Universal architecture of bacterial chemoreceptor arrays

Abstract

Chemoreceptors are key components of the high-performance signal transduction system that controls bacterial chemotaxis. Chemoreceptors are typically localized in a cluster at the cell pole, where interactions among the receptors in the cluster are thought to contribute to the high sensitivity, wide dynamic range, and precise adaptation of the signaling system. Previous structural and genomic studies have produced conflicting models, however, for the arrangement of the chemoreceptors in the clusters. Using whole-cell electron cryo-tomography, here we show that chemoreceptors of different classes and in many different species representing several major bacterial phyla are all arranged into a highly conserved, 12-nm hexagonal array consistent with the proposed "trimer of dimers" organization. The various observed lengths of the receptors confirm current models for the methylation, flexible bundle, signaling, and linker sub-domains in vivo. Our results suggest that the basic mechanism and function of receptor clustering is universal among bacterial species and was thus conserved during evolution.

Fig. 1.

Characteristic appearance of chemoreceptor arrays in vivo. (A) A 55-nm-thick tomographic slice through a T. maritima cell pole (signaling domain class 44H). Typical features like the inner membrane (IM) and outer membrane (OM) and the enclosed extended periplasm are clearly visible. The arrows indicate the location of the chemoreceptor array within the inner membrane and densely packed cytoplasm. (Scale bar: 100 nm.) (B) A 3-nm-thick tomographic slice through the pole of a T. maritima cell treated with polymyxin B. The reduced cytoplasmic crowding clarifies chemoreceptor features compared with those in untreated cells. (Scale bar: 100 nm.) (C) Enlarged view of the array shown in B: 1, periplasmic receptor domains; 2, inner membrane; 3, cytoplasmic receptor domains; 4, CheA-CheW base plate. The line between the white arrows illustrates how the array heights were measured (from the center of the inner membrane to the center of the CheA-CheW base layer). (Scale bar: 25 nm.)

Fig. 2.

Chemoreceptor arrays in diverse bacteria. Tomographic slices through cells of 11 different species illuminating the varied location but consistent appearance of the arrays. (T. maritima and C. crescentus are not shown, because they are available in Fig. 1 and ref. , respectively.) (Scale bars: 100 nm.)

Fig. 3.

Correlation between observed physical length and predicted sequence length. (A) Organisms possessing a single class of topology type I receptors. Physical length and sequence length were measured as described in Materials and Methods. The sequence length is an average of all topology type I MCPs in the given genome. Vertical bars indicate SD of measurements from different cryo-tomograms and positions within the array, horizontal bars indicate the larger of the SD of the various MCP sequence lengths present in the genome or the estimated uncertainty in the position of the transmembrane region (≈5 residues, see Materials and Methods). The line is a least-squares fit whose slope confirms that the cytoplasmic domains of the receptors form extended coiled coils. Al, A. longum; Ec, E. coli; Hn, H. neapolitanus; Lm, L. monocytogenes; Rs, R. sphaeroides; Tm, T. maritima; and Vc, V. cholera. (B) All topology type I MCPs in all 13 organisms imaged. Each MCP sequence in each organism is represented by a symbol, color- and shape-coded by organism (Right). All the MCPs of a particular organism appear at the same height on the graph (the measured distance between the inner membrane and base plate layer), even though it is not known which were actually imaged. MCPs of particular signaling domain classes cluster closely (3), and are labeled with the color of the label itself (e.g., 34H, 36H) indicating whether the receptors of that class are typical (black), contain extra linkers (blue), or contain both extra linkers and a second HAMP domain (red; see Fig. S1C). The sequence lengths of typical receptors (i.e., those without extra linkers and HAMP domains) are seen to progress steadily with class number across the graph from left to right. Receptors with additional linkers or a second HAMP domain (blue and red labels) appear further to the right than expected because of their extra residues. The Unc label represents an MCP that does not correspond to a known length class, but was given a sequence length measurement as described in Materials and Methods. The graph shows that within the organisms that possess 2 classes of receptors (C. jejuni, H. hepaticus, B. burgdorferi, T. primitia, M. magneticum, and C. crescentus), only one class matches the trend line found in A, suggesting that it was the receptor class forming the arrays.

Fig. 4.

Universally conserved 12-nm hexagonal arrangement of receptor. (A) “Top” view of a chemoreceptor array (black arrows) in T. maritima (signaling domain class 44H). (Scale bar: 50 nm.) (B–K) Top views (Left) and power spectra (Right) of receptor arrays all reveal the same ≈12-nm hexagonal lattice. B, T. maritima; C, A. longum; D, C. jejuni; E, H. hepaticus; F, M. magneticum; G, H. neapolitanus; H, R. sphaeroides; I, E. coli; J, V. cholerae; K, T. primitia. (Scale bars: 25 nm; power spectra enlarged.) (L) Trimer of dimers (blue) fit into the vertices of the hexagonal lattice in a chemoreceptor array (V. cholerae). Six trimers of dimers (red) enclose one hexagon. The spacing from the center of one hexagon to the center of an adjacent one is consistently 12 nm (blue asterisks).