Enzymes of the shikimic acid pathway encoded in the genome of a basal metazoan, Nematostella vectensis, have microbial origins

Abstract

The shikimic acid pathway is responsible for the biosynthesis of many aromatic compounds by a broad range of organisms, including bacteria, fungi, plants, and some protozoans. Animals are considered to lack this pathway, as evinced by their dietary requirement for shikimate-derived aromatic amino acids. We challenge the universality of this traditional view in this report of genes encoding enzymes for the shikimate pathway in an animal, the starlet sea anemone Nematostella vectensis. Molecular evidence establishes horizontal transfer of ancestral genes of the shikimic acid pathway into the N. vectensis genome from both bacterial and eukaryotic (dinoflagellate) donors. Bioinformatic analysis also reveals four genes that are closely related to those of Tenacibaculum sp. MED152, raising speculation for the existence of a previously unsuspected bacterial symbiont. Indeed, the genome of the holobiont (i.e., the entity consisting of the host and its symbionts) comprises a high content of Tenacibaculum-like gene orthologs, including a 16S rRNA sequence that establishes the phylogenetic position of this associate to be within the family Flavobacteriaceae. These results provide a complementary view for the biogenesis of shikimate-related metabolites in marine Cnidaria as a "shared metabolic adaptation" between the partners.

Fig. 1.

Phylogenetic tree showing the relationship of the predicted protein sequence of the N. vectensis aroA-like gene to the predicted murA protein sequences of the seven best hits in a BLAST analysis and to those in E. coli and Tenacibaculum. Distances were calculated from a CLUSTAL W alignment using the Jones-Taylor-Thornton matrix, and the tree was constructed by using the neighbor-joining algorithm in programs of the PHYLIP package (version 3.63). The distance is proportion of amino acid substitutions.

Fig. 2.

Phylogenetic tree showing the relationship of the deduced protein sequence of the aroB part of the AroB-O-methyltransferase protein of N. vectensis to homologous dinoflagellate proteins. Sequences were aligned with CLUSTALW and the tree was constructed by using the neighbor-joining algorithm with distances derived from the Jones-Taylor-Thornton model (using PHYLIP version 3.63). The tree was rooted by using Anabaena variabilis as an out group. The distances are the proportion of amino acid substitutions, and the bootstrap values based on 100 samples are shown.

Fig. 3.

Phylogenetic tree of PCNA protein sequences. The sequence of the PCNA protein of O. marina was used for a BLAST search against the translated genomic sequences of N. vectensis. The BLAST alignments were used to assemble the protein sequence from N. vectensis. The sequences from the two species were used for BLAST searches of GenBank, and a selection of the best hits for each species was used to construct a phylogenetic tree by using the neighbor-joining algorithm in programs of the PHYLIP package (version 3.63). The distance is proportion of nucleotide substitutions.

Fig. 4.

Phylogenetic tree showing the relationship of the 16S rRNA gene sequence found in the N. vectensis genome sequence (720-bp fragment in entry c429301624.Contig1 of StellaBase, http://evodevo.bu.edu/stellabase; SI Dataset 8a) to the sequences of the closest type strains in Ribosomal Data Base Project II (release 9.52; http://rdp.cme.msu.edu). Distances were calculated from a CLUSTAL W alignment using the F84 model, and the tree was constructed as in Fig. 3.