Evolution of Invasion in a Diverse Set of Fusobacterium Species

Gene categories expanded in active and passive invaders (Q < 0.0005). (A) The top 12 GO terms expanded in the active invaders were largely membrane related. (B) Pfam domains expanded in the active invaders include the known virulence-related adhesins FadA and RadD, as well as a massive expansion of MORN2 domains of unknown function. (C) A different set of adhesins, including the trimeric autotransporter adhesion protein YadA, is expanded in the passive invaders. (See Table S5 in the supplemental material for a full listing of categories expanded in both active and passive invaders for Q < 0.05.) (D) Clade-specific summary of expanded Pfam domains. The number of dots represents the average number of domains present in a genome from each of the five clades. For MORN2, there can be multiple domains per gene.

Gene families expanded in active invaders clustered in the genome. This multiple alignment of our set of seven finished F. nucleatum genomes shows an example of a region with close physical association among FadA, RadD, and MORN2 family proteins. The gray-shaded connectors represent orthologous protein pairs. This genomic region also contains an ompA gene shown to be involved in biofilm formation in Fusobacterium (69), as well as numerous strain-specific genes, transposases, IS elements, and genes previously identified as being differentially expressed under aggregation conditions (11). In two genomes (F. nucleatum subsp. nucleatum ATCC 25586 and F. nucleatum subsp. polymorphum ATCC 10953), a synteny break (indicated with a black line) placed the canonical fadA gene (FN0264) in this region rather than a second radD gene. Several regions similar to this are located in the genome.

Species distribution of MORN2 orthogroups. Each column represents an orthogroup. The boxes are colored according to the average number of MORN2 domains per protein, and for each orthogroup containing two or more paralogs, the numbers indicate the number of paralogs. There is tremendous variation in the number and structure of proteins containing MORN2 domains across genomes. Active invaders (species names shaded in dark gray) contain longer, more complex MORN2-containing proteins than passive invaders (species names shaded in light gray). Passive invaders contain only a small complement of short, “ancestral” orthogroups, which are present across all species. Expansions of active invader orthogroups, especially in F. periodonticum, can be seen by the presence of paralogs.