Cold Et12 was a
weaker competitor to Et23 binding, since a noticeable decrease in band intensity demanded 500-fold molar excess of Et12 (Figure 3B). The results with Pb18 extracts presented in Figures 3A and 3B were similar with extracts from Pb339 and Pb3 (data not shown), suggesting that the same protein selleck inhibitor in each isolate binds to both probes; however affinity for Et23 is possibly higher. Therefore, a DNA binding motif might include the overlapping region from nt -243 to -229 (CTGTTGATCTTTT), for which there are no motifs recognized by the TFsearch computer program (Figure 1). We also designed an Et23Δ probe to verify the influence in EMSA of substitution at -230 (C/A). We initially noticed that the Et23Δ band was reproducibly less intense than the Et23 band when assayed with protein extracts from Pb18 (Figure 3C) and Pb339 (data not shown), but equally intense with Pb3 extracts (Figure 3C). In terms of competition with the Et12 complex, Et23Δ was as good a competitor as Et23, while cold Et12 could apparently Lorlatinib inhibit band formation with Et23Δ more effectively
than with Et23 (Figure 3D). Therefore, a C (instead of an A) at position -230 seems to be important for stronger Pb18 protein binding to Et23. Figure 3 Radioautograms showing EMSA results with radio labeled (*) Et12, Et23, and Et23Δ probes. When not specified, protein extracts from Pb18 were used. In A, specificity of the EMSA bands was suggested by effective competition with 100 × molar excess of cold homologous probe. In B and D, cross-competition experiments with the indicated
cold probes at 100 Methane monooxygenase × or 500 × molar excess. In C, the intensity of Et23 and Et23Δ (ACY-1215 chemical structure mutated in -230 to A) bands are compared with different protein extracts (Pb3 or Pb18, as indicated). In E, migration of Et12 and Et23 bands are compared with protein extracts from different isolates (indicated). The position of shifted bands is indicated with arrows. Figure 3E shows the Et12 and Et23 bands obtained with protein extracts from Pb18, Pb339 and Pb3 comparatively in the same radioautogram. It is noticeable that while the bands migrated similarly for each individual isolate, the Pb3 bands (both Et12 and Et23) migrated faster. It is worth mentioning that we observed similar behavior with Bs8.1Δ, which was also positive in EMSA with protein extracts from Pb18 and Pb3; the shifted band migrated similarly for Pb18 and Pb339, but faster for Pb3 (data not shown). Bs8.1 and Bs8.2Δ were only assayed with Pb339 extracts. Manual search through the PbGP43 promoter region revealed the existence of two CreA-like DNA binding motifs (C/GC/TGGA/GG), whose sequences (CTGGTG and ATGGTG) are observed in the Et6 and Et7 probes (Figure 1, Table 1). CreA is a zinc-finger catabolic repressor in A. nidulans  and we tested the probes with Pb339 extracts.