Cyanobacteriochrome-like GAF folds in phages revealed via AlphaFold proteomic modelling

Accurate protein structure prediction followed by structural homology detection enable the functional annotation of otherwise obscure viral protein-coding genes. Here we employ AlphaFold proteomic modelling and structural homology searches on the genome of CrV-01T, a representative freshwater cyanophage, to reveal previously unknown structural homologs. One of these cryptic viral proteins is found to be a cyanobacteriochrome-like GAF fold (CGF) protein. Cyanobacteriochromes (CBCRs) are known to regulate phototaxis, cyclic nucleotide metabolism and optimization of light harvesting in cyanobacteria. Phylogenetic analyses indicate that the CGF protein of CrV-01T was probably acquired from a cyanobacterial host. We then use experimentally determined CBCR structures to query the Big Fantastic Virus Database and discover that CGFs are present among many different bacteriophages. The GAF domain sequence, which is a hallmark of CBCRs, can still be detected in some of these divergent viral proteins. Remarkably, viral CGF proteins harbor an N-terminal extension that in most cases is predicted to contain a transmembrane α-helix, indicating that they may bind the host membrane after being synthesized in the virocell. The presence of CGF protein-coding genes in cyanophage genomes suggests novel ways in which viruses may manipulate the metabolism of cyanobacteria, the most abundant oxygenic phototrophs on Earth. Overall, the findings reported here emphasize the importance of applying structural homology detection methods when annotating viral genomes and highlight the potential of AlphaFold for exploring the dark matter of the aquatic virosphere.