As a result of molecular domestication of the gag gene of errantiviruses, the Gagr gene was formed in the genome of Drosophila melanogaster. It has previously been shown that the Gagr gene is transcribed at the highest level in gut tissues relative to other tissues, and its transcription is most effectively induced in females in response to ammonium persulfate added to the nutrient medium. In the present work, the gut transcriptome of females with knockdown of the Gagr gene was studied in all tissues under standard conditions and under stress conditions caused by ammonium persulfate. It was revealed that in females with knockdown of the Gagr gene, the genes of antimicrobial peptides controlled by the Toll and Imd signaling pathways are activated in the gut. Induction of a stress response by ammonium persulfate revealed disruption of the JAK/STAT and JNK/MAPK signaling pathways and an almost complete absence of activation of the ER- stress and UPR-stress pathways in flies with the Gagr gene knockdown. The data obtained confirm the important role of the Gagr gene in maintaining homeostasis and the immune response.