Axial patterning in snakes and caecilians: Evidence for an alternative interpretation of the Hox code

It is generally assumed that the characteristic deregionalized body plan of species with a snake-like morphology evolved through a corresponding homogenization of Hox gene expression domains along the primary axis. Here, we examine the expression of Hox genes in snake embryos and show that a collinear pattern of Hox expression is retained within the paraxial mesoderm of the trunk. Genes expressed at the anterior and most posterior, regionalized, parts of the skeleton correspond to the expected anatomical boundaries. Unexpectedly however, also the dorsal (thoracic), homogenous rib-bearing region of trunk, is regionalized by unconventional gradual anterior limits of Hox expression that are not obviously reflected in the skeletal anatomy. In the lateral plate mesoderm we also detect regionalized Hox expression yet the forelimb marker Tbx5 is not restricted to a rudimentary forelimb domain but is expressed throughout the entire flank region. Analysis of several Hox genes in a caecilian amphibian, which convergently evolved a deregionalized body plan, reveals a similar global collinear pattern of Hox expression. The differential expression of posterior, vertebra-modifying or even rib-suppressing Hox genes within the dorsal region is inconsistent with the homogeneity in vertebral identity. Our results suggest that the evolution of a deregionalized, snake-like body involved not only alterations in Hox gene cis-regulation but also a different downstream interpretation of the Hox code.     

Regulation of Respiration and Fermentation to Control the Plant Internal Oxygen Concentration

Plant internal oxygen concentrations can drop well below ambient even when the plant grows under optimal conditions. Using pea (Pisum sativum) roots, we show how amenable respiration adapts to hypoxia to save oxygen when the oxygen availability decreases. The data cannot simply be explained by oxygen being limiting as substrate but indicate the existence of a regulatory mechanism, because the oxygen concentration at which the adaptive response is initiated is independent of the actual respiratory rate. Two phases can be discerned during the adaptive reaction: an initial linear decline of respiration is followed by a nonlinear inhibition in which the respiratory rate decreased progressively faster upon decreasing oxygen availability. In contrast to the cytochrome c pathway, the inhibition of the alternative oxidase pathway shows only the linear component of the adaptive response. Feeding pyruvate to the roots led to an increase of the oxygen consumption rate, which ultimately led to anoxia. The importance of balancing the in vivo pyruvate availability in the tissue was further investigated. Using various alcohol dehydrogenase knockout lines of Arabidopsis (Arabidopsis thaliana), it was shown that even under aerobic conditions, alcohol fermentation plays an important role in the control of the level of pyruvate in the tissue. Interestingly, alcohol fermentation appeared to be primarily induced by a drop in the energy status of the tissue rather than by a low oxygen concentration, indicating that sensing the energy status is an important component of optimizing plant metabolism to changes in the oxygen availability.Plants are obligate aerobic organisms, with oxygen being an essential substrate for mitochondrial energy production. However, the poor distribution efficiency for oxygen through root, tuber, seed, or stem tissue of various species results in steep drops of the internal oxygen concentration, ranging from values near above zero to just below 40% of air saturation (e.g. Armstrong et al., 1994; Geigenberger et al., 2000; Rolletschek et al., 2002; van Dongen et al., 2003, 2004; Vigeolas et al., 2003).These low levels of internal oxygen strongly affect plant metabolism. Several studies showed that energy-consuming metabolic pathways are adjusted to the actual oxygen availability (for review, see Geigenberger, 2003; Bailey-Serres and Voesenek, 2008). By saving energy, the plant decreases the demand for respiratory oxygen consumption that could help to postpone or even prevent the tissue from becoming anoxic. Indeed, it was observed that the metabolic flux through glycolysis slows down, respiratory oxygen consumption decreases, and adenylate levels drop in response to low internal oxygen (Geigenberger et al., 2000; Bologa et al., 2003). This inhibition of respiration is not easily explained by substrate limitation of cytochrome c oxidase (COX). First, the reduction of respiration becomes apparent already at oxygen concentrations around 20% of air saturation, whereas the K_m value for oxygen of COX lies around 0.05% of air saturation (which equals 0.14 μm under standard conditions; Drew, 1997). Second, the inhibition of respiration could be clearly distinguished from the induction of fermentation, which did not occur until oxygen fell to levels close to zero (Geigenberger, 2003).Based on these studies, it is reasonable to assume that a sensitive tuning mechanism must exist that allows the plant to regulate oxygen consumption while simultaneously preventing anoxia. However, hardly anything is known about the mechanism by which a plant induces adaptive responses to low oxygen (Bailey-Serres and Chang, 2005). Vice versa, comparably little is known about how metabolic activity affects the plant internal oxygen concentration. Previous studies focused on the effect that feeding of different sugars had on the respiration rate of tissue slices (Loef et al., 2001) or used transgenic approaches to stimulate metabolism by introducing a more energy-consuming route of Suc degradation via invertase in growing tubers (Bologa et al., 2003). In the latter case, respiration rates were increased and internal oxygen concentrations fell to very low levels that were close to zero. This shows that plant internal oxygen concentrations respond very sensitively to changes in metabolic activities. However, the underlying mechanism remains unclear.Glycolysis is part of the central backbone of primary carbohydrate metabolism and respiration. Pyruvate serves as a key metabolite linking glycolysis in the cytosol with mitochondrial respiration. Under aerobic conditions, pyruvate is transported into mitochondria and is oxidized through the tricarboxylic acid (TCA) cycle into organic acids and NADH. Moreover, pyruvate has regulatory potential, as it was shown that alternative oxidase (AOX) becomes more active in the presence of α-keto acids such as pyruvate (Millar et al., 1993, 1996; Vanlerberghe et al., 1995; Vanlerberghe and McIntosh, 1997), thus affecting the efficiency of ATP production per unit of oxygen being respired. Under oxygen-limiting conditions, pyruvate can either be converted into ethanol by pyruvate decarboxylase (PDC) and alcohol dehydrogenase (ADH) or to lactate by lactate dehydrogenase. Pyruvate also serves as a precursor for the synthesis of Ala via the reversible reaction catalyzed by Ala amino transferase, which was shown to play a crucial role in the rapid conversion of Ala to pyruvate during recovery from low-oxygen stress (Miyashita et al., 2007). Furthermore, pyruvate is the substrate of acetolactate synthase, which is the first enzyme committed to the biosynthesis of the branched-chain amino acids Val, Leu, and Ile. Inhibition of acetolactate synthase by the herbicide imazethapyr induces aerobic fermentation in plants (Gaston et al., 2002). Despite its central role in energy metabolism under both oxygen-rich and oxygen-depleted conditions, no investigations were made, to our knowledge, until now on the impact pyruvate has on the plant internal oxygen concentration.The aim of this study was to investigate the regulation of respiration and its relation to the plant internal oxygen concentration. To investigate this, we changed the oxygen concentration of the nutrient solution of hydroponically grown pea (Pisum sativum) plants and tested the influence of several sugars and organic acids. We measured root internal oxygen concentrations as well as the energy status of the tissue and related this to the rate of oxygen consumption by both the cytochrome c pathway and the AOX. The results are investigated in relation to the function and regulation of fermentative metabolism.     

The X-ray Structure of RU486 Bound to the Progesterone Receptor in a Destabilized Agonistic Conformation

Here we describe the 1.95 Å structure of the clinically used antiprogestin RU486 (mifepristone) in complex with the progesterone receptor (PR). The structure was obtained by taking a crystal of the PR ligand binding domain containing the agonist norethindrone and soaking it in a solution containing the antagonist RU486 for extended times. Clear ligand exchange could be observed in one copy of the PR ligand binding domain dimer in the crystal. RU486 binds while PR is in an agonistic conformation without displacing helix 12. Although this is probably because of the constraints of the crystal lattice, it demonstrates that helix 12 displacement is not a prerequisite for RU486 binding. Interestingly, B-factor analysis clearly shows that helix 12 becomes more flexible after RU486 binding, suggesting that RU486, being a model antagonist, does not induce one fixed conformation of helix 12 but changes its positional equilibrium. This conclusion is confirmed by comparing the structures of RU486 bound to PR and RU486 bound to the glucocorticoid receptor.The drug RU486, also known as mifepristone, is the only clinically approved antiprogestin (trade name Mifegyne® or Mifeprex®). It is applied to terminate pregnancy and has been clinically tested in many more indications (1, 2). Recently, it was shown that RU486 can prevent mammary tumorigenesis in Brca1/p53-deficient mice, implying a use for RU486 in breast cancer therapy (3).RU486 exerts its clinical effect by binding to the ligand binding domain of the progesterone receptor, although RU486 can also bind to the glucocorticoid receptor (GR)² and weakly to the androgen receptor (4). All these nuclear receptors are close sequence homologs (5). Because the anti-GR activity of RU486 might be problematic in chronic administration (1), past research has focused on finding RU486 variants with more selectivity (4, 6–10) (Open in a separate windowDespite the clinical importance of RU486, there is currently no three-dimensional structure of it bound to PR, its principal target. However, other complexes have been informative, such as that between the PR ligand binding domain and asoprisnil, which is biochemically a full antagonist and is chemically related to RU486 (11). Also informative is the crystal structure of RU486 bound to the GR LBD (12). In all these structures the antagonists bind to a receptor conformation in which the C-terminal helix (called helix 12) is displaced compared with structures of bound agonists. This so-called helix 12 displacement was first seen in the structure of raloxifene bound to the estrogen receptor α, and it is commonly thought to be a general nuclear receptor mechanism (5, 13).The indications from x-ray structures that in PR, RU486 can induce displacement of helix 12 are supported by biochemical data. For instance the truncation of the PR C terminus induces RU486 to act as agonist (14). Also, the C terminus of PR becomes prone to proteolysis when RU486 binds (15). Finally, from modeling RU486 into the structure of bound progesterone, it has been concluded that the 11β substitution of RU486 (16).Despite the evidence that RU486 can induce displacement of helix 12, it is still unclear if RU486 obligately dissociates helix 12 through steric repulsion or if RU486 allows multiple positions of helix 12 but changes their dynamic equilibrium. In this latter theory, called the dynamic model, RU486 would also be able to bind when helix 12 is in an agonist conformation. Indeed, under rare conditions RU486 can function as an agonist (7), and the compound asoprisnil, in vivo, is known as a partial agonist (11). The use of corepressor peptides in crystal complexes, such as in the PR-asoprisnil complex (11), might lock helix 12 into its final antagonist position, whereas the compound alone would have more subtle effects. The dynamic model controversy has also arisen with other nuclear receptors, indicating its wider scope (13, 17).To further elucidate the mechanism of RU486, we have determined the three-dimensional structure of RU486 bound to PR. For this, we developed a novel protocol in which ligands are exchanged in an existing PR crystal in which norethindrone is bound. The crystal lattice restricts the position of helix 12 to the agonist position, but RU486 is still able to bind, proving that it is sterically compatible with an agonist position of helix 12 and suggesting that RU486 works through changing the dynamic equilibrium of helix 12. Comparing our structure with the asoprisnil complex gives insight into the mechanism of helix 12 destabilization, which is confirmed by comparing our structure to that of RU486 bound to GR.     

Greater Transport Efficiencies of the Membrane Fatty Acid Transporters FAT/CD36 and FATP4 Compared with FABPpm and FATP1 and Differential Effects on Fatty Acid Esterification and Oxidation in Rat Skeletal Muscle

In selected mammalian tissues, long chain fatty acid transporters (FABPpm, FAT/CD36, FATP1, and FATP4) are co-expressed. There is controversy as to whether they all function as membrane-bound transporters and whether they channel fatty acids to oxidation and/or esterification. Among skeletal muscles, the protein expression of FABPpm, FAT/CD36, and FATP4, but not FATP1, correlated highly with the capacities for oxidative metabolism (r ≥ 0.94), fatty acid oxidation (r ≥ 0.88), and triacylglycerol esterification (r ≥ 0.87). We overexpressed independently FABPpm, FAT/CD36, FATP1, and FATP4, within a normal physiologic range, in rat skeletal muscle, to determine the effects on fatty acid transport and metabolism. Independent overexpression of each fatty acid transporter occurred without altering either the expression or plasmalemmal content of other fatty acid transporters. All transporters increased fatty acid transport, but FAT/CD36 and FATP4 were 2.3- and 1.7-fold more effective than FABPpm and FATP1, respectively. Fatty acid transporters failed to alter the rates of fatty acid esterification into triacylglycerols. In contrast, all transporters increased the rates of long chain fatty acid oxidation, but the effects of FABPpm and FAT/CD36 were 3-fold greater than for FATP1 and FATP4. Thus, fatty acid transporters exhibit different capacities for fatty acid transport and metabolism. In vivo, FAT/CD36 and FATP4 are the most effective fatty acid transporters, whereas FABPpm and FAT/CD36 are key for stimulating fatty acid oxidation.Uptake of long chain fatty acids across the plasma membrane had long been considered to occur via passive diffusion. However, in recent years, there has been a fundamental shift in our understanding, and it is now widely recognized that long chain fatty acids cross the plasma membrane via a protein-mediated mechanism (for reviews, see Refs. 1–3). A number of fatty acid transporters have been identified, including fatty acid translocase/CD36 (FAT/CD36), plasma membrane-associated fatty acid binding proteins (FABPpm), and a family of fatty acid transport proteins (FATP1–6)⁵ (for reviews, see Refs. 1 and 4). Selected stimuli (muscle contraction, insulin, and AICAR) induce the translocation of selected fatty acid transporters (FABPpm, FAT/CD36, and FATP1) from an intracellular depot to the plasma membrane, in both heart and skeletal muscle, resulting in concurrently increased rates of fatty acid transport (for a review, see Ref. 1). Some fatty acid transporters have now also been implicated in the dysregulation of fatty acid metabolism in heart and skeletal muscle in models of insulin resistance and type 1 and 2 diabetes, including FAT/CD36 (5–9), FATP1 (10, 11), and possibly FATP4 (11, 12) but not FABPpm (5–7). Thus, in recent years, it has become widely accepted that (a) long chain fatty acids traverse the plasma membrane via a protein-mediated mechanism and (b) some of the fatty acid transporters are central to the dysregulation in skeletal muscle fatty acid metabolism in obesity and type 2 diabetes.In vivo, many of the fatty acid transporters are frequently co-expressed in different tissues. FAT/CD36 and FABPpm are ubiquitously expressed (1), whereas FATP1–6 exhibit a somewhat tissue-specific distribution pattern (13, 14). The reason for the co-expression of different fatty acid transporters within the same tissue remains unclear. It has been speculated that selected fatty acid transporters may need to interact with each other (15, 16). Alternatively, it is also possible that (a) different fatty acid transporters have discrepant transport capacities, and (b) selected transporters may channel fatty acids differentially to fatty acid oxidation and esterification into triacylglycerols in mammalian tissue.Recent evidence has shown that the transport capacities among FATPs can differ substantially, as revealed by overexpression (14, 17, 18) or knockdown studies (19), but there is little agreement as to which FATP is most effective. Extensive studies by DiRusso et al. (17) in yeast revealed that when FATP1–6 were overexpressed to similar levels (qualitative assessment), FATP4 exhibited 1.7- and 3-fold greater fatty acid transport effectiveness compared with FATP1 and FATP2, respectively, whereas no fatty acid transport capacities were attributable to FATP3, -5, and -6 (17). In contrast, in HEK293 cells, the FATP6 transport capacity was 3- and 6.5-fold greater than FATP1 and FATP4, respectively (14), whereas in 3T3-L1 adipocytes, a fatty acid transport role was evident only for FATP1 and not FATP4 (19). Others have also questioned the transport role of FATP4 (20). These discrepant findings with respect to the transport effectiveness of FATPs may reflect, in part, the use of diverse cell types with ill defined metabolic needs and/or machinery for fatty acid uptake and metabolism. Indeed, several recent reports indicate that fatty acid transport cannot be adequately examined in some cells, because these appear to lack accessory proteins that may be involved in fatty acid transport (21, 22). In addition, extrapolation of results from cultured cells to metabolically important tissue in vivo may also be problematic, since cells and mammalian tissues probably have different requirements for fatty acid utilization, and their regulation of fatty acid uptake may also differ. For example, the mechanisms regulating the acute contraction-induced up-regulation of fatty acid transport and oxidation, such as occurs in heart and skeletal muscle, is probably absent in selected cell cultures.Assessment of fatty acid transporter effectiveness, in vivo, cannot be determined in knock-out animals, since compensatory responses in some fatty acid transporters (FATP1 and -4) occur when another fatty acid transporter (FAT/CD36) has been ablated (23, 24). Thus, the relative effectiveness of selected fatty acid transporters on fatty acid transport in vivo remains unknown. In addition, whether fatty acid transporters channel fatty acids to a particular metabolic fate, as has been suggested based on studies in cultured cells (18, 19, 25), may depend on the cell type being examined.It is desirable to discern the effectiveness of selected fatty acid transporters in mammalian tissues that have a well known system for transporting and utilizing fatty acids and in which fatty acid transporters can be independently up-regulated without disturbing the expression of other fatty acid transporters. These criteria can be satisfied in rat skeletal muscle in which genes can be up-regulated under controlled conditions within a physiologically meaningful range (26–28). Therefore, in the present study, we have compared the independent transport effectiveness of fatty acid transporters (FABPpm, FAT/CD36, FATP1, and FATP4) in skeletal muscle, without disturbing the expression and plasmalemmal content of other fatty acid transporters. In addition, we also examined the contributions of these transporters to fatty acid oxidation and esterification into triacylglycerols. These are the first studies to reveal that in vivo (a) the fatty acid transport effectiveness of fatty acid transporters differs considerably, and (b) in skeletal muscle, these transporters serve to channel fatty acids to oxidation, not esterification into triacylglycerols.     

Analysis of severely affected patients with dihydropyrimidine dehydrogenase deficiency reveals large intragenic rearrangements of DPYD and a de novo interstitial deletion del(1)(p13.3p21.3)

Dihydropyrimidine dehydrogenase (DPD) deficiency is an infrequently described autosomal recessive disorder of the pyrimidine degradation pathway and can lead to mental and motor retardation and convulsions. DPD deficiency is also known to cause a potentially lethal toxicity following administration of the antineoplastic agent 5-fluorouracil. In an ongoing study of 72 DPD deficient patients, we analysed the molecular background of 5 patients in more detail in whom initial sequence analysis did not reveal pathogenic mutations. In three patients, a 13.8 kb deletion of exon 12 was found and in one patient a 122 kb deletion of exon 14–16 of DPYD. In the fifth patient, a c.299_302delTCAT mutation in exon 4 was found and also loss of heterozygosity of the entire DPD gene. Further analysis demonstrated a de novo deletion of approximately 14 Mb of chromosome 1p13.3–1p21.3, which includes DPYD. Haploinsufficiency of NTNG1, LPPR4, GPSM2, COL11A1 and VAV3 might have contributed to the severe psychomotor retardation and unusual craniofacial features in this patient. Our study showed for the first time the presence of genomic deletions affecting DPYD in 7% (5/72) of all DPD deficient patients. Therefore, screening of DPD deficient patients for genomic deletions should be considered.     

Septal pore complex morphology in the Agaricomycotina (Basidiomycota) with emphasis on the Cantharellales and Hymenochaetales

The ultrastructure of septa and septum-associated septal pore caps are important taxonomic markers in the Agaricomycotina (Basidiomycota, Fungi). The septal pore caps covering the typical basidiomycetous dolipore septum are divided into three main phenotypically recognized morphotypes: vesicular-tubular (including the vesicular, sacculate, tubular, ampulliform, and globular morphotypes), imperforate, and perforate. Until recently, the septal pore cap-type reflected the higher-order relationships within the Agaricomycotina. However, the new classification of Fungi resulted in many changes including revision of existing and addition of new orders. Therefore, the septal pore cap ultrastructure of more than 325 species as reported in literature was related to this new classification. In addition, the septal pore cap ultrastructures of Rickenella fibula and Cantharellus formosus were examined by transmission electron microscopy. Both fungi have dolipore septa associated with perforate septal pore caps. These results combined with data from the literature show that the septal pore cap-type within orders of the Agaricomycotina is generally monomorphic, except for the Cantharellales and Hymenochaetales.It appears from the fungal phylogeny combined with the septal pore cap ultrastructure that the vesicular-tubular and the imperforate type both may have arisen from endoplasmic reticulum. Thereafter, the imperforate type eventually gave rise to the perforate septal pore cap-type.     

A Probabilistic Framework for Peptide and Protein Quantification from Data-Dependent and Data-Independent LC-MS Proteomics Experiments

Abstract A probability-based quantification framework is presented for the calculation of relative peptide and protein abundance in label-free and label-dependent LC-MS proteomics data. The results are accompanied by credible intervals and regulation probabilities. The algorithm takes into account data uncertainties via Poisson statistics modified by a noise contribution that is determined automatically during an initial normalization stage. Protein quantification relies on assignments of component peptides to the acquired data. These assignments are generally of variable reliability and may not be present across all of the experiments comprising an analysis. It is also possible for a peptide to be identified to more than one protein in a given mixture. For these reasons the algorithm accepts a prior probability of peptide assignment for each intensity measurement. The model is constructed in such a way that outliers of any type can be automatically reweighted. Two discrete normalization methods can be employed. The first method is based on a user-defined subset of peptides, while the second method relies on the presence of a dominant background of endogenous peptides for which the concentration is assumed to be unaffected. Normalization is performed using the same computational and statistical procedures employed by the main quantification algorithm. The performance of the algorithm will be illustrated on example data sets, and its utility demonstrated for typical proteomics applications. The quantification algorithm supports relative protein quantification based on precursor and product ion intensities acquired by means of data-dependent methods, originating from all common isotopically-labeled approaches, as well as label-free ion intensity-based data-independent methods.