Biomedical subjects

Harukazu Suzuki

Publications and source records attributed to Harukazu Suzuki.

10 recordsLinked to original sources

PubMed2004

Solution structure of a BolA-like protein from Mus musculus.

The BolA-like proteins are widely conserved from prokaryotes to eukaryotes. The BolA-like proteins seem to be involved in cell proliferation or cell-cycle regulation, but the molecular function is still unknown. Here we determined the structure of a mouse BolA-like protein. The overall topology is alphabetabetaalphaalphabetaalpha, in which beta(1) and beta(2) are antiparallel, and beta(3) is parallel to beta(2). This fold is similar to the class II KH fold, except for the absence of the GXXG loop, which is well conserved in the KH fold. The conserved residues in the BolA-like proteins are assembled on the one side of the protein.

Amino Acid Sequence↗

PubMed2003

The PDZ protein tax-interacting protein-1 inhibits beta-catenin transcriptional activity and growth of colorectal cancer cells.

Wnt signaling is essential during development while deregulation of this pathway frequently leads to the formation of various tumors including colorectal carcinomas. A key component of the pathway is beta-catenin that, in association with TCF-4, directly regulates the expression of Wnt-responsive genes. To identify novel binding partners of beta-catenin that may control its transcriptional activity, we performed a mammalian two-hybrid screen and isolated the Tax-interacting protein (TIP-1). The in vivo complex formation between beta-catenin and TIP-1 was verified by coimmunoprecipitation, and a direct physical association was revealed by glutathione S-transferase pull-down experiments in vitro. By using a panel of deletion mutants of both proteins, we demonstrate that the interaction is mediated by the PDZ (PSD-95/DLG/ZO-1 homology) domain of TIP-1 and requires primarily the last four amino acids of beta-catenin. TIP-1 overexpression resulted in a dose-dependent decrease in the transcriptional activity of beta-catenin when tested on the TOP/FOPFLASH reporter system. Conversely, siRNA-mediated knock-down of endogenous TIP-1 slightly increased endogenous beta-catenin transactivation function. Moreover, we show that overexpression of TIP-1 reduced the proliferation and anchorage-independent growth of colorectal cancer cells. These data suggest that TIP-1 may represent a novel regulatory element in the Wnt/beta-catenin signaling pathway.

Agar↗

PubMed2003

Construction of reliable protein-protein interaction networks with a new interaction generality measure.

MOTIVATION: Recent screening techniques have made large amounts of protein-protein interaction data available, from which biologically important information such as the function of uncharacterized proteins, the existence of novel protein complexes, and novel signal-transduction pathways can be discovered. However, experimental data on protein interactions contain many false positives, making these discoveries difficult. Therefore computational methods of assessing the reliability of each candidate protein-protein interaction are urgently needed. RESULTS: We developed a new 'interaction generality' measure (IG2) to assess the reliability of protein-protein interactions using only the topological properties of their interaction-network structure. Using yeast protein-protein interaction data, we showed that reliable protein-protein interactions had significantly lower IG2 values than less-reliable interactions, suggesting that IG2 values can be used to evaluate and filter interaction data to enable the construction of reliable protein-protein interaction networks.

Binding Sites↗

PubMed2003

Global insights into protein complexes through integrated analysis of the reliable interactome and knockout lethality.

We performed an integrated computational analysis of data derived from a comprehensive set of protein-protein interactions (interactome) and a phenotype dataset on lethality in Saccharomyces cerevisiae. For the analysis, we selected reliable interactome data using our previous 'interaction generality,' a computational approach to assess reliability of interactions. Those efforts gave clear evidence that proteins with lethal phenotypes in knockout studies (lethal proteins) may interact with each other to form functional protein complexes to perform their cellular roles. However, our analysis indicates that interactions between lethal proteins are rather restricted to the same cellular pathway or function, and it is quite unlikely that they interact with other lethal proteins functioning in different cellular roles. Furthermore, our results allowed us predictions on the functions of thus far uncharacterized lethal proteins with an estimated 93% accuracy. Thus, the analysis described in here can provide global insights into the biological features of the protein complexes.

Computational Biology↗

PubMed2003

Inferring higher functional information for RIKEN mouse full-length cDNA clones with FACTS.

FACTS (Functional Association/Annotation of cDNA Clones from Text/Sequence Sources) is a semiautomated knowledge discovery and annotation system that integrates molecular function information derived from sequence analysis results (sequence inferred) with functional information extracted from text. Text-inferred information was extracted from keyword-based retrievals of MEDLINE abstracts and by matching of gene or protein names to OMIM, BIND, and DIP database entries. Using FACTS, we found that 47.5% of the 60,770 RIKEN mouse cDNA FANTOM2 clone annotations were informative for text searches. MEDLINE queries yielded molecular interaction-containing sentences for 23.1% of the clones. When disease MeSH and GO terms were matched with retrieved abstracts, 22.7% of clones were associated with potential diseases, and 32.5% with GO identifiers. A significant number (23.5%) of disease MeSH-associated clones were also found to have a hereditary disease association (OMIM Morbidmap). Inferred neoplastic and nervous system disease represented 49.6% and 36.0% of disease MeSH-associated clones, respectively. A comparison of sequence-based GO assignments with informative text-based GO assignments revealed that for 78.2% of clones, identical GO assignments were provided for that clone by either method, whereas for 21.8% of clones, the assignments differed. In contrast, for OMIM assignments, only 28.5% of clones had identical sequence-based and text-based OMIM assignments. Sequence, sentence, and term-based functional associations are included in the FACTS database (http://facts.gsc.riken.go.jp/), which permits results to be annotated and explored through web-accessible keyword and sequence search interfaces. The FACTS database will be a critical tool for investigating the functional complexity of the mouse transcriptome, cDNA-inferred interactome (molecular interactions), and pathome (pathologies).

Animals↗

PubMed2003

CDS annotation in full-length cDNA sequence.

The identification of coding sequences (CDS) is an important step in the functional annotation of genes. CDS prediction for mammalian genes from genomic sequence is complicated by the vast abundance of intergenic sequence in the genome, and provides little information about how different parts of potential CDS regions are expressed. In contrast, mammalian gene CDS prediction from cDNA sequence offers obvious advantages, yet encounters a different set of complexities when performed on high-throughput cDNA (HTC) sequences, such as the set of 60,770 cDNAs isolated from full-length enriched libraries of the FANTOM2 project. We developed a CDS annotation strategy that uses a variety of different CDS prediction programs to annotate the CDS regions of FANTOM2 cDNAs. These include rsCDS, which uses sequence similarity to known proteins; ProCrest; Longest-ORF and Truncated-ORF, which are ab initio based predictors; and finally, DECODER and NCBI CDS predictor, which use a combination of both principles. Aided by graphical displays of these CDS prediction results in the context of other sequence similarity results for each cDNA, FANTOM2 CDS inspection by curators and follow-up quality control procedures resulted in high quality CDS predictions for a total of 14,345 FANTOM2 clones.

Animals↗

PubMed2003

The mammalian protein-protein interaction database and its viewing system that is linked to the main FANTOM2 viewer.

Here, we describe the development of a mammalian protein-protein interaction (PPI) database and of a PPI Viewer application to display protein interaction networks (http://fantom21.gsc.riken.go.jp/PPI/). In the database, we stored the mammalian PPIs identified through our PPI assays (internal PPIs), as well as those we extracted and processed (external PPIs) from publicly available data sources, the DIP and BIND databases and MEDLINE abstracts by using FACTS, a new functional inference and curation system. We integrated the internal and external PPIs into the PPI database, which is linked to the main FANTOM2 viewer. In addition, we incorporated into the PPI Viewer information regarding the luciferase reporter activity of internal PPIs and the data confidence of external PPIs; these data enable visualization and evaluation of the reliability of each interaction. Using the described system, we successfully identified several interactions of biological significance. Therefore, the PPI Viewer is a useful tool for exploring FANTOM2 clone-related protein interactions and their potential effects on signaling and cellular communication.

Animals↗

PubMed2002

NF-kappaB activator Act1 associates with IL-1/Toll pathway adaptor molecule TRAF6.

NF-kappaB activator 1 (Act1), also called CIKS, is a recently identified protein with NF-kappaB and AP-1 activation activities through its association with the IkappaB kinase complex. We identified and confirmed that Act1 interacts with tumor necrosis factor receptor-associated factor 6 (TRAF6); notably, Act1 binds to TRAF6 only among TRAF family proteins. The amino-terminal half of Act1 is required for its interaction with the TRAF domain. Act1-mediated NF-kappaB activation was inhibited by a dominant-negative mutant of TRAF6 in a dose-dependent manner, and IL-1-induced NF-kappaB activation was inhibited by a high level of Act1 expression. Our results suggest that Act1 is involved in IL-1/Toll-mediated signaling through TRAF6.

Adaptor Proteins, Signal Transducing↗

PubMed2002

Interaction generality, a measurement to assess the reliability of a protein-protein interaction.

Here we introduce the 'interaction generality' measure, a new method for computationally assessing the reliability of protein-protein interactions obtained in biological experiments. This measure is basically the number of proteins involved in a given interaction and also adopts the idea that interactions observed in a complicated interaction network are likely to be true positives. Using a group of yeast protein-protein interactions identified in various biological experiments, we show that interactions with low generalities are more likely to be reproducible in other independent assays. We constructed more reliable networks by eliminating interactions whose generalities were above a particular threshold. The rate of interactions with common cellular roles increased from 63% in the unadjusted estimates to 79% in the refined networks. As a result, the rate of cross-talk between proteins with different cellular roles decreased, enabling very clear predictions of the functions of some unknown proteins. The results suggest that the interaction generality measure will make interaction data more useful in all organisms and may yield insights into the biological roles of the proteins studied.

Computational Biology↗

PubMed2002

T2BP, a novel TRAF2 binding protein, can activate NF-kappaB and AP-1 without TNF stimulation.

TRAF2 is a key molecule involved in TNF signaling, which is crucial for the regulation of inflammatory processes. We have identified a novel TRAF2 binding protein, designated as T2BP (TRAF2 binding protein), by a mammalian two-hybrid screening approach. T2BP is a relatively small protein of 184 amino acids, which includes a forkhead-associated domain, the phosphopeptide binding motif. The interaction domain search showed that the TRAF domain in TRAF2 is required for the binding to T2BP whereas almost the entire protein in T2BP binds to TRAF2. The interaction was further confirmed by co-immunoprecipitation. Expression profiling for T2BP and TRAF2 revealed an ubiquitous expression in adult mouse tissues. Overexpression of T2BP in HEK293 cells activated NF-kappaB and AP-1 in a dose dependent manner as well as seen in the TNF-treated control cells. Our results suggest that T2BP is involved in the TNF-mediated signaling by its interaction with TRAF2.

Adaptor Proteins, Signal Transducing↗