A DNA element recognised by the molybdenum-responsive transcription factor ModE is conserved in Proteobacteria, green sulphur bacteria and Archaea

Abstract

Background: The transition metal molybdenum is essential for life. Escherichia coli imports this metal into the cell in the form of molybdate ions, which are taken up via an ABC transport system. In E. coli and other Proteobacteria molybdenum metabolism and homeostasis are regulated by the molybdate-responsive transcription factor ModE.

Results: Orthologues of ModE are widespread amongst diverse prokaryotes, but not ubiquitous. We identified probable ModE-binding sites upstream of genes implicated in molybdenum metabolism in green sulphur bacteria and methanogenic Archaea as well as in Proteobacteria. We also present evidence of horizontal transfer of nitrogen fixation genes between green sulphur bacteria and methanogenic Archaea.

Conclusions: Whereas most of the archaeal helix-turn-helix-containing transcription factors belong to families that are Archaea-specific, ModE is unusual in that it is found in both Archaea and Bacteria. Moreover, its cognate upstream DNA recognition sequence is also conserved between Archaea and Bacteria, despite the fundamental differences in their core transcription machinery. ModE is the third example of a transcriptional regulator with a binding signal that is conserved in Bacteria and Archaea.

Figure 1

Alignment of the helix-turn-helix (HTH) domains homologous to the molybdenum-responsive transcriptional regulator ModE. Amino acid residues predicted to directly interact with the target DNA are marked with asterisks (*). The alignment was taken from the Pfam database .

Figure 2

Domain architectures of some example members of the HTH_9 family as defined by Pfam (Bateman et al., 2002). The domains are described in the text. A. Q9I631 (Pseudomonas aeruginosa), Q88AA0 (Ps. syringae), Q88QX4 (Ps. putida), Q9CMR6 (Pasteurella multocida), MODE_HAEIN (Haemophilus influenzae), Q8Z8A6 (Salmonella Typhi), Q8ZQR8 (Salmonella Typhimurium), MODE_ECOLI (E. coli), MODE_YERPE (Yersinia pestis), Q8EAN6 (Shewanella oneidensis), Q8XQR8 (Ralstonia solanacearum), Q8KC82 (Chlorobium tepidum), MODE_AZOVI (Azotobacter vinelandii), Q9ABA4 (Caulobater crescentus), MOPA_RHOCA (Rhodobacter capsulatus), MOPA_RHOCA (Rhodobacter capsulatus), Q9F4K4 (Herbaspirillum seropedicae). B. Q8PWN4 (Methanosarcina mazei), and Q8TTZ2 (M. acetivorans). C. Q9RBF7 (Alcaligenes eutrophus), Q8XXM1 (Ralstonia solanacearum), and Q8ZZY3 (Pyrobaculum aerophilum). D. Q9PMF6 (Campylobacter jejuni). E. Q97Z66 (Sulfolobus solfataricus), Q97ET9 (Sulfolobus tokodaii), Q8ZYE6 (P. aerophilum), O29240 (Archaeglobus fulgidus), Q8TVF9 (Methanopyrus kandleri), and Q98KI4 (Rhizobium loti).

Figure 3

Alignment of known and strongly suspected ModE-binding sites used to generate the weight matrix.

Figure 4

Sequence logo representation of the alignment of known and strongly suspected ModE-binding in Figure 3. A graphic representation of an aligned set of binding sites. The relative heights of the letters are proportional to the frequencies of bases at each position. The degree of sequence conservation is measured in bits of information and is indicated by the total height of a stack of letters. The vertical scale is in bits, with a maximum of 2 bits possible at each position. The logo was generated using WebLogo [27].

Figure 5

Position-specific weight matrix derived from the alignment of known and strongly suspected ModE-binding sites used to generate the weight matrix in Figure 1.

Figure 6

Formula used to calculate I_seq, the Kullback-Leibler distance [26], where i is the position within the site, p_b is the frequency of that base in the genome, and f_b,i is the observed frequency of each base at that position (from the weight matrix). Values for p_b were calculated from the percentage G+C content of the genome sequence.