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Background The Solanaceae family includes several economically important vegetable crops. The tomato ( Solanum lycopersicum ) is regarded as a model plant of the Solanaceae family. Recently, a number of tomato resources have been developed in parallel with the ongoing tomato genome sequencing project. In particular, a miniature cultivar, Micro-Tom, is regarded as a model system in tomato genomics, and a number of genomics resources in the Micro-Tom-background, such as ESTs and mutagenized lines, have been established by an international alliance. Results To accelerate the progress in tomato genomics, we developed a collection of fully-sequenced 13,227 Micro-Tom full-length cDNAs. By checking redundant sequences, coding sequences, and chimeric sequences, a set of 11,502 non-redundant full-length cDNAs (nrFLcDNAs) was generated. Analysis of untranslated regions demonstrated that tomato has longer 5'- and 3'-untranslated regions than most other plants but rice. Classification of functions of proteins predicted from the coding sequences demonstrated that nrFLcDNAs covered a broad range of functions. A comparison of nrFLcDNAs with genes of sixteen plants facilitated the identification of tomato genes that are not found in other plants, most of which did not have known protein domains. Mapping of the nrFLcDNAs onto currently available tomato genome sequences facilitated prediction of exon-intron structure. Introns of tomato genes were longer than those of Arabidopsis and rice. According to a comparison of exon sequences between the nrFLcDNAs and the tomato genome sequences, the frequency of nucleotide mismatch in exons between Micro-Tom and the genome-sequencing cultivar (Heinz 1706) was estimated to be 0.061%. Conclusion The collection of Micro-Tom nrFLcDNAs generated in this study will serve as a valuable genomic tool for plant biologists to bridge the gap between basic and applied studies. The nrFLcDNA sequences will help annotation of the tomato whole-genome sequence and aid in tomato functional genomics and molecular breeding. Full-length cDNA sequences and their annotations are provided in the database KaFTom http://www.pgb.kazusa.or.jp/kaftom/ via the website of the National Bioresource Project Tomato http://tomato.nbrp.jp .

NPR1 is a central regulator of salicylic-acid (SA)-mediated defense signaling in Arabidopsis. Here, we report the characterization of OsNPR1, an Oryzae sativa (rice) ortholog of NPR1, focusing on its role in blast disease resistance and identification of OsNPR1-regulated genes. Blast resistance tests using OsNPR1 knockdown and overexpressing rice lines demonstrated the essential role of OsNPR1 in benzothiadiazole (BTH)-induced blast resistance. Genome-wide transcript profiling using OsNPR1-knockdown lines revealed that 358 genes out of 1,228 BTH-upregulated genes and 724 genes out of 1,069 BTH-downregulated genes were OsNPR1-dependent with respect to BTH responsiveness, thereby indicating that OsNPR1 plays a more vital role in gene downregulation. The OsNPR1-dependently downregulated genes included many of those involved in photosynthesis and in chloroplast translation and transcription. Reduction of photosynthetic activity after BTH treatment and its negation by OsNPR1 knockdown were indeed reflected in the changes in Fv/Fm values in leaves. These results imply the role of OsNPR1 in the reallocation of energy and resources during defense responses. We also examined the OsNPR1-dependence of SA-mediated suppression of ABA-induced genes.

Myo -inositol monophosphatase (IMP) catalyzes the dephosphorylation of myo -inositol 3-phosphate in the last step of myo -inositol biosynthesis. IMP is also important in phosphate metabolism and is required for the biosynthesis of cell wall polysaccharides, phytic acid, and phosphatidylinositol. In Arabidopsis, IMP is encoded by VTC4 . There are, however, two additional IMP candidate genes, IMPL1 and IMPL2 , which have not yet been elucidated. In our genetic studies of Arabidopsis IMP genes, only the loss-of-function mutant impl2 showed embryonic lethality at the globular stage. All IMP genes were expressed in a similar manner both in the vegetative and reproductive organs. In developing seeds, expression of IMP genes was not coupled with the expression of the genes encoding myo -inositol phosphate synthases, which supply the substrate for IMPs in the de novo synthesis pathway. Instead, expression of IMP genes was correlated with expression of the gene for myo -inositol polyphosphate 1-phosphatase ( SAL1 ), which is involved in the myo -inositol salvage pathway, suggesting a possible salvage pathway role in seed development. Moreover, the partial rescue of the impl2 phenotype by histidine application implies that IMPL2 is also involved in histidine biosynthesis during embryo development.

C-LEC1, an orthologue of Arabidopsis LEC1, is thought to be an essential transcriptional activator required for normal development during the early and late phases of embryogenesis. C-LEC1 is similar in sequence to the HAP3 subunits of other organisms. To understand C-LEC1 function better, a cDNA library of carrot somatic embryos was screened for factors that form complexes with C-LEC1. Two carrot HAP5 homologues and two carrot HAP2 homologues were identified; these factors have significant sequence similarity to the conserved regions of HAP5 and HAP2, respectively. Some of these proteins form heterotrimeric complexes that bind specifically to DNA fragments containing a CCAAT sequence in vitro. The results suggest that C-LEC1 is a component of the CCAAT-box-binding factor and forms a complex with C-HAP2B and C-HAP5A or C-HAP5B that regulates gene expression during carrot embryo development.

In order to clarify the mechanism of the abnormal expression of Lewisb antigen, which was specific for uterine endometrial cancer tissue, the activities of α1→2fucosyltransferase, α1→3fucosyltransferase, and α1→4fucosyltransferase in normal endometrial tissues and uterine endometrial cancer tissues were determined. Further, an immunocytochemical study of the expression of blood group‐related carbohydrate antigens in 6 cultured cell lines derived from various gynecologic malignant tumors was performed and the α1→2fucosyltransferase, α1→3fucosyltransferase, and α1→4fucosyltransferase activities of these cell lines were determined. Compared with normal endometrium, uterine endometrial cancer tissues showed significantly higher values of α1→2fucosyltransferase, α1→3fucosyltransferase, and α1→4fucosyltransferase activities. The specifically strong expression of type I carbohydrate chains, particularly the Lewisb antigen, was recognized in cultured cell lines derived from uterine endometrial cancer. Compared with those cell lines derived from uterine cervical cancer and ovarian cancer, the cultured cell lines derived from uterine endometrial cancer showed higher activities of α1→2fucosyltransferase and α1→4fucosyltransferase, which are enzymes related to the synthesis of Lewisb antigen. The cell lines derived from uterine endometrial cancer showed specifically high values of α1→4fucosyltransferase activity. These results suggest that the α1→2fucosyltransferase and α1→4fucosyltransferase activities, especially the α1→4fucosyltransferase activity, contribute to the abnormal expression of the Lewisb antigen in uterine endometrial cancer.

In order to clarify the mechanism of the abnormal expression of Lewisb antigen, which was specific for uterine endometrial cancer tissue, the activities of α1→2fucosyltransferase, α1→3fucosyltransferase, and α1→4fucosyltransferase in normal endometrial tissues and uterine endometrial cancer tissues were determined. Further, an immunocytochemical study of the expression of blood group‐related carbohydrate antigens in 6 cultured cell lines derived from various gynecologic malignant tumors was performed and the α1→2fucosyltransferase, α1→3fucosyltransferase, and α1→4fucosyltransferase activities of these cell lines were determined. Compared with normal endometrium, uterine endometrial cancer tissues showed significantly higher values of α1→2fucosyltransferase, α1→3fucosyltransferase, and α1→4fucosyltransferase activities. The specifically strong expression of type I carbohydrate chains, particularly the Lewisb antigen, was recognized in cultured cell lines derived from uterine endometrial cancer. Compared with those cell lines derived from uterine cervical cancer and ovarian cancer, the cultured cell lines derived from uterine endometrial cancer showed higher activities of α1→2fucosyltransferase and α1→4fucosyltransferase, which are enzymes related to the synthesis of Lewisb antigen. The cell lines derived from uterine endometrial cancer showed specifically high values of α1→4fucosyltransferase activity. These results suggest that the α1→2fucosyltransferase and α1→4fucosyltransferase activities, especially the α1→4fucosyltransferase activity, contribute to the abnormal expression of the Lewisb antigen in uterine endometrial cancer.