Chlorophyll Catabolites – Chemical and Structural Footprints of a Fascinating Biological Phenomenon

Twenty years ago, the molecular basis for the seasonal disappearance of chlorophyll was still enigmatic. In the meantime, our knowledge on chlorophyll breakdown has grown considerably. As outlined here, it has been possible to decipher the basic transformations involved in natural chlorophyll breakdown by identification of chlorophyll catabolites in higher plants, and with the help of the synthesis of (putative) catabolic intermediates. In vascular plants, chlorophyll breakdown typically converts the green plant pigments efficiently into colorless and non-fluorescent tetrapyrroles. It involves colored intermediates only fleetingly and in an (elusive) enzyme-bound form. The non-fluorescent chlorophyll catabolites accumulate in the vacuoles of degreened leaves and are considered the products, primarily, of a detoxification process. However, they are effective antioxidants, and may thus also have physiologically beneficial chemical properties.(© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2009

Chlorophyll breakdown in oilseed rape

Chlorophyll catabolism accompanying leaf senescence is one of the most spectacular natural phenomena. Despite this fact, the metabolism of chlorophyll has been largely neglegted until recently. Oilseed rape has been used extensively as a model plant for the recent elucidating of structures of chlorophyll catabolites and for investigation of the enzymic reactions of the chlorophyll breakdown pathway. The key reaction which causes loss of green color is catalyzed in a two-step reaction by pheophorbide a oxygenase and red chlorophyll catabolite reductase. In this Minireview, we summarize the actual knowledge about catabolites and enzymes of chlorophyll catabolism in oilseed rape and discuss the significance of this pathway in respect to chlorophyll degradation during Brassica napus seed developmen

Access to Organometallic Arylcobaltcorrins through Radical Synthesis: 4‐Ethylphenylcobalamin, a Potential “Antivitamin B 12 ”

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/96761/1/anie_201209651_sm_miscellaneous_information.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/96761/2/2606_ftp.pd

Non-iterative and exact method for constraining particles in a linear geometry

We present a practical numerical method for evaluating the Lagrange multipliers necessary for maintaining a constrained linear geometry of particles in dynamical simulations. The method involves no iterations, and is limited in accuracy only by the numerical methods for solving small systems of linear equations. As a result of the non-iterative and exact (within numerical accuracy) nature of the procedure there is no drift in the constrained geometry, and the method is therefore readily applied to molecular dynamics simulations of, e.g., rigid linear molecules or materials of non-spherical grains. We illustrate the approach through implementation in the commonly used second-order velocity explicit Verlet method.Comment: 12 pages, 2 figure

Residual structure in a peptide fragment of the outer membrane protein X under denaturing conditions: a molecular dynamics study

The Escherichia coli outer membrane protein X (OmpX) contains two polypeptide segments that present nonrandom residual structure in 8M aqueous urea, whereas the remainder of the protein is in a flexibly disordered conformation (Tafer et al. in Biochemistry 43:860-869, 2004). In the present study, the results of two long-timescale (0.4μs) unrestrained explicit-solvent molecular dynamics (MD) simulations of a tetradecapeptide representative of one of these two segments in 8M aqueous urea are reported and analyzed. The two simulations were initiated either from the conformation of the corresponding segment in an NMR model structure of the unfolded protein or from an entirely extended configuration. The sampled conformational ensembles agree qualitatively with the experimentally observed NOEs, but not quantitatively, suggesting that a number of relevant configurations were not visited on the 2×0.4μs timescale. Major conformational transitions occur on the 0.1μs timescale, and the ensembles corresponding to the two independent simulations overlap only to a limited extent. However, both simulations show in multiple events the reversible formation and disruption of α-helical secondary structure (characteristic of the urea-denatured state) and β-turn secondary structure (characteristic of the native state). Events of helix formation are correlated with the appearance of hydrogen bonds between two side chains (Asp75-Ser78) and of a persistent hydrophobic contact (Trp76-Tyr80). They also evidence a peculiar helix stabilization and N-terminal capping role for a negatively charged residue (Asp75). These features are in good qualitative agreement with the NMR model for the structured state of the corresponding segment in the urea-denatured protein. The analysis of the simulations provides a detailed picture of the structural and dynamic features of the considered peptide at atomic resolution that is of high relevance in the understanding of the OmpX folding proces

Structure elucidation of chlorophyll catabolites (phyllobilins) by ESI-mass spectrometry—Pseudo-molecular ions and fragmentation analysis of a nonfluorescent chlorophyll catabolite (NCC)

AbstractThe hyphenation of high performance chromatography with modern mass spectrometric techniques providing high-resolution data as well as structural information from MS/MS experiments has become a versatile tool for rapid natural product identification and characterization. A recent application of this methodology concerned the investigation of the annually occurring degradation of green plant pigments. Since the first structural elucidation of a breakdown product in the early 1990s, a number of similarly structured, tetrapyrrolic catabolites have been discovered with the help of chromatographic, spectroscopic and spectrometric methods. A prerequisite for a satisfactory, manually operated or database supported analysis of mass spectrometric fragmentation patterns is a deeper knowledge of the underlying gas phase chemistry. Still, a thorough investigation of the common fragmentation behavior of these ubiquitous, naturally occurring chlorophyll breakdown products is lacking. This study closes the gap and gives a comprehensive overview of collision-induced fragmentation reactions of a tetrapyrrolic nonfluorescent chlorophyll catabolite, which is intended to serve as a model compound for the substance class of phyllobilins

Extraktion und Amplifikation von Pilz-DNA aus Kleinsäugerkotproben

Das Sammeln von Kotproben von Kleinsäugern und deren genetische Analyse stellt eine nicht invasive Art der Beprobung dar. Diese kommt vor allem dann zum Einsatz, wenn es sich um seltene, unauffällige oder störungsanfällige Arten handelt, oder wenn invasive Probenentnahmen nicht erlaubt bzw. nicht durchführbar sind. Solche Proben bergen eine Reihe von technischen Problemen. Der geringe Probenumfang von wenigen Milligramm Kot kann die molekularen Analysen beeinträchtigen. Die Proben enthalten unter Umständen nur sehr geringe Mengen der zu extrahierenden und amplifizierenden DNA. Es wurde ein gegenüber existierenden Methoden verbessertes Extraktionsprotokoll entwickelt, optimiert für die Beurteilung von Mykophagie unter Kleinsäugern. Kotproben von vier Kleinsäugerarten (Myodes glareolus, Apodemus flavicollis, Microtus agrestis und Sorex minutus), mit unterschiedlich enthaltener Menge an Pilzsporen wurden verwendet, um die Extraktionsleistung zweier kommerzieller Extraktionskits und zweier selbsthergestellter Extraktionspuffer mit modifiziertem Extraktionsprotokoll, zu vergleichen. Die besten Resultate bezüglich Menge und Amplifikation der extrahierten Ziel-DNA erzielte der einfachere der beiden selbstgemachten Extraktionspuffern in Kombination mit mechanischem Aufschluss und Hitzebehandlung. Die Puffersimplizität, einfache Extraktions- und Aufreinigungsschritte und vor allem die Möglichkeit der Arbeit mit sehr kleinen Probenmengen lassen den Schluss zu, dass das neu entwickelte Extraktionsprotokoll neben der Extraktion von (Pilz) DNA aus Säugetierkot möglicherweise auch passend für andere, ähnliche Studien wäre (andere Vektorart, andere DNA-Quellen). Weiters sollte die Frage geklärt werden, welche Pilze die Kleinsäuger bevorzugt konsumieren. Nach Klonierung und Sequenzierung von elf Proben konnten in neun Proben Ektomykorrhizapilze nachgewiesen werden.DNA-based analysis of faecal samples is essential for research about ecology of rare, elusive or endangered species, where invasive sampling is impossible or not practicable. When investigating small species, sample size constraints risk impairing molecular investigations, because of low DNA amounts present in sample sizes of a few milligrams. Comparison of existing methods led to the development of an improved protocol for DNA extraction optimised for the assessment of mycophagy among small mammals. Stool samples from four different species (Myodes glareolus, Apodemus flavicollis, Microtus agrestis and Sorex minutus) containing varying amounts of fungal spores were used to assess the extraction ability of two commercial stool DNA extraction kits and of two different in-house extraction protocols. The simplest extraction buffer in combination with an adequate mechanical and heat lysis treatment yielded best results regarding amount and amplification of the extracted DNA. Because of the possibility to work with very small samples, buffer simplicity, and easy extraction and purification procedure, we regard our newly developed extraction protocol for (fungal) DNA from mammalian faeces as very suitable for use in other studies, possibly involving different vector species as well as other sources of DNA, with probably only minor modifications necessary for adaptation. Further molecular work was done with the faecal samples extracted with the improved in-house protocols to find out which fungi were preferably eaten by small mammals. In nine out of eleven samples ectomycorrhizal fungi were identified

Is small mammal mycophagy relevant for truffle cultivation?

The role of small mammal mycophagy as vectors of hypogeous fungi is well established. However, little is known about dispersal of gourmet truffle species by mammal vectors, or about the potential role of mycophagy in truffle plantations. We hypothesize that small mammal mycophagy contributes to the productivity of truffle plantations by providing inoculum for truffle mycelium establishment and mating. Spread of non-desired competitors of gourmet truffles is a potential adverse effect of small mammal mycophagy