Genome of Enterobacteriophage Lula/phi80 and Insights into Its Ability To Spread in the Laboratory Environment

The novel temperate bacteriophage Lula, contaminating laboratoryEscherichia coli strains, turned out to be the well-known lambdoid phage phi80. Our previous studies revealed that two characteristics of Lula/phi80 facilitate its spread in the laboratory environment: cryptic lysogen productivity and stealthy infectivity. To understand the genetics/genomics behind these traits, we sequenced and annotated the Lula/phi80 genome, encountering anE. coli -toxic gene revealed as a gap in the sequencing contig and analyzing a few genes in more detail. Lula/phi80's genome layout copies that of lambda, yet homology with other lambdoid phages is mostly limited to the capsid genes. Lula/phi80's DNA is resistant to cutting with several restriction enzymes, suggesting DNA modification, but deletion of the phage'sdamL gene, coding for DNA adenine methylase, did not make DNA cuttable. ThedamL mutation of Lula/phi80 also did not change the phage titer in lysogen cultures, whereas the hostdam mutation did increase it almost 100-fold. Since the high phage titer in cultures of Lula/phi80 lysogens is apparently in response to endogenous DNA damage, we deleted the only Lula/phi80 SOS-controlled gene,dinL . We found thatdinL mutant lysogens release fewer phage in response to endogenous DNA damage but are unchanged in their response to external DNA damage. The toxic gene of Lula/phi80,gamL , encodes an inhibitor of the host ATP-dependent exonucleases, RecBCD and SbcCD. Its own antidote,agt , apparently encoding a modifier protein, was found nearby. Interestingly, Lula/phi80 lysogens arerecD andsbcCD phenocopies, so GamL and Agt are part of lysogenic conversion.