Novel route to chaetomellic acid A and analogues: Serendipitous discovery of a more competent FTase inhibitor

A new practical route to chaetomellic acid A (ACA), based on the copper catalysed radical cyclization (RC) of (Z)-3-(2,2-dichloropropanoyl)-2-pentadecylidene-1,3-thiazinane, is described. Remarkably, the process entailed: (i) a one-pot preparation of the intermediate N-α-perchloroacyl-2-(Z)-alkyliden-1,3-thiazinanes starting from N-(3-hydroxypropyl)palmitamide, (ii) a two step smooth transformation of the RC products into ACA and (iii) only one intermediate chromatographic purification step. The method offers a versatile approach to the preparation of ACA analogues, through the synthesis of an intermediate maleic anhydride with a vinylic group at the end of the aliphatic tail, a function that can be transformed through a thiol–ene coupling. Serendipitously, the disodium salt of 2-(9-(butylthio)nonyl)-3-methylmaleic acid, that we prepared as a representative sulfurated ACA analogue, was a more competent FTase inhibitor than ACA. This behaviour was analysed by a molecular docking study.     

Preceding hydrophobic and beta-branched amino acids attenuate splicing by the CnePRP8 intein

As the Cne PRP8 intein is active and exists in an essential gene of an important fungal pathogen, inhibitors of splicing and assays for intein activity are of interest. The self-splicing activity of Cne PRP8, the intein from the Prp8 gene of Cryptococcus neoformans, was assessed in different heterologous fusion proteins expressed in Escherichia coli. Placement of a putatively inactive variant of the intein adjacent to the alpha-complementation peptide abolished the peptide's ability to restore beta-galactosidase activity, while an active variant allowed complementation. This alpha-complementation peptide therefore provides a facile assay of splicing which can be used to test potential inhibitors. When placed between two heterologous protein domains, splicing was impaired by a beta-branched amino acid immediately preceding the intein, while splicing occurred only with a hydroxyl or thiol immediately following the intein. Both these assays sensitively report impairment of splicing and provide information on how context constrains the splicing ability of Cne PRP8.     

The nuclear-encoded inteins of fungi

An intein is a protein sequence embedded within a precursor protein that is excised during protein maturation. Inteins were first found encoded in the VMA gene of Saccharomyces cerevisiae. Subsequently, they have been found in diverse organisms (eukaryotes, archaea, eubacteria and viruses). The VMA intein has been found in various saccharomycete yeasts but not in other fungi. Different inteins have now been found widely in the fungi (ascomycetes, basidiomycetes, zygomycetes and chytrids) and in diverse proteins. A protein distantly related to inteins, but closely related to metazoan hedgehog proteins, has been described from Glomeromycota. Many of the newly described inteins contain homing endonucleases and some of these are apparently active. The enlarged fungal intein data set permits insight into the evolution of inteins, including the role of horizontal transfer in their persistence. The diverse fungal inteins provide a resource for biotechnology using their protein splicing or homing endonuclease capabilities.     

Regional trends and drivers of the global methane budget

The ongoing development of the Global Carbon Project (GCP) global methane (CH₄) budget shows a continuation of increasing CH₄ emissions and CH₄ accumulation in the atmosphere during 2000–2017. Here, we decompose the global budget into 19 regions (18 land and 1 oceanic) and five key source sectors to spatially attribute the observed global trends. A comparison of top-down (TD) (atmospheric and transport model-based) and bottom-up (BU) (inventory- and process model-based) CH₄ emission estimates demonstrates robust temporal trends with CH₄ emissions increasing in 16 of the 19 regions. Five regions—China, Southeast Asia, USA, South Asia, and Brazil—account for >40% of the global total emissions (their anthropogenic and natural sources together totaling >270 Tg CH₄ yr^?1 in 2008–2017). Two of these regions, China and South Asia, emit predominantly anthropogenic emissions (>75%) and together emit more than 25% of global anthropogenic emissions. China and the Middle East show the largest increases in total emission rates over the 2000 to 2017 period with regional emissions increasing by >20%. In contrast, Europe and Korea and Japan show a steady decline in CH₄ emission rates, with total emissions decreasing by ~10% between 2000 and 2017. Coal mining, waste (predominantly solid waste disposal) and livestock (especially enteric fermentation) are dominant drivers of observed emissions increases while declines appear driven by a combination of waste and fossil emission reductions. As such, together these sectors present the greatest risks of further increasing the atmospheric CH₄ burden and the greatest opportunities for greenhouse gas abatement.     

Biallelic Mutations in the Autophagy Regulator DRAM2 Cause Retinal Dystrophy with Early Macular Involvement

Retinal dystrophies are an overlapping group of genetically heterogeneous conditions resulting from mutations in more than 250 genes. Here we describe five families affected by an adult-onset retinal dystrophy with early macular involvement and associated central visual loss in the third or fourth decade of life. Affected individuals were found to harbor disease-causing variants in DRAM2 (DNA-damage regulated autophagy modulator protein 2). Homozygosity mapping and exome sequencing in a large, consanguineous British family of Pakistani origin revealed a homozygous frameshift variant (c.140delG [p.Gly47Valfs^∗3]) in nine affected family members. Sanger sequencing of DRAM2 in 322 unrelated probands with retinal dystrophy revealed one European subject with compound heterozygous DRAM2 changes (c.494G>A [p.Trp165^∗] and c.131G>A [p.Ser44Asn]). Inspection of previously generated exome sequencing data in unsolved retinal dystrophy cases identified a homozygous variant in an individual of Indian origin (c.64_66del [p.Ala22del]). Independently, a gene-based case-control association study was conducted via an exome sequencing dataset of 18 phenotypically similar case subjects and 1,917 control subjects. Using a recessive model and a binomial test for rare, presumed biallelic, variants, we found DRAM2 to be the most statistically enriched gene; one subject was a homozygote (c.362A>T [p.His121Leu]) and another a compound heterozygote (c.79T>C [p.Tyr27His] and c.217_225del [p.Val73_Tyr75del]). DRAM2 encodes a transmembrane lysosomal protein thought to play a role in the initiation of autophagy. Immunohistochemical analysis showed DRAM2 localization to photoreceptor inner segments and to the apical surface of retinal pigment epithelial cells where it might be involved in the process of photoreceptor renewal and recycling to preserve visual function.     

Self-Incompatibility-Induced Programmed Cell Death in Field Poppy Pollen Involves Dramatic Acidification of the Incompatible Pollen Tube Cytosol

Self-incompatibility (SI) is an important genetically controlled mechanism to prevent inbreeding in higher plants. SI involves highly specific interactions during pollination, resulting in the rejection of incompatible (self) pollen. Programmed cell death (PCD) is an important mechanism for destroying cells in a precisely regulated manner. SI in field poppy (Papaver rhoeas) triggers PCD in incompatible pollen. During SI-induced PCD, we previously observed a major acidification of the pollen cytosol. Here, we present measurements of temporal alterations in cytosolic pH ([pH]_cyt); they were surprisingly rapid, reaching pH 6.4 within 10 min of SI induction and stabilizing by 60 min at pH 5.5. By manipulating the [pH]_cyt of the pollen tubes in vivo, we show that [pH]_cyt acidification is an integral and essential event for SI-induced PCD. Here, we provide evidence showing the physiological relevance of the cytosolic acidification and identify key targets of this major physiological alteration. A small drop in [pH]_cyt inhibits the activity of a soluble inorganic pyrophosphatase required for pollen tube growth. We also show that [pH]_cyt acidification is necessary and sufficient for triggering several key hallmark features of the SI PCD signaling pathway, notably activation of a DEVDase/caspase-3-like activity and formation of SI-induced punctate actin foci. Importantly, the actin binding proteins Cyclase-Associated Protein and Actin-Depolymerizing Factor are identified as key downstream targets. Thus, we have shown the biological relevance of an extreme but physiologically relevant alteration in [pH]_cyt and its effect on several components in the context of SI-induced events and PCD.Programmed cell death (PCD) in plants is relatively well documented and characterized (Jones and Dangl, 1996; van Doorn, 2011; van Doorn et al., 2011). There is considerable biochemical evidence for the involvement of caspase-like activities in plant PCD (van Doorn and Woltering, 2005). For example, the vacuolar processing enzyme has YVADase (caspase-1-like) activity (Hatsugai et al., 2004; Rojo et al., 2004; Hara-Nishimura et al., 2005), DEVDase (caspase-3-like) and YVADases are associated with PCD in several plant systems (del Pozo and Lam, 1998; Korthout et al., 2000; Danon et al., 2004), and VEIDase (caspase-6-like) is the main caspase-like activity involved in embryonic pattern formation (Bozhkov et al., 2004). However, because plants have no caspase gene homologs (Sanmartín et al., 2005), the nature of their caspase-like enzymes is the subject of considerable debate. Vacuolar cell death is one of two major classes of PCD in plants (van Doorn et al., 2011). It is thought that collapse of the vacuole is a key irreversible step in several plant PCD systems, including during tissue and organ formation, such as the classic differentiation of tracheary elements (Hara-Nishimura and Hatsugai, 2011). Exactly how this is achieved and what processes are involved remain unknown. Until very recently, it was generally thought that the rupturing vacuole releases proteases, hydrolases, and nucleases, allowing cellular disassembly by an autophagy-like process. Some PCD systems cannot be assigned to either class; these include PCD triggered by the hypersensitive response to biotrophic pathogens, PCD in cereal endosperm, and self-incompatibility (SI)-induced PCD (van Doorn et al., 2011).SI is a genetically controlled pollen-pistil cell-cell recognition system. Self-pollen is recognized by the stigma as being genetically identical, resulting in inhibition of pollen tube growth. Most SI systems use tightly linked polymorphic genes: the pollen (male) and pistil (female) S-determinants. In field poppy (Papaver rhoeas), the S-determinants are a 14-kD signaling ligand field poppy stigma S (PrsS) and a unique transmembrane protein field poppy pollen S (PrpS; Foote et al., 1994; Wheeler et al., 2010). These interact in an S-specific manner, and increases in cytosolic free calcium ([Ca2+]_cyt) are triggered in incompatible pollen tubes (Franklin-Tong et al., 1993), resulting in phosphorylation of soluble inorganic pyrophosphatases (sPPases; Rudd et al., 1996; de Graaf et al., 2006), activation of a Mitogen-Activated Protein Kinase (MAPK; Rudd et al., 2003), and increases in reactive oxygen species (ROS) and nitric oxide (Wilkins et al., 2011, 2014). Most of these components are integrated into a signaling network leading to PCD (Bosch et al., 2008; Wilkins et al., 2014). The actin cytoskeleton is a key target in the field poppy SI response, undergoing depolymerization (Snowman et al., 2002) followed by polymerization into highly stable F-actin foci decorated with the actin binding proteins (ABPs) Actin-Depolymerizing Factor (ADF) and Cyclase-Associated Protein (CAP; Poulter et al., 2010, 2011), with both processes being involved in mediating PCD (Thomas et al., 2006). A major player in SI-mediated PCD is a caspase-3-like/DEVDase-like activity (Thomas and Franklin-Tong, 2004; Bosch and Franklin-Tong, 2007). The SI-induced caspase-3-like/DEVDase exhibits maximum substrate cleavage in vitro at pH 5, with peak activity 5 h after SI induction in vivo (Bosch and Franklin-Tong, 2007). The low pH optimum for this caspase-3-like/DEVDase activity is unusual, because most of the cytosolic plant caspase-like activities identified to date have optimal activity close to normal physiological pH (approximate pH, 6.5–7.0; Korthout et al., 2000; Bozhkov et al., 2004; Coffeen and Wolpert, 2004). Because the SI-induced cytosolic-located DEVDase requires a low pH for activity, this suggested that, during SI, the pollen tube cytosol undergoes dramatic acidification. In vivo pH measurements of the cytosol at 1 to 4 h after SI induction confirmed this, when cytosolic pH ([pH]_cyt) had dropped from pH 6.9 to pH 5.5 (Bosch and Franklin-Tong, 2007). This fits the in vitro pH optimum of the caspase-3-like/DEVDase almost exactly, implicating pollen cytosolic acidification as playing a vital role in creating optimal conditions for the activation of the caspase-3-like/DEVDase-like activity and progression of PCD.Under normal cellular conditions, [pH]_cyt is between approximately 6.9 and 7.5 (Kurkdjian and Guern, 1989; Felle, 2001). Pollen tubes, like other tip-growing cells, have [pH]_cyt gradients (Gibbon and Kropf, 1994; Feijó et al., 1999). The [pH]_cyt of the pollen tube shank is an approximate pH of 6.9 to 7.11 (Fricker et al., 1997; Messerli and Robinson, 1998). There has been much debate about the [pH]_cyt gradient, comprising an apical domain with an approximate pH of 6.8 and a subapical alkaline band with an approximate pH of 7.2 to 7.8 in Lilium longiflorum and Lilium formosanum pollen tubes (Fricker et al., 1997; Messerli and Robinson, 1998; Feijó et al., 2001; Lovy-Wheeler et al., 2006). Oscillations of [pH]_cyt between approximate pH values of 6.9 and 7.3 have been linked to tip growth in L. formosanum pollen tubes (Lovy-Wheeler et al., 2006). The vacuole and the apoplast have a highly acidic pH between pH 5 and pH 6 (Katsuhara et al., 1989; Feijó et al., 1999). The majority of studies of pH changes in plant cells reports modest, transient changes in [pH]_cyt of approximately 0.4 and 0.7 pH units during development, gravitropic responses, decreases in light intensity, and addition of elicitors, hormones, and other treatments. For example, during root hair development in Arabidopsis (Arabidopsis thaliana), root [pH]_cyt was elevated from an approximate pH of 7.3 to 7.7 (Bibikova et al., 1998). Root gravitropic responses stimulate small transient [pH]_cyt alterations (Scott and Allen, 1999; Fasano et al., 2001; Johannes et al., 2001). More recently, it has been shown that the [pH]_cyt drops during PCD controlling root cap development; however, exactly how many units the [pH]_cyt decreased was not measured (Fendrych et al., 2014). Other studies investigating [pH]_cyt in response to physiologically relevant signals also report small transient alterations. Light-adapted cells respond to a decrease in light intensity with a rapid transient cytosolic acidification by approximately 0.3 pH units (Felle et al., 1986). Addition of nodulation factors resulted in an increase of 0.2 pH units in root hairs (Felle et al., 1998), and abscisic acid increased the [pH]_cyt of guard cells by 0.3 pH units (Blatt and Armstrong, 1993). Changes in [pH]_cyt are thought to activate stress responses (Felle, 2001). Elicitor treatments resulted in a [pH]_cyt drop of between 0.4 and 0.7 pH units in suspension cells (Mathieu et al., 1996; Kuchitsu et al., 1997), a drop of 0.2 pH units in Nitellopsis obtusa cells treated with salt (Katsuhara et al., 1989), and a drop of 0.3 to 0.7 pH units in Eschscholzia californica (Roos et al., 1998).Here, we investigate SI-induced acidification of the cytosol, providing measurements of physiologically relevant temporal alterations in [pH]_cyt, and identify key targets of this, providing mechanistic insights into these events. The SI-induced acidification plays a pivotal role in the activation of a caspase-3-like/DEVDase activity, the formation of punctate F-actin foci, and ABP localization during SI PCD. We investigate the vacuole as a potential contributor to SI-induced [pH]_cyt acidification.     

Mutagenesis of isopentenyl phosphate kinase to enhance geranyl phosphate kinase activity

Isopentenyl phosphate kinase (IPK) catalyzes the ATP-dependent phosphorylation of isopentenyl phosphate (IP) to form isopentenyl diphosphate (IPP) during biosynthesis of isoprenoid metabolites in Archaea. The structure of IPK from the archeaon Thermoplasma acidophilum (THA) was recently reported and guided the reconstruction of the IP binding site to accommodate the longer chain isoprenoid monophosphates geranyl phosphate (GP) and farnesyl phosphate (FP). We created four mutants of THA IPK with different combinations of alanine substitutions for Tyr70, Val73, Val130, and Ile140, amino acids with bulky side chains that limited the size of the side chain of the isoprenoid phosphate substrate that could be accommodated in the active site. The mutants had substantially increased GP kinase activity, with 20-200-fold increases in k(cat)(GP) and 30-130-fold increases in k(cat)(GP)/K(M)(GP) relative to those of wild-type THA IPK. The mutations also resulted in a 10(6)-fold decrease in k(cat)(IP)/K(M)(IP) compared to that of wild-type IPK. No significant change in the kinetic parameters for the cosubstrate ATP was observed, signifying that binding between the nucleotide binding site and the IP binding site was not cooperative. The shift in substrate selectivity from IP to GP, and to a lesser extent, FP, in the mutants could act as a starting point for the creation of more efficient GP or FP kinases whose products could be exploited for the chemoenzymatic synthesis of radiolabeled isoprenoid diphosphates.     

Mutations in c4orf26, encoding a Peptide with in vitro hydroxyapatite crystal nucleation and growth activity, cause amelogenesis imperfecta

Autozygosity mapping and clonal sequencing of an Omani family identified mutations in the uncharacterized gene, C4orf26, as a cause of recessive hypomineralized amelogenesis imperfecta (AI), a disease in which the formation of tooth enamel fails. Screening of a panel of 57 autosomal-recessive AI-affected families identified eight further families with loss-of-function mutations in C4orf26. C4orf26 encodes a putative extracellular matrix acidic phosphoprotein expressed in the enamel organ. A mineral nucleation assay showed that the protein's phosphorylated C terminus has the capacity to promote nucleation of hydroxyapatite, suggesting a possible function in enamel mineralization during amelogenesis.     

Regulation of phenylacetic acid degradation genes of Burkholderia cenocepacia K56-2

Background  

Metabolically versatile soil bacteria Burkholderia cepacia complex (Bcc) have emerged as opportunistic pathogens, especially of cystic fibrosis (CF). Previously, we initiated the characterization of the phenylacetic acid (PA) degradation pathway in B. cenocepacia, a member of the Bcc, and demonstrated the necessity of a functional PA catabolic pathway for full virulence in Caenorhabditis elegans. In this study, we aimed to characterize regulatory elements and nutritional requirements that control the PA catabolic genes in B. cenocepacia K56-2.     

Differential regulation of corticotropin releasing factor 1alpha receptor endocytosis and trafficking by beta-arrestins and Rab GTPases

The corticotropin releasing factor (CRF) type 1alpha receptor, a member of the G protein-coupled receptor (GPCR) subfamily B, is involved in the aetiology of anxiety and depressive disorders. In the present study, we examined the internalization and trafficking of the CRF1alpha receptor in both human embryonic kidney (HEK)293 cells and primary cortical neurons. We found that CRF1alpha receptor activation leads to the selective recruitment of beta-arrestin2 in both HEK293 cells and neurons. We observed distinct distribution patterns of CRF1alpha receptor and beta-arrestin2 in HEK293 cells and cortical neurons. In HEK293 cells, beta-arrestin2-green fluorescent protein (GFP) co-localized with CRF1alpha receptor in vesicles at the plasma membrane but was dissociated from the receptor in endosomes. In contrast, in primary cortical neurons, beta-arrestin2 and CRF1alpha receptor were internalized in distinct endocytic vesicles. By bioluminescence resonance energy transfer, we demonstrated that beta-arrestin2 association with CRF1alpha receptor was increased in cells transfected with G protein-coupled receptor kinase (GRK)3 and GRK6 and decreased in cells transfected with GRK2 and GRK5. In both HEK293 cells and cortical neurons, internalized CRF1alpha receptor transited from Rab5-positive early endosomes to Rab4-positive recycling endosomes and was not targeted to lysosomes. However, CRF1alpha receptor resensitization was blocked by the overexpression of wild-type, but not dominant-negative, Rab5 and Rab4 GTPases. Taken together, our results suggest that beta-arrestin trafficking differs between HEK293 cells and neurons, and that CRF1alpha receptor resensitization is regulated in an atypical manner by Rab GTPases.