Phage genomes are enriched with genes to overcome diverse bacterial immune systems

Abstract

Phages and bacteria are engaged in an evolutionary arms race, where phages continually evolve new strategies to overcome bacterial defenses. To systematically investigate the functions of all genes within phage genomes, we constructed a gene deletion library of the Escherichia coli phage phiDruSM1, belonging to the Queuovirinae subfamily, the Seuratvirus genus, whose morphotype is siphovirus morphology, encompassing 105 open reading frames ( orfs ). By infecting various E. coli clinical isolates with 73 orf knockout phages, we demonstrated that each gene is essential for host range mechanisms. Furthermore, we identified 21 potential pairs of antiphage defense systems (ADSs) and phage-encoded anti-defense systems (ADSs). Experimental validation confirmed that phiDruSM1-derived ADSs are effective against multiple defense systems, including Druantia type I, Brex type I, AVAST type III, Sir2+HerA, DUF4297+HerA, and Gao_Hhe ( hhe ). These findings highlight that a major portion of the phage genome is dedicated to counteracting ADSs.