Baez et al. 2020 (PRJNA564991)

General Details

Title Flavobacterium johnsoniae ribosome profiling
Organism
Number of Samples 3
Release Date 2019/09/11 00:00
Sequencing Types
Protocol Details

Study Links

Repository Details

SRA SRP221399
ENA SRP221399
GEO 0.0
BioProject PRJNA564991

Publication

Title
Authors Baez WD, Roy B, McNutt ZA, Shatoff EA, Chen S, Bundschuh R, Fredrick K
Journal Nucleic acids research
Publication Date 2019 Nov 18
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. © The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.
PMC PMC6847099
PMID 31602466
DOI
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)
SRR10100142 PRJNA564991 Flavobacterium johnsoniae ATCC:17061 0.0 0.0
SRR10100141 PRJNA564991 Flavobacterium johnsoniae ATCC:17061 0.0 0.0
SRR10100140 PRJNA564991 Flavobacterium johnsoniae ATCC:17061 0.0 0.0
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)

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