Metabolomics, transcript omics, proteomics, oh my!
and so much to learn by characterizing these molecules and understanding Most research in —omics hardly raises their function.” an eyebrow these days. Genome seOn the protein front, the team identiquencing as well as transcriptome and fied 195 proteins, of which 11 were more proteome profiling have become so rouabundant and 107 were less abundant at tine they barely merit attention. Yet, one the lower temperature; the remainder molecular domain remains a technical were unchanged. For 39 of those 107 and analytic challenge: metabolomics. down-regulated proteins, expression For nucleic acids (DNA and RNA) and of the corresponding gene was also proteins, the small pool of molecular diminished; for two others, mRNA building blocks constrains the problem abundance actually increased. of identification. But that’s not the case Down-regulated proteins included for metabolites. Nor are there many those involved in energy metabolism, limits on how they can be assembled. amino acid biosynthesis, transcription, As a result, researchers looking to and translation; among the up-reguplumb the metabolome really have lated proteins, one was implicated in their work cut out for them. oxidative stress response. But for sev“We have about 2500 endogenous eral of these proteins, this study marked metabolites in our METLIN database,” the first time they were observed. says Gary Siuzdak of the Scripps Re“A lot of the proteins and genes of this search Institute. “But when [we] do organism remain hypothetical,” says an experiment, there are Trauger. “Many are not hythousands of metabolites we pothetical now that we have NH 2 N H2N H P. furiosus 72 ºC 107 cannot identify.” identified the proteins. So in P. furiosus 95 ºC In work published in JPR that sense, it is an exciting (2008, 7, 1027–1035), Siuzdak frontier for understanding NH2 and his colleagues describe the interaction between the NH2 N NH H2N a step in the right direcdifferent macromolecules NH2 NH2 H2N O H2N N H tion. The team combined and metabolites.” H OH N HN N H2N HN transcriptome, proteome, Yet, as often happens at O NH2 and metabolome profiling the frontier, rough patches 4 4 0 Arginine Agmatine Spermidine N -Amino- N -(N-Acetylto derive a holistic picture of remain. The three data sets propylaminopropyl)spermidine spermidine how the extremophile Pyrohad relatively little overlap, coccus furiosus adapts to cold for instance. And though Hot-blooded. Metabolic profiling of P. furiosus at cold (purple) and temperatures. metabolites from the polywarm (magenta) temperatures reveals up-regulation of an alternate P. furiosus is a hypertheramine biosynthetic pathway polyamine biosynthesis pathway. mophilic organism that were up-regulated, none of grows optimally near the the biosynthetic enzymes boiling point of water, a temperature at These five metabolites are part of in that pathway were temperaturewhich most proteins and nucleic acids an alternate polyamine synthesis regulated at the RNA level. And none unfold. “The fundamental biochemistry pathway, which was previously identiof those enzymes were detected at the of how these organisms function at high fied in another thermophile, Thermus protein level, suggesting an as-yet-untemperatures, where most biomolecules thermophilus. Because T. thermophilus identified level of regulation. degrade, is interesting,” says Sunia up-regulates this pathway when its According to Siuzdak, the next step is Trauger, associate director of the Scripps temperature increases from 65 °C (its to map protein–metabolite interactions, MS facility and lead author of the study. normal temperature) to 75 °C, Trauger a project Trauger has already largely To gain insight into that biochemspeculates that this metabolic change completed. But the ultimate goal, he istry, Siuzdak and his team looked at could highlight a common thermosays—and one in line with the objechow mRNA, protein, and metabolite philic defense against stress. tives of the U.S. Department of Energy, abundances differed between cultures The identification of the novel which is funding the work—is to use the grown at 95 °C and 72 °C. metabolite N4-(N-acetylaminopropyl)insights gained from these studies to Using a custom DNA microarray, spermidine highlights the benefit of support metabolic engineering efforts the team profiled the expression of the unbiased experimental approaches. such as biofuel production. organism’s 2065 open reading frames “Our platform gives a window into an “If you have a more complete underunder both conditions. They then comarea that is just fraught with discovery,” standing of the biochemistry, you can pared those numbers with protein and Siuzdak says. “So many molecules hopefully design an organism that will metabolite data they collected via semihaven’t been identified, and you could achieve your goals more effectively,” quantitative single-stage and tandem call that a problem. But I look at it the Siuzdak says. LC/MS by using two in-house bioinforother way: there’s so much to discover —Jeffrey M. Perkel Peak area
matics tools to aid their analyses. One of those tools is METLIN, a metabolite database. The other is XCMS. XCMS “aligns and statistically evaluates the data, ultimately pulling out the molecules that are most interesting, with the most significant changes,” explains Siuzdak. “Then we focus on those molecules, looking at our or other databases to identify the metabolites.” The study’s numbers hint at the challenge for metabolic researchers. Of the >100 metabolites whose abundances changed across conditions, the team putatively identified 12 that were downregulated and 5 that were up-regulated. Five metabolites were identified definitively with chemical standards and MS/ MS: arginine; agmatine; spermidine; N4-aminopropylspermidine; and one novel compound, N4-(N-acetylamino propyl)spermidine.
Journal of Proteome Research • Vol. 7, No. 3, 2008 839
