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.
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.
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.
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.
Barry, Rachael M, et al.Large-scale filament formation inhibits the activity of CTP synthetase.”. Elife 3 (2014): , 3, e03638. Web.Abstract
CTP Synthetase (CtpS) is a universally conserved and essential metabolic enzyme. While many enzymes form small oligomers, CtpS forms large-scale filamentous structures of unknown function in prokaryotes and eukaryotes. By simultaneously monitoring CtpS polymerization and enzymatic activity, we show that polymerization inhibits activity, and CtpS's product, CTP, induces assembly. To understand how assembly inhibits activity, we used electron microscopy to define the structure of CtpS polymers. This structure suggests that polymerization sterically hinders a conformational change necessary for CtpS activity. Structure-guided mutagenesis and mathematical modeling further indicate that coupling activity to polymerization promotes cooperative catalytic regulation. This previously uncharacterized regulatory mechanism is important for cellular function since a mutant that disrupts CtpS polymerization disrupts E. coli growth and metabolic regulation without reducing CTP levels. We propose that regulation by large-scale polymerization enables ultrasensitive control of enzymatic activity while storing an enzyme subpopulation in a conformationally restricted form that is readily activatable.
Drescher, Knut, et al.Solutions to the public goods dilemma in bacterial biofilms.”. Curr Biol 24.1 (2014): , 24, 1, 50-5. Web.Abstract
Bacteria frequently live in densely populated surface-bound communities, termed biofilms [1-4]. Biofilm-dwelling cells rely on secretion of extracellular substances to construct their communities and to capture nutrients from the environment [5]. Some secreted factors behave as cooperative public goods: they can be exploited by nonproducing cells [6-11]. The means by which public-good-producing bacteria avert exploitation in biofilm environments are largely unknown. Using experiments with Vibrio cholerae, which secretes extracellular enzymes to digest its primary food source, the solid polymer chitin, we show that the public goods dilemma may be solved by two very different mechanisms: cells can produce thick biofilms that confine the goods to producers, or fluid flow can remove soluble products of chitin digestion, denying access to nonproducers. Both processes are unified by limiting the distance over which enzyme-secreting cells provide benefits to neighbors, resulting in preferential benefit to nearby clonemates and allowing kin selection to favor public good production. Our results demonstrate new mechanisms by which the physical conditions of natural habitats can interact with bacterial physiology to promote the evolution of cooperation.
Castellana, Michele, et al.Enzyme clustering accelerates processing of intermediates through metabolic channeling.”. Nat Biotechnol 32.10 (2014): , 32, 10, 1011-8. Web.Abstract
We present a quantitative model to demonstrate that coclustering multiple enzymes into compact agglomerates accelerates the processing of intermediates, yielding the same efficiency benefits as direct channeling, a well-known mechanism in which enzymes are funneled between enzyme active sites through a physical tunnel. The model predicts the separation and size of coclusters that maximize metabolic efficiency, and this prediction is in agreement with previously reported spacings between coclusters in mammalian cells. For direct validation, we study a metabolic branch point in Escherichia coli and experimentally confirm the model prediction that enzyme agglomerates can accelerate the processing of a shared intermediate by one branch, and thus regulate steady-state flux division. Our studies establish a quantitative framework to understand coclustering-mediated metabolic channeling and its application to both efficiency improvement and metabolic regulation.
Haselwandter, Christoph A, and Ned S Wingreen. “The role of membrane-mediated interactions in the assembly and architecture of chemoreceptor lattices.”. PLoS Comput Biol 10.12 (2014): , 10, 12, e1003932. Web.Abstract
In vivo fluorescence microscopy and electron cryo-tomography have revealed that chemoreceptors self-assemble into extended honeycomb lattices of chemoreceptor trimers with a well-defined relative orientation of trimers. The signaling response of the observed chemoreceptor lattices is remarkable for its extreme sensitivity, which relies crucially on cooperative interactions among chemoreceptor trimers. In common with other membrane proteins, chemoreceptor trimers are expected to deform the surrounding lipid bilayer, inducing membrane-mediated anisotropic interactions between neighboring trimers. Here we introduce a biophysical model of bilayer-chemoreceptor interactions, which allows us to quantify the role of membrane-mediated interactions in the assembly and architecture of chemoreceptor lattices. We find that, even in the absence of direct protein-protein interactions, membrane-mediated interactions can yield assembly of chemoreceptor lattices at very dilute trimer concentrations. The model correctly predicts the observed honeycomb architecture of chemoreceptor lattices as well as the observed relative orientation of chemoreceptor trimers, suggests a series of "gateway" states for chemoreceptor lattice assembly, and provides a simple mechanism for the localization of large chemoreceptor lattices to the cell poles. Our model of bilayer-chemoreceptor interactions also helps to explain the observed dependence of chemotactic signaling on lipid bilayer properties. Finally, we consider the possibility that membrane-mediated interactions might contribute to cooperativity among neighboring chemoreceptor trimers.
Bassler, Bonnie L, and Ned S Wingreen. “Working together at the interface of physics and biology.”. Phys Biol 11.5 (2014): , 11, 5, 053010. Web.Abstract
Good communication, whether it is between quorum-sensing bacteria or the different scientists studying those critters, is the key to a successful interdisciplinary collaboration, Bonnie Bassler and Ned Wingreen provide a personal perspective on working at the interface between the physical and biological sciences.
Wang, Siyuan, and Ned S Wingreen. “Cell shape can mediate the spatial organization of the bacterial cytoskeleton.”. Biophys J 104.3 (2013): , 104, 3, 541-52. Web.Abstract
The bacterial cytoskeleton guides the synthesis of cell wall and thus regulates cell shape. Because spatial patterning of the bacterial cytoskeleton is critical to the proper control of cell shape, it is important to ask how the cytoskeleton spatially self-organizes in the first place. In this work, we develop a quantitative model to account for the various spatial patterns adopted by bacterial cytoskeletal proteins, especially the orientation and length of cytoskeletal filaments such as FtsZ and MreB in rod-shaped cells. We show that the combined mechanical energy of membrane bending, membrane pinning, and filament bending of a membrane-attached cytoskeletal filament can be sufficient to prescribe orientation, e.g., circumferential for FtsZ or helical for MreB, with the accuracy of orientation increasing with the length of the cytoskeletal filament. Moreover, the mechanical energy can compete with the chemical energy of cytoskeletal polymerization to regulate filament length. Notably, we predict a conformational transition with increasing polymer length from smoothly curved to end-bent polymers. Finally, the mechanical energy also results in a mutual attraction among polymers on the same membrane, which could facilitate tight polymer spacing or bundling. The predictions of the model can be verified through genetic, microscopic, and microfluidic approaches.
Skoge, Monica, et al.Chemical sensing by nonequilibrium cooperative receptors.”. Phys Rev Lett 110.24 (2013): , 110, 24, 248102. Web.Abstract
Cooperativity arising from local interactions in equilibrium receptor systems provides gain, but does not increase sensory performance, as measured by the signal-to-noise ratio (SNR) due to a fundamental tradeoff between gain and intrinsic noise. Here we allow sensing to be a nonequilibrium process and show that energy dissipation cannot circumvent the fundamental tradeoff, so that the SNR is still optimal for independent receptors. For systems requiring high gain, nonequilibrium 2D-coupled receptors maximize the SNR, revealing a new design principle for biological sensors.
Skoge, Monica, et al.Chemical Sensing by Nonequilibrium Cooperative Receptors.”. Phys Rev Lett 110.24 (2013). Web.Abstract
Cooperativity arising from local interactions in equilibrium receptor systems provides gain, but does not increase sensory performance, as measured by the signal-to-noise ratio (SNR) due to a fundamental tradeoff between gain and intrinsic noise. Here we allow sensing to be a nonequilibrium process and show that energy dissipation cannot circumvent the fundamental tradeoff, so that the SNR is still optimal for independent receptors. For systems requiring high gain, nonequilibrium 2D-coupled receptors maximize the SNR, revealing a new design principle for biological sensors.
Borenstein, David Bruce, et al.Non-local interaction via diffusible resource prevents coexistence of cooperators and cheaters in a lattice model.”. PLoS One 85 (2013): , 8, 5, e63304. Web.Abstract
Many cellular populations cooperate through the secretion of diffusible extracellular resources, such as digestive enzymes or virulence factors. Diffusion of these resources leads to long-range intercellular interactions, creating the possibility of cooperation but also the risk of exploitation by non-producing neighbors. In the past, considerable attention has been given to game-theoretic lattice models of intercellular cooperation. In these models, coexistence is commonly observed between cooperators (corresponding to resource producers) and cheaters (corresponding to nonproducers). However, these models consider only interactions between direct competitors. We find that when individuals are allowed to interact non-locally through the diffusion of a shared resource coexistence between cooperators and cheaters is lost. Instead, we find population dynamics similar to simple competition, either neutral or biased, with no balancing selection that would favor coexistence. Our results highlight the importance of an accurate treatment of diffusion of shared resources and argue against the generality of the conclusions of game-theoretic lattice models.
Dwyer, Robert S, et al.Predicting functionally informative mutations in Escherichia coli BamA using evolutionary covariance analysis.”. Genetics 195.2 (2013): , 195, 2, 443-55. Web.Abstract
The essential outer membrane β-barrel protein BamA forms a complex with four lipoprotein partners BamBCDE that assembles β-barrel proteins into the outer membrane of Escherichia coli. Detailed genetic studies have shown that BamA cycles through multiple conformations during substrate assembly, suggesting that a complex network of residues may be involved in coordinating conformational changes and lipoprotein partner function. While genetic analysis of BamA has been informative, it has also been slow in the absence of a straightforward selection for mutants. Here we take a bioinformatic approach to identify candidate residues for mutagenesis using direct coupling analysis. Starting with the BamA paralog FhaC, we show that direct coupling analysis works well for large β-barrel proteins, identifying pairs of residues in close proximity in tertiary structure with a true positive rate of 0.64 over the top 50 predictions. To reduce the effects of noise, we designed and incorporated a novel structured prior into the empirical correlation matrix, dramatically increasing the FhaC true positive rate from 0.64 to 0.88 over the top 50 predictions. Our direct coupling analysis of BamA implicates residues R661 and D740 in a functional interaction. We find that the substitutions R661G and D740G each confer OM permeability defects and destabilize the BamA β-barrel. We also identify synthetic phenotypes and cross-suppressors that suggest R661 and D740 function in a similar process and may interact directly. We expect that the direct coupling analysis approach to informed mutagenesis will be particularly useful in systems lacking adequate selections and for dynamic proteins with multiple conformations.
Cooper, Robert M, Ned S Wingreen, and Edward C Cox. “An excitable cortex and memory model successfully predicts new pseudopod dynamics.”. PLoS One 73 (2012): , 7, 3, e33528. Web.Abstract
Motile eukaryotic cells migrate with directional persistence by alternating left and right turns, even in the absence of external cues. For example, Dictyostelium discoideum cells crawl by extending distinct pseudopods in an alternating right-left pattern. The mechanisms underlying this zig-zag behavior, however, remain unknown. Here we propose a new Excitable Cortex and Memory (EC&M) model for understanding the alternating, zig-zag extension of pseudopods. Incorporating elements of previous models, we consider the cell cortex as an excitable system and include global inhibition of new pseudopods while a pseudopod is active. With the novel hypothesis that pseudopod activity makes the local cortex temporarily more excitable--thus creating a memory of previous pseudopod locations--the model reproduces experimentally observed zig-zag behavior. Furthermore, the EC&M model makes four new predictions concerning pseudopod dynamics. To test these predictions we develop an algorithm that detects pseudopods via hierarchical clustering of individual membrane extensions. Data from cell-tracking experiments agrees with all four predictions of the model, revealing that pseudopod placement is a non-Markovian process affected by the dynamics of previous pseudopods. The model is also compatible with known limits of chemotactic sensitivity. In addition to providing a predictive approach to studying eukaryotic cell motion, the EC&M model provides a general framework for future models, and suggests directions for new research regarding the molecular mechanisms underlying directional persistence.
Sourjik, Victor, and Ned S Wingreen. “Responding to chemical gradients: bacterial chemotaxis.”. Curr Opin Cell Biol 24.2 (2012): , 24, 2, 262-8. Web.Abstract
Chemotaxis allows bacteria to follow gradients of nutrients and other environmental stimuli. The bacterium Escherichia coli performs chemotaxis via a run-and-tumble strategy in which sensitive temporal comparisons lead to a biased random walk, with longer runs in the preferred gradient direction. The chemotaxis network of E. coli has developed over the years into one of the most thoroughly studied model systems for signal transduction and behavior, yielding general insights into such properties of cellular networks as signal amplification, signal integration, and robustness. Despite its relative simplicity, the operation of the E. coli chemotaxis network is highly refined and evolutionarily optimized at many levels. For example, recent studies revealed that the network adjusts its signaling properties dependent on the extracellular environment, apparently to optimize chemotaxis under particular conditions. The network can even utilize potentially detrimental stochastic fluctuations in protein levels and reaction rates to maximize the chemotactic performance of the population.
Daly, Kristopher E, et al.Mechanics of membrane bulging during cell-wall disruption in gram-negative bacteria.”. Phys Rev E Stat Nonlin Soft Matter Phys 83.4 Pt 1 (2011): , 83, 4 Pt 1, 041922. Web.Abstract
The bacterial cell wall is a network of sugar strands crosslinked by peptides that serve as the primary structure for bearing osmotic stress. Despite its importance in cellular survival, the robustness of the cell wall to network defects has been relatively unexplored. Treatment of the gram-negative bacterium Escherichia coli with the antibiotic vancomycin, which disrupts the crosslinking of new material during growth, leads to the development of pronounced bulges and eventually of cell lysis. Here, we model the mechanics of the bulging of the cytoplasmic membrane through pores in the cell wall. We find that the membrane undergoes a transition between a nearly flat state and a spherical bulge at a critical pore radius of ~20 nm. This critical pore size is large compared to the typical distance between neighboring peptides and glycan strands, and hence pore size acts as a constraint on network integrity. We also discuss the general implications of our model to membrane deformations in eukaryotic blebbing and vesiculation in red blood cells.
Furchtgott, Leon, Ned S Wingreen, and Kerwyn Casey Huang. “Mechanisms for maintaining cell shape in rod-shaped Gram-negative bacteria.”. Mol Microbiol 81.2 (2011): , 81, 2, 340-53. Web.Abstract
For the rod-shaped Gram-negative bacterium Escherichia coli, changes in cell shape have critical consequences for motility, immune system evasion, proliferation and adhesion. For most bacteria, the peptidoglycan cell wall is both necessary and sufficient to determine cell shape. However, how the synthesis machinery assembles a peptidoglycan network with a robustly maintained micron-scale shape has remained elusive. To explore shape maintenance, we have quantified the robustness of cell shape in three Gram-negative bacteria in different genetic backgrounds and in the presence of an antibiotic that inhibits division. Building on previous modelling suggesting a prominent role for mechanical forces in shape regulation, we introduce a biophysical model for the growth dynamics of rod-shaped cells to investigate the roles of spatial regulation of peptidoglycan synthesis, glycan-strand biochemistry and mechanical stretching during insertion. Our studies reveal that rod-shape maintenance requires insertion to be insensitive to fluctuations in cell-wall density and stress, and even a simple helical pattern of insertion is sufficient for over sixfold elongation without significant loss in shape. In addition, we demonstrate that both the length and pre-stretching of newly inserted strands regulate cell width. In sum, we show that simple physical rules can allow bacteria to achieve robust, shape-preserving cell-wall growth.
Mora, Thierry, et al.Non-genetic individuality in Escherichia coli motor switching.”. Phys Biol 82 (2011): , 8, 2, 024001. Web.Abstract
By analyzing 30 min, high-resolution recordings of single Escherichia coli flagellar motors in the physiological regime, we show that two main properties of motor switching-the mean clockwise and mean counter-clockwise interval durations-vary significantly. When we represent these quantities on a two-dimensional plot for several cells, the data do not fall on a one-dimensional curve, as expected with a single control parameter, but instead spread in two dimensions, pointing to motor individuality. The largest variations are in the mean counter-clockwise interval, and are attributable to variations in the concentration of the internal signaling molecule CheY-P. In contrast, variations in the mean clockwise interval are interpreted in terms of motor individuality. We argue that the sensitivity of the mean counter-clockwise interval to fluctuations in CheY-P is consistent with an optimal strategy of run and tumble. The concomittent variability in mean run length may allow populations of cells to better survive in rapidly changing environments by 'hedging their bets'.
Oleksiuk, Olga, et al.Thermal robustness of signaling in bacterial chemotaxis.”. Cell 145.2 (2011): , 145, 2, 312-21. Web.Abstract
Temperature is a global factor that affects the performance of all intracellular networks. Robustness against temperature variations is thus expected to be an essential network property, particularly in organisms without inherent temperature control. Here, we combine experimental analyses with computational modeling to investigate thermal robustness of signaling in chemotaxis of Escherichia coli, a relatively simple and well-established model for systems biology. We show that steady-state and kinetic pathway parameters that are essential for chemotactic performance are indeed temperature-compensated in the entire physiological range. Thermal robustness of steady-state pathway output is ensured at several levels by mutual compensation of temperature effects on activities of individual pathway components. Moreover, the effect of temperature on adaptation kinetics is counterbalanced by preprogrammed temperature dependence of enzyme synthesis and stability to achieve nearly optimal performance at the growth temperature. Similar compensatory mechanisms are expected to ensure thermal robustness in other systems.
Swanson, Douglas, and Ned S Wingreen. “Active biopolymers confer fast reorganization kinetics.”. Phys Rev Lett 107.21 (2011): , 107, 21, 218103. Web.Abstract
Many cytoskeletal biopolymers are "active," consuming energy in large quantities. In this Letter, we identify a fundamental difference between active polymers and passive, equilibrium polymers: for equal mean lengths, active polymers can reorganize faster than equilibrium polymers. We show that equilibrium polymers are intrinsically limited to linear scaling between mean lifetime (or mean first-passage time, or MFPT) and mean length, MFPT∼, by analogy to 1D Potts models. By contrast, we present a simple active-polymer model that improves upon this scaling, such that MFPT∼(1/2). Since, to be biologically useful, structural biopolymers must typically be many monomers long yet respond dynamically to the needs of the cell, the difference in reorganization kinetics may help to justify the active polymers' greater energy cost.
Teng, Shu-Wen, et al.Active regulation of receptor ratios controls integration of quorum-sensing signals in Vibrio harveyi.”. Mol Syst Biol 7 (2011): , 7, 491. Web.Abstract
Quorum sensing is a chemical signaling mechanism used by bacteria to communicate and orchestrate group behaviors. Multiple feedback loops exist in the quorum-sensing circuit of the model bacterium Vibrio harveyi. Using fluorescence microscopy of individual cells, we assayed the activity of the quorum-sensing circuit, with a focus on defining the functions of the feedback loops. We quantitatively investigated the signaling input-output relation both in cells with all feedback loops present as well as in mutants with specific feedback loops disrupted. We found that one of the feedback loops regulates receptor ratios to control the integration of multiple signals. Together, the feedback loops affect the input-output dynamic range of signal transmission and the noise in the output. We conclude that V. harveyi employs multiple feedback loops to simultaneously control quorum-sensing signal integration and to ensure signal transmission fidelity.
van Teeffelen, Sven, et al.The bacterial actin MreB rotates, and rotation depends on cell-wall assembly.”. Proc Natl Acad Sci U S A 108.38 (2011): , 108, 38, 15822-7. Web.Abstract
Bacterial cells possess multiple cytoskeletal proteins involved in a wide range of cellular processes. These cytoskeletal proteins are dynamic, but the driving forces and cellular functions of these dynamics remain poorly understood. Eukaryotic cytoskeletal dynamics are often driven by motor proteins, but in bacteria no motors that drive cytoskeletal motion have been identified to date. Here, we quantitatively study the dynamics of the Escherichia coli actin homolog MreB, which is essential for the maintenance of rod-like cell shape in bacteria. We find that MreB rotates around the long axis of the cell in a persistent manner. Whereas previous studies have suggested that MreB dynamics are driven by its own polymerization, we show that MreB rotation does not depend on its own polymerization but rather requires the assembly of the peptidoglycan cell wall. The cell-wall synthesis machinery thus either constitutes a novel type of extracellular motor that exerts force on cytoplasmic MreB, or is indirectly required for an as-yet-unidentified motor. Biophysical simulations suggest that one function of MreB rotation is to ensure a uniform distribution of new peptidoglycan insertion sites, a necessary condition to maintain rod shape during growth. These findings both broaden the view of cytoskeletal motors and deepen our understanding of the physical basis of bacterial morphogenesis.
McIsaac, Scott R, et al.Does the potential for chaos constrain the embryonic cell-cycle oscillator?”. PLoS Comput Biol 77 (2011): , 7, 7, e1002109. Web.Abstract
Although many of the core components of the embryonic cell-cycle network have been elucidated, the question of how embryos achieve robust, synchronous cellular divisions post-fertilization remains unexplored. What are the different schemes that could be implemented by the embryo to achieve synchronization? By extending a cell-cycle model previously developed for embryos of the frog Xenopus laevis to include the spatial dimensions of the embryo, we establish a novel role for the rapid, fertilization-initiated calcium wave that triggers cell-cycle oscillations. Specifically, in our simulations a fast calcium wave results in synchronized cell cycles, while a slow wave results in full-blown spatio-temporal chaos. We show that such chaos would ultimately lead to an unpredictable patchwork of cell divisions across the embryo. Given this potential for chaos, our results indicate a novel design principle whereby the fast calcium-wave trigger following embryo fertilization synchronizes cell divisions.
Skoge, Monica, Yigal Meir, and Ned S Wingreen. “Dynamics of cooperativity in chemical sensing among cell-surface receptors.”. Phys Rev Lett 107.17 (2011): , 107, 17, 178101. Web.Abstract
Cooperative interactions among sensory receptors provide a general mechanism to increase the sensitivity of signal transduction. In particular, bacterial chemotaxis receptors interact cooperatively to produce an ultrasensitive response to chemoeffector concentrations. However, cooperativity between receptors in large macromolecular complexes is necessarily based on local interactions and consequently is fundamentally connected to slowing of receptor-conformational dynamics, which increases intrinsic noise. Therefore, it is not clear whether or under what conditions cooperativity actually increases the precision of the concentration measurement. We explicitly calculate the signal-to-noise ratio (SNR) for sensing a concentration change using a simple, Ising-type model of receptor-receptor interactions, generalized via scaling arguments, and find that the optimal SNR is always achieved by independent receptors.
Banigan, Edward J, et al.Filament depolymerization can explain chromosome pulling during bacterial mitosis.”. PLoS Comput Biol 79 (2011): , 7, 9, e1002145. Web.Abstract
Chromosome segregation is fundamental to all cells, but the force-generating mechanisms underlying chromosome translocation in bacteria remain mysterious. Caulobacter crescentus utilizes a depolymerization-driven process in which a ParA protein structure elongates from the new cell pole, binds to a ParB-decorated chromosome, and then retracts via disassembly, pulling the chromosome across the cell. This poses the question of how a depolymerizing structure can robustly pull the chromosome that disassembles it. We perform Brownian dynamics simulations with a simple, physically consistent model of the ParABS system. The simulations suggest that the mechanism of translocation is "self-diffusiophoretic": by disassembling ParA, ParB generates a ParA concentration gradient so that the ParA concentration is higher in front of the chromosome than behind it. Since the chromosome is attracted to ParA via ParB, it moves up the ParA gradient and across the cell. We find that translocation is most robust when ParB binds side-on to ParA filaments. In this case, robust translocation occurs over a wide parameter range and is controlled by a single dimensionless quantity: the product of the rate of ParA disassembly and a characteristic relaxation time of the chromosome. This time scale measures the time it takes for the chromosome to recover its average shape after it is has been pulled. Our results suggest explanations for observed phenomena such as segregation failure, filament-length-dependent translocation velocity, and chromosomal compaction.
Wang, Yufang, et al.Protein-level fluctuation correlation at the microcolony level and its application to the Vibrio harveyi quorum-sensing circuit.”. Biophys J 100.12 (2011): , 100, 12, 3045-53. Web.Abstract
Gene expression is stochastic, and noise that arises from the stochastic nature of biochemical reactions propagates through active regulatory links. Thus, correlations in gene-expression noise can provide information about regulatory links. We present what to our knowledge is a new approach to measure and interpret such correlated fluctuations at the level of single microcolonies, which derive from single cells. We demonstrated this approach mathematically using stochastic modeling, and applied it to experimental time-lapse fluorescence microscopy data. Specifically, we investigated the relationships among LuxO, LuxR, and the small regulatory RNA qrr4 in the model quorum-sensing bacterium Vibrio harveyi. Our results show that LuxR positively regulates the qrr4 promoter. Under our conditions, we find that qrr regulation weakly depends on total LuxO levels and that LuxO autorepression is saturated. We also find evidence that the fluctuations in LuxO levels are dominated by intrinsic noise. We furthermore propose LuxO and LuxR interact at all autoinducer levels via an unknown mechanism. Of importance, our new method of evaluating correlations at the microcolony level is unaffected by partition noise at cell division. Moreover, the method is first-order accurate and requires less effort for data analysis than single-cell-based approaches. This new correlation approach can be applied to other systems to aid analysis of gene regulatory circuits.
Doucette, Christopher D, et al.α-Ketoglutarate coordinates carbon and nitrogen utilization via enzyme I inhibition.”. Nat Chem Biol 712 (2011): , 7, 12, 894-901. Web.Abstract
Microbes survive in a variety of nutrient environments by modulating their intracellular metabolism. Balanced growth requires coordinated uptake of carbon and nitrogen, the primary substrates for biomass production. Yet the mechanisms that balance carbon and nitrogen uptake are poorly understood. We find in Escherichia coli that a sudden increase in nitrogen availability results in an almost immediate increase in glucose uptake. The concentrations of glycolytic intermediates and known regulators, however, remain homeostatic. Instead, we find that α-ketoglutarate, which accumulates in nitrogen limitation, directly blocks glucose uptake by inhibiting enzyme I, the first step of the sugar-phosphoenolpyruvate phosphotransferase system (PTS). This inhibition enables rapid modulation of glycolytic flux without marked changes in the concentrations of glycolytic intermediates by simultaneously altering import of glucose and consumption of the terminal glycolytic intermediate phosphoenolpyruvate. Quantitative modeling shows that this previously unidentified regulatory connection is, in principle, sufficient to coordinate carbon and nitrogen utilization.
Goyal, Sidhartha, et al.Achieving optimal growth through product feedback inhibition in metabolism.”. PLoS Comput Biol 66 (2010): , 6, 6, e1000802. Web.Abstract
Recent evidence suggests that the metabolism of some organisms, such as Escherichia coli, is remarkably efficient, producing close to the maximum amount of biomass per unit of nutrient consumed. This observation raises the question of what regulatory mechanisms enable such efficiency. Here, we propose that simple product-feedback inhibition by itself is capable of leading to such optimality. We analyze several representative metabolic modules--starting from a linear pathway and advancing to a bidirectional pathway and metabolic cycle, and finally to integration of two different nutrient inputs. In each case, our mathematical analysis shows that product-feedback inhibition is not only homeostatic but also, with appropriate feedback connections, can minimize futile cycling and optimize fluxes. However, the effectiveness of simple product-feedback inhibition comes at the cost of high levels of some metabolite pools, potentially associated with toxicity and osmotic imbalance. These large metabolite pool sizes can be restricted if feedback inhibition is ultrasensitive. Indeed, the multi-layer regulation of metabolism by control of enzyme expression, enzyme covalent modification, and allostery is expected to result in such ultrasensitive feedbacks. To experimentally test whether the qualitative predictions from our analysis of feedback inhibition apply to metabolic modules beyond linear pathways, we examine the case of nitrogen assimilation in E. coli, which involves both nutrient integration and a metabolic cycle. We find that the feedback regulation scheme suggested by our mathematical analysis closely aligns with the actual regulation of the network and is sufficient to explain much of the dynamical behavior of relevant metabolite pool sizes in nutrient-switching experiments.
Zee, Barry M, et al.In vivo residue-specific histone methylation dynamics.”. J Biol Chem 285.5 (2010): , 285, 5, 3341-50. Web.Abstract
Methylation of specific histone residues is capable of both gene activation and silencing. Despite vast work on the function of methylation, most studies either present a static snapshot of methylation or fail to assign kinetic information to specific residues. Using liquid chromatography-tandem mass spectrometry on a high-resolution mass spectrometer and heavy methyl-SILAC labeling, we studied site-specific histone lysine and arginine methylation dynamics. The detection of labeled intermediates within a methylation state revealed that mono-, di-, and trimethylated residues generally have progressively slower rates of formation. Furthermore, methylations associated with active genes have faster rates than methylations associated with silent genes. Finally, the presence of both an active and silencing mark on the same peptide results in a slower rate of methylation than the presence of either mark alone. Here we show that quantitative proteomic approaches such as this can determine the dynamics of multiple methylated residues, an understudied portion of histone biology.
Teng, Shu-Wen, et al.Measurement of the copy number of the master quorum-sensing regulator of a bacterial cell.”. Biophys J 98.9 (2010): , 98, 9, 2024-31. Web.Abstract
Quorum-sensing is the mechanism by which bacteria communicate and synchronize group behaviors. Quantitative information on parameters such as the copy number of particular quorum-sensing proteins should contribute strongly to understanding how the quorum-sensing network functions. Here, we show that the copy number of the master regulator protein LuxR in Vibrio harveyi can be determined in vivo by exploiting small-number fluctuations of the protein distribution when cells undergo division. When a cell divides, both its volume and LuxR protein copy number, N, are partitioned with slight asymmetries. We measured the distribution functions describing the partitioning of the protein fluorescence and the cell volume. The fluorescence distribution is found to narrow systematically as the LuxR population increases, whereas the volume partitioning is unchanged. Analyzing these changes statistically, we determined that N = 80-135 dimers at low cell density and 575 dimers at high cell density. In addition, we measured the static distribution of LuxR over a large (3000) clonal population. Combining the static and time-lapse experiments, we determine the magnitude of the Fano factor of the distribution. This technique has broad applicability as a general in vivo technique for measuring protein copy number and burst size.
Kidd, Philip B, and Ned S Wingreen. “Modeling the role of covalent enzyme modification in Escherichia coli nitrogen metabolism.”. Phys Biol 71 (2010): , 7, 1, 016006. Web.Abstract
In the bacterium Escherichia coli, the enzyme glutamine synthetase (GS) converts ammonium into the amino acid glutamine. GS is principally active when the cell is experiencing nitrogen limitation, and its activity is regulated by a bicyclic covalent modification cascade. The advantages of this bicyclic-cascade architecture are poorly understood. We analyze a simple model of the GS cascade in comparison to other regulatory schemes and conclude that the bicyclic cascade is suboptimal for maintaining metabolic homeostasis of the free glutamine pool. Instead, we argue that the lag inherent in the covalent modification of GS slows the response to an ammonium shock and thereby allows GS to transiently detoxify the cell, while maintaining homeostasis over longer times.
Tu, Kimberly C, et al.Negative feedback loops involving small regulatory RNAs precisely control the Vibrio harveyi quorum-sensing response.”. Mol Cell 37.4 (2010): , 37, 4, 567-79. Web.Abstract
Quorum-sensing (QS) bacteria assess population density through secretion and detection of molecules called autoinducers (AIs). We identify and characterize two Vibrio harveyi negative feedback loops that facilitate precise transitions between low-cell-density (LCD) and high-cell-density (HCD) states. The QS central regulator LuxO autorepresses its own transcription, and the Qrr small regulatory RNAs (sRNAs) posttranscriptionally repress luxO. Disrupting feedback increases the concentration of AIs required for cells to transit from LCD to HCD QS modes. Thus, the two cooperative negative feedback loops determine the point at which V. harveyi has reached a quorum and control the range of AIs over which the transition occurs. Negative feedback regulation also constrains the range of QS output by preventing sRNA levels from becoming too high and preventing luxO mRNA levels from reaching zero. We suggest that sRNA-mediated feedback regulation is a network design feature that permits fine-tuning of gene regulation and maintenance of homeostasis.
Ng, Wai-Leung, et al.Probing bacterial transmembrane histidine kinase receptor-ligand interactions with natural and synthetic molecules.”. Proc Natl Acad Sci U S A 107.12 (2010): , 107, 12, 5575-80. Web.Abstract
Bacterial histidine kinases transduce extracellular signals into the cytoplasm. Most stimuli are chemically undefined; therefore, despite intensive study, signal recognition mechanisms remain mysterious. We exploit the fact that quorum-sensing signals are known molecules to identify mutants in the Vibrio cholerae quorum-sensing receptor CqsS that display altered responses to natural and synthetic ligands. Using this chemical-genetics approach, we assign particular amino acids of the CqsS sensor to particular roles in recognition of the native ligand, CAI-1 (S-3 hydroxytridecan-4-one) as well as ligand analogues. Amino acids W104 and S107 dictate receptor preference for the carbon-3 moiety. Residues F162 and C170 specify ligand head size and tail length, respectively. By combining mutations, we can build CqsS receptors responsive to ligand analogues altered at both the head and tail. We suggest that rationally designed ligands can be employed to study, and ultimately to control, histidine kinase activity.
Neumann, Silke, et al.Differences in signalling by directly and indirectly binding ligands in bacterial chemotaxis.”. EMBO J 29.20 (2010): , 29, 20, 3484-95. Web.Abstract
In chemotaxis of Escherichia coli and other bacteria, extracellular stimuli are perceived by transmembrane receptors that bind their ligands either directly, or indirectly through periplasmic-binding proteins (BPs). As BPs are also involved in ligand uptake, they provide a link between chemotaxis and nutrient utilization by cells. However, signalling by indirectly binding ligands remains much less understood than signalling by directly binding ligands. Here, we compared intracellular responses mediated by both types of ligands and developed a new mathematical model for signalling by indirectly binding ligands. We show that indirect binding allows cells to better control sensitivity to specific ligands in response to their nutrient environment and to coordinate chemotaxis with ligand transport, but at the cost of the dynamic range being much narrower than for directly binding ligands. We further demonstrate that signal integration by the chemosensory complexes does not depend on the type of ligand. Overall, our data suggest that the distinction between signalling by directly and indirectly binding ligands is more physiologically important than the traditional distinction between high- and low-abundance receptors.
Hansen, Clinton H, Victor Sourjik, and Ned S Wingreen. “A dynamic-signaling-team model for chemotaxis receptors in Escherichia coli.”. Proc Natl Acad Sci U S A 107.40 (2010): , 107, 40, 17170-5. Web.Abstract
The chemotaxis system of Escherichia coli is sensitive to small relative changes in ambient chemoattractant concentrations over a broad range. Interactions among receptors are crucial to this sensitivity, as is precise adaptation, the return of chemoreceptor activity to prestimulus levels in a constant chemoeffector environment through methylation and demethylation of receptors. Signal integration and cooperativity have been attributed to strongly coupled, mixed teams of receptors, but receptors become individually methylated according to their ligand occupancy states. Here, we present a model of dynamic signaling teams that reconciles strong coupling among receptors with receptor-specific methylation. Receptor trimers of dimers couple to form a honeycomb lattice, consistent with cryo-electron microscopy (cryoEM) tomography, within which the boundaries of signaling teams change rapidly. Our model helps explain the inferred increase in signaling team size with receptor modification, and indicates that active trimers couple more strongly than inactive trimers.
Wyart, Matthieu, David Botstein, and Ned S Wingreen. “Evaluating gene expression dynamics using pairwise RNA FISH data.”. PLoS Comput Biol 611 (2010): , 6, 11, e1000979. Web.Abstract
Recently, a novel approach has been developed to study gene expression in single cells with high time resolution using RNA Fluorescent In Situ Hybridization (FISH). The technique allows individual mRNAs to be counted with high accuracy in wild-type cells, but requires cells to be fixed; thus, each cell provides only a "snapshot" of gene expression. Here we show how and when RNA FISH data on pairs of genes can be used to reconstruct real-time dynamics from a collection of such snapshots. Using maximum-likelihood parameter estimation on synthetically generated, noisy FISH data, we show that dynamical programs of gene expression, such as cycles (e.g., the cell cycle) or switches between discrete states, can be accurately reconstructed. In the limit that mRNAs are produced in short-lived bursts, binary thresholding of the FISH data provides a robust way of reconstructing dynamics. In this regime, prior knowledge of the type of dynamics--cycle versus switch--is generally required and additional constraints, e.g., from triplet FISH measurements, may also be needed to fully constrain all parameters. As a demonstration, we apply the thresholding method to RNA FISH data obtained from single, unsynchronized cells of Saccharomyces cerevisiae. Our results support the existence of metabolic cycles and provide an estimate of global gene-expression noise. The approach to FISH data presented here can be applied in general to reconstruct dynamics from snapshots of pairs of correlated quantities including, for example, protein concentrations obtained from immunofluorescence assays.
Nara, Peter L, et al.How can vaccines against influenza and other viral diseases be made more effective?”. PLoS Biol 812 (2010): , 8, 12, e1000571. Web.
Mora, Thierry, and Ned S Wingreen. “Limits of sensing temporal concentration changes by single cells.”. Phys Rev Lett 104.24 (2010): , 104, 24, 248101. Web.Abstract
Berg and Purcell [Biophys. J. 20, 193 (1977)] calculated how the accuracy of concentration sensing by single-celled organisms is limited by noise from the small number of counted molecules. Here we generalize their results to the sensing of concentration ramps, which is often the biologically relevant situation (e.g., during bacterial chemotaxis). We calculate lower bounds on the uncertainty of ramp sensing by three measurement devices: a single receptor, an absorbing sphere, and a monitoring sphere. We contrast two strategies, simple linear regression of the input signal versus maximum likelihood estimation, and show that the latter can be twice as accurate as the former. Finally, we consider biological implementations of these two strategies, and identify possible signatures that maximum likelihood estimation is implemented by real biological systems.
Meir, Yigal, et al.Precision and kinetics of adaptation in bacterial chemotaxis.”. Biophys J 99.9 (2010): , 99, 9, 2766-74. Web.Abstract
The chemotaxis network of the bacterium Escherichia coli is perhaps the most studied model for adaptation of a signaling system to persistent stimuli. Although adaptation in this system is generally considered to be precise, there has been little effort to quantify this precision, or to understand how and when precision fails. Using a Förster resonance energy transfer-based reporter of signaling activity, we undertook a systematic study of adaptation kinetics and precision in E. coli cells expressing a single type of chemoreceptor (Tar). Quantifiable loss of precision of adaptation was observed at levels of the attractant MeAsp as low 10 μM, with pronounced differences in both kinetics and precision of adaptation between addition and removal of attractant. Quantitative modeling of the kinetic data suggests that loss of precise adaptation is due to a slowing of receptor methylation as available modification sites become scarce. Moreover, the observed kinetics of adaptation imply large cell-to-cell variation in adaptation rates-potentially providing genetically identical cells with the ability to "hedge their bets" by pursuing distinct chemotactic strategies.
Endres, Robert G, and Ned S Wingreen. “Accuracy of direct gradient sensing by cell-surface receptors.”. Prog Biophys Mol Biol 100.1-3 (2009): , 100, 1-3, 33-9. Web.Abstract
Chemotactic cells of eukaryotic organisms are able to accurately sense shallow chemical concentration gradients using cell-surface receptors. This sensing ability is remarkable as cells must be able to spatially resolve small fractional differences in the numbers of particles randomly arriving at cell-surface receptors by diffusion. An additional challenge and source of uncertainty is that particles, once bound and released, may rebind the same or a different receptor, which adds to noise without providing any new information about the environment. We recently derived the fundamental physical limits of gradient sensing using a simple spherical-cell model, but not including explicit particle-receptor kinetics. Here, we use a method based on the fluctuation-dissipation theorem (FDT) to calculate the accuracy of gradient sensing by realistic receptors. We derive analytical results for two receptors, as well as two coaxial rings of receptors, e.g. one at each cell pole. For realistic receptors, we find that particle rebinding lowers the accuracy of gradient sensing, in line with our previous results.
Ndifon, Wilfred, Ned S Wingreen, and Simon A Levin. “Differential neutralization efficiency of hemagglutinin epitopes, antibody interference, and the design of influenza vaccines.”. Proc Natl Acad Sci U S A 106.21 (2009): , 106, 21, 8701-6. Web.Abstract
It is generally assumed that amino acid mutations in the surface protein, hemagglutinin (HA), of influenza viruses allow these viruses to circumvent neutralization by antibodies induced during infection. However, empirical data on circulating influenza viruses show that certain amino acid changes to HA actually increase the efficiency of neutralization of the mutated virus by antibodies raised against the parent virus. Here, we suggest that this surprising increase in neutralization efficiency after HA mutation could reflect steric interference between antibodies. Specifically, if there is a steric competition for binding to HA by antibodies with different neutralization efficiencies, then a mutation that reduces the binding of antibodies with low neutralization efficiencies could increase overall viral neutralization. We use a mathematical model of virus-antibody interaction to elucidate the conditions under which amino acid mutations to HA could lead to an increase in viral neutralization. Using insights gained from the model, together with genetic and structural data, we predict that amino acid mutations to epitopes C and E of the HA of influenza A/H3N2 viruses could lead on average to an increase in the neutralization of the mutated viruses. We present data supporting this prediction and discuss the implications for the design of more effective vaccines against influenza viruses and other pathogens.
Yuan, Jie, et al.Metabolomics-driven quantitative analysis of ammonia assimilation in E. coli.”. Mol Syst Biol 5 (2009): , 5, 302. Web.Abstract
Despite extensive study of individual enzymes and their organization into pathways, the means by which enzyme networks control metabolite concentrations and fluxes in cells remains incompletely understood. Here, we examine the integrated regulation of central nitrogen metabolism in Escherichia coli through metabolomics and ordinary-differential-equation-based modeling. Metabolome changes triggered by modulating extracellular ammonium centered around two key intermediates in nitrogen assimilation, alpha-ketoglutarate and glutamine. Many other compounds retained concentration homeostasis, indicating isolation of concentration changes within a subset of the metabolome closely linked to the nutrient perturbation. In contrast to the view that saturated enzymes are insensitive to substrate concentration, competition for the active sites of saturated enzymes was found to be a key determinant of enzyme fluxes. Combined with covalent modification reactions controlling glutamine synthetase activity, such active-site competition was sufficient to explain and predict the complex dynamic response patterns of central nitrogen metabolites.
Long, Tao, et al.Quantifying the integration of quorum-sensing signals with single-cell resolution.”. PLoS Biol 73 (2009): , 7, 3, e68. Web.Abstract
Cell-to-cell communication in bacteria is a process known as quorum sensing that relies on the production, detection, and response to the extracellular accumulation of signaling molecules called autoinducers. Often, bacteria use multiple autoinducers to obtain information about the vicinal cell density. However, how cells integrate and interpret the information contained within multiple autoinducers remains a mystery. Using single-cell fluorescence microscopy, we quantified the signaling responses to and analyzed the integration of multiple autoinducers by the model quorum-sensing bacterium Vibrio harveyi. Our results revealed that signals from two distinct autoinducers, AI-1 and AI-2, are combined strictly additively in a shared phosphorelay pathway, with each autoinducer contributing nearly equally to the total response. We found a coherent response across the population with little cell-to-cell variation, indicating that the entire population of cells can reliably distinguish several distinct conditions of external autoinducer concentration. We speculate that the use of multiple autoinducers allows a growing population of cells to synchronize gene expression during a series of distinct developmental stages.
Greenfield, Derek, et al.Self-organization of the Escherichia coli chemotaxis network imaged with super-resolution light microscopy.”. PLoS Biol 76 (2009): , 7, 6, e1000137. Web.Abstract
The Escherichia coli chemotaxis network is a model system for biological signal processing. In E. coli, transmembrane receptors responsible for signal transduction assemble into large clusters containing several thousand proteins. These sensory clusters have been observed at cell poles and future division sites. Despite extensive study, it remains unclear how chemotaxis clusters form, what controls cluster size and density, and how the cellular location of clusters is robustly maintained in growing and dividing cells. Here, we use photoactivated localization microscopy (PALM) to map the cellular locations of three proteins central to bacterial chemotaxis (the Tar receptor, CheY, and CheW) with a precision of 15 nm. We find that cluster sizes are approximately exponentially distributed, with no characteristic cluster size. One-third of Tar receptors are part of smaller lateral clusters and not of the large polar clusters. Analysis of the relative cellular locations of 1.1 million individual proteins (from 326 cells) suggests that clusters form via stochastic self-assembly. The super-resolution PALM maps of E. coli receptors support the notion that stochastic self-assembly can create and maintain approximately periodic structures in biological membranes, without direct cytoskeletal involvement or active transport.
Mora, Thierry, et al.Steps in the bacterial flagellar motor.”. PLoS Comput Biol 510 (2009): , 5, 10, e1000540. Web.Abstract
The bacterial flagellar motor is a highly efficient rotary machine used by many bacteria to propel themselves. It has recently been shown that at low speeds its rotation proceeds in steps. Here we propose a simple physical model, based on the storage of energy in protein springs, that accounts for this stepping behavior as a random walk in a tilted corrugated potential that combines torque and contact forces. We argue that the absolute angular position of the rotor is crucial for understanding step properties and show this hypothesis to be consistent with the available data, in particular the observation that backward steps are smaller on average than forward steps. We also predict a sublinear speed versus torque relationship for fixed load at low torque, and a peak in rotor diffusion as a function of torque. Our model provides a comprehensive framework for understanding and analyzing stepping behavior in the bacterial flagellar motor and proposes novel, testable predictions. More broadly, the storage of energy in protein springs by the flagellar motor may provide useful general insights into the design of highly efficient molecular machines.
Mukhopadhyay, Ranjan, and Ned S Wingreen. “Curvature and shape determination of growing bacteria.”. Phys Rev E Stat Nonlin Soft Matter Phys 80.6 Pt 1 (2009): , 80, 6 Pt 1, 062901. Web.Abstract
Bacterial cells come in a variety of shapes, determined by the stress-bearing cell wall. Though many molecular details about the cell wall are known, our understanding of how a particular shape is produced during cell growth is at its infancy. Experiments on curved Escherichia coli grown in microtraps, and on naturally curved Caulobacter crescentus, reveal different modes of growth: one preserving arc length and the other preserving radius of curvature. We present a simple model for curved cell growth that relates these two growth modes to distinct but related growth rules--"hooplike growth" and "self-similar growth"--and discuss the implications for microscopic growth mechanisms.
Mehta, Pankaj, et al.Information processing and signal integration in bacterial quorum sensing.”. Mol Syst Biol 5 (2009): , 5, 325. Web.Abstract
Bacteria communicate using secreted chemical signaling molecules called autoinducers in a process known as quorum sensing. The quorum-sensing network of the marine bacterium Vibrio harveyi uses three autoinducers, each known to encode distinct ecological information. Yet how cells integrate and interpret the information contained within these three autoinducer signals remains a mystery. Here, we develop a new framework for analyzing signal integration on the basis of information theory and use it to analyze quorum sensing in V. harveyi. We quantify how much the cells can learn about individual autoinducers and explain the experimentally observed input-output relation of the V. harveyi quorum-sensing circuit. Our results suggest that the need to limit interference between input signals places strong constraints on the architecture of bacterial signal-integration networks, and that bacteria probably have evolved active strategies for minimizing this interference. Here, we analyze two such strategies: manipulation of autoinducer production and feedback on receptor number ratios.
Endres, Robert G, and Ned S Wingreen. “Maximum likelihood and the single receptor.”. Phys Rev Lett 103.15 (2009): , 103, 15, 158101. Web.Abstract
The accuracy by which biological cells sense chemical concentration is ultimately limited by the random arrival of particles at the receptors by diffusion. This fundamental physical limit is generally considered to be the Berg-Purcell limit [Biophys. J. 20, 193 (1977)]. Here we derive a lower limit by applying maximum likelihood to the time series of receptor occupancy. The increased accuracy stems from solely considering the unoccupied time intervals--disregarding the occupied time intervals as these do not contain any information about the external particle concentration, and only decrease the accuracy of the concentration estimate. Receptors which minimize the bound time intervals achieve the highest possible accuracy. We discuss how a cell could implement such an optimal sensing strategy by absorbing or degrading bound particles.
Mora, Thierry, Howard Yu, and Ned S Wingreen. “Modeling torque versus speed, shot noise, and rotational diffusion of the bacterial flagellar motor.”. Phys Rev Lett 103.24 (2009): , 103, 24, 248102. Web.Abstract
We present a minimal physical model for the flagellar motor that enables bacteria to swim. Our model explains the experimentally measured torque-speed relationship of the proton-driven E. coli motor at various pH and temperature conditions. In particular, the dramatic drop of torque at high rotation speeds (the "knee") is shown to arise from saturation of the proton flux. Moreover, we show that shot noise in the proton current dominates the diffusion of motor rotation at low loads. This suggests a new way to probe the discreteness of the energy source, analogous to measurements of charge quantization in superconducting tunnel junctions.
Endres, Robert G, and Ned S Wingreen. “Accuracy of direct gradient sensing by single cells.”. Proc Natl Acad Sci U S A 105.41 (2008): , 105, 41, 15749-54. Web.Abstract
Many types of cells are able to accurately sense shallow gradients of chemicals across their diameters, allowing the cells to move toward or away from chemical sources. This chemotactic ability relies on the remarkable capacity of cells to infer gradients from particles randomly arriving at cell-surface receptors by diffusion. Whereas the physical limits of concentration sensing by cells have been explored, there is no theory for the physical limits of gradient sensing. Here, we derive such a theory, using as models a perfectly absorbing sphere and a perfectly monitoring sphere, which, respectively, infer gradients from the absorbed surface particle density or the positions of freely diffusing particles inside a spherical volume. We find that the perfectly absorbing sphere is superior to the perfectly monitoring sphere, both for concentration and gradient sensing, because previously observed particles are never remeasured. The superiority of the absorbing sphere helps explain the presence at the surfaces of cells of signal-degrading enzymes, such as PDE for cAMP in Dictyostelium discoideum (Dicty) and BAR1 for mating factor alpha in Saccharomyces cerevisiae (budding yeast). Quantitatively, our theory compares favorably with recent measurements of Dicty moving up a cAMP gradient, suggesting these cells operate near the physical limits of gradient detection.
Hansen, Clinton H, Robert G Endres, and Ned S Wingreen. “Chemotaxis in Escherichia coli: a molecular model for robust precise adaptation.”. PLoS Comput Biol 41 (2008): , 4, 1, e1. Web.Abstract
The chemotaxis system in the bacterium Escherichia coli is remarkably sensitive to small relative changes in the concentrations of multiple chemical signals over a broad range of ambient concentrations. Interactions among receptors are crucial to this sensitivity as is precise adaptation, the return of chemoreceptor activity to prestimulus levels in a constant chemoeffector environment. Precise adaptation relies on methylation and demethylation of chemoreceptors by the enzymes CheR and CheB, respectively. Experiments indicate that when transiently bound to one receptor, these enzymes act on small assistance neighborhoods (AN) of five to seven receptor homodimers. In this paper, we model a strongly coupled complex of receptors including dynamic CheR and CheB acting on ANs. The model yields sensitive response and precise adaptation over several orders of magnitude of attractant concentrations and accounts for different responses to aspartate and serine. Within the model, we explore how the precision of adaptation is limited by small AN size as well as by CheR and CheB kinetics (including dwell times, saturation, and kinetic differences among modification sites) and how these kinetics contribute to noise in complex activity. The robustness of our dynamic model for precise adaptation is demonstrated by randomly varying biochemical parameters.
Swem, Lee R, et al.Deducing receptor signaling parameters from in vivo analysis: LuxN/AI-1 quorum sensing in Vibrio harveyi.”. Cell 134.3 (2008): , 134, 3, 461-73. Web.Abstract
Quorum sensing, a process of bacterial cell-cell communication, relies on production, detection, and response to autoinducer signaling molecules. LuxN, a nine-transmembrane domain protein from Vibrio harveyi, is the founding example of membrane-bound receptors for acyl-homoserine lactone (AHL) autoinducers. We used mutagenesis and suppressor analyses to identify the AHL-binding domain of LuxN and discovered LuxN mutants that confer both decreased and increased AHL sensitivity. Our analysis of dose-response curves of multiple LuxN mutants pins these inverse phenotypes on quantifiable opposing shifts in the free-energy bias of LuxN for occupying its kinase and phosphatase states. To understand receptor activation and to characterize the pathway signaling parameters, we exploited a strong LuxN antagonist, one of fifteen small-molecule antagonists we identified. We find that quorum-sensing-mediated communication can be manipulated positively and negatively to control bacterial behavior and, more broadly, that signaling parameters can be deduced from in vivo data.
Mehta, Pankaj, Ranjan Mukhopadhyay, and Ned S Wingreen. “Exponential sensitivity of noise-driven switching in genetic networks.”. Phys Biol 52 (2008): , 5, 2, 026005. Web.Abstract
There is increasing experimental evidence that cells can utilize biochemical noise to switch probabilistically between distinct gene-expression states. In this paper, we demonstrate that such noise-driven switching is dominated by tails of probability distributions and is therefore exponentially sensitive to changes in physiological parameters such as transcription and translation rates. Exponential sensitivity limits the robustness of noise-driven switching, suggesting cells may use other mechanisms in order to switch reliably. We discuss our results in the context of competence in the bacterium Bacillus subtilis.
Vizcarra, Christina L, et al.An improved pairwise decomposable finite-difference Poisson-Boltzmann method for computational protein design.”. J Comput Chem 29.7 (2008): , 29, 7, 1153-62. Web.Abstract
Our goal is to develop accurate electrostatic models that can be implemented in current computational protein design protocols. To this end, we improve upon a previously reported pairwise decomposable, finite difference Poisson-Boltzmann (FDPB) model for protein design (Marshall et al., Protein Sci 2005, 14, 1293). The improvement involves placing generic sidechains at positions with unknown amino acid identity and explicitly capturing two-body perturbations to the dielectric environment. We compare the original and improved FDPB methods to standard FDPB calculations in which the dielectric environment is completely determined by protein atoms. The generic sidechain approach yields a two to threefold increase in accuracy per residue or residue pair over the original pairwise FDPB implementation, with no additional computational cost. Distance dependent dielectric and solvent-exclusion models were also compared with standard FDPB energies. The accuracy of the new pairwise FDPB method is shown to be superior to these models, even after reparameterization of the solvent-exclusion model.
Mukhopadhyay, Ranjan, Kerwyn Casey Huang, and Ned S Wingreen. “Lipid localization in bacterial cells through curvature-mediated microphase separation.”. Biophys J 95.3 (2008): , 95, 3, 1034-49. Web.Abstract
Although many proteins are known to localize in bacterial cells, for the most part our understanding of how such localization takes place is limited. Recent evidence that the phospholipid cardiolipin localizes to the poles of rod-shaped bacteria suggests that targeting of some proteins may rely on the heterogeneous distribution of membrane lipids. Membrane curvature has been proposed as a factor in the polar localization of high-intrinsic-curvature lipids, but the small size of lipids compared to the dimensions of the cell means that single molecules cannot stably localize. At the other extreme, phase separation of the membrane energetically favors a single domain of such lipids at one pole. We have proposed a physical mechanism in which osmotic pinning of the membrane to the cell wall naturally produces microphase separation, i.e., lipid domains of finite size, whose aggregate sensitivity to cell curvature can support spontaneous and stable localization to both poles. Here, we demonstrate that variations in the strength of pinning of the membrane to the cell wall can also act as a strong localization mechanism, in agreement with observations of cardiolipin relocalization from the poles to the septum during sporulation in the bacterium Bacillus subtilis. In addition, we rigorously determine the relationship between localization and the domain-size distribution including the effects of entropy, and quantify the strength of domain-domain interactions. Our model predicts a critical concentration of cardiolipin below which domains will not form and hence polar localization will not take place. This observation is consistent with recent experiments showing that in Escherichia coli cells with reduced cardiolipin concentrations, cardiolipin and the osmoregulatory protein ProP fail to localize to the poles.
Endres, Robert G, et al.Variable sizes of Escherichia coli chemoreceptor signaling teams.”. Mol Syst Biol 4 (2008): , 4, 211. Web.Abstract
Like many sensory receptors, bacterial chemotaxis receptors form clusters. In bacteria, large-scale clusters are subdivided into signaling teams that act as 'antennas' allowing detection of ligands with remarkable sensitivity. The range of sensitivity is greatly extended by adaptation of receptors to changes in concentrations through covalent modification. However, surprisingly little is known about the sizes of receptor signaling teams. Here, we combine measurements of the signaling response, obtained from in vivo fluorescence resonance energy transfer, with the statistical method of principal component analysis, to quantify the size of signaling teams within the framework of the previously successful Monod-Wyman-Changeux model. We find that size of signaling teams increases 2- to 3-fold with receptor modification, indicating an additional, previously unrecognized level of adaptation of the chemotaxis network. This variation of signaling-team size shows that receptor cooperativity is dynamic and likely optimized for sensing noisy ligand concentrations.
Pompeani, Audra J, et al.The Vibrio harveyi master quorum-sensing regulator, LuxR, a TetR-type protein is both an activator and a repressor: DNA recognition and binding specificity at target promoters.”. Mol Microbiol 70.1 (2008): , 70, 1, 76-88. Web.Abstract
Quorum sensing is the process of cell-to-cell communication by which bacteria communicate via secreted signal molecules called autoinducers. As cell population density increases, the accumulation of autoinducers leads to co-ordinated changes in gene expression across the bacterial community. The marine bacterium, Vibrio harveyi, uses three autoinducers to achieve intra-species, intra-genera and inter-species cell-cell communication. The detection of these autoinducers ultimately leads to the production of LuxR, the quorum-sensing master regulator that controls expression of the genes in the quorum-sensing regulon. LuxR is a member of the TetR protein superfamily; however, unlike other TetR repressors that typically repress their own gene expression and that of an adjacent operon, LuxR is capable of activating and repressing a large number of genes. Here, we used protein binding microarrays and a two-layered bioinformatics approach to show that LuxR binds a 21 bp consensus operator with dyad symmetry. In vitro and in vivo analyses of two promoters directly regulated by LuxR allowed us to identify those bases that are critical for LuxR binding. Together, the in silico and biochemical results enabled us to scan the genome and identify novel targets of LuxR in V. harveyi and thus expand the understanding of the quorum-sensing regulon.
Huang, Kerwyn Casey, et al.Cell shape and cell-wall organization in Gram-negative bacteria.”. Proc Natl Acad Sci U S A 105.49 (2008): , 105, 49, 19282-7. Web.Abstract
In bacterial cells, the peptidoglycan cell wall is the stress-bearing structure that dictates cell shape. Although many molecular details of the composition and assembly of cell-wall components are known, how the network of peptidoglycan subunits is organized to give the cell shape during normal growth and how it is reorganized in response to damage or environmental forces have been relatively unexplored. In this work, we introduce a quantitative physical model of the bacterial cell wall that predicts the mechanical response of cell shape to peptidoglycan damage and perturbation in the rod-shaped Gram-negative bacterium Escherichia coli. To test these predictions, we use time-lapse imaging experiments to show that damage often manifests as a bulge on the sidewall, coupled to large-scale bending of the cylindrical cell wall around the bulge. Our physical model also suggests a surprising robustness of cell shape to peptidoglycan defects, helping explain the observed porosity of the cell wall and the ability of cells to grow and maintain their shape even under conditions that limit peptide crosslinking. Finally, we show that many common bacterial cell shapes can be realized within the same model via simple spatial patterning of peptidoglycan defects, suggesting that minor patterning changes could underlie the great diversity of shapes observed in the bacterial kingdom.
Guberman, Jonathan M, et al.PSICIC: noise and asymmetry in bacterial division revealed by computational image analysis at sub-pixel resolution.”. PLoS Comput Biol 411 (2008): , 4, 11, e1000233. Web.Abstract
Live-cell imaging by light microscopy has demonstrated that all cells are spatially and temporally organized. Quantitative, computational image analysis is an important part of cellular imaging, providing both enriched information about individual cell properties and the ability to analyze large datasets. However, such studies are often limited by the small size and variable shape of objects of interest. Here, we address two outstanding problems in bacterial cell division by developing a generally applicable, standardized, and modular software suite termed Projected System of Internal Coordinates from Interpolated Contours (PSICIC) that solves common problems in image quantitation. PSICIC implements interpolated-contour analysis for accurate and precise determination of cell borders and automatically generates internal coordinate systems that are superimposable regardless of cell geometry. We have used PSICIC to establish that the cell-fate determinant, SpoIIE, is asymmetrically localized during Bacillus subtilis sporulation, thereby demonstrating the ability of PSICIC to discern protein localization features at sub-pixel scales. We also used PSICIC to examine the accuracy of cell division in Esherichia coli and found a new role for the Min system in regulating division-site placement throughout the cell length, but only prior to the initiation of cell constriction. These results extend our understanding of the regulation of both asymmetry and accuracy in bacterial division while demonstrating the general applicability of PSICIC as a computational approach for quantitative, high-throughput analysis of cellular images.
Mehta, Pankaj, Sidhartha Goyal, and Ned S Wingreen. “A quantitative comparison of sRNA-based and protein-based gene regulation.”. Mol Syst Biol 4 (2008): , 4, 221. Web.Abstract
Small non-coding RNAs (sRNAs) have important functions as genetic regulators in prokaryotes. sRNAs act post-transcriptionally through complementary pairing with target mRNAs to regulate protein expression. We use a quantitative approach to compare and contrast sRNAs with conventional transcription factors (TFs) to better understand the advantages of each form of regulation. In particular, we calculate the steady-state behavior, noise properties, frequency-dependent gain (amplification), and dynamical response to large input signals of both forms of regulation. Although the mean steady-state behavior of sRNA-regulated proteins exhibits a distinctive tunable threshold linear behavior, our analysis shows that transcriptional bursting leads to significantly higher intrinsic noise in sRNA-based regulation than in TF-based regulation in a large range of expression levels and limits the ability of sRNAs to perform quantitative signaling. Nonetheless, we find that sRNAs are better than TFs at filtering noise in input signals. Additionally, we find that sRNAs allow cells to respond rapidly to large changes in input signals. These features suggest a 'niche' for sRNAs in allowing cells to transition quickly yet reliably between distinct states. This functional niche is consistent with the widespread appearance of sRNAs in stress response and quasi-developmental networks in prokaryotes.
Wang, Hui, Ned S Wingreen, and Ranjan Mukhopadhyay. “Self-organized periodicity of protein clusters in growing bacteria.”. Phys Rev Lett 101.21 (2008): , 101, 21, 218101. Web.Abstract
Chemotaxis receptors in E. coli form clusters at the cell poles and also laterally along the cell body, and this clustering plays an important role in signal transduction. Recently, experiments using fluorescence imaging have shown that, during cell growth, lateral clusters form at positions approximately periodically spaced along the cell body. In this Letter, we demonstrate within a lattice model that such spatial organization could arise spontaneously from a stochastic nucleation mechanism. The same mechanism may explain the recent observation of periodic aggregates of misfolded proteins in E. coli.
Weitz, Joshua S, Philip N Benfey, and Ned S Wingreen. “Evolution, interactions, and biological networks.”. PLoS Biol 51 (2007): , 5, 1, e11. Web.
Goyal, Sidhartha, and Ned S Wingreen. “Growth-induced instability in metabolic networks.”. Phys Rev Lett 98.13 (2007): , 98, 13, 138105. Web.Abstract
Product-feedback inhibition is a ubiquitous regulatory scheme for maintaining homeostasis in living cells. Individual metabolic pathways with product-feedback inhibition are stable as long as one pathway step is rate limiting. However, pathways are often coupled both by the use of a common substrate and by stoichiometric utilization of their products for cell growth. We show that such a coupled network with product-feedback inhibition may exhibit limit-cycle oscillations which arise via a Hopf bifurcation. Our results highlight novel evolutionary constraints on the architecture of metabolism.
Li, Je-Luen, et al.Hydrophobic interaction and hydrogen-bond network for a methane pair in liquid water.”. Proc Natl Acad Sci U S A 104.8 (2007): , 104, 8, 2626-30. Web.Abstract
We employ fully quantum-mechanical molecular dynamics simulations to evaluate the force between two methanes dissolved in water, as a model for hydrophobic association. A stable configuration is found near the methane-methane contact separation, while a shallow second potential minimum occurs for the solvent-separated configuration. The strength and shape of the potential of mean force are in conflict with earlier classical force-field simulations but agree well with a simple hydrophobic burial model which is based on solubility experiments. Examination of solvent dynamics reveals stable water cages at several specific methane-methane separations.
Ureta, Alejandro R, et al.Kinetic analysis of the assembly of the outer membrane protein LamB in Escherichia coli mutants each lacking a secretion or targeting factor in a different cellular compartment.”. J Bacteriol 189.2 (2007): , 189, 2, 446-54. Web.Abstract
Outer membrane beta-barrel proteins in gram-negative bacteria, such as Escherichia coli, must be translocated from their site of synthesis in the cytoplasm to the periplasm and finally delivered to the outer membrane. At least a dozen proteins located in the cytoplasm, the periplasm, and both the inner and outer membranes are required to catalyze this complex assembly process. At normal growth temperatures and conditions the transport and assembly processes are so fast that assembly intermediates cannot be detected. Using cells grown at a low temperature to slow the assembly process and pulse-chase analysis with immunodetection methods, we followed newly synthesized LamB molecules during their transit through the cell envelope. The quality and reproducibility of the data allowed us to calculate rate constants for three different subassembly reactions. This kinetic analysis revealed that secB and secD mutants exhibit nearly identical defects in precursor translocation from the cytoplasm. However, subsequent subassembly reaction rates provided no clear evidence for an additional role for SecD in LamB assembly. Moreover, we found that surA mutants are qualitatively indistinguishable from yfgL mutants, suggesting that the products of both of these genes share a common function in the assembly process, most likely the delivery of LamB to the YaeT assembly complex in the outer membrane.
Endres, Robert G, Joseph J Falke, and Ned S Wingreen. “Chemotaxis receptor complexes: from signaling to assembly.”. PLoS Comput Biol 37 (2007): , 3, 7, e150. Web.Abstract
Complexes of chemoreceptors in the bacterial cytoplasmic membrane allow for the sensing of ligands with remarkable sensitivity. Despite the excellent characterization of the chemotaxis signaling network, very little is known about what controls receptor complex size. Here we use in vitro signaling data to model the distribution of complex sizes. In particular, we model Tar receptors in membranes as an ensemble of different sized oligomer complexes, i.e., receptor dimers, dimers of dimers, and trimers of dimers, where the relative free energies, including receptor modification, ligand binding, and interaction with the kinase CheA determine the size distribution. Our model compares favorably with a variety of signaling data, including dose-response curves of receptor activity and the dependence of activity on receptor density in the membrane. We propose that the kinetics of complex assembly can be measured in vitro from the temporal response to a perturbation of the complex free energies, e.g., by addition of ligand.
Sourjik, Victor, and Ned S Wingreen. “Turning to the cold.”. Nat Cell Biol 99 (2007): , 9, 9, 1029-31. Web.
Keymer, Juan E, et al.Chemosensing in Escherichia coli: two regimes of two-state receptors.”. Proc Natl Acad Sci U S A 103.6 (2006): , 103, 6, 1786-91. Web.Abstract
The chemotaxis network in Escherichia coli is remarkable for its sensitivity to small relative changes in the concentrations of multiple chemical signals. We present a model for signal integration by mixed clusters of interacting two-state chemoreceptors. Our model results compare favorably to the results obtained by Sourjik and Berg with in vivo fluorescence resonance energy transfer. Importantly, we identify two distinct regimes of behavior, depending on the relative energies of the two states of the receptors. In regime I, coupling of receptors leads to high sensitivity, while in regime II, coupling of receptors leads to high cooperativity, i.e., high Hill coefficient. For homogeneous receptors, we predict an observable transition between regime I and regime II with increasing receptor methylation or amidation.
Emberly, Eldon, and Ned S Wingreen. “Hourglass model for a protein-based circadian oscillator.”. Phys Rev Lett 96.3 (2006): , 96, 3, 038303. Web.Abstract
Many organisms possess internal biochemical clocks, known as circadian oscillators, which allow them to regulate their biological activity with a 24-hour period. It was recently discovered that the circadian oscillator of photosynthetic cyanobacteria is able to function in a test tube with only three proteins, KaiA, KaiB, and KaiC, and ATP. Biochemical events are intrinsically stochastic, and this tends to desynchronize oscillating protein populations. We propose that stability of the Kai-protein oscillator relies on active synchronization by (i) monomer exchange between KaiC hexamers during the day, and (ii) formation of clusters of KaiC hexamers at night. Our results highlight the importance of collective assembly or disassembly of proteins in biochemical networks, and may help guide design of novel protein-based oscillators.
Wingreen, Ned, and David Botstein. “Back to the future: education for systems-level biologists.”. Nat Rev Mol Cell Biol 711 (2006): , 7, 11, 829-32. Web.Abstract
We describe a graduate course in quantitative biology that is based on original path-breaking papers in diverse areas of biology; each of these papers depends on quantitative reasoning and theory as well as experiment. Close reading and discussion of these papers allows students with backgrounds in physics, computational sciences or biology to learn essential ideas and to communicate in the languages of disciplines other than their own.
Wingreen, Ned S, and Simon A Levin. “Cooperation among microorganisms.”. PLoS Biol 49 (2006): , 4, 9, e299. Web.
Huang, Kerwyn Casey, Ranjan Mukhopadhyay, and Ned S Wingreen. “A curvature-mediated mechanism for localization of lipids to bacterial poles.”. PLoS Comput Biol 211 (2006): , 2, 11, e151. Web.Abstract
Subcellular protein localization is a universal feature of eukaryotic cells, and the ubiquity of protein localization in prokaryotic species is now acquiring greater appreciation. Though some targeting anchors are known, the origin of polar and division-site localization remains mysterious for a large fraction of bacterial proteins. Ultimately, the molecular components responsible for such symmetry breaking must employ a high degree of self-organization. Here we propose a novel physical mechanism, based on the two-dimensional curvature of the membrane, for spontaneous lipid targeting to the poles and division site of rod-shaped bacterial cells. If one of the membrane components has a large intrinsic curvature, the geometrical constraint of the plasma membrane by the more rigid bacterial cell wall naturally leads to lipid microphase separation. We find that the resulting clusters of high-curvature lipids are large enough to spontaneously and stably localize to the two cell poles. Recent evidence of localization of the phospholipid cardiolipin to the poles of bacterial cells suggests that polar targeting of some proteins may rely on the membrane's differential lipid content. More generally, aggregates of lipids, proteins, or lipid-protein complexes may localize in response to features of cell geometry incapable of localizing individual molecules.
Endres, Robert G, and Ned S Wingreen. “Precise adaptation in bacterial chemotaxis through "assistance neighborhoods".”. Proc Natl Acad Sci U S A 103.35 (2006): , 103, 35, 13040-4. Web.Abstract
The chemotaxis network in Escherichia coli is remarkable for its sensitivity to small relative changes in the concentrations of multiple chemical signals over a broad range of ambient concentrations. Key to this sensitivity is an adaptation system that relies on methylation and demethylation (or deamidation) of specific modification sites of the chemoreceptors by the enzymes CheR and CheB, respectively. It was recently discovered that these enzymes can access five to seven receptors when tethered to a particular receptor. We show that these "assistance neighborhoods" are necessary for precise adaptation in a model for signaling by clusters of chemoreceptors. In agreement with experiment, model clusters composed of receptors of different types exhibit high sensitivity and precise adaptation over a wide range of chemical concentrations and the response of adapted clusters to addition/removal of attractant scales with free-energy change. We predict two limits of precise adaptation at large attractant concentrations: Either receptors reach full methylation and turn off, or receptors become saturated and cease to respond to attractant but retain their adapted activity.
Skoge, Monica L, Robert G Endres, and Ned S Wingreen. “Receptor-receptor coupling in bacterial chemotaxis: evidence for strongly coupled clusters.”. Biophys J 90.12 (2006): , 90, 12, 4317-26. Web.Abstract
Receptor coupling is believed to explain the high sensitivity of the Escherichia coli chemotaxis network to small changes in levels of chemoattractant. We compare in detail the activity response of coupled two-state receptors for different models of receptor coupling: weakly-coupled extended one-dimensional and two-dimensional lattice models and the Monod-Wyman-Changeux model of isolated strongly-coupled clusters. We identify features in recent data that distinguish between the models. Specifically, researchers have measured the receptor activity response to steps of chemoattractant for a variety of engineered E. coli strains using in vivo fluorescence resonance energy transfer. We find that the fluorescence resonance energy transfer results for wild-type and for a low-activity mutant are inconsistent with the lattice models of receptor coupling, but consistent with the Monod-Wyman-Changeux model of receptor coupling, suggesting that receptors form isolated strongly-coupled clusters.
Endres, Robert G, and Ned S Wingreen. “Weight matrices for protein-DNA binding sites from a single co-crystal structure.”. Phys Rev E Stat Nonlin Soft Matter Phys 73.6 Pt 1 (2006): , 73, 6 Pt 1, 061921. Web.Abstract
Transcription-factor proteins bind to specific DNA sequences to regulate gene expression in cells. DNA-binding sites are often identified using weight matrices calculated from multiple known binding sites. However, in many cases the number of examples is limited. Here, we report on an atomistic method that starts from an x-ray co-crystal structure of the protein bound to one particular DNA sequence, and infers other binding sites, which are used to construct a weight matrix. The emphasis of the paper is on using the Wang-Landau Monte Carlo algorithm to efficiently sample high-affinity binding sites, which demonstrates that sampling can produce accurate weight matrices in analogy to bioinformatics approaches. For cases of low complexity, we compare to the exhaustive (but slow) dead-end elimination algorithm. To recover crystal binding sites, it is important to include bound water in the protein-DNA interface. Our approach can, in principle, even be applied when no native protein-DNA co-crystal structure is available, only the structure of a closely related homologous protein whose amino-acid sequence is changed to the protein of interest.
Kruus, Erik, et al.Gibbs sampling and helix-cap motifs.”. Nucleic Acids Res 33.16 (2005): , 33, 16, 5343-53. Web.Abstract
Protein backbones have characteristic secondary structures, including alpha-helices and beta-sheets. Which structure is adopted locally is strongly biased by the local amino acid sequence of the protein. Accurate (probabilistic) mappings from sequence to structure are valuable for both secondary-structure prediction and protein design. For the case of alpha-helix caps, we test whether the information content of the sequence-structure mapping can be self-consistently improved by using a relaxed definition of the structure. We derive helix-cap sequence motifs using database helix assignments for proteins of known structure. These motifs are refined using Gibbs sampling in competition with a null motif. Then Gibbs sampling is repeated, allowing for frameshifts of +/-1 amino acid residue, in order to find sequence motifs of higher total information content. All helix-cap motifs were found to have good generalization capability, as judged by training on a small set of non-redundant proteins and testing on a larger set. For overall prediction purposes, frameshift motifs using all training examples yielded the best results. Frameshift motifs using a fraction of all training examples performed best in terms of true positives among top predictions. However, motifs without frameshifts also performed well, despite a roughly one-third lower total information content.
Emberly, Eldon G, et al.Flexibility of beta-sheets: principal component analysis of database protein structures.”. Proteins 55.1 (2004): , 55, 1, 91-8. Web.Abstract
Protein folds are built primarily from the packing together of two types of structures: alpha-helices and beta-sheets. Neither structure is rigid, and the flexibility of helices and sheets is often important in determining the final fold (e.g., coiled coils and beta-barrels). Recent work has quantified the flexibility of alpha-helices using a principal component analysis (PCA) of database helical structures (J. Mol. Bio. 2003, 327, pp. 229-237). Here, we extend the analysis to beta-sheet flexibility using PCA on a database of beta-sheet structures. For sheets of varying dimension and geometry, we find two dominant modes of flexibility: twist and bend. The distributions of amplitudes for these modes are found to be Gaussian and independent, suggesting that the PCA twist and bend modes can be identified as the soft elastic normal modes of sheets. We consider the scaling of mode eigenvalues with sheet size and find that parallel beta-sheets are more rigid than antiparallel sheets over the entire range studied. Finally, we discuss the application of our PCA results to modeling and design of beta-sheet proteins.
Wingreen, Ned S. “Ammonia Transport.”. EcoSal Plus 11 (2004). Web.Abstract
This review reviews the ammonium/methylammonium transport (Amt) proteins of Escherichia coli and Salmonella enterica serovar Typhimurium. The Amt proteins and their homologs, the methylammonium/ammonium permease proteins of Saccharomyces cerevisiae, constitute a distinct class of membrane-associated ammonia transporters. Members of the Amt family are found in archaea, bacteria, fungi, plants, and invertebrate animals. In E. coli and serovar Typhimurium, the Amt proteins are essential to maintain maximal growth at low concentrations of ammonia, the preferred nitrogen source. Soupene and coworkers showed that a mutant of E. coli with only the low-affinity glutamate dehydrogenase pathway for assimilation of ammonia, which therefore grows slowly at low ammonia concentrations, is not relieved of its growth defect by overexpression of AmtB. A recent study on an Amt protein from tomato concluded that it was a specific transporter for NH4+. A trimeric stoichiometry for AmtB is supported by the observation of a direct interaction between AmtB and the trimeric signal-transduction protein GlnK. In E. coli, GlnK has been observed to associate with the membrane in an AmtB-dependent fashion. Both GlnK and GlnB are sensors of nitrogen status. Their interaction with AmtB suggests a role for AmtB in nitrogen regulation. In summary, AmtB is a membrane-associated ammonia transporter that is important for growth at external concentrations of the uncharged species (NH3) below about 50 nM. The preponderance of evidence suggests that AmtB specifically transports the charged species (NH4+) and that this transport is passive and, hence, bidirectional.
Zhang, Naigong, Chen Zeng, and Ned S Wingreen. “Fast accurate evaluation of protein solvent exposure.”. Proteins 57.3 (2004): , 57, 3, 565-76. Web.Abstract
Protein solvation energies are often taken to be proportional to solvent-accessible surface areas. Computation of these areas is numerically demanding and may become a bottleneck for folding and design applications. Fast graph-based methods, such as dead-end elimination (DEE), become possible if all energies, including solvation energies, are expressed as single-residue and pair-residue terms. To this end, Street and Mayo originated a pair-residue approximation for solvent-accessible surface areas (Street AG, Mayo SL. Pairwise calculation of protein solvent accessible surface areas. Fold Des 1998;3:253-258). The dominant source of error in this method is the overlapping burial of side-chain surfaces in the protein core. Here we report a new pair-residue approximation, which greatly reduces this overlap error by the use of optimized generic side-chains. We have tested the generic-side-chain method for the ten proteins studied by Street and Mayo and for 377 single-domain proteins from the CATH database (Orengo CA, Michie AD, Jones S, Jones DT, Swindells MB, Thornton JM. CATH-A hierarchic classification of protein domain structures. Structure 1997;5:1093-1108). With little additional cost in computation, the new method consistently reduces error for total areas and residue-by-residue areas by more than a factor of two. For example, the residue-by-residue error (for buried area) is reduced from 7.42 A(2) to 3.70 A(2). This difference translates into a solvation energy difference of approximately 0.2 kcal/mol per residue, amounting to a reduction in root-mean-square energy error of 2 kcal/mol for a 100 residue chain, a potentially critical difference for both protein folding and design applications.
Huang, Kerwyn Casey, and Ned S Wingreen. “Min-protein oscillations in round bacteria.”. Phys Biol 13-4 (2004): , 1, 3-4, 229-35. Web.Abstract
In rod-shaped Escherichia coli cells, the Min proteins, which are involved in division-site selection, oscillate from pole-to-pole. The homologs of the Min proteins from the round bacterium Neisseria gonorrhoeae also form a spatial oscillator when expressed in wild-type and round, rodA- mutants of E. coli, suggesting that the Min proteins form an oscillator in N. gonorrhoeae. Here we report that a numerical model for Min-protein oscillations in rod-shaped cells also produces oscillations in round cells (cocci). Our numerical results explain why the MinE-protein rings found in wild-type E. coli are absent in round mutants. In addition, we find that for round cells there is a minimum radius below which oscillations do not occur, and a maximum radius above which oscillations become mislocalized. Finally, we demonstrate that Min-protein oscillations can select the long axis in nearly round cells based solely on geometry, a potentially important factor in division-plane selection in cocci.
Kulkarni, Rahul V, et al.Pattern formation within Escherichia coli: diffusion, membrane attachment, and self-interaction of MinD molecules.”. Phys Rev Lett 93.22 (2004): , 93, 22, 228103. Web.Abstract
In E. coli, accurate cell division depends upon the oscillation of Min proteins from pole to pole. We provide a model for the polar localization of MinD based only on diffusion, a delay for nucleotide exchange, and different rates of attachment to the bare membrane and the occupied membrane. We derive analytically the probability density, and correspondingly the length scale, for MinD attachment zones. Our simple analytical model illustrates the processes giving rise to the observed localization of cellular MinD zones.
Wingreen, Ned S. “Physics. Quantum many-body effects in a single-electron transistor.”. Science 304.5675 (2004): , 304, 5675, 1258-9. Web.
Lenz, Derrick H, et al.The small RNA chaperone Hfq and multiple small RNAs control quorum sensing in Vibrio harveyi and Vibrio cholerae.”. Cell 118.1 (2004): , 118, 1, 69-82. Web.Abstract
Quorum-sensing bacteria communicate with extracellular signal molecules called autoinducers. This process allows community-wide synchronization of gene expression. A screen for additional components of the Vibrio harveyi and Vibrio cholerae quorum-sensing circuits revealed the protein Hfq. Hfq mediates interactions between small, regulatory RNAs (sRNAs) and specific messenger RNA (mRNA) targets. These interactions typically alter the stability of the target transcripts. We show that Hfq mediates the destabilization of the mRNA encoding the quorum-sensing master regulators LuxR (V. harveyi) and HapR (V. cholerae), implicating an sRNA in the circuit. Using a bioinformatics approach to identify putative sRNAs, we identified four candidate sRNAs in V. cholerae. The simultaneous deletion of all four sRNAs is required to stabilize hapR mRNA. We propose that Hfq, together with these sRNAs, creates an ultrasensitive regulatory switch that controls the critical transition into the high cell density, quorum-sensing mode.