Does autophagy mediate age-dependent effect of dietary restriction responses in the filamentous fungus Podospora anserina?

Autophagy is a well-conserved catabolic process, involving the degradation of a cell''s own components through the lysosomal/vacuolar machinery. Autophagy is typically induced by nutrient starvation and has a role in nutrient recycling, cellular differentiation, degradation and programmed cell death. Another common response in eukaryotes is the extension of lifespan through dietary restriction (DR). We studied a link between DR and autophagy in the filamentous fungus Podospora anserina, a multicellular model organism for ageing studies and mitochondrial deterioration. While both carbon and nitrogen restriction extends lifespan in P. anserina, the size of the effect varied with the amount and type of restricted nutrient. Natural genetic variation for the DR response exists. Whereas a switch to carbon restriction up to halfway through the lifetime resulted in extreme lifespan extension for wild-type P. anserina, all autophagy-deficient strains had a shorter time window in which ageing could be delayed by DR. Under nitrogen limitation, only PaAtg1 and PaAtg8 mediate the effect of lifespan extension; the other autophagy-deficient mutants PaPspA and PaUth1 had a similar response as wild-type. Our results thus show that the ageing process impinges on the DR response and that this at least in part involves the genetic regulation of autophagy.     

Combined effect of temperature and bleaching herbicides on photosynthesis,pigment and fatty acid composition of Chlamydomonas reinhardtii

Norflurazon (Nf) and fluridone (Fd) are phytoene desaturase inhibitor herbicides that are widely used for the control of grasses and invasive aquatic weeds, respectively. These herbicides enter aquatic environments where they can negatively affect non-target plant species (e.g. algae). Their toxicity towards algae may be modified by abiotic factors such as light intensity, temperature, pH and nutrients. Investigating the effect of low temperature on the toxicity of Nf and Fd is particularly important because both temperature and herbicides affect some of the same physiological process (e.g. carotenoid biosynthesis). Here we demonstrate that Nf reduced photosynthesis in the green alga Chlamydomonas reinhardtii more strongly at 15 than at 25ºC, while Fd showed stronger effects at 25 than at 15ºC. Neither herbicide significantly inhibited photosynthesis at 8ºC. Although the overall pigment content decreased with lower temperature, there was an increase in photo-protective carotenoids relative to chlorophylls at both 15 and 8ºC in the absence of herbicides. Moreover, most of the measured pigments decreased markedly in the presence of Nf and Fd at 15 and 25ºC, including β-carotene which fell to below detection limits. The fatty acid composition was modified by temperature and the level of unsaturation noticeably increased at 15 compared with 25ºC. At 8ºC, however, despite a 2.4 times decrease in fatty acid content, the unsaturation level was similar to 25ºC acclimated cells. Monounsaturated fatty acids increased concomitant with a decrease in polyunsaturated fatty acid in the 2.5 µM Nf treatment at 25ºC. Differences in the effect of Nf and Fd on photosynthesis at 15 and 25ºC can be attributed to the marked decrease in carotenoids, which play an important role in photoprotection. At 8ºC, the apparent lack of inhibitory effects compared with control cultures could be due to enhanced photoprotection and/or decreased uptake of herbicides by the alga.     

Impact of plant architecture and extraguild prey density on intraguild predation in an agroecosystem

Several models and experimental studies conducted in confined environments have shown that intraguild predation (IGP) can modulate population abundances and structure communities. A number of ecological and abiotic factors determine the nature and frequency of IGP. This study examined the effect of plant architecture and extraguild prey density, and their interactions, on the occurrence of IGP between two species of ladybird, Harmonia axyridis (Pallas) and Propylea quatuordecimpunctata L. (both Coleoptera: Coccinellidae). Theoretical concepts predict that IGP levels would increase with a decrease of both extraguild prey density and plant structural complexity. We conducted a factorial experiment in an open soybean field into which coccinellid larvae were introduced in experimental plots for a period of 5 days. We tested two levels of soybean aphid [Aphis glycines Matsumara (Hemiptera: Aphididae)] density, low and high (100 and 1 000 aphids per plot, respectively), and two levels of plant complexity, low (by removing half of the branches from the soybean plants) and high (by leaving plants intact). We used species‐specific molecular markers to detect the presence of P. quatuordecimpunctata in the digestive tract of H. axyridis. Molecular gut‐content analysis of H. axyridis revealed that rates of IGP were higher (20%) at low aphid density than at high aphid density (<6%). Decreased plant complexity did not impact the frequency of IGP. In accordance with existing literature, this study demonstrates that IGP is amplified at low extraguild prey density. We conclude that considering environmental factors, such as extraguild prey density, is crucial to improve our ability to predict the impact of intraguild predation on community structure and, from an applied perspective, biological control.     

New horizons in schizophrenia treatment: autophagy protection is coupled with behavioral improvements in a mouse model of schizophrenia

Autophagy plays a key role in the pathophysiology of schizophrenia as manifested by a 40% decrease in BECN1/Beclin 1 mRNA in postmortem hippocampal tissues relative to controls. This decrease was coupled with the deregulation of the essential ADNP (activity-dependent neuroprotector homeobox), a binding partner of MAP1LC3B/LC3B (microtubule-associated protein 1 light chain 3 β) another major constituent of autophagy. The drug candidate NAP (davunetide), a peptide fragment from ADNP, enhanced the ADNP-LC3B interaction. Parallel genetic studies have linked allelic variation in the gene encoding MAP6/STOP (microtubule-associated protein 6) to schizophrenia, along with altered MAP6/STOP protein expression in the schizophrenic brain and schizophrenic-like behaviors in Map6-deficient mice. In this study, for the first time, we reveal significant decreases in hippocampal Becn1 mRNA and reversal by NAP but not by the antipsychotic clozapine (CLZ) in Map6-deficient (Map6^+/−) mice. Normalization of Becn1 expression by NAP was coupled with behavioral protection against hyperlocomotion and cognitive deficits measured in the object recognition test. CLZ reduced hyperlocomotion below control levels and did not significantly affect object recognition. The combination of CLZ and NAP resulted in normalized outcome behaviors. Phase II clinical studies have shown NAP-dependent augmentation of functional activities of daily living coupled with brain protection. The current studies provide a new mechanistic pathway and a novel avenue for drug development.     

Genome-wide association mapping of three important traits using bread wheat elite breeding populations

The exponential development of molecular markers enables a more effective study of the genetic architecture of traits of economic importance, like test weight in wheat (Triticum aestivum L.), for which a high value is desired by most end-users. The association mapping (AM) method now allows more precise exploration of the entire genome. AM requires populations with substantial genetic variability of the traits of interest. The breeding lines at the end of a selection cycle, characterized for numerous traits, represent a potentially useful population for AM studies. Using three elite line populations, selected by several breeders and genotyped with about 2,500 Diversity Arrays Technology markers, several associations were identified between these markers and test weight, grain yield and heading date. To minimize spurious associations, we compared the general linear model and mixed linear model (MLM), which adjust for population structure and kinship differently. The MLM model with the kinship matrix was the most efficient. Finally, elite lines from several breeding programs had sufficient genetic variability to allow for the mapping of several chromosomal regions involved in the variation of three important traits.     

The invasive Leptoglossus seed bug,a threat for commercial seed crops,but for conifer diversity?

Among the recent introductions of alien insects in Europe, the polyphagous western conifer seed bug, Leptoglossus occidentalis Heidemann (Heteroptera; Coreidae) can seriously be regarded as a major threat for all the European conifer forests. In the current study combining laboratory and field experimentations, we characterized first bug damage by developing specific damage categories on seeds of different conifer species by the use of X-ray. Secondly, we investigated the impact of the invasive bug on key conifer species used for afforestation in Western and Central Europe. For this purpose, we performed germination tests on predated seeds which revealed that even light damage (consumption of <1/3 of the whole seed content) strongly reduced the germination capability of the seed. We also compared the impact of feeding on the proportion of filled seeds. Second year cones of Pinus sylvestris and Pinus nigra have been enclosed and offered to different life stages (nymphs and adults) and the results showed a significant reduction of filled seeds whatever the life stage. In field, we annually surveyed the bug seed damage for six different conifer species planted in southwestern French seed orchards. Taking into account the economic value of improved seeds in seed orchards, economic impact of bug damage was important although never exceeded 25 %. Two natural or semi-natural alpine pine stands were also surveyed and appeared to be highly affected by the bug (up to 70 % of damaged seeds). Therefore, bug damage could also be considered as a serious threat for seed production in natural stands.     

Prioritizing causal disease genes using unbiased genomic features

Background

Cardiovascular disease (CVD) is the leading cause of death in the developed world. Human genetic studies, including genome-wide sequencing and SNP-array approaches, promise to reveal disease genes and mechanisms representing new therapeutic targets. In practice, however, identification of the actual genes contributing to disease pathogenesis has lagged behind identification of associated loci, thus limiting the clinical benefits.

Results

To aid in localizing causal genes, we develop a machine learning approach, Objective Prioritization for Enhanced Novelty (OPEN), which quantitatively prioritizes gene-disease associations based on a diverse group of genomic features. This approach uses only unbiased predictive features and thus is not hampered by a preference towards previously well-characterized genes. We demonstrate success in identifying genetic determinants for CVD-related traits, including cholesterol levels, blood pressure, and conduction system and cardiomyopathy phenotypes. Using OPEN, we prioritize genes, including FLNC, for association with increased left ventricular diameter, which is a defining feature of a prevalent cardiovascular disorder, dilated cardiomyopathy or DCM. Using a zebrafish model, we experimentally validate FLNC and identify a novel FLNC splice-site mutation in a patient with severe DCM.

Conclusion

Our approach stands to assist interpretation of large-scale genetic studies without compromising their fundamentally unbiased nature.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-014-0534-8) contains supplementary material, which is available to authorized users.     

Characterization of Glycosaminoglycan (GAG) Sulfatases from the Human Gut Symbiont Bacteroides thetaiotaomicron Reveals the First GAG-specific Bacterial Endosulfatase

Despite the importance of the microbiota in human physiology, the molecular bases that govern the interactions between these commensal bacteria and their host remain poorly understood. We recently reported that sulfatases play a key role in the adaptation of a major human commensal bacterium, Bacteroides thetaiotaomicron, to its host (Benjdia, A., Martens, E. C., Gordon, J. I., and Berteau, O. (2011) J. Biol. Chem. 286, 25973–25982). We hypothesized that sulfatases are instrumental for this bacterium, and related Bacteroides species, to metabolize highly sulfated glycans (i.e. mucins and glycosaminoglycans (GAGs)) and to colonize the intestinal mucosal layer. Based on our previous study, we investigated 10 sulfatase genes induced in the presence of host glycans. Biochemical characterization of these potential sulfatases allowed the identification of GAG-specific sulfatases selective for the type of saccharide residue and the attachment position of the sulfate group. Although some GAG-specific bacterial sulfatase activities have been described in the literature, we report here for the first time the identity and the biochemical characterization of four GAG-specific sulfatases. Furthermore, contrary to the current paradigm, we discovered that B. thetaiotaomicron possesses an authentic GAG endosulfatase that is active at the polymer level. This type of sulfatase is the first one to be identified in a bacterium. Our study thus demonstrates that bacteria have evolved more sophisticated and diverse GAG sulfatases than anticipated and establishes how B. thetaiotaomicron, and other major human commensal bacteria, can metabolize and potentially tailor complex host glycans.     

F-Box Only Protein 31 (FBXO31) Negatively Regulates p38 Mitogen-activated Protein Kinase (MAPK) Signaling by Mediating Lysine 48-linked Ubiquitination and Degradation of Mitogen-activated Protein Kinase Kinase 6 (MKK6)

The p38 MAPK signal transduction pathway plays an important role in inflammatory and stress responses. MAPKK6 (MKK6), a dual specificity protein kinase, is a p38 activator. Activation of the MKK6-p38 pathway is kept in check by multiple layers of regulations, including autoinhibition, dimerization, scaffold proteins, and Lys-63-linked polyubiquitination. However, the mechanisms underlying deactivation of MKK6-p38, which is crucial for maintaining the magnitude and duration of signal transduction, are not well understood. Lys-48-linked ubiquitination, which marks substrates for proteasomal degradation, is an important negative posttranslational regulatory machinery for signal pathway transduction. Here we report that the accumulation of F-box only protein 31 (FBXO31), a component of Skp1·Cul1·F-box protein E3 ligase, negatively regulated p38 activation in cancer cells upon genotoxic stresses. Our results show that FBXO31 binds to MKK6 and mediates its Lys-48-linked polyubiquitination and degradation, thereby functioning as a negative regulator of MKK6-p38 signaling and protecting cells from stress-induced cell apoptosis. Taken together, our findings uncover a new mechanism of deactivation of MKK6-p38 and substantiate a novel regulatory role of FBXO31 in stress response.