Title Deciphering chemotaxis pathways using cross species comparisons Permalink

Background: Chemotaxis is the process by which motile bacteria sense their chemical environment and move towards more favourable conditions. Escherichia coli utilises a single sensory pathway, but little is known about signalling pathways in species with more complex systems. Results: To investigate whether chemotaxis pathways in other bacteria follow the E. coli paradigm, we analysed 206 species encoding at least 1 homologue of each of the 5 core chemotaxis proteins (CheA, CheB, CheR, CheW and CheY). 61 species encode more than one of all of these 5 proteins, suggesting they have multiple chemotaxis pathways. Operon information is not available for most bacteria, so we developed a novel statistical approach to cluster che genes into putative operons. Using operon-based models, we reconstructed putative chemotaxis pathways for all 206 species. We show that cheA-cheW and cheR-cheB have strong preferences to occur in the same operon as two-gene blocks, which may reflect a functional requirement for co-transcription. However, other che genes, most notably cheY, are more dispersed on the genome. Comparison of our operons with shuffled equivalents demonstrates that specific patterns of genomic location may be a determining factor for the observed in vivo chemotaxis pathways. We then examined the chemotaxis pathways of Rhodobacter sphaeroides. Here, the PpfA protein is known to be critical for correct partitioning of proteins in the cytoplasmically-localised pathway. We found ppfA in che operons of many species, suggesting that partitioning of cytoplasmic Che protein clusters is common. We also examined the apparently non-typical chemotaxis components, CheA3, CheA4 and CheY6. We found that though variants of CheA proteins are rare, the CheY6 variant may be a common type of CheY, with a significantly disordered C-terminal region which may be functionally significant. Conclusions: We find that many bacterial species potentially have multiple chemotaxis pathways, with grouping of che genes into operons likely to be a major factor in keeping signalling pathways distinct. Gene order is highly conserved with cheA-cheW and cheR-cheB blocks, perhaps reflecting functional linkage. CheY behaves differently to other Che proteins, both in its genomic location and its putative protein interactions, which should be considered when modelling chemotaxis pathways. Background Chemotaxis is the process by which motile bacteria move towards more favourable conditions by sensing their chemical environment. It is of significant medical interest, as many pathogenic bacteria depend on chemotaxis and motility to invade their hosts. For example, Helicobacter pylori, which colonizes the mucus lining of the stomach, has a chemotactic response to gastric mucin [1]. Biofilm development depends on chemotaxis, and their formation in the lungs of cystic fibrosis patients and on medical implants can have serious consequences [2,3]. Chemotaxis is also essential for symbiotic associations of bacteria, for example the colonization of wheat roots by the nitrogen fixing bacterium Azospirillum brasilense [4]. In addition, chemotaxis is the canonical system used to study signalling pathways in systems biology, due to its relative simplicity for modelling purposes, and the ease with which it can be studied experimentally. A detailed, quantitative understanding of chemotaxis pathways would pave the way for the study of other, more complex signalling systems. * Correspondence: deane@stats.ox. ac.uk † Contributed equally Department of Statistics, University of Oxford, Oxford, UK Hamer et al. BMC Systems Biology 2010, 4:3 http://www.biomedcentral. com/1752-0509/4/3 © 2010 Hamer et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Escherichia coli chemotaxis has been extensively studied and is known to use a single 2-component histidine protein kinase-dependent signal transduction pathway consisting of the Che proteins A, B, R, W, Y and Z [5]. Any reduction in chemoattractant or increase in chemorepellent in the periplasm is sensed by membranespanning methyl-accepting chemotaxis receptors (MCPs) which are linked via CheW to a dimeric histidine protein kinase, CheA, to form a large, polar, quaternary protein complex. On activation, the monomers of CheA transautophosphorylate and the phosphoryl group is then transferred to one of two response regulators, either CheY or CheB. Phosphorylated CheY is able to diffuse and bind to the FliM component of the flagellar motor, resulting in a change in motor rotation from counter-clockwise to clockwise. This causes a switch from smooth swimming to tumbling, allowing the bacteria to change direction. The motor has a baseline stochastic switching frequency in the absence of any stimulation, but binding of phosphorylated CheY increases this rate. CheY is dephosphorylated by CheZ, which terminates the signal. The constitutively active methyltransferase CheR transfers methyl groups to the MCPs, increasing their ability to activate CheA. Phosphorylated CheB competes with CheR, by removing methyl groups from the MCPs, so reducing their ability to activate CheA. This decreases the rate of CheA transphosphorylation and so resets the rate of direction changing to pre-stimulus levels, resulting in adaptation. A schematic of a generalised chemotaxis pathway, consisting of the core chemotaxis proteins (CheA, CheB, CheR, CheW and CheY) is shown in Figure 1. CheZ is not included here as many species do not have a CheZ homologue. E. coli chemotaxis is a relatively simple biological system which is conserved across many bacterial and archaeal species, and has inspired the development of numerous mathematical models of chemotaxis [6,7]. However, some bacteria have multiple homologues of the Che proteins which probably form more than one chemotaxis pathway. Rhodobacter sphaeroides is a well studied example of a species with multiple chemotaxis pathways. It has several homologues of E. coli CheA, B, R, W and Y proteins but none of CheZ. There are three operons encoding the majority of the chemotaxis genes (CheOp1, CheOp2 and CheOp3), as well as other unlinked loci encoding chemoreceptors and CheY homologues [8]. CheOp2 and CheOp3 are essential for chemotaxis in the laboratory, while the physiological role of CheOp1 has not yet been established [9-13]. Of the 13 chemoreceptor homologues, 4 lack transmembrane regions and are referred to as transducer-like proteins (Tlps). These are cytoplasmic and sense the metabolic state of the cell rather than the exterior environment. Studies have shown the presence of two discrete protein clusters in the cell, with the proteins encoded by CheOp2 localising with the MCPs at the cell pole, and proteins encoded by CheOp3 localising with cytoplasmic Tlps [14]. Chemotaxis requires signals from both these clusters to be integrated to produce a response at the single flagellar motor. Exactly how these clusters are formed and targeted to the correct position Figure 1 Schematic representation of the core chemotaxis pathway. Reduction in chemoattractant or increase in chemorepellant is sensed by membrane-bound methyl-accepting chemotaxis receptors. This activates CheA and triggers transphosphorylation. The phosphoryl group is then transferred to either CheY or CheB. Phosphorylated CheY is able to diffuse and bind to the FliM component of the flagellar motor, resulting in a change in motor rotation from counter-clockwise to clockwise. This causes a switch from smooth swimming to tumbling and hence a change in swimming direction. Phosphorylated CheB competes with the constitutively active methyltransferase CheR, causing demethylation of the receptors, which reduces their ability to activate CheA. This resets the rate of direction changing to prestimulus levels, a process known as adaptation. Hamer et al. BMC Systems Biology 2010, 4:3 http://www.biomedcentral. com/1752-0509/4/3 Page 2 of 19