2.A.56 The Tripartite ATP-independent Periplasmic Transporter (TRAP-T) Family

TRAP-T family permeases generally consist of three components, and these systems have so far been found in Gram-negative bacteria, Gram-positive bacteria and archaea. Several members of the family have been both sequenced and functionally characterized. The first system to be characterized was the DctPQM system of Rhodobacter capsulatus (Forward et al., 1997), and it is the prototype for the TRAP-T family (Kelly and Thomas, 2001; Rabus et al., 1999).

DctP is a periplasmic dicarboxylate (malate, fumarate, succinate) binding receptor that is biochemically well-characterized. The 3-dimensional structure of a homologue, SiaTP (TC #2.A.56.1.3) has been solved (Muller et al., 2006). DctQ is an integral cytoplasmic membrane protein (25 kDa) with 4 putative transmembrane α-helical spanners (TMSs). DctM is a second integral cytoplasmic membrane protein (50 kDa) with 12 putative TMSs. These three proteins have been shown to be both necessary and sufficient for the proton motive force-dependent uptake of dicarboxylates into R. capsulatus. An involvement of ATP in transport energization was excluded.  The substrate-binding protein, SiaP, imposes directionality on an electrochemical sodium gradient-driven TRAP transporter, SiaPQM (Mulligan et al., 2009).

In several TRAP-T systems, fused Q-M-type proteins instead of two separate Q- and M-type proteins are found, while in others, Q-P-type fusion proteins are found. The operon encoding the Synechocystis system includes a protein homologous to the glutamine binding protein, and biochemical evidence has suggested that a glutamate transporter from Rhodobacter sphaeroides is a periplasmic binding protein-dependent, pmf-dependent secondary carrier (Jacobs et al., 1996). Homologous systems in Halomonas elongata and Rhodobacter spheroides take up ectoine/hydroxyectoine and taurine, respectively (Bruggemann et al., 2004; Grammann et al., 2002). The DctP dicarboxylate receptor is homologous to both the YiaO monocarboxylate receptor and the TeaA ectoine receptor. Thus, the TRAP-T family of permeases may be involved in the uptake of widely divergent compounds, mostly carboxylate derivatives (Kelly and Thomas, 2001; Thomas et al., 2006; Mulligan et al., 2007).

The crystal structure of SiaP (the receptor for SiaTP; TC #2.A.56.1.3) reveals an overall topology similar to ATP binding cassette receptors, which is not apparent from the sequence, demonstrating that primary and secondary transporters can share a common structural component (Müller et al., 2006). The structure of SiaP in the presence of the sialic acid analogue 2,3-didehydro-2-deoxy-N-acetylneuraminic acid reveals the ligand bound in a deep cavity with its carboxylate group forming a salt bridge with a highly conserved Arg residue. Sialic acid binding, which obeys simple bimolecular association kinetics, is accompanied by domain closure about a hinge region and the kinking of an α-helix hinge component. The structure provides insight into the evolution, mechanism, and substrate specificity of TRAP-transporters (Müller et al., 2006).

The solute binding receptor, DctP, has a structure comprised of two domains connected by a hinge that closes upon substrate binding, similar to those in ABC uptake porters. Substrate binding is mediated through a conserved and specific arginine/carboxylate interaction in the receptor. Mulligan et al. (2011) have reviewed the expanding repertoire of substrates and physiological roles for experimentally characterized TRAP transporters in bacteria and discuss mechanistic aspects. TRAP transporters are high-affinity, Na+-dependent unidirectional secondary transporters.

A subfamily of TRAP-Ts [tetratricopeptide repeat-protein associated TRAP transporters (TPATs)] has four components. Three are common to both TRAP-Ts and TPATs. TPATs are distinguished from TRAP-Ts by the presence of a protein called the 'T component'. In Treponema pallidum, this protein (TatT) is a water-soluble trimer whose protomers are each perforated by a pore. Its respective P component (TatP(T)) interacts with TatT. Co-crystal structures of two complexes showed that up to three monomers of TatP(T) can bind to the TatT trimer. A putative ligand-binding cleft of TatP(T) aligns with the pore of TatT, strongly suggesting ligand transfer between T and P(T) (Brautigam et al., 2012).

The generalized transport reaction presumed to be catalyzed by TRAP-T family permeases is:

solute (out) + nH+ (out) → solute (in) + nH+ (in)



This family belongs to the .

 

References:

Allen, S., A. Zaleski, J.W. Johnston, B.W. Gibson, M.A. Apicella. (2005). Novel sialic acid transporter of Haemophilus influenzae. Infect. Immun. 73: 5291-5300.

Brautigam CA., Deka RK., Schuck P., Tomchick DR. and Norgard MV. (2012). Structural and thermodynamic characterization of the interaction between two periplasmic Treponema pallidum lipoproteins that are components of a TPR-protein-associated TRAP transporter (TPAT). J Mol Biol. 420(1-2):70-86.

Bruggemann, C., K. Denger, A.M. Cook, and J. Ruff. (2004 ). Enzymes and genes of taurine and isethionate dissimilation in Paracoccus denitrificans. Microbiology 150: 805-816.

Chae, J.C. and G.J. Zylstra. (2006). 4-Chlorobenzoate uptake in Comamonas sp. strain DJ-12 is mediated by a tripartite ATP-independent periplasmic transporter. J. Bacteriol. 188: 8407-8412.

Chen, A.M., Y.B. Wang, S. Jie, A.Y. Yu, L. Luo, G.Q. Yu, J.B. Zhu, and Y.Z. Wang. (2010). Identification of a TRAP transporter for malonate transport and its expression regulated by GtrA from Sinorhizobium meliloti. Res. Microbiol. 161: 556-564.

Deka, R.K., C.A. Brautigam, M. Goldberg, P. Schuck, D.R. Tomchick, and M.V. Norgard. (2012). Structural, Bioinformatic, and In Vivo Analyses of Two Treponema pallidum Lipoproteins Reveal a Unique TRAP Transporter. J. Mol. Biol. 416: 678-696.

Denger, K., T.H. Smits, and A.M. Cook. (2006). Genome-enabled analysis of the utilization of taurine as sole source of carbon or of nitrogen by Rhodobacter sphaeroides 2.4.1. Microbiology 152: 3197-3206.

Forward, J., M.C. Behrendt, N.R. Wyborn, R. Cross, and D.J. Kelly. (1997). TRAP Transporters: a new family of periplasmic solute transport systems encoded by the dctPQM genes of Rhodobacter capsulatus and by homologs in diverse Gram-negative bacteria. J. Bacteriol. 179: 5482-5493.

Grammann, K., A. Volke, and H.J. Kunte. (2002). New type of osmoregulated solute transporter identified in halophilic members of the Bacteria domain: TRAP transporter TeaABC mediates uptake of ectoine and hydroxyectoine in Halomonas elongata DSM 2581T. J. Bacteriol. 184: 3078-3085.

Hopkins AP., Hawkhead JA. and Thomas GH. (2013). Transport and catabolism of the sialic acids N-glycolylneuraminic acid and 3-keto-3-deoxy-D-glycero-D-galactonononic acid by Escherichia coli K-12. FEMS Microbiol Lett. 347(1):14-22.

Jacobs, M.H.J., T. van der Heide, A.J.M. Driessen, and W.N. Konings. (1996). Glutamate transport in Rhodobacter sphaeroides is mediated by a novel binding-protein dependent secondary transport system. Proc. Natl. Acad. Sci. USA 93: 12786-12790.

Johnston, J.W., N.P. Coussens, S. Allen, J.C. Houtman, K.H. Turner, A. Zaleski, S. Ramaswamy, B.W. Gibson, and M.A. Apicella. (2008). Characterization of the N-acetyl-5-neuraminic acid-binding site of the extracytoplasmic solute receptor (SiaP) of nontypeable Haemophilus influenzae strain 2019. J. Biol. Chem. 283(2): 855-865.

Kelly, D.J. and G.H. Thomas. (2001). The tripartite ATP-independent periplasmic (TRAP) transporters of bacteria and archaea. FEMS Microbiol. Rev. 25: 405-424.

Lee, M., S.G. Woo, G. Park, and M.K. Kim. (2011). Paracoccus caeni sp. nov., isolated from sludge. Int J Syst Evol Microbiol 61: 1968-1972.

Meinert, C., J. Senger, M. Witthohn, J.H. Wübbeler, and A. Steinbüchel. (2017). Carbohydrate uptake in Advenella mimigardefordensis strain DPN7T is mediated by periplasmic sugar oxidation and a TRAP-transport system. Mol. Microbiol. [Epub: Ahead of Print]

Müller, A., E. Severi, C. Mulligan, A.G. Watts, D.J. Kelly, K.S. Wilsonz, A.J. Wilkinson, and G.H. Thomas. (2006). Conservation of structure and mechanism in primary and secondary transporters exemplified by SiaP, a sialic acid binding virulence factor from Haemophilus influenzae. J. Biol. Chem. 281: 22212-22222.

Mulligan, C., A.P. Leech, D.J. Kelly, and G.H. Thomas. (2012). The membrane proteins SiaQ and SiaM form an essential stoichiometric complex in the sialic acid tripartite ATP-independent periplasmic (TRAP) transporter SiaPQM (VC1777-1779) from Vibrio cholerae. J. Biol. Chem. 287: 3598-3608.

Mulligan, C., D.J. Kelly, and G.H. Thomas. (2007). Tripartite ATP-independent periplasmic (TRAP) transporters: application of a relational database (TRAPDb) for genome-wide analysis of transporter gene frequency and organization. J. Mol. Microbiol. Biotechnol. (in press).

Mulligan, C., E.R. Geertsma, E. Severi, D.J. Kelly, B. Poolman, and G.H. Thomas. (2009). The substrate-binding protein imposes directionality on an electrochemical sodium gradient-driven TRAP transporter. Proc. Natl. Acad. Sci. USA 106: 1778-1783.

Mulligan, C., M. Fischer, and G.H. Thomas. (2011). Tripartite ATP-independent periplasmic (TRAP) transporters in bacteria and archaea. FEMS Microbiol. Rev. 35: 68-86.

Pernil, R., A. Herrero, and E. Flores. (2010). A TRAP transporter for pyruvate and other monocarboxylate 2-oxoacids in the cyanobacterium Anabaena sp. strain PCC 7120. J. Bacteriol. 192: 6089-6092.

Quintero, M.J., M.L. Montesinos, A. Herrero, and E. Flores. (2001). Identification of genes encoding amino acid permeases by inactivation of selected ORFs from the Synechocystis genomic sequence. Genome Res. 11: 2034-2040.

Rabus, R., D.L. Jack, D.J. Kelly, and M.H. Saier, Jr. (1999). TRAP transporters: an ancient family of extracytoplasmic solute-receptor-dependent secondary active transporters. Microbiology 145: 3431-3445.

Rodionov, D.A., M.S. Gelfand, and N. Hugouvieux-Cotte-Pattat. (2004). Comparative genomics of the KdgR regulon in Erwinia chrysanthemi 3937 and other γ-proteobacteria. Microbiology 150: 3571-3590.

Rodionov, D.A., P. Hebbeln, A. Eudes, J. ter Beek, I.A. Rodionova, G.B. Erkens, D.J. Slotboom, M.S. Gelfand, A.L. Osterman, A.D. Hanson, and T. Eitinger. (2009). A novel class of modular transporters for vitamins in prokaryotes. J. Bacteriol. 191: 42-51.

Salmon, R.C., M.J. Cliff, J.B. Rafferty, and D.J. Kelly. (2013). The CouPSTU and TarPQM transporters in Rhodopseudomonas palustris: redundant, promiscuous uptake systems for lignin-derived aromatic substrates. PLoS One 8: e59844.

Severi, E., G. Randle, P. Kivlin, K. Whitfield, R. Young, R. Moxon, D. Kelly, D. Hood, and G.H. Thomas. (2005). Sialic acid transport in Haemophilus influenzae is essential for lipopolysaccharide sialylation and serum resistance and is dependent on a novel tripartite ATP-independent periplasmic transporter. Mol. Microbiol. 58: 1173-1185.

Thomas, G.H., T. Southworth, M.R. León-Kempis, A. Leech, and D.J. Kelly. (2006). Novel ligands for the extracellular solute receptors of two bacterial TRAP transporters. Microbiology 152: 187-198.

Wubbeler JH., Hiessl S., Schuldes J., Thurmer A., Daniel R. and Steinbuchel A. (2014). Unravelling the complete genome sequence of Advenella mimigardefordensis strain DPN7T and novel insights in the catabolism of the xenobiotic polythioester precursor 3,3'-dithiodipropionate. Microbiology. 160(Pt 7):1401-16.

Examples:

TC#NameOrganismal TypeExample
2.A.56.1.1Tripartite dicarboxylate:H+ symporter (substrates include: fumarate, D- and L-malate, succinate, succinamide, orotate, iticonate and mesaconate) (Forward et al., 1997)Gram-negative bacteria DctPQM dicarboxylate transporter of Rhodobacter capsulatus
DctP (R)
DctQ (M, 4 TMS)
DctM (M, 12 TMS)
 
2.A.56.1.10

Transporter for lignin derived aromatic compounds, TarPQM (Salmon et al. 2013).  The purple photosynthetic bacterium Rhodopseudomonas palustris is able to grow photoheterotrophically under anaerobic conditions on a range of phenylpropeneoid lignin monomers, including coumarate, ferulate, caffeate, and cinnamate. TarPQM is encoded at the same locus as CouPSTW (TC# 3.A.1.4.11) and several other genes involved in coumarate metabolism. The periplasmic binding-protein of this system (TarP) binds coumarate, ferulate, caffeate, and cinnamate with nanomolar KD values. Thus, R. palustris uses two redundant but energetically distinct primary and secondary transporters that both employ high-affinity periplasmic binding-proteins to maximize the uptake of lignin-derived aromatic substrates from the environment (Salmon et al. 2013).

Proteobacteria

TarPQM of Rhodopseudomonas palustris
TarP (R; 336 aas)
TarQ (small M; 217 aas)
TarM (large M; 435 aas)

 
2.A.56.1.11Tripartite high affinity ectoine/hydroxyectoine uptake system (Grammann et al., 2002)BacteriaTeaABC ectoine transporter of Halomonas elongata
TeaA (R)
TeaB (M, 4 TMS)
TeaC (M, 12 TMS)
 
2.A.56.1.12

2-Oxoglutarate, 2OG (α-ketoglutarate, αKG) uptake porter of 677 aas and 20 TMSs (Large + small subunits fused) plus a periplasmic solute binding protein of 318 aas and 1 N-terminal TMS.

αKG uptake porter of Shewanella oneidensis

 
2.A.56.1.13Putative transporterBacteriaPutative transporter of Fusobacterium nucleatum (gi 19704274)
 
2.A.56.1.2The 2,3-diketo-L-gulonate (2,3-DKG) transporter, YiaMNO [2,3-KDG is a breakdown product of L-ascorbate] (Thomas et al., 2006) BacteriaYiaMNO of E. coli
YiaM (M, 4 TMSs; most like TauL) (P37674)
YiaN (M, 12 TMSs; most like DctM) (P37675)
YiaO (R, like DctP and TauK) (P37676)
 
2.A.56.1.3

Na+-dependent (smf-driven) sialic acid (N-acetyl neuraminic acid) transporter, SiaTP (Allen et al., 2005; Severi et al., 2005; Johnston et al., 2008). SiaT is also called SiaQM (Mulligan et al., 2009).  Also transports the related sialic acids, N-glycolylneuraminic acid (Neu5Gc) and 3-keto-3-deoxy-D-glycero-D-galactonononic acid (KDN) (Hopkins et al. 2013).

Bacteria

SiaTP of Haemophilus influenzae
SiaT (a fusion protein equivalent to both DctM and DctQ) (616 aas; 16 TMSs) (P44543)
SiaP (R) (P44542)

 
2.A.56.1.4

Putative tripartite taurine uptake system, TauKLM (Bruggemann et al., 2004; Denger et al., 2006)

Bacteria

TauKLM of Rhodobacter sphaeroides
TauK (Rsph2615) (R) (Q3IVI6)
TauL (Rsph2614) (M, 4 TMS) (Q3IVI5)
TauM (Rsph2613) (M, 12 TMS) (Q3IVI4)

 
2.A.56.1.5

The putative rhamnogalacturonide transporter (Rodionov et al. 2004)

Proteobacteria

RhiABC of Salmonella typhimurium
RhiA (R) (P43020)
RhiB (M, 4 TMSs) (Q8ZKR9)
RhiC (M, 12 TMSs) (Q8ZKS0)

 
2.A.56.1.6

The Na+-dependent sialic acid uptake porter, SiaPQM. SiaQ and SiaM form a 1:1 stoichiometric complex (Mulligan et al., 2012).

Bacteria

SiaPQM of Vibrio cholerae
SiaP (R) (Q9KR64)
SiaQ (M, 4TMSs) (B9TSN0)
SiaM (M, 12 TMSs) (B9TSM9)

 
2.A.56.1.7

The malonate uptake transporter, MatPQM. Regulated by the GtrA transcriptional activator (Chen et al. 2010). MatM is fused in a single protein C-terminal to MatA (malonyl-CoA decarboxylase).

α-Proteobacteria

MatPQM of Sinorhizobium meliloti
MatP (R) (Q930W1)
MatQ (M, 4TMSs) (Q930W2)
MatM (M, 12TMSs) (Q930W3)

 
2.A.56.1.8

Sialic acid uptake transporter, DctMPQ

Proteobacteria

DctMPQ of E. coli 
DctM (Q8FA80)
DctQ (Q8FA79)
DctP (Q8FA78) 

 
2.A.56.1.9

The possible disulfide 3,3'-dithiodipropionic acid (DTDP) tripartite transporter, DctMPQ (Wübbeler et al. 2014).  More probably takes up an array of oxidized sugar onic acids, D-gluconate, D-galactonate, L-arabonate, D-fuconate and D-xylonate. The sugars are oxidized by a broad-range, membrane bound sogar oxidase.  The acids that have been studied kineticall have Kms between 8 and 15 μM (Meinert et al. 2017; ).

Proteobacteria

DTDP transporter of Advenella mimigardefordensis strain DPN7
DctM (M, large)
DctP (R)
DctQ (M, small)

 
Examples:

TC#NameOrganismal TypeExample
2.A.56.2.1

TRAP transporter for a hydrophobic substrate (3-d structure known; tp0958 has 18-20 TMSs) (Deka et al., 2012). The substrate could be a lipoprotein, tp0956 (O83922) which is encoded in the same operon with tp0957 and tp058. This protein differs from all other members of the TRAP-T family in having 19 predicted TMSs with extra TMSs at its N-terminus.

Bacteria

TRAP-T transporter of Treponema pallidum
tp0957 (R) (O83923)
tp0958 (M) (O83924) 

 
Examples:

TC#NameOrganismal TypeExample
2.A.56.3.1Tripartite glutamate:Na+ symporter (Quintero et al., 2001)Gram-negative bacteriaGtrABC glutamate:Na+ symporter of Synechocystis strain PCC6803
GtrA (M) (like DctQ)
GtrB (M) (like DctM)
GtrC (R) (like GlnH of E. coli)
 
2.A.56.3.2Tripartite 4-chlorobenzoate symporter (also binds and may transport 4-bromo-, 4-iodo-, and 4-fluorobenzoate and with a lower affinity, 3-chlorobenzoate, 2-chlorobenzoate, 4-hydroxybenzoate, 3-hydroxybenzoate, and benzoate) (Chae and Zylstra, 2006)Gram-negative bacteriaFcbT1/T2/T3 of Comamonas sp. strain DJ-12
FcbT1 (R) (AAF16407)
FcbT2 (M-sm) (AAF16408)
FcbT3 (M-lg) (AAF16409)
 
2.A.56.3.3

The 2-oxo monocarboxylate transporter (Pernil et al., 2010). Transports pyruvate which is inhibited by various 2-ketoacids.

Bacteria

The 2-oxo monocarboxylate transporter of Anabaena (nostoc) sp. strain PCC7120
DctQ (Alr3026) (Q8YSQ8)
DctM (Alr3027) (Q8YSQ7)
DctP (Alr3028) (Q8YSQ6) 

 
2.A.56.3.4

The 2-ketomonocarboxylate transporter (presented in order of affinity - 2-oxovalerate [highest affinity, KD=0.1 μM], 2-oxoisovalerate, 2-oxobutyrate, 2-oxoisocaproate, 2-oxo-3-methylvalerate, pyruvate [lowest affinity, KD=3 μM]) (Thomas et al., 2006).

Bacteria

The 2-ketomonocarboxylate transporter of Rhodobacter capsulatus
DctM-2, M-large (D5ATK1)
DctQ-2, M-small (D5ATK0)
DctP-2, Receptor (R) (D5ALT6)

 
Examples:

TC#NameOrganismal TypeExample