In the Section on Nutrient Control of Gene expression (SNCGE), we study molecular mechanisms of gene regulation at the translational and transcriptional levels, using the regulation of amino acid biosynthetic genes in budding yeast as a model system. Transcription of these and many other genes is coordinately induced by the transcriptional activator Gcn4 in response to starvation for any amino acid. Expression of GCN4 is coupled to amino acid levels by a conserved translational control mechanism involving upstream open reading frames (uORFs) in GCN4 mRNA and phosphorylation of the general translation initiation factor eIF2α by protein kinase Gcn2. In the area of translational control, we are investigating molecular pathways involved in recruiting mRNAs by the small (40S) ribosomal subunit and scanning of mRNA leaders for the correct AUG start codon. This work is divided into two parts: (i) analysis of translation initiation factors and 40S proteins that regulate conformational transitions in scanning 40S subunits to insure high-fidelity selection of AUG start codons, and (ii) studies of the m7G-cap binding initiation factors eIF4F and eIF4B, poly(A)-binding protein (Pab1), and auxiliary DEAD-box helicases Ded1 and Dbp1 that stimulate ribosome attachment and scanning by resolving mRNA structures. We also examine the in vivo functions of general repressors of translation, Scd6, Pat1, and helicase Dhh1 in sculpting the yeast translatome in response to nutrient starvation and stress. In the area of transcriptional control, we are examining the chromatin remodeling (CR) complexes, histone acetyl transferases (HATs), and general regulatory factors (GRFs) involved in remodeling and evicting nucleosomes that occlude promoter sequences and impede preinitiation complex (PIC) assembly by RNA Polymerase II (Pol II) at the hundreds of genes co-regulated by Gcn4, and genome-wide. We also seek to identify the functional consequences and regulation by chromatin regulators of the cryptic internal promoters we found recently to be activated by Gcn4 binding within gene coding sequences (CDSs).

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