Bacterial Membrane Transport: Superfamilies of Transport Proteins

Abstract

The bacterial transport systems enable bacteria to accumulate needed nutrients, extrude unwanted by products and maintain cytoplasmic content of protons and salts conducive to growth and development. Two most widely spread superfamilies of transporters are the ion‐coupled systems that take part in chemiosmotic circuits, and the ABC solute ATPases (adenosine triphosphatases), whose operation is linked to ATP hydrolysis. The crystal structure of several bacterial transporters has recently been determined, a major breakthrough in the research of transporters. It opened the field to a combined study of structure, function and computation. Several of the structurally deciphered bacterial transporters have eukaryotic orthologues including neurotransmitter transporters that play major roles in health and disease and are major drug targets. Hence, the bacterial transport systems are important both for elucidating the mechanism of transport as well as drug design.

Key concepts:

  • Crystal structures are essential for understanding the mechanism of transport.

  • Topology model of transporters obtained from the primary amino acid sequence, the positive‐inside rule and experimental data have been validated by the crystal structure.

  • Primary transporters utilize external source of energy to drive active transport.

  • The secondary transporters utilize the energy stored in a pre‐existing gradient to drive transport.

  • The MFS, major facilitator superfamily, encompasses the largest number of evolutionary related most diverse group of secondary transporters and the extensively studied LacY and GlpT with their crystal structures are educative examples.

  • Na+/H+ antiporters are essential for sodium and pH homeostasis in all cells and the most studied Escherichia coli NhaA with its crystal structure is an educative example.

  • The sodium‐coupled secondary transporter LeuT is a bacterial homologue of human neurotransmitters transporters and therefore its crystal structure is an essential step in drug design.

  • The alternating access model is the mechanism of activity of secondary transporters.

  • The molecules of many secondary transporters exhibit internal symmetry that implies a unique evolution.

  • The internal symmetry of secondary transporters with the inverted repeats and the interrupted helices in the middle of the membrane is the structural basis of the activity mechanism.

Keywords: ion‐coupled transporters; secondary transporters; major facilitator superfamily; ABC solute ATPase superfamily; transporter crystal structure

Figure 1.

Classification of transporting proteins. The four recognized classes of transporter proteins (1, channels and pores; 2, group translocators; 3, primary transporters; 4, secondary transporters) are shown. This article emphasizes secondary transporters for which atomic structure has recently been determined. ETC, electron transport chain and PTS, phosphotransferase system.

Figure 2.

Secondary structure (schematic topology model) and crystal structure of NhaA Na+/H+ antiporter. (a) The 12‐helix topology model of many secondary transporters is illustrated using NhaA as the example. The topology model of NhaA is based on the crystal structure (Hunte et al., ). The distribution of positive (blue circled) and negative (red circled) residues in loops is consistent with the ‘positive‐inside’ rule discussed in the text. (b) Ribbon representation of the crystal structure of NhaA viewed parallel to the membrane (broken line). The 12 TMSs are labelled with Roman numerals. N and C indicate the N‐ and C‐temini. Cytoplasmic and periplasmic funnels are marked by continuous black line; c and p denote helices in the cytoplasmic or periplasmic sides, respectively.

Figure 3.

The crystal structure of LacY. (a) Ribbon representation of LacY viewed parallel to the membrane. The 12 TMSs are labelled with Roman numerals and coloured from the N‐terminus in purple to the C‐terminus in pink. The lactose‐substrate analogue TDG (β‐d‐galactopyranosyl‐1thio‐β‐d‐galactopyranoside) is shown in black spheres. (b) Ribbon representation of LacY viewed along the membrane normal from the cytoplasmic side. For clarity the loops are omitted. The figure was reproduced with permission from Abramson et al..

Figure 4.

Topology models of secondary transporters, LacY, LeuT and NhaA with emphasis on intramolecular symmetry. The secondary structure of the secondary transporters is schematically represented. (a) In LacY (Abramson et al., ), the large hydrophilic cavity is designated by a green triangle with TDG the lactose analogue. The TMSs are shown in rectangles and designated in Roman numerals. h1–4 are small helices in the cytoplasmic side of the membrane. The dual symmetry between the N‐terminus domain (blue, TMS I–IV) and the C‐terminus domain (red, TMSs VII–XII) can be superimposed on each other. (b) In LeuT (Yamashita et al., ), TMSs I–V (light blue rectangle background) are symmetrically related to TMSs VI–X (light pink inverted rectangle background) following inversion by pseudo 2‐fold symmetry axis located in the plane of the membrane. The disrupted helices I and VI with the respective small helices (Ia and Ib and VIa VIb) are shown with the extended chains and the active site (L) in the middle of the membrane. IL1 and 5 are small helices at the cytoplasmic side and EL2, 3, 4a and 4b at the periplasmic side of the membrane. The arrows depict a β sheet. (c) In NhaA (Hunte et al., ), TMSs III–V (light blue triangle background) and X–XII (light pink inverted triangle background) are symmetrically related and exhibit inverted topology. The TMSs assembly of the interrupted helices IV and XI, the extended chains and the putative Na+‐binding site are shown. The arrows depict a β sheet.

Figure 5.

Gate and rocker switches. Schematic representation of the transport mechanism of secondary transporters. The crystal structure of SGLT1 (Faham et al., ) suggests that rotation of two broken helices permit alternating access of the substrates to the opposing sides of the membranes. The crystal structure of LacY (Abramson et al., ) and GlpT (Huang et al., ) suggests the rocker switches which are thought to function by the rotation of two domains towards one another, alternatively exposing the substrate‐binding site to each side of the membrane.

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Further Reading

Law CJ, Maloney PC and Wang DN (2008) Ins and outs of major facilitator superfamily antiporters. Annual Review of Microbiology 62: 289–305.

Murakami S (2008) Multidrug efflux transporter, AcrB – the pumping mechanism. Current Opinion of Structural Biology 18: 459–465.

Nikaido H and Takatsuka Y (2009) Mechanisms of RND multidrug efflux pumps. Biochimica et Biophysica Acta 1794: 769–781.

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Padan, Etana(Sep 2009) Bacterial Membrane Transport: Superfamilies of Transport Proteins. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0003743.pub2]