Phylogeny and Expansion of Serine/Threonine Kinases in Phagocytotic Bacteria in the Phylum Planctomycetota

Abstract The recently isolated bacterium “Candidatus Uabimicrobium amorphum” is the only known prokaryote that can engulf other bacterial cells. Its proteome contains a high fraction of proteins involved in signal transduction systems, which is a feature normally associated with multicellularity in eukaryotes. Here, we present a protein-based phylogeny which shows that “Ca. Uabimicrobium amorphum” represents an early diverging lineage that clusters with the Saltatorellus clade within the phylum Planctomycetota. A gene flux analysis indicated a gain of 126 protein families for signal transduction functions in “Ca. Uabimicrobium amorphum”, of which 66 families contained eukaryotic-like Serine/Threonine kinases (STKs) with Pkinase domains. In total, we predicted 525 functional STKs in “Ca. Uabimicrobium amorphum”, which represent 8% of the proteome and is the highest fraction of STKs in a bacterial proteome. The majority of STKs in this species are membrane proteins and 30% contain long, tandem arrays of WD40 or TPR domains. The pKinase domain was predicted to be located in the cytoplasm, while the WD40 and TPR domains were predicted to be located in the periplasm. Such domain combinations were also identified in the STKs of other species in the Planctomycetota, although in much lower abundances. A phylogenetic analysis of the STKs in the Planctomycetota inferred from the Pkinase domain alone provided support for lineage-specific expansions of the STKs in “Ca. Uabimicrobium amorphum”. The results imply that expansions of eukaryotic-like signal transduction systems are not restricted to multicellular organisms, but have occurred in parallel in prokaryotes with predatory lifestyles and phagocytotic-like behaviors.