- Defining the essential genome of diverse phages with phage Tn-seq
- Systematic mapping of bacteriophage gene essentiality with HIDEN-SEQ
Most tailed phages have genomes of 50–200 kb in size, of which one part is composed of operons of core genes encoding functions involved in phage replication, gene expression and virion assembly. The other genes, largely coding for hypothetical proteins, are often dispensable under standard laboratory conditions and their proportion increases with genome size. Based on a few previous studies, these accessory genes seem to provide functions that enhance the ability of the phage to survive and adapt to specific hosts or environmental conditions. Well-known examples are T4 genes encoding inhibitors of specific antiviral defence systems such as rIIA/rIIB for RexAB or dmd for RnlAB and various anti-CRISPR proteins encoded in different phages. Accessory genes of bacteriophages thus seem to largely form their arsenal of tools and tricks to prevail in the virus–host arms race. To systematically uncover the biological functions of these genes, scalable genome-wide approaches linking viral genes to specific phenotypes are required. Existing methods have offered valuable insights but remain laborious and not broadly applicable. In bacteria, this challenge has been overcome by transposon-insertion sequencing (TnSeq), a technique that quantifies the fitness of all viable transposon insertions in a genome by comparative deep sequencing before and after growth under a given condition. While TnSeq has revolutionized bacterial microbiology, no analogous approach has so far been available for phages. Although transposition into phage genomes had occasionally been reported, its scale and application have been limited by the lack of broadly applicable genetic selection markers.
Read here: https://www.nature.com/articles/s41564-026-02455-8
