribosome entry site (IGR IRES) of the Dicistroviridae viral family can directly assemble 80S ribosomes and initiate translation at a non-AUG codon from the ribosomal A-site. These functions are directed by two independently folded domains of the IGR IRES. One domain, composed of overlapping pseudoknots II and III (PKII/III), mediates ribosome recruitment. The seco...

Ribosome profiling identifies ribosome positions on translated mRNAs. A prominent feature of published datasets is the near complete absence of ribosomes in 3' untranslated regions (3'UTR) although substantial ribosome density can be observed on non-coding RNAs. Here we perform ribosome profiling in cultured Drosophila and human cells and show that different features of translation are revealed...

extended abstract 1. introduction one of the important issues in crisis management is providing settlement and help to the injured. in fact, the location of rescue and help centers should be designed in such a way that after the incident, there is the best chance ofgiving response to victims. in this regard, one of the important tasks of urban planners is to identify suitable locations for evac...

In Escherichia coli, rRNAs are initially transcribed with precursor sequences, which are subsequently removed through processing reactions. To investigate the role of precursor sequences, we analyzed ribosome assembly in strains containing mutations in the processing RNases. We observed that defects in 23S rRNA processing resulted in an accumulation of ribosomal subunits and caused a significan...

During translation elongation, the ribosome ratchets along its mRNA template, incorporating each new amino acid and translocating from one codon to the next. The elongation cycle requires dramatic structural rearrangements of the ribosome. We show here that deep sequencing of ribosome-protected mRNA fragments reveals not only the position of each ribosome but also, unexpectedly, its particular ...