The outer membrane Omp85-like protein P39 influences metabolic homeostasis in mature Arabidopsis thaliana.

The Omp85 proteins form a large membrane protein family in bacteria and eukaryotes. Omp85 proteins are composed of a C-terminal ß-barrel-shaped membrane domain and one or more N-terminal polypeptide transport-associated (POTRA) domains. However, Arabidopsis thaliana contains two genes coding for Omp85 proteins without a POTRA domain. One gene is designated P39, according to the molecular weight of the encoded protein. The protein is targeted to plastids and it was established that p39 has electrophysiological properties similar to other Omp85 family members, particularly to that designated as Toc75V/Oep80. We analysed expression of the gene and characterised two T-DNA insertion mutants, focusing on alterations in photosynthetic activity, plastid ultrastructure, global expression profile and metabolome. We observed pronounced expression of P39, especially in veins. Mutants of P39 show growth aberrations, reduced photosynthetic activity and changes in plastid ultrastructure, particularly in the leaf tip. Further, they display global alteration of gene expression and metabolite content in leaves of mature plants. We conclude that the function of the plastid-localised and vein-specific Omp85 family protein p39 is important, but not essential, for maintenance of metabolic homeostasis of full-grown A. thaliana plants. Further, the function of p39 in veins influences the functionality of other plant tissues. The link connecting p39 function with metabolic regulation in mature A. thaliana is discussed.

Reduction techniques for network validation in systems biology.

The rapidly increasing amount of experimental biological data enables the development of large and complex, often genome-scale models of molecular systems. The simulation and analysis of these computer models of metabolism, signal transduction, and gene regulation are standard applications in systems biology, but size and complexity of the networks limit the feasibility of many methods. Reduction of networks provides a hierarchical view of complex networks and gives insight knowledge into their coarse-grained structural properties. Although network reduction has been extensively studied in computer science, adaptation and exploration of these concepts are still lacking for the analysis of biochemical reaction systems. Using the Petri net formalism, we describe two local network structures, common transition pairs and minimal transition invariants. We apply these two structural elements for network reduction. The reduction preserves the CTI-property (covered by transition invariants), which is an important feature for completeness of biological models. We demonstrate this concept for a selection of metabolic networks including a benchmark network of Saccharomyces cerevisiae whose straightforward treatment is not yet feasible even on modern supercomputers.

Transitions of gene expression induced by short-term blue light.

Blue light modulates many processes in plants and plant cells. It influences global and long-term responses, such as seedling development and phototropism, and induces short-term adaptations like stomatal opening and chloroplast movement. Three genes were identified as important for the latter process, namely PHOT1, PHOT2 and CHUP1. The former two phototropin blue light receptors act in perception of the blue light signal. The protein CHUP1 is localised to the outer envelope membrane of chloroplasts and is involved in chloroplast movement. To explore whether short-term reactions required for chloroplast movement are under transcriptional control, we analysed the transcriptome in wild-type Arabidopsis thaliana, phot1, phot2 and chup1 with different blue light treatments for 5 or 30 min. Blue light-induced changes in transcription depended on illumination time and intensity. Illumination with 100 µmol·m(-2) · s(-1) blue light induced down-regulation of several genes and might point to cascades that could be important for sensing low levels of blue light. Analysis of the transcriptome of the mutants in response to the different light regimes suggests that the transcriptional response to blue light in the wild-type can be attributed to phot1 rather than phot2, suggesting that blue light-induced alteration of expression is a function of phot1. In contrast, the blue light response at the transcriptional level of chup1 plants was unique, and confirmed the higher light sensitivity of this mutant.