The oligomeric stromal proteome of Arabidopsis thaliana chloroplasts.

This study presents an analysis of the stromal proteome in its oligomeric state extracted from highly purified chloroplasts of Arabidopsis thaliana. 241 proteins (88% with predicted cTP), mostly assembled in oligomeric complexes, were identified by mass spectrometry with emphasis on distinguishing between paralogues. This is critical because different paralogues in a gene family often have different subcellular localizations and/or different expression patterns and functions. The native protein masses were determined for all identified proteins. Comparison with the few well characterized stromal complexes from A. thaliana confirmed the accuracy of the native mass determination, and by extension, the usefulness of the native mass data for future in-depth protein interaction studies. Resolved protein interactions are discussed and compared with an extensive collection of native mass data of orthologues in other plants and bacteria. Relative protein expression levels were estimated from spot intensities and also provided estimates of relative concentrations of individual proteins. No such quantification has been reported so far. Surprisingly proteins dedicated to chloroplast protein synthesis, biogenesis, and fate represented nearly 10% of the total stroma protein mass. Oxidative pentose phosphate pathway, glycolysis, and Calvin cycle represented together about 75%, nitrogen assimilation represented 5-7%, and all other pathways such as biosynthesis of e.g. fatty acids, amino acids, nucleotides, tetrapyrroles, and vitamins B(1) and B(2) each represented less than 1% of total protein mass. Several proteins with diverse functions outside primary carbon metabolism, such as the isomerase ROC4, lipoxygenase 2 involved in jasmonic acid biosynthesis, and a carbonic anhydrase (CA1), were surprisingly abundant in the range of 0.75-1.5% of the total stromal mass. Native images with associated information are available via the Plastid Proteome Database.

Infrared photodissociation spectroscopy of electrosprayed ions in a Fourier transform mass spectrometer.

Previous gas-phase methods for infrared photodissociation spectroscopy (IRPD) require sample volatility. Our method instead uses electrospray ionization to introduce even large nonvolatile molecules into a Fourier transform mass spectrometer, where extended (>15 s) ion storage makes possible high sensitivity spectral measurements with an OPO laser over a range of 3050-3800 cm(-1). The spectra of 22 gaseous proton-bound amino acid complexes are generally correlated with the H-stretching frequencies established for O-H and N-H functional groups in solution. For theoretical structure predictions of the Gly2H+ and N-acylated Asp2H+ dimers, IRPD spectra clearly differentiate between the predicted lowest energy conformers. In contrast to solution, in the gas phase the glycine zwitterion is approximately 20 kcal/mol less stable than the neutral; however, glycine is clearly zwitterionic in the gaseous GlyLysH+ dimer. The level of theory is inadequate for the larger Lys2H+ dimer, as all low energy predicted structures have free carboxyl O-H groups, in contrast to the IR spectrum. IRPD appears to be a promising new technique for providing unique information on a broad range of biomolecular and other gaseous ions, especially on noncovalent bonding involving O-H and N-H groups.

Structural analysis of phosphatidylcholines by post-source decay matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

The utility of post-source decay (PSD) matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) was investigated for the structural analysis of phosphatidylcholine (PC). PC did not produce detectable negative molecular ion from MALDI, but positive ions were observed as both [PC+H](+) and [PC+Na](+). The PSD spectra of the protonated PC species contained only one fragment corresponding to the head group (m/z 184), while the sodiated precursors produced many fragment ions, including those derived from the loss of fatty acids. The loss of fatty acid from the C-1 position (sn-1) of the glycerol backbone was favored over the loss of fatty acid from the C-2 position (sn-2). Ions emanating from the fragmentation of the head group (phosphocholine) included [PC+Na-59](+), [PC+Na-183](+) and [PC+Na-205](+), which corresponded to the loss of trimethylamine (TMA), non-sodiated choline phosphate and sodiated choline phosphate, respectively. Other fragments reflecting the structure of the head group were observed at m/z 183, 146 and 86. The difference in the fragmentation patterns for the PSD of [PC+Na](+) compared to [PC+H](+) is attributed to difference in the binding of Na(+) and H(+). While the proton binds to a negatively charged oxygen of the phosphate group, the sodium ion can be associated with several regions of the PC molecule. Hence, in the sodiated PC, intermolecular interaction of the negatively charged oxygen of the phosphate group, along with sodium association at multiple sites, can lead to a complex and characteristic ion fragmentation pattern. The preferential loss of sn-1 fatty acid group could be explained by the formation of an energetically favorable six-member ring intermediate, as apposed to the five-member ring intermediate formed prior to the loss of sn-2 fatty acid group.

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry of lipids: ionization and prompt fragmentation patterns.

Ionization and prompt fragmentation patterns of triacylglycerols, phospholipids (PLs) and galactolipids were investigated using matrix-assisted laser desorption/ionization (MALDI). Positive ions of non-nitrogen-containing lipids appeared only in the sodiated form, while nitrogen-containing lipids were detected as both sodiated and protonated adducts. Lipids containing acidic hydroxyls were detected as multiple sodium adducts or deprotonated ions in the positive and negative modes, respectively, with the exception of phosphatidylcholines. The positive MALDI spectra of triacylglycerols contained prompt fragments equivalent to the loss of RCOO(-) from the neutral molecules. Prompt fragment ions [PL-polar head](+) were observed in the positive MALDI spectra of all phospholipids except phosphatidylcholines. The phosphatidylcholines produced only a minor positive fragment corresponding to the head group itself (m/z 184). Galactolipids did not undergo prompt fragmentation. Post-source decay (PSD) was used to examine the source of prompt fragments. PSD fragment patterns indicated that the lipid prompt fragment ions did not originate from the observed molecular ions (sodiated or protonated), and suggested that the prompt fragmentation followed the formation of highly unstable, probably protonated, precursor ions. Pathways leading to the formation of prompt fragment ions are proposed.

Oxidative metabolism and the physiological age of seed potatoes are affected by increased alpha-linolenate content.

The effects of high alpha-linolenate content on lipid peroxidation, oxidative stress and loss of plant growth potential during ageing of potato (Solanum tuberosum L.) seed-tubers was examined. Endoplasmic reticulum (FAD3) and plastidal (FAD7) 18:2 fatty acid desaturases were upregulated in potato (cv. Desiree), resulting in a 2-fold average increase in mol percentage 18:3 in the total lipid fraction across all transgenic clones. In double-transformed (FAD3+7) tubers, high alpha-linolenate phenotype effected accelerated ageing, resulting in growth responses characteristic of older seed-tubers. Although respiration rates of wild-type (WT) and FAD3+7 tubers were equal at 7 months of storage, rates had increased by 23% and 50% in WT and FAD3+7 tubers, respectively, by 19 months of storage. Electrolyte leakage of tissue from 19-month-old FAD3+7 tubers was significantly greater than that from WT tubers of the same age, indicating that the high alpha-linolenate phenotype was detrimental to membrane integrity during long-term storage. On average, indices of lipid peroxidation (malondialdehyde, ethane, C-6 aldehydes) were higher in older FAD3+7 tubers, relative to WT tubers. Activities of glucose-6-phosphate dehydrogenase, peroxidase, glutathione reductase, ascorbate peroxidase and monodehydroascorbate reductase increased in tubers with advancing age and were higher, on average, in FAD3+7 tubers. Dehydroascorbate reductase activity decreased with age, with no difference between transgenic and WT lines. Collectively, these results indicate that FAD3+7 tubers underwent a higher degree of oxidative stress during ageing. The age-induced increase in respiration of FAD3+7 tubers was at least partly a response to fuel increased free radical scavenging through the ascorbate-glutathione antioxidant pathway. By affecting the susceptibility of lipids to peroxidation, the degree of fatty acid unsaturation influenced the development of oxidative stress and the overall rate at which growth potential was lost from seed-tubers during ageing. Thus, oxidative stress plays an integral role in modulating the ageing process to affect growth potential from potato seed-tubers.

Lipid metabolism during aging of high-alpha-linolenate-phenotype potato tubers.

Previous studies demonstrated that high levels of alpha-linolenate in cell membranes of potato tubers (achieved by overexpressing fatty acid desaturases) enhances lipid peroxidation, oxidative stress, and tuber metabolic rate, effectively accelerating the physiological age of tubers. This study details the changes in lipid molecular species of microsomal and mitochondrial membranes from wild-type (WT) and high-alpha-linolenate tubers during aging. The microsomal and mitochondrial polar lipids of high-alpha-linolenate tubers were dominated by 18:3/18:3 and 16:0/18:3 molecular species. Relative to WT tubers, high-alpha-linolenate tubers had a substantially higher 16:0/18:n to 18:n/18:n molecular species ratio in mitochondria and microsomes, potentially reflecting a compensatory response to maintain membrane biophysical properties in the face of increased unsaturation. Phosphatidylcholine (PC) and phosphatidylethanolamine (PE) accounted for 53 and 37% of polar lipids, respectively, in mitochondria from younger WT and high-alpha-linolenate tubers. The relative proportions of these phospholipids (PL) did not change during aging of WT tubers. In contrast, PE increased to dominate the PL pool of mitochondria during aging of high-alpha-linolenate tubers. While aging effected an increase in mitochondrial 18:3-bearing PCs and PEs in WT tubers, the concentration of 18:3-bearing PCs fell with a concomitant increase in 18:3-bearing PEs during aging of high-alpha-linolenate tubers. These age- and high-alpha-linolenate-induced changes had no effect on the respiration rate and functional integrity of isolated mitochondria. Differential increases in the respiration rates of WT and high-alpha-linolenate tubers during aging were therefore a consequence of unsaturation-dependent alterations in the microenvironments of cells. Microsomal 18:3-bearing PCs, PEs, digalactosyldiacylglycerols (DGDG), and monogalactosyldiacylglycerols all increased in WT tubers during aging. In contrast, a selective loss of 18:3-bearing PCs and DGDGs from microsomes of high-alpha-linolenate tubers likely reflects a greater susceptibility of membranes to peroxidative catabolism during aging. Aging resulted in an increase in sterol/PL ratio in microsomes from WT tubers, due primarily to a decline in PL. In high-alpha-linolenate tubers, the increase in sterol/PL ratio during aging was due to increases in Delta 5-avenasterol and stigmasterol, indicating membrane rigidification and likely contributing to increased membrane permeability. Age-induced changes in 18:3-bearing lipids in membranes of transformed tubers are discussed relative to the development of oxidative stress and accelerated aging.

Changes in lipid molecular species and sterols of microsomal membranes during aging of potato (Solanum tuberosum L.) seed-tubers.

Changes in sterols and the molecular species composition of polar lipids from microsomal membranes were characterized as a prerequisite to determining how lipid chemistry affects membrane susceptibility to peroxidation during aging of potato tubers. Polar lipid content of the microsomal fraction fell 17% (protein basis) as tubers aged from 22 to 38 mon at 4 degrees C. In younger seed-tubers, PC concentration (protein basis) was the highest, followed by digalactosyldiacylglycerol (DGDG), PE, monogalactosyldiacylglycerol (MGDG), and PI. PC and PE increased 14 and 27%, respectively, whereas glycolipids fell 64 and PI 43% with advancing age. These changes resulted in PC and PE dominating the microsomal membrane lipids of 38-mon-old tubers. Nonpositional analysis of lipid molecular species across lipid pools showed an increase in 16:0/18:3, 18:3/18:3, and 18:2/18:3 (PC and PE only), and a decline in 18:2/18:2 and 16:0/18:2 (except for MGDG) with advancing tuber age. The increase in 18:3-bearing species effected a linear increase in double-bond index (DBI) of PC and PE during aging. The DBI of DGDG did not change with age; however, it fell 65% for MGDG, resulting in an overall decrease in average microsomal DBI. In addition, A5-avenasterol and stigmasterol concentrations increased 1.6- and 3.3-fold, respectively, effecting a significant increase in the sterol/phospholipid ratio with advancing tuber age. The increase in sterol/phospholipid ratio and the possibility that the increased unsaturation of microsomal membranes reflects a compensatory response to maintain optimal membrane function in light of the age-induced loss of galactolipid and PI are discussed.