NEAT: a domain duplicated in genes near the components of a putative Fe3+ siderophore transporter from Gram-positive pathogenic bacteria

Abstract

Background: Iron uptake from the host is essential for bacteria that infect animals. To find potential targets for drugs active against pathogenic bacteria, we have searched all completely sequenced genomes of pathogenic bacteria for genes relevant for iron transport.

Results: We identified a protein domain that appears in variable copy number in bacterial genes that are usually in the vicinity of a putative Fe3+ siderophore transporter. Accordingly, we have denoted this domain NEAT for 'near transporter'. Most of the bacterial species containing this domain are pathogenic. Sequence features indicate that the domain is anchored to the extracellular side of the membrane. The domain seems to be under high selective pressure for rapid independent duplications that are typical of sequences involved in signaling and binding.

Conclusions: The NEAT domain might be functionally related to iron transport. The taxonomic specificity of this domain and its predicted extracellular position could make it an interesting target for designing new drugs against some highly pathogenic bacteria.

Figure 1

Conserved genome organization around the components of a putative Fe³⁺ siderophore transporter (from STRING [26,27] or from the literature when the genome is not present in STRING). Each gene is represented with an arrow-shaped box (as inSTRING) pointing in the direction of transcription. The genes in yellow contain the NEAT domain; the pink ovals indicate the number of occurrences of the domain within the gene. Genes in green are related to Escherichia coli fecB, fepB, or fhuD (Fe³⁺ siderophore transporter, periplasmic component). Genes in red are related to fecC, fepG, fhuB (Fe³⁺ siderophore transporter, transmembrane component). Genes in violet are related to fecE, fepC, fhuC (Fe³⁺ siderophore transporter, ATPase component). Remaining genes (in white) did not show significant sequence similarity to any of the other genes displayed in the figure. Codes for genes containing the NEAT domain are shown in Table 1. For the neighboring genes the names used correspond to those from the corresponding genomic project. Spy1797 should be shown between S_pyog (Spy1798) and Spy1796, but is not displayed here because there was no such corresponding entry in GenBank. Note that there was no neighboring ATPase (violet gene) in S. aureus; the most similar sequence in this species is SA0602 (not shown).

Figure 2

Multiple alignment of the occurrences of the NEAT domain, generated with the ClustalW program [28]. SMART [9,10], which identifies repeats using prospero [29,30], was used to search for domains in some sequences. The internal repeats detected in this manual analysis were used to generate subsequences that were used for building the first alignment. Then, we followed an iterative procedure by building a Hidden Markov Model (HMM) of the alignment and adding to the alignment significant hits from an HMM search [31,32] comparison of the HMM to the NCBI's nonredundant protein database. For the final HMM (derived from the alignment presented in this figure) no more similar sequences were detected below a standard E-value threshold (E = 0.001). The consensus in 70% of the sequences is reported below the alignment. Residue ranges are listed next to the protein code name. The letters h, l, and p indicate hydrophobic, aliphatic, and polar residues, respectively. Hydrophobic residues are highlighted in dark blue, polar residues in green, and a fairly conserved arginine (R in the consensus sequence) in red. Codes are the same as in Figure 1 and Table 1. The predicted secondary structure [8], mostly beta sheet, is displayed at the bottom of the figure. Although the B_anth sequence corresponds to a fragment of the domain, examination of the corresponding DNA sequence indicates that the actual translation product might extend further in both the amino- and carboxy-terminal directions.

Figure 3

Modular arrangements of sequences containing the NEAT domain. Protein codes are the same as those shown in Figure 1 and Table 1. The red line indicates the signal peptide; the blue box represents a transmembrane helix; the gray box indicates the Gram-positive anchor as detected by Pfam [15,16]; the black box represents a hydrophobic carboxy-terminal anchoring domain proposed for two Listeria sequences [23]. PKD is the polycystic kidney disease domain (present in PKD1, chitinases, and collagenases, among others), and LRR stands for leucine-rich repeat (ten copies detected in S_pyog, using the program REP [33,34]). The scale bar indicates the length in amino acids.

Figure 4

Phylogenetic tree of the domain instances generated from the multiple alignment shown in Figure 2. Bootstrapping values range from 0 to 100. The labels indicate the sequence and position of the repeat in the sequence. Domains from the same sequence have identical color (for example, all B_hal1 repeats are red). Domains from sequences of the same species have similar colors (for example, the S. aureus domains are colored in different hues of green).