Publications

2017
Posfai, Anna, Thibaud Taillefumier, and Ned S Wingreen. “Metabolic Trade-Offs Promote Diversity in a Model Ecosystem.”. Phys Rev Lett 118.2 (2017): , 118, 2, 028103. Web.Abstract
In nature, a large number of species can coexist on a small number of shared resources; however, resource-competition models predict that the number of species in steady coexistence cannot exceed the number of resources. Motivated by recent studies of phytoplankton, we introduce trade-offs into a resource-competition model and find that an unlimited number of species can coexist. Our model spontaneously reproduces several notable features of natural ecosystems, including keystone species and population dynamics and abundances characteristic of neutral theory, despite an underlying non-neutral competition for resources.
Taillefumier, Thibaud, et al.Microbial consortia at steady supply.”. Elife 6 (2017). Web.Abstract
Metagenomics has revealed hundreds of species in almost all microbiota. In a few well-studied cases, microbial communities have been observed to coordinate their metabolic fluxes. In principle, microbes can divide tasks to reap the benefits of specialization, as in human economies. However, the benefits and stability of an economy of microbial specialists are far from obvious. Here, we physically model the population dynamics of microbes that compete for steadily supplied resources. Importantly, we explicitly model the metabolic fluxes yielding cellular biomass production under the constraint of a limited enzyme budget. We find that population dynamics generally leads to the coexistence of different metabolic types. We establish that these microbial consortia act as cartels, whereby population dynamics pins down resource concentrations at values for which no other strategy can invade. Finally, we propose that at steady supply, cartels of competing strategies automatically yield maximum biomass, thereby achieving a collective optimum.
2016
Drescher, Knut, et al.Architectural transitions in Vibrio cholerae biofilms at single-cell resolution.”. Proc Natl Acad Sci U S A 113.14 (2016): , 113, 14, E2066-72. Web.Abstract
Many bacterial species colonize surfaces and form dense 3D structures, known as biofilms, which are highly tolerant to antibiotics and constitute one of the major forms of bacterial biomass on Earth. Bacterial biofilms display remarkable changes during their development from initial attachment to maturity, yet the cellular architecture that gives rise to collective biofilm morphology during growth is largely unknown. Here, we use high-resolution optical microscopy to image all individual cells in Vibrio cholerae biofilms at different stages of development, including colonies that range in size from 2 to 4,500 cells. From these data, we extracted the precise 3D cellular arrangements, cell shapes, sizes, and global morphological features during biofilm growth on submerged glass substrates under flow. We discovered several critical transitions of the internal and external biofilm architectures that separate the major phases of V. cholerae biofilm growth. Optical imaging of biofilms with single-cell resolution provides a new window into biofilm formation that will prove invaluable to understanding the mechanics underlying biofilm development.
Sonnenburg, Erica D, et al.Diet-induced extinctions in the gut microbiota compound over generations.”. Nature 529.7585 (2016): , 529, 7585, 212-5. Web.Abstract
The gut is home to trillions of microorganisms that have fundamental roles in many aspects of human biology, including immune function and metabolism. The reduced diversity of the gut microbiota in Western populations compared to that in populations living traditional lifestyles presents the question of which factors have driven microbiota change during modernization. Microbiota-accessible carbohydrates (MACs) found in dietary fibre have a crucial involvement in shaping this microbial ecosystem, and are notably reduced in the Western diet (high in fat and simple carbohydrates, low in fibre) compared with a more traditional diet. Here we show that changes in the microbiota of mice consuming a low-MAC diet and harbouring a human microbiota are largely reversible within a single generation. However, over several generations, a low-MAC diet results in a progressive loss of diversity, which is not recoverable after the reintroduction of dietary MACs. To restore the microbiota to its original state requires the administration of missing taxa in combination with dietary MAC consumption. Our data illustrate that taxa driven to low abundance when dietary MACs are scarce are inefficiently transferred to the next generation, and are at increased risk of becoming extinct within an isolated population. As more diseases are linked to the Western microbiota and the microbiota is targeted therapeutically, microbiota reprogramming may need to involve strategies that incorporate dietary MACs as well as taxa not currently present in the Western gut.
Bitbol, Anne-Florence, et al.Inferring interaction partners from protein sequences.”. Proc Natl Acad Sci U S A 113.43 (2016): , 113, 43, 12180-12185. Web.Abstract
Specific protein-protein interactions are crucial in the cell, both to ensure the formation and stability of multiprotein complexes and to enable signal transduction in various pathways. Functional interactions between proteins result in coevolution between the interaction partners, causing their sequences to be correlated. Here we exploit these correlations to accurately identify, from sequence data alone, which proteins are specific interaction partners. Our general approach, which employs a pairwise maximum entropy model to infer couplings between residues, has been successfully used to predict the 3D structures of proteins from sequences. Thus inspired, we introduce an iterative algorithm to predict specific interaction partners from two protein families whose members are known to interact. We first assess the algorithm's performance on histidine kinases and response regulators from bacterial two-component signaling systems. We obtain a striking 0.93 true positive fraction on our complete dataset without any a priori knowledge of interaction partners, and we uncover the origin of this success. We then apply the algorithm to proteins from ATP-binding cassette (ABC) transporter complexes, and obtain accurate predictions in these systems as well. Finally, we present two metrics that accurately distinguish interacting protein families from noninteracting ones, using only sequence data.
Aquino, Gerardo, Ned S Wingreen, and Robert G Endres. “Know the Single-Receptor Sensing Limit? Think Again.”. J Stat Phys 162 (2016): , 162, 1353-1364. Web.Abstract
How cells reliably infer information about their environment is a fundamentally important question. While sensing and signaling generally start with cell-surface receptors, the degree of accuracy with which a cell can measure external ligand concentration with even the simplest device-a single receptor-is surprisingly hard to pin down. Recent studies provide conflicting results for the fundamental physical limits. Comparison is made difficult as different studies either suggest different readout mechanisms of the ligand-receptor occupancy, or differ on how ligand diffusion is implemented. Here we critically analyse these studies and present a unifying perspective on the limits of sensing, with wide-ranging biological implications.
Castellana, Michele, Sophia Hsin-Jung Li, and Ned S Wingreen. “Spatial organization of bacterial transcription and translation.”. Proc Natl Acad Sci U S A 113.33 (2016): , 113, 33, 9286-91. Web.Abstract
In bacteria such as Escherichia coli, DNA is compacted into a nucleoid near the cell center, whereas ribosomes-molecular complexes that translate mRNAs into proteins-are mainly localized to the poles. We study the impact of this spatial organization using a minimal reaction-diffusion model for the cellular transcriptional-translational machinery. Although genome-wide mRNA-nucleoid segregation still lacks experimental validation, our model predicts that [Formula: see text] of mRNAs are segregated to the poles. In addition, our analysis reveals a "circulation" of ribosomes driven by the flux of mRNAs, from synthesis in the nucleoid to degradation at the poles. We show that our results are robust with respect to multiple, biologically relevant factors, such as mRNA degradation by RNase enzymes, different phases of the cell division cycle and growth rates, and the existence of nonspecific, transient interactions between ribosomes and mRNAs. Finally, we confirm that the observed nucleoid size stems from a balance between the forces that the chromosome and mRNAs exert on each other. This suggests a potential global feedback circuit in which gene expression feeds back on itself via nucleoid compaction.
Yan, Jing, et al.Vibrio cholerae biofilm growth program and architecture revealed by single-cell live imaging.”. Proc Natl Acad Sci U S A 113.36 (2016): , 113, 36, E5337-43. Web.Abstract
Biofilms are surface-associated bacterial communities that are crucial in nature and during infection. Despite extensive work to identify biofilm components and to discover how they are regulated, little is known about biofilm structure at the level of individual cells. Here, we use state-of-the-art microscopy techniques to enable live single-cell resolution imaging of a Vibrio cholerae biofilm as it develops from one single founder cell to a mature biofilm of 10,000 cells, and to discover the forces underpinning the architectural evolution. Mutagenesis, matrix labeling, and simulations demonstrate that surface adhesion-mediated compression causes V. cholerae biofilms to transition from a 2D branched morphology to a dense, ordered 3D cluster. We discover that directional proliferation of rod-shaped bacteria plays a dominant role in shaping the biofilm architecture in V. cholerae biofilms, and this growth pattern is controlled by a single gene, rbmA Competition analyses reveal that the dense growth mode has the advantage of providing the biofilm with superior mechanical properties. Our single-cell technology can broadly link genes to biofilm fine structure and provides a route to assessing cell-to-cell heterogeneity in response to external stimuli.
2015
Tikhonov, Mikhail, Robert W Leach, and Ned S Wingreen. “Interpreting 16S metagenomic data without clustering to achieve sub-OTU resolution.”. ISME J 91 (2015): , 9, 1, 68-80. Web.Abstract
The standard approach to analyzing 16S tag sequence data, which relies on clustering reads by sequence similarity into Operational Taxonomic Units (OTUs), underexploits the accuracy of modern sequencing technology. We present a clustering-free approach to multi-sample Illumina data sets that can identify independent bacterial subpopulations regardless of the similarity of their 16S tag sequences. Using published data from a longitudinal time-series study of human tongue microbiota, we are able to resolve within standard 97% similarity OTUs up to 20 distinct subpopulations, all ecologically distinct but with 16S tags differing by as little as one nucleotide (99.2% similarity). A comparative analysis of oral communities of two cohabiting individuals reveals that most such subpopulations are shared between the two communities at 100% sequence identity, and that dynamical similarity between subpopulations in one host is strongly predictive of dynamical similarity between the same subpopulations in the other host. Our method can also be applied to samples collected in cross-sectional studies and can be used with the 454 sequencing platform. We discuss how the sub-OTU resolution of our approach can provide new insight into factors shaping community assembly.
Rutherford, Steven T, et al.Comprehensive analysis reveals how single nucleotides contribute to noncoding RNA function in bacterial quorum sensing.”. Proc Natl Acad Sci U S A 112.44 (2015): , 112, 44, E6038-47. Web.Abstract
Five homologous noncoding small RNAs (sRNAs), called the Qrr1-5 sRNAs, function in the Vibrio harveyi quorum-sensing cascade to drive its operation. Qrr1-5 use four different regulatory mechanisms to control the expression of ∼ 20 mRNA targets. Little is known about the roles individual nucleotides play in mRNA target selection, in determining regulatory mechanism, or in defining Qrr potency and dynamics of target regulation. To identify the nucleotides vital for Qrr function, we developed a method we call RSort-Seq that combines saturating mutagenesis, fluorescence-activated cell sorting, high-throughput sequencing, and mutual information theory to explore the role that every nucleotide in Qrr4 plays in regulation of two mRNA targets, luxR and luxO. Companion biochemical assays allowed us to assign specific regulatory functions/underlying molecular mechanisms to each important base. This strategy yielded a regional map of nucleotides in Qrr4 vital for stability, Hfq interaction, stem-loop formation, and base pairing to both luxR and luxO, to luxR only, and to luxO only. In terms of nucleotides critical for sRNA function, the RSort-Seq analysis provided strikingly different results from those predicted by commonly used regulatory RNA-folding algorithms. This approach is applicable to any RNA-RNA interaction, including sRNAs in other bacteria and regulatory RNAs in higher organisms.
Nadell, Carey D, et al.Extracellular matrix structure governs invasion resistance in bacterial biofilms.”. ISME J 98 (2015): , 9, 8, 1700-9. Web.Abstract
Many bacteria are highly adapted for life in communities, or biofilms. A defining feature of biofilms is the production of extracellular matrix that binds cells together. The biofilm matrix provides numerous fitness benefits, including protection from environmental stresses and enhanced nutrient availability. Here we investigate defense against biofilm invasion using the model bacterium Vibrio cholerae. We demonstrate that immotile cells, including those identical to the biofilm resident strain, are completely excluded from entry into resident biofilms. Motile cells can colonize and grow on the biofilm exterior, but are readily removed by shear forces. Protection from invasion into the biofilm interior is mediated by the secreted protein RbmA, which binds mother-daughter cell pairs to each other and to polysaccharide components of the matrix. RbmA, and the invasion protection it confers, strongly localize to the cell lineages that produce it.
Bitbol, Anne-Florence, and Ned S Wingreen. “Fundamental constraints on the abundances of chemotaxis proteins.”. Biophys J 108.5 (2015): , 108, 5, 1293-305. Web.Abstract
Flagellated bacteria, such as Escherichia coli, perform directed motion in gradients of concentration of attractants and repellents in a process called chemotaxis. The E. coli chemotaxis signaling pathway is a model for signal transduction, but it has unique features. We demonstrate that the need for fast signaling necessitates high abundances of the proteins involved in this pathway. We show that further constraints on the abundances of chemotaxis proteins arise from the requirements of self-assembly both of flagellar motors and of chemoreceptor arrays. All these constraints are specific to chemotaxis, and published data confirm that chemotaxis proteins tend to be more highly expressed than their homologs in other pathways. Employing a chemotaxis pathway model, we show that the gain of the pathway at the level of the response regulator CheY increases with overall chemotaxis protein abundances. This may explain why, at least in one E. coli strain, the abundance of all chemotaxis proteins is higher in media with lower nutrient content. We also demonstrate that the E. coli chemotaxis pathway is particularly robust to abundance variations of the motor protein FliM.
Persat, Alexandre, et al.The mechanical world of bacteria.”. Cell 161.5 (2015): , 161, 5, 988-97. Web.Abstract
In the wild, bacteria are predominantly associated with surfaces as opposed to existing as free-swimming, isolated organisms. They are thus subject to surface-specific mechanics, including hydrodynamic forces, adhesive forces, the rheology of their surroundings, and transport rules that define their encounters with nutrients and signaling molecules. Here, we highlight the effects of mechanics on bacterial behaviors on surfaces at multiple length scales, from single bacteria to the development of multicellular bacterial communities such as biofilms.
Wasnik, Vaibhav, Ned S Wingreen, and Ranjan Mukhopadhyay. “Modeling curvature-dependent subcellular localization of the small sporulation protein SpoVM in Bacillus subtilis.”. PLoS One 10.1 (2015): , 10, 1, e0111971. Web.Abstract
Recent in vivo experiments suggest that in the bacterium, Bacillus subtilis, the cue for the localization of the small sporulation protein, SpoVM, an essential factor in spore coat formation, is curvature of the bacterial plasma membrane. In vitro measurements of SpoVM adsorption to vesicles of varying sizes also find high sensitivity of adsorption to vesicle radius. This curvature-dependent adsorption is puzzling given the orders of magnitude difference in length scale between an individual protein and the radius of curvature of the cell or vesicle, suggesting protein clustering on the membrane. Here we develop a minimal model to study the relationship between curvature-dependent membrane adsorption and clustering of SpoVM. Based on our analysis, we hypothesize that the radius dependence of SpoVM adsorption observed in vitro is governed primarily by membrane tension, while for in-vivo localization of SpoVM, we propose a highly sensitive mechanism for curvature sensing based on the formation of macroscopic protein clusters on the membrane.
Taillefumier, Thibaud, and Ned S Wingreen. “Optimal census by quorum sensing.”. PLoS Comput Biol 11.5 (2015): , 11, 5, e1004238. Web.Abstract
Quorum sensing is the regulation of gene expression in response to changes in cell density. To measure their cell density, bacterial populations produce and detect diffusible molecules called autoinducers. Individual bacteria internally represent the external concentration of autoinducers via the level of monitor proteins. In turn, these monitor proteins typically regulate both their own production and the production of autoinducers, thereby establishing internal and external feedbacks. Here, we ask whether feedbacks can increase the information available to cells about their local density. We quantify available information as the mutual information between the abundance of a monitor protein and the local cell density for biologically relevant models of quorum sensing. Using variational methods, we demonstrate that feedbacks can increase information transmission, allowing bacteria to resolve up to two additional ranges of cell density when compared with bistable quorum-sensing systems. Our analysis is relevant to multi-agent systems that track an external driver implicitly via an endogenously generated signal.
Feng, Lihui, et al.A qrr noncoding RNA deploys four different regulatory mechanisms to optimize quorum-sensing dynamics.”. Cell 160.1-2 (2015): , 160, 1-2, 228-40. Web.Abstract
Quorum sensing is a cell-cell communication process that bacteria use to transition between individual and social lifestyles. In vibrios, homologous small RNAs called the Qrr sRNAs function at the center of quorum-sensing pathways. The Qrr sRNAs regulate multiple mRNA targets including those encoding the quorum-sensing regulatory components luxR, luxO, luxM, and aphA. We show that a representative Qrr, Qrr3, uses four distinct mechanisms to control its particular targets: the Qrr3 sRNA represses luxR through catalytic degradation, represses luxM through coupled degradation, represses luxO through sequestration, and activates aphA by revealing the ribosome binding site while the sRNA itself is degraded. Qrr3 forms different base-pairing interactions with each mRNA target, and the particular pairing strategy determines which regulatory mechanism occurs. Combined mathematical modeling and experiments show that the specific Qrr regulatory mechanism employed governs the potency, dynamics, and competition of target mRNA regulation, which in turn, defines the overall quorum-sensing response.
Borenstein, David Bruce, et al.Established Microbial Colonies Can Survive Type VI Secretion Assault.”. PLoS Comput Biol 11.10 (2015): , 11, 10, e1004520. Web.Abstract
Type VI secretion (T6S) is a cell-to-cell injection system that can be used as a microbial weapon. T6S kills vulnerable cells, and is present in close to 25% of sequenced Gram-negative bacteria. To examine the ecological role of T6S among bacteria, we competed self-immune T6S+ cells and T6S-sensitive cells in simulated range expansions. As killing takes place only at the interface between sensitive and T6S+ strains, while growth takes place everywhere, sufficiently large domains of sensitive cells can achieve net growth in the face of attack. Indeed T6S-sensitive cells can often outgrow their T6S+ competitors. We validated these findings through in vivo competition experiments between T6S+ Vibrio cholerae and T6S-sensitive Escherichia coli. We found that E. coli can survive and even dominate so long as they have an adequate opportunity to form microcolonies at the outset of the competition. Finally, in simulated competitions between two equivalent and mutually sensitive T6S+ strains, the more numerous strain has an advantage that increases with the T6S attack rate. We conclude that sufficiently large domains of T6S-sensitive individuals can survive attack and potentially outcompete self-immune T6S+ bacteria.
Wingreen, Ned S, and Kerwyn Casey Huang. “Physics of Intracellular Organization in Bacteria.”. Annu Rev Microbiol 69 (2015): , 69, 361-79. Web.Abstract
With the realization that bacteria achieve exquisite levels of spatiotemporal organization has come the challenge of discovering the underlying mechanisms. In this review, we describe three classes of such mechanisms, each of which has physical origins: the use of landmarks, the creation of higher-order structures that enable geometric sensing, and the emergence of length scales from systems of chemical reactions coupled to diffusion. We then examine the diversity of geometric cues that exist even in cells with relatively simple geometries, and end by discussing both new technologies that could drive further discovery and the implications of our current knowledge for the behavior, fitness, and evolution of bacteria. The organizational strategies described here are employed in a wide variety of systems and in species across all kingdoms of life; in many ways they provide a general blueprint for organizing the building blocks of life.
2014
Broedersz, Chase P, et al.Condensation and localization of the partitioning protein ParB on the bacterial chromosome.”. Proc Natl Acad Sci U S A 111.24 (2014): , 111, 24, 8809-14. Web.Abstract
The ParABS system mediates chromosome segregation and plasmid partitioning in many bacteria. As part of the partitioning mechanism, ParB proteins form a nucleoprotein complex at parS sites. The biophysical basis underlying ParB-DNA complex formation and localization remains elusive. Specifically, it is unclear whether ParB spreads in 1D along DNA or assembles into a 3D protein-DNA complex. We show that a combination of 1D spreading bonds and a single 3D bridging bond between ParB proteins constitutes a minimal model for a condensed ParB-DNA complex. This model implies a scaling behavior for ParB-mediated silencing of parS-flanking genes, which we confirm to be satisfied by experimental data from P1 plasmids. Furthermore, this model is consistent with experiments on the effects of DNA roadblocks on ParB localization. Finally, we show experimentally that a single parS site is necessary and sufficient for ParB-DNA complex formation in vivo. Together with our model, this suggests that ParB binding to parS triggers a conformational switch in ParB that overcomes a nucleation barrier. Conceptually, the combination of spreading and bridging bonds in our model provides a surface tension ensuring the condensation of the ParB-DNA complex, with analogies to liquid-like compartments such as nucleoli in eukaryotes.
Neumann, Silke, et al.Imprecision of adaptation in Escherichia coli chemotaxis.”. PLoS One 91 (2014): , 9, 1, e84904. Web.Abstract
Adaptability is an essential property of many sensory systems, enabling maintenance of a sensitive response over a range of background stimulus levels. In bacterial chemotaxis, adaptation to the preset level of pathway activity is achieved through an integral feedback mechanism based on activity-dependent methylation of chemoreceptors. It has been argued that this architecture ensures precise and robust adaptation regardless of the ambient ligand concentration, making perfect adaptation a celebrated property of the chemotaxis system. However, possible deviations from such ideal adaptive behavior and its consequences for chemotaxis have not been explored in detail. Here we show that the chemotaxis pathway in Escherichia coli shows increasingly imprecise adaptation to higher concentrations of attractants, with a clear correlation between the time of adaptation to a step-like stimulus and the extent of imprecision. Our analysis suggests that this imprecision results from a gradual saturation of receptor methylation sites at high levels of stimulation, which prevents full recovery of the pathway activity by violating the conditions required for precise adaptation. We further use computer simulations to show that limited imprecision of adaptation has little effect on the rate of chemotactic drift of a bacterial population in gradients, but hinders precise accumulation at the peak of the gradient. Finally, we show that for two major chemoeffectors, serine and cysteine, failure of adaptation at concentrations above 1 mM might prevent bacteria from accumulating at toxic concentrations of these amino acids.

Pages