Evaluation of the mobile content in Magnetospirillum magneticum AMB-1 genome using bioinformatical approaches reveals a new genome size for the magnetosome island

Abstract

After completing its sequence/annotation in 2005, Magnetospirillum magneticum AMB-1 had become one of the most important magnetotactic genomes used to facilitate analysis of the magnetosome formation process. In this paper we investigate the genome contents of AMB-1 and other magnetotactic bacteria to demonstrate the size of mobile genome and number of conserved genes in M. magneticum AMB-1. The preliminary analysis presented here shows the mosaic structure of these genomes. 100 genomic islands were identified in AMB-1 by IslandPick. Moreover, the size of AMB-1 magnetosome island (MAI), previously known to be 100 kb, was re-estimated to be in the size range of 110 kb. Thus more genes were included to be part of this GI. The investigation included the use of comparative approaches to elucidate conserved protein coding sequences. 13 CDS were identified to be conserved among three magnetotactic genomes. One CDS (amb3135) was conserved in five magnetotactic genomes. The amino acid sequence for this CDS (amb3135) was used to draw a phylogenetic tree among magnetotactic bacteria. The phylogeny based on amb3135 is in concordance with previous studies indicating a close relationship between strain AMB-1 and other Magnetospirillum species.