Combined analysis of transcriptome and proteome data as a tool for the identification of candidate biomarkers in renal cell carcinoma

Results obtained from expression profilings of renal cell carcinoma using different "ome"-based approaches and comprehensive data analysis demonstrated that proteome-based technologies and cDNA microarray analyses complement each other during the discovery phase for disease-related candidate biomarkers. The integration of the respective data revealed the uniqueness and complementarities of the different technologies. While comparative cDNA microarray analyses though restricted to up-regulated targets largely revealed genes involved in controlling gene/protein expression (19%) and signal transduction processes (13%), proteomics/PROTEOMEX-defined candidate biomarkers include enzymes of the cellular metabolism (36%), transport proteins (12%), and cell motility/structural molecules (10%). Candidate biomarkers defined by proteomics and PROTEOMEX are frequently shared, whereas the sharing rate between cDNA microarray and proteome-based profilings is limited. Putative candidate biomarkers provide insights into their cellular (dys)function and their diagnostic/prognostic value but still warrant further validation in larger patient numbers. Based on the fact that merely three candidate biomarkers were shared by all applied technologies, namely annexin A4, tubulin alpha-1A chain, and ubiquitin carboxyl-terminal hydrolase L1, the analysis at a single hierarchical level of biological regulation seems to provide only limited results thus emphasizing the importance and benefit of performing rather combinatorial screenings which can complement the standard clinical predictors.

Inactivation of Lgt allows systematic characterization of lipoproteins from Listeria monocytogenes

Lipoprotein anchoring in bacteria is mediated by the prolipoprotein diacylglyceryl transferase (Lgt), which catalyzes the transfer of a diacylglyceryl moiety to the prospective N-terminal cysteine of the mature lipoprotein. Deletion of the lgt gene in the gram-positive pathogen Listeria monocytogenes (i) impairs intracellular growth of the bacterium in different eukaryotic cell lines and (ii) leads to increased release of lipoproteins into the culture supernatant. Comparative extracellular proteome analyses of the EGDe wild-type strain and the Delta lgt mutant provided systematic insight into the relative expression of lipoproteins. Twenty-six of the 68 predicted lipoproteins were specifically released into the extracellular proteome of the Delta lgt strain, and this proved that deletion of lgt is an excellent approach for experimental verification of listerial lipoproteins. Consequently, we generated Delta lgt Delta prfA double mutants to detect lipoproteins belonging to the main virulence regulon that is controlled by PrfA. Overall, we identified three lipoproteins whose extracellular levels are regulated and one lipoprotein that is posttranslationally modified depending on PrfA. It is noteworthy that in contrast to previous studies of Escherichia coli, we unambiguously demonstrated that lipidation by Lgt is not a prerequisite for activity of the lipoprotein-specific signal peptidase II (Lsp) in Listeria.

“LANESPECTOR”, a tool for membrane proteome profiling based on sodium dodecyl sulfate-polyacrylamide gel electrophoresis/liquid chromatography - tandem mass spectrometry analysis: Application toListeria monocytogenes membrane proteins

Proteomics is required to provide insight into any type of subproteome. While the workflow based on two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) can be applied for many subproteomes and comprises well-established strategies for data presentation and data analysis, the comprehensive investigation of membrane proteomes remains a challenging task. We present a number of procedures that provide an insight into such systems. We have established a novel protocol for the efficient preparation of membrane fractions, which is used here for the human pathogen Listeria monocytogenes that overcomes difficulties associated with ribosomes. Subsequently, we have used the combination of sodium dodecyl sulfate (SDS)-PAGE and liquid chromatography-tandem mass spectrometry for the characterization of the membrane proteome. Three hundred and one different membrane proteins could be identified, including 70 proteins that exhibited 2-15 transmembrane domains. However, a remarkably high ratio of proteins was detected in gel sections that were not in accordance with their expected migration behavior during SDS-PAGE. Protein identifications based on MASCOT significance criteria could be shown to be of high quality and therefore could not be the explanation of this observation. Consequently we have developed LaneSpector, a general visualization tool that allows the systematic comparison between apparent and calculated protein masses, which is routinely applicable to any high-throughput approach using a mass-dependent separation dimension prior to LC-MS/MS. The detailed presentation of the LaneSpector plot promotes the validation of the analytical process and might help to reveal relevant biological processes such as proteolysis or other post-translational modifications.

Effect of adaptation to ethanol on cytoplasmic and membrane protein profiles of Oenococcus oeni

The practical application of commercial malolactic starter cultures of Oenococcus oeni surviving direct inoculation in wine requires insight into mechanisms of ethanol toxicity and of acquired ethanol tolerance in this organism. Therefore, the site-specific location of proteins involved in ethanol adaptation, including cytoplasmic, membrane-associated, and integral membrane proteins, was investigated. Ethanol triggers alterations in protein patterns of O. oeni cells stressed with 12% ethanol for 1 h and those of cells grown in the presence of 8% ethanol. Levels of inosine-5'-monophosphate dehydrogenase and phosphogluconate dehydrogenase, which generate reduced nicotinamide nucleotides, were decreased during growth in the presence of ethanol, while glutathione reductase, which consumes NADPH, was induced, suggesting that maintenance of the redox balance plays an important role in ethanol adaptation. Phosphoenolpyruvate:mannose phosphotransferase system (PTS) components of mannose PTS, including the phosphocarrier protein HPr and EII(Man), were lacking in ethanol-adapted cells, providing strong evidence that mannose PTS is absent in ethanol-adapted cells, and this represents a metabolic advantage to O. oeni cells during malolactic fermentation. In cells grown in the presence of ethanol, a large increase in the number of membrane-associated proteins was observed. Interestingly, two of these proteins, dTDT-glucose-4,6-dehydratase and D-alanine:D-alanine ligase, are known to be involved in cell wall biosynthesis. Using a proteomic approach, we provide evidence for an active ethanol adaptation response of O. oeni at the cytoplasmic and membrane protein levels.

Structure of the bc1 complex from Seculamonas ecuadoriensis, a jakobid flagellate with an ancestral mitochondrial genome

In eubacteria, the respiratory bc(1) complex (complex III) consists of three or four different subunits, whereas that of mitochondria, which have descended from an alpha-proteobacterial endosymbiont, contains about seven additional subunits. To understand better how mitochondrial protein complexes evolved from their simpler bacterial predecessors, we purified complex III of Seculamonas ecuadoriensis, a member of the jakobid protists, which possess the most bacteria-like mitochondrial genomes known. The S. ecuadoriensis complex III has an apparent molecular mass of 460 kDa and exhibits antimycin-sensitive quinol:cytochrome c oxidoreductase activity. It is composed of at least eight subunits between 6 and 46 kDa in size, including two large "core" subunits and the three "respiratory" subunits. The molecular mass of the S. ecuadoriensis bc(1) complex is slightly lower than that reported for other eukaryotes, but about 2x as large as complex III in bacteria. This indicates that the departure from the small bacteria-like complex III took place at an early stage in mitochondrial evolution, prior to the divergence of jakobids. We posit that the recruitment of additional subunits in mitochondrial respiratory complexes is a consequence of the migration of originally alpha-proteobacterial genes to the nucleus.

[Sonographic diagnosis of fetal development disorders at the 1st Gynecologic Clinic of the Munich University 1984]

The diagnostic accuracy of sonographic screening is demonstrated by the results obtained in 171 pregnant women referred to the Department of Gynaecology of the University of Munich during 1984 for on-target sonography of foetal developmental disturbances. The accuracy was found to be 80%. Examination of pregnant women at risk shows a very low rate of developmental disturbances. The consequences arising from the observed disturbances of development are discussed.

[Selective removal of one twin with trisomy 21 by sectio parva in the 23rd week of pregnancy and later spontaneous birth of the healthy twin]

In a 41-year old tertipara with twin pregnancy, foetal chromosome analysis showed a boy without abnormal findings, 46, XY, and a boy with free trisomy 21. Abortion of the abnormal twin was performed in the 23rd week of pregnancy via sectio parva. Despite preoperative onset of tocolysis and ultimately performed circular suture of the cervix, premature rupture of the membranes occurred in the 28th pregnancy week, followed by spontaneous birth of the second twin weighing 1010 g. Raising of the premature baby did not present any special problems.

[Cefoperazone, cefsulodin and ceftazidime--3 cephalosporins active against Pseudomonas in comparison with their monobactam analogs]

This study compares the in vitro activity of three cephalosporins - ceftazidime, cefoperazone, cefsulodin and their monobactam analogues for 144 strains of Pseudomonas aeruginosa. Media variation studies are performed and the effect of human serum and anaerobic conditions on MIC is investigated. A significant inoculum effect is considered as a sign of instability against beta-lactamases. Ceftazidine inhibits nearly all pseudomonads at concentrations between 2 and 4 micrograms/ml being significantly more active than the other antibiotics tested. The level of activity of all monobactams tested is lower than that of the homologous cephalosporins. The counterpart of ceftazidine is also the most effective monobactam but the counterpart of cefsulodin shows no activity against pseudomonads.

[Comparison of antimicrobial activity and stability to beta-lactamases of cefoperazone, cefotaxime, lamoxactam and ceftriaxon]

Ceftriaxon (Ro 13-9904) is a new cephalosporin, whose structure resembles cefotaxime. This study compares the minimal inhibitory concentrations (MIC-s) of Ceftriaxon, cefoperazone, cefotaxime, lamoxactam and gentamicin against 622 isolates of various Enterobacteriaceae, non-fermenters and Aeromonas hydrophila. Furthermore the minimal bactericidal concentrations (MBC-s) were determined for some organism; additionally destruction of beta-lactamantibiotics in the presence of beta-lactamases was studied by a bioassay technique. The in vitro activity of Ceftriaxon against gramnegative bacteria was found very similar to that of cefotaxime. The susceptibility of Enterobacter sp. to the three cephalosporines was exceeded by lamoxactam while cefoperazone was the most active beta-lactam-antibiotic against Pseudomonas. Lactamases, which inactivated cefotaxime also destroyed Ceftriaxon in a greater extend. No hydrolysis of lamoxactam and cefoperazone occurred by nearly all bacterial extracts tested.