Bacterial Membrane Transport: Secondary Transport Proteins


Membrane transport proteins enable cells to accumulate nutrients, extrude unwanted by‐products and maintain cytoplasmic content of protons and salts conducive to growth and development. Bacterial secondary active transporters for which crystal structures have recently been determined produced major breakthroughs in the study of transporters, opening the field to diverse disciplines such as structural biology, biochemistry, biophysics, molecular biology and computation. The insights derived from these structures are particularly important in light of the fact that many of the structurally deciphered bacterial transporters have eukaryotic orthologues that play crucial roles in health and disease and are important drug targets.

Key Concepts

  • Transport of solutes across bacterial membrane.
  • The different transport proteins.
  • Primary and secondary active transport in bacteria.
  • Possible evolution of transporters.
  • Crystal structure of transporters, a breakthrough in transport research.

Keywords: secondary active transport; active transport; membrane proteins; transporters; H+ coupled transporters; Na+ coupled transporters

Figure 1. Classification of transporter proteins. The four recognised classes of transporter proteins are shown: (1) channels and pores; (2) group translocators; (3) primary transporters; (4) secondary transporters. This article emphasises secondary transporters for which atomic structures have recently been determined. ETC, electron transport chain; PTS, phosphotransferase system; S(number), different substrates.
Figure 2. Secondary structure (schematic topology model) and crystal structure of NhaA Na+/H+ antiporter. (a) The12‐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 TM segments are labelled with Roman numerals. N and C indicate the N‐ and C‐ termini. Cytoplasmic and periplasmic funnels are marked by a 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 TM segments are labelled with Roman numerals and coloured from the N‐terminus in purple to the C‐terminus in pink. The lactose‐substrate analogue TDG (b‐d‐galactopyranosyl‐1 thio‐b‐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 position of the sugars is based on biochemical observations.
Figure 4. Topology models of secondary transporters LacY, LeuT and NhaA with emphasis on intramolecular symmetry. The secondary structure of each secondary transporter 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 TM segments 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–VI) the C‐terminus domain (red, TMs 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., ), TMs III–V (light blue triangle background) and X–XII (light pink inverted triangle background) are symmetrically related and exhibit inverted topology. The TM 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. Alternating‐access mechanisms. The major conformations of the alternating‐access mechanism observed in (a) rocker‐switch and (b) rocking‐bundle proteins. The substrate (red sphere) binds between two domains, catalysing the rearrangement of the protein around the central substrate‐binding site. In rocker‐switch proteins, two structurally similar domains rock to afford alternating accessibility. In rocking‐bundle proteins, one structurally dissimilar domain rearranges against a less labile domain to afford accessibility. Transport in rocker‐switch and rocking‐bundle proteins further involves local, substrate‐induced gating rearrangements by helices located in either one or both of the domains (depicted here as curved lines). (c) The elevator mechanism. The substrate (red sphere) binds to one of the domains, which moves against a structurally dissimilar immobile domain to physically translocate the substrate to the other side of a fixed barrier. Substrate binding and release in each state are likely facilitated by local gating transitions, primarily in the moving domain (gates are depicted here as curved lines). Adapted from Drew and Boudker .


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Further Reading

Bai X , Moraes TF and Reithmeier RAF (2018) Structural biology of solute carrier (SLC) membrane transport proteins. Molecular Membrane Biology. DOI: 10.1080/09687688.2018.1448123.

Forrest LR and Rudnick G (2009) The rocking bundle: a mechanism for ion‐coupled solute flux by symmetrical transporters. Physiology (Bethesda) 24: 377–386. DOI: 10.1152/physiol.00030.2009.

Ito M , Morino M and Krulwich TA (2017) Mrp antiporters have important roles in diverse bacteria and archaea. Frontiers in Microbiology 8: 2325. DOI: 10.3389/fmicb.2017.02325.

Kristensen AS , Andersen J , Jørgensen TN , et al. (2011) SLC6 neurotransmitter transporters: structure, function, and regulation. Pharmacological Reviews 63: 585–640.

Kunji ER , Aleksandrova A , King MS , et al. (2016) The transport mechanism of the mitochondrial ADP/ATP carrier. Biochimica et Biophysica Acta 1863: 2379–2393. DOI: 10.1016/j.bbamcr.2016.03.015.

Masi M , Réfregiers M , Pos KM and Pagès JM (2017) Mechanisms of envelope permeability and antibiotic influx and efflux in Gram‐negative bacteria. Nature Microbiology 2: 17001. DOI: 10.1038/nmicrobiol.2017.1.

Padan E (2014) Functional and structural dynamics of NhaA, a prototype for Na(+) and H(+) antiporters, which are responsible for Na(+) and H(+) homeostasis in cells. Biochimica et Biophysica Acta 1837: 1047–1062. DOI: 10.1016/j.bbabio.2013.12.007.

Penmatsa A and Gouaux E (2014) How LeuT shapes our understanding of the mechanisms of sodium‐coupled neurotransmitter transporters. The Journal of Physiology 592 (5): 863–869.

Preiss L , Hicks DB , Suzuki S , Meier T and Krulwich TA (2015) Alkaliphilic bacteria with impact on industrial applications, concepts of early life forms, and bioenergetics of ATP synthesis. Frontiers in Bioengineering and Biotechnology 3: 75. DOI: 10.3389/fbioe.2015.00075.

Zomot E , Yardeni EH , Vargiu AV , et al. (2018) A new critical conformational determinant of multidrug efflux by an MFS transporter. Journal of Molecular Biology 430: 1368–1385. DOI: 10.1016/j.jmb.2018.02.026.

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Padan, Etana(Feb 2019) Bacterial Membrane Transport: Secondary Transport Proteins. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0003743.pub3]