Molecular basis for the selective recognition and ubiquitination of centromeric histone H3 by yeast E3 ligase Psh1

Centromeres are chromosomal loci marked by histone variant Cen H3(centromeric histone H3) and essential for genomic stability and cell division. The budding yeast E3 ubiquitin ligase Psh1 selectively recognizes the yeast Cen H3(Cse4) for ubiquitination and controls the cellular level of Cse4 for proteolysis,but the underlying mechanism remains largely unknown. Here, we show that Psh1 uses a Cse4-binding domain(CBD, residues 1-211) to interact with Cse4-H4 instead of H3-H4, yielding a dissociation constant(K_d) of 27 nM. Psh1 recognizes Cse4-specific residues in the L1 loop and a2 helix to ensure Cse4 binding and ubiquitination. We map the Psh1-binding region of Cse4-H4 and identify a wide range of Cse4-specific residues required for the Psh1-mediated Cse4 recognition and ubiquitination. Further analyses reveal that histone chaperone Scm3 can impair Cse4 ubiquitination by abrogating Psh1-Cse4 binding. Together, our study reveals a novel Cse4-binding mode distinct from those of known Cen H3 chaperones and elucidates the mechanism by which Scm3 competes with Psh1 for Cse4 binding.     

Design a system for measuring individual cow feed intake in commercial dairies

Monitoring individual cow feed intake is necessary for calculating the cow individual feed efficiency. The cost and maintenance time necessary for research systems make them impractical for most of the commercial producers. We developed a measurement system with producer convenience and low investment as key design criteria. The goal of this study was to design the system and validate its ability to rank cows by their feed conversion efficiency in commercial farms. The new system consisted of three principal parts: (a) a hanging weighing system, (b) a visual cow identification system and (c) an automatic cleaning system. The weighing system consisted of hanging a single load cell to provide feed mass measurements. The image-based cow identification system (replacing Radio-Frequency Identification) entailed cameras installed above the feeding area and an image processing algorithm that recognized cows by their collar numbers. The new system worked within normal farm routines: the feed supplying truck distributed the animal feed, and a tractor cleaned feed residual. To validate the accuracy and convenience of the system and to rank the cows by their efficiency, an experiment with six scales and 12 cows was conducted in a research barn, succeeded by eight-scale system in a commercial farm with 16 cows. The feed intake of each cow participating in the experiments was monitored for one month. The validation experiment showed that the system had the following specification: scales were accurate within 120 g; the visual cow identification rate was greater than 96%; feeding duration was accurate to 52 s; and routine farm practices (feed distribution, pushing, and residual removal) continued as usual. The cost for a feeding station (utilized consequently for a number of cows) was about 1 500 USD. An example of application of the system to rank cows by their efficiency under commercial conditions was shown. The system can potentially be used for ranking cows by their efficiency in commercial facilities.     

Seasonal changes in cuticular hydrocarbons in response to polyphenism in the host-alternating aphid Prociphilus oriens

In most terrestrial arthropods, cuticular hydrocarbons (CHCs) function to assist in desiccation tolerance and chemical communications. However, few studies have clarified whether CHC profiles change among developmental stages or among different morphs in non-social insects. In the present study, we evaluated how CHC profiles change in accordance with polyphenism in the host-alternating aphid Prociphilus oriens, which exhibits a complex life cycle and five distinct morphs. These morphs are sexual or asexual and adapt to different host plants. We found that all generations of P. oriens shared high proportions of n-alkanes, but its composition varied among morphs. Three morphs that are attended by ants were characterized by relatively high proportions of n-C25 to n-C27, whereas two morphs that are not attended by ants had higher proportions of longer-chain n-alkanes, such as n-C27 and n-C29. The CHC profiles of sexual females were largely different from those of males. Considering that sexual females of Prociphilus spp. lack organs that secrete sex pheromones (scent plaques), the CHCs of sexual females are likely to function as a sex attractant. High proportions of methyl-branched alkanes were detected in the long and flocculent waxy substances of autumnal migrants. These methyl-branched alkanes are considered a cue to recognize conspecifics. We concluded that the functions and components of CHCs differ among morphs, and that those of sexual females differ from those of males and asexual generations because of their function in sexual communication.     

Multicomponent shell traits are consistent with an individual recognition function of the appearance of common murre (Uria aalge) eggs: A biological replication study

In dense breeding colonies, and despite having no nest structure, common murres (or guillemots: Uria aalge) are still able to identify their own eggs. Each female murre''s egg is thought to be recognized individually by the shell''s avian‐perceivable traits. This is because the eggshells’ visible traits conform to expectations of the identity‐signaling hypothesis in that they show both high intraindividual repeatability and high interindividual variability. Identity signaling also predicts a lack of correlation between each of the putative multicomponent recognition traits, yielding no significant relationships between those eggshell traits that are generated by mutually exclusive physiological factors. Using a multivariate analysis across eggshell size and shape, avian‐perceivable background coloration, spot (maculation) shape, and spot density, we detected no unexpected statistical correlations between Icelandic common murre egg traits lacking known physiological or mathematical relationships with one another. These results biologically replicate the conclusions of a recent eggshell trait study of Canadian common murres using similar methodology. We also demonstrate the use of static correlations to infer identity signaling function without direct behavioral observations, which in turn may also be applied to rare or extinct species and provide valuable insight into otherwise unknown communicative and behavioral functions.     

Multicoloured greenbeards,bacteriocin diversity and the rock‐paper‐scissors game

Greenbeard genes identify copies of themselves in other individuals and cause their bearer to behave nepotistically towards those individuals. Bacterial toxins (bacteriocins) exemplify the greenbeard effect because producer strains carry closely linked genes for immunity, such that toxicity is limited to nonproducer strains. Bacteriocin producers can be maintained in a dynamic polymorphism, known as rock‐paper‐scissors (RPS) dynamics, with immune and susceptible strains. However, it is unclear whether and how such dynamics will be maintained in the presence of multiple toxin types (multiple beard ‘colours’). Here, we analyse strain dynamics using models of recurrent patch colonization and population growth. We find that (i) polymorphism is promoted by a small number of founding lineages per patch, strong local resource competition and the occurrence of mutations; (ii) polymorphism can be static or dynamic, depending on the intensity of local interactions and the costs of toxins and immunity; (iii) the occurrence of multiple toxins can promote RPS dynamics; and (iv) strain diversity can be maintained even when toxins differ in toxicity or lineages can exhibit multitoxicity/multi‐immunity. Overall, the factors that maintain simple RPS dynamics can also promote the coexistence of multiple toxin types (multiple beard colours), thus helping to explain the remarkable levels of bacteriocin diversity in nature. More generally, we contrast these results with the maintenance of marker diversity in genetic kin recognition.     

Conformational insights on the molecular recognition processes of carbohydrate molecules by proteins and enzymes: A 3D view by using NMR

This review focuses, in a non-exhaustive manner, on the essential structural and conformational features of protein–carbohydrate interactions and on some applications of NMR spectroscopy to deal with this topic from different levels of complexity.     

All roads lead to Rome (but some may be harder to travel): SRP-independent translocation into the endoplasmic reticulum

Abstract

Translocation into the endoplasmic reticulum (ER) is the first biogenesis step for hundreds of eukaryotic secretome proteins. Over the past 30 years, groundbreaking biochemical, structural and genetic studies have delineated one conserved pathway that enables ER translocation- the signal recognition particle (SRP) pathway. However, it is clear that this is not the only pathway which can mediate ER targeting and insertion. In fact, over the past decade, several SRP-independent pathways have been uncovered, which recognize proteins that cannot engage the SRP and ensure their subsequent translocation into the ER. These SRP-independent pathways face the same challenges that the SRP pathway overcomes: chaperoning the preinserted protein while in the cytosol, targeting it rapidly to the ER surface and generating vectorial movement that inserts the protein into the ER. This review strives to summarize the various mechanisms and machineries which mediate these stages of SRP-independent translocation, as well as examine why SRP-independent translocation is utilized by the cell. This emerging understanding of the various pathways utilized by secretory proteins to insert into the ER draws light to the complexity of the translocational task, and underlines that insertion into the ER might be more varied and tailored than previously appreciated.     

Beyond Eyeballing: Fitting Models to Experimental Data

Abstract

As we learn more about the biology of the Toll-like receptors (TLRs), a wide range of molecules that can activate this fascinating family of pattern recognition receptors emerges. In addition to conserved pathogenic components, endogenous danger signals created upon tissue damage are also sensed by TLRs. Detection of these types of stimuli results in TLR mediated inflammation that is vital to fight pathogenic invasion and drive tissue repair. Aberrant activation of TLRs by pathogenic and endogenous ligands has also been linked with the pathogenesis of an increasing number of infectious and autoimmune diseases, respectively. Most recently, allergen activation of TLRs has also been described, creating a third broad class of TLR stimulus that has helped to shed light on the pathogenesis of allergic disease. To date, microbial activation of TLRs remains best characterized. Each member of the TLR family senses a specific subset of pathogenic ligands, pathogen associated molecular patterns (PAMPS), and a wealth of structural and biochemical data continues to reveal the molecular mechanisms of TLR activation by PAMPs, and to demonstrate how receptor specificity is achieved. In contrast, the mechanisms by which endogenous molecules and allergens activate TLRs remain much more mysterious. Here, we provide an overview of our current knowledge of how very diverse stimuli activate the same TLRs and the structural basis of these modes of immunity.     

Dopamine Receptor Microdomains Involved in Molecular Recognition and the Regulation of Drug Affinity and Function

A cationic protonatable amine moiety on dopaminergic ligands forms a high affinity reinforced ionic bond with an anionic aspartic acid at position 3.32 of dopamine receptors. When present, catechol hydroxyls of the ligands form hydrogen bonds with serines at position 5.42, 5.43, and 5.46, and this network of hydrogen bonds serves to orient ligands in the binding-site crevice and increase their binding affinity. A steric clash between aromatic moieties of the ligands and aromatic amino acids of the receptor (e.g., H6.55, F6.52 or F6.51 and W6.48) is likely to be propagated in domino-like fashion along the length of TM6, which is believed to trigger activation of the receptor. Specifically, it is the change in the conformation of W6.48 from an orientation perpendicular to the plane of the lipid membrane to one that is parallel that is believed to result in activation. Molecular determinants that mediate the D4/D2-selectivity of many extremely D4-selective 1,4-DAP ligands, include a nonconserved cluster of bulky amino acids at the TM2/TM3 interface (positions 2.61, 3.28 and 3.29).     

ANALYSIS OF LIGAND–RECEPTOR INTERACTIONS IN CELLS BY ATOMIC FORCE MICROSCOPY

ABSTRACT

Atomic force microscopy (AFM) increasingly has been used to analyse “receptor” function, either by using purified proteins (“molecular recognition microscopy”) or, more recently, in situ in living cells. The latter approach has been enabled by the use of a modified commercial AFM, linked to a confocal microscope, which has allowed adhesion forces between ligands and receptors in cells to be measured and mapped, and downstream cellular responses analysed. We review the application of AFM to cell biology and, in particular, to the study of ligand–receptor interactions and draw examples from our own work and that of others to show the utility of AFM, including for the exploration of cell surface functionalities. We also identify shortcomings of AFM in comparison to “standard” methods, such as receptor auto-radiography or immuno-detection, that are widely applied in cell biology and pharmacological analysis.