Abstract:
:Mitochondrial-DNA diseases have no effective treatments. Allotopic expression-synthesis of a wild-type version of the mutated protein in the nuclear-cytosolic compartment and its importation into mitochondria-has been proposed as a gene-therapy approach. Allotopic expression has been successfully demonstrated in yeast, but in mammalian mitochondria results are contradictory. The evidence available is based on partial phenotype rescue, not on the incorporation of a functional protein into mitochondria. Here, we show that reliance on partial rescue alone can lead to a false conclusion of successful allotopic expression. We recoded mitochondrial mt-Nd6 to the universal genetic code, and added the N-terminal mitochondrial-targeting sequence of cytochrome c oxidase VIII (C8) and the HA epitope (C8Nd6HA). The protein apparently co-localized with mitochondria, but a significant part of it seemed to be located outside mitochondria. Complex I activity and assembly was restored, suggesting successful allotopic expression. However, careful examination of transfected cells showed that the allotopically-expressed protein was not internalized in mitochondria and that the selected clones were in fact revertants for the mt-Nd6 mutation. These findings demonstrate the need for extreme caution in the interpretation of functional rescue experiments and for clear-cut controls to demonstrate true rescue of mitochondrial function by allotopic expression.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Perales-Clemente E,Fernández-Silva P,Acín-Pérez R,Pérez-Martos A,Enríquez JAdoi
10.1093/nar/gkq769subject
Has Abstractpub_date
2011-01-01 00:00:00pages
225-34issue
1eissn
0305-1048issn
1362-4962pii
gkq769journal_volume
39pub_type
杂志文章abstract::Detecting recombinations in the genome sequence of human immunodeficiency virus (HIV-1) is crucial for epidemiological studies and for vaccine development. Herein, we present a web server for subtyping and localization of phylogenetic breakpoints in HIV-1. Our software is based on a jumping profile Hidden Markov Model...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl255
更新日期:2006-07-01 00:00:00
abstract::Specific guanine-rich regions in human genome can form higher-order DNA structures called G-quadruplexes, which regulate many relevant biological processes. For instance, the formation of G-quadruplex at telomeres can alter cellular functions, inducing apoptosis. Thus, developing small molecules that are able to bind ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku247
更新日期:2014-05-01 00:00:00
abstract::The modified nucleoside, 7-(4,5-cis-dihydroxy-1-cyclopenten-3-yl-aminomethyl)-7-deazaguanosine, designated as Q, and its derivative, Q*, were found in tRNA's from various organisms, including several mammalian tissues, other animals such as starfish, lingula and hagfish, and wheat germ. Q isolated from rat liver tRNA ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/2.10.1931
更新日期:1975-10-01 00:00:00
abstract::HotSpot Wizard is a web server used for the automated identification of hotspots in semi-rational protein design to give improved protein stability, catalytic activity, substrate specificity and enantioselectivity. Since there are three orders of magnitude fewer protein structures than sequences in bioinformatic datab...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky417
更新日期:2018-07-02 00:00:00
abstract::Backscattering interferometry (BSI) has been used to successfully monitor molecular interactions without labeling and with high sensitivity. These properties suggest that this approach might be useful for detecting biomarkers of infection. In this report, we identify interactions and characteristics of nucleic acid pr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt165
更新日期:2013-05-01 00:00:00
abstract::Among a collection of 74 aprt mutations induced by treatment of plateau phase Chinese hamster ovary CHO cells with the radiomimetic DNA double-strand cleaving agent neocarzinostatin, nine were large-scale rearrangements. Molecular analysis indicated that all nine were highly conservative, non-homologous reciprocal exc...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkf369
更新日期:2002-06-15 00:00:00
abstract::Wybutine (Ywye), situated next to the 3'-side of the anticodon of tRNAPhe from Saccharomyces cerevisiae, can be photo-crosslinked to mRNA when bound to Escherichia coli ribosomes. Crosslinking can be obtained with poly(U) as well as with oligonucleotides such as pAUGUUU or p(U)6. In order to identify the site of react...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.21.8181
更新日期:1984-11-12 00:00:00
abstract::Pfam is a widely used database of protein families, currently containing more than 13,000 manually curated protein families as of release 26.0. Pfam is available via servers in the UK (http://pfam.sanger.ac.uk/), the USA (http://pfam.janelia.org/) and Sweden (http://pfam.sbc.su.se/). Here, we report on changes that ha...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr1065
更新日期:2012-01-01 00:00:00
abstract::Infection of Escherichia coli by a bacteriophage T4 regA, gene 44 double mutant leads to about a 7-fold increase in the amount of RNA ligase obtained after infection by wild-type phage. Using cells infected by the double mutant, RNA ligase was purified to homogeneity with a 20% yield. Unlike previous preparations of t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/4.9.3175
更新日期:1977-09-01 00:00:00
abstract::A new E. coli strain has been constructed that contains the dinD1::LacZ+ fusion and is deficient in methylation-dependent restriction systems (McrA-, McrBC-, Mrr-). This strain has been used to clone restriction endonuclease genes directly into E. coli. When E. coli cells are not fully protected by the cognate methyla...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.12.2399
更新日期:1994-06-25 00:00:00
abstract::The Mediator complex transmits activation signals from DNA bound transcription factors to the core transcription machinery. Genome wide localization studies have demonstrated that Mediator occupancy not only correlates with high levels of transcription, but that the complex also is present at transcriptionally silence...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr551
更新日期:2011-10-01 00:00:00
abstract::The Escherichia coli RuvC protein is an endonuclease that resolves Holliday junctions. In vitro, the protein shows efficient structure-specific binding of Holliday junctions, yet the rate of junction resolution is remarkably low. We have mapped the sites of cleavage on a synthetic junction through which a crossover ca...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.13.2490
更新日期:1994-07-11 00:00:00
abstract::Most proteins from higher organisms are known to be multi-domain proteins and contain substantial numbers of intrinsically disordered (ID) regions. To analyse such protein sequences, those from human for instance, we developed a special protein-structure-prediction pipeline and accumulated the products in the Structur...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq1057
更新日期:2011-01-01 00:00:00
abstract::We present YOGY a web-based resource for orthologous proteins from nine eukaryotic organisms: Homo sapiens, Mus musculus, Rattus norvegicus, Arabidopsis thaliana, Drosophila melanogaster, Caenorhabditis elegans, Plasmodium falciparum, Schizosaccharomyces pombe and Saccharomyces cerevisiae. Using a gene name from any o...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl311
更新日期:2006-07-01 00:00:00
abstract::The European Nucleotide Archive (ENA; https://www.ebi.ac.uk/ena), provided from EMBL-EBI, has for more than three decades been responsible for archiving the world's public sequencing data and presenting this important resource to the scientific community to support and accelerate the global research effort. Here, we o...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky1078
更新日期:2019-01-08 00:00:00
abstract::Hippo pathway is involved in tumorigenesis, and its regulation in cytosol has been extensively studied, but its regulatory mechanisms in the nuclear are not clear. In the current study, using a FBS-inducing model following serum starvation, we identified KDM3A, a demethylase of histone H3K9me1/2, as a positive regulat...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky1317
更新日期:2019-03-18 00:00:00
abstract::We previously found that the splicing of exon 5 to exon 6 in the rat beta-TM gene required that exon 6 first be joined to the downstream common exon 8 (Helfman et al., Genes and Dev. 2, 1627-1638, 1988). Pre-mRNAs containing exon 5, intron 5 and exon 6 are not normally spliced in vitro. We have carried out a mutationa...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.12.2318
更新日期:1994-06-25 00:00:00
abstract::As an approach to gene therapy for the respiratory manifestations of cystic fibrosis (CF), in vivo plasmid-mediated direct transfer of the normal CF transmembrane conductance regulator (CFTR) gene to the airway epithelium was investigated in mice. To evaluate the feasibility of this strategy, pRSVL, a plasmid composed...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.12.3233
更新日期:1992-06-25 00:00:00
abstract::We have used paired-end sequencing of yeast nucleosomal DNA to obtain accurate genomic maps of nucleosome positions and occupancies in control cells and cells treated with 3-aminotriazole (3AT), an inducer of the transcriptional activator Gcn4. In control cells, 3AT-inducible genes exhibit a series of distinct nucleos...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr643
更新日期:2011-12-01 00:00:00
abstract::Tubercidin may be directly brominated by reaction with N-bromosuccinimide in DMF to give 5-bromotubercidin, a reversible inhibitor of RNA synthesis. When buffered with potassium acetate the major product is 6-bromotubercidin. 5,6-Dibromotubercidin is formed in minor amounts under both conditions. N-Chlorosuccinimide a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/8.24.6213
更新日期:1980-12-20 00:00:00
abstract::The promoter of the human BCR gene, regulating the transcription of the chimeric BCR/ABL mRNA in leukemia, has been isolated and characterized. A region of 1.1 kb immediately 5' to the transcription start site was analyzed in detail by sequencing, DNase 1 footprinting, gel retardation and functional studies. These exp...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.23.7119
更新日期:1990-12-11 00:00:00
abstract::We developed a framework for quick and reliable construction of complex gene circuits for genetically engineering mammalian cells. Our hierarchical framework is based on a novel nucleotide addressing system for defining the position of each part in an overall circuit. With this framework, we demonstrate construction o...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt605
更新日期:2013-09-01 00:00:00
abstract::WebProAnalyst is a web-accessible analysis tool (http://wwwmgs.bionet.nsc.ru/mgs/programs/panalyst/) designed for scanning quantitative structure-activity relationships in protein families. The tool allows users to search correlations between protein activity and physicochemical characteristics (i.e. hydrophobicity or...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki421
更新日期:2005-07-01 00:00:00
abstract::Most RNA molecules collapse rapidly and reach the native state through a pathway that contains numerous traps and unproductive intermediates. The D135 group II intron ribozyme is unusual in that it can fold slowly and directly to the native state, despite its large size and structural complexity. Here we use hydroxyl ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki973
更新日期:2005-11-27 00:00:00
abstract::Twenty AdoMet-dependent methyltransferases (MTases) have been characterized structurally by X-ray crystallography and NMR. These include seven DNA MTases, five RNA MTases, four protein MTases and four small molecule MTases acting on the carbon, oxygen or nitrogen atoms of their substrates. The MTases share a common co...
journal_title:Nucleic acids research
pub_type: 杂志文章,评审
doi:10.1093/nar/29.18.3784
更新日期:2001-09-15 00:00:00
abstract::Large-scale automatic annotation of protein sequences remains challenging in postgenomics era. E1DS is designed for annotating enzyme sequences based on a repository of 1D signatures. The employed sequence signatures are derived using a novel pattern mining approach that discovers long motifs consisted of several sequ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn324
更新日期:2008-07-01 00:00:00
abstract::In this paper, we describe a new method for selecting RNA aptamers that cooperatively bind to two specific sites within a target RNA. We designed a selection system in which two RNAs, a target RNA and a RNA pool, were assembled by employing a pre-organized GAAA tetraloop-11-nt receptor interaction. This allows us to s...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn1012
更新日期:2009-02-01 00:00:00
abstract::The Comparative Toxicogenomics Database (CTD; http://ctdbase.org/) is a premier public resource for literature-based, manually curated associations between chemicals, gene products, phenotypes, diseases, and environmental exposures. In this biennial update, we present our new chemical-phenotype module that codes chemi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky868
更新日期:2019-01-08 00:00:00
abstract::The DNA sequence of a 225.4 kilobase segment of the Escherichia coli K-12 genome is described here, from 76.0 to 81.5 minutes on the genetic map. This brings the total of contiguous sequence from the E.coli genome project to 725.1 kb (76.0 to 92.8 minutes). We found 191 putative coding genes (ORFs) of which 72 genes w...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.13.2576
更新日期:1994-07-11 00:00:00
abstract::Mitochondrial DNA is a sensitive target of chemical carcinogens (Backer and Weinstein (1980) Science 209, 297-299), suggesting that mutations of the mitochondrial genome occur in tumor cells. We examined this point by comparing mitochondrial DNA sequences in four rat tumors with those of normal rat liver. Some novel m...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/11.6.1635
更新日期:1983-03-25 00:00:00