We analyzed 6,749 lines tagged by the gene trap vector pGA2707. This resulted in the isolation of 3,793 genomic sequences flanking the T-DNA. Among the insertions, 1,846 T-DNAs were integrated into genic regions, and 1,864 were located in intergenic regions. Frequencies were also higher at the beginning and end of the coding regions and upstream near the ATG start codon. The overall GC content at the insertion sites was close to that measured from the entire rice (Oryza sativa) genome. Functional classification of these 1,846 tagged genes showed a distribution similar to that observed for all the genes in the rice chromosomes. This indicates that T-DNA insertion is not biased toward a particular class of genes. There were 764, 327, and 346 T-DNA insertions in chromosomes 1, 4 and 10, respectively. Insertions were not evenly distributed; frequencies were higher at the ends of the chromosomes and lower near the centromere. At certain sites, the frequency was higher than in the surrounding regions. This sequence database will be valuable in identifying knockout mutants for elucidating gene function in rice. This resource is available to the scientific community at http://www.postech.ac.kr/life/pfg/risd.Insertional mutagenesis is one of the most useful methods for analyzing gene function. When foreign DNA is inserted into a gene, it not only creates a mutation but also tags the affected gene, facilitating its isolation and characterization (Azpiroz-Leehan and Feldmann, 1997). Transposons and T-DNA have been used most widely as an insertional mutagen (Mathur et al., 1998;Wisman et al., 1998; Krysan et al., 1999;Parinov et al., 1999;Speulman et al., 1999;Tissier et al., 1999). It is believed that T-DNA insertion is a random event and that the inserted sequences are stable through multiple generations (Azpiroz- Leehan and Feldmann, 1997;Parinov and Sundaresan, 2000). Insertional mutant pools have been constructed in Arabidopsis and used for functional analysis of a number of genes (Feldmann, 1991; Koncz et al., 1992; Azpiroz-Leehan and Feldmann, 1997; Bechtold and Pelletier, 1998; Krysan et al., 1999; Galbiati et al., 2000;Parinov and Sundaresan, 2000; Bouché and Bouchez, 2001;Sessions et al., 2002;Szabados et al., 2002). The procedure for T-DNA insertional mutagenesis has also been applied to rice (Oryza sativa) using the Agrobacterium tumefaciensmediated transformation method (Hiei et al., 1994). Jeon et al. (2000) have reported the construction of over 20,000 T-DNA-tagged rice lines. A T-DNA insertional mutagen can be modified to trap a gene by inserting a reporter gene, such as gus (␤-glucuronidase), next to the T-DNA border (Sundaresan et al., 1995; Jeon et al., 2000;Springer, 2000). Approximately 5% to 10% of the mutagenized lines are GUS positive, demonstrating the efficiency of this gene-trapping system (Chin et al., 1999; Jeon et al., 2000).Completion of the genome sequencing for both Arabidopsis and rice has provided new reverse genetic means for assigning biological functions to sequenced genes (Kumar...

Circulating endothelial progenitor cell (EPC) numbers and functions are reduced in migraine patients, suggesting that EPCs can be an underlying link between migraine and cardiovascular risk.

Cdc48 (also called VCP and p97) is an abundant protein that plays essential regulatory functions in a broad array of cellular processes. Working with various cofactors, Cdc48 utilizes its ATPase activity to promote the assembly and disassembly of protein complexes. Here, we review key biological functions and regulation of Cdc48 in ubiquitin-related events. Given the broad employment of Cdc48 in cell biology and its intimate ties to human diseases (e.g., amyotrophic lateral sclerosis), studies of Cdc48 will bring significant insights into the mechanism and function of ubiquitin in health and diseases.

Ufd2 is the founding member of E4 enzymes that are specifically involved in ubiquitin chain elongation but whose roles in proteolysis remain scarce. Here, using a genome-wide screen, we identified one cellular target of yeast Ufd2 as the membrane protein Pex29. The ubiquitin chains assembled on Pex29 in vivo by Ufd2 mainly contain Lys-48 linkages. We found that the ubiquitin-protein E3 ligase for overexpressed Pex29 is Doa10, which is known to be involved in protein quality control. Interestingly, not all Doa10 substrates are regulated by Ufd2, suggesting that E4 involvement is not specific to a particular E3, but may depend on the spatial arrangement of the E3-substrate interaction. Cells lacking UFD2 elicit an unfolded protein response, expanding the physiological function of Ufd2. Our results lead to novel insights into the biological role of Ufd2 and further underscore the significance of Ufd2 in proteolysis.

Background: Ufd2 is a U-box-containing ubiquitin-protein ligase. Results: Mps1 turnover is regulated by Ufd2 in yeast and mammalian cells. Conclusion: Our study leads to novel insights into the cell cycle control and physiological significance of the Ufd2 pathway. Significance: Understanding the functions of Ufd2 will elucidate a poorly characterized pathway in proteolysis that may be crucial to unravel the mechanisms underlying human diseases.