The purification and properties of chicken liver RNase: An enzyme which is useful in distinguishing between cytidylic and uridylic acid residues

Chemical and Enzymatic Probing of Viral RNAs: From Infancy to Maturity and Beyond

RNA molecules are key players in a variety of biological events, and this is particularly true for viral RNAs. To better understand the replication of those pathogens and try to block them, special attention has been paid to the structure of their RNAs. Methods to probe RNA structures have been developed since the 1960s; even if they have evolved over the years, they are still in use today and provide useful information on the folding of RNA molecules, including viral RNAs. The aim of this review is to offer a historical perspective on the structural probing methods used to decipher RNA structures before the development of the selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) methodology and to show how they have influenced the current probing techniques. Actually, these technological breakthroughs, which involved advanced detection methods, were made possible thanks to the development of next-generation sequencing (NGS) but also to the previous works accumulated in the field of structural RNA biology. Finally, we will also discuss how high-throughput SHAPE (hSHAPE) paved the way for the development of sophisticated RNA structural techniques.

Isolation of a new ribonuclease from fresh fruiting bodies of the straw mushroom

Although ribonucleases have been isolated from numerous organisms in the animal and plant kingdoms, only a few have been reported from mushrooms. In this investigation, a novel ribonuclease, with an N-terminal amino acid sequence distinctly different from those of the previously published mushroom ribonucleases, was isolated from the fruiting bodies of the straw mushroom. It exhibited a molecular weight of 42.5 kDa in sodium dodecyl sulfate-polyacrylamide gel electrophoresis which was larger than those of ribonucleases from other organisms. The isolation procedure entailed extraction with aqueous buffer, (NH(4))(2)SO(4) precipitation, ion exchange chromatography on DEAE-cellulose, affinity chromatography on Affi-gel blue gel, ion exchange chromatography on CM-Sepharose CL6B, and gel filtration on Superdex 75 using fast protein liquid chromatography. Straw mushroom ribonuclease was relatively specific for polyU and hydrolyzed yeast tRNA with a pH optimum between 6.5 and 7.5.

Structure-function relationships of acid ribonucleases: lysosomal, vacuolar, and periplasmic enzymes

It is surprising that only relatively recently has attention been directed to the characterization of the properties of acid ribonucleases (RNases), leading to some understanding of their biochemistry and their functional roles. The present review summarizes current progress in this field under the following general topics: (1) the wide distribution of acid RNases in organisms from viruses to animals; (2) recent findings concerning their primary and three-dimensional structure; (3) the structure-function relationship of acid RNases, with a fungal RNase from Rhizopus niveus as a model enzyme; (4) the unique localization of acid RNases in the periplasm of bacteria, vacuoles in plants, and lysosomes of animals and protozoa; and (5) the diversity of physiological roles, depending on the organism, such as self-incompatibility factors and defense proteins in some plants, the surface protein of an animal virus related to pathogenicity, and possible relationship to human cancer.

Yolk granules are the major compartment for bullfrog (Rana catesbeiana) oocyte-specific ribonuclease

Rana catesbeiana ribonuclease (RC-RNase) is a pyrimidine guanine sequence-specific ribonuclease found only in R. catesbeiana (bullfrog) oocytes, not in other organs. An immunohistochemical assay showed that RC-RNase was present in the regular yolk granules, but not in forming yolk granules, yolk platelets, pigment granules, mitochondria clouds or the nucleus. The RC-RNase was restricted to the lateral amorphous area of the yolk granules, and was absent from the central area that has a vitellogenin crystal lattice. The RC-RNase was extracted from yolk granules by 0.5 M NaCl and purified by dialysis and affinity chromatography. Most of the RC-RNase (94%) was found in the yolk granules, the rest RC-RNase (6%) was found in the cytosol in the form of free RNase and latent RNase. The RC-RNase extracted from yolk granules was further analyzed by immunoprecipitation and RNase activity assay on an SDS/polyacrylamide gel. Our results suggest that the RC-RNase activity is regulated by both compartmentation and inhibitor binding.

Cusativin, a new cytidine-specific ribonuclease accumulated in seeds of Cucumis sativus L

Dry seeds of Cucumis sativus L. were found to contain a heat-sensitive endoribonuclease of a novel type which we have named cusativin. It was purified to apparent electrophoretic homogeneity by chromatography through S-Sepharose Fast Flow, Sephadex G-75, CM-Sepharose, Superdex 75-FPLC (fast protein liquid chromatography) and Mono S-FPLC. It is a single unglycosylated polypeptide chain with an apparent molecular mass (M(r)) of 22900. Polyclonal anti-cusativin antibodies raised in rabbits only reacted with melonin, the translation inhibitor from Cucumis melo L. Functional, Western blot and enzyme-linked immunosorbent assay (ELISA) analyses indicated that cusativin is present in the coat and cotyledons of dry seeds, but not in embryonic axes. Cusativin is accumulated in maturing seeds. By contrast, after seed germination there is degradation of the cusativin present in cotyledons but not that present in the seed coat. The preference of cusativin for polynucleotide cleavage was poly(C) >> poly(A) acids, poly(U) and poly(G) being unaffected by cusativin. Under the denaturing conditions used for RNA sequencing, cusativin acted only on poly(C). Cusativin proved to be useful for RNA sequencing, in particular, complementing the data obtained with RNase CL3. Cusativin represents a new class of plant RNase and, as far as we are aware, is the first plant enzyme that shows cleavage specificity for cytidine under the denaturing conditions of RNA sequencing.

Identification of an intracellular pyrimidine-specific endoribonuclease from Bacillus subtilis

Two intracellular RNases which were easily separated by fractionation on strong anion- or cation-exchange resins were identified from Bacillus subtilis. One cleaved any phosphodiester bond, while the second cleaved only pyrimidine-N bonds. The enzyme with pyrimidine-N specificity was approximately 15 kDa, had a pH optimum of approximately 6.2, degraded C-C bonds approximately 10 times faster than U-U bonds, and was completely inactive against single-stranded DNA. The enzyme is called RNase C and may be the first reported broad-specificity endoribonuclease from B. subtilis.

Porcine thyroid cytosolic, latent alkaline ribonuclease: resistance to protein denaturants

1. A ribonuclease isolated from porcine thyroid cytosol using phenol: sodium dodecylsulfate treatment was associated with RNA and identical to latent alkaline ribonuclease. 2. Distribution of activity between aqueous and phenolic phases depended on pH, RNA, and ribonuclease inhibitor. 3. The ribonuclease was totally resistant to urea, guanidinium: HCl, chloroform:isoamyl alcohol, ethanol, heating at 100 degrees C for 10 min or at 80 degrees C plus 100 mM NaCl. It was highly resistant to hydrolysis by proteinase K except in the presence of detergent. 4. The extreme stability and other properties of latent alkaline ribonuclease could be the result of its association with RNA.

Purification and characterization of two ribonucleases from developing tomato fruit

Two neutral ribonucleases have been purified from developing tomato fruit. Their activity is maximal 5 days after anthesis, declines during maturation, and then increases slightly in the mature green through breaker stages. The ribonucleases Tf1 and Tf2 have molecular weights of 59 and 29 K, respectively, based on sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and are glycoproteins. The reduced and denatured Tf1 is composed of two subunits, 30 and 29 K, of which only the 30-K subunit displays ribonuclease activity after renaturation. Reduced and denatured Tf2 is a single 29-K polypeptide that is renaturable to an active ribonuclease. Only the 30-K, active subunit of Tf1 is immunologically cross-reactive with Tf2. Both ribonucleases are cyclyzing endoribonucleases with a strong preference for cleavage at pyrimidine residues, thus generating oligonucleotide products ending with pyrimidine 2',3'-cyclic phosphate. These tomato fruit ribonucleases share a number of properties in common with the S-glycoprotein ribonucleases that are involved in self-incompatibility reactions in some solanaceous plants.

Double-stranded ribonuclease coinduced with interferon

Double-stranded (ds) RNA and many viruses are inducers of interferon (IFN), the latter presumably because they contain, or can form, dsRNA. Concomitant with the induction of IFN in chicken embryo cells was the induction of a novel double-stranded ribonuclease (dsRNase), which was released into the medium and continued to accumulate long after IFN production ceased. Only avian cells (chicken, quail, turkey, or duck) expressed high levels of this dsRNase; mammalian, turtle, or fish cells did not. Production of the nuclease was inducer dose-dependent. Optimum pH and cation requirements distinguished it from other dsRNase activities. Degradation of dsRNA was endonucleolytic. Activity resided in a molecule of an Mr of approximately 34,500. Low levels of a single-stranded (ss) RNase activity were inseparable from the dsRNase. The role for a dsRNA-inducible dsRNase released from cells is unknown.

Discontinuous transcription or RNA processing of vaccinia virus late messengers results in a 5' poly(A) leader

We have demonstrated by primer elongation and cap analysis that mature vaccinia virus late transcripts are discontinuously synthesized. We have shown that RNA transcripts from a translocated 11K and from the authentic 11K and 4b late promoters are extended by approximately 35 nucleotides beyond the "start site" determined by S1 mapping using vaccinia genomic DNA as a probe. Sequencing of the RNA and of the first strand cDNA reveal that a homopolymeric poly(A) sequence is linked to the 5' terminus of the RNA transcripts. S1 mapping of RNA transcripts with a DNA probe containing an A-stretch, replacing promoter sequences upstream of position -1, confirms the existence of a poly(A) leader of approximately 35 A-residues.

A new ribonuclease from cobra venom (Naja naja) showing specificity towards cytidylic acid

A ribonuclease was isolated and purified to homogeneity from cobra venom. The enzyme was found to be homogeneous on SDS and non-SDS polyacrylamide gel electrophoreses, and high performance liquid chromatography. The purified enzyme hydrolysed poly(rC), but not poly(rA), poly(rU), poly(rG), poly(rI), or poly(rI).poly(rC). The presence of magnesium was found to be an essential requirement for the nucleolytic activity of this enzyme.

Purification of a uridine-specific acid nuclease from chicken liver by fast protein liquid chromatography

A rapid purification procedure for a novel uridine-specific nuclease from chicken liver based on the Pharmacia fast protein liquid chromatography (FPLC) system is presented. The purification was achieved by applying crude extract to a Mono S cation-exchange column equilibrated with 10 mM potassium phosphate buffer (pH 6.0). The enzyme was eluted in 20 min with a potassium chloride gradient at a flow-rate of 2 ml/min. The enzyme was then chromatographed on a Superose 12 size-exclusion column in less than 1 h at a flow-rate of 0.5 ml/min (Kav = 0.77). The enzyme was re-chromatographed on a second Mono S column to concentrate the protein. The uridine-specific nuclease hydrolyzed poly(U) and Escherichia coli 5S RNA. Poly(A) was hydrolyzed by the nuclease less efficiently (about 10% of the poly(U) activity). No hydrolysis was detected with poly(C), poly(G), poly(dT) or poly(dA) as substrate. The speed with which each purification step could be carried out facilitated the determination of optimal chromatographic conditions. We found that the resolution of the Mono S and Superose 12 columns was superior to that of conventional ion exchangers and size-exclusion columns respectively.

Reverse transcription of 7S L RNA by an avian retrovirus

Linial et al. isolated a quail cell line, SE21Q1b, that is transformed by a single integrated provirus of Rous sarcoma virus. Virus particles are released from these cells, but because of a provirus defect, cellular rather than viral RNA is packaged. When these virus particles are disrupted with melittin in the presence of an appropriate reaction mixture containing actinomycin D, there is significant reverse transcription of packaged cellular RNA species. We have shown that (i) cellular 7S L RNA is an efficient template; (ii) initiation is on a unique tRNA-like primer; (iii) synthesis produces a 135-base strong-stop DNA product; and (iv) after synthesis, RNase H acts to remove the 135 bases of the 7S L RNA which acted as the template. A possible facilitator of such specific transcription may be that, in the virus particles but not in the cell, the majority of the 7S L RNA species exist complexed with the tRNA, even before the disruption of the virus. From the size and sequence features of the reverse transcript of 7S L RNA, we speculate that such events may have participated in the process by which animal cell genomes have, in the course of evolution, accumulated multiple copies of Alu-like elements.

Structural comparison of human, bovine, rat, and Walker 256 carcinosarcoma asparaginyl-tRNA

The complete nucleotide sequences of human placenta, human liver, and bovine liver tRNAAsn have been determined. A comparison of these tRNA structures with the previously reported nucleotide sequences of rat liver and Walker 256 carcinosarcoma tRNAAns reveals that the primary nucleotide sequences of the major species of mammalian cytoplasmic tRNAasn are conserved in higher eucaryotes. The complete nucleotide sequence of these tRNAs is: pG-U-C-U-C-U-G-U-m1G-m2G-C-G-C-A-A-D-C-G-G-D-X-A-G-C-G-C-m2(2)G-psi-psi-C-G-G-C-U-Q(G)-U-U-t6A-A-C-C-G-A-A-A-G-m7G-D-U-G-G-U-G-G-Z-psi-C-G-m1A-G-C-C-C-A-C-C-C-A-G-G-G-A-C-G-C-C-AOH where X is 3-(3-amino-3-carboxyl-n-propyl)uridine, Q is 7-(4,5-cis-dihydroxyl-1-cyclopenten-3-yl-aminomethyl)-7-deazaguanosine, Z is an unknown modified nucleotide, and Q(G) represents the replacement of Q nucleoside by G nucleoside in Walker 256 carcinosarcoma tRNAAsn. These primary structures were determined by combined use of the 3H- and 32P-post-labeling techniques. Sequences were compared by tritium nucleoside trialcohol analysis, completed RNAase T1 digestion followed by 3H-labeled fingerprinting on polyethylenimine-impregnated cellulose by two-dimensional thin-layer chromatography (TLC), and polyacrylamide gel electrophoresis of either 5'-32P- and/or 3'-[32P]pCp-labeled tRNA after partial ribonuclease digestions.