Effects of mutations in phage restriction sites during escape from restriction–modification

Abstract

Restriction-modification systems are widespread genetic elements that protect bacteria from bacteriophage infections by recognizing and cleaving heterologous DNA at short, well-defined sequences called restriction sites. Bioinformatic evidence shows that restriction sites are significantly underrepresented in bacteriophage genomes, presumably because bacteriophages with fewer restriction sites are more likely to escape cleavage by restriction-modification systems. However, how mutations in restriction sites affect the likelihood of bacteriophage escape is unknown. Using the bacteriophage λ and the restriction-modification system EcoRI, we show that while mutation effects at different restriction sites are unequal, they are independent. As a result, the probability of bacteriophage escape increases with each mutated restriction site. Our results experimentally support the role of restriction site avoidance as a response to selection imposed by restriction-modification systems and offer an insight into the events underlying the process of bacteriophage escape.

Prokaryotic genome expansion is facilitated by phages and plasmids but impaired by CRISPR

“…Our results also imply that CRISPR immune systems might be more sensitive towards invading phages than plasmids, consistent with the differential fitness burdens brought by the two types of foreign invaders to the hosts (37,(39)(40)(41).…”

ΦX174 Attenuation by Whole Genome Codon Deoptimization

“…However, there are many other compositional features within the DNA sequences of protein coding genes upon which selection acts. These features include: the genic GC content (4-6) , CpG or TpA dinucleotides (7)(8)(9)(10)(11) , codon pairs (12)(13)(14)(15) , endonuclease recognition sites (16)(17)(18)(19) , intron splicing motifs (20) , mRNA folding stability (21)(22)(23)(24)(25) , ribosomal pausing sites (26,27) , concentration of non-preferred codons at transcripts 5' end (28)(29)(30) , autocorrelation of codons on transcript (31) , and capacity of codon order to influence co-translational folding of proteins (32,33) . At any given site, natural selection may act on one or more of these features to favor the use of certain codons over other synonymous ones (34) .…”

Hypothesis: a Plastically Produced Phenotype Predicts Host Specialization and Can Precede Subsequent Mutations in Bacteriophage

“…Sequencing could reveal whether the phages that bypassed the R-M system contained new mutations. The restriction barrier of the new host could be increased or decreased by increasing or decreasing the number of motifs recognized by the R-M system in the genome of the phage ( 29 ) or perhaps by increasing or decreasing the expression levels of the host restriction endonucleases and methyltransferases. Finally, the mutation rate of the phage can be adjusted by growing the phage in the presence of a mutagen.…”