Taking advantage of the completed draft sequence of the rice genome, Antonius Koller, John Yates, et. al. of the Torrey Mesa Research Institute in La Jolla report on a proteomic analysis of rice in a paper, “Proteomic survey of metabolic pathways in rice,” published August 5 in the Proceedings of the National Academy of Sciences. In their study, the authors used 2D gel electrophoresis combined with tandem mass spectrometry, and multidimensional protein identification technology to analyze the proteins of Oryza sativa leaf, root, and seed tissue, finding 2,528 unique proteins. In addition to discovering that enzymes involved in central metabolic pathways are found in all tissues, the group identified previously characterized allergenic proteins in the rice seed sample, indicating that proteomics may serve as a tool for profiling the allergenicity of food samples.
Building on the idea of using a small molecule microarrays to probe cell lysates for active proteins, Nicolas Winssinger, Jennifer Harris, et. al. of the Genomics Institute of the Novartis Research Foundation and Scripps Research Institute describe a new approach that could potentially screen up to 400,000 enzyme activity probes in a volume of 300 µl. In a paper published August 5 in PNAS, the authors describe their technique: After covalently binding a small molecule to a peptide nucleic acid, whose sequence serves as an identifier for the small molecule, the researchers use the probes to screen for the presence of functionally-active enzymes in a sample. Harris et. al. use size exclusion filtration to remove any small molecule probes not bound to enzymes, and then hybridize the peptide nucleic acid sequences from the remaining probes to an oligonucleotide array. Because each probe is tagged with a single fluorescein molecule, the intensity of the fluorescence is proportional to the abundance of the protein in the sample. The authors demonstrated the technique using small molecules selective for cysteine proteases in the presence of cytotoxic lymphocyte-mediated cell death.
In the August issue of Nature Biotechnology, Benjamin Cravatt (see Proteomics Pioneer, p. 6), Gregory Adam, et. al. of the Scripps Research Institute report on a strategy for combinatorially generating chemical probes for profiling proteins. To build a library of candidate probes, Cravatt and his colleagues synthesized compounds with a sulfonate ester reactive group coupled to a variable alkyl/aryl-binding group, and either biotinylated or tagged the probes with fluorescent labels. In their study, the researchers demonstrated that they could use the probe library to isolate six mechanistically distinct enzyme classes from complex mixtures of proteins, none of which had been targeted previously by known probes, the authors claim. In addition, Cravatt and his team used the probes to identify an omega-class glutathione S-transferase whose activity was upregulated in invasive human breast cancer cell lines.