Tripartite ATP-independent Periplasmic Transporter
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Tripartite ATP-independent periplasmic transporters (TRAP transporters) are a large family of solute transporters found in
bacteria Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were am ...
and archaea, but not in
eukaryotes Eukaryotes () are organisms whose cells have a nucleus. All animals, plants, fungi, and many unicellular organisms, are Eukaryotes. They belong to the group of organisms Eukaryota or Eukarya, which is one of the three domains of life. Bact ...
, that appear to be specific for the uptake of
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 ...
s or related molecules containing a carboxylate or sulfonate group. They are unique in that they utilize a substrate binding protein (SBP) in combination with a secondary transporter.


History

TRAP transporters were discovered in the laboratory of Prof. David J. Kelly at the
University of Sheffield The University of Sheffield (informally Sheffield University or TUOS) is a public university, public research university in Sheffield, South Yorkshire, England. Its history traces back to the foundation of Sheffield Medical School in 1828, Firth C ...
, UK. His group were working on the mechanism used by the photosynthetic bacterium ''
Rhodobacter capsulatus ''Rhodobacter capsulatus'' is a species of purple bacteria, a group of bacteria that can obtain energy through photosynthesis. Its name is derived from the Latin adjective "capsulatus" ("with a chest", "encapsulated"), itself derived Latin noun " ...
'' to take up certain
dicarboxylic acid In organic chemistry, a dicarboxylic acid is an organic compound containing two carboxyl groups (). The general molecular formula for dicarboxylic acids can be written as , where R can be aliphatic or aromatic. In general, dicarboxylic acids show ...
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 The ATP-binding cassette transporters (ABC transporters) are a transport system superfamily that is one of the largest and possibly one of the oldest gene families. It is represented in all extant phyla, from prokaryotes to humans. ABC transpo ...
, 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 (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were am ...
and archaea, 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 Succinic acid () is a dicarboxylic acid with the chemical formula (CH2)2(CO2H)2. The name derives from Latin ''succinum'', meaning amber. In living organisms, succinic acid takes the form of an anion, succinate, which has multiple biological ro ...
,
malate Malic acid is an organic compound with the molecular formula . It is a dicarboxylic acid that is made by all living organisms, contributes to the sour taste of fruits, and is used as a food additive. Malic acid has two stereoisomeric forms ...
and
fumarate Fumaric acid is an organic compound with the formula HO2CCH=CHCO2H. A white solid, fumaric acid occurs widely in nature. It has a fruit-like taste and has been used as a food additive. Its E number is E297. The salts and esters are known as f ...
, keto-acids such as
pyruvate Pyruvic acid (CH3COCOOH) is the simplest of the alpha-keto acids, with a carboxylic acid and a ketone functional group. Pyruvate, the conjugate base, CH3COCOO−, is an intermediate in several metabolic pathways throughout the cell. Pyruvic aci ...
and alpha-ketobutyrate and the sugar acid, ''N''-acetyl neuraminic acid (or
sialic acid Sialic acids are a class of alpha-keto acid sugars with a nine-carbon backbone. The term "sialic acid" (from the Greek for saliva, - ''síalon'') was first introduced by Swedish biochemist Gunnar Blix in 1952. The most common member of this ...
). 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''.


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 Gram-negative bacteria are bacteria that do not retain the crystal violet stain used in the Gram staining method of bacterial differentiation. They are characterized by their cell envelopes, which are composed of a thin peptidoglycan cell wa ...
, the SBP is usually free in the
periplasm The periplasm is a concentrated gel-like matrix in the space between the inner cytoplasmic membrane and the bacterial outer membrane called the ''periplasmic space'' in gram-negative bacteria. Using cryo-electron microscopy it has been found tha ...
and expressed at relatively high levels compared to the membrane domains. In
Gram positive bacteria In bacteriology, gram-positive bacteria are bacteria that give a positive result in the Gram stain test, which is traditionally used to quickly classify bacteria into two broad categories according to their type of cell wall. Gram-positive bacte ...
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 substrate 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 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.


Structure


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 Arginine is the amino acid with the formula (H2N)(HN)CN(H)(CH2)3CH(NH2)CO2H. The molecule features a guanidino group appended to a standard amino acid framework. At physiological pH, the carboxylic acid is deprotonated (−CO2−) and both the a ...
residue in the TRAP SBPs forms a salt bridge with a carboxylate group on the substrate, which is important for substrate recognition.


Membrane subunits

The first structure of the membrane domains was solved for the sialic acid transporter from ''Haemophilus influenzae''. Confirmed by another TRAP transporter structure, the structures reveal a monomeric elevator-like transport mechanism for TRAP transporter. While the larger M-subunit forms the stator- and elevator-domain, the Q-subunit seems to enlarge and stabilize the stator-domain of the monomeric transporter. Current models suggest a binding of the SBP with both functional parts of the transporter, the stator- and elevator domain, and show a matched conformational coupling between the inward-open and outward-open state of the membrane subunits to the opened and closed state of the SBP.


References

{{reflist, 2


External links



The lab page of Prof. David Kelly, University of Sheffield, UK

The lab page of Dr. Gavin Thomas, University of York, UK. Transport proteins