Publications by authors named "Chenyi Fei"

10 Publications

  • Page 1 of 1

Hierarchical transitions and fractal wrinkling drive bacterial pellicle morphogenesis.

Proc Natl Acad Sci U S A 2021 May;118(20)

Department of Molecular Biology, Princeton University, Princeton, NJ 08544;

Bacterial cells can self-organize into structured communities at fluid-fluid interfaces. These soft, living materials composed of cells and extracellular matrix are called pellicles. Cells residing in pellicles garner group-level survival advantages such as increased antibiotic resistance. The dynamics of pellicle formation and, more generally, how complex morphologies arise from active biomaterials confined at interfaces are not well understood. Here, using as our model organism, a custom-built adaptive stereo microscope, fluorescence imaging, mechanical theory, and simulations, we report a fractal wrinkling morphogenesis program that differs radically from the well-known coalescence of wrinkles into folds that occurs in passive thin films at fluid-fluid interfaces. Four stages occur: growth of founding colonies, onset of primary wrinkles, development of secondary curved ridge instabilities, and finally the emergence of a cascade of finer structures with fractal-like scaling in wavelength. The time evolution of pellicle formation depends on the initial heterogeneity of the film microstructure. Changing the starting bacterial seeding density produces three variations in the sequence of morphogenic stages, which we term the bypass, crystalline, and incomplete modes. Despite these global architectural transitions, individual microcolonies remain spatially segregated, and thus, the community maintains spatial and genetic heterogeneity. Our results suggest that the memory of the original microstructure is critical in setting the morphogenic dynamics of a pellicle as an active biomaterial.
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http://dx.doi.org/10.1073/pnas.2023504118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8157956PMC
May 2021

LuxT controls specific quorum-sensing-regulated behaviors in Vibrionaceae spp. via repression of qrr1, encoding a small regulatory RNA.

PLoS Genet 2021 Apr 1;17(4):e1009336. Epub 2021 Apr 1.

Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America.

Quorum sensing (QS) is a process of chemical communication bacteria use to transition between individual and collective behaviors. QS depends on the production, release, and synchronous response to signaling molecules called autoinducers (AIs). The marine bacterium Vibrio harveyi monitors AIs using a signal transduction pathway that relies on five small regulatory RNAs (called Qrr1-5) that post-transcriptionally control target genes. Curiously, the small RNAs largely function redundantly making it difficult to understand the necessity for five of them. Here, we identify LuxT as a transcriptional repressor of qrr1. LuxT does not regulate qrr2-5, demonstrating that qrr genes can be independently controlled to drive unique downstream QS gene expression patterns. LuxT reinforces its control over the same genes it regulates indirectly via repression of qrr1, through a second transcriptional control mechanism. Genes dually regulated by LuxT specify public goods including an aerolysin-type pore-forming toxin. Phylogenetic analyses reveal that LuxT is conserved among Vibrionaceae and sequence comparisons predict that LuxT represses qrr1 in additional species. The present findings reveal that the QS regulatory RNAs can carry out both shared and unique functions to endow bacteria with plasticity in their output behaviors.
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http://dx.doi.org/10.1371/journal.pgen.1009336DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8043402PMC
April 2021

Competitive binding of independent extension and retraction motors explains the quantitative dynamics of type IV pili.

Proc Natl Acad Sci U S A 2021 02;118(8)

Department of Molecular Biology, Princeton University, Princeton, NJ 08540;

Type IV pili (TFP) function through cycles of extension and retraction. The coordination of these cycles remains mysterious due to a lack of quantitative measurements of multiple features of TFP dynamics. Here, we fluorescently label TFP in the pathogen and track full extension and retraction cycles of individual filaments. Polymerization and depolymerization dynamics are stochastic; TFP are made at random times and extend, pause, and retract for random lengths of time. TFP can also pause for extended periods between two extension or two retraction events in both wild-type cells and a slowly retracting PilT mutant. We developed a biophysical model based on the stochastic binding of two dedicated extension and retraction motors to the same pilus machine that predicts the observed features of the data with no free parameters. We show that only a model in which both motors stochastically bind and unbind to the pilus machine independent of the piliation state of the machine quantitatively explains the experimentally observed pilus production rate. In experimental support of this model, we show that the abundance of the retraction motor dictates the pilus production rate and that PilT is bound to pilus machines even in their unpiliated state. Together, the strong quantitative agreement of our model with a variety of experiments suggests that the entire repetitive cycle of pilus extension and retraction is coordinated by the competition of stochastic motor binding to the pilus machine, and that the retraction motor is the major throttle for pilus production.
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http://dx.doi.org/10.1073/pnas.2014926118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7923367PMC
February 2021

Identification of signaling pathways, matrix-digestion enzymes, and motility components controlling biofilm dispersal.

Proc Natl Acad Sci U S A 2020 12 7;117(51):32639-32647. Epub 2020 Dec 7.

Department of Molecular Biology, Princeton University, Princeton, NJ 08544;

Bacteria alternate between being free-swimming and existing as members of sessile multicellular communities called biofilms. The biofilm lifecycle occurs in three stages: cell attachment, biofilm maturation, and biofilm dispersal. biofilms are hyperinfectious, and biofilm formation and dispersal are considered central to disease transmission. While biofilm formation is well studied, almost nothing is known about biofilm dispersal. Here, we conducted an imaging screen for mutants that fail to disperse, revealing three classes of dispersal components: signal transduction proteins, matrix-degradation enzymes, and motility factors. Signaling proteins dominated the screen and among them, we focused on an uncharacterized two-component sensory system that we term DbfS/DbfR for dispersal of biofilm sensor/regulator. Phospho-DbfR represses biofilm dispersal. DbfS dephosphorylates and thereby inactivates DbfR, which permits dispersal. Matrix degradation requires two enzymes: LapG, which cleaves adhesins, and RbmB, which digests matrix polysaccharides. Reorientation in swimming direction, mediated by CheY3, is necessary for cells to escape from the porous biofilm matrix. We suggest that these components act sequentially: signaling launches dispersal by terminating matrix production and triggering matrix digestion, and subsequent cell motility permits escape from biofilms. This study lays the groundwork for interventions aimed at modulating biofilm dispersal to ameliorate disease.
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http://dx.doi.org/10.1073/pnas.2021166117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7768729PMC
December 2020

Cell position fates and collective fountain flow in bacterial biofilms revealed by light-sheet microscopy.

Science 2020 07 11;369(6499):71-77. Epub 2020 Jun 11.

Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.

Bacterial biofilms represent a basic form of multicellular organization that confers survival advantages to constituent cells. The sequential stages of cell ordering during biofilm development have been studied in the pathogen and model biofilm-former It is unknown how spatial trajectories of individual cells and the collective motions of many cells drive biofilm expansion. We developed dual-view light-sheet microscopy to investigate the dynamics of biofilm development from a founder cell to a mature three-dimensional community. Tracking of individual cells revealed two distinct fates: one set of biofilm cells expanded ballistically outward, while the other became trapped at the substrate. A collective fountain-like flow transported cells to the biofilm front, bypassing members trapped at the substrate and facilitating lateral biofilm expansion. This collective flow pattern was quantitatively captured by a continuum model of biofilm growth against substrate friction. Coordinated cell movement required the matrix protein RbmA, without which cells expanded erratically. Thus, tracking cell lineages and trajectories in space and time revealed how multicellular structures form from a single founder cell.
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http://dx.doi.org/10.1126/science.abb8501DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7426073PMC
July 2020

Nonuniform growth and surface friction determine bacterial biofilm morphology on soft substrates.

Proc Natl Acad Sci U S A 2020 04 19;117(14):7622-7632. Epub 2020 Mar 19.

Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, NJ 08544;

During development, organisms acquire three-dimensional (3D) shapes with important physiological consequences. While basic mechanisms underlying morphogenesis are known in eukaryotes, it is often difficult to manipulate them in vivo. To circumvent this issue, here we present a study of developing biofilms grown on agar substrates in which the spatiotemporal morphological patterns were altered by varying the agar concentration. Expanding biofilms are initially flat but later undergo a mechanical instability and become wrinkled. To gain mechanistic insights into this dynamic pattern-formation process, we developed a model that considers diffusion of nutrients and their uptake by bacteria, bacterial growth/biofilm matrix production, mechanical deformation of both the biofilm and the substrate, and the friction between them. Our model shows quantitative agreement with experimental measurements of biofilm expansion dynamics, and it accurately predicts two distinct spatiotemporal patterns observed in the experiments-the wrinkles initially appear either in the peripheral region and propagate inward (soft substrate/low friction) or in the central region and propagate outward (stiff substrate/high friction). Our results, which establish that nonuniform growth and friction are fundamental determinants of stress anisotropy and hence biofilm morphology, are broadly applicable to bacterial biofilms with similar morphologies and also provide insight into how other bacterial biofilms form distinct wrinkle patterns. We discuss the implications of forming undulated biofilm morphologies, which may enhance the availability of nutrients and signaling molecules and serve as a "bet hedging" strategy.
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http://dx.doi.org/10.1073/pnas.1919607117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7148565PMC
April 2020

Mechanical instability and interfacial energy drive biofilm morphogenesis.

Elife 2019 03 8;8. Epub 2019 Mar 8.

Department of Molecular Biology, Princeton University, Princeton, United States.

Surface-attached bacterial communities called biofilms display a diversity of morphologies. Although structural and regulatory components required for biofilm formation are known, it is not understood how these essential constituents promote biofilm surface morphology. Here, using as our model system, we combine mechanical measurements, theory and simulation, quantitative image analyses, surface energy characterizations, and mutagenesis to show that mechanical instabilities, including wrinkling and delamination, underlie the morphogenesis program of growing biofilms. We also identify interfacial energy as a key driving force for mechanomorphogenesis because it dictates the generation of new and the annihilation of existing interfaces. Finally, we discover feedback between mechanomorphogenesis and biofilm expansion, which shapes the overall biofilm contour. The morphogenesis principles that we discover in bacterial biofilms, which rely on mechanical instabilities and interfacial energies, should be generally applicable to morphogenesis processes in tissues in higher organisms.
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http://dx.doi.org/10.7554/eLife.43920DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6453567PMC
March 2019

Bacterial Biofilm Material Properties Enable Removal and Transfer by Capillary Peeling.

Adv Mater 2018 Nov 8;30(46):e1804153. Epub 2018 Oct 8.

Department of Mechanical and Aerospace Engineering, Princeton University, D328 E-Quad, Olden St., Princeton, NJ, 08544, USA.

Biofilms, surface-attached communities of bacterial cells, are a concern in health and in industrial operations because of persistent infections, clogging of flows, and surface fouling. Extracellular matrices provide mechanical protection to biofilm-dwelling cells as well as protection from chemical insults, including antibiotics. Understanding how biofilm material properties arise from constituent matrix components and how these properties change in different environments is crucial for designing biofilm removal strategies. Here, using rheological characterization and surface analyses of Vibrio cholerae biofilms, it is discovered how extracellular polysaccharides, proteins, and cells function together to define biofilm mechanical and interfacial properties. Using insight gained from our measurements, a facile capillary peeling technology is developed to remove biofilms from surfaces or to transfer intact biofilms from one surface to another. It is shown that the findings are applicable to other biofilm-forming bacterial species and to multiple surfaces. Thus, the technology and the understanding that have been developed could potentially be employed to characterize and/or treat biofilm-related infections and industrial biofouling problems.
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http://dx.doi.org/10.1002/adma.201804153DOI Listing
November 2018

Design principles for enhancing phase sensitivity and suppressing phase fluctuations simultaneously in biochemical oscillatory systems.

Nat Commun 2018 04 12;9(1):1434. Epub 2018 Apr 12.

IBM T. J. Watson Research Center, Yorktown Heights, New York, NY, 10598, USA.

Biological systems need to function accurately in the presence of strong noise and at the same time respond sensitively to subtle external cues. Here we study design principles in biochemical oscillatory circuits to achieve these two seemingly incompatible goals. We show that energy dissipation can enhance phase sensitivity linearly by driving the phase-amplitude coupling and increase timing accuracy by suppressing phase diffusion. Two general design principles in the key underlying reaction loop formed by two antiparallel pathways are found to optimize oscillation performance with a given energy budget: balancing the forward-to-backward flux ratio between the two pathways to reduce phase diffusion and maximizing the net flux of the phase-advancing pathway relative to that of the phase-retreating pathway to enhance phase sensitivity. Experimental evidences consistent with these design principles are found in the circadian clock of cyanobacteria. Future experiments to test the predicted dependence of phase sensitivity on energy dissipation are proposed.
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http://dx.doi.org/10.1038/s41467-018-03826-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5897384PMC
April 2018