Combined Transcriptome and Metabolome Analysis Reveals That Carbon Catabolite Repression Governs Growth and Pathogenicity in Verticillium dahliae

Carbon catabolite repression (CCR) is a common transcriptional regulatory mechanism that microorganisms use to efficiently utilize carbon nutrients, which is critical for the fitness of microorganisms and for pathogenic species to cause infection. Here, we characterized two CCR genes, <i>VdCreA</i> and <i>VdCreC</i>, in <i>Verticillium dahliae</i> that cause cotton Verticillium wilt disease. The <i>VdCreA</i> and <i>VdCreC</i> knockout mutants displayed slow growth with decreased conidiation and microsclerotium production and reduced virulence to cotton, suggesting that <i>VdCreA</i> and <i>VdCreC</i> are involved in growth and pathogenicity in <i>V. dahliae</i>. We further generated 36 highly reliable and stable <i>ΔVdCreA</i> and <i>ΔVdCreC</i> libraries to comprehensively explore the dynamic expression of genes and metabolites when grown under different carbon sources and CCR conditions. Based on the weighted gene co-expression network analysis (WGCNA) and correlation networks, <i>VdCreA</i> is co-expressed with a multitude of downregulated genes. These gene networks span multiple functional pathways, among which seven genes, including PYCR (pyrroline-5-carboxylate reductase), are potential target genes of <i>VdCreA</i>. Different carbon source conditions triggered entirely distinct gene regulatory networks, yet they exhibited similar changes in metabolic pathways. Six genes, including 6-phosphogluconolactonase and 2-ODGH (2-oxoglutarate dehydrogenase E1), may serve as hub genes in this process. Both <i>VdCreA</i> and <i>VdCreC</i> could comprehensively influence the expression of plant cell wall-degrading enzyme (PCWDE) genes, suggesting that they have a role in pathogenicity in <i>V. dahliae</i>. The integrated expression profiles of the genes and metabolites involved in the glycolysis/gluconeogenesis and pentose phosphate pathways showed that the two major sugar metabolism-related pathways were completely changed, and GADP (glyceraldehyde-3-phosphate) may be a pivotal factor for CCR under different carbon sources. All these results provide a more comprehensive perspective for further analyzing the role of Cre in CCR.