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Yeast curation pipeline; functional annotation; Pichia pastoris; cis-acting DNA elements; transcription factors; phylogenetic footprinting; Saccharomyces cerevisiae
  • Beste Avcı,
  • Oğuz Yaman,
  • Pinar Calik
Beste Avcı
Orta Doğu Teknik Üniversitesi Mühendislik Fakültesi
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Oğuz Yaman
Middle East Technical University
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Pinar Calik
Middle East Technical University

Corresponding Author:[email protected]

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The design and engineering of promoter architectures with tunable and improved promoter activity is a major challenge that substantially impacts recombinant protein production and industrial biotechnology. Pichia pastoris and Saccharomyces cerevisiae are of industrial interest owing to their recombinant protein production capacities, genetic accessibility, and simple nutrient requirements. We annotated the binding sites for the targeted transcription factors (TFs) in P. pastoris through the constructed yeast curation pipeline using phylogenetic footprints of TF binding sites (TFBSs) in the model yeast S. cerevisiae. The upstream regulatory regions of the genes encoding the enzymes in central carbon metabolism for putative TFBSs in S. cerevisiae and P. pastoris were analyzed with a direct scanning algorithm. The conserved putative TFBSs located in the promoters of the orthologous genes in P. pastoris were identified by the pairwise sequence alignments between the promoters of the two species. Among the putative TFBSs annotated in P. pastoris, the probable functional regions of those in coordination with the TFs play a role in the regulation of central carbon metabolism was evaluated based on the functional regions of their counterparts in S. cerevisiae. The consensus sequence of TFBS motifs in P. pastoris was also determined. The structural analysis we presented is invaluable for designing novel engineered promoters and ensuring transcriptional robustness in P. pastoris and phylogenetic footprinting analyses of other yeast species.