Thermodynamic and Kinetic Characterization of Antisense Oligodeoxynucleotide Binding to a Structured mRNA

Antisense oligonucleotides act as exogenous inhibitors of gene expression by binding to a complementary sequence on the target mRNA, preventing translation into protein. Antisense technology is being applied successfully as a research tool and as a molecular therapeutic. However, a quantitative understanding of binding energetics between short oligonucleotides and longer mRNA targets is lacking, and selecting a high-affinity antisense oligonucleotide sequence from the many possibilities complementary to a particular RNA is a critical step in designing an effective antisense inhibitor. Here, we report measurements of the thermodynamics and kinetics of hybridization for a number of oligodeoxynucleotides (ODNs) complementary to the rabbit β-globin (RBG) mRNA using a binding assay that facilitates rapid separation of bound from free species in solution. A wide range of equilibrium dissociation constants were observed, and association rate constants within the measurable range correlated strongly with binding affinity. In addition, a significant correlation was observed of measured binding affinities with binding affinity values predicted using a thermodynamic model involving DNA and RNA unfolding, ODN hybridization, and RNA restructuring to a final free energy minimum. In contrast to the behavior observed for hybridization of short strands, the association rate constant increased with temperature, suggesting that the kinetics of association are related to disrupting the native structure of the target RNA. The rate of cleavage of the RBG mRNA in the presence of ribonuclease H and ODNs of varying association kinetics displayed apparent first-order kinetics, with the rate constant exhibiting binding-limited behavior at low association rates and reaction-limited behavior at higher rates. Implications for the rational design of effective antisense reagents are discussed.     

Insertions of a Novel Class of Transposable Elements with a Strong Target Site Preference at the R Locus of Maize

The r locus of maize regulates anthocyanin synthesis in various tissues of maize through the production of helix-loop-helix DNA binding proteins capable of inducing expression of structural genes in the anthocyanin biosynthetic pathway. The complex r variant, R-r:standard (R-r), undergoes frequent mutation through a variety of mechanisms including displaced synapsis and crossing over, and intrachromosomal recombination. Here we report a new mechanism for mutation at the R-r complex: insertion of a novel family of transposable elements. Because the elements were first identified in the R-p gene of the R-r complex, they have been named P Instability Factor (PIF). Two different PIF elements were cloned and found to have identical sequences at their termini but divergent internal sequences. In addition, the PIF elements showed a marked specificity of insertion sites. Six out of seven PIF-containing derivatives examined had an element inserted at an identical location. Two different members of the PIF element family were identified at this position. The seventh PIF-containing derivative examined had the element inserted at a distinct position within r. Even at this location, however, the element inserted into a conserved target sequence. The timing of PIF excision is unusual. Germinal excision rates can range up to several percent of progeny. Yet somatic sectors are rare, even in lines exhibiting high germinal reversion rates.     

Identification of a good c-myc antisense oligodeoxynucleotide target site and the inactivity at this site of novel NCH triplet--targeting ribozymes.

A region of c-myc mRNA was identified which permitted very efficient antisense effects to be achieved in living cells using chimeric methylphosphonate--phosphodiester antisense effectors. Novel inosine--containing ribozymes (which cleave after NCH triplets) were directed to an ACA triplet within this region and delivered into living cells. No ribozyme intracellular activity could be identified. Very low ribozyme function was also observed in in vitro assays using a 1700nt substrate RNA.     

靶向基质金属蛋白酶14类血红素结构域特异活性位点的确定及反义肽虚拟筛选

目的:确定基质金属蛋白酶14(MMP-14)类血红素结构域(HPX14)特异活性位点,虚拟筛选获得能与HPX14特异结合的短肽。方法:用metaPocket预测HPX14的活性口袋,多序列比对分析活性口袋的氨基酸残基特异性;基于M-I和R-B理论设计以特异活性位点为正义肽的反义肽库,并进行虚拟筛研究及结合特异性确定。结果:生物信息学分析确定了KGRGLTD为HPX14的特异活性位点,并构建了其1036条反义肽;通过2轮虚拟筛选,获得10条得分居前的与HPX14结合较好的反义肽,它们与HPX14具有较高的亲和力,并可能影响MMP-14同源二聚体的形成和MMP-14活性的抑制;VSETAPF、IGEPPPF是对接打分最好的2条短肽,与HPX14的结合具有特异性。结论:KGRGLTD是HPX14的特异活性位点,虚拟筛选得到的VSETAPF、IGEPPPF等反义肽与HPX14具有较高的亲和力,这为基于MMP-14的HPX结构域的靶向小分子多肽先导药物的发现提供了重要的前期工作基础与新思路。     

用于鉴定microRNA靶基因的新型双萤光素酶报告基因系统的构建及应用

目的:构建用于鉴定microRNA靶基因的报告基因系统。方法:在pGL3-Basic载体的luc基因上游插入CMV启动子,下游插入用于克隆靶基因3’UTR的多克隆位点,构建报告基因载体pMIR-luciferase;将pMIR-lu-ciferase载体的luc基因替换成Rluc基因,构建内参载体pMIR-control;将补体因子H(CFH)的3’UTR插入pMIR-luciferase载体的多克隆位点处,构建含有CFH 3’UTR的报告基因载体;用pIRES2-EGFP载体构建microRNA146a真核表达载体;将含有CFH 3’UTR的报告基因载体、microRNA146a真核表达载体及内参载体共转染HepG2细胞,进行报告基因的活性检测。结果:构建了报告基因载体、内参载体和microRNA146a真核表达载体,经酶切和测序鉴定正确;microRNA146a真核表达载体转染细胞72 h后,经荧光显微镜观察确认载体转染及表达;用实时定量PCR检测,microRNA146a的表达水平显著上调(P<0.01);用构建的报告基因系统检测,结果表明microRNA146a显著地抑制了含CFH 3’UTR的报告基因的活性(P<0.05)。结论:构建了一种新型的报告基因载体系统,该系统可用于miRNA靶基因的鉴定。     

Identification of gp96 as a Novel Target for Treatment of Autoimmune Disease in Mice

Heat shock proteins have been implicated as endogenous activators for dendritic cells (DCs). Chronic expression of heat shock protein gp96 on cell surfaces induces significant DC activations and systemic lupus erythematosus (SLE)-like phenotypes in mice. However, its potential as a therapeutic target against SLE remains to be evaluated. In this work, we conducted chemical approach to determine whether SLE-like phenotypes can be compromised by controlling surface translocation of gp96. From screening of chemical library, we identified a compound that binds and suppresses surface presentation of gp96 by facilitating its oligomerization and retrograde transport to endoplasmic reticulum. In vivo administration of this compound reduced maturation of DCs, populations of antigen presenting cells, and activated B and T cells. The chemical treatment also alleviated the SLE-associated symptoms such as glomerulonephritis, proteinuria, and accumulation of anti-nuclear and –DNA antibodies in the SLE model mice resulting from chronic surface exposure of gp96. These results suggest that surface translocation of gp96 can be chemically controlled and gp96 as a potential therapeutic target to treat autoimmune disease like SLE.     

IS481 and IS1002 of Bordetella pertussis Create a 6-Base-Pair Duplication upon Insertion at a Consensus Target Site

The insertion sequence IS481 and its isoform IS1002 have been observed to transpose into the bvgAS locus of Bordetella pertussis, for which the DNA sequence has previously been determined. Upon insertion of IS481 at three different sites and IS1002 at one site, a 6-bp sequence originally present was found at the junction of bvg and insertion sequence DNA. This indicates that, contrary to prior reports, IS481 and IS1002 do create a duplication upon insertion. In this light, examination of these and other examples of IS481 and IS1002 reported in the literature leads to the observation that the 6-bp recognition sequence usually fits the consensus NCTAGN. The near-palindromic nature of this sequence, when directly repeated at the ends of IS481 or IS1002, apparently led to the interpretation that 5 of these base pairs were part of the terminal inverted repeats flanking these elements.     

一株嗜盐菌新种的分离与鉴定

从舟山册子岛船舶压载水泥样中分离到一株细菌S3-22,其与已知细菌的16S rDNA序列相似性低于97%,G+C mol%为54.9 mol%,主要脂肪酸iso-C17:1ω9c(24.99%),细胞醌型为甲基萘醌MK-5。革兰氏染色阴性,最适生长条件为30～37℃、pH7、3%NaCl。嗜盐,氧化酶、接触酶、淀粉酶、酯酶呈阳性,可还原硝酸盐。依据其16S rDNA序列相似性、系统发育学分析及细胞与分子水平的鉴定表明,该菌是Kordiimonas属的一个新种,菌株S3-22的16S rDNA序列登陆号为FJ847942。     

Identification of the Tryptophan Residue Located at the Substrate-binding Site of Rye Seed Chitinase-c

Chemical modifications of rye seed chitinase-c (RSC-c) with various reagents suggested the involvements of tryptophan and glutamic/aspartic acid residues in the activity. Of these, the modification of tryptophan residues with N-bromosuccinimide (NBS) was investigated in detail.

In the NBS-oxidation at pH 4.0, two of the six tryptophan residues in RSC-c were rapidly oxidized and the chitinase activity was almost completely lost. On the other hand, in the NBS-oxidation at pH 5.9, only one tryptophan residue was oxidized and the activity was greatly reduced. Analyses of the oxidized tryptophan-containing peptides from the tryptic and chymotryptic digests of the modified RSC-c showed that two tryptophan residues oxidized at pH 4.0 are Trp72 and Trp82, and that oxidized at pH 5.9 is Trp72.

The NBS-oxidation of Trp72 at pH 5.9 was protected by a tetramer of N-acetylglucosamine (NAG₄), a very slowly reactive substrate for RSC-c, and the activity was almost fully retained. In the presence of NAG4, RSC-c exhibited an UV -difference spectrum with maxima at 284 nm and 293 nm, attributed to the red shift of the tryptophan residue, as well as a small trough around 300 nm probably due to an alteration of the environment of the tryptophan residue. From these results, it was suggested that Trp72 is exposed on the surface of the RSC-c molecule and involved in the binding to substrate.     

Identification of the Serine 307 of LKB1 as a Novel Phosphorylation Site Essential for Its Nucleocytoplasmic Transport and Endothelial Cell Angiogenesis

LKB1, a master kinase that controls at least 13 downstream protein kinases including the AMP-activated protein kinase (AMPK), resides mainly in the nucleus. A key step in LKB1 activation is its export from the nucleus to the cytoplasm. Here, we identified S307 of LKB1 as a putative novel phosphorylation site which is essential for its nucleocytoplasmic transport. In a cell-free system, recombinant PKC-ζ phosphorylates LKB1 at S307. AMPK-activating agents stimulate PKC-ζ activity and LKB1 phosphorylation at S307 in endothelial cells, hepatocytes, skeletal muscle cells, and vascular smooth muscle cells. Like the kinase-dead LKB1 D194A mutant (mutation of Asp194 to Ala), the constitutively nucleus-localized LKB1 SL26 mutant and the LKB1 S307A mutant (Ser307 to Ala) exhibit a decreased association with STRADα. Interestingly, the PKC-ζ consensus sequence surrounding LKB1 S307 is disrupted in the LKB1 SL26 mutant, thus providing a likely molecular explanation for this mutation causing LKB1 dysfunction. In addition, LKB1 nucleocytoplasmic transport and AMPK activation in response to peroxynitrite are markedly reduced by pharmacological inhibition of CRM1, which normally facilitates nuclear export of LKB1-STRAD complexes. In comparison to the LKB1 wild type, the S307A mutant complexes show reduced association with CRM1. Finally, adenoviral overexpression of wild-type LKB1 suppresses, while the LKB1 S307A mutant increases, tube formation and hydrogen peroxide-enhanced apoptosis in cultured endothelial cells. Taken together, our results suggest that, in multiple cell types the signaling pathways engaged by several physiological stimuli converge upon PKC-ζ-dependent LKB1 phosphorylation at S307, which directs the nucleocytoplasmic transport of LKB1 and consequent AMPK activation.LKB1 is a tumor suppressor (3, 25, 33, 42, 59) that is mutated in Peutz-Jeghers cancer syndrome (20, 24). This serine/threonine protein kinase phosphorylates and activates at least 13 downstream kinases, which in turn regulate multiple cellular processes, including the cell cycle, cellular proliferation, apoptosis, and energy metabolism (1, 30). One of the key downstream kinases of LKB1 is the 5′-AMP-activated protein kinase (AMPK), a serine/threonine kinase that serves as a master regulator of energy metabolism (18, 19, 28). LKB1 is ubiquitously expressed in adult and fetal tissue, particularly pancreatic, liver, testicular, cardiac, and skeletal muscle tissue (21, 25, 43, 60). In humans, LKB1 comprises 433 amino acids (436 residues in mouse LKB1) and is located predominantly in the nucleus due to its nuclear localization signal in the N-terminal noncatalytic region (residues 38 to 43) (36, 53). Paradoxically, LKB1 activation takes place predominantly in the cytoplasm, after it complexes with STRAD (STE-related adapter) and MO25 (mouse protein 25). As a result, the nucleocytoplasmic transport and subsequent association of LKB1 with STRAD and MO25 in the cytoplasm are required for full activation of LKB1 (2, 5) and its downstream kinases, including AMPK. Consistent with this theory, 12 mutants of LKB1 (including the SL26 mutants) found in patients with Peutz-Jeghers cancer syndrome are constitutively nuclear (5, 6). Further, a recent study from Macara''s group (13) shows that STRAD regulates LKB1 localization by blocking access to importin and by association with CRM1 and exportin-7, two nuclear protein exportins.LKB1 is phosphorylated at S325, T366, and S431 by upstream kinases. In addition, LKB1 autophosphorylates at S31, T185, T189, T336, and S404 (1). Mutation of any of these phosphorylation sites to Ala (to abolish phosphorylation) or Glu (to mimic phosphorylation) does not significantly affect the in vitro catalytic activity of LKB1 or its intracellular localization (5, 44, 45). Recently, we demonstrated that phosphorylation of LKB1 S428 is required for metformin-enhanced AMPK activation (56). Nevertheless, several questions such as the precise mechanism(s) underlying LKB1 activation, the relevant phosphorylation sites, and the upstream activating kinase(s) remain unclear. While it has been shown that LKB1 S428 phosphorylation is required for nucleocytoplasmic transport of LKB1, the translocation of LKB1 to the cytosol could be further regulated by unknown mechanisms. Here, we have identified S307 as a novel phosphorylation site in LKB1 and provide evidence that, in multiple cell types, phosphorylation of this site by protein kinase C ζ (PKC-ζ) induces nucleocytoplasmic transport of LKB1 and subsequent activation of AMPK and suppression of angiogenesis and apoptosis. Importantly, we provide a molecular explanation for the constitutive nuclear localization of the LKB1 SL26 mutant. Taken together, our results suggest that the phosphorylation of LKB1 S307 by PKC-ζ is essential for LKB1 regulation of cell cycle progression, proliferation, angiogenesis, and apoptosis.     

Source Bioaerosol Concentration and rRNA Gene-Based Identification of Microorganisms Aerosolized at a Flood Irrigation Wastewater Reuse Site

Reuse of partially treated domestic wastewater for agricultural irrigation is a growing practice in arid regions throughout the world. A field sampling campaign to determine bioaerosol concentration, culturability, and identity at various wind speeds was conducted at a flooded wastewater irrigation site in Mexicali, Baja California, Mexico. Direct fluorescent microscopy measurements for total microorganisms, culture-based assays for heterotrophs and gram-negative enteric bacteria, and small-subunit rRNA gene-based cloning were used for microbial characterizations of aerosols and effluent wastewater samples. Bioaerosol results were divided into two wind speed regimens: (i) below 1.9 m/s, average speed 0.5 m/s, and (ii) above 1.9 m/s, average speed 4.5 m/s. Average air-borne concentration of total microorganisms, culturable heterotrophs, and gram-negative enteric bacteria were, respectively, 1.1, 4.2, and 6.2 orders of magnitude greater during the high-wind-speed regimen. Small-subunit rRNA gene clone libraries processed from samples from air and the irrigation effluent wastewater during a high-wind sampling event indicate that the majority of air clone sequences were more than 98% similar to clone sequences retrieved from the effluent wastewater sample. Overall results indicate that wind is a potential aerosolization mechanism of viable wastewater microorganisms at flood irrigation sites.     

Identification of a Novel Palmitylation Site Essential for Membrane Association and Isomerohydrolase Activity of RPE65

RPE65 is a membrane-associated protein abundantly expressed in the retinal pigment epithelium, which converts all-trans-retinyl ester to 11-cis-retinol, a key step in the retinoid visual cycle. Although three cysteine residues (Cys-231, Cys-329, and Cys-330) were identified to be palmitylated in RPE65, recent studies showed that a triple mutant, with all three Cys replaced by an alanine residue, was still palmitylated and remained membrane-associated, suggesting that there are other yet to be identified palmitylated Cys residues in RPE65. Here we mapped the entire RPE65 using mass spectrometry analysis and demonstrated that a trypsin-digested RPE65 fragment (residues 98-118), which contains two Cys residues (Cys-106 and Cys-112), was singly palmitylated in both native bovine and recombinant human RPE65. To determine whether Cys-106 or Cys-112 is the palmitylation site, these Cys were separately replaced by alanine. Mass spectrometry analysis of purified wild-type RPE65 and C106A and C112A mutants showed that mutation of Cys-106 did not affect the palmitylation status of the fragment 98-118, whereas mutation of Cys-112 abolished palmitylation in this fragment. Subcellular fractionation and immunocytochemistry analyses both showed that mutation of Cys-112 dissociated RPE65 from the membrane, whereas the C106A mutant remained associated with the membrane. In vitro isomerohydrolase activity assay showed that C106A has an intact enzymatic activity similar to that of wtRPE65, whereas C112A lost its enzymatic activity. These results indicate that the newly identified Cys-112 palmitylation site is essential for the membrane association and activity of RPE65.Both rod and cone visual pigments in vertebrates require 11-cis-retinal as the chromophore. Isomerization of 11-cis-retinal to all-trans-retinal by a photon triggers the phototransduction cascade and initiates vision (1, 2). Recycling of 11-cis-retinal through the retinoid visual cycle is an essential process for the regeneration of visual pigments and for normal vision (3, 4). The key step in the visual cycle is to isomerize all-trans-retinyl ester to 11-cis-retinol in retinal pigment epithelium (RPE)² (5, 6). This isomerization process is known to be catalyzed by an isomerohydrolase in the RPE. Several recent lines of evidence suggest that RPE65 is the isomerohydrolase in the visual cycle (7-9).RPE65 is a microsomal protein, abundantly expressed in the RPE (10-12). RPE65 knock-out (Rpe65^-/-) mice showed a lack of 11-cis-retinoids, overaccumulation of all-trans-retinyl ester, impaired visual function, and early degeneration of cone photoreceptors (7-9). RPE65 is an iron(II)-dependent enzyme, in which an iron is coordinated by four conserved histidine (His) residues (His-180, -241, -313, and -527) based on molecular modeling using a crystal structure of apocarotenoid monooxygenase as a template (8, 13-15). RPE65 lacks any predicted transmembrane helix and is associated with the microsomal membrane (11). Previous studies have shown that membrane association of RPE65 is essential for its isomerohydrolase activity (7). However, the structural basis for its membrane association has not been revealed. An earlier study showed that three Cys residues (Cys-231, 329 and 330) in RPE65 were palmitylated, which were suggested to be responsible for its membrane association (16). However, triple mutations of all the three Cys residues did not completely dissociate RPE65 from the membrane (17, 18). Moreover, the triple Cys mutant remains palmitylated (17). These results suggested that either the site of palmitylation responsible for the membrane association of RPE65 had not yet been identified or other mechanisms, such as hydrophobic interactions, anchor the protein to cellular membranes (17, 19).In this study, we used the combination of mass spectrometric analysis and site-directed mutagenesis to identify the palmitylated site in RPE65. Moreover, we determined the role of this site in the membrane association and enzymatic activity of RPE65.