Chemical biology

Genetically encodable aldehyde tag

New bioorthogonal tags are always welcome additions to the chemical biologist's toolbox. Carrico et al. describe a new such handle, a genetically encodable aldehyde tag. A 6-amino-acid motif is recognized by formylglycine-generating enzyme, which oxidizes cysteine to the aldehyde-containing formylglycine. The aldehyde serves as a convenient attachment site for aminooxy- and hydrazine-functionalized labels.

Carrico, I.S. et al. Nat. Chem. Biol.; published online 22 April 2007.

Proteomics

The Drosophila protein catalog

Brunner et al. present a catalog of 63% of the predicted proteome of the model organism Drosophila melanogaster, using shotgun mass spectrometry. They obtained high coverage by using diverse samples, an extensive fractionation strategy and a statistical bioinformatic approach called analysis-driven experimentation, which allowed them to optimize experimental conditions to target under-represented portions of the proteome.

Brunner, E. et al. Nat. Biotechnol. 25, 576–583 (2007).

Gene regulation

A tool to upregulate gene expression

Whereas RNAi has come into its own as a means to knock down gene expression, no good corresponding tool has been available to do the opposite: upregulate gene expression. Xiao et al. describe the development of a cell-permeable synthetic transcription factor mimic, which activates gene expression in living cells by binding to a specially designed promoter. They were able to achieve a fivefold upregulation of expression in HeLa cells.

Xiao, X. et al. Angew. Chem. Int. Edn. 46, 2865–2868 (2007).

Spectroscopy

Aligning with nanotubes

Liquid crystalline media are used to weakly align protein molecules during an NMR experiment, facilitating the measurement of residual dipolar couplings, which aid in structure solution. These media, however, are generally incompatible with the detergents used in membrane protein preparations. Douglas et al. report the design and synthesis of detergent-resistant DNA nanotubes as a viable alternative for the weak alignment of membrane proteins in NMR experiments.

Douglas, S.M. et al. Proc. Natl. Acad. Sci. USA, 104, 6644–6648 (2007).

Genomics

A gene expression resource for fission yeast

With the goal of understanding the multiple levels of regulation of gene expression, Lackner et al. present genome-wide data sets identifying key gene expression intermediates in the fission yeast Schizosaccharomyces pombe. Using microarray analysis, they collected data under standardized conditions, revealing new insights about systems-level regulation from transcription to translation.

Lackner, D.H. et al. Mol. Cell 26, 145–155 (2007).