Adaptive evolution has targeted the C-terminal domain of the RXLR effectors of plant pathogenic oomycetes

Oomycete plant pathogens deliver effector proteins inside host cells to modulate plant defense circuitry and to enable parasitic colonization. These effectors are defined by a conserved motif, termed RXLR (for Arg, any amino acid, Leu, Arg), that is located downstream of the signal peptide and that has been implicated in host translocation. Because the phenotypes of RXLR effectors extend to plant cells, their genes are expected to be the direct target of the evolutionary forces that drive the antagonistic interplay between pathogen and host. We used the draft genome sequences of three oomycete plant pathogens, Phytophthora sojae, Phytophthora ramorum, and Hyaloperonospora parasitica, to generate genome-wide catalogs of RXLR effector genes and determine the extent to which these genes are under positive selection. These analyses revealed that the RXLR sequence is overrepresented and positionally constrained in the secretome of Phytophthora relative to other eukaryotes. The three examined plant pathogenic oomycetes carry complex and diverse sets of RXLR effector genes that have undergone relatively rapid birth and death evolution. We obtained robust evidence of positive selection in more than two-thirds of the examined paralog families of RXLR effectors. Positive selection has acted for the most part on the C-terminal region, consistent with the view that RXLR effectors are modular, with the N terminus involved in secretion and host translocation and the C-terminal domain dedicated to modulating host defenses inside plant cells.     

Effects of diapause on post‐diapause reproductive investment in the moth Ostrinia scapulalis

Diapause is a strategy used by many insect species to survive adverse environmental conditions. However, diapause incurs costs that may have adverse effects on post‐diapause development and reproduction. We herein investigated the effects of diapause on the post‐diapause reproductive investment of males and females in a multivoltine moth, the adzuki bean borer, Ostrinia scapulalis (Walker) (Lepidoptera: Crambidae). We found that (1) post‐diapause males and females were smaller and had lower mating success than non‐diapause individuals, (2) post‐diapause females had lower fecundity and shorter longevity than non‐diapause females, (3) post‐diapause males transferred similar numbers of eupyrene and apyrene sperm as non‐diapause males, (4) the fecundity and longevity of non‐diapause females mated with post‐diapause males and those mated with non‐diapause males were not significantly different, and (5) no significant relationship was found between diapause duration (short and long) and post‐diapause reproductive investments in both males and females. These results suggest that post‐diapause males did not reduce reproductive investment in spite of the cost of diapause, and the significant decline in reproductive output in post‐diapause females was due to their reduced body weight and longevity, which appeared to be direct consequences of the cost of diapause.     

454 Genome sequencing of Pseudoperonospora cubensis reveals effector proteins with a QXLR translocation motif

Pseudoperonospora cubensis is a biotrophic oomycete pathogen that causes downy mildew of cucurbits, a devastating foliar disease threatening cucurbit production worldwide. We sequenced P. cubensis genomic DNA using 454 pyrosequencing and obtained random genomic sequences covering approximately 14% of the genome, thus providing the first set of useful genomic sequence information for P. cubensis. Using bioinformatics approaches, we identified 32 putative RXLR effector proteins. Interestingly, we also identified 29 secreted peptides with high similarity to RXLR effectors at the N-terminal translocation domain, yet containing an R-to-Q substitution in the first residue of the translocation motif. Among these, a family of QXLR-containing proteins, designated as PcQNE, was confirmed to have a functional signal peptide and was further characterized as being localized in the plant nucleus. Internalization of secreted PcQNE into plant cells requires the QXLR-EER motif. This family has a large number of near-identical copies within the P. cubensis genome, is under diversifying selection at the C-terminal domain, and is upregulated during infection of plants, all of which are common characteristics of characterized oomycete effectors. Taken together, the data suggest that PcQNE are bona fide effector proteins with a QXLR translocation motif, and QXLR effectors are prevalent in P. cubensis. Furthermore, the massive duplication of PcQNE suggests that they might play pivotal roles in pathogen fitness and pathogenicity.     

New furin inhibitors based on weakly basic amidinohydrazones

A novel series of amidinohydrazone-derived furin inhibitors was prepared; the most potent compounds 17 and 21 inhibit furin with K_i values of 0.46 and 0.59 μM, respectively. In contrast to inhibitor 17, which still contains a guanidino residue, compound 21 possesses only weakly basic amidinohydrazone groups.     

Isolation and characterization of endocellulase-free multienzyme complex from newly isolated Thermoanaerobacterium thermosaccharolyticum strain NOI-1

An endocellulase-free multienzyme complex was produced by a thermophilic anaerobic bacterium, Thermoanaerobacterium thermosaccharolyticum strain NOI-1, when grown on xylan. The temperature and pH optima for growth were 60 degrees C and 6.0, respectively. The bacterial cells were found to adhere to insoluble xylan and Avicel. A scanning electron microscopy analysis showed the adhesion of xylan to the cells. An endocellulase-free multienzyme complex was isolated from the crude enzyme of strain NOI-1 by affinity purification on cellulose and Sephacryl S-300 gel filtration. The molecular mass of the multienzyme complex was estimated to be about 1,200 kDa. The multienzyme complex showed one protein on native PAGE, one xylanase on a native zymogram, 21 proteins on SDS-PAGE, and 5 xylanases on a SDS zymogram. The multienzyme complex consisted of xylanase, beta-xylosidase, alpha-L-arabinofuranosidase, beta-glucosidase, and cellobiohydrolase. The multienzyme complex was effective in hydrolyzing xylan and corn hulls. This is the first report of an endocellulase-free multienzyme complex produced by a thermophilic anaerobic bacterium, T. thermosaccharolyticum strain NOI-1.     

An artifacts removal post-processing for epiphyseal region-of-interest (EROI) localization in automated bone age assessment (BAA)

Background

Guidewire (GW) size and stenosis dimensions are the two major factors affecting the translesional pressure drop. Studying the combined effect of these parameters on the mean pressure drop (Δp) across the stenosis is of high practical importance.

Methods

In this study, time averaged mass and momentum conservation equations are solved analytically to obtain pressure drop-flow, Δp-Q, curves for three different percentage area blockages corresponding to moderate (64%), intermediate (80%), and severe (90%) stenoses. Stenosis is considered to be axisymmetric consisting of three different sections namely converging, throat, and diverging regions. Analytical expressions for pressure drop are obtained for each of these regions separately. Using this approach, effects of lesion length and GW insertion on the mean translesional pressure drop and its component (loss due to momentum change and viscous loss) are analyzed.

Results and Conclusion

It is observed that for a given percent area stenosis (AS), increase in the throat length only increases the viscous loss. However, increase in the severity of stenosis and GW insertion increase both loss due to momentum change and viscous loss. GW insertion has greater contribution to the rise in viscous loss (increase by 2.14 and 2.72 times for 64% and 90% AS, respectively) than loss due to momentum change (1.34% increase for 64% AS and 25% decrease for 90% AS). It also alters the hyperemic pressure drop in moderate (48% increase) to intermediate (30% increase) stenoses significantly. However, in severe stenoses GW insertion has a negligible effect (0.5% increase) on hyperemic translesional pressure drop. It is also observed that pressure drop in a severe stenosis is less sensitive to lesion length variation (4% and 14% increase in Δp for without and with GW, respectively) as compared to intermediate (10% and 30% increase in Δp for without and with GW, respectively) and moderate stenoses (22% and 48% increase in Δp for without and with GW, respectively). Based on the contribution of pressure drop components to the total translesional pressure drop, it is found that viscous losses are dominant in moderate stenoses, while in severe stenoses losses due to momentum changes are significant. It is also shown that this simple analytical solution can provide valuable information regarding interpretation of coronary diagnostic parameters such as fractional flow reserve (FFR).     

Patterns of diversifying selection in the phytotoxin-like scr74 gene family of Phytophthora infestans

Phytophthora infestans, the organism responsible for the Irish famine, causes late blight, a re-emerging disease of potato and tomato. Little is known about the molecular evolution of P. infestans genes. To identify candidate effector genes (virulence or avirulence genes) that may have co-evolved with the host, we mined expressed sequence tag (EST) data from infection stages of P. infestans for secreted and potentially polymorphic genes. This led to the identification of scr74, a gene that encodes a predicted 74-amino acid secreted cysteine-rich protein with similarity to the Phytophthora cactorum phytotoxin PcF. The expression of scr74 was upregulated approximately 60-fold 2 to 4 days after inoculation of tomato and was also significantly induced during early stages of colonization of potato. The scr74 gene was found to belong to a highly polymorphic gene family within P. infestans with 21 different sequences identified. Using the approximate and maximum likelihood (ML) methods, we found that diversifying selection likely caused the extensive polymorphism observed within the scr74 gene family. Pairwise comparisons of 17 scr74 sequences revealed elevated ratios of nonsynonymous to synonymous nucleotide-substitution rates, particularly in the mature region of the proteins. Using ML, all 21 polymorphic amino acid sites were identified to be under diversifying selection. Of these 21 amino acids, 19 are located in the mature protein region, suggesting that selection may have acted on the functional portions of the proteins. Further investigation of gene copy number and organization revealed that the scr74 gene family comprises at least three copies located in a region of no more than 300 kb of the P. infestans genome. We found evidence that recombination contributed to sequence divergence within at least one gene locus. These results led us to propose an evolutionary model that involves gene duplication and recombination, followed by functional divergence of scr74 genes. This study provides support for using diversifying selection as a criterion for identifying candidate effector genes from sequence databases.     

γ-L-glutamyltaurine

Summary. The discovery of the dipeptide γ-glutamyltaurine (γ-GT; glutaurine, Litoralon) in the parathyroid in 1980 and later in the brain of mammals gave rise to studies on intrinsic and synthetic taurine peptides of this type. It was suggested that γ-glutamyltransferase (GGT; γ-glutamyltranspeptidase) in the brain is responsible for the in vivo formation of this unusual dipeptide. γ-GT has been prepared by both synthetic and enzymatic methods. The chemical syntheses included the use of protecting groups and coupling methods. A wide spectrum of analytical and spectroscopic methods was used to confirm the structure of the synthetic compounds and to elucidate the position of the peptide bond. Enzymatic preparation of γ-GT from taurine takes advantage of the selective transpeptidation action of GGT on L-glutamine, glutathione, γ-glutamyl-p-nitroanilide or other glutamine donors. Although the functional roles of γ-GT in the brain are only poorly understood, many of its established CNS effects have been reported in the last 25 years. Its effect on emotional arousal and its anti-conflict potencies are synergistic with the anxiolytic drug diazepam. γ-GT exhibits anti-conflict potency, which is exerted by reducing aversion or phobia and/or the anxiety levels. γ-GT also acts as endogenous modulator in excitatory aminoacidergic neurotransmission. It is suggested that such acidic peptides through N-methyl-D-aspartic acid receptors could be part of the neurochemical substrate underlying self-stimulation of the medial prefrontal cortex. Other γ-GT effects in neural systems include: effects on the monoamine concentration in the brain; effects on aggressive behavior in the cat; effects on thyroid hormones in the rat; amelioration of electroshock-induced amnesia; potent and long-lasting antiepileptic action (on intra-amygdaloid injection); affect the glutamatergic system in schizophrenic disorders. Roles for γ-GT in non-neural systems have also been reported, e.g., effects on the metamorphosis of amphibians; on plasma rennin regulation; on radiation protection; on uric acid levels; on human antibody-dependent cell-mediated cytotoxicity (ADCC) and many more.     

Modeling and simulation of the swelling behavior of pH-stimulus-responsive hydrogels

The modulation of the swelling ability of the hydrogel matrix by pH-stimulus enables the dynamic control of the swelling forces, thereby obtaining effective diffusivity and permeability of the solutes, or mechanical energy from the hydrogel. In this work, a chemo-electro-mechanical model describing hydrogel behavior, based on multi-field effects, is developed to simulate the swelling and shrinking of these fascinating bio-materials, and it is termed the multi-effect-coupling pH-stimulus (MECpH) model. This model accounts for the ionic fluxes within both the hydrogel and solution, the coupling between the electric field, ionic fluxes, and mechanical deformations of the hydrogel. The main contribution of this model is to incorporate the relationship between the concentrations of the ionized fixed-charge groups and the diffusive hydrogen ion, which follows a Langmuir isotherm, into the Poisson-Nernst-Planck system. To validate this MECpH model, one-dimensional steady-state simulations under varying pH solution are carried out via a meshless Hermite-Cloud methodology, and the numerical results are compared with available experimental data. It is shown that the presently developed MECpH model is accurate, efficient, and numerically stable.     

Mutations of the PC2 substrate binding pocket alter enzyme specificity

By taking advantage of the recently published furin structure, whose catalytic domain shares high homology with other proprotein convertases, we designed mutations in the catalytic domain of PC2, altering residues Ser206, Thr271, Asp278, ArgGlu282, AlaSer323, Leu341, Asn365, and Ser380, which are both conserved and specific to this convertase, and substituting residues specific to PC1 and/or furin. In order to investigate the determinants of PC2 specificity, we have tested the mutated enzymes against a set of proenkephalin-derived substrates, as well as substrates representing Arg, Ala, Leu, Phe, and Glu positional scanning variants of a peptide B-derived substrate. We found that the exchange of the Ser206 residue with Arg or Lys led to a total loss of activity. Increased positive charge of the substrate generally resulted in an increased specificity constant. Most intriguingly, the RE281GR mutation, corresponding to a residue placed distantly in the S6 pocket, evoked the largest changes in the specificity pattern. The D278E and N356S mutations resulted in distinct alterations in PC2 substrate preferences. However, when other residues that distinguish PC2 from other convertases were substituted with PC1-like or furin-like equivalents, there was no significant alteration of the PC2 specificity pattern, suggesting that the overall structure of the substrate binding cleft rather than individual residues specifies substrate binding.