The cis-regulatory map of Shewanella genomes

Abstract

While hundreds of microbial genomes are sequenced, the challenge remains to define their cis-regulatory maps. Here, we present a comparative genomic analysis of the cis-regulatory map of Shewanella oneidensis, an important model organism for bioremediation because of its extraordinary abilities to use a wide variety of metals and organic molecules as electron acceptors in respiration. First, from the experimentally verified transcriptional regulatory networks of Escherichia coli, we inferred 24 DNA motifs that are conserved in S. oneidensis. We then applied a new comparative approach on five Shewanella genomes that allowed us to systematically identify 194 nonredundant palindromic DNA motifs and corresponding regulons in S. oneidensis. Sixty-four percent of the predicted motifs are conserved in at least three of the seven newly sequenced and distantly related Shewanella genomes. In total, we obtained 209 unique DNA motifs in S. oneidensis that cover 849 unique transcription units. Besides conservation in other genomes, 77 of these motifs are supported by at least one additional type of evidence, including matching to known transcription factor binding motifs and significant functional enrichment or expression coherence of the corresponding target genes. Using the same approach on a more focused gene set, 990 differentially expressed genes derived from published microarray data of S. oneidensis during exposure to metal ions, we identified 31 putative cis-regulatory motifs (16 with at least one type of additional supporting evidence) that are potentially involved in the process of metal reduction. The majority (18/31) of those motifs had been found in our whole-genome comparative approach, further demonstrating that such an approach is capable of uncovering a large fraction of the regulatory map of a genome even in the absence of experimental data. The integrated computational approach developed in this study provides a useful strategy to identify genome-wide cis-regulatory maps and a novel avenue to explore the regulatory pathways for particular biological processes in bacterial systems.

Figure 1.

Flow chart of the procedure of identifying conserved cis-regulatory motifs in S. oneidensis by comparative analysis.

Figure 2.

Conservation of the known E. coli transcriptional regulatory interactions in S. oneidensis. The logos of the E. coli TFBS were drawn based on the motif weight matrix models obtained from RegulonDB (Version 5.0). ^aThe number of binding sites used to build the motif profiles. Multiple binding sites may be from the same gene. ^bOnly the first genes of the target operons of a TF were considered when we counted the number of conserved target genes. A few target genes in RegulonDB were not included due to discrepancies in gene names.

Figure 3.

Estimation of neutral distances between five Shewanella species. The numbers shown are neutral substitution rates (K_s) measured by synonymous substitutions in coding sequences.

Figure 4.

Conservation of the 183 motifs identified from Dataset II in the distantly related Shewanella species. The black bars represent the percentage of motifs identified from the five Shewanella genomes that are also conserved in the seven newly sequenced Shewanella species. The white bars represent the results from the control sequence sets.

Figure 5.

Venn diagrams showing the numbers of predicted motifs supported by different types of evidence, including matching to known TF-binding motifs, significant functional enrichment of the target genes in GO or KEGG pathway terms (GO/KG) and EC of the target genes in microarray experiments (EC). (A) Motifs identified from Dataset I (see Table 2 for detailed information). (B) Motifs identified from Dataset II (see Table 3 for detailed information).