Systems Biology and Biochemistry of Intracellular Transport Processes in Plants

Research in the Weber-lab in the Institute for Plant Biochemistry at the Heinrich-Heine-University is focused on intra-cellular transport processes in plant cells.

Specifically, we are interested in how metabolites are transported across the membranes surrounding plastids, peroxisomes, and mitochondria. Understanding intracellular transport processes at the molecular level is important because many metabolic pathways in eukaryotic cells are compartmentalized. That is, individual steps of a particular pathway are distributed over several cellular compartments. As a consequence, precursors, metabolic intermediates, and end products need to be transported between cellular compartments.

Only a relatively minor share of intracellular transporters have been identified to date. We employ molecular, biochemical, physiological, and multiple 'omics technologies to gain understanding of intracellular metabolite transport in plant cells. This includes bioinformatical analysis of genome sequences, whole-genome shotgun sequencing and massively-parallel sequencing of cDNAs, proteomics of various membrane systems, and recombinant expression and reconstitution of membrane transporters.

OPTIMAS - Systems Biology of Maize Plants

OPTIMAS is a systems biology approach to address the question how to increase yield and plant biomass for food, feed and bioenergy purposes. Furthermore it will provide new useful insights in the distribution of plant resources between vegetative biomass and corn yield. The goal of OPTIMAS is the identification of metabolic processes and of unigenes, which correlate positively with a high biomass production and yield in the C4-plant maize. To reach this goal a correlation between physiological, biochemical and molecular data with agronomically relevant parameters has to be established in a reductionistic approach. Afterwards the predicted processes/unigenes will be examined in a largely diverse population of maize genotypes. Based on these results there will be molecular or biochemical markers available which can be used for precision breeding and for the creation of transgenic plants.
As a long-term perspective, systems biology tools will be provided to allow the breeding of an efficient and ressource-effective maize for farming under optimal and suboptimal environmental conditions.
In coordinated modules excessive amounts of molecular and physiological data will be collected and used for derivation of mathematical models of yield generation. Subsequently, these models will be tested in terms of their transferability to agriculturally relevant conditions.

OPTIMAS Website:

Photorespiration: Origin and Metabolic Integration in Interacting Compartments (PROMICS; DFG Research Unit FOR 1186)

Photorespiration represents one of the major highways of plant primary metabolism. By mass flow, excelled only by photosynthesis, it actually constitutes the second-most important process in the land-based biosphere. Related CO2 losses can be very high and are further elevated by warmer temperatures and drought, hence reducing the yields of important crops.
In light of the importance of this process for plant metabolism, adaptation and productivity, and significantly boosted by new tools, our network addresses major unresolved questions of the origins, metabolic integration, and cellular biology of photorespiratory metabolism. To this end, we have combined the multivalent expertise of ten research groups and associated partners as well as advanced technology platforms to pursue two new approaches. A Systems Biology approach will provide a comprehensive understanding of the dynamic interactions that take place between the components of photorespiration in order to appreciate the system as a whole and allow quantitative predictions. Complementary to this, an integrated Synthetic Biology approach promotes plant breeding for sustainable energy production.

PROMICS Website:

The Role of Bundle-Sheath Cells in C3 Plants (TP B9, SFB 590)

Similar to C4 plants, foliar veins of the C3 plant Arabidopsis thaliana are surrounded by a sheath of chloroplast containing cells. Very little is known about the function these bundle sheath cells. Mutant analysis showed that impaired chloroplast metabolism in the bundle sheath is associated with impaired mesophyll cell development. We hypothesize that bundle sheath cells generate a metabolic signal that is required for mesophyll cell differentiation. We will test this hypothesis by inactivation of metabolic pathways in the bundle sheath and analyzing the effects on mesophyll development.

SFB 590: undefined

Primary carbon partitioning in red algae and green plants

While the primary path of carbon is remarkably conserved in photosynthetic organisms, significant variation exists in the ways that carbon exits the Calvin cycle, especially when all photosynthetic organisms are considered, not just plants. Most terrestrial eukaryotic photosynthetic organisms belong to the Viridiplantae, which are characterized by (1) chloroplasts that are bounded by two envelope membranes, (2) use of chlorophyll a and b, (3) storage of starch inside the chloroplast stroma, and (4) synthesis of sucrose in the cytosol. In land plants and green algae, the export of the products of the Calvin-Benson cycle, triose phosphates GAP and DAP, from chloroplasts to the cytosol is mediated by a triose phosphate/phosphate antiporter [1]. Paralogous genes encoding this class of transporters can also be found in the genomes of the red algae and in members of the Chromalveolata [2]. However, only members of the Viridiplantae partition photoassimilates between a plastidic starch pool and cytosolic sucrose biosynthesis. We hypothesize that different strategies of carbon partitioning are reflected by the kinetic properties of plastidic phosphate translocators. This hypothesis will be tested by in vitro and in vivo experiments using phosphate translocators from red algae.

This project is funded by the Deutsche Forschungsgemeinschaft
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Understanding the role of the plastid outer envelope membrane for integrating plastids into cellular metabolic and regulatory networks

This collaborative research project aims at identifying the role of the chloroplast outer envelope membrane in integrating plastids with the metabolic and regulatory networks in plant cells. To this end, proteins localized in the outer plastid envelope membrane of pea will be identified by proteomics. Their localization in plant cells will be independently assessed in Arabidopsis by tagging with the green fluorescent protein and biarsenical-dye assays. Comprehensive massively-parallel transcriptome sequencing of pea will be conducted to generate a sequence database that is required for proteomics. Arabidopsis mutants deficient in genes encoding proteins of the plastid outer envelope membrane will be isolated and analyzed jointly with several thousand other mutants deficient in plastid-targeted and peroxisomal proteins, using a mutant and data analysis pipeline that was established at Michigan State University with funding from the NSF Arabidopsis 2010 program. Graduate students funded through this AFGN project will be trained in large-scale mutant and multivariate data analysis at Michigan State University. This project will provide the plant research community with information on intracellular protein localization and with a comprehensive database of the pea transcriptome. Using a consistent pipeline for the analysis of several thousand mutants will provide a unique opportunity to gain insight into the role of the plastid envelope membrane in integrating plastids with other cellular compartments and for generating testable hypotheses of protein function.

This project is funded by the Deutsche Forschungsgemeinschaft (WE 2231/4-1) in the framework of the undefinedArabidopsis Functional Genomics Network (AFGN)

Annotation and functional characterization of novel components of the plastid permeome through comparative analysis of C3 and C4 plants

All plastids trace their origin to a single ancient endosymbiotic event approximately 1.6 billion years ago in which a photoautotrophic cyanobacterium was engulfed by a primitive mitochondriate eukaryote – resulting in the first photosynthetic eukaryote. One of the crucial steps in forging endosymbiosis was connecting and coordinating the metabolisms of host and cyanobiont. Establishing this connection required the recruitment of metabolite transporters to the evolving plastid envelope membrane.

Despite their importance for both, understanding endosymbiosis and function of photosynthetic eukaryotic cells, relatively little is known about the molecular identities of the metabolite transporters that connect the plastid with the cytosol. We hypothesize that novel transporter functions can be identified by comparative transcriptomics and proteomics of C3 and C4 plants. Metabolite transporters required for maintaining the enormous metabolic fluxes caused by C4 photosynthesis should be much more abundant in C4 plants than in C3 plants. Since the biochemistry of C4 photosynthesis is well understood, testable hypotheses about transporter functions can be developed for those transporters that are highly expressed in leaves of C4 plants in comparison to C3 plants.
Based on previous comparative proteomics and transcriptomics results, we have identified a number of novel transporters in C4 plants that will be functionally characterized in the proposed work. The proposed work will thus extend the repertoire of functionally annotated chloroplast metabolite transporters and will thus contribute to a better understanding of the metabolic integration of plastids into plant cells.

This project is funded by the Deutsche Forschungsgemeinschaft in the framework of the undefinedTransregional Research Center TR1, project C12.

Functional and comparative analysis of the chloroplast proteomes of the red algae Galdieria sulphuraria and Cyanidioschyzon merolae

All plastids are believed to trace their origin to a single ancient endosymbiotic event approximately 1.6 billion years ago that involved the engulfment and maintenance of a photoautotrophic cyanobacterium by a primitive mitochondriate eukaryote – resulting in the first photosynthetic eukaryote, the protoalga. Within a period of 0.15 billion years, establishment of the plastid and divergence of the three major lineages of the Archaeplastida (i.e., the red algae [Rhodophyta], green algae/land plants [Viridiplantae], and glaucophytes [Glaucocystophyceae]), began. The endosymbiotic origin of plastids required many steps, including the evolution of a protein import apparatus and plastid targeting sequences, the transfer of genetic material from the endosymbiont to the nuclear genome of the host, and the establishment of genome – plastome intracellular communication and regulation.  In addition, connecting and coordinating the metabolisms of both partners taking part in endosymbiosis was certainly crucial for the success of the newly formed organism. Our current understanding of the proteome of modern plastids is predominantly influenced by studies of the chloroplasts of the Viridiplantae. Comparatively little is known about the plastids of the other lineages of the Archaeplastida. To achieve a comprehensive understanding of the endosymbiotic origin of chloroplasts, it is required to comparatively analyze the plastid proteomes of all three lines of the Archaeplastida. To this end, we will (i) catalogue the plastidial proteomes of the red algae C. merolae and G. sulphuraria and of the glaucocystophyceaen alga C. paradoxa and (ii) functionally characterize the interaction of plastidial and cytosolic nitrogen metabolism in these algae.

This project is funded by the Deutsche Forschungsgemeinschaft in the framework of the undefinedTransregional Research Center TR1, project B9.

Association of the C4 syndrome with adaptation to abiotic stress

In this project, we will test the hypothesis that the C4 syndrome is not only associated with higher water use efficiency and heat tolerance, but also with more general adaptations to abiotic stress, due to the selective pressure exerted by abiotic environments that favor the evolution of C4 metabolism. This hypothesis will be tested in close collaboration with Drs. Lercher and Westhoff at HHU and Drs. Farré, Buell, and Cui at MSU, using a systems biology approach that includes detailed physiological, biochemical, metabolic, genetic, and genomic characterization of a range of C3, C3-C4 intermediate, and C4 species of the genus Flaveria. Thus, this project is complementary to projects P2, P5, and P10 of IRTG 1525 by adding experimental data at the levels of the transcriptome, metabolome, and enzymatic activities. Jointly with the groups at FZJ (P7 and P8), we will also employ non-invasive phenotyping of various species of the genus Flaveria to provide a solid database for associating plant performance under various conditions with specific molecular traits that are part of the C4 syndrome. 

This project is part of the undefinedInternational Research Training Grant 1525, a joint project between Heinrich-Heine-University, the Julich Research Center, and the Michigan State University. Funded by undefinedDFG grant IRTG 1525.




Prof. Dr. Andreas Weber

Biochemie der Pflanzen Heinrich-Heine-Universität Universitätsstraße 1
Gebäude: 26.03
Etage/Raum: 01.30
40225 Düsseldorf
Tel.: +49 211 81-12347
Verantwortlich für den Inhalt: E-Mail sendenProf.Dr. Andreas Paul M. Weber