A novel host-specific restriction system associated with DNA backbone S-modification in Salmonella.

Abstract:

:A novel, site-specific, DNA backbone S-modification (phosphorothioation) has been discovered, but its in vivo function(s) have remained obscure. Here, we report that the enteropathogenic Salmonella enterica serovar Cerro 87, which possesses S-modified DNA, restricts DNA isolated from Escherichia coli, while protecting its own DNA by site-specific phosphorothioation. A cloned 15-kb gene cluster from S. enterica conferred both host-specific restriction and DNA S-modification on E. coli. Mutational analysis of the gene cluster proved unambiguously that the S-modification prevented host-specific restriction specified by the same gene cluster. Restriction activity required three genes in addition to at least four contiguous genes necessary for DNA S-modification. This functional overlap ensures that restriction of heterologous DNA occurs only when the host DNA is protected by phosphorothioation. Meanwhile, this novel type of host-specific restriction and modification system was identified in many diverse bacteria. As in the case of methylation-specific restriction systems, targeted inactivation of this gene cluster should facilitate genetic manipulation of these bacteria, as we demonstrate in Salmonella.

journal_name

Nucleic Acids Res

journal_title

Nucleic acids research

authors

Xu T,Yao F,Zhou X,Deng Z,You D

doi

10.1093/nar/gkq610

subject

Has Abstract

pub_date

2010-11-01 00:00:00

pages

7133-41

issue

20

eissn

0305-1048

issn

1362-4962

pii

gkq610

journal_volume

38

pub_type

杂志文章
  • Affinity proteomic dissection of the human nuclear cap-binding complex interactome.

    abstract::A 5',7-methylguanosine cap is a quintessential feature of RNA polymerase II-transcribed RNAs, and a textbook aspect of co-transcriptional RNA processing. The cap is bound by the cap-binding complex (CBC), canonically consisting of nuclear cap-binding proteins 1 and 2 (NCBP1/2). Interest in the CBC has recently renewed...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkaa743

    authors: Dou Y,Kalmykova S,Pashkova M,Oghbaie M,Jiang H,Molloy KR,Chait BT,Rout MP,Fenyö D,Jensen TH,Altukhov I,LaCava J

    更新日期:2020-10-09 00:00:00

  • QDMR: a quantitative method for identification of differentially methylated regions by entropy.

    abstract::DNA methylation plays critical roles in transcriptional regulation and chromatin remodeling. Differentially methylated regions (DMRs) have important implications for development, aging and diseases. Therefore, genome-wide mapping of DMRs across various temporal and spatial methylomes is important in revealing the impa...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkr053

    authors: Zhang Y,Liu H,Lv J,Xiao X,Zhu J,Liu X,Su J,Li X,Wu Q,Wang F,Cui Y

    更新日期:2011-05-01 00:00:00

  • Different sequence signatures in the upstream regions of plant and animal tRNA genes shape distinct modes of regulation.

    abstract::In eukaryotes, the transcription of tRNA genes is initiated by the concerted action of transcription factors IIIC (TFIIIC) and IIIB (TFIIIB) which direct the recruitment of polymerase III. While TFIIIC recognizes highly conserved, intragenic promoter elements, TFIIIB binds to the non-coding 5'-upstream regions of the ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkq1257

    authors: Zhang G,Lukoszek R,Mueller-Roeber B,Ignatova Z

    更新日期:2011-04-01 00:00:00

  • Role of modified nucleosides in tRNA: effect of modification of the 2-thiouridine derivative located at the 5'-end of the anticodon of yeast transfer RNA Lys2.

    abstract::Yeast tRNA Lys2 codes preferentially for AAA and contains a 2-thiouridine derivative (U) at the 5'-position of the anticodon. Removal of the 2-thio group from U by treatment with CNBr did not affect the amino acid accepting activity of the modified tRNA Lys2. CNBr treated tRNA Lys2 was active in protein synthesis but ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/3.3.523

    authors: Sen GC,Ghosh HP

    更新日期:1976-03-01 00:00:00

  • Eliminating helper phage from phage display.

    abstract::Phage display technology involves the display of proteins or peptides, as coat protein fusions, on the surface of a phage or phagemid particles. Using standard technology, helper phage are essential for the replication and assembly of phagemid particles, during library production and biopanning. We have eliminated the...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkl772

    authors: Chasteen L,Ayriss J,Pavlik P,Bradbury AR

    更新日期:2006-01-01 00:00:00

  • A comparison between mammalian and avian fast skeletal muscle alkali myosin light chain genes: regulatory implications.

    abstract::A single locus in the mouse, rat and chicken encodes both alkali myosin light chains, MLC1F and MLC3F. This gene has two distinct promoters and gives rise to two different primary transcripts, which are processed by alternative and different modes of splicing to form MLC1F and MLC3F mRNAs. The MLC1F/MLC3F gene is very...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/13.13.4623

    authors: Daubas P,Robert B,Garner I,Buckingham M

    更新日期:1985-07-11 00:00:00

  • Structural dynamics of double-stranded DNA with epigenome modification.

    abstract::Modification of cytosine plays an important role in epigenetic regulation of gene expression and genome stability. Cytosine is converted to 5-methylcytosine (5mC) by DNA methyltransferase; in turn, 5mC may be oxidized to 5-hydroxymethylcytosine (5hmC) by ten-eleven translocation enzyme. The structural flexibility of D...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkaa1210

    authors: Furukawa A,Walinda E,Arita K,Sugase K

    更新日期:2021-01-25 00:00:00

  • Molecular mechanism of introduction of the hidden break into the 28S rRNA of insects: implication based on structural studies.

    abstract::We determined the structure around the gap region between 28S alpha and 28S beta rRNA of Bombyx mori, a lepidopteran insect, to know the introduction mechanism of the hidden break, an interruption of the phosphodiester bond specific to the 28S rRNA of protostomes. Sequence analysis and S1 nuclease mapping suggested th...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/14.16.6393

    authors: Fujiwara H,Ishikawa H

    更新日期:1986-08-26 00:00:00

  • Rapid synthesis of oligodeoxyribonucleotides. II. Machine-aided solid-phase syntheses of two nonanucleotides and an octanucleotide.

    abstract::Preparation of the two nonanucleotides, d(pG-G-A-G-G-A-G-A-A) and d(pT-T-C-T-G-T-T-G-A), and the octanucleotide, d(pT-G-G-C-C-C-A-T) is described by a rapid solid-phase method on a polyamide support. The syntheses were carried out using a modified solid-phase peptide synthesiser and required one day for each nucleotid...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/4.12.4391

    authors: Gait MJ,Sheppard RC

    更新日期:1977-12-01 00:00:00

  • Anisotropic overall and internal motions of short DNA fragments.

    abstract::Anisotropic motions of DNA fragments in the size range 6-118 base pairs are studied by the steady-state fluorescence polarization of different excitation transitions in the intercalated ethidium cation. Calculated effective tumbling and twisting times are found to be shorter than predicted for overall motions of rigid...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/14.9.3945

    authors: Härd T,Kearns DR

    更新日期:1986-05-12 00:00:00

  • Epitope mapping using combinatorial phage-display libraries: a graph-based algorithm.

    abstract::A phage-display library of random peptides is a combinatorial experimental technique that can be harnessed for studying antibody-antigen interactions. In this technique, a phage peptide library is scanned against an antibody molecule to obtain a set of peptides that are bound by the antibody with high affinity. This s...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkl975

    authors: Mayrose I,Shlomi T,Rubinstein ND,Gershoni JM,Ruppin E,Sharan R,Pupko T

    更新日期:2007-01-01 00:00:00

  • DNA binding and oligomerization of NtrC studied by fluorescence anisotropy and fluorescence correlation spectroscopy.

    abstract::Fluorescence anisotropy and fluorescence correlation spectroscopy measurements of rhodamine-labeled DNA oligonucleotide duplexes have been used to determine equilibrium binding constants for DNA binding of the prokaryotic transcription activator protein NtrC. Measurements were made with wild-type NtrC from Escherichia...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/26.6.1373

    authors: Sevenich FW,Langowski J,Weiss V,Rippe K

    更新日期:1998-03-15 00:00:00

  • The use of R-looping for structural gene identification and mRNA purification.

    abstract::A method is presented for the purification of mRNAs and the identification of structural gene sequences in recombinant DNA molecules. RNA is hybridized to double-stranded linear DNA such that R-loops are formed between most DNAs and their complementary RNA sequences. These R-loops are purified from unhybridized RNAs b...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/6.7.2483

    authors: Woolford JL Jr,Rosbash M

    更新日期:1979-06-11 00:00:00

  • Deoxyribozymes that recode sequence information.

    abstract::Allosteric nucleic acid ligases have been used previously to transform analyte-binding into the formation of oligonucleotide templates that can be amplified and detected. We have engineered binary deoxyribozyme ligases whose two components are brought together by bridging oligonucleotide effectors. The engineered liga...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkl176

    authors: Tabor JJ,Levy M,Ellington AD

    更新日期:2006-04-28 00:00:00

  • ArrayOme: a program for estimating the sizes of microarray-visualized bacterial genomes.

    abstract::ArrayOme is a new program that calculates the size of genomes represented by microarray-based probes and facilitates recognition of key bacterial strains carrying large numbers of novel genes. Protein-coding sequences (CDS) that are contiguous on annotated reference templates and classified as 'Present' in the test st...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gni005

    authors: Ou HY,Smith R,Lucchini S,Hinton J,Chaudhuri RR,Pallen M,Barer MR,Rajakumar K

    更新日期:2005-01-07 00:00:00

  • Repressor CopG prevents access of RNA polymerase to promoter and actively dissociates open complexes.

    abstract::Replication of the promiscuous plasmid pMV158 requires expression of the initiator repB gene, which is controlled by the repressor CopG. Genes repB and copG are co-transcribed from promoter P(cr). We have studied the interactions between RNA polymerase, CopG and the promoter to elucidate the mechanism of repression by...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkp503

    authors: Hernández-Arriaga AM,Rubio-Lepe TS,Espinosa M,del Solar G

    更新日期:2009-08-01 00:00:00

  • GeConT 2: gene context analysis for orthologous proteins, conserved domains and metabolic pathways.

    abstract::The Gene Context Tool (GeConT) allows users to visualize the genomic context of a gene or a group of genes and their orthologous relationships within fully sequenced bacterial genomes. The new version of the server incorporates information from the COG, Pfam and KEGG databases, allowing users to have an integrated gra...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkn330

    authors: Martinez-Guerrero CE,Ciria R,Abreu-Goodger C,Moreno-Hagelsieb G,Merino E

    更新日期:2008-07-01 00:00:00

  • A mostly traditional approach improves alignment of bisulfite-converted DNA.

    abstract::Cytosines in genomic DNA are sometimes methylated. This affects many biological processes and diseases. The standard way of measuring methylation is to use bisulfite, which converts unmethylated cytosines to thymines, then sequence the DNA and compare it to a reference genome sequence. We describe a method for the cri...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gks275

    authors: Frith MC,Mori R,Asai K

    更新日期:2012-07-01 00:00:00

  • Pharos: Collating protein information to shed light on the druggable genome.

    abstract::The 'druggable genome' encompasses several protein families, but only a subset of targets within them have attracted significant research attention and thus have information about them publicly available. The Illuminating the Druggable Genome (IDG) program was initiated in 2014, has the goal of developing experimental...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkw1072

    authors: Nguyen DT,Mathias S,Bologa C,Brunak S,Fernandez N,Gaulton A,Hersey A,Holmes J,Jensen LJ,Karlsson A,Liu G,Ma'ayan A,Mandava G,Mani S,Mehta S,Overington J,Patel J,Rouillard AD,Schürer S,Sheils T,Simeonov A,Sklar L

    更新日期:2017-01-04 00:00:00

  • On the cooperative and noncooperative binding of ethidium to DNA.

    abstract::The equilibrium binding of ethidium bromide to native DNAs and to poly(dG-dC) X poly(dG-dC) has been studied by both phase partition and direct spectrophotometric techniques. The binding isotherms obtained from both experimental techniques show that ethidium binds in a cooperative manner to E. coli DNA. On the other h...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/10.24.8211

    authors: Winkle SA,Rosenberg LS,Krugh TR

    更新日期:1982-12-20 00:00:00

  • Detection of oligonucleotide hybridization at femtomolar level and sequence-specific gene analysis of the Arabidopsis thaliana leaf extract with an ultrasensitive surface plasmon resonance spectrometer.

    abstract::A flow-injection (FI) device is combined, through the use of a low-volume (4 microl) flow cell, with an ultrasensitive surface plasmon resonance (SPR) spectrometer equipped with a bi-cell photodiode detector. The application of this novel FI-SPR device for sequence-specific ultratrace analysis of oligodeoxynucleotides...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gnf072

    authors: Song F,Zhou F,Wang J,Tao N,Lin J,Vellanoweth RL,Morquecho Y,Wheeler-Laidman J

    更新日期:2002-07-15 00:00:00

  • Pseudomonas aeruginosa MutL promotes large chromosomal deletions through non-homologous end joining to prevent bacteriophage predation.

    abstract::Pseudomonas aeruginosa is an opportunistic pathogen with a relatively large genome, and has been shown to routinely lose genomic fragments during environmental selection. However, the underlying molecular mechanisms that promote chromosomal deletion are still poorly understood. In a recent study, we showed that by del...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gky160

    authors: Shen M,Zhang H,Shen W,Zou Z,Lu S,Li G,He X,Agnello M,Shi W,Hu F,Le S

    更新日期:2018-05-18 00:00:00

  • A coronary artery disease-associated tRNAThr mutation altered mitochondrial function, apoptosis and angiogenesis.

    abstract::The tissue specificity of mitochondrial tRNA mutations remains largely elusive. In this study, we demonstrated the deleterious effects of tRNAThr 15927G>A mutation that contributed to pathogenesis of coronary artery disease. The m.15927G>A mutation abolished the highly conserved base-pairing (28C-42G) of anticodon ste...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gky1241

    authors: Jia Z,Zhang Y,Li Q,Ye Z,Liu Y,Fu C,Cang X,Wang M,Guan MX

    更新日期:2019-02-28 00:00:00

  • A new method for predicting signal sequence cleavage sites.

    abstract::A new method for identifying secretory signal sequences and for predicting the site of cleavage between a signal sequence and the mature exported protein is described. The predictive accuracy is estimated to be around 75-80% for both prokaryotic and eukaryotic proteins. ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/14.11.4683

    authors: von Heijne G

    更新日期:1986-06-11 00:00:00

  • Gene F of plasmid RSF1010 codes for a low-molecular-weight repressor protein that autoregulates expression of the repAC operon.

    abstract::The repAC operon of plasmid RSF1010 consists of the genes for proteins E, F, RepA (DNA helicase), and RepC (origin-binding initiator protein) and is transcriptionally initiated by a promoter called P4. We have studied the expression of the repAC operon in vivo by using fusions to the lacZ reporter gene. The results sh...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/18.21.6215

    authors: Maeser S,Scholz P,Otto S,Scherzinger E

    更新日期:1990-11-11 00:00:00

  • Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4): an archaeal DinB-like DNA polymerase with lesion-bypass properties akin to eukaryotic poleta.

    abstract::Phylogenetic analysis of Y-family DNA polymerases suggests that it can be subdivided into several discrete branches consisting of UmuC/DinB/Rev1/Rad30/Rad30A and Rad30B. The most diverse is the DinB family that is found in all three kingdoms of life. Searches of the complete genome of the crenarchaeon Sulfolobus solfa...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/29.22.4607

    authors: Boudsocq F,Iwai S,Hanaoka F,Woodgate R

    更新日期:2001-11-15 00:00:00

  • Mutations in the RNA polymerase recognition sequence of the Klebsiella pneumoniae nifH promoter permitting transcriptional activation in the absence of NifA binding to upstream activator sequences.

    abstract::Positive control of the wild-type Klebsiella pneumoniae nifH promoter by the NifA protein requires that NifA is bound at the upstream activator sequence (UAS). By introducing base substitutions at -15 to -17 in the RNA polymerase recognition sequence of the nifH promoter, positive control by a form of NifA unable to b...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/17.7.2597

    authors: Buck M,Cannon W

    更新日期:1989-04-11 00:00:00

  • Regulation of UMSBP activities through redox-sensitive protein domains.

    abstract::UMSBP is a CCHC-type zinc finger protein, which functions during replication initiation of kinetoplast DNA minicircles and the segregation of kinetoplast DNA networks. Interactions of UMSBP with origin sequences, as well as the protein oligomerization, are affected by its redox state. Reduction yields UMSBP monomers a...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkn927

    authors: Sela D,Shlomai J

    更新日期:2009-01-01 00:00:00

  • Exogenous RNAi mechanisms contribute to transcriptome adaptation by phased siRNA clusters in Paramecium.

    abstract::Extensive research has characterized distinct exogenous RNAi pathways interfering in gene expression during vegetative growth of the unicellular model ciliate Paramecium. However, role of RNAi in endogenous transcriptome regulation, and environmental adaptation is unknown. Here, we describe the first genome-wide profi...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkz553

    authors: Karunanithi S,Oruganti V,Marker S,Rodriguez-Viana AM,Drews F,Pirritano M,Nordström K,Simon M,Schulz MH

    更新日期:2019-09-05 00:00:00

  • WDHD1 modulates the post-transcriptional step of the centromeric silencing pathway.

    abstract::The centromere is a highly specialized chromosomal element that is essential for chromosome segregation during mitosis. Centromere integrity must therefore be properly preserved and is strictly dependent upon the establishment and maintenance of surrounding chromatin structure. Here we identify WDHD1, a WD40-domain an...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkq1338

    authors: Hsieh CL,Lin CL,Liu H,Chang YJ,Shih CJ,Zhong CZ,Lee SC,Tan BC

    更新日期:2011-05-01 00:00:00