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Gupta R, Rhee KY, Beagle SD, Chawla R, Perdomo N, Lockless SW, Lele PP. Indole modulates cooperative protein-protein interactions in the flagellar motor. PNAS NEXUS 2022; 1. [PMID: 35719892 PMCID: PMC9205328 DOI: 10.1093/pnasnexus/pgac035] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Indole is a major component of the bacterial exometabolome, and the mechanisms for its wide-ranging effects on bacterial physiology are biomedically significant, although they remain poorly understood. Here, we determined how indole modulates the functions of a widely conserved motility apparatus, the bacterial flagellum. Our experiments in Escherichia coli revealed that indole influences the rotation rates and reversals in the flagellum’s direction of rotation via multiple mechanisms. At concentrations higher than 1 mM, indole decreased the membrane potential to dissipate the power available for the rotation of the motor that operates the flagellum. Below 1 mM, indole did not dissipate the membrane potential. Instead, experiments and modeling indicated that indole weakens cooperative protein interactions within the flagellar complexes to inhibit motility. The metabolite also induced reversals in the rotational direction of the motor to promote a weak chemotactic response, even when the chemotaxis response regulator, CheY, was lacking. Experiments further revealed that indole does not require the transporter Mtr to cross the membrane and influence motor functions. Based on these findings, we propose that indole modulates intra- and inter-protein interactions in the cell to influence several physiological functions.
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Affiliation(s)
- Rachit Gupta
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843-3122, USA
| | - Kathy Y Rhee
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843-3122, USA
| | - Sarah D Beagle
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, 63130, USA
| | - Ravi Chawla
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA 92037, USA
| | - Nicolas Perdomo
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843-3122, USA
| | - Steve W Lockless
- Department of Biology, Texas A&M University, College Station, TX 77843-3258, USA
| | - Pushkar P Lele
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843-3122, USA
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2
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Antani JD, Sumali AX, Lele TP, Lele PP. Asymmetric random walks reveal that the chemotaxis network modulates flagellar rotational bias in Helicobacter pylori. eLife 2021; 10:63936. [PMID: 33493107 PMCID: PMC7834020 DOI: 10.7554/elife.63936] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 01/12/2021] [Indexed: 12/14/2022] Open
Abstract
The canonical chemotaxis network modulates the bias for a particular direction of rotation in the bacterial flagellar motor to help the cell migrate toward favorable chemical environments. How the chemotaxis network in Helicobacter pylori modulates flagellar functions is unknown, which limits our understanding of chemotaxis in this species. Here, we determined that H. pylori swim faster (slower) whenever their flagella rotate counterclockwise (clockwise) by analyzing their hydrodynamic interactions with bounding surfaces. This asymmetry in swimming helped quantify the rotational bias. Upon exposure to a chemo-attractant, the bias decreased and the cells tended to swim exclusively in the faster mode. In the absence of a key chemotaxis protein, CheY, the bias was zero. The relationship between the reversal frequency and the rotational bias was unimodal. Thus, H. pylori’s chemotaxis network appears to modulate the probability of clockwise rotation in otherwise counterclockwise-rotating flagella, similar to the canonical network.
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Affiliation(s)
- Jyot D Antani
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843, United States
| | - Anita X Sumali
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843, United States
| | - Tanmay P Lele
- Department of Biomedical Engineering, Texas A&M University, College Station, TX 77840, College Station, TX 77840, United States.,Department of Translational Medical Sciences, Texas A&M University, Houston, TX 77030, United States
| | - Pushkar P Lele
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843, United States
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3
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Polyphosphate is an extracellular signal that can facilitate bacterial survival in eukaryotic cells. Proc Natl Acad Sci U S A 2020; 117:31923-31934. [PMID: 33268492 DOI: 10.1073/pnas.2012009117] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Polyphosphate is a linear chain of phosphate residues and is present in organisms ranging from bacteria to humans. Pathogens such as Mycobacterium tuberculosis accumulate polyphosphate, and reduced expression of the polyphosphate kinase that synthesizes polyphosphate decreases their survival. How polyphosphate potentiates pathogenicity is poorly understood. Escherichia coli K-12 do not accumulate detectable levels of extracellular polyphosphate and have poor survival after phagocytosis by Dictyostelium discoideum or human macrophages. In contrast, Mycobacterium smegmatis and Mycobacterium tuberculosis accumulate detectable levels of extracellular polyphosphate, and have relatively better survival after phagocytosis by D. discoideum or macrophages. Adding extracellular polyphosphate increased E. coli survival after phagocytosis by D. discoideum and macrophages. Reducing expression of polyphosphate kinase 1 in M. smegmatis reduced extracellular polyphosphate and reduced survival in D. discoideum and macrophages, and this was reversed by the addition of extracellular polyphosphate. Conversely, treatment of D. discoideum and macrophages with recombinant yeast exopolyphosphatase reduced the survival of phagocytosed M. smegmatis or M. tuberculosis D. discoideum cells lacking the putative polyphosphate receptor GrlD had reduced sensitivity to polyphosphate and, compared to wild-type cells, showed increased killing of phagocytosed E. coli and M. smegmatis Polyphosphate inhibited phagosome acidification and lysosome activity in D. discoideum and macrophages and reduced early endosomal markers in macrophages. Together, these results suggest that bacterial polyphosphate potentiates pathogenicity by acting as an extracellular signal that inhibits phagosome maturation.
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4
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Rhee KY, Chawla R, Lele PP. Protein expression-independent response of intensity-based pH-sensitive fluorophores in Escherichia coli. PLoS One 2020; 15:e0234849. [PMID: 32555627 PMCID: PMC7302705 DOI: 10.1371/journal.pone.0234849] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 06/02/2020] [Indexed: 12/02/2022] Open
Abstract
Fluorescent proteins that modulate their emission intensities when protonated serve as excellent probes of the cytosolic pH. Since the total fluorescence output fluctuates significantly due to variations in the fluorophore levels in cells, eliminating the dependence of the signal on protein concentration is crucial. This is typically accomplished with the aid of ratiometric fluorescent proteins such as pHluorin. However, pHluorin is excited by blue light, which can complicate pH measurements by adversely impacting bacterial physiology. Here, we characterized the response of intensity-based, pH-sensitive fluorescent proteins that excite at longer wavelengths where the blue light effect is diminished. The pH-response was interpreted in terms of an analytical model that assumed two emission states for each fluorophore: a low intensity protonated state and a high intensity deprotonated state. The model suggested a scaling to eliminate the dependence of the signal on the expression levels as well as on the illumination and photon-detection settings. Experiments successfully confirmed the scaling predictions. Thus, the internal pH can be readily determined with intensity-based fluorophores with appropriate calibrations irrespective of the fluorophore concentration and the signal acquisition setup. The framework developed in this work improves the robustness of intensity-based fluorophores for internal pH measurements in E. coli, potentially extending their applications.
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Affiliation(s)
- Kathy Y. Rhee
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas, United States of America
| | - Ravi Chawla
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas, United States of America
| | - Pushkar P. Lele
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas, United States of America
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5
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Biphasic chemotaxis of Escherichia coli to the microbiota metabolite indole. Proc Natl Acad Sci U S A 2020; 117:6114-6120. [PMID: 32123098 DOI: 10.1073/pnas.1916974117] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Bacterial chemotaxis to prominent microbiota metabolites such as indole is important in the formation of microbial communities in the gastrointestinal (GI) tract. However, the basis of chemotaxis to indole is poorly understood. Here, we exposed Escherichia coli to a range of indole concentrations and measured the dynamic responses of individual flagellar motors to determine the chemotaxis response. Below 1 mM indole, a repellent-only response was observed. At 1 mM indole and higher, a time-dependent inversion from a repellent to an attractant response was observed. The repellent and attractant responses were mediated by the Tsr and Tar chemoreceptors, respectively. Also, the flagellar motor itself mediated a repellent response independent of the receptors. Chemotaxis assays revealed that receptor-mediated adaptation to indole caused a bipartite response-wild-type cells were attracted to regions of high indole concentration if they had previously adapted to indole but were otherwise repelled. We propose that indole spatially segregates cells based on their state of adaptation to repel invaders while recruiting beneficial resident bacteria to growing microbial communities within the GI tract.
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Koganitsky A, Tworowski D, Dadosh T, Cecchini G, Eisenbach M. A Mechanism of Modulating the Direction of Flagellar Rotation in Bacteria by Fumarate and Fumarate Reductase. J Mol Biol 2019; 431:3662-3676. [PMID: 31412261 DOI: 10.1016/j.jmb.2019.08.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 07/31/2019] [Accepted: 08/01/2019] [Indexed: 02/04/2023]
Abstract
Fumarate, an electron acceptor in anaerobic respiration of Escherichia coli, has an additional function of assisting the flagellar motor to shift from counterclockwise to clockwise rotation, with a consequent modulation of the bacterial swimming behavior. Fumarate transmits its effect to the motor via the fumarate reductase complex (FrdABCD), shown to bind to FliG-one of the motor's switch proteins. How binding of the FrdABCD respiratory enzyme to FliG enhances clockwise rotation and how fumarate is involved in this activity have remained puzzling. Here we show that the FrdA subunit in the presence of fumarate is sufficient for binding to FliG and for clockwise enhancement. We further demonstrate by in vitro binding assays and super-resolution microscopy in vivo that the mechanism by which fumarate-occupied FrdA enhances clockwise rotation involves its preferential binding to the clockwise state of FliG (FliGcw). Continuum electrostatics combined with docking analysis and conformational sampling endorsed the experimental conclusions and suggested that the FrdA-FliGcw interaction is driven by the positive electrostatic potential generated by FrdA and the negatively charged areas of FliG. They further demonstrated that fumarate changes FrdA's conformation to one that can bind to FliGcw. These findings also show that the reason for the failure of the succinate dehydrogenase flavoprotein SdhA (an almost-identical analog of FrdA shown to bind to FliG equally well) to enhance clockwise rotation is that it has no binding preference for FliGcw. We suggest that this mechanism is physiologically important as it can modulate the magnitude of ΔG0 between the clockwise and counterclockwise states of the motor to tune the motor to the growth conditions of the bacteria.
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Affiliation(s)
- Anna Koganitsky
- Department of Biomolecular Sciences, The Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Dmitry Tworowski
- Department of Structural Biology, The Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Tali Dadosh
- Department of Chemical Research Support, The Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Gary Cecchini
- Molecular Biology Division, San Francisco VA Health Care System, San Francisco, CA 94121, USA; Department of Biochemistry & Biophysics, University of California, San Francisco, CA 94158, USA
| | - Michael Eisenbach
- Department of Biomolecular Sciences, The Weizmann Institute of Science, 7610001 Rehovot, Israel.
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7
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Sakai T, Miyata T, Terahara N, Mori K, Inoue Y, Morimoto YV, Kato T, Namba K, Minamino T. Novel Insights into Conformational Rearrangements of the Bacterial Flagellar Switch Complex. mBio 2019; 10:e00079-19. [PMID: 30940700 PMCID: PMC6445934 DOI: 10.1128/mbio.00079-19] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 02/26/2019] [Indexed: 01/01/2023] Open
Abstract
The flagellar motor can spin in both counterclockwise (CCW) and clockwise (CW) directions. The flagellar motor consists of a rotor and multiple stator units, which act as a proton channel. The rotor is composed of the transmembrane MS ring made of FliF and the cytoplasmic C ring consisting of FliG, FliM, and FliN. The C ring is directly involved in rotation and directional switching. The Salmonella FliF-FliG deletion fusion motor missing 56 residues from the C terminus of FliF and 94 residues from the N terminus of FliG keeps a domain responsible for the interaction with the stator intact, but its motor function is reduced significantly. Here, we report the structure and function of the FliF-FliG deletion fusion motor. The FliF-FliG deletion fusion not only resulted in a strong CW switch bias but also affected rotor-stator interactions coupled with proton translocation through the proton channel of the stator unit. The energy coupling efficiency of the deletion fusion motor was the same as that of the wild-type motor. Extragenic suppressor mutations in FliG, FliM, or FliN not only relieved the strong CW switch bias but also increased the motor speed at low load. The FliF-FliG deletion fusion made intersubunit interactions between C ring proteins tighter compared to the wild-type motor, whereas the suppressor mutations affect such tighter intersubunit interactions. We propose that a change of intersubunit interactions between the C ring proteins may be required for high-speed motor rotation as well as direction switching.IMPORTANCE The bacterial flagellar motor is a bidirectional rotary motor for motility and chemotaxis, which often plays an important role in infection. The motor is a large transmembrane protein complex composed of a rotor and multiple stator units, which also act as a proton channel. Motor torque is generated through their cyclic association and dissociation coupled with proton translocation through the proton channel. A large cytoplasmic ring of the motor, called C ring, is responsible for rotation and switching by interacting with the stator, but the mechanism remains unknown. By analyzing the structure and function of the wild-type motor and a mutant motor missing part of the C ring connecting itself with the transmembrane rotor ring while keeping a stator-interacting domain for bidirectional torque generation intact, we found interesting clues to the change in the C ring conformation for the switching and rotation involving loose and tight intersubunit interactions.
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Affiliation(s)
- Tomofumi Sakai
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
| | - Tomoko Miyata
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
| | - Naoya Terahara
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
| | - Koichiro Mori
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
| | - Yumi Inoue
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
| | - Yusuke V Morimoto
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
- RIKEN Center for Biosystems Dynamics Research, Suita, Osaka, Japan
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Iizuka, Fukuoka, Japan
| | - Takayuki Kato
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
| | - Keiichi Namba
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
- RIKEN Center for Biosystems Dynamics Research, Suita, Osaka, Japan
- RIKEN SPring-8 Center, Suita, Osaka, Japan
| | - Tohru Minamino
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
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8
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Ford KM, Antani JD, Nagarajan A, Johnson MM, Lele PP. Switching and Torque Generation in Swarming E. coli. Front Microbiol 2018; 9:2197. [PMID: 30279682 PMCID: PMC6153309 DOI: 10.3389/fmicb.2018.02197] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 08/28/2018] [Indexed: 12/14/2022] Open
Abstract
Escherichia coli swarm on semi-solid surfaces with the aid of flagella. It has been hypothesized that swarmer cells overcome the increased viscous drag near surfaces by developing higher flagellar thrust and by promoting surface wetness with the aid of a flagellar switch. The switch enables reversals between clockwise (CW) and counterclockwise (CCW) directions of rotation of the flagellar motor. Here, we measured the behavior of flagellar motors in swarmer cells. Results indicated that although the torque was similar to that in planktonic cells, the tendency to rotate CCW was higher in swarmer cells. This suggested that swarmers likely have a smaller pool of phosphorylated CheY. Results further indicated that the upregulation of the flagellin gene was not critical for flagellar thrust or swarming. Consistent with earlier reports, moisture added to the swarm surface restored swarming in a CCW-only mutant, but not in a FliG mutant that rotated motors CW-only (FliGCW). Fluorescence assays revealed that FliGCW cells grown on agar surfaces carried fewer flagella than planktonic FliGCW cells. The surface-dependent reduction in flagella correlated with a reduction in the number of putative flagellar preassemblies. These results hint toward a possibility that the conformational dynamics of switch proteins play a role in the proper assembly of flagellar complexes and flagellar export, thereby aiding bacterial swarming.
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Affiliation(s)
- Katie M Ford
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, United States
| | - Jyot D Antani
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, United States
| | - Aravindh Nagarajan
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, United States
| | - Madeline M Johnson
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, United States
| | - Pushkar P Lele
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, United States
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Choi MK, Jo S, Lee BH, Kim MH, Choi JB, Kim K, Kim MK. Dynamic characteristics of a flagellar motor protein analyzed using an elastic network model. J Mol Graph Model 2017; 78:81-87. [PMID: 29054097 DOI: 10.1016/j.jmgm.2017.10.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Revised: 10/02/2017] [Accepted: 10/03/2017] [Indexed: 12/23/2022]
Abstract
At the base of a flagellar motor, its rotational direction and speed are regulated by the interaction between rotor and stator proteins. A switching event occurs when the cytoplasmic rotor protein, called C-ring, changes its conformation in response to binding of the CheY signal protein. The C-ring structure consists of FliG, FliM, and FliN proteins and its conformational changes in FliM and FliG including HelixMC play an important role in switching the motor direction. Therefore, clarifying their dynamic properties as well as conformational changes is a key to understanding the switching mechanism of the motor protein. In this study, to elucidate dynamic characteristics of the C-ring structure, both harmonic (intrinsic vibration) and anharmonic (transition pathway) analyses are conducted by using the symmetry-constrained elastic network model. As a result, the first three normal modes successfully capture the essence of transition pathway from wild type to CW-biased state. Their cumulative square overlap value reaches up to 0.842. Remarkably, it is also noted from the transition pathway that the cascade of interactions from the signal protein to FliM to FliG, highlighted by the major mode shapes from the first three normal modes, induces the reorientation (∼100° rotation of FliGC5) of FliG C-terminal that directly interacts with the stator protein. Presumably, the rotational direction of the motor protein is switched by this substantial change in the stator-rotor interaction.
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Affiliation(s)
- Moon-Ki Choi
- School of Mechanical Engineering, Sungkyunkwan University, Suwon, 16419, Korea
| | - Soojin Jo
- School of Mechanical Engineering, Sungkyunkwan University, Suwon, 16419, Korea
| | - Byung Ho Lee
- School of Mechanical Engineering, Sungkyunkwan University, Suwon, 16419, Korea
| | - Min Hyeok Kim
- Korea Institute for Advanced Study, Seoul, 02455, Korea
| | - Jae Boong Choi
- School of Mechanical Engineering, Sungkyunkwan University, Suwon, 16419, Korea
| | - Kyunghoon Kim
- School of Mechanical Engineering, Sungkyunkwan University, Suwon, 16419, Korea
| | - Moon Ki Kim
- School of Mechanical Engineering, Sungkyunkwan University, Suwon, 16419, Korea.
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10
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Impact of fluorescent protein fusions on the bacterial flagellar motor. Sci Rep 2017; 7:12583. [PMID: 28974721 PMCID: PMC5626733 DOI: 10.1038/s41598-017-11241-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 08/22/2017] [Indexed: 01/16/2023] Open
Abstract
Fluorescent fusion proteins open a direct and unique window onto protein function. However, they also introduce the risk of perturbation of the function of the native protein. Successful applications of fluorescent fusions therefore rely on a careful assessment and minimization of the side effects, but such insight is still lacking for many applications. This is particularly relevant in the study of the internal dynamics of motor proteins, where both the chemical and mechanical reaction coordinates can be affected. Fluorescent proteins fused to the stator of the Bacterial Flagellar Motor (BFM) have previously been used to unveil the motor subunit dynamics. Here we report the effects on single motors of three fluorescent proteins fused to the stators, all of which altered BFM behavior. The torque generated by individual stators was reduced while their stoichiometry remained unaffected. MotB fusions decreased the switching frequency and induced a novel bias-dependent asymmetry in the speed in the two directions. These effects could be mitigated by inserting a linker at the fusion point. These findings provide a quantitative account of the effects of fluorescent fusions to the stator on BFM dynamics and their alleviation- new insights that advance the use of fluorescent fusions to probe the dynamics of protein complexes.
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11
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Bacterial Flagellar Motor Switch in Response to CheY-P Regulation and Motor Structural Alterations. Biophys J 2016; 110:1411-20. [PMID: 27028650 DOI: 10.1016/j.bpj.2016.02.023] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 02/16/2016] [Accepted: 02/17/2016] [Indexed: 11/20/2022] Open
Abstract
The bacterial flagellar motor (BFM) is a molecular machine that rotates the helical filaments and propels the bacteria swimming toward favorable conditions. In our previous works, we built a stochastic conformational spread model to explain the dynamic and cooperative behavior of BFM switching. Here, we extended this model to test whether it can explain the latest experimental observations regarding CheY-P regulation and motor structural adaptivity. We show that our model predicts a strong correlation between rotational direction and the number of CheY-Ps bound to the switch complex, in agreement with the latest finding from Fukuoka et al. It also predicts that the switching sensitivity of the BFM can be fine-tuned by incorporating additional units into the switch complex, as recently demonstrated by Yuan et al., who showed that stoichiometry of FliM undergoes dynamic change to maintain ultrasensitivity in the motor switching response. In addition, by locking some rotor switching units on the switch complex into the stable clockwise-only conformation, our model has accurately simulated recent experiments expressing clockwise-locked FliG(ΔPAA) into the switch complex and reproduced the increased switching rate of the motor.
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12
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Pandini A, Morcos F, Khan S. The Gearbox of the Bacterial Flagellar Motor Switch. Structure 2016; 24:1209-20. [PMID: 27345932 PMCID: PMC4938800 DOI: 10.1016/j.str.2016.05.012] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 04/26/2016] [Accepted: 05/23/2016] [Indexed: 12/11/2022]
Abstract
Switching of flagellar motor rotation sense dictates bacterial chemotaxis. Multi-subunit FliM-FliG rotor rings couple signal protein binding in FliM with reversal of a distant FliG C-terminal (FliGC) helix involved in stator contacts. Subunit dynamics were examined in conformer ensembles generated by molecular simulations from the X-ray structures. Principal component analysis extracted collective motions. Interfacial loop immobilization by complex formation coupled elastic fluctuations of the FliM middle (FliMM) and FliG middle (FliGM) domains. Coevolved mutations captured interfacial dynamics as well as contacts. FliGM rotation was amplified via two central hinges to the FliGC helix. Intrinsic flexibility, reported by the FliGMC ensembles, reconciled conformers with opposite FliGC helix orientations. FliG domain stacking deformed the inter-domain linker and reduced flexibility; but conformational changes were not triggered by engineered linker deletions that cause a rotation-locked phenotype. These facts suggest that binary rotation states arise from conformational selection by stacking interactions. Switch complex exploits differential subunit stiffness for mechanical amplification Distinct rotor protein X-ray structures generate overlapping conformer ensembles Stacking constraints on a flexible helix linker could select diverse rotation states Non-contact elastic couplings at the subunit interface in the complex have coevolved
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Affiliation(s)
- Alessandro Pandini
- Department of Computer Science and Synthetic Biology Theme, Brunel University London, Uxbridge UB8 3PH, UK; Computational Cell and Molecular Biology, The Francis Crick Institute, London NW1 1AT, UK
| | - Faruck Morcos
- Department of Biological Sciences, University of Texas at Dallas, Richardson, TX 75080, USA
| | - Shahid Khan
- Molecular Biology Consortium, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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13
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Onoue Y, Kojima S, Homma M. Effect of FliG three amino acids deletion in Vibrio polar-flagellar rotation and formation. J Biochem 2015; 158:523-9. [PMID: 26142283 DOI: 10.1093/jb/mvv068] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 06/03/2015] [Indexed: 11/14/2022] Open
Abstract
Most of bacteria can swim by rotating flagella bidirectionally. The C ring, located at the bottom of the flagellum and in the cytoplasmic space, consists of FliG, FliM and FliN, and has an important function in flagellar protein secretion, torque generation and rotational switch of the motor. FliG is the most important part of the C ring that interacts directly with a stator subunit. Here, we introduced a three-amino acids in-frame deletion mutation (ΔPSA) into FliG from Vibrio alginolyticus, whose corresponding mutation in Salmonella confers a switch-locked phenotype, and examined its phenotype. We found that this FliG mutant could not produce flagellar filaments in a fliG null strain but the FliG(ΔPSA) protein could localize at the cell pole as does the wild-type protein. Unexpectedly, when this mutant was expressed in a wild-type strain, cells formed flagella efficiently but the motor could not rotate. We propose that this different phenotype in Vibrio and Salmonella might be due to distinct interactions between FliG mutant and FliM in the C ring between the bacterial species.
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Affiliation(s)
- Yasuhiro Onoue
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan
| | - Seiji Kojima
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan
| | - Michio Homma
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan
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