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Abstract
The bacterial strategy of chemotaxis relies on temporal comparisons of chemical concentrations, where the probability of maintaining the current direction of swimming is modulated by changes in stimulation experienced during the recent past. A short-term memory required for such comparisons is provided by the adaptation system, which operates through the activity-dependent methylation of chemotaxis receptors. Previous theoretical studies have suggested that efficient navigation in gradients requires a well-defined adaptation rate, because the memory time scale needs to match the duration of straight runs made by bacteria. Here we demonstrate that the chemotaxis pathway of Escherichia coli does indeed exhibit a universal relation between the response magnitude and adaptation time which does not depend on the type of chemical ligand. Our results suggest that this alignment of adaptation rates for different ligands is achieved through cooperative interactions among chemoreceptors rather than through fine-tuning of methylation rates for individual receptors. This observation illustrates a yet-unrecognized function of receptor clustering in bacterial chemotaxis.
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Ghosh SK, Kundu T, Sain A. From chemosensing in microorganisms to practical biosensors. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012; 86:051910. [PMID: 23214817 DOI: 10.1103/physreve.86.051910] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Revised: 09/24/2012] [Indexed: 06/01/2023]
Abstract
Microorganisms like bacteria can sense concentrations of chemoattractants in their medium very accurately. They achieve this through interaction between the receptors on their cell surfaces and chemoattractant molecules (like sugar). Physical processes like diffusion set some limits on the accuracy of detection, which was discussed by Berg and Purcell in the late seventies. We re-examine their work in order to assess what insight it may offer for making efficient, practical biosensors. We model the functioning of a typical biosensor as a reaction-diffusion process in a confined geometry. Using available data first we characterize the system by estimating the kinetic constants for the binding and unbinding reactions between the chemoattractants and the receptors. Then we compute the binding flux for this system, which Berg and Purcell had discussed. Unlike in microorganisms where the interval between successive measurements determines the efficiency of the nutrient searching process, it turns out that biosensors depend on long time properties like signal saturation time, which we study in detail. We also develop a mean field description of the kinetics of the system.
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Affiliation(s)
- Surya K Ghosh
- Department of Physics, Indian Institute of Technology, Bombay, Powai, Mumbai 400 076, India
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Li Z, Jensen GJ. Electron cryotomography: a new view into microbial ultrastructure. Curr Opin Microbiol 2009; 12:333-40. [PMID: 19427259 PMCID: PMC2747746 DOI: 10.1016/j.mib.2009.03.007] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2009] [Revised: 03/20/2009] [Accepted: 03/25/2009] [Indexed: 10/20/2022]
Abstract
Electron cryotomography (ECT) is an emerging technology that allows thin samples such as small bacterial cells to be imaged in 3D in a nearly native state to 'molecular' (approximately 4nm) resolution. As such, ECT is beginning to deliver long-awaited insight into the positions and structures of cytoskeletal filaments, cell wall elements, motility machines, chemoreceptor arrays, internal compartments, and other ultrastructures. Here we briefly explain ECT, review its recent contributions to microbiology, and conclude with a discussion of future prospects.
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Affiliation(s)
- Zhuo Li
- Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
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Shimizu TS, Le Novère N. Looking inside the box: bacterial transistor arrays. Mol Microbiol 2008; 69:5-9. [PMID: 18484950 DOI: 10.1111/j.1365-2958.2008.06240.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
One often compares cells to computers, and signalling proteins to transistors. Location and wiring of those molecular transistors is paramount in defining the function of the subcellular chips. The bacterial chemotactic sensing apparatus is a large, stable assembly consisting of thousands of receptors, signal transducing kinases and linking proteins, and is responsible for the motile response of the bacterium to environmental signals, whether chemical, mechanical, or thermal. Because of its rich functional repertoire despite its relative simplicity, this chemosome has attracted much attention from both experimentalists and theoreticians, and the bacterial chemotaxis response becoming a benchmark in Systems Biology. Structural and functional models of the chemotactic device have been developed, often based on particular assumptions regarding the topology of the receptor lattice. In this issue of Molecular Microbiology, Briegel et al. provide a detailed view of the receptor arrangement, unravelling the wiring of the molecular signal processors.
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Affiliation(s)
- Thomas S Shimizu
- Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Ave, Cambridge, MA 02138, USA
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Briegel A, Ding HJ, Li Z, Werner J, Gitai Z, Dias DP, Jensen RB, Jensen GJ. Location and architecture of the Caulobacter crescentus chemoreceptor array. Mol Microbiol 2008; 69:30-41. [PMID: 18363791 DOI: 10.1111/j.1365-2958.2008.06219.x] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A new method for recording both fluorescence and cryo-EM images of small bacterial cells was developed and used to identify chemoreceptor arrays in cryotomograms of intact Caulobacter crescentus cells. We show that in wild-type cells preserved in a near-native state, the chemoreceptors are hexagonally packed with a lattice spacing of 12 nm, just a few tens of nanometers away from the flagellar motor that they control. The arrays were always found on the convex side of the cell, further demonstrating that Caulobacter cells maintain dorsal/ventral as well as anterior/posterior asymmetry. Placing the known crystal structure of a trimer of receptor dimers at each vertex of the lattice accounts well for the density and agrees with other constraints. Based on this model for the arrangement of receptors, there are between one and two thousand receptors per array.
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Affiliation(s)
- Ariane Briegel
- Division of Biology, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA
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Fujinami S, Sato T, Trimmer JS, Spiller BW, Clapham DE, Krulwich TA, Kawagishi I, Ito M. The voltage-gated Na+ channel NaVBP co-localizes with methyl-accepting chemotaxis protein at cell poles of alkaliphilic Bacillus pseudofirmus OF4. MICROBIOLOGY-SGM 2008; 153:4027-4038. [PMID: 18048917 DOI: 10.1099/mic.0.2007/012070-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Na(V)BP, found in alkaliphilic Bacillus pseudofirmus OF4, is a member of the bacterial voltage-gated Na(+) channel superfamily. The alkaliphile requires Na(V)BP for normal chemotaxis responses and for optimal pH homeostasis during a shift to alkaline conditions at suboptimally low Na(+) concentrations. We hypothesized that interaction of Na(V)BP with one or more other proteins in vivo, specifically methyl-accepting chemotaxis proteins (MCPs), is involved in activation of the channel under the pH conditions that exist in the extremophile and could underpin its role in chemotaxis; MCPs transduce chemotactic signals and generally localize to cell poles of rod-shaped cells. Here, immunofluorescence microscopy and fluorescent protein fusion studies showed that an alkaliphile protein (designated McpX) that cross-reacts with antibodies raised against Bacillus subtilis McpB co-localizes with Na(V)BP at the cell poles of B. pseudofirmus OF4. In a mutant in which Na(V)BP-encoding ncbA is deleted, the content of McpX was close to the wild-type level but McpX was significantly delocalized. A mutant of B. pseudofirmus OF4 was constructed in which cheAW expression was disrupted to assess whether this mutation impaired polar localization of McpX, as expected from studies in Escherichia coli and Salmonella, and, if so, whether Na(V)BP would be similarly affected. Polar localization of both McpX and Na(V)BP was decreased in the cheAW mutant. The results suggest interactions between McpX and Na(V)BP that affect their co-localization. The inverse chemotaxis phenotype of ncbA mutants may result in part from MCP delocalization.
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Affiliation(s)
- Shun Fujinami
- Graduate School of Life Sciences, Toyo University, Oura-gun, Gunma 374-0193, Japan
| | - Takako Sato
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima, Yokosuka 237-0061, Japan
| | - James S Trimmer
- Department of Pharmacology, School of Medicine, University of California, Davis, CA 95616, USA
| | - Benjamin W Spiller
- Howard Hughes Medical Institute, Department of Cardiovascular Research, Children's Hospital and Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - David E Clapham
- Howard Hughes Medical Institute, Department of Cardiovascular Research, Children's Hospital and Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Terry A Krulwich
- Department of Pharmacology and Systems Therapeutics, Mount Sinai School of Medicine, NY 10029, USA
| | - Ikuro Kawagishi
- Department of Frontier Bioscience, Faculty of Engineering, Hosei University 3-7-2 Kajino-cho, Koganei, Tokyo 184-8584, Japan
| | - Masahiro Ito
- Graduate School of Life Sciences, Toyo University, Oura-gun, Gunma 374-0193, Japan
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Li Y, Hu Y, Fu W, Xia B, Jin C. Solution structure of the bacterial chemotaxis adaptor protein CheW from Escherichia coli. Biochem Biophys Res Commun 2007; 360:863-7. [PMID: 17631272 DOI: 10.1016/j.bbrc.2007.06.146] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2007] [Accepted: 06/28/2007] [Indexed: 10/23/2022]
Abstract
The bacterial chemotaxis adaptor protein CheW physically links the chemoreceptors (MCPs) and the histidine kinase CheA. Extensive investigations using bacterium Escherichia coli have established the central role of CheW in the MCP-modulated activation of CheA. Here we report the solution structure of CheW from E. coli determined by NMR spectroscopy. The results show that E. coli CheW shares an overall fold with previously reported structure of CheW from Thermotoga maritima, whereas local conformational deviations are observed. In particular, the C-terminal alpha-helix is considerably longer in E. coli CheW and appears to shrink the active binding pocket with CheA. Our study provides the structural basis for further investigations in E. coli chemotaxis.
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Affiliation(s)
- You Li
- Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing 100871, China
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Borbat PP, Freed JH. Measuring distances by pulsed dipolar ESR spectroscopy: spin-labeled histidine kinases. Methods Enzymol 2007; 423:52-116. [PMID: 17609127 DOI: 10.1016/s0076-6879(07)23003-4] [Citation(s) in RCA: 118] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Applications of dipolar ESR spectroscopy to structural biology are rapidly expanding, and it has become a useful method that is aimed at resolving protein structure and functional mechanisms. The method of pulsed dipolar ESR spectroscopy (PDS) is outlined in the first half of the chapter, and it illustrates the simplicity and potential of this developing technology with applications to various biological systems. A more detailed description is presented of the implementation of PDS to reconstruct the ternary structure of a large dimeric protein complex from Thermotoga maritima, formed by the histidine kinase CheA and the coupling protein CheW. This protein complex is a building block of an extensive array composed of coupled supramolecular structures assembled from CheA/CheW proteins and transmembrane signaling chemoreceptors, which make up a sensor that is key to controlling the motility in bacterial chemotaxis. The reconstruction of the CheA/CheW complex has employed several techniques, including X-ray crystallography and pulsed ESR. Emphasis is on the role of PDS, which is part of a larger effort to reconstruct the entire signaling complex, including chemoreceptor, by means of PDS structural mapping. In order to precisely establish the mode of coupling of CheW to CheA and to globally map the complex, approximately 70 distances have already been determined and processed into molecular coordinates by readily available methods of distance geometry constraints.
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Affiliation(s)
- Peter P Borbat
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
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