Expression of ␣-amylase genes in both rice suspension cells and germinating embryos is repressed by sugars and the mechanism involves transcriptional regulation. The promoter of a rice ␣-amylase gene ␣Amy3 was analyzed by both loss-and gain-of-function studies and the major sugar response sequence (SRS) was located between 186 and 82 base pairs upstream of the transcription start site. The SRS conferred sugar responsiveness to a minimal promoter in an orientation-independent manner. It also converted a sugar-insensitive rice actin gene promoter into a sugar-sensitive promoter in a dosedependent manner. Linker-scan mutation studies identified three essential motifs: the GC box, the G box, and the TATCCA element, within the SRS. Sequences containing either the GC box plus G box or the TATCCA element each mediated sugar response, however, they acted synergistically to give a high level glucose starvation-induced expression. Nuclear proteins from rice suspension cells binding to the TATCCA element in a sequence-specific and sugar-dependent manner were identified. The TATCCA element is also an important component of the gibberellin response complex of the ␣-amylase genes in germinating cereal grains, suggesting that the regulation of ␣-amylase gene expression by sugar and hormone signals may share common regulatory machinery.Sugar repression of gene expression is a fundamental and ubiquitous regulatory system for adjusting to changes in nutrient availability in both prokaryotic and eukaryotic cells. In microorganisms, glucose or other rapidly metabolizable carbon sources repress the expression of genes that code for enzymes related to the metabolism of other carbon sources. Our understanding of the mechanisms of sugar repression has been based largely on studies of microorganisms. In the case of Escherichia coli, a model to explain at the molecular level, the mechanism of sugar repression has been determined (1, 2). The mechanism of glucose repression in yeast is more complicated and is less understood than it is in E. coli (3-5). Studies using Saccharomyces cerevisiae mutants have revealed many of the components involved in the response to carbon catabolite repression (5), but it is still unclear how all of these components interact to regulate transcription. A universal signaling pathway which leads to the regulation of all glucose-repressible genes has yet to be determined.As in microorganisms, sugar repression of gene expression also allows plant cells to cope effectively with changes in the carbon sources present in their environment. However, in multicellular plants, feedback repression by excess sugars provides an additional mechanism for maintaining an economical balance between supply (source) and demand (sink) for carbohydrate allocation and utilization among tissues and organs (6 -8). Despite the fact that sugar repression of gene expression is likely a central control mechanism mediating energy homeostasis and carbohydrate distribution in plants, the molecular mechanism of sugar feedback regulation remain...

The elucidation and prediction of how changes in a protein give altered activities and selectivities remains a major challenge in chemistry. Two hurdles have prevented accurate family-wide models: i) obtaining diverse datasets and ii) suitable parameter frameworks that encapsulate activities in large sets. Here we show that a relatively small but broad activity dataset is sufficient to train algorithms for functional prediction over the entire glycosyltransferase superfamily 1 (GT1) of the plant Arabidopsis thaliana. Whilst sequence analysis alone fails for GT1 substrate utilization patterns, our chemical-bioinformatic model, GT-Predict, succeeds by coupling physicochemical features with isozyme recognition patterns over the family. GT-Predict identified GT1 biocatalysts for novel substrates and allowed functional annotation for uncharacterized GT1s. Finally, analyses of GT-Predict decision pathways revealed structural modulators of substrate recognition, informing mechanism. This multifaceted approach to enzyme prediction could guide streamlined utilization (and design) of biocatalysts and discovery of other family-wide protein functions.

The neurotrophic tyrosine kinase receptor type 2 (Ntrk2, also known as TrkB) and its ligands brain derived neurotrophic factor (Bdnf), neurotrophin-4 (NT-4/5), and neurotrophin-3 (NT-3) are known primarily for their multiple effects on neuronal differentiation and survival. Here, we provide evidence that Ntrk2 plays a role in the pathologic remodeling of the spleen that accompanies chronic infection. We show that in Leishmania donovani-infected mice, Ntrk2 is aberrantly expressed on splenic endothelial cells and that new maturing blood vessels within the white pulp are intimately associated with F4/80hiCD11bloCD11c+ macrophages that express Bdnf and NT-4/5 and have pro-angiogenic potential in vitro. Furthermore, administration of the small molecule Ntrk2 antagonist ANA-12 to infected mice significantly inhibited white pulp neovascularization but had no effect on red pulp vascular remodeling. We believe this to be the first evidence of the Ntrk2/neurotrophin pathway driving pathogen-induced vascular remodeling in lymphoid tissue. These studies highlight the therapeutic potential of modulating this pathway to inhibit pathological angiogenesis.