Protocol for Genome-Scale Reconstruction and Melanogenesis Analysis of Exophiala dermatitidis

Wheaton L. Schroeder, Rajib Saha

Research output: Contribution to journalArticlepeer-review

Abstract

Exophiala dermatitidis is a polyextremotolerant fungus with a small genome, thus suitable as a model system for melanogenesis and carotenogensis. A genome-scale model, iEde2091, is reconstructed to increase metabolic understanding and used in a shadow price analysis of pigments, as detailed here. Important to this reconstruction is OptFill, a recently developed alternative gap-filling method useful in the holistic and conservative reconstruction of genome-scale models of metabolism, particularly for understudied organisms like E. dermatitidis where gaps in metabolic knowledge are abundant. For complete details on the use and execution of this protocol, please refer to Schroeder and Saha (2020) and Schroeder et al. (2020).

Original languageEnglish (US)
Article number100105
JournalSTAR Protocols
Volume1
Issue number2
DOIs
StatePublished - Sep 18 2020

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Neuroscience(all)
  • Immunology and Microbiology(all)

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