Effect of depleting BFD1-regulated gene-expression factors (TGME49_253790, TGME49_208020, TGME49_224630, TGME49_306620, TGME49_311100) on the Toxoplasma transcriptome during alkaline stress

The transcription factor BFD1 is the master regulator of the Toxoplasma chronic-stage differentiation program, which is induced under alkaline stress. Prior work indicated that BFD1 transcriptionally activates five other putative RNA- and DNA-binding proteins during differentiation, suggesting potential secondary roles in shaping the Toxoplasma chronic-stage transcriptome. To describe the distinct genetic cohorts controlled by these factors, we generated individual knockdown strains for each candidate using the auxin inducible degron system (TIR1/AID) and examined the transcriptomic effects of their depletion under alkaline stress. Comparative gene expression RNA-seq analysis of conditional knockdown strains of ME49 Toxoplasma, cultured for 96h under alkaline stress in either the presence or absence of TGME49_200385 (BFD1), TGME49_306620, TGME49_311100, TGME49_224630, TGME49_253790, or TGME49_208020. Experiments were performed in biological duplicate (separate infections).