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Japanese Team Sequences Genome of Magnetic Bacteria

NEW YORK (GenomeWeb News) – Japanese researchers have sequenced the genome of a magnetic bacterial species called Desulfovibrio magneticus — work that they say uncovers hints about magnetic structures found in this and some other bacteria.

The team sequenced the more than 5.3 million bases in the D. magneticus genome using whole-genome sequencing. By comparing this sequence with genetic and genomic sequences for other bacteria — including magnetic bacteria from a slightly different group — the researchers pinpointed three gene regions believed to contribute to the formation and function of magnetic structures in the bacteria called magnetosomes.

The study, published in the advanced, online edition of Genome Research today, also suggests that these genes moved horizontally from one bacterial species to the next.

"Our findings suggest the presence of core genetic components for magnetosome biosynthesis," senior author Tadashi Matsunaga, a biotechnology researcher at the Tokyo University of Agriculture and Technology, and his colleagues wrote, "these genes may have been acquired into the magnetotactic bacterial genomes by multiple gene transfer events during proteobacterial evolution."

D. magneticus is a gamma-proteobacterial species that belongs to a larger group of magnetic microbes known as magnetotactic bacteria. These microbes accumulate iron particles from the environment and organize them into magnetic particle structures called magnetosomes, which help them use the Earth's magnetic field for directional and other information.

While past genomic, proteomic, and transcriptomic studies have delved into magnetosome function to a certain extent, the authors noted, most work has been done on alpha-proteobacteria, leaving questions about which genes orchestrate magnetosome function in other types of magnetotactic bacteria.

Matsunaga and his colleagues used whole-genome shotgun sequencing with an ABI 3700 DNA Analyzer to sequence the more than 5.3 million base of a D. magneticus strain called RS-1.

The genome is housed on a 5.2 million base pair circular chromosome containing 4,629 open reading frames and two smaller plasmids containing 65 ORFs and 10 ORFs, respectively, the researchers explained.

After sequencing the D. magneticus genome, the team found that it was larger than those of magnetic bacteria sequenced before it and contained G and C nucleotides in non-uniform clumps in the genome.

The researchers then used BLAST to search the Universal Protein Resource database for sequences that resembled those in D. magneticus. Dozens of the genes resembled those in other magnetic bacteria such as Magnetospirillium magneticum or M. gryphiswaldense and reciprocal matches between the genomes of five different magnetotactic bacteria turned up 456 core magnetotactic genes.

When they compared the D. magneticus genome with whole genome data for three other bacteria in the same genera as well as four magnetic bacteria strains in the alpha-proteobacterial group, the team fingered a trio of gene regions that seem to contribute to magnetosome functioning.

The regions were well conserved in the all of the species tested. One, called the nuo gene cluster, was also present in the genomes of three iron-reducing bacteria, the team noted, while a mamaAB-like gene cluster, which apparently governs processes such as iron transport and magnetosome alignment, was present in islands throughout the genomes of the magnetic bacteria. Similar islands have been observed previously for magnetosome membrane protein-coding genes.

Based on these patterns — and the discovery that a cryptic plasmid carrying several genes resembling those in magnetic bacteria — the team speculated that gene regions related to magnetosome function have spread from one species to the next via horizontal gene transfer rather than common descent.

Matsunaga said in a statement that studies such as this may eventually reveal not only insights into the biology underlying magnetosomes, but also clues for applying such structures to develop new technology. He highlighted the potential value of being able to synthesize magnetosomes with a given morphology, which he says "provide opportunities to their applications in electromagnetic tapes, drug delivery, magnetic resonance imaging, and cell separation."

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