Excisionase in Pf filamentous prophage controls lysis‐lysogeny decision‐making in Pseudomonas aeruginosa

Abstract

Pf filamentous prophages are prevalent among clinical and environmental Pseudomonas aeruginosa isolates. Pf4 and Pf5 prophages are integrated into the host genomes of PAO1 and PA14, respectively, and play an important role in biofilm development. However, the genetic factors that directly control the lysis-lysogeny switch in Pf prophages remain unclear. Here, we identified and characterized the excisionase genes in Pf4 and Pf5 (named xisF4 and xisF5, respectively). XisF4 and XisF5 represent two major subfamilies of functional excisionases and are commonly found in Pf prophages. While both of them can significantly promote prophage excision, only XisF5 is essential for Pf5 excision. XisF4 activates Pf4 phage replication by upregulating the phage initiator gene (PA0727). In addition, xisF4 and the neighboring phage repressor c gene pf4r are transcribed divergently and their 5′-untranslated regions overlap. XisF4 and Pf4r not only auto-activate their own expression but also repress each other. Furthermore, two H-NS family proteins, MvaT and MvaU, coordinately repress Pf4 production by directly repressing xisF4. Collectively, we reveal that Pf prophage excisionases cooperate in controlling lysogeny and phage production.

Pf Bacteriophage and Their Impact on Pseudomonas Virulence, Mammalian Immunity, and Chronic Infections

“…At this point, the phage must decide whether it will initiate a chronic infection and produce progeny virions or initiate a lysogenic lifecycle and integrate into the bacterial chromosome as a prophage (80). If conditions favor Pf entering a lysogenic lifecycle after infecting a naïve bacterial host, the RF can be integrated into the bacterial chromosome as a prophage by the Pf-encoded site-specific tyrosine recombinase IntF (84).…”

“…When pf4r is suppressed, as it is by OxyR, or when sufficiently high titers of infecting Pf virions overwhelm Pf4r, as may happen during superinfection, XisF4 is free to promote the transcription of the operon encoding the replication initiator protein (PA0727) and IntF (84). The initiator protein binds to RF DNA at the origin of replication, recruits the host helicase UvrD and DNA polymerase III, and initiates rolling circle replication (87).…”

Prophage encoding toxin/antitoxin system PfiT/PfiA inhibits Pf4 production in Pseudomonas aeruginosa

“…We recently reannotated the Pf4 genome during the identification of the phage excisionase gene xisF4 (Li et al , 2019). Two neighbouring genes that are only 9 bp apart, PA0729 and Rorf0727 , are located at the right end of the Pf4 prophage.…”

“…In PAO1, Pf4 is integrated between PA0714 and tRNA Gly , while Pf5 is integrated inside the coding region of the PA14_49040 gene. The genome regions that encode phage replication, structure and assembly genes in the prophages Pf4 and Pf5 share much higher sequence identity than accessory gene regions (Li et al , 2019). The PfiT/PfiA TA system is located at the end of the Pf4 prophage and is not found in the Pf5 prophage.…”

Temperate Bacteriophages (Prophages) in Pseudomonas aeruginosa Isolates Belonging to the International Cystic Fibrosis Clone (CC274)

“…Three of these showed high similarity to the Pseudomonas Pf inovirus, constituted by 9-15 proteins in isolates AUS411, AUS531, and FQSE15-1110. The inoviruses present in isolates AUS531 and FQSE15 were similar to the Pseudomonas Pf4 and Pf5 inoviruses, but the prophage detected in AUS411 was a new phage, designated Pf8_ST274-AUS411 (hereinafter referred to as Pf8) (Hay and Lithgow, 2019;Li et al, 2019). The genome of the Pf8 filamentous phage is of size 10 Kb and has a total of 16 proteins and one tRNA coding region (Genbank:MN710383).…”