Drosophila melanogaster is a proven model system for many aspects of human biology. Here we present a two-hybrid-based protein-interaction map of the fly proteome. A total of 10,623 predicted transcripts were isolated and screened against standard and normalized complementary DNA libraries to produce a draft map of 7048 proteins and 20,405 interactions. A computational method of rating two-hybrid interaction confidence was developed to refine this draft map to a higher confidence map of 4679 proteins and 4780 interactions. Statistical modeling of the network showed two levels of organization: a short-range organization, presumably corresponding to multiprotein complexes, and a more global organization, presumably corresponding to intercomplex connections. The network recapitulated known pathways, extended pathways, and uncovered previously unknown pathway components. This map serves as a starting point for a systems biology modeling of multicellular organisms, including humans.

No abstract

Galectin-3 is a multifunctional oncogenic protein found in the nucleus and cytoplasm and also the extracellular milieu. Although recent studies demonstrated an anti-apoptotic activity of galectin-3, neither the functional site nor the mechanism of how galectin-3 regulates apoptosis is known. In this study, we examined the subcellular localization of galectin-3 during apoptosis and investigated its anti-apoptotic actions. We report that galectin-3 translocates to the perinuclear membrane following a variety of apoptotic stimuli. Confocal microscopy and biochemical analysis revealed that galectin-3 is enriched in the mitochondria and prevents mitochondrial damage and cytochrome c release. Using a yeast two-hybrid system, we screened for galectin-3-interacting proteins that regulate galectin-3 localization and anti-apoptotic activity. Synexin, a Ca 2؉ -and phospholipid-binding protein, was one of the proteins identified. We confirmed direct interaction between galectin-3 and synexin by glutathione S-transferase pulldown assay in vitro. We showed that galectin-3 failed to translocate to the perinuclear membranes when expression of synexin was down-regulated using an oligodeoxyribonucleotide complementary to the synexin mRNA, suggesting a role for synexin in galectin-3 trafficking. Furthermore, synexin down-regulation abolished anti-apoptotic activity of galectin-3. Taken together, these results suggest that synexin mediates galectin-3 translocation to the perinuclear mitochondrial membranes, where it regulates mitochondrial integrity critical for apoptosis regulation.Galectin-3 is a 31-kDa member of the ␤-galactoside-binding family of proteins found widely in epithelial and immune cells. Expression of galectin-3 is associated with neoplastic progression and metastatic potential (1-5) in head and neck (6), thyroid (7), gastric (3), and colon (8) cancers, suggesting a role in oncogenesis. Galectin-3 modulates a variety of cellular processes. Extracellular galectin-3 mediates cell migration, cell adhesion, and cell/cell interactions, whereas nuclear galectin-3 is involved in pre-mRNA splicing (9 -11). Interestingly, recent studies showed that cytoplasmic, but not nuclear, galectin-3 is associated with tumor progression (12, 13). Yet, the role of cytoplasmic galectin-3 is unknown.We (15-17) and others (14,18,19) have previously shown that galectin-3 inhibits T-cell apoptosis induced by anti-Fas antibody and epithelial cell apoptosis induced by staurosporine, cisplatin, genistein, and anoikis. The anti-apoptotic activity of galectin-3 was also demonstrated in galectin-3-deficient mice. Peritoneal macrophages from galectin-3-deficient mice were more sensitive to apoptotic stimuli than those from control mice (20). The ability of galectin-3 to protect cells against apoptosis induced by agents working through different mechanisms suggests that galectin-3 regulates the common apoptosis commitment step.During the past decade, explosive progress has been made toward understanding the molecular basis for the regulation of the a...

DroID (http://droidb.org/), the Drosophila Interactions Database, is a comprehensive public resource for Drosophila gene and protein interactions. DroID contains genetic interactions and experimentally detected protein–protein interactions curated from the literature and from external databases, and predicted protein interactions based on experiments in other species. Protein interactions are annotated with experimental details and periodically updated confidence scores. Data in DroID is accessible through user-friendly, intuitive interfaces that allow simple or advanced searches and graphical visualization of interaction networks. DroID has been expanded to include interaction types that enable more complete analyses of the genetic networks that underlie biological processes. In addition to protein–protein and genetic interactions, the database now includes transcription factor–gene and regulatory RNA–gene interactions. In addition, DroID now has more gene expression data that can be used to search and filter interaction networks. Orthologous gene mappings of Drosophila genes to other organisms are also available to facilitate finding interactions based on gene names and identifiers for a number of common model organisms and humans. Improvements have been made to the web and graphical interfaces to help biologists gain a comprehensive view of the interaction networks relevant to the genes and systems that they study.

Background: Data from large-scale protein interaction screens for humans and model eukaryotes have been invaluable for developing systems-level models of biological processes. Despite this value, only a limited amount of interaction data is available for prokaryotes. Here we report the systematic identification of protein interactions for the bacterium Campylobacter jejuni, a foodborne pathogen and a major cause of gastroenteritis worldwide.

We characterized interactions between Drosophila melanogaster cell cycle regulatory proteins by a yeast interaction-mating technique. The results were displayed as two-dimensional matrices that revealed individual binary interactions between proteins. Each protein (Cdi, cyclindependent kinase interactor) interacted with a distinct spectrum of cyclin-dependent kinases (Cdk) from Drosophila and other organisms. Some Cdis interacted with other Cdis, indicating that these proteins may form trimeric complexes that include Cdks. Similar analysis of interaction matrices may be generally useful in detecting other multiprotein complexes and in establishing connectivity between individual complex members. Moreover, such analysis may also help assign function to newly identified proteins, identify domains involved in proteinprotein interactions, and aid the dissection of genetic regulatory networks.

No abstract

Cytochrome c oxidase (COX) is the terminal enzyme of the electron transport chain, made up of 13 subunits encoded by both mitochondrial and nuclear DNA. Subunit 4 (COX4), a key regulatory subunit, exists as two isoforms, the ubiquitous isoform 1 and the tissue-specific (predominantly lung) isoform 2 (COX4I2). COX4I2 renders lung COX about 2-fold more active compared with liver COX, which lacks COX4I2. We previously identified a highly conserved 13-bp sequence in the proximal promoter of COX4I2 that functions as an oxygen responsive element (ORE), maximally active at a 4% oxygen concentration. Here, we have identified three transcription factors that bind this conserved ORE, namely recombination signal sequence–binding protein Jκ (RBPJ), coiled-coil-helix-coiled-coil-helix domain 2 (CHCHD2) and CXXC finger protein 5 (CXXC5). We demonstrate that RBPJ and CHCHD2 function towards activating the ORE at 4% oxygen, whereas CXXC5 functions as an inhibitor. To validate results derived from cultured cells, we show using RNA interference a similar effect of these transcription factors in the gene regulation of COX4I2 in primary pulmonary arterial smooth muscle cells. Depending on the oxygen tension, a concerted action of the three transcription factors regulates the expression of COX4I2 that, as we discuss, could augment both COX activity and its ability to cope with altered cellular energy requirements.