Sequence and analysis of the 46.6-kb plasmid pA1 from Sphingomonas sp A1 that corresponds to the typical IncP-1β plasmid backbone without any accessory gene

Sphingomonas sp. A1 (strain A1) is capable of directly incorporating macromolecules (e.g., alginate) through the specialized import system-"super-channel." Here, we report the complete DNA sequence and genetic organization of plasmid pA1 from strain A1. Nucleotide sequence analysis revealed that pA1 comprises 46,557bp encoding 49 open reading frames (ORFs) with 65% G+C content and abundant GCCG/CGGC motifs. Many predicted pA1ORFs showed high similarity to pA81 ORFs; pA81 is supposedly a self-transmissible promiscuous incompatibility (Inc) group P-1 beta plasmid. Unlike any reported IncP-1 plasmids, pA1 contains no inserted mobile genetic elements. The genetic organization and predicted pA1 ORFs showed greater similarity to the IncP-1 beta plasmid backbone than to the IncP-1 alpha plasmid backbone. pA1 contains restriction site-associated repeat sequences typical of the IncP-1 beta but absent in the IncP-lot and 6 subgroups. Thus, the overall pA1 structure corresponds to that of the typical IncP-1 beta plasmids. Phylogenetic analysis of the replication-associated proteins suggested that pA1 may have diverged later along with the two IncP-1 beta plasmids-pA81 and pB4. The 2.4-kb duplicates of stable inheritance genes klcAB and korC in pA1 possibly resulted from insertion and/or recombination events via the repeat sequences flanking these duplicates. (c) 2005 Elsevier Inc. All rights reserved.