User:Betrick9/sandbox

Ribosomal pause refers to the queueing or stacking of ribosomes during translation of the nucleotide sequence of mRNA transcripts. These transcripts are decoded and converted into amino acid sequence during protein synthesis by ribosomes. The pause sites of the mRNAs only briefly interrupt the progress of translation. Within the ribosome, transfer RNA molecules recognize specific trinucleotide codons on the mRNA, and add their cognate amino acids to nascent protein chains.

It's been known since the 1980s that different mRNAs are translated at different rates. The main reason for these differences was thought to be the concentration of rarer varieties of tRNA limiting the rate at which some transcripts could be decoded.

Two techniques can localize the ribosomal pause site in vivo; a micrococcal nuclease protection assay and isolation of polynomial transcript. This works by taking the tissue that is extracted through a sucrose cushion with the translation elongation that inhabit it and centrifuging the whole.

The ribosome pausing can be detected during preprolactin synthesis on free polysomes, when the ribosome is paused the other ribosomes are tightly stacked together. When the ribosome pauses while the translation takes place, the fragments that started to translate before the pause took place is over presented. However, along with the mRNA if the ribosome pauses then specific bands will be improved in the trailing edge of the ribosome.

Some of the elongation inhibitors such as cycloheximide (in eukaryotes) or chloramphenicol cause the ribosomal pause and accumulate at the start codons. EFP factor regulates the ribosomal pause at polyproline in bacteria, and when there is no EFP the density of ribosomes decreases from the polypro line motifs. If there are multiple ribosome pauses then the EFP won't resolve it.

Effects on gene expression
During protein synthesis, rapidly changing conditions in the cell can cause ribosomal pausing. In bacteria and viruses, this can affect growth rate and trigger translational abandonment. This releases the ribosome from the mRNA and the incomplete polypeptide is targeted for destruction.

In eukaryotes, ribosomal pausing can initiate an analogous process which triggers endonucleolytic attack of the mRNA, a process termed mRNA no-go decay. Ribosomal pausing also aids co-translational folding of the nascent polypeptide on the ribosome, and delays protein translation while its encoding mRNA. This can trigger ribosomal frameshifting.

Advantage of the ribosomal pause
By the time, the ribosome movement on the mRNA is not a liner, and the ribosome gets paused at different regions with unknown reason. The ribosome pause position will help to identify the mRNA sequence features and structure and the transacting factor that modulate this process. The advantage of ribosomal pause sites that are located at protein domain boundaries are aiding folding of a protein.

The location of the ribosome pause event in vitro
It is known that ribosomes pause at distinct sites, but the reasons for these pauses are not known. Also, the ribosome gets paused if the pseudoknot is disrupted. 10% of the ribosome pause at the pseudoknot and 4% of the ribosomes are terminated. Before the ribosome is obstructed it passes the pseudoknot. An assay was put together by a group from the University of California in an effort to show a model of mRNA and the translation was monitored in two in vitro systems. It was found that translating ribosomes aren't uniformly distributed along an mRNA.

Ribosome Profiling
Ribosome profiling is a method that sequences the ribosome protected fragment to reveal the occupancy of mRNA. The ribosome profiling has the ability to reveal the ribosome pause sites in the whole transcriptome, and when the kinetics layer is added, it discloses the time of the pause, and the translation takes place.