Tripartite ATP-independent periplasmic transporter
Encyclopedia
Tripartite ATP-independent periplasmic transporters (TRAP transporters) are a large family of solute transporters found in bacteria
and archaea
, but not in eukaryotes, that appear to be specific for the uptake of organic acid
s. They are unique in that they utilize a substrate binding protein (SBP) in combination with a secondary transporter
.
, UK. His group were working on the mechanism used by the photosynthetic bacterium Rhodobacter
capsulatus to take up certain dicarboxylic acid
s. They characterised a binding protein component (DctP) of a transporter that recognized these compounds, which they assumed would form part of a typical ABC transporter, but when they sequenced the genes surrounding dctP they found two other genes encoding integral membrane proteins, dctQ and dctM, but no genes encoding components of an ABC transporter. They further showed that uptake of the same dicarboxylates was independent of ATP and that uptake required an electrochemical ion gradient, making this a unique binding protein-dependent secondary transporter.
Since these early studies, it has become clear that TRAP transporters are present in many bacteria
and archaea
, with many bacterial having multiple TRAP transporters, some having over 20 different systems.
and expressed at relatively high levels compared to the membrane domains. In Gram positive bacteria and archaea, the SBP is tethered to the cytoplasmic membrane. In both types of systems the SBP binds to substrate, usually with low micromolar affinity, which causes a significant conformation change in the protein, akin to a Venus flytrap closing. The trapped subtrate is then delivered to the membrane domains of the transporter, where the electrochemical ion gradient is somehow exploited to open the SBP, extract the substrate and catalyse its movement across the membrane. For the SiaPQM TRAP transporter which has been studied in a fully reconstituted in vitro form, uptake uses a Na+ gradient and not proton gradient to drive uptake. The SiaPQM systems also exhibits unique properties for a secondary transporter in that it cannot catalyse bidirectional transport as the SBP imposes that movement is only in the direction of uptake into the cell.
Bacteria
Bacteria are a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals...
and archaea
Archaea
The Archaea are a group of single-celled microorganisms. A single individual or species from this domain is called an archaeon...
, but not in eukaryotes, that appear to be specific for the uptake of organic acid
Organic acid
An organic acid is an organic compound with acidic properties. The most common organic acids are the carboxylic acids, whose acidity is associated with their carboxyl group –COOH. Sulfonic acids, containing the group –SO2OH, are relatively stronger acids. The relative stability of the conjugate...
s. They are unique in that they utilize a substrate binding protein (SBP) in combination with a secondary transporter
Secondary active transport
In secondary active transport or co-transport, uses energy to transport molecules across a membrane; however, in contrast to primary active transport, there is no direct coupling of ATP; instead, the electrochemical potential difference created by pumping ions out of the cell is used...
.
History
TRAP transporters were discovered in the laboratory of Prof. David J. Kelly at the University of SheffieldUniversity of Sheffield
The University of Sheffield is a research university based in the city of Sheffield in South Yorkshire, England. It is one of the original 'red brick' universities and is a member of the Russell Group of leading research intensive universities...
, UK. His group were working on the mechanism used by the photosynthetic bacterium Rhodobacter
Rhodobacter
In taxonomy, Rhodobacter is a genus of the Rhodobacteraceae.The most famous species of Rhodobacter is Rhodobacter sphaeroides, which is commonly used to express proteins.-External links:...
capsulatus to take up certain dicarboxylic acid
Dicarboxylic acid
Dicarboxylic acids are organic compounds that contain two carboxylic acid functional groups. In molecular formulae for dicarboxylic acids, these groups are often written as HOOC-R-COOH, where R may be an alkyl, alkenyl, alkynyl, or aryl group...
s. They characterised a binding protein component (DctP) of a transporter that recognized these compounds, which they assumed would form part of a typical ABC transporter, but when they sequenced the genes surrounding dctP they found two other genes encoding integral membrane proteins, dctQ and dctM, but no genes encoding components of an ABC transporter. They further showed that uptake of the same dicarboxylates was independent of ATP and that uptake required an electrochemical ion gradient, making this a unique binding protein-dependent secondary transporter.
Since these early studies, it has become clear that TRAP transporters are present in many bacteria
Bacteria
Bacteria are a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals...
and archaea
Archaea
The Archaea are a group of single-celled microorganisms. A single individual or species from this domain is called an archaeon...
, with many bacterial having multiple TRAP transporters, some having over 20 different systems.
Substrates
To date, most substrates for TRAP transporters contain a common feature which is that they are organic acids. This includes C4-dicarboxylates such as succinate, malate and fumarate, keto-acids such as pyruvate and alpha-ketobutyrate and the sugar acid, N-acetyl neuraminic acid (or sialic acid). Other substrates include the compatible solute ectoine and hydroxyectoine and pyroglutamate.Composition
All known TRAP transporters contain 3 protein domains. These are the solute binding protein (the SBP), the small membrane protein domain and the large membrane protein domain. Following the nomenclature for the first characterized TRAP transporter, DctPQM, these subunits are usually named P, Q and M respectively. Around 10% of TRAP transporters have natural genetic fusions between the two membrane protein components, and in the one well studied example of this in the sialic acid specific TRAP transporter from Haemophilus influenzae the fused gene has been named siaQM. The large M subunit is predicted to have 12 transmembrane helices and the small Q subunit to have 4 transmembrane helices and the fused QM proteins are predicted to have 17 transmembrane helices.Mechanism
By using an SBP, TRAP transporters share some similarity to ABC transporters in that the substrate for the transporter is initially recognized outside of the cytoplasmic membrane. In Gram-negative bacteria, the SBP is usually free in the periplasmPeriplasmic space
The periplasmic space or periplasm is a space between the peptidoglycan cell wall and inner membrane of Gram-negative bacteria or the equivalent space outside the inner membrane of Gram-positive bacteria. It may constitute up to 40% of the total cell volume in Gram-negative species, and is...
and expressed at relatively high levels compared to the membrane domains. In Gram positive bacteria and archaea, the SBP is tethered to the cytoplasmic membrane. In both types of systems the SBP binds to substrate, usually with low micromolar affinity, which causes a significant conformation change in the protein, akin to a Venus flytrap closing. The trapped subtrate is then delivered to the membrane domains of the transporter, where the electrochemical ion gradient is somehow exploited to open the SBP, extract the substrate and catalyse its movement across the membrane. For the SiaPQM TRAP transporter which has been studied in a fully reconstituted in vitro form, uptake uses a Na+ gradient and not proton gradient to drive uptake. The SiaPQM systems also exhibits unique properties for a secondary transporter in that it cannot catalyse bidirectional transport as the SBP imposes that movement is only in the direction of uptake into the cell.
Substrate binding protein (SBP)
Following the first structure of a TRAP SBP in 2005, there are now over 10 different structures available. They all have very similar overall structures, with two globular domains linked by a hinge. The substrate binding site is formed by both the domains which enclose the substrate. A highly conserved arginine residue in the TRAP SBPs forms a salt bridge with a carboxylate group on the substrate, which is important for substrate recognition.Membrane subunits
There are currently no structures for the membrane domains of any TRAP transporter. It is not even known which subunit(s) made a direct interaction with the SBP subunit during the transport cycle.External links
- http://www.sheffield.ac.uk/mbb/staff/kelly The lab page of Prof. David Kelly, University of Sheffield, UK
- http://www.york.ac.uk/biology/research/biochemistry-biophysics/gavin-h-thomas/ The lab page of Dr. Gavin Thomas, University of York, UK.