Graphical analysis and experimental evaluation of Saccharomyces cerevisiae PTRK1|2 and PBMH1|2 promoter region.
We designed a simple graphical presentation for the results of a transcription factor (TF) pattern matching analysis. The TF analysis algorithm utilized known sequence signature motifs from several databases. The graphical presentation enabled a quick overview of potential TF binding sites, their frequency and spacing on both DNA strands and thus straight forward identification of promising candidates for further experimental investigations. The developed tool was applied on in total four Saccharomyces cerevisiae gene promoter regions. The selected differentially expressed genes belong to functionally different families and encode duplicate functions, TRK1 and TRK2 as ion transporters and BMH1 and BMH2 as multiple regulators. Output evaluation revealed a number of TFs with promising differences in the promoter regions of each gene pair. Experimental investigations were performed by using corresponding TF yeast mutants for either phenotypic analysis of ion transport mediated growth or expression analysis of BMH1,2 genes. Upon phenotypic testing one TF mutant exhibited severely impaired growth under non-permissive conditions. This TF, Mot3p was identified as of most abundant potential binding sites and distinctive patterns among the TRK promoter regions.
Group of Theoretical Biophysics, MNF I, Humboldt University of Berlin, Invalidenstrasse 42, 10115 Berlin, Germany. gerber@molgen.mpg.de
Susanne
S
Gerber
Guido
G
Hasenbrink
Wouter
W
Hendriksen
Paul
P
Van Heusden
Jost
J
Ludwig
Edda
E
Klipp
Hella
H
Lichtenberg-Fraté
D048948:14-3-3 Proteins / Q000235:genetics* / Q000378:metabolism; D001483:Base Sequence; D001665:Binding Sites; D027682:Cation Transport Proteins / Q000235:genetics* / Q000378:metabolism; D019295:Computational Biology; D003196:Computer Graphics; D004271:DNA, Fungal / Q000235:genetics / Q000378:metabolism; D015966:Gene Expression Regulation, Fungal; D008969:Molecular Sequence Data; D009154:Mutation / Q000235:genetics; D010641:Phenotype; D011401:Promoter Regions, Genetic / Q000235:genetics*; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics* / Q000378:metabolism; D012689:Sequence Homology, Nucleic Acid; D014157:Transcription Factors / Q000235:genetics* / Q000378:metabolism
D048948:14-3-3 Proteins; C075852:BMH1 protein, S cerevisiae; C097164:BMH2 protein, S cerevisiae; D027682:Cation Transport Proteins; D004271:DNA, Fungal; C112006:MOT3 protein, S cerevisiae; D029701:Saccharomyces cerevisiae Proteins; C085258:TRK2 protein, S cerevisiae; D014157:Transcription Factors; C068664:TRK1 protein, S cerevisiae