Tuesday, May 17, 2011

The Reporter Gene Hoax


Recently, it has come to light that Christian Bök is trying to engineer some kind of protein poem, but the fact that he mentioned a protein that fluoresces was in fact too much butter in the brûlée. All he has to do is retrofit a cipher to a known and common reporter gene / protein sequence. Not easy that, but not either what he says he is doing. I'm calling it a pseudo-hoax. He is not designing a reporter gene / protein combo, but designing a cipher for a set of data already known. I'll bet on it. I mean he could be modifying a common reporter gene, and that would be cool. It seems more likely he is tinkering with the scaffolding of something fairly well known rather than cooking from scratch. I suppose anything is possible, and he is of course a very intelligent person, but it just seems more likely it is something of this nature to me.


I like Bök enough, but I just don't think he's doing what he says he's doing. He is not the first Proteomics poet, but, like Eugene Thacker, he has joined the ranks of the trans-disci-planaria..

He is a disco worm.

Why doesn't he fluroesce red himself. That would be really something, I guess, although I prefer
the green or blue tones..


Here are some abstracts concerning cobA a reporter gene that causes a red fluorescence.

cobA, a red fluorescent transcriptional reporter for Escherichia coli, yeast, and mammalian cells
Stefan Wildt1,2 & Ulrich Deuschle1

We demonstrate the use of Propionibacterium freudenreichii uroporphyrinogen III methyltransferase (cobA) as a reporter of gene expression in Escherichia coli, fission yeast, and mammalian cells. Overexpression of cobA in cells resulted in bright red fluorescence that was visualized with standard fluorescence microscopy and fluorescence-activated cell sorting analysis at the single-cell level. As with green fluorescent protein (GFP), no addition of exogenous substrate was required. When expressed in Chinese hamster ovary cells from a bicistronic transcript, cobA and GFP gave rise to fluorescence signals of similar intensity. The bright red fluorescence generated by the cobA reporter promises a better signal-to-noise ratio than blue and green fluorescent reporter systems, as autofluorescence and light scattering of cells, media, and materials are reduced in the red wavelengths.

"CobA gene provides an excellent opportunity for its use as a reporter gene in some extremophilic Bacillus"

More useful news!

A common problem encountered when using fluorescence detection in real samples analysis is that the matrix may contain compounds that autofluorescence or that can be excited at the wavelengths of commonly employed fluorescent reporter molecules. This causes an increase in background fluorescence, which in turn tends to compromise the detection limits of the system. To address this issue, we investigated the use of a reporter enzyme that produces fluorescent compounds, which can be excited at wavelengths that are not commonly encountered in compounds present in real samples. For that, a whole cell-based sensing system for arsenite that employs cobA as the reporter gene was developed. The system utilizes genetically engineered bacteria that incorporate the specificity of the ars operon with the sensitivity of the cobA gene. The cobA gene codes for uroporphyrinogen III methyltransferase that converts the substrate uroporphyrinogen (urogen) III into two fluorescent compounds sirohydrochlorin and trimethylpyrrocorphin. Urogen III is ubiquitous within the cell, however, because the cells use it for vitamin B12 and siroheme biosynthesis, this sensing system is limited by substrate availability. By supplementing the media with ALA, a precursor of urogen III, a more stable and reproducible response was obtained. We observed three excitation maxima at 357, 378, and 498 nm, with a single emission maximum at 605 nm. Excitation at 498 nm was selected because it results in less background interference as most endogenous substances are not active at this wavelength. Advantages and limitations of using the cobA gene in whole-cell sensing applications are presented.