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Author = Sharma, Virag;
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Displaying Results 1 - 2 of 2 on page 1 of 1
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Analysis of tetra- and hepta-nucleotides motifs promoting -1 ribosomal frameshifting in Escherichia coli
(2014)
Sharma, Virag; Prère, Marie-Francoise; Canal, Isabelle; Firth, Andrew E.; Atkins, John ...
Analysis of tetra- and hepta-nucleotides motifs promoting -1 ribosomal frameshifting in Escherichia coli
(2014)
Sharma, Virag; Prère, Marie-Francoise; Canal, Isabelle; Firth, Andrew E.; Atkins, John F.; Baranov, Pavel V.; Fayet, Olivier
Abstract:
Programmed ribosomal -1 frameshifting is a non-standard decoding process occurring when ribosomes encounter a signal embedded in the mRNA of certain eukaryotic and prokaryotic genes. This signal has a mandatory component, the frameshift motif: it is either a Z_ZZN tetramer or a X_XXZ_ZZN heptamer (where ZZZ and XXX are three identical nucleotides) allowing cognate or near-cognate repairing to the -1 frame of the A site or A and P sites tRNAs. Depending on the signal, the frameshifting frequency can vary over a wide range, from less than 1% to more than 50%. The present study combines experimental and bioinformatics approaches to carry out (i) a systematic analysis of the frameshift propensity of all possible motifs (16 Z_ZZN tetramers and 64 X_XXZ_ZZN heptamers) in Escherichia coli and (ii) the identification of genes potentially using this mode of expression amongst 36 Enterobacteriaceae genomes. While motif efficiency varies widely, a major distinctive rule of bacterial -1 framesh...
http://hdl.handle.net/10468/5017
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Retapamulin-assisted ribosome profiling reveals the alternative bacterial proteome
(2019)
Meydan, Sezen; Marks, James; Klepacki, Dorota; Sharma, Virag; Baranov, Pavel V.; Firth,...
Retapamulin-assisted ribosome profiling reveals the alternative bacterial proteome
(2019)
Meydan, Sezen; Marks, James; Klepacki, Dorota; Sharma, Virag; Baranov, Pavel V.; Firth, Andrew E.; Margus, Tonu; Kefi, Amira; Vázquez-Laslop, Nora; Mankin, Alexander S.
Abstract:
The use of alternative translation initiation sites enables production of more than one protein from a single gene, thereby expanding the cellular proteome. Although several such examples have been serendipitously found in bacteria, genome-wide mapping of alternative translation start sites has been unattainable. We found that the antibiotic retapamulin specifically arrests initiating ribosomes at start codons of the genes. Retapamulin-enhanced Ribo-seq analysis (Ribo-RET) not only allowed mapping of conventional initiation sites at the beginning of the genes, but strikingly, it also revealed putative internal start sites in a number of Escherichia coli genes. Experiments demonstrated that the internal start codons can be recognized by the ribosomes and direct translation initiation in vitro and in vivo. Proteins, whose synthesis is initiated at internal in-frame and out-of-frame start sites, can be functionally important and contribute to the “alternative” bacterial proteome. The i...
http://hdl.handle.net/10468/7933
Displaying Results 1 - 2 of 2 on page 1 of 1
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