Queueing or stacking of ribosomes during translation of the nucleotide sequence of mRNA transcripts
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 an amino acid sequence during protein synthesis by ribosomes. Due to the pause sites of some mRNA's, there is a disturbance caused in translation.[1] Ribosomal pausing occurs in both eukaryotes and prokaryotes.[2][3] A more severe pause is known as a ribosomal stall.[4]
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 varieties of rare tRNAs limiting the rate at which some transcripts could be decoded.[5] However, with research techniques such as ribosome profiling, it was found that at certain sites there were higher concentrations of ribosomes than average, and these pause sites were tested with specific codons. No link was found between the occupancy of specific codons and amount of their tRNAs. Thus, the early findings about rare tRNAs causing pause sites doesn't seem plausible.[2]
Two techniques can localize the ribosomal pause site in vivo; a micrococcal nuclease protection assay and isolation of polysomal transcript.[6] Isolation of polysomal transcripts occurs by centrifuging tissue extracts through a sucrose cushion with translation elongation inhibitors, for example cycloheximide.[7]
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, during translation, the fragments that started to translate before the pause took place are overrepresented. However, along with the mRNA if the ribosome pauses then specific bands will be improved in the trailing edge of the ribosome.[8]
Some of the elongation inhibitors, such as: cycloheximide (in eukaryotes) or chloramphenicol, cause the ribosomes to pause and to accumulate in the start codons. Elongation Factor P regulates the ribosomal pause at polyproline in bacteria, and when there is no EFP the density of ribosomes decreases from the polyproline motifs. If there are multiple ribosome pauses, then the EFP won't resolve it.[9]
^Gawroński P, Jensen PE, Karpiński S, Leister D, Scharff LB (March 2018). "Pausing of Chloroplast Ribosomes Is Induced by Multiple Features and Is Linked to the Assembly of Photosynthetic Complexes". Plant Physiology. 176 (3): 2557–2569. doi:10.1104/pp.17.01564. PMC 5841727. PMID 29298822.
^ abLi GW, Oh E, Weissman JS (March 2012). "The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria". Nature. 484 (7395): 538–41. Bibcode:2012Natur.484..538L. doi:10.1038/nature10965. PMC 3338875. PMID 22456704.
^Lopinski JD, Dinman JD, Bruenn JA (February 2000). "Kinetics of ribosomal pausing during programmed -1 translational frameshifting". Molecular and Cellular Biology. 20 (4): 1095–103. doi:10.1128/MCB.20.4.1095-1103.2000. PMC 85227. PMID 10648594.
^Buskirk, Allen R.; Green, Rachel (19 March 2017). "Ribosome pausing, arrest and rescue in bacteria and eukaryotes". Philosophical Transactions of the Royal Society B: Biological Sciences. 372 (1716): 20160183. doi:10.1098/rstb.2016.0183. PMC 5311927. PMID 28138069.
^Kontos H, Napthine S, Brierley I (December 2001). "Ribosomal pausing at a frameshifter RNA pseudoknot is sensitive to reading phase but shows little correlation with frameshift efficiency". Molecular and Cellular Biology. 21 (24): 8657–70. doi:10.1128/MCB.21.24.8657-8670.2001. PMC 100026. PMID 11713298.
^Jha SS, Komar AA (July 2012). "Isolation of ribosome bound nascent polypeptides in vitro to identify translational pause sites along mRNA". Journal of Visualized Experiments (65). doi:10.3791/4026. PMC 3471273. PMID 22806127.
^Kim JK, Hollingsworth MJ (October 1992). "Localization of in vivo ribosome pause sites". Analytical Biochemistry. 206 (1): 183–8. doi:10.1016/s0003-2697(05)80031-4. PMID 1456432.
^Wolin SL, Walter P (November 1988). "Ribosome pausing and stacking during translation of a eukaryotic mRNA". The EMBO Journal. 7 (11): 3559–69. doi:10.1002/j.1460-2075.1988.tb03233.x. PMC 454858. PMID 2850168.
^Brar GA, Yassour M, Friedman N, Regev A, Ingolia NT, Weissman JS (February 2012). "High-resolution view of the yeast meiotic program revealed by ribosome profiling". Science. 335 (6068): 552–7. Bibcode:2012Sci...335..552B. doi:10.1126/science.1215110. PMC 3414261. PMID 22194413.
Ribosomalpause refers to the queueing or stacking of ribosomes during translation of the nucleotide sequence of mRNA transcripts. These transcripts are...
Ribosomal frameshifting, also known as translational frameshifting or translational recoding, is a biological phenomenon that occurs during translation...
affected by ribosomalpausing, which can trigger endonucleolytic attack of the tRNA, a process termed mRNA no-go decay. Ribosomalpausing also aids co-translational...
HIV ribosomal frameshift signal is a ribosomal frameshift (PRF) that human immunodeficiency virus (HIV) uses to translate several different proteins from...
protein synthesis, rapidly changing conditions in the cell can cause ribosomalpausing. In coronaviruses, this can affect growth rate and trigger translational...
for ribosome profiling to show pause sites within the transcriptome at specific codons. These sites of slow or paused translation are demonstrated by...
ORF, pausing of translation is caused by scanning ribosome with three conserved sequences that are complementary to the 3’ hairpin of 18S ribosomal RNA...
commonly studied in Saccharomyces cerevisiae. RRM3 formally stands for Ribosomal DNArecombination mutation 3. The gene codes for nuclear protein Rrm3p...
acids to growing polypeptide chains at the ribosomal site of protein synthesis during translation; Ribosomal RNA (rRNA) Incorporates into ribosomes; Micro...
hundreds of ribosomal DNA repeats, sometimes distributed over multiple chromosomes. Termination of transcription occurs in the ribosomal intergenic spacer...
Pol I) is, in higher eukaryotes, the polymerase that only transcribes ribosomal RNA (but not 5S rRNA, which is synthesized by RNA polymerase III), a type...
number of bacteria species. This pseudoknot stimulates programmed -1 ribosomal frameshifting (PRF-1) which in turn stimulates the express of transposase...
modifications. Most of the RNA modifications are found on transfer-RNA and ribosomal-RNA, but also eukaryotic mRNA has been shown to be modified with multiple...
(1979). "Reverse transcriptase pauses at N2-methylguanine during in vitro transcription of Escherichia coli 16S ribosomal RNA". Proceedings of the National...
is a limiting component of the multisubunit complex that recruits 40S ribosomal subunits to the 5' end of mRNAs. Interaction of this protein with eIF4E...
experimentally supported. First, the translation of the leader peptide and ribosomal stalling are directly evidenced to be necessary for inhibiting the transcription...
important genes unusable, they are still essential to keep a species' ribosomal DNA intact over the generations, preventing infertility. Retrotransposons...
RNA-dependent RNA polymerase pauses to release the new mRNA when it encounters an intergenic sequence. When the RNA polymerase is paused, a chance exists that...
one of these is initiation factor-4G, which in turn recruits the 40S ribosomal subunit. However, a poly(A) tail is not required for the translation of...
Escherichia coli cells starved for amino acids and inhibit synthesis of ribosomal and transfer RNAs. It is now known that (p)ppGpp is also produced in response...
that involves pausing of transcription elongation and release of both the pre-ribosomal RNA and Pol I from the DNA template. The pausing is mediated by...
degradable substrates include nonfunctional protein fragments produced from ribosomal stalling during translation, misfolded or unfolded proteins, aggregated...
polymerase III, the polymerase responsible for synthesizing transfer and small ribosomal RNAs in eukaryotes. The carboxy-terminal domain of this subunit shares...