Sugar transport across the peritubular face of renal cells of the flounder

The transport of some sugars at the antiluminal face of renal cells was studied using teased tubules of flounder (Pseudopleuronectes americanus). The analytical procedure allowed the determination of both free and total (free plus phosphorylated) tissue sugars. The inulin space of the preparation was 0.333 ± 0.017 kg/kg wet wt (7 animals, 33 analyses). The nonmetabolizable α-methyl-D-glucoside entered the cells by a carrier-mediated (phloridzin-sensitive), ouabain-insensitive process. The steady-state tissue/medium ratio was systematically below that for diffusion equilibrium. D-Glucose was a poor inhibitor of α-methyl-glucoside transport, D-galactose was ineffective. The phloridzin-sensitive transport processes of 2-deoxy-D-glucose,D-galactose,and 2-deoxy-D-galactose were associated with considerable phosphorylation. Kinetic evidence suggested that these sugars were transported in free form and subsequently were phosphorylated. 2-Deoxy-D-glucose accumulated in the cells against a slight concentration gradient. This transport was greatly inhibited by D-glucose, whereas α-methyl-glucoside and also D-galactose and its 2-deoxy-derivative were ineffective. D-Galactose and 2-deoxy-D-galactose mutually competed for transport; D-glucose, 2-deoxy-D-glucose, and α-methyl-D-glucoside were ineffective. Studies using various sugars as inhibitors suggest the presence of three carrier-mediated pathways of sugar transport at the antiluminal cell face of the flounder renal tubule: the pathway of α-methyl-D-glucoside (not shared by D-glucose); the pathway commonly shared by 2-deoxy-D-glucose and D-glucose; the pathway shared by D-galactose and 2-deoxy-D-galactose.     

Active Sugar Transport by the Small Intestine : The effects of sugars,amino acids,hexosamines, sulfhydryl-reacting compounds,and cations on the preferential binding of D-glucose to Tris-disrupted brush borders

Tris-disrupted and intact brush border membrane preparations from mucosa of hamster jejunum were capable of preferentially binding actively transported D-glucose in a similar manner. Density gradient centrifugation of the Tris-disrupted brush borders indicated that D-glucose was bound to a fraction containing the cores or inner material of the microvilli. The properties of this binding were examined with the Tris-disrupted brush border preparation. Actively transported sugars competitively inhibited preferential D-glucose binding, whereas no effect was observed with nonactively transported sugars. Neither actively nor nonactively transported amino acids affected D-glucose binding. D-Glucosamine, which is not actively transported, was inhibitory to preferential D-glucose binding as well as to the active transport of D-glucose by everted sacs of hamster jejunum. No inhibitory effect was observed with the same concentration of D-galactosamine. Preferential D-glucose binding was also inhibited by sulfhydryl-reacting compounds, Ca²⁺, and Li⁺ ions. On the other hand, Mg²⁺ was shown to be stimulatory and Na⁺, NH₄ ⁺, and K⁺ had no effect on this phenomenon. The results of these experiments suggest that preferential D-glucose binding to brush borders is related to the initial step in active sugar transport by the small intestine.     

Glutamate, glutamine, aspartate, asparagine, glucose and ketone-body metabolism in chick intestinal brush-border cells

1. Suspensions of isolated chick jejunal columnar absorptive (brush-border) cells respired on endogenous substrates at a rate 40% higher than that shown by rat brush-border cells. 2. Added d-glucose (5 or 10mm), l-glutamine (2.5mm) and l-glutamate (2.5mm) were the only individual substrates which stimulated respiration by chick cells; l-aspartate (2.5 or 6.7mm), glutamate (6.7mm), glutamine (6.7mm), l-alanine (1 or 10mm), pyruvate (1 or 2mm), l-lactate (5 or 10mm), butyrate (10mm) and oleate (1mm) did not stimulate chick cell respiration; l-asparagine (6.7mm) inhibited slightly; glucose (5mm) stimulated more than did 10mm-glucose. 3. Acetoacetate (10mm) and d-3-hydroxybutyrate (10mm) were rapidly consumed but, in contrast to rat brush-border cells, did not stimulate respiration. 4. Glucose (10mm) was consumed more slowly than 5mm-glucose; the dominant product of glucose metabolism during vigorous respiration was lactate; the proportion of glucose converted to lactate was greater with 10mm- than with 5mm-glucose. 5. Glutamate and aspartate consumption rates decreased, and alanine and glutamine consumption rates increased when their initial concentrations were raised from 2.5 to 6.7 or 10mm. 6. The metabolic fate of glucose was little affected by concomitant metabolism of any one of aspartate, glutamate or glutamine except for an increased production of alanine; the glucose-stimulated respiration rate was unaffected by concomitant metabolism of these individual amino acids. 7. Chick cells produced very little alanine from aspartate and, in contrast to rat cells, likewise produced very little alanine from glutamate or glutamine; in chick cells alanine appeared to be predominantly a product of transmination of pyruvate derived from glucose metabolism. 8. In chick cells, glutamate and glutamine were formed from aspartate (2.5 or 6.7mm); aspartate and glutamine were formed from glutamate (2.5mm) but only aspartate from 6.7mm-glutamate; glutamate was the dominant product formed from glutamine (6.7mm) but aspartate only was formed from 2.5mm-glutamine. 9. Chick brush-border cells can thus both catabolize and synthesize glutamine; glutamine synthesis is always diminished by concomitant metabolism of glucose, presumably by allosteric inhibition of glutamine synthetase by alanine. 10. Proline was formed from glutamine (2.5mm) but not from glutamine (2.5mm)+glucose (5mm) and not from 2.5mm-glutamate; ornithine was formed from glutamine (2.5mm)+glucose (5.0mm) but not from glutamine alone; serine was formed from glutamine (2.5mm)+glucose (5mm) and from these two substrates plus aspartate (2.5mm). 11. Total intracellular adenine nucleotides (22μmol/g dry wt.) remained unchanged during incubation of chick cells with glucose. 12. Intracellular glutathione (0.7–0.8mm) was depleted by 40% during incubation of respiring chick cells without added substrates for 75min at 37°C; partial restoration of the lost glutathione was achieved by incubating cells with l-glutamate+l-cysteine+glycine.     

Difference in Topology of Normal and Tumour Cell Membranes shown by Different Surface Distributions of Ferritin-conjugated Concanavalin A

THE observations of Burger and Goldberg¹ on the differential agglutinability of malignant cells by the saccharide-binding protein, wheat germ agglutinin (WGA), have prompted other investigators to study the nature of tumour cell surfaces using similar reagents. A variety of other plant agglutinins specifically agglutinate certain oncogenic virus-transformed cells at much lower concentrations than those required to agglutinate their normal parental lines. In addition to WGA^1,2 (specific for binding N-acetyl-D-glucosamine-like residues¹), these include concanavalin A (Con A)^3,4 (specific for binding α-D-glucose or α-D-mannose-like residues⁵), soy bean agglutinin (SBA)^6,7 (specific for binding N-acetyl-D-galactosamine and D-galactose-like residues⁶) and Ricinus communis agglutinin (specific for binding D-galactose and L-arabinose-like residues) (G. L. N. and J. Blaustein, in preparation). To explain this differential agglutinability phenomenon, Burger² proposed that the agglutinin-binding sites on normal cells could have undergone three possible types of change after transformation: (a) the normal parent cell may have no agglutinin sites and after transformation a complete de novo synthesis of agglutinin sites occurs; (b) the normal parent cell may have agglutinin sites, but not enough for agglutination and transformation results in an increase in the number of agglutinin sites; or (c) the normal parent cell agglutinin sites remain constant in number after transformation; but this process results in an exposure of “cryptic” agglutinin sites and the transformed cell is rendered agglutinable. Several workers^8,10,19 postulate a fourth type of change: (d) the normal parent cell agglutinin sites remain constant in number after transformation but the topological distribution of agglutinin sites changes to a distribution more favourable for agglutination. The first and second mechanisms have proved to be unlikely as originally suggested², because agglutinin surface receptors are present on normal cells² and they are present in the same amounts on normal or transformed cells. This latter finding has been demonstrated in saturation binding experiments using purified ¹²⁵I-labelled WGA⁸, Con A^8,9 and SBA¹⁰, with results contrary to earlier reports using ⁶³Ni-labelled Con A³.     

Amino Acid and Sugar Transport in Rabbit Ileum

L-Alanine and 3-O-methyl-D-glucose accumulation by mucosal strips from rabbit ileum has been investigated with particular emphasis on the interaction between Na and these transport processes. L-Alanine is rapidly accumulated by mucosal tissue and intracellular concentrations of approximately 50 mM are reached within 30 min when extracellular L-alanine concentration is 5 mM. Evidence is presented that intracellular alanine exists in an unbound, osmotically active form and that accumulation is an active transport process. In the absence of extracellular Na, the final ratio of intracellular to extracellular L-alanine does not differ significantly from unity and the rate of net uptake is markedly inhibited. Amino acid accumulation is also inhibited by 5 x 10^-5 M ouabain. 3-O-methyl-D-glucose accumulation by this preparation is similarly affected by ouabain and by incubation in a Na-free medium. The effects of amino acid accumulation, of ouabain, and of incubation in a Na-free medium on cell water content and intracellular Na and K concentrations have also been investigated. These results are discussed with reference to the two hypotheses which have been suggested to explain the interaction between Na and intestinal nonelectrolyte transport.     

l-Glutamate-Dependent Medium Alkalinization by Asparagus Mesophyll Cells : Cotransport or Metabolism?

Mechanically isolated Asparagus sprengeri Regel mesophyll cells cause alkalinization of the suspension medium on the addition of l-glutamate or its analog l-methionine-d,l-sulfoximine. Using a radiolabeled pH probe, it was found that both compounds caused internal acidification whereas l-aspartate did not. Fusicoccin stimulated H⁺ efflux from the cells by 111% and the uptake of l-[U-¹⁴C]glutamate by 55%. Manometric experiments demonstrated that, unlike l-methionine-d,l-sulfoximine, l-glutamate stimulated CO₂ evolution from nonilluminated cells. Simultaneous measurements of medium alkalinization and ¹⁴CO₂ evolution upon the addition of labeled l-glutamate showed that alkalinization was immediate and reached a maximum value after 45 minutes whereas ¹⁴CO₂ evolution exhibited a lag before its appearance and continued in a linear manner for at least 100 minutes. Rates of alkalinization and uptake of l-[U-¹⁴C]glutamate were higher in the light while rates of ¹⁴CO₂ evolution were higher in the dark. The major labeled product of glutamate decarboxylation, γ-aminobutyric acid, was found in the cells and the suspension medium. Its addition to the cell suspension did not result in medium alkalinization and evidence indicates that it is lost from the cell to the medium. The data suggest that the origin of medium alkalinization is co-transport not metabolism, and that the loss of labeled CO₂ and γ-aminobutyric acid from the cell result in an overestimation of the stoichiometry of the H⁺/l-glutamate uptake process.     

Fast Protein Loop Sampling and Structure Prediction Using Distance-Guided Sequential Chain-Growth Monte Carlo Method

Loops in proteins are flexible regions connecting regular secondary structures. They are often involved in protein functions through interacting with other molecules. The irregularity and flexibility of loops make their structures difficult to determine experimentally and challenging to model computationally. Conformation sampling and energy evaluation are the two key components in loop modeling. We have developed a new method for loop conformation sampling and prediction based on a chain growth sequential Monte Carlo sampling strategy, called Distance-guided Sequential chain-Growth Monte Carlo (DiSGro). With an energy function designed specifically for loops, our method can efficiently generate high quality loop conformations with low energy that are enriched with near-native loop structures. The average minimum global backbone RMSD for 1,000 conformations of 12-residue loops is Å, with a lowest energy RMSD of Å, and an average ensemble RMSD of Å. A novel geometric criterion is applied to speed up calculations. The computational cost of generating 1,000 conformations for each of the x loops in a benchmark dataset is only about cpu minutes for 12-residue loops, compared to ca cpu minutes using the FALCm method. Test results on benchmark datasets show that DiSGro performs comparably or better than previous successful methods, while requiring far less computing time. DiSGro is especially effective in modeling longer loops (– residues).     

Anecdotal,Historical and Critical Commentaries on Genetics: In the Beginning Was the Worm …

The replicative life span (RLS) of Saccharomyces cerevisiae has been established as a model for the genetic regulation of longevity despite the inherent difficulty of the RLS assay, which requires separation of mother and daughter cells by micromanipulation after every division. Here we present the mother enrichment program (MEP), an inducible genetic system in which mother cells maintain a normal RLS—a median of 36 generations in the diploid MEP strain—while the proliferative potential of daughter cells is eliminated. Thus, the viability of a population over time becomes a function of RLS, and it displays features of a survival curve such as changes in hazard rate with age. We show that viability of mother cells in liquid culture is regulated by SIR2 and FOB1, two opposing regulators of RLS in yeast. We demonstrate that viability curves of these short- and long-lived strains can be easily distinguished from wild type, using a colony formation assay. This provides a simplified screening method for identifying genetic or environmental factors that regulate RLS. Additionally, the MEP can provide a cohort of cells at any stage of their life span for the analysis of age-associated phenotypes. These capabilities effectively remove the hurdles presented by RLS analysis that have hindered S. cerevisiae aging studies since their inception 50 years ago.THE budding yeast Saccharomyces cerevisiae is a popular model system for studying fundamental processes of cellular aging (reviewed in Steinkraus et al. 2008). Analyses over the past 50 years have led to the idea that budding yeast can be used to study three types of cellular aging. Replicative aging describes the division potential of individual cells and relies on the asymmetric cell divisions of budding yeast that yield distinct mother and daughter cells. Replicative life span (RLS) is defined as the number of times an individual cell divides before it undergoes senescence (Mortimer and Johnston 1959). Chronological aging describes the capacity of cells in stationary phase (analogous to G₀ in higher eukaryotes) to maintain viability over time, which is assayed by their ability to reenter the cell cycle when nutrients are reintroduced (Longo et al. 1996). Finally, budding yeast have been used to study clonal senescence, which is analogous to the Hayflick limit imposed on mammalian tissue culture cells and characterized by a finite number of times a population of cells can divide. Although wild-type yeast populations do not senesce, this phenomenon has been observed in mutant strains such as those lacking telomerase components (Lundblad and Szostak 1989; Singer and Gottschling 1994).While genetic screens have been applied to examine clonal and chronological aging (Lundblad and Szostak 1989; Powers et al. 2006; Murakami et al. 2008), they have been limited in their application to studying replicative aging (Kaeberlein and Kennedy 2005; Kaeberlein et al. 2005b). This limitation arises from the arduous nature of isolating replicatively aged yeast cells. The current “gold standard” for isolating aged mother cells is by micromanipulation, where daughter cells are counted and removed after every division (Park et al. 2002). Although micromanipulation is currently the only method capable of accurately measuring RLS in yeast, it is severely constrained by the small number of cells that can be analyzed. Thus, genetic analysis of the regulation of RLS has been limited to a candidate gene approach (reviewed in Steinkraus et al. 2008).True genetic analysis of RLS will require large populations of aged cells. However, there are two confounding issues that make isolation of aged individuals difficult. First, single-cell pedigree analysis has shown that age-associated phenotypes, such as replicative life span potential, segregate asymmetrically between mother and daughter cells, rendering age-associated phenotypes nonheritable (Egilmez and Jazwinski 1989; Kennedy et al. 1994). Thus, daughter cells are generally “reset” to a young state with every generation. Second, when age is measured in terms of cell divisions, an unfractionated population is predominately young. The fraction of the population at an age of n cell divisions is ∼1/2ⁿ. Individual cells that reach the median RLS, which is ∼26 generations for haploid cells of the S288C strain background (Kaeberlein et al. 2005a), represent an insignificant fraction of the total population. In fact, it is unlikely that any cell reaches such an advanced age because nutrient depletion will limit the division potential of the population (Dickinson and Schweizer 1999).As an alternative to micromanipulation, methods were developed to isolate aged cells from liquid cultures (Smeal et al. 1996; Sinclair and Guarente 1997; Chen and Contreras 2007). However, due to the exponential growth of progeny cells, these populations are technically limited to 7–12 generations before nutrient depletion interferes with replicative aging. While sequential rounds of growth and purification are possible, the inability to continuously follow an undisturbed cohort of cells prevents the measurement of RLS by these methods. Instead, purification methods are primarily used for the examination of molecular changes associated with aging cells. Unfortunately, low yields and loss of viability due to purification methods diminish their utility for analyzing phenotypes that affect cells of advanced age. As an alternative to purification from natural populations, a strategy to genetically regulate the replicative capacity of daughter cells and avoid the limits imposed by exponential growth has been described (Jarolim et al. 2004). While this system effectively prevents division of daughter cells, it unintentionally decreases the median RLS of mother cells to four cell divisions, thus restricting its usefulness.Here we describe the development of a novel genetic selection against newborn daughter cells, the “mother enrichment program” (MEP), which restricts the replicative capacity of daughter cells while allowing mother cells to achieve a normal RLS. We demonstrate that upon induction of the selection, the viability of MEP strains growing in liquid culture is determined by the RLS of the initial population of mother cells. MEP cultures therefore allow the comparison of RLS between strains without the need for micromanipulation. Additionally, because MEP cultures are not subject to nutrient limitation, single-step affinity purification of aged cells can be achieved at any point during their life span. Together, these capabilities substantially resolve the technical hurdles that have made replicative aging studies in S. cerevisiae exceptionally challenging.     

l-Serine Deficiency Elicits Intracellular Accumulation of Cytotoxic Deoxysphingolipids and Lipid Body Formation

l-Serine is required to synthesize membrane lipids such as phosphatidylserine and sphingolipids. Nevertheless, it remains largely unknown how a diminished capacity to synthesize l-serine affects lipid homeostasis in cells and tissues. Here, we show that deprivation of external l-serine leads to the generation of 1-deoxysphingolipids (doxSLs), including 1-deoxysphinganine, in mouse embryonic fibroblasts (KO-MEFs) lacking d-3-phosphoglycerate dehydrogenase (Phgdh), which catalyzes the first step in the de novo synthesis of l-serine. A novel mass spectrometry-based lipidomic approach demonstrated that 1-deoxydihydroceramide was the most abundant species of doxSLs accumulated in l-serine-deprived KO-MEFs. Among normal sphingolipid species in KO-MEFs, levels of sphinganine, dihydroceramide, ceramide, and hexosylceramide were significantly reduced after deprivation of external l-serine, whereas those of sphingomyelin, sphingosine, and sphingosine 1-phosphate were retained. The synthesis of doxSLs was suppressed by supplementing the culture medium with l-serine but was potentiated by increasing the ratio of l-alanine to l-serine in the medium. Unlike with l-serine, depriving cells of external l-leucine did not promote the occurrence of doxSLs. Consistent with results obtained from KO-MEFs, brain-specific deletion of Phgdh in mice also resulted in accumulation of doxSLs in the brain. Furthermore, l-serine-deprived KO-MEFs exhibited increased formation of cytosolic lipid bodies containing doxSLs and other sphingolipids. These in vitro and in vivo studies indicate that doxSLs are generated in the presence of a high ratio of l-alanine to l-serine in cells and tissues lacking Phgdh, and de novo synthesis of l-serine is necessary to maintain normal sphingolipid homeostasis when the external supply of this amino acid is limited.     

Regulation of sulfate uptake by amino acids in cultured tobacco cells

The sulfur requirements of tobacco (Nicotiana tabacum L. var. Xanthi) XD cells grown in chemically defined liquid media can be satisfied by sulfate, thiosulfate, l-cyst(e)ine, l-methionine or glutathione, and somewhat less effectively by d-cyst (e) ine, d-methionine or dl-homocyst (e)ine. Sulfate uptake is inhibited after a 2 hr lag by l-cyst (e)ine, l-methionine, l-homocyst(e)ine or l-isoleucine, but not by any of the other protein amino acids, nor by d-cyst(e)ine. l-cyst(e)ine is neither a competitive nor a non-competitive inhibitor of sulfate uptake. Its action most closely resembles apparent uncompetitive inhibition. Inhibition of sulfate uptake by l-cyst(e)ine can be partially prevented by equimolar l-arginine, l-lysine, l-leucine, l-phenylalanine, l-tyrosine or l-tryptophan, but is little affected by any of the other protein amino acids. The effective amino acids are apparent competitive inhibitors of l-cyst(e)ine uptake after a 2 hr lag. Inhibition of sulfate uptake by l-methionine cannot be prevented, nor can uptake of l-methionine be inhibited by any single protein amino acid. The results suggest the occurrence of negative feedback control of sulfate assimilation by the end products, the sulfur amino acids, in cultured tobacco cells.     

Cross-Species RNAi Rescue Platform in Drosophila melanogaster

RNAi-mediated gene knockdown in Drosophila melanogaster is a powerful method to analyze loss-of-function phenotypes both in cell culture and in vivo. However, it has also become clear that false positives caused by off-target effects are prevalent, requiring careful validation of RNAi-induced phenotypes. The most rigorous proof that an RNAi-induced phenotype is due to loss of its intended target is to rescue the phenotype by a transgene impervious to RNAi. For large-scale validations in the mouse and Caenorhabditis elegans, this has been accomplished by using bacterial artificial chromosomes (BACs) of related species. However, in Drosophila, this approach is not feasible because transformation of large BACs is inefficient. We have therefore developed a general RNAi rescue approach for Drosophila that employs Cre/loxP-mediated recombination to rapidly retrofit existing fosmid clones into rescue constructs. Retrofitted fosmid clones carry a selection marker and a phiC31 attB site, which facilitates the production of transgenic animals. Here, we describe our approach and demonstrate proof-of-principle experiments showing that D. pseudoobscura fosmids can successfully rescue RNAi-induced phenotypes in D. melanogaster, both in cell culture and in vivo. Altogether, the tools and method that we have developed provide a gold standard for validation of Drosophila RNAi experiments.RNAi-mediated gene knockdown, whereby an exogenous double stranded RNA (dsRNA) is used to trigger homology-dependent suppression of the target gene, is an effective loss-of-function method to interrogate gene function. The RNAi technology in Drosophila melanogaster is widely used for genomewide RNAi screens in cell culture (see review by Perrimon and Mathey-Prevot 2007a), and more recently has been extended to large scale in vivo studies (Dietzl et al. 2007; Ni et al. 2009; Mummery-Widmer et al. 2009). Gene knockdown by RNAi is achieved by the introduction of dsRNAs into cultured cells or by inducible overexpression of “hairpin” dsRNAs in transgenic flies. In the context of in vivo RNAi screening, the combination of a tissue-specific GAL4 driver with a GAL4-responsive hairpin dsRNA transgene allows knockdown of the target gene only in the desired cells, thus providing a powerful way of probing biological processes that have been so far difficult to investigate.Analysis of the specificity of long dsRNAs in Drosophila cells has revealed that these reagents, depending on their sequences and levels of expression, can knock down genes others than the intended target (Kulkarni et al. 2006; Ma et al. 2006). This phenomenon is not specific to long dsRNAs and has also been commonly observed with 21-nt long siRNAs and shRNAs used in mammalian RNAi screens. In fact the rate of false positives associated with off-target effects observed in mammalian screens is usually higher than those observed with long dsRNAs (Echeverri and Perrimon 2006). Unwanted false positives created by off-target effects are a major problem in RNAi screens and require lengthy secondary validation tests (Echeverri and Perrimon 2006; Perrimon and Mathey-Prevot 2007b; Ramadan et al. 2007). Further, false positives associated with RNAi reagents are not limited to tissue culture experiments, as they have also been reported in the context of transgenic RNAi. For example, ∼25% of the hairpins targeting nonessential genes cause lethality when driven by the constitutively expressed Act5C-GAL4 driver (Dietzl et al. 2007; Ni et al. 2009).A number of approaches can be used to validate the specificity of RNAi-induced phenotypes (Echeverri and Perrimon 2006). These include validation by multiple dsRNAs that target the same gene but that do not overlap in sequence, comparison of knockdown efficiencies of multiple dsRNAs and the phenotypic strengths, and rescue of the phenotype by either cDNAs or genomic DNAs. Rescue of RNAi phenotypes constitutes the gold standard in the field as it provides unambiguous proof that the targeted gene is indeed responsible for the phenotype observed. In Drosophila cell culture experiments, cDNAs that lack the original 3′-untranslated region (UTR) have been used to rescue phenotypes induced by dsRNAs targeting the 3′-UTR (Yokokura et al. 2004; Stielow et al. 2008). In mammalian cell culture experiments, cDNAs that have a silent point mutation in the region targeted by an siRNA are commonly used (Lassus et al. 2002). The intrinsic problem of these approaches, however, is that overexpression of cDNAs alone can evoke abnormal cellular responses on their own, complicating interpretation of the results. A cleaner method is based on cross-species rescue that uses genomic DNA from a different species whose sequence is divergent enough from the host species to make it refractory to the RNAi reagent directed against the host gene. This approach effectively addresses the issue of overexpression artifact, as the rescue transgene is expressed from its endogenous promoter, ensuring proper levels and precise spatiotemporal regulation of gene expression. Cross-species rescue methods that use bacterial artificial chromosome (BACs) retrofitted with an appropriate selection marker have been described for mammals and C. elegans (Kittler et al. 2005; Sarov et al. 2006). However, the BAC strategies are not realistic for large-scale studies, because transformation of BACs, which are typically larger than 100 kb, is inefficient, albeit not impossible, in Drosophila (Venken et al. 2006).To provide a feasible way to validate large-scale RNAi screening results, we decided to develop a universal method for cross-species RNAi rescue in Drosophila. We chose to use fosmids, which are single-copy bacterial vectors with a cloning capacity of ∼40 kb, rather than BACs because (1) transformation of plasmids around this size is relatively efficient (Venken et al. 2006) and (2) end-sequenced fosmid clones for 11 different Drosophila species generated by the Drosophila species genome project are now publicly available (Richards et al. 2005; Drosophila 12 Genomes Consortium 2007).     

Amino Acid Isomerization in the Production of l-Phenylalanine from d-Phenylalanine by Bacteria

To establish an advantageous method for the production of l-amino acids, microbial isomerization of d- and dl-amino acids to l-amino acids was studied. Screening experiments on a number of microorganisms showed that cell suspensions of Pseudomonas fluorescens and P. miyamizu were capable of isomerizing d- and dl-phenylalanines to l-phenylalanine. Various conditions suitable for isomerization by these organisms were investigated. Cells grown in a medium containing d-phenylalanine showed highest isomerization activity, and almost completely converted d- or dl-phenylalanine into l-phenylalanine within 24 to 48 hr of incubation. Enzymatic studies on this isomerizing system suggested that the isomerization of d- or dl-phenylalanine is not catalyzed by a single enzyme, “amino acid isomerase,” but the conversion proceeds by a two step system as follows: d-pheylalanine is oxidized to phenylpyruvic acid by d-amino acid oxidase, and the acid is converted to l-phenylalanine by transamination or reductive amination.     

Gene expression and activity of cartilage degrading glycosidases in human rheumatoid arthritis and osteoarthritis synovial fibroblasts

Introduction

Similar to matrix metalloproteinases, glycosidases also play a major role in cartilage degradation. Carbohydrate cleavage products, generated by these latter enzymes, are released from degrading cartilage during arthritis. Some of the cleavage products (such as hyaluronate oligosaccharides) have been shown to bind to Toll-like receptors and provide endogenous danger signals, while others (like N-acetyl glucosamine) are reported to have chondroprotective functions. In the current study for the first time we systematically investigated the expression of glycosidases within the joints.

Methods

Expressions of β-D-hexosaminidase, β-D-glucuronidase, hyaluronidase, sperm adhesion molecule 1 and klotho genes were measured in synovial fibroblasts and synovial membrane samples of patients with rheumatoid arthritis and osteoarthritis by real-time PCR. β-D-Glucuronidase, β-D-glucosaminidase and β-D-galactosaminidase activities were characterized using chromogenic or fluorogenic substrates. Synovial fibroblast-derived microvesicles were also tested for glycosidase activity.

Results

According to our data, β-D-hexosaminidase, β-D-glucuronidase, hyaluronidase, and klotho are expressed in the synovial membrane. Hexosaminidase is the major glycosidase expressed within the joints, and it is primarily produced by synovial fibroblasts. HexA subunit gene, one of the two genes encoding for the alpha or the beta chains of hexosaminidase, was characterized by the strongest gene expression. It was followed by the expression of HexB subunit gene and the β-D-glucuronidase gene, while the expression of hyaluronidase-1 gene and the klotho gene was rather low in both synovial fibroblasts and synovial membrane samples. Tumor growth factor-β1 profoundly downregulated glycosidase expression in both rheumatoid arthritis and osteoarthritis derived synovial fibroblasts. In addition, expression of cartilage-degrading glycosidases was moderately downregulated by proinflammatory cytokines including TNFα, IL-1β and IL-17.

Conclusions

According to our present data, glycosidases expressed by synovial membranes and synovial fibroblasts are under negative regulation by some locally expressed cytokines both in rheumatoid arthritis and osteoarthritis. This does not exclude the possibility that these enzymes may contribute significantly to cartilage degradation in both joint diseases if acting in collaboration with the differentially upregulated proteases to deplete cartilage in glycosaminoglycans.     

Indirect evidence for a strict negative control of S-adenosyl-l-methionine decarboxylase by spermidine in rat hepatoma cells

1. Direct or indirect inhibitors of l-ornithine decarboxylase (EC 4.1.1.17), structurally related or unrelated to l-ornithine, including dl-α-difluoromethylornithine, α-methylornithine and 1,3-diaminopropane, used alone or in combination, decreased polyamine concentrations in rat hepatoma tissue culture (HTC) cells and increased S-adenosyl-l-methionine decarboxylase activity (EC 4.1.1.50). 2. Comparison of the catalytic properties of S-adenosyl-l-methionine from cells with elevated and normal activities revealed no apparent modification of the catalytic site as judged by affinity for the substrate, stimulation by di- and tri-amines and inhibition by methylglyoxal bis-(guanylhydrazone). 3. Actinomycin D and cycloheximide, and RNA and a proteinsynthesis inhibitor respectively, blocked the increase of S-adenosyl-l-methionine decarboxylase activity elicited by α-difluoromethylornithine. In polyamine-depleted cells the apparent half-life of elevated S-adenosyl-l-methionine decarboxylase activity, determined by inhibition of protein synthesis, was 2.5-fold longer than in control cells. The present results suggest that elevation of S-adenosyl-l-methionine decarboxylase activity by α-difluoromethylornithine is due to stabilization of the enzyme. 4. Restoration of the normal intracellular putrescine content, by addition of putrescine to the medium of polyamine-deficient cells, transiently increased S-adenosyl-l-methionine decarboxylase activity. Thereafter, intracellular conversion of putrescine into spermidine was accompanied by inactivation of the enzyme at a rate that was similar to that found on addition of spermidine itself. No relationship between total intracellular spermine content and S-adenosyl-l-methionine decarboxylase activity could be established. 5. Addition of 1mm-1,3-diaminopropane to polyamine-deficient cells did not cause a decrease in the activity of S-adenosyl-l-methionine decarboxylase, whereas addition of 1,5-diaminopentane (cadaverine) did. 1,3-Diamino-N-(3-aminopropyl)propane did not accumulate in cells treated with α-difluoromethylornithine and 1,3-diaminopropane, whereas addition of 1,5-diaminopentane led to the accumulation of 1,5-diamino-N-(3-aminopropyl)pentane. 1,3-Diamino-N-(3-aminopropyl)propane (10μm) was as effective as spermidine in decreasing S-adenosyl-l-methionine decarboxylase activity. Thus effectiveness of a diamine in decreasing enzyme activity is related to its capability of being converted into a closely structurally related homologue of spermidine by spermidine synthase. 6. The spermidine site of action appears to be post-translational since (a) the spermidine-induced decrease of S-adenosyl-l-methionine activity was not prevented by actinomycin D and (b) spermidine in the presence of cycloheximide led to a synergistic inactivation of the enzyme with a decay rate that progressively approached control values. Altogether these results are indirect evidence for a strict negative control of S-adenosyl-l-methionine decarboxylase by spermidine and substantiate previous findings [Mamont, Duchesne, Grove & Tardif (1978) Exp. Cell Res. 115, 387–393]. Spermidine appears to act on some processes involved in denaturation and/or degradation of the enzyme protein. Putrescine appears to decrease the rate of these processes. The physiological significance of the regulatory control of S-adenosyl-l-methionine decarboxylase is discussed.     

Deficiency in l-Serine Deaminase Interferes with One-Carbon Metabolism and Cell Wall Synthesis in Escherichia coli K-12

Escherichia coli K-12 provided with glucose and a mixture of amino acids depletes l-serine more quickly than any other amino acid even in the presence of ammonium sulfate. A mutant without three 4Fe4S l-serine deaminases (SdaA, SdaB, and TdcG) of E. coli K-12 is unable to do this. The high level of l-serine that accumulates when such a mutant is exposed to amino acid mixtures starves the cells for C₁ units and interferes with cell wall synthesis. We suggest that at high concentrations, l-serine decreases synthesis of UDP-N-acetylmuramate-l-alanine by the murC-encoded ligase, weakening the cell wall and producing misshapen cells and lysis. The inhibition by high l-serine is overcome in several ways: by a large concentration of l-alanine, by overproducing MurC together with a low concentration of l-alanine, and by overproducing FtsW, thus promoting septal assembly and also by overexpression of the glycine cleavage operon. S-Adenosylmethionine reduces lysis and allows an extensive increase in biomass without improving cell division. This suggests that E. coli has a metabolic trigger for cell division. Without that reaction, if no other inhibition occurs, other metabolic functions can continue and cells can elongate and replicate their DNA, reaching at least 180 times their usual length, but cannot divide.The Escherichia coli genome contains three genes, sdaA, sdaB, and tdcG, specifying three very similar 4Fe4S l-serine deaminases. These enzymes are very specific for l-serine for which they have unusually high K_m values (3, 32). Expression of the three genes is regulated so that at least one of the gene products is synthesized under all common growth conditions (25). This suggests an important physiological role for the enzymes. However, why E. coli needs to deaminate l-serine has been a long-standing problem of E. coli physiology, the more so since it cannot use l-serine as the sole carbon source.We showed recently that an E. coli strain devoid of all three l-serine deaminases (l-SDs) loses control over its size, shape, and cell division when faced with complex amino acid mixtures containing l-serine (32). We attributed this to starvation for single-carbon (C₁) units and/or S-adenosylmethionine (SAM). C₁ units are usually made from serine via serine hydroxymethyl transferase (GlyA) or via glycine cleavage (GCV). The l-SD-deficient triple mutant strain is starved for C₁ in the presence of amino acids, because externally provided glycine inhibits GlyA and a very high internal l-serine concentration along with several other amino acids inhibits glycine cleavage. While the parent cell can defend itself by reducing the l-serine level by deamination, this crucial reaction is missing in the ΔsdaA ΔsdaB ΔtdcG triple mutant. We therefore consider these to be “defensive” serine deaminases.The fact that an inability to deaminate l-serine leads to a high concentration of l-serine and inhibition of GlyA is not surprising. However, it is not obvious why a high level of l-serine inhibits cell division and causes swelling, lysis, and filamentation. Serine toxicity due to inhibition of biosynthesis of isoleucine (11) and aromatic amino acids (21) has been reported but is not relevant here, since these amino acids are provided in Casamino Acids.We show here that at high internal concentrations, l-serine also causes problems with peptidoglycan synthesis, thus weakening the cell wall. Peptidoglycan is a polymer of long glycan chains made up of alternating N-acetylglucosamine and N-acetylmuramic acid residues, cross-linked by l-alanyl-γ-d-glutamyl-meso-diaminopimelyl-d-alanine tetrapeptides (1, 28). The glucosamine and muramate residues and the pentapeptide (from which the tetrapeptide is derived) are all synthesized in the cytoplasm and then are exported to be polymerized into extracellular peptidoglycan (2).In this paper, we show that lysis is caused by l-serine interfering with the first step of synthesis of the cross-linking peptide, the addition of l-alanine to uridine diphosphate-N-acetylmuramate. This interference is probably due to a competition between serine and l-alanine for the ligase, MurC, which adds the first l-alanine to UDP-N-acetylmuramate (7, 10, 15). As described here, the weakening of the cell wall by l-serine can be overcome by a variety of methods that reduce the endogenous l-serine pool or counteract the effects of high levels of l-serine.