Insights from the genome annotation of Elizabethkingia anophelis from the malaria vector Anopheles gambiae

Abstract

Elizabethkingia anophelis is a dominant bacterial species in the gut ecosystem of the malaria vector mosquito Anopheles gambiae. We recently sequenced the genomes of two strains of E. anophelis, R26T and Ag1, isolated from different strains of A. gambiae. The two bacterial strains are identical with a few exceptions. Phylogenetically, Elizabethkingia is closer to Chryseobacterium and Riemerella than to Flavobacterium. In line with other Bacteroidetes known to utilize various polymers in their ecological niches, the E. anophelis genome contains numerous TonB dependent transporters with various substrate specificities. In addition, several genes belonging to the polysaccharide utilization system and the glycoside hydrolase family were identified that could potentially be of benefit for the mosquito carbohydrate metabolism. In agreement with previous reports of broad antibiotic resistance in E. anophelis, a large number of genes encoding efflux pumps and β-lactamases are present in the genome. The component genes of resistance-nodulation-division type efflux pumps were found to be syntenic and conserved in different taxa of Bacteroidetes. The bacterium also displays hemolytic activity and encodes several hemolysins that may participate in the digestion of erythrocytes in the mosquito gut. At the same time, the OxyR regulon and antioxidant genes could provide defense against the oxidative stress that is associated with blood digestion. The genome annotation and comparative genomic analysis revealed functional characteristics associated with the symbiotic relationship with the mosquito host.

Figure 1. Subsystem category distribution statistics for the genome of E. Anophelis as annotated by RAST.

The pie chart represents relative abundance of each subsystem category and numbers depict subsystem feature counts.

Figure 2. Graphic view of a syntenic gene cluster that is conserved in five taxa of Bacteroidetes.

The genes encoding the components of TonB dependent transporters are ExbB, ExbD and TonB. Locus ID of each gene is given in the boxes, with taxon prefix (e.g. D505_ for E.a.) in the ExbB box for each species. The box with * in D. fermentans represents a predicted gene encoding a hypothetic protein. The scale bar represents 1 kb in length. Phylogenetically, E. anophelis and F. johnsoniae belong to the class Flavobacteria, Dyadobacter fermentans belongs to the class Cytophagia, Arcticibacter svalbardensis is in the class Sphingobacteriia, and Bacteroides thetaiotaomicron is located in the class Bacteroidia.

Figure 3. Graphic view of four Sus-like loci in the genome of E. anophelis R26^T.

Locus ID of each gene is given in the boxes. HP: hypothetic protein. The scale bar represents 1 kb in length.

Figure 4. Graphic view of a locus where three component genes of an RND efflux pump are located syntenically in four taxa of Bacteroidetes.

Gene name was given on the top of each box. Locus ID of each gene is given in the boxes. OMP, outer membrane protein; RND: HAE1, Hydrophobe/amphiphile efflux-1; MFP, membrane fusion protein; HP: hypothetic protein. The scale bar represents 1 kb in length.

Figure 5. Phylogenetic relationship of homologues of three selected lactam degrading enzymes in E. anophelis and other taxa.

(A) D505_10647; (B) D505_08675; (C) D505_08350. Numbers above clades are bootstrap values (1,000 replicates). The trees were constructed by Neighbor Joining criterion implemented in MEGA 5.1. The GenBank accession numbers of the sequences were listed in Table S5.

Figure 6. Isoprenoid synthesis pathway in four bacterial species.

The color code represents the enzymes that are present in the species.