Basal Promoter Elements Basal Promoter Element = BPE TATA Box: (G or A)TATA(A or T)AA –Nature 381: (1996) –Science 272: (1996) CAAT Box: GGCCAATC GC Box: GCCACACCC –From class lectures Control Gene Transcription

Diauxic Shift Decrease in [Glucose] causes changes in gene transcription –Effect of shift on transcription of every ORF in S. cerevisiae quantified by Yeast Gene Expression Database

Questions Is the sequence quality of one BPE higher than another? Does diauxic shift regulation correlate with the quality of TATA, CAAT, or GC boxes? –Quality: How well does the actual sequence match the “ideal”?

The Program I wrote a program which finds the closest match to any given “ideal” sequence. Scoring: Points given for each ‘correct’ base, then normalized to 1. The search is exhaustive. –Entire sequence between previous stop codon and start codon scanned for matches

3 types of diauxic regulation Upregulated (22 sequences): –<2X at [Glucose] = 14 g/L –>5X at [Glucose] = 0.2 g/L Downregulated (18 sequences): –>0.47X at [Glucose] = 14 g/L –<0.23X at [Glucose] = 0.2 g/L Control (10 sequences) –Never >2X or <0.5X

Method The program analyzed each sequence. Average BPE quality scores for Upregulated, Downregulated, and Control sequences were computed.

Results

Future Directions Are the ideal sequences accurate for Saccharomyces? Does the quality of the boxes correlate with other relative events? –e.g., pH, temperature, salt concentration Do other protein binding sequences correlate with diauxic shift?