The effects of archipelago spatial structure on island diversity and endemism: predictions from a spatially‐structured neutral model

Islands are particularly suited to testing hypotheses about the ecological and evolutionary mechanisms underpinning community assembly. Yet the complex spatial arrangements of real island systems have received little attention from both empirical studies and theoretical models. Here, we investigate the extent to which the spatial structure of archipelagos affects species diversity and endemism. We start by proposing a new spatially structured neutral model that explicitly considers archipelago structure, and then investigate its predictions under a diversity of scenarios. Our results suggest that considering the spatial structure of archipelagos is crucial to understanding their diversity and endemism, with structured island systems acting both as “museums” and “cradles” of biodiversity. These dynamics of diversification may change the traditionally expected pattern of decrease in species richness with distance from the mainland, even potentially leading to increasing patterns for taxa with high speciation rates in archipelagos off species‐poor continental areas. Our results also predict that, within spatially structured archipelagos, metapopulation dynamics and evolutionary processes can generate higher diversity on islands more centrally placed than at the periphery. We derive from our results a set of theoretical predictions, potentially testable with empirical data.     

Differential quantitative proteome analysis of Escherichia coli grown on acetate versus glucose

Relative protein abundances of Escherichia coli MG1655 growing exponentially on minimal medium with acetate or glucose as the sole carbon source were investigated in a quantitative shotgun proteome analysis with TMT6‐plex isobaric tags. Peptides were separated by high resolution high/low pH 2D‐LC, using an optimized fraction pooling scheme followed by mass spectrometric analysis. Quantitative data were acquired for 2099 proteins covering 49% of the predicted E. coli proteins, showing system‐wide effects of growth conditions. In total, 507 proteins showed a fold change of at least 1.5 and 205 proteins changed by more than twofold. Significant differences in abundance were observed for most of the proteins in the central carbon metabolism and in proteins relevant for amino acid and protein synthesis, processing of environmental information and scavenging of a variety of alternate carbon sources. Periplasmic‐binding proteins were also more abundant on acetate, especially proteins involved in scavenging extracellular resources such as sugars. All MS data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository (dataset identifier PXD003863).     

Structural basis for the antagonistic roles of RNP-8 and GLD-3 in GLD-2 poly(A)-polymerase activity

Cytoplasmic polyadenylation drives the translational activation of specific mRNAs in early metazoan development and is performed by distinct complexes that share the same catalytic poly(A)-polymerase subunit, GLD-2. The activity and specificity of GLD-2 depend on its binding partners. In Caenorhabditis elegans, GLD-2 promotes spermatogenesis when bound to GLD-3 and oogenesis when bound to RNP-8. GLD-3 and RNP-8 antagonize each other and compete for GLD-2 binding. Following up on our previous mechanistic studies of GLD-2–GLD-3, we report here the 2.5 Å resolution structure and biochemical characterization of a GLD-2–RNP-8 core complex. In the structure, RNP-8 embraces the poly(A)-polymerase, docking onto several conserved hydrophobic hotspots present on the GLD-2 surface. RNP-8 stabilizes GLD-2 and indirectly stimulates polyadenylation. RNP-8 has a different amino-acid sequence and structure as compared to GLD-3. Yet, it binds the same surfaces of GLD-2 by forming alternative interactions, rationalizing the remarkable versatility of GLD-2 complexes.     

Le Crocodilien longirostre Gavialosuchus dans le Miocène moyen de Polastron (Gers,France)

A left maxilla fragment from the newly discovered Miocene vertebrate locality of Polastron (Gers, southwestern France) is described and referred to the longsnouted eusuchian crocodilian Gavialosuchus, which had never been reported from the Miocene of this area, in which crocodilian remains are scarce. On the basis of its mammal fauna, the locality is slightly older than Sansan. Although Gavialosuchus is usually found in marine beds, its occurrence in the fluviatile deposits of Polastron shows that it also inhabited rivers.     

Biochemical characterisation of recombinant Streptomyces pristinaespiralis L-lysine cyclodeaminase

L-Lysine cyclodeaminase from Streptomyces pristinaespiralis was heterologously expressed in Escherichia coli, isolated to 90% purity after two purification steps and characterised. The size of the isolated recombinant enzyme was in agreement with the theoretical size calculated from the corresponding gene. We demonstrated that our preparation converts L-lysine to L-pipecolic acid (enantiomeric excess >95%) after isolating and identifying the conversion product by LC/MS, NMR and IR. This conversion followed Michaelis-Menten kinetics with a K(m) of 1.39+/-0.32 mM. The enzyme activity was maximal at pH 6.7. Reducing conditions, the presence of glycerol and in particular the presence of iron(II) significantly enhanced the L-lysine cyclodeaminase activity. Although the heat stability of the enzyme diminished significantly after 37 degrees C, the initial rate of reaction was maximal at 61 degrees C. We found no requirement for an external cofactor for full activity, although sequence data indicate NAD+ as cofactor. Upon enzyme denaturation, NAD+ release was observed, which indicates very tight binding of NAD+ to the enzyme. In parallel we developed selection and screening assays for lysine cyclodeaminase, which we adapted to microtitre plate format and validated. Among twenty-eight lysine analogues screened for turnover/binding to the enzyme, three were identified as substrates (L-ornithine, 5-hydroxylysine and L-4-thialysine), while another six (4-azalysine, L-2,4-diaminobutyric acid, 1,5-diaminopentane, N-epsilon-trifluoroacetyl-L-lysine, N-epsilon-Boc-L-lysine and N-epsilon-methyl-L-lysine) were shown to compete against L-lysine turnover without being converted by the enzyme. All substrates displayed Michaelis-Menten kinetics upon turnover by lysine cyclodeaminase. Our results indicate that the lysine cyclodeaminase from Streptomyces pristinaespiralis is a highly enantioselective enzyme at the substrate recognition and conversion levels, in both cases in favour of the l-isomer.