Identification of a novel glyoxylate reductase supports phylogeny-based enzymatic substrate specificity prediction

Phylogenetic analysis of the superfamily of D-2-hydroxyacid dehydrogenases identified the previously unrecognized cluster of glyoxylate/hydroxypyruvate reductases (GHPR). Based on the genome sequence of Rhizobium etli, the nodulating endosymbiont of the common bean plant, we predicted a putative 3-phosphoglycerate dehydrogenase to exhibit GHPR activity instead. The protein was overexpressed and purified. The enzyme is homodimeric under native conditions and is indeed capable of reducing both glyoxylate and hydroxypyruvate. Other substrates are phenylpyruvate and ketobutyrate. The highest activity was observed with glyoxylate and phenylpyruvate, both having approximately the same kcat/Km ratio. This kind of substrate specificity has not been reported previously for a GHPR. The optimal pH for the reduction of phenylpyruvate to phenyllactate is pH 7. These data lend support to the idea of predicting enzymatic substrate specificity based on phylogenetic clustering.     

Specialized edaphic niches of threatened copper endemic plant species in the D.R. Congo: implications for ex situ conservation

Background and aims

Copper (Cu) rich soils derived from rocks of the Katangan Copperbelt in the south-eastern Democratic Republic of Congo (DRC) support a rich diversity of metallophytes including 550 heavy metal tolerant; 24 broad Cu soil endemic; and 33 strict Cu soil endemic plant species. The majority of the plant species occur on prominent Cu hills scattered along the copperbelt. Heavy metal mining on the Katangan Copperbelt has resulted in extensive degradation and destruction of the Cu hill ecosystems. As a result, approximately 80 % of the strict Cu endemic plant species are classified as threatened according to IUCN criteria and represent a conservation priority. Little is known about the soil Cu tolerance optimum of the Cu endemic plant species. The purpose of this study was to quantify the soil Cu concentration (Cu edaphic niche) of four Cu endemic plant species to inform soil propagation conditions and microhabitat site selection for planting of the species in Cu hill ecosystem restoration.

Methods

The soil Cu concentration tolerance of Cu endemic plant species was studied including Crotalaria cobalticola (CRCO); Gladiolus ledoctei (GLLE); Diplolophium marthozianum (DIMA); and Triumfetta welwitschii var. rogersii (TRWE-RO). The in situ natural habitat distributions of the Cu endemic plant species with respect to soil Cu concentration (Cu edaphic niche) was calculated by means of a generalised additive model. Additionally, the seedling emergence and growth of the four Cu endemic plant species in three soil Cu concentrations was tested ex situ and the results were compared to that of the natural habitat soil Cu concentration optimum (Cu edaphic niche).

Results

CRCO exhibited greater performance on the highest soil Cu concentration, consistent with its calculated Cu edaphic niche occurring at the highest soil Cu concentrations. In contrast, both DIMA and TRWE-RO exhibited greatest performance at the lowest soil Cu concentration, despite the calculated Cu edaphic niche occurring at moderate soil Cu concentrations. GLLE exhibited equal performances in the entire range of soil Cu concentrations.

Conclusions

These results suggest that CRCO evolved via the edaphic specialization model where it is most competitive in Cu hill habitat with the highest soil Cu concentration. In comparison, DIMA and TRWE-RO appear to have evolved via the endemism refuge model, which indicates that the species were excluded into (i.e., took refuge in) the lower plant competition Cu hill habitat due to their inability to effectively compete with higher plant competition on normal soils. The soil Cu edaphic niche determined for the four species will be useful in conservation activities including informing soil propagation conditions and microhabitat site selection for planting of the species in Cu hill ecosystem restoration.

     

Epitope characterization of anti-JAM-A antibodies using orthogonal mass spectrometry and surface plasmon resonance approaches

Junctional adhesion molecule-A (JAM-A) is an adherens and tight junction protein expressed by endothelial and epithelial cells and associated with cancer progression. We present here the extensive characterization of immune complexes involving JAM-A antigen and three monoclonal antibodies (mAbs), including hz6F4-2, a humanized version of anti-tumoral 6F4 mAb identified by a functional and proteomic approach in our laboratory. A specific workflow that combines orthogonal approaches has been designed to determine binding stoichiometries along with JAM-A epitope mapping determination at high resolution for these three mAbs. Native mass spectrometry experiments revealed different binding stoichiometries and affinities, with two molecules of JAM-A being able to bind to hz6F4-2 and F11 Fab, while only one JAM-A was bound to J10.4. Surface plasmon resonance indirect competitive binding assays suggested epitopes located in close proximity for hz6F4-2 and F11. Finally, hydrogen-deuterium exchange mass spectrometry was used to precisely identify epitopes for all mAbs. The results obtained by orthogonal biophysical approaches showed a clear correlation between the determined epitopes and JAM-A binding characteristics, allowing the basis for molecular recognition of JAM-A by hz6F4-2 to be definitively established for the first time. Taken together, our results highlight the power of MS-based structural approaches for epitope mapping and mAb conformational characterization.     

Prognostic factors of 10-year radiographic outcome in early rheumatoid arthritis: a prospective study

Introduction  

The objectives of this study were to determine the predictive factors of long-term radiographic outcome of rheumatoid arthritis (RA) and to describe the relationship between joint damage and disability over the course of the disease.     

Novel benzimidazole derivatives as selective CB2 agonists

The preparation and evaluation of a novel class of CB2 agonists based on a benzimidazole moiety are reported. They showed binding affinities up to 1nM towards the CB2 receptor with partial to full agonist potencies. They also demonstrated good to excellent selectivity (>1000-fold) over the CB1 receptor.     

Ca regulation of connexin 43 hemichannels in C6 glioma and glial cells

Connexin hemichannels have a low open probability under normal conditions but open in response to various stimuli, forming a release pathway for small paracrine messengers. We investigated hemichannel-mediated ATP responses triggered by changes of intracellular Ca²⁺ ([Ca²⁺]_i) in Cx43 expressing glioma cells and primary glial cells. The involvement of hemichannels was confirmed with gja1 gene-silencing and exclusion of other release mechanisms. Hemichannel responses were triggered when [Ca²⁺]_i was in the 500 nM range but the responses disappeared with larger [Ca²⁺]_i transients. Ca²⁺-triggered responses induced by A23187 and glutamate activated a signaling cascade that involved calmodulin (CaM), CaM-dependent kinase II, p38 mitogen activated kinase, phospholipase A2, arachidonic acid (AA), lipoxygenases, cyclo-oxygenases, reactive oxygen species, nitric oxide and depolarization. Hemichannel responses were also triggered by activation of CaM with a Ca²⁺-like peptide or exogenous application of AA, and the cascade was furthermore operational in primary glial cells isolated from rat cortex. In addition, several positive feed-back loops contributed to amplify the responses. We conclude that an elevation of [Ca²⁺]_i triggers hemichannel opening, not by a direct action of Ca²⁺ on hemichannels but via multiple intermediate signaling steps that are adjoined by distinct signaling mechanisms activated by high [Ca²⁺]_i and acting to restrain cellular ATP loss.     

Cadmium uptake and distribution in Arabidopsis thaliana exposed to low chronic concentrations depends on plant growth

This study tested the hypothesis that Cd uptake is correlated with the shoot or root growth of Arabidopsis thaliana ecotype Columbia cultivated hydroponically at environmentally relevant Cd concentrations: 20, 100 and 350 nmol L^?1. Growth of both roots and shoots were delayed at 350 nmol L^?1. The rate of Cd uptake determined by spiking the nutrient solution with ¹⁰⁹Cd for 24 h, was significantly correlated with the root growth rate. The fraction of Cd absorbed that was allocated to shoots was constant with time but decreased with increasing exposure to Cd. Autoradiography and gamma counting showed that Cd was preferentially allocated to developing leaves. Hence, the quantity of Cd in shoots depended both on the root growth, which probably governed the uptake, and on the maturity of the leaves, which may have determined the Cd allocated to shoots through changes in the transpiration stream.     

Soil decomposition of wheat internodes of different maturity stages: relative impact of the soluble and structural fractions

The aim of this study was to clarify the importance of the soluble fraction on cell wall decomposition. Wheat plant was chosen as a model and was harvested at three stages of maturity: anthesis (A stage), 20 days after anthesis (B stage) and physiological maturity (PM stage). Wheat third internode (numbered down from the ear) were selected for this study. Internode age influenced the cumulative CO(2) kinetics with internodes from wheat stem harvested at anthesis mineralizing 62.1%+/-2.2 of added residue C whereas those harvested at the B and PM stages mineralized 58.8%+/-1.4 and 51.6%+/-1.7, respectively of the added C. Chemical analyses revealed that maturation of the selected internodes mainly altered residue quality by modifying the proportion of soluble to cell wall fractions rather than the quality of these fractions. The hexose to pentose ratios were good biomarkers of microbial sugars for both soluble and cell wall fractions, as were the uronic acids, which are not commonly determined in soil decomposition studies. This study clearly demonstrated that the contents of the internode soluble fraction did not affect the extent of cell wall C mineralization. Therefore, the soluble content of crop residues would not regulate the soil microbial populations able to mineralize cell wall C. However, this needs to be validated on a broader range of residue types with different nature of cell wall C or soluble compounds.     

Towards calixarene-based prodrugs: Drug release and antibacterial behaviour of a water-soluble nalidixic acid/calix[4]arene ester adduct

A water-soluble calixarene-based heterocyclic podand incorporating a quinolone antibiotic subunit, the nalidixic acid, was synthesised and fully characterised. Its prodrug behaviour was assessed in vitro by HPLC, demonstrating the release of the tethered quinolone in model biological conditions. Microbiological studies performed on various Gram-positive and Gram-negative reference strains showed very interesting antibacterial activities.