The Development of an Information Criterion for Change-Point Analysis

Change-point analysis is a flexible and computationally tractable tool for the analysis of times series data from systems that transition between discrete states and whose observables are corrupted by noise. The change point algorithm is used to identify the time indices (change points) at which the system transitions between these discrete states. We present a unified information-based approach to testing for the existence of change points. This new approach reconciles two previously disparate approaches to change-point analysis (frequentist and information based) for testing transitions between states. The resulting method is statistically principled, parameter and prior free, and widely applicable to a wide range of change-point problems.

Physical modeling of chromosome segregation in escherichia coli reveals impact of force and DNA relaxation

The physical mechanism by which Escherichia coli segregates copies of its chromosome for partitioning into daughter cells is unknown, partly due to the difficulty in interpreting the complex dynamic behavior during segregation. Analysis of previous chromosome segregation measurements in E. coli demonstrates that the origin of replication exhibits processive motion with a mean displacement that scales as t(0.32). In this work, we develop a model for segregation of chromosomal DNA as a Rouse polymer in a viscoelastic medium with a force applied to a single monomer. Our model demonstrates that the observed power-law scaling of the mean displacement and the behavior of the velocity autocorrelation function is captured by accounting for the relaxation of the polymer chain and the viscoelastic environment. We show that the ratio of the mean displacement to the variance of the displacement during segregation events is a critical metric that eliminates the compounding effects of polymer and medium dynamics and provides the segregation force. We calculate the force of oriC segregation in E. coli to be ∼0.49 pN.

Kin cell lysis is a danger signal that activates antibacterial pathways of Pseudomonas aeruginosa

The perception and response to cellular death is an important aspect of multicellular eukaryotic life. For example, damage-associated molecular patterns activate an inflammatory cascade that leads to removal of cellular debris and promotion of healing. We demonstrate that lysis of Pseudomonas aeruginosa cells triggers a program in the remaining population that confers fitness in interspecies co-culture. We find that this program, termed P. aeruginosa response to antagonism (PARA), involves rapid deployment of antibacterial factors and is mediated by the Gac/Rsm global regulatory pathway. Type VI secretion, and, unexpectedly, conjugative type IV secretion within competing bacteria, induce P. aeruginosa lysis and activate PARA, thus providing a mechanism for the enhanced capacity of P. aeruginosa to target bacteria that elaborate these factors. Our finding that bacteria sense damaged kin and respond via a widely distributed pathway to mount a complex response raises the possibility that danger sensing is an evolutionarily conserved process.

DOI:http://dx.doi.org/10.7554/eLife.05701.001

Bacteria live in diverse and changing environments where resources such as nutrients and space are often limited. They have thus evolved many survival strategies, including competitive and cooperative behaviors. In the first case, bacteria antagonize or prevent the growth of other microorganisms competing with them for resources, such as by generating antibiotics that specifically target rivals. During cooperation, bacteria may coordinate the production of compounds that have a shared benefit for members of their community.

In multicellular organisms, some cell types sense harmful microorganisms by the injury they cause in neighboring cells. This triggers a process that can lead to the production of molecules that kill the invaders and factors that promote the repair of cellular damage. An equivalent process has so far not been described for single-celled organisms such as bacteria. However, bacteria often live in structured groups containing many different species. In this type of growth environment, the ability of bacteria to sense when others of their species are attacked and to respond by taking measures to defend themselves could improve their chances of survival.

Now, LeRoux et al. reveal that the bacterium Pseudomonas aeruginosa is able to detect ‘danger signals’ released when neighboring P. aeruginosa cells are killed by other bacteria. These signals trigger a response in surviving cells by turning on a pathway that controls a number of antibacterial factors. These include the production of the so-called ‘type VI secretion system’, a molecular machine that delivers a potent cocktail of antibacterial toxins directly into nearby bacteria.

This process, which LeRoux et al. have named ‘P. aeruginosa response to antagonism’, or PARA for short, enables P. aeruginosa to thrive when grown with competing bacterial species. P. aeruginosa is notorious for infecting the lungs of people with the genetic disease cystic fibrosis, as well as chronic wounds often found in people with diabetes. In both cases, when P. aeruginosa is present, the numbers of other, often less harmful organisms, tend to decrease. PARA may be one reason for the success of P. aeruginosa in these multi-species infections.

DOI:http://dx.doi.org/10.7554/eLife.05701.002

Cytoplasmic dynamics reveals two modes of nucleoid-dependent mobility

It has been proposed that forces resulting from the physical exclusion of macromolecules from the bacterial nucleoid play a central role in organizing the bacterial cell, yet this proposal has not been quantitatively tested. To investigate this hypothesis, we mapped the generic motion of large protein complexes in the bacterial cytoplasm through quantitative analysis of thousands of complete cell-cycle trajectories of fluorescently tagged ectopic MS2-mRNA complexes. We find the motion of these complexes in the cytoplasm is strongly dependent on their spatial position along the long axis of the cell, and that their dynamics are consistent with a quantitative model that requires only nucleoid exclusion and membrane confinement. This analysis also reveals that the nucleoid increases the mobility of MS2-mRNA complexes, resulting in a fourfold increase in diffusion coefficients between regions of the lowest and highest nucleoid density. These data provide strong quantitative support for two modes of nucleoid action: the widely accepted mechanism of nucleoid exclusion in organizing the cell and a newly proposed mode, in which the nucleoid facilitates rapid motion throughout the cytoplasm.

Genome-scale quantitative characterization of bacterial protein localization dynamics throughout the cell cycle

Bacterial cells display both spatial and temporal organization, and this complex structure is known to play a central role in cellular function. Although nearly one-fifth of all proteins in Escherichia coli localize to specific subcellular locations, fundamental questions remain about how cellular-scale structure is encoded at the level of molecular-scale interactions. One significant limitation to our understanding is that the localization behavior of only a small subset of proteins has been characterized in detail. As an essential step toward a global model of protein localization in bacteria, we capture and quantitatively analyze spatial and temporal protein localization patterns throughout the cell cycle for nearly every protein in E. coli that exhibits nondiffuse localization. This genome-scale analysis reveals significant complexity in patterning, notably in the behavior of DNA-binding proteins. Complete cell-cycle imaging also facilitates analysis of protein partitioning to daughter cells at division, revealing a broad and robust assortment of asymmetric partitioning behaviors.

RNA mango aptamer-fluorophore: a bright, high-affinity complex for RNA labeling and tracking

Because RNA lacks strong intrinsic fluorescence, it has proven challenging to track RNA molecules in real time. To address this problem and to allow the purification of fluorescently tagged RNA complexes, we have selected a high affinity RNA aptamer called RNA Mango. This aptamer binds a series of thiazole orange (fluorophore) derivatives with nanomolar affinity, while increasing fluorophore fluorescence by up to 1,100-fold. Visualization of RNA Mango by single-molecule fluorescence microscopy, together with injection and imaging of RNA Mango/fluorophore complex in C. elegans gonads demonstrates the potential for live-cell RNA imaging with this system. By inserting RNA Mango into a stem loop of the bacterial 6S RNA and biotinylating the fluorophore, we demonstrate that the aptamer can be used to simultaneously fluorescently label and purify biologically important RNAs. The high affinity and fluorescent properties of RNA Mango are therefore expected to simplify the study of RNA complexes.

Unidirectional P-body transport during the yeast cell cycle

P-bodies belong to a large family of RNA granules that are associated with post-transcriptional gene regulation, conserved from yeast to mammals, and influence biological processes ranging from germ cell development to neuronal plasticity. RNA granules can also transport RNAs to specific locations. Germ granules transport maternal RNAs to the embryo, and neuronal granules transport RNAs long distances to the synaptic dendrites. Here we combine microfluidic-based fluorescent microscopy of single cells and automated image analysis to follow p-body dynamics during cell division in yeast. Our results demonstrate that these highly dynamic granules undergo a unidirectional transport from the mother to the daughter cell during mitosis as well as a constrained “hovering” near the bud site half an hour before the bud is observable. Both behaviors are dependent on the Myo4p/She2p RNA transport machinery. Furthermore, single cell analysis of cell size suggests that PBs play an important role in daughter cell growth under nutrient limiting conditions.

Estimating podocyte number and density using a single histologic section

The reduction in podocyte density to levels below a threshold value drives glomerulosclerosis and progression to ESRD. However, technical demands prohibit high-throughput application of conventional morphometry for estimating podocyte density. We evaluated a method for estimating podocyte density using single paraffin-embedded formalin-fixed sections. Podocyte nuclei were imaged using indirect immunofluorescence detection of antibodies against Wilms' tumor-1 or transducin-like enhancer of split 4. To account for the large size of podocyte nuclei in relation to section thickness, we derived a correction factor given by the equation CF=1/(D/T+1), where T is the tissue section thickness and D is the mean caliper diameter of podocyte nuclei. Normal values for D were directly measured in thick tissue sections and in 3- to 5-μm sections using calibrated imaging software. D values were larger for human podocyte nuclei than for rat or mouse nuclei (P<0.01). In addition, D did not vary significantly between human kidney biopsies at the time of transplantation, 3-6 months after transplantation, or with podocyte depletion associated with transplant glomerulopathy. In rat models, D values also did not vary with podocyte depletion, but increased approximately 10% with old age and in postnephrectomy kidney hypertrophy. A spreadsheet with embedded formulas was created to facilitate individualized podocyte density estimation upon input of measured values. The correction factor method was validated by comparison with other methods, and provided data comparable with prior data for normal human kidney transplant donors. This method for estimating podocyte density is applicable to high-throughput laboratory and clinical use.

c-di-GMP heterogeneity is generated by the chemotaxis machinery to regulate flagellar motility

Individual cell heterogeneity is commonly observed within populations, although its molecular basis is largely unknown. Previously, using FRET-based microscopy, we observed heterogeneity in cellular c-di-GMP levels. In this study, we show that c-di-GMP heterogeneity in Pseudomonas aeruginosa is promoted by a specific phosphodiesterase partitioned after cell division. We found that subcellular localization and reduction of c-di-GMP levels by this phosphodiesterase is dependent on the histidine kinase component of the chemotaxis machinery, CheA, and its phosphorylation state. Therefore, individual cell heterogeneity in c-di-GMP concentrations is regulated by the activity and the asymmetrical inheritance of the chemotaxis organelle after cell division. c-di-GMP heterogeneity results in a diversity of motility behaviors. The generation of diverse intracellular concentrations of c-di-GMP by asymmetric partitioning is likely important to the success and survival of bacterial populations within the environment by allowing a variety of motility behaviors.

DOI:http://dx.doi.org/10.7554/eLife.01402.001

Bacterial populations have traditionally been assumed to be made up of identical cells. However, while the bacteria within a population may be genetically identical, individual cells have different growth rates, metabolisms and motilities, among other things. This ‘phenotypic heterogeneity’ has been observed in many different species of bacteria, and in some cases it can be attributed to changes in the concentration of molecules called second messengers that help to relay signals from the external environment to targets within the cell.

It can be challenging to monitor changes in the concentration of specific molecules inside cells, but researchers recently developed a form of microscopy based on FRET (short for Forster resonance energy transfer) that can measure the levels of a second messenger molecule called cyclic di-guanylate (c-di-GMP) inside individual cells. This technique was used to study P. aeruginosa, a bacterium that has a single corkscrew-shaped propeller that enables it to swim through liquid. P. aeruginosa divides to form two daughter cells—one with a propeller and one without.

Although the daughter cell that does not have a propeller quickly grows one, FRET-based microscopy revealed that the daughter cell with a propeller had less c-di-GMP than the daughter without a propeller, but the reasons underlying this difference and its effects on bacterial behavior were not clear.

Now Kulasekara et al. show that the cell that inherits the propeller contains an enzyme that degrades c-di-GMP, and that the low levels of this second messenger molecule—caused by the enzyme being concentrated near the base of the propeller, and the presence of a protein (CheA) that enables the bacteria to swim towards sources of nutrients—result in faster swimming speeds and increased responsiveness to nutrients. In other words, although the two daughter cells are genetically identical, they behave quite differently because of the different levels of this second messenger molecule.

The existence of heterogeneity within a bacterial population likely leads to increased success and survival within changing diverse environments, and this work sets the stage for similar investigations into what establishes heterogeneity in other bacterial populations.

DOI:http://dx.doi.org/10.7554/eLife.01402.002

Mapping the driving forces of chromosome structure and segregation in Escherichia coli

The mechanism responsible for the accurate partitioning of newly replicated Escherichia coli chromosomes into daughter cells remains a mystery. In this article, we use automated cell cycle imaging to quantitatively analyse the cell cycle dynamics of the origin of replication (oriC) in hundreds of cells. We exploit the natural stochastic fluctuations of the chromosome structure to map both the spatial and temporal dependence of the motional bias segregating the chromosomes. The observed map is most consistent with force generation by an active mechanism, but one that generates much smaller forces than canonical molecular motors, including those driving eukaryotic chromosome segregation.

Diverse type VI secretion phospholipases are functionally plastic antibacterial effectors

Membranes allow the compartmentalization of biochemical processes and are therefore fundamental to life. The conservation of the cellular membrane, combined with its accessibility to secreted proteins, has made it a common target of factors mediating antagonistic interactions between diverse organisms. Here we report the discovery of a diverse superfamily of bacterial phospholipase enzymes. Within this superfamily, we defined enzymes with phospholipase A1 (PLA₁) and A2 (PLA₂) activity, which are common in host cell-targeting bacterial toxins and the venoms of certain insects and reptiles^1,2. However, we find that the fundamental role of the superfamily is to mediate antagonistic bacterial interactions as effectors of the type VI secretion system (T6SS) translocation apparatus; accordingly, we name these proteins type VI lipase effectors (Tle). Our analyses indicate that PldA of Pseudomonas aeruginosa, a eukaryotic-like phospholipase D (PLD)³, is a member of the Tle superfamily and the founding substrate of the haemolysin co-regulated protein secretion island II T6SS (H2-T6SS). While prior studies have specifically implicated PldA and the H2-T6SS in pathogenesis^3–5, we uncovered a specific role for the effector and its secretory machinery in intra- and inter-species bacterial interactions. Furthermore we find that this effector achieves its antibacterial activity by degrading phosphatidylethanolamine (PE), the major component of bacterial membranes. The surprising finding that virulence-associated phospholipases can serve as specific antibacterial effectors suggests that interbacterial interactions are a relevant factor driving the ongoing evolution of pathogenesis.

Surface sensing and lateral subcellular localization of WspA, the receptor in a chemosensory-like system leading to c-di-GMP production

Pseudomonas aeruginosa responds to growth on agar surfaces to produce cyclic-di-GMP, which stimulates biofilm formation. This is mediated by an alternative cellular function chemotaxis-like system called Wsp. The receptor protein WspA, is bioinformatically indistinguishable from methyl-accepting chemotaxis proteins. However, unlike standard chemoreceptors, WspA does not form stable clusters at cell poles. Rather, it forms dynamic clusters at both polar and lateral subcellular locations. To begin to study the mechanism of Wsp signal transduction in response to surfaces, we carried out a structure-function study of WspA and found that its C-terminus is important for its lateral subcellular localization and function. When this region was replaced with that of a chemoreceptor for amino acids, WspA became polarly localized. In addition, introduction of mutations in the C-terminal region of WspA that rendered this protein able to form more stable receptor-receptor interactions, also resulted in a WspA protein that was less capable of activating signal transduction. Receptor chimeras with a WspA C-terminus and N-terminal periplasmic domains from chemoreceptors that sense amino acids or malate responded to surfaces to produce c-di-GMP. Thus, the amino acid sequence of the WspA periplasmic region did not need to be conserved for the Wsp system to respond to surfaces.

Measuring chromosome conformation with degenerate labels

Although DNA conformation plays an integral role in all genetic processes from transcription to chromosome segregation, there is as yet no tractable method for capturing the in vivo conformation of a chromosome at high resolution. Labeling and fluorescently imaging thousands of loci along the chromosome would readily yield a conformation if each locus could be uniquely distinguished in the image, but this would unrealistically require thousands of distinguishable labels and a tedious experimental process. Here we present a computational method for extracting conformations when the total number of labels far exceeds the number of distinguishable labels. We evaluate our technique using simulated conformations with lengths ranging from 10 to 100 kilobases, and discuss the prospects for an experiment.

A model for Escherichia coli chromosome packaging supports transcription factor-induced DNA domain formation

What physical mechanism leads to organization of a highly condensed and confined circular chromosome? Computational modeling shows that confinement-induced organization is able to overcome the chromosome's propensity to mix by the formation of topological domains. The experimentally observed high precision of separate subcellular positioning of loci (located on different chromosomal domains) in Escherichia coli naturally emerges as a result of entropic demixing of such chromosomal loops. We propose one possible mechanism for organizing these domains: regulatory control defined by the underlying E. coli gene regulatory network requires the colocalization of transcription factor genes and target genes. Investigating this assumption, we find the DNA chain to self-organize into several topologically distinguishable domains where the interplay between the entropic repulsion of chromosomal loops and their compression due to the confining geometry induces an effective nucleoid filament-type of structure. Thus, we propose that the physical structure of the chromosome is a direct result of regulatory interactions. To reproduce the observed precise ordering of the chromosome, we estimate that the domain sizes are distributed between 10 and 700 kb, in agreement with the size of topological domains identified in the context of DNA supercoiling.

Protein-mediated molecular bridging: a key mechanism in biopolymer organization

Protein-mediated bridging is ubiquitous and essential for shaping cellular structures in all organisms. Here we dissect this mechanism for a model system: the Histone-like Nucleoid-Structuring protein (H-NS). We present data from two complementary single-molecule assays that probe the H-NS-DNA interaction: a dynamic optical-trap-driven unzipping assay and an equilibrium H-NS-mediated DNA looping scanning force microscopy imaging assay. To quantitatively analyze and compare these assays, we employ what we consider a novel theoretical framework that describes the bridging motif. The interplay between the experiments and our theoretical model not only infers the effective interaction free energy, the bridging conformation and the duplex-duplex spacing, but also reveals a second, unresolved, cis-binding mode that challenges our current understanding of the role of bridging proteins in chromatin structure. We expect that this theoretical framework for describing protein-mediated bridging will be applicable to proteins acting in chromatin and cytoskeletal organization.