Synthetic biology has played a major role in engineering microbial cell factories to convert plant biomass (lignocellulose) to fuels and bioproducts by fermentation. However, the final product yield is limited by inhibition of microbial growth and fermentation by toxic phenolic compounds generated during lignocellulosic pre-treatment and hydrolysis. Advances in the development of systems biology technologies (genomics, transcriptomics, proteomics, metabolomics) have rapidly resulted in large datasets which are necessary to obtain a holistic understanding of complex biological processes underlying phenolic compound toxicity. Here, we review and compare different systems biology tools that have been utilized to identify molecular mechanisms that modulate phenolic compound toxicity in Saccharomyces cerevisiae. By focusing on and comparing functional genomics and transcriptomics approaches we identify common mechanisms potentially underlying phenolic toxicity. Additionally, we discuss possible ways by which integration of data obtained across multiple unbiased approaches can result in new avenues to develop yeast strains with a significant improvement in tolerance to phenolic fermentation inhibitors.

中文翻译：

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多面系统生物学方法展示了酿酒酵母中酚类化合物抑制的细胞景观

合成生物学在工程微生物细胞工厂中发挥了重要作用，通过发酵将植物生物质（木质纤维素）转化为燃料和生物产品。然而，最终产品产量受到木质纤维素预处理和水解过程中产生的有毒酚类化合物抑制微生物生长和发酵的限制。系统生物学技术（基因组学、转录组学、蛋白质组学、代谢组学）的发展迅速产生了大型数据集，这些数据集对于全面了解酚类化合物毒性背后的复杂生物过程是必不可少的。在这里，我们回顾并比较了不同的系统生物学工具，这些工具已被用于确定调节酿酒酵母中酚类化合物毒性的分子机制。通过关注和比较功能基因组学和转录组学方法，我们确定了潜在的酚类毒性的常见机制。此外，我们讨论了可能的方法，通过哪些方法整合通过多种无偏方法获得的数据可以产生新的途径来开发酵母菌株，并显着提高对酚类发酵抑制剂的耐受性。