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Koler M, Parkinson JS, Vaknin A. Signal integration in chemoreceptor complexes. Proc Natl Acad Sci U S A 2024; 121:e2312064121. [PMID: 38530894 PMCID: PMC10998596 DOI: 10.1073/pnas.2312064121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 03/01/2024] [Indexed: 03/28/2024] Open
Abstract
Motile bacteria use large receptor arrays to detect chemical and physical stimuli in their environment, process this complex information, and accordingly bias their swimming in a direction they deem favorable. The chemoreceptor molecules form tripod-like trimers of receptor dimers through direct contacts between their cytoplasmic tips. A pair of trimers, together with a dedicated kinase enzyme, form a core signaling complex. Hundreds of core complexes network to form extended arrays. While considerable progress has been made in revealing the hierarchical structure of the array, the molecular properties underlying signal processing in these structures remain largely unclear. Here we analyzed the signaling properties of nonnetworked core complexes in live cells by following both conformational and kinase control responses to attractant stimuli and to output-biasing lesions at various locations in the receptor molecule. Contrary to the prevailing view that individual receptors are binary two-state devices, we demonstrate that conformational coupling between the ligand binding and the kinase-control receptor domains is, in fact, only moderate. In addition, we demonstrate communication between neighboring receptors through their trimer-contact domains that biases them to adopt similar signaling states. Taken together, these data suggest a view of signaling in receptor trimers that allows significant signal integration to occur within individual core complexes.
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Affiliation(s)
- Moriah Koler
- The Racah Institute of Physics, The Hebrew University, Jerusalem91904, Israel
| | - John S. Parkinson
- School of Biological Sciences, University of Utah, Salt Lake City, UT84112
| | - Ady Vaknin
- The Racah Institute of Physics, The Hebrew University, Jerusalem91904, Israel
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2
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Griffith M, Araújo A, Travasso R, Salvador A. The architecture of redox microdomains: Cascading gradients and peroxiredoxins' redox-oligomeric coupling integrate redox signaling and antioxidant protection. Redox Biol 2024; 69:103000. [PMID: 38150990 PMCID: PMC10829873 DOI: 10.1016/j.redox.2023.103000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 12/07/2023] [Accepted: 12/14/2023] [Indexed: 12/29/2023] Open
Abstract
In the cytosol of human cells under low oxidative loads, hydrogen peroxide is confined to microdomains around its supply sites, due to its fast consumption by peroxiredoxins. So are the sulfenic and disulfide forms of the 2-Cys peroxiredoxins, according to a previous theoretical analysis [Travasso et al., Redox Biology 15 (2017) 297]. Here, an extended reaction-diffusion model that for the first time considers the differential properties of human peroxiredoxins 1 and 2 and the thioredoxin redox cycle predicts important new aspects of the dynamics of redox microdomains. The peroxiredoxin 1 sulfenates and disulfides are more localized than the corresponding peroxiredoxin 2 forms, due to the former peroxiredoxin's faster resolution step. The thioredoxin disulfides are also localized. As the H2O2 supply rate (vsup) approaches and then surpasses the maximal rate of the thioredoxin/thioredoxin reductase system (V), these concentration gradients become shallower, and then vanish. At low vsup the peroxiredoxin concentration determines the H2O2 concentrations and gradient length scale, but as vsup approaches V, the thioredoxin reductase activity gains influence. A differential mobility of peroxiredoxin disulfide dimers vs. reduced decamers enhances the redox polarity of the cytosol: as vsup approaches V, reduced decamers are preferentially retained far from H2O2 sources, attenuating the local H2O2 buildup. Substantial total protein concentration gradients of both peroxiredoxins emerge under these conditions, and the concentration of reduced peroxiredoxin 1 far from the H2O2 sources even increases with vsup. Altogether, the properties of 2-Cys peroxiredoxins and thioredoxin are such that localized H2O2 supply induces a redox and functional polarization between source-proximal regions (redox microdomains) that facilitate peroxiredoxin-mediated signaling and distal regions that maximize antioxidant protection.
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Affiliation(s)
- Matthew Griffith
- CNC - Centre for Neuroscience Cell Biology, University of Coimbra, UC-Biotech, Parque Tecnológico de Cantanhede, Núcleo 4, Lote 8, 3060-197, Cantanhede, Portugal; Department of Mathematical Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Adérito Araújo
- CMUC, Department of Mathematics, University of Coimbra, Largo D. Dinis, 3004-143, Coimbra, Portugal.
| | - Rui Travasso
- CFisUC, Department of Physics, University of Coimbra, Coimbra, Rua Larga, 3004-516, Coimbra, Portugal.
| | - Armindo Salvador
- CNC - Centre for Neuroscience Cell Biology, University of Coimbra, UC-Biotech, Parque Tecnológico de Cantanhede, Núcleo 4, Lote 8, 3060-197, Cantanhede, Portugal; Coimbra Chemistry Center - Institute of Molecular Sciences (CQC-IMS), University of Coimbra, Rua Larga, 3004-535, Coimbra, Portugal; Institute for Interdisciplinary Research, University of Coimbra, Casa Costa Alemão, Rua Dom Francisco de Lemos, 3030-789, Coimbra, Portugal.
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Uchida Y, Hamamoto T, Che YS, Takahashi H, Parkinson JS, Ishijima A, Fukuoka H. The Chemoreceptor Sensory Adaptation System Produces Coordinated Reversals of the Flagellar Motors on an Escherichia coli Cell. J Bacteriol 2022; 204:e0027822. [PMID: 36448786 PMCID: PMC9765175 DOI: 10.1128/jb.00278-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 11/01/2022] [Indexed: 12/05/2022] Open
Abstract
In isotropic environments, an Escherichia coli cell exhibits coordinated rotational switching of its flagellar motors, produced by fluctuations in the intracellular concentration of phosphorylated CheY (CheY-P) emanating from chemoreceptor signaling arrays. In this study, we show that these CheY-P fluctuations arise through modifications of chemoreceptors by two sensory adaptation enzymes: the methyltransferase CheR and the methylesterase CheB. A cell containing CheR, CheB, and the serine chemoreceptor Tsr exhibited motor synchrony, whereas a cell lacking CheR and CheB or containing enzymatically inactive forms did not. Tsr variants with different combinations of methylation-mimicking Q residues at the adaptation sites also failed to show coordinated motor switching in cells lacking CheR and CheB. Cells containing CheR, CheB, and Tsr [NDND], a variant in which the adaptation site residues are not substrates for CheR or CheB modifications, also lacked motor synchrony. TsrΔNWETF, which lacks a C-terminal pentapeptide-binding site for CheR and CheB, and the ribose-galactose receptor Trg, which natively lacks this motif, failed to produce coordinated motor switching, despite the presence of CheR and CheB. However, addition of the NWETF sequence to Trg enabled Trg-NWETF to produce motor synchrony, as the sole receptor type in cells containing CheR and CheB. Finally, CheBc, the catalytic domain of CheB, supported motor coordination in combination with CheR and Tsr. These results indicate that the coordination of motor switching requires CheR/CheB-mediated changes in receptor modification state. We conclude that the opposing receptor substrate-site preferences of CheR and CheB produce spontaneous blinking of the chemoreceptor array's output activity. IMPORTANCE Under steady-state conditions with no external stimuli, an Escherichia coli cell coordinately switches the rotational direction of its flagellar motors. Here, we demonstrate that the CheR and CheB enzymes of the chemoreceptor sensory adaptation system mediate this coordination. Stochastic fluctuations in receptor adaptation states trigger changes in signal output from the receptor array, and this array blinking generates fluctuations in CheY-P concentration that coordinate directional switching of the flagellar motors. Thus, in the absence of chemoeffector gradients, the sensory adaptation system controls run-tumble swimming of the cell, its optimal foraging strategy.
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Affiliation(s)
- Yumiko Uchida
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Tatsuki Hamamoto
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Yong-Suk Che
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Hiroto Takahashi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Miyagi, Japan
| | - John S. Parkinson
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, USA
| | - Akihiko Ishijima
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Hajime Fukuoka
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
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4
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Wang P, Zhang G, Xu Z, Chen Z, Liu X, Wang C, Zheng C, Wang J, Zhang H, Yan A. Whole-cell FRET monitoring of transcription factor activities enables functional annotation of signal transduction systems in living bacteria. J Biol Chem 2022; 298:102258. [PMID: 35839853 PMCID: PMC9396075 DOI: 10.1016/j.jbc.2022.102258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 06/29/2022] [Accepted: 07/01/2022] [Indexed: 11/24/2022] Open
Abstract
Bacteria adapt to their constantly changing environments largely by transcriptional regulation through the activities of various transcription factors (TFs). However, techniques that monitor TF–promoter interactions in situ in living bacteria are lacking. Herein, we developed a whole-cell TF–promoter binding assay based on the intermolecular FRET between an unnatural amino acid, l-(7-hydroxycoumarin-4-yl) ethylglycine, which labels TFs with bright fluorescence through genetic encoding (donor fluorophore) and the live cell nucleic acid stain SYTO 9 (acceptor fluorophore). We show that this new FRET pair monitors the intricate TF–promoter interactions elicited by various types of signal transduction systems, including one-component (CueR) and two-component systems (BasSR and PhoPQ), in bacteria with high specificity and sensitivity. We demonstrate that robust CouA incorporation and FRET occurrence is achieved in all these regulatory systems based on either the crystal structures of TFs or their simulated structures, if 3D structures of the TFs were unavailable. Furthermore, using CueR and PhoPQ systems as models, we demonstrate that the whole-cell FRET assay is applicable for the identification and validation of complex regulatory circuit and novel modulators of regulatory systems of interest. Finally, we show that the FRET system is applicable for single-cell analysis and monitoring TF activities in Escherichia coli colonizing a Caenorhabditis elegans host. In conclusion, we established a tractable and sensitive TF–promoter binding assay, which not only complements currently available approaches for DNA–protein interactions but also provides novel opportunities for functional annotation of bacterial signal transduction systems and studies of the bacteria–host interface.
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Affiliation(s)
- Pengchao Wang
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China; Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China
| | - Guangming Zhang
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Zeling Xu
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Zhe Chen
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Xiaohong Liu
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 15 Datun Road, Chaoyang District, Beijing 100101, China
| | - Chenyin Wang
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Chaogu Zheng
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Jiangyun Wang
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 15 Datun Road, Chaoyang District, Beijing 100101, China.
| | - Hongmin Zhang
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China.
| | - Aixin Yan
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China.
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Dominick C, Yeung C, Wu XL. Accurate delivery of chemicals to a small target using a pressure-driven valved micropipette. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2022; 93:034103. [PMID: 35364991 DOI: 10.1063/5.0076514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 03/03/2022] [Indexed: 06/14/2023]
Abstract
We describe a new method for accurately and reproducibly delivering a minute amount of a chemical to a small target in an aqueous environment. Our method is based on a micropipette with a check valve at its tip that can be opened and closed on demand. We demonstrate that this device can produce a flux of 10-12 l in a short pulse lasting less than 100 ms. The finite width of the pulse is due to molecular dispersion of the chemical, in this case, fluorescein. The chemical distribution near the micropipette tip is measured and compared with the results of a numerical integration assuming stokeslet flow. Our technique is of general utility and has applications in microbiology and neuroscience when a precise control of the spatiotemporal chemical distribution around a specimen is desired.
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Affiliation(s)
- Corey Dominick
- Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | - Chuck Yeung
- School of Science, Pennsylvania State University at Erie, The Behrend College, Erie, Pennsylvania 16563, USA
| | - X L Wu
- Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
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6
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Suppression of cell-cell variation by cooperative interaction of phosphatase and response regulator. Biophys J 2022; 121:319-326. [PMID: 34896368 PMCID: PMC8790193 DOI: 10.1016/j.bpj.2021.12.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 10/27/2021] [Accepted: 12/07/2021] [Indexed: 01/21/2023] Open
Abstract
In bacterial chemotaxis, the output of chemosensing, the concentration of the response regulator CheY-P that was constantly adjusted by the opposing action of the kinase CheA and the phosphatase CheZ, serves as the input of the ultrasensitive flagellar motor that drives bacterial motility. The steady-state kinase activity exhibits large cell-to-cell variation that may result in similar variation in CheY-P concentration. Here, we found that the in vivo phosphatase activity is highly cooperative with respect to CheY-P concentration, and this suppresses the cell-to-cell variation of CheY-P concentration so that it falls within the operational range of the flagellar motor. Therefore, the cooperativity of the CheZ and CheY-P interaction we identified here provided a mechanism of robust coupling between the output of chemosensing and the input of the flagellar motor. Suppression of cell heterogeneity by cooperativity of protein-protein interaction is likely a common feature in many biological signaling systems.
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7
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Zheng CR, Singh A, Libby A, Silver PA, Libby EA. Modular and Single-Cell Sensors of Bacterial Ser/Thr Kinase Activity. ACS Synth Biol 2021; 10:2340-2350. [PMID: 34463482 DOI: 10.1021/acssynbio.1c00250] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
At the single-cell level, protein kinase activity is typically inferred from downstream transcriptional reporters. However, promoters are often coregulated by several pathways, making the activity of a specific kinase difficult to deconvolve. Here, we present modular, direct, and specific sensors of bacterial kinase activity, including FRET-based sensors, as well as a synthetic transcription factor based on the lactose repressor (LacI) that has been engineered to respond to phosphorylation. We demonstrate the utility of these sensors in measuring the activity of PrkC, a conserved bacterial Ser/Thr kinase, in different growth conditions from single cells to colonies. We also show that PrkC activity increases in response to a cell-wall active antibiotic that blocks the late steps in peptidoglycan synthesis (cefotaxime), but not the early steps (fosfomycin). These sensors have a modular design that should generalize to other bacterial signaling systems in the future.
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Affiliation(s)
- Christine R. Zheng
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
| | - Abhyudai Singh
- Electrical and Computer Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Alexandra Libby
- Princeton Neuroscience Institute, Princeton University, Princeton, New Jersey 08544, United States
| | - Pamela A. Silver
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
| | - Elizabeth A. Libby
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
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8
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Dominick CN, Wu XL. Bacterial cell-body rotation driven by a single flagellar motor and by a bundle. Biophys J 2021; 120:2454-2460. [PMID: 33932433 DOI: 10.1016/j.bpj.2021.04.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 04/05/2021] [Accepted: 04/07/2021] [Indexed: 10/21/2022] Open
Abstract
Using self-trapped Escherichia coli bacteria that have intact flagellar bundles on glass surfaces, we study statistical fluctuations of cell-body rotation in a steady (unstimulated) state. These fluctuations underline direction randomization of bacterial swimming trajectories and plays a fundamental role in bacterial chemotaxis. A parallel study is also conducted using a classical rotation assay in which cell-body rotation is driven by a single flagellar motor. These investigations allow us to draw the important conclusion that during periods of counterclockwise motor rotation, which contributes to a run, all flagellar motors are strongly correlated, but during the clockwise period, which contributes to a tumble, individual motors are uncorrelated in long times. Our observation is consistent with the physical picture that formation and maintenance of a coherent flagellar bundle is provided by a single dominant flagellum in the bundle.
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Affiliation(s)
- Corey N Dominick
- Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Xiao-Lun Wu
- Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, Pennsylvania.
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9
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How an unusual chemosensory system forms arrays on the bacterial nucleoid. Biochem Soc Trans 2021; 48:347-356. [PMID: 32129822 DOI: 10.1042/bst20180450] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 02/04/2020] [Accepted: 02/05/2020] [Indexed: 11/17/2022]
Abstract
Chemosensory systems are signaling pathways elegantly organized in hexagonal arrays that confer unique functional features to these systems such as signal amplification. Chemosensory arrays adopt different subcellular localizations from one bacterial species to another, yet keeping their supramolecular organization unmodified. In the gliding bacterium Myxococcus xanthus, a cytoplasmic chemosensory system, Frz, forms multiple clusters on the nucleoid through the direct binding of the FrzCD receptor to DNA. A small CheW-like protein, FrzB, might be responsible for the formation of multiple (instead of just one) Frz arrays. In this review, we summarize what is known on Frz array formation on the bacterial chromosome and discuss hypotheses on how FrzB might contribute to the nucleation of multiple clusters. Finally, we will propose some possible biological explanations for this type of localization pattern.
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Hsu IS, Moses AM. Stochastic models for single-cell data: Current challenges and the way forward. FEBS J 2021; 289:647-658. [PMID: 33570798 DOI: 10.1111/febs.15760] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 12/22/2020] [Accepted: 02/10/2021] [Indexed: 11/28/2022]
Abstract
Although the quantity and quality of single-cell data have progressed rapidly, making quantitative predictions with single-cell stochastic models remains challenging. The stochastic nature of cellular processes leads to at least three challenges in building models with single-cell data: (a) because variability in single-cell data can be attributed to multiple different sources, it is difficult to rule out conflicting mechanistic models that explain the same data equally well; (b) the distinction between interesting biological variability and experimental variability is sometimes ambiguous; (c) the nonstandard distributions of single-cell data can lead to violations of the assumption of symmetric errors in least-squares fitting. In this review, we first discuss recent studies that overcome some of the challenges or set up a promising direction and then introduce some powerful statistical approaches utilized in these studies. We conclude that applying and developing statistical approaches could lead to further progress in building stochastic models for single-cell data.
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Affiliation(s)
- Ian S Hsu
- Department of Cell & Systems Biology, University of Toronto, ON, Canada
| | - Alan M Moses
- Department of Cell & Systems Biology, University of Toronto, ON, Canada
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Liu X, Liu Y, Johnson KS, Dong X, Xie Z. Protein Residues and a Novel Motif Involved in the Cellular Localization of CheZ in Azorhizobium caulinodans ORS571. Front Microbiol 2020; 11:585140. [PMID: 33365019 PMCID: PMC7750401 DOI: 10.3389/fmicb.2020.585140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 11/16/2020] [Indexed: 12/26/2022] Open
Abstract
Chemotaxis is essential for the competitiveness of motile bacteria in complex and harsh environments. The localization of chemotactic proteins in the cell is critical for coordinating a maximal response to chemotactic signals. One chemotaxis protein with a well-defined subcellular localization is the phosphatase CheZ. CheZ localizes to cell poles by binding with CheA in Escherichia coli and other enteric bacteria, or binding with a poorly understood protein called ChePep in epsilon-Proteobacteria. In alpha-Proteobacteria, CheZ lacks CheA-binding sites, and its cellular localization remains unknown. We therefore determined the localization of CheZ in the alpha-Proteobacteria Azorhizobium caulinodans ORS571. A. caulinodans CheZ, also termed as CheZAC, was found to be located to cell poles independently of CheA, and we suspect that either the N-terminal helix or the four-helix bundle of CheZAC is sufficient to locate to cell poles. We also found a novel motif, AXXFQ, which is adjacent to the phosphatase active motif DXXXQ, which effects the monopolar localization of CheZAC. This novel motif consisting of AXXFQ is conserved in CheZ and widely distributed among Proteobacteria. Finally, we found that the substitution of phosphatase active site affects the polar localization of CheZAC. In total, this work characterized the localization pattern of CheZ containing a novel motif, and we mapped the regions of CheZAC that are critical for its polar localization.
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Affiliation(s)
- Xiaolin Liu
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Yanan Liu
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Kevin Scot Johnson
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Xiaoyan Dong
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Zhihong Xie
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.,National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment of Shandong Agricultural University, Taian, China
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12
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Fluctuations in Intracellular CheY-P Concentration Coordinate Reversals of Flagellar Motors in E. coli. Biomolecules 2020; 10:biom10111544. [PMID: 33198296 PMCID: PMC7696710 DOI: 10.3390/biom10111544] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/09/2020] [Accepted: 11/09/2020] [Indexed: 11/17/2022] Open
Abstract
Signal transduction utilizing membrane-spanning receptors and cytoplasmic regulator proteins is a fundamental process for all living organisms, but quantitative studies of the behavior of signaling proteins, such as their diffusion within a cell, are limited. In this study, we show that fluctuations in the concentration of the signaling molecule, phosphorylated CheY, constitute the basis of chemotaxis signaling. To analyze the propagation of the CheY-P signal quantitatively, we measured the coordination of directional switching between flagellar motors on the same cell. We analyzed the time lags of the switching of two motors in both CCW-to-CW and CW-to-CCW switching (∆tCCW-CW and ∆tCW-CCW). In wild-type cells, both time lags increased as a function of the relative distance of two motors from the polar receptor array. The apparent diffusion coefficient estimated for ∆t values was ~9 µm2/s. The distance-dependency of ∆tCW-CCW disappeared upon loss of polar localization of the CheY-P phosphatase, CheZ. The distance-dependency of the response time for an instantaneously applied serine attractant signal also disappeared with the loss of polar localization of CheZ. These results were modeled by calculating the diffusion of CheY and CheY-P in cells in which phosphorylation and dephosphorylation occur in different subcellular regions. We conclude that diffusion of signaling molecules and their production and destruction through spontaneous activity of the receptor array generates fluctuations in CheY-P concentration over timescales of several hundred milliseconds. Signal fluctuation coordinates rotation among flagella and regulates steady-state run-and-tumble swimming of cells to facilitate efficient responses to environmental chemical signals.
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13
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Duvall SW, Childers WS. Design of a Histidine Kinase FRET Sensor to Detect Complex Signal Integration within Living Bacteria. ACS Sens 2020; 5:1589-1596. [PMID: 32495620 DOI: 10.1021/acssensors.0c00008] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Histidine kinases (HK) switch between conformational states that promote kinase and phosphatase activities to regulate diverse cellular processes. Past studies have shown that these functional states can display heterogeneity between cells in microbial communities and can vary at the subcellular level. Methods to track and correlate the kinase conformational state with the phenotypic response of living bacteria cells will offer new opportunities to interrogate bacterial signaling mechanisms. As a proof of principle, we incorporated both mClover3 (donor) and mRuby3 (acceptor) fluorescent proteins into the Caulobacter crescentus cell-cycle HK CckA as an in vivo fluorescence resonance energy transfer (FRET) sensor to detect these structural changes. Our engineered FRET sensor was responsive to CckA-specific input signals and detected subcellular changes in CckA signal integration that occurs as cells develop. We demonstrated the potential of using the CckA FRET sensor as an in vivo screening tool for HK inhibitors. In summary, we have developed a new HK FRET sensor design strategy that can be adopted to monitor in vivo changes for interrogation of a broad range of signaling mechanisms in living bacteria.
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Affiliation(s)
- Samuel W. Duvall
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - W. Seth Childers
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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Abstract
Prokaryotic organisms occupy the most diverse set of environments and conditions on our planet. Their ability to sense and respond to a broad range of external cues remain key research areas in modern microbiology, central to behaviors that underlie beneficial and pathogenic interactions of bacteria with multicellular organisms and within complex ecosystems. Advances in our understanding of the one- and two-component signal transduction systems that underlie these sensing pathways have been driven by advances in imaging the behavior of many individual bacterial cells, as well as visualizing individual proteins and protein arrays within living cells. Cryo-electron tomography continues to provide new insights into the structure and function of chemosensory receptors and flagellar motors, while advances in protein labeling and tracking are applied to understand information flow between receptor and motor. Sophisticated microfluidics allow simultaneous analysis of the behavior of thousands of individual cells, increasing our understanding of how variance between individuals is generated, regulated and employed to maximize fitness of a population. In vitro experiments have been complemented by the study of signal transduction and motility in complex in vivo models, allowing investigators to directly address the contribution of motility, chemotaxis and aggregation/adhesion on virulence during infection. Finally, systems biology approaches have demonstrated previously uncharted areas of protein space in which novel two-component signal transduction pathways can be designed and constructed de novo These exciting experimental advances were just some of the many novel findings presented at the 15th Bacterial Locomotion and Signal Transduction conference (BLAST XV) in January 2019.
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15
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Probing chemotaxis activity in Escherichia coli using fluorescent protein fusions. Sci Rep 2019; 9:3845. [PMID: 30846802 PMCID: PMC6405996 DOI: 10.1038/s41598-019-40655-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 02/19/2019] [Indexed: 12/27/2022] Open
Abstract
Bacterial chemotaxis signaling may be interesting for the development of rapid biosensor assays, but is difficult to quantify. Here we explore two potential fluorescent readouts of chemotactically active Escherichia coli cells. In the first, we probed interactions between the chemotaxis signaling proteins CheY and CheZ by fusing them individually with non-fluorescent parts of stable or unstable ‘split’-Green Fluorescent Protein. Wild-type chemotactic cells but not mutants lacking the CheA kinase produced distinguishable fluorescence foci, two-thirds of which localize at the cell poles with the chemoreceptors and one-third at motor complexes. Fluorescent foci based on stable split-eGFP displayed small fluctuations in cells exposed to attractant or repellent, but those based on an unstable ASV-tagged eGFP showed a higher dynamic behaviour both in the foci intensity changes and the number of foci per cell. For the second readout, we expressed the pH-sensitive fluorophore pHluorin in the cyto- and periplasm of chemotactically active E. coli. Calibrations of pHluorin fluorescence as a function of pH demonstrated that cells accumulating near a chemo-attractant temporally increase cytoplasmic pH while decreasing periplasmic pH. Both readouts thus show promise for biosensor assays based on bacterial chemotaxis activity.
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16
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Dominick CN, Wu XL. Rotating Bacteria on Solid Surfaces without Tethering. Biophys J 2018; 115:588-594. [PMID: 30041887 DOI: 10.1016/j.bpj.2018.06.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 06/12/2018] [Accepted: 06/19/2018] [Indexed: 11/19/2022] Open
Abstract
Bacterial motion is strongly affected by the presence of a surface. One of the hallmarks of swimming near a surface is a defined curvature of bacterial trajectories, underlining the importance of counter rotations of the cell body and flagellum for locomotion of the microorganism. We find that there is another mode of bacterial motion on solid surfaces, i.e., self trapping due to fluid flows created by a rotating flagellum perpendicular to the surface. For a rod-like bacterium, such as Escherichia coli, this creates a peculiar situation in that the bacterium appears to swim along a minor axis of the cell body and is pressed against the surface. Although a full hydrodynamic theory is still lacking to explain the self-trapping phenomenon, the effect is intriguing and can be exploited to study a variety of biophysical phenomena of swimming bacteria. In particular, we showed that self-trapped E. coli cells display a chemotaxis response that is identical to the classical rotation assay in which antibodies are used to physically "glue" a flagellum to the surface.
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Affiliation(s)
- Corey N Dominick
- Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Xiao-Lun Wu
- Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, Pennsylvania.
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17
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Nandi SK, Safran SA. Protein gradients in single cells induced by their coupling to "morphogen"-like diffusion. J Chem Phys 2018; 148:205101. [PMID: 29865807 DOI: 10.1063/1.5021086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
One of the many ways cells transmit information within their volume is through steady spatial gradients of different proteins. However, the mechanism through which proteins without any sources or sinks form such single-cell gradients is not yet fully understood. One of the models for such gradient formation, based on differential diffusion, is limited to proteins with large ratios of their diffusion constants or to specific protein-large molecule interactions. We introduce a novel mechanism for gradient formation via the coupling of the proteins within a single cell with a molecule, that we call a "pronogen," whose action is similar to that of morphogens in multi-cell assemblies; the pronogen is produced with a fixed flux at one side of the cell. This coupling results in an effectively non-linear diffusion degradation model for the pronogen dynamics within the cell, which leads to a steady-state gradient of the protein concentration. We use stability analysis to show that these gradients are linearly stable with respect to perturbations.
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Affiliation(s)
- Saroj Kumar Nandi
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sam A Safran
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
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18
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Waite AJ, Frankel NW, Emonet T. Behavioral Variability and Phenotypic Diversity in Bacterial Chemotaxis. Annu Rev Biophys 2018; 47:595-616. [PMID: 29618219 DOI: 10.1146/annurev-biophys-062215-010954] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Living cells detect and process external signals using signaling pathways that are affected by random fluctuations. These variations cause the behavior of individual cells to fluctuate over time (behavioral variability) and generate phenotypic differences between genetically identical individuals (phenotypic diversity). These two noise sources reduce our ability to predict biological behavior because they diversify cellular responses to identical signals. Here, we review recent experimental and theoretical advances in understanding the mechanistic origin and functional consequences of such variation in Escherichia coli chemotaxis-a well-understood model of signal transduction and behavior. After briefly summarizing the architecture and logic of the chemotaxis system, we discuss determinants of behavior and chemotactic performance of individual cells. Then, we review how cell-to-cell differences in protein abundance map onto differences in individual chemotactic abilities and how phenotypic variability affects the performance of the population. We conclude with open questions to be addressed by future research.
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Affiliation(s)
- Adam James Waite
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520; .,Current affiliation: Calico Life Sciences, LLC, South San Francisco, California 94080
| | - Nicholas W Frankel
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520; .,Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158
| | - Thierry Emonet
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520; .,Department of Physics, Yale University, New Haven, Connecticut 06520
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19
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Keegstra JM, Kamino K, Anquez F, Lazova MD, Emonet T, Shimizu TS. Phenotypic diversity and temporal variability in a bacterial signaling network revealed by single-cell FRET. eLife 2017; 6:e27455. [PMID: 29231170 PMCID: PMC5809149 DOI: 10.7554/elife.27455] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 11/17/2017] [Indexed: 11/13/2022] Open
Abstract
We present in vivo single-cell FRET measurements in the Escherichia coli chemotaxis system that reveal pervasive signaling variability, both across cells in isogenic populations and within individual cells over time. We quantify cell-to-cell variability of adaptation, ligand response, as well as steady-state output level, and analyze the role of network design in shaping this diversity from gene expression noise. In the absence of changes in gene expression, we find that single cells demonstrate strong temporal fluctuations. We provide evidence that such signaling noise can arise from at least two sources: (i) stochastic activities of adaptation enzymes, and (ii) receptor-kinase dynamics in the absence of adaptation. We demonstrate that under certain conditions, (ii) can generate giant fluctuations that drive signaling activity of the entire cell into a stochastic two-state switching regime. Our findings underscore the importance of molecular noise, arising not only in gene expression but also in protein networks.
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Affiliation(s)
| | | | | | | | - Thierry Emonet
- Department of Molecular, Cellular and Developmental BiologyYale UniversityNew HavenUnited States
- Department of PhysicsYale UniversityNew HavenUnited States
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20
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Bardy SL, Briegel A, Rainville S, Krell T. Recent advances and future prospects in bacterial and archaeal locomotion and signal transduction. J Bacteriol 2017; 199:e00203-17. [PMID: 28484047 PMCID: PMC5573076 DOI: 10.1128/jb.00203-17] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Unraveling the structure and function of two-component and chemotactic signaling along with different aspects related to motility of bacteria and archaea are key research areas in modern microbiology. Escherichia coli is the traditional model organism to study chemotaxis signaling and motility. However, the recent study of a wide range of bacteria and even some archaea with different lifestyles has provided new insight into the eco-physiology of chemotaxis, which is essential for the host establishment of different pathogens or beneficial bacteria. The expanded range of model organisms has also permitted the study of chemosensory pathways unrelated to chemotaxis, multiple chemotaxis pathways within an organism, and new types of chemoreceptors. This research has greatly benefitted from technical advances in the field of cryo-microscopy that continues to reveal with increasing resolution the complexity and diversity of large protein complexes like the flagellar motor or chemoreceptor arrays. In addition, sensitive instruments now allow for an increasing number of experiments to be conducted at the single-cell level, thereby revealing information that is beginning to bridge the gap between individual cells and population behavior. Evidence has also accumulated showing that bacteria have evolved different mechanisms for surface sensing, which appears to be mediated by flagella and possibly type IV pili, and that the downstream signaling involves chemosensory pathways and two-component system based processes. Herein we summarize the recent advances and research tendencies in this field as presented at the latest Bacterial Locomotion and Signal Transduction (BLAST XIV) conference.
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Affiliation(s)
- Sonia L. Bardy
- University of Wisconsin—Milwaukee, Biological Sciences, Milwaukee, Wisconsin, USA
| | | | - Simon Rainville
- Laval University, Department of Physics, Engineering Physics and Optics, Quebec City, Québec, Canada
| | - Tino Krell
- Estación Experimental del Zaidín, Granada, Spain
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21
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Koutsoumanis KP, Aspridou Z. Individual cell heterogeneity in Predictive Food Microbiology: Challenges in predicting a "noisy" world. Int J Food Microbiol 2016; 240:3-10. [PMID: 27412586 DOI: 10.1016/j.ijfoodmicro.2016.06.021] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 06/13/2016] [Accepted: 06/19/2016] [Indexed: 11/25/2022]
Abstract
Gene expression is a fundamentally noisy process giving rise to a significant cell to cell variability at the phenotype level. The phenotypic noise is manifested in a wide range of microbial traits. Heterogeneous behavior of individual cells is observed at the growth, survival and inactivation responses and should be taken into account in the context of Predictive Food Microbiology (PMF). Recent methodological advances can be employed for the study and modeling of single cell dynamics leading to a new generation of mechanistic models which can provide insight into the link between phenotype, gene-expression, protein and metabolic functional units at the single cell level. Such models however, need to deal with an enormous amount of interactions and processes that influence each other, forming an extremely complex system. In this review paper, we discuss the importance of noise and present the future challenges in predicting the "noisy" microbial responses in foods.
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Affiliation(s)
- Konstantinos P Koutsoumanis
- Laboratory of Food Microbiology and Hygiene, Department of Food Science and Technology, School of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece.
| | - Zafiro Aspridou
- Laboratory of Food Microbiology and Hygiene, Department of Food Science and Technology, School of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece
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22
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Fundamental constraints on the abundances of chemotaxis proteins. Biophys J 2016; 108:1293-305. [PMID: 25762341 DOI: 10.1016/j.bpj.2015.01.024] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 01/25/2015] [Accepted: 01/28/2015] [Indexed: 01/01/2023] Open
Abstract
Flagellated bacteria, such as Escherichia coli, perform directed motion in gradients of concentration of attractants and repellents in a process called chemotaxis. The E. coli chemotaxis signaling pathway is a model for signal transduction, but it has unique features. We demonstrate that the need for fast signaling necessitates high abundances of the proteins involved in this pathway. We show that further constraints on the abundances of chemotaxis proteins arise from the requirements of self-assembly both of flagellar motors and of chemoreceptor arrays. All these constraints are specific to chemotaxis, and published data confirm that chemotaxis proteins tend to be more highly expressed than their homologs in other pathways. Employing a chemotaxis pathway model, we show that the gain of the pathway at the level of the response regulator CheY increases with overall chemotaxis protein abundances. This may explain why, at least in one E. coli strain, the abundance of all chemotaxis proteins is higher in media with lower nutrient content. We also demonstrate that the E. coli chemotaxis pathway is particularly robust to abundance variations of the motor protein FliM.
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23
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Single-cell E. coli response to an instantaneously applied chemotactic signal. Biophys J 2015; 107:730-739. [PMID: 25099812 DOI: 10.1016/j.bpj.2014.06.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Revised: 05/27/2014] [Accepted: 06/10/2014] [Indexed: 01/31/2023] Open
Abstract
In response to an attractant or repellant, an Escherichia coli cell controls the rotational direction of its flagellar motor by a chemotaxis system. When an E. coli cell senses an attractant, a reduction in the intracellular concentration of a chemotaxis protein, phosphorylated CheY (CheY-P), induces counterclockwise (CCW) rotation of the flagellar motor, and this cellular response is thought to occur in several hundred milliseconds. Here, to measure the signaling process occurring inside a single E. coli cell, including the recognition of an attractant by a receptor cluster, the inactivation of histidine kinase CheA, and the diffusion of CheY and CheY-P molecules, we applied a serine stimulus by instantaneous photorelease from a caged compound and examined the cellular response at a temporal resolution of several hundred microseconds. We quantified the clockwise (CW) and CCW durations immediately after the photorelease of serine as the response time and the duration of the response, respectively. The results showed that the response time depended on the distance between the receptor and motor, indicating that the decreased CheY-P concentration induced by serine propagates through the cytoplasm from the receptor-kinase cluster toward the motor with a timing that is explained by the diffusion of CheY and CheY-P molecules. The response time included 240 ms for enzymatic reactions in addition to the time required for diffusion of the signaling molecule. The measured response time and duration of the response also revealed that the E. coli cell senses a similar serine concentration regardless of whether the serine concentration is increasing or decreasing. These detailed quantitative findings increase our understanding of the signal transduction process that occurs inside cells during bacterial chemotaxis.
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24
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25
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Clausznitzer D, Micali G, Neumann S, Sourjik V, Endres RG. Predicting chemical environments of bacteria from receptor signaling. PLoS Comput Biol 2014; 10:e1003870. [PMID: 25340783 PMCID: PMC4207464 DOI: 10.1371/journal.pcbi.1003870] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Accepted: 08/19/2014] [Indexed: 11/19/2022] Open
Abstract
Sensory systems have evolved to respond to input stimuli of certain statistical properties, and to reliably transmit this information through biochemical pathways. Hence, for an experimentally well-characterized sensory system, one ought to be able to extract valuable information about the statistics of the stimuli. Based on dose-response curves from in vivo fluorescence resonance energy transfer (FRET) experiments of the bacterial chemotaxis sensory system, we predict the chemical gradients chemotactic Escherichia coli cells typically encounter in their natural environment. To predict average gradients cells experience, we revaluate the phenomenological Weber's law and its generalizations to the Weber-Fechner law and fold-change detection. To obtain full distributions of gradients we use information theory and simulations, considering limitations of information transmission from both cell-external and internal noise. We identify broad distributions of exponential gradients, which lead to log-normal stimuli and maximal drift velocity. Our results thus provide a first step towards deciphering the chemical nature of complex, experimentally inaccessible cellular microenvironments, such as the human intestine. Outside the laboratory, bacteria live in complex microenvironments characterized by competition for space and available nutrients. Although often inaccessible by experiments, understanding the spatio-temporal dynamics of bacterial microenvironments is biomedically important. For instance, the chemical environment that symbiotic Escherichia coli encounter in the human gut relates to health of the gastrointestinal tract, gut metabolism, immune response, and tissue homeostasis. Other complex microenvironments include soil and biofilms. Assuming that bacterial sensory systems have evolved to optimally sense typical gradients, we treat signaling data, the signaling pathway with its architecture and reaction rates, and computer simulations of swimming bacteria in different gradients as “prior knowledge” to “reverse engineer” E. coli's habitat. Our identified gradients are exponentially shaped with wide-ranging rate values. These microenvironments most likely stem from local fluctuating nutrient sources and degradation by competing species, in which bacteria have evolved to swim with optimal performance.
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Affiliation(s)
- Diana Clausznitzer
- Department of Life Sciences, Imperial College, London, United Kingdom
- Centre for Integrative Systems Biology and Bioinformatics, Imperial College, London, United Kingdom
- BioQuant, Heidelberg University, Heidelberg, Germany
- Institute for Medical Informatics and Biometry, Technische Universität Dresden, Dresden, Germany
| | - Gabriele Micali
- Department of Life Sciences, Imperial College, London, United Kingdom
- Centre for Integrative Systems Biology and Bioinformatics, Imperial College, London, United Kingdom
| | - Silke Neumann
- Centre of Molecular Biology, Heidelberg University, DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Victor Sourjik
- Centre of Molecular Biology, Heidelberg University, DKFZ-ZMBH Alliance, Heidelberg, Germany
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Robert G. Endres
- Department of Life Sciences, Imperial College, London, United Kingdom
- Centre for Integrative Systems Biology and Bioinformatics, Imperial College, London, United Kingdom
- * E-mail:
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26
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Campbell-Valois FX, Sansonetti PJ. Tracking bacterial pathogens with genetically-encoded reporters. FEBS Lett 2014; 588:2428-36. [PMID: 24859085 DOI: 10.1016/j.febslet.2014.05.022] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 05/12/2014] [Indexed: 11/15/2022]
Abstract
During the infectious process, bacterial pathogens are subject to changes in environmental conditions such as nutrient availability, immune response challenges, bacterial density and physical contacts with targeted host cells. These conditions occur in the colonized organs, in diverse regions within infected tissues or even at the subcellular level for intracellular pathogens. Integration of environmental cues leads to measurable biological responses in the bacterium required for adaptation. Recent progress in technology enabled the study of bacterial adaptation in situ using genetically encoded reporters that allow single cell analysis or whole body imaging based on fluorescent proteins, alternative fluorescent assays or luciferases. This review presents a historical perspective and technical details on the methods used to develop transcriptional reporters, protein-protein interaction assays and secretion detection assays to study pathogenic bacteria adaptation in situ. Finally, studies published in the last 5 years on gram positive and gram negative bacterial adaptation to the host during infection are discussed. However, the methods described here could easily be extended to study complex microbial communities within host tissue and in the environment.
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Affiliation(s)
- F-X Campbell-Valois
- Institut Pasteur, Unité de Pathogénie Microbienne Moléculaire, 25-28 rue du Docteur-Roux, 75724 Paris, France; INSERM, U786, 75015 Paris, France
| | - Philippe J Sansonetti
- Institut Pasteur, Unité de Pathogénie Microbienne Moléculaire, 25-28 rue du Docteur-Roux, 75724 Paris, France; INSERM, U786, 75015 Paris, France; Collège de France, Chaire de Microbiologie et Maladies infectieuses, 11 Place Marcelin Berthelot, 75005 Paris, France.
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27
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Neumann S, Løvdok L, Bentele K, Meisig J, Ullner E, Paldy FS, Sourjik V, Kollmann M. Exponential signaling gain at the receptor level enhances signal-to-noise ratio in bacterial chemotaxis. PLoS One 2014; 9:e87815. [PMID: 24736435 PMCID: PMC3988002 DOI: 10.1371/journal.pone.0087815] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 01/01/2014] [Indexed: 11/18/2022] Open
Abstract
Cellular signaling systems show astonishing precision in their response to external stimuli despite strong fluctuations in the molecular components that determine pathway activity. To control the effects of noise on signaling most efficiently, living cells employ compensatory mechanisms that reach from simple negative feedback loops to robustly designed signaling architectures. Here, we report on a novel control mechanism that allows living cells to keep precision in their signaling characteristics – stationary pathway output, response amplitude, and relaxation time – in the presence of strong intracellular perturbations. The concept relies on the surprising fact that for systems showing perfect adaptation an exponential signal amplification at the receptor level suffices to eliminate slowly varying multiplicative noise. To show this mechanism at work in living systems, we quantified the response dynamics of the E. coli chemotaxis network after genetically perturbing the information flux between upstream and downstream signaling components. We give strong evidence that this signaling system results in dynamic invariance of the activated response regulator against multiplicative intracellular noise. We further demonstrate that for environmental conditions, for which precision in chemosensing is crucial, the invariant response behavior results in highest chemotactic efficiency. Our results resolve several puzzling features of the chemotaxis pathway that are widely conserved across prokaryotes but so far could not be attributed any functional role.
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Affiliation(s)
- Silke Neumann
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Linda Løvdok
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Kajetan Bentele
- Institute for Theoretical Biology, Humboldt Universität zu Berlin, Berlin, Germany
| | - Johannes Meisig
- Institute for Theoretical Biology, Humboldt Universität zu Berlin, Berlin, Germany
| | - Ekkehard Ullner
- Department of Physics and Institute for Complex Systems and Mathematical Biology (ICSMB), Aberdeen, United Kingdom
| | - Ferencz S. Paldy
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Victor Sourjik
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Markus Kollmann
- Department Biologie, Heinrich-Heine-Universität, Düsseldorf, Düsseldorf, Germany
- * E-mail:
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28
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Frank V, Vaknin A. Prolonged stimuli alter the bacterial chemosensory clusters. Mol Microbiol 2013; 88:634-44. [PMID: 23551504 DOI: 10.1111/mmi.12215] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/21/2013] [Indexed: 11/27/2022]
Abstract
The clustering of membrane-bound receptors plays an essential role in various biological systems. A notable model system for studying this phenomenon is the bacterial chemosensory cluster that allows motile bacteria to navigate along chemical gradients in their environment. While the basic structure of these chemosensory clusters is becoming clear, their dynamic nature and operation are not yet understood. By measuring the fluorescence polarization of tagged receptor clusters in live Escherichia coli cells, we provide evidence for stimulus-induced dynamics in these sensory clusters. We find that when a stimulus is applied, the packing of the receptors slowly decreases and that the process reverses when the stimulus is removed. Consistent with these physical changes we find that the effective cooperativity of the kinase response slowly evolves in the presence of a stimulus. Time-lapse fluorescence imaging indicates that, despite these changes, the receptor clusters do not generally dissociate upon ligand binding. These data reveal stimulus-dependent plasticity in chemoreceptor clusters.
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Affiliation(s)
- Vered Frank
- The Racah Institute of Physics, The Hebrew University, Jerusalem, 91904, Israel
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29
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Zhou Y, Chu K, Zhen H, Fang Y, Yao C. Visualizing Hg2+ ions in living cells using a FRET-based fluorescent sensor. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2013; 106:197-202. [PMID: 23380148 DOI: 10.1016/j.saa.2012.12.092] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 12/23/2012] [Accepted: 12/30/2012] [Indexed: 06/01/2023]
Abstract
A novel FRET fluorescent sensor for Hg2+ imaging in living cells is rationally designed based on a coumarin-rhodamine platform. RBC1 exhibit high selectivity and excellent sensitivity in both absorbance and fluorescence detection of Hg2+ in aqueous solution. After addition of increasing concentrations of Hg2+, it result in the decrease of coumarin emission at 467 nm and a new emission profile of rhodamine at 590 nm gradually increased. The response time to Hg2+ is less than 2 min, and other metal ions including Fe2+, Mn2+, Ni2+, Co2+, Cu2+, Zn2+, Cd2+, Pb2+, and Cr3+ had no interference. In addition, fluorescent imaging of Hg2+ in A375 cells is also successfully demonstrated. The design strategy of two fluorophores switching in this work would help to extend the development of FRET fluorescent sensors.
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Affiliation(s)
- Yi Zhou
- State Key Laboratory of Materials-Oriented Chemical Engineering and College of Science, Nanjing University of Technology, Nanjing 210009, PR China
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30
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Tropini C, Rabbani N, Huang KC. Physical constraints on the establishment of intracellular spatial gradients in bacteria. BMC BIOPHYSICS 2012; 5:17. [PMID: 22931750 PMCID: PMC3496868 DOI: 10.1186/2046-1682-5-17] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Accepted: 07/17/2012] [Indexed: 11/25/2022]
Abstract
Background Bacteria dynamically regulate their intricate intracellular organization involving proteins that facilitate cell division, motility, and numerous other processes. Consistent with this sophisticated organization, bacteria are able to create asymmetries and spatial gradients of proteins by localizing signaling pathway components. We use mathematical modeling to investigate the biochemical and physical constraints on the generation of intracellular gradients by the asymmetric localization of a source and a sink. Results We present a systematic computational analysis of the effects of other regulatory mechanisms, such as synthesis, degradation, saturation, and cell growth. We also demonstrate that gradients can be established in a variety of bacterial morphologies such as rods, crescents, spheres, branched and constricted cells. Conclusions Taken together, these results suggest that gradients are a robust and potentially common mechanism for providing intracellular spatial cues.
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Affiliation(s)
- Carolina Tropini
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
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31
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Tindall MJ, Gaffney EA, Maini PK, Armitage JP. Theoretical insights into bacterial chemotaxis. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2012; 4:247-59. [PMID: 22411503 DOI: 10.1002/wsbm.1168] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Research into understanding bacterial chemotactic systems has become a paradigm for Systems Biology. Experimental and theoretical researchers have worked hand-in-hand for over 40 years to understand the intricate behavior driving bacterial species, in particular how such small creatures, usually not more than 5 µm in length, detect and respond to small changes in their extracellular environment. In this review we highlight the importance that theoretical modeling has played in providing new insight and understanding into bacterial chemotaxis. We begin with an overview of the bacterial chemotaxis sensory response, before reviewing the role of theoretical modeling in understanding elements of the system on the single cell scale and features underpinning multiscale extensions to population models.
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Affiliation(s)
- Marcus J Tindall
- School of Biological Sciences, University of Reading, Whiteknights, Reading, UK.
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32
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Charon NW, Cockburn A, Li C, Liu J, Miller KA, Miller MR, Motaleb M, Wolgemuth CW. The unique paradigm of spirochete motility and chemotaxis. Annu Rev Microbiol 2012; 66:349-70. [PMID: 22994496 PMCID: PMC3771095 DOI: 10.1146/annurev-micro-092611-150145] [Citation(s) in RCA: 128] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Spirochete motility is enigmatic: It differs from the motility of most other bacteria in that the entire bacterium is involved in translocation in the absence of external appendages. Using the Lyme disease spirochete Borrelia burgdorferi (Bb) as a model system, we explore the current research on spirochete motility and chemotaxis. Bb has periplasmic flagella (PFs) subterminally attached to each end of the protoplasmic cell cylinder, and surrounding the cell is an outer membrane. These internal helix-shaped PFs allow the spirochete to swim by generating backward-moving waves by rotation. Exciting advances using cryoelectron tomography are presented with respect to in situ analysis of cell, PF, and motor structure. In addition, advances in the dynamics of motility, chemotaxis, gene regulation, and the role of motility and chemotaxis in the life cycle of Bb are summarized. The results indicate that the motility paradigms of flagellated bacteria do not apply to these unique bacteria.
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Affiliation(s)
- Nyles W. Charon
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Health Sciences Center, Box 9177, Morgantown, WV. 26506-9177
| | - Andrew Cockburn
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Health Sciences Center, Box 9177, Morgantown, WV. 26506-9177
| | - Chunhao Li
- Department of Oral Biology, The State University of New York at Buffalo, NY 14214-3092
| | - Jun Liu
- The University of Texas - Houston Medical School, Department of Pathology and Laboratory Medicine, 6431 Fannin, MSB 2.228, Houston, TX 77030
| | - Kelly A. Miller
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Health Sciences Center, Box 9177, Morgantown, WV. 26506-9177
| | - Michael R. Miller
- Department of Biochemistry, West Virginia University, Health Sciences Center, Post Office Box 9177, Morgantown, WV. 26506-9177
| | - Md. Motaleb
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, NC 27834
| | - Charles W. Wolgemuth
- Department of Cell Biology and Center for Cell Analysis and Modeling, University of Connecticut Health Center, Farmington, CT 06030-3505
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33
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Griffin EE, Odde DJ, Seydoux G. Regulation of the MEX-5 gradient by a spatially segregated kinase/phosphatase cycle. Cell 2011; 146:955-68. [PMID: 21925318 DOI: 10.1016/j.cell.2011.08.012] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2011] [Revised: 06/17/2011] [Accepted: 08/08/2011] [Indexed: 10/17/2022]
Abstract
Protein concentration gradients encode spatial information across cells and tissues and often depend on spatially localized protein synthesis. Here, we report that a different mechanism underlies the MEX-5 gradient. MEX-5 is an RNA-binding protein that becomes distributed in a cytoplasmic gradient along the anterior-to-posterior axis of the one-cell C. elegans embryo. We demonstrate that the MEX-5 gradient is a direct consequence of an underlying gradient in MEX-5 diffusivity. The MEX-5 diffusion gradient arises when the PAR-1 kinase stimulates the release of MEX-5 from slow-diffusive, RNA-containing complexes in the posterior cytoplasm. PAR-1 directly phosphorylates MEX-5 and is antagonized by the spatially uniform phosphatase PP2A. Mathematical modeling and in vivo observations demonstrate that spatially segregated phosphorylation and dephosphorylation reactions are sufficient to generate stable protein concentration gradients in the cytoplasm. The principles demonstrated here apply to any spatially segregated modification cycle that affects protein diffusion and do not require protein synthesis or degradation.
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Affiliation(s)
- Erik E Griffin
- Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Center for Cell Dynamics, Johns Hopkins School of Medicine, 725 N. Wolfe Street, PCTB 706, Baltimore, MD 21205, USA
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34
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Terasawa S, Fukuoka H, Inoue Y, Sagawa T, Takahashi H, Ishijima A. Coordinated reversal of flagellar motors on a single Escherichia coli cell. Biophys J 2011; 100:2193-200. [PMID: 21539787 DOI: 10.1016/j.bpj.2011.03.030] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Revised: 03/04/2011] [Accepted: 03/14/2011] [Indexed: 10/18/2022] Open
Abstract
An Escherichia coli cell transduces extracellular stimuli sensed by chemoreceptors to the state of an intracellular signal molecule, which regulates the switching of the rotational direction of the flagellar motors from counterclockwise (CCW) to clockwise (CW) and from CW back to CCW. Here, we performed high-speed imaging of flagellar motor rotation and show that the switching of two different motors on a cell is controlled coordinatedly by an intracellular signal protein, phosphorylated CheY (CheY-P). The switching is highly coordinated with a subsecond delay between motors in clear correlation with the distance of each motor from the chemoreceptor patch localized at a cell pole, which would be explained by the diffusive motion of CheY-P molecules in the cell. The coordinated switching becomes disordered by the expression of a constitutively active CheY mutant that mimics the CW-rotation stimulating function. The coordinated switching requires CheZ, which is the phosphatase for CheY-P. Our results suggest that a transient increase and decrease in the concentration of CheY-P caused by a spontaneous burst of its production by the chemoreceptor patch followed by its dephosphorylation by CheZ, which is probably a wavelike propagation in a subsecond timescale, triggers and regulates the coordinated switching of flagellar motors.
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Affiliation(s)
- Shun Terasawa
- Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai, Japan
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35
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Zhao Q, Yi M, Liu Y. Spatial distribution and dose-response relationship for different operation modes in a reaction-diffusion model of the MAPK cascade. Phys Biol 2011; 8:055004. [PMID: 21832801 DOI: 10.1088/1478-3975/8/5/055004] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The mitogen-activated protein kinase (MAPK) cascade plays a critical role in the control of cell growth. Deregulation of this pathway contributes to the development of many cancers. To better understand its signal transduction, we constructed a reaction-diffusion model for the MAPK pathway. We modeled the three layers of phosphorylation-dephosphorylation reactions and diffusion processes from the cell membrane to the nucleus. Based on different types of feedback in the MAPK cascade, four operation modes are introduced. For each of the four modes, spatial distributions and dose-response curves of active kinases (i.e. ppMAPK) are explored by numerical simulation. The effects of propagation length, diffusion coefficient and feedback strength on the pathway dynamics are investigated. We found that intrinsic bistability in the MAPK cascade can generate a traveling wave of ppMAPK with constant amplitude when the propagation length is short. ppMAPK in this mode of intrinsic bistability decays more slowly than it does in all other modes as the propagation length increases. Moreover, we examined the global and local responses to Ras-GTP of these four modes, and demonstrated how the shapes of these dose-response curves change as the propagation length increases. Also, we found that larger diffusion constant gives a higher response level on the zero-order regime and makes the ppMAPK profiles flatter under strong Ras-GTP stimulus. Furthermore, we observed that spatial responses of ppMAPK are more sensitive to negative feedback than to positive feedback in the broader signal range. Finally, we showed how oscillatory signals pass through the kinase cascade, and found that high frequency signals are damped faster than low frequency ones.
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Affiliation(s)
- Qi Zhao
- Department of Mathematics, Liaoning University, Shenyang 110036, People's Republic of China
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36
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Frank V, Koler M, Furst S, Vaknin A. The physical and functional thermal sensitivity of bacterial chemoreceptors. J Mol Biol 2011; 411:554-66. [PMID: 21718703 DOI: 10.1016/j.jmb.2011.06.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Revised: 05/29/2011] [Accepted: 06/03/2011] [Indexed: 10/18/2022]
Abstract
The bacterium Escherichia coli exhibits chemotactic behavior at temperatures ranging from approximately 20 °C to at least 42 °C. This behavior is controlled by clusters of transmembrane chemoreceptors made from trimers of dimers that are linked together by cross-binding to cytoplasmic components. By detecting fluorescence energy transfer between various components of this system, we studied the underlying molecular behavior of these receptors in vivo and throughout their operating temperature range. We reveal a sharp modulation in the conformation of unclustered and clustered receptor trimers and, consequently, in kinase activity output. These modulations occurred at a characteristic temperature that depended on clustering and were lower for receptors at lower adaptational states. However, in the presence of dynamic adaptation, the response of kinase activity to a stimulus was sustained up to 45 °C, but sensitivity notably decreased. Thus, this molecular system exhibits a clear thermal sensitivity that emerges at the level of receptor trimers, but both receptor clustering and adaptation support the overall robust operation of the system at elevated temperatures.
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Affiliation(s)
- Vered Frank
- The Racah Institute of Physics, The Hebrew University, Jerusalem 91904, Israel
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37
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Identification of an anchor residue for CheA-CheY interactions in the chemotaxis system of Escherichia coli. J Bacteriol 2011; 193:3894-903. [PMID: 21642453 DOI: 10.1128/jb.00426-11] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Transfer of a phosphoryl group from autophosphorylated CheA (P-CheA) to CheY is an important step in the bacterial chemotaxis signal transduction pathway. This reaction involves CheY (i) binding to the P2 domain of P-CheA and then (ii) acquiring the phosphoryl group from the P1 domain. Crystal structures indicated numerous side chain interactions at the CheY-P2 binding interface. To investigate the individual contributions of the P2 side chains involved in these contacts, we analyzed the effects of eight alanine substitution mutations on CheA-CheY binding interactions. An F214A substitution in P2 caused ∼1,000-fold reduction in CheA-CheY binding affinity, while Ala substitutions at other P2 positions had small effects (E171A, E178A, and I216A) or no detectable effects (H181A, D202A, D207A, and C213A) on binding affinity. These results are discussed in relation to previous in silico predictions of hot-spot and anchor positions at the CheA-CheY interface. We also investigated the consequences of these mutations for chemotaxis signal transduction in living cells. CheA(F214A) was defective in mediating localization of CheY-YFP to the large clusters of signaling proteins that form at the poles of Escherichia coli cells, while the other CheA variants did not differ from wild-type (wt) CheA (CheA(wt)) in this regard. In our set of mutants, only CheA(F214A) exhibited a markedly diminished ability to support chemotaxis in motility agar assays. Surprisingly, however, in FRET assays that monitored receptor-regulated production of phospho-CheY, CheA(F214A) (and each of the other Ala substitution mutants) performed just as well as CheA(wt). Overall, our findings indicate that F214 serves as an anchor residue at the CheA-CheY interface and makes an important contribution to the binding energy in vitro and in vivo; however, loss of this contribution does not have a large negative effect on the overall ability of the signaling pathway to modulate P-CheY levels in response to chemoattractants.
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38
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CheY3 of Borrelia burgdorferi is the key response regulator essential for chemotaxis and forms a long-lived phosphorylated intermediate. J Bacteriol 2011; 193:3332-41. [PMID: 21531807 DOI: 10.1128/jb.00362-11] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Spirochetes have a unique cell structure: These bacteria have internal periplasmic flagella subterminally attached at each cell end. How spirochetes coordinate the rotation of the periplasmic flagella for chemotaxis is poorly understood. In other bacteria, modulation of flagellar rotation is essential for chemotaxis, and phosphorylation-dephosphorylation of the response regulator CheY plays a key role in regulating this rotary motion. The genome of the Lyme disease spirochete Borrelia burgdorferi contains multiple homologues of chemotaxis genes, including three copies of cheY, referred to as cheY1, cheY2, and cheY3. To investigate the function of these genes, we targeted them separately or in combination by allelic exchange mutagenesis. Whereas wild-type cells ran, paused (flexed), and reversed, cells of all single, double, and triple mutants that contained an inactivated cheY3 gene constantly ran. Capillary tube chemotaxis assays indicated that only those strains with a mutation in cheY3 were deficient in chemotaxis, and cheY3 complementation restored chemotactic ability. In vitro phosphorylation assays indicated that CheY3 was more efficiently phosphorylated by CheA2 than by CheA1, and the CheY3-P intermediate generated was considerably more stable than the CheY-P proteins found in most other bacteria. The results point toward CheY3 being the key response regulator essential for chemotaxis in B. burgdorferi. In addition, the stability of CheY3-P may be critical for coordination of the rotation of the periplasmic flagella.
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39
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Wu K, Walukiewicz HE, Glekas GD, Ordal GW, Rao CV. Attractant binding induces distinct structural changes to the polar and lateral signaling clusters in Bacillus subtilis chemotaxis. J Biol Chem 2010; 286:2587-95. [PMID: 21098025 DOI: 10.1074/jbc.m110.188664] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Bacteria employ a modified two-component system for chemotaxis, where the receptors form ternary complexes with CheA histidine kinases and CheW adaptor proteins. These complexes are arranged in semi-ordered arrays clustered predominantly at the cell poles. The prevailing models assume that these arrays are static and reorganize only locally in response to attractant binding. Recent studies have shown, however, that these structures may in fact be much more fluid. We investigated the localization of the chemotaxis signaling arrays in Bacillus subtilis using immunofluorescence and live cell fluorescence microscopy. We found that the receptors were localized in clusters at the poles in most cells. However, when the cells were exposed to attractant, the number exhibiting polar clusters was reduced roughly 2-fold, whereas the number exhibiting lateral clusters distinct from the poles increased significantly. These changes in receptor clustering were reversible as polar localization was reestablished in adapted cells. We also investigated the dynamic localization of CheV, a hybrid protein consisting of an N-terminal CheW-like adaptor domain and a C-terminal response regulator domain that is known to be phosphorylated by CheA, using immunofluorescence. Interestingly, we found that CheV was localized predominantly at lateral clusters in unstimulated cells. However, upon exposure to attractant, CheV was found to be predominantly localized to the cell poles. Moreover, changes in CheV localization are phosphorylation-dependent. Collectively, these results suggest that the chemotaxis signaling arrays in B. subtilis are dynamic structures and that feedback loops involving phosphorylation may regulate the positioning of individual proteins.
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Affiliation(s)
- Kang Wu
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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40
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Kentner D, Sourjik V. Use of Fluorescence Microscopy to Study Intracellular Signaling in Bacteria. Annu Rev Microbiol 2010; 64:373-90. [DOI: 10.1146/annurev.micro.112408.134205] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- David Kentner
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany;
| | - Victor Sourjik
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany;
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41
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Spatial organization in bacterial chemotaxis. EMBO J 2010; 29:2724-33. [PMID: 20717142 DOI: 10.1038/emboj.2010.178] [Citation(s) in RCA: 119] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2010] [Accepted: 07/07/2010] [Indexed: 11/09/2022] Open
Abstract
Spatial organization of signalling is not an exclusive property of eukaryotic cells. Despite the fact that bacterial signalling pathways are generally simpler than those in eukaryotes, there are several well-documented examples of higher-order intracellular signalling structures in bacteria. One of the most prominent and best-characterized structures is formed by proteins that control bacterial chemotaxis. Signals in chemotaxis are processed by ordered arrays, or clusters, of receptors and associated proteins, which amplify and integrate chemotactic stimuli in a highly cooperative manner. Receptor clusters further serve to scaffold protein interactions, enhancing the efficiency and specificity of the pathway reactions and preventing the formation of signalling gradients through the cell body. Moreover, clustering can also ensure spatial separation of multiple chemotaxis systems in one bacterium. Assembly of receptor clusters appears to be a stochastic process, but bacteria evolved mechanisms to ensure optimal cluster distribution along the cell body for partitioning to daughter cells at division.
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42
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Soh S, Byrska M, Kandere-Grzybowska K, Grzybowski BA. Reaction-diffusion systems in intracellular molecular transport and control. Angew Chem Int Ed Engl 2010; 49:4170-98. [PMID: 20518023 PMCID: PMC3697936 DOI: 10.1002/anie.200905513] [Citation(s) in RCA: 127] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Chemical reactions make cells work only if the participating chemicals are delivered to desired locations in a timely and precise fashion. Most research to date has focused on active-transport mechanisms, although passive diffusion is often equally rapid and energetically less costly. Capitalizing on these advantages, cells have developed sophisticated reaction-diffusion (RD) systems that control a wide range of cellular functions-from chemotaxis and cell division, through signaling cascades and oscillations, to cell motility. These apparently diverse systems share many common features and are "wired" according to "generic" motifs such as nonlinear kinetics, autocatalysis, and feedback loops. Understanding the operation of these complex (bio)chemical systems requires the analysis of pertinent transport-kinetic equations or, at least on a qualitative level, of the characteristic times of the constituent subprocesses. Therefore, in reviewing the manifestations of cellular RD, we also describe basic theory of reaction-diffusion phenomena.
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Affiliation(s)
- Siowling Soh
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Rd, Evanston, IL 60208
| | - Marta Byrska
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Rd, Evanston, IL 60208
| | - Kristiana Kandere-Grzybowska
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Rd, Evanston, IL 60208
| | - Bartosz A. Grzybowski
- Department of Chemistry, Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Rd, Evanston, IL 60208, Homepage: http://www.dysa.northwestern.edu
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43
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Soh S, Byrska M, Kandere-Grzybowska K, Grzybowski B. Reaktions-Diffusions-Systeme für intrazellulären Transport und Kontrolle. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200905513] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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44
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Jiang L, Ouyang Q, Tu Y. Quantitative modeling of Escherichia coli chemotactic motion in environments varying in space and time. PLoS Comput Biol 2010; 6:e1000735. [PMID: 20386737 PMCID: PMC2851563 DOI: 10.1371/journal.pcbi.1000735] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2009] [Accepted: 03/03/2010] [Indexed: 11/18/2022] Open
Abstract
Escherichia coli chemotactic motion in spatiotemporally varying environments is studied by using a computational model based on a coarse-grained description of the intracellular signaling pathway dynamics. We find that the cell's chemotaxis drift velocity v(d) is a constant in an exponential attractant concentration gradient [L] proportional, variantexp(Gx). v(d) depends linearly on the exponential gradient G before it saturates when G is larger than a critical value G(C). We find that G(C) is determined by the intracellular adaptation rate k(R) with a simple scaling law: G(C) infinity k(1/2)(R). The linear dependence of v(d) on G = d(ln[L])/dx directly demonstrates E. coli's ability in sensing the derivative of the logarithmic attractant concentration. The existence of the limiting gradient G(C) and its scaling with k(R) are explained by the underlying intracellular adaptation dynamics and the flagellar motor response characteristics. For individual cells, we find that the overall average run length in an exponential gradient is longer than that in a homogeneous environment, which is caused by the constant kinase activity shift (decrease). The forward runs (up the gradient) are longer than the backward runs, as expected; and depending on the exact gradient, the (shorter) backward runs can be comparable to runs in a spatially homogeneous environment, consistent with previous experiments. In (spatial) ligand gradients that also vary in time, the chemotaxis motion is damped as the frequency omega of the time-varying spatial gradient becomes faster than a critical value omega(c), which is controlled by the cell's chemotaxis adaptation rate k(R). Finally, our model, with no adjustable parameters, agrees quantitatively with the classical capillary assay experiments where the attractant concentration changes both in space and time. Our model can thus be used to study E. coli chemotaxis behavior in arbitrary spatiotemporally varying environments. Further experiments are suggested to test some of the model predictions.
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Affiliation(s)
- Lili Jiang
- Center for Theoretical Biology and School of Physics, Peking University, Beijing, China
- IBM T. J. Watson Research Center, Yorktown Heights, New York, United States of America
| | - Qi Ouyang
- Center for Theoretical Biology and School of Physics, Peking University, Beijing, China
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing, China
| | - Yuhai Tu
- Center for Theoretical Biology and School of Physics, Peking University, Beijing, China
- IBM T. J. Watson Research Center, Yorktown Heights, New York, United States of America
- * E-mail:
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45
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Scharf BE. Summary of useful methods for two-component system research. Curr Opin Microbiol 2010; 13:246-52. [DOI: 10.1016/j.mib.2010.01.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2009] [Revised: 01/10/2010] [Accepted: 01/11/2010] [Indexed: 10/19/2022]
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46
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Silversmith RE. Auxiliary phosphatases in two-component signal transduction. Curr Opin Microbiol 2010; 13:177-83. [PMID: 20133180 DOI: 10.1016/j.mib.2010.01.004] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2009] [Revised: 01/05/2010] [Accepted: 01/07/2010] [Indexed: 11/18/2022]
Abstract
Signal termination in two-component systems occurs by loss of the phosphoryl group from the response regulator protein. This review explores our current understanding of the structures, catalytic mechanisms and means of regulation of the known families of phosphatases that catalyze response regulator dephosphorylation. The CheZ and CheC/CheX/FliY families, despite different overall structures, employ identical catalytic strategies using an amide side chain to orient a water molecule for in-line attack of the aspartyl phosphate. Spo0E phosphatases contain sequence and structural features that suggest a strategy similar to the chemotaxis phosphatases but the mechanism used by the Rap phosphatases is not yet elucidated. Identification of features shared by phosphatase families may aid in the identification of currently unrecognized classes of response regulator phosphatases.
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Affiliation(s)
- Ruth E Silversmith
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599-7290, USA.
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47
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Abstract
Specific CheA-short (CheA(S)) residues, L123 and L126, were identified as critical for CheZ binding. In the CheA(S) 'P1-CheZ nuclear magnetic resonance structure, these residues form an interaction surface on alpha-helix E in the 'P1 domain. Both L123 and L126 are buried in CheA-long (CheA(L)), providing an explanation for why CheA(L) fails to bind CheZ.
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48
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Abstract
CheZ localizes to chemoreceptor patches by binding CheA-short (CheA(S)). Residues 70 to 134 of CheZ, constituting the apical loops and part of the dimerization domain, suffice for localization. Replacements of Tyr-118, Ile-119, Leu-123, Arg-124, and Leu-126 of CheA interfere with localization. These residues are exposed in the 'P1 domain of CheA(S).
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49
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Tindall MJ, Porter SL, Wadhams GH, Maini PK, Armitage JP. Spatiotemporal modelling of CheY complexes in Escherichia coli chemotaxis. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2009; 100:40-6. [PMID: 19540260 DOI: 10.1016/j.pbiomolbio.2009.06.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The chemotaxis pathway of Escherichia coli is one of the best studied and modelled biological signalling pathways. Here we extend existing modelling approaches by explicitly including a description of the formation and subcellular localization of intermediary complexes in the phosphotransfer pathway. The inclusion of these complexes shows that only about 60% of the total output response regulator (CheY) is uncomplexed at any moment and hence free to interact with its target, the flagellar motor. A clear strength of this model is its ability to predict the experimentally observable subcellular localization of CheY throughout a chemotactic response. We have found good agreement between the model output and experimentally determined CheY localization patterns.
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Affiliation(s)
- M J Tindall
- Institute for Cardiovascular and Metabolic Research and School of Biological Sciences and Department of Mathematics, University of Reading, Whiteknights, Reading, Berkshire RG6 6AP, UK.
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50
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Structural basis for the localization of the chemotaxis phosphatase CheZ by CheAS. J Bacteriol 2009; 191:5842-4. [PMID: 19502407 DOI: 10.1128/jb.00323-09] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
CheA-short interacts with CheZ to localize CheZ to cell poles. The fifth helical region (residues 112 to 133) from the phosphotransfer domain of CheA interacts with CheZ and becomes ordered and helical, although it lacks a stable fold in the CheA fragment comprising residues 98 to 150 alone. One CheA molecule binds to one CheZ dimer.
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