Toxoplasma gondii is an intracellular parasite that relies on intricate molecular mechanisms for its proliferation and survival. Here, we investigate the role of TgUAE1 in these processes and shed light on the underlying regulatory network. We demonstrate that TgUAE1 is crucial for maintaining the proliferation of T. gondii and the normal morphology of mitochondria. To elucidate the molecular basis of TgUAE1's essential functions, we conducted transcriptome sequencing to identify the genes regulated by this factor. Total RNA was extracted from TATi-3HA-TgUba1 strains cultured under 0.5 µg/ml ATc (knockout strain) and DMSO (wild strain), and subjected to deep sequencing using the Illumina Novaseq TM 6000 platform. Subsequently, sequence reads were mapped to the T. gondii genome, resulting in a comprehensive transcriptome containing 8637 detected genes. Among these genes, 934 were dysregulated in the absence of TgUAE1, comprising 60 downregulated and 874 upregulated genes. Functional enrichment analysis revealed their involvement in various GO categories and KEGG pathways. Our findings provide novel insights into the profound impact of TgUAE1 on the expression landscape of the T. gondii genome, highlighting the significance of this factor in parasite biology. Overall design: RNA profiles of TgUAE1 knockdown and wild-type strains.