In silico tools for signal transduction research

Signal transduction is a fundamental process that takes place in all living organisms and understanding how this event occurs at the cellular level is of vital importance to virtually all fields of biomedicine. There are several major steps involved in deciphering the signalling pathways: (a) Which molecules are involved in signalling? (b) Who talks to whom?, ie making sense of the molecular interactions in a context-dependent way. (c) Where are the signalling events taking place?, eg when a resting cell becomes activated. The challenge lies in reconstructing signalling modules and networks evoked in a particular response to a single input as well as correlating the signalling response to different cellular inputs. There is also the need for interpretation of cross-talk between signalling modules in response to single and multiple inputs. To follow up these questions there are many good databases that provide an information system on regulatory networks. This review aims to find some of the bioinformatics tools and websites available to conduct signal transduction research and to discuss the representation of databases available for the processes of signalling. The databases considered here can provide a well-structured overview on the subject and a basis for advanced bioinformatics analysis to interpret the function of genomic sequences or to analyse signalling networks within a cell. However, the knowledge of most signalling pathways is incomplete and for this reason the existing databases will provide insight, but very rarely a more complete picture.     

苏云金芽孢杆菌双组份信号转导系统的生物信息学分析

苏云金芽孢杆菌(Bacillus thuringiensis)能产生杀虫晶体蛋白等多种活性成分,是目前应用最广泛的微生物杀虫剂。本文采用生物信息学方法,系统分析了由本实验室完成全基因组测序的苏云金芽孢杆菌YBT-1520、CT-43和BMB171 3个菌株的双组分信号转导系统(Two-componentsignal transduction system,TCS)的分布、结构及功能,并初步构建了部分TCS的调控网络关系图。本研究旨在为深入研究苏云金芽孢杆菌的生长、代谢以及毒力因子的表达与调控,全面了解伴孢晶体的形成机制开辟新的研究方向。     

伤害信号分子及其信号转导

伤害对于植物是一种常见的环境刺激。目前,对伤害刺激产生的防御反应及其机理都有了较为广泛的研究。简述了目前已确定的参与伤害反应的信号分子：寡糖素,系统素,脱落酸,茉莉酸,乙烯和电信号等,并初步探讨了伤害信号分子的信号转导途径。     

Calcium and signal transduction in plants

Environmental and hormonal signals control diverse physiological processes in plants. The mechanisms by which plant cells perceive and transduce these signals are poorly understood. Understanding biochemical and molecular events involved in signal transduction pathways has become one of the most active areas of plant research. Research during the last 15 years has established that Ca2+ acts as a messenger in transducing external signals. The evidence in support of Ca2+ as a messenger is unequivocal and fulfills all the requirements of a messenger. The role of Ca2+ becomes even more important because it is the only messenger known so far in plants. Since our last review on the Ca2+ messenger system in 1987, there has been tremendous progress in elucidating various aspects of Ca(2+) -signaling pathways in plants. These include demonstration of signal-induced changes in cytosolic Ca2+, calmodulin and calmodulin-like proteins, identification of different Ca2+ channels, characterization of Ca(2+) -dependent protein kinases (CDPKs) both at the biochemical and molecular levels, evidence for the presence of calmodulin-dependent protein kinases, and increased evidence in support of the role of inositol phospholipids in the Ca(2+) -signaling system. Despite the progress in Ca2+ research in plants, it is still in its infancy and much more needs to be done to understand the precise mechanisms by which Ca2+ regulates a wide variety of physiological processes. The purpose of this review is to summarize some of these recent developments in Ca2+ research as it relates to signal transduction in plants.     

Bacterial signal transduction networks via connectors and development of the inhibitors as alternative antibiotics

Bacterial cells possess a signal transduction system that differs from those described in higher organisms, including human cells. These so-called two-component signal transduction systems (TCSs) consist of a sensor (histidine kinase, HK) and a response regulator, and are involved in cellular functions, such as virulence, drug resistance, biofilm formation, cell wall synthesis, cell division. They are conserved in bacteria across all species. Although TCSs are often studied and characterized individually, they are assumed to interact with each other and form signal transduction networks within the cell. In this review, I focus on the formation of TCS networks via connectors. I also explore the possibility of using TCS inhibitors, especially HK inhibitors, as alternative antimicrobial agents.     

拟南芥QUA1基因在光信号途径中的表达与功能分析

光信号在植物生长发育过程中具有非常重要的作用。不同的光信号通过调节植物下游基因的表达,进而影响细胞分化、结构和功能的改变,以及组织和器官的形成,参与植物光形态建成。QUA1 (QUASIMODO1)是拟南芥糖基转移酶家族中的一个成员,参与植物细胞壁中果胶的合成。本文以拟南芥qua1-1/cry1以及qua1-1/phyB双突变体为材料,对QUA1基因在光信号途径中的功能进行了分析。结果显示,qua1-1突变体在暗、蓝光、红光以及远红外光培养条件下下胚轴的伸长均受到抑制,QUA1基因的表达同样受到光信号的调节,而且突变体中多种光信号调节基因的表达也受到了影响。通过对qua1-1突变体下胚轴的观察发现,突变体下胚轴表皮细胞长度明显变短。与cry1以及phyB突变体相比,qua1-1/cry1和qua1-1/phyB双突变体下胚轴长度明显变短,而且双突变体中光信号调节基因的表达也有明显变化,表明QUA1可能参与了CRY1以及PHYB介导的蓝光及红光信号传导。以上结果表明QUA1影响了下胚轴细胞的伸长以及光信号调节基因的表达,并参与调控多种光信号传导途径。     

Attractor analysis of asynchronous Boolean models of signal transduction networks

Prior work on the dynamics of Boolean networks, including analysis of the state space attractors and the basin of attraction of each attractor, has mainly focused on synchronous update of the nodes’ states. Although the simplicity of synchronous updating makes it very attractive, it fails to take into account the variety of time scales associated with different types of biological processes. Several different asynchronous update methods have been proposed to overcome this limitation, but there have not been any systematic comparisons of the dynamic behaviors displayed by the same system under different update methods. Here we fill this gap by combining theoretical analysis such as solution of scalar equations and Markov chain techniques, as well as numerical simulations to carry out a thorough comparative study on the dynamic behavior of a previously proposed Boolean model of a signal transduction network in plants. Prior evidence suggests that this network admits oscillations, but it is not known whether these oscillations are sustained. We perform an attractor analysis of this system using synchronous and three different asynchronous updating schemes both in the case of the unperturbed (wild-type) and perturbed (node-disrupted) systems. This analysis reveals that while the wild-type system possesses an update-independent fixed point, any oscillations eventually disappear unless strict constraints regarding the timing of certain processes and the initial state of the system are satisfied. Interestingly, in the case of disruption of a particular node all models lead to an extended attractor. Overall, our work provides a roadmap on how Boolean network modeling can be used as a predictive tool to uncover the dynamic patterns of a biological system under various internal and environmental perturbations.     

植物体内磷脂代谢和信号转导

磷脂不但作为细胞结构的重要组成部分，其代谢产物主料可作为人信号分子，这一推断日益受到人们重视，并为越来越多的实验所证实。本文综述磷脂酶类、磷酸肌醇激酶及其代谢产物参与的植物细胞内的信号转导，阐述它们与植物激素和钙信使系统的关系。     

Genetic engineering of plant signal transduction mechanisms

Signal transduction is used by plants to coordinate their development and to sense and respond to fluctuations in their surroundings. Of prime importance is the ability to defend against pathogens and other environmental hazards such as cold temperatures, drought or wounding. Many transduction pathways are now characterized and the underlying genes are known. This suggests an obvious question—can we engineer signal transduction mechanisms for plant improvement? We address this question by presenting a rationale for an engineering approach and by discussing results from recent attempts to apply this approach. Calmodulin-like domain protein kinase (CDPK) and mitogen-activated protein kinase (MAPK) pathways are used as primary examples. New technology that will aid these efforts is also covered.     

A possible degree of motional freedom in bacterial chemoreceptor cytoplasmic domains and its potential role in signal transduction

We describe an array of gaps in an antiparallel four-helix bundle structure, the cytoplasmic domains of bacterial chemoreceptors. For a given helix, the side chain interactions that define a helix’s position are analyzed in terms of residue interfaces, the most important of which are a-a, g-g, d-d, g-d, and a-d. It was found that the interdigitation of the side groups does not entirely fill the space along the long axis of the structure, which results in a rather regular array of gaps. A simulated piston motion of helix CD1 along the helical axis direction by 1.2Å shows that 85% of the side chain interactions still satisfy Van der Waals criteria, while the remaining clashes could be avoided by small rotations of side chains. Therefore, two states could exist in the structure, related by a piston motion. Analysis of the crystal structure of a small four-helix bundle, the P1_short domain of CheA in Thermotoga Maritima, reveals that the two coexisting states related by a 1.3-1.7Å piston motion are defined by the same mechanism. This two-state model is a plausible candidate mechanism for the long distance signal transduction in bacterial chemoreceptors and is qualitatively consistent with literature chemoreceptor mutagenesis results. Such a mechanism could exist in many other structures with interdigitating α-helices.     

Ca-modulated ONE-GC odorant signal transduction

In a subset of olfactory epithelium the odorant receptor guanylate cyclase, ONE-GC, is a central transduction component of the cyclic GMP signaling pathway. The odorant binds to the extracellular domain and activates its intracellular catalytic domain to generate the odorant second messenger, cyclic GMP. The present study demonstrates that it is a two-step, Ca²⁺-independent and Ca²⁺-dependent, sequential process. In step one, the odorant, uroguanylin, binds ONE-GC and primes it for stimulation. In step two, Ca²⁺-bound neurocalcin δ binds to the defined intracellular domain and saturates ONE-GC activity. A prototype model is proposed that depicts this signal transduction process.     

Synthetic modular systems--reverse engineering of signal transduction

During the last decades, biology has decomposed cellular systems into genetic, functional and molecular networks. It has become evident that these networks consist of components with specific functions (e.g., proteins and genes). This has generated a considerable amount of knowledge and hypotheses concerning cellular organization. The idea discussed here is to test the extent of this knowledge by reconstructing, or reverse engineering, new synthetic biological systems from known components. We will discuss how integration of computational methods with proteomics and engineering concepts might lead us to a deeper and more abstract understanding of signal transduction systems. Designing and successfully introducing synthetic proteins into cellular pathways would provide us with a powerful research tool with many applications, such as development of biosensors, protein drugs and rewiring of biological pathways.     

Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction

Large‐scale protein signalling networks are useful for exploring complex biochemical pathways but do not reveal how pathways respond to specific stimuli. Such specificity is critical for understanding disease and designing drugs. Here we describe a computational approach—implemented in the free CNO software—for turning signalling networks into logical models and calibrating the models against experimental data. When a literature‐derived network of 82 proteins covering the immediate‐early responses of human cells to seven cytokines was modelled, we found that training against experimental data dramatically increased predictive power, despite the crudeness of Boolean approximations, while significantly reducing the number of interactions. Thus, many interactions in literature‐derived networks do not appear to be functional in the liver cells from which we collected our data. At the same time, CNO identified several new interactions that improved the match of model to data. Although missing from the starting network, these interactions have literature support. Our approach, therefore, represents a means to generate predictive, cell‐type‐specific models of mammalian signalling from generic protein signalling networks.     

Peptides as probes for G protein signal transduction

Triggered by agonist binding to cell surface receptors, the heterotrimeric G proteins dissociate into and βγ subunits, each activating distinct second messenger pathways. Peptides from the primary sequences of receptors, G proteins, and effectors have been used to study the molecular interactions between these proteins. Receptor-derived peptides from the second, third and fourth intracellular loops and certain naturally occurring peptides antagonize G protein interactions and can directly activate G protein. These peptides bind to G protein sites that include the N and C terminal regions of the subunit and a yet to be identified region of the β subunit. Peptides have also been useful in characterizing G protein-effector interactions. The identification of the contact sites between proteins involved in G protein signal transduction should aid in the development of non-peptide mimetic therapeutics which could specifically modify G protein-mediated cellular responses.     

Towards an understating of signal transduction protein interaction networks

Protein network analysis has witnessed a number of advancements in the past for understanding molecular characteristics for important network topologies in biological systems. The signaling pathway regulates cell cycle progression and anti-apoptotic molecules. This pathway is also involved in maintaining cell survival by modulating the activity of apoptosis through RAS, P13K, AKT and BAD activities. The importance of protein-protein interactions to improve usability of the interactome by scoring and ranking interaction data for proteins in signal transduction networks is illustrated using available data and resources.     

p38 MAPK信号传导通路

丝裂原活化蛋白激酶（ｍｉｔｏｇｅｎ－ａｃｔｉｖａｔｅｄｐｏｒｏｔｅｉｎｋｉｎａｓｅ,ＭＡＰＫ）介导了生长、发育,分裂,死亡,以及细胞间的功能同步等多种细胞生理功能,在哺乳动物细胞中已发现和克隆了ＥＲＫ、ＪＮＫ／ＳＡＰＫ,ＥＲＫ５／ＢＭＫ１和ｐ３８／ＲＫ四个ＭＡＰＫ亚族,这些新的ＭＡＰＫ介导了物理,化学反激,细菌产物,炎性细胞因子等多种刺激引起的细胞反应,ｐ３８亚族至少包括ｐ３８（α）,ｐ３８β,ｐ     

树突状细胞免疫调节作用及其信号转导机制

树突状细胞（DC）是最强效的抗原提呈细胞。,在抗原的刺激下,DC通过趋化因子作用由外周组织迁移至淋巴组织和器官,同时上调主要组织相容性复合体分子、共刺激分子和黏附分子的表达,分泌细胞因子,获得预激幼稚T细胞的独特能力。DC通过不同的受体吞饮、吞噬和胞吞抗原,例如C型凝集素受体捕获和呈递抗原,通过Toll样受体识别病原体和激活DC。本文主要综述了DC的免疫调节效应及其不同病原体识别受体活化和细胞内信号机制。     

赤霉素信号转导与棉纤维的分子发育

赤霉素(Gas)作为一种高效能的植物生长调节物质对棉纤维的分化和发育有着非常重要的影响, 但是, 一直以来有关赤霉素与棉纤维分化和发育的分子机制的研究还很少。文章论述了近年来GA信号组分、转导途径的分子生物学研究进展以及GA与棉纤维分子发育的相关研究成果, 旨在为揭示赤霉素调控棉纤维分化和发育的分子机制以及改善棉纤维品质的棉花育种工作提供新的思路。     

Neurotrophin signal transduction by the Trk receptor

The initial event in the neuronal differentiation of PC12 cells is the binding of the neurotrophin nerve growth factor (NGF) to the Trk receptor. This interaction stimulates the intrinsic tyrosine kinase activity of TRk, initiating a signalling cascade involving the phosphorylation of intracellular proteins on tyrosine, serine, and threonine residues. These signals are then in turn propagated to other messengers, ultimately leading to differentiation, neurotrophin-dependent survival and the loss of proliferative capacity. To transmit NGF signals, NGF-activated Trk rapidly associated with the cytoplasmic proteins, SHC, PI-3 kinase, and PLC-γ1. These proteins are involved in stimulating the formation of various second messenger molecules and activating the Ras signal transduction pathway. Studies with Trk mutants indicate that the acivation of the Ras pathway is necessary for complete differentiation of PC12-derived cells and for the maintenance of the differentiated phenotype. Trk also induces the tyrosine phosphorylation of SNT, a specific target of neurotrophic factor activity in neuronal cells. This review will discuss the potential roles of Trk and the proteins of the Trk signalling pathways in NGF function, and summarize our attempts to understand the mechanisms used by Trk to generate dthe many phenotypic responses of PC12 cells to NGF. 1994 John Wiley & Sons, Inc.     

脂筏与T细胞信号转导

抗原提呈细胞将抗原加工处理后通过MHCⅠ/MHCⅡ类分子提呈供T细胞识别。TCR对抗原的识别引起一系列下游信号事件的发生,最终使T细胞激活,但对TCR复合物结合抗原后引起胞内区磷酸化的早期事件机制还不是很清楚。最近的研究揭示脂筏参与了这一早期信号事件的发生。脂筏是一种膜脂双层内含有的特殊微区,T细胞膜表面参与T细胞激活的各种关键信号分子都定位于脂筏。T细胞激活过程中脂筏通过聚集和重分配形成一个信号转导的平台。