High-throughput transient transformation of Arabidopsis roots enables systematic colocalization analysis of GFP-tagged proteins

Determination of the subcellular localization of an unknown protein is a major step towards the elucidation of its function. Lately, the expression of proteins fused to fluorescent markers has been very popular and many approaches have been proposed to express these proteins. Stable transformation using Agrobacterium tumefaciens generates stable lines for downstream experiments, but is time-consuming. If only colocalization is required, transient techniques save time and effort. Several methods for transient assays have been described including protoplast transfection, biolistic bombardment, Agrobacterium tumefaciens cocultivation and infiltration. In general colocalizations are preferentially performed in intact tissues of the same species, resembling the native situation. High transformation rates were described for cotyledons of Arabidopsis, but never for roots. Here we report that it is possible to transform Arabidopsis root epidermal cells with an efficiency that is sufficient for colocalization purposes.Key words: Arabidopsis, GFP-fusions, protein localization, root, transient transformationSince the release of the Arabidopsis thaliana genome sequence plant biologists set the goal to elucidate the functions of all coded genes. Apart from the spatio-temporal expression patterns of genes, the subcellular localization of gene products can play an essential role in deciphering their function. Classical immunological approaches to localize proteins can be hindered by cross-reactivity, time-consuming generation of antibodies and the low temporal resolution. Expression of tagged proteins forms a suitable alternative. Lately, fusions with fluorescent proteins in combination with confocal (CLSM)¹ or spinning disc microscopy² allow real time protein localization and even subcellular trafficking at high resolution. An overview of fluorescent tagging approaches can be found elsewhere.³Currently several techniques to introduce the coding region for a tagged protein in a plant are available. The generation of stable lines transformed by Agrobacterium tumefaciens offers a continuous source of plant material, but it is time-consuming especially when only colocalization experiments are required. Transient assays, on the other hand, offer the advantage of being fast and amenable to high throughput strategies. Each of these techniques, however, has some limitations and drawbacks. Particle bombardment (biolistics) ^4–6 for example circumvents the host specificity of Agrobacterium strains, but requires expensive equipment. Moreover, it is rather disruptive and imposes a significant stress upon the plants, possibly influencing the results. Protoplasts lack a cell wall and protoplast transformation^7,8 is therefore not suitable for certain experiments related to cell wall proteins or when interactions between cells on tissue level might be important.⁹ Moreover, protoplasts have lost their identity which might be critical for the correct functioning of certain transgenic constructs. Agrobacterium infiltration of tobacco leaves¹⁰ is regularly used and represents an efficient, fast and relatively easy transformation technique. However, tobacco leaves easily show autofluoresence due to tissue damage as a result of experimental manipulations. As it has been reported that some protein fusions expressed in an heterologous system localize to different subcellular localizations11 it is advisable not to use tobacco when localizing Arabidopsis proteins. Leaf infiltrations have been performed in Arabidopsis,¹² but apparently their leaves are much more prone to mechanical damage and the leaf developmental stage is critical, complicating this technique. Cocultivation of Agrobacterium with seedlings offers a rapid and efficient approach applicable to many mono and dicot species. It was reported to work efficiently in Arabidopsis cotyledons, but not in roots.⁹ As an alternative method, Agrobacterium infiltration of Arabidopsis seedlings¹¹ seems an efficient technique for transient expression. However, expression in root cells could not be obtained. Colocalizations are required in the native cells or tissue for the correct localization of an unknown protein or proteins that need interaction partners. As a consequence this technique can not be reliably used when root expressed gene products are studied. Here we show evidence that it is possible to use the described technique¹¹ to induce transient expression in Arabidopsis roots.We used the Agrobacterium infiltration of Arabidopsis seedlings technique¹¹ to colocalize several C-terminal (S65T)-sGFP fusions generated in the plant binary vector pGWB6.¹³ Each construct was transformed into Agrobacterium tumefaciens (C59C1Rif^R) containing the helper plasmid pMP90. Subsequently different stable marker lines, wild type Arabidopsis (Col-0) bearing mCherry fusion constructs,¹⁴ were transiently transformed.¹¹ After 2 or 3 days seedlings were studied using CLSM. Besides being expressed in cotyledons fusion proteins were clearly observed in root epidermis and root cap cells (Fig. 1A and B). As reported¹¹ the transformation efficiency in cotyledons was considerably higher than in root cells. However, in each experiment we obtained a considerable amount of transformed root epidermal cells which was more than sufficient for colocalization studies (Fig. 2). It was remarkable that transformation was repeatedly successful in groups of cells, adjacent or close to each other.Open in a separate windowFigure 1Transient transformation of Arabidopsis root cells. Expression of the protein-GFP fusion product can be seen in the epidermal (A) and root cap cells (B) on fluorescence/transmission merged images. As seen in (A) high efficiencies of root transformation can be reached.Open in a separate windowFigure 2Colocalization of mCherry and GFP constructs. Confocal image of the mCherry fluorescence (A), the GFP signal (B) and the merged image (C).In contrast to what was reported earlier we show here that the Agrobacterium infiltration technique¹¹ is perfectly capable of transiently transforming Arabidopsis root epidermal cells. It allows the transient production and study of proteins in their native environment, considerably increasing the reliability of such experiments. Additionaly the use of RFP marker constructs in colocalisation studies in the root is free of interference by the red background autofluorescence of chlorophyll.     

Eph receptor signalling casts a wide net on cell behaviour

Eph receptor tyrosine kinases mould the behaviour of many cell types by binding membrane-anchored ligands, ephrins, at sites of cell-cell contact. Eph signals affect both of the contacting cells and can produce diverse biological responses. New models explain how quantitative variations in the densities and signalling abilities of Eph receptors and ephrins could account for the different effects that are elicited on axon guidance, cell adhesion and cell migration during development, homeostasis and disease.     

Control of cell behaviour by signalling through Eph receptors and ephrins

Eph receptor tyrosine kinases and ephrins mediate contact-dependent cell interactions that regulate the repulsion and adhesion mechanisms involved in the guidance and assembly of cells. Recent work has revealed a role of overlapping Eph receptor and ephrin expression in modulating neuronal growth cone repulsion, and has shown that bidirectional activation restricts intermingling and communication between cell populations. In addition, progress has been made in understanding how Eph receptors and ephrins control cell adhesion.     

Deterministic chaos and the first positive Lyapunov exponent: a nonlinear analysis of the human electroencephalogram during sleep

Under selected conditions, nonlinear dynamical systems, which can be described by deterministic models, are able to generate so-called deterministic chaos. In this case the dynamics show a sensitive dependence on initial conditions, which means that different states of a system, being arbitrarily close initially, will become macroscopically separated for sufficiently long times. In this sense, the unpredictability of the EEG might be a basic phenomenon of its chaotic character. Recent investigations of the dimensionality of EEG attractors in phase space have led to the assumption that the EEG can be regarded as a deterministic process which should not be mistaken for simple noise. The calculation of dimensionality estimates the degrees of freedom of a signal. Nevertheless, it is difficult to decide from this kind of analysis whether a process is quasiperiodic or chaotic. Therefore, we performed a new analysis by calculating the first positive Lyapunov exponent L₁ from sleep EEG data. Lyapunov exponents measure the mean exponential expansion or contraction of a flow in phase space. L₁ is zero for periodic as well as quasiperiodic processes, but positive in the case of chaotic processes expressing the sensitive dependence on initial conditions. We calculated L₁ for sleep EEG segments of 15 healthy men corresponding to the sleep stages I, II, III, IV, and REM (according to Rechtschaffen and Kales). Our investigations support the assumption that EEG signals are neither quasiperiodic waves nor a simple noise. Moreover, we found statistically significant differences between the values of L₁ for different sleep stages. All together, this kind of analysis yields a useful extension of the characterization of EEG signals in terms of nonlinear dynamical system theory.     

Bayesian analysis of signaling networks governing embryonic stem cell fate decisions

MOTIVATION: Signaling events that direct mouse embryonic stem (ES) cell self-renewal and differentiation are complex and accordingly difficult to understand in an integrated manner. We address this problem by adapting a Bayesian network learning algorithm to model proteomic signaling data for ES cell fate responses to external cues. Using this model we were able to characterize the signaling pathway influences as quantitative, logic-circuit type interactions. Our experimental dataset includes measurements for 28 signaling protein phosphorylation states across 16 different factorial combinations of cytokine and matrix stimuli as reported previously. RESULTS: The Bayesian network modeling approach allows us to uncover previously reported signaling activities related to mouse ES cell self-renewal, such as the roles of LIF and STAT3 in maintaining undifferentiated ES cell populations. Furthermore, the network predicts novel influences such as between ERK phosphorylation and differentiation, or RAF phosphorylation and differentiated cell proliferation. Visualization of the influences detected by the Bayesian network provides intuition about the underlying physiology of the signaling pathways. We demonstrate that the Bayesian networks can capture the linear, nonlinear and multistate logic interactions that connect extracellular cues, intracellular signals and consequent cell functional responses.     

Changing neighbours,changing behaviour: cell adhesion molecule-mediated signalling during tumour progression

Changes in cell-cell and cell-matrix adhesion accompany the transition from benign tumours to invasive, malignant cancer and the subsequent metastatic dissemination of tumour cells. This review discusses a possible role of cell adhesion molecules not only in redirecting a tumour cell's adhesive capabilities but also in modulating intracellular signalling, and with it, tumour malignancy.     

Additional factors governing specialized cell dynamics based on deductive systems analysis

Summary This paper presents the findings of an engineering style systems analysis performed on the cell in an effort to understand how specialized cell dynamics can be described in an end-to-end manner. Of unique interest is the projection of additional internal cell functions, beyond the many recent discoveries, for facilitating precision growth. Potential cell mechanisms for fulfilling the projected functions are then deduced through comparative systems techniques ANSER is a not-for-profit public service research institute. This paper does not reflect the official opinion of ANSER and the U.S. government.     

Transmembrane signalling and modulation of neutrophil behaviour

Neutrophils are blood cells which respond to chemotactic stimuli and phagocytize invading microorganisms. The activation of oriented locomotion, the formation of pseudopods, and the production and secretion of factors toxic to the endycytized organisms all require the transmission and amplification of external stimuli by the neutrophil plasma membrane. Ca²⁺ mobilization, the transient elevation of cyclic AMP, protein phosphorylation and lipid turnover may all be involved in transmembrane signalling and the modulation of neutrophil functions.     

Insights into the behaviour of systems biology models from dynamic sensitivity and identifiability analysis: a case study of an NF-kappaB signalling pathway

Mathematical modelling offers a variety of useful techniques to help in understanding the intrinsic behaviour of complex signal transduction networks. From the system engineering point of view, the dynamics of metabolic and signal transduction models can always be described by nonlinear ordinary differential equations (ODEs) following mass balance principles. Based on the state-space formulation, many methods from the area of automatic control can conveniently be applied to the modelling, analysis and design of cell networks. In the present study, dynamic sensitivity analysis is performed on a model of the IkappaB-NF-kappaB signal pathway system. Univariate analysis of the Euclidean-form overall sensitivities shows that only 8 out of the 64 parameters in the model have major influence on the nuclear NF-kappaB oscillations. The sensitivity matrix is then used to address correlation analysis, identifiability assessment and measurement set selection within the framework of least squares estimation and multivariate analysis. It is shown that certain pairs of parameters are exactly or highly correlated to each other in terms of their effects on the measured variables. The experimental design strategy provides guidance on which proteins should best be considered for measurement such that the unknown parameters can be estimated with the best statistical precision. The whole analysis scheme we describe provides efficient parameter estimation techniques for complex cell networks.     

Direct quantification of in vitro cell growth through image analysis

Summary Objective, accurate, non-intrusive measurement of in vitro cell growth was realized through microcomputerized video image analysis. Recently-released video and digitizing hardware and software were incorporated into an analytical system which accurately quantified visual differences between cultures on a cell number or fresh mass basis. Sequential measurements during culture incubation further detected and quantified subtle changes in colony area and density resulting from growth. Each measurement was acquired rapidly, without encroaching on the in vitro environment, so cell growth was undisturbed. Custom software routines coordinated the quantification of this detailed record into precise cumulative growth curves.     

Genetic analysis of Ras signalling pathways in cell proliferation,migration and survival

We have used mouse embryonic fibroblasts (MEFs) devoid of Ras proteins to illustrate that they are essential for proliferation and migration, but not for survival, at least in these cells. These properties are unique to the Ras subfamily of proteins because ectopic expression of other Ras‐like small GTPases, even when constitutively active, could not compensate for the absence of Ras proteins. Only constitutive activation of components of the Raf/Mek/Erk pathway was sufficient to sustain normal proliferation and migration of MEFs devoid of Ras proteins. Activation of the phosphatidylinositol 3‐kinase (PI3K)/PTEN/Akt and Ral guanine exchange factor (RalGEF)/Ral pathways, either alone or in combination, failed to induce proliferation or migration of Rasless cells, although they cooperated with Raf/Mek/Erk signalling to reproduce the full response mediated by Ras signalling. In contrast to current hypotheses, Ras signalling did not induce proliferation by inducing expression of D‐type Cyclins. Rasless MEFs had normal levels of Cyclin D1/Cdk4 and Cyclin E/Cdk2. However, these complexes were inactive. Inactivation of the pocket proteins or knock down of pRb relieved MEFs from their dependence on Ras signalling to proliferate.     

Elucidation of T cell signalling models

A potential mechanism that allows T cells to reliably discriminate pMHC ligands involves an interplay between kinetic proofreading, negative feedback and a destruction of this negative feedback. We analyse a detailed model of these mechanisms which involves the TCR, SHP1 and ERK. We discover that the behaviour of pSHP1 negative feedback is of primary importance, and particularly the influence of a kinetic proofreading base negative feedback state on pSHP1 dynamics. The CD8 co-receptor is shown to benefit from a kinetic proofreading locking mechanism and is able to overcome pSHP1 negative influences to sensitise a T cell.     

Physicochemical modelling of cell signalling pathways

Physicochemical modelling of signal transduction links fundamental chemical and physical principles, prior knowledge about regulatory pathways, and experimental data of various types to create powerful tools for formalizing and extending traditional molecular and cellular biology.     

A parametric study of wind chill equivalent temperatures by a dimensionless steady-state analysis

A first order analytical approximation of steady-state heat conduction in a hollow cylinder exchanging heat at its external surface by convection with a cold and windy environment is presented. The model depicts the thermal behavior of certain body elements, e.g., head/face, when exposed to such environments. The results are presented by dimensionless parameters and facilitate the estimation of wind chill equivalent temperatures (WCETs). The effects of several variables on determining WCETs were studied using specific examples, leading to the following generalizations: (1) the conditions assumed for "calm" wind speed appear to be a dominant factor in determining WCET; (2) the effects, on both (skin) surface temperature and on WCET, of a 1°C change in environmental temperature appear to be more pronounced than those of a 1 m/s change in wind speed; (3) similarly, predicted WCETs are more sensitive to the geometrical dimensions assumed for the modeled entity than they are to wind speeds; and (4) tissue thermal conductivity, the angle at which the convective heat transfer coefficient is measured relative to wind direction, and the factor used to establish "effective" wind speeds in the domain occupied by humans relative to reported values, all seem to have relatively small effects on the determination of WCET. These conclusions strongly suggest, among other things, that for any given combination of environmental conditions, wind chill indices may best be presented as ranges rather than as single values. This seems to apply even when worst-case scenarios are considered. Also emphasized is the need for careful and realistic selection of all the parameter values used in the determination of WCETs.     

PhosR enables processing and functional analysis of phosphoproteomic data

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