GC-MS-based analysis of the metabolic response of Escherichia coli exposed to four different stress conditions reveals reduction of energy expensive pathways.Time-resolved response of E. coli to changing environmental conditions is more specific on the metabolite as compared with the transcript level.Cease of growth during stress response as compared with stationary phase response invokes similar transcript but dissimilar metabolite responses.Condition-dependent associations between metabolites and transcripts are revealed applying co-clustering and canonical correlation analysis.

There is current debate whether genetically modified (GM) plants might contain unexpected, potentially undesirable changes in overall metabolite composition. However, appropriate analytical technology and acceptable metrics of compositional similarity require development. We describe a comprehensive comparison of total metabolites in field-grown GM and conventional potato tubers using a hierarchical approach initiating with rapid metabolome "fingerprinting" to guide more detailed profiling of metabolites where significant differences are suspected. Central to this strategy are data analysis procedures able to generate validated, reproducible metrics of comparison from complex metabolome data. We show that, apart from targeted changes, these GM potatoes in this study appear substantially equivalent to traditional cultivars.

The primary walls of grasses are composed of cellulose microfibrils, glucuronoarabinoxylans (GAXs), and mixed-linkage ␤-glucans, together with smaller amounts of xyloglucans, glucomannans, pectins, and a network of polyphenolic substances. Chemical imaging by Fourier transform infrared microspectroscopy revealed large differences in the distributions of many chemical species between different tissues of the maize (Zea mays) coleoptile. This was confirmed by chemical analyses of isolated outer epidermal tissues compared with mesophyll-enriched preparations. Glucomannans and esterified uronic acids were more abundant in the epidermis, whereas ␤-glucans were more abundant in the mesophyll cells. The localization of ␤-glucan was confirmed by immunocytochemistry in the electron microscope and quantitative biochemical assays. We used field emission scanning electron microscopy, infrared microspectroscopy, and biochemical characterization of sequentially extracted polymers to further characterize the cell wall architecture of the epidermis. Oxidation of the phenolic network followed by dilute NaOH extraction widened the pores of the wall substantially and permitted observation by scanning electron microscopy of up to six distinct microfibrillar lamellae. Sequential chemical extraction of specific polysaccharides together with enzymic digestion of ␤-glucans allowed us to distinguish two distinct domains in the grass primary wall. First, a ␤-glucan-enriched domain, coextensive with GAXs of low degrees of arabinosyl substitution and glucomannans, is tightly associated around microfibrils. Second, a GAX that is more highly substituted with arabinosyl residues and additional glucomannan provides an interstitial domain that interconnects the ␤-glucan-coated microfibrils. Implications for current models that attempt to explain the biochemical and biophysical mechanism of wall loosening during cell growth are discussed.Biochemical studies have provided a reasonably complete catalog of the major polysaccharides and phenolic substances that constitute the primary cell walls of angiosperms (McCann and Roberts, 1991;Carpita and Gibeaut, 1993). The walls of grasses and related monocots (commelinoids) have quite different compositions compared with those of all dicots and of the non-commelinoid monocot species (Carpita, 1996). The "type II" cell walls of commelinoid monocots are characterized by cellulose microfibrils cross-linked by glucuronoarabinoxylans (GAXs) and a network of polyphenolic substances (Carpita and Gibeaut, 1993;Carpita, 1996). Maize (Zea mays) and other members of the Poales also contain developmentally regulated polymers, the mixed-linkage (133),(134)-␤-dglucans (hereafter, called ␤-glucans). The ␤-glucans are initially absent from meristematic cells but accumulate up to about 20% dry mass of the cell wall coincident with the most rapid rates of coleoptile elongation (Kim et al., 2000). As the elongation rate slows, the ␤-glucan is hydrolyzed by exo-and endo-␤-d-glucanases located in the wall. Concomitant with th...

A new strategy for direct infusion-based metabolite analysis employing a combination of high-resolution mass spectrometry and (13)C-isotope labeling of entire metabolomes is described. Differentially isotope labeled metabolite extracts from otherwise identically grown reference plants were prepared and infused into a Fourier transform ion cyclotron resonance mass spectrometer. The derived accurate mass lists from each extract were searched, using an in-house-developed database search tool, against a number of comprehensive metabolite databases. Comparison of the retrieved chemical formulas from both, the (12)C and (13)C samples, leads to two major advantages compared to nonisotope-based metabolite fingerprinting: first, removal of background contaminations from the result list, due to the (12)C/(13)C peak pairing principle and therefore positive identification of compounds of true biological origin; second, elimination of ambiguity in chemical formula assignment due to the same principle, leading to the clear association of one measured mass to only one chemical formula. Applying this combination of strategies to metabolite extracts of the model plant Arabidopsis thaliana therefore resulted in the reproducible identification of more than 1000 unambiguous chemical sum formulas of biological origin of which more than 80% have not been associated to Arabidopsis before.