Additional file 1: Figure S1. of Exogenous glutamate rapidly induces the expression of genes involved in metabolism and defense responses in rice roots

Glutamate is a precursor for many important molecules in plants. Figure S2. Amino acid contents of 17-day-old rice seedlings. Figure S3. Regulation of glutamate-responsive genes by different concentrations of glutamate. Figure S4. Effects of different nitrogen treatments on the expression of glutamate-responsive genes. Table S1. Effects of exogenous glutamate treatment on endogenous amino acid content in rice roots. Table S2. List of glutamate up-regulated genes in representative functional categories derived from gene ontology (GO) enrichment analysis. Table S3. KEGG analysis of glutamate up-regulated genes in rice roots. Table S4. KEGG pathway enrichment analysis of glutamate up-regulated genes in rice root. Table S5. Effects of glutamate on the expression of glutamate receptor genes in rice roots. Table S6. Sequences of primers used for quantitative RT-PCR analysis. (PDF 2009 kb

Near-atomic resolution visualization of human transcription promoter opening

In eukaryotic transcription initiation, a large multi-subunit pre-initiation complex (PIC) that assembles at the core promoter is required for the opening of the duplex DNA and identification of the start site for transcription by RNA polymerase II. Here we use cryo-electron microscropy (cryo-EM) to determine near-atomic resolution structures of the human PIC in a closed state (engaged with duplex DNA), an open state (engaged with a transcription bubble), and an initially transcribing complex (containing six base pairs of DNA–RNA hybrid). Our studies provide structures for previously uncharacterized components of the PIC, such as TFIIE and TFIIH, and segments of TFIIA, TFIIB and TFIIF. Comparison of the different structures reveals the sequential conformational changes that accompany the transition from each state to the next throughout the transcription initiation process. This analysis illustrates the key role of TFIIB in transcription bubble stabilization and provides strong structural support for a translocase activity of XPB