Protein Staining Influences the Quality of Mass Spectra Obtained by Peptide Mass Fingerprinting after Separation on 2-D Gels. A Comparison of Staining with Coomassie Brilliant Blue and Sypro Ruby

When separating protein mixtures on 2-D gels for proteomics purposes, fluorescent staining is superior in sensitivity and linear response as compared to Coomassie Brilliant Blue (CBB) and silver staining, respectively. We have compared the quality of mass spectra for proteins obtained from gels stained with CBB and SYPRO Ruby (SR) and found significant differences. These differences can be seen both in inferior signal/noise ratios and number of peptides detected with the fluorescent stain.

Antifibrinolytic proCPU is present in the peritoneal cavity during surgery

The fibrinolytic capacity of the peritoneum plays a pivotal role in peritoneal wound healing. During surgery the balance between fibrin deposition and degradation is tilted towards deposition, leading to the formation of adhesions. In blood, carboxypeptidase U (CPU) stabilizes clots by retarding fibrinolysis. The purpose of this study was to investigate whether the more stable zymogen, proCPU, is also present in the peritoneal cavity and, if so, to examine its origin. Levels of proCPU were measured in plasma and serosal peritoneal fluid collected during surgery. Peritoneal biopsies were stained for proCPU. Two-dimensional gel electrophoresis was performed to study the protein composition of the serosal fluid compared to plasma and Western blotting to identify differences in glycosylation of proCPU, indicating possible different cellular origin. Cultured human mesothelial cells were examined for proCPU production under normal conditions and conditions mimicking surgery. We found comparable and correlating levels of proCPU in serosal fluid and plasma. ProCPU was also found where fibrin covered the injured peritoneal surface. A protein composition very similar in serosal fluid and plasma was shown by two-dimensional gel electrophoresis, and the proCPU pattern did not indicate a different origin. No proCPU production was found in cultured mesothelial cells. This is the first study to report on the presence of proCPU in the peritoneal cavity, which seems to be the result of plasma oozing out during the inflammatory reaction to the surgical trauma. This is likely to be important for the balance between fibrin deposition and degradation and thereby in the formation of postoperative adhesions.

Hepatic protein expression of lean mice and obese diabetic mice treated with peroxisome proliferator-activated receptor activators

The peroxisome proliferator-activated receptors (PPARs) are ligand-activated transcription factors that modulate lipid and glucose homeostasis. In the clinic, PPARalpha and PPARgamma agonists are used to treat hypertriglyceridemia and insulin resistance of diabetes, respectively. To gain further insight into the molecular mechanisms underlying the therapeutic actions of these drugs, we have by two-dimensional electrophoresis and mass spectrometry performed a comparative analysis of the hepatic protein expression profiles of lean and obese (ob/ob) mice, and obese mice treated with WY14643 (PPARalpha agonist) or rosiglitazone (PPARgamma agonist). We found that livers from obese mice displayed higher levels of enzymes involved in fatty acid oxidation and lipogenesis compared to lean mice and these differences were further amplified by treatment with both PPAR activators. WY14643 normalized the expression levels of several enzymes involved in glycolysis, gluconeogenesis and amino acid metabolism in the obese mice to the levels of lean mice, whereas rosiglitazone partially normalized levels of enzymes involved in amino acid metabolism. In summary, a classical proteomics approach was successfully used to characterize differences at the hepatic proteome level between lean and obese diabetic mice, to map metabolic pathways affected by treatment, and to discriminate between effects caused by treatment with agonists of the closely related PPARalpha and PPARgamma receptors.

Isolation and identification of a novel mitochondrial metalloprotease (PreP) that degrades targeting presequences in plants

Most of the nuclear encoded mitochondrial precursor proteins contain an N-terminal extension called the presequence that carries targeting information and that is cleaved off after import into mitochondria. The presequences are amphiphilic, positively charged, membrane-interacting peptides with a propensity to form alpha-helices. Here we have investigated the proteolysis of the presequences that have been cleaved off inside mitochondria. A presequence derived from the overexpressed F(1)beta subunit of the ATP synthase and specific synthetic fluorescent peptides (Pep Tag Protease assay) have been shown to undergo rapid degradation catalyzed by a matrix located protease. We have developed a three-step chromatographic procedure including affinity and anion exchange chromatography for isolation of the protease from potato tuber mitochondria. Two-dimensional gel electrophoresis of the isolated proteolytically active fraction followed by electrospray ionization-mass spectrometry/mass spectrometry and data base searches allowed identification of the presequence peptide-degrading protease in Arabidopsis thaliana data base as a novel mitochondrial metalloendoprotease with a molecular mass of 105 kDa. The identified metalloprotease contains an inverted zinc-binding motif and belongs to the pitrilysin family.