Analysis of the N-terminal DNA binding domain of the IS30 transposase

IS30 is the founding member of a large family of widely spread bacterial insertion sequences with closely related transposases. The N-terminal end of the IS30 transposase had been shown to retain sequence-specific DNA binding activity and to protect the IS30 terminal inverted repeats. Structural predictions revealed the presence of a helix-helix-turn-helix motif (H-HTH2) which, in the case of IS30, is preceded by an additional helix-turn-helix motif (HTH1). Analysis of deletion and point mutants in this region revealed that both motifs are important for IS30 transposition. IS30 exhibits two types of insertion specificity preferring either a 24 bp palindromic hot-spot (GOHS) or sequences resembling its ends [left and right terminal inverted repeat (IRL and IRR)]. Results are presented suggesting that the HTH1 region is required for GOHS targeting and interferes with the inverted repeat (IR) targeting. On the other hand, H-HTH2 appears to be required for both. The binding activities of the mutant proteins to the terminal IS30 IRs as measured by gel retardation correlated well with these results. Furthermore, close inspection of the H-HTH2 region revealed significant amino acid identity with a similar predicted secondary structure carried by the transcriptional regulator FixJ of Sinorhizobium meliloti and involved in FixJ binding to its target sequence. This suggests that FixJ and IS30 transposase share similar sequence-specific DNA binding mechanisms.