Pseudomonas putida AlkA and AlkB Proteins Comprise Different Defense Systems for the Repair of Alkylation Damage to DNA – In Vivo, In Vitro, and In Silico Studies
Figure 1
The genes encoding proteins involved in the repair of alkylation damage to DNA in (A) P. putida (tag1 – locus tag: PputGB1_0078, alkA – PputGB1_0739, ada – PputGB1_0740, tag2 – PputGB1_1244, alkA2 – PputGB1_2545, alkB – PputGB1_2549, ogt – PputGB1_2805, gcdH – PputGB1_3505, atl – PputGB1_4493, aidB – PputGB1_4834, aag – PputGB1_4865, adap – promoter region containing putative Ada box, hp – hypothetical protein) and (B) E. coli species (atl – ECDH10B_0410, ogt – ECDH10B_1455, alkA – ECDH10B_2218, alkB – ECDH10B_2369, ada – ECDH10B_2370, tag – ECDH10B_3728, aidB – ECDH10B_4382).
The CLANS protein clustering of P. putida and E. coli AlkA, Tag, and Aag sequences (C) indicates that PpAlkA2s are 3meA glycosylases most closely related to EcAlkA proteins. The CLANS clustering of P. putida and E. coli AidB protein sequences (family cd01154, NCBI) (D) clearly shows that the P. putida acyl-CoA dehydrogenases represented by P. putida KT2440 locus PP_4780 are most closely related to E. coli AidB proteins but the subfamily of PpGcdH, comprising other acyl-CoA dehydrogenases represented by P. putida KT2440 locus PP_0158, preserve perfect Ada boxes in their promoter regions (see Figure 3).