scholarly journals Cryo-EM study of start codon selection during archaeal translation initiation

2016 ◽  
Vol 7 (1) ◽  
Author(s):  
Pierre-Damien Coureux ◽  
Christine Lazennec-Schurdevin ◽  
Auriane Monestier ◽  
Eric Larquet ◽  
Lionel Cladière ◽  
...  
Keyword(s):  
Translation Initiation ◽  
Start Codon ◽  
Codon Selection

scholarly journals eIF2α interactions with mRNA control accurate start codon selection by the translation preinitiation complex

2020 ◽  
Vol 48 (18) ◽  
pp. 10280-10296
Author(s):  
Anil Thakur ◽  
Swati Gaikwad ◽  
Anil K Vijjamarri ◽  
Alan G Hinnebusch
Keyword(s):  
Translation Initiation ◽  
Ternary Complex ◽  
Start Codon ◽  
Preinitiation Complex ◽  
Closed Conformation ◽  
Open Conformation ◽  
Kozak Context ◽  
Codon Selection

Abstract In translation initiation, AUG recognition triggers rearrangement of the 48S preinitiation complex (PIC) from an open conformation to a closed state with more tightly-bound Met-tRNAi. Cryo-EM structures have revealed interactions unique to the closed complex between arginines R55/R57 of eIF2α with mRNA, including the −3 nucleotide of the ‘Kozak’ context. We found that R55/R57 substitutions reduced recognition of a UUG start codon at HIS4 in Sui− cells (Ssu− phenotype); and in vitro, R55G-R57E accelerated dissociation of the eIF2·GTP·Met-tRNAi ternary complex (TC) from reconstituted PICs with a UUG start codon, indicating destabilization of the closed complex. R55/R57 substitutions also decreased usage of poor-context AUGs in SUI1 and GCN4 mRNAs in vivo. In contrast, eIF2α-R53 interacts with the rRNA backbone only in the open complex, and the R53E substitution enhanced initiation at a UUG codon (Sui− phenotype) and poor-context AUGs, while reducing the rate of TC loading (Gcd− phenotype) in vivo. Consistently, R53E slowed TC binding to the PIC while decreasing TC dissociation at UUG codons in vitro, indicating destabilization of the open complex. Thus, distinct interactions of eIF2α with rRNA or mRNA stabilize first the open, and then closed, conformation of the PIC to influence the accuracy of initiation in vivo.

A Stable Upstream Stem-loop Structure Enhances Selection of the First 5′-ORF-AUG as a Main Start Codon for Translation Initiation of Human ACAT1 mRNA

2004 ◽  
Vol 36 (4) ◽  
pp. 259-268 ◽  
Author(s):  
Li Yang ◽  
Jiang Chen ◽  
Catherine C. Y. Chang ◽  
Xin-Ying Yang ◽  
Zhen-Zhen Wang ◽  
...  
Keyword(s):  
Translation Initiation ◽  
Start Codon ◽  
Loop Structure ◽  
Stem Loop ◽  
Reading Frame ◽  
Stem Loop Structure ◽  
Codon Selection ◽  
Mutation Analyses ◽  
Enzymatic Activity Assay ◽  
Selection Of

Abstract Human ACAT1 cDNA K1 was first cloned and functionally expressed in 1993. There are two adjacent in-frame AUG codons, AUG1397–1399 and AUG1415–1417, at 5′-terminus of the open reading frame (ORF, nt 1397–3049) of human ACAT1 mRNA corresponding to cDNA K1. In current work, these two adjacent inframe AUGs at 5′-terminus of the predicted ORF (5′-ORF-AUGs) as start codons for translation initiation of human ACAT1 mRNA were characterized in detail. Codon mutations indicated that both of these two adjacent 5′-ORF-AUGs can be selected as start codons but the first 5′-ORF-AUG1397–1399 is a main start codon consistent with that of the predicted ORF of human ACAT1 mRNA. Further deletion and mutation analyses demonstrated that a stable upstream stem-loop structure enhanced the selection of the first 5′-ORF-AUG1397–1399 as a main start codon, in addition to upstream nucleotide A in the –3 position, which is a key site of Kozak sequence. In addition, result of ACAT1 enzymatic activity assay showed no obvious difference between these two ACAT1 proteins respectively initiated from the two adjacent 5′-ORF-AUGs. This work showed that a stable upstream stem-loop structure could modulate the start codon selection during translation initiation of mRNAs that contain adjacent multi-5′-ORF-AUGs.

scholarly journals Stringency of start codon selection modulates autoregulation of translation initiation factor eIF5

2011 ◽  
Vol 40 (7) ◽  
pp. 2898-2906 ◽  
Author(s):  
Gary Loughran ◽  
Matthew S. Sachs ◽  
John F. Atkins ◽  
Ivaylo P. Ivanov
Keyword(s):  
Translation Initiation ◽  
Translation Initiation Factor ◽  
Initiation Factor ◽  
Start Codon ◽  
Codon Selection

scholarly journals Bi-directional ribosome scanning controls the stringency of start codon selection

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Yifei Gu ◽  
Yuanhui Mao ◽  
Longfei Jia ◽  
Leiming Dong ◽  
Shu-Bing Qian
Keyword(s):  
Translation Initiation ◽  
Current Knowledge ◽  
Start Codon ◽  
Entry Site ◽  
Internal Ribosome Entry ◽  
Eukaryotic Translation ◽  
Operational Mechanism ◽  
Codon Recognition ◽  
Codon Selection ◽  
Selection Of

AbstractThe fidelity of start codon recognition by ribosomes is paramount during protein synthesis. The current knowledge of eukaryotic translation initiation implies unidirectional 5ʹ→3ʹ migration of the pre-initiation complex (PIC) along the 5ʹ UTR. In probing translation initiation from ultra-short 5ʹ UTR, we report that an AUG triplet near the 5ʹ end can be selected via PIC backsliding. Bi-directional ribosome scanning is supported by competitive selection of closely spaced AUG codons and recognition of two initiation sites flanking an internal ribosome entry site. Transcriptome-wide PIC profiling reveals footprints with an oscillation pattern near the 5ʹ end and start codons. Depleting the RNA helicase eIF4A leads to reduced PIC oscillations and impaired selection of 5ʹ end start codons. Enhancing the ATPase activity of eIF4A promotes nonlinear PIC scanning and stimulates upstream translation initiation. The helicase-mediated PIC conformational switch may provide an operational mechanism that unifies ribosome recruitment, scanning, and start codon selection.

scholarly journals A combinatorial model predicts leaderless mRNA start codon selection in C. crescentus

2020 ◽  
Author(s):  
Mohammed-Husain M. Bharmal ◽  
Jared M. Schrader
Keyword(s):  
Translation Initiation ◽  
Mrna Translation ◽  
Start Codon ◽  
Leaderless Mrna ◽  
Combinatorial Model ◽  
Shine Dalgarno Sequence ◽  
Codon Selection ◽  
Relationship Of ◽  
Bacterial Translation

AbstractBacterial translation is thought to initiate by base-pairing of the 16S rRNA and the Shine-Dalgarno sequence in the mRNA’s 5’ UTR. However, transcriptomics has revealed that leaderless mRNAs, which completely lack any 5’ UTR, are broadly distributed across bacteria and can initiate translation in the absence of the Shine-Dalgarno sequence. To investigate the mechanism of leaderless mRNA translation initiation, synthetic in vivo translation reporters were designed that systematically tested the effects of start codon accessibility, leader length, and start codon identity on leaderless mRNA translation initiation. Using this data, a simple computational model was built based on the combinatorial relationship of these mRNA features which can accurately classify leaderless mRNAs and predict the translation initiation efficiency of leaderless mRNAs. Thus, start codon accessibility, leader length, and start codon identity combine to define leaderless mRNA translation initiation in bacteria.

scholarly journals Translation initiation factor 3 antagonizes authentic start codon selection on leaderless mRNAs

1999 ◽  
Vol 31 (1) ◽  
pp. 67-77 ◽  
Author(s):  
Karsten Tedin ◽  
Isabella Moll ◽  
Sonja Grill ◽  
Armin Resch ◽  
Anton Graschopf ◽  
...  
Keyword(s):  
Translation Initiation ◽  
Translation Initiation Factor ◽  
Initiation Factor ◽  
Start Codon ◽  
Codon Selection ◽  
Translation Initiation Factor 3

scholarly journals eIF3b and eIF3i relocate together to the ribosomal subunit interface during translation initiation and modulate start codon selection

2018 ◽  
Author(s):  
Jose L. Llácer ◽  
Tanweer Hussain ◽  
Jinsheng Dong ◽  
Yuliya Gordiyenko ◽  
Alan G. Hinnebusch
Keyword(s):  
Translation Initiation ◽  
Ribosomal Subunit ◽  
Start Codon ◽  
High Fidelity ◽  
Electron Cryomicroscopy ◽  
Translational Initiation ◽  
Closed Conformation ◽  
Subunit Interface ◽  
Codon Selection

ABSTRACTDuring eukaryotic translational initiation, the 48S ribosomal pre-initiation complex (PIC) scans the 5’ untranslated region of mRNA until it encounters a start codon. We present a single particle electron cryomicroscopy (cryo-EM) reconstruction of a yeast 48S PIC in an open scanning-competent state in which eIF3b is observed bound on the 40S subunit interface. eIF3b is re-located with eIF3i from their solvent-interface locations observed in other PIC structures; however, eIF3i is not in contact with the 40S. Re-processing of micrographs of our previous 48S PIC in a closed state using currently available tools reveal a similar re-location of eIF3b and eIF3i from the solvent to subunit interface. Genetic analysis indicates that high fidelity initiation in vivo depends strongly on eIF3b interactions at the subunit interface that either promote the closed conformation of the PIC on start codon selection or facilitate subsequent relocation back to the solvent side of the 40S subunit.

scholarly journals Roles of helix H69 of 23S rRNA in translation initiation

2015 ◽  
Vol 112 (37) ◽  
pp. 11559-11564 ◽  
Author(s):  
Qi Liu ◽  
Kurt Fredrick
Keyword(s):  
Translation Initiation ◽  
Start Codon ◽  
23S Rrna ◽  
Initiator Trna ◽  
Lethal Phenotype ◽  
Initiation Factors ◽  
Dominant Lethal ◽  
Initiation Of Translation ◽  
Codon Selection ◽  
Subunit Joining

Initiation of translation involves the assembly of a ribosome complex with initiator tRNA bound to the peptidyl site and paired to the start codon of the mRNA. In bacteria, this process is kinetically controlled by three initiation factors—IF1, IF2, and IF3. Here, we show that deletion of helix H69 (∆H69) of 23S rRNA allows rapid 50S docking without concomitant IF3 release and virtually eliminates the dependence of subunit joining on start codon identity. Despite this, overall accuracy of start codon selection, based on rates of formation of elongation-competent 70S ribosomes, is largely uncompromised in the absence of H69. Thus, the fidelity function of IF3 stems primarily from its interplay with initiator tRNA rather than its anti-subunit association activity. While retaining fidelity, ∆H69 ribosomes exhibit much slower rates of overall initiation, due to the delay in IF3 release and impedance of an IF3-independent step, presumably initiator tRNA positioning. These findings clarify the roles of H69 and IF3 in the mechanism of translation initiation and explain the dominant lethal phenotype of the ∆H69 mutation.

scholarly journals Conformational rearrangements upon start codon recognition in human 48S translation initiation complex

2021 ◽  
Author(s):  
Sung-Hui Yi ◽  
Valentyn Petrychenko ◽  
Jan Erik Schliep ◽  
Akanksha Goyal ◽  
Andreas Linden ◽  
...  
Keyword(s):  
Translation Initiation ◽  
Population Distribution ◽  
Start Codon ◽  
Translation Start Codon ◽  
Initiation Factors ◽  
Codon Recognition ◽  
Translation Start ◽  
Conformational Rearrangements ◽  
Codon Selection ◽  
Selection Of

Selection of the translation start codon is a key step during protein synthesis in human cells. We obtained cryo-EM structures of human 48S initiation complexes and characterized the intermediates of codon recognition by kinetic methods using eIF1A as a reporter. Both approaches capture two distinct ribosome populations formed on an mRNA with a cognate AUG codon in the presence of eIF1, eIF1A, eIF2–GTP–Met-tRNAiMet, and eIF3. The ‘open’ 40S subunit conformation differs from the human 48S scanning complex and represents an intermediate preceding the codon recognition step. The ‘closed’ form is similar to reported structures of complexes from yeast and mammals formed upon codon recognition, except for the orientation of eIF1A, which is unique in our structure. Kinetic experiments show how various initiation factors mediate the population distribution of open and closed conformations until 60S subunit docking. Our results provide insights into the timing and structure of human translation initiation intermediates and suggest the differences in the mechanisms of start codon selection between mammals and yeast.

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