Soybean Proteome Database 2012: update on the comprehensive data repository for soybean proteomics

The Soybean Proteome Database (SPD) was created to provide a data repository for functional analyses of soybean responses to flooding stress, thought to be a major constraint for establishment and production of this plant. Since the last publication of the SPD, we thoroughly enhanced the contents of database, particularly protein samples and their annotations from several organelles. The current release contains 23 reference maps of soybean (Glycine max cv. Enrei) proteins collected from several organs, tissues, and organelles including the maps for plasma membrane, cell wall, chloroplast, and mitochondrion, which were analyzed by two-dimensional polyacrylamide gels. Furthermore, the proteins analyzed with gel-free proteomics technique have been added and are available online. In addition to protein fluctuations under flooding, those of salt and drought stress have been included in the current release. A case analysis employing a portion of those newly released data was conducted, and the results will be shown. An ‘omics table has also been provided to reveal relationships among mRNAs, proteins, and metabolites with a unified temporal-profile tag in order to facilitate retrieval of the data based on the temporal profiles. An intuitive user interface based on dynamic HTML enables users to browse the network as well as the profiles of the multiple “omes” in an integrated fashion. The SPD is available at: http://proteome.dc.affrc.go.jp/Soybean

The Rice Annotation Project Database (RAP-DB): hub for Oryza sativa ssp. japonica genome information

With the completion of the rice genome sequencing, a standardized annotation is necessary so that the information from the genome sequence can be fully utilized in understanding the biology of rice and other cereal crops. An annotation jamboree was held in Japan with the aim of annotating and manually curating all the genes in the rice genome. Here we present the Rice Annotation Project Database (RAP-DB), which has been developed to provide access to the annotation data. The RAP-DB has two different types of annotation viewers, BLAST and BLAT search, and other useful features. By connecting the annotations to other rice genomics data, such as full-length cDNAs and Tos17 mutant lines, the RAP-DB serves as a hub for rice genomics. All of the resources can be accessed through

KAIKObase: An integrated silkworm genome database and data mining tool

<p>Abstract</p> <p>Background</p> <p>The silkworm, <it>Bombyx mori</it>, is one of the most economically important insects in many developing countries owing to its large-scale cultivation for silk production. With the development of genomic and biotechnological tools, <it>B. mori </it>has also become an important bioreactor for production of various recombinant proteins of biomedical interest. In 2004, two genome sequencing projects for <it>B. mori </it>were reported independently by Chinese and Japanese teams; however, the datasets were insufficient for building long genomic scaffolds which are essential for unambiguous annotation of the genome. Now, both the datasets have been merged and assembled through a joint collaboration between the two groups.</p> <p>Description</p> <p>Integration of the two data sets of silkworm whole-genome-shotgun sequencing by the Japanese and Chinese groups together with newly obtained fosmid- and BAC-end sequences produced the best continuity (~3.7 Mb in N50 scaffold size) among the sequenced insect genomes and provided a high degree of nucleotide coverage (88%) of all 28 chromosomes. In addition, a physical map of BAC contigs constructed by fingerprinting BAC clones and a SNP linkage map constructed using BAC-end sequences were available. In parallel, proteomic data from two-dimensional polyacrylamide gel electrophoresis in various tissues and developmental stages were compiled into a silkworm proteome database. Finally, a <it>Bombyx </it>trap database was constructed for documenting insertion positions and expression data of transposon insertion lines.</p> <p>Conclusion</p> <p>For efficient usage of genome information for functional studies, genomic sequences, physical and genetic map information and EST data were compiled into KAIKObase, an integrated silkworm genome database which consists of 4 map viewers, a gene viewer, and sequence, keyword and position search systems to display results and data at the level of nucleotide sequence, gene, scaffold and chromosome. Integration of the silkworm proteome database and the <it>Bombyx </it>trap database with KAIKObase led to a high-grade, user-friendly, and comprehensive silkworm genome database which is now available from URL: <url>http://sgp.dna.affrc.go.jp/KAIKObase/</url>.</p

TriAnnot: A Versatile and High Performance Pipeline for the Automated Annotation of Plant Genomes

In support of the international effort to obtain a reference sequence of the bread wheat genome and to provide plant communities dealing with large and complex genomes with a versatile, easy-to-use online automated tool for annotation, we have developed the TriAnnot pipeline. Its modular architecture allows for the annotation and masking of transposable elements, the structural, and functional annotation of protein-coding genes with an evidence-based quality indexing, and the identification of conserved non-coding sequences and molecular markers. The TriAnnot pipeline is parallelized on a 712 CPU computing cluster that can run a 1-Gb sequence annotation in less than 5 days. It is accessible through a web interface for small scale analyses or through a server for large scale annotations. The performance of TriAnnot was evaluated in terms of sensitivity, specificity, and general fitness using curated reference sequence sets from rice and wheat. In less than 8 h, TriAnnot was able to predict more than 83% of the 3,748 CDS from rice chromosome 1 with a fitness of 67.4%. On a set of 12 reference Mb-sized contigs from wheat chromosome 3B, TriAnnot predicted and annotated 93.3% of the genes among which 54% were perfectly identified in accordance with the reference annotation. It also allowed the curation of 12 genes based on new biological evidences, increasing the percentage of perfect gene prediction to 63%. TriAnnot systematically showed a higher fitness than other annotation pipelines that are not improved for wheat. As it is easily adaptable to the annotation of other plant genomes, TriAnnot should become a useful resource for the annotation of large and complex genomes in the future

The early evolution of eukaryotes with special reference to ribosome export factors

　It is believed that primordial eukaryotes were derived from prokaryotes, acquiringnucleus.　A number of attempts have been made to reveal the early evolution ofeukaryotes, and some hypotheses for the emergence of the early eukaryotes areproposed so far. However, the evolutionary process of early eukaryotes is still acontroversial issue and remains one of the biggest questions in current biology. In thisstudy, with the eventual goal toward elucidation of the evolutionary origin and processof early eukaryotes, I conducted molecular evolutionary analyses of transporter proteinsof ribosomes between the nucleus and the cytoplasm, called ribosome export factors(REFs).　This　thesis consists of four chapters and an appendix. In Chapter 1, I described theresearch background for this study, with particular emphasis on the molecular functionof the REFs. The ribosome, one of the largest complexes in eukaryotic cells, is to beexported from the nucleus to the cytoplasm through nuclear pores. As discovered inrecent years, the kinetic steps in this nucleocytoplasmic transport pathway arestimulated by the REFs. The REFs would be worth focusing on because they can beconsidered as one of the components in the eukaryotic core system, translation, and asone of the key genes in the evolutionary process of early eukaryotes for maintaining themobility of the ribosomes under the existence of nuclear membrane in thethen-emerging eukaryotic cells. 　In Chapter 2, with the aim of revealing the functional significance of the REFs inthe process of eukaryotic evolution, I examined the functional constraints of the entiretranslation system, the ribosomal proteins and the REF proteins. Estimating the relativeevolutionary rates of the yeast REF proteins, I found that, although not as much as theribosomal proteins, the REF proteins do slowly evolve. More interestingly, theevolutionary rates of the REFs can be classified into two groups. In order to explain thisdifference in evolutionary rates between the two groups, I considered two subcategoriesfor the REFs, according to the steps in which the REFs are involved. Those twosubcategories are non-membranous REFs (non-mREFs) and membranous REFs(mREFs). Interestingly, this categorization was coincided with the evolutionary ratedifference: Namely, the rapidly evolving REFs were the non-mREFs while the slowlyevolving REFs were the mREFs. These results show that the mREF proteins evolveslower than the non-mREF proteins, suggesting the functional importance of mREFs inthe evolutionary process of eukaryotes. 　In Chapter 3, I examined the evolutionary origin of the eukaryotic nucleus byconducting the ortholog detection analysis of the REFs in prokaryotic lineages. Theevolutionary origin of the nucleus is still unclear, although a number of hypotheses havebeen proposed so far. I searched for the origin of the REFs in archaeal and eubacteriallineages by the method of PSI-BLAST. The results obtained showed that thenon-mREFs originated exclusively from eubacterial proteins whereas the mREFs werefrom both archaeal and eubacterial proteins. Thus, the REFs working inside the nuclearmembrane (i.e.non-mREFs) are derived only from eubacteria, while alternatively, theREFs shuttling between the nucleus and the cytoplasm (i.e. mREFs) are from botharchaea and eubacteria. If we assume that the early nucleus has parsimoniouslyemployed intranuclear proteins as the intranuclear transporters (i.e. non-mREFs), thesedata suggest that the structure of the nucleus may be a descendant of the eubacterial cell. At least, it is suggested that the nucleus arose in a cell that contained chromosomespossessing a substantial fraction of eubacterial genes. Therefore, from the viewpoint ofribosome transport, it is plausible that the nuclear structure is not originated fromarchaea, but from eubacteria. 　Lastly, in Chapter 4,I provided a summary and conclusions for the present study. Ihave shown that the REFs evolve slowly, in addition, the mREFs evolve more slowly, suggesting that the entire eukaryotic translation system is under the functionalconstraints, and in particular, that the mREFs are functionally important in the processof eukaryotic evolution. Moreover, from the prokaryotic origin of the REFs, it issuggested that the nucleus is rather a descendant of the eubacterial cell, not the archaeal cell. 　In Appendix, I made particular mention to the biological database projects foreukaryotes, in which I have been involved. Comprehensive annotations of modeleukaryotes and integrated databases for such annotations are becoming more and more important in the current post-genome era. Moreover, such databases are useful for the study of early evolution of eukaryotes that is the main aim of the present study. Suchdatabases are also invaluable for comprehensive access to the information resources, and will stimulate the comparative evolutionary genomics. With the eventual goal toknow the early evolution of eukaryotes, here I refer to three eukaryotic database projectsin which I have been involved, the Molecular Database of Hydra Cells, the RiceAnnotation Project Database (RAP-DB), and the H-Invitational Database (H-InvDB). 　The Molecular Database of Hydra Cells includes the invaluable data of expressionpatterns of cell type-specific genes in Hydra, a member of phylum Cnidaria, whichbranched more than 500 million years ago from the main stem leading to all bilateriananimals. The database framework was developed by myself, and it serves a uniqueopportunity for graphically browsing more than 100 cell type-specific genes in Hydra. All of the resources can be accessed through http://hydra.lab.nig.ac.jp/hydra/.　The RAP-DB is a database for Oryza sativa ssp. Japonica, one of the modeleukaryotes, and has been developed in order to comprehensively house all theannotations produced by the RAP (Rice Annotation Project), which is internationallyorganized with the aim of providing standardized and highly accurate annotations of therice genome. The latest version of the RAP-DB contains 3l,439 genes validated bycDNAs. The RAP-DB has been also developed by myself, and employed in the analyseswithin Chapter 2. The RAP-DB is available at http://rapdb.lab.nig.ac.jp/.　The H-Invitational Database (H-InvDB) was originally developed as an integrateddatabase of the human transcriptome that was based on extensive annotation of largesets of full-length cDNA (FLcDNA) clone. I participated in the Annotation Meeting ofGenome Information Integration Project for the further development of the humangenome annotations. Now, the database provides annotation for 175,537 humantranscripts and 120,558 human mRNAs extracted from the public DNA databank, inaddition to 54,978 human FLcDNA, in the latest release, H-InvDB_4.3. The H-InvDBis available at http://www.h-invitational jp/.　The three projects in which I have been involved produced comprehensiveinformation for the model eukaryotes. Each database provides a nice implementation foreach biological resource and will stimulate the further exploration in the early evolutionof eukaryotes

Loss of variation of state detected in soybean metabolic and human myelomonocytic leukaemia cell transcriptional networks under external stimuli

Soybean (Glycine max) is sensitive to flooding stress, and flood damage at the seedling stage is a barrier to growth. We constructed two mathematical models of the soybean metabolic network, a control model and a flooded model, from metabolic profiles in soybean plants. We simulated the metabolic profiles with perturbations before and after the flooding stimulus using the two models. We measured the variation of state that the system could maintain from a state–space description of the simulated profiles. The results showed a loss of variation of state during the flooding response in the soybean plants. Loss of variation of state was also observed in a human myelomonocytic leukaemia cell transcriptional network in response to a phorbol-ester stimulus. Thus, we detected a loss of variation of state under external stimuli in two biological systems, regardless of the regulation and stimulus types. Our results suggest that a loss of robustness may occur concurrently with the loss of variation of state in biological systems. We describe the possible applications of the quantity of variation of state in plant genetic engineering and cell biology. Finally, we present a hypothetical “external stimulus-induced information loss” model of biological systems