Genetic control of processes of bacterial interactions with plants in associations

This review is devoted to the mechanisms and genetic control of processes underlying the formation and efficiency of associative relationships between bacteria and plants. The role of different polysaccharides and cellular fibrils in the appearance of associative relations and the biosynthetic pathway of these compounds and structures is considered. The molecular mechanisms of bacterial systems responsible for stimulating plant growth and development--nitrogen fixation and synthesis of a plant hormone, indoleacetic acid--are presented. The properties of associative bacteria are discussed in comparison with the relevant characteristics of the most studied free-living or symbiotic model species of bacteria.     

Spatiotemporal specificity of synaptic plasticity: cellular rules and mechanisms

Recent experimental results on spike-timing-dependent plasticity (STDP) and heterosynaptic interaction in various systems have revealed new temporal and spatial properties of activity-dependent synaptic plasticity. These results challenge the conventional understanding of Hebb's rule and raise intriguing questions regarding the fundamental processes of cellular signaling. In this article, I review these new findings that lead to formulation of a new set of cellular rules. Emphasis is on evaluating potential molecular and cellular mechanisms that may underlie the spike-timing window of STDP and different patterns of heterosynaptic modifications. I also highlight several unresolved issues, and suggest future lines of research.     

Transition metal homeostasis: from yeast to human disease

Transition metal ions are essential nutrients to all forms of life. Iron, copper, zinc, manganese, cobalt and nickel all have unique chemical and physical properties that make them attractive molecules for use in biological systems. Many of these same properties that allow these metals to provide essential biochemical activities and structural motifs to a multitude of proteins including enzymes and other cellular constituents also lead to a potential for cytotoxicity. Organisms have been required to evolve a number of systems for the efficient uptake, intracellular transport, protein loading and storage of metal ions to ensure that the needs of the cells can be met while minimizing the associated toxic effects. Disruptions in the cellular systems for handling transition metals are observed as a number of diseases ranging from hemochromatosis and anemias to neurodegenerative disorders including Alzheimer??s and Parkinson??s disease. The yeast Saccharomyces cerevisiae has proved useful as a model organism for the investigation of these processes and many of the genes and biological systems that function in yeast metal homeostasis are conserved throughout eukaryotes to humans. This review focuses on the biological roles of iron, copper, zinc, manganese, nickel and cobalt, the homeostatic mechanisms that function in S. cerevisiae and the human diseases in which these metals have been implicated.     

What Part of NO Don't You Understand? Some Answers to the Cardinal Questions in Nitric Oxide Biology

Nitric oxide (NO) regulates biological processes through signaling mechanisms that exploit its unique biochemical properties as a free radical. For the last several decades, the key aspects of the chemical properties of NO relevant to biological systems have been defined, but it has been a challenge to assign these to specific cellular processes. Nevertheless, it is now clear that the high affinity of NO for transition metal centers, particularly iron, and the rapid reaction of NO with oxygen-derived free radicals can explain many of its biological and pathological properties. Emerging studies also highlight a growing importance of the secondary metabolites of NO-dependent reactions in the post-translational modification of key metabolic and signaling proteins. In this minireview, we emphasize the current understanding of the biochemistry of NO and place it in a biological context.     

Contamination of abiotic surfaces: what a colonizing bacterium sees and how to blur it

Many microbes are able to interfere with solid surfaces and trigger highly sophisticated colonization responses that include expression of specific properties such as increased resistances to antimicrobial agents. An anticontamination strategy might be to prevent adhesion by interfering with the surface-sensing processes and repelling the pioneering cells, to maintain the cellular sensitivity to antimicrobial agents. Recent studies have shown that differences in the physiological state of free-floating and attached bacteria, which could explain the increased levels of resistance, are triggered very early during attachment. Two-component-mediated signalling mechanisms are involved in these surface-sensing processes. Drugs and surface treatments able to interfere with the stimulation factors of these sensing systems (water activity and accumulation of proteins within the periplasm) could "blind" the colonizing bacteria and delay surface contamination.     

Regulatory modules: Coupling protein stability to phopshoregulation during cell division

Multiple post-translational regulation systems regulate cell biology. Two key mechanisms that coordinate the myriad processes of cell replication are phosphorylation and ubiquitin-mediated degradation of proteins. Regulatory modules have evolved to integrate these two control systems at key decision points in the cell division cycle. These modules enable information to be processed with high fidelity by filtering noise, improving specificity, generating feedback loops, and optimizing spatiotemporal coordination of cellular processes. This review provides examples of these modules and considers the advantages of this signaling nexus.     

The glutaredoxin mono- and di-thiol mechanisms for deglutathionylation are functionally equivalent: implications for redox systems biology

Glutathionylation plays a central role in cellular redox regulation and anti-oxidative defence. Grx (Glutaredoxins) are primarily responsible for reversing glutathionylation and their activity therefore affects a range of cellular processes, making them prime candidates for computational systems biology studies. However, two distinct kinetic mechanisms involving either one (monothiol) or both (dithiol) active-site cysteines have been proposed for their deglutathionylation activity and initial studies predicted that computational models based on either of these mechanisms will have different structural and kinetic properties. Further, a number of other discrepancies including the relative activity of active-site mutants and contrasting reciprocal plot kinetics have also been reported for these redoxins. Using kinetic modelling, we show that the dithiol and monothiol mechanisms are identical and, we were also able to explain much of the discrepant data found within the literature on Grx activity and kinetics. Moreover, our results have revealed how an apparently futile side-reaction in the monothiol mechanism may play a significant role in regulating Grx activity in vivo.     

PDZ domains and their binding partners: structure, specificity, and modification

PDZ domains are abundant protein interaction modules that often recognize short amino acid motifs at the C-termini of target proteins. They regulate multiple biological processes such as transport, ion channel signaling, and other signal transduction systems. This review discusses the structural characterization of PDZ domains and the use of recently emerging technologies such as proteomic arrays and peptide libraries to study the binding properties of PDZ-mediated interactions. Regulatory mechanisms responsible for PDZ-mediated interactions, such as phosphorylation in the PDZ ligands or PDZ domains, are also discussed. A better understanding of PDZ protein-protein interaction networks and regulatory mechanisms will improve our knowledge of many cellular and biological processes.     

哺乳动物大脑中神经活动如何改变突触

大脑最基本性质是快速适应周围环境改变的能力,这主要是通过改变各个神经细胞之间的连接来实现的。有多种不同机制可以调节突触的强度,包括突触效率的稳态调节、突触增强和减弱的形态学表现以及钙在其中的作用。当开始了解这些突触改变的细胞生物学机制的时候,也应该考虑这种突触可塑性在完整大脑中的功能意义。因此,应用最新的成像手段来研究经验如何影响皮层环路中突触的改变,尤其是在体双光子显微技术可以在新皮层的单个神经元水平上研究形态和功能可塑性。这些实验将逐渐填补传统的细胞水平和系统水平研究之间的空白,并将有助于更全面充分地理解突触可塑性这种现象及其在皮层功能乃至动物行为中所起的作用。     

Coated-vesicle formation in vitro: conflicting results using different assays

Cell-free systems provide essential tools for elucidating the molecular mechanisms underlying complex cellular processes such as vesicular transport. The biochemical utility of these model systems is strengthened by assays that allow rapid, quantitative detection of the events being studied. Two model systems have recently been developed to reconstitute coated-vesicle budding, and two different biochemical assays are used to detect this event. Striking differences in the biochemical requirements for 'coated-vesicle budding' are detected by these two assays, suggesting that two distinct events are being measured. These findings have wide implications for the use of cell-free assay systems in cell biology.     

FGF signaling in flies and worms: more and more relevant to vertebrate biology

FGF signaling in the invertebrate model systems Drosophila melanogaster and Caenorhabditis elegans was initially most obviously involved in cell motility events. More recently, however, FGFs and FGF signaling in these systems have been shown to affect many additional cellular processes. This recent work has shown that the pleiotropies of these FGF receptors resemble those of their vertebrate counterparts, and, in many cases, serve as excellent models for understanding the fundamental molecular mechanisms controlling these events.     

Intracellular sterol dynamics

We review the cellular mechanisms implicated in cholesterol trafficking and distribution. Recent studies have provided new information about the distribution of sterols within cells, including analysis of its transbilayer distribution. The cholesterol interaction with other lipids and its engagement in various trafficking processes will determine its proper level in a specific membrane; making the cholesterol distribution uneven among the various intracellular organelles. The cholesterol content is important since cholesterol plays an essential role in membranes by controlling their physicochemical properties as well as key cellular events such as signal transduction and protein trafficking. Cholesterol movement between cellular organelles is highly dynamic, and can be achieved by vesicular and non-vesicular processes. Various studies have analyzed the proteins that play a significant role in these processes, giving us new information about the relative importance of these two trafficking pathways in cholesterol transport. Although still poorly characterized in many trafficking routes, several potential sterol transport proteins have been described in detail; as a result, molecular mechanisms for sterol transport among membranes start to be appreciated.     

Dissecting the mechanisms of environment sensitivity of smart probes for quantitative assessment of membrane properties

The plasma membrane, as a highly complex cell organelle, serves as a crucial platform for a multitude of cellular processes. Its collective biophysical properties are largely determined by the structural diversity of the different lipid species it accommodates. Therefore, a detailed investigation of biophysical properties of the plasma membrane is of utmost importance for a comprehensive understanding of biological processes occurring therein. During the past two decades, several environment-sensitive probes have been developed and become popular tools to investigate membrane properties. Although these probes are assumed to report on membrane order in similar ways, their individual mechanisms remain to be elucidated. In this study, using model membrane systems, we characterized the probes Pro12A, NR12S and NR12A in depth and examined their sensitivity to parameters with potential biological implications, such as the degree of lipid saturation, double bond position and configuration (cis versus trans), phospholipid headgroup and cholesterol content. Applying spectral imaging together with atomistic molecular dynamics simulations and time-dependent fluorescent shift analyses, we unravelled individual sensitivities of these probes to different biophysical properties, their distinct localizations and specific relaxation processes in membranes. Overall, Pro12A, NR12S and NR12A serve together as a toolbox with a wide range of applications allowing to select the most appropriate probe for each specific research question.     

On the dynamics of controlled metabolic network and cellular behavior

The existence of elaborate control mechanisms for the various biochemical processes inside and within living cells is responsible for the coherent behaviour observed in its spatio-temporal organisation. Stability and sensitivity are both necessary properties of living systems and these are achieved through negetive and positive feedback loops as in other control systems. We have studied a three-step reaction scheme involving a negative and a positive feedback loop in the form of end-product inhibition and allosteric activation. The variety of behaviour exhibited by this system, under different conditions, includes steady state, simple limit cycle oscillations, complex oscillations and period bifurcations leading to random oscillations or chaos. The system also shows the existence of two distinct chaotic regimes under the variation of a single parameter. These results, in comparison with single biochemical control loops, show that new behaviours can be exhibited in a more complex network which are not seen in the single control loops. The results are discussed in the light of a diverse variety of cellular functions in normal and altered cells indicating the role of controlled metabolic network as the underlying basis for cellular behaviour.     

Reciprocal interactions between cells and extracellular matrix during remodeling of tissue constructs

Cells remodel extracellular matrix during tissue development and wound healing. Similar processes occur when cells compress and stiffen collagen gels. An important task for cell biologists, biophysicists, and tissue engineers is to guide these remodeling processes to produce tissue constructs that mimic the structure and mechanical properties of natural tissues. This requires an understanding of the mechanisms by which this remodeling occurs. Quantitative measurements of the contractile force developed by cells and the extent of compression and stiffening of the matrix describe the results of the remodeling processes. Not only do forces exerted by cells influence the structure of the matrix but also external forces exerted on the matrix can modulate the structure and orientation of the cells. The mechanisms of these processes remain largely unknown, but recent studies of the regulation of myosin-dependent contractile force and of cell protrusion driven by actin polymerization provide clues about the regulation of cellular functions during remodeling.     

Exploiting biological complexity for strain improvement through systems biology

Cellular complexity makes it difficult to build a complete understanding of cellular function but also offers innumerable possibilities for modifying the cellular machinery to achieve a specific purpose. The exploitation of cellular complexity for strain improvement has been a challenging goal for applied biological research because it requires the coordinated understanding of multiple cellular processes. It is therefore pursued most efficiently in the framework of systems biology. Progress in strain improvement will depend not only on advances in technologies for high-throughput measurements but, more importantly, on the development of theoretical methods that increase the information content of these measurements and, as such, facilitate the elucidation of mechanisms and the identification of genetic targets for modification.     

Measurement techniques for cellular biomechanics in vitro

Living cells and tissues experience mechanical forces in their physiological environments that are known to affect many cellular processes. Also of importance are the mechanical properties of cells, as well as the microforces generated by cellular processes themselves in their microenvironments. The difficulty associated with studying these phenomena in vivo has led to alternatives such as using in vitro models. The need for experimental techniques for investigating cellular biomechanics and mechanobiology in vitro has fueled an evolution in the technology used in these studies. Particularly noteworthy are some of the new biomicroelectromechanical systems (Bio-MEMS) devices and techniques that have been introduced to the field. We describe some of the cellular micromechanical techniques and methods that have been developed for in vitro studies, and provide summaries of the ranges of measured values of various biomechanical quantities. We also briefly address some of our experiences in using these methods and include modifications we have introduced in order to improve them.