Manipulation of IME4 expression, a global regulation strategy for metabolic engineering in Saccharomyces cerevisiae

Metabolic engineering has been widely used for production of natural medicinal molecules. However, engineering high-yield platforms is hindered in large part by limited knowledge of complex regulatory machinery of metabolic network. N6-Methyladenosine (m6A) modification of RNA plays critical roles in regulation of gene expression. Herein, we identify 1470 putatively m6A peaks within 1151 genes from the haploid Saccharomyces cerevisiae strain. Among them, the transcript levels of 94 genes falling into the pathways which are frequently optimized for chemical production, are remarkably altered upon overexpression of IME4 (the yeast m6A methyltransferase). In particular, IME4 overexpression elevates the mRNA levels of the methylated genes in the glycolysis, acetyl-CoA synthesis and shikimate/ aromatic amino acid synthesis modules. Furthermore, ACS1 and ADH2, two key genes responsible for acetyl-CoA synthesis, are induced by IME4 overexpression in a transcription factor-mediated manner. Finally, we show IME4 overexpression can significantly increase the titers of isoprenoids and aromatic compounds. Manipulation of m6A therefore adds a new layer of metabolic regulatory machinery and may be broadly used in bioproduction of various medicinal molecules of terpenoid and phenol classes. & COPY; 2023 Chinese Pharmaceutical Association and Institute of Materia Medica, Chinese Academy of Medical Sciences. Production and hosting by Elsevier B.V. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

Automated summary

Metabolic engineering has been widely used for the production of natural medicinal molecules. However, the limited knowledge of the complex regulatory machinery of the metabolic network hindered the engineering of high-yield platforms. The N6-methyladenosine (m6A) modification of RNA plays a critical role in the regulation of gene expression. Overexpression of the yeast m6A methyltransferase IME4 remarkably altered the transcript levels of genes involved in pathways optimized for chemical production, such as glycolysis, acetyl-CoA synthesis, and shikimate/ aromatic amino acid synthesis. Furthermore, IME4 overexpression induced the key genes ACS1 and ADH2 responsible for acetyl-CoA synthesis in a transcription factor-mediated manner and significantly increased the production of isoprenoids and aromatic compounds. Manipulation of m6A adds a new layer of metabolic regulatory machinery and has the potential to be widely used in the bioproduction of various medicinal molecules.