The methylotrophic yeast Pichia pastoris is widely used for recombinant protein production due to its ability to grow to high cell densities as well as possession of an inducible methanol utilization pathway (MUT). The expression of genes encoding enzymes of the MUT pathway is very tightly regulated. These genes are turned on when methanol but not glucose is used as the sole carbon source. Thus, P. pastoris cells can be grown to high densities in glucose containing medium and expression of genes of MUT pathway can be turned on by changing the carbon source to methanol. This strategy is widely used for recombinant protein production wherein the gene of interest is cloned downstream of the methanol-inducible promoter of the gene encoding the first enzyme of the MUT pathway, alcohol oxidase I (AOXI). Despite production of a large number of recombinant proteins using the AOXI promoter, the mechanism of transcriptional activation of AOXI is not very well understood. It is only recently that a zinc finger protein known as Mxr1p (methanol expression regulator 1) was shown to play a key role in the regulation of AOXI as well as other genes of methanol utilization pathway (1) P. pastoris strains that do not express Mxr1p (mxr1) are unable to grow on peroxisomal substrates such as methanol and oleic acid. Methanol-inducible expression of genes involved in MUT pathway as well as those involved in peroxisome biogenesis (peroxins,) is severely impaired in mxr1 strains. While Mxr1p is constitutively expressed in cells cultured on glucose as well as methanol, it is cytosolic in glucose-grown cells, but nuclear in methanol-grown cells (1). The exact nucleotide sequence to which Mxr1p binds and regulates the expression of genes of MUT pathway is not known. The aim of this thesis is to map the Mxr1p binding sites in the promoters of methanol-inducible genes of P. pastoris. As a first step towards understanding the mechanism of transcriptional regulation of AOXI and other methanol inducible genes of P. pastoris by Mxr1p, the N-terminal region comprising of 150 amino acids, including the zinc finger DNA binding domain of Mxr1p was cloned into an E. coli expression vector and the recombinant protein was purified from E. coli cells. This recombinant protein (referred to as Mxr1p in this study) was used in an electrophoretic mobility shift assay (EMSA) to identify Mxr1p binding sites in the AOXI promoter. EMSA was carried out with sixteen different oligonucleotides spanning AOXI promoter region between -940 and -114 bp. Such studies led to the identification of six Mxr1p binding sites in AOXI promoter. Using a combination of DNase I footprinting as well as EMSA with chimeric double stranded oligonucleotides, the minimal Mxr1p binding site was identified as a 20 bp DNA sequence containing a core 5’CYCC 3’ sequence. Using methylation interference as well as extensive mutagenesis studies, nucleotides critical for Mxr1p binding were identified. Comparative analysis of Mxr1p binding sites identified in our study with the AOXI promoter deletion studies of Hartner et al (2) suggested that the Mxr1p binding sites identified in our study are likely to function as methanol-inducible enhancers in vivo, since deletion of AOXI promoter regions comprising Mxr1p binding sites results in a significant loss of methanol-inducible promoter activity. Thus, Mxr1p binding sites are likely to function as Mxr1p response elements (MXREs) in vivo. Mxr1p is considered to be the P. pastoris homologue of S. cerevisiae Adr1p (alcohol dehydrogenase II [ADH2] synthesis regulator). Adr1p is a key regulator of S. cerevisiae genes involved in the metabolism of glycerol, ethanol and oleic acid. The DNA binding domains of Adr1p and Mxr1p share 82% similarity and 70% identity. We therefore examined whether Mxr1p can bind to the Adr1p binding site of ADH2 promoter(ADH2-UAS1). Our studies indicate that Mxr1p does not bind to ADH2-UAS1. Interestingly, a single point mutation restores Mxr1p binding to ADH2-UAS1. Since Mxr1p is involved in the regulation of a number of genes including AOXI, we examined whether promoters of other Mxr1p-regulated genes also harbour MXREs similar to those identified in AOXI promoter. The promoters of genes encoding dihydroxyacetone synthase (DHAS) and peroxin 8 (PEX8) were chosen for this purpose. A detailed analysis of Mxr1p binding to these promoter sequences led to the conclusion that DHAS and PEX8 promoters also harbour Mxr1p binding sites similar to those of AOXI promoter. Based on these studies, we have derived a consensus sequence for Mxr1p binding. This study is the first report on detailed characterization of Mxr1p binding sites in three methanol-inducible promoters of P. pastoris and thus provides the molecular framework by which this transcription factor functions as a master regulator of genes involved in methanol utilization pathway of P. pastoris. Our study provides the blue print for mapping Mxr1p binding sites in the promoters of other Mxr1p-regulated genes.