Transcriptomic elucidation of itaconic acid production by Methylorubrum extorquens AM1 and its phaR mutant derivative

Methylorubrum extorquens AM1 is engineered to produce itaconic acid by heterologous expression of cis-aconitic acid decarboxylase. Mutation was also performed on phaR in Methylorubrum extorquens AM1, which regulate poly-beta-hydroxybutyrate accumulation, in attempt to increase carbon flux toward itaconic acid production. However, in our case, itaconic acid production by phaR mutant strain was not higher than that of the wildtype. Transcriptomic analysis was utilized in order to examine the cause for this phenomenon. RNA-seq analysis revealed that phaR mutation in the itaconic acid-producing strain might result in a complex regulatory rewiring at the gene expression level, which could cause a reduced resource flux toward ITA production. Also, RNA profiling gave a hint at the broad regulatory role of PhaR. Comparison of RNA profiles between Methylorubrum extorquens AM1 wildtype strain carrying pTE101 control plasmid, wildtype strain with itaconic acid-producing plasmid (pTE101a-CAD) and its phaR mutant derivative carrying the itaconic acid-producing plasmid using RNA-seq.