Enzymatic Hydrolysis of Esters Containing a Tetrazole Ring

The lipase‐catalyzed enantioselective hydrolysis of acetates containing tetrazole moiety was studied. Among all tested lipases, Novozyme SP 435 allowed to obtain optically active 4‐(5‐aryl‐2H‐tetrazol‐2yl)butan‐2‐ol and 1‐(5‐aryl‐2H‐tetrazol‐2yl)‐propan‐2‐ol and their acetates with the highest optical purities (ee = 95%‐99%) and excellent enantioselectivity (E>100). Some of the synthesized tetrazole derivatives were screened for their antifungal activity. Racemic mixtures of 4‐[5‐(4‐chlorophenyl)‐2H‐tetrazol‐2‐yl)butan‐2‐ol as well as pure enantiomers of this compound showed promising antifungal activity against F. sambucinum, F. oxysporum, C. coccodes, and A. niger. Chirality 26: 811–816, 2014. © 2014 Wiley Periodicals, Inc.     

Enzymatic Synthesis of Rhamnose Containing Chemicals by Reverse Hydrolysis

Rhamnose containing chemicals (RCCs) are widely occurred in plants and bacteria and are known to possess important bioactivities. However, few of them were available using the enzymatic synthesis method because of the scarcity of the α-L-rhamnosidases with wide acceptor specificity. In this work, an α-L-rhamnosidase from Alternaria sp. L1 was expressed in Pichia pastroris strain GS115. The recombinant enzyme was purified and used to synthesize novel RCCs through reverse hydrolysis in the presence of rhamnose as donor and mannitol, fructose or esculin as acceptors. The effects of initial substrate concentrations, reaction time, and temperature on RCC yields were investigated in detail when using mannitol as the acceptor. The mannitol derivative achieved a maximal yield of 36.1% by incubation of the enzyme with 0.4 M L-rhamnose and 0.2 M mannitol in pH 6.5 buffers at 55°C for 48 h. In identical conditions except for the initial acceptor concentrations, the maximal yields of fructose and esculin derivatives reached 11.9% and 17.9% respectively. The structures of the three derivatives were identified to be α-L-rhamnopyranosyl-(1→6'')-D-mannitol, α-L-rhamnopyranosyl-(1→1'')-β-D-fructopyranose, and 6,7-dihydroxycoumarin α-L-rhamnopyranosyl-(1→6'')-β-D-glucopyranoside by ESI-MS and NMR spectroscopy. The high glycosylation efficiency as well as the broad acceptor specificity of this enzyme makes it a powerful tool for the synthesis of novel rhamnosyl glycosides.     

Hydrolysis of DNA by a Branched Peptide without Aromatic Residues

A branched peptide Nα, Nɛ-di (l-leucyl)-l-lysine was found to efficiently cleave supercoiled double-strand DNA such as PUC19 DNA at optimum pH 4.0 in 40 mmol/l Britton–Robbinson buffer. The T4 ligase experiment implied that the DNA cleavage occurs via a hydrolytic path. The dependence of the cleavage reaction on the ionic strength indicated that the interaction of DNA with the branched peptide involve only electrostatic binding.     

Histidine kinase regulation by a cyclophilin-like inhibitor

The sensor histidine kinase A (KinA) from Bacillus subtilis triggers a phosphorelay that activates sporulation. The antikinase KipI prevents sporulation by binding KinA and inhibiting the autophosphorylation reaction. Using neutron contrast variation, mutagenesis, and fluorescence data, we show that two KipI monomers bind via their C-domains at a conserved proline in the KinA dimerization and histidine-phosphotransfer (DHp) domain. Our crystal structure of the KipI C-domain reveals the binding motif has a distinctive hydrophobic groove formed by a five-stranded antiparallel β-sheet; a characteristic of the cyclophilin family of proteins that bind prolines and often act as cis-trans peptidyl-prolyl isomerases. We propose that the DHp domain of KinA transmits conformational signals to regulate kinase activity via this proline-mediated interaction. Given that both KinA and KipI homologues are widespread in the bacterial kingdom, this mechanism has broad significance in bacterial signal transduction.     

Histidine Production by Auxotrophic Histidine Analog-resistant Mutants of Corynebacterinm glutamicum

Corynebacterium glutamicum mutants carrying both auxotrophy and histidine analog-resistance were derived by a mutagenic treatment, and their histidine productivity was compared with that of a triazolealanine (TRA)-resistant histidine producer, C. glutamicum KY-10260. As a result, a leucine auxotrophic TRA-resistant mutant, Rα-88 was selected out of 164 auxotrophic derivatives of KY-10260. It produced histidine at a distinctly higher concentration than the parent strain under every condition tested. The concentration reached 11 mg/ml or 5.8% (w/w) of the initial sugar. Addition of an excessive amount of leucine to the medium inhibited the histidine production together with the by-production of valine by this mutant. Thiazolealanine-resistant mutants derived from a tyrosine auxotroph, a phenylalanine auxotroph and a tryptophan auxotroph gave the same or lower production in comparison with KY-10260.     

Sunflower Seed Aminopeptidase-Catalyzed Hydrolysis of Phe-Xaa Dipeptides — Exploring the S1′ Specificity of the Enzyme

The S₁′ substrate specificity of the sunflower seed major aminopeptidase was studied with a series of dipeptide substrates with phenylalanine at P₁ and a hydrophobic amino acid at P₁′ position. The kinetic parameters of hydrolysis are significantly affected by the structure, side chain hydrophobicity and configuration of the P₁′ moiety. Its binding during enzyme-substrate complex formation takes place at a hydrophobic site of limited size following an extraction mechanism as seen from the applied structure-activity correlation. Attempts to establish such dependencies for the catalytic step of the reaction reveal the presence of additional S₁′-P₁′ enzyme-substrate interactions of greater complexity.     

Real-time Direct Observation of Single-molecule DNA Hydrolysis by Exonuclease III

Abstract

Single-molecule DNA digestion by exonuclease III, which has 3′ to 5′ exonuclease activity, was analyzed using a micro-channel with two-layer laminar flow. First, a DNA-bead complex was optically trapped in one layer in the absence of exonuclease III permitted the DNA to be stretched by the laminar flow. The exonuclease III reaction was initiated by moving the trapped DNA-bead complex to another layer of flow, which contained exonuclease III. As the reaction proceeded, the fluorescently-stained DNA was observed to shorten. The process was photographed; examination of the photographs showed that the DNA molecule shortened in a linear fashion with respect to the reaction time. The digestion rate obtained from the single-molecule experiment was compared to that measured from a bulk experiment and was found to be ca. 28 times higher than the bulk digestion rate.     

NMR Studies of a DNA Containing 8-Methoxydeoxyguanosine

Abstract

¹H NMR experiments have been undertaken to elucidate the structural effects of methoxy substitution at the C8 of a deoxyguanosine residue in a self-complementary dodecadeoxyribonucleotide, d(C-G-C-mo⁸G-A-A-T-T-C-G-C-G), duplex, which has an 8-methoxy-2′-deoxyguanosine (mo⁸dG) residue at the 4th position. NMR data indicate that the mo⁸dG residue takes an anti glycosidic conformation in a mo⁸dG(anti):dC(anti) base-pair structure in a B-form duplex. The thermal stability of the duplex is reduced, but the overall structure is much the same as that of the unmodified d(C-G-C-G-A-A-T-T-C-G-C-G) duplex.     

Histidine production by a regulatory mutant of Streptomyces coelicolor

Streptomyces coelicolor mutant RF-59, isolated as a revertant of a histidine auxotroph after mutagenic treatment with N-methylN'-nitro-N-nitrosoguanidine, was found to accumulate L-histidine. The mutant was sensitive to 2-thiazo-lealanine and L-2,4-diaminobutyric acid and partially sensitive to alpha-methylhistidine but resistant to 1,2,4-triazolealanine, indicating that repression of the histidine operon was modified in the mutant. Culture conditions were investigated, and optimal media for L-histidine production were developed, resulting in L-histidine accumulation of 2.1 to 3.5 g/liter.     

Histidine production by a regulatory mutant of Streptomyces coelicolor.

Streptomyces coelicolor mutant RF-59, isolated as a revertant of a histidine auxotroph after mutagenic treatment with N-methylN'-nitro-N-nitrosoguanidine, was found to accumulate L-histidine. The mutant was sensitive to 2-thiazo-lealanine and L-2,4-diaminobutyric acid and partially sensitive to alpha-methylhistidine but resistant to 1,2,4-triazolealanine, indicating that repression of the histidine operon was modified in the mutant. Culture conditions were investigated, and optimal media for L-histidine production were developed, resulting in L-histidine accumulation of 2.1 to 3.5 g/liter.     

Mechanism of CpG DNA Methyltransferases M.SssI and Dnmt3a Studied by DNA Containing 2-Aminopurine

Murine DNA methyltransferases Dnmt3a-CD and M.SssI from Spiroplasma methylate cytosines at CpG sites. The role of 6-oxo groups of guanines in DNA methylation by these enzymes has been studied using DNA substrates, which contained 2-aminopurine at different positions. Removal of the 6-oxo group of the guanine located adjacent to the target cytosine in the CpG site dramatically reduces the stability of the methyltransferase–DNA complexes and leads to a significant decrease in the methylation. Apparently, O6 of this guanine is involved in the recognition of CpG sites by the enzymes. Cooperative binding of Dnmt3a-CD to 2-aminopurine-containing DNA and the formation of nonproductive enzyme–substrate complexes were observed.     

Dipeptides as Leaving Group in the Enzyme‐Catalyzed DNA Synthesis

Conjugates of 2′‐deoxyadenosine monophosphate with dipeptides have been synthesized and tested as substrates for several polymerases. Although the incorporation efficiency is not very high, it demonstrates that some of these dipeptides can be accommodated in the active site of polymerases and function as leaving groups in the enzymatic synthesis of DNA.     

Mechanism of Dephosphorylation of Glucosyl-3-phosphoglycerate by a Histidine Phosphatase

Mycobacterium tuberculosis (Mtb) synthesizes polymethylated polysaccharides that form complexes with long chain fatty acids. These complexes, referred to as methylglucose lipopolysaccharides (MGLPs), regulate fatty acid biosynthesis in vivo, including biosynthesis of mycolic acids that are essential for building the cell wall. Glucosyl-3-phosphoglycerate phosphatase (GpgP, EC 5.4.2.1), encoded by Rv2419c gene, catalyzes the second step of the pathway for the biosynthesis of MGLPs. The molecular basis for this dephosphorylation is currently not understood. Here, we describe the crystal structures of apo-, vanadate-bound, and phosphate-bound MtbGpgP, depicting unliganded, reaction intermediate mimic, and product-bound views of MtbGpgP, respectively. The enzyme consists of a single domain made up of a central β-sheet flanked by α-helices on either side. The active site is located in a positively charged cleft situated above the central β-sheet. Unambiguous electron density for vanadate covalently bound to His¹¹, mimicking the phosphohistidine intermediate, was observed. The role of residues interacting with the ligands in catalysis was probed by site-directed mutagenesis. Arg¹⁰, His¹¹, Asn¹⁷, Gln²³, Arg⁶⁰, Glu⁸⁴, His¹⁵⁹, and Leu²⁰⁹ are important for enzymatic activity. Comparison of the structures of MtbGpgP revealed conformational changes in a key loop region connecting β1 with α1. This loop regulates access to the active site. MtbGpgP functions as dimer. L209E mutation resulted in monomeric GpgP, rendering the enzyme incapable of dephosphorylation. The structures of GpgP reported here are the first crystal structures for histidine-phosphatase-type GpgPs. These structures shed light on a key step in biosynthesis of MGLPs that could be targeted for development of anti-tuberculosis therapeutics.     

ATP Binding and Hydrolysis by Mcm2 Regulate DNA Binding by Mcm Complexes

The essential minichromosome maintenance (Mcm) proteins Mcm2 through Mcm7 likely comprise the replicative helicase in eukaryotes. In addition to Mcm2-7, other subcomplexes, including one comprising Mcm4, Mcm6, and Mcm7, unwind DNA. Using Mcm4/6/7 as a tool, we reveal a role for nucleotide binding by Saccharomyces cerevisiae Mcm2 in modulating DNA binding by Mcm complexes. Previous studies have shown that Mcm2 inhibits DNA unwinding by Mcm4/6/7. Here, we show that interaction of Mcm2 and Mcm4/6/7 is not sufficient for inhibition; rather, Mcm2 requires nucleotides for its regulatory role. An Mcm2 mutant that is defective for ATP hydrolysis (K549A), as well as ATP analogues, was used to show that ADP binding by Mcm2 is required to inhibit DNA binding and unwinding by Mcm4/6/7. This Mcm2-mediated regulation of Mcm4/6/7 is independent of Mcm3/5. Furthermore, the importance of ATP hydrolysis by Mcm2 to the regulation of the native complex was apparent from the altered DNA binding properties of Mcm2^KA-7. Moreover, together with the finding that Mcm2_K549A does not support yeast viability, these results indicate that the nucleotide-bound state of Mcm2 is critical in regulating the activities of Mcm4/6/7 and Mcm2-7 complexes.     

Hydrolysis of phospholipids by a lysosomal enzyme

The phospholipid-hydrolyzing activity of rat liver lysosomes has been studied. These lysosomes contain a phospholipase that cleaves both fatty acid ester linkages of lecithin and of phosphatidyl ethanolamine and releases free fatty acids from both positional isomers of lysolecithin. The enzyme does not require calcium for maximum activity, and is inhibited by diethyl ether and sodium deoxycholate. Mercuric ions and cetyltrimethyl ammonium bromide also inhibit the hydrolysis. Compared with lipase activity, this enzyme is relatively stable to heat. The specific activity of the hydrolysis of lecithin by the lysosomal enzyme is considerably higher than those reported for mitochondrial and microsomal phospholipases. The enzyme resembles other hydrolases of the lysosome in that it has an acid pH optimum (pH 4.5). This enzymic activity is present in both the lysosomal soluble enzyme fraction and in the lysosomal membrane fraction. The enzyme may participate in the intracellular digestion of mitochondria that is carried out by the intact lysosome in vivo. Localized inflammation and changes in vascular permeability following tissue damage could be catalyzed by this phospholipase.     

Transfection of KB Cells by Liposomes Containing Adenovirus Type 2 DNA

Adenovirus type 2 DNA was entrapped in liposomes which were then used to transfect KB cells with an efficiency of ~4,000 plaques per μg of encapsulated DNA.     

Enzymatic Hydrolysis and Biological Activity of Oligonucleotides Containing 5-Substituted Pyrrmidine Bases

Abstract

Two series of alternating ODNs containing 5-n.alkyl-, alkenyl- and alkynyl-dU and -dC units have been prepared in order to study the kinetics of their hydrolysis by SV PDE and human serum, respectively. Both in (r⁵dUpdA)₁₀ and (r⁵dCpdG)₆ series the rate of hydrolysis decreased with increasing length of side-chain. Replacement of thymidines by 5-hexynyl-dU in different antisense oligomers resulted in considerably higher biological activity relative to that of the thymidine-containing counterparts.