Fig 1.
Number of MCP genes in 43 enterobacterial genomes with and without CheV.
Each dot represents a genome. The dashed lines indicate the average number of MCPs for each distribution.
Fig 2.
Analysis of patterns in sequence conservation suggests interaction between CheVRR domain and CheA-P1.
A) Comparison between sequence logos of CheAP1 from genomes with and without CheV. The CheAP1 active site His48 (black dot) and the only different position between the two sets Gly55 (red dot) are marked. B) Comparison between sequence logos of CheY and the CheVRR domain. Positions that are conserved in both sets are marked (blue dots for solvent exposed positions (10 25 57 65 68 72 82 83 107 116) and blue stars for buried positions (13 18 60 61 63 64 94 103 106 109 111)). C) Cartoon representation of the CheY (white) and CheAP1 (blue) [35]. Solvent exposed positions conserved in CheY and CheVRR datasets localize to the protein interface region (blue spheres). The single position that is different between the sets of CheAP1 with and without CheV, Gly55 (red sphere), lays in the C-terminal part of the second α-helix involved in the interaction protein region that also contains the active site His48 (white CPK representation).
Fig 3.
Clusters of orthologous groups of chemoreceptors from 43 enterobacterial genomes.
Each node represents a chemoreceptor sequence. MCPs from E. coli (blue) and S. enterica (red) are labeled by name and a corresponding COG number. See S1 Dataset and Materials and Methods for details.
Table 1.
COG assignment of chemoreceptors in E. coli and S. enterica.
Fig 4.
Co-Evolution of CheV and McpC orthologs.
Phylogenetic profile shows the correlation of presence and absence of CheV (orange) and McpC orthologs (black). Left, 16S phylogenetic tree of the organisms used in this study.
Fig 5.
Changes in conservation patterns in chemoreceptors.
Comparison of the sequence logo from sequences in COG1, COG2 and COG6 of the 20 amino-acid region around the Gly278 (A) and Ser406 (B), both marked with a star. The sequence is inverted in the B panel (right to left) to depict the difference in helix where the two positions are found. Gly278 is found in the descending helix and S406 is found in the ascending helix of the receptor. C) Cartoon representation based on the crystal structure (PDB code: 1QU7) [56] of the chemoreceptor signaling domain (white ribbons) and the methylation sites (blue spheres) with mapping of the 10 amino-acid region (red ribbons) around the two positions (yellow spheres) with significantly different pattern in sequences from COG2 compared to sequences from COG1 and COG6.
Fig 6.
Analysis of the sequence conservation between CheW and CheVW.
A) Sequence logo of CheVW (top logo) and CheW (bottom logo). Positions conserved in both groups (20, 22, 24, 25, 27, 30, 35, 38, 39, 49, 57, 62, 67, 70, 71, 102, 105, 111, 132, 148, 151) (blue circles) and position conserved within each groups (28, 32, 33, 34, 36, 37, 41, 42, 50, 51, 54, 58, 61, 66, 68, 86, 89, 91, 92,98, 99, 100, 101, 104, 108, 110, 116, 133, 135, 142, 144, 145, 147, 149, 150) (red stars) are highlighted. Numbers for E. coli CheW. Proposed CheW regions for binding CheA [24, 58] and chemoreceptors [24, 50] are underlined in dashed and solid lines, correspondingly. B) Mapping of marked positions onto E. coli CheW NMR model [57] in ribbons (top) and accessible surface area (bottom).
Fig 7.
Schematic models of possible integration of CheV into the chemoreceptor array.
Top-view of the arrangement of the array components showing the known and proposed interaction sites between chemoreceptor trimers (blue), CheA (yellow) and CheW (red) [36, 37], as well as potential locations of CheV (green). Chemoreceptors that interact with CheV are marked with asterisks. A) CheV occupies the proposed empty ring and does not interact with CheAP5 or CheW. B) CheV might be incorporated with CheW and CheAP5 into the hexagonal ring.