当前位置： SCI文献检索 > NUCLEIC ACIDS RESEARCH期刊下所有文献 > A type IV modification-dependent restriction enzyme SauUSI from Staphylococcus aureus subsp. aureus USA300.

A type IV modification-dependent restriction enzyme SauUSI from Staphylococcus aureus subsp. aureus USA300.

Abstract：

:A gene encoding a putative DNA helicase from Staphylococcus aureus USA300 was cloned and expressed in Escherichia coli. The protein was purified to over 90% purity by chromatography. The purified enzyme, SauUSI, predominantly cleaves modified DNA containing 5mC and 5-hydroxymethylcytosine. Cleavage of 5mC-modified plasmids indicated that the sites S5mCNGS (S = C or G) are preferentially digested. The endonuclease activity requires the presence of adenosine triphosphate (ATP) or dATP whereas the non-hydrolyzable γ-S-ATP does not support activity. SauUSI activity was inhibited by ethylenediaminetetraacetic acid. It is most active in Mg(++) buffers. No companion methylase gene was found near the SauUSI restriction gene. The absence of a cognate methylase and cleavage of modified DNA indicate that SauUSI belongs to type IV restriction endonucleases, a group that includes EcoK McrBC and Mrr. SauUSI belongs to a family of highly similar homologs found in other sequenced S. aureus, S. epidermidis and S. carnosus genomes. More distant SauUSI orthologs can be found in over 150 sequenced bacterial/archaea genomes. Finally, we demonstrated the biological function of the type IV REase in restricting 5mC-modified plasmid DNA by transformation into clinical S. aureus strain SA564, and in restricting phage λ infection when the endonuclease is expressed in E. coli.

journal_name

Nucleic Acids Res

journal_title

Nucleic acids research

authors

Xu SY,Corvaglia AR,Chan SH,Zheng Y,Linder P

doi

10.1093/nar/gkr098

subject

Has Abstract

pub_date

2011-07-01 00:00:00

pages

5597-610

issue

13

eissn

0305-1048

issn

1362-4962

pii

gkr098

journal_volume

39

pub_type

杂志文章

相关文献

NUCLEIC ACIDS RESEARCH文献大全
  • Aging Chart: a community resource for rapid exploratory pathway analysis of age-related processes.

    abstract：:Aging research is a multi-disciplinary field encompassing knowledge from many areas of basic, applied and clinical research. Age-related processes occur on molecular, cellular, tissue, organ, system, organismal and even psychological levels, trigger the onset of multiple debilitating diseases and lead to a loss of fun...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkv1287

    authors： Moskalev A,Zhikrivetskaya S,Shaposhnikov M,Dobrovolskaya E,Gurinovich R,Kuryan O,Pashuk A,Jellen LC,Aliper A,Peregudov A,Zhavoronkov A

    更新日期：2016-01-04 00:00:00

  • c-MYC empowers transcription and productive splicing of the oncogenic splicing factor Sam68 in cancer.

    abstract：:The splicing factor Sam68 is upregulated in many human cancers, including prostate cancer (PCa) where it promotes cell proliferation and survival. Nevertheless, in spite of its frequent upregulation in cancer, the mechanism(s) underlying its expression are largely unknown. Herein, bioinformatics analyses identified th...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkz344

    authors： Caggiano C,Pieraccioli M,Panzeri V,Sette C,Bielli P

    更新日期：2019-07-09 00:00:00

  • Elastic network models for RNA: a comparative assessment with molecular dynamics and SHAPE experiments.

    abstract：:Elastic network models (ENMs) are valuable and efficient tools for characterizing the collective internal dynamics of proteins based on the knowledge of their native structures. The increasing evidence that the biological functionality of RNAs is often linked to their innate internal motions poses the question of whet...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkv708

    authors： Pinamonti G,Bottaro S,Micheletti C,Bussi G

    更新日期：2015-09-03 00:00:00

  • Real-time measurement of in vitro transcription.

    abstract：:We have developed a simple method to measure RNA synthesis in real time. In this technique, transcription reactions are performed in the presence of molecular beacons that possess a 2'-O-methylribonucleotide backbone. These probes become fluorescent as they hybridize to nascent RNA during the course of synthesis. We f...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gnh068

    authors： Marras SA,Gold B,Kramer FR,Smith I,Tyagi S

    更新日期：2004-05-20 00:00:00

  • Chloroplast transit peptide prediction: a peek inside the black box.

    abstract：:Previous work in predicting protein localization to the chloroplast organelle in plants led to the development of an artificial neural network-based approach capable of remarkable accuracy in its prediction (ChloroP). A common criticism against such neural network models is that it is difficult to interpret the criter...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/29.16.e82

    authors： Schein AI,Kissinger JC,Ungar LH

    更新日期：2001-08-15 00:00:00

  • CAMP: Collection of sequences and structures of antimicrobial peptides.

    abstract：:Antimicrobial peptides (AMPs) are gaining importance as anti-infective agents. Here we describe the updated Collection of Antimicrobial Peptide (CAMP) database, available online at http://www.camp.bicnirrh.res.in/. The 3D structures of peptides are known to influence antimicrobial activity. Although there exists datab...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkt1157

    authors： Waghu FH,Gopi L,Barai RS,Ramteke P,Nizami B,Idicula-Thomas S

    更新日期：2014-01-01 00:00:00

  • RF-Cloning.org: an online tool for the design of restriction-free cloning projects.

    abstract：:Restriction-free cloning (RF-cloning) is a PCR-based technology that expands on the QuikChange™ mutagenesis process originally popularized by Stratagene in the mid-1990s, and allows the insertion of essentially any sequence into any plasmid at any location. While RF-cloning is a powerful tool for the design of custom ...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gks396

    authors： Bond SR,Naus CC

    更新日期：2012-07-01 00:00:00

  • The structure of tRNA 5 Lys from Drosophila melanogaster.

    abstract：:The nucleotide sequence of Drosophila melanogaster tRNA 5 Lys is pGCCCGGAUAm2GCUCAGDCGGDAGAGCA psi psi GGACUsU*UUt6A*A psi CCAAGGm7GDm5CCAGGGTm psi CAm1AGUCCCUGUUCGGGCGCCA. The sU* is probably 5-methylcarboxymethyl-2-thiouridine and t6A* is a mixture of modified derivatives of t6A including t6A itself and a component ...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/10.20.6393

    authors： Cribbs DL,Gillam IC,Tener GM

    更新日期：1982-10-25 00:00:00

  • Synergistic effects of ATP and RNA binding to human DEAD-box protein DDX1.

    abstract：:RNA helicases of the DEAD-box protein family form the largest group of helicases. The human DEAD-box protein 1 (DDX1) plays an important role in tRNA and mRNA processing, is involved in tumor progression and is also hijacked by several virus families such as HIV-1 for replication and nuclear export. Although important...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkv106

    authors： Kellner JN,Reinstein J,Meinhart A

    更新日期：2015-03-11 00:00:00

  • Characterization of the 3' exonuclease subunit DP1 of Methanococcus jannaschii replicative DNA polymerase D.

    abstract：:The B-subunits associated with the replicative DNA polymerases are conserved from Archaea to humans, whereas the corresponding catalytic subunits are not related. The latter belong to the B and D DNA polymerase families in eukaryotes and archaea, respectively. Sequence analysis places the B-subunits within the calcine...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkh558

    authors： Jokela M,Eskelinen A,Pospiech H,Rouvinen J,Syväoja JE

    更新日期：2004-04-30 00:00:00

  • DNA compaction by the bacteriophage protein Cox studied on the single DNA molecule level using nanofluidic channels.

    abstract：:The Cox protein from bacteriophage P2 forms oligomeric filaments and it has been proposed that DNA can be wound up around these filaments, similar to how histones condense DNA. We here use fluorescence microscopy to study single DNA-Cox complexes in nanofluidic channels and compare how the Cox homologs from phages P2 ...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkw352

    authors： Frykholm K,Berntsson RP,Claesson M,de Battice L,Odegrip R,Stenmark P,Westerlund F

    更新日期：2016-09-06 00:00:00

  • Cas9-chromatin binding information enables more accurate CRISPR off-target prediction.

    abstract：:The CRISPR system has become a powerful biological tool with a wide range of applications. However, improving targeting specificity and accurately predicting potential off-targets remains a significant goal. Here, we introduce a web-based CR: ISPR/Cas9 O: ff-target P: rediction and I: dentification T: ool (CROP-IT) th...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkv575

    authors： Singh R,Kuscu C,Quinlan A,Qi Y,Adli M

    更新日期：2015-10-15 00:00:00

  • Spectral clustering of protein sequences.

    abstract：:An important problem in genomics is automatically clustering homologous proteins when only sequence information is available. Most methods for clustering proteins are local, and are based on simply thresholding a measure related to sequence distance. We first show how locality limits the performance of such methods by...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkj515

    authors： Paccanaro A,Casbon JA,Saqi MA

    更新日期：2006-03-17 00:00:00

  • Long noncoding RNA HCP5 participates in premature ovarian insufficiency by transcriptionally regulating MSH5 and DNA damage repair via YB1.

    abstract：:The genetic etiology of premature ovarian insufficiency (POI) has been well established to date, however, the role of long noncoding RNAs (lncRNAs) in POI is largely unknown. In this study, we identified a down-expressed lncRNA HCP5 in granulosa cells (GCs) from biochemical POI (bPOI) patients, which impaired DNA dama...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkaa127

    authors： Wang X,Zhang X,Dang Y,Li D,Lu G,Chan WY,Leung PCK,Zhao S,Qin Y,Chen ZJ

    更新日期：2020-05-07 00:00:00

  • BSD: the Biodegradative Strain Database.

    abstract：:The Biodegradative Strain Database (BSD) is a freely-accessible, web-based database providing detailed information on degradative bacteria and the hazardous substances that they degrade, including corresponding literature citations, relevant patents and links to additional web-based biological and chemical data. The B...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkg032

    authors： Urbance JW,Cole J,Saxman P,Tiedje JM

    更新日期：2003-01-01 00:00:00

  • ELM--the database of eukaryotic linear motifs.

    abstract：:Linear motifs are short, evolutionarily plastic components of regulatory proteins and provide low-affinity interaction interfaces. These compact modules play central roles in mediating every aspect of the regulatory functionality of the cell. They are particularly prominent in mediating cell signaling, controlling pro...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkr1064

    authors： Dinkel H,Michael S,Weatheritt RJ,Davey NE,Van Roey K,Altenberg B,Toedt G,Uyar B,Seiler M,Budd A,Jödicke L,Dammert MA,Schroeter C,Hammer M,Schmidt T,Jehl P,McGuigan C,Dymecka M,Chica C,Luck K,Via A,Chatr-Aryamont

    更新日期：2012-01-01 00:00:00

  • H/ACA snoRNA levels are regulated during stem cell differentiation.

    abstract：:H/ACA small nucleolar RNAs (snoRNAs) guide pseudouridylation as part of a small nucleolar ribonucleoprotein complex (snoRNP). Disruption of H/ACA snoRNA levels in stem cells impairs pluripotency, yet it remains unclear how H/ACA snoRNAs contribute to differentiation. To determine if H/ACA snoRNA levels are dynamic dur...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkaa612

    authors： McCann KL,Kavari SL,Burkholder AB,Phillips BT,Hall TMT

    更新日期：2020-09-04 00:00:00

  • The folding of the hepatitis C virus internal ribosome entry site depends on the 3'-end of the viral genome.

    abstract：:Hepatitis C virus (HCV) translation initiation is directed by an internal ribosome entry site (IRES) and regulated by distant regions at the 3'-end of the viral genome. Through a combination of improved RNA chemical probing methods, SHAPE structural analysis and screening of RNA accessibility using antisense oligonucl...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gks927

    authors： Romero-López C,Barroso-Deljesus A,García-Sacristán A,Briones C,Berzal-Herranz A

    更新日期：2012-12-01 00:00:00

  • TropGeneDB, the multi-tropical crop information system updated and extended.

    abstract：:TropGeneDB (http://tropgenedb.cirad.fr) was created to store genetic, molecular and phenotypic data on tropical crop species. The most common data stored in TropGeneDB are molecular markers, quantitative trait loci, genetic and physical maps, genetic diversity, phenotypic diversity studies and information on genetic r...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gks1105

    authors： Hamelin C,Sempere G,Jouffe V,Ruiz M

    更新日期：2013-01-01 00:00:00

  • Structural basis for substrate binding and catalytic mechanism of a human RNA:m5C methyltransferase NSun6.

    abstract：:5-methylcytosine (m5C) modifications of RNA are ubiquitous in nature and play important roles in many biological processes such as protein translational regulation, RNA processing and stress response. Aberrant expressions of RNA:m5C methyltransferases are closely associated with various human diseases including cancer...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkx473

    authors： Liu RJ,Long T,Li J,Li H,Wang ED

    更新日期：2017-06-20 00:00:00

  • Hexameric RSF1010 helicase RepA: the structural and functional importance of single amino acid residues.

    abstract：:In the known monoclinic crystals the 3-dimensional structure of the hexameric, replicative helicase RepA encoded by plasmid RSF1010 shows 6-fold rotational symmetry. In contrast, in the cubic crystal form at 2.55 A resolution described here RepA has 3-fold symmetry and consists of a trimer of dimers. To study structur...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkg790

    authors： Ziegelin G,Niedenzu T,Lurz R,Saenger W,Lanka E

    更新日期：2003-10-15 00:00:00

  • Overexpression of eIF5 or its protein mimic 5MP perturbs eIF2 function and induces ATF4 translation through delayed re-initiation.

    abstract：:ATF4 is a pro-oncogenic transcription factor whose translation is activated by eIF2 phosphorylation through delayed re-initiation involving two uORFs in the mRNA leader. However, in yeast, the effect of eIF2 phosphorylation can be mimicked by eIF5 overexpression, which turns eIF5 into translational inhibitor, thereby ...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkw559

    authors： Kozel C,Thompson B,Hustak S,Moore C,Nakashima A,Singh CR,Reid M,Cox C,Papadopoulos E,Luna RE,Anderson A,Tagami H,Hiraishi H,Slone EA,Yoshino KI,Asano M,Gillaspie S,Nietfeld J,Perchellet JP,Rothenburg S,Masai H,W

    更新日期：2016-10-14 00:00:00

  • Displacement of a DNA binding protein by Dda helicase.

    abstract：:Bacteriophage T4 Dda helicase has recently been shown to be active as a monomer for unwinding of short duplex oligonucleotides and for displacing streptavidin from 3'-biotinylated oligonucleotides. However, its activity for streptavidin displacement and DNA unwinding has been shown to increase as the number of Dda mol...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkl369

    authors： Byrd AK,Raney KD

    更新日期：2006-05-31 00:00:00

  • Importance of the reverse Hoogsteen base pair 54-58 for tRNA function.

    abstract：:To elucidate the general constraints imposed on the structure of the D- and T-loops in functional tRNAs, active suppressor tRNAs were selected in vivo from a combinatorial tRNA gene library in which several nucleotide positions of these loops were randomized. Analysis of the nucleotide sequences of the selected clones...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkg448

    authors： Zagryadskaya EI,Doyon FR,Steinberg SV

    更新日期：2003-07-15 00:00:00

  • Triple helix formation at distant sites: hybrid oligonucleotides containing a polymeric linker.

    abstract：:An oligonucleotide hybrid is described which possesses two triple helix forming oligonucleotides which have been connected by a flexible polymeric linker chain. As a prototype, binding of this class of oligonucleotide to duplex DNA has been studied using a segment of the HSV-1 D-glycoprotein promoter, which possesses ...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/21.20.4810

    authors： Kessler DJ,Pettitt BM,Cheng YK,Smith SR,Jayaraman K,Vu HM,Hogan ME

    更新日期：1993-10-11 00:00:00

  • A multi-fingerprint browser for the ZINC database.

    abstract：:To confirm the activity of an initial small molecule 'hit compound' from an activity screening, one needs to probe the structure-activity relationships by testing close analogs. The multi-fingerprint browser presented here (http://dcb-reymond23.unibe.ch:8080/MCSS/) enables one to rapidly identify such close analogs am...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gku379

    authors： Awale M,Reymond JL

    更新日期：2014-07-01 00:00:00

  • PCR performance of the B-type DNA polymerase from the thermophilic euryarchaeon Thermococcus aggregans improved by mutations in the Y-GG/A motif.

    abstract：:The effect of mutations in the highly conserved Y-GG/A motif of B-type DNA polymerases was studied in the DNA polymerase from the hyperthermophilic euryarchaeon Thermococcus aggregans. This motif plays a critical role in the balance between the synthesis and degradation of the DNA chain. Five different mutations of th...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/28.20.3910

    authors： Böhlke K,Pisani FM,Vorgias CE,Frey B,Sobek H,Rossi M,Antranikian G

    更新日期：2000-10-15 00:00:00

  • Femtosecond near-infrared laser microirradiation reveals a crucial role for PARP signaling on factor assemblies at DNA damage sites.

    abstract：:Laser microirradiation is a powerful tool for real-time single-cell analysis of the DNA damage response (DDR). It is often found, however, that factor recruitment or modification profiles vary depending on the laser system employed. This is likely due to an incomplete understanding of how laser conditions/dosages affe...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkv976

    authors： Saquilabon Cruz GM,Kong X,Silva BA,Khatibzadeh N,Thai R,Berns MW,Yokomori K

    更新日期：2016-02-18 00:00:00

  • HMMCONVERTER 1.0: a toolbox for hidden Markov models.

    abstract：:Hidden Markov models (HMMs) and their variants are widely used in Bioinformatics applications that analyze and compare biological sequences. Designing a novel application requires the insight of a human expert to define the model's architecture. The implementation of prediction algorithms and algorithms to train the m...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkp662

    authors： Lam TY,Meyer IM

    更新日期：2009-11-01 00:00:00

  • Structure and transcription of the Drosophila mulleri alcohol dehydrogenase genes.

    abstract：:The D. melanogaster Adh gene is transcribed from two different promoters; a proximal (larval) promoter is active during late embryonic and larval stages, and a distal (adult) promoter is active primarily in third instar larvae and in adult flies (1). Genetic analyses suggest that several species of the mulleri subgrou...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/13.19.6899

    authors： Fischer JA,Maniatis T

    更新日期：1985-10-11 00:00:00