Tripartite ATP-Independent Periplasmic (TRAP) Transporters and Tripartite Tricarboxylate Transporters (TTT): From Uptake to Pathogenicity

Abstract

The ability to efficiently scavenge nutrients in the host is essential for the viability of any pathogen. All catabolic pathways must begin with the transport of substrate from the environment through the cytoplasmic membrane, a role executed by membrane transporters. Although several classes of cytoplasmic membrane transporters are described, high-affinity uptake of substrates occurs through Solute Binding-Protein (SBP) dependent systems. Three families of SBP dependant transporters are known; the primary ATP-binding cassette (ABC) transporters, and the secondary Tripartite ATP-independent periplasmic (TRAP) transporters and Tripartite Tricarboxylate Transporters (TTT). Far less well understood than the ABC family, the TRAP transporters are found to be abundant among bacteria from marine environments, and the TTT transporters are the most abundant family of proteins in many species of β-proteobacteria. In this review, recent knowledge about these families is covered, with emphasis on their physiological and structural mechanisms, relating to several examples of relevant uptake systems in pathogenicity and colonization, using the SiaPQM sialic acid uptake system from Haemophilus influenzae and the TctCBA citrate uptake system of Salmonella typhimurium as the prototypes for the TRAP and TTT transporters, respectively. High-throughput analysis of SBPs has recently expanded considerably the range of putative substrates known for TRAP transporters, while the repertoire for the TTT family has yet to be fully explored but both types of systems most commonly transport carboxylates. Specialized spectroscopic techniques and site-directed mutagenesis have enriched our knowledge of the way TRAP binding proteins capture their substrate, while structural comparisons show conserved regions for substrate coordination in both families. Genomic and protein sequence analyses show TTT SBP genes are strikingly overrepresented in some bacteria, especially in the β-proteobacteria and some α-proteobacteria. The reasons for this are not clear but might be related to a role for these proteins in signaling rather than transport.

Keywords: carboxylic acids; high-affinity; periplasmic binding-proteins; secondary transporter; solute transport.

Figure 1

Overall topologies and structures of the different Solute Binding Protein (SBP dependant) transporter families. The ABC transporters are represented by the E. coli maltose transporter MalEFGK2 (PDB 2R6G). It is composed of a solute binding protein (red), two Transmembrane (TM) domains (blue), and two Nucleotide binding domains (NBD) (orange); The secondary Tripartite ATP-independent periplasmic (TRAP) Transporters are composed of a 12 TM domain channel DctM (blue) and a 4 TM domain protein DctQ (green), which can be fused together by an additional TM domain (yellow) in a DctQM protein, and a DctP or TAXI SBP protein, represented respectively by the SiaP from H. influenza (PDB 2CEY) (light red) and the TT1099 from T. thermophilus (PDB 1US4) (dark red). TAXI-TRAP were always found associated with fused DctQM proteins; The Tripartite Tricarboxylate Transporter (TTT), is formed also by a 12 TM channel TctA (purple), a 4 TM protein TctB (cyan) and a TctC solute binding protein, represented by Bug27 from B. pertussis (PDB 2QPQ) (Brown). In some rare cases, TctAB proteins may be also fused. Although sharing similar topology, the TRAP and TTT systems share no sequence similarity.

Figure 2

Examples of genetic organization for different secondary SBP dependant transporters. (A) Gene organizations for TRAP systems. (B) Gene organization for TTT systems. ^* represents an amido-hydrolase gene.

Figure 3

Comparison between TRAP and TTT SBP crystal structures. (A) Overall structure of SiaP, a sialic acid binding SBP from the TRAP family in H. influenzae (PDB 3B50). Domain 1 is represented in cyan (α-helix) and purple (β-sheet), and domain 2 is represented in blue (α-helix) and green (β-sheet). A sialic acid molecule is shown in the binding pocket. Arg147, important to perform a salt bridge with the carboxylic group of the substrate in most SiaP homologs is shown in red. (B) Overall structure of BugD, a aspartate binding SBP from the TTT family in B. pertussis (PDB 2F5X). Domain 1 is represented in green (α-helix) and orange (β-sheet), and domain 2 is represented in blue (α-helix) and brown (β-sheet). An aspartate molecule is shown in the binding pocket. Two loops, between β1 and α1 and between β7 and α6, are involved in the conserved coordination of two water molecules, which bridge hydrogen bonds with the proximal carboxylic group in the substrate. These loops and waters are shown in red (C) Binding pocket of SiaP, showing the coordination of the sialic acid molecule. Arg147 perform a salt bridge with the carboxylic group in the substrate. The remaining of the molecule is coordinated by hydrogen bonds and water molecules which are variable inside the TRAP family. (D) Binding pocket of BugD, showing the coordination of the aspartate molecule. The residues Ala-15, gly-16, gly-17, and Asp-20 participate in the loop between β1 and α1, coordinating two water molecules which bridge hydrogen bonds with the proximal carboxylic group in the substrate. This coordination is very conserved among the TTT family. The remaining substrate coordination occur through non-conserved hydrogen bonds and water bridging.

Figure 4

Numbers of genomes containing different ranges of homologs for tctC and tctA.