| Summary: | The putative methyltransferase Lae1 is a global regulator in <i>Trichoderma,</i> which modulates the expression of secondary metabolite gene clusters, possibly via chromatin remodeling. Here we aimed to explore the specific transcription and metabolites profiles regulated by Lae1 in <i>T. atroviride</i> 23. Comparative transcriptomics and metabolome analyses between the <i>lae1</i> deletion (Mlae1) and over-expressing (Olae1) mutants were performed using RNA sequencing and QTOF-UPLC-MS techniques. In total, 1344 unique differentially expressed genes (DEGs) and 92 metabolites were identified across three strains. The significantly altered metabolic profiles revealed that the <i>lae1</i> gene modulates central carbon metabolism, amino acid metabolism, secondary metabolism, and phospholipid metabolism. The effects of <i>lae1</i> on phospholipid metabolism were further explored, and the findings showed that <i>lae1</i> modulates the composition and function of cell membranes and other metabolic activities, including the phosphotransferase system (PTS) and biosynthesis of secondary metabolites (SM). Phospholipid metabolism is related to energy metabolism, signal transduction, and environmental adaptability of microorganisms. These data showed that <i>Lae1</i> affects the primary metabolites, phospholipid, as well as the regulation of secondary metabolites in Trichoderma. This study could potentially provoke in-depth investigations of the Lae1-mediated target genes in phospholipid synthesis. The Lae1 may act as a novel target that is associated with disease defense and drug development in the future.
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