Branchpoint Sugar Stereochemistry Determines the Hydrolytic Susceptibility of Branched RNA Fragments by the Yeast Debranching Enzyme (YDBR)

Abstract

A series of branched RNAs (Y-shaped) related to yeast pre-mRNA splicing intermediates were synthesized incorporating both natural (i.e., ribose) and non-natural (i.e., arabinose, xylose and acyclic nucleoside) branchpoints in order to examine the effect of sugar conformation and phosphodiester configuration on yDBR hydrolytic efficiency. The results indicate that 2′-phosphodiester scission with yDBR occurs only with a cis-arrangement of phosphate groups at the branchpoint (i.e., ribose) thereby discriminating between all other configurations.     

Synthesis of 1, 7-Dideazapurine Ribonucleosides and Deoxyribonucleosides

Abstract

The synthesis of hydroxylamino derivatives of 1,7-dideazaadenosine and of 1,7-dideaza-2′-deoxyadenosine, starting from 4-nitro-1H-pyrrolo[2,3-b]pyridine (1), is described. None of the synthesized compounds are substrates of adenosine deaminase and two of them (3 and 18) are weak inhibitors.     

Purification and characterization of a thermostable pullulanase fromThermoactinomyces thalpophilus

Summary Thermoactinomyces thalpophilus No. 15 produced an extracellular pullulanase in an aerobic fermentation with soluble starch, salts, and complex nitrogen sources. Acetone fractionation, ion-exchange chromatography, and gel filtration purified the enzyme from cell-free broth 16-fold to an electrophoretically homogeneous state (specific activity, 1352 U/mg protein; yield, 4%). The purified enzyme (estimated MW 79 000) was optimally active at pH 7.0 and 70°C and retained 90% relative activity at 80°C (30 min) in the absence of substrate. The enzyme was activated by Co²⁺, inhibited by Hg²⁺, and exhibited enhanced stability in the presence of Ca²⁺. The enzyme hydrolyzed pullulan (K _m 0.32%, w/v) forming maltotriose, and hydrolyzed amylopectin (K _m 0.36%, w/v), amylopectin beta-limit dextrin (K _m 0.45%, w/v) and glycogen beta-limit dextrin (K _m 1.11%, w/v) forming maltotriose and maltose.     

Synthesis and Biological Activity of 6-Hydroxyguanidino-and 6-Hydroxyureidopurine And Their Ribonucleosides

Abstract

N ⁶ ?(1-hydroxyguanidino)purine IIa, and its 9-β-D-ribonucleoside derivative IIb were prepared by reacting at room temperature 6-hydroxyadenine Ia and 6-hydroxyadenosine Ib, with 1-guanyl-3,5-dimethylpyrazole nitrate in DMF. Refluxing IIa and IIb in 95% ethanol gave N⁶?(1-hydroxyureido)purine and its ribonucleoside derivative respectively; the latter compound was also obtained by refluxing Ib with 1-guanyl-3,5-dimethylpyrazole nitrate in ethanol. The two base analogs were inactive against L1210 cells in vitro, but the nucleoside derivatives inhibited the growth of these cells by 50% at 5 × 10 ^-6 and 6 × 10^?7 M respectively. Compound IIb, at 200 mg/kg/day × 5, increased the life span of L1210-bearing DBA/2N mice by 57%. Cytofluorometric determinations showed that IIb inhibited cell growth in the G₂ phase of the cell cycle. also found to inhibit adenosine deaminase activity with a K_i = 3.47 μM.     

Alkaline detergent enzymes from alkaliphiles: enzymatic properties, genetics, and structures

The cleaning power of detergents seems to have peaked; all detergents contain similar ingredients and are based on similar detergency mechanisms. To improve detergency, modern types of heavy-duty powder detegents and automatic dishwasher detergents usually contain one or more enzymes, such as protease, amylase, cellulase, and lipase. Alkaliphilic Bacillus strains are often good sources of alkaline extracellular enzymes, the properties of which fulfil the essential requirements for enzymes to be used in detergents. We have isolated numbers of alkaliphilic Bacillus that produce such alkaline detergent enzymes, including cellulase (CMCase), protease, α-amylase, and debranching enzymes, and have succeeded in large-scale industrial production of some of these enzymes. Here, we describe the enzymatic properties, genetics, and structures of the detergent enzymes that we have developed. Received: January 22, 1998 / Accepted: February 16, 1998     

Molecular recognition of a branched peptide with HIV-1 Rev Response Element (RRE) RNA

Interaction of HIV-1 rev response element (RRE) RNA with its cognate protein, Rev, is critical for HIV-1 replication. Understanding the mode of interaction between RRE RNA and ligands at the binding site can facilitate RNA molecular recognition as well as provide a strategy for developing anti-HIV therapeutics. Our approach utilizes branched peptides as a scaffold for multivalent binding to RRE IIB (high affinity rev binding site) with incorporation of unnatural amino acids to increase affinity via non-canonical interactions with the RNA. Previous high throughput screening of a 46,656-member library revealed several hits that bound RRE IIB RNA in the sub-micromolar range. In particular, the lead compound, 4B3, displayed a K_d value of 410?nM and demonstrated selectivity towards RRE. A ribonuclease protection assay revealed that 4B3 binds to the stem-loop structure of RRE IIB RNA, which was confirmed by SHAPE analysis with 234 nt long NL4-3 RRE RNA. Our studies further indicated interaction of 4B3 with both primary and secondary Rev binding sites.     

Specific detection of pullulanase type I in polyacrylamide gels

Abstract A specific detection of pullulanase type I which hydrolyzes the α-1,6-glycosidic linkages on pullulan and starch was developed using impregnation of gels with soluble starch and staining for amylose with iodine. It was a simple and highly sensitive zymogram method capable of detecting as little as 0.001 unit of pullulanase type I activity in polyacrylamide gels after electrophoresis. After fractionation of crude enzyme using DEAE ion exchange chromatography to avoid possible co-migration of amylolytic enzymes which disturb the interaction between amylose and iodine, the high and critical sensitivity of the detection was achieved. The specific detection is based on the fact that when pullulanase type I hydrolyzes the α-1,6-glycosidic bonds in soluble starch increased amounts of α-1,4-linked amylose is formed which yields more intensely blue colored conjugate with iodine. Thus, blue bands on the lighter background signal the presence of pullulanase type I. In contrast, amylolytic enzymes give 'white' bands on the lightly stained background because they remove amylose. This procedure is effective in enzyme screening to distinguish debranching enzyme (pullulanase type I) from other pullulan-degrading enzymes.     

Improved Protocol for the Synthesis of Flexibly Protected Morpholino Monomers from Unprotected Ribonucleosides

An inexpensive and much improved protocol has been developed for the synthesis of protected morpholino monomers from unprotected ribonucleosides in high overall yield, using oxidative glycol cleavage and reductive amination strategy. Unlike the previous methods, the present strategy allows installing the exocyclic amine protections at a later stage, and thus avoids the use of expensive, or commercially unavailable, exocyclic amine-protected ribonucleosides as starting materials. To demonstrate the flexibility of the present method in choosing protecting groups, the monomers have been protected with several such groups of different deblocking properties at the exocyclic amine position.     

Building Blocks for Synthesis of Oligoarabinonucleotides: Preparation of Arabinonucleoside H-Phosphonates from Protected Ribonucleosides

Abstract

A straightforward and inexpensive synthesis of arabinonucleoside H-phosphonates has been developed. Arabinonucleosides were synthesised from protected ribonucleosides via 2′-keto derivatives. Reaction conditions have been optimised for compounds bearing labile N-protections. Further protecting group manipulation and phosphonylation gave the required H-phosphonate monomers.     

VARIATION OF ENZYME ACTIVITIES AT A BRANCHED PATHWAY INVOLVED IN THE UTILIZATION OF GLUCONATE IN ESCHERICHIA COLI

Abstract.— Twenty‐four strains of Escherichia coli from the ECOR collection were characterized for growth rate in gluconate minimal salts medium and for Vmax and Km of the three enzymes (gluconokinase, 6‐phosphogluconate dehydrogenase, and 6‐phosphogluconate dehydratase) that form a branch point for the utilization of gluconate. A total of 11 characters–growth rate, three Vmax values, four Km values, and three Vmax/Km values–were determined for these 24 ECOR strains. Most of the characters were normally distributed. Statistical tests showed that growth rate is significantly less variable than enzyme activities. Also, analyses of variance showed significant differences among strains and among the extant five genetic groups of E. coli for the characters measured. A Mantel test showed that, for some characters, closely related strains shared similar character values. Two hypotheses regarding the relationships between growth rate and enzyme activity and between various enzyme activities were tested. None of the expected correlations between growth rate and enzyme activity or between enzyme activities was detected. The results were discussed in terms of metabolic control analysis and neutral theory.     

Synthesis and mesomorphic properties of glycosyl dialkyl- and diacyl-glycerols bearing saturated, unsaturated and methyl branched fatty acid and fatty alcohol chains. Part I. Synthesis

Glycosyl dialkyl- and diacyl-glycerols bearing saturated, unsaturated or chiral methyl branched chains in the tail and disaccharide and trisaccharide carbohydrate headgroups were synthesised. Standard procedures were used for the preparation of the educts and the glyco lipids: trichloracetimidate procedure for the preparation of long-chained compounds, glycosylation using the beta-peracetate and boron trifluoride etherate was successful for the preparation of lipids with a medium-alkyl chain length. Preparation of the ester was afforded in a multi-step synthesis according to published procedures. Thus, several lipids were synthesised in a few synthetic steps in good yields. The introduction of unsaturated or methyl branched chains lead to liquid crystallinity at ambient temperature, because these compounds will be used as model compounds for biological systems. The biophysical properties of these compounds will be reported in a following paper.     

Photochemical Synthesis of 6-Aryluridines1)

Abstract

Synthesis of 6-aryluridines was effected by photochemical arylation of 6-iodo-2′,3′-O-isopropylidene-5′-O-methoxymethyluridine.     

Photochemical Synthesis and Multiphoton Luminescence of Monodisperse Silver Nanocrystals

A rapid, photochemical solution-phase synthesis has been developed for the production of monodisperse, nanometer-sized silver particles. The stabilizer used in the synthesis can be used to control the average diameter of the particles over a range from 1 to 7 nm. The same reaction mixture can also be employed to deposit patterns of nanoparticles with a laser via multiphoton absorption. The particles exhibit strong multiphoton absorption-induced luminescence when irradiated with 800-nm light, allowing emission from single nanoparticles to be observed readily.     

Amino acid substitutions of the limit dextrinase gene in barley are associated with enzyme thermostability

Limit dextrinase (LD) is a key enzyme in determining the malting quality. A survey of 60 barley varieties showed a wide range of variation for the enzyme activity and thermostability. Galleon showed low enzyme activity and high thermostability while Maud showed high activity and low thermostability. Alignment of the LD amino acid sequences of Galleon and Maud identified seven amino acid substitutions Lys/Arg-102, Thr/Ala-233, Ser/Gly-235, Gly/Ala-298, Cys/Arg-415, Ala/Ser-885 and Gly/Cys-888. Genetic diversity of LD was investigated using single strand conformation polymorphism based on the amino acid substitutions. Only limited genetic variation was detected in the current malting barley varieties, although wide variation was observed in the wider barley germplasm. The Thr/Ala-233 and Ala/Ser-885 substitutions were associated with enzyme thermostability (P < 0.0001), but no polymorphism was associated with the enzyme activity. This result was confirmed from further sequence analysis. The results will provide a tool for understanding and selection of high LD thermostability.     

Characterization and in vitro activity of a branched peptide boronic acid that interacts with HIV-1 RRE RNA

A branched peptide containing multiple boronic acids was found to bind RRE IIB selectively and inhibit HIV-1 p24 capsid production in a dose-dependent manner. Structure–activity relationship studies revealed that branching in the peptide is crucial for the low micromolar binding towards RRE IIB, and the peptide demonstrates selectivity towards RRE IIB in the presence of tRNA. Footprinting studies suggest a binding site on the upper stem and internal loop regions of the RNA, which induces enzymatic cleavage of the internal loops of RRE IIB upon binding.     

Synthesis of Fused Cyclopropane-Containing Nucleosides by [1,2]-Hydride Shift Rearrangements and B-Elimination Reactions of Sulfonylated Ribonucleosides

Abstract

(1′R, 3′S and R, 5′S)-4′-Oxo-2′-oxabicyclo[3.1.0]hexan-3′-yl pyrimidines and purines were synthesized from ribonucleosides in 2-5 steps. The configurations of the base moieties in the cyclopropano keto-nucleosides were determined by NOE difference spectroscopy.     

Synthesis of oligosaccharides related to the repeating unit of the capsular polysaccharide from Streptococcus pneumoniae type 37

A tetra- and a pentasaccharide were synthesized as analogues to the structure of the Streptococcus pneumoniae type 37 capsular polysaccharide, a homopolymer with a disaccharide-repeating unit of -->3)[beta-D-Glcp-(1-->2)]-beta-D-Glcp-(1-->. Synthesis of the tetrasaccharide employed a beta-(1-->2)-diglycosylation of a beta-(1-->3)-linked disaccharide. Subsequently, the pentasaccharide was synthesized from a suitably protected tetrasaccharide derivative by a beta-(1-->3)-extension at O-3'. Steric crowding was found to be an important factor in the formation of the pentasaccharide.     

RNase P cleaves the adenine riboswitch and stabilizes pbuE mRNA in Bacillus subtilis

RNase P from Bacillus subtilis cleaves in vitro the adenine riboswitch upstream of pbuE, which codes for an adenine efflux pump. The guanine riboswitch, encoded upstream of xpt-pbuX operon, is not cleaved. The cleavage sites do not occur at any predicted structures that should be recognized by RNase P in the theoretical model of the adenine riboswitch. However, it is possible to draw alternative secondary structure models that match the apparent requirements for RNase P substrates at these cleavage sites. Support for these models is provided by appropriate mutagenesis experiments. Adenine showed no effect on the cleavage in vitro of the pbuE adenine riboswitch by RNase P holoenzyme from B. subtilis. The results of genetic experiments performed in B. subtilis support the cleavage of adenine riboswitch by RNase P in vivo and suggest that it induces the stabilization of pbuE mRNA under normal conditions.     

Fluorogenic substrates of glycogen debranching enzyme for assaying debranching activity

Glycogen debranching enzyme (GDE) degrades glycogen in concert with glycogen phosphorylase. GDE has two distinct active sites for maltooligosaccharide transferase and amylo-1,6-glucosidase activities. Phosphorylase limit dextrin from glycogen is debranched by cooperation of the two activities. Fluorogenic branched dextrins were prepared as substrates of GDE from pyridylaminated maltooctaose (PA-maltooctaose) and maltotetraose, taking advantage of the synthetic action of Klebsiella pneumoniae pullulanase. Their structures were as follows: Glcalpha1-4Glcalpha1-4Glcalpha1-4Glcalpha1-4Glcalpha1-4(Glcalpha1-4Glcalpha1-4Glcalpha1-4Glcalpha1-6)Glcalpha1-4Glcalpha1-4GlcPA (B3), Glcalpha1-4Glcalpha1-4Glcalpha1-4Glcalpha1-4(Glcalpha1-4Glcalpha1-4Glcalpha1-4Glcalpha1-6)Glcalpha1-4Glcalpha1-4Glcalpha1-4GlcPA (B4), Glcalpha1-4Glcalpha1-4Glcalpha1-4(Glcalpha1-4Glcalpha1-4Glcalpha1-4Glcalpha1-6)Glcalpha1-4Glcalpha1-4Glcalpha1-4Glcalpha1-4GlcPA (B5), Glcalpha1-4Glcalpha1-4(Glcalpha1-4Glcalpha1-4Glcalpha1-4Glcalpha1-6)Glcalpha1-4Glcalpha1-4Glcalpha1-4Glcalpha1-4Glcalpha1-4GlcPA (B6), Glcalpha1-4(Glcalpha1-4Glcalpha1-4Glcalpha1-4Glcalpha1-6)Glcalpha1-4Glcalpha1-4Glcalpha1-4Glcalpha1-4Glcalpha1-4Glcalpha1-4GlcPA (B7), and Glcalpha1-4Glcalpha1-4Glcalpha1-4Glcalpha1-6Glcalpha1-4Glcalpha1-4Glcalpha1-4Glcalpha1-4Glcalpha1-4Glcalpha1-4Glcalpha1-4GlcPA (B8). These dextrins were incubated with porcine skeletal muscle GDE. No fluorogenic product was found in the digest of B8. The fluorogenic products from B3, B4, and B5 were PA-maltooctaose only. PA-maltooctaose, PA-maltoundecaose, and 6(7)-O-alpha-glucosyl-PA-maltooctaose were from B7. PA-maltooctaose and 6(6)-O-alpha-glucosyl-PA-maltooctaose were from B6. These results indicate that the maltooligosaccharide transferase removed the maltotriosyl residues from the maltotetraosyl branches by hydrolysis or intramolecular transglycosylation to expose 6-O-alpha-glucosyl residues, and then the amylo-1,6-glucosidase hydrolyzed the alpha-1,6-glycosidic linkages of the products rapidly. Probably, 6-O-alpha-glucosyl-PA-maltooctaoses from B7 and B6 were less susceptible to the amylo-1,6-glucosidase than were those from B3, B4, and B5. Taking this into account, B3, B4, and B5 are suitable substrates for GDE assay.