Making new molecules - evolution of pathways for novel metabolites in plants

Plants have adapted to their environments by diversifying in various ways. This diversification is reflected at the phytochemical level in their production of numerous specialized secondary metabolites that provide protection against biotic and abiotic stresses. Plant speciation is therefore intimately linked to metabolic diversification, yet we do not currently have a deep understanding of how new metabolic pathways evolve. Recent evidence indicates that genes for individual secondary metabolic pathways can be either distributed throughout the genome or clustered, but the relative frequencies of these two pathway organizations remain to be established. While it is possible that clustering is a feature of pathways that have evolved in recent evolutionary time, the answer to this and how dispersed and clustered pathways may be related remain to be addressed. Recent advances enabled by genomics and systems biology are beginning to yield the first insights into network evolution in plant metabolism. This review focuses on recent progress in understanding the evolution of clustered and dispersed pathways for new secondary metabolites in plants.     

Current understanding of the regulation of methionine biosynthesis in plants

Plants can provide most of the nutrients for the human diet. However, the major crops are often deficient in some of the nutrients. Thus, malnutrition, with respect to micronutrients such as vitamin A, iron, and zinc, but also macronutrients such as the essential amino acids lysine and methionine, affects more than 40% of the world's population. Recent advances in molecular biology, but also the grasp of biochemical pathways, metabolic fluxes, and networks can now be exploited to produce crops enhanced in key nutrients to increase the nutritional value of plant-derived foods and feeds. Some of the predictions appear to be accurate, while others not, reflecting the fact that plant metabolism is more complex than presently understood. A good example for a complex regulation is the methionine biosynthetic pathway in plants. The nutritional importance of Met and cysteine has motivated extensive studies of their roles in plant molecular physiology, especially regarding to their transport, synthesis, and accumulation in plants. Recent studies have demonstrated that Met metabolism is regulated differently in various plant species.     

Comparative biology comes into bloom: genomic and genetic comparison of flowering pathways in rice and Arabidopsis

Huge advances in plant biology are possible now that we have the complete genome sequences of several flowering plants. Now, genomes can be comprehensively compared and map-based cloning can be performed more easily. Association study is emerging as a powerful method for the functional identification of genes and molecular genetics has begun to reveal the basis of plant diversity. Taking the flowering pathways as an example, we discuss the potential of several approaches to comparative biology.     

The Roles of Phytohormones in Development as Studied in Transgenic Plants

The study of transgenic plants has greatly advanced our understanding of the control of development and metabolism. The ability to isolate and modify genes greatly extends the range of what is technically feasible. In the area of hormone biology, transgenic plants have helped to elucidate the pathways of synthesis, the metabolic control points, and the biological functions of the various phytohormones. This review covers the available genes that modulate the metabolism and perception of the phytohormones. One of the most significant conclusions coming out of transgenic plant work is the complex interaction among the different classes of phytohormones. For example, increasing the level of the auxin indole-3-acetic acid (IAA) in a plant has the secondary effect of inducing ethylene biosynthesis. This complication can be circumvented by combining transgenic plants modulating multiple hormones or through the use of available mutants. In this manner, transgenic plants have been utilized to unambiguously define the roles of auxin, cytokinin, and ethylene in the control of apical dominance. The power of transgenic plants as tools in hormone biology is perhaps best illustrated by work on ethylene. In this case, the modular characterization of genes led to elucidation of the biosynthetic pathway. Availability of the biosynthetic genes has permitted detailed analysis of the regulation of synthesis, definition of the role of ethylene in the control of several developmental processes, and the application of that knowledge for agricultural improvement.     

Thiamine in plants: Aspects of its metabolism and functions

Thiamine diphosphate (vitamin B₁) plays a fundamental role as an enzymatic cofactor in universal metabolic pathways including glycolysis, the pentose phosphate pathway, and the tricarboxylic acid cycle. In addition, thiamine diphosphate has recently been shown to have functions other than as a cofactor in response to abiotic and biotic stress in plants. Recently, several steps of the plant thiamine biosynthetic pathway have been characterized, and a mechanism of feedback regulation of thiamine biosynthesis via riboswitch has been unraveled. This review focuses on these most recent advances made in our understanding of thiamine metabolism and functions in plants. Phenotypes of plant mutants affected in thiamine biosynthesis are described, and genomics, proteomics, and metabolomics data that have increased further our knowledge of plant thiamine metabolic pathways and functions are summarized. Aspects of thiamine metabolism such as catabolism, salvage, and transport in plants are discussed.     

植物次生代谢基因工程

植物次生代谢基因工程,是利用基因工程技术对植物次生代谢途径的遗传特性进行改造,进而改变植物次生代谢产物。植物次生代谢基因工程的出现是人类对次生代谢途径的深入了解和分子生物学向纵深发展的结果,同时它又促进了次生代谢分子生物学的发展。调控因子的应用和多基因的协同转化为植物次生代谢基因工程拓宽了思路。从次生代谢图谱、植物基因工程策略和植物转基因方法等方面对植物次生代谢的基因工程研究进展做一简要概述。     

植物苯丙烷代谢途径

众所周知,固着生长的植物经常受到环境中各种生物和非生物胁迫的威胁。所以在漫长的进化过程中,植物必须将多样的环境信号整合到其发育过程中,以实现适应性形态的发生和代谢途径的精确调控,最终使植物完成整个生长周期。研究显示,苯丙烷代谢作为植物重要的次级代谢途径之一,其代谢产物,例如木质素、孢粉素、花青素和有机酸等,在调控植物适应性生长的过程中发挥着重要功能。特别是在药用植物中,苯丙烷代谢还与众多药用活性成分的合成息息相关,几乎所有包含苯丙烷骨架的天然药效成分均由苯丙烷代谢途径直接或间接合成,例如黄酮类、萜类和酚类等。此外,经苯丙烷代谢途径产生的一些次级代谢产物还能由植物根系外泌到周际土壤中,通过改变根系微生物的菌群生态,而影响植物生长和抵抗生物或非生物胁迫的能力。同时,苯丙烷代谢介导的这种植物-微生物互作也与药用植物的道地品质密不可分。本文综述了近年来植物苯丙烷代谢途径的最新研究进展,重点对该代谢途径中代谢产物的生理功能及表达调控机制进行了介绍,以期更深入地理解药用植物苯丙烷代谢与药材性状之间的潜在关系,旨在指导优良中草药的遗传育种,以进一步促进我国中医药事业的蓬勃发展。     

Rewiring and regulation of cross-compartmentalized metabolism in protists

Plastid acquisition, endosymbiotic associations, lateral gene transfer, organelle degeneracy or even organelle loss influence metabolic capabilities in many different protists. Thus, metabolic diversity is sculpted through the gain of new metabolic functions and moderation or loss of pathways that are often essential in the majority of eukaryotes. What is perhaps less apparent to the casual observer is that the sub-compartmentalization of ubiquitous pathways has been repeatedly remodelled during eukaryotic evolution, and the textbook pictures of intermediary metabolism established for animals, yeast and plants are not conserved in many protists. Moreover, metabolic remodelling can strongly influence the regulatory mechanisms that control carbon flux through the major metabolic pathways. Here, we provide an overview of how core metabolism has been reorganized in various unicellular eukaryotes, focusing in particular on one near universal catabolic pathway (glycolysis) and one ancient anabolic pathway (isoprenoid biosynthesis). For the example of isoprenoid biosynthesis, the compartmentalization of this process in protists often appears to have been influenced by plastid acquisition and loss, whereas for glycolysis several unexpected modes of compartmentalization have emerged. Significantly, the example of trypanosomatid glycolysis illustrates nicely how mathematical modelling and systems biology can be used to uncover or understand novel modes of pathway regulation.     

植物次生代谢基因工程研究进展

随着对植物代谢网络日渐全面的认识,应用基因工程技术对植物次生代谢途径进行遗传改良已取得了可喜的进展.对次生代谢途径进行基因修饰的策略包括:导入单个、多个靶基因或一个完整的代谢途径,使宿主植物合成新的目标物质;通过反义RNA和RNA干涉等技术降低靶基因的表达水平,从而抑制竞争性代谢途径,改变代谢流和增加目标物质的含量;对控制多个生物合成基因的转录因子进行修饰,更有效地调控植物次生代谢以提高特定化合物的积累.作者结合对大豆种子异黄酮类代谢调控和基因工程改良的研究,着重介绍了花青素和黄酮类物质、生物碱、萜类化合物和安息香酸衍生物等次生代谢产物生物合成的基因工程研究进展.     

Production and engineering of terpenoids in plant cell culture

Terpenoids are a diverse class of natural products that have many functions in the plant kingdom and in human health and nutrition. Their chemical diversity has led to the discovery of over 40,000 different structures, with several classes serving as important pharmaceutical agents, including the anticancer agents paclitaxel (Taxol) and terpenoid-derived indole alkaloids. Many terpenoid compounds are found in low yield from natural sources, so plant cell cultures have been investigated as an alternate production strategy. Metabolic engineering of whole plants and plant cell cultures is an effective tool to both increase terpenoid yield and alter terpenoid distribution for desired properties such as enhanced flavor, fragrance or color. Recent advances in defining terpenoid metabolic pathways, particularly in secondary metabolism, enhanced knowledge concerning regulation of terpenoid accumulation, and application of emerging plant systems biology approaches, have enabled metabolic engineering of terpenoid production. This paper reviews the current state of knowledge of terpenoid metabolism, with a special focus on production of important pharmaceutically active secondary metabolic terpenoids in plant cell cultures. Strategies for defining pathways and uncovering rate-influencing steps in global metabolism, and applying this information for successful terpenoid metabolic engineering, are emphasized.     

Les protéines phosphatases et protéines kinases des plantes supérieures

The recent gain in knowledge concerning enzymes involved in signal transduction pathways is a direct consequence of the considerable advances made in molecular biology. Protein kinases and protein phosphatases, the two major enzymes implicated in post-translational modifications, have been studied in particular. The number of characterized plant genes and/or cDNAs encoding these enzymes is increasing everyday. Since 1991, 26 genes and cDNAs coding for plant protein phosphatases have been isolated and characterized. The huge number of protein kinases (estimated at several thousands) makes it impossible to give an exhaustive list of the genes already identified, but a classification of these enzymes, based on phylogenetic criteria, allows us to appreciate the range of functions this protein family may play in plants.     

Plant Metabolic Modeling: Achieving New Insight into Metabolism and Metabolic Engineering

Models are used to represent aspects of the real world for specific purposes, and mathematical models have opened up new approaches in studying the behavior and complexity of biological systems. However, modeling is often time-consuming and requires significant computational resources for data development, data analysis, and simulation. Computational modeling has been successfully applied as an aid for metabolic engineering in microorganisms. But such model-based approaches have only recently been extended to plant metabolic engineering, mainly due to greater pathway complexity in plants and their highly compartmentalized cellular structure. Recent progress in plant systems biology and bioinformatics has begun to disentangle this complexity and facilitate the creation of efficient plant metabolic models. This review highlights several aspects of plant metabolic modeling in the context of understanding, predicting and modifying complex plant metabolism. We discuss opportunities for engineering photosynthetic carbon metabolism, sucrose synthesis, and the tricarboxylic acid cycle in leaves and oil synthesis in seeds and the application of metabolic modeling to the study of plant acclimation to the environment. The aim of the review is to offer a current perspective for plant biologists without requiring specialized knowledge of bioinformatics or systems biology.     

Flavonoids as developmental regulators

Flavonoids, usually regarded as dispensable phytochemicals derived from plant secondary metabolism, play important roles in the biology of plants by affecting several developmental processes. Bioactive flavonoids also signal to microbes, serve as allelochemicals and are important nutraceuticals in the animal diet. Despite the significant progress made in identifying flavonoid pathway genes and regulators, little is currently known about the protein targets of flavonoids in plant or animal cells. Recently, there have been advances in our understanding of the roles that flavonoids play in developmental processes of plants. The multiple cellular roles of flavonoids can reflect their chemical diversity, or might suggest the existence of cellular targets shared between many of these seemingly disparate processes.     

Metabolic cartography: experimental quantification of metabolic fluxes from isotopic labelling studies

For the past decade, flux maps have provided researchers with an in-depth perspective on plant metabolism. As a rapidly developing field, significant headway has been made recently in computation, experimentation, and overall understanding of metabolic flux analysis. These advances are particularly applicable to the study of plant metabolism. New dynamic computational methods such as non-stationary metabolic flux analysis are finding their place in the toolbox of metabolic engineering, allowing more organisms to be studied and decreasing the time necessary for experimentation, thereby opening new avenues by which to explore the vast diversity of plant metabolism. Also, improved methods of metabolite detection and measurement have been developed, enabling increasingly greater resolution of flux measurements and the analysis of a greater number of the multitude of plant metabolic pathways. Methods to deconvolute organelle-specific metabolism are employed with increasing effectiveness, elucidating the compartmental specificity inherent in plant metabolism. Advances in metabolite measurements have also enabled new types of experiments, such as the calculation of metabolic fluxes based on (13)CO(2) dynamic labelling data, and will continue to direct plant metabolic engineering. Newly calculated metabolic flux maps reveal surprising and useful information about plant metabolism, guiding future genetic engineering of crops to higher yields. Due to the significant level of complexity in plants, these methods in combination with other systems biology measurements are necessary to guide plant metabolic engineering in the future.     

异戊二烯类植物激素赤霉素和脱落酸的代谢调控

赤霉素和脱落酸在植物生理过程中具有重要的调控作用,其生物合成途径迄今已基本阐明。赤霉素与类胡萝卜素的生物合成途径具有共同前体牻牛儿基牻牛儿基二磷酸,而脱落酸则直接来自于类胡萝卜素。参与这两种植物激素和类胡萝卜素代谢过程的大多数酶基因已经从不同植物中获得克隆;各种调控方式也随着分子生物学的研究工作而得到鉴定。本文就近年来对赤霉素和脱落酸等代谢调控机制及其与植物类胡萝卜素代谢之间关系的研究工作做简要回顾。     

Integrated view of plant metabolic defense with particular focus on chewing herbivores

Success of plants largely depends on their ability to defend against herbivores. Since emergence of the first voracious consumers, plants maintained adapting their structures and chemistry to escape from extinction. The constant pressure was further accelerated by adaptation of herbivores to plant defenses, which all together sparked the rise of a chemical empire comprised of thousands of specialized metabolites currently found in plants. Metabolic diversity in the plant kingdom is truly amazing, and although many plant metabolites have already been identified, a large number of potentially useful chemicals remain unexplored in plant bio-resources. Similarly, biosynthetic routes for plant metabolites involve many enzymes, some of which still wait for identification and biochemical characterization. Moreover, regulatory mechanisms that control gene expression and enzyme activities in specialized metabolism of plants are scarcely known. Finally, understanding of how plant defense chemicals exert their toxicity and/or repellency against herbivores remains limited to typical examples, such as proteinase inhibitors, cyanogenic compounds and nicotine. In this review, we attempt summarizing the current status quo in metabolic defense of plants that is predominantly based on the survey of ubiquitous examples of plant interactions with chewing herbivores.