A rapid staining technique for detection of RNase after polyacrylamide gel electrophoresis

Enzymatic and Chemical-Based Methods to Inactivate Endogenous Blood Ribonucleases for Nucleic Acid Diagnostics

There are ongoing research efforts into simple and low-cost point-of-care nucleic acid amplification tests (NATs) addressing widespread diagnostic needs in resource-limited clinical settings. Nucleic acid testing for RNA targets in blood specimens typically requires sample preparation that inactivates robust blood ribonucleases (RNases) that can rapidly degrade exogenous RNA. Most NATs rely on decades-old methods that lyse pathogens and inactivate RNases with high concentrations of guanidinium salts. Herein, we investigate alternatives to standard guanidinium-based methods for RNase inactivation using an activity assay with an RNA substrate that fluoresces when cleaved. The effects of proteinase K, nonionic surfactants, SDS, dithiothreitol, and other additives on RNase activity in human serum are reported. Although proteinase K has been widely used in protocols for nuclease inactivation, it was found that high concentrations of proteinase K are unable to eliminate RNase activity in serum, unless used in concert with denaturing concentrations of SDS. It was observed that SDS must be combined with proteinase K, dithiothreitol, or both for irreversible and complete RNase inactivation in serum. This work provides an alternative chemistry for inactivating endogenous RNases for use in simple, low-cost point-of-care NATs for blood-borne pathogens.

Assignment of RFLP, RAPD and isoenzyme markers to Aspergillus nidulans chromosomes, using chromosome-substituted segregants of a hybrid of A. nidulans and A. quadrilineatus

Chromosome-substituted haploid segregants were selected from among the benomyl-induced progeny of an interspecific hybrid produced by polyethylene-glycol-induced fusion of protoplasts of an Aspergillus nidulans 'master strain' and an A. quadrilineatus auxotrophic mutant. These segregants were examined by RFLP, RAPD, and isoenzyme analysis. The A. nidulans ribosomal repeat unit was assigned to chromosome V, while the benA and the pyrG genes were assigned to linkage groups VIII and I, respectively, of A. nidulans. None of the other cloned genes tested (gdhA, amdS and 25s rRNA) showed polymorphism between the two parents. The method was also used to assign RAPD markers and isoenzyme bands of beta-arylesterase, phosphatases, NAD-dependent malate dehydrogenase, and cellulase, to A. nidulans chromosomes and/or to their A. quadrilineatus equivalents. The isoenzyme and DNA sequences assigned to chromosomes could be used to saturate the genetic map of A. nidulans, or could serve as starting points for the construction of a genetic map of A. quadrilineatus. No method affording the same possibilities has been described so far in Aspergilli. This chromosome-assay method may be a useful alternative to pulsed-field-gel electrophoretic procedures for the assignment of molecular markers to chromosomes.

Identification, characterization, and comparison of RNA-degrading enzymes of wheat and barley

RNA-degrading enzymes play an important role in regulating gene expression, and sequence analyses have revealed significant homology among several plant RNA-degrading enzymes. In this study we surveyed crude extracts of the above-ground part of the common wheat (Triticum aestivum L.) and the cultivated barley (Hordeum vulgare L.) for major RNA-degrading enzymes using a substrate-based SDS-PAGE assay. Fifteen wheat and fourteen barley RNA-degrading enzymes, with apparent molecular masses ranging from 16.3 to 40.1 kD, were identified. These RNA-degrading enzymes were characterized by their response to pH changes and addition of EDTA and ZnCl2 to the preincubation or incubation buffers. The 33.2- to 40.1-kD wheat and barley, 31.7-kD wheat, and 32.0-kD barley enzyme activities were inhibited by both zinc and EDTA and were relatively tolerant to alkaline environment. The 22.7- to 28.2-kD enzymes were inhibited by zinc but stimulated by EDTA. The 18.8-kD enzyme exists in both wheat and barley. It was active in an acid environment, was inhibited by zinc, but was not affected by EDTA. Two enzyme activities (31.0 and 32.0 kD) are unique to the common wheat.

Extracellular RNase produced by Yarrowia lipolytica

Production of extracellular RNase(s) by Yarrowia lipolytica CX161-1B was examined in media between pHs 5 and 7. RNase production occurred during the exponential growth phase. High-molecular-weight nitrogen compounds supported the highest levels of RNase production. Several RNases were detected in the supernatant medium. Based on sodium dodecyl sulfate-polyacrylamide gel electrophoresis, the RNases had estimated molecular weights of 45,000, 43,000, and 34,000. It was found that Y. lipolytica secretes only one RNase (the 45,000-molecular-weight RNase) and that the 43,000 and 34,000-molecular-weight RNases are degradation products of this RNase. The alkaline extracellular protease secreted by Y. lipolytica was shown to have a major role in the 45,000- to 43,000-molecular-weight conversion, and it was demonstrated that the 45,000-molecular-weight RNase could be purified from a mutant which does not produce the alkaline extracellular protease. Purification of the RNase from a wild-type strain resulted in purification of the 43,000-molecular-weight RNase. This RNase was a glycoprotein with a molecular weight of 44,000 as estimated by gel filtration, an isoelectric point of pH 4.8, and a pH optimum between 6.5 and 7.0.

Detection of plasma proteins during sequential ultrafiltration/dialysis

Elimination of low molecular weight proteins during sequential ultrafiltration/dialysis was studied in 29 uremic patients. Beta-2-microglobulin, retinol binding protein, free light chains lambda and kappa, Zn-alpha-2-glycoprotein, hemopexin, prealbumin, hemoglobin, albumin, acid alpha-1-glycoprotein, haptoglobin, alpha-1-antichymotrypsin, ribonuclease, lysozyme, amylase, non-specific esterase, and proteolytic activity were detected in all ultrafiltrates tested. The level of total protein and ribonuclease was determined in 36 crude ultrafiltrates from 23 patients. Concentrated ultrafiltrates were used to quantitate retinol binding protein, prealbumin, albumin, lysozyme, and amylase. Other proteins identified in the ultrafiltrates are present in trace amounts. The question was discussed whether ++inextensive but systematic loss of proteins during hemofiltration in chronic RDT might be the cause of patient homeostasis disturbances.

Isoelectric focusing--polynucleotide/polyacrylamide-gel electrophoresis. A technique to separate and characterize nuclease activities

Individual native nuclease activities from human leucocytes are separated by using two-dimensional gel electrophoresis in an apparatus that allows the simultaneous running of 28 gels. Proteins are separated by isoelectric focusing in a disc gel, followed by electrophoresis into a slab gel containing DNA. Protein denaturants are avoided in the second dimension by the use of a running pH well above the optimal pH for DNAase (deoxyribonuclease) activity. Electrophoresed gels are incubated in appropriate buffers to activate nuclease activity. After staining for intact DNA, the positions of active enzymes, unobscured by the presence of other proteins, are revealed as colourless spots in a reddish-purple field. The technique is easy to use and is sensitive to 50pg of DNAase I. Versatility is provided by the use of either acidic or basic electrophoresis running buffers and by the use of specific gel incubation conditions to reveal different sets of enzyme activities. Two DNAases active at pH 7.4 in the presence of Mg2+ and Ca2+, and sixteen DNAases active at acidic pH and not requiring metals, are detected. Treatment of the human enzymes with specific glycosidases reveals that many of the human DNAases are glycoproteins containing negatively charged moieties and may be derived from modification of parent activities.

Ribonuclease of Entamoeba invadens

Two bands of RNAase activity were observed on gel electrophoresis of fractions obtained during partial purification of the RNAase of Entamoeba invadens. The faster migrating band which was responsible for most of the RNAase activity was isolated by gel electrophoresis. A pI of 5.5 was determined for this RNAase activity and estimates of its molecular weight and sedimentation coefficient gave values of about 25 000 and approximately 2.8 S. It exhibited maximum activity around pH 6, and digestion of RNA showed a pattern expected of an endoribonuclease.

Pancreatic ribonucleases of mammals with ruminant-like digestion. Amino-acid sequences of hippopotamus and sloth ribonucleases

High levels of pancreatic ribonucleases are found in ruminants, species that have a ruminant-like digestion and several species with coecal digestion. Pancreatic ribonucleases from several independently evolved species with ruminant-like digestion were investigated to test a hypothesis that glycosylation of ribonucleases may have some function in species with coecal digestion and that glycosylation of the enzyme may not be advantageous for ruminants. Ribonucleases from the hippopotamus, two-toed sloth and three-toed sloth were isolated by extraction with sulfuric acid and affinity chromatography. Complete amino acid sequences were determined for the ribonucleases from the hippopotamus and two-toed sloth and a partial sequence for the enzyme from the three-toed sloth. The amino acids 75-78 of hippopotamus ribonuclease were positioned by homology with other artiodactyl ribonucleases. In hippopotamus ribonuclease a heterogeneity was found at position 37, half of the molecules containing glutamine acid the other half lysine. Hippopotamus ribonuclease differs less from pig and bovine ribonuclease than these differ from each other, because more ancestral characteristics have been retained. Although hippopotamus ribonuclease contains all four Asn-X-Ser/Thr sequences previously found to be glycosylation sites in one or more pancreatic ribonucleases, only the sequence Ans-Met-Thr (34-36) is glycosylated in the variant with glutamine at position 37, while the variant with lysine at this position is carbohydrate-free. Both sloth ribonucleases are completely glycosylated at the sequence Ans-Met-Thr (34-36) with a simple type of carbohydrate chain. The amino acid sequence of two-toed sloth ribonuclease shows some interesting coupled replacements.

Use of polynucleotide/polyacrylamide-gel electrophoresis as a sensitive technique for the detection and comparison of ribonuclease activities

A technique is described in which the incorporation of a polynucleotide substrate into the matrix of a polyacrylamide gel allows the use of electrophoresis for the detection of polycationic ribonuclease activity rather than simply the presence of protein. Because use is made of the catalytic properties of ribonucleases, polynucleotide/polyacrylamide-gel electrophoresis is apparoximately 10(5) times more sensitive for the detection of these enzymes than conventional gel electrophoresis with the use of protein-staining dyes. Initial studies showed that the poor migration, in the gels, of highly charged polycationic ribonucleases in the presence of negatively charged synthetic polynucleotides could be overcome by high concentrations of spermine. The positively charged polyamine, by neutralizing the polyanionic polynucleotide, enabled these basic enzymes to migrate considerable distances in the gel. Electrophoresis of the RNAases under conditions of low pH, and incubation of the gel at neutral pH followed by staining for polynucleotide, resulted in coloured gels containing clear bands that define regions of enzyme activity. Alterations in spermine concentration or substrate identity caused changes in the positions of these bands, suggesting a dynamic interaction among the enzyme, polyamine and polynucleotide. Because of the advantages, in terms of selectivity and sensitivity of polynucleotide/polyacrylamide-gel electrophoresis, this technique was used to demonstrate the nuclease homogenity of three purified bovine muscle enzymes, and to compare these enzymes with each other, as well as with bovine pancreatic ribonuclease A.

The amino-acid sequence of kangaroo pancreatic ribonuclease

Red kangaroo (Macropus rufus) ribonuclease was isolated from pancreatic tissue by affinity chromatography. The amino acid sequence was determined by automatic sequencing of overlapping large fragments and by analysis of shorter peptides obtained by digestion with a number of proteolytic enzymes. The polypeptide chain consists of 122 amino acid residues. Compared to other ribonucleases, the N-terminal residue and residue 114 are deleted. In other pancreatic ribonucleases position 114 is occupied by a cis proline residue in an external loop at the surface of the molecule. Other remarkable substitutions are the presence of a tyrosine residue at position 123 instead of a serine which forms a hydrogen bond with the pyrimidine ring of a nucleotide substrate, and a number of hydrophobichydrophilic interchanges in the sequence 51-55, which forms part of an alpha-helix in bovine ribonuclease and exhibits few substitutions in the placental mammals. Kangaroo ribonuclease contains no carbohydrate, although the enzyme possesses a recognition site for carbohydrate attachment in the sequence Asn-Val-Thr (62-64). The enzyme differs at about 35-40% of the positions from all other mammalian pancreatic ribonucleases sequenced to date, which is in agreement with the early divergence between the marsupials and the placental mammals. From fragmentary data a tentative sequence of red-necked wallaby (Macropus rufogriseus) pancreatic ribonuclease has been derived. Eight differences with the kangaroo sequence were found.

Guinea-pig pancreatic ribonucleases. Isolation, properties, primary structure and glycosidation

Two ribonucleases were isolated from guinea-pig pancreas by extraction with 0.125 M sulfuric acid, precipitation with acetone and chromatography on carboxymethyl-cellulose. The amino acid sequences were determined from tryptic digests of the aminoethylated proteins. The tryptic peptides were positioned in the sequence by homology with other pancreatic ribonucleases. Both ribonucleases not only differ in the presence (ribonuclease B) or absence of carbohydrate (ribonuclease A), but also at 31 positions of the amino acid sequence. In guinea-pig ribonuclease B a leucine/proline heterogeneity was found at position 64. The carbohydrate in guinea-pig ribonuclease B is attached to asparagine residues at positions 21 and 34. The carbohydrate-free guinea-pig ribonuclease A possesses a recognition site for sugar attachment in the sequence Asn-Val-Ser (62-64).

Isolation, properties and primary structure of coypu and chinchilla pancreatic ribonuclease

Pancreatic ribonucleases from the hystricomorph rodent species: coypu and chinchilla were isolated using chromatography on carboxymethyl-cellulose. The amino acid sequences were determined from tryptic digests of the aminoethylated proteins. The tryptic peptides were positioned in the sequence by homology with other pancreatic ribonucleases. Coypu pancreas contains one carbohydrate-containing ribonuclease component. From chinchilla pancreas two carbohydrate-containing ribonuclease components were obtained; one homogeneous and the other heterogeneous. The latter differs from the first in being more acidic; it exhibits heterogeneity both in its carbohydrate moiety (glycopeptides both with and without sialic acid were isolated) and in amino acid sequence (probably glycine at position 32 has been partially substituted by aspartic acid). In both ribonucleases the carbohydrate is attached to asparagine 34. Earlier results on the titration behaviour of histidine residues in both proteins obtained by nuclear magnetic resonance spectroscopy are discussed. An ion bridge between the invariant glutamic acid 49 and histidine 80 may explain the high pK value of the latter.

Allelic polymorphism in arabian camel ribonuclease and the amino acid sequence of bactrian camel ribonuclease

Pancreatic ribonucleases from several species (whitetail deer, roe deer, guinea pig, and arabian camel) exhibit more than one amino acid at particular positions in their amino acid sequences. Since these enzymes were isolated from pooled pancreas, the origin of this heterogeneity is not clear. The pancreatic ribonucleases from 11 individual arabian camels (Camelus dromedarius) have been investigated with respect to the lysine-glutamine heterogeneity at position 103 (Welling et al., 1975). Six ribonucleases showed only one basic band and five showed two bands after polyacrylamide gel electrophoresis, suggesting a gene frequency of about 0.75 for the Lys gene and about 0.25 for the Gln gene. The amino acid sequence of bactrian camel (Camelus bactrianus) ribonuclease isolated from individual pancreatic tissue was determined and compared with that of arabian camel ribonuclease. The only difference was observed at position 103. In the ribonucleases from two unrelated bactrian camels, only glutamine was observed at that position.

Differential activity staining: its use in characterization of guanylyl-specific ribonuclease in the genus Ustilago

Guanylyl-specific ribonuclease can be identified by a novel technique employing electrophoresis in polyacrylamide slabs followed by differential activity staining. The technique requires as little as 7 ng of enzyme which may be grossly admixed with contaminants, including other ribonucleases. Upon electrophoresis and activity staining, a variety of ribonucleases can be visualized as light or clear bands in a colored background formed by toluidine blue complexed with oligonucleotide substrate. Guanylyl-specific ribonuclease, which is detectable when using an oligonucleotide substrate of random base sequence, does not yield a band when using oligonucleotides bearing guanylyl residues at the 3'-termini only and containing, therefore, no susceptible internucleotide bonds; in contrast, a ribonuclease with a different base specificity or no base specificity yields a band with either substrate. This differential activity staining method for establishing guanylyl specificity permits estimation of the extent of nonspecific cleavage of internucleotide linkages by a putatively guanylyl-specific enzyme and is at least as sensitive as conventional procedures for determination of base specificity. With this new technique guanyloribonuclease has been identified in the unfractionated culture medium of 10 organisms belonging to the phytopathogenic fungal genus Ustilago. It is suggested that guanylyl-specific ribonuclease is widely distributed among Ustilago species; its electrophoretic properties may be revealing of phylogenetic relationships among these plant parasites and among their hosts. The general technique of differential activity staining, developed for determination of the base specificity of ribonucleases, may be widely applicable to analysis of enzymes catalyzing depolymerization reactions.

The amino acid sequence of dromedary pancreatic ribonuclease

Dromedary (Camelus dromedarius) RNAase (ribonuclease) was isolated from pancreatic tissue by affinity chromatography. Peptides obtained by digestion with different proteolytic enzymes and CNBr were isolated by gel filtration, preparative high-voltage paper electrophoresis and paper chromatography. Peptides were sequenced by the dansyl-Edman method. All peptide bonds were overlapped by one or more peptides. The polypeptide chain consists of 123 amino acids. A deletion (position 39) was observed in an external loop of the polypeptide chain (residues 35-40), as was found earlier to horse RNAase (Scheffer & Beintema, 1974). A heterogeneity was found at position 103 (glutamine and lysine). Dromedary RNAase differs at 23-32% of the positions from all other pancreatic RNAases sequenced to date. In evolutionary terms this indicates that dromedary RNAase has evolved independently during the larger part of the evolution of the mammals. Detailed evidence for the sequence has been deposited as Supplementary Publication SUP 50046 (14 pages) at the British Library (Lending Division), Boston Spa, Wetherby, W. Yorks. LS23 7BQ, U.K., from whom copies may be obtained on the terms given in Biochem. J. (1975) 145, 5.

Spermidine requirement for Bacillus thuringiensis ribosomes in cell-free phenylalanine incorporation

A cell-free system from Bacillus thuringiensis was found to actively incorporate phenylalanine into hot trichloroacetic acid-precipitable material in the presence of synthetic polynucleotide, ribosomes, S-100 supernatant, an energy-generating system, and guanosine triphosphate. Phenylalanine incorporation was absolutely dependent on the presence of spermidine in addition to magnesium ions, even when highly purified ribosomes were used. The spermidine effect could not be attributed to inhibition of nucleases. The ribosomal and supernatant fractions from Escherichia coli and B. thuringiensis could be substituted for each other in this system. The spermidine requirement was shown to be limited to the B. thuringiensis ribosome fraction.