Figure 1.
The Bacterial Inorganic Nitrogen Cycle
The ammonification, denitrification, detoxification, nitrogen fixation, and nitrification pathways are shown by colored solid lines with genes names involved in the pathway. The dashed black line shows possible non-enzymatic interconversions of nitrogen oxides. The dotted line shows additional formation of NO and hydroxylamine during nitrite ammonification.
Figure 2.
Genomic Organization of Genes Regulated by HcpR
Yellow circles with numbers denote candidate HcpR sites with different consensus sequences. These numbers correspond to the HcpR profile numbers in Figure 3.
Figure 3.
Maximum Likelihood Phylogenetic Tree of the FNR/CRP Family of Transcriptional Regulators
The third column contains sequences of helix-turn-helix motifs in the proteins. Two specificity-determining positions correlated with DNA motifs are colored (R180 and E181 in proteins correlate with G3 and A6 in DNA sites, respectively). The fourth column includes sequence logos for presumably homogeneous and large site sets and sequence consensi for small sets of DNA sites and for well-established motifs of other factors (FNR, CRP, CooA, NtcA, ArcR). The last column indicates the name of a search profile constructed in this study.
Figure 4.
Genomic Organization of Genes Regulated by NsrR, NorR, and DNR in β-Proteobacteria
Magenta, green, and blue circles denote candidate NsrR, NorR, and DNR sites, respectively. Candidate σ54 promoters associated with NorR sites are shown by angle arrows. Experimentally known sites of NorR and DNR are marked by “s.” Additional sites of the NarP and FNR factors are indicated by purple squares and black triangles, respectively.
Figure 5.
Genomic Organization of Genes Regulated by NnrR and NsrR in α-Proteobacteria
Orange and magenta circles denote candidate NnrR and NsrR sites, respectively. Experimentally known NnrR sites are marked by “s.”
Figure 6.
Genomic Organization of Genes Regulated by NsrR, NorR, and DNR in γ-Proteobacteria
Magenta, green, and blue circles denote candidate NsrR, NorR, and DNR sites, respectively. Candidate σ54 promoters associated with NorR sites are shown by angle arrows. Experimentally known sites of NorR and DNR are marked by “s.” Additional sites of the NarP and FNR factors are indicated by purple squares and black triangles, respectively.
Figure 7.
Sequence Logos for the Identified NsrR-Binding Sites in Various Bacterial Taxa
Figure 8.
Sequence Logos for the Identified NorR-Binding Sites in Various Species of Proteobacteria
Table 1.
Predicted Members of Regulatory and Metabolic Networks of the Nitrogen Oxides Dissimilatory Metabolism
Table 1.
Continued
Figure 9.
Maximum Likelihood Phylogenetic Tree of the Hybrid Cluster (Prismane) Proteins
Genes predicted to be regulated by the nitrogen oxides–related factors are highlighted by respective colors. Additionally, predicted FNR-regulated genes are denoted by black circles. Genes positionally linked to the NADH oxidoreductase hcr and the hypothetical ferredoxin frdX genes are shown by red and blue lines, respectively. Archaeal genes are shown by pointed lines.
Figure 10.
Regulatory Interactions between Genes for Dissimilatory Nitrogen Oxides Metabolism in Bacteria
(A) Distribution of regulators and regulated genes. The number of cases when a gene is regulated by a specific transcription factor is indicated by the length of a colored bar in the histogram. The white bar in the histogram shows the cases when the gene is present in a genome possessing at least one of the studied regulons, but is not regulated by any of them.
(B) Combined regulatory network. Arrows denote regulatory interactions, with the thickness reflecting the frequency of the interaction in the analyzed genomes. Experimentally established (for DNR, NnrR, NsrR, and NorR) and predicted based on the regulon content (for HcpR) signal molecules are shown in filled ovals, and the protein family for each transcription factor is shown below.
Table 2.
List of Genome Abbreviations Used in This Study
Table 2.
Continued
Table 3.
Distribution of Predicted Regulatory Sites in Bacterial Genomes