Computational protocol: Competitive folding of anti-terminator/terminator hairpins monitored by single molecule FRET

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Protocol publication

[…] RAT sequences in complete bacterial genomes have been searched using the nucleotide blastn web server, hosted by the NCBI server (http://blast.ncbi.nlm.nih.gov) and the RAT sequences of licS, sacB, sacX, sacP or ptsG from B. subtilis. Each putative RAT sequence has been checked manually and only those for which the downstream regulated gene and the cognate anti-terminator protein could be unambiguously inferred have been retrieved. The identified target genes have been eventually renamed as their orthologues in B. subtilis or E. coli. Formation of the predicted downstream terminator hairpins have been checked using the RNAfold server (http://rna.tbi.univie.ac.at). No apparent RAT-overlapping terminator could be found in case of sacX encoding the negative SacY-regulator in the three B. subtilis sub-species we analysed, RNAfold detecting only an imperfect palindrome (Supplementary Figure S1, in grey) overlapping the RAT sequence over only 3 or 5 nt (underlined in black) and comprising a very small putative terminator (in red); nevertheless, previous studies have shown that sucrose-induction of the sacXY operon relies on this regulatory RAT element as well as downstream sequences possibly forming alternative mRNA secondary structures (). […]

Pipeline specifications

Software tools BLASTN, RNAfold
Application RNA structure analysis
Organisms Bacillus subtilis