bprom algorithm  (Softberry Inc)

Journal: Frontiers in Cellular and Infection Microbiology

Article Title: CodY Regulates Thiol Peroxidase Expression as Part of the Pneumococcal Defense Mechanism against H 2 O 2 Stress

doi: 10.3389/fcimb.2017.00210

Figure Lengend Snippet: Identification of tpxD regulatory promoter elements. (A) In silico analysis of tpxD proximal promoter region. Identification of tpxD promoter elements using BPROM algorithm: ATG start codon (1); Shine Dalgarno (2); transcription start site at A (3); −10 and −35 elements of the σ 70 promoter (4 and 5, respectively). The first nucleotide included in each of the Δ tpxD comp mutants (1–6) is indicated by arrow. (B) Influence of tpxD putative regulatory elements on TpxD expression levels under H 2 O 2 stress. TpxD levels, determined by Western blotting, were measured in D39, Δ tpxD and Δ tpxD comp1-6 (described in Figure ). Bacteria were grown anaerobically to OD 620 = 0.25 and then challenged with 1 mM H 2 O 2 for 40 min. Separated proteins were electroblotted onto 0.45 μm nitrocellulose membrane, and stained with Ponceau S to ensure equal loading, before incubation with antibodies. Membranes were exposed for long time intervals to ensure the absence of bands in Δ tpxD comp1-4 and are lined up, as indicated in the figure. Densitometry was performed using ImageJ software.

Article Snippet: Promoter elements were predicted using the Softberry BPROM algorithm of bacterial promoters ( http://www.softberry.com/berry.phtml?topic=bprom&group=programs&subgroup=gfindb ).

Techniques: In Silico, Expressing, Western Blot, Staining, Incubation, Software