RNA N-glycosidase Research Articles

The membrane insertion of trichosanthin is membrane-surface-pH dependent.

Trichosanthin (TCS) is the active component extracted from Tianhuafen, a traditional herbal medicine that has been used for abortion in China for centuries. It belongs to the type-I ribosome-inactivating protein (RIP) family and can inactivate the eukaryotic ribosome through its RNA N-glycosidase activity. Recent studies have shown TCS to be multifunctional, its pharmacological properties including immunomodulatory, anti-tumour and anti-HIV activities. The membrane-insertion property of TCS is thought to be essential for its physiological effect, for it must get across the membrane before it can enter the cytoplasm and exert its RIP function. In this paper, the membrane-insertion mechanism of TCS was studied. The monolayer experiment revealed that TCS's membrane-insertion ability was dependent on low pH. Fluorescence spectroscopy using 1-anilinonaphthalene-8-sulphonic acid as a probe showed that low pH may induce the conformational change of TCS that leads to the hydrophobic-site exposure, and the CD result showed that this conformational change did not alter its secondary structure. Such conformational change leads to an intermediate state, called the 'molten globular state' by previous investigators. The pH-dependent membrane insertion and conformational change were related by the fact that the optimal membrane-surface pH needed was the same for the two events. From these and other results, a membrane-insertion model was proposed.

Characterization and molecular cloning of two different type 2 ribosome-inactivating proteins from the monocotyledonous plant Polygonatum multiflorum.

Leaves of the monocotyledonous plant Polygonatum multiflorum L. (Solomon's seal) contain besides a monocot mannose-binding lectin two galactose/N-acetylgalactosamine (Gal/GalNAc)-binding type 2 ribosome-inactivating proteins (RIPs). Both RIPs were purified using a combination of classical protein purification techniques and affinity chromatography. Although both RIPs consist of protomers of 65 kDa, the P. multiflorum RIP monomer (PMRIPm) occurs as a monomer of approximately 60 kDa, whereas the tetramer (PMRIPt) is a tetramer of 240 kDa. Both RIPs exhibit similar RNA N-glycosidase activity but differ in their specific agglutination activity and carbohydrate-binding specificity, PMRIPt being a GalNAc-specific lectin whereas PMRIPm is Gal/GalNAc-specific. Toxicity tests indicated that both Polygonatum RIPs exhibit a very low cytotoxicity towards human and animal cells. Analysis of the genomic clones encoding both RIPs revealed a high degree of sequence similarity to other type 2 RIPs. Molecular modelling confirmed that both Polygonatum RIPs have a similar structure to ricin.

Crystal structures of the complexes of trichosanthin with four substrate analogs and catalytic mechanism of RNA N-glycosidase

Four substrate analogs-nicotinamide adenine dinucleotide, adenylyl (3', 5') guanosine, guanylyl (3',5') adenosine, and adenosine 2', 5'-diphosphate-have been used to prepare the complexes with trichosanthin (TCS), a type I ribosome-inactivating protein that possesses the activity of N-glycosidase. The crystal structures of the complexes have been determined and refined at high resolution. The refined structures show that the N-glycosidic bonds of all the four substrate analogues are hydrolyzed and a common structure is shared by the four complexes, in which only adenine, the product of the enzymatic reaction, is bound in the active center. The structure is compared with those of native trichosanthin and a previously reported trichosanthin-NADPH complex in which the N-glycosidic bond is uncleaved. The structural comparison shows that the conformation of Tyr70 obviously differs from those in the latter two structures, i.e., the side chain of Tyr70 is rotated along its Cbeta-Cgamma bond by approximately 70 degrees. The water molecule found to be preassociated with the N-glycosidic bond in the TCS-NADPH complex structure and proposed to be the water candidate responsible for hydrolyzing the N-glycosidic bond disappears in the trichosanthin-product complex structure. Based on the comparison of the three structures representing the different stages of the enzymatic reaction, the catalytic mechanism of RNA N-glycosidase has been further elucidated. Proteins 2000;39:37-46.

Crystal structures of the complexes of trichosanthin with four substrate analogs and catalytic mechanism of RNA N-glycosidase

Crystal structures of the complexes of trichosanthin with four substrate analogs and catalytic mechanism of RNA N-glycosidase

Effects of the active aldehyde group generated by RNA N-glycosidase in the sarcin/ricin domain of rat 28S ribosomal RNA on peptide elongation.

Effects of the active aldehyde group of ribose C1' at position 4324 of rat 28S rRNA, in the inactivated ribosome generated by RNA N-glycosidases (trichosanthin, A-chain of cinnamomin and ricin), on peptide elongation have been studied. The aldehyde group inhibits the activities of eEF1A-dependent aminoacyl-tRNA binding to the inactivated ribosome and eEF1A-dependent GTPase, but increases eEF2-dependent activity. At a high concentration of RNA N-glycosidase, the generated aldehyde group also inhibits aminoacyl-tRNA binding to the inactivated ribosome in the absence of elongation factor and translocation activity. When the aldehyde group is reduced into a hydroxyl group by sodium borohydride or blocked with an amino acid through nucleophilic addition, the activities of eEF1A-dependent aminoacyl-tRNA binding and eEF1A-dependent GTPase of the inactivated ribosome are partially restored, but the altered activities of eEF2-dependent GTPase, translocation and aminoacyl-tRNA binding in the absence of elongation factor are not normalized. Thus, reduction or blockage of the aldehyde group with sodium borohydride or amino acids might change the conformation of the S/R domain in rat 28S ribosomal RNA to meet the requirement for eEF1A-dependent reactions, but not eEF2-involved reactions.

Polynucleotide: Adenosine Glycosidase Activity of Immunotoxins Containing Ribosome-Inactivating Proteins

Polynucleotide:adenosine glycosidases (rRNA N-glycosidases, EC 3.2.2.22, more commonly known as ribosome-inactivating proteins, RIP) are a numerous family of plant and bacterial enzymes, shown to release also adenine from DNA in vitro. They are well suited for the preparation of specifically toxic conjugates with several carriers, including monoclonal antibodies (immunotoxins). Here we show that (i) immunotoxins containing various PNAG (dianthin, gelonin, momordin I, PAP-S, PDS-2, ricin A-chain, saporin-L1, saporin-S6) all act on DNA; (ii) activity on DNA in vitro is less compromised by disulphide linkage to antibody than is inhibition of cell-free protein translation; and (iii) specific cytotoxicity of immunotoxin does not correlate with substrate specificity.

Site-Specific Mutagenesis of Mistletoe Lectin: The Role of RIP Activity in Apoptosis

Recombinant mistletoe lectin (rML) belongs to the class of type II ribosome-inactivating proteins (RIP) composed of a catalytically active A-chain with rRNA N-glycosidase activity and a B-chain with carbohydrate binding properties. To investigate the contribution of the enzymatic activity of the rML A-chain to the observed cytotoxic and apoptotic effects, an rMLA E166Q R169Q molecule was developed by means of site-specific mutagenesis. Following heterologous expression, the activity of mutant rMLA was measured in a cell-free assay for rRNA–N-glycosidase activity. Moreover, after generation of heterodimer, the activities of mutant rML E166Q R169Q and rML wild type were determined in a cytotoxicity and apoptosis assay. Although the reduction of activity as measured in the cell-free RIP assay was more pronounced (factor 237) than in both cellular assays (factors 20–22), the data clearly indicate a close correlation between cytotoxicity, apoptosis, and the enzymatic activity of the rML A-chain. Thus, RIP activity is an essential feature of rML and therefore a prerequisite for its biological function as an anticancer agent.

Solution Structure of Anti-HIV-1 and Anti-Tumor Protein MAP30: Structural Insights into Its Multiple Functions

We present the solution structure of MAP30, a plant protein with anti-HIV and anti-tumor activities. Structural analysis and subsequent biochemical assays lead to several novel discoveries. First, MAP30 acts like a DNA glycosylase/apurinic (ap) lyase, an additional activity distinct from its known RNA N-glycosidase activity toward the 28S rRNA. Glycosylase/ap lyase activity explains MAP30's apparent inhibition of the HIV-1 integrase, MAP30's ability to irreversibly relax supercoiled DNA, and may be an alternative cytotoxic pathway that contributes to MAP30's anti-HIV/anti-tumor activities. Second, two distinct, but contiguous, subsites are responsible for MAP30's glycosylase/ap lyase activity. Third, Mn 2+ and Zn 2+ interact with negatively charged surfaces next to the catalytic sites, facilitating DNA substrate binding instead of directly participating in catalysis.

Characterization of recombinant and plant-derived mistletoe lectin and their B-chains.

Mistletoe lectin I (pML) and its isoforms ML II and III constitute the active principle in extract preparations from mistletoe, commonly used as immunomodulator in adjuvant tumour therapy. The heterodimeric disulfide-linked cytotoxic protein is classified as type II ribosome inactivating protein (RIP). Recently, the sequence coding for the mistletoe lectin prepro-protein was identified and the existence of a single intron-free gene was shown [Eck, J., Langer, M., Möckel, B., Baur, A., Rothe, M., Zinke, H. & Lentzen, H. (1999) Eur. J. Biochem. 264, 775-784]. The aim of this study was to prepare pure and homogeneous rMLB-chain as well as rML heterodimer for studying the carbohydrate binding specificity of recombinant versus natural protein and its contribution to the observed cytotoxic effect. Expression in E. coli resulted in the production of insoluble protein (inclusion bodies). A procedure for generating correctly folded, biochemically and biologically active rMLB was established starting from the insoluble single chain. Carbohydrate binding and specificity of pMLB and rMLB were analysed by a competitive enzyme linked lectin assay (ELLA). Asialofetuin was able to compete with binding of both chains (50% at 0.8 microM). The specificity of the B-chains to lactose was more distinct with halfmaximal competition at 4.9 mM (pMLB) and > 90 mM (rMLB), respectively. Furthermore, in a coassociation process rMLA- and rMLB inclusion bodies were associated in one step by defined dilution yielding active rML-heterodimer. The activities of recombinant (rML) and plant derived mistletoe lectin (pML) were compared. Cytotoxicity was determined using MOLT-4 cells and enzymatic rRNA N-glycosidase activity was measured in a coupled transcription/translation assay. The IC50 values of the two heterodimers were similar in both assays; rMLB-chain did not show any cytotoxic effect. In the ELLA with lactose as a competitor 50% competition of binding to asialofetuin was achieved at 1.6 mM (rML) and 1.8 mM (pML). Hence, using three different assays we found no significant differences between the recombinant protein and the glycosylated form of ML. Comparing the biological activities of the single chains with those of the heterodimer we conclude, that both, lectin activity and the rRNA N-glycosidase activity, are prerequisites for the cytotoxic effects on target cells.

Deguanylation of Human Immunodeficiency Virus (HIV-1) RNA by Recombinant Pokeweed Antiviral Protein

Modeling studies, combined with the molecular docking of the trinucleotide GGG into the active site of the deadenylating RNA N-glycosidase pokeweed antiviral protein (PAP), indicated that a guanine base can fit into the active site pocket of PAP without disturbing its unique geometry and is sandwiched between residues Tyr72 and Tyr123 very much like an adenine base. The guanine base can form two specific hydrogen bonds with the active site residues Ser121 and Val73 and the attached negatively charged phosphate groups can entertain stabilizing electrostatic interactions with two clusters of positively charged patches on the PAP surface formed by Lys210 and Arg179 from one side and Arg122 and Arg135 from the other side of the active site. These observations prompted the hypothesis that the RNA depurinating activity of PAP may not be restricted to adenine residues and PAP should be capable of deguanylating ribosomal and viral RNA as well. This hypothesis was experimentally confirmed by direct demonstration that guanine base is released from both ribosomal and HIV-1 RNA after treatment with purified recombinant PAP using quantitative high performance liquid chromatography. Recombinant PAP released adenine and guanine residues at a 1:1 ratio from HIV-1 RNA and at an approximately 3:1 (adenine:guanine) ratio from Escherichia coli ribosomal RNA. At a concentration of 5 μM, recombinant PAP released 263 ± 10 pmol of adenine and 100 ± 11 pmol of guanine from 1 μg of E. coli ribosomal RNA (16S + 23S) within 4 h of treatment. By comparison, 138 ± 12 pmol of adenine and 143 ± 10 pmol of guanine were released from 1 μg of HIV-1 RNA under identical treatment conditions (5 μM recombinant PAP, 4 h treatment). The deguanylation of the ribosomal and viral RNA targets by recombinant PAP was concentration-dependent and is abolished by alanine substitutions of the catalytic active site residues Tyr72 and Tyr123. To our knowledge, these findings provide the first evidence that PAP can deguanylate both ribosomal and viral RNA.

Three-dimensional structure of beta-momorcharin at 2.55 A resolution.

Beta-Momorcharin (Mr approximately 29 kDa) is a single-chained ribosome-inactivating protein (RIP) with a branched hexasaccharide bound to Asn51. The crystal structure of beta-momorcharin has been determined using the molecular-replacement method and refined to 2. 55 A resolution. The final structural model gave an R factor of 17. 2% and root-mean-square deviations of 0.016 A and 1.76 degrees from ideal bond lengths and bond angles, respectively. beta-Momorcharin contains nine alpha-helices, two 310 helices and three beta-sheets, and its overall structure is similar to those of other single-chained RIPs. Residues Tyr70, Tyr109, Glu158 and Arg161 are expected to define the active site of beta-momorcharin as an rRNA N-glycosidase. The oligosaccharide is linked to the protein through an N-glycosidic bond, beta-GlcNAc-(1-N)-Asn51, and stretches from the surface of the N-terminal domain far from the active site, which suggests that it should not play a role in enzymatic function. The oligosaccharide of each beta-momorcharin molecule interacts with the protein through hydrogen bonds, although in the crystals most of these are intermolecular interactions with the protein atoms in an adjacent unit cell. This is the first example of an RIP structure which provides information about the three-dimensional structure and binding site of the oligosaccharide in the active chains of RIPs.

Role of TYR70 in the N-glycosidase activity of neo-trichosanthin

Trichosanthin (TCS) is a type I ribosome-inactivating protein (RIP) which possesses rRNA N-glycosidase activity. TCS has long been used as an abortifacient in China. In recent years, its immunomodulatory, anti-tumor and anti-HIV properties have attracted more and more attention. An isoform of trichosanthin, neo-trichosanthin (n-TCS), has been cloned and expressed as recombinant protein. The biochemical studies revealed that n-TCS has virtually the same rRNA N-glycosidase activity as TCS. The crystal structure of n-TCS is similar to TCS. The crystal of Y70A n-TCS, the mutant of recombinant n-TCS, was soaked in sodium citrate buffer (pH 5.5) containing 25% KCl and AMP (10 mg/ml) prior to data collection. After structure determination and refinement, no electron density corresponding to adenine can be detected around the active pocket. Furthermore, the reaction products of Y70A n-TCS and AMP incubated at various reaction times were analyzed using HPLC. No adenine can be detected. These results suggest that Tyr70 is crucial to n-TCS for its substrate recognition, binding and perhaps N-glycosidase activity.

Purification and characterization of trichomaglin--a novel ribosome-inactivating protein with abortifacient activity.

Trichomaglin, a novel ribosome-inactivating protein, has been isolated from root tuber of a plant Maganlin (Trichosanthes Lepiniate, Cucurbitaceae). The isolation and purification procedure included ammonium sulfate precipitation, Sephadex G-75 chromatography and CM-Sephadex C-50 chromatography. The protein was identified to be homogeneous by SDS-PAGE and FPLC analysis. Its molecular weight is 24,673 dalton and isoelectric point is 5.8, determined by electrospray ionization mass spectroscopy and isoelectric focusing gel electrophoresis respectively. Trichomaglin can inhibit protein synthesis in rabbit reticulocyte lysate with ID50 of 10.1 nM. When rat ribosome was incubated with trichomaglin, a diagnostic RNA fragment appeared on polyacrylamide gel after ribosomal RNAs were treated with acidic aniline. It was concluded that trichomaglin is an RNA N-glycosidase. In addition, it has been verified to be an abortifacient protein.

Prediction of a conserved, neutralizing epitope in ribosome-inactivating proteins

The secondary structures, side-chain solvent accessibilities, and superpositioned crystal structures of the A-chain of ricin and four other plant rRNA N-glycosidases (ribosome-inactivating proteins, RIPs) were examined. Previously, a 26-residue fragment from the A-chain of ricin was determined to bind to a neutralizing monoclonal antibody. The region in the native ricin A-chain, to which this peptide corresponds, is solvent-exposed and contains a negatively charged residue that has been hypothesized to participate in the toxin’s function, namely, rRNA binding and/or enzymatic activity. This region appears to be conserved in all of the structurally defined plant RIPs examined. Moreover, other plant RIPs, whose tertiary structures are, as yet, unknown, were predicted to have an analogous, solvent-exposed region containing a conserved, negatively charged residue. By analogy, these conserved structural and functional features lead to the suggestion that this exposed region represents a logical starting point for experiments designed to locate neutralizing epitopes in these RIPs. In contrast, the tertiary structure of the analogous region in a bacteria-derived RIP (Shiga toxin) is a less solvent-exposed, truncated loop and is a structure that is not as likely to be a neutralizing epitope. Because most of the amino acid residues are not conserved within this exposed region, these RIPs are predicted to be antigenically distinct.

Purification and Characterization of Novel Ribosome Inactivating Proteins, Alpha- and Beta-Pisavins, from Seeds of the Garden PeaPisum Sativum

Two ribosome inactivating proteins designated α- and β-pisavins were isolated from seeds of the garden peaPisum sativum var. arvense Poirwith a procedure involving affinity chromatography on Affi-gel Blue gel, immobilized metal ion affinity chromatography on Iminodiacetic acid-agarose, cation exchange chromatography on Resource-S, and gel filtration on Superose 12. α- and β-pisavins are nonglycoproteins with a molecular weight of 20.5 kDa and 18.7 kDa respectively. The sequences of the fist sixty N-terminal amino acids of α- and β-pisavins were identical. In isoelectric focusing these two proteins merged into one band with a pI greater than 9.3. Inhibition of protein synthesis by a rabbit reticulocyte lysate system was achieved at an IC50of approximately 0.5 nM. Activity of the proteins toward tRNA was observed. The proteins acted on ribosomal RNA through its RNA N-glycosidase activity to release an Endo's fragment, and converted the conformation of DNA from supercoiled and circular forms into a linear form.

Involvement of the amino acids outside the active-site cleft in the catalysis of ricin A chain.

The A chain of ricin (RA) is a cytotoxic RNA N-glycosidase that inactivates ribosomes by depurination of the adenosine residue at position 4324 in 28S rRNA. Of the 267 amino acids in the protein, 231 could be deleted in one or another of 83 mutants, without the loss of the capacity to catalyze hydrolysis of a single specific nucleotide in rRNA [Morris, K. N. & Wool, I. G. (1992) Proc. Natl Acad. Sci. USA 89, 4869-4873]. Expression of 29 selected deletion mutants of RA in prokaryotic cell-free coupled transcription-translation reactions was carried out and the activities of the mutants were assessed by monitoring depurination of reticulocyte ribosomes. Kinetic analysis of five deletion mutants which retained detectable activity was performed. Deletion of amino acids outside the putative active-site cleft in these mutants significantly affected the catalytic rate rather than the interaction with ribosomes. From these data, the amino acids far from the active-site cleft appeared to be involved in alignment of the key residues for catalysis and interaction with the target tetraloop structure of 28S rRNA.

A novel type-1 ribosome-inactivating protein isolated from the supernatant of transformed suspension cultures of Trichosanthes kirilowii.

A type-1 ribosome-inactivating protein (RIP) designated TK-35 has been purified from the supernatant of suspension cultures of Agrobacterium rhizogenes-transformed stem sections of Trichosanthes kirilowii. The protein was purified from the supernatant by PerSeptive SH/M cation exchange and Sephadex G-75 S gel permeation chromatography. The protein occurs as a monomer, with a molecular weight of 35,117, and is glycosylated. A protein translation inhibition assay indicates that TK-35 has an IC50 value of 2.45 nM and is able to release the rRNA N-glycosidase diagnostic fragment from rabbit reticulocyte lysate. TK-35 is quite thermally stable. Analysis of its N-terminal sequence and two lys-C-protease-digested polypeptides (internal) amino acid sequence indicates that this protein is not homologous to trichosanthin and other type-1 RIPs in Cucurbitaceae family.

Mechanisms of Action of Ribotoxins

AbstractThe ribotoxins α-sarcin and ricin and their homologs catalyze covalent modifications in adjacent nucleotides in the large RNA of ribosomes. α-Sarcin is a ribonuclease that cleaves the phosphodiester bond on the 3’ side of G4325 in a universal, 14-nucleotide, purine-rich sequence in 28SrRNA. The A-chain of ricin and of other related toxins such as Shiga toxin and Vero toxin is a RNA N-glycosidase that catalyses the depurination of the 5’ adjacent A4324. There are nearly 7000 nucleotides in mammalian ribosomes. The toxins, however, catalyze only a single covalent modification that inactivates the ribosomes and is entirely responsible for the toxicity.

Purification and activity study of the A- and B-chains of cinnamomin, a type II ribosome-inactivating protein.

The strong hydrophobic interaction between the A- and B-chains of cinnamomin, a type II ribosome-inactivating protein, makes it difficult to separate A- and B-chains after the disulfide bond is broken. We failed to separate the A-chain from B-chain of cinnamomin using methods under usual conditions. A convenient method for purification of the A- and B-chains of cinnamomin on a large scale has been developed. We chose urea to weaken the non-covalent interaction between the A- and B-chains. In the presence of 4M urea, the A- and B-chains of the reduced cinnamomin are separated effectively by DEAE-cellulose chromatography. The purified A-chain still displays the RNA N-glycosidase activity and the B-chain loses the lectin activity. After refolding in vitro in the presence of lactose, the B-chain is renatured and the active B-chain with lectin activity can be further purified by Sepharose 4B affinity chromatography. From 80 mg of cinnamomin, 10 mg of A-chain (25%) and 38 mg of the B-chain (95%) were obtained. In addition, the intrinsic fluorescence spectra of the A- and B-chains were employed to study the structural changes in the active and the non-active forms of cinnamomin A- and B-chains.

Bifunctional plant defence enzymes with chitinase and ribosome inactivating activities from Trichosanthes kirilowii cell cultures

Three bifunctional plant enzymes (named TKC 15, TKC 28-I, and TKC 28-II) with both chitinase and RIP activity were purified from the medium of Trichosanthes kirilowii plant cell cultures. Highly purified preparations of these proteins exhibited endochitolytic activity as well as the specific 28S rRNA N-glycosidase activity characteristic of ribosome inactivating proteins (RIPs). In addition to providing a competitive advantage to the plant, these enzymes offer the possibility of improved antifungal protection when expressed in transgenic plants.