A picky eater: exploring the mechanisms of selective autophagy in human pathologies

Autophagy is a catabolic process conserved among all eukaryotes essential for the cellular and organismal homeostasis. One of the principal roles of this pathway is to maintain an accurate balance between synthesis, degradation and subsequent recycling of cellular components. Under certain conditions, however, cells are also able to modulate autophagy and specifically remove a number of structures that are potentially harmful. Aberrant protein aggregates, damaged organelles or pathogens can be selectively incorporated into large double-membrane vesicles called autophagosomes to be delivered into lysosomes for destruction. This ability to eliminate specific structures is exploited by the cells in several physiological processes as well as in multiple pathological situations, making autophagy a precious multitask cellular degradative pathway. In this review, we will first examine what is known about the basic mechanisms of autophagy and then discuss in a second part the nature of the cargoes that are selectively sequestered into autophagosomes, what provides the specificity and the possible implications of selective types of autophagy in human pathologies.     

Sex and pollen: the role of males in stabilising a plant-seed eater pollinating mutualism

Some plants are exclusively pollinated by an insect whose larvae feed on their seeds. The net outcome of a single visit for the plant depends on the number of ovules fertilised by the visitor, the number of eggs laid, and the number of seeds eaten by each larva. Unlike other known plant-seed eater pollinating mutualisms, the globeflower-globeflower fly mutualism (Trollius europaeus-Chiastocheta spp.) is unique in that not only females but also males visit flowers, and both sexes are potential pollinators. I analysed the relative efficiency of Chiastocheta males versus females in transporting pollen and fertilising globeflower ovules. I show that there is no sex-specific morphological adaptation or behaviour to enhance pollen collection and transportation in Chiastocheta flies, and that males contribute to pollination. However, because of their smaller body size, males transport significantly less pollen than females. Less seeds are produced after a visit from a male than after a visit from a female. A single female visit contributes to about 12% of total seed production, and a single male visit to only 5.4%. Females tend to spend more time inside the flower than males, and the number of ovules fertilised is significantly correlated with the time insects spent inside the closed corolla. The lower efficiency of ovule fertilisation by a male's single visit is compensated for by the higher rate of flower visitation by males: a flower receives about twice as many visits from males as from females during a time unit. The contribution of males to pollination is of major importance with respect to understanding the evolutionary stability of the globeflower-globeflower fly mutualism, as males satiate pollen requirement of flowers, masking the antagonistic effect of ovipositing females.     

Profiling the IgOme: Meeting the challenge

The entire repertoire of antibodies in our serum, the IgOme, is a historical record of our past experiences and a reflection of our immune status at any given moment. Understanding the dynamics of the IgOme and how the diversity and specificities of serum antibodies change in response to disease and maintenance of homeostasis can directly impact the ability to design and develop novel vaccines, diagnostics and therapeutics. Here we review both direct and indirect methodologies that are being developed to map the complexity and specificities of the antibodies in polyclonal serum – the IgOme.     

The paradox of the adventurous young and the cautious old: natural selection vs. rational calculation.

Younger people are more adventurous and less willing to reduce the risk to life. This seems to be fitness reducing since the gene cannot be passed on if one dies before leaving offsprings. However, due to the cumulative nature of knowledge and the complementarity of learning and adventurousness, it is shown in a simple model that it enhances fitness. Nevertheless, the higher willingness of the old to pay to reduce the risk to life may also be due to the rational calculation of expected utility maximization. A positive real rate of interest makes accumulation of wealth desirable and hence may make the dollar value of life increase dramatically until a fairly old age. Even if the lifetime earnings of everyone are the same and everyone can lend and borrow at the same rate of interest, the old may be willing to pay much more to reduce the risk to life.     

Postprandial responses in the African rhombig egg eater (Dasypeltis scabra)

The African rhombic egg eater (Dasypeltis scabra) is a colubrid snake feeding exclusively on bird eggs. Frequency of feeding is governed by the seasonal availability of bird eggs; i.e., long fasting intervals change with relatively short periods when plenty of food is available. Intermittent feeding snakes show a remarkable postprandial increase of metabolic rate and digestive organ size. The postprandial increase in metabolic rate (specific dynamic action, SDA) in snakes is affected by meal size, temperature, and meal composition. A major portion of SDA in snakes is allocated to gastric function and the breakdown of the meal. We hypothesize that SDA in egg eaters is lower than in other snake species, because egg eaters feed on “liquid” food that does not require enzymatic breakdown in the stomach. We also hypothesized that other components of the postprandial response of egg eaters (e.g., size changes of the intestine and the liver) do not differ from other snakes. The standard metabolic rate and metabolic response to feeding were measured using closed-chamber respirometry. Size changes of small intestine and liver were measured using high-resolution transcutaneous ultrasonography. Standard metabolic rates of fasting egg eaters were in the same range of mass specific values as known from other snakes. Within 24 h after feeding, oxygen consumption doubled and peaked at 2 days after feeding. At the same time, the size of the small intestine and the cross-sectional diameter of the liver increased. Within 2 days after feeding, the size of the mucosal epithelium doubled its thickness. Liver size increased significantly within 24 h reaching maximum size 2–4 days after feeding. The size of both organs returned to fasting values within 7–10 days after feeding. The postprandial response of African rhombic egg eaters shows the same pattern and dynamics as known from other snake species. However, the factorial increase of metabolic rate during SDA is the lowest reported for any snake. A comparison with literature data supports the idea that SDA is mainly determined by gastric function and that it is low in egg eaters because they do not have to break down solid meals in the stomach as other snake species do.     

Microsatellite loci in the European bee‐eater,Merops apiaster

Twelve polymorphic microsatellite markers have been developed for the European bee‐eater, Merops apiaster (Coraciiformes: Meropidae). Screening of eight individuals at these loci showed that the average allelic diversity was 5.8, with a range of two to 11 alleles per locus. The loci reported here will provide insight into the levels of extra‐pair parentage, kin selection and dispersal in this species, which has co‐operative breeding and nests in large colonies.     

The role of the cell surface in social and adventurous behaviour of myxobacteria

The myxobacteria are an unusually social group of prokaryotic organisms that form fruiting bodies containing dormant myxospores in response to nutritional stress. Social behaviour is controlled by a multigene system known as 'S' and by a series of intercellular signals that are released during development. The genes controlling these communication systems have been identified by mutational analysis and current research is directed toward examining the functions of these genes. S- mutants are generally nondevelopmental and noncohesive. They lack pili, a Congo red receptor, and 50-nm-wide fibrils which extend outward from the cell surface. Changes in the architecture of the cell surface have been studied by means of surface labelling and with monoclonal antibodies directed against cell-surface antigens. The cell surface undergoes dramatic changes during the course of development. Most vegetative antigens decrease in concentration or disappear completely while new development-specific antigens appear.     

Morphology of a picky eater: a novel mechanism underlies premaxillary protrusion and retraction within cyprinodontiforms

Upper jaw protrusion is hypothesized to improve feeding performance in teleost fishes by enhancing suction production and stealth of the feeding event. However, many cyprinodontiform fishes (mid-water feeders, such as mosquitofish, killifish, swordtails, mollies and pupfish) use upper jaw protrusion for "picking" prey out of the water column or off the substrate; this feeding mode may require improved jaw dexterity, but does not necessarily require increased stealth and/or suction production. We describe functional aspects of the bones, muscles and ligaments of the anterior jaws in three cyprinodontiform genera: Fundulus (Fundulidae), Gambusia and Poecilia (Poeciliidae). All three genera possess a premaxillomandibular ligament that connects the premaxilla of the upper jaw to the mandible. The architecture of this ligament is markedly different from the upper-lower jaw connections previously described for basal atherinomorphs or other teleosts, and this loose ligamentous connection allows for more pronounced premaxillary protrusion in this group relative to closely related outgroup taxa. Within poeciliids, a novel insertion of the second division of the adductor mandibulae (A2) onto the premaxilla has also evolved, which allows this jaw adductor to actively retract the premaxilla during mouth closing. This movement is in contrast with most other teleosts, where the upper jaw is retracted passively via pressure applied by the adduction of the lower jaw. We postulate that this mechanism of premaxillary protrusion mediates the cyprinodontiforms' ability to selectively pick specific food items from the water column, surface or bottom, as a picking-based feeding mechanism requires controlled and coordinated "forceps-like" movements of the upper and lower jaws. This mechanism is further refined in some poeciliids, where direct muscular control of the premaxillae may facilitate picking and/or scraping material from the substrate.     

Identification of genes required for adventurous gliding motility in Myxococcus xanthus with the transposable element mariner

Myxococcus xanthus glides over solid surfaces without the use of flagella, dependent upon two large sets of adventurous (A) and social (S) genes, using two different mechanisms of gliding motility. Myxococcus xanthus A-S- double mutants form non-motile colonies lacking migratory cells at their edges. We have isolated 115 independent mutants of M. xanthus with insertions of transposon magellan-4 in potential A genes by screening for insertions that reduce the motility of a mutant S- parental strain. These insertions are found not only in the three loci known to be required for A motility, mglBA, cglB, and aglU, but also in 30 new genes. Six of these new genes encode different homologues of the TolR, TolB, and TolQ transport proteins, suggesting that adventurous motility is dependent on biopolymer transport. Other insertions which affect both A and S motility suggest that both systems share common energy and cell wall determinants. Because the spectrum of magellan-4 insertions in M. xanthus is extraordinarily broad, transposon mutagenesis with this eukaryotic genetic element permits the rapid genetic analysis of large sets of genes that contribute to a complex microbial behaviors such as A motility.     

Profiling cancer

In the past couple of years, several very exciting studies have demonstrated the enormous power of gene-expression profiling for cancer classification and prediction of patient survival. In addition to promising a more accurate classification of cancer and therefore better treatment of patients, gene-expression profiling can result in the identification of novel potential targets for cancer therapy and a better understanding of the molecular mechanisms leading to cancer.     

Profiling the Trypanosoma cruzi phosphoproteome

Protein phosphorylation is a reversible post-translational modification essential for the regulation of several signal transduction pathways and biological processes in the living cell. Therefore, the identification of protein phosphorylation sites is crucial to understand cell signaling control at the molecular level. Based on mass spectrometry, recent studies have reported the large-scale mapping of phosphorylation sites in various eukaryotes and prokaryotes. However, little is known about the impact of phosphorylation in protozoan parasites. To in depth characterize the phosphoproteome of Trypanosoma cruzi, a parasite of the Kinetoplastida class, protein samples from cells at different phases of the metacyclogenesis--differentiation process of the parasites from non-infective epimastigotes to infective metacyclic trypomastigotes--were enriched for phosphopeptides using TiO(2) chromatography and analyzed on an LTQ-Orbitrap mass spectrometer. In total, 1,671 proteins were identified, including 753 phosphoproteins, containing a total of 2,572 phosphorylation sites. The distribution of phosphorylated residues was 2,162 (84.1%) on serine, 384 (14.9%) on threonine and 26 (1.0%) on tyrosine. Here, we also report several consensus phosphorylation sequence motifs and as some of these conserved groups have enriched biological functions, we can infer the regulation by protein kinases of this functions. To our knowledge, our phosphoproteome is the most comprehensive dataset identified until now for Kinetoplastida species. Here we also were able to extract biological information and infer groups of sites phosphorylated by the same protein kinase. To make our data accessible to the scientific community, we uploaded our study to the data repositories PHOSIDA, Proteome Commons and TriTrypDB enabling researchers to access information about the phosphorylation sites identified here.     

Phytohormone Profiling across the Bryophytes

BackgroundBryophytes represent a very diverse group of non-vascular plants such as mosses, liverworts and hornworts and the oldest extant lineage of land plants. Determination of endogenous phytohormone profiles in bryophytes can provide substantial information about early land plant evolution. In this study, we screened thirty bryophyte species including six liverworts and twenty-four mosses for their phytohormone profiles in order to relate the hormonome with phylogeny in the plant kingdom.MethodologySamples belonging to nine orders (Pelliales, Jungermanniales, Porellales, Sphagnales, Tetraphidales, Polytrichales, Dicranales, Bryales, Hypnales) were collected in Central and Northern Bohemia. The phytohormone content was analysed with a high performance liquid chromatography electrospray tandem-mass spectrometry (HPLC-ESI-MS/MS).ConclusionThe apparent differences in conjugation and/or degradation strategies of growth hormones between liverworts and mosses might potentially show a hidden link between vascular plants and liverworts. On the other hand, the complement of stress hormones in bryophytes probably correlate rather with prevailing environmental conditions and plant survival strategy than with plant evolution.     

AglZ is a filament-forming coiled-coil protein required for adventurous gliding motility of Myxococcus xanthus

The aglZ gene of Myxococcus xanthus was identified from a yeast two-hybrid assay in which MglA was used as bait. MglA is a 22-kDa cytoplasmic GTPase required for both adventurous and social gliding motility and sporulation. Genetic studies showed that aglZ is part of the A motility system, because disruption or deletion of aglZ abolished movement of isolated cells and aglZ sglK double mutants were nonmotile. The aglZ gene encodes a 153-kDa protein that interacts with purified MglA in vitro. The N terminus of AglZ shows similarity to the receiver domain of two-component response regulator proteins, while the C terminus contains heptad repeats characteristic of coiled-coil proteins, such as myosin. Consistent with this motif, expression of AglZ in Escherichia coli resulted in production of striated lattice structures. Similar to the myosin heavy chain, the purified C-terminal coiled-coil domain of AglZ forms filament structures in vitro.