Plant Genome DataBase Japan (PGDBj): a portal website for the integration of plant genome-related databases.

The Plant Genome DataBase Japan (PGDBj, http://pgdbj.jp/?ln=en) is a portal website that aims to integrate plant genome-related information from databases (DBs) and the literature. The PGDBj is comprised of three component DBs and a cross-search engine, which provides a seamless search over the contents of the DBs.

SABRE2: a database connecting plant EST/full-length cDNA clones with Arabidopsis information.

The SABRE (Systematic consolidation of Arabidopsis and other Botanical REsources) database cross-searches plant genetic resources through publicly available Arabidopsis information. In SABRE, plant expressed sequence tag (EST)/cDNA clones are related to TAIR (The Arabidoposis Information Resource) gene models and their annotations through sequence similarity. By entering a keyword, SABRE searches and retrieves TAIR gene models and annotations, together with homologous gene clones from various plant species.

Development of full-length cDNAs from Chinese cabbage (Brassica rapa Subsp. pekinensis) and identification of marker genes for defence response.

Arabidopsis belongs to the Brassicaceae family and plays an important role as a model plant for which researchers have developed fine-tuned genome resources. Genome sequencing projects have been initiated for other members of the Brassicaceae family. Among these projects, research on Chinese cabbage (Brassica rapa subsp.

The RIKEN integrated database of mammals.

The RIKEN integrated database of mammals (http://scinets.org/db/mammal) is the official undertaking to integrate its mammalian databases produced from multiple large-scale programs that have been promoted by the institute. The database integrates not only RIKEN's original databases, such as FANTOM, the ENU mutagenesis program, the RIKEN Cerebellar Development Transcriptome Database and the Bioresource Database, but also imported data from public databases, such as Ensembl, MGI and biomedical ontologies.

NBRP databases: databases of biological resources in Japan.

The National BioResource Project (NBRP) is a Japanese project that aims to establish a system for collecting, preserving and providing bioresources for use as experimental materials for life science research. It is promoted by 27 core resource facilities, each concerned with a particular group of organisms, and by one information center. The NBRP database is a product of this project.

Analysis of multiple occurrences of alternative splicing events in Arabidopsis thaliana using novel sequenced full-length cDNAs.

Alternative splicing (AS) is a mechanism by which multiple types of mature mRNAs are generated from a single pre-mature mRNA. In this study, we completely sequenced 1800 full-length cDNAs from Arabidopsis thaliana, which had 5' and/or 3' sequences that were previously found to have AS events or alternative transcription start sites. Unexpectedly, these sequences gave us further evidence of AS, as 601 out of 1800 transcripts showed novel AS events.

A tree of life based on protein domain organizations.

It is desirable to estimate a tree of life, a species tree including all available species in the 3 superkingdoms, Archaea, Bacteria, and Eukaryota, using not a limited number of genes but full-scale genome information. Here, we report a new method for constructing a tree of life based on protein domain organizations, that is, sequential order of domains in a protein, of all proteins detected in a genome of an organism. The new method is free from the identification of orthologous gene sets and therefore does not require the burdensome and error-prone computation.

Genomic evolution of MHC class I region in primates.

To elucidate the origins of the MHC-B-MHC-C pair and the MHC class I chain-related molecule (MIC)A-MICB pair, we sequenced an MHC class I genomic region of humans, chimpanzees, and rhesus monkeys and analyzed the regions from an evolutionary stand-point, focusing first on LINE sequences that are paralogous within each of the first two species and orthologous between them. Because all the long interspersed nuclear element (LINE) sequences were fragmented and nonfunctional, they were suitable for conducting phylogenetic study and, in particular, for estimating evolutionary time. Our study has revealed that MHC-B and MHC-C duplicated 22.

Construction and characterization of chimeric proteins composed of type-1 and type-2 periplasmic binding proteins MglB and ArgT.

The respective type-1 and type-2 periplasmic binding proteins (PBPs) MglB and ArgT are believed to have evolved from a common ancestor into siblings showing topological differences in their main chain connectivity. At first glance, they show similar structure. But, more detailed examination reveals that the chain connectivity of ArgT is more convoluted than that of MglB.

Characterization of folding pathways of the type-1 and type-2 periplasmic binding proteins MglB and ArgT.

The family of periplasmic binding proteins (PBPs) is believed to have arisen from a common ancestor and to have differentiated into two types. At first approximation, both types of PBPs have the same fold pattern, reflecting their common origin. However, the connection between the main chains of a type 2 PBP is more complicated than a type 1 PBP's.

Parallel evolution of ligand specificity between LacI/GalR family repressors and periplasmic sugar-binding proteins.

The bacterial LacI/GalR family repressors such as lactose operon repressor (LacI), purine nucleotide synthesis repressor (PurR), and trehalose operon repressor (TreR) consist of not only the N-terminal helix-turn-helix DNA-binding domain but also the C-terminal ligand-binding domain that is structurally homologous to periplasmic sugar-binding proteins. These structural features imply that the repressor family evolved by acquiring the DNA-binding domain in the N-terminal of an ancestral periplasmic binding protein (PBP). Phylogenetic analysis of the LacI/GalR family repressors and their PBP homologues revealed that the acquisition of the DNA-binding domain occurred first in the family, and ligand specificity then evolved.