Baez et al. 2020 (PRJNA564991)
General Details
| Title | Flavobacterium johnsoniae ribosome profiling |
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| Organism | |
| Number of Samples | 3 |
| Release Date | 2019/09/11 00:00 |
| Sequencing Types | |
| Protocol Details |
Study Links
| GWIPS-viz | Trips-Viz |
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Repository Details
| SRA | SRP221399 |
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| ENA | SRP221399 |
| GEO | |
| BioProject | PRJNA564991 |
Publication
| Title | |
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| 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) | ||
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| SRR10100142 | PRJNA564991 | Flavobacterium johnsoniae | ATCC:17061 |  |
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| SRR10100141 | PRJNA564991 | Flavobacterium johnsoniae | ATCC:17061 | |
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| SRR10100140 | PRJNA564991 | Flavobacterium johnsoniae | ATCC:17061 | |
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| 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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