Insights into the mechanism of dihydropyrimidine dehydrogenase from site-directed mutagenesis targeting the active site loop and redox cofactor coordination

In mammals, the pyrimidines uracil and thymine are metabolised by a three-step reductive degradation pathway. Dihydropyrimidine dehydrogenase (DPD) catalyses its first and rate-limiting step, reducing uracil and thymine to the corresponding 5,6-dihydropyrimidines in an NADPH-dependent reaction. The enzyme is an adjunct target in cancer therapy since it rapidly breaks down the anti-cancer drug 5-fluorouracil and related compounds. Five residues located in functionally important regions were targeted in mutational studies to investigate their role in the catalytic mechanism of dihydropyrimidine dehydrogenase from pig. Pyrimidine binding to this enzyme is accompanied by active site loop closure that positions a catalytically crucial cysteine (C671) residue. Kinetic characterization of corresponding enzyme mutants revealed that the deprotonation of the loop residue H673 is required for active site closure, while S670 is important for substrate recognition. Investigations on selected residues involved in binding of the redox cofactors revealed that the first FeS cluster, with unusual coordination, cannot be reduced and displays no activity when Q156 is mutated to glutamate, and that R235 is crucial for FAD binding.     

Glycoprotein Capture and Quantitative Phosphoproteomics Indicate Coordinated Regulation of Cell Migration upon Lysophosphatidic Acid Stimulation

The lipid mediator lysophosphatidic acid (LPA) is a serum component that regulates cellular functions such as proliferation, migration, and survival via specific G protein-coupled receptors. The underlying signaling mechanisms are still incompletely understood, including those that operate at the plasma membrane to modulate cell-cell and cell-matrix interactions in LPA-promoted cell migration. To explore LPA-evoked phosphoregulation with a focus on cell surface proteins, we combined glycoproteome enrichment by immobilized lectins with SILAC-based quantitative phosphoproteomics. We performed biological replicate analyses in SCC-9 squamous cell carcinoma cells and repeatedly quantified the effect of 1.5- and 5-min LPA treatment on more than 700 distinct phosphorylations in lectin-purified proteins. We detected many regulated phosphorylation events on various types of plasma membrane proteins such as cell adhesion molecules constituting adherens junctions, desmosomes, and hemidesmosomes. Several of these LPA-regulated phosphorylation sites have been characterized in a biological context other than G protein-coupled receptor signaling, and the transfer of this functional information suggests coordinated and multifactorial cell adhesion control in LPA-induced cell migration. Additionally, we identified LPA-mediated activation loop phosphorylation of the serine/threonine kinase Wnk1 and verified a role of Wnk1 for LPA-induced cell migration in knock-down experiments. In conclusion, the glycoproteome phosphoproteomics strategy described here sheds light on incompletely understood mechanisms in LPA-induced cell migratory behavior.The plasma membrane separates the interior of a mammalian cell from the environment. To respond to external signals such as growth factors, cells possess various types of plasma membrane-spanning receptors that communicate to the intracellular signaling machinery in a ligand-regulated manner. G protein-coupled receptors (GPCRs),1 which are integral membrane proteins with seven transmembrane helices, constitute the largest superfamily of cell surface receptors. GPCRs mediate intracellular activation of heterotrimeric G proteins in response to extracellular ligand binding. A plethora of different factors are known to act on GPCRs, including peptide ligands, proteases, nucleotides as well as bioactive lipid molecules such as lysophosphatidic acid (LPA). LPA induces various biological responses including proliferation and migration in a wide range of mammalian cell types and has been implicated in the progression of several human cancers (1, 2). Upon LPA binding to its cognate receptors, heterotrimeric G proteins from the G_i, G_q, and G_12/13 families are activated by guanine nucleotide exchange factors resulting in their dissociation into activated Gα and Gβγ subunits. Activated G protein subunits interact with various effector proteins including phospholipase C and adenylate cyclase isoforms as well as guanine nucleotide exchange factors for Rho family GTPases, which either directly or via second messenger production communicate to cellular kinase signaling. GPCR activation by LPA is also known to trigger the proteolytic activity of ADAM transmembrane metalloproteases, such as ADAM17, which processes epidermal growth factor receptor (EGFR) ligand precursors on the extracellular side to release mature growth factors triggering EGFR activation (3–8). The molecular mechanisms involved in the control of ADAM metalloprotease activity are not clear yet. The resulting transactivation of the EGFR tyrosine kinase provides a link to signaling modules such as mitogen-activated protein kinase cascades and has been implicated in the control of cell proliferation and migration upon LPA treatment (9). Regarding the induction of cell motility upon LPA, previous studies have reported several signaling elements in addition to EGFR transactivation that contribute to this complex cellular behavior. In particular, RhoGTPase-dependent signals that activate downstream effectors such as Rho kinase and focal adhesion kinase are involved in the control of cytoskeletal organization and cell attachment to the surrounding extracellular matrix (ECM) (10, 11). The coordinated regulation of such integrin-mediated interactions is required to enable cell movement and occurs in dedicated macromolecular assemblies such as focal adhesion complexes and hemidesmosomes (12, 13). Despite the key role of integrins, the molecular mechanisms that underlie their functional modulation upon GPCR activation are poorly understood. Moreover, cell-cell contacts such as adherens junctions and desmosomes have to dissociate prior to cell migration. Likewise, it is unclear how the components of these structures, such as members of the cadherin family, might be regulated by GPCR-mediated signaling pathways. Both LPA levels and LPA_1–3 receptor expression are often elevated in cancer patients, and the bioactive lipid acts as a potent inducer of cell migration and invasion in vitro. Due to the key role of protein phosphorylation in LPA-induced signal transmission, comprehensive phosphorylation analysis of regulated proteins might generate new insights into pro-migratory signaling mechanisms in cancer cells. Mass spectrometry (MS)-based analysis has emerged as the key method for unbiased protein phosphorylation studies due to various technological advances in recent years (14, 15). Because of the substoichiometric nature of many site-specific phosphorylation events, phosphopeptides constitute only a small fraction in total peptide samples. Therefore, they need to be efficiently enriched prior to MS analysis, which has become routinely possible by phosphate group-selective purification strategies employing capture reagents such as immobilized metal ion affinity chromatography or titanium dioxide beads (16). Moreover, phosphopeptide analysis has benefited enormously from the availability of hybrid mass spectrometers that combine the sensitivity and speed of linear ion traps with the high resolution and accuracy of orbitrap mass analyzers (17). These advances together with quantitative approaches such as stable isotope labeling by amino acids in cell cultures (SILAC) (18, 19) and substantial progress in computational proteomics (20) now allow for concomitant identification and quantification of several thousand phosphorylation sites from single cellular extracts (21–23).We previously analyzed cell signaling responses in A498 kidney carcinoma cells upon LPA and heparin-binding EGF-like growth factor treatment by monitoring phosphorylation changes in total cell lysate and protein kinase-enriched fractions (24). In a complementary approach, we now aimed for a systematic survey of LPA-induced phosphorylation changes on plasma membrane proteins and their interaction partners. Furthermore, we were interested in time-resolved analysis of LPA-induced phosphorylation changes on ADAM17 and the EGFR to gain further insights into possible mechanisms underlying the still enigmatic EGFR transactivation process. In our present study, we therefore analyzed SCC-9 squamous carcinoma cells due to their pronounced EGFR transactivation response upon LPA. As plasma membrane proteins usually contain covalently attached carbohydrate structures, we performed lectin affinity enrichment of glycosylated proteins prior to SILAC-based quantitative phosphoproteomics (25). This experimental strategy enabled us to acquire in-depth data about LPA regulation of diverse glycoproteins and revealed coordinated phosphoregulation of cell adhesion proteins as likely mechanism underlying cell migratory behavior.     

Postnatal growth restriction and gene expression changes in a mouse model of fetal alcohol syndrome

Growth restriction, craniofacial dysmorphology, and central nervous system defects are the main diagnostic features of fetal alcohol syndrome. Studies in humans and mice have reported that the growth restriction can be prenatal or postnatal, but the underlying mechanisms remain unknown.We recently described a mouse model of moderate gestational ethanol exposure that produces measurable phenotypes in line with fetal alcohol syndrome (e.g., craniofacial changes and growth restriction in adolescent mice). In this study, we characterize in detail the growth restriction phenotype by measuring body weight at gestational day 16.5, cross-fostering from birth to weaning, and by extending our observations into adulthood. Furthermore, in an attempt to unravel the molecular events contributing to the growth phenotype, we have compared gene expression patterns in the liver and kidney of nonfostered, ethanol-exposed and control mice at postnatal day 28.We find that the ethanol-induced growth phenotype is not detectable prior to birth, but is present at weaning, even in mice that have been cross-fostered to unexposed dams. This finding suggests a postnatal growth restriction phenotype that is not due to deficient postpartum care by dams that drank ethanol, but rather a physiologic result of ethanol exposure in utero. We also find that, despite some catch-up growth after 5 weeks of age, the effect extends into adulthood, which is consistent with longitudinal studies in humans.Genome-wide gene expression analysis revealed interesting ethanol-induced changes in the liver, including genes involved in the metabolism of exogenous and endogenous compounds, iron homeostasis, and lipid metabolism.     

Molecular Basis for the Dual Function of Eps8 on Actin Dynamics: Bundling and Capping

Actin capping and cross-linking proteins regulate the dynamics and architectures of different cellular protrusions. Eps8 is the founding member of a unique family of capping proteins capable of side-binding and bundling actin filaments. However, the structural basis through which Eps8 exerts these functions remains elusive. Here, we combined biochemical, molecular, and genetic approaches with electron microscopy and image analysis to dissect the molecular mechanism responsible for the distinct activities of Eps8. We propose that bundling activity of Eps8 is mainly mediated by a compact four helix bundle, which is contacting three actin subunits along the filament. The capping activity is mainly mediated by a amphipathic helix that binds within the hydrophobic pocket at the barbed ends of actin blocking further addition of actin monomers. Single-point mutagenesis validated these modes of binding, permitting us to dissect Eps8 capping from bundling activity in vitro. We further showed that the capping and bundling activities of Eps8 can be fully dissected in vivo, demonstrating the physiological relevance of the identified Eps8 structural/functional modules. Eps8 controls actin-based motility through its capping activity, while, as a bundler, is essential for proper intestinal morphogenesis of developing Caenorhabditis elegans.     

Fidelity variants of RNA dependent RNA polymerases uncover an indirect, mutagenic activity of amiloride compounds

In a screen for RNA mutagen resistance, we isolated a high fidelity RNA dependent RNA polymerase (RdRp) variant of Coxsackie virus B3 (CVB3). Curiously, this variant A372V is also resistant to amiloride. We hypothesize that amiloride has a previously undescribed mutagenic activity. Indeed, amiloride compounds increase the mutation frequencies of CVB3 and poliovirus and high fidelity variants of both viruses are more resistant to this effect. We hypothesize that this mutagenic activity is mediated through alterations in intracellular ions such as Mg2+ and Mn2+, which in turn increase virus mutation frequency by affecting RdRp fidelity. Furthermore, we show that another amiloride-resistant RdRp variant, S299T, is completely resistant to this mutagenic activity and unaffected by changes in ion concentrations. We show that RdRp variants resist the mutagenic activity of amiloride via two different mechanisms: 1) increased fidelity that generates virus populations presenting lower basal mutation frequencies or 2) resisting changes in divalent cation concentrations that affect polymerase fidelity. Our results uncover a new antiviral approach based on mutagenesis.     

Androgen action via testicular arteriole smooth muscle cells is important for Leydig cell function, vasomotion and testicular fluid dynamics

Regulation of blood flow through the testicular microvasculature by vasomotion is thought to be important for normal testis function as it regulates interstitial fluid (IF) dynamics which is an important intra-testicular transport medium. Androgens control vasomotion, but how they exert these effects remains unclear. One possibility is by signalling via androgen receptors (AR) expressed in testicular arteriole smooth muscle cells. To investigate this and determine the overall importance of this mechanism in testis function, we generated a blood vessel smooth muscle cell-specific AR knockout mouse (SMARKO). Gross reproductive development was normal in SMARKO mice but testis weight was reduced in adulthood compared to control littermates; this reduction was not due to any changes in germ cell volume or to deficits in testosterone, LH or FSH concentrations and did not cause infertility. However, seminiferous tubule lumen volume was reduced in adult SMARKO males while interstitial volume was increased, perhaps indicating altered fluid dynamics; this was associated with compensated Leydig cell failure. Vasomotion was impaired in adult SMARKO males, though overall testis blood flow was normal and there was an increase in the overall blood vessel volume per testis in adult SMARKOs. In conclusion, these results indicate that ablating arteriole smooth muscle AR does not grossly alter spermatogenesis or affect male fertility but does subtly impair Leydig cell function and testicular fluid exchange, possibly by locally regulating microvascular blood flow within the testis.     

Poles Apart: The “Bipolar” Pteropod Species Limacina helicina Is Genetically Distinct Between the Arctic and Antarctic Oceans

The shelled pteropod (sea butterfly) Limacina helicina is currently recognised as a species complex comprising two sub-species and at least five “forma”. However, at the species level it is considered to be bipolar, occurring in both the Arctic and Antarctic oceans. Due to its aragonite shell and polar distribution L. helicina is particularly vulnerable to ocean acidification. As a key indicator of the acidification process, and a major component of polar ecosystems, L. helicina has become a focus for acidification research. New observations that taxonomic groups may respond quite differently to acidification prompted us to reassess the taxonomic status of this important species. We found a 33.56% (±0.09) difference in cytochrome c oxidase subunit I (COI) gene sequences between L. helicina collected from the Arctic and Antarctic oceans. This degree of separation is sufficient for ordinal level taxonomic separation in other organisms and provides strong evidence for the Arctic and Antarctic populations of L. helicina differing at least at the species level. Recent research has highlighted substantial physiological differences between the poles for another supposedly bipolar pteropod species, Clione limacina. Given the large genetic divergence between Arctic and Antarctic L. helicina populations shown here, similarly large physiological differences may exist between the poles for the L. helicina species group. Therefore, in addition to indicating that L. helicina is in fact not bipolar, our study demonstrates the need for acidification research to take into account the possibility that the L. helicina species group may not respond in the same way to ocean acidification in Arctic and Antarctic ecosystems.     

Mechanisms ensuring optimal conditions of implantation and embryo development in the pig

The paper summarizes results of a series of studies concerning luteolysis and early pregnancy in pigs. The involvement of the oxytocin (OT)/OT receptor system in the mechanism of corpus luteum (CL) protection during early pregnancy as well as the implication of luteinizing hormone (LH) in the endometrial prostaglandin (PG) release and synthesis are described. In addition, the role of leptin in the regulation of ovarian steroidogenesis and the expression of leptin and its receptor (OB-Rb) genes in hypothalamus, pituitary and reproductive tissues are reported. Moreover, a strong emphasis was placed on the mechanism of PGE2 participation in the local endocrine regulations of reproductive processes occurring in the utero-ovarian area as well as on the vascular endothelial growth factor (VEGF) ligand-receptor system in the ovary and uterus.