Catalytic and Functional Roles of Conserved Amino Acids in the SET Domain of the S. cerevisiae Lysine Methyltransferase Set1

In S. cerevisiae, the lysine methyltransferase Set1 is a member of the multiprotein complex COMPASS. Set1 catalyzes mono-, di- and trimethylation of the fourth residue, lysine 4, of histone H3 using methyl groups from S-adenosylmethionine, and requires a subset of COMPASS proteins for this activity. The methylation activity of COMPASS regulates gene expression and chromosome segregation in vivo. To improve understanding of the catalytic mechanism of Set1, single amino acid substitutions were made within the SET domain. These Set1 mutants were evaluated in vivo by determining the levels of K4-methylated H3, assaying the strength of gene silencing at the rDNA and using a genetic assessment of kinetochore function as a proxy for defects in Dam1 methylation. The findings indicate that no single conserved active site base is required for H3K4 methylation by Set1. Instead, our data suggest that a number of aromatic residues in the SET domain contribute to the formation of an active site that facilitates substrate binding and dictates product specificity. Further, the results suggest that the attributes of Set1 required for trimethylation of histone H3 are those required for Pol II gene silencing at the rDNA and kinetochore function.     

PTM MarkerFinder,a software tool to detect and validate spectra from peptides carrying post‐translational modifications

Mass spectrometry (MS) analysis of peptides carrying post‐translational modifications is challenging due to the instability of some modifications during MS analysis. However, glycopeptides as well as acetylated, methylated and other modified peptides release specific fragment ions during CID (collision‐induced dissociation) and HCD (higher energy collisional dissociation) fragmentation. These fragment ions can be used to validate the presence of the PTM on the peptide. Here, we present PTM MarkerFinder, a software tool that takes advantage of such marker ions. PTM MarkerFinder screens the MS/MS spectra in the output of a database search (i.e., Mascot) for marker ions specific for selected PTMs. Moreover, it reports and annotates the HCD and the corresponding electron transfer dissociation (ETD) spectrum (when present), and summarizes information on the type, number, and ratios of marker ions found in the data set. In the present work, a sample containing enriched N‐acetylhexosamine (HexNAc) glycopeptides from yeast has been analyzed by liquid chromatography‐mass spectrometry on an LTQ Orbitrap Velos using both HCD and ETD fragmentation techniques. The identification result (Mascot .dat file) was submitted as input to PTM MarkerFinder and screened for HexNAc oxonium ions. The software output has been used for high‐throughput validation of the identification results.     

Generative FDG-PET and MRI Model of Aging and Disease Progression in Alzheimer's Disease

The failure of current strategies to provide an explanation for controversial findings on the pattern of pathophysiological changes in Alzheimer''s Disease (AD) motivates the necessity to develop new integrative approaches based on multi-modal neuroimaging data that captures various aspects of disease pathology. Previous studies using [18F]fluorodeoxyglucose positron emission tomography (FDG-PET) and structural magnetic resonance imaging (sMRI) report controversial results about time-line, spatial extent and magnitude of glucose hypometabolism and atrophy in AD that depend on clinical and demographic characteristics of the studied populations. Here, we provide and validate at a group level a generative anatomical model of glucose hypo-metabolism and atrophy progression in AD based on FDG-PET and sMRI data of 80 patients and 79 healthy controls to describe expected age and symptom severity related changes in AD relative to a baseline provided by healthy aging. We demonstrate a high level of anatomical accuracy for both modalities yielding strongly age- and symptom-severity- dependant glucose hypometabolism in temporal, parietal and precuneal regions and a more extensive network of atrophy in hippocampal, temporal, parietal, occipital and posterior caudate regions. The model suggests greater and more consistent changes in FDG-PET compared to sMRI at earlier and the inversion of this pattern at more advanced AD stages. Our model describes, integrates and predicts characteristic patterns of AD related pathology, uncontaminated by normal age effects, derived from multi-modal data. It further provides an integrative explanation for findings suggesting a dissociation between early- and late-onset AD. The generative model offers a basis for further development of individualized biomarkers allowing accurate early diagnosis and treatment evaluation.     

A Large Plasmodium vivax Reservoir and Little Population Structure in the South Pacific

Introduction

The importance of Plasmodium vivax in malaria elimination is increasingly being recognized, yet little is known about its population size and population genetic structure in the South Pacific, an area that is the focus of intensified malaria control.

Methods

We have genotyped 13 microsatellite markers in 295 P. vivax isolates from four geographically distinct sites in Papua New Guinea (PNG) and one site from Solomon Islands, representing different transmission intensities.

Results

Diversity was very high with expected heterozygosity values ranging from 0.62 to 0.98 for the different markers. Effective population size was high (12′872 to 19′533 per site). In PNG population structuring was limited with moderate levels of genetic differentiation. F _ST values (adjusted for high diversity of markers) were 0.14–0.15. Slightly higher levels were observed between PNG populations and Solomon Islands (F _ST = 0.16).

Conclusions

Low levels of population structure despite geographical barriers to transmission are in sharp contrast to results from regions of low P. vivax endemicity. Prior to intensification of malaria control programs in the study area, parasite diversity and effective population size remained high.     

First experimental evidence of corals feeding on seagrass matter

We present the first experimental evidence of a coral (Oulastrea crispata) ingesting and assimilating seagrass material. Tropical seagrass meadows export a substantial portion of their productivity and can provide an important source of nutrients to neighbouring systems such as coral reefs; however, little is known about the mechanisms of this link. To investigate whether seagrass nutrient uptake via coral heterotrophy is possible, we conducted a feeding experiment with seagrass particulate and dissolved organic matter. Using gut extractions and stable isotope analyses, we determined that O. crispata ingested ¹⁵N-enriched seagrass particles and assimilated the nitrogen into its tissue at a rate of 0.75 μg N cm^?2 h^?1. Corals took up nitrogen from dissolved matter at a comparable rate of 0.98 μg N cm^?2 h^?1. While other ecological connections between seagrass meadows and reef ecosystems are well known, our results suggest a previously unstudied direct nutritional link between seagrasses and corals.     

Lipoxygenase6-Dependent Oxylipin Synthesis in Roots Is Required for Abiotic and Biotic Stress Resistance of Arabidopsis

Jasmonates are oxylipin signals that play important roles in the development of fertile flowers and in defense against pathogens and herbivores in leaves. The aim of this work was to understand the synthesis and function of jasmonates in roots. Grafting experiments with a jasmonate-deficient mutant demonstrated that roots produce jasmonates independently of leaves, despite low expression of biosynthetic enzymes. Levels of 12-oxo-phytodienoic acid, jasmonic acid, and its isoleucine derivative increased in roots upon osmotic and drought stress. Wounding resulted in a decrease of preformed 12-oxo-phytodienoic acid concomitant with an increase of jasmonic acid and jasmonoyl-isoleucine. 13-Lipoxygenases catalyze the first step of lipid oxidation leading to jasmonate production. Analysis of 13-lipoxygenase-deficient mutant lines showed that only one of the four 13-lipoxygenases, LOX6, is responsible and essential for stress-induced jasmonate accumulation in roots. In addition, LOX6 was required for production of basal 12-oxo-phytodienoic acid in leaves and roots. Loss-of-function mutants of LOX6 were more attractive to a detritivorous crustacean and more sensitive to drought, indicating that LOX6-derived oxylipins are important for the responses to abiotic and biotic factors.Oxylipins are ubiquitous signaling molecules that are derived from polyunsaturated fatty acids by enzymatic and nonenzymatic processes. In plants, the biosynthesis and function of oxylipins of the jasmonate family in aboveground tissues has been investigated in detail. Jasmonates comprise 12-oxo-phytodienoic acid (OPDA), jasmonic acid (JA), and derivatives of JA. In leaves, jasmonates accumulate in response to abiotic factors such as wounding, drought, osmotic stress, darkness, and ozone and during interactions with organisms such as herbivores, pathogens, and mutualistic organisms (Wasternack, 2007). The relevance of jasmonates in wound response, ozone tolerance, and the defense against herbivores and necrotrophic pathogens in leaves has been well investigated using mutants in JA biosynthesis and signaling (Browse, 2009a). In addition, jasmonates play an important role in flower development, and Arabidopsis (Arabidopsis thaliana) mutants in the JA pathway are male sterile (Browse, 2009b). The first step in jasmonate biosynthesis is catalyzed by 13-lipoxygenases (LOXs). The resulting 13(S)-hydroperoxyoctadecatrienoic acid (13-HPOTE) is converted by allene oxide synthase (AOS) and allene oxide cyclase to OPDA (Wasternack, 2007). These enzymatic steps are located in plastids. OPDA is transported to peroxisomes and converted to JA. JA can be further metabolized to different derivatives that take place mainly in the cytosol. The conjugation of JA with Ile is an important step because jasmonoyl-Ile (JA-Ile) has been identified as a biologically active jasmonate (Staswick and Tiryaki, 2004). OPDA is also biologically active without conversion to JA derivatives. In contrast to all other jasmonates, the OPDA structure contains an electrophilic α,β-unsaturated carbonyl group that renders OPDA more reactive than JA. Therefore, OPDA is classified as a reactive electrophile species with unique signaling properties different from other jasmonates (Farmer and Davoine, 2007).Of the six lipoxygenase genes present in Arabidopsis, four genes encode 13-LOX. For the respective enzymes LOX2, LOX3, LOX4, and LOX6, it was shown that linolenic acid is the preferred substrate and that 13-HPOTE is formed in vitro (Bannenberg et al., 2009). All four enzymes are proposed to be located in plastids. LOX2 is highly expressed in leaves; expression is up-regulated by jasmonates and stress treatments such as wounding and osmotic stress (Bell and Mullet, 1993; Seltmann et al., 2010a). LOX2 was shown to contribute the majority of jasmonate synthesis upon wounding and osmotic stress and during senescence in leaves (Bell et al., 1995; Glauser et al., 2009). LOX2 is also responsible for the accumulation of arabidopsides (Glauser et al., 2009), which are galactolipids containing esterified OPDA in plastids by direct oxidation of galactolipids (Zoeller et al., 2012). LOX3 and LOX4 are required for the development of fertile flowers (Caldelari et al., 2011). LOX6 shows overall low expression (Bannenberg et al., 2009). Recently, it was reported that LOX6 contributes to the fast accumulation of JA and JA-Ile in wounded leaves and is required for the fast increase of JA and JA-Ile in distal leaves after wounding (Chauvin et al., 2013).In contrast to leaves and flowers, little is known on jasmonate biosynthesis and function in roots. Expression of the plastid-localized enzymes of jasmonate synthesis LOX2, AOS, and allene oxide cyclase2 is very low in roots (Zimmermann et al., 2004). By contrast, enzymes such as 9-LOX and α-dioxygenase1 are strongly expressed in roots. These enzymes are involved in the biosynthesis of oxylipins different from jasmonates, and 9-LOX products have been shown to regulate lateral root development because mutants in LOX1 and LOX5 produce more lateral roots (Vellosillo et al., 2007). However, jasmonate function in roots is still obscure. Here, we analyzed jasmonate accumulation in roots upon different stress treatments and show that mutants defective in LOX6 are impaired in stress-induced jasmonate synthesis and are more susceptible to drought and detritivore feeding.