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PubMed2005

Paramyxovirus mRNA editing, the "rule of six" and error catastrophe: a hypothesis.

The order Mononegavirales includes three virus families that replicate in the cytoplasm: the Paramyxoviridae, composed of two subfamilies, the Paramyxovirinae and Pneumovirinae, the Rhabdoviridae and the Filoviridae. These viruses, also called non-segmented negative-strand RNA viruses (NNV), contain five to ten tandemly linked genes, which are separated by conserved junctional sequences that act as mRNA start and poly(A)/stop sites. For the NNV, downstream mRNA synthesis depends on termination of the upstream mRNA, and all NNV RNA-dependent RNA polymerases reiteratively copy ("stutter" on) a short run of template uridylates during transcription to polyadenylate and terminate their mRNAs. The RNA-dependent RNA polymerase of a subset of the NNV, all members of the Paramyxovirinae, also stutter in a very controlled fashion to edit their phosphoprotein gene mRNA, and Ebola virus, a filovirus, carries out a related process on its glycoprotein mRNA. Remarkably, all viruses that edit their phosphoprotein mRNA are also governed by the "rule of six", i.e. their genomes must be of polyhexameric length (6n+0) to replicate efficiently. Why these two seemingly unrelated processes are so tightly linked in the Paramyxovirinae has been an enigma. This paper will review what is presently known about these two processes that are unique to viruses of this subfamily, and will discuss whether this enigmatic linkage could be due to the phenomenon of RNA virus error catastrophe.

Base Sequence↗
PubMed1993

Dolphin and porpoise morbilliviruses are genetically distinct from phocine distemper virus.

The morbilliviruses recently isolated from two cetacean species in the North and Mediterranean Seas have been shown to differ from phocine distemper virus isolated from European seals using monoclonal antibodies. We have identified a "universal" morbillivirus primer set, based on highly conserved regions of the morbillivirus phosphoprotein (P) gene and used this to amplify a region surrounding the RNA editing site from all known members of the group. Sequence analysis of this region of the gene shows that the dolphin and porpoise viruses are related but quite different from all other members of the group, forming a distinct lineage more closely related to the ruminant morbilliviruses than to the carnivore viruses.

Animals↗
PubMed1993

Editing of the chloroplast rpoB transcript is independent of chloroplast translation and shows different patterns in barley and maize.

Sequence analysis of amplified cDNAs derived from the maize chloroplast rpoB transcript which encodes the beta subunit of a chloroplast specific, DNA dependent RNA polymerase reveals four C-to-U editing sites clustered within 150 nucleotides of the 5' terminal region of the rpoB message. These newly identified editing sites confirm the bias of chloroplast editing for certain codon transitions and for second codon positions which both appear suggestive for an involvement of the translational apparatus in the editing process. This supposition prompted us to investigate editing of the rpoB transcript from ribosome deficient, and hence protein synthesis deficient, plastids of the barley mutant albostrians. In this mutant editing is, however, not impaired at any of the editing sites functional in the barley wild type rpoB transcript. This demonstrates that chloroplast editing is neither linked to nor dependent on the chloroplast translational apparatus. As a further consequence any peptide components required for chloroplast editing must be encoded in the nuclear genome. In spite of strong sequence conservation only three of the four editing sites identified in the maize rpoB transcript are functional in barley. This indicates that sequences surrounding an editing site alone are not sufficient as determinants for the editing process in chloroplasts, but that trans-acting templates carrying the editing information for each individual site may also be required.

Amino Acid Sequence↗
PubMed1999

Editing of cytochrome b mRNA in physarum mitochondria.

The reading frame in the mRNA for the cytochrome b apoprotein in mitochondria of Physarum polycephalum is created by the insertion of 43 nucleotides in the mRNA relative to the mtDNA sequence encoding it (RNA editing). Most of these insertions (31) are single cytidines; however, single uridines are inserted at six sites, and the dinucleotides, CU and GC, are inserted at two sites and one site, respectively. These insertions create a 392-codon reading frame in the mature mRNA. The amino acid sequence inferred from this reading frame has similarity to cytochrome b apoproteins encoded by other mtDNAs. The insertions are quite evenly distributed throughout the length of the reading frame with an average spacing of 27 nucleotides. This mRNA has the highest percentage (23%) of noncytidine insertions of any Physarum RNA characterized to date. cDNAs corresponding to partially edited RNAs can be enriched by selective amplification. Some cDNAs that lack the GC dinucleotide insertion are fully edited at sites flanking the GC dinucleotide insertion site. Similarly some cDNAs lack the CT dinucleotide insertion or have a CC or TT insertion flanked by a fully edited sequence. These results imply that dinucleotide editing occurs by a process separate from the global insertion of cytidines.

Amino Acid Sequence↗
PubMed1996

RNA editing in the cox3 mRNA of Magnolia is more extensive than in other dicot or monocot plants.

The Magnoliaceae are discussed as one of the key species at the root of the flowering plants. To obtain molecular information for one of these phylogenetically interesting plant species, we determined genomic and cDNA sequences of the mitochondrial cox3 gene in Magnolia grandiflora. Twenty-two RNA editing events are identified to alter cytidines in the mRNA to uridines, all but one of which change the encoded amino acid identity. RNA editing in the cox3 coding region is thus more frequent in Magnolia than in other dicot or monocot plants investigated and almost as predominant as in some gymnosperms. The cox3 RNA editing frequency in Magnolia thus occupies an intermediate position between angiosperms and gymnosperms consistent with the phylogenetic position of the Magnoliales.

Amino Acid Sequence↗
PubMed2004

Systematic identification of abundant A-to-I editing sites in the human transcriptome.

RNA editing by members of the ADAR (adenosine deaminases acting on RNA) family leads to site-specific conversion of adenosine to inosine (A-to-I) in precursor messenger RNAs. Editing by ADARs is believed to occur in all metazoa, and is essential for mammalian development. Currently, only a limited number of human ADAR substrates are known, whereas indirect evidence suggests a substantial fraction of all pre-mRNAs being affected. Here we describe a computational search for ADAR editing sites in the human transcriptome, using millions of available expressed sequences. We mapped 12,723 A-to-I editing sites in 1,637 different genes, with an estimated accuracy of 95%, raising the number of known editing sites by two orders of magnitude. We experimentally validated our method by verifying the occurrence of editing in 26 novel substrates. A-to-I editing in humans primarily occurs in noncoding regions of the RNA, typically in Alu repeats. Analysis of the large set of editing sites indicates the role of editing in controlling dsRNA stability.

Adenosine↗
PubMed1992

The bacteriophage phi 29 DNA polymerase, a proofreading enzyme.

The bacteriophage phi 29 DNA polymerase, involved both in the protein-primed initiation and elongation steps of the viral DNA replication, displays a very processive 3',5'-exonuclease activity acting preferentially on single-stranded DNA. This exonucleolytic activity showed a marked preference for excision of a mismatched versus a correctly paired 3' terminus. These characteristics enable the phi 29 DNA polymerase to act as a proofreading enzyme. A comparative analysis of the wild-type phi 29 DNA polymerase and a mutant lacking 3',5'-exonuclease activity indicated that a productive coupling between the exonuclease and polymerase activities is necessary to prevent fixation of polymerization errors. Based on these data, the phi 29 DNA polymerase, a model enzyme for protein-primed DNA replication, appears to share the same mechanism for the editing function as that first proposed for T4 DNA polymerase and Escherichia coli DNA polymerase I on the basis of functional and structural studies.

Bacteriophages↗
PubMed2004

Dentocase - open-source education management system in dentistry.

Since 2001, an interdisciplinary project on multimedia education in medicine has been sponsored by the Federal Ministry of Education and Research at the Charité. One part of the project is on dentistry. In the light of the results of a survey of dental students, an Internet-based education management system was created using open-source back-end systems. It supports four didactic levels for editing documentation of patient treatments. Each level corresponds to the learning abilities of the students. The patient documentation is organized to simulate the working methods of a physician or dentist. The system was tested for the first time by students in the summer semester of 2003 and has been used since the winter semester of 2003 as part of the curriculum.

Computer-Assisted Instruction↗
PubMed2005

Modulation of microRNA processing and expression through RNA editing by ADAR deaminases.

Adenosine deaminases acting on RNA (ADARs) are involved in editing of adenosine residues to inosine in double-stranded RNA (dsRNA). Although this editing recodes and alters functions of several mammalian genes, its most common targets are noncoding repeat sequences, indicating the involvement of this editing system in currently unknown functions other than recoding of protein sequences. Here we show that specific adenosine residues of certain microRNA (miRNA) precursors are edited by ADAR1 and ADAR2. Editing of pri-miR-142, the precursor of miRNA-142, expressed in hematopoietic tissues, resulted in suppression of its processing by Drosha. The edited pri-miR-142 was degraded by Tudor-SN, a component of RISC and also a ribonuclease specific to inosine-containing dsRNAs. Consequently, mature miRNA-142 expression levels increased substantially in ADAR1 null or ADAR2 null mice. Our results demonstrate a new function of RNA editing in the control of miRNA biogenesis.

Adenosine Deaminase↗
PubMed1993

Molecular cloning of an apolipoprotein B messenger RNA editing protein.

Mammalian apolipoprotein B (apo B) exists in two forms, each the product of a single gene. The shorter form, apo B48, arises by posttranscriptional RNA editing whereby cytidine deamination produces a UAA termination codon. A full-length complementary DNA clone encoding an apo B messenger RNA editing protein (REPR) was isolated from rat small intestine. The 229-residue protein contains consensus phosphorylation sites and leucine zipper domains. HepG2 cell extracts acquire editing activity when mixed with REPR from oocyte extracts. REPR is essential for apo B messenger RNA editing, and the isolation and characterization of REPR may lead to the identification of other eukaryotic RNA editing proteins.

APOBEC-1 Deaminase↗
PubMed2000

Wilms' tumor suppressor gene WT1: from structure to renal pathophysiologic features.

Normal development of the kidney is a highly complex process that requires precise orchestration of proliferation, differentiation, and apoptosis. In the past few years, a number of genes that regulate these processes, and hence play pivotal roles in kidney development, have been identified. The Wilms' tumor suppressor gene WT1 has been shown to be one of these essential regulators of kidney development, and mutations in this gene result in the formation of tumors and developmental abnormalities such as the Denys-Drash and Frasier syndromes. A fascinating aspect of the WT1 gene is the multitude of isoforms produced from its genomic locus. In this review, our current understanding of the structural features of WT1, how they modulate the transcriptional and post-transcriptional activities of the protein, and how mutations affecting individual isoforms can lead to diseased kidneys is summarized. In addition, results from transgenic experiments, which have yielded important findings regarding the function of WT1 in vivo, are discussed. Finally, data on the unusual feature of RNA editing of WT1 transcripts are presented, and the relevance of RNA editing for the normal functioning of the WT1 protein in the kidney is discussed.

Animals↗
PubMed1995

Ethanol modulates apolipoprotein B mRNA editing in the rat.

We have studied the rat ethanol-liquid diet model for chronic ethanol modulation of lipid homeostasis, apolipoprotein (apo) B production and apoB mRNA editing. Male Wistar rats were fed one of three diets: i) regular chow, ii) an isocaloric liquid diet, or iii) isocaloric ethanol-liquid diet where ethanol accounts for 35.5% of the total calories, for up to 40 days. There was no difference in body weight or liver/body weight ratio among the three groups of animals at the end of the feeding period. Hepatic and plasma triglycerides were elevated in the ethanol-treated animals only, correlated with an accumulation of lipid particles in the liver of these animals. By DNA excess hybridization, the steady state mRNA levels of apoB and apoB mRNA-editing protein relative to actin were not significantly altered. The proportion of edited apoB mRNA; i.e., apoB-48 mRNA/(apoB-48 + B-100) mRNA, increased in a time-dependent manner from approximately 50% to 100% in the ethanol-treated group. It remained unchanged in the chow- and liquid diet-fed animals. The proportion of apoB-48/apoB-100 protein synthesis was determined by [35S]methionine labeling followed by specific immunoprecipitation and SDS-polyacrylamide gel electrophoresis. The amount of newly synthesized apoB-48 increased from 30-50% to > 99% of the total apoB (apoB-48 + apoB-100). This increase in apoB-48 biosynthesis is reflected by an increase in circulating plasma apoB-48 from barely detectable to approximately 50% of total plasma apoB. Fractionation of plasma lipoproteins by fast protein liquid chromatography (FPLC) indicates that the ethanol-induced hypertriglyceridemia is completely accounted for by an increase in plasma very low density lipoprotein (VLDL). The proportion of apoB-48 as a percent of total apoB in the VLDL fraction increased from approximately 50% in controls to > 90% in ethanol-treated animals. Furthermore, there is a strong correlation between plasma triglyceride concentration and proportion of edited apoB-mRNA in the liver of ethanol-treated rats, but no direct correlation of the latter with intrahepatic triglyceride content. Ethanol-treated rats represent a new model for studying the regulation of apoB mRNA editing by dietary factors in vivo.

Animals↗
PubMed1992

The nad4L gene is encoded between exon c of nad5 and orf25 in the Arabidopsis mitochondrial genome.

In the Arabidopsis thaliana mitochondrial genome the gene coding for subunit 4L of NADH dehydrogenase (nad4L) is located between exon c of the nad5 open reading frame and orf25. The physical proximity of these genes further supports the trans-splicing model for assembly of the nad5 mRNA. Some transcripts comprise the nad4L open reading frame cotranscribed with nad5 exon c and orf25, while other mRNAs contain only nad4L and orf25. Both open reading frames for nad4L and orf25 are edited in several positions with different frequencies.

Amino Acid Sequence↗
PubMed1993

RNA editing in maize chloroplasts is a processing step independent of splicing and cleavage to monocistronic mRNAs.

The psbB operon contained in the plastomes of higher plants consists of the genes psbB, psbH, petB and petD. The primary transcript of this operon is subject to a series of processing steps which include cleavages resulting in four monocistronic mRNAs and splicing of the petB and petD transcripts. A search for editing sites within the two latter transcripts from maize led us to the detection of one editing site within the petB coding region which is conserved at the DNA level in other graminean species and in tobacco. This shows that editing must be considered as an additional processing step of the psbB operon encoded primary transcript. As is evident from cDNA sequences derived from the dicistronic and/or unspliced petB/D transcripts which are completely edited, editing is an early step of mRNA processing which precedes both splicing and cleavage to the monocistronic mRNAs and which must, therefore, be independent of the latter two steps. This conclusion is confirmed by a similar observation with the editing site of the rpl2 transcript which is contained in the polycistronic transcript of the rpoA operon, although here only partial editing is observed for the unspliced dicistronic rpl23/rpl2 transcript.

Animals↗
PubMed1994

RNA editing of human kainate receptor subunits.

RNA editing has been shown to be critical in generating the molecular diversity of rodent kainate receptors. We have examined cDNAs derived from various human brain sources to assess the occurrence and extent of RNA editing in human brain. Comparison of genomic and cDNA sequences revealed extensive editing of the human EAA4 (GluR6) mRNA at the isoleucine/valine, tyrosine/cysteine sites of the transmembrane I region, and the glutamine/arginine site of the transmembrane II region. Of the eight potential molecular variants generated by the nucleotide exchange, five were observed in the tissues examined. The distribution of the various RNA editing combinations were not uniform, and displayed tissue and/or age dependent distribution. Editing of the glutamine/arginine site was also confirmed for EAA3 (GluR5), which displays a significantly higher extent of editing in specific human brain regions compared with rodent whole brain. Hence, it can be concluded that RNA editing is a determinant of the phenotype of human kainate receptor complexes.

Aged↗
PubMed2002

TROSY-NMR studies of the 91kDa TRAP protein reveal allosteric control of a gene regulatory protein by ligand-altered flexibility.

The tryptophan biosynthesis genes of several Bacilli are controlled through terminator/anti-terminator transcriptional attenuation. This process is regulated by tryptophan-dependent binding of the trp RNA-binding attenuation protein (TRAP) to the leader region of the trp operon mRNA, precluding formation of the antiterminator RNA hairpin, and allowing formation of the less stable terminator hairpin. Crystal structures are available of TRAP in complex with tryptophan and in ternary complex with tryptophan and RNA. However, no structure of TRAP in the absence of tryptophan is available; thus, the mechanism of allostery remains unclear. We have used transverse relaxation optimized spectroscopy (TROSY)-based NMR experiments to study the mechanism of ligand-mediated allosteric regulation in the 90.6kDa 11-mer TRAP. By recording a series of two-dimensional 15N-edited TROSY NMR spectra of TRAP from the thermophile Bacillus stearothermophilus over an extended range of temperatures, we have found tryptophan binding to be temperature-dependent, in agreement with the previously observed temperature-dependent RNA binding. Triple-resonance TROSY-based NMR spectra recorded at 55 degrees C have allowed us to obtain backbone resonance assignments for uniformly 2H,13C,15N-labeled TRAP in the inactive form and in the active form (free and bound to tryptophan). On the basis of ligand-dependent differential line-broadening and chemical shift perturbations, coupled with the results of proteolytic sensitivity measurements, we infer that tryptophan-modulated protein flexibility (dynamics) plays a central role in TRAP function by altering its RNA-binding affinity. Furthermore, because the crystal structures show that the ligand is buried completely in the bound state, we speculate that such dynamic behavior may be important to enable rapid response to changes in intracellular tryptophan levels. Thus, we propose that allosteric control of TRAP is accomplished by ligand-altered protein dynamics.

Bacterial Proteins↗
PubMed1999

Long RNA hairpins that contain inosine are present in Caenorhabditis elegans poly(A)+ RNA.

Adenosine deaminases that act on RNA (ADARs) are RNA-editing enzymes that convert adenosine to inosine within double-stranded RNA. In the 12 years since the discovery of ADARs only a few natural substrates have been identified. These substrates were found by chance, when genomically encoded adenosines were identified as guanosines in cDNAs. To advance our understanding of the biological roles of ADARs, we developed a method for systematically identifying ADAR substrates. In our first application of the method, we identified five additional substrates in Caenorhabditis elegans. Four of those substrates are mRNAs edited in untranslated regions, and one is a noncoding RNA edited throughout its length. The edited regions are predicted to form long hairpin structures, and one of the RNAs encodes POP-1, a protein involved in cell fate decisions.

3' Untranslated Regions↗
PubMed1996

A promiscuous chloroplast DNA fragment is transcribed in plant mitochondria but the encoded RNA is not edited.

The RNA editing processes in chloroplasts and mitochondira of higher plants show several similarities which are suggestive of common components and/or biochemical steps between the two plant organelles. The existence of various promiscuous DNA fragments of chloroplast origin in plant mitochondrial genomes allowed us to test the possibility that chloroplast sequences are also edited in mitochondria. An rpoB fragment transferred from chloroplasts to mitochondria in rice was chosen as it contains several editing sites, two of which match sequence motifs surrounding even non-homologous editing sites in both chloroplast and mitochondrial transcripts. Rice chloroplast and mitochondrial rpoB DNA and cDNA sequences were selectively amplified and the editing status of the cDNA sequences was determined. Three of the four potential rpoB editing sites previously detected in maize were found to be edited in the rice chloroplast rpoB transcript, whereas the fourth was found to remain unedited. In mitochondria, however, all four editing sites remain unmodified at the cDNA level. This indicates that the editing processes of higher plant mitochondria and chloroplasts are not identical and that organelle-specific factors are required for eliciting the respective editing events.

Amino Acid Sequence↗