The genome of the amoeba symbiont Candidatus Amoebophilus asiaticus encodes an afp-like prophage possibly used for protein secretion

The recently sequenced genome of the obligate intracellular amoeba symbiont Candidatus Amoebophilus asiaticus is unique among prokaryotic genomes due to its extremely large fraction of genes encoding proteins harboring eukaryotic domains such as ankyrin-repeats, TPR/SEL1 repeats, leucine-rich repeats, as well as F-and U-box domains, most of which likely serve in the interaction with the amoeba host. Here we provide evidence for the presence of additional proteins, which are presumably presented extracellularly and should thus also be important for host cell interaction. Surprisingly, we did not find homologs of any of the well-known protein secretion systems required to translocate effector proteins into the host cell in the A. asiaticus genome, and the type six secretion system seems to be incomplete. Here we describe the presence of a putative prophage in the A. asiaticus genome, which shows similarity to the antifeeding prophage from the insect pathogen Serratia entomophila. In S. entomophila this system is used to deliver toxins into insect hosts. This putative antifeeding-like prophage might thus represent the missing protein secretion apparatus in A. asiaticus.