Abstract:
:enod40 is a plant gene that participates in the regulation of symbiotic interaction between leguminous plants and bacteria or fungi. Furthermore, it has been suggested to play a general role in non-symbiotic plant development. Although enod40 seems to have multiple functions, being present in many land plants, the molecular mechanisms of its activity are unclear; they may be determined though, by short peptides and/or RNA structures encoded in the enod40 genes. We utilized conserved RNA structures in enod40 sequences to search nucleotide sequence databases and identified a number of new enod40 homologues in plant species that belong to known, but also, to yet unknown enod40-containing plant families. RNA secondary structure predictions and comparative sequence analysis of enod40 RNAs allowed us to determine the most conserved structural features, present in all known enod40 genes. Remarkably, the topology and evolution of one of the conserved structural domains are similar to those of the expansion segments found in structural RNAs such as rRNAs, RNase P and SRP RNAs. Surprisingly, the enod40 RNA structural elements are much more stronger conserved than the encoded peptides. This finding suggests that some general functions of enod40 gene could be determined by the encoded RNA structure, whereas short peptides may be responsible for more diverse functions found only in certain plant families.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Gultyaev AP,Roussis Adoi
10.1093/nar/gkm173subject
Has Abstractpub_date
2007-01-01 00:00:00pages
3144-52issue
9eissn
0305-1048issn
1362-4962pii
gkm173journal_volume
35pub_type
杂志文章abstract::Eukaryotic gene expression is regulated by enhancer-promoter interactions but the molecular mechanisms that govern specificity have remained elusive. Genome-wide studies utilizing STARR-seq identified two enhancer classes in Drosophila that interact with different core promoters: housekeeping enhancers (hkCP) and deve...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw1114
更新日期:2017-02-28 00:00:00
abstract::Calf lens messenger fractions have been purified on poly(dT)-cellulose. The purified RNA's have been analyzed as nucleosides by a method which can be used on a micro-scale with highly reproduceble results. Both the 10S and 14S lens mRNA contain poly A sequences. The poly A content found in 14S mRNA cannot account for ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/1.2.245
更新日期:1974-02-01 00:00:00
abstract::Eukaryotic transcription factor B (TFB) proteins are homologous to KsgA/Dim1 ribosomal RNA (rRNA) methyltransferases. The mammalian TFB1, mitochondrial (TFB1M) factor is an essential protein necessary for mitochondrial gene expression. TFB1M mediates an rRNA modification in the small ribosomal subunit and thus plays a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt547
更新日期:2013-09-01 00:00:00
abstract::We have developed a new COFACTOR webserver for automated structure-based protein function annotation. Starting from a structural model, given by either experimental determination or computational modeling, COFACTOR first identifies template proteins of similar folds and functional sites by threading the target structu...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks372
更新日期:2012-07-01 00:00:00
abstract::The selective and potent inhibition of mitochondrial translation in Saccharomyces cerevisiae by pentamidine suggests a novel antimicrobial action for this drug. Electrophoresis mobility shift assay, T1 ribonuclease footprinting, hydroxyl radical footprinting and isothermal titration calorimetry collectively demonstrat...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm1180
更新日期:2008-03-01 00:00:00
abstract::To prevent progressive telomere shortening as a result of conventional DNA replication, new telomeric DNA must be added onto the chromosome end. The de novo DNA synthesis involves elongation of the G-rich strand of the telomere by telomerase. In human cells, the CST complex (CTC1-STN1-TEN1) also functions in telomere ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx125
更新日期:2017-05-05 00:00:00
abstract::Mitochondrial DNA (mtDNA) is entirely dependent on nuclear genes for its transcription and replication. One of these genes is TOP1MT, which encodes the mitochondrial DNA topoisomerase IB, involved in mtDNA relaxation. To elucidate TOP1MT regulation, we performed genome-wide profiling across the 60-cell line panel (the...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr208
更新日期:2011-08-01 00:00:00
abstract::Bacteria occupy a diverse set of environmental niches with differing oxygen availability. Anaerobic environments such as mammalian digestive tracts and industrial reactors harbor an abundance of both obligate and facultative anaerobes, many of which play significant roles in human health and biomanufacturing. Studying...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw580
更新日期:2016-09-30 00:00:00
abstract::As a trial practical application, we have applied optimized microfabricated electrophoresis devices, combined with enzymatic mutation detection methods, to the determination of single nucleotide polymorphism (SNP) sites in the p53 suppressor gene. Using clinical samples, we have achieved robust assays with quality fac...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.9.e43
更新日期:2000-05-01 00:00:00
abstract::(19)F NMR spectroscopy has proved to be a valuable tool to monitor functionally important conformational transitions of nucleic acids. Here, we present a systematic investigation on the application of 5-fluoro pyrimidines to probe DNA and RNA secondary structures. Oligonucleotides with the propensity to adapt secondar...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp862
更新日期:2009-12-01 00:00:00
abstract::A new system, ZCURVE 1.0, for finding protein- coding genes in bacterial and archaeal genomes has been proposed. The current algorithm, which is based on the Z curve representation of the DNA sequences, lays stress on the global statistical features of protein-coding genes by taking the frequencies of bases at three c...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg254
更新日期:2003-03-15 00:00:00
abstract::The formation of interstrand cross-links in nucleic acids can have a strong impact on biological function of nucleic acids; therefore, many cross-linking agents have been developed for biological applications. Despite numerous studies, there remains a need for cross-linking agents that exhibit both efficiency and sele...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt197
更新日期:2013-07-01 00:00:00
abstract::Methylation of CpG motifs in DNA is involved in the control of gene expression and in several other epigenic effects. It suppresses also the immuno-stimulation properties of bacterial or viral DNAs that contain CPGS: However, effects of methylation on the DNA structure and dynamics are not clear. Here we carried out a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.11.2314
更新日期:2001-06-01 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::Transposition of Saccharomyces cerevisiae Ty1 retroelements has been shown to involve reverse transcription in intracytoplasmic virus-like particles (Ty-VLPs). Ty DNA present in the particles specified by Ty1-H3 element was found to consist of the full-length genomic DNA as well as incomplete cDNAs mainly of plus pola...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.15.3513
更新日期:1993-07-25 00:00:00
abstract::Methylation of miRNAs at the 2'-hydroxyl group on the ribose at 3'-end (2'-O-methylation, 2'Ome) is critical for miRNA function in plants and Drosophila. Whether this methylation phenomenon exists for mammalian miRNA remains unknown. Through LC-MS/MS analysis, we discover that majority of miR-21-5p isolated from human...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa504
更新日期:2020-07-27 00:00:00
abstract::Polyploidy, the presence of multiple sets of chromosomes that are similar but not identical, complicates both chromosome walking and assembly of sequence-ready contigs for many plant taxa including a large number of economically-significant crops. Traditional 'dot-blot hybridization' or PCR-based assays for identifyin...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.7.e23
更新日期:2000-04-01 00:00:00
abstract::SINE-VNTR-Alu (SVA) elements are non-autonomous, hominid-specific non-LTR retrotransposons and distinguished by their organization as composite mobile elements. They represent the evolutionarily youngest, currently active family of human non-LTR retrotransposons, and sporadically generate disease-causing insertions. S...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr863
更新日期:2012-02-01 00:00:00
abstract::The major mRNA degradation pathway involves deadenylation of the target molecule followed by decapping and, finally, 5'-->3' exonuclease digestion of the mRNA body. While yeast factors involved in the decapping and exonuclease degradation steps have been identified, the nature of the factor(s) involved in the deadenyl...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.12.2448
更新日期:2001-06-15 00:00:00
abstract::The design and synthesis of metal complexes that can specifically target DNA secondary structure has attracted considerable attention. Chiral metallosupramolecular complexes (e.g. helicates) in particular display unique DNA-binding behavior, however until recently few examples which are both water-compatible and enant...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx244
更新日期:2017-05-19 00:00:00
abstract::The editing function of aminoacyl-tRNA synthetases (aaRSs) is indispensible for formation of the correct aminoacyl-tRNAs. Editing deficiency may lead to growth inhibition and the pathogenesis of various diseases. Herein, we confirmed that norvaline (Nva) but not isoleucine or valine is the major threat to the editing ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx487
更新日期:2017-07-07 00:00:00
abstract::Interleukin 2 (IL2) mRNA has a short half-life in the cytoplasm of T lymphocytes, relative to most mRNA. We have discovered a candidate ribonuclease to account for the rapid turnover of IL2 mRNA in the cytosol of the human T lymphocyte cell line Jurkat. In partially purified form, this RNase is about 7 times as active...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.1.155
更新日期:1993-01-11 00:00:00
abstract::DNA restriction fragments located 5' to the human c-myc gene display anomalous electrophoretic mobility on polyacrylamide gels. Computer modeling of the c-myc flanking DNA suggests that the slow-moving DNA fragments spanning nucleotides -1690 to -1054 (relative to c-myc promoter P1) and -718 to -452 form large left ha...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.7.2819
更新日期:1989-04-11 00:00:00
abstract::The self-assembly of bis-biotinylated double-stranded DNA and the tetravalent biotin-binding protein streptavidin (STV) have been studied by non-denaturing gel electrophoresis and atomic force microscopy (AFM). The rapid self-assembly reproducibly generated populations of individual oligomeric complexes. Most striking...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.23.4553
更新日期:1999-12-01 00:00:00
abstract::A 200 bp sequence including a stretch of 54 base pairs of alternating guanosine and adenosine nucleotide residues [(dG-dA)27.(dT-dC)27] was cloned in the simian virus 40 (SV40) genome between the KpnI and HpaII sites. This sequence was discovered earlier as part of a region limiting the amplification of sequences adja...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.16.8077
更新日期:1988-08-25 00:00:00
abstract::Single-walled carbon nanotubes (SWNTs) have been considered as the leading candidate for nanodevice applications ranging from gene therapy and novel drug delivery to membrane separations. The miniaturization of DNA-nanotube devices for biological applications requires fully understanding DNA-nanotube interaction mecha...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl513
更新日期:2006-08-02 00:00:00
abstract::Although the involvement of Ser/Arg-rich (SR) proteins in RNA metabolism is well documented, their role in vertebrate development remains elusive. We, therefore, elected to take advantage of the zebrafish model organism to study the SR genes' functions using the splicing morpholino (sMO) microinjection and the program...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx638
更新日期:2017-09-19 00:00:00
abstract::We have isolated a rat cDNA, named FE65, hybridizing to an mRNA of about 2,300 nucleotides present in rat brain, undetectable in rat liver and very poorly represented in other tissues. An mRNA of the same size is present in human neuroblastoma cells and is absent from other human cell lines. The FE65 cDNA contains an ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.19.5269
更新日期:1991-10-11 00:00:00
abstract::Sas2p is a histone acetyltransferase implicated in the regulation of transcriptional silencing, and ORC is the six-subunit origin recognition complex involved in the initiation of DNA replication and the establishment of transcriptionally silent chromatin by silencers in yeast. We show here that SAS2 deletion (sas2Del...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn465
更新日期:2008-09-01 00:00:00
abstract::Helicase-nuclease systems dedicated to DNA end resection in preparation for homologous recombination (HR) are present in all kingdoms of life. In thermophilic archaea, the HerA helicase and NurA nuclease cooperate with the highly conserved Mre11 and Rad50 proteins during HR-dependent DNA repair. Here we show that HerA...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr1157
更新日期:2012-04-01 00:00:00