Regulation of transcriptional silencing in yeast by growth temperature.

Abstract:

:Increasing evidence indicates that transcriptionally silent chromatin structure is dynamic and may change its conformation in response to external or internal stimuli. We show that growth temperature affects all three forms of transcriptional silencing in Saccharomyces cerevisiae. In general, increasing the temperature within the range of 23-37 degrees C strengthens HM and telomeric silencing but reduces rDNA silencing. High temperature (37 degrees C) can suppress the silencing defects of histone H4 mutants. We demonstrate that DNA at the silent HML locus becomes more and more negatively supercoiled as temperature increases in a Sir-dependent manner, which is indicative of enhanced silent chromatin. This enhancement of silent chromatin is not dependent on silencers and therefore does not require de novo assembly of silent chromatin. We also present evidence suggesting that MAP kinase-mediated Sir3p hyperphosphorylation, which plays a role in regulating silencing in response to certain stress conditions, is not involved in high temperature-induced strengthening of silencing. In addition, Pnc1p, a positive regulator of Sir2p activity, plays no role in thermal regulation of silencing. Therefore, growth temperature regulates transcriptional silencing by a novel mechanism.

journal_name

J Mol Biol

authors

Bi X,Yu Q,Sandmeier JJ,Elizondo S

doi

10.1016/j.jmb.2004.10.002

keywords:

subject

Has Abstract

pub_date

2004-12-03 00:00:00

pages

893-905

issue

4

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(04)01270-7

journal_volume

344

pub_type

杂志文章
  • Structure-function relationships within the peptide deformylase family. Evidence for a conserved architecture of the active site involving three conserved motifs and a metal ion.

    abstract::Thermus thermophilus peptide deformylase was characterized. Its enzymatic properties as well as its organization in domains proved to share close resemblances with those of the Escherichia coli enzyme despite few sequence identities. In addition to the HEXXH signature sequence of the zinc metalloprotease family, a sec...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1997.0904

    authors: Meinnel T,Lazennec C,Villoing S,Blanquet S

    更新日期:1997-04-04 00:00:00

  • A model for the mechanism of polymerase translocation.

    abstract::A general mechanism for polymerase translocation is elaborated. The central feature of this mechanism is that a rapid translocational equilibrium is established after each cycle of nucleoside monophosphate incorporation such that the polymerase distributes itself by diffusional sliding between all accessible positions...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1996.0707

    authors: Guajardo R,Sousa R

    更新日期:1997-01-10 00:00:00

  • Characterisation of epitopes on human p53 using phage-displayed peptide libraries: insights into antibody-peptide interactions.

    abstract::We previously described the use of a phage-displayed library of random hexapeptides to define and localise the epitope on the human tumor suppressor protein p53 recognised by the monoclonal antibody PAb240. Here we have extended these results to a further eight anti-p53 monoclonal antibodies and to two further librari...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1995.0202

    authors: Stephen CW,Helminen P,Lane DP

    更新日期:1995-04-21 00:00:00

  • Structural and Functional Characterization of the BcsG Subunit of the Cellulose Synthase in Salmonella typhimurium.

    abstract::Many bacteria secrete cellulose, which forms the structural basis for bacterial multicellular aggregates, termed biofilms. The cellulose synthase complex of Salmonella typhimurium consists of the catalytic subunits BcsA and BcsB and several auxiliary subunits that are encoded by two divergently transcribed operons, bc...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2018.07.008

    authors: Sun L,Vella P,Schnell R,Polyakova A,Bourenkov G,Li F,Cimdins A,Schneider TR,Lindqvist Y,Galperin MY,Schneider G,Römling U

    更新日期:2018-09-14 00:00:00

  • Crystal structure of ferric Aplysia limacina myoglobin at 2 X 0 A resolution.

    abstract::The three-dimensional structure of ferric myoglobin from the mollusc Aplysia limacina has been refined at 2 X 0 A resolution. The crystallographic R factor, calculated at this stage, is 0 X 194. Despite its high content of apolar residues (both aromatic and aliphatic), Aplysia limacina myoglobin, which contains only o...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(85)90285-2

    authors: Bolognesi M,Coda A,Gatti G,Ascenzi P,Brunori M

    更新日期:1985-05-05 00:00:00

  • Cloning and sequence analysis of the Escherichia coli 4.5 S RNA gene.

    abstract::The structure of the Escherichia coli gene coding for the metabolically stable 4.5 S RNA has been determined by cloning and DNA sequence analysis. Results from Southern hybridization assays carried out prior to cloning show the 4.5 S DNA to be limited to a single locus in the E. coli K12 genome. A 5.4 X 10(3) base DNA...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(84)90236-5

    authors: Hsu LM,Zagorski J,Fournier MJ

    更新日期:1984-09-25 00:00:00

  • The reliability of in vivo structure-function analysis of tRNA aminoacylation.

    abstract::The G.U wobble base-pair in the acceptor helix of Escherichia coli tRNAAlais critical for aminoacylation by the alanine synthetase. Previous work by several groups probed the mechanism of enzyme recognition of G.U by a structure-function analysis of mutant tRNAs using either a cell assay (amber suppressor tRNA) or a t...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1999.2884

    authors: McClain WH,Jou YY,Bhattacharya S,Gabriel K,Schneider J

    更新日期:1999-07-09 00:00:00

  • Atomic force microscopy of cholera toxin B-oligomers bound to bilayers of biologically relevant lipids.

    abstract::Cholera toxin B-oligomer was imaged by atomic force microscopy (AFM) on biologically relevant model membranes, such as 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine and egg yolk phosphatidylcholine at room temperature in solution at a resolution in the range of 1 to 2 nm. In addition, two-dimensional arrays we...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1995.0238

    authors: Mou J,Yang J,Shao Z

    更新日期:1995-05-05 00:00:00

  • Monitoring sequence space as a test for the target of selection in viruses.

    abstract::An essential feature of viral quasispecies, predicted from quasispecies theory, is that the target of selection is the mutant distribution as a whole. To test molecularly the mutant composition selected from a viral quasispecies we reconstructed a mutant distribution using 19 antigenic variants of foot-and-mouth disea...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2004.10.066

    authors: Perales C,Martín V,Ruiz-Jarabo CM,Domingo E

    更新日期:2005-01-21 00:00:00

  • The structural basis of riboflavin binding to Schizosaccharomyces pombe 6,7-dimethyl-8-ribityllumazine synthase.

    abstract::Riboflavin is an essential cofactor in all organisms. Its direct biosynthetic precursor, 6,7-dimethyl-8-ribityllumazine, is synthesised by the enzyme 6,7-dimethyl-8-ribityllumazine synthase. Recently, we have found that the enzyme from Schizosaccharomyces pombe binds riboflavin, the final product of the pathway with a...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(02)00116-x

    authors: Gerhardt S,Haase I,Steinbacher S,Kaiser JT,Cushman M,Bacher A,Huber R,Fischer M

    更新日期:2002-05-17 00:00:00

  • An on-pathway hidden intermediate and the early rate-limiting transition state of Rd-apocytochrome b562 characterized by protein engineering.

    abstract::The folding pathway of Rd-apocytochrome b562, a four-helix bundle protein, was characterized using Trp and Ala/Gly pair mutations. We found that the Trp mutants (F65W) of both the fully folded Rd-apocytochrome b562 and a partially unfolded intermediate with the N-terminal helix (helix I) unfolded, fold with identical ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2005.07.057

    authors: Zhou Z,Huang Y,Bai Y

    更新日期:2005-09-30 00:00:00

  • Nature of recombination involved in excision and rearrangement of human repetitive DNA.

    abstract::An alphoid-like human repetitive DNA of the Sau3A family is present extrachromosomally and in the chromosomes. In the chromosomes, the DNA is located on chromosome 11 but related sequences are present in chromosome 17. We characterized the nature of the recombination involved in the excision of the extrachromosomal DN...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(87)90202-6

    authors: Kiyama R,Okumura K,Matsui H,Bruns GA,Kanda N,Oishi M

    更新日期:1987-12-20 00:00:00

  • Biochemical Differences and Similarities between the DEAD-Box Helicase Orthologs DDX3X and Ded1p.

    abstract::DDX3X is a conserved DEAD-box RNA helicase involved in translation initiation and other processes of RNA metabolism. Mutations in human DDX3X and deregulation of its expression are linked to tumorigenesis and intellectual disability. The protein is also targeted by diverse viruses. Previous studies demonstrated helica...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2017.10.008

    authors: Sharma D,Putnam AA,Jankowsky E

    更新日期:2017-11-24 00:00:00

  • Bacteriophage p22 portal vertex formation in vivo.

    abstract::Bacteriophage with double-stranded, linear DNA genomes package DNA into pre-assembled icosahedral procapsids through a unique vertex. The packaging vertex contains an oligomeric ring of a portal protein that serves as a recognition site for the packaging enzymes, a conduit for DNA translocation, and the site of tail a...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2001.5275

    authors: Moore SD,Prevelige PE Jr

    更新日期:2002-02-01 00:00:00

  • X-ray crystal structure of the rotavirus inner capsid particle at 3.8 A resolution.

    abstract::The rotavirus inner capsid particle, known as the "double-layered particle" (DLP), is the "payload" delivered into a cell in the process of viral infection. Its inner and outer protein layers, composed of viral protein (VP) 2 and VP6, respectively, package the 11 segments of the double-stranded RNA (dsRNA) of the vira...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2010.01.055

    authors: McClain B,Settembre E,Temple BR,Bellamy AR,Harrison SC

    更新日期:2010-03-26 00:00:00

  • Solution structure of the WNK1 autoinhibitory domain, a WNK-specific PF2 domain.

    abstract::WNK1 [with no lysine (K)-1] is a 250-kDa serine/threonine protein kinase involved in the maintenance of cellular salt levels and is directly linked to a hereditary form of hypertension. Here, we report the solution NMR structure of the autoinhibitory domain of WNK1 (WNK1-AI), a small regulatory subunit that lies immed...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2013.01.031

    authors: Moon TM,Correa F,Kinch LN,Piala AT,Gardner KH,Goldsmith EJ

    更新日期:2013-04-26 00:00:00

  • Identification of three aspartic acid residues essential for catalysis by the RusA holliday junction resolvase.

    abstract::RusA is a Holliday junction resolvase encoded by the cryptic prophage DLP12 of Escherichia coli K-12 that can be activated to promote homologous recombination and DNA repair in resolution-deficient mutants lacking the RuvABC proteins. Database searches with the 120 amino acid residue RusA sequence identified 11 homolo...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1998.2499

    authors: Bolt EL,Sharples GJ,Lloyd RG

    更新日期:1999-02-19 00:00:00

  • Allosteric changes in protein structure computed by a simple mechanical model: hemoglobin TR2 transition.

    abstract::Information on protein dynamics has been usually inferred from spectroscopic studies of parts of the proteins, or indirectly from the comparison of the conformations assumed in the presence of different substrates or ligands. While molecular simulations also provide information on protein dynamics, they usually suffer...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2003.08.027

    authors: Xu C,Tobi D,Bahar I

    更新日期:2003-10-10 00:00:00

  • Desmin and vimentin intermediate filament networks: their viscoelastic properties investigated by mechanical rheometry.

    abstract::We have investigated the viscoelastic properties of the cytoplasmic intermediate filament (IF) proteins desmin and vimentin. Mechanical measurements were supported by time-dependent electron microscopy studies of the assembly process under similar conditions. Network formation starts within 2 min, but it takes more th...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2009.03.005

    authors: Schopferer M,Bär H,Hochstein B,Sharma S,Mücke N,Herrmann H,Willenbacher N

    更新日期:2009-04-24 00:00:00

  • Identification of elements essential for transcription in Brugia malayi promoters.

    abstract::Little is known concerning promoter structure in the filarial parasites. Recently, transient transfection methods have been developed for the human filarial parasite Brugia malayi. These methods have been employed to localize the promoter for the 70kDa heat shock protein (BmHSP70) to a region extending 394nt upstream ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2005.08.014

    authors: Higazi TB,Deoliveira A,Katholi CR,Shu L,Barchue J,Lisanby M,Unnasch TR

    更新日期:2005-10-14 00:00:00

  • Characterization of the heterogeneity and specificity of interpolypeptide interactions in amyloid protofibrils by measurement of site-specific fluorescence anisotropy decay kinetics.

    abstract::The aggregation of proteins often results in highly ordered fibrillar structures. While significant insights have been obtained on structural aspects of amyloid fibrils, little is known about the structures of protofibrils, which are presumed to be the precursors of fibrils. An understanding of the molecular mechanism...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2009.08.053

    authors: Jha A,Udgaonkar JB,Krishnamoorthy G

    更新日期:2009-10-30 00:00:00

  • Differential surface accessibility of alpha(187-199) in the Torpedo acetylcholine receptor alpha subunits.

    abstract::We have probed the surface accessibility of residues alpha187 to alpha199 of the Torpedo acetylcholine receptor with monoclonal antibody 383C, which binds uniquely to these residues. However, 383C binds to only one of the two alpha subunits in the membrane-bound receptor, neither of the two subunits in carbamylcholine...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1998.2001

    authors: Fairclough RH,Twaddle GM,Gudipati E,Lin MY,Richman DP

    更新日期:1998-09-18 00:00:00

  • Contribution of the hydrophobic effect to globular protein stability.

    abstract::The decrease in conformational stability, delta(delta G), has been measured for 72 aliphatic side-chain mutants from four proteins in which a larger side-chain is replaced by a smaller side-chain so that steric effects are minimal. When these delta(delta G) values are corrected to the same accessibility, namely 100% b...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(92)90121-y

    authors: Pace CN

    更新日期:1992-07-05 00:00:00

  • Nascent β Structure in the Elongated Hydrophobic Region of a Gerstmann-Sträussler-Scheinker PrP Allele.

    abstract::Prion diseases are neurodegenerative disorders caused by the misfolding of the cellular prion protein (PrPC). Gerstmann-Sträussler-Scheinker syndrome is an inherited prion disease with one early-onset allele (HRdup) containing an eight-amino-acid insertion; this LGGLGGYV insert is positioned after valine 129 (human Pr...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2019.04.027

    authors: Fu ZL,Holmes PC,Westaway D,Sykes BD

    更新日期:2019-06-28 00:00:00

  • Parallel and antiparallel Holliday junctions differ in structure and stability.

    abstract::Two Holliday junction analogs, JA and JP, containing identical base-paired arms have been constructed from oligonucleotides. The former is constrained to adopt an antiparallel Sigal-Alberts structure, and the latter a parallel structure, by means of single strand d(T)9 tethers. We evaluate here the free energy differe...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(91)90942-y

    authors: Lu M,Guo Q,Seeman NC,Kallenbach NR

    更新日期:1991-10-20 00:00:00

  • Crystal structure of the dog lipocalin allergen Can f 2: implications for cross-reactivity to the cat allergen Fel d 4.

    abstract::The dog lipocalin allergen Can f 2 is an important cause of allergic sensitization in humans worldwide. Here, the first crystal structure of recombinant rCan f 2 at 1.45 A resolution displays a classical lipocalin fold with a conserved Gly-Xaa-Trp motif, in which Trp19 stabilizes the overall topology of the monomeric ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2010.05.043

    authors: Madhurantakam C,Nilsson OB,Uchtenhagen H,Konradsen J,Saarne T,Högbom E,Sandalova T,Grönlund H,Achour A

    更新日期:2010-08-06 00:00:00

  • Atomic-Resolution Structures of the APC/C Subunits Apc4 and the Apc5 N-Terminal Domain.

    abstract::Many essential biological processes are mediated by complex molecular machines comprising multiple subunits. Knowledge on the architecture of individual subunits and their positions within the overall multimeric complex is key to understanding the molecular mechanisms of macromolecular assemblies. The anaphase-promoti...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2015.08.023

    authors: Cronin NB,Yang J,Zhang Z,Kulkarni K,Chang L,Yamano H,Barford D

    更新日期:2015-10-09 00:00:00

  • DNA polymerase X from African swine fever virus: quantitative analysis of the enzyme-ssDNA interactions and the functional structure of the complex.

    abstract::Interactions of polymerase X from African swine fever virus with single-stranded DNA (ssDNA) have been studied, using quantitative fluorescence titration and analytical ultracentrifugation techniques. Experiments were performed with a fluorescent etheno-derivative of ssDNA oligomers. Studies of unmodified ssDNA oligom...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2005.10.061

    authors: Jezewska MJ,Marcinowicz A,Lucius AL,Bujalowski W

    更新日期:2006-02-10 00:00:00

  • Computer modelling of the alpha-helical coiled coil: packing of side-chains in the inner core.

    abstract::In order to predict the structure of alpha-helical coiled-coil proteins from their sequences, it is necessary to know how the side-chains pack in the interface between the alpha-helical strands. Since in alpha-fibrous proteins leucine is the most common residue at both the a and d positions of the heptad repeat, which...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1995.0352

    authors: Offer G,Sessions R

    更新日期:1995-06-23 00:00:00

  • Observing membrane protein diffusion at subnanometer resolution.

    abstract::Single sodium-driven rotors from a bacterial ATP synthase were embedded into a lipid membrane and observed in buffer solution at subnanometer resolution using atomic force microscopy (AFM). Time-lapse AFM topographs show the movement of single proteins within the membrane. Subsequent analysis of their individual traje...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(03)00206-7

    authors: Müller DJ,Engel A,Matthey U,Meier T,Dimroth P,Suda K

    更新日期:2003-04-11 00:00:00