RNA editing, introns and evolution

Caries activity tests are an essential part of any programme concerned with the study or treatment of dental caries. Most of the caries activity tests require expensive kits or specially prepared media or facilities for incubation which limits their use in clinical practice. The present study sample consisted of twenty five children with dental caries and twenty five controls, free of caries, gingivitis and other oral ailments. The test is simple and consists of rinsing the mouth with 10 ml of sterile milk, 3 ml of which is mixed with 0.12 ml of 0.1% methylene blue dye and observed for colour change. The present study demonstrated the potential uses of this test in a pediatric dental clinic setup.     

Lactone-ring-cleaving enzyme: genetic analysis, novel RNA editing, and evolutionary implications

A lactonohydrolase from Fusarium oxysporum AKU 3702 is an enzyme catalyzing the hydrolysis of aldonate lactones to the corresponding aldonic acids. The amino acid sequences of the NH2 terminus and internal peptide fragments of the enzyme were determined to prepare synthetic oligonucleotides as primers for the PCR. An approximate 1, 000-base genomic DNA fragment thus amplified was used as the probe to clone both genomic DNA and cDNA for the enzyme. The lactonohydrolase genomic gene consists of six exons separated by five short introns. A novel type of RNA editing, in which lactonohydrolase mRNA included the insertion of guanosine and cytidine residues, was observed. The predicted amino acid sequence of the cloned lactonohydrolase cDNA showed significant similarity to those of the gluconolactonase from Zymomonas mobilis, and paraoxonases from human and rabbit, forming a unique superfamily consisting of C-O cleaving enzymes and P-O cleaving enzymes. Lactonohydrolase was expressed under the control of the lac promoter in Escherichia coli.     

Guide RNA-directed uridine insertion RNA editing in vitro

Guide RNAs (gRNAs) have been proposed to mediate uridine (U) addition/deletion editing of mitochondrial mRNAs in kinetoplastid protozoa. The Us are proposed to be derived either from UTP by two successive cleavage-ligations or transesterifications, or from the 3' end of the gRNA by the same mechanisms. We have demonstrated gRNA-dependent U insertions into a specific editing site of a pre-edited mRNA which was incubated in a mitochondrial extract from Leishmania tarentolae. The predominant number of U insertions was determined by the number of guiding nucleotides in the added gRNA, and the formation of a gRNA-mRNA anchor duplex was necessary for activity. UTP and alpha-beta bond hydrolysis of ATP were required, and the activity was inhibited above 50-100 mM KCl. A gRNA-independent insertion of up to approximately 13 Us occurred in the absence of the added cognate gRNA; the extent of this activity was affected by sequences upstream and downstream of the edited region. Heparin inhibited the gRNA-independent U insertion activity and had no effect on the gRNA-dependent activity. Blocking the 3' OH of the gRNA had little effect on the gRNA-dependent U insertion activity. The data are consistent with a cleavage-ligation model in which the Us are derived directly from UTP.     

Assays for investigating RNA editing in plant mitochondria

Dendritic cells (DCs) pulsed with unfractionated tumor cell lysates or defined tumor peptides provide potent vaccines which elicit strong antitumor immunity. In this study, we generated DCs from the 2-h adherent progenitor cells obtained from the peripheral blood of melanoma patients. These DCs were able to capture biotinylated melanoma tumor cell lysates. We examined the efficacy of immunogens composed of DCs loaded either with the melanoma peptide gp100 [amino acids 280-288 (DC/gp100)] or with lysates from melanoma tumor cells (DC/lysates) in inducing cytotoxic T-cells from autologous PBLs of HLA-A2 melanoma patients. After four to five weekly stimulations of bulk PBLs with DC/gp100 or DC/lysates, the cultures were enriched with CD3+ T-cells and exhibited one of three phenotypic and functional patterns: (1) Predominant expression of CD8+ and MHC class I-restricted CTLs which displayed strong lytic activity against melanoma cells and T2 cells loaded with the gp100 peptide, (2) mixed CD4+/CD8+ phenotype and weak lytic activity, or (3) nonlytic and predominantly CD4+ cultures. Interestingly, T-cell cultures from each patient exhibited similar phenotypes and lytic activities whether the stimulant was DC/gp100 or DC/cell lysates. Our study demonstrates that DCs pulsed with soluble melanoma peptides or cell lysates are capable of inducing CD8+ CTLs from autologous PBLs of some, but not all, melanoma patients. The function and phenotype of the generated T-cell cultures are governed by DCs since both antigens (the gp100 peptide and melanoma lysates), when presented by a given DC preparation, induced similar T-cell cultures. In summary, it may be difficult to predict the nature of the cellular responses elicited by DC/tumor antigen vaccines from patient to patient.     

RNA enzymes with two small-molecule substrates

BACKGROUND: The 'RNA world' hypothesis posits ancient organisms employing versatile catalysis by RNAs. In particular, such a metabolism would have required RNA catalysts that join small molecules. Such anabolic reactions now occur very widely, for example in phospholipid, terpene, amino acid and nucleotide synthetic pathways in modern organisms. Present RNA systems, however, do not perform such reactions using substrates that do not base pair. Here we ask whether this lack is a methodological artifact due to the practice of selection-amplification, or a fundamental property of active sites reconstructed within RNA structures. RESULTS: Three rationally modified RNA enzymes, Iso6-G, Iso6-2G and Iso63G, catalyze the formation of (5'-->5') polyphosphate-linked oligonucleotides in trans. One of these, Iso6-G RNA, has a specific substrate site for a guanosine triphosphate, GTP, dGTP or ddGTP, and one nonspecific substrate site for a terminal-phosphate-containing small molecule. This ribozyme catalyzes multiple turnovers, proceeding at a constant rate. Guanosine specificity is probably not attributable to Watson-Crick base pairing. CONCLUSIONS: Ribozymes can readily bind multiple small-molecule substrates simultaneously and catalyze reactions that build up larger products, apparently independent of substrate-RNA Watson-Crick base pairing. RNA enzymes therefore parallel proteins, which often overcome the entropic difficulties of positioning multiple small substrates for catalysis of anabolic reactions. These results support the idea of a complex ancestral metabolism based on RNA catalysis.     

Accurate and efficient insertional RNA editing in isolated Physarum mitochondria

RNA editing is a process whereby nucleotide insertion, deletion, or base substitution results in the production of an RNA whose sequence differs from that of its template. The mitochondrial RNAs of Physarum polycephalum are processed specifically at multiple sites by both mono- and dinucleotide insertions, as well as apparent cytidine (C) to uridine (U) changes. The precise mechanism and timing of these processing events are currently unknown. We describe here the development of an isolated mitochondrial system in which exogenously supplied nucleotides can be incorporated into RNAs under defined conditions. The results of S1 nuclease protection, nearest neighbor and RNase T1 fingerprint analyses indicate that the vast majority of these newly synthesized mitochondrial RNAs have been accurately and efficiently processed by both mono- and dinucleotide insertions. This work provides a direct demonstration of faithful nucleotide insertion in a mitochondrial editing system. In contrast, the newly synthesized RNAs are not processed by C to U changes in the isolated mitochondria, suggesting that the base changes observed in Physarum are unlikely to occur via a deletion/insertion mechanism.     

RNA editing of a chimeric maize mitochondrial gene transcript is sequence specific

Fentanyl and its derivatives are considered among the most potent opiate analgesic/euphoriants. The pharmacological literature generally supports a mu opiate receptor site of action for the fentanyl derivatives, but some observations suggest that other sites of action may be involved in producing the extremely potent fentanyl effects. In order to investigate the mechanism of action of fentanyl-like drugs further, [3H]carfentanil was used as a radioligand to image high-affinity carfentanil binding sites in slidemounted sections of the rat brain (receptor autoradiography). In parallel studies the prototypical mu opiate agonist radioligand [3H]DAMGO ([D-Ala2-MePhe4-Gly-ol5]enkephalin) was also used. The working hypothesis was that if carfentanil was acting through another high-affinity site besides the mu opiate receptor, the distribution pattern of the autoradiographic image produced by [3H]carfentanil should be significantly different than the autoradiographic pattern displayed by the well-characterized and selective mu opiate [3H]DAMGO. Thirty-five brain regions were examined for specific [3H]carfentanil and [3H]DAMGO binding. The absolute and relative densities of the sites were essentially identical. The highest levels of binding were observed in the "patch" areas of the striatum (131 +/- 5 fmol/mg T.E. for [3H]carfentanil; 162 +/- 13 fmol/mg T.E. for [3H]DAMGO). The lowest levels were observed in the cerebellum where no specific binding of either radioligand was observed. The overall distribution pattern of the two radioligands produced a correlation coefficient of 0.95; the distribution pattern was prototypical for the mu opiate receptor as reported previously by other groups.(ABSTRACT TRUNCATED AT 250 WORDS)     

Enzymatic RNA synthesis and RNase P. Evolutionary aspects

TransferRNA recognition was used as leit-motiv in the illustration of possible links between a hypothetical primordial RNA world and the contemporary DNA world. In an RNA world, 'proto-tRNA' could have functioned as replication origin and as primitive telomere. Possibly, this primitive structure is preserved in a 'universal substrate' for modern tRNA-specific enzymes. The combination of acceptor stem and T arm (plus a linker) was finally revealed as sufficient for the recognition by prokaryotic and eukaryotic RNase P, as well as other tRNA enzymes. In modern life forms, a tRNA-like element in viral RNAs still serves as replication origin, and furthermore, the recognition of similar structures as cryptic promoters is universally conserved for template-dependent RNA polymerases. Another common property of modern polymerases is their high, but clearly limited and condition-dependent substrate specificity. Very likely, also substrate recognition by primitive polymerases was not more stringent, and this lead to the occurrence of mixed nucleic acids as intermediates in the transition of genomic RNA to contemporary genomic DNA.     

Direct visualization of uridylate deletion in vitro suggests a mechanism for kinetoplastid RNA editing

Deletion of uridylates from the 3'-most editing site of synthetic ATPase 6 pre-mRNA can be visualized directly by coincubation of a radiolabeled substrate RNA and a synthetic gRNA in 20S fractions of T.brucie mitochondrial lysates. Substrate RNA cleavage is gRNA directed and occurs 3' to the uridylates to be deleted. U residues appear to be sequentially removed from the 3' end of the 5' cleavage product prior to religation of the two pre-mRNA halves. gRNA/mRNA chimeric molecules are also produced. Time course experiments indicate that chimeras appear after cleavage intermediates and edited product. Furthermore, a mutant gRNA promotes formation of edited product but not detectable chimeras. Our results suggest a model for kinetoplastid RNA editing in which chimeric molecules are nonproductive end products of editing and not intermediates that serve as a repository for deleted U's.     

RNA editing of the barley (Hordeum vulgare) mitochondrial ATP synthase subunit 9

1. Single Comb White Leghorn adult cockerels were fed on 50 g/kg protein diet, 200 g/kg protein diet or 50 g/kg protein diet plus urea and in vitro ammoniagenesis from urea and uric acid in the caeca was determined. 2. Four-fold protein intake caused about 4.6-fold increase in caecal ammonia production from urea (P < 0.05), and tended to increase it from uric acid as compared with 50 g/kg protein-fed birds. 3. Dietary urea significantly increased caecal ammonia production from urea and uric acid by about 2 and 3 times as much as those of control birds, respectively (P < 0.05). 4. It is concluded that increased protein intake and the feeding of urea are able to induce ammoniagenesis from urea and uric acid in the caeca of fowls.