Comparative genome analysis of four magnetotactic bacteria reveals a complex set of group-specific genes implicated in magnetosome biomineralization and function

Abstract

Magnetotactic bacteria (MTB) are a heterogeneous group of aquatic prokaryotes with a unique intracellular organelle, the magnetosome, which orients the cell along magnetic field lines. Magnetotaxis is a complex phenotype, which depends on the coordinate synthesis of magnetosomes and the ability to swim and orient along the direction caused by the interaction with the Earth's magnetic field. Although a number of putative magnetotaxis genes were recently identified within a conserved genomic magnetosome island (MAI) of several MTB, their functions have remained mostly unknown, and it was speculated that additional genes located outside the MAI might be involved in magnetosome formation and magnetotaxis. In order to identify genes specifically associated with the magnetotactic phenotype, we conducted comparisons between four sequenced magnetotactic Alphaproteobacteria including the nearly complete genome of Magnetospirillum gryphiswaldense strain MSR-1, the complete genome of Magnetospirillum magneticum strain AMB-1, the complete genome of the magnetic coccus MC-1, and the comparative-ready preliminary genome assembly of Magnetospirillum magnetotacticum strain MS-1 against an in-house database comprising 426 complete bacterial and archaeal genome sequences. A magnetobacterial core genome of about 891 genes was found shared by all four MTB. In addition to a set of approximately 152 genus-specific genes shared by the three Magnetospirillum strains, we identified 28 genes as group specific, i.e., which occur in all four analyzed MTB but exhibit no (MTB-specific genes) or only remote (MTB-related genes) similarity to any genes from nonmagnetotactic organisms and which besides various novel genes include nearly all mam and mms genes previously shown to control magnetosome formation. The MTB-specific and MTB-related genes to a large extent display synteny, partially encode previously unrecognized magnetosome membrane proteins, and are either located within (18 genes) or outside (10 genes) the MAI of M. gryphiswaldense. These genes, which represent less than 1% of the 4,268 open reading frames of the MSR-1 genome, as yet are mostly of unknown functions but are likely to be specifically involved in magnetotaxis and, thus, represent prime targets for future experimental analysis.

FIG. 1.

Phylogenetic affiliation of best BLAST hits of all conserved ORFs from MSR-1. Bars represent the top-10 numbers of the best E-value hits from each conserved gene in MSR-1. (A) Distribution with all database species from genomesDB included. (B) Distribution after closest relatives AMB-1, MS-1, and R. rubrum were excluded from analysis.

FIG. 2.

Comparative gene content analysis of MTB based on reciprocal best matches. The Venn diagrams illustrate the shared gene content between the four genomes. For visualization, individual diagrams for three genomes are shown. The numbers of species-specific genes and shared genes are indicated. (A) Shared gene content between MSR-1, AMB-1, and MS-1. (B) Shared gene content between MSR-1, AMB-1, and strain MC-1.

FIG. 3.

Phylogenetic tree of MamH (MGR4089) orthologous and paralogous proteins including the MTB-related MGR4148 (maximum-likelihood analysis). MamH represents a typical example for an MTB-related protein defined in this study; i.e., it forms a coherent phylogenetic branch within its family tree. In addition, the newly identified MTB-related MGR4148 gene is related to MamH but forms a distinct group. The three major clusters are indicated by different colors. The numbers indicate the bootstrap support for selected nodes.

FIG. 4.

Gene neighborhood representation of selected group-specific genes. Identical colors indicate homologous genes in the corresponding genomes. Arrows in bold lines indicate identification of the gene product within the magnetosome membrane. (A) mamXY cluster. Conserved gene neighborhood of MGR4148, mamX (MGR4149), and mamY (MGR4150) (top). Schematic representation of the different Pfam domain structure of the MTB-related gene MGR4148 compared to mamH (bottom) (B) Gene neighborhood of mtxA. The corrected annotation for the MGR0208 homolog of AMB-1 is shown. (C) Gene neighborhood of MGR3500. (D) Gene neighborhood of mmsF (MGR4072).