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 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.

scholarly journals eIF1 Controls Multiple Steps in Start Codon Recognition during Eukaryotic Translation Initiation

2009 ◽  
Vol 394 (2) ◽  
pp. 268-285 ◽  
Author(s):  
Jagpreet S. Nanda ◽  
Yuen-Nei Cheung ◽  
Julie E. Takacs ◽  
Pilar Martin-Marcos ◽  
Adesh K. Saini ◽  
...  
Keyword(s):  
Translation Initiation ◽  
Start Codon ◽  
Eukaryotic Translation ◽  
Codon Recognition ◽  
Eukaryotic Translation Initiation

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.

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