The MicrobesOnline Web site for comparative genomics

Abstract

At present, hundreds of microbial genomes have been sequenced, and hundreds more are currently in the pipeline. The Virtual Institute for Microbial Stress and Survival has developed a publicly available suite of Web-based comparative genomic tools (http://www.microbesonline.org) designed to facilitate multispecies comparison among prokaryotes. Highlights of the MicrobesOnline Web site include operon and regulon predictions, a multispecies genome browser, a multispecies Gene Ontology browser, a comparative KEGG metabolic pathway viewer, a Bioinformatics Workbench for in-depth sequence analysis, and Gene Carts that allow users to save genes of interest for further study while they browse. In addition, we provide an interface for genome annotation, which like all of the tools reported here, is freely available to the scientific community.

Figure 1.

Comparative Genome Browser. In a subgroup of the γ-Proteobacteria, two ancient operons for adjacent steps in the TCA cycle, sdhCDAB and sucABCD, have been merged into one larger operon. This view from the Comparative Genome Browser shows the sdhA locus across an archaeon (Halobacterium sp.), a Gram-positive bacterium (Mycobacterium tuberculosis), and a diverse range of proteobacteria. Note that the larger operon is present in only a single clade, yet it is highly conserved within this group, suggesting that it may reflect a recent innovation within the γ-Proteobacteria.

Figure 2.

The VertiGO Browser. The VertiGO Browser uses the Gene Ontology (Camon et al. 2003) to display and highlight differences in the physiological capabilities among a set of bacteria. In the figure, the unusually large number of signal transduction proteins in the metal-reducing bacteria, D. vulgaris and Geobacter metallireducens, is evident when compared to other model organisms. Users can view any number of genomes in this way by selecting them from the menu at left, and navigate the GO hierarchy by clicking the boxes to the left of each term. In addition, users can retrieve all genes that match a particular GO annotation by clicking the number corresponding to the appropriate term and species (for terms with <200 genes).

Figure 3.

Comparative Metabolic Maps. Differences in the tricarboxylic acid (TCA) cycle are shown for the Gram-positive bacterium B. subtilis and the Gram-negative Proteobacterium D. vulgaris. Reactions highlighted with filled boxes indicate that corresponding enzymes were identified in both species (gray boxes), only in B. subtilis (blue boxes), or only in D. vulgaris (yellow boxes). As expected, B. subtilis is found to contain a complete complement of enzymes for the TCA cycle. In contrast, the strictly anaerobic bacterium D. vulgaris is shown to lack a complete cycle, and likely uses different enzymes for conversion between 2-oxoglutarate and succinate.

Figure 4.

Regulon Browser. The Regulon Browser page for flgH of Shewanella oneidensis MR-1 is shown. Genes predicted to be possible transcriptional regulators are highlighted with yellow boxes; other genes are blue. Genes in the same predicted operon are connected, and operons in the same predicted regulon appear inside the same gray box (e.g., the two operons in the top right regulon). Red lines connecting regulons indicate strong similarity in expression patterns, while blue lines indicate chromosomal proximity of the orthologs, one or more component genes from each regulon in several distantly related species. Most of the genes highlighted in this view are flagellar-related, and the fliA gene highlighted in yellow is the alternative σ factor responsible for expression of flagellar genes.

Figure 5.

Bioinformatics Workbench. The Bioinformatics Workbench allows users to perform basic sequence analysis on the genes and features of interest they have collected in their Gene Carts while browsing the MicrobesOnline Web site. (A) Gene Cart including α and β subunits of dissimilatory sulfite reductase (dsrAB), and a related hydrogenase as an outgroup. (B,C) A multiple sequence alignment and phylogenetic tree generated for the genes in the Gene Cart using the built-in tools. Colors in the tree indicate taxonomy, and numbers show quartet-puzzling scores from TREE-PUZZLE (Schmidt et al. 2002).