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Xia X, Li Y, Xiao X, Zhang Z, Mao C, Li T, Wan M. Chemotactic Micro/Nanomotors for Biomedical Applications. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2306191. [PMID: 37775935 DOI: 10.1002/smll.202306191] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 09/12/2023] [Indexed: 10/01/2023]
Abstract
In nature, many organisms respond chemotactically to external chemical stimuli in order to extract nutrients or avoid danger. Inspired by this natural chemotaxis, micro/nanomotors with chemotactic properties have been developed and applied to study a variety of disease models. This chemotactic strategy has shown promising results and has attracted the attention of an increasing number of researchers. This paper mainly reviews the construction methods of different types of chemotactic micro/nanomotors, the mechanism of chemotaxis, and the potential applications in biomedicine. First, based on the classification of materials, the construction methods and therapeutic effects of chemotactic micro/nanomotors based on natural cells and synthetic materials in cellular and animal experiments will be elaborated in detail. Second, the mechanism of chemotaxis of micro/nanomotors is elaborated in detail: chemical reaction induced chemotaxis and physical process driven chemotaxis. In particular, the main differences and significant advantages between chemotactic micro/nanomotors and magnetic, electrical and optical micro/nanomotors are described. The applications of chemotactic micro/nanomotors in the biomedical fields in recent years are then summarized, focusing on the mechanism of action and therapeutic effects in cancer and cardiovascular disease. Finally, the authors are looking forward to the future development of chemotactic micro/nanomotors in the biomedical fields.
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Affiliation(s)
- Xue Xia
- National and Local Joint Engineering Research Center of Biomedical Functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, China
| | - Yue Li
- National and Local Joint Engineering Research Center of Biomedical Functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, China
| | - Xiangyu Xiao
- National and Local Joint Engineering Research Center of Biomedical Functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, China
| | - Ziqiang Zhang
- National and Local Joint Engineering Research Center of Biomedical Functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, China
| | - Chun Mao
- National and Local Joint Engineering Research Center of Biomedical Functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, China
| | - Ting Li
- National and Local Joint Engineering Research Center of Biomedical Functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, China
| | - Mimi Wan
- National and Local Joint Engineering Research Center of Biomedical Functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, China
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2
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Bano R, Mears P, Golding I, Chemla YR. Flagellar dynamics reveal fluctuations and kinetic limit in the Escherichia coli chemotaxis network. Sci Rep 2023; 13:22891. [PMID: 38129516 PMCID: PMC10739816 DOI: 10.1038/s41598-023-49784-w] [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: 09/11/2023] [Accepted: 12/12/2023] [Indexed: 12/23/2023] Open
Abstract
The Escherichia coli chemotaxis network, by which bacteria modulate their random run/tumble swimming pattern to navigate their environment, must cope with unavoidable number fluctuations ("noise") in its molecular constituents like other signaling networks. The probability of clockwise (CW) flagellar rotation, or CW bias, is a measure of the chemotaxis network's output, and its temporal fluctuations provide a proxy for network noise. Here we quantify fluctuations in the chemotaxis signaling network from the switching statistics of flagella, observed using time-resolved fluorescence microscopy of individual optically trapped E. coli cells. This approach allows noise to be quantified across the dynamic range of the network. Large CW bias fluctuations are revealed at steady state, which may play a critical role in driving flagellar switching and cell tumbling. When the network is stimulated chemically to higher activity, fluctuations dramatically decrease. A stochastic theoretical model, inspired by work on gene expression noise, points to CheY activation occurring in bursts, driving CW bias fluctuations. This model also shows that an intrinsic kinetic ceiling on network activity places an upper limit on activated CheY and CW bias, which when encountered suppresses network fluctuations. This limit may also prevent cells from tumbling unproductively in steep gradients.
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Affiliation(s)
- Roshni Bano
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Patrick Mears
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Ido Golding
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Yann R Chemla
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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3
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Lu S, Chemla YR. Optical traps induce fluorophore photobleaching by two-photon excitation. Biophys J 2023; 122:4316-4325. [PMID: 37828742 PMCID: PMC10698272 DOI: 10.1016/j.bpj.2023.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 09/20/2023] [Accepted: 10/10/2023] [Indexed: 10/14/2023] Open
Abstract
Techniques combining optical tweezers with fluorescence microscopy have become increasingly popular. Unfortunately, the high-power, infrared lasers used to create optical traps can have a deleterious effect on dye stability. Previous studies have shown that dye photobleaching is enhanced by absorption of visible fluorescence excitation plus infrared trap photons, a process that can be significantly reduced by minimizing simultaneous exposure to both light sources. Here, we report another photobleaching pathway that results from direct excitation by the trapping laser alone. Our results show that this trap-induced fluorescence loss is a two-photon absorption process, as demonstrated by a quadratic dependence on the intensity of the trapping laser. We further show that, under conditions typical of many trap-based experiments, fluorescence emission of certain fluorophores near the trap focus can drop by 90% within 1 min. We investigate how photostability is affected by the choice of dye molecule, excitation and emission wavelength, and labeled molecule. Finally, we discuss the different photobleaching pathways in combined trap-fluorescence measurements, which guide the selection of optimal dyes and conditions for more robust experimental protocols.
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Affiliation(s)
- Suoang Lu
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Yann R Chemla
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois; Center of the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, Illinois.
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4
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Melamed S, Zhang A, Jarnik M, Mills J, Silverman A, Zhang H, Storz G. σ 28-dependent small RNA regulation of flagella biosynthesis. eLife 2023; 12:RP87151. [PMID: 37843988 PMCID: PMC10578931 DOI: 10.7554/elife.87151] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2023] Open
Abstract
Flagella are important for bacterial motility as well as for pathogenesis. Synthesis of these structures is energy intensive and, while extensive transcriptional regulation has been described, little is known about the posttranscriptional regulation. Small RNAs (sRNAs) are widespread posttranscriptional regulators, most base pairing with mRNAs to affect their stability and/or translation. Here, we describe four UTR-derived sRNAs (UhpU, MotR, FliX and FlgO) whose expression is controlled by the flagella sigma factor σ28 (fliA) in Escherichia coli. Interestingly, the four sRNAs have varied effects on flagellin protein levels, flagella number and cell motility. UhpU, corresponding to the 3´ UTR of a metabolic gene, likely has hundreds of targets including a transcriptional regulator at the top flagella regulatory cascade connecting metabolism and flagella synthesis. Unlike most sRNAs, MotR and FliX base pair within the coding sequences of target mRNAs and act on ribosomal protein mRNAs connecting ribosome production and flagella synthesis. The study shows how sRNA-mediated regulation can overlay a complex network enabling nuanced control of flagella synthesis.
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Affiliation(s)
- Sahar Melamed
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human DevelopmentBethesdaUnited States
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of JerusalemJerusalemIsrael
| | - Aixia Zhang
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human DevelopmentBethesdaUnited States
| | - Michal Jarnik
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human DevelopmentBethesdaUnited States
| | - Joshua Mills
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human DevelopmentBethesdaUnited States
| | - Aviezer Silverman
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of JerusalemJerusalemIsrael
| | - Hongen Zhang
- Bioinformatics and Scientific Computing Core, Eunice Kennedy Shriver National Institute of Child Health and Human DevelopmentBethesdaUnited States
| | - Gisela Storz
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human DevelopmentBethesdaUnited States
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Tan A, Alsenani Q, Lanz M, Birchall C, Drage LKL, Picton D, Mowbray C, Ali A, Harding C, Pickard RS, Hall J, Aldridge PD. Evasion of toll-like receptor recognition by Escherichia coli is mediated via population level regulation of flagellin production. Front Microbiol 2023; 14:1093922. [PMID: 37032848 PMCID: PMC10078357 DOI: 10.3389/fmicb.2023.1093922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 03/03/2023] [Indexed: 04/11/2023] Open
Abstract
Uropathogenic Escherichia coli is a major cause of urinary tract infections. Analysis of the innate immune response in immortalized urothelial cells suggests that the bacterial flagellar subunit, flagellin, is key in inducing host defenses. A panel of 48 clinical uro-associated E. coli isolates recovered from either cystitis, pyelonephritis asymptomatic bacteriuria (ABU) or UTI-associated bacteraemia infections were characterized for motility and their ability to induce an innate response in urothelial cells stably transfected with a NF-κB luciferase reporter. Thirty-two isolates (67%) were identified as motile with strains recovered from cystitis patients exhibiting an uneven motility distribution pattern; seven of the cystitis isolates were associated with a > 5-fold increase in NF-κB signaling. To explore whether the NF-κB signaling response reflected antigenic variation, flagellin was purified from 14 different isolates. Purified flagellin filaments generated comparable NF-κB signaling responses, irrespective of either the source of the isolate or H-serotype. These data argued against any variability between isolates being related to flagellin itself. Investigations also argued that neither TLR4 dependent recognition of bacterial lipopolysaccharide nor growth fitness of the isolates played key roles in leading to the variable host response. To determine the roles, if any, of flagellar abundance in inducing these variable responses, flagellar hook numbers of a range of cystitis and ABU isolates were quantified. Images suggested that up to 60% of the isolate population exhibited flagella with the numbers averaging between 1 and 2 flagella per bacterial cell. These data suggest that selective pressures exist in the urinary tract that allow uro-associated E. coli strains to maintain motility, but exploit population heterogeneity, which together function to prevent host TLR5 recognition and bacterial killing.
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Affiliation(s)
- Aaron Tan
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Qusai Alsenani
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Marcello Lanz
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Christopher Birchall
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Lauren K. L. Drage
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - David Picton
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Catherine Mowbray
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Ased Ali
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Christopher Harding
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
- Urology Department, Freeman Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Robert S. Pickard
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
- Urology Department, Freeman Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Judith Hall
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
- *Correspondence: Judith Hall,
| | - Phillip D. Aldridge
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
- Phillip D. Aldridge,
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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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7
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Voliotis M, Rosko J, Pilizota T, Liverpool TB. Steady-state running rate sets the speed and accuracy of accumulation of swimming bacteria. Biophys J 2022; 121:3435-3444. [PMID: 36045575 PMCID: PMC9515231 DOI: 10.1016/j.bpj.2022.08.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 07/31/2022] [Accepted: 08/15/2022] [Indexed: 11/21/2022] Open
Abstract
We study the chemotaxis of a population of genetically identical swimming bacteria undergoing run and tumble dynamics driven by stochastic switching between clockwise and counterclockwise rotation of the flagellar rotary system, where the steady-state rate of the switching changes in different environments. Understanding chemotaxis quantitatively requires that one links the measured steady-state switching rates of the rotary system, as well as the directional changes of individual swimming bacteria in a gradient of chemoattractant/repellant, to the efficiency of a population of bacteria in moving up/down the gradient. Here we achieve this by using a probabilistic model, parametrized with our experimental data, and show that the response of a population to the gradient is complex. We find the changes to the steady-state switching rate in the absence of gradients affect the average speed of the swimming bacterial population response as well as the width of the distribution. Both must be taken into account when optimizing the overall response of the population in complex environments.
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Affiliation(s)
- Margaritis Voliotis
- College of Engineering, Mathematics and Physical Sciences, University of Exeter, Exeter, United Kingdom.
| | - Jerko Rosko
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Teuta Pilizota
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, United Kingdom.
| | - Tanniemola B Liverpool
- School of Mathematics, University of Bristol, Bristol, United Kingdom; BrisSynBio, Life Sciences Building, University of Bristol, Bristol, United Kingdom.
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8
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Junot G, Darnige T, Lindner A, Martinez VA, Arlt J, Dawson A, Poon WCK, Auradou H, Clément E. Run-to-Tumble Variability Controls the Surface Residence Times of E. coli Bacteria. PHYSICAL REVIEW LETTERS 2022; 128:248101. [PMID: 35776449 DOI: 10.1103/physrevlett.128.248101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 04/19/2022] [Indexed: 06/15/2023]
Abstract
Motile bacteria are known to accumulate at surfaces, eventually leading to changes in bacterial motility and biofilm formation. We use a novel two-color, three-dimensional Lagrangian tracking technique to follow simultaneously the body and the flagella of a wild-type Escherichia coli. We observe long surface residence times and surface escape corresponding mostly to immediately antecedent tumbling. A motility model accounting for a large behavioral variability in run-time duration reproduces all experimental findings and gives new insights into surface trapping efficiency.
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Affiliation(s)
- Gaspard Junot
- PMMH, UMR 7636 CNRS, ESPCI Paris, PSL Research University, Sorbonne Université and Université Paris Cité, 7-9 quai Saint-Bernard, Paris, 75005, France
| | - Thierry Darnige
- PMMH, UMR 7636 CNRS, ESPCI Paris, PSL Research University, Sorbonne Université and Université Paris Cité, 7-9 quai Saint-Bernard, Paris, 75005, France
| | - Anke Lindner
- PMMH, UMR 7636 CNRS, ESPCI Paris, PSL Research University, Sorbonne Université and Université Paris Cité, 7-9 quai Saint-Bernard, Paris, 75005, France
| | - Vincent A Martinez
- SUPA and the School of Physics and Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - Jochen Arlt
- SUPA and the School of Physics and Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - Angela Dawson
- SUPA and the School of Physics and Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - Wilson C K Poon
- SUPA and the School of Physics and Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - Harold Auradou
- Université Paris-Saclay, CNRS, FAST, 91405 Orsay, France
| | - Eric Clément
- PMMH, UMR 7636 CNRS, ESPCI Paris, PSL Research University, Sorbonne Université and Université Paris Cité, 7-9 quai Saint-Bernard, Paris, 75005, France
- Institut Universitaire de France (IUF)
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9
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Flagellin outer domain dimerization modulates motility in pathogenic and soil bacteria from viscous environments. Nat Commun 2022; 13:1422. [PMID: 35301306 PMCID: PMC8931119 DOI: 10.1038/s41467-022-29069-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 02/24/2022] [Indexed: 12/01/2022] Open
Abstract
Flagellar filaments function as the propellers of the bacterial flagellum and their supercoiling is key to motility. The outer domains on the surface of the filament are non-critical for motility in many bacteria and their structures and functions are not conserved. Here, we show the atomic cryo-electron microscopy structures for flagellar filaments from enterohemorrhagic Escherichia coli O157:H7, enteropathogenic E. coli O127:H6, Achromobacter, and Sinorhizobium meliloti, where the outer domains dimerize or tetramerize to form either a sheath or a screw-like surface. These dimers are formed by 180° rotations of half of the outer domains. The outer domain sheath (ODS) plays a role in bacterial motility by stabilizing an intermediate waveform and prolonging the tumbling of E. coli cells. Bacteria with these ODS and screw-like flagellar filaments are commonly found in soil and human intestinal environments of relatively high viscosity suggesting a role for the dimerization in these environments. It has been suggested that the outer domains of bacterial flagellins are not needed for motility. Here, the authors show that flagellar filament outer domains from some bacteria have unique structures which can alter the motility of the bacteria.
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Pareek V, Gupta R, Devineau S, Sivasankaran SK, Bhargava A, Khan MA, Srikumar S, Fanning S, Panwar J. Does Silver in Different Forms Affect Bacterial Susceptibility and Resistance? A Mechanistic Perspective. ACS APPLIED BIO MATERIALS 2022; 5:801-817. [PMID: 35073697 DOI: 10.1021/acsabm.1c01179] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The exceptional increase in antibiotic resistance in past decades motivated the scientific community to use silver as a potential antibacterial agent. However, due to its unknown antibacterial mechanism and the pattern of bacterial resistance to silver species, it has not been revolutionized in the health sector. This study deciphers mechanistic aspects of silver species, i.e., ions and lysozyme-coated silver nanoparticles (L-Ag NPs), against E. coli K12 through RNA sequencing analysis. The obtained results support the reservoir nature of nanoparticles for the controlled release of silver ions into bacteria. This study differentiates between the antibacterial mechanism of silver species by discussing the pathway of their entry in bacteria, sequence of events inside cells, and response of bacteria to overcome silver stress. Controlled release of ions from L-Ag NPs not only reduces bacterial growth but also reduces the likelihood of resistance development. Conversely, direct exposure of silver ions, leads to rapid activation of the bacterial defense system leading to development of resistance against silver ions, like the well-known antibiotic resistance problem. These findings provide valuable insight on the mechanism of silver resistance and antibacterial strategies deployed by E. coli K12, which could be a potential target for the generation of aim-based and effective nanoantibiotics.
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Affiliation(s)
- Vikram Pareek
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani 333031, India.,School of Public Health, Physiotherapy and Sports Science, Centre for Food Safety, Science Centre South, University College Dublin, Dublin 4, Ireland
| | - Rinki Gupta
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani 333031, India
| | | | | | - Arpit Bhargava
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani 333031, India
| | - Mohd Azeem Khan
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani 333031, India
| | - Shabrinath Srikumar
- Department of Food, Nutrition and Health, College of Food and Agriculture, UAE University, Al Ain 15551, UAE
| | - Séamus Fanning
- School of Public Health, Physiotherapy and Sports Science, Centre for Food Safety, Science Centre South, University College Dublin, Dublin 4, Ireland.,Institute for Global Food Security, Queen's University Belfast, Belfast BT7 1NN, United Kingdom
| | - Jitendra Panwar
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani 333031, India
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11
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Schröder NCH, Korša A, Wami H, Mantel O, Dobrindt U, Kurtz J. Serial passage in an insect host indicates genetic stability of the human probiotic Escherichia coli Nissle 1917. Evol Med Public Health 2022; 10:71-86. [PMID: 35186295 PMCID: PMC8853844 DOI: 10.1093/emph/eoac001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 12/17/2021] [Indexed: 11/14/2022] Open
Abstract
Background and objectives The probiotic Escherichia coli strain Nissle 1917 (EcN) has been shown to effectively prevent and alleviate intestinal diseases. Despite the widespread medical application of EcN, we still lack basic knowledge about persistence and evolution of EcN outside the human body. Such knowledge is important also for public health aspects, as in contrast to abiotic therapeutics, probiotics are living organisms that have the potential to evolve. This study made use of experimental evolution of EcN in an insect host, the red flour beetle Tribolium castaneum, and its flour environment. Methodology Using a serial passage approach, we orally introduced EcN to larvae of T.castaneum as a new host, and also propagated it in the flour environment. After eight propagation cycles, we analyzed phenotypic attributes of the passaged replicate EcN lines, their effects on the host in the context of immunity and infection with the entomopathogen Bacillus thuringiensis, and potential genomic changes using WGS of three of the evolved lines. Results We observed weak phenotypic differences between the ancestral EcN and both, beetle and flour passaged EcN lines, in motility and growth at 30°C, but neither any genetic changes, nor the expected increased persistence of the beetle-passaged lines. One of these lines displayed distinct morphological and physiological characteristics. Conclusions and implications Our findings suggest that EcN remains rather stable during serial passage in an insect. Weak phenotypic changes in growth and motility combined with a lack of genetic changes indicate a certain degree of phenotypic plasticity of EcN. Lay Summary For studying adaptation of the human probiotic Escherichia coli strain Nissle 1917, we introduced it to a novel insect host system and its environment using a serial passage approach. After passage, we observed weak phenotypic changes in growth and motility but no mutations or changes in persistence inside the host.
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Affiliation(s)
- Nicolas C H Schröder
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Ana Korša
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Haleluya Wami
- Institute for Hygiene, UKM Münster, Münster, Germany
| | - Olena Mantel
- Institute for Hygiene, UKM Münster, Münster, Germany
| | | | - Joachim Kurtz
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
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12
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Colin R, Ni B, Laganenka L, Sourjik V. Multiple functions of flagellar motility and chemotaxis in bacterial physiology. FEMS Microbiol Rev 2021; 45:fuab038. [PMID: 34227665 PMCID: PMC8632791 DOI: 10.1093/femsre/fuab038] [Citation(s) in RCA: 90] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 07/02/2021] [Indexed: 12/13/2022] Open
Abstract
Most swimming bacteria are capable of following gradients of nutrients, signaling molecules and other environmental factors that affect bacterial physiology. This tactic behavior became one of the most-studied model systems for signal transduction and quantitative biology, and underlying molecular mechanisms are well characterized in Escherichia coli and several other model bacteria. In this review, we focus primarily on less understood aspect of bacterial chemotaxis, namely its physiological relevance for individual bacterial cells and for bacterial populations. As evident from multiple recent studies, even for the same bacterial species flagellar motility and chemotaxis might serve multiple roles, depending on the physiological and environmental conditions. Among these, finding sources of nutrients and more generally locating niches that are optimal for growth appear to be one of the major functions of bacterial chemotaxis, which could explain many chemoeffector preferences as well as flagellar gene regulation. Chemotaxis might also generally enhance efficiency of environmental colonization by motile bacteria, which involves intricate interplay between individual and collective behaviors and trade-offs between growth and motility. Finally, motility and chemotaxis play multiple roles in collective behaviors of bacteria including swarming, biofilm formation and autoaggregation, as well as in their interactions with animal and plant hosts.
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Affiliation(s)
- Remy Colin
- Max Planck Institute for Terrestrial Microbiology & Center for Synthetic Microbiology (SYNMIKRO), Karl-von-Frisch Strasse 16, Marburg D-35043, Germany
| | - Bin Ni
- Max Planck Institute for Terrestrial Microbiology & Center for Synthetic Microbiology (SYNMIKRO), Karl-von-Frisch Strasse 16, Marburg D-35043, Germany
- College of Resources and Environmental Science, National Academy of Agriculture Green Development, China Agricultural University, Yuanmingyuan Xilu No. 2, Beijing 100193, China
| | - Leanid Laganenka
- Institute of Microbiology, D-BIOL, ETH Zürich, Vladimir-Prelog-Weg 4, Zürich 8093, Switzerland
| | - Victor Sourjik
- Max Planck Institute for Terrestrial Microbiology & Center for Synthetic Microbiology (SYNMIKRO), Karl-von-Frisch Strasse 16, Marburg D-35043, Germany
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13
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Liu G, Liu Z, Zhu L, Zhang R, Yuan J. Upcoming flow promotes the bundle formation of bacterial flagella. Biophys J 2021; 120:4391-4398. [PMID: 34509505 DOI: 10.1016/j.bpj.2021.09.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 07/21/2021] [Accepted: 09/07/2021] [Indexed: 11/15/2022] Open
Abstract
Flagellated bacteria swim by rotating a bundle of helical flagella and commonly explore the surrounding environment in a "run-and-tumble" motility mode. Here, we show that the upcoming flow could impact the bacterial run-and-tumble behavior by affecting the formation and dispersal of the flagellar bundle. Using a dual optical tweezers setup to trap individual bacteria, we characterized the effects of the imposed fluid flow and cell body rotation on the run-and-tumble behavior. We found that the two factors affect the behavior differently, with the imposed fluid flow increasing the running time and decreasing the tumbling time and the cell body rotation decreasing the tumbling time only. Using numerical simulations, we computed the flagellar bundling time as a function of flow velocity, which agrees well with our experimental observations. The mechanical effects we characterized here provide novel, to our knowledge, ingredients for further studies of bacterial chemotaxis in complex environments such as dynamic fluid environments.
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Affiliation(s)
- Guangzhe Liu
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Physics, Hefei, China
| | - Zhaorong Liu
- State Key Laboratory of Fire Science, University of Science and Technology of China, Hefei, China
| | - Lailai Zhu
- Department of Mechanical Engineering, National University of Singapore, Singapore, Singapore
| | - Rongjing Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Physics, Hefei, China.
| | - Junhua Yuan
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Physics, Hefei, China.
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14
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Ni B, Colin R, Sourjik V. Production and Characterization of Motile and Chemotactic Bacterial Minicells. ACS Synth Biol 2021; 10:1284-1291. [PMID: 34081866 PMCID: PMC8218304 DOI: 10.1021/acssynbio.1c00012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
![]()
Minicells are nanosized
membrane vesicles produced by bacteria.
Minicells are chromosome-free but contain cellular biosynthetic and
metabolic machinery, and they are robust due to the protection provided
by the bacterial cell envelope, which makes them potentially highly
attractive in biomedical applications. However, the applicability
of minicells and other nanoparticle-based delivery systems is limited
by their inefficient accumulation at the target. Here we engineered
the minicell-producing Escherichia coli strain to
overexpress flagellar genes, which enables the generation of motile
minicells. We subsequently performed an experimental and theoretical
analysis of the minicell motility and their responses to gradients
of chemoeffectors. Despite important differences between the motility
of minicells and normal bacterial cells, minicells were able to bias
their movement in chemical gradients and to accumulate toward the
sources of chemoattractants. Such motile and chemotactic minicells
may thus be applicable for an active effector delivery and specific
targeting of tissues and cells according to their metabolic profiles.
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Affiliation(s)
- Bin Ni
- Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology, Marburg D-35043, Germany
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), Philipps University Marburg, Marburg D-35043, Germany
| | - Remy Colin
- Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology, Marburg D-35043, Germany
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), Philipps University Marburg, Marburg D-35043, Germany
| | - Victor Sourjik
- Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology, Marburg D-35043, Germany
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), Philipps University Marburg, Marburg D-35043, Germany
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15
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Tao A, Zhang R, Yuan J. Direct Mapping from Intracellular Chemotaxis Signaling to Single-Cell Swimming Behavior. Biophys J 2020; 119:2461-2468. [PMID: 33189681 DOI: 10.1016/j.bpj.2020.10.040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 09/22/2020] [Accepted: 10/21/2020] [Indexed: 10/23/2022] Open
Abstract
Bacterial chemotaxis allows bacteria to sense the chemical environment and modulate their swimming behavior accordingly. Although the intracellular chemotaxis signaling pathway has been studied extensively, experimental studies are still lacking that could provide direct link from the pathway output (the intracellular concentration of the phosphorylated form of the response regulator phosphorylated CheY (CheY-P)) to single-cell swimming behavior. Here, we measured the swimming behavior of individual Escherichia coli cells while simultaneously detecting the intracellular CheY-P concentration, thereby providing a direct relationship between the intracellular CheY-P concentration and the single-cell run-and-tumble behavior. The measured relationship is consistent with the ultrasensitivity of the motor switch and a "veto model" that describes the interaction among individual flagella, although contribution from the voting mechanism could not be ruled out.
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Affiliation(s)
- Antai Tao
- Hefei National Laboratory for Physical Sciences at the Microscale, and Department of Physics, University of Science and Technology of China, Hefei, Anhui, China
| | - Rongjing Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale, and Department of Physics, University of Science and Technology of China, Hefei, Anhui, China.
| | - Junhua Yuan
- Hefei National Laboratory for Physical Sciences at the Microscale, and Department of Physics, University of Science and Technology of China, Hefei, Anhui, China.
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16
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Rhine K, Makurath MA, Liu J, Skanchy S, Lopez C, Catalan KF, Ma Y, Fare CM, Shorter J, Ha T, Chemla YR, Myong S. ALS/FTLD-Linked Mutations in FUS Glycine Residues Cause Accelerated Gelation and Reduced Interactions with Wild-Type FUS. Mol Cell 2020; 80:666-681.e8. [PMID: 33159856 PMCID: PMC7688085 DOI: 10.1016/j.molcel.2020.10.014] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 08/06/2020] [Accepted: 10/09/2020] [Indexed: 12/12/2022]
Abstract
The RNA-binding protein fused in sarcoma (FUS) can form pathogenic inclusions in neurodegenerative diseases like amyotrophic lateral sclerosis (ALS) and frontotemporal lobar dementia (FTLD). Over 70 mutations in Fus are linked to ALS/FTLD. In patients, all Fus mutations are heterozygous, indicating that the mutant drives disease progression despite the presence of wild-type (WT) FUS. Here, we demonstrate that ALS/FTLD-linked FUS mutations in glycine (G) strikingly drive formation of droplets that do not readily interact with WT FUS, whereas arginine (R) mutants form mixed condensates with WT FUS. Remarkably, interactions between WT and G mutants are disfavored at the earliest stages of FUS nucleation. In contrast, R mutants physically interact with the WT FUS such that WT FUS recovers the mutant defects by reducing droplet size and increasing dynamic interactions with RNA. This result suggests disparate molecular mechanisms underlying ALS/FTLD pathogenesis and differing recovery potential depending on the type of mutation.
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Affiliation(s)
- Kevin Rhine
- Program in Cell, Molecular, Developmental Biology, and Biophysics, Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218, USA; Department of Biology, Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218, USA
| | - Monika A Makurath
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Physics, Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - James Liu
- Department of Biology, Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218, USA; Medical Genetics and Ophthalmic Genomics Unit, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sophie Skanchy
- Department of Biophysics, Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218, USA
| | - Christian Lopez
- Department of Biology, Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218, USA
| | - Kevin F Catalan
- Program in Cell, Molecular, Developmental Biology, and Biophysics, Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218, USA; Department of Biology, Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218, USA
| | - Ye Ma
- Department of Biomedical Engineering, Johns Hopkins Medical Institute, 615 N Wolfe St, Baltimore, MD 21231, USA
| | - Charlotte M Fare
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - James Shorter
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Taekjip Ha
- Program in Cell, Molecular, Developmental Biology, and Biophysics, Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218, USA; Department of Physics, Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Biophysics, Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218, USA; Department of Biomedical Engineering, Johns Hopkins Medical Institute, 615 N Wolfe St, Baltimore, MD 21231, USA; Howard Hughes Medical Institute, Baltimore, MD 21218, USA
| | - Yann R Chemla
- Department of Physics, Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Sua Myong
- Program in Cell, Molecular, Developmental Biology, and Biophysics, Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218, USA; Department of Physics, Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Biophysics, Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218, USA.
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17
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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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18
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Agmon E, Spangler RK. A Multi-Scale Approach to Modeling E. coli Chemotaxis. ENTROPY 2020; 22:e22101101. [PMID: 33286869 PMCID: PMC7597207 DOI: 10.3390/e22101101] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/25/2020] [Accepted: 09/25/2020] [Indexed: 12/25/2022]
Abstract
The degree to which we can understand the multi-scale organization of cellular life is tied to how well our models can represent this organization and the processes that drive its evolution. This paper uses Vivarium-an engine for composing heterogeneous computational biology models into integrated, multi-scale simulations. Vivarium's approach is demonstrated by combining several sub-models of biophysical processes into a model of chemotactic E. coli that exchange molecules with their environment, express the genes required for chemotaxis, swim, grow, and divide. This model is developed incrementally, highlighting cross-compartment mechanisms that link E. coli to its environment, with models for: (1) metabolism and transport, with transport moving nutrients across the membrane boundary and metabolism converting them to useful metabolites, (2) transcription, translation, complexation, and degradation, with stochastic mechanisms that read real gene sequence data and consume base pairs and ATP to make proteins and complexes, and (3) the activity of flagella and chemoreceptors, which together support navigation in the environment.
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19
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From indication to decision: A hierarchical approach to model the chemotactic behavior of Escherichia coli. J Theor Biol 2020; 495:110253. [PMID: 32201302 DOI: 10.1016/j.jtbi.2020.110253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 03/16/2020] [Accepted: 03/18/2020] [Indexed: 10/24/2022]
Abstract
Reducing the complex behavior of living entities to its underlying physical and chemical processes is a formidable task in biology. Complex behaviors can be characterized as decision making: the ability to process the incoming information via an intracellular network and act upon this information to choose appropriate strategies. Motility is one such behavior that has been the focus many modeling efforts in the past. Our aim is to reduce the chemotactic behavior in Escherichia coli to its molecular constituents in order to paint a comprehensive and end-to-end picture of this intricate behavior. We utilize a hierarchical approach, consisting of three layers, to achieve this goal: at the first level, chemical reactions involved in chemotaxis are simulated. In the second level, the chemical reactions give rise to the mechanical movement of six independent flagella. At the last layer, the two lower layers are combined to allow a digital bacterium to receive information from its environment and swim through it with verve. Our results are in concert with the experimental studies concerning the motility of E.coli cells. In addition, we show that our detailed model of chemotaxis is reducible to a non-homogeneous Markov process.
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20
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Mousavi SM, Gompper G, Winkler RG. Wall entrapment of peritrichous bacteria: a mesoscale hydrodynamics simulation study. SOFT MATTER 2020; 16:4866-4875. [PMID: 32424390 DOI: 10.1039/d0sm00571a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Microswimmers such as E. coli bacteria accumulate and exhibit an intriguing dynamics near walls, governed by hydrodynamic and steric interactions. Insight into the underlying mechanisms and predominant interactions demand a detailed characterization of the entrapment process. We employ a mesoscale hydrodynamics simulation approach to study entrapment of an E. coli-type cell at a no-slip wall. The cell is modeled by a spherocylindrical body with several explicit helical flagella. Three stages of the entrapment process can be distinguished: the approaching regime, where a cell swims toward a wall on a nearly straight trajectory; a scattering regime, where the cell touches the wall and reorients; and a surface-swimming regime. Our simulations show that steric interactions may dominate the entrapment process, yet, hydrodynamic interactions slow down the adsorption dynamics close to the boundary and imply a circular motion on the wall. The locomotion of the cell is characterized by a strong wobbling dynamics, with cells preferentially pointing toward the wall during surface swimming.
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Affiliation(s)
- S Mahdiyeh Mousavi
- Theoretical Soft Matter and Biophysics, Institute of Complex Systems and Institute for Advanced Simulation, Forschungszentrum Jülich and JARA, D-52425 Jülich, Germany.
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21
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Nguyen HV, Faivre V. Targeted drug delivery therapies inspired by natural taxes. J Control Release 2020; 322:439-456. [PMID: 32259545 DOI: 10.1016/j.jconrel.2020.04.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/02/2020] [Accepted: 04/03/2020] [Indexed: 12/18/2022]
Abstract
A taxis is the movement responding to a stimulus of an organism. This behavior helps organisms to migrate, to find food or to avoid dangers. By mimicking and using natural taxes, many bio-inspired and bio-hybrid drug delivery systems have been synthesized. Under the guidance of physical and chemical stimuli, drug-loaded carriers are led to a target, for example tumors, then locally release the drug, inducing a therapeutic effect without influencing other parts of the body. On the other hand, for moving targets, for example metastasis cancer cells or bacteria, taking advantage of their taxes behavior is a solution to capture and to eliminate them. For instance, several traps and ecological niches have been fabricated to attract cancer cells by releasing chemokines. Cancer cells are then eliminated by drug loaded inside the trap, by radiotherapy focusing on the trap location or by simply removing the trap. Further research is needed to deeply understand the taxis behavior of organisms, which is essential to ameliorate the performance of taxes-inspired drug delivery application.
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Affiliation(s)
- Hung V Nguyen
- Université Paris-Saclay, CNRS, Institut Galien Paris Sud, 5 rue JB Clément, 92296 Châtenay-Malabry, France
| | - Vincent Faivre
- Université Paris-Saclay, CNRS, Institut Galien Paris Sud, 5 rue JB Clément, 92296 Châtenay-Malabry, France.
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22
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Dakheel MM, Alkandari FAH, Mueller-Harvey I, Woodward MJ, Rymer C. Antimicrobial in vitro activities of condensed tannin extracts on avian pathogenic Escherichia coli. Lett Appl Microbiol 2020; 70:165-172. [PMID: 31782190 DOI: 10.1111/lam.13253] [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] [Received: 08/20/2019] [Revised: 11/23/2019] [Accepted: 11/25/2019] [Indexed: 12/16/2022]
Abstract
Condensed tannins (CTs), which extracted from yew leaves, tilia flower and black locust leaves, were examined for their antimicrobial in vitro activity against avian pathogenic Escherichia coli (APEC). Past research demonstrated that CTs which contain procyanidins and prodelphinidins that could inhibit the growth of a wide range of bacteria. However, there is no information on how these affect pathogenic bacteria from chickens such as APEC. The high concentration of extracts, 10, 5, 2·5 mg ml-1 , affected the growth curves of APEC, which gave different inhibition values for the three CT extracts. Furthermore, these CTs had significant effects (P ≤ 0·05) on APEC biofilm and motility depending on each CT concentration and composition. However, at low concentration (0·6 mg ml-1 ), the tilia flowers, a high molar percentage of procyanidins, enhanced bacterial cell attachment and improved the swimming motility of APEC. In contrast, yew, an equal molar percentage of procyanidins/prodelphinidins, and black locust, a high molar percentage of prodelphinidins, interrupted and blocked swarming and swimming motility. The data suggested that the antimicrobial activity of the CT extracts was elicited by a positive relationship between anti-biofilm formation and anti-motility capacities. SIGNIFICANCE AND IMPACT OF THE STUDY: This study showed that condensed tannins (CTs), which were a group of secondary metabolites of many plants and rich in prodelphinidins (PD), had greater antibacterial activity against avian pathogenic Escherichia coli (APEC) than CTs that were rich in procyanidins (PC). The mode of action of the CTs was to inhibit the swimming and swarming motility of APEC, and its ability to form biofilms. The significance of this finding is that the use of PD-rich CTs to control APEC should not encourage the development of antibiotic resistance by APEC because a different mechanism is used. If confirmed in vivo, this could provide the poultry industry with a valuable and novel means of controlling the antibiotic resistance.
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Affiliation(s)
- M M Dakheel
- Department of Veterinary Public Health, College of Veterinary Medicine, University of Baghdad, Baghdad, Iraq
| | | | - I Mueller-Harvey
- School of Agriculture, Policy and Development, University of Reading, Reading, UK
| | - M J Woodward
- Department of Food and Nutritional Sciences, The University of Reading, Reading, UK
| | - C Rymer
- School of Agriculture, Policy and Development, University of Reading, Reading, UK
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23
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Abstract
Optical tweezers have great potential in microbiology for holding and manipulating single cells under a microscope. However, the methodology to use optical tweezers for live cell studies is still at its infancy. In this work, we determined suitable parameters for stable trapping of single Escherichia coli bacteria, and identified the upper limits of IR-exposure that can be applied without affecting viability. We found that the maximum tolerable IR-exposure is 2.5-fold higher when employing oscillating instead of stationary optical trapping (20 J and 8 J, respectively). We found that good stability of cells in an oscillating trap is achieved when the effective trap length is 20% larger than the cell length, the oscillation frequency higher than 100 Hz and the trap oriented perpendicular to the medium flow direction. Further, we show, using an IR power just sufficient for stable holding, that bacteria remain viable during at least 30 min of holding in an oscillating trap. In this work, we established a method for long-term stable handling of single E. coli cells using optical tweezers. This work will pave the way for future use of optical tweezers in microbiology.
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24
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Ma G, Hu C, Li S, Gao X, Li H, Hu X. Simultaneous, hybrid single-molecule method by optical tweezers and fluorescence. NANOTECHNOLOGY AND PRECISION ENGINEERING 2019. [DOI: 10.1016/j.npe.2019.11.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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25
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Micali G, Endres RG. Maximal information transmission is compatible with ultrasensitive biological pathways. Sci Rep 2019; 9:16898. [PMID: 31729454 PMCID: PMC6858467 DOI: 10.1038/s41598-019-53273-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 10/29/2019] [Indexed: 11/16/2022] Open
Abstract
Cells are often considered input-output devices that maximize the transmission of information by converting extracellular stimuli (input) via signaling pathways (communication channel) to cell behavior (output). However, in biological systems outputs might feed back into inputs due to cell motility, and the biological channel can change by mutations during evolution. Here, we show that the conventional channel capacity obtained by optimizing the input distribution for a fixed channel may not reflect the global optimum. In a new approach we analytically identify both input distributions and input-output curves that optimally transmit information, given constraints from noise and the dynamic range of the channel. We find a universal optimal input distribution only depending on the input noise, and we generalize our formalism to multiple outputs (or inputs). Applying our formalism to Escherichia coli chemotaxis, we find that its pathway is compatible with optimal information transmission despite the ultrasensitive rotary motors.
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Affiliation(s)
- Gabriele Micali
- Department of Life Sciences, Imperial College, London, UK.,Centre for Integrative Systems Biology and Bioinformatics, Imperial College, London, UK.,Department of Environmental Microbiology, Eawag, Dübendorf, Switzerland.,Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
| | - Robert G Endres
- Department of Life Sciences, Imperial College, London, UK. .,Centre for Integrative Systems Biology and Bioinformatics, Imperial College, London, UK.
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26
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Gasperotti A, Brameyer S, Fabiani F, Jung K. Phenotypic heterogeneity of microbial populations under nutrient limitation. Curr Opin Biotechnol 2019; 62:160-167. [PMID: 31698311 DOI: 10.1016/j.copbio.2019.09.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 09/18/2019] [Accepted: 09/19/2019] [Indexed: 12/16/2022]
Abstract
Phenotypic heterogeneity is a phenomenon in which genetically identical individuals have different characteristics. This behavior can also be found in bacteria, even if they grow as monospecies in well-mixed environments such as bioreactors. Here it is discussed how phenotypic heterogeneity is generated by internal factors and how it is promoted under nutrient-limited growth conditions. A better understanding of the molecular levels that control phenotypic heterogeneity could improve biotechnological production processes.
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Affiliation(s)
- Ana Gasperotti
- Department of Microbiology, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany
| | - Sophie Brameyer
- Department of Microbiology, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany
| | - Florian Fabiani
- Department of Microbiology, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany
| | - Kirsten Jung
- Department of Microbiology, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany.
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27
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orf20 in prophage phiv142-3 contributes to the adhesion and colonization ability of avian pathogenic Escherichia coli strain DE142 by affecting the formation of flagella and I fimbriae. Vet Microbiol 2019; 235:301-309. [PMID: 31383317 DOI: 10.1016/j.vetmic.2019.07.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/17/2019] [Accepted: 07/20/2019] [Indexed: 12/21/2022]
Abstract
We have previously demonstrated that prophage phiv142-3 enhances the colonization ability of avian pathogenic Escherichia coli (APEC) strain DE142. However, the mechanism of this action remains unknown. In this study, we demonstrate that deletion of phiv142-3 orf20 leads to a decrease in the survival ability in chicken serum, adhesion, and ability to invade DF-1 cells of mutant strain DE142Δorf20 compared with that of wild type (WT). Avian infection assays showed that bacterial loads in lungs and hearts of chickens challenged with the mutant are decreased to 7% and 8.3% compared with those challenged with the WT. The number of flagella and I fimbriae of the mutant are decreased and the mutant exhibits filamentation. However, protein ORF20 shows no adhesion ability to DF-1 cells in adherence inhibition experiments, indicating that it does not directly participate in adhesion. qRT-PCR revealed that the deletion of orf20 leads to reduction in the expression of nine genes related to the exportation of flagellar protein and two I-fimbriae-related genes (fimA and fimH), but does not affect genes related to the synthesis of flagella and other adhesins. Compared with the WT, the transcription level of the cell-division-associated genes minC and minD was increased 1.4-fold and 2.5-fold in mutant DE142Δorf20, respectively, indicating that orf20 affects the morphology of DE142 by regulating expression of minC and minD. Thus, our study revealed that orf20 in prophage phiv142-3 played a role in flagellar exportation, cell morphology, and I fimbriae synthesis.
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Danis U, Rasooli R, Chen CY, Dur O, Sitti M, Pekkan K. Thrust and Hydrodynamic Efficiency of the Bundled Flagella. MICROMACHINES 2019; 10:mi10070449. [PMID: 31277385 PMCID: PMC6680724 DOI: 10.3390/mi10070449] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 05/23/2019] [Accepted: 05/26/2019] [Indexed: 01/09/2023]
Abstract
The motility mechanism of prokaryotic organisms has inspired many untethered microswimmers that could potentially perform minimally invasive medical procedures in stagnant fluid regions inside the human body. Some of these microswimmers are inspired by bacteria with single or multiple helical flagella to propel efficiently and fast. For multiple flagella configurations, the direct measurement of thrust and hydrodynamic propulsion efficiency has been challenging due to the ambiguous mechanical coupling between the flow field and mechanical power input. To address this challenge and to compare alternative micropropulsion designs, a methodology based on volumetric velocity field acquisition is developed to acquire the key propulsive performance parameters from scaled-up swimmer prototypes. A digital particle image velocimetry (PIV) analysis protocol was implemented and experiments were conducted with the aid of computational fluid dynamics (CFD). First, this methodology was validated using a rotating single-flagellum similitude model. In addition to the standard PIV error assessment, validation studies included 2D vs. 3D PIV, axial vs. lateral PIV and simultaneously acquired direct thrust force measurement comparisons. Compatible with typical micropropulsion flow regimes, experiments were conducted both for very low and higher Reynolds (Re) number regimes (up to a Re number = 0.01) than that are reported in the literature. Finally, multiple flagella bundling configurations at 0°, 90° and 180° helical phase-shift angles were studied using scaled-up multiple concentric flagella thrust elements. Thrust generation was found to be maximal for the in-phase (0°) bundling configuration but with ~50% lower hydrodynamic efficiency than the single flagellum. The proposed measurement protocol and static thrust test-bench can be used for bio-inspired microscale propulsion methods, where direct thrust and efficiency measurement are required.
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Affiliation(s)
- Umit Danis
- Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Reza Rasooli
- Department of Mechanical Engineering, Koc University, Istanbul 34450, Turkey
| | - Chia-Yuan Chen
- Department of Mechanical Engineering, National Cheng Kung University, Tainan 701, Taiwan
| | - Onur Dur
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Metin Sitti
- Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Department of Mechanical Engineering, Koc University, Istanbul 34450, Turkey
- Physical Intelligence Department, Max Planck Institute for Intelligent Systems, Stuttgart 70569, Germany
| | - Kerem Pekkan
- Department of Mechanical Engineering, Koc University, Istanbul 34450, Turkey.
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
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Blue Light Is a Universal Signal for Escherichia coli Chemoreceptors. J Bacteriol 2019; 201:JB.00762-18. [PMID: 30858302 DOI: 10.1128/jb.00762-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 03/04/2019] [Indexed: 12/31/2022] Open
Abstract
Blue light has been shown to elicit a tumbling response in Escherichia coli, a nonphototrophic bacterium. The exact mechanism of this phototactic response is still unknown. Here, we quantify phototaxis in E. coli by analyzing single-cell trajectories in populations of free-swimming bacteria before and after light exposure. Bacterial strains expressing only one type of chemoreceptor reveal that all five E. coli receptors (Aer, Tar, Tsr, Tap, and Trg) are capable of mediating responses to light. In particular, light exposure elicits a running response in the Tap-only strain, the opposite of the tumbling responses observed for all other strains. Therefore, light emerges as a universal stimulus for all E. coli chemoreceptors. We also show that blue light exposure causes a reversible decrease in swimming velocity, a proxy for proton motive force. This result is consistent with a previously proposed hypothesis that, rather than sensing light directly, chemoreceptors sense light-induced perturbations in proton motive force, although other factors are also likely to contribute.IMPORTANCE Our findings provide new insights into the mechanism of E. coli phototaxis, showing that all five chemoreceptor types respond to light and their interactions play an important role in cell behavior. Our results also open up new avenues for examining and manipulating E. coli taxis. Since light is a universal stimulus, it may provide a way to quantify interactions among different types of receptors. Because light is easier to control spatially and temporally than chemicals, it may be used to study swimming behavior in complex environments. Since phototaxis can cause migration of E. coli bacteria in light gradients, light may be used to control bacterial density for studying density-dependent processes in bacteria.
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30
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Navarrete B, Leal-Morales A, Serrano-Ron L, Sarrió M, Jiménez-Fernández A, Jiménez-Díaz L, López-Sánchez A, Govantes F. Transcriptional organization, regulation and functional analysis of flhF and fleN in Pseudomonas putida. PLoS One 2019; 14:e0214166. [PMID: 30889223 PMCID: PMC6424431 DOI: 10.1371/journal.pone.0214166] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 03/07/2019] [Indexed: 11/25/2022] Open
Abstract
The Pseudomonas putida flhA-flhF-fleN-fliA cluster encodes a component of the flagellar export gate and three regulatory elements potentially involved in flagellar biogenesis and other functions. Here we show that these four genes form an operon, whose transcription is driven from the upstream PflhA promoter. A second promoter, PflhF, provides additional transcription of the three distal genes. PflhA and PflhF are σN-dependent, activated by the flagellar regulator FleQ, and negatively regulated by FleN. Motility, surface adhesion and colonization defects of a transposon insertion mutant in flhF revealed transcriptional polarity on fleN and fliA, as the former was required for strong surface adhesion and biofilm formation, and the latter was required for flagellar synthesis. On the other hand, FlhF and FleN were necessary to attain proper flagellar location and number for a fully functional flagellar complement. FleN, along with FleQ and the second messenger c-di-GMP differentially regulated transcription of lapA and the bcs operon, encoding a large adhesion protein and cellulose synthase. FleQ positively regulated the PlapA promoter and activation was antagonized by FleN and c-di-GMP. PbcsD was negatively regulated by FleQ and FleN, and repression was antagonized by c-di-GMP. FleN promoted FleQ binding to both PlapA and PbcsD in vitro, while c-di-GMP antagonized interaction with PbcsD and stimulated interaction with PlapA. A single FleQ binding site in PlapA was critical to activation in vivo. Our results suggest that FleQ, FleN and c-di-GMP cooperate to coordinate the regulation of flagellar motility and biofilm development.
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Affiliation(s)
- Blanca Navarrete
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/Consejo Superior de Investigaciones Científicas/Junta de Andalucía, Sevilla, Spain
- Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, Sevilla, Spain
| | - Antonio Leal-Morales
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/Consejo Superior de Investigaciones Científicas/Junta de Andalucía, Sevilla, Spain
- Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, Sevilla, Spain
| | - Laura Serrano-Ron
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/Consejo Superior de Investigaciones Científicas/Junta de Andalucía, Sevilla, Spain
- Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, Sevilla, Spain
| | - Marina Sarrió
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/Consejo Superior de Investigaciones Científicas/Junta de Andalucía, Sevilla, Spain
- Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, Sevilla, Spain
| | - Alicia Jiménez-Fernández
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/Consejo Superior de Investigaciones Científicas/Junta de Andalucía, Sevilla, Spain
- Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, Sevilla, Spain
| | - Lorena Jiménez-Díaz
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/Consejo Superior de Investigaciones Científicas/Junta de Andalucía, Sevilla, Spain
- Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, Sevilla, Spain
| | - Aroa López-Sánchez
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/Consejo Superior de Investigaciones Científicas/Junta de Andalucía, Sevilla, Spain
- Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, Sevilla, Spain
| | - Fernando Govantes
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/Consejo Superior de Investigaciones Científicas/Junta de Andalucía, Sevilla, Spain
- Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, Sevilla, Spain
- * E-mail:
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Driving the expression of the Salmonella enterica sv Typhimurium flagellum using flhDC from Escherichia coli results in key regulatory and cellular differences. Sci Rep 2018; 8:16705. [PMID: 30420601 PMCID: PMC6232118 DOI: 10.1038/s41598-018-35005-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 10/28/2018] [Indexed: 11/09/2022] Open
Abstract
The flagellar systems of Escherichia coli and Salmonella enterica exhibit a significant level of genetic and functional synteny. Both systems are controlled by the flagellar specific master regulator FlhD4C2. Since the early days of genetic analyses of flagellar systems it has been known that E. coli flhDC can complement a ∆flhDC mutant in S. enterica. The genomic revolution has identified how genetic changes to transcription factors and/or DNA binding sites can impact the phenotypic outcome across related species. We were therefore interested in asking: using modern tools to interrogate flagellar gene expression and assembly, what would the impact be of replacing the flhDC coding sequences in S. enterica for the E. coli genes at the flhDC S. entercia chromosomal locus? We show that even though all strains created are motile, flagellar gene expression is measurably lower when flhDCEC are present. These changes can be attributed to the impact of FlhD4C2 DNA recognition and the protein-protein interactions required to generate a stable FlhD4C2 complex. Furthermore, our data suggests that in E. coli the internal flagellar FliT regulatory feedback loop has a marked difference with respect to output of the flagellar systems. We argue due diligence is required in making assumptions based on heterologous expression of regulators and that even systems showing significant synteny may not behave in exactly the same manner.
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Najafi J, Shaebani MR, John T, Altegoer F, Bange G, Wagner C. Flagellar number governs bacterial spreading and transport efficiency. SCIENCE ADVANCES 2018; 4:eaar6425. [PMID: 30263953 PMCID: PMC6157962 DOI: 10.1126/sciadv.aar6425] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Accepted: 08/22/2018] [Indexed: 05/31/2023]
Abstract
Peritrichous bacteria synchronize and bundle their flagella to actively swim, while disruption of the bundle leads to a slow motility phase with a weak propulsion. It is still not known whether the number of flagella represents an evolutionary adaptation toward optimizing bacterial navigation. We study the swimming dynamics of differentially flagellated Bacillus subtilis strains in a quasi-two-dimensional system. We find that decreasing the number of flagella N f reduces the average turning angle between two successive run phases and enhances the run time and the directional persistence of the run phase. As a result, having fewer flagella is beneficial for long-distance transport and fast spreading, while having a lot of flagella is advantageous for the processes that require a slower spreading, such as biofilm formation. We develop a two-state random walk model that incorporates spontaneous switchings between the states and yields exact analytical expressions for transport properties, in remarkable agreement with experiments. The results of numerical simulations based on our two-state model suggest that the efficiency of searching and exploring the environment is optimized at intermediate values of N f. The optimal choice of N f, for which the search time is minimized, decreases with increasing the size of the environment in which the bacteria swim.
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Affiliation(s)
- Javad Najafi
- Center for Biophysics, Saarland University, 66041 Saarbrücken, Germany
| | | | - Thomas John
- Center for Biophysics, Saarland University, 66041 Saarbrücken, Germany
| | - Florian Altegoer
- Department of Chemistry and LOEWE Center for Synthetic Microbiology, Philipps University Marburg, 35043 Marburg, Germany
| | - Gert Bange
- Department of Chemistry and LOEWE Center for Synthetic Microbiology, Philipps University Marburg, 35043 Marburg, Germany
| | - Christian Wagner
- Center for Biophysics, Saarland University, 66041 Saarbrücken, Germany
- Physics and Materials Science Research Unit, University of Luxembourg, 1511 Luxembourg, Luxembourg
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33
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Riley EE, Das D, Lauga E. Swimming of peritrichous bacteria is enabled by an elastohydrodynamic instability. Sci Rep 2018; 8:10728. [PMID: 30013040 PMCID: PMC6048115 DOI: 10.1038/s41598-018-28319-8] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 06/20/2018] [Indexed: 11/25/2022] Open
Abstract
Peritrichously-flagellated bacteria, such as Escherichia coli, self-propel in fluids by using specialised motors to rotate multiple helical filaments. The rotation of each motor is transmitted to a short flexible segment called the hook which in turn transmits it to a flagellar filament, enabling swimming of the whole cell. Since multiple motors are spatially distributed on the body of the organism, one would expect the propulsive forces from the filaments to push against each other leading to negligible swimming. We use a combination of computations and theory to show that the swimming of peritrichous bacteria is enabled by an elastohydrodynamic bending instability occurring for hooks more flexible than a critical threshold. Using past measurements of hook bending stiffness, we demonstrate how real bacteria are safely on the side of the instability that promotes systematic swimming.
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Affiliation(s)
- Emily E Riley
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, UK.,Centre for Ocean Life, Technical University of Denmark, Kongens Lyngby, DK-2800, Denmark
| | - Debasish Das
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, UK
| | - Eric Lauga
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, UK.
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34
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Kinosita Y, Nishizaka T. Cross-kymography analysis to simultaneously quantify the function and morphology of the archaellum. Biophys Physicobiol 2018; 15:121-128. [PMID: 29955563 PMCID: PMC6018435 DOI: 10.2142/biophysico.15.0_121] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 03/29/2018] [Indexed: 12/13/2022] Open
Abstract
In many microorganisms helical structures are important for motility, e.g., bacterial flagella and kink propagation in Spiroplasma eriocheiris. Motile archaea also form a helical-shaped filament called the ‘archaellum’ that is functionally equivalent to the bacterial flagellum, but structurally resembles type IV pili. The archaellum motor consists of 6–8 proteins called fla accessory genes, and the filament assembly is driven by ATP hydrolysis at catalytic sites in FlaI. Remarkably, previous research using a dark-field microscopy showed that right-handed filaments propelled archaeal cells forwards or backwards by clockwise or counterclockwise rotation, respectively. However, the shape and rotational rate of the archaellum during swimming remained unclear, due to the low signal and lack of temporal resolution. Additionally, the structure and the motor properties of the archaellum and bacterial flagellum have not been precisely determined during swimming because they move freely in three-dimensional space. Recently, we developed an advanced method called “cross-kymography analysis”, which enables us to be a long-term observation and simultaneously quantify the function and morphology of helical structures using a total internal reflection fluorescence microscope. In this review, we introduce the basic idea of this analysis, and summarize the latest information in structural and functional characterization of the archaellum motor.
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Affiliation(s)
- Yoshiaki Kinosita
- Department of Physics, Gakushuin University, Toshima-ku, Tokyo 171-8588, Japan
| | - Takayuki Nishizaka
- Department of Physics, Gakushuin University, Toshima-ku, Tokyo 171-8588, Japan
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35
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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: 36] [Impact Index Per Article: 6.0] [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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36
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Hintsche M, Waljor V, Großmann R, Kühn MJ, Thormann KM, Peruani F, Beta C. A polar bundle of flagella can drive bacterial swimming by pushing, pulling, or coiling around the cell body. Sci Rep 2017; 7:16771. [PMID: 29196650 PMCID: PMC5711944 DOI: 10.1038/s41598-017-16428-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 11/06/2017] [Indexed: 01/30/2023] Open
Abstract
Bacteria swim in sequences of straight runs that are interrupted by turning events. They drive their swimming locomotion with the help of rotating helical flagella. Depending on the number of flagella and their arrangement across the cell body, different run-and-turn patterns can be observed. Here, we present fluorescence microscopy recordings showing that cells of the soil bacterium Pseudomonas putida that are decorated with a polar tuft of helical flagella, can alternate between two distinct swimming patterns. On the one hand, they can undergo a classical push-pull-push cycle that is well known from monopolarly flagellated bacteria but has not been reported for species with a polar bundle of multiple flagella. Alternatively, upon leaving the pulling mode, they can enter a third slow swimming phase, where they propel themselves with their helical bundle wrapped around the cell body. A theoretical estimate based on a random-walk model shows that the spreading of a population of swimmers is strongly enhanced when cycling through a sequence of pushing, pulling, and wrapped flagellar configurations as compared to the simple push-pull-push pattern.
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Affiliation(s)
- Marius Hintsche
- University of Potsdam, Institute of Physics and Astronomy, 14476, Potsdam, Germany
| | - Veronika Waljor
- University of Potsdam, Institute of Physics and Astronomy, 14476, Potsdam, Germany
| | - Robert Großmann
- Université Côte d'Azur, Laboratoire J. A. Dieudonné, UMR 7351 CNRS, F-06108, Nice Cedex 02, France
| | - Marco J Kühn
- Institut für Mikrobiologie und Molekularbiologie, Justus-Liebig-Universität Giessen, 35392, Giessen, Germany
| | - Kai M Thormann
- Institut für Mikrobiologie und Molekularbiologie, Justus-Liebig-Universität Giessen, 35392, Giessen, Germany
| | - Fernando Peruani
- Université Côte d'Azur, Laboratoire J. A. Dieudonné, UMR 7351 CNRS, F-06108, Nice Cedex 02, France
| | - Carsten Beta
- University of Potsdam, Institute of Physics and Astronomy, 14476, Potsdam, Germany.
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37
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Micali G, Colin R, Sourjik V, Endres RG. Drift and Behavior of E. coli Cells. Biophys J 2017; 113:2321-2325. [PMID: 29111155 DOI: 10.1016/j.bpj.2017.09.031] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 09/20/2017] [Accepted: 09/26/2017] [Indexed: 11/30/2022] Open
Abstract
Chemotaxis of the bacterium Escherichia coli is well understood in shallow chemical gradients, but its swimming behavior remains difficult to interpret in steep gradients. By focusing on single-cell trajectories from simulations, we investigated the dependence of the chemotactic drift velocity on attractant concentration in an exponential gradient. Whereas maxima of the average drift velocity can be interpreted within analytical linear-response theory of chemotaxis in shallow gradients, limits in drift due to steep gradients and finite number of receptor-methylation sites for adaptation go beyond perturbation theory. For instance, we found a surprising pinning of the cells to the concentration in the gradient at which cells run out of methylation sites. To validate the positions of maximal drift, we recorded single-cell trajectories in carefully designed chemical gradients using microfluidics.
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Affiliation(s)
- Gabriele Micali
- Department of Life Sciences, Imperial College, London, United Kingdom; Centre for Integrative Systems Biology and Bioinformatics, Imperial College, London, United Kingdom; Department of Environmental Microbiology, Eawag, Dübendorf, Switzerland; Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
| | - Rémy Colin
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany; LOEWE Center for Synthetic Microbiology, Marburg, Germany
| | - Victor Sourjik
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany; LOEWE Center for Synthetic 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.
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38
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Colin R, Sourjik V. Emergent properties of bacterial chemotaxis pathway. Curr Opin Microbiol 2017; 39:24-33. [PMID: 28822274 DOI: 10.1016/j.mib.2017.07.004] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Accepted: 07/27/2017] [Indexed: 11/17/2022]
Abstract
The chemotaxis pathway of Escherichia coli is the most studied sensory system in prokaryotes. The highly conserved general architecture of this pathway consists of two modules which mediate signal transduction and adaptation. The signal transduction module detects and amplifies changes in environmental conditions and rapidly transmits these signals to control bacterial swimming behavior. The adaptation module gradually resets the activity and sensitivity of the first module after initial stimulation and thereby enables the temporal comparisons necessary for bacterial chemotaxis. Recent experimental and theoretical work has unraveled multiple quantitative features emerging from the interplay between these two modules. This has laid the groundwork for rationalization of these emerging properties in the context of the evolutionary optimization of the chemotactic behavior.
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Affiliation(s)
- Remy Colin
- Max Planck Institute for Terrestrial Microbiology and LOEWE Center for Synthetic Microbiology, Karl-von-Frisch-strasse 16, 35043 Marburg, Germany
| | - Victor Sourjik
- Max Planck Institute for Terrestrial Microbiology and LOEWE Center for Synthetic Microbiology, Karl-von-Frisch-strasse 16, 35043 Marburg, Germany.
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39
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Visualizing Flagella while Tracking Bacteria. Biophys J 2017; 111:630-639. [PMID: 27508446 DOI: 10.1016/j.bpj.2016.05.053] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 05/23/2016] [Accepted: 05/26/2016] [Indexed: 10/21/2022] Open
Abstract
A complete description of the swimming behavior of a bacterium requires measurement of the displacement and orientation of the cell body together with a description of the movement of the flagella. We rebuilt a tracking microscope so that we could visualize flagellar filaments of tracked cells by fluorescence. We studied Escherichia coli (cells of various lengths, including swarm cells), Bacillus subtilis (wild-type and a mutant with fewer flagella), and a motile Streptococcus (now Enterococcus). The run-and-tumble statistics were nearly the same regardless of cell shape, length, and flagellation; however, swarm cells rarely tumbled, and cells of Enterococcus tended to swim in loops when moving slowly. There were events in which filaments underwent polymorphic transformations but remained in bundles, leading to small deflections in direction of travel. Tumble speeds were ∼2/3 as large as run speeds, and the rates of change of swimming direction while running or tumbling were smaller when cells swam more rapidly. If a smaller fraction of filaments were involved in tumbles, the tumble intervals were shorter and the angles between runs were smaller.
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40
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Cell morphology governs directional control in swimming bacteria. Sci Rep 2017; 7:2061. [PMID: 28515428 PMCID: PMC5435708 DOI: 10.1038/s41598-017-01565-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 03/31/2017] [Indexed: 11/12/2022] Open
Abstract
The ability to rapidly detect and track nutrient gradients is key to the ecological success of motile bacteria in aquatic systems. Consequently, bacteria have evolved a number of chemotactic strategies that consist of sequences of straight runs and reorientations. Theoretically, both phases are affected by fluid drag and Brownian motion, which are themselves governed by cell geometry. Here, we experimentally explore the effect of cell length on control of swimming direction. We subjected Escherichia coli to an antibiotic to obtain motile cells of different lengths, and characterized their swimming patterns in a homogeneous medium. As cells elongated, angles between runs became smaller, forcing a change from a run-and-tumble to a run-and-stop/reverse pattern. Our results show that changes in the motility pattern of microorganisms can be induced by simple morphological variation, and raise the possibility that changes in swimming pattern may be triggered by both morphological plasticity and selection on morphology.
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Applying torque to the Escherichia coli flagellar motor using magnetic tweezers. Sci Rep 2017; 7:43285. [PMID: 28266562 PMCID: PMC5339722 DOI: 10.1038/srep43285] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 01/24/2017] [Indexed: 01/06/2023] Open
Abstract
The bacterial flagellar motor of Escherichia coli is a nanoscale rotary engine essential for bacterial propulsion. Studies on the power output of single motors rely on the measurement of motor torque and rotation under external load. Here, we investigate the use of magnetic tweezers, which in principle allow the application and active control of a calibrated load torque, to study single flagellar motors in Escherichia coli. We manipulate the external load on the motor by adjusting the magnetic field experienced by a magnetic bead linked to the motor, and we probe the motor’s response. A simple model describes the average motor speed over the entire range of applied fields. We extract the motor torque at stall and find it to be similar to the motor torque at drag-limited speed. In addition, use of the magnetic tweezers allows us to force motor rotation in both forward and backward directions. We monitor the motor’s performance before and after periods of forced rotation and observe no destructive effects on the motor. Our experiments show how magnetic tweezers can provide active and fast control of the external load while also exposing remaining challenges in calibration. Through their non-invasive character and straightforward parallelization, magnetic tweezers provide an attractive platform to study nanoscale rotary motors at the single-motor level.
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Hashemi Shabestari M, Meijering AEC, Roos WH, Wuite GJL, Peterman EJG. Recent Advances in Biological Single-Molecule Applications of Optical Tweezers and Fluorescence Microscopy. Methods Enzymol 2016; 582:85-119. [PMID: 28062046 DOI: 10.1016/bs.mie.2016.09.047] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Over the past two decades, single-molecule techniques have evolved into robust tools to study many fundamental biological processes. The combination of optical tweezers with fluorescence microscopy and microfluidics provides a powerful single-molecule manipulation and visualization technique that has found widespread application in biology. In this combined approach, the spatial (~nm) and temporal (~ms) resolution, as well as the force scale (~pN) accessible to optical tweezers is complemented with the power of fluorescence microscopy. Thereby, it provides information on the local presence, identity, spatial dynamics, and conformational dynamics of single biomolecules. Together, these techniques allow comprehensive studies of, among others, molecular motors, protein-protein and protein-DNA interactions, biomolecular conformational changes, and mechanotransduction pathways. In this chapter, recent applications of fluorescence microscopy in combination with optical trapping are discussed. After an introductory section, we provide a description of instrumentation together with the current capabilities and limitations of the approaches. Next we summarize recent studies that applied this combination of techniques in biological systems and highlight some representative biological assays to mark the exquisite opportunities that optical tweezers combined with fluorescence microscopy provide.
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Affiliation(s)
| | | | - W H Roos
- Moleculaire Biofysica, Zernike Institute, Rijksuniversiteit Groningen, Groningen, The Netherlands
| | - G J L Wuite
- Vrije Universiteit, Amsterdam, The Netherlands
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Dufour YS, Gillet S, Frankel NW, Weibel DB, Emonet T. Direct Correlation between Motile Behavior and Protein Abundance in Single Cells. PLoS Comput Biol 2016; 12:e1005041. [PMID: 27599206 PMCID: PMC5012591 DOI: 10.1371/journal.pcbi.1005041] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 06/29/2016] [Indexed: 01/26/2023] Open
Abstract
Understanding how stochastic molecular fluctuations affect cell behavior requires the quantification of both behavior and protein numbers in the same cells. Here, we combine automated microscopy with in situ hydrogel polymerization to measure single-cell protein expression after tracking swimming behavior. We characterized the distribution of non-genetic phenotypic diversity in Escherichia coli motility, which affects single-cell exploration. By expressing fluorescently tagged chemotaxis proteins (CheR and CheB) at different levels, we quantitatively mapped motile phenotype (tumble bias) to protein numbers using thousands of single-cell measurements. Our results disagreed with established models until we incorporated the role of CheB in receptor deamidation and the slow fluctuations in receptor methylation. Beyond refining models, our central finding is that changes in numbers of CheR and CheB affect the population mean tumble bias and its variance independently. Therefore, it is possible to adjust the degree of phenotypic diversity of a population by adjusting the global level of expression of CheR and CheB while keeping their ratio constant, which, as shown in previous studies, confers functional robustness to the system. Since genetic control of protein expression is heritable, our results suggest that non-genetic diversity in motile behavior is selectable, supporting earlier hypotheses that such diversity confers a selective advantage. Cell-to-cell variations in protein numbers due to random fluctuations at the molecular level lead to cell-to-cell variations in behavior. To maintain predictable responses, signaling networks have evolved robustness against noise, but in some situations phenotypic diversity in a clonal population can be beneficial as a bet hedging or division of labor strategy. Investigating of how random molecular fluctuations affect cell behavior requires to measure biological parameters at different scales. Here, we report a new experiment that allows the measure of both protein numbers and behavior in cells that are free to move in their environment. Using Escherichia coli, a model system for the study of cellular behavior, we investigated the effects variations in the numbers of the chemo-receptor modification enzymes on single-cell swimming behavior. We found that the mean and variance of the behavior can be adjusted independently in the population by adjusting protein expression. This mechanism allows for the genetic selection of phenotypic diversity without disrupting correlations in protein expression that are important for the overall robustness of the chemotaxis system.
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Affiliation(s)
- Yann S Dufour
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, United States of America
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America
| | - Sébastien Gillet
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, United States of America
| | - Nicholas W Frankel
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, United States of America
| | - Douglas B Weibel
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Thierry Emonet
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, United States of America
- Department of Physics, Yale University, New Haven, Connecticut, United States of America
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Diepold A, Armitage JP. Type III secretion systems: the bacterial flagellum and the injectisome. Philos Trans R Soc Lond B Biol Sci 2016; 370:rstb.2015.0020. [PMID: 26370933 DOI: 10.1098/rstb.2015.0020] [Citation(s) in RCA: 138] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The flagellum and the injectisome are two of the most complex and fascinating bacterial nanomachines. At their core, they share a type III secretion system (T3SS), a transmembrane export complex that forms the extracellular appendages, the flagellar filament and the injectisome needle. Recent advances, combining structural biology, cryo-electron tomography, molecular genetics, in vivo imaging, bioinformatics and biophysics, have greatly increased our understanding of the T3SS, especially the structure of its transmembrane and cytosolic components, the transcriptional, post-transcriptional and functional regulation and the remarkable adaptivity of the system. This review aims to integrate these new findings into our current knowledge of the evolution, function, regulation and dynamics of the T3SS, and to highlight commonalities and differences between the two systems, as well as their potential applications.
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Affiliation(s)
- Andreas Diepold
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Judith P Armitage
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
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45
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Chemotaxis for enhanced immobilization ofEscherichia coliandLegionella pneumophilaon biofunctionalized surfaces of GaAs. Biointerphases 2016; 11:021004. [PMID: 27098616 DOI: 10.1116/1.4947048] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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46
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Gao Z, Li H, Chen X, Zhang HP. Using confined bacteria as building blocks to generate fluid flow. LAB ON A CHIP 2015; 15:4555-62. [PMID: 26496967 DOI: 10.1039/c5lc01093d] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
In many technological applications, materials are transported by fluid flow at micro/nanometer scales. Conventionally, macroscopic apparatuses, such as syringe pumps, are used to drive the flow. This work explores the possibility of utilizing motile bacteria as microscopic pumps. We used micro-fabricated structures to confine smooth-swimming bacteria in a prescribed configuration. The flagella of confined bacteria rotate to collectively generate flow that can transport materials along designed trajectories. Different structures are combined to realize complex functions, such as collection or dispersion of particles. Experimental findings are reproduced in numerical simulations. Our method opens new ways to generate transport flow at the micrometer scale and to drive bio-hybrid devices.
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Affiliation(s)
- Zhiyong Gao
- Department of Physics and Astronomy and Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai, China.
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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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Schuhmacher JS, Thormann KM, Bange G. How bacteria maintain location and number of flagella? FEMS Microbiol Rev 2015. [PMID: 26195616 DOI: 10.1093/femsre/fuv034] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Bacteria differ in number and location of their flagella that appear in regular patterns at the cell surface (flagellation pattern). Despite the plethora of bacterial species, only a handful of these patterns exist. The correct flagellation pattern is a prerequisite for motility, but also relates to biofilm formation and the pathogenicity of disease-causing flagellated bacteria. However, the mechanisms that maintain location and number of flagella are far from being understood. Here, we review our knowledge on mechanisms that enable bacteria to maintain their appropriate flagellation pattern. While some peritrichous flagellation patterns might occur by rather simple stochastic processes, other bacterial species appear to rely on landmark systems to define the designated flagellar position. Such landmarks are the Tip system of Caulobacter crescentus or the signal recognition particle (SRP)-GTPase FlhF and the MinD/ParA-type ATPase FlhG (synonyms: FleN, YlxH and MinD2). The latter two proteins constitute a regulatory circuit essential for diverse flagellation patterns in many Gram-positive and negative species. The interactome of FlhF/G (e.g. C-ring proteins FliM, FliN, FliY or the transcriptional regulator FleQ/FlrA) seems evolutionary adapted to meet the specific needs for a respective pattern. This variability highlights the importance of the correct flagellation pattern for motile species.
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Affiliation(s)
- Jan S Schuhmacher
- LOEWE Center for Synthetic Microbiology & Dep. of Chemistry, Philipps University Marburg, Hans-Meerwein-Strasse, D-35043 Marburg, Germany
| | - Kai M Thormann
- Justus-Liebig University, Department of Microbiology and Molecular Biology, Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany
| | - Gert Bange
- LOEWE Center for Synthetic Microbiology & Dep. of Chemistry, Philipps University Marburg, Hans-Meerwein-Strasse, D-35043 Marburg, Germany
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Limits of feedback control in bacterial chemotaxis. PLoS Comput Biol 2014; 10:e1003694. [PMID: 24967937 PMCID: PMC4072517 DOI: 10.1371/journal.pcbi.1003694] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 05/13/2014] [Indexed: 01/03/2023] Open
Abstract
Inputs to signaling pathways can have complex statistics that depend on the environment and on the behavioral response to previous stimuli. Such behavioral feedback is particularly important in navigation. Successful navigation relies on proper coupling between sensors, which gather information during motion, and actuators, which control behavior. Because reorientation conditions future inputs, behavioral feedback can place sensors and actuators in an operational regime different from the resting state. How then can organisms maintain proper information transfer through the pathway while navigating diverse environments? In bacterial chemotaxis, robust performance is often attributed to the zero integral feedback control of the sensor, which guarantees that activity returns to resting state when the input remains constant. While this property provides sensitivity over a wide range of signal intensities, it remains unclear how other parameters such as adaptation rate and adapted activity affect chemotactic performance, especially when considering that the swimming behavior of the cell determines the input signal. We examine this issue using analytical models and simulations that incorporate recent experimental evidences about behavioral feedback and flagellar motor adaptation. By focusing on how sensory information carried by the response regulator is best utilized by the motor, we identify an operational regime that maximizes drift velocity along chemical concentration gradients for a wide range of environments and sensor adaptation rates. This optimal regime is outside the dynamic range of the motor response, but maximizes the contrast between run duration up and down gradients. In steep gradients, the feedback from chemotactic drift can push the system through a bifurcation. This creates a non-chemotactic state that traps cells unless the motor is allowed to adapt. Although motor adaptation helps, we find that as the strength of the feedback increases individual phenotypes cannot maintain the optimal operational regime in all environments, suggesting that diversity could be beneficial. The biased random walk is a fundamental strategy used by many organisms to navigate their environment. Drift along the desired direction is achieved by reducing the probability to reorient whenever conditions improve. In the chemotaxis system of Escherichia coli, this is accomplished with a sensory module that implements negative integral feedback control, the output of which is relayed to the flagellar motors (the actuators) by a response regulator to control the probability to change direction. The proper dynamical coupling between sensor and actuator is critical for the performance of the random walker. Here, we identify an optimal regime for this coupling that maximizes drift velocity in the direction of the gradient in multiple environments. Our analysis reveals that feedback of the behavior onto the system in steep gradients can constrain individual cell performance, by causing bi-stable behavior that can trap cells in non-chemotactic states. These limitations are inherent in the biased random walk strategy with integral feedback control, but can be alleviated if the output of the pathway adapts, as recently characterized for the flagellar motors in Escherichia coli.
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Fukuoka H, Sagawa T, Inoue Y, Takahashi H, Ishijima A. Direct Imaging of Intracellular Signaling Components That Regulate Bacterial Chemotaxis. Sci Signal 2014; 7:ra32. [DOI: 10.1126/scisignal.2004963] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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