Organization of Physical Interactomes as Uncovered by Network Schemas

Large-scale protein-protein interaction networks provide new opportunities for understanding cellular organization and functioning. We introduce network schemas to elucidate shared mechanisms within interactomes. Network schemas specify descriptions of proteins and the topology of interactions among them. We develop algorithms for systematically uncovering recurring, over-represented schemas in physical interaction networks. We apply our methods to the S. cerevisiae interactome, focusing on schemas consisting of proteins described via sequence motifs and molecular function annotations and interacting with one another in one of four basic network topologies. We identify hundreds of recurring and over-represented network schemas of various complexity, and demonstrate via graph-theoretic representations how more complex schemas are organized in terms of their lower-order constituents. The uncovered schemas span a wide range of cellular activities, with many signaling and transport related higher-order schemas. We establish the functional importance of the schemas by showing that they correspond to functionally cohesive sets of proteins, are enriched in the frequency with which they have instances in the H. sapiens interactome, and are useful for predicting protein function. Our findings suggest that network schemas are a powerful paradigm for organizing, interrogating, and annotating cellular networks

Food and parasites - life-history decisions in copepods

In the freshwater copepod, Macrocyclops albidus, food availability, rearing conditions and tapeworm infection clearly affected various life-history traits and their trade-offs. I found that low food availability clearly constrained resource allocations to several life-history (often phenotypically plastic) traits, whereas high food availability either allowed for adjustments in resource allocation patterns or allowed to be allocated to several traits withou apparent trade-offs. Both maile and female copepods allocated resources according to food availability; developing more slowly and achieving smaller adult body size when food was scarce. When food availability was low females were constrained and produced fewer eggs (in total and per clutch), and started reproduction later than females with more food available. Males under low food availability allocated reletively more spermatophore size (current reproduction) with decreasing body size. In contrast, when food availability was high males allocated resources to body size as well as spermatophore size. Overall, at maturity, copepods of both sexes were more similar in size than in age, suggesting that large body size was more important for fitness than fast development. In nature the prevalence of copepods infected with cestode tapeworms was found to be low (0-3%). Female copepods, experimentally infected with the cestode Schistocephalus solidus, showed lower overall fecundity, especially when food availability was low. However, infected females produced a larger proportion of their life-time egg production early in life than non-infected females. This might be an adaptation to reduce future fitness costs of infection. Females grown under bad rearing conditions, but with high food availability, produced their first clutch earlier than females grown under good rearing conditions, indicating an adjustment in timing reproduction. These findings contribute to our fundamental evolutionary understanding of how environmental conditions interact with life-history traits.Introduction................................................7 Body size.................................................8 Current vs. future reproduction...........................9 Aim........................................................11 Study species..............................................12 The parasite.............................................13 General methods..........................................15 Results and Discussion.....................................17 Age and size at maturity - paper I.......................17 Resource allocation in males - paper II..................19 Female life-histories and food availability - paper III..21 A field study - paper IV.................................23 Resource allocation and cost of infection in females - paper V................................................. 25 Conclusion.................................................28 Acknowledgments............................................30 Sammanfattning.............................................32 References.................................................3

Causes and consequences of mass loss upon predator encounter: feeding interruption, stress or fit-for-flight?

1. Birds have been shown to lose mass upon predator encounters. This mass loss has generally been assumed to be caused by the feeding interruption the birds experience upon encountering the predator. However, birds may lose this mass because of predator stress and because they prepare themselves for flight (fit-for-flight). In this experiment the aim was to distinguish between effects of feeding interruptions and stress or fit-for-flight on the mass loss of Yellowhammers (Emberiza citrinella L.) upon predator exposure. 2. When exposed to a 45-min feeding interruption, the birds lost only a quarter of the mass they lost when they were moved to another room and exposed to a stuffed Sparrowhawk (Accipiter nisus) for 1 min at that beginning of the feeding interruption. This indicates that mass loss upon predator exposure is not just due to the feeding interruption birds experience upon encountering a predator, but is probably, to a large extent, due to both predator stress and fit-for-flight. 3. When the stuffed Sparrowhawk was replaced with a dummy (an opaque plastic bottle), mass loss upon exposure was similar to the loss in the Sparrowhawk treatment. This indicates that moving the birds to another room, which occurred in both these treatments, may to a large extent be the cause of the mass loss. 4. During the same day, the birds regained 92% of their losses. However, regaining those losses was partly postponed to the end of the day, which indicates that the birds faced a trade-off between starvation and predation risk, and were able to respond to that trade-off by altering their diurnal trajectory of mass increase. By postponing foraging to the end of the day, the birds decreased the mass-dependent costs of predation risk

Causes and consequences of mass loss upon predator encounter: feeding interruption, stress or fit-for-flight?

1. Birds have been shown to lose mass upon predator encounters. This mass loss has generally been assumed to be caused by the feeding interruption the birds experience upon encountering the predator. However, birds may lose this mass because of predator stress and because they prepare themselves for flight (fit-for-flight). In this experiment the aim was to distinguish between effects of feeding interruptions and stress or fit-for-flight on the mass loss of Yellowhammers (Emberiza citrinella L.) upon predator exposure. 2. When exposed to a 45-min feeding interruption, the birds lost only a quarter of the mass they lost when they were moved to another room and exposed to a stuffed Sparrowhawk (Accipiter nisus) for 1 min at that beginning of the feeding interruption. This indicates that mass loss upon predator exposure is not just due to the feeding interruption birds experience upon encountering a predator, but is probably, to a large extent, due to both predator stress and fit-for-flight. 3. When the stuffed Sparrowhawk was replaced with a dummy (an opaque plastic bottle), mass loss upon exposure was similar to the loss in the Sparrowhawk treatment. This indicates that moving the birds to another room, which occurred in both these treatments, may to a large extent be the cause of the mass loss. 4. During the same day, the birds regained 92% of their losses. However, regaining those losses was partly postponed to the end of the day, which indicates that the birds faced a trade-off between starvation and predation risk, and were able to respond to that trade-off by altering their diurnal trajectory of mass increase. By postponing foraging to the end of the day, the birds decreased the mass-dependent costs of predation risk

Protein pre-fractionation in detergent-polymer aqueous two-phase systems for facilitated proteomic studies of membrane proteins

Pre-fractionation of a complex mixture of proteins increases the resolution in analytical separations of proteins from cells, tissues or organisms. Here we demonstrate a novel method for pre-fractionation of membrane proteins by a detergent-based aqueous two-phase system. Membrane proteins are strongly under-represented in proteomic studies based on two-dimensional electrophoresis (2-DE). As a model system, we have isolated mitochondria from the yeast Saccharomyces cerevisiae. Mitochondrial proteins were fractionated in an aqueous two-phase system consisting of the polymer poly(ethylene glycol) and either of two commonly used non-ionic detergents, Triton X-114 or dodecyl maltoside (DDM). Soluble proteins partitioned mainly to the polymer phase while membrane proteins were enriched in the detergent phase, as identified from one-dimensional electrophoresis (I-DE) and/or 2-DE followed by mass spectrometric analysis. Pre-fractionation was further enhanced by addition of an anionic detergent, sodium dodecyl sulfate, or a chaotropic salt, NaClO4, and by raising the pH in the system. The two-phase system pre-fractionation was furthermore combined with an alternative two-dimensional high-resolution separation method, namely ion-exchange chromatography and 1-DE. By this approach a larger number of membrane proteins could be identified compared to separation with conventional 2-DE. Thus, pre-fractionation of complex protein mixtures using the aqueous two-phase systems developed here will help to disclose larger proportions of membrane proteins in different proteomes. (C) 2004 Elsevier B.V. All rights reserved

Structural mechanism of host Rab1 activation by the bifunctional Legionella type IV effector SidM/DrrA

Bacterial pathogens deliver effector proteins with diverse biochemical activities into host cells, thereby modulating various host functions. Legionella pneumophila hijacks host vesicle trafficking to avoid phagosome–lysosome fusion, a mechanism that is dependent on the Legionella Dot/Icm type IV secretion system. SidM/DrrA, a Legionella type IV effector, is important for the interactions of Legionella-containing vacuoles with host endoplasmic reticulum–derived vesicles. SidM is the only known protein that catalyzes both the exchange of GDP for GTP and GDI displacement from small GTPase Rab1. We determined the crystal structures of SidM alone (residues 317–647) and SidM (residues 193–550) in complex with nucleotide-free WT Rab1. The SidM structure contains an N-terminal helical domain with a potential new function, a Rab1-activation domain, and a C-terminal phosphatidylinositol 4-phosphate–binding P4M domain. The Rab1-activation domain has extensive strong interactions mainly with Rab1 switch I and II regions that undergo substantial conformational changes on SidM binding. Mutations of switch-contacting residues in SidM attenuate both the nucleotide exchange and GDI displacement activities. Structural comparisons of Rab1 in the SidM complex with Rab1-GDP and Ypt1-GDP in the GDI complex identify key conformational changes that disrupt the nucleotide and GDI binding of Rab1. Further biochemical and structural analyses reveal a unique mechanism of coupled GDP release and GDI displacement likely triggered by the SidM-induced drastic displacement of switch I of Rab1