Prokaryotic coding regions have little if any specific depletion of Shine-Dalgarno motifs
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چکیده
منابع مشابه
Depletion of Shine-Dalgarno Sequences Within Bacterial Coding Regions Is Expression Dependent
Efficient and accurate protein synthesis is crucial for organismal survival in competitive environments. Translation efficiency-the number of proteins translated from a single mRNA in a given time period-is the combined result of differential translation initiation, elongation, and termination rates. Previous research identified the Shine-Dalgarno (SD) sequence as a modulator of translation ini...
متن کاملThe Frequency of Internal Shine–Dalgarno-like Motifs in Prokaryotes
In prokaryotes, translation initiation typically depends on complementary binding between a G-rich Shine-Dalgarno (SD) motif in the 5' untranslated region of mRNAs, and the 3' tail of the 16S ribosomal RNA (the anti-SD sequence). In some cases, internal SD-like motifs in the coding region generate "programmed" ribosomal pauses that are beneficial for protein folding or accurate targeting. On th...
متن کاملSelection of Shine-Dalgarno sequences in plastids
Like bacterial genes, most plastid (chloroplast) genes are arranged in operons and transcribed as polycistronic mRNAs. Plastid protein biosynthesis occurs on bacterial-type 70S ribosomes and translation initiation of many (but not all) mRNAs is mediated by Shine-Dalgarno (SD) sequences. To study the mechanisms of SD sequence recognition, we have analyzed translation initiation from mRNAs contai...
متن کاملEvaluating Representations for the Shine-Dalgarno Site in Escherichia coli
Several methods for identifying individual motif instance by exhaustive evaluation of k-mers (k ≤ 10) are applied to the pooled Upstream Regions (USR) of all 4289 Escherichia coli ORFs. Instances of the Shine-Dalgarno (SD) site are readily identified using these methods. Using these motif instances as starting points, various motif representations and training methods, including several new alg...
متن کاملConserved small mRNA with an unique, extended Shine-Dalgarno sequence
Up to now, very small protein-coding genes have remained unrecognized in sequenced genomes. We identified an mRNA of 165 nucleotides (nt), which is conserved in Bradyrhizobiaceae and encodes a polypeptide with 14 amino acid residues (aa). The small mRNA harboring a unique Shine-Dalgarno sequence (SD) with a length of 17 nt was localized predominantly in the ribosome-containing P100 fraction of ...
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ژورنال
عنوان ژورنال: PLOS ONE
سال: 2018
ISSN: 1932-6203
DOI: 10.1371/journal.pone.0202768