Photorhabdus antibacterial Rhs polymorphic toxin inhibits translation through ADP-ribosylation of 23S ribosomal RNA

Bacteria have evolved sophisticated mechanisms to deliver potent toxins into bacterial competitors or into eukaryotic cells in order to destroy rivals and gain access to a specific niche or to hijack essential metabolic or signaling pathways in the host. Delivered effectors carry various activities such as nucleases, phospholipases, peptidoglycan hydrolases, enzymes that deplete the pools of NADH or ATP, compromise the cell division machinery, or the host cell cytoskeleton. Effectors categorized in the family of polymorphic toxins have a modular structure, in which the toxin domain is fused to additional elements acting as cargo to adapt the effector to a specific secretion machinery. Here we show that Photorhabdus laumondii, an entomopathogen species, delivers a polymorphic antibacterial toxin via a type VI secretion system. This toxin inhibits protein synthesis in a NAD⁺-dependent manner. Using a biotinylated derivative of NAD, we demonstrate that translation is inhibited through ADP-ribosylation of the ribosomal 23S RNA. Mapping of the modification further showed that the adduct locates on helix 44 of the thiostrepton loop located in the GTPase-associated center and decreases the GTPase activity of the EF-G elongation factor.     

Polycyclic nitrogen heterocycles as potential thymidine phosphorylase inhibitors: synthesis,biological evaluation,and molecular docking study

New polycyclic heterocycles were synthesised and evaluated as potential inhibitors of thymidine phosphorylase (TP). Inspired by the pharmacophoric pyrimidinedione core of the natural substrate, four series have been designed in order to interact with large empty pockets of the active site: pyrimidoquinoline-2,4-diones (series A), pyrimidinedione linked to a pyrroloquinoline-1,3-diones (series B and C), the polycyclic heterocycle has been replaced by a pyrimidopyridopyrrolidinetetraone (series D). In each series, the tricyclic nitrogen heterocyclic moiety has been synthesised by a one-pot multicomponent reaction. Compared to 7-DX used as control, 2d, 2l, 2p (series A), 28a (series D), and the open intermediate 30 showed modest to good activities. A kinetic study confirmed that the most active compounds 2d, 2p are competitive inhibitors. Molecular docking analysis confirmed the interaction of these new compounds at the active binding site of TP and highlighted a plausible specific interaction in a pocket that had not yet been explored.     

A combinatorial mutagenesis approach for functional epitope mapping on phage-displayed target antigen: Application to antibodies against epidermal growth factor

Although multiple different procedures to characterize the epitopes recognized by antibodies have been developed, site-directed mutagenesis remains the method of choice to define the energetic contribution of antigen residues to binding. These studies are useful to identify critical residues and to delineate functional maps of the epitopes. However, they tend to underestimate the roles of residues that are not critical for binding on their own, but contribute to the formation of the target epitope in an additive, or even cooperative, way. Mapping antigenic determinants with a diffuse energetic landscape, which establish multiple individually weak interactions with the antibody paratope, resulting in high affinity and specificity recognition of the epitope as a whole, is thus technically challenging. The current work was aimed at developing a combinatorial strategy to overcome the limitations of site-directed mutagenesis, relying on comprehensive randomization of discrete antigenic regions within phage-displayed antigen libraries. Two model antibodies recognizing epidermal growth factor were used to validate the mapping platform. Abrogation of antibody recognition due to the introduction of simultaneous replacements was able to show the involvement of particular amino acid clusters in epitope formation. The abundance of some of the original residues (or functionally equivalent amino acids sharing their physicochemical properties) among the set of mutated antigen variants selected on a given antibody highlighted their contributions and allowed delineation of a detailed functional map of the corresponding epitope. The use of the combinatorial approach could be expanded to map the interactions between other antigens/antibodies.     

Exploring a new biodiversity frontier: subterranean ants in northern Australia

Although it is common for ant surveys to uncover previously uncollected species, a recent study of subterranean ants in Amazonian Ecuador has indicated that an entire ant fauna may remain largely undiscovered. Here we report on the first systematic investigation of subterranean ants in northern Australia, in order to assess the extent to which the high abundance and diversity of subterranean ants in Amazonia is apparent in tropical Australia. We use a novel sampling technique that combines elements of an attractant bait and a pitfall trap, and allows many traps to be deployed simultaneously. Our main study was conducted at three closely approximated sites in Darwin, where the local ant fauna has been intensively surveyed using conventional (above-ground) sampling techniques. The 720 traps deployed resulted in 421 species records, representing 29 species from 17 genera. Sixteen of these species have cryptobiotic morphology, with four recorded here for the first time. Remarkably, one of these four (a blind species of Solenopsis) was the second most frequently caught species in subterranean traps, with 70 records. Ant abundance, species richness and composition varied markedly between sites, despite site similarity in soils and vegetation. Total ant records were greater in the middle compared with start of the wet season, declined with depth, and were greater after 4 days than one. Sampling at six sites in the Mitchell Falls area of the northern Kimberley region, 1,200 km southwest of Darwin, also revealed several cryptobiotic species new to science, including a new genus record (Pseudolasius) for Western Australia. Our underground sampling has therefore revealed an abundant and diverse subterranean ant fauna in northern Australia, containing many cryptobiotic species not previously collected. We use our results to provide methodological guidelines for most effectively sampling this fauna. Combined with the Amazonian study, our findings indicate that a specialist subterranean ant fauna, including numerous species remaining to be discovered, might be a feature of tropical landscapes throughout the world.     

Genetic polymorphism of CYP4A11 and CYP4A22 genes and in silico insights from comparative 3D modelling in a French population

The CYP4A subfamily is known to ω-hydroxylate the endogenous arachidonic acid into 20-hydroxyeicosatetranoic acid, which has renovascular and tubular functions. The aim of this work was to report a comprehensive investigation of the CYP4A11 and CYP4A22 genetic polymorphisms in a French population. Using PCR-SSCP and sequencing strategies, a total of 26 sequence variations were identified comprising 3 missense mutations for CYP4A11 (Ser404Phe, Phe434Ser and Arg505His) and 7 missense mutations for CYP4A22 (Arg126Trp, Gly130Ser, Asn152Tyr, Val185Phe, Cys231Arg, Leu428Pro and Leu509Phe). In comparison with SNPs reported in the database (dbSNP) of the National Center for Biotechnology information (NCBI), 6 and 3 novel polymorphisms were identified in CYP4A11 and CYP4A22, respectively. The potential impact of the amino acid substitutions on the structure and/or catalytic activity of the enzymes has been estimated by the construction and validation of the CYP4A 3D models. These results could be helpful for further investigations of the potential role of CYP4A variants in the genetic susceptibility to cardiovascular diseases in humans such as arterial hypertension.     

Under which conditions is character displacement a likely outcome of secondary contact?

Sympatric character displacement is one possible mechanism that prevents competitive exclusion. This mechanism is thought to be behind the radiation of Darwin's finches, where character displacement is assumed to have followed secondary contact of ecologically similar species. We use a model to evaluate under which ecological and environmental conditions this mechanism is likely. Using the adaptive dynamics theory, we analyse different ecological models embedded in the secondary contact scenario. We highlight two necessary conditions for character displacement in sympatry: (i) very strong premating isolation between the two populations, and (ii) secondary contact to occur at an evolutionary branching point. Character displacement is then driven by adaptation to interspecific competition. We determine how ecological and environmental parameters influence the probability of ecological divergence. Finally, we discuss the likelihood of sympatric character displacement under disruptive selection in natural populations.     

The evolution of postreproductive life span as an insurance against indeterminacy

Postreproductive life span remains a puzzle for evolutionary biologists. The explanation of increased inclusive fitness through parental care after reproduction that applies for humans is unrealistic for many species. We propose a new selective mechanism, independent of parental care, which relies on the hypothesis that postreproductive life span can evolve as an insurance against indeterminacy: longer life expectancy reduces the risk of dying by chance before the cessation of reproductive activity. We demonstrate numerically that the duration of evolved postreproductive life span is indeed expected to increase with variability in life span duration. An unprecedented assay of 11 strains of the collembola Folsomia candida shows the existence of (1) postreproductive life span in the absence of parental care; (2) genetic variability in mean postreproductive life span and postreproductive life span variability itself; (3) strong genetic correlation between latter traits. This new explanation brings along the novel idea that loose canalization of a trait (here, somatic life span) can itself act as a selective pressure on other traits.     

miR-196 regulates axial patterning and pectoral appendage initiation

Vertebrate Hox clusters contain protein-coding genes that regulate body axis development and microRNA (miRNA) genes whose functions are not yet well understood. We overexpressed the Hox cluster microRNA miR-196 in zebrafish embryos and found four specific, viable phenotypes: failure of pectoral fin bud initiation, deletion of the 6th pharyngeal arch, homeotic aberration and loss of rostral vertebrae, and reduced number of ribs and somites. Reciprocally, miR-196 knockdown evoked an extra pharyngeal arch, extra ribs, and extra somites, confirming endogenous roles of miR-196. miR-196 injection altered expression of hox genes and the signaling of retinoic acid through the retinoic acid receptor gene rarab. Knocking down rarab mimicked the pectoral fin phenotype of miR-196 overexpression, and reporter constructs tested in tissue culture and in embryos showed that the rarab 3′UTR is a miR-196 target for pectoral fin bud initiation. These results show that a Hox cluster microRNA modulates development of axial patterning similar to nearby protein-coding Hox genes, and acts on appendicular patterning at least in part by modulating retinoic acid signaling.