Genome of Controversial Arsenic Bacterium Sequenced

Our data show evidence for arsenate in macromolecules that normally contain phosphate, most notably nucleic acids and proteins.

One year ago those 18 words ignited quite a media controversy when Felisa Wolfe-Simon and her colleagues held a press conference to announce the discovery of a bacterium that not only survived high levels of arsenic in its environment but also seemed to use that element in its DNA. Five months later, the debate resurfaced with the publication of critical comments on the original research.

Last week, the genome of the bacterium, known as GFAJ-1, was posted in Genbank, the public repository of DNA sequences for all who care to take a look. But it doesn't settle the debate over whether arsenic is used in DNA.

Simon Silver, an arsenic microbiologist at the University of Illinois, Chicago, and one of the most vocal critics of the arsenic bacterium research, and his colleagues sequenced the bacterium and found 3400 genes in its 3.5 million bases. Of note is that even the common gut bacterium, Escherichia coli, has more of the genes known to help it survive arsenic exposure than GFAJ-1, Silver said in a phone interview. Silver didn't expect the genome to address the core of the controversy, but then again, he doesn't think any test will convince Wolfe-Simon and her co-authors that they are wrong. "This sort of stuff never gets resolved," he says. "It eventually goes away." Silver and his colleagues intend to compare this genome with three others from other microbes living in arsenic-rich environments to better understand arsenic-related chemistry.

Wolfe-Simon calls the genome "an important step forward. But it may take some time, data mining, and modeling to understand its implications" because the functions of so many genes are unknown. The result "begs the question even more strongly of how GFAJ‑1 survives in the high arsenic conditions we grow it in," she notes.

Her collaborator, Ronald S. Oremland from the U.S. Geological Survey in Menlo Park, California, is glad to see the genome available and, with Wolfe-Simon, still stands behind the 18 words spoken 1 year ago. Wolfe-Simon is now at working at Lawrence Berkeley National Laboratory (LBNL) with John Tainer. They have spent the past several months learning how to better grow the bacterium in hopes of more carefully characterizing the DNA and other biomolecules, such as the ribosome.

A blog at MSNBC provides a rundown of the past year and where researchers now stand in this controversy.

A time-lapse video taken by James Lim at LBNL of GFAJ-1 is here.