PSAT: a web tool to compare genomic neighborhoods of multiple prokaryotic genomes

Abstract

Background: The conservation of gene order among prokaryotic genomes can provide valuable insight into gene function, protein interactions, or events by which genomes have evolved. Although some tools are available for visualizing and comparing the order of genes between genomes of study, few support an efficient and organized analysis between large numbers of genomes. The Prokaryotic Sequence homology Analysis Tool (PSAT) is a web tool for comparing gene neighborhoods among multiple prokaryotic genomes.

Results: PSAT utilizes a database that is preloaded with gene annotation, BLAST hit results, and gene-clustering scores designed to help identify regions of conserved gene order. Researchers use the PSAT web interface to find a gene of interest in a reference genome and efficiently retrieve the sequence homologs found in other bacterial genomes. The tool generates a graphic of the genomic neighborhood surrounding the selected gene and the corresponding regions for its homologs in each comparison genome. Homologs in each region are color coded to assist users with analyzing gene order among various genomes. In contrast to common comparative analysis methods that filter sequence homolog data based on alignment score cutoffs, PSAT leverages gene context information for homologs, including those with weak alignment scores, enabling a more sensitive analysis. Features for constraining or ordering results are designed to help researchers browse results from large numbers of comparison genomes in an organized manner. PSAT has been demonstrated to be useful for helping to identify gene orthologs and potential functional gene clusters, and detecting genome modifications that may result in loss of function.

Conclusion: PSAT allows researchers to investigate the order of genes within local genomic neighborhoods of multiple genomes. A PSAT web server for public use is available for performing analyses on a growing set of reference genomes through any web browser with no client side software setup or installation required. Source code is freely available to researchers interested in setting up a local version of PSAT for analysis of genomes not available through the public server. Access to the public web server and instructions for obtaining source code can be found at http://www.nwrce.org/psat.

Figure 1

Evidence of gene orthology through sequence homology and gene order conservation. The Francisella tularensis subspecies novicida U112 gene FTN_0453 does not have any homologous genes in other Francisella strains. The PSAT genomic neighborhood browser, however, highlighted a gene cluster between F t novicida U112 and genomes from genera such as Shewanella and Vibrio. The conserved order of the homologs provided secondary evidence that the genes in this cluster are orthologs.

Figure 2

Loss of function suggested by disruption of the leu operon. The leu operon is known to be involved with leucine biosynthesis in Francisella tularensis subspecies novicida U112 (ilvE, leuA, leuC, leuD, and leuB). The PSAT graphic demonstrated that genes in this operon are missing in Francisella tularensis subspecies tularensis SchuS4 suggesting that leucine biosynthesis may be impaired in this strain of the bacteria.

Figure 3

Genes related to glucose metabolism neighbor a pair of regulator genes. Pseudomonas aeruginosa genes gltR and gltS make up a putative sensor kinase-response regulator pair. PSAT demonstrated that the gene pair is located near a cluster of genes involved with glucose metabolism in several genomes. Previous studies have shown that gltR is indeed required for glucose transport in Pseudomonas aeruginosa.