GenoBase: comprehensive resource database of Escherichia coli K-12.

Comprehensive experimental resources, such as ORFeome clone libraries and deletion mutant collections, are fundamental tools for elucidation of gene function. Data sets by omics analysis using these resources provide key information for functional analysis, modeling and simulation both in individual and systematic approaches. With the long-term goal of complete understanding of a cell, we have over the past decade created a variety of clone and mutant sets for functional genomics studies of Escherichia coli K-12. We have made these experimental resources freely available to the academic community worldwide. Accordingly, these resources have now been used in numerous investigations of a multitude of cell processes. Quality control is extremely important for evaluating results generated by these resources. Because the annotation has been changed since 2005, which we originally used for the construction, we have updated these genomic resources accordingly. Here, we describe GenoBase (http://ecoli.naist.jp/GB/), which contains key information about comprehensive experimental resources of E. coli K-12, their quality control and several omics data sets generated using these resources.

The spatial expression patterns of DROOPING LEAF orthologs suggest a conserved function in grasses.

The DROOPING LEAF (DL) gene regulates carpel specification in the flower and midrib formation in the leaf in Oryza sativa (rice). Loss-of-function mutations in the dl locus cause homeotic transformation of carpels into stamens and lack of midrib, resulting in the drooping leaf phenotype. DL is a member of the YABBY gene family and is closely related to the CRABS CLAW (CRC) gene in Arabidopsis thaliana. The function of Arabidopsis CRC, however, differs from that of rice DL: it is responsible for nectary development and is partially involved in carpel identity. Thus, genes related to DL/CRC seem to have functionally diversified during angiosperm evolution. To assess the conservation of DL function in related species, here we examined the in situ expression patterns of DL orthologs in three grass species, i.e., maize, wheat and sorghum, which is assigned to subfamilies different from Ehrhartoideae including O. sativa. The results clearly show that the temporal and spatial expression patterns of DL orthologs in the three species are identical to those of rice DL in both flower and leaf development, suggesting that DL-related genes are functionally conserved within the grass family. It is likely that DL may have been recruited to carpel specification and midrib formation within the lineage of the grass family after divergence of their ancestor from that of eudicots.