Availability of a second upstream AUG can completely overcome inhibition of protein synthesis initiation engendered by mRNA secondary structure encompassing the start codon

AbstractThe ribosome is a dynamic machine that undergoes many conformational rearrangements during the initiation of protein synthesis. Significant differences exist between the process of protein synthesis initiation in eubacteria and eukaryotes. In particular, the initiation of eukaryotic protein synthesis requires roughly an order of magnitude more initiation factors to promote efficient mRNA recruitment and ribosomal recognition of the start codon than are needed for eubacterial initiation. The mechanisms by which these initiation factors promote ribosome conformational changes during stages of initiation have been studied using cross-linking, footprinting, site-directed probing, cryo-electron microscopy, X-ray crystallography, fluorescence spectroscopy and single-molecule techniques. Here, we review how the results of these different approaches have begun to converge to yield a detailed molecular understanding of the dynamic motions that the eukaryotic ribosome cycles through during the initiation of protein synthesis.

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Minigene-like inhibition of protein synthesis mediated by hungry codons near the start codon

Nucleic Acids Research ◽

10.1093/nar/gkn395 ◽

2008 ◽

Vol 36 (13) ◽

pp. 4233-4241 ◽

Cited By ~ 5

Author(s):

E. Jacinto-Loeza ◽

S. Vivanco-Dominguez ◽

G. Guarneros ◽

J. Hernandez-Sanchez

Keyword(s):

Protein Synthesis ◽

Start Codon ◽

Inhibition Of Protein Synthesis

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Global analysis of protein synthesis in Flavobacterium johnsoniae reveals the use of Kozak-like sequences in diverse bacteria

Nucleic Acids Research ◽

10.1093/nar/gkz855 ◽

2019 ◽

Vol 47 (20) ◽

pp. 10477-10488 ◽

Cited By ~ 9

Author(s):

William D Baez ◽

Bappaditya Roy ◽

Zakkary A McNutt ◽

Elan A Shatoff ◽

Shicheng Chen ◽

...

Keyword(s):

Escherichia Coli ◽

Protein Synthesis ◽

Comparative Analysis ◽

Translation Initiation ◽

Global Analysis ◽

Start Codon ◽

Mrna Secondary Structure ◽

Kozak Sequence ◽

Flavobacterium Johnsoniae ◽

Initiation Of Translation

Abstract In all cells, initiation of translation is tuned by intrinsic features of the mRNA. Here, we analyze translation in Flavobacterium johnsoniae, a representative of the Bacteroidetes. Members of this phylum naturally lack Shine–Dalgarno (SD) sequences in their mRNA, and yet their ribosomes retain the conserved anti-SD sequence. Translation initiation is tuned by mRNA secondary structure and by the identities of several key nucleotides upstream of the start codon. Positive determinants include adenine at position –3, reminiscent of the Kozak sequence of Eukarya. Comparative analysis of Escherichia coli reveals use of the same Kozak-like sequence to enhance initiation, suggesting an ancient and widespread mechanism. Elimination of contacts between A-3 and the conserved β-hairpin of ribosomal protein uS7 fails to diminish the contribution of A-3 to initiation, suggesting an indirect mode of recognition. Also, we find that, in the Bacteroidetes, the trinucleotide AUG is underrepresented in the vicinity of the start codon, which presumably helps compensate for the absence of SD sequences in these organisms.

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