Analyzing yeast protein-protein interaction data obtained from different sources

High-throughput methods for detecting protein interactions, such as mass spectrometry and yeast two-hybrid assays, continue to produce vast amounts of data that may be exploited to infer protein function and regulation. As this article went to press, the pool of all published interaction information on Saccharomyces cerevisiae was 15,143 interactions among 4,825 proteins, and power-law scaling supports an estimate of 20,000 specific protein interactions. To investigate the biases, overlaps, and complementarities among these data, we have carried out an analysis of two high-throughput mass spectrometry (HMS)-based protein interaction data sets from budding yeast, comparing them to each other and to other interaction data sets. Our analysis reveals 198 interactions among 222 proteins common to both data sets, many of which reflect large multiprotein complexes. It also indicates that a "spoke" model that directly pairs bait proteins with associated proteins is roughly threefold more accurate than a "matrix" model that connects all proteins. In addition, we identify a large, previously unsuspected nucleolar complex of 148 proteins, including 39 proteins of unknown function. Our results indicate that existing large-scale protein interaction data sets are nonsaturating and that integrating many different experimental data sets yields a clearer biological view than any single method alone.     

Proteomic analysis reveals alterations in the renal kallikrein pathway during hypoxia-induced hypertension

Obstructive sleep apnea syndrome (OSAS), a disorder characterized by episodic hypoxia (EH) during sleep, is associated with systemic hypertension. We used proteomic analysis to examine differences in rat kidney protein expression during EH, and their potential relationship to EH-induced hypertension. Young male Sprague-Dawley rats were exposed to either EH or sustained hypoxia (SH) for 14 (EH14/SH14) and 30 (EH30/SH30) days. Mean arterial blood pressure was significantly increased only in EH30 (p < 0.0002). Kidney proteins were resolved by two-dimensional-PAGE and were identified by MALDI-MS. Renal expression of kallistatin, a potent vasodilator, was down-regulated in all animals. Expression of alpha-1-antitrypsin, an inhibitor of kallikrein activation, was up-regulated in EH but down-regulated in SH. Western blotting showed significant elevation of B(2)-bradykinin receptor expression in all normotensive animals but remained unchanged in hypertensive animals. Proteins relevant to vascular hypertrophy, such as smooth muscle myosin and protein-disulfide isomerase were up-regulated in EH30 but were down-regulated in SH30. These data indicate that EH induces changes in renal protein expression consistent with impairment of vasodilation mediated by the kallikrein-kallistatin pathway and vascular hypertrophy. In contrast, SH-induced changes suggest the kallikrein- and bradykinin-mediated compensatory mechanisms for prevention of hypertension and vascular remodeling. To test the hypothesis suggested by the proteomic data, we measured the effect of EH on blood pressure in transgenic hKLK1 rats that overexpress human kallikrein. Transgenic hKLK1 animals were protected from EH-induced hypertension. We conclude that EH-induced hypertension may result, at least in part, from altered regulation of the renal kallikrein system.     

Calcium-regulated exocytosis of dense-core vesicles requires the activation of ADP-ribosylation factor (ARF)6 by ARF nucleotide binding site opener at the plasma membrane

Vacuole fusion requires a coordinated cascade of priming, docking, and fusion. SNARE proteins have been implicated in the fusion itself, although their precise role in the cascade remains unclear. We now report that the vacuolar SNAP-23 homologue Vam7p is a mobile element of the SNARE complex, which moves from an initial association with the cis-SNARE complex via a soluble intermediate to the docking site. Soluble Vam7p is specifically recruited to vacuoles and can rescue a fusion reaction poisoned with antibodies to Vam7p. Both the recombinant Vam7p PX domain and a FYVE domain construct of human Hrs block the recruitment of Vam7p and vacuole fusion, demonstrating that phosphatidylinositol 3-phosphate is a primary receptor of Vam7p on vacuoles. We propose that the Vam7p cycle is linked to the availability of a lipid domain on yeast vacuoles, which is essential for coordinating the fusion reaction prior to and beyond docking.     

Greedily building protein networks with confidence

MOTIVATION: With genome sequences complete for human and model organisms, it is essential to understand how individual genes and proteins are organized into biological networks. Much of the organization is revealed by proteomics experiments that now generate torrents of data. Extracting relevant complexes and pathways from high-throughput proteomics data sets has posed a challenge, however, and new methods to identify and extract networks are essential. We focus on the problem of building pathways starting from known proteins of interest. RESULTS: We have developed an efficient, greedy algorithm, SEEDY, that extracts biologically relevant biological networks from protein-protein interaction data, building out from selected seed proteins. The algorithm relies on our previous study establishing statistical confidence levels for interactions generated by two-hybrid screens and inferred from mass spectrometric identification of protein complexes. We demonstrate the ability to extract known yeast complexes from high-throughput protein interaction data with a tunable parameter that governs the trade-off between sensitivity and selectivity. DNA damage repair pathways are presented as a detailed example. We highlight the ability to join heterogeneous data sets, in this case protein-protein interactions and genetic interactions, and the appearance of cross-talk between pathways caused by re-use of shared components. SIGNIFICANCE AND COMPARISON: The significance of the SEEDY algorithm is that it is fast, running time O[(E + V) log V] for V proteins and E interactions, a single adjustable parameter controls the size of the pathways that are generated, and an associated P-value indicates the statistical confidence that the pathways are enriched for proteins with a coherent function. Previous approaches have focused on extracting sub-networks by identifying motifs enriched in known biological networks. SEEDY provides the complementary ability to perform a directed search based on proteins of interest. AVAILABILITY: SEEDY software (Perl source), data tables and confidence score models (R source) are freely available from the author.     

Influence of culture time on the expression of drug-metabolizing enzymes in primary human hepatocytes and hepatoma cell line HepG2

Primary cultures of human hepatocytes and hepatoma cell line HepG2 are frequently used to evaluate the hepatic disposition of drugs and other xenobiotics. To check the variability of the expression of drug-metabolizing enzymes in these in vitro models, expression of genes coding for several cytochrome P450 isoforms and phase II enzymes was quantified during culture time by real-time RT-PCR. Gene expression was determined daily for primary hepatocytes maintained in a sandwich culture over 1 week and for HepG2, during the first 10 passages. In primary hepatocytes characteristic expression trends were observed which could be abstracted into three major classes of time curves. Genes of the first and the second class had an expression maximum around day 6 and day 4 in culture, respectively. The third class of genes had two expression peaks: at day 1 and 5 in culture. Surprisingly, also the cell line HepG2 showed significant expression changes during passages. For example, gene expression of cytochrome 1A1 varied 8-fold, that of cytochrome 2B6 30-fold, and that of NADP-quinone reductase 1 more than 200-fold within the first 10 passages. In conclusion, neither primary hepatocytes nor HepG2 cell line display a model for constant expression of drug-metabolizing enzymes.     

Dependence of the flash-induced oxygen evolution pattern on the chemically and far red light-modulated redox condition in cyanobacterial photosynthetic electron transport

Flash-induced photosynthetic oxygen evolution was measured in cells and thylakoid preparations from the coccoid cyanobacteria Synechocystis sp. PCC 6803 and Synechococcus sp. PCC 7942 and from the filamentous cyanobacterium Oscillatoria chalybea. The resulting characteristic flash patterns from these cyanobacteria can be chemically altered by addition of exogenously added substances like CCCP, DCPiP and inorganic salts. Potassium chloride, manganese sulfate and calcium chloride affected the sequences by specific increases in the flash yield and/or effects on the transition parameters. Chloride appeared to exert the strongest stimulatory effect on the oxygen yield. In comparison to chloride, both manganese and calcium did not significantly stimulate the flash amplitudes as such, but improved the functioning of the oxygen evolving complex by decreasing the miss parameter alpha. Particular effects were observed with respect to the time constants of the relaxation kinetics of the first two flash signals Y1/Y2 of the cyanobacterial patterns. In the presence of the investigated chemicals the amplitudes of the first two flash signals (Y2 in particular) were increased and the relaxation kinetics were enhanced so that the time constant became about identical to the conditions of steady state oxygen flash amplitudes. The results provide further evidence against a possible participation of either PS I or respiratory processes to Y1/Y2 of cyanobacterial flash patterns. Dramatic effects were observed when protoplasts from Oscillatoria chalybea or cells from Synechocystis sp. PCC 6803 and Synechococcus sp. PCC 7942 were exposed to weak far red background illumination. Under these conditions, Y2 (and to a smaller extent Y1) of otherwise unchanged flash sequences were specifically modified. Y2 was substantially increased and again the relaxation kinetics were accelerated making the signal indistinguishable from a Y(SS) signal. From the mathematical fit of the sequences we conclude that S2 contributes to 10-20% of the S-state distribution (in comparison to 0% in the control). Thus, far red background illumination might represent a valuable means for photosynthetic investigations where high amounts of S2 are required like e. g. EPR measurements. In such experiments the corresponding EPR signals appeared substantially enhanced following far red preillumination (Ahrling and Bader, unpublished observations). Our results clearly show that the 'controversial results' from parts of the literature suggesting the participation of different mechanisms (net oxygen evolution, inhibited uptake processes etc.) are not required to explain the flash-induced oxygen evolution in cyanobacteria: the seemingly 'incompatible' conditions and conformations can be perfectly interconverted by different modulation techniques (chemicals, far red) of the respective redox condition within the water oxidation complex of photosynthesis.     

The crystal structure of dihydrofolate reductase from Thermotoga maritima: molecular features of thermostability

Two high-resolution structures have been obtained for dihydrofolate reductase from the hyperthermophilic bacterium Thermotoga maritima in its unliganded state, and in its ternary complex with the cofactor NADPH and the inhibitor, methotrexate. While the overall fold of the hyperthermophilic enzyme is closely similar to monomeric mesophilic dihydrofolate reductase molecules, its quaternary structure is exceptional, in that T. maritima dihydrofolate reductase forms a highly stable homodimer. Here, the molecular reasons for the high intrinsic stability of the enzyme are elaborated and put in context with the available data on the physical parameters governing the folding reaction. The molecule is extremely rigid, even with respect to structural changes during substrate binding and turnover. Subunit cooperativity can be excluded from structural and biochemical data. Major contributions to the high intrinsic stability of the enzyme result from the formation of the dimer. Within the monomer, only subtle stabilizing interactions are detectable, without clear evidence for any of the typical increments of thermal stabilization commonly reported for hyperthermophilic proteins. The docking of the subunits is optimized with respect to high packing density in the dimer interface, additional salt-bridges and beta-sheets. The enzyme does not show significant structural changes upon binding its coenzyme, NADPH, and the inhibitor, methotrexate. The active-site loop, which is known to play an important role in catalysis in mesophilic dihydrofolate reductase molecules, is rearranged, participating in the association of the subunits; it no longer participates in catalysis.     

Chondrocyte deformation within compressed agarose constructs at the cellular and sub-cellular levels

Mechanotransduction events in articular cartilage may be resolved into extracellular components followed by intracellular signalling events, which finally lead to altered cell response. Cell deformation is one of the former components, which has been examined using a model involving bovine chondrocytes seeded in agarose constructs. Viable fluorescent labels and confocal laser scanning microscopy were used to examine cellular and sub-cellular morphology. It was observed that cell size increased up to day 6 in culture, associated with an increase in the contents of proteoglycan and collagen. In addition, the organisation of the cytoskeleton components, described using a simple scoring scale, revealed temporal changes for actin fibres, microtubules and vimentin intermediate filaments. The constructs on day 1 were also subjected to unconfined compressive strains. A series of confocal scans through the centre of individual cells revealed a change from a spherical to an elliptical morphology. This was demonstrated by a change in diameter ratio, from a mean value of 1.00 at 0% strain to 0.60 at 25% strain. Using simple equations, the volume and surface areas were also estimated from the scans. Although the former revealed little change with increasing construct strain, surface area appeared to increase significantly. However further examination, using transmission electron microscopy to reveal fine ultrastructural detail at the cell periphery, suggest that this increase may be due to an unravelling of folds at the cell membrane. Cell deformation was associated with a decrease in the nuclear diameter, in the direction of the applied strain. The resulting nuclear strain in one direction increased in constructs compressed at later time points, although its values at all three assessment times were less than the corresponding values for cell strain. It is suggested that the nuclear behaviour may be a direct result of temporal changes observed in the organisation of the cytoskeleton. The study demonstrated that the chondrocyte-agarose model provides a useful system for the examination of compression events at both cellular and sub-cellular levels.     

Inducer exclusion by glucose 6-phosphate in Escherichia coli

The main mechanism causing catabolite repression by glucose and other carbon sources transported by the phosphotransferase system (PTS) in Escherichia coli involves dephosphorylation of enzyme IIA^Glc as a result of transport and phosphorylation of PTS carbohydrates. Dephosphorylation of enzyme IIA^Glc leads to 'inducer exclusion': inhibition of transport of a number of non-PTS carbon sources (e.g. lactose, glycerol), and reduced adenylate cyclase activity. In this paper, we show that the non-PTS carbon source glucose 6-phosphate can also cause inducer exclusion. Glucose 6-phosphate was shown to cause inhibition of transport of lactose and the non-metabolizable lactose analogue methyl-β- D -thiogalactoside (TMG). Inhibition was absent in mutants that lacked enzyme IIA^Glc or were insensitive to inducer exclusion because enzyme IIA^Glc could not bind to the lactose carrier. Furthermore, we showed that glucose 6-phosphate caused dephosphorylation of enzyme IIA^Glc. In a mutant insensitive to enzyme IIA^Glc-mediated inducer exclusion, catabolite repression by glucose 6-phosphate in lactose-induced cells was much weaker than that in the wild-type strain, showing that inducer exclusion is the most important mechanism contributing to catabolite repression in lactose-induced cells. We discuss an expanded model of enzyme IIA^Glc-mediated catabolite repression which embodies repression by non- PTS carbon sources.