Arsenic Based Life: the story continues

An update to the debate regarding the possibility of bacteria that can incorporate arsenic into DNA and other biomolecules (as described in the recent Science paper by Felicia Wolfe-Simon et al): the first published rebuttal has appeared in the chemical literature (n.b. many thanks to @BoraZ and @bmossop on Twitter for the alert). The rebuttal by Fekry, Tipton and Gates was published in ACS Chemical Biology on January 18th, and examines the potential consequences for DNA's chemical kinetics of a switch from arsenic to phosphate within the backbone structure.  This argument should sound familiar to those who have been following the online debate regarding the Wolfe-Simon's paper, and the article details the problems the GFAJ-1 would need to overcome if it replaced incredibly stable phosphate bonds with inherently unstable arsenate bonds. As quantified by the authors, the half-life of hydrolytic cleavage of the normal phosphate DNA backbone has been estimated as approximately 30 million years. This is in stark comparison with the estimated half-life for hydrolytic cleavage of the proposed arsenate-containing DNA backbone, 0.06 seconds. Such a difference would present a rather extreme challenge for GFAJ-1. As the article notes:

The estimates presented in preceding paragraphs suggest that, if exposed to bulk water, half of the arsenodiester linkages in the genome of Halomonadacea GFAJ-1 would be hydrolytically cleaved in less than 0.1 s. While some bacteria have evolved mechanisms for protecting their DNA under conditions of stress,(36, 37) overcoming such dramatic kinetic instability in its genetic material would be a significant feat for Halomonadacea GFAJ-1. Finally, we note that the use of arsenate esters in cell signaling, enzyme regulation, and cellular respiration would present a similar set of difficulties to the microbe.

This article moves the debate regarding the interpretations of the Wolfe-Simon's paper into arena of the official publication record. It is to be hoped that the original authors will now respond (as they promised to do), thus allowing a somewhat one-sided barrage of criticisms to evolve into a productive scientific discussion.

To celebrate this anticipated shift (and to remind readers of the reported results/interpretations plus major criticisms of the Wolfe-Simon's paper), a video presentation of the article from a recent session of the Stanford Neurosciences Ph.D Program Journal Club.

Unfortunately, the video did not preserve the projected slides as well as expected, so underneath the video readers will find the slides posted (fullscreen view is suggested - an option that can accessed by selecting the Menu button).

Neurosciences Journal Club Presentation Pt 1

Neuroscience Journal Club Presentation Pt 2

Presentation Slides

[slideshare id=6715316&doc=winter2011jc-110126233904-phpapp01]