Conservation of proteobacterial magnetosome genes and structures in an uncultivated member of the deep-branchingNitrospiraphylum

Abstract

Magnetotactic bacteria (MTB) are a phylogenetically diverse group which uses intracellular membrane-enclosed magnetite crystals called magnetosomes for navigation in their aquatic habitats. Although synthesis of these prokaryotic organelles is of broad interdisciplinary interest, its genetic analysis has been restricted to a few closely related members of the Proteobacteria, in which essential functions required for magnetosome formation are encoded within a large genomic magnetosome island. However, because of the lack of cultivated representatives from other phyla, it is unknown whether the evolutionary origin of magnetotaxis is monophyletic, and it has been questioned whether homologous mechanisms and structures are present in unrelated MTB. Here, we present the analysis of the uncultivated "Candidatus Magnetobacterium bavaricum" from the deep branching Nitrospira phylum by combining micromanipulation and whole genome amplification (WGA) with metagenomics. Target-specific sequences obtained by WGA of cells, which were magnetically collected and individually sorted from sediment samples, were used for PCR screening of metagenomic libraries. This led to the identification of a genomic cluster containing several putative magnetosome genes with homology to those in Proteobacteria. A variety of advanced electron microscopic imaging tools revealed a complex cell envelope and an intricate magnetosome architecture. The presence of magnetosome membranes as well as cytoskeletal magnetosome filaments suggests a similar mechanism of magnetosome formation in "Cand. M. bavaricum" as in Proteobacteria. Altogether, our findings suggest a monophyletic origin of magnetotaxis, and relevant genes were likely transferred horizontally between Proteobacteria and representatives of the Nitrospira phylum.M agnetotactic bacteria (MTB) are widespread aquatic microorganisms that use unique intracellular organelles called magnetosomes to navigate along the earth's magnetic field while searching for growth-favoring microoxic zones within stratified sediments. In strains of Magnetospirillum, it was shown that magnetosomes consist of magnetite (Fe 3 O 4 ) crystals enclosed by a dedicated phospholipid membrane. The magnetosome membrane (MM) contains a specific set of proteins (1-3), which direct the biomineralization of highly ordered crystals along actin-like cytoskeletal filaments that control the assembly and intracellular positioning of a linear magnetosome chain (4-7). Synthesis of magnetosomes has recently emerged as a model for prokaryotic organelle formation and biomineralization (8-11). The trait of magnetotaxis is widely spread among Proteobacteria including members from the α-, δ-and γ-subdivisions, as well as uncultivated species from the deep branching Nitrospira phylum (8). The presence of MTB within unrelated lines of various phylogenetic groups, as well as their stunning diversity with respect to magnetosome shape, composition, and intracellular organization lead to speculations of whether the evolutionary origin of magnetota...

Genomic insights into the uncultured genus ‘Candidatus Magnetobacterium’ in the phylum Nitrospirae

“…Comparative genomic analyses of MAIs from Alphaproteobacteria and Deltaproteobacteria MTB and an incomplete MAI from Mbav have suggested a common set of magnetosome genes existed in these MTB (Nakazawa et al, 2009;Jogler et al, 2011;Lefèvre and Wu, 2013;Lefèvre et al, 2013b). The complete MAI of Mcas presented here confirms the presence of these core genes (mamKPMQBAIEO) that should be essential for magnetosome biomineralization in both Nitrospirae and Proteobacteria MTB (Figure 4).…”

“…Although unlike their Proteobacteria counterparts, the hallmarks of MTB in 'Ca. Magnetobacterium' genus are their ability to forms hundreds to a thousand bullet-shaped magnetite magnetosomes organized into multiple bundles of chains (Spring et al, 1993;Jogler et al, 2011). In this study, the complete sequence of magnetosome protein MamK, a key protein for organizing magnetosomes into chain arrangement in Proteobacteria MTB (Komeili et al, 2006;Ozyamak et al, 2013), has been identified, suggesting a similar strategy of magnetosomes chain organization in both Nitrospirae and Proteobacteria MTB.…”

“…(i) Two 16S rRNA gene clone libraries were constructed from the extracted genomic DNA, and 36 clones were randomly chosen for Sanger sequencing. All 31 successfully sequenced genes showed high similarities (499%) and were mostly similar to Mbav (Spring et al, 1993;Jogler et al, 2011). (ii) The fluorescence in situ hybridization analysis (Figure 1d) indicates that the enriched culture was pure.…”

“…Recent studies have suggested that these organisms may be capable of oxidizing sulfur (Spring and Bazylinski, 2006;Jogler et al, 2010), thus linking this genus to the key steps of iron and sulfur cycles in nature. However, except for a few short genomic fragments (Jogler et al, 2010;Jogler et al, 2011;Lin et al, 2011), very little genetic data of this genus are available owing to their unculturability. Consequently, knowledge of their trophic strategy, physiology and intracellular biomineralization remains very limited.…”

Common ancestry of iron oxide- and iron-sulfide-based biomineralization in magnetotactic bacteria

“…A number of magnetosome-related genes, including mamA, mamB, mamE, mamI, mamM, mamP and mamQ, were recently found to be present in the genome of Candidatus Magnetobacterium bavaricum, a magnetite-producing MTB phylogenetically affiliated with the Nitrospirae phylum (Jogler et al, 2011). These genes not only show similar sequence homologies to others of their type, the organization of these genes show similar short intergenic distances between them and an identical direction of transcription, providing evidence that they are organized as an operon as described for other MTB (Schü bbe et al, 2006).…”