Naeij Hamta Babaei, Etemadifar Zahra, Kilbane John, Karimi-Jafari Mohammad Hossein, Mofidifar Sepideh
Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran.
Division of Biology, Illinois Institute of Technology, Chicago, IL, United States of America.
PLoS One. 2025 Jan 29;20(1):e0317796. doi: 10.1371/journal.pone.0317796. eCollection 2025.
Exophiala spinifera strain FM, a black yeast and melanized ascomycete, shows potential for oil biodesulfurization by utilizing dibenzothiophene (DBT) as its sole sulfur source. However, the specific pathway and enzymes involved in this process remain unclear due to limited genome sequencing and metabolic understanding of E. spinifera. In this study, we sequenced the complete genome of E. spinifera FM to construct the first genome-scale metabolic model (GSMM) for this organism. Through bioinformatics analysis, we identified genes potentially involved in DBT desulfurization and degradation pathways for hazardous pollutants. We focused on understanding the cost associated with metabolites in sulfur assimilation pathway to assess economic feasibility, optimize resource allocation, and guide metabolic engineering and process design. To overcome knowledge gaps, we developed a genome-scale model for E. spinifera, iEsp1694, enabling a comprehensive investigation into its metabolism. The model was rigorously validated against growth phenotypes and gene essentiality data. Through shadow price analysis, we identified costly metabolites such as 3'-phospho-5'-adenylyl sulfate, 5'-adenylyl sulfate, and choline sulfate when DBT was used as the sulfur source. iEsp1694 encompasses the degradation of aromatic compounds, which serves as a crucial first step in comprehending the pan metabolic capabilities of this strain.
棘状外瓶霉菌株FM是一种黑色酵母和黑化子囊菌，它以二苯并噻吩（DBT）作为唯一硫源，具有石油生物脱硫的潜力。然而，由于对棘状外瓶霉的基因组测序和代谢了解有限，该过程涉及的具体途径和酶仍不清楚。在本研究中，我们对棘状外瓶霉FM的全基因组进行了测序，以构建该生物体的首个基因组规模代谢模型（GSMM）。通过生物信息学分析，我们鉴定了可能参与DBT脱硫和有害污染物降解途径的基因。我们着重了解硫同化途径中与代谢物相关的成本，以评估经济可行性、优化资源分配，并指导代谢工程和工艺设计。为了填补知识空白，我们开发了棘状外瓶霉的基因组规模模型iEsp1694，以便对其代谢进行全面研究。该模型针对生长表型和基因必需性数据进行了严格验证。通过影子价格分析，我们确定了当使用DBT作为硫源时，诸如3'-磷酸-5'-腺苷硫酸、5'-腺苷硫酸和硫酸胆碱等成本高昂的代谢物。iEsp1694涵盖了芳香化合物的降解，这是理解该菌株泛代谢能力的关键第一步。
