DNA-binding specificity of the Lon protease α-domain from Brevibacillus thermoruber WR-249

Lon protease has been well studied in many aspects; however, the DNA-binding specificity of Lon in prokaryotes has not been clearly identified. Here we examined the DNA-binding activity of Lon protease α-domains from Brevibacillus thermoruber (Bt), Bacillus subtilis (Bs), and Escherichia coli (Ec). MALDI-TOF mass spectroscopy showed that the α-domain from Bt-Lon binds to the duplex nucleotide sequence 5′-CTGTTAGCGGGC-3′ (ms1) and protected it from DNase I digestion. Surface plasmon resonance showed that the Bt-Lon α-domain binds with ms1 double-stranded DNA tighter than Bs- and Ec-Lon α-domains, whereas the Bt-Lon α-domain has dramatically lower affinity for double-stranded DNA with 0 and 50% identity to the ms1 binding sequence. Our results indicated that Bt-Lon α-domain plays a critical role with ms1 sequence in the DNA-binding specificity.