Abstract:
:We have sequenced the genome of Shigella flexneri serotype 2a, the most prevalent species and serotype that causes bacillary dysentery or shigellosis in man. The whole genome is composed of a 4 607 203 bp chromosome and a 221 618 bp virulence plasmid, designated pCP301. While the plasmid shows minor divergence from that sequenced in serotype 5a, striking characteristics of the chromosome have been revealed. The S.flexneri chromosome has, astonishingly, 314 IS elements, more than 7-fold over those possessed by its close relatives, the non-pathogenic K12 strain and enterohemorrhagic O157:H7 strain of Escherichia coli. There are 13 translocations and inversions compared with the E.coli sequences, all involve a segment larger than 5 kb, and most are associated with deletions or acquired DNA sequences, of which several are likely to be bacteriophage-transmitted pathogenicity islands. Furthermore, S.flexneri, resembling another human-restricted enteric pathogen, Salmonella typhi, also has hundreds of pseudogenes compared with the E.coli strains. All of these could be subjected to investigations towards novel preventative and treatment strategies against shigellosis.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Jin Q,Yuan Z,Xu J,Wang Y,Shen Y,Lu W,Wang J,Liu H,Yang J,Yang F,Zhang X,Zhang J,Yang G,Wu H,Qu D,Dong J,Sun L,Xue Y,Zhao A,Gao Y,Zhu J,Kan B,Ding K,Chen S,Cheng H,Yao Z,He B,Chen R,Ma D,Qiang B,doi
10.1093/nar/gkf566keywords:
subject
Has Abstractpub_date
2002-10-15 00:00:00pages
4432-41issue
20eissn
0305-1048issn
1362-4962journal_volume
30pub_type
杂志文章abstract::Cancer-associated somatic mutations outside protein-coding regions remain largely unexplored. Analyses of the TERT locus have indicated that non-coding regulatory mutations can be more frequent than previously suspected and play important roles in oncogenesis. Using a computational method called SASE-hunter, developed...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv419
更新日期:2015-06-23 00:00:00
abstract::In silico prediction of transcription factor binding sites (TFBSs) is central to the task of gene regulatory network elucidation. Genomic DNA sequence information provides a basis for these predictions, due to the sequence specificity of TF-binding events. However, DNA sequence alone is an impoverished source of infor...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn866
更新日期:2009-01-01 00:00:00
abstract::Escherichia coli MutY is an adenine and a weak guanine DNA glycosylase involved in reducing mutagenic effects of 7,8-dihydro-8-oxo-guanine (8-oxoG). The C-terminal domain of MutY is required for 8-oxoG recognition and is critical for mutation avoidance of oxidative damage. To determine which residues of this domain ar...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg434
更新日期:2003-06-15 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::CENP-A and CENP-B are major components of centromeric chromatin. CENP-A is the histone H3 variant, which forms the centromere-specific nucleosome. CENP-B specifically binds to the CENP-B box DNA sequence on the centromere-specific repetitive DNA. In the present study, we found that the CENP-A nucleosome more stably re...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv405
更新日期:2015-05-26 00:00:00
abstract::Recent rapid advances in next generation RNA sequencing (RNA-Seq)-based provide researchers with unprecedentedly large data sets and open new perspectives in transcriptomics. Furthermore, RNA-Seq-based transcript profiling can be applied to non-model and newly discovered organisms because it does not require a predefi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks540
更新日期:2012-07-01 00:00:00
abstract::In vitro selection of RNA-cleaving DNAzymes is a powerful method for isolating metal-specific DNA. A few successful examples are known, but it is still difficult to target some thiophilic metals such as Cd(2+) due to limited functional groups in DNA. While using modified bases expands the chemical functionality of DNA...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv519
更新日期:2015-07-13 00:00:00
abstract::The polymerase encoded by human hepatitis B virus, which has reverse transcriptase and RNase H activity, binds to its pregenomic RNA template in a two-step process involving a terminal redundancy. Both first strand and second strand DNA synthesis involve primer translocation and second strand synthesis involves a temp...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.17.3295
更新日期:1996-09-01 00:00:00
abstract::Simian cells have been transformed with SV40 origin-defective recombinant plasmids containing the tsA209 T-antigen gene. These plasmids contain deletions of either 5 or 52 nucleotides that include the BglI site at the SV40 ori, are defective for replication in COS-1 cells but retain a functional SV40 early promoter. T...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.22.7913
更新日期:1985-11-25 00:00:00
abstract::MicroRNAs (miRNA) are short single-stranded RNA molecules derived from hairpin-forming precursors that play a crucial role as post-transcriptional regulators in eukaryotes and viruses. In the past years, many microRNA target genes (MTGs) have been identified experimentally. However, because of the high costs of experi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw1085
更新日期:2017-01-25 00:00:00
abstract::EcoRI digestion of total mouse DNA yields a prominant 1.3 kb fragment amounting to between 1 and 2% of the mouse genome. The majority of the 1.3 kb EcoRI fragments have a single Bg1II site 800 bp from one end. This EcoRI-Bg1II sequence family shows HindIII and HaeIII sequence heterogeneity. We have cloned representati...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/8.21.5031
更新日期:1980-11-11 00:00:00
abstract::Rotaviruses are a major cause of acute, often fatal, gastroenteritis in infants and young children world-wide. Virions contain an 11 segment double-stranded RNA genome. Little is known about the cis-acting sequences and structural elements of the viral RNAs. Using a database of 1621 full-length sequences of mammalian ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq663
更新日期:2010-11-01 00:00:00
abstract::Argonaute (Ago) proteins function in RNA silencing as components of the RNA-induced silencing complex (RISC). In lower organisms, the small interfering RNA and miRNA pathways diverge due in part to sorting mechanisms that direct distinct small RNA (sRNA) duplexes onto specific Ago-RISCs. However, such sorting mechanis...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku137
更新日期:2014-04-01 00:00:00
abstract::In conditions that mimic those of the living cell, where various biomolecules and other components are present, DNA strands can adopt many structures in addition to the canonical B-form duplex. Previous studies in the presence of cosolutes that induce molecular crowding showed that thermal stabilities of DNA structure...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv1133
更新日期:2015-12-02 00:00:00
abstract::Analysis of 41 histone homologous clones from an isogenic gene library of Drosophila melanogaster showed that non-histone fragments interrupt the histone repetitive clusters at several sites. Long (L) and short (S) forms of the repeating units are distinguished by the insertion of 240 bp into the spacer between H1 and...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.1.225
更新日期:1989-01-11 00:00:00
abstract::Genetic screens in Saccharomyces cerevisiae have identified the roles of ribosome components, tRNAs and translation factors in translational fidelity. These screens rely on the suppression of altered start codons, nonsense codons or frameshift mutations in genes involved in amino acid or nucleotide metabolism. Many of...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki765
更新日期:2005-08-12 00:00:00
abstract::Immunoglobulin (Ig) diversification by somatic hypermutation in germinal center B cells is instrumental for maturation of the humoral immune response, but also bears the risk of excessive or aberrant genetic changes. Thus, introduction of DNA damage by activation-induced cytidine deaminase as well as DNA repair by mul...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt1378
更新日期:2014-04-01 00:00:00
abstract::Non-protein-coding RNAs (ncRNAs) fulfill a wide range of cellular functions from protein synthesis to regulation of gene expression. Identification of novel regulatory ncRNAs by experimental approaches commonly includes the generation of specialized cDNA libraries encoding small ncRNA species. However, such identifica...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm244
更新日期:2007-01-01 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv1500
更新日期:2016-02-29 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa174
更新日期:2020-05-07 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl361
更新日期:2006-05-22 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
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更新日期:2014-05-01 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa368
更新日期:2020-07-02 00:00:00
abstract::The intrinsic stiffness of DNA limits its ability to be bent and twisted over short lengths, but such deformations are required for gene regulation. One classic paradigm is DNA looping in the regulation of the Escherichia coli lac operon. Lac repressor protein binds simultaneously to two operator sequences flanking th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm419
更新日期:2007-01-01 00:00:00
abstract::The Mouse Genome Database (MGD) (http://www.informatics.jax.org) is the community model organism database resource for the laboratory mouse, a premier animal model for the study of genetic and genomic systems relevant to human biology and disease. MGD maintains a comprehensive catalog of genes, functional RNAs and oth...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt1225
更新日期:2014-01-01 00:00:00
abstract::Previous studies have shown that the yeast Candida albicans encodes a unique seryl-tRNA(CAG) that should decode the leucine codon CUG as serine. However, in vitro translation of several different CUG-containing mRNAs in the presence of this unusual seryl-tRNA(CAG) result in an apparent increase in the molecular weight...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.9.1481
更新日期:1995-05-11 00:00:00
abstract::The presence of the C.C mispair in a defined duplex oligodeoxynucleotide enhanced its capacity to serve as a substrate for highly purified human DNA methyltransferase. Analysis of tritiated reaction products showed that the C.C mispair acted as a "methylation acceptor" in that it was itself rapidly methylated. The m5C...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.17.6899
更新日期:1987-09-11 00:00:00
abstract::Splicing of mammalian introns requires that the intron possess at least 80 nucleotides. This length requirement presumably reflects the constraints of accommodating multiple snRNPs simultaneously in the same intron. In the free-living nematode, C. elegans, introns typically are 45 to 55 nucleotides in length. In this ...
journal_title:Nucleic acids research
pub_type: 杂志文章
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更新日期:1990-01-11 00:00:00
abstract::Cis-elements (-933 to -641) upstream of the human M creatine kinase gene cap site contain an enhancer that confers developmental and tissue-specific expression to the chloramphenicol acetyltransferase gene in C2C12 myogenic cells transfected in culture. Division of the enhancer at -770 into a 5' fragment that includes...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.9.2313
更新日期:1992-05-11 00:00:00
abstract::Hepatitis C virus (HCV) is the major etiological agent of non-A, non-B hepatitis. Current therapies are not effective in all patients and can result in the generation of resistant mutants, leading to a need for new therapeutic options. HCV has an RNA genome that contains a well-defined and highly conserved secondary s...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh706
更新日期:2004-07-19 00:00:00