Tadasu Shin-i et al. (2007) International Worm Meeting "The extension of the nematode expression pattern map database (NEXTDB) for comparative genomics."

Takanori Narita, Ikuko Muramatsu, Hiroko Ohchi, Tadasu SHIN-I, Yuji KOHARA, Tomoko Endoh, Masumi Obara, Hisayo Nomoto, Chihiro Ebata, Hiroshi KAGOSHIMA, Kazuko Oishi, Keiko Nogata, Fumiko Ohta, Wakako Hamano, Yumiko Ueta, Sachiko Wakazuki

[International Worm Meeting, 2007]

We are updating the database "NEXTDB" to integrate all the information of ESTs, gene expression patterns and gene functions of C.elegans which are being produced and analyzed in this laboratory. In addition to the EST sequences from the previous 130,000 cDNA clones (lambda ZAP clones and oligo-cap clones) which were classified into 14,000 unique transcripts, this time we obtained ESTs from new full-length cDNA clones made by the V-capping method. This method generates cDNA clones of more full length and less mutation. We classified tag sequences of the 100,000 clones and found additional 1,000 unique transcripts, as well as 6,500 kinds which were also found in the previous clones. Then they were compared to genome sequences by use of BLASTN and predicted structures of genes strictly. BLASTX searches and motif searches by HMM are also done to predict functions of CDSs. As to whole mount in-situ hybridization of 11,000 genes, we continue to annotate their developmental stages and expression patterns. The images and their description of RNAi phenotypes of 900 genes and antibody staining images which showed localization of 660 proteins were also stored in the database. All the images and annotations are arranged based on the corresponding cDNA clones. All the data are integrated with the genome map based on WWW, and the information of maps and their relations are displayed visually. The latest version is opened through the following URL. http://nematode.lab.nig.ac.jp We also have started EST/genome analysis of other nematode Diploscapter coronatus in collaboration with Dr. Einhard Schierenberg at Univ. of Koeln, since we are interested with its different cell cleavage and arrangement pattern to gastrulation stage. EST sequencing and preliminary assembling of low-coverage whole genome shotgun sequencing are in progress. All the results were also incorporated to NEXTDB.

Tsuyoshi Kawano et al. (2004) East Asia Worm Meeting "Gene-disruptions of C. elegans insulin-like genes Ceinsulin-1 and -2"

Naoya Kataoka, Keiko Gengyo-Ando, Shuji Honda, Tsuyoshi Kawano, Yasuo Kimura, Shohei MItani, Ikuko Tanaka

[East Asia Worm Meeting, 2004]

Gene-disruptions of C. elegans insulin-like genes Ceinsulin-1 and -2Tsuyoshi Kawano1, Naoya Kataoka1, Ikuko Tanaka1, Yasuo Kimura1, Shuji Honda2, Keiko Gengyo-Ando3 and Shohei Mitani31Department of Biological and Environmental Chemistry, Tottori University, 4-101, Minami, Koyama-cho, Tottori 680-8553, Japan2Tokyo Metropolitan Institute of Gerontology, 35-2, Sakae-cho, Itabashi-ku, Tokyo 173-0015, Japan3Department of Physiology, Tokyo Women , s Medical University School of Medicine, 8-1, Kawada-cho, Shinjuku-ku. Tokyo 162-8666, Japan In C. elegans, the insulin-signaling regulates the diapause, longevity and fat metabolism via the DAF-2, a homolog of insulin/IGF-I receptors. Our search for the DAF-2 ligands revealed two insulin/IGF-like peptides named Ceinsulin-1 and -2. We will also show phenotypes of the mutants lacking the genes.At first, Ceinsulin-1::gfp and Ceinsulin-2::gfp were constructed in a translational fusion manner and introduced into wild-type animals to search the cell expressing the Ceinsulin genes. The Ceinsulin-1::gfp is expressed at several neurons in the head and tail, whereas the Ceinsulin-2::gfp is expressed at several neurons only in the head. These cells do not overlap with chemosensory neurons filling DiI. Next, to Ceinsulin-1 and -2 deletion mutants designated tm339 and tm790, respectively, were generated and isolated with the TMP/UV method followed by the sib-screening. The tm339 has deletion of approximately 1.4 kb covering two of three exons in the T28B8.2 gene. The tm790 lays approximately deletion of 0.6 kb on two exons in the F56F3.6 gene. The tm339 exhibits a slightly extended life span as our previous RNAi experiment, while the tm790 shows almost the same life span as wild-type animals. Now, we are examining effects of these gene-disruptions on dauer larva formation.Gengyo-Ando, K and Mitani, S. (2000) Biochem. Biophys. Res. Commun. 269: 64-69.Kawano, T. et al. (2000) Biochem. Biophys. Res. Commun. 273: 431-436.Kawano, T. et al. (2003) Biosci. Biotechnol.Biochem. 67: 2678-2682.

Chen, Baohui et al. (2009) International Worm Meeting "res-1 cooperates with tat-1 to regulate PS asymmetry and membrane trafficking in C. elegans."

Yu, Lina, Li, Xin, Jiang, Yue, Wang, Xiaochen, Yan, Jiacong, Chen, Baohui, Zeng, Sheng

[International Worm Meeting, 2009]

The asymmetrical distribution of phosphatidylserine (PS) across plasma membrane is disrupted in apoptotic cells, which leads to the exposure of PS on the cell surface that serves as an "eat-me" signal for their clearance. How PS asymmetry is maintained and regulated during apoptosis and in other cellular processes is poorly understood. From a genetic screen for regulators of engulfment signal, we isolated several alleles of tat-1 (transbilayer amphipath transporters) and one allele of res-1 (regulator of engulfment signals). tat-1 encodes a P-type ATPase that is suggested to promote the inward movement of aminophospholipids such as PS and PE, which restricts them to the inner leaflet of cell membrane. Consistent with previous findings (1), we found that in the tat-1 mutants, the surface-exposed PS is detected not only on apoptotic cells, but also on living cells. Identical phenotypes were also observed in the res-1(qx36) mutants, indicating that res-1 is also involved in maintaining PS asymmetry on plasma membrane. Interestingly, we found that both tat-1 and res-1 mutants display severe defects in membrane trafficking including intestinal vacuolation and endocytosis defects in both intestine and coelomocytes. TAT-1 is localized to plasma membrane and intracellular vesicles, which is consistent with its function in maintaining PS asymmetry across cell membrane and in endocytosis (1, 2). Importantly, the membranous and vesicular localization of TAT-1 is totally disrupted in the res-1(qx36) mutants. On the other hand, RES-1::GFP showed similar localization pattern to that of TAT-1, which is abolished in the tat-1(qx30) mutants. Therefore, RES-1 and TAT-1 likely cooperates with each other to regulate PS asymmetry and membrane trafficking in C. elegans. We will report our characterizations of RES-1 and TAT-1 in the meeting. 1.Monica Darland-Ransom, Xiaochen Wang, Chun-Ling Sun, James Mapes, Keiko Gengyo-Ando, Shohei Mitani, Ding Xue, 2008. Role of C. elegans TAT-1 protein in maintaining plasma membrane phosphatidylserine asymmetry. Science 320: 528-531 2.Anne-Francoise Ruaud, Lars Nilssoon, Fabrice Richard, Morten Krog Larsen, Jen-Louis Bessereau and Simon Tuck, 2009. The C. elegans P4-ATPase TAT-1 regulates lysosome biogenesis and endocytosis. Traffic 10(1): 88-100.