Controlled vocabularies are increasingly used by databases to describe genes and gene products because they facilitate identification of similar genes within an organism or among different organisms. One of The Arabidopsis Information Resource's goals is to associate all Arabidopsis genes with terms developed by the Gene Ontology Consortium that describe the molecular function, biological process, and subcellular location of a gene product. We have also developed terms describing Arabidopsis anatomy and developmental stages and use these to annotate published gene expression data. As of March 2004, we used computational and manual annotation methods to make 85,666 annotations representing 26,624 unique loci. We focus on associating genes to controlled vocabulary terms based on experimental data from the literature and use The Arabidopsis Information Resource-developed PubSearch software to facilitate this process. Each annotation is tagged with a combination of evidence codes, evidence descriptions, and references that provide a robust means to assess data quality. Annotation of all Arabidopsis genes will allow quantitative comparisons between sets of genes derived from sources such as microarray experiments. The Arabidopsis annotation data will also facilitate annotation of newly sequenced plant genomes by using sequence similarity to transfer annotations to homologous genes. In addition, complete and up-to-date annotations will make unknown genes easy to identify and target for experimentation. Here, we describe the process of Arabidopsis functional annotation using a variety of data sources and illustrate several ways in which this information can be accessed and used to infer knowledge about Arabidopsis and other plant species.

Background: Microarray technology is a widely used approach for monitoring genome-wide gene expression. For Arabidopsis, there are over 1,800 microarray hybridizations representing many different experimental conditions on Affymetrix™ ATH1 gene chips alone. This huge amount of data offers a unique opportunity to infer the principles that govern the regulation of gene expression in plants.

This is the first report on using green fluorescent protein (GFP) as a pH reporter in plants. Proton fluxes and pH regulation play important roles in plant cellular activity and therefore, it would be extremely helpful to have a plant gene reporter system for rapid, non-invasive visualization of intracellular pH changes. In order to develop such a system, we constructed three vectors for transient and stable transformation of plant cells with a pH-sensitive derivative of green fluorescent protein. Using these vectors, transgenic Arabidopsis thaliana and tobacco plants were produced. Here the application of pH-sensitive GFP technology in plants is described and, for the first time, the visualization of pH gradients between different developmental compartments in intact whole-root tissues of A. thaliana is reported. The utility of pH-sensitive GFP in revealing rapid, environmentally induced changes in cytoplasmic pH in roots is also demonstrated.

Studies of plant tropisms, the directed growth toward or away from external stimuli such as light and gravity, began more than a century ago. Yet biochemical, physiological, and especially molecular mechanisms of plant tropic responses remain for the most part unclear. We examined expression of 8,300 genes during early stages of the gravitropic response using high-density oligonucleotide probe microarrays. Approximately 1.7% of the genes represented on the array exhibited significant expression changes within the first 30 min of gravity stimulation. Among gravity-induced genes were a number of genes previously implicated to be involved in gravitropism. However, a much larger number of the identified genes have not been previously associated with gravitropism. Because reorientation of plants may also expose plants to mechanical perturbations, we also compared the effects of a gentle mechanical perturbation on mRNA levels during the gravity response. It was found that approximately 39% of apparently gravity-regulated genes were also regulated by the mechanical perturbation caused by plant reorientation. Our study revealed the induction of complex gene expression patterns as a consequence of gravitropic reorientation and points to an interplay between the gravitropic and mechanical responses and to the extreme sensitivity of plants to even very gentle mechanical perturbations.Though studies of plant tropisms began more than a century ago (Knight, 1806; Ciesielski, 1872; Darwin, 1880), the mechanisms of plant tropic responses, including gravitropism, are for the most part still unknown. It is believed that the gravitropic response is a well-coordinated process regulated through gravity signal perception and transduction, gene transcription, and translation. Previous research findings, based largely on physiological, biochemical, and genetic experimental evidence, have implicated a role for starch-filled plastids, amyloplasts, as statoliths in gravity perception (Volkmann and Sievers, 1979;Sack, 1991; Blancaflor et al., 1998;Moctezuma and Feldman, 1999a), and Ca 2ϩ (Belyavskaya, 1996; Lu and Feldman, 1997;Sinclair and Trewavas, 1997) , 1981;Zieschang et al., 1993;Scott and Allen, 1999), K ϩ (Philippar et al., 1999), auxin (Cholodny, 1928;Went, 1928; Feldman, 1985;Parker and Briggs, 1990; Konings, 1995; Chen et al., 1999;Moctezuma and Feldman, 1999b), the cytoskeleton (Baluska and Hasenstein, 1997), and the cell wall (Cosgrove, 1997; Edelmann, 1997; Hejnowicz, 1997) in gravity signal transduction. Earlier work has also implicated a need for both transcription and translation regulation in the root gravity response (Feldman, 1981). Yet in only a few studies have attempts been made to analyze gravity-induced changes at the transcriptional level (Guilfoyle et al., 1993; Li et al., 1999;Philippar et al., 1999). Recently developed cDNA and oligonucleotide probe microarray technologies now allow for accurate measurement of mRNA transcript abundance for hundreds or thousands of genes in parallel (Schena et al., 1995(Sc...