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Plant Physiology 135:599-600 (2004) © 2004 American Society of Plant Biologists Functional Annotation of the Arabidopsis GenomeThe most recent version of the Arabidopsis genome annotation includes 26,207 protein-coding genes and 3,786 pseudogenes. A central goal of The Arabidopsis Information Resource (TAIR) project, as discussed by Berardini et al. (pp. 745–755), is to integrate information from various data sources and present the research community with a comprehensive view of each Arabidopsis gene. Functional annotation is the process of collecting information about and describing a gene's biological identity—its various aliases, molecular function, biological role(s), subcellular location, and its expression domains within the plant. 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 TAIR's specific goals is to associate all Arabidopsis genes with terms developed by the Gene Ontology (GO) Consortium. The GO vocabularies are gaining widespread acceptance as the standard set of terms to use for functional annotation. The terms are organized into three categories that represent molecular functions, biological processes, and subcellular compartment. Molecular function terms describe the biochemical activity performed by a gene product (e.g. kinase activity). Biological process terms describe the ordered assembly of more than one molecular function (e.g. flower development). Cellular component terms describe the subcellular compartments of a cell (e.g. nucleus). The terms are used to describe these separate aspects of a gene product's biological identity. The vocabularies are developed and maintained by a consortium of model organism databases (MODs). Curators from the MODs work together to ensure that the terms are uniformly agreed upon, clearly defined, and broadly applicable to a wide taxonomic range of species. There are several advantages to using controlled vocabularies for functional annotation of a genome. First, it allows one to perform powerful intraspecific and cross-specific genome queries. Second, one can quantitatively assess the similarity and/or dissimilarity of any two sets of genes or genomes by comparing the distribution of their annotations. Third, one can use the annotated genome of any one species to extrapolate to another genome. Trehalose and Carbon Utilization in Plants Trehalose usually brings to mind anhydrobiotic species, such as the resurrection plant (Selaginella lepidophylla), which are able to survive complete dehydration. In these organisms, it is well established that trehalose accumulation helps protect proteins from extreme dehydration. In typical plants, which lack these amazing dehydrative abilities, trehalose levels are barely detectable, and few researchers previously considered trehalose to be of much importance. New evidence, however, is challenging this idea and indicating that even miniscule levels of trehalose are important, indeed, essential for basic plant function. A trehalose biosynthetic pathway, similar to that which occurs in Saccharomyces, has recently been identified in Arabidopsis. Moreover, an Arabidopsis mutant (Attps1) that cannot synthesize trehalose because of a defect in trehalose-6-phosphate synthase (TPS) fails to develop mature seeds. In this issue, van Dijken et al. (pp. 969–977) report on their analysis of AtTPS1 expression during development of wild-type Arabidopsis plants as well as the effect of TPS1 deletion. They report that a generally low expression is observed in all organs analyzed, peaking in metabolic sinks such as flower buds, ripening siliques, and young rosette leaves. Plants that had reduced AtTPS1 expression exhibit depressed root growth, unusual root meristems, small leaves with brown margins, and a failure to flower. Taken together, the AtTPS1 expression data and the phenotypes observed for the tps1 mutant suggest an essential role for AtTPS1 throughout the Arabidopsis life cycle. In a companion paper, Schluepmann et al. (pp. 879–890) examine the effects of trehalose-6-phosphate (T6P) titer on plant function. Recent studies have shown that T6P is essential for carbon utilization in Arabidopsis and may affect glycolysis. Moreover, T6P levels have been shown to influence photosynthetic capacity per leaf area. In this issue, the authors show that wild-type Arabidopsis seedlings grown on 100 mM trehalose rapidly accumulate T6P and stop growing, but seedlings expressing Escherichia coli trehalose phosphate hydrolase develop normally on such media. The authors suggest that T6P accumulation may result from a strong reduction in T6P dephosphorylation when trehalose levels are high. Metabolizable sugars added to trehalose medium rescue T6P inhibition of growth. Sucrose feeding, which rapidly induces the expression of trehalose phosphate synthase AtTPS5 to high levels, also leads to a progressive increase in T6P concentrations. These findings suggest that the control of T6P control over carbon utilization may only occur when carbon availability is low. An examination of expression profile data from seedlings with altered T6P content suggests that T6P levels are correlated with the expression of a specific set of genes, including the S6 ribosomal kinase ATPK19, independently of carbon status. Interestingly, sucrose addition represses 15 of these genes, one of which is AtKIN11, encoding a SNF1 related kinase known to play a role in sucrose utilization. Engineering Very Long Chain Polyunsaturated Fatty Acids Very long chain polyunsaturated fatty acids (VLCPUFAs), such as arachidonic acid (AA), docosahexaenoic acid (DHA), and eicosapentaenoic acid (EPA), have profound effects on animal cell function and development. In animal cells, VLCPUFAS serve as precursors for the synthesis of prostaglandins, thromboxanes, and leukotrienes. AA and DHA are also important in pre- and postnatal development, and EPA and DHA may reduce strokes and heart attacks by stabilizing atherosclerotic plaques. Since higher plants do not contain these fatty acids, there is considerable interest in genetically engineering the capacity to synthesize them in commercial oilseed species. Such transgenic seed crops could potentially be important sources of these fatty acids for the nutraceutical/pharmaceutical industries. In this issue, Fraser et al. (pp. 859–866) report on the effects of genetically engineering a gene encoding a linolenic and linoleic acid-specific fatty acid elongating enzyme (IgASE1) from Isochrysis galbana, a marine microalga rich in DHA and EPA, into Arabidopsis. The constitutive expression of IgASE1 in Arabidopsis resulted in the accumulation of eicosadienoic acid (EDA) and eicosatrienoic acid (ETrA) in all tissues examined, with no visible effects on plant morphology. The synthesis of significant quantities of EDA and ETrA in a higher plant is a key step in the long-term goal of producing VLCPUFAs in oil-seed species, since EDA and EtrA are potential precursors of these physiologically important fatty acids. Alternative Action of Heterotrimeric G-Proteins in Seed Germination
Heterotrimeric G-proteins physically couple the recognition of many extracellular signals by seven-transmembrane (7TM) cell-surface receptors to the activation of enzyme activities in the cytoplasm. Some responses perceived by 7TM receptors in amoeboid cells and possibly in human cells can initiate downstream action independently of heterotrimeric G-proteins. Plants use heterotrimeric G-protein signaling in the regulation of growth and development, particularly in hormonal control of seed germination, but it is not yet clear whether these responses utilize a 7TM receptor. The Arabidopsis protein GCR1, although localized in a punctate manner beneath the plasma membrane, has a predicted 7TM-spanning domain and other features characteristic of 7TM receptors. Previously, it has been reported that one of the phenotypes caused by overexpression of GCR1 in Arabidopsis is loss of seed dormancy. In this issue, Chen et al. (pp. 907–915) demonstrate that the Arabidopsis null mutants of GCR1 are less sensitive to the enhancement of seed germination by gibberellic acid (GA) and brassinosteroid (BR). This phenotype is similar to that previously observed for null mutants of the heterotrimeric G-protein Salicylate and Cold Tolerance Salicylic acid (SA) has received much attention due to its involvement in plant responses to disease and other stresses. Recent studies have indicated that salicylate treatment may enhance the cold tolerance of many species. However, unlike most species previously studied, Arabidopsis is chilling-resistant and able to grow to maturity at 5°C. In this issue, Scott et al. (pp. 1040–1049) take advantage of many SA-signalling and metabolism mutants to test the hypothesis that the growth of Arabidopsis plants under chilling conditions is related to SA. Plants with the SA hydroxylase NahG transgene have reduced levels of SA and grew at similar rates to wild types at 23°C. Transfer to 5°C slowed the growth of both genotypes, but the NahG plants displayed relative growth rates about one-third greater than wild type, so that by 2 months NahG plants were typically 2.7-fold larger. The partially SA-insensitive npr1 mutant displayed growth intermediate between NahG and wild type, while the SA-deficient eds5 mutant behaved like NahG. In contrast, the cpr1 mutant, that normally has a high titer of SA, accumulated very high levels of SA at 5oC and its growth was much more inhibited than WT. At both temperatures, cpr1 was the only SA-responsive genotype in which oxidative damage was significantly different to WT. These results involving long-term endogenous effects of SA seem contradictory to previous reports in the literature concerning the beneficial effects of exogenous short-term SA treatments in enhancing cold tolerance. The authors suggest that the seeming discrepancy may be related to the length of time studied or the source of SA (endogenous or exogenous).
Department of Natural Sciences Mercy College Dobbs Ferry, New York 10522 FOOTNOTES www.plantphysiol.org/cgi/doi/10.1104/pp.104.900110 Related articles in Plant Physiol.:
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-subunit, gpa1. However, the reduced sensitivities toward GA and BR in the single gcr1, gpa1, and agb1 (heterotrimeric G-protein 
-subunit) mutants are additive or synergistic in the double and triple mutants. Thus, GCR1, unlike a typical 7TM receptor, apparently acts independently of the heterotrimeric G-protein in at least some aspects of seed germination, suggesting that this alternative mode of 7TM receptor action also functions in the plant kingdom. 
9 Polyunsaturated Fatty Acid Specific Elongase Component Alters Arabidopsis Glycerolipid Profiles