Plant Systems Biology Research Articles

AtPID: Arabidopsis thaliana protein interactome database--an integrative platform for plant systems biology.

Arabidopsis thaliana Protein Interactome Database (AtPID) is an object database that integrates data from several bioinformatics prediction methods and manually collected information from the literature. It contains data relevant to protein–protein interaction, protein subcellular location, ortholog maps, domain attributes and gene regulation. The predicted protein interaction data were obtained from ortholog interactome, microarray profiles, GO annotation, and conserved domain and genome contexts. This database holds 28 062 protein–protein interaction pairs with 23 396 pairs generated from prediction methods. Among the rest 4666 pairs, 3866 pairs of them involving 1875 proteins were manually curated from the literature and 800 pairs were from enzyme complexes in KEGG. In addition, subcellular location information of 5562 proteins is available. AtPID was built via an intuitive query interface that provides easy access to the important features of proteins. Through the incorporation of both experimental and computational methods, AtPID is a rich source of information for system-level understanding of gene function and biological processes in A. thaliana. Public access to the AtPID database is available at http://atpid.biosino.org/.

Responses of higher plants to abiotic stresses and agricultural sustainable development

Higher plants play the most important role in keeping a stable environment on the earth, which regulates global circumstances in many ways at different levels (molecular, individual, community, and so on), but the nature of the mechanism is the gene expression and control temporally and spatially at the molecular level. In a persistently changing environment, there are many adverse stress conditions such as cold, drought, salinity and UV-B (280–320 mm), which consistently influence plant growth and crop production by causing significant losses in agriculture. Agricultural sustainable development is the most important part of global sustainable development. Unlike animals, higher plants, which are sessile, cannot escape from the surroundings, and adapt themselves to the changing environments by a series of molecular responses aimed to cope with these challenges. The physiological basis for these molecular responses is the integration of many transduced events into a comprehensive network of signalling pathways. Plant hormones occupy a central place in this transduction network, frequently acting in conjunction with other signals, to co-ordinately regulate cellular processes such as cell division, elongation and differentiation, which are the fundamental basis for higher plant development and related character expressions. In a word, it is at the molecular level-gene expression and control in time and space that we can bring out the mystery of living organisms and explore the nature of environmental changes. Ecological science is a fused and ramified field gathering natural sciences and social sciences, where the frontier is molecular ecology. It is obvious that molecular biology is the purposeful basis for improving diverse types of eco-environment. The common stress factors mentioned above are those important ecological factors influencing the environment, which are general environmental stimuli and cues to higher plants. Molecular responses to such common environmental stresses have been studied intensively over the last few years, in which there is an intricate network of signalling pathways controlling perception of these environmental stress signals, the generation of second messengers and signal transduction. Therefore, deeper understanding of these molecular processes is even vital to agricultural production in the semiarid area and arid areas of the world. In this review, updated progresses were introduced in terms of functional analysis of signalling components and problems with respect to bio-watersaving, agricultural eco-environment, and a possible general network of stress-responsive gene expression control model were summarized, with an emphasis on the integration between stress signal transduction pathways and agricultural eco-environment. The viewpoint is that the molecular information from higher plant cells, tissues, and organs should be efficiently popularized to levels of individuals, community, and ecosystem, which can play a greater role, and which is also one of the greatest challenges for plant systems biology during the 21st century.

ProMEX: a mass spectral reference database for proteins and protein phosphorylation sites.

BackgroundIn the last decade, techniques were established for the large scale genome-wide analysis of proteins, RNA, and metabolites, and database solutions have been developed to manage the generated data sets. The Golm Metabolome Database for metabolite data (GMD) represents one such effort to make these data broadly available and to interconnect the different molecular levels of a biological system [1]. As data interpretation in the light of already existing data becomes increasingly important, these initiatives are an essential part of current and future systems biology.ResultsA mass spectral library consisting of experimentally derived tryptic peptide product ion spectra was generated based on liquid chromatography coupled to ion trap mass spectrometry (LC-IT-MS). Protein samples derived from Arabidopsis thaliana, Chlamydomonas reinhardii, Medicago truncatula, and Sinorhizobium meliloti were analysed. With currently 4,557 manually validated spectra associated with 4,226 unique peptides from 1,367 proteins, the database serves as a continuously growing reference data set and can be used for protein identification and quantification in uncharacterized biological samples. For peptide identification, several algorithms were implemented based on a recently published study for peptide mass fingerprinting [2] and tested for false positive and negative rates. An algorithm which considers intensity distribution for match correlation scores was found to yield best results. For proof of concept, an LC-IT-MS analysis of a tryptic leaf protein digest was converted to mzData format and searched against the mass spectral library. The utility of the mass spectral library was also tested for the identification of phosphorylated tryptic peptides. We included in vivo phosphorylation sites of Arabidopsis thaliana proteins and the identification performance was found to be improved compared to genome-based search algorithms. Protein identification by ProMEX is linked to other levels of biological organization such as metabolite, pathway, and transcript data. The database is further connected to annotation and classification services via BioMoby.ConclusionThe ProMEX protein/peptide database represents a mass spectral reference library with the capability of matching unknown samples for protein identification. The database allows text searches based on metadata such as experimental information of the samples, mass spectrometric instrument parameters or unique protein identifier like AGI codes. ProMEX integrates proteomics data with other levels of molecular organization including metabolite, pathway, and transcript information and may thus become a useful resource for plant systems biology studies. The ProMEX mass spectral library is available at .

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.

Top-down Phenomics of Arabidopsis thaliana: METABOLIC PROFILING BY ONE- AND TWO-DIMENSIONAL NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY AND TRANSCRIPTOME ANALYSIS OF ALBINO MUTANTS

Elucidating the function of each gene in a genome is important for understanding the whole organism. We previously constructed 4000 disruptant mutants of Arabidopsis by insertion of Ds transposons. Here, we describe a top-down phenomics approach based on metabolic profiling that uses one-dimensional 1H and two-dimensional 1H,13C NMR analyses and transcriptome analysis of albino mutant lines of Arabidopsis. One-dimensional 1H NMR metabolic fingerprinting revealed global metabolic changes in the albino mutants, notably a decrease in aromatic metabolites and changes in aliphatic metabolites. NMR measurements of plants fed with 13C6-glucose showed that the albino lines had dramatically different 13C-labeling patterns and increased levels of several amino acids, especially Asn and Gln. Microarray analysis of one of the albino lines revealed a unique expression profile and showed that changes in the expression of genes encoding metabolic enzymes did not correspond with changes in the levels of metabolites. Collectively, these results suggest that albino mutants lose the normal carbon/nitrogen balance, presumably mainly through lack of photosynthesis. Our study offers an idea of how much the metabolite network is affected by chloroplast function in plants and shows the effectiveness of NMR-based metabolic analysis for metabolite profiling. On the basis of these findings, we propose that future investigations of plant systems biology combine transcriptomic, metabolomic, and phenomic analyses of gene disruptant lines.

Flux quantification in central carbon metabolism of Catharanthus roseus hairy roots by 13C labeling and comprehensive bondomer balancing

Methods for accurate and efficient quantification of metabolic fluxes are desirable in plant metabolic engineering and systems biology. Toward this objective, we introduce the application of “bondomers”, a computationally efficient and intuitively appealing alternative to the commonly used isotopomer concept, to flux evaluation in plants, by using Catharanthus roseus hairy roots as a model system. We cultured the hairy roots on (5% w/w U– 13C, 95% w/w naturally abundant) sucrose, and acquired two-dimensional [ 13C, 1H] and [ 1H, 1H] NMR spectra of hydrolyzed aqueous extract from the hairy roots. Analysis of these spectra yielded a data set of 116 bondomers of β-glucans and proteinogenic amino acids from the hairy roots. Fluxes were evaluated from the bondomer data by using comprehensive bondomer balancing. We identified most fluxes in a three-compartmental model of central carbon metabolism with good precision. We observed parallel pentose phosphate pathways in the cytosol and the plastid with significantly different fluxes. The anaplerotic fluxes between phosphoenolpyruvate and oxaloacetate in the cytosol and between malate and pyruvate in the mitochondrion were relatively high (60.1 ± 2.5 mol per 100 mol sucrose uptake, or 22.5 ± 0.5 mol per 100 mol mitochondrial pyruvate dehydrogenase flux). The development of a comprehensive flux analysis tool for this plant hairy root system is expected to be valuable in assessing the metabolic impact of genetic or environmental changes, and this methodology can be extended to other plant systems.

From genes to patterns: Auxin distribution and auxin-dependent gene regulation in plant pattern formation

It has long been recognized that the plant hormone auxin plays integral roles in a variety of plant processes. More recently, it has become clear that these processes include some of the most basic pattern formation mechanisms needed to establish a functional plant body. Considerable insight into how this regulation plays out at the molecular level has been attained in recent years. Of special note are the complementary actions of the auxin efflux carrier proteins responsible for the formation of instructive auxin concentration gradients and the transcription factor complexes required for the appropriate interpretation of such instructions. The numerous players involved and the complexity of their regulation provide insight into how a single plant hormone can operate in such a multifunctional fashion. Many new features of auxin action can now be quantified and visualized, and three-dimensional models of auxin patterning can be tested and mathematically modeled. With these new advances, the developmental biology of auxin-mediated patterning has turned into a subject of plant systems biology research.

Recent applications of NMR spectroscopy in plant metabolomics

Recent research has established NMR as a key method for high-throughput comparative analysis of plant extracts. We discuss recent examples of the use of NMR to provide metabolomic data for various applications in plant science and look forward to the key role that NMR will play in data provision for plant systems biology.

Towards plant systems biology – novel mathematical approaches to enable quantitative analysis of growth processes

Towards plant systems biology – novel mathematical approaches to enable quantitative analysis of growth processes

INTEGRATIVE PLANT BIOLOGY: Role of Phloem Long-Distance Macromolecular Trafficking

Recent studies have revealed the operation of a long-distance communication network operating within the vascular system of higher plants. The evolutionary development of this network reflects the need to communicate environmental inputs, sensed by mature organs, to meristematic regions of the plant. One consequence of such a long-distance signaling system is that newly forming organs can develop properties optimized for the environment into which they will emerge, mature, and function. The phloem translocation stream of the angiosperms contains, in addition to photosynthate and other small molecules, a variety of macromolecules, including mRNA, small RNA, and proteins. This review highlights recent progress in the characterization of phloem-mediated transport of macromolecules as components of an integrated long-distance signaling network. Attention is focused on the role played by these proteins and RNA species in coordination of developmental programs and the plant's response to both environmental cues and pathogen challenge. Finally, the importance of developing phloem transcriptome and proteomic databases is discussed within the context of advances in plant systems biology.

DRASTIC--INSIGHTS: querying information in a plant gene expression database

DRASTIC––Database Resource for the Analysis of Signal Transduction In Cells () has been created as a first step towards a data-based approach for constructing signal transduction pathways. DRASTIC is a relational database of plant expressed sequence tags and genes up- or down-regulated in response to various pathogens, chemical exposure or other treatments such as drought, salt and low temperature. More than 17700 records have been obtained from 306 treatments affecting 73 plant species from 512 peer-reviewed publications with most emphasis being placed on data from Arabidopsis thaliana. DRASTIC has been developed by the Scottish Crop Research Institute and the University of Abertay Dundee and allows rapid identification of plant genes that are up- or down-regulated by multiple treatments and those that are regulated by a very limited (or perhaps a single) treatment. The INSIGHTS (INference of cell SIGnaling HypoTheseS) suite of web-based tools allows intelligent data mining and extraction of information from the DRASTIC database. Potential response pathways can be visualized and comparisons made between gene expression patterns in response to various treatments. The knowledge gained informs plant signalling pathways and systems biology investigations.

The Arabidopsis genome: A foundation for plant research

The sequence of the first plant genome was completed and published at the end of 2000. This spawned a series of large-scale projects aimed at discovering the functions of the 25,000+ genes identified in Arabidopsis thaliana (Arabidopsis). This review summarizes progress made in the past five years and speculates about future developments in Arabidopsis research and its implications for crop science. The provision of large populations of gene disruption lines to the research community has greatly accelerated the impact of genomics on many areas of plant science. The tools and community organization required for plant integrative and systems biology approaches are now ready to accomplish the next big step in plant biology--the integration of knowledge and modeling of biological processes. In the future, plant science will continue to be enriched by the alignment of high-quality basic research (generally conducted in Arabidopsis), with strategic objectives in crop plants. The sequence and analysis of an increasing number of crop plant genomes enhance this alignment and provide new insights into genome evolution and crop plant domestication.

The role of mass spectrometry in plant systems biology

Large-scale analyses of proteins and metabolites are intimately bound to advancements in MS technologies. The aim of these non-targeted "omic" technologies is to extend our understanding beyond the analysis of only parts of the system. Here, metabolomics and proteomics emerged in parallel with the development of novel mass analyzers and hyphenated techniques such as gas chromatography coupled to time-of-flight mass spectrometry (GC-TOF-MS) and multidimensional liquid chromatography coupled to mass spectrometry (LC-MS). The analysis of (i) proteins (ii) phosphoproteins, and (iii) metabolites is discussed in the context of plant physiology and environment and with a focus on novel method developments. Recently published studies measuring dynamic (quantitative) behavior at these levels are summarized; for these works, the completely sequenced plants Arabidopsis thaliana and Oryza sativa (rice) have been the primary models of choice. Particular emphasis is given to key physiological processes such as metabolism, development, stress, and defense. Moreover, attempts to combine spatial, tissue-specific resolution with systematic profiling are described. Finally, we summarize the initial steps to characterize the molecular plant phenotype as a corollary of environment and genotype.

Plant systems biology: linking theory and experiment

Plant systems biology: linking theory and experiment

On systems thinking, systems biology, and the in silico plant.

The recent summary report of a Department of Energy Workshop on Plant Systems Biology (P.V. Minorsky [2003] Plant Physiol 132: 404-409) offered a welcomed advocacy for systems analysis as essential in understanding plant development, growth, and production. The goal of the Workshop was to consider methods for relating the results of molecular research to real-world challenges in plant production for increased food supplies, alternative energy sources, and environmental improvement. The rather surprising feature of this report, however, was that the Workshop largely overlooked the rich history of plant systems analysis extending over nearly 40 years (Sinclair and Seligman, 1996) that has considered exactly those challenges targeted by the Workshop. Past systems research has explored and incorporated biochemical and physiological knowledge into plant simulation models from a number of perspectives. The research has resulted in considerable understanding and insight about how to simulate plant systems and the relative contribution of various factors in influencing plant production. These past activities have contributed directly to research focused on solving the problems of increasing biomass production and crop yields. These modeling approaches are also now providing an avenue to enhance integration of molecular genetic technologies in plant improvement (Hammer et al., 2002).

Plant Systems Biology

This Arabidopsis special issue devoted to Plant Systems Biology goes to press on the heels of the 50th anniversary of the discovery of the structure of DNA. With the more recent advent of genome scale data, we have gone from studying one gene—one protein at a time—to the whole genome. In the new

GE specialty materials completes Osmonics deal

Traditional modeling methods using rate equations and enzyme kinetics aloneare insufficient for large-scale plant modeling. As the development of methods to address the challenges posed by plant systems biology is a priority, plant systems biology should take advantage of current modeling strategies and advances in system-wide analysis that have been developed in efforts to achieve both unicellular and multi-cellular modeling.There are currently two large-scale modeling projects undertaken by E-Cell:e2coli, which aims to simulate the E. coli bacterium, and e-Rice, which aims at simulating the rice plant. e-Rice is one of the first attempts to simulate a whole plant organism. Our preliminary goal is to create a generic model for the basic metabolism in a plant cell that can then be adapted to cells residing at different sites in a rice plant. The current version of the basic model consists of reactions that take place in the chloroplast, mitochondrion, peroxisome, and cytosol.The reconstruction of even a prokaryotic cell poses many challenges.3, 20, 21With plants, a huge amount of data and many data types are involved, complicating the process even further.22–24 Even in the same genome, these data vary depending on the type of organelles, cells, tissues, and organs involving multiple development phases. However, by obtaining cell-wide data at two different levels—the genome for global properties and the metabolome for expressed physical properties, a basic dataset for cell simulation can be prepared for computer simulations. Our endeavor to simulate a whole plant is still in its initial stages where we are developing the tools and algorithms necessary for integrating vast amounts of available data and information. The tools and algorithms being developed are indispensable for reliable and comprehensive large-scale simulations, and can be adapted to various organisms including plants and mammals.In summary, our integrative approach and methods addresses large-scale modeling that is being developed at the Institute for Advanced Biosciences. Our approach for constructing the cell model consists of using 1) the Genome to E-Cell System (GEM System) for modeling pathways based on genomic information, 2) rice metabolome research using capillary electrophoresis mass spectrometry (CE-MS), 3) Atomic Reconstruction of Metabolism (ARM), and 4) the hybrid static/dynamic algorithm for integrating static models based on pathway stoichiometry and dynamic models using kinetics. These applications provide a systematic method for acquiring and integrating various data types for whole cell modeling using the E-Cell simulation environment.