Regulation and function of tetrapyrrole biosynthesis in plants and algae

AbstractTetrapyrroles are macrocyclic molecules with various structural variants and multiple functions in Prokaryotes and Eukaryotes. Present knowledge about the metabolism of tetrapyrroles reflects the complex evolution of the pathway in different kingdoms of organisms, the complexity of structural and enzymatic variations of enzymatic steps, as well as a wide range of regulatory mechanisms, which ensure adequate synthesis of tetrapyrrole end-products at any time of development and environmental condition. This review intends to highlight new findings of research on tetrapyrrole biosynthesis in plants and algae. In the course of the heme and chlorophyll synthesis in these photosynthetic organisms, glutamate, one of the central and abundant metabolites, is converted into highly photoreactive tetrapyrrole intermediates. Thereby, several mechanisms of posttranslational control are thought to be essential for a tight regulation of each enzymatic step. Finally, we wish to discuss the potential role of tetrapyrroles in retrograde signaling and point out perspectives of the formation of macromolecular protein complexes in tetrapyrrole biosynthesis as an efficient mechanism to ensure a fine-tuned metabolic flow in the pathway. This article is part of a Special Issue entitled: Chloroplast Biogenesis

Impact of Porphyrin Binding to GENOMES UNCOUPLED 4 on Tetrapyrrole Biosynthesis in planta

Plant tetrapyrrole biosynthesis (TPS) provides the indispensable chlorophyll (Chl) and heme molecules in photosynthetic organisms. Post-translational mechanisms control the enzymes to ensure a balanced flow of intermediates in the pathway and synthesis of appropriate amounts of both endproducts. One of the critical regulators of TPS is GENOMES UNCOUPLED 4 (GUN4). GUN4 interacts with magnesium chelatase (MgCh), and its binding of the catalytic substrate and product of the MgCh reaction stimulates the insertion of Mg2+ into protoporphyrin IX. Despite numerous in vitro studies, knowledge about the in vivo function of the GUN4:porphyrin interaction for the whole TPS pathway, particularly in plants, is still limited. To address this, we focused on two highly conserved amino acids crucial for porphyrin-binding to GUN4 and analyzed GUN4-F191A, R211A, and R211E substitution mutants in vitro and in vivo. Our analysis confirmed the importance of these amino acids for porphyrin-binding and the stimulation of plant MgCh by GUN4 in vitro. Expression of porphyrin-binding deficient F191A, R211A, and R211E in the Arabidopsis gun4-2 knockout mutant background revealed that, unlike in cyanobacteria and green algae, GUN4:porphyrin interactions did not affect the stability of GUN4 or other Arabidopsis TPS pathway enzymes in vivo. In addition, although they shared diminished porphyrin-binding and MgCh activation in vitro, expression of the different GUN4 mutants in gun4-2 had divergent effects on the TPS and the accumulation of Chl and Chl-binding proteins. For instance, expression of R211E, but not R211A, induced a substantial decrease of ALA synthesis rate, lower TPS intermediate and Chl level, and strongly impaired accumulation of photosynthetic complexes compared to wild-type plants. Furthermore, the presence of R211E led to significant growth retardation and paler leaves compared to GUN4 knockdown mutants, indicating that the exchange of R211 to glutamate compromised TPS and Chl accumulation more substantially than the almost complete lack of GUN4. Extensive in vivo analysis of GUN4 point mutants suggested that F191 and R211 might also play a role beyond porphyrin-binding.Peer Reviewe

A Constraint Programming Approach for Non-Preemptive Evacuation Scheduling

Large-scale controlled evacuations require emergency services to select evacuation routes, decide departure times, and mobilize resources to issue orders, all under strict time constraints. Existing algorithms almost always allow for preemptive evacuation schedules, which are less desirable in practice. This paper proposes, for the first time, a constraint-based scheduling model that optimizes the evacuation flow rate (number of vehicles sent at regular time intervals) and evacuation phasing of widely populated areas, while ensuring a nonpreemptive evacuation for each residential zone. Two optimization objectives are considered: (1) to maximize the number of evacuees reaching safety and (2) to minimize the overall duration of the evacuation. Preliminary results on a set of real-world instances show that the approach can produce, within a few seconds, a non-preemptive evacuation schedule which is either optimal or at most 6% away of the optimal preemptive solution.Comment: Submitted to the 21st International Conference on Principles and Practice of Constraint Programming (CP 2015). 15 pages + 1 reference pag

Exact Gap Computation for Code Coverage Metrics in ISO-C

Test generation and test data selection are difficult tasks for model based testing. Tests for a program can be meld to a test suite. A lot of research is done to quantify the quality and improve a test suite. Code coverage metrics estimate the quality of a test suite. This quality is fine, if the code coverage value is high or 100%. Unfortunately it might be impossible to achieve 100% code coverage because of dead code for example. There is a gap between the feasible and theoretical maximal possible code coverage value. Our review of the research indicates, none of current research is concerned with exact gap computation. This paper presents a framework to compute such gaps exactly in an ISO-C compatible semantic and similar languages. We describe an efficient approximation of the gap in all the other cases. Thus, a tester can decide if more tests might be able or necessary to achieve better coverage.Comment: In Proceedings MBT 2012, arXiv:1202.582

Geometrical enhancement of the proximity effect in quantum wires with extended superconducting tunnel contacts

We study Andreev reflection in a ballistic one-dimensional channel coupled in parallel to a superconductor via a tunnel barrier of finite length $L$. The dependence of the low-energy Andreev reflection probability $R_A$ on $L$ reveals the existence of a characteristic length scale $\xi_N$ beyond which $R_A(L)$ is enhanced up to unity despite the low interfacial transparency. The Andreev reflection enhancement is due to the strong mixing of particle and hole states that builds up in contacts exceeding the coherence length $\xi_N$, leading to a small energy gap (minigap) in the density of states of the normal system. The role of the geometry of such hybrid contacts is discussed in the context of the experimental observation of zero-bias Andreev anomalies in the resistance of extended carbon nanotube/superconductor junctions in field effect transistor setups.Comment: 11 pages, 8 figures; minor revisions including added Ref. 7 and inset to Fig. 3b; version as accepted for publication to Phys. Rev.

The J_1-J_2 antiferromagnet with Dzyaloshinskii-Moriya interaction on the square lattice: An exact diagonalization study

We examine the influence of an anisotropic interaction term of Dzyaloshinskii-Moriya (DM) type on the groundstate ordering of the J_1-J_2 spin-1/2-Heisenberg antiferromagnet on the square lattice. For the DM term we consider several symmetries corresponding to different crystal structures. For the pure J_1-J_2 model there are strong indications for a quantum spin liquid in the region of 0.4 < J_2/J_1 < 0.65. We find that a DM interaction influences the breakdown of the conventional antiferromagnetic order by i) shifting the spin liquid region, ii) changing the isotropic character of the groundstate towards anisotropic correlations and iii) creating for certain symmetries a net ferromagnetic moment.Comment: 7 pages, RevTeX, 6 ps-figures, to appear in J. Phys.: Cond. Ma