scholarly journals Deconstructing the individual steps of vertebrate translation initiation

2019 ◽  
Author(s):  
Adam Giess ◽  
Yamila N. Torres Cleuren ◽  
Håkon Tjeldnes ◽  
Maximilian Krause ◽  
Teshome Tilahun Bizuayehu ◽  
...  
Keyword(s):  
Translation Initiation ◽  
Stop Codon ◽  
Small Subunit ◽  
Codon Recognition ◽  
Rate Determining Step ◽  
Expression Control ◽  
Gene Expression Control ◽  
Stop Codon Recognition ◽  
Specific Regulation ◽  
The Individual

AbstractTranslation initiation is often attributed as the rate determining step of eukaryotic protein synthesis and key to gene expression control 1. Despite this centrality the series of steps involved in this process are poorly understood 2,3. Here we capture the transcriptome-wide occupancy of ribosomes across all stages of translation initiation, enabling us to characterize the transcriptome-wide dynamics of ribosome recruitment to mRNAs, scanning across 5’ UTRs and stop codon recognition, in a higher eukaryote. We provide mechanistic evidence for ribosomes attaching to the mRNA by threading the mRNA through the small subunit. Moreover, we identify features regulating the recruitment and processivity of scanning ribosomes, redefine optimal initiation contexts and demonstrate endoplasmic reticulum specific regulation of initiation. Our approach enables deconvoluting translation initiation into separate stages and identifying the regulators at each step.

scholarly journals Eukaryotic Release Factor 1 Phosphorylation by CK2 Protein Kinase Is Dynamic but Has Little Effect on the Efficiency of Translation Termination in Saccharomyces cerevisiae

2006 ◽  
Vol 5 (8) ◽  
pp. 1378-1387 ◽  
Author(s):  
Adam K. Kallmeyer ◽  
Kim M. Keeling ◽  
David M. Bedwell
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Protein Synthesis ◽  
Protein Kinase ◽  
Stop Codon ◽  
Translation Termination ◽  
Release Factor ◽  
Codon Recognition ◽  
Number Of Factors ◽  
Stop Codon Recognition

ABSTRACT Protein synthesis requires a large commitment of cellular resources and is highly regulated. Previous studies have shown that a number of factors that mediate the initiation and elongation steps of translation are regulated by phosphorylation. In this report, we show that a factor involved in the termination step of protein synthesis is also subject to phosphorylation. Our results indicate that eukaryotic release factor 1 (eRF1) is phosphorylated in vivo at serine 421 and serine 432 by the CK2 protein kinase (previously casein kinase II) in the budding yeast Saccharomyces cerevisiae. Phosphorylation of eRF1 has little effect on the efficiency of stop codon recognition or nonsense-mediated mRNA decay. Also, phosphorylation is not required for eRF1 binding to the other translation termination factor, eRF3. In addition, we provide evidence that the putative phosphatase Sal6p does not dephosphorylate eRF1 and that the state of eRF1 phosphorylation does not influence the allosuppressor phenotype associated with a sal6Δ mutation. Finally, we show that phosphorylation of eRF1 is a dynamic process that is dependent upon carbon source availability. Since many other proteins involved in protein synthesis have a CK2 protein kinase motif near their extreme C termini, we propose that this represents a common regulatory mechanism that is shared by factors involved in all three stages of protein synthesis.

scholarly journals PABP enhances release factor recruitment and stop codon recognition during translation termination

2016 ◽  
Vol 44 (16) ◽  
pp. 7766-7776 ◽  
Author(s):  
Alexandr Ivanov ◽  
Tatyana Mikhailova ◽  
Boris Eliseev ◽  
Lahari Yeramala ◽  
Elizaveta Sokolova ◽  
...  
Keyword(s):  
Stop Codon ◽  
Translation Termination ◽  
Release Factor ◽  
Codon Recognition ◽  
Stop Codon Recognition

scholarly journals Structural basis for stop codon recognition in eukaryotes

Nature ◽  
2015 ◽  
Vol 524 (7566) ◽  
pp. 493-496 ◽  
Author(s):  
Alan Brown ◽  
Sichen Shao ◽  
Jason Murray ◽  
Ramanujan S. Hegde ◽  
V. Ramakrishnan
Keyword(s):  
Stop Codon ◽  
Structural Basis ◽  
Codon Recognition ◽  
Stop Codon Recognition

scholarly journals Two-step model of stop codon recognition by eukaryotic release factor eRF1

2013 ◽  
Vol 41 (8) ◽  
pp. 4573-4586 ◽  
Author(s):  
Polina Kryuchkova ◽  
Alexander Grishin ◽  
Boris Eliseev ◽  
Anna Karyagina ◽  
Ludmila Frolova ◽  
...  
Keyword(s):  
Stop Codon ◽  
Release Factor ◽  
Codon Recognition ◽  
Step Model ◽  
Stop Codon Recognition

scholarly journals Kinetics of Stop Codon Recognition by Release Factor 1

Biochemistry ◽  
2009 ◽  
Vol 48 (47) ◽  
pp. 11178-11184 ◽  
Author(s):  
Byron Hetrick ◽  
Kristin Lee ◽  
Simpson Joseph
Keyword(s):  
Stop Codon ◽  
Release Factor ◽  
Codon Recognition ◽  
Stop Codon Recognition ◽  
Kinetics Of

Functional characterization of polypeptide release factor 1b in the ciliate Euplotes

2010 ◽  
Vol 30 (6) ◽  
pp. 425-431 ◽  
Author(s):  
Yan Wang ◽  
Baofeng Chai ◽  
Wei Wang ◽  
Aihua Liang
Keyword(s):  
Stop Codon ◽  
Functional Characterization ◽  
Subcellular Location ◽  
Class I ◽  
Release Factor ◽  
Amino Acid Motif ◽  
Codon Recognition ◽  
Stop Codon Recognition ◽  
Higher Eukaryotes

In higher eukaryotes, RF-I (class I release factor) [eRF1 (eukaryotic release factor 1)] is responsible for stop codon recognition and promotes nascent polypeptide release from the ribosome. Interestingly, two class I RFs, eRF1a and eRF1b, have been identified among the ciliates Euplotes, which are variant code organisms. In the present study, we analysed the comparative expression of eRF1a and eRF1b in Euplotes cells, demonstrating that the expression of eRF1b was higher than that of eRF1a. An interaction between eRF1b and eRF3 was confirmed, suggesting that an eRF1b function is facilitated by eRF3. Co-localization of both eRF1s indicated that they function in the same subcellular location in Euplotes cells. We also analysed the characteristics of stop codon discrimination by eRF1b. Like eRF1a, eRF1b recognized UAA and UAG as stop codons, but not UGA. This finding disagreed with the deduced characteristics of eRF1a/eRF1b from the classic hypothesis of ‘anticodon-mimicry’ proposed by Muramatsu et al. [Muramatsu, Heckmann, Kitanaka and Kuchino (2001) FEBS Lett. 488, 105–109]. Mutagenesis experiments indicated that the absolutely conserved amino acid motif ‘G31T32’ (numbered as for human eRF1) in eRF1b was the key to efficient stop codon recognition by eRF1b. In conclusion, these findings support and improve the ‘cavity model’ of stop codon discrimination by eRF1 proposed by Bertram et al. [Bertram, Bell, Ritchie, Fullerton and Stansfield (2000) RNA 6, 1236–1247] and Inagaki et al. [Inagaki, Blouin, Doolittle and Roger (2002) Nucleic Acids Res. 30, 532–544].

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