The Wolbachia genome of Brugia malayi: endosymbiont evolution within a human pathogenic nematode

Abstract

Complete genome DNA sequence and analysis is presented for Wolbachia, the obligate alpha-proteobacterial endosymbiont required for fertility and survival of the human filarial parasitic nematode Brugia malayi. Although, quantitatively, the genome is even more degraded than those of closely related Rickettsia species, Wolbachia has retained more intact metabolic pathways. The ability to provide riboflavin, flavin adenine dinucleotide, heme, and nucleotides is likely to be Wolbachia's principal contribution to the mutualistic relationship, whereas the host nematode likely supplies amino acids required for Wolbachia growth. Genome comparison of the Wolbachia endosymbiont of B. malayi (wBm) with the Wolbachia endosymbiont of Drosophila melanogaster (wMel) shows that they share similar metabolic trends, although their genomes show a high degree of genome shuffling. In contrast to wMel, wBm contains no prophage and has a reduced level of repeated DNA. Both Wolbachia have lost a considerable number of membrane biogenesis genes that apparently make them unable to synthesize lipid A, the usual component of proteobacterial membranes. However, differences in their peptidoglycan structures may reflect the mutualistic lifestyle of wBm in contrast to the parasitic lifestyle of wMel. The smaller genome size of wBm, relative to wMel, may reflect the loss of genes required for infecting host cells and avoiding host defense systems. Analysis of this first sequenced endosymbiont genome from a filarial nematode provides insight into endosymbiont evolution and additionally provides new potential targets for elimination of cutaneous and lymphatic human filarial disease.

Figure 1. Genogram of the Complete Circular Genome of wBm

The scale indicates coordinates in kilobase pairs (kbp) with the putative origin of replication positioned at 0 kbp. The outermost ring indicates the GC-skew over all bases in the forward strand using a window size of 40 kbp and a step size of 1 kbp. Positive and negative skew are shaded gold and blue, respectively. Features are shown as paired rings separated by a circular baseline. In each pair, the outer and inner rings represent the forward and reverse DNA strands, respectively. Working inward from the scale, the features displayed are as follows: identified genes and their broad functional classification (multihued, as listed); tRNA (blue)/rRNA (red) genes; putative pseudogenes (green); repeated sequences (red) and transposon-related repeats (blue).

Figure 2. Venn Diagram Showing Comparison of Conserved and Unique Genes and Pseudogenes in wBm (Wolbachia from B. malayi), Rickettsia prowazekii, Rickettsia conorii, and in wBm and wMel (among Those Assigned to COGs)

(A) Predicted functional protein-coding genes. (B) Pseudogenes. (C) Combined results for comparison between wBm and wMel. G, intact gene; P, pseudogene.

Figure 3. Metabolic Pathways Retained in wBm

Pathways shared by Wolbachia and Rickettsia are shown with black arrows. Pathways present in Wolbachia but not in Rickettsia are shown with green arrows. Numbering alongside pathway arrows reflects enzyme annotation, a table of which is available at http://tools.neb.com/wolbachia/.

Figure 4. Organization of Direct and Palindromic Repeats in wBm

Circles represent the complete genomic sequence of wBm. Repeats were identified using the REPuter program [182] and are connected by line segments. Direct repeats are shown in the graphs in the top row, while palindromic repeats are shown in the lower row of graphs. The left column graphs display repeats of 50 to 500 bp in length. The rightmost graphs display repeats of greater than 500 bp in length.

Figure 5. Absence of Gene Order Colinearity between wBm and Rickettsia and Disruption of Gene Colinearity between wBm and wMel

Each dot represents a pair of probable orthologs defined as reciprocal BLAST best hits with E-value less than 0.001. (A) Genome dot-plot comparison of wBm (Wolbachia from B. malayi) and Rpro (R. prowazekii). (B) Genome dot-plot comparison of wBm (Wolbachia from B. malayi) and Rcon (R. conorii). (C) Genome dot-plot comparison of Rpro (R. prowazekii) and Rcon (R. conorii). (D) Genome dot-plot comparison of wBm and wMel.