Dinucleotide Phosphate Research Articles

Amino Acids Involved in Polyphosphate Synthesis and Its Mobilization Are Distinct in Polyphosphate Kinase-1 from Mycobacterium tuberculosis

BackgroundIn bacteria polyphosphates (poly-P) are involved in cellular metabolism and development especially during stress. The enzyme, principally involved in polyphosphate biosynthesis and its mobilization leading to generation of NTPs, is known as polyphosphate kinase (PPK).Principal FindingsAmong two genes of polyphosphate kinases present in Mycobacterium tuberculosis, we cloned and expressed PPK1 in Escherichia coli as histidine-tagged protein. This ∼86 kDa protein is capable of autophosphorylation and synthesis of poly-P as well as NTP. Among 22 conserved histidine residues, we found only His-491 is autophosphorylated and crucial for any enzymatic activity. Substitution of His-510 caused mPPK1 protein deficient but not defective in autophosphorylation, thereby contrary to earlier reports negating any role of this residue in the process. However, mutation of His-510 with either Ala or Gln affected ATP or poly-P synthesis depending on the substitution; while such effects were severe with H510A but mild with H510Q. Furthermore, mPPK1 also renders auxiliary nucleotide diphosphate kinase function by synthesizing virtually all NTPs/dNTPs from their cognate NDPs/dNDPs by utilizing poly-P as the phosphate donor albeit with varied efficiency. To assess the influence of other catalytic domain residues of mPPK1 towards its functionality, we designed mutations based on E. coli PPK1 crystal structure since it owes 68% amino acid sequence similarity with mPPK1. Interestingly, our results revealed that mutations in mPPK1 affecting poly-P synthesis always affected its ATP synthesizing ability; however, the reverse may not be true.Conclusions/SignificanceWe conclude that amino acid residues involved in poly-P and ATP synthesizing activities of mPPK1 are distinct. Considering conserved nature of PPK1, it seems our observations have broader implications and not solely restricted to M. tuberculosis only.

Location and conformation of pantothenate and its derivatives inMycobacterium tuberculosispantothenate kinase: insights into enzyme action

Previous studies of complexes of Mycobacterium tuberculosis PanK (MtPanK) with nucleotide diphosphates and nonhydrolysable analogues of nucleoside triphosphates in the presence or the absence of pantothenate established that the enzyme has dual specificity for ATP and GTP, revealed the unusual movement of ligands during enzyme action and provided information on the effect of pantothenate on the location and conformation of the nucleotides at the beginning and the end of enzyme action. The X-ray analyses of the binary complexes of MtPanK with pantothenate, pantothenol and N-nonylpantothenamide reported here demonstrate that in the absence of nucleotide these ligands occupy, with a somewhat open conformation, a location similar to that occupied by phosphopantothenate in the `end' complexes, which differs distinctly from the location of pantothenate in the closed conformation in the ternary `initiation' complexes. The conformation and the location of the nucleotide were also different in the initiation and end complexes. An invariant arginine appears to play a critical role in the movement of ligands that takes place during enzyme action. The work presented here completes the description of the locations and conformations of nucleoside diphosphates and triphosphates and pantothenate in different binary and ternary complexes, and suggests a structural rationale for the movement of ligands during enzyme action. The present investigation also suggests that N-alkylpantothenamides could be phosphorylated by the enzyme in the same manner as pantothenate.

Purification and biochemical characterization of a novel ecto-apyrase, MP67, from Mimosa pudica.

We have previously reported the presence of an apyrase in Mimosa pudica. However, only limited information is available for this enzyme. Thus, in this study, the apyrase was purified to homogeneity. The purified enzyme had a molecular mass of around 67 kD and was able to hydrolyze both nucleotide triphosphate and nucleotide diphosphate as substrates. The ratio of ATP to ADP hydrolysis velocity of the purified protein was 0.01 in the presence of calcium ion, showing extremely high substrate specificity toward ADP. Thus, we designated this novel apyrase as MP67. A cDNA clone of MP67 was obtained using primers designed from the amino acid sequence of trypsin-digested fragments of the protein. In addition, rapid amplification of cDNA ends-polymerase chain reaction was performed to clone a conventional apyrase (MpAPY2). Comparison of the deduced amino acid sequences showed that MP67 is similar to ecto-apyrases; however, it was distinct from conventional apyrase based on phylogenetic classification. MP67 and MpAPY2 were expressed in Escherichia coli, and the recombinant proteins were purified. The recombinant MP67 showed high substrate specificity toward ADP rather than ATP. A polyclonal antibody raised against the recombinant MP67 was used to examine the tissue distribution and localization of native MP67 in the plant. The results showed that MP67 was ubiquitously distributed in various tissues, most abundantly in leaves, and was localized to plasma membranes. Thus, MP67 is a novel ecto-apyrase with extremely high substrate specificity for ADP.

Diphosphate Regulation of Adenosine Triphosphate Sensitive Potassium Channel in Human Bladder Smooth Muscle Cells

To clarify the properties of adenosine triphosphate sensitive K+ channel in human detrusor smooth muscle we examined the effect of the representative nicotinic acid derivatives β-nicotinamide adenine dinucleotide, cyclic adenosine diphosphate ribose and nicotinic acid adenine dinucleotide phosphate (Sigma-Aldrich®) on human detrusor adenosine triphosphate sensitive K+ channels. Patch clamp procedures were done in human detrusor cells. Reverse transcriptase and real-time polymerase chain reaction were performed to clarify the subunit components of adenosine triphosphate sensitive K+ channels. The K+ channel opener levcromakalim induced a long lasting outward current that was inhibited by glibenclamide (Sigma-Aldrich) under the whole cell configuration. The single channel study revealed that the unitary conductance of the adenosine triphosphate sensitive K+ channel in the human detrusor was 11 pS and nucleotide diphosphates increased its open probability. Applying β-nicotinamide adenine dinucleotide also activated the adenosine triphosphate sensitive K+ channel but applying cyclic adenosine diphosphate ribose or nicotinic acid adenine dinucleotide phosphate had little effect on channel activation. Molecular studies indicated that Kir6.1 and SUR2B were the predominant components of the adenosine triphosphate sensitive K+ channel in the human detrusor. To our knowledge we report the first single channel study of the adenosine triphosphate sensitive K+ channel in the human detrusor. The properties of this channel, ie unitary conductance, adenosine triphosphate sensitivity and diphosphate activation, were consistent with those of other smooth muscle organs. β-Nicotinamide adenine dinucleotide has the potency to activate adenosine triphosphate sensitive K+ channels in the human detrusor. This channel likely has some role during ischemic conditions as well as physiological muscle motion leading to the activation of cell metabolism.

Insights Into Mutagenesis Using Escherichia coli Chromosomal lacZ Strains That Enable Detection of a Wide Spectrum of Mutational Events

Strand misalignments at DNA repeats during replication are implicated in mutational hotspots. To study these events, we have generated strains carrying mutations in the Escherichia coli chromosomal lacZ gene that revert via deletion of a short duplicated sequence or by template switching within imperfect inverted repeat (quasipalindrome, QP) sequences. Using these strains, we demonstrate that mutation of the distal repeat of a quasipalindrome, with respect to replication fork movement, is about 10-fold higher than the proximal repeat, consistent with more common template switching on the leading strand. The leading strand bias was lost in the absence of exonucleases I and VII, suggesting that it results from more efficient suppression of template switching by 3' exonucleases targeted to the lagging strand. The loss of 3' exonucleases has no effect on strand misalignment at direct repeats to produce deletion. To compare these events to other mutations, we have reengineered reporters (designed by Cupples and Miller 1989) that detect specific base substitutions or frameshifts in lacZ with the reverting lacZ locus on the chromosome rather than an F' element. This set allows rapid screening of potential mutagens, environmental conditions, or genetic loci for effects on a broad set of mutational events. We found that hydroxyurea (HU), which depletes dNTP pools, slightly elevated templated mutations at inverted repeats but had no effect on deletions, simple frameshifts, or base substitutions. Mutations in nucleotide diphosphate kinase, ndk, significantly elevated simple mutations but had little effect on the templated class. Zebularine, a cytosine analog, elevated all classes.

Abstract 5380: Synergistic effects of clofarabine and decitabine in acute myeloid leukemia

Abstract Clofarabine (CLO) is a purine nucleoside analog with promising efficacy in acute myeloid leukemia (AML). Its mechanism of action involves inhibition of the ribonucleotide reductase (RR) that converts nucleotide diphosphates to the corresponding deoxynucleotide diphosphates. Expression of the small RR subunit, p53R2 (product of RRM2B), demonstrated that a shorter protein is associated with CLO resistance. We have also shown that decitabine (DEC), another active drug in AML, induces p53R2 mRNA and protein expression and therefore asked herein whether the combination will be synergistic in a human AML cell line, HEL. To understand the role of p53R2 in this interaction, we knocked it down (KD) with shRNAmir. HEL and HEL-p53R2KD cells were exposed to CLO and DEC for 24,48,72, and 96-hr. Cells were stained with trypan blue for cell viability. The Hill model was fit to each concentration-response curve for each drug. After fitting and determination of 50% inhibition concentration (IC50), five combination ratios of the IC50 (CLO:DEC; 1:1, 1:4, 4:1, 1.5:3.5; 3.5:1.5) were characterized. In addition, western blot analysis was performed for both cell lines to determine levels of P53R2 expression for the same concentration range and exposure time to each drug, and in combination. Bands in western blot were quantitated using densitometry. HSC70 was used as a house keeping gene. At 24 hr, the IC50 values for CLO and DEC in HEL cells were 500 nM. In p53R2KD cells, the IC50 values for CLO and DEC were 700 nM and 120 nM. As exposure time increased to 48, 72, or 96 hr, the potency increased 10-15-fold for clofarabine, while only 2-4-fold for decitabine. At 48 hr, IC50 values were less than 50 nM for clofarabine in both HEL and p53R2KD cells, while it was 145 and 215 nM for decitabine. For the combination treatment, a pharmacodynamic (PD) interaction model was developed to assess the degree of synergy between CLO and DEC on cell viability. A PD parameter, labeled as ψ, characterized the extent of the interaction. When ψ >=1, the interaction between the two drugs may be additive, while ψ<1 represents synergy and ψ>1 indicates antagonism. Following 24 hr of drug exposure of CLO and DEC at the 50% of the IC50 values for each drug combination, ψ was estimated to be 1.00 (CI 0.850-1.22) for P53R2KD and >1 for HEL cells. In addition, western blot analyses performed at 24-hr following combined drug exposure revealed that the upper band did not change as a function of drug concentration, while the lower band showed a concentration-dependent increase in p53R2 protein expression, especially in p53R2KD. The PD model demonstrated a synergistic effect for CLO and DEC in the AML cell line HEL; knocking down p53R2 decreased this synergism, attesting to p53R2's role in both drugs’ mechanism of action. The increase in the lower band supports its role as part of clofarabine resistance. A clinical trial combining CLO and DEC in AML is warranted. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 5380. doi:10.1158/1538-7445.AM2011-5380

Extracellular nucleotide derivatives protect cardiomyocytes against hypoxic stress

Rationale Extracellular nucleotides have widespread effects and various cell responses. Whereas the effect of a purine nucleotide (ATP) and a pyrimidine nucleotide (UTP) on myocardial infarction has been examined, the role of different purine and pyrimidine nucleotides and nucleosides in cardioprotection against hypoxic stress has not been reported. Objective To investigate the role of purine and pyrimidine nucleotides and nucleosides in protective effects in cardiomyocytes subjected to hypoxia. Methods and results Rat cultured cardiomyocytes were treated with various extracellular nucleotides and nucleosides, before or during hypoxic stress. The results revealed that GTP or CTP exhibit cardioprotective ability, as revealed by lactate dehydrogenase (LDH) release, by propidium iodide (PI) staining, by cell morphology, and by preserved mitochondrial activity. Pretreatment with various P2 antagonists (suramin, RB-2, or PPADS) did not abolish the cardioprotective effect of the nucleotides. Moreover, P2Y 2 −/− , P2Y 4 −/−, and P2Y 2 −/−/P2Y 4 −/− receptor knockouts mouse cardiomyocytes were significantly protected against hypoxic stress when treated with UTP. These results indicate that the protective effect is not mediated via those receptors. We found that a wide variety of triphosphate and diphosphate nucleotides (TTP, ITP, deoxyGTP, and GDP), provided significant cardioprotective effect. GMP, guanosine, and ribose phosphate provided no cardioprotective effect. Moreover, we observed that tri/di-phosphate alone assures cardioprotection. Treatment with extracellular nucleotides, or with tri/di-phosphate, administered under normoxic conditions or during hypoxic conditions, led to a decrease in reactive oxygen species production. Conclusions Extracellular tri/di-phosphates are apparently the molecule responsible for cardioprotection against hypoxic damage, probably by preventing free radicals formation.

Enzymatic Activity of the Soybean Ecto-Apyrase GS52 Is Essential for Stimulation of Nodulation

Nitrogen is an essential nutrient for plant growth. In the Rhizobium-legume symbiosis, root nodules are the sites of bacterial nitrogen fixation, in which atmospheric nitrogen is converted into a form that plants can utilize. While recent studies suggested an important role for the soybean (Glycine max) ecto-apyrase GS52 in rhizobial root hair infection and root nodule formation, precisely how this protein impacts the nodulation process remains undetermined. In this study, the biochemical characteristics of the GS52 enzyme were investigated. Computer modeling of the GS52 apyrase structure identified key amino acid residues important for catalytic activity, which were subsequently mutagenized. Although the GS52 enzyme exhibited broad substrate specificity, its activity on pyrimidine nucleotides and diphosphate nucleotides was significantly higher than on ATP. This result was corroborated by structural modeling of GS52, which predicted a low specificity for the adenine base within the substrate-binding pocket of the enzyme. The wild-type enzyme and its inactive mutant forms were expressed in soybean roots in order to evaluate the importance of GS52 enzymatic activity for nodulation. The results indicated a clear correlation between GS52 enzymatic activity and nodule number. Altogether, our study indicates that the catalytic activity of the GS52 apyrase, likely acting on extracellular nucleotides, is critical for rhizobial infection and nodulation.

Influence of Ligand Chirality on the Catalytic Efficiency of Human 3-Phosphoglycerate Kinase

L-nucleoside analogues form an important class of antiviral and anticancer drug candidates. To be pharmacologically active, they need to be phosphorylated in multiple steps by cellular kinases. Human phosphoglycerate kinase (hPGK) was shown to exhibit low specificity for nucleotide diphosphate analogues and its catalytic efficiency in phosphorylation was also affected. Revealing the mechanism of action and functional motions of hPGK gains importance in in silico drug-design to provide efficient phosphorylation process.To elucidate the effect of ligand chirality on dynamics and catalytic efficiency, molecular dynamics simulations were performed on four different nucleotides (D-/L-ADP and D-/L-CDP) in complex with hPGK and 1,3-bisphospho-D-glycerate (bPG). The simulation results confirm high affinity for the natural substrate (D-ADP), while L-ADP shows only moderate affinity for hPGK. The observed short residence time of both CDP enantiomers at the active site suggests very weak binding affinity which may result in poor catalytic efficiency shown for hPGK with D-/L-CDP. Analysis of the simulations unravels important dynamic conditions for efficient phosphorylation replacing the single requirement of a tight binding. These are: 1) over the strength of the binding, the flexibility of the substrate within the binding site gains importance, especially for the phosphate groups; 2) the hinge bending motion of the domains upon substrates binding should be more correlated and directional, and consequently should imply a lower number of hinge residues; 3) the nucleotide binding site should have an increased flexibility allowing significant dynamic freedoms for the substrates.

Wheat Mitochondrial Proteomes Provide New Links between Antioxidant Defense and Plant Salinity Tolerance

The mitochondrial proteome and differences associated with salt tolerance have been investigated in Australian commercial varieties of wheat. Mitochondria isolated from shoots were used to generate a wheat mitochondrial reference map; 68 unique wheat mitochondrial proteins were identified from 192 gel spots using 2D PAGE and LC-MS/MS. This analysis also provided MS/MS spectra for 199 proteotypic peptides as a foundation for the development of targeted proteomics to study the respiratory apparatus in wheat. Using this reference map and 2D DIGE, we have found quantitative differences in the shoot mitochondrial proteomes of v. Wyalkatchem and v. Janz, two commercially important wheat varieties that are known from a range of experiments to differ in salinity tolerance. These proteins included Mn-superoxide dismutase (Mn-SOD), cysteine synthase, nucleotide diphosphate kinase, and the voltage dependent anion channel (VDAC). Antibodies to the mitochondrial alternative oxidase (AOX), previously linked to reduced ROS formation from the electron transport chain and salt tolerance in Arabidopsis, also showed a commensurate higher abundance in v. Wyakatchem in both control and salt-treated conditions. Together, the data presented here suggest that differences in mitochondrial ROS defense pathways in the mitochondrial proteomes of key Australian wheat varieties correlate with whole-plant salinity tolerance.

Mechanism of Regulation of Native Cardiac Muscle Thin Filaments by Rigor Cardiac Myosin-S1 and Calcium

We have studied the mechanism of activation of native cardiac thin filaments by calcium and rigor myosin. The acceleration of the rate of 2'-deoxy-3'-O-(N-methylanthraniloyl)ADP (mdADP) dissociation from cardiac myosin-S1-mdADP-P(i) and cardiac myosin-S1-mdADP by native cardiac muscle thin filaments was measured using double mixing stopped-flow fluorescence. Relative to inhibited thin filaments (no bound calcium or rigor S1), fully activated thin filaments (with both calcium and rigor-S1 bound) increase the rate of product dissociation from the physiologically important pre-power stroke myosin-mdADP-P(i) by a factor of ∼75. This can be compared with only an ∼6-fold increase in the rate of nucleotide diphosphate dissociation from nonphysiological myosin-mdADP by the fully activated thin filaments relative to the fully inhibited thin filaments. These results show that physiological levels of regulation are not only dependent on the state of the thin filament but also on the conformation of the myosin. Less than 2-fold regulation is due to a change in affinity of myosin-ADP-P(i) for thin filaments such as would be expected by a simple "steric blocking" of the myosin-binding site of the thin filament by tropomyosin. Although maximal activation requires both calcium and rigor myosin-S1 bound to the cardiac filament, association with a single ligand produces ∼70% maximal activation. This can be contrasted with skeletal thin filaments in which calcium alone only activated the rate of product dissociation ∼20% of maximum, and rigor myosin produces ∼30% maximal activation.

The C-terminal α–α superhelix of Pat is required for mRNA decapping in metazoa

Pat proteins regulate the transition of mRNAs from a state that is translationally active to one that is repressed, committing targeted mRNAs to degradation. Pat proteins contain a conserved N-terminal sequence, a proline-rich region, a Mid domain and a C-terminal domain (Pat-C). We show that Pat-C is essential for the interaction with mRNA decapping factors (i.e. DCP2, EDC4 and LSm1–7), whereas the P-rich region and Mid domain have distinct functions in modulating these interactions. DCP2 and EDC4 binding is enhanced by the P-rich region and does not require LSm1–7. LSm1–7 binding is assisted by the Mid domain and is reduced by the P-rich region. Structural analysis revealed that Pat-C folds into an α–α superhelix, exposing conserved and basic residues on one side of the domain. This conserved and basic surface is required for RNA, DCP2, EDC4 and LSm1–7 binding. The multiplicity of interactions mediated by Pat-C suggests that certain of these interactions are mutually exclusive and, therefore, that Pat proteins switch decapping partners allowing transitions between sequential steps in the mRNA decapping pathway.

Dynamic Effects of Cofactors and DNA on the Oligomeric State of the Human Mitochondrial DNA Helicase

Mitochondria are the essential energy‐producing organelle in eukaryotes, and represent the only organelle in animals that contains its own genome. Maintenance of the mitochondrial DNA (mtDNA) genome is dependent on myriad nuclear‐encoded proteins including the mtDNA helicase, which is an essential component of the replicative machinery. Human mtDNA helicase shares a high degree of sequence similarity with the bacteriophage T7 primase‐helicase gene 4 protein, and catalyzes duplex unwinding in the 5’‐3’ direction. We have shown that it is an oligomer in solution that is destabilized under low salt conditions. We present here the effects of cofactors on its stability and oligomerization state. We show that the low salt sensitivity of the mtDNA helicase is alleviated by the presence of magnesium, nucleotide and increased temperature. Electron microscopic and glutaraldehyde cross‐linking analyses provide the first evidence of a heptameric oligomer, and its interconversion from a hexameric form. Limited proteolysis by trypsin shows that binding of nucleoside triphosphate produces a conformational change that is distinct from the conformation observed in the presence of nucleotide diphosphate. We find that single‐stranded DNA binding occurs in the absence of cofactors, and renders the mtDNA helicase more susceptible to proteolytic digestion. Experiments to examine oligomeric state upon DNA binding are underway to evaluate the functional form of the enzyme, and its dynamic changes along the reaction pathway. This research was supported by NIH grant GM45295.

Myelin protein composition is altered in mice lacking either sulfated or both sulfated and non‐sulfated galactolipids

Myelin is highly enriched in galactocerebroside (GalCer) and its sulfated form sulfatide. Mice, unable to synthesize GalCer and sulfatide (CGT(null)) or sulfatide alone (CST(null)), exhibit disorganized paranodal structures and progressive dysmyelination. To obtain insights into the molecular mechanisms underlying these defects, we examined myelin composition of these mutants by two-dimensional differential fluorescence intensity gel electrophoresis proteomic approach and immunoblotting. We identified several proteins whose expressions were significantly altered in these mutants. These proteins are known to regulate cytoskeletal dynamics, energy metabolism, vesicular trafficking or adhesion, suggesting a disruption in these physiological processes in the absence of myelin galactolipids. Further analysis of one of these proteins, nucleotide diphosphate kinase (NDK)/Nm23, showed that it was reduced in myelin of CGT(null) and increased in CST(null), but not in whole brain homogenate. Immunostaining showed an increase in its expression in the cell bodies of CGT(null)- and a decrease in CST(null)-oligodenrocytes, together leading to the hypothesis that transport of NDK/Nm23 from oligodenrocyte cell bodies into myelin may be differentially dysregulated in the absence of these galactolipids. This study provides new insights into the changes that occur in the composition/distribution of myelin proteins in mice lacking either unsulfated and/or sulfated galactolipids and reinforces the role of these lipids in intracellular trafficking.

NDP Kinase 유전자를 과발현시킨 형질전환 톨 페스큐 식물체의 저온 스트레스에 대한 내성 특성

저온 스트레스에 대한 내성을 지닌 신품종 톨 페스큐를 개발할 목적으로 CaMV35S 프로모터 하류에 NDP kinase 2 유전자가 항상적으로 발현하도록 제작한 벡터를 Agrobacterium법을 이용하여 톨 페스큐에 도입하였다. Hygromycin이 첨가된 선발배지에서 내성을 나타내며 재분화된 형질전환 식물체를 pot로 이식하여 기내순화 시킨 후, Southern blot 분석을 실시하여 본 결과, NDP kinase 2 유전자가 형질전환 식물체의 genome에 정상적으로 도입되었음을 확인하였다. 프로테옴 분석을 통하여 도입유전자의 조절을 받는 항산화관련 유전자들의 발현이 유도되었음을 확인 할 수 있었다. 형질전환 식물체 잎 절편을 산화스트레스 중의 하나인 저온 스트레스를 처리하여 세포의 손상 정도를 조사한 결과, 비형질전환체에 비해 형질전환체는 강한 내성을 나타내었다. 또한 유식물체 수준에서 저온 스트레스를 처리하여 내성을 비교한 결과, 비형질전환체에 비해 형질전환체는 높은 내성을 나타내었다. 이 형질전환 톨페스큐는 산화스트레스 내성 품종개발을 위한 소재로 활용 될 수 있을 것이다. Oxidative stress is the main limiting factor in crop productivity. To solve global environmental problems using the plant biotechnology, we have developed on the oxidative stress-tolerant transgenic tall fescue plants via Agrobacterium-mediated genetic transformation method. In order to develop transgenic tall fescue (Festuca arundinacea Schreb.) plants with enhanced tolerance to multiple environmental stresses, nucleotide diphosphate kinase gene under the control of CaMV35S promoter were introduced into genome of tall fescue plants. Proteomic analysis revealed that transgenic tall fescue not only accumulated NDP kinase 2 protein in their cells, but also induced several other antioxindative enzyme-related proteins. When leaf discs of transgenic plants were subjected to cold stress, they showed approximately 30% less damage than wild-type plants. In addition, transgenic tall fescue plants showed normal growth when transgenic plants were subjected to <TEX>$4^{\circ}C$</TEX> for 3 days treatments. These results suggest that transgene is important in ROS scavenging by induction of antioxidative proteins, and could improve abiotic stress tolerance in transgenic tall fescue plants.

Regulation of Transforming Growth Factor-β-dependent Cyclooxygenase-2 Expression in Fibroblasts

Abnormal transforming growth factor-beta (TGF-beta) signaling is a critical contributor to the pathogenesis of various human diseases ranging from tissue fibrosis to tumor formation. Excessive TGF-beta signaling stimulates fibrotic responses. Recent research has focused in the main on the antiproliferative effects of TGF-beta in fibroblasts, and it is presently understood that TGF-beta-stimulated cyclooxygenase-2 (COX-2) induction in fibroblasts is essential for antifibroproliferative effects of TGF-beta. Both TGF-beta and COX-2 have been implicated in tumor growth, invasion, and metastasis, and therefore tumor-associated fibroblasts are a recent topic of interest. Here we report the identification of positive and negative regulatory factors of COX-2 expression induced by TGF-beta as determined using proteomic approaches. We show that TGF-beta coordinately up-regulates three factors, heterogeneous nuclear ribonucleoprotein A/B (HNRPAB), nucleotide diphosphate kinase A (NDPK A), and nucleotide diphosphate kinase A (NDPK B). Functional pathway analysis showed that HNRPAB augments mRNA and protein levels of COX-2 and subsequent prostaglandin E(2) (PGE(2)) production by suppressing degradation of COX-2 mRNA. In contrast, NDPK A and NDPK B attenuated mRNA and protein levels of COX-2 by affecting TGF-beta-Smad2/3/4 signaling at the receptor level. Collectively, we report on a new regulatory pathway of TGF-beta in controlling expression of COX-2 in fibroblasts, which advances our understanding of pathophysiological mechanisms of TGF-beta.

The Structure and Assembly Dynamics of Plasmid Actin AlfA Imply a Novel Mechanism of DNA Segregation

Bacterial cytoskeletal proteins participate in a variety of processes, including cell division and DNA segregation. Polymerization of one plasmid-encoded, actin-like protein, ParM, segregates DNA by pushing two plasmids in opposite directions and forms the current paradigm for understanding active plasmid segregation. An essential feature of ParM assembly is its dynamically instability, the stochastic switching between growth and disassembly. It is unclear whether dynamic instability is an essential feature of all actin-like protein-based segregation mechanisms or whether bacterial filaments can segregate plasmids by different mechanisms. We expressed and purified AlfA, a plasmid-segregating actin-like protein from Bacillus subtilis, and found that it forms filaments with a unique structure and biochemistry; AlfA nucleates rapidly, polymerizes in the presence of ATP or GTP, and forms highly twisted, ribbon-like, helical filaments with a left-handed pitch and protomer nucleotide binding pockets rotated away from the filament axis. Intriguingly, AlfA filaments spontaneously associate to form uniformly sized, mixed-polarity bundles. Most surprisingly, our biochemical characterization revealed that AlfA does not display dynamic instability and is relatively stable in the presence of diphosphate nucleotides. These results (i) show that there is remarkable structural diversity among bacterial actin filaments and (ii) indicate that AlfA filaments partition DNA by a novel mechanism.

Effects of tumor metastasis suppressor gene nm23-H1 on invasion and proliferation of cervical cancer cell lines

Previous studies have shown that nm23-H1 is a tumor metastasis suppressor gene. Nucleotide diphosphate kinase 1 (NDPK1) encoded by nm23-H1 is involved in cancer cellular differentiation, proliferation, apoptosis and metastasis. This study was to investigate the effects of nm23-H1 on proliferation and invasion of cervical cancer cells. The eukaryotic expression vector pcDNA3.1-nm23-H1 was transfected into cervical cancer cells. Cell invasion potential was determined by the Transwell assay. Cell proliferation was measured by MTT assay and changes in cell cycle distribution were analyzed by flow cytometry (FCM). Compared with parent cells (Caski and SiHa) and vector control cells (Caski-3.1 and SiHa-3.1), the proliferation and invasion of pcDNA3.1-nm23-H1 transfected cells (SiHa-N and Caski-N) were apparently decreased (P<0.05); the proportions of G2/M and S cells were obviously decreased while that of G0/G1 cells was increased (P<0.05). However, transfection of nm23-H1 gene had no influence on proliferation, cell cycle and invasion of HeLa cells (P>0.05). nm23-H1 gene could inhibit proliferation and invasion of cervical cancer cells in a cell-dependent manner.

Fermentative Production of Thymidine by a Metabolically Engineered Escherichia coli Strain

Thymidine is an important precursor in the production of various antiviral drugs, including azidothymidine for the treatment of AIDS. Since thymidine-containing nucleotides are synthesized only by the de novo pathway during DNA synthesis, it is not easy to produce a large amount of thymidine biologically. In order to develop a host strain to produce thymidine, thymidine phosphorylase, thymidine kinase, and uridine phosphorylase genes were deleted from an Escherichia coli BL21 strain to develop BLdtu. Since the genes coding for the enzymes related to the nucleotide salvage pathway were disrupted, BLdtu was unable to utilize thymidine or thymine, and thymidine degradation activity was completely abrogated. We additionally expressed T4 thymidylate synthase, T4 nucleotide diphosphate reductase, bacteriophage PBS2 TMP phosphohydrolase, E. coli dCTP deaminase, and E. coli uridine kinase in the BLdtu strain to develop a thymidine-producing strain (BLdtu24). BLdtu24 produced 649.3 mg liter(-1) of thymidine in a 7-liter batch fermenter for 24 h, and neither thymine nor uridine was detected. However, the dUTP/dTTP ratio was increased in BLdtu24, which could lead to increased double-strand breakages and eventually to cell deaths during fermentation. To enhance thymidine production and to prevent cell deaths during fermentation, we disrupted a gene (encoding uracil-DNA N-glycosylase) involved in DNA excision repair to suppress the consumption of dTTP and developed BLdtug24. Compared with the thymidine production in BLdtu24, the thymidine production in BLdtug24 was increased by approximately 1.2-fold (740.3 mg liter(-1)). Here, we show that a thymidine-producing strain with a relatively high yield can be developed using a metabolic engineering approach.

Characterization and Optimization of a Red-Shifted Fluorescence Polarization ADP Detection Assay

ATP depletion and ADP formation are generic detection methods used for the identification of kinase and other ATP-utilizing enzyme inhibitors in high-throughput screening campaigns. However, the most widely used nucleotide detection approaches require high ATP consumption rates or involve the use of coupling enzymes, which can complicate the selection of lead compounds. As an alternative, we have developed the Transcreener (BellBrook Labs, Madison, WI) platform, which relies on the direct immunodetection of nucleotides. Here we describe the development of antibodies with >100-fold selectivity for ADP versus ATP, which enable robust detection of initial velocity rates (Z' > 0.7 at 10% substrate consumption) at ATP concentrations ranging from 0.1 microM to 1,000 microM in a competitive fluorescence polarization (FP) immunoassay. Competitive binding experiments indicate similar affinities for other nucleotide diphosphates, including 2' -deoxy ADP, GDP, and UDP. The antibody-tracer complex and the red-shifted, ratiometric FP signal are stable for at least 24 h at room temperature, providing suitable conditions for high-throughput screening. A method for calculating a kinase ATP Km with this FP immunoassay is also presented. The Transcreener ADP assay provides a simple, generic assay platform for inhibitor screening and selectivity profiling that can be used for any ADP-generating enzyme.