Understanding flux in plant metabolic networks

The revolutionary growth in our ability to identify the 'parts list' of cellular infrastructure in plants in detail, and to alter it with precision, challenges us to develop methods to quantify how these parts function. For components of metabolism, this means mapping fluxes at the level of metabolic networks. Advances in experimental, analytical and software tools for metabolic flux analysis now allow maps of the fluxes through central metabolism to be obtained from the results of stable-isotope-labeling experiments. Such maps have led to notable successes in understanding and engineering metabolic function in microorganisms. Recent studies in plants are giving insight into particular fluxes, such as those of the pentose phosphate pathway, and into general phenomena, such as substrate- or futile-cycles and compartmentation. The importance of experimental design and statistical analysis have been illustrated, and analyses of fluxes in heterotrophic plant tissues have been carried out recently.     

Multi-criteria optimization of regulation in metabolic networks

Determining the regulation of metabolic networks at genome scale is a hard task. It has been hypothesized that biochemical pathways and metabolic networks might have undergone an evolutionary process of optimization with respect to several criteria over time. In this contribution, a multi-criteria approach has been used to optimize parameters for the allosteric regulation of enzymes in a model of a metabolic substrate-cycle. This has been carried out by calculating the Pareto set of optimal solutions according to two objectives: the proper direction of flux in a metabolic cycle and the energetic cost of applying the set of parameters. Different Pareto fronts have been calculated for eight different "environments" (specific time courses of end product concentrations). For each resulting front the so-called knee point is identified, which can be considered a preferred trade-off solution. Interestingly, the optimal control parameters corresponding to each of these points also lead to optimal behaviour in all the other environments. By calculating the average of the different parameter sets for the knee solutions more frequently found, a final and optimal consensus set of parameters can be obtained, which is an indication on the existence of a universal regulation mechanism for this system.The implications from such a universal regulatory switch are discussed in the framework of large metabolic networks.     

Measuring multiple fluxes through plant metabolic networks

Fluxes through metabolic networks are crucial for cell function, and a knowledge of these fluxes is essential for understanding and manipulating metabolic phenotypes. Labeling provides the key to flux measurement, and in network flux analysis the measurement of multiple fluxes allows a flux map to be superimposed on the metabolic network. The principles and practice of two complementary methods, dynamic and steady-state labeling, are described, emphasizing best practice and illustrating their contribution to network flux analysis with examples taken from the plant and microbial literature. The principal analytical methods for the detection of stable isotopes are also described, as well as the procedures for obtaining flux maps from labeling data. A series of boxes summarizing the key concepts of network flux analysis is provided for convenience.     

Insights into plant metabolic networks from steady-state metabolic flux analysis

Steady-state metabolic flux analysis (MFA) is an experimental approach that allows the measurement of multiple fluxes in the core network of primary carbon metabolism. It is based on isotopic labelling experiments, and although well established in the analysis of micro-organisms, and some mammalian systems, the extension of the method to plant cells has been challenging because of the extensive subcellular compartmentation of the metabolic network. Despite this difficulty there has been substantial progress in developing robust protocols for the analysis of heterotrophic plant metabolism by steady-state MFA, and flux maps have now been published that reflect the metabolic phenotypes of excised root tips, developing embryos and cotyledons, hairy root cultures, and cell suspensions under a variety of physiological conditions. There has been a steady improvement in the quality, extent and statistical reliability of these analyses, and new information is emerging on the performance of the plant metabolic network and the contributions of specific pathways.     

Chromatin regulation of plant development

Chromatin remodeling factors are being identified as genetic modifiers of developmental mutations in plants. These mutations result in lethality in metazoans, whereas in plants, they are viable and affect a wide range of developmental and physiological processes. Recent studies have begun to define the many functions of chromatin remodeling factors in plants and have revealed apparent differences between these factors in the two kingdoms.     

Experimental and mathematical approaches to modeling plant metabolic networks

To support their sessile and autotrophic lifestyle higher plants have evolved elaborate networks of metabolic pathways. Dynamic changes in these metabolic networks are among the developmental forces underlying the functional differentiation of organs, tissues and specialized cell types. They are also important in the various interactions of a plant with its environment. Further complexity is added by the extensive compartmentation of the various interconnected metabolic pathways in plants. Thus, although being used widely for assessing the control of metabolic flux in microbes, mathematical modeling approaches that require steady-state approximations are of limited utility for understanding complex plant metabolic networks. However, considerable progress has been made when manageable metabolic subsystems were studied. In this article, we will explain in general terms and using simple examples the concepts underlying stoichiometric modeling (metabolic flux analysis and metabolic pathway analysis) and kinetic approaches to modeling (including metabolic control analysis as a special case). Selected studies demonstrating the prospects of these approaches, or combinations of them, for understanding the control of flux through particular plant pathways are discussed. We argue that iterative cycles of (dry) mathematical modeling and (wet) laboratory testing will become increasingly important for simulating the distribution of flux in plant metabolic networks and deriving rational experimental designs for metabolic engineering efforts.     

Fortune telling: metabolic markers of plant performance

Background

In the last decade, metabolomics has emerged as a powerful diagnostic and predictive tool in many branches of science. Researchers in microbes, animal, food, medical and plant science have generated a large number of targeted or non-targeted metabolic profiles by using a vast array of analytical methods (GC–MS, LC–MS, ¹H-NMR….). Comprehensive analysis of such profiles using adapted statistical methods and modeling has opened up the possibility of using single or combinations of metabolites as markers. Metabolic markers have been proposed as proxy, diagnostic or predictors of key traits in a range of model species and accurate predictions of disease outbreak frequency, developmental stages, food sensory evaluation and crop yield have been obtained.

Aim of review

(i) To provide a definition of plant performance and metabolic markers, (ii) to highlight recent key applications involving metabolic markers as tools for monitoring or predicting plant performance, and (iii) to propose a workable and cost-efficient pipeline to generate and use metabolic markers with a special focus on plant breeding.

Key message

Using examples in other models and domains, the review proposes that metabolic markers are tending to complement and possibly replace traditional molecular markers in plant science as efficient estimators of performance.

     

虫害诱导的植物挥发物代谢调控机制研究进展

长期受自然界的非生物/生物侵害,植物逐步形成了复杂的防御机制,为防御植食性昆虫的为害,植物释放虫害诱导产生的挥发性化合物(herbivore-induced plant volatiles,HIPVs)。HIPVs是植物-植食性昆虫-天敌三级营养关系之间协同进化的结果。HIPVs的化学组分因植物、植食性昆虫种类的不同而有差异。生态系统中,HIPVs可在植物与节肢动物、植物与微生物、虫害植物与邻近的健康植物、或同一植株的受害和未受害部位间起作用,介导防御性反应。HIPVs作为寄主定位信号,在吸引捕食性、寄生性天敌过程中起着重要作用。HIPVs还可以作为植物间信息交流的工具,启动植株的防御反应而增强抗虫性。不论从生态学还是经济学角度来看,HIPVs对于农林生态系中害虫综合治理策略的完善具有重要意义。前期的研究在虫害诱导植物防御的化学生态学方面奠定了良好基础,目前更多的研究转向阐述虫害诱导植物抗性的分子机制。为了深入了解HIPVs的代谢调控机制,主要从以下几个方面进行了综述。因为植食性昆虫取食造成的植物损伤是与昆虫口腔分泌物共同作用的结果,所以首先阐述口腔分泌物在防御反应中的作用。挥发物诱导素volicitin和β-葡萄糖苷酶作为口腔分泌物的组分,是产生HIPVs的激发子,通过调节伤信号诱发HIPVs的释放。接着阐述了信号转导途径对HIPVs释放的调节作用,并讨论了不同信号途径之间的交互作用。就HIPVs的代谢过程而言,其过程受信号转导途径(包括茉莉酸、水杨酸、乙烯、过氧化氢信号途径)的调控,其中茉莉酸信号途径是诱发HIPVs释放的重要途径。基于前人的研究,综述了HIPVs的主要代谢过程及其过程中关键酶类的调控作用。文中的HIPVs主要包括萜烯类化合物、绿叶挥发物和莽草酸途径产生的芳香族化合物,如水杨酸甲酯和吲哚等。作为化学信号分子,这些化合物中的一部分还能激活邻近植物防御基因的表达。萜烯合酶是各种萜烯类化合物合成的关键酶类,脂氧合酶、过氧化氢裂解酶也是绿叶挥发物代谢途径中的研究热点,而苯丙氨酸裂解酶和水杨酸羧基甲基转移酶分别是合成水杨酸及其衍生物水杨酸甲酯的关键酶类。这些酶类的基因在转录水平上调控着HIPVs代谢途径。最后展望了HIPVs的研究前景。     

Gibberellin biosynthesis and the regulation of plant development

Gibberellins (GAs) form a large family of plant growth substances with distinct functions during the whole life cycle of higher plants. The rate of GA biosynthesis and catabolism determines how the GA hormone pool occurs in plants in a tissue and developmentally regulated manner. With the availability of genes coding for GA biosynthetic enzymes, our understanding has improved dramatically of how GA plant hormones regulate and integrate a wide range of growth and developmental processes. This review focuses on two plant systems, pumpkin and Arabidopsis, which have added significantly to our understanding of GA biosynthesis and its regulation. In addition, we present models for regulation of GA biosynthesis in transgenic plants, and discuss their suitability for altering plant growth and development.     

Hormonal regulation during plant fruit development

The modern concept of the hormonal regulation of fruit set, growth, maturation, and ripening is considered. Pollination and fertilization induce ovule activation by surmounting the blocking action of ethylene and ABA to be manifested in auxin accumulation. Active fruit growth by pericarp cell division and elongation is due to the syntheses of auxin in the developing seed and of gibberellins in the pericarp. In climacteric fleshy fruits, the maturation is controlled by ethylene via so-called System 1 combining the possibilities of autoinhibition and autocatalysis by ethylene of its own biosynthesis. Transition of tomato fruits from maturation to ripening is characterized by highly active synthesis of ethylene and its receptors due to the functioning of regulatory System 2 resulting in the up-regulation of much greater number of ethylene-inducible genes. In peach fruits, the hormonal regulation of ripening includes also an active auxin involvement in the ethylene biosynthesis, which is combined with the ethylene-induced expression of genes encoding both auxin biosynthesis and the response to auxin. Ethylene induces the expression of genes responsible for the fruit softening, its taste, color, and flavor. Nonclimacteric fleshy fruits produce very small amounts of ethylene; its evolution increases only by the very end of ripening and can be described by a reduced System 1. The ripening of nonclimacteric fruits only weakly depends on ethylene but is stimulated by abscisic acid.     

Hormone regulation of development in plant cells

Summary Hormonal stimulation of dedifferentiation and redifferentiation can be studied in explanted, cultured plant tissues. Some of the questions about development which one would like to answer with such a system revolve around the role of quiescence in the stabilization of the differentiated state, the role of replication in the stimulation of redifferentiation and the means by which cells are brought out of the quiescent state. Such a system also offers the potential for revealing the level(s) at which plant hormones operate in the stimulation of replication and differentiation since the responses to hormones can be achieved in vitro. The pea-root cortical parenchyma system has been utilized as a model system in the study of cytokinin plus auxin stimulation of redevelopment of mature, quiescent root cells. The first detected response of the root parenchyma to excision and culture with both of these hormones is an enhanced rate of RNA synthesis between 9 and 12 hr after the initiation of culture. DNA synthesis is stimulated 36 to 39 hr after RNA synthesis (after 48 hr in culture). During this 48-hr period various cytological changes have been observed which are compatible with renewed nucleic acid synthesis, but cytological changes have not been observed prior to the onset of hormone-stimulated RNA synthesis. The first mitoses and cytokineses occur after 60 and 72 hr, respectively. Terminally differentiated tracheary elements are first formed in these cultures after 120 to 168 hr when both the cytokinin and auxin are present at adequate levels. Studies employing inhibitors suggest that tracheary element differentiation is dependent upon the DNA replication that normally accompanies cell replication. Temperature probes of the period between the initiation of cultures and the appearance of the terminally differentiated tracheary elements have been initiated and, in conjunction with previous studies employing inhibitors and analogues, may allow one to distinguish between a variety of potential models of hormone-stimulated redifferentiation. Presented in the Opening Symposium on Nutritional Factors and Differentiation at the 28th Annual Meeting of the Tissue Culture Association, New Orleans, Louisiana, June 6–9, 1977. Supported in part by grants from the National Science Foundation (GB 36948) and the Public Health Service (RR 07092).