Bacterial repression loops require enhanced DNA flexibility.

Abstract:

:The Escherichia coli lac operon provides a classic paradigm for understanding regulation of gene transcription. It is now appreciated that lac promoter repression involves cooperative binding of the bidentate lac repressor tetramer to pairs of lac operators via DNA looping. We have adapted components of this system to create an artificial assay of DNA flexibility in E.coli. This approach allows for systematic study of endogenous and exogenous proteins as architectural factors that enhance apparent DNA flexibility in vivo. We show that inducer binding does not completely remove repression loops but it does alter their geometries. Deletion of the E.coli HU protein drastically destabilizes small repression loops, an effect that can be partially overcome by expression of a heterologous mammalian HMG protein. These results emphasize that the inherent torsional inflexibility of DNA restrains looping and must be modulated in vivo.

journal_name

J Mol Biol

authors

Becker NA,Kahn JD,Maher LJ 3rd

doi

10.1016/j.jmb.2005.04.035

keywords:

subject

Has Abstract

pub_date

2005-06-17 00:00:00

pages

716-30

issue

4

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(05)00455-9

journal_volume

349

pub_type

杂志文章
  • The anticodon loop is a major identity determinant of Saccharomyces cerevisiae tRNA(Leu).

    abstract::The recognition of tRNALeu, one of the class II tRNAs having a long variable arm, by leucyl-tRNA synthetase in Saccharomyces cerevisiae was studied using the T7 transcription system. Exchanging the anticodon arm of tRNALeu but not the D- or T psi C-arm to that of tRNASer seriously affected the leucine accepting activi...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1996.0610

    authors: Soma A,Kumagai R,Nishikawa K,Himeno H

    更新日期:1996-11-15 00:00:00

  • The RecG branch migration protein of Escherichia coli dissociates R-loops.

    abstract::The RuvAB and RecG proteins of Escherichia coli promote branch migration of Holliday junction intermediates in genetic recombination. Both are structure-specific helicases that unwind and rewind DNA at the junction point. The helicase activities of these proteins were investigated using RNA:DNA hybrid molecules. RuvAB...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1996.0671

    authors: Vincent SD,Mahdi AA,Lloyd RG

    更新日期:1996-12-13 00:00:00

  • Recognition elements in rRNA for the tylosin resistance methyltransferase RlmA(II).

    abstract::The methyltransferase RlmA(II) (formerly TlrB) is found in many Gram-positive bacteria, and methylates the N-1 position of nucleotide G748 within the loop of hairpin 35 in 23S rRNA. Methylation of the rRNA by RlmA(II) confers resistance to tylosin and other mycinosylated 16-membered ring macrolide antibiotics. We have...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2007.06.068

    authors: Lebars I,Husson C,Yoshizawa S,Douthwaite S,Fourmy D

    更新日期:2007-09-14 00:00:00

  • A novel disulfide bond in the SH2 Domain of the C-terminal Src kinase controls catalytic activity.

    abstract::The SH2 domain of the C-terminal Src kinase [Csk] contains a unique disulfide bond that is not present in other known SH2 domains. To investigate whether this unusual disulfide bond serves a novel function, the effects of disulfide bond formation on catalytic activity of the full-length protein and on the structure of...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2006.10.076

    authors: Mills JE,Whitford PC,Shaffer J,Onuchic JN,Adams JA,Jennings PA

    更新日期:2007-02-02 00:00:00

  • The central PPT of the yeast retrotransposon Ty1 is not essential for transposition.

    abstract::The yeast retrotransposon Ty1 has structural and functional similarities to retroviruses. We report here that, as in retroviruses, the plus-strand DNA of Ty1 is synthesized as two segments. A central DNA flap is formed during reverse transcription consecutive to elongation (with strand displacement) of the upstream se...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(03)00812-x

    authors: Heyman T,Wilhelm M,Wilhelm FX

    更新日期:2003-08-08 00:00:00

  • Nerve growth factor in different crystal forms displays structural flexibility and reveals zinc binding sites.

    abstract::Murine beta-nerve growth factor (beta NGF) is a 118 amino acid residue polypeptide which, as a functional dimer, plays an important role in the survival and development of certain neuronal populations. The structure of the bis-desocta1-8 form of murine beta NGF has been determined in two different crystal modification...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1994.1380

    authors: Holland DR,Cousens LS,Meng W,Matthews BW

    更新日期:1994-06-10 00:00:00

  • A TOPRIM domain in the crystal structure of the catalytic core of Escherichia coli primase confirms a structural link to DNA topoisomerases.

    abstract::Primases synthesize short RNA strands on single-stranded DNA templates, thereby generating the hybrid duplexes required for the initiation of synthesis by DNA polymerases. We present the crystal structure of the catalytic unit of a primase enzyme, that of a approximately 320 residue fragment of Escherichia coli primas...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2000.3844

    authors: Podobnik M,McInerney P,O'Donnell M,Kuriyan J

    更新日期:2000-07-07 00:00:00

  • Characterization of in vitro and in vivo mutations in non-conserved nucleotides in the ribosomal RNA recognition domain for the ribotoxins ricin and sarcin and the translation elongation factors.

    abstract::The sarcin/ricin domain in 23 S/28 S rRNA is crucial for ribosome function, since it constitutes at least part of the binding site for the elongation factors and hence is essential for binding aminoacyl-tRNA and for translocation. The domain is also the site of action of ricin and sarcin and analysis of the effect of ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1998.2337

    authors: Macbeth MR,Wool IG

    更新日期:1999-01-15 00:00:00

  • Structural analysis of CYP2R1 in complex with vitamin D3.

    abstract::The activation of vitamin D to its hormonal form is mediated by cytochrome P450 enzymes. CYP2R1 catalyzes the initial step converting vitamin D into 25-hydroxyvitamin D. A CYP2R1 gene mutation causes an inherited form of rickets due to 25-hydroxylase deficiency. To understand the narrow substrate specificity of CYP2R1...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2008.03.065

    authors: Strushkevich N,Usanov SA,Plotnikov AN,Jones G,Park HW

    更新日期:2008-06-27 00:00:00

  • The Alternate Pathway for BCR Signaling Induced by IL-4 Requires Lyn Tyrosine Kinase.

    abstract::BCR signaling triggers a cascade of intracellular mediators that eventuates in transcription factor activation. Signaling is proximally mediated by Src family tyrosine kinases, the most abundant being Lyn. Key mediators are grouped together as the signalosome, and failure of any single member of this group leads to fa...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.jmb.2020.10.002

    authors: Khan N,Rothstein TL

    更新日期:2021-01-08 00:00:00

  • Robust mechanosensing and tension generation by myosin VI.

    abstract::Myosin VI is a molecular motor that is thought to function both as a transporter and as a cytoskeletal anchor in vivo. Here we use optical tweezers to examine force generation by single molecules of myosin VI under physiological nucleotide concentrations. We find that myosin VI is an efficient transporter at loads of ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2010.10.010

    authors: Chuan P,Spudich JA,Dunn AR

    更新日期:2011-01-07 00:00:00

  • Structure of the minimal interface between ApoE and LRP.

    abstract::Clusters of complement-type ligand-binding repeats (CRs) in the low-density lipoprotein receptor (LDLR) family are thought to mediate the interactions with their various ligands. Apolipoprotein E (ApoE), a key ligand for cholesterol homeostasis, has been shown to interact with LDLR-related protein 1 (LRP) through thes...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2010.03.022

    authors: Guttman M,Prieto JH,Handel TM,Domaille PJ,Komives EA

    更新日期:2010-04-30 00:00:00

  • Heterocyst-forming filamentous cyanobacteria encode proteins that resemble eukaryotic RNA-binding proteins of the RNP family.

    abstract::Heterocyst-forming cyanobacteria have multiple genes encoding proteins that are similar to the RNP family of eukaryotic RNA-binding proteins. Three genes from two strains of cyanobacteria (Anabaena and Chlorogloeopsis) have been sequenced. All three putative gene products contain a single RNA Recognition Motif (RRM) t...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1994.1070

    authors: Mulligan ME,Jackman DM,Murphy ST

    更新日期:1994-01-21 00:00:00

  • The antiterminator RNA of phage HK022.

    abstract::The put sites of phage HK022 increase the processivity of transcription and thereby promote the expression of viral genes that are located downstream of transcription terminators. RNA polymerase molecules that have traversed a put site are converted to a terminator-resistant form by the put transcript. We analyzed the...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1997.1251

    authors: Banik-Maiti S,King RA,Weisberg RA

    更新日期:1997-10-10 00:00:00

  • Molecular and structural basis for redox regulation of beta-actin.

    abstract::An essential consequence of growth factor-mediated signal transduction is the generation of intracellular H(2)O(2). It operates as a second messenger in the control of actin microfilament dynamics, causing rapid and dramatic changes in the morphology and motile activity of stimulated cells. Little is understood about ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2007.04.056

    authors: Lassing I,Schmitzberger F,Björnstedt M,Holmgren A,Nordlund P,Schutt CE,Lindberg U

    更新日期:2007-07-06 00:00:00

  • ABCF ATPases Involved in Protein Synthesis, Ribosome Assembly and Antibiotic Resistance: Structural and Functional Diversification across the Tree of Life.

    abstract::Within the larger ABC superfamily of ATPases, ABCF family members eEF3 in Saccharomyces cerevisiae and EttA in Escherichia coli have been found to function as ribosomal translation factors. Several other ABCFs including biochemically characterized VgaA, LsaA and MsrE confer resistance to antibiotics that target the pe...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2018.12.013

    authors: Murina V,Kasari M,Takada H,Hinnu M,Saha CK,Grimshaw JW,Seki T,Reith M,Putrinš M,Tenson T,Strahl H,Hauryliuk V,Atkinson GC

    更新日期:2019-08-23 00:00:00

  • Recognition of the highly conserved GTPase center of 23 S ribosomal RNA by ribosomal protein L11 and the antibiotic thiostrepton.

    abstract::The antibiotic thiostrepton, a thiazole-containing peptide, inhibits translation and ribosomal GTPase activity by binding directly to a limited and highly conserved region of the large subunit ribosomal RNA termed the GTPase center. We have previously used a filter binding assay to examine the binding of ribosomal pro...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(91)90932-v

    authors: Ryan PC,Lu M,Draper DE

    更新日期:1991-10-20 00:00:00

  • Identification of pregnane X receptor binding sites in the regulatory regions of genes involved in bile acid homeostasis.

    abstract::The nuclear receptor pregnane X receptor (PXR) acts as a sensor for a broad variety of natural and synthetic lipophilic compounds, such as bile acids and rifampicin, and regulates the expression of proteins that are involved in the metabolism and transport of these compounds. PXR binds as a heterodimer with the retino...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2004.12.003

    authors: Frank C,Makkonen H,Dunlop TW,Matilainen M,Väisänen S,Carlberg C

    更新日期:2005-02-18 00:00:00

  • Thermodynamic and structural basis for transition-state stabilization in antibody-catalyzed hydrolysis.

    abstract::Catalytic antibodies 6D9 and 9C10, which were induced by immunization with a haptenic transition-state analog (TSA), catalyze the hydrolysis of a nonbioactive chloramphenicol monoester derivative to generate a bioactive chloramphenicol. These antibodies stabilize the transition state to catalyze the hydrolysis reactio...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2007.03.023

    authors: Oda M,Ito N,Tsumuraya T,Suzuki K,Sakakura M,Fujii I

    更新日期:2007-05-25 00:00:00

  • Nucleotide sequences of Caenorhabditis elegans core histone genes. Genes for different histone classes share common flanking sequence elements.

    abstract::We have determined the nucleotide sequence of core histone genes and flanking regions from two of approximately 11 different genomic histone clusters of the nematode Caenorhabditis elegans. Four histone genes from one cluster (H3, H4, H2B, H2A) and two histone genes from another (H4 and H2A) were analyzed. The predict...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(89)90566-4

    authors: Roberts SB,Emmons SW,Childs G

    更新日期:1989-04-20 00:00:00

  • Monitoring Ligand-Induced Protein Ordering in Drug Discovery.

    abstract::While the gene for p53 is mutated in many human cancers causing loss of function, many others maintain a wild-type gene but exhibit reduced p53 tumor suppressor activity through overexpression of the negative regulators, Mdm2 and/or MdmX. For the latter mechanism of loss of function, the activity of endogenous p53 can...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2016.01.016

    authors: Grace CR,Ban D,Min J,Mayasundari A,Min L,Finch KE,Griffiths L,Bharatham N,Bashford D,Kiplin Guy R,Dyer MA,Kriwacki RW

    更新日期:2016-03-27 00:00:00

  • DNA double-strand break in vivo at the 3' extremity of exons located upstream of group II introns. Senescence and circular DNA introns in Podospora mitochondria.

    abstract::In the filamentous fungus Podospora anserina, the unavoidable phenomenon of senescence is associated with the amplification of the first intron of the mitochondrial cox1 that accumulates as circular DNA molecules consisting of tandem repeats. This group II intron (cox1-i1 or alpha) is able to transpose and contains an...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1994.1613

    authors: Sainsard-Chanet A,Begel O,Belcour L

    更新日期:1994-10-07 00:00:00

  • A thermodynamic and kinetic analysis of the folding pathway of an SH3 domain entropically stabilised by a redesigned hydrophobic core.

    abstract::The folding thermodynamics and kinetics of the alpha-spectrin SH3 domain with a redesigned hydrophobic core have been studied. The introduction of five replacements, A11V, V23L, M25V, V44I and V58L, resulted in an increase of 16% in the overall volume of the side-chains forming the hydrophobic core but caused no remar...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(03)00273-0

    authors: Cobos ES,Filimonov VV,Vega MC,Mateo PL,Serrano L,Martínez JC

    更新日期:2003-04-18 00:00:00

  • Organization and evolution of repeated DNA sequences in closely related plant genomes.

    abstract::In common with many other eukaryotic species, the genomes of species in the genus Allium contain a high proportion of repeated DNA sequences, which may be implicated in the considerable differences in genome size that are seen between even very closely related species. The gross organization of repetitive sequences wi...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(83)80189-2

    authors: Evans IJ,James AM,Barnes SR

    更新日期:1983-11-15 00:00:00

  • Base sequence and helix structure variation in B and A DNA.

    abstract::The observed propeller twist in base-pairs of crystalline double-helical DNA oligomers improves the stacking overlap along each individual helix strand. But, as proposed by Calladine, it also leads to clash or steric hindrance between purines at adjacent base-pairs on opposite strands of the helix. This clash can be r...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(83)80093-x

    authors: Dickerson RE

    更新日期:1983-05-25 00:00:00

  • Threshold occupancy and specific cation binding modes in the hammerhead ribozyme active site are required for active conformation.

    abstract::The relationship between formation of active in-line attack conformations and monovalent (Na(+)) and divalent (Mg(2+)) metal ion binding in hammerhead ribozyme (HHR) has been explored with molecular dynamics simulations. To stabilize repulsions between negatively charged groups, different requirements of the threshold...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2009.02.054

    authors: Lee TS,Giambaşu GM,Sosa CP,Martick M,Scott WG,York DM

    更新日期:2009-04-24 00:00:00

  • Folding pathway of FKBP12 and characterisation of the transition state.

    abstract::The folding pathway of human FKBP12, a 12 kDa FK506-binding protein (immunophilin), has been characterised. Unfolding and refolding rate constants have been determined over a wide range of denaturant concentrations and data are shown to fit to a two-state model of folding in which only the denatured and native states ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1999.2941

    authors: Main ER,Fulton KF,Jackson SE

    更新日期:1999-08-13 00:00:00

  • A pi-helix switch selective for porphyrin deprotonation and product release in human ferrochelatase.

    abstract::Ferrochelatase (protoheme ferrolyase, EC 4.99.1.1) is the terminal enzyme in heme biosynthesis and catalyzes the insertion of ferrous iron into protoporphyrin IX to form protoheme IX (heme). Due to the many critical roles of heme, synthesis of heme is required by the vast majority of organisms. Despite significant inv...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2007.08.040

    authors: Medlock AE,Dailey TA,Ross TA,Dailey HA,Lanzilotta WN

    更新日期:2007-11-02 00:00:00

  • Mitochondrial DNA Purifying Selection in Mammals and Invertebrates.

    abstract::Numerous mitochondrial quality control mechanisms exist within cells, but none have been shown to effectively assess and control the quality of mitochondrial DNA (mtDNA). One reason such mechanisms have yet to be elucidated is that they do not appear to be particularly active in most somatic cells, where many studies ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.jmb.2018.10.019

    authors: Palozzi JM,Jeedigunta SP,Hurd TR

    更新日期:2018-12-07 00:00:00

  • Stability and DNA-binding ability of the bZIP dimers formed by the ATF-2 and c-Jun transcription factors.

    abstract::The dimer formed by the ATF-2 and c-Jun transcription factors is one of the main components of the human interferon-beta enhanceosome. Although these two transcription factors are able to form two homodimers and one heterodimer, it is mainly the heterodimer that participates in the formation of this enhanceosome, bind...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2009.11.050

    authors: Carrillo RJ,Dragan AI,Privalov PL

    更新日期:2010-02-19 00:00:00