Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Base editing”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,225 records · Page 68Linked to original sources
PubMed2004

High resolution crystal structure of a key editosome enzyme from Trypanosoma brucei: RNA editing ligase 1.

Trypanosomatids are causative agents of several devastating tropical diseases such as African sleeping sickness, Chagas' disease and leishmaniasis. There are no effective vaccines available to date for treatment of these protozoan diseases, while current drugs have limited efficacy, significant toxicity and suffer from increasing resistance. Trypanosomatids have several remarkable and unique metabolic and structural features that are of great interest for developing new anti-protozoan therapeutics. One such feature is "RNA editing", an essential process in these pathogenic protozoa. Transcripts for key trypanosomatid mitochondrial proteins undergo extensive post-transcriptional RNA editing by specifically inserting or deleting uridylates from pre-mature mRNA in order to create mature mRNAs that encode functional proteins. The RNA editing process is carried out in a approximately 1.6 MDa multi-protein complex, the editosome. In Trypanosoma brucei, one of the editosome's core enzymes, the RNA editing ligase 1 (TbREL1), has been shown to be essential for survival of both insect and bloodstream forms of the parasite. We report here the crystal structure of the catalytic domain of TbREL1 at 1.2 A resolution, in complex with ATP and magnesium. The magnesium ion interacts with the beta and gamma-phosphate groups and is almost perfectly octahedrally coordinated by six phosphate and water oxygen atoms. ATP makes extensive direct and indirect interactions with the ligase via essentially all its atoms while extending its base into a deep pocket. In addition, the ATP makes numerous interactions with residues that are conserved in the editing ligases only. Further away from the active site, TbREL1 contains a unique loop containing several hydrophobic residues that are highly conserved among trypanosomatid RNA editing ligases which may play a role in protein-protein interactions in the editosome. The distinct characteristics of the adenine-binding pocket, and the absence of any close homolog in the human genome, bode well for the design of selective inhibitors that will block the essential RNA ligase function in a number of major protozoan pathogens.

Adenosine Triphosphate↗
PubMed1994

Differential RNA editing in closely related introns in Oenothera mitochondria.

Introns a/b of the nad2 gene and b/c of the nad1 gene in Oenothera mitochondria were found to be closely related. Within a scaffold of conserved sequence regions, a 48 bp sequence element covering intron domain V and flanking nucleotides is identical in both group II introns. The third nucleotide of this element is edited in the nad2, but not in the nad1 intervening sequence. The C to U editing event compensates an nad2-specific nucleotide mismatch in the stem domain IV and thus improves secondary structure stability. This differential editing event indicates that the identical upstream 2 and downstream 45 nucleotides are not sufficient to specify this editing site. Comparison of adjacent exon editing patterns in spliced and unspliced transcripts shows a higher degree of editing in processed sequences, confirming that RNA editing is a posttranscriptional process in plant mitochondria.

Amino Acid Sequence↗
PubMed2002

Assembly and function of the RNA editing complex in Trypanosoma brucei requires band III protein.

Trypanosome RNA editing, the posttranscriptional insertion and deletion of U residues in mitochondrial transcripts, is catalyzed by a protein complex containing seven distinct proteins. In this study, we cloned the gene for band III, a 555-amino-acid protein with two separate zinc finger motifs. We prepared antibodies that showed band III protein cofractionates with the previously characterized band IV protein throughout the purification of the editing complex and is not found free or in other protein associations; therefore, it is a true constituent of the editing complex. Double-stranded RNA interference efficiently depleted band III protein and demonstrated that band III expression is essential for growth of procyclic trypanosomes and for RNA editing. These depleted cell extracts were deficient specifically in guide RNA-directed endonuclease cleavage at both U deletion and U insertion sites and in the activity of the band IV ligase, but they retained the 3'-U-exonuclease and terminal-U-transferase activities as well as band V ligase of the editing complex. Loss of band III protein also resulted in almost complete loss of the band IV ligase protein and altered sedimentation of the band V ligase. These data indicate that band III is either the RNA editing endonuclease or a factor critical for cleavage activity in the editing complex. They also demonstrate that band III is required for proper assembly of the editing complex.

Amino Acid Sequence↗
PubMed1995

Mutagenesis of apobec-1, the catalytic subunit of the mammalian apolipoprotein B mRNA editing enzyme, reveals distinct domains that mediate cytosine nucleoside deaminase, RNA binding, and RNA editing activity.

Apolipoprotein (apo) B48 is synthesized by mammalian small intestine as a result of post-transcriptional RNA editing. This process is mediated by an enzyme complex containing a catalytic subunit, apobec-1, which is homologous to other cytidine deaminases, particularly in a domain (H/C)-(A/V)-E-(X)24-30-P-C-(X)2-C which coordinates zinc, apobec-1, expressed as a glutathione S-transferase fusion protein, demonstrates both apoB RNA editing and cytidine deaminase activity. His61, Cys93, and Cys96, the putative zinc-coordinating residues, were mutated to Arg, Ser, and Ser, respectively, with loss of RNA editing activity and either great reduction or abolition of cytidine deaminase activity. Mutation of the catalytically active Glu63 residue to Gln and Pro92 to Leu abolished both cytidine deaminase and RNA editing activity. The conservative His61-->Cys mutation, which should coordinate zinc, retained both editing and cytidine deaminase activity. Thus, zinc binding is required for both apoB RNA editing and cytidine deaminase activity. Mutation of the first four leucines within the heptad repeat of the leucine-rich region (LRR) of apobec-1 resulted in reduced RNA editing but preservation of wild-type cytidine deaminase activity. GST/APOBEC-1 was also demonstrated to cross-link to apoB RNA. Mutation of His61-->Arg abolished RNA binding, while the Glu63-->Gln and Cys96-->Ser mutant proteins showed wild-type levels of RNA binding. The remaining mutants had reduced levels of activity. Overexpression of wild-type apobec-1 in McA 7777 cells resulted in a 5-6-fold increase in editing of endogenous apoB. Transfection of the His61-->Cys, LRR, and Cys93-->Ser mutants increased endogenous editing 2-3-fold, while Glu63-->Gln and His61-->Arg mutants acted as dominant negatives, reducing endogenous editing. These data suggest that apobec-1 has distinct functional domains which modulate activity in the context of the apoB mRNA editing enzyme.

APOBEC-1 Deaminase↗
PubMed1995

Editing of alpha-amino-3-hydroxy-5-methylisoxazole-4-propionic acid receptor GluR-B pre-mRNA in vitro reveals site-selective adenosine to inosine conversion.

In neurons of the mammalian brain primary transcripts of genes encoding subunits of glutamate receptor channels can undergo RNA editing, leading to altered properties of the transmitter-activated channel. Editing of these transcripts is a nuclear process that targets specific adenosines and requires a double-stranded RNA structure configured from complementary exonic and intronic sequences. We show here that the two independent editing sites in alpha-amino-3-hydroxy-5-methylisoxazole-4-propionic acid receptor GluR-B pre-mRNA are edited with positional accuracy by nuclear extract from HeLa cells. Nucleotide analysis by thin layer chromatography of the edited RNA sequences revealed selective adenosine to inosine conversion, most likely reflecting the participation of double-stranded RNA adenosine deaminase. Our results predict the presence of inosine-containing codons in other mammalian mRNAs.

Adenosine↗
PubMed1996

Synthesis of leader RNA and editing of P mRNA during transcription by rinderpest virus.

Purified rinderpest virus was earlier shown to transcribe in vitro, all virus-specific mRNAs with the promoter-proximal N mRNA being the most abundant. Presently, this transcription system has been shown to synthesize full length monocistronic mRNAs comparable to those made in infected cells. Small quantities of bi- and tricistronic mRNAs are also synthesized. Rinderpest virus synthesizes in vitro, a leader RNA of approximately 55 nucleotides in length. Purified rinderpest virus also exhibits RNA editing activity during the synthesis of P mRNA as shown by primer extension analysis of the mRNA products.

Animals↗
PubMed1997

Apobec-1 and apolipoprotein B mRNA editing.

Apolipoprotein (apo)B mRNA editing is a novel mechanism for the post-transcriptional regulation of gene expression in mammals. It consists of a C-->U conversion of the first base of the codon CAA, encoding glutamine-2153, to UAA, an in-frame stop codon, in apoB mRNA. Since its initial description in 1987, substantial progress has been made in the last few years on the mechanism of editing. Apobec-1, the catalytic component of the apoB mRNA editing enzyme complex, has been cloned. This article begins with an overview of the general biology of apoB mRNA editing. It then provides an in-depth analysis of the structure, evolution and possible mechanism of action of apobec-1. ApoB mRNA editing is the prototype of RNA editing in mammals. What we learn from apoB mRNA editing will be useful in our understanding of other examples of RNA editing in vertebrates which are being described with increasing frequency.

APOBEC-1 Deaminase↗
PubMed1997

Purification and characterization of a human RNA adenosine deaminase for glutamate receptor B pre-mRNA editing.

The glutamate receptor subunit B (GluR-B) pre-mRNA is edited at two adenosine residues, resulting in amino acid changes that alter the electrophysiologic properties of the glutamate receptor. Previous studies showed that these amino acid changes are due to adenosine to inosine conversions in two codons resulting from adenosine deamination. Here, we describe the purification and characterization of an activity from human HeLa cells that efficiently and accurately edits GluR-B pre-mRNA at both of these sites. The purified activity contains a human homolog of the recently reported rat RED1 (rRED1) protein, a member of the family of double-stranded RNA-dependent deaminase proteins. Recombinant human RED1 (hRED1), but not recombinant dsRAD, another member of the family, efficiently edits both the Q/R and R/G sites of GluR-B RNA. We conclude that the GluR-B editing activity present in HeLa cell extracts and the recombinant hRED1 protein are indistinguishable.

Adenosine↗
PubMed1995

The World Health Organization's histologic classification of bone tumors. A commentary on the second edition.

BACKGROUND: The World Health Organization's histologic classification of bone tumors was revised in 1993. METHODS: The first edition was reviewed by an international panel of pathologists from nine countries and modified to incorporate advances made in the twenty years since it appeared. RESULTS: The framework and concept of the classification remain the same (i.e., based on histologic criteria in terms of differentiation shown by the tumor cells via conventional light microscopy supplemented by immunohistochemistry). New entities not described in the first edition include, for example, benign and malignant fibrous histiocytomas, well differentiated osteosarcoma, round-cell osteosarcoma, clear cell chondrosarcoma, primitive neuroectodermal tumor of bone, osteofibrous dysplasia, and giant cell reparative granuloma. CONCLUSION: The revised and expanded classification reflects advances in our knowledge, but is similar in concept and framework to the original version to allow comparisons between data collected in the past and future.

Humans↗
PubMed1996

RNA editing in plant mitochondria and chloroplasts.

In the mitochondria and chloroplasts of higher plants there is an RNA editing activity responsible for specific C-to-U conversions and for a few U-to-C conversions leading to RNA sequences different from the corresponding DNA sequences. RNA editing is a post-transcriptional process which essentially affects the transcripts of protein coding genes, but has also been found to modify non-coding transcribed regions, structural RNAs and intron sequences. RNA editing is essential for correct gene expression: proteins translated from edited transcripts are different from the ones deduced from the genes sequences and usually present higher similarity to the corresponding non-plant homologues. Initiation and stop codons can also be created by RNA editing. RNA editing has also been shown to be required for the stabilization of the secondary structure of introns and tRNAs. The biochemistry of RNA editing in plant organelles is still largely unknown. In mitochondria, recent experiments indicate that RNA editing may be a deamination process. A plastid transformation technique showed to be a powerful tool for the study of RNA editing. The biochemistry as well as the evolutionary features of RNA editing in both organelles are compared in order to identify common as well as organelle-specific components.

Amino Acid Sequence↗
PubMed1988

Cocrystal structure of an editing complex of Klenow fragment with DNA.

High-resolution crystal structures of editing complexes of both duplex and single-stranded DNA bound to Escherichia coli DNA polymerase I large fragment (Klenow fragment) show four nucleotides of single-stranded DNA bound to the 3'-5' exonuclease active site and extending toward the polymerase active site. Melting of the duplex DNA by the protein is stabilized by hydrophobic interactions between Phe-473, Leu-361, and His-666 and the last three bases at the 3' terminus. Two divalent metal ions interacting with the phosphodiester to be hydrolyzed are proposed to catalyze the exonuclease reaction by a mechanism that may be related to mechanisms of other enzymes that catalyze phospho-group transfer including RNA enzymes. We suggest that the editing active site competes with the polymerase active site some 30 A away for the newly formed 3' terminus. Since a 3' terminal mismatched base pair favors the melting of duplex DNA, its binding and excision at the editing exonuclease site that binds single-stranded DNA is enhanced.

Computer Simulation↗
PubMed2004

Recognition of psychiatric disorders in musculoskeletal and cardiovascular rehabilitation patients.

OBJECTIVE: To investigate the detection rate of psychiatric disorders in rehabilitation inpatients with musculoskeletal and cardiovascular diseases (CVDs). DESIGN: Cross-sectional survey; analysis of medical charts and discharge reports, combined with standardized diagnostic interviews. SETTING: Four orthopedic and 6 cardiovascular rehabilitation hospitals in southwest Germany. PARTICIPANTS: More than 1700 inpatients with different musculoskeletal disorders and CVDs participated in the survey. On the basis of their General Health Questionnaire score, 205 patients with musculoskeletal diseases and 164 patients with CVDs were selected randomly for standardized interviews. Discharge reports of interviewed patients were analyzed. INTERVENTIONS: Not applicable. MAIN OUTCOME MEASURES: Clinical interview (Composite International Diagnostic Interview [CIDI]) to obtain diagnoses of psychiatric disorders as defined by the Diagnostic and Statistical Manual of Mental Disorders, 4th edition (DSM-IV). Assessment of psychosocial burden and diagnoses of mental disorders, as well as admission to psychologic treatments, based on discharge reports of the attending physicians. RESULTS: The detection rate (sensitivity) of mental disorders was 48% in the orthopedic rehabilitation patients and 32% in the cardiovascular patients. Specificity was 80% in musculoskeletal patients and 87% in cardiovascular patients. Differential diagnostic competencies were lacking, and only half of the physicians' diagnoses corresponded to the CIDI diagnoses. CONCLUSIONS: The results showed a need for current DSM-IV or International Classification of Diseases, 10th edition, psychodiagnostics in medical rehabilitation to detect mental disorders in patients in the rehabilitation process at an earlier stage and to refer patients with comorbid mental disorders to adequate treatment.

Adult↗
PubMed2002

PharmGKB: the Pharmacogenetics Knowledge Base.

The Pharmacogenetics Knowledge Base (PharmGKB; http://www.pharmgkb.org/) contains genomic, phenotype and clinical information collected from ongoing pharmacogenetic studies. Tools to browse, query, download, submit, edit and process the information are available to registered research network members. A subset of the tools is publicly available. PharmGKB currently contains over 150 genes under study, 14 Coriell populations and a large ontology of pharmacogenetics concepts. The pharmacogenetic concepts and the experimental data are interconnected by a set of relations to form a knowledge base of information for pharmacogenetic researchers. The information in PharmGKB, and its associated tools for processing that information, are tailored for leading-edge pharmacogenetics research. The PharmGKB project was initiated in April 2000 and the first version of the knowledge base went online in February 2001.

Biotransformation↗
PubMed2003

The method to compare nucleotide sequences based on the minimum entropy principle.

A new method to compare two (or several) symbol sequences is developed. The method is based on the comparison of the frequencies of the small fragments of the compared sequences; it requires neither string editing, nor other transformations of the compared objects. The comparison is executed through a calculation of the specific entropy of a frequency dictionary against the special dictionary called the hybrid one; this latter is the statistical ancestor of the group of sequences under comparison. Some applications of the developed method in the fields of genetics and bioinformatics are discussed.

Animals↗