Time to be versatile: regulation of the replication timing program in budding yeast.

Abstract:

:Eukaryotic replication origins are activated at different times during the S phase of the cell cycle, following a temporal program that is stably transmitted to daughter cells. Although the mechanisms that control initiation at the level of individual origins are now well understood, much less is known on how cells coordinate replication at hundreds of origins distributed on the chromosomes. In this review, we discuss recent advances shedding new light on how this complex process is regulated in the budding yeast Saccharomyces cerevisiae. The picture that emerges from these studies is that replication timing is regulated in cis by mechanisms modulating the chromatin structure and the subnuclear organization of origins. These mechanisms do not affect the licensing of replication origins but determine their ability to compete for limiting initiation factors, which are recycled from early to late origins throughout the length of the S phase.

journal_name

J Mol Biol

authors

Yoshida K,Poveda A,Pasero P

doi

10.1016/j.jmb.2013.09.020

subject

Has Abstract

pub_date

2013-11-29 00:00:00

pages

4696-705

issue

23

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(13)00604-9

journal_volume

425

pub_type

杂志文章,评审
  • The LcrG Tip Chaperone Protein of the Yersinia pestis Type III Secretion System Is Partially Folded.

    abstract::The type III secretion system (T3SS) is essential in the pathogenesis of Yersinia pestis, the causative agent of plague. A small protein, LcrG, functions as a chaperone to the tip protein LcrV, and the LcrG-LcrV interaction is important in regulating protein secretion through the T3SS. The atomic structure of the LcrG...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2015.07.024

    authors: Chaudhury S,de Azevedo Souza C,Plano GV,De Guzman RN

    更新日期:2015-09-25 00:00:00

  • Evolutionary stabilization of the gene-3-protein of phage fd reveals the principles that govern the thermodynamic stability of two-domain proteins.

    abstract::The gene-3-protein (G3P) of filamentous phage is essential for their propagation. It consists of three domains. The CT domain anchors G3P in the phage coat, the N2 domain binds to the F pilus of Escherichia coli and thus initiates infection, and the N1 domain continues by interacting with the TolA receptor. Phage are ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(03)00359-0

    authors: Martin A,Schmid FX

    更新日期:2003-05-09 00:00:00

  • Catabolism of phenylalanine by Pseudomonas putida: the NtrC-family PhhR regulator binds to two sites upstream from the phhA gene and stimulates transcription with sigma70.

    abstract::Pseudomonas putida uses L-phenylalanine as the sole nitrogen source for growth by converting L-phenylalanine to L-tyrosine, which acts as a donor of the amino group. This metabolic step requires the products of the phhA and phhB genes, which form an operon. Expression of the phhA promoter is mediated by the phhR gene ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2006.12.008

    authors: Herrera MC,Ramos JL

    更新日期:2007-03-09 00:00:00

  • Accomodation of S-cis-tamoxifen-N(2)-guanine adduct within a bent and widened DNA minor groove.

    abstract::The non-steroidal anti-estrogen tamoxifen [TAM] has been in clinical use over the last two decades as a potent adjunct chemotherapeutic agent for treatment of breast cancer. It has also been given prophylactically to women with a strong family history of breast cancer. However, tamoxifen treatment has also been associ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2000.4071

    authors: Shimotakahara S,Gorin A,Kolbanovskiy A,Kettani A,Hingerty BE,Amin S,Broyde S,Geacintov N,Patel DJ

    更新日期:2000-09-15 00:00:00

  • Negative regulation of AAA + ATPase assembly by two component receiver domains: a transcription activation mechanism that is conserved in mesophilic and extremely hyperthermophilic bacteria.

    abstract::Only a few transcriptional regulatory proteins have been characterized in extremely hyperthermophilic organisms, and most function as repressors. Structural features of the NtrC1 protein from the hyperthermophilic bacterium Aquifex aeolicus suggested that this protein functions similarly to the sigma(54)-polymerase ac...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2005.08.003

    authors: Doucleff M,Chen B,Maris AE,Wemmer DE,Kondrashkina E,Nixon BT

    更新日期:2005-10-21 00:00:00

  • A conformational switch involved in maturation of Staphylococcus aureus bacteriophage 80α capsids.

    abstract::Bacteriophages are involved in many aspects of the spread and establishment of virulence factors in Staphylococcus aureus, including the mobilization of genetic elements known as S. aureus pathogenicity islands (SaPIs), which carry genes for superantigen toxins and other virulence factors. SaPIs are packaged into phag...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2010.11.047

    authors: Spilman MS,Dearborn AD,Chang JR,Damle PK,Christie GE,Dokland T

    更新日期:2011-01-21 00:00:00

  • Solution Conformation of Bovine Leukemia Virus Gag Suggests an Elongated Structure.

    abstract::Bovine leukemia virus (BLV) is a deltaretrovirus that infects domestic cattle. The structural protein Gag, found in all retroviruses, is a polyprotein comprising three major functional domains: matrix (MA), capsid (CA), and nucleocapsid (NC). Previous studies have shown that both mature BLV MA and NC are able to bind ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2019.01.036

    authors: Qualley DF,Cooper SE,Ross JL,Olson ED,Cantara WA,Musier-Forsyth K

    更新日期:2019-03-15 00:00:00

  • Intrinsically disordered C-terminal tails of E. coli single-stranded DNA binding protein regulate cooperative binding to single-stranded DNA.

    abstract::The homotetrameric Escherichia coli single-stranded DNA binding protein (SSB) plays a central role in DNA replication, repair and recombination. E. coli SSB can bind to long single-stranded DNA (ssDNA) in multiple binding modes using all four subunits [(SSB)65 mode] or only two subunits [(SSB)35 binding mode], with th...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2014.12.020

    authors: Kozlov AG,Weiland E,Mittal A,Waldman V,Antony E,Fazio N,Pappu RV,Lohman TM

    更新日期:2015-02-27 00:00:00

  • Nuclear transport of Ras-associated tumor suppressor proteins: different transport receptor binding specificities for arginine-rich nuclear targeting signals.

    abstract::Ras proteins regulate a wide range of biological processes by interacting with a variety of effector proteins. In addition to the known role in tumorigensis, the activated form of Ras exhibits growth-inhibitory effects by unknown mechanisms. Several Ras effector proteins identified as mediators of apoptosis and cell-c...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2007.01.026

    authors: Kumari G,Singhal PK,Rao MR,Mahalingam S

    更新日期:2007-04-13 00:00:00

  • Monomer/dimer ratios of replication protein modulate the DNA strand-opening in a replication origin.

    abstract::DNA opening is an essential step in the initiation of replication via the Cairns mode of replication. The opening reaction was investigated in a gamma ori system by using hyperactive variants of plasmid R6K-encoded initiator protein, pi. Reactivity to KMnO4 (indicative of opening) within gamma ori DNA occurred in both...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2000.4426

    authors: Krüger R,Konieczny I,Filutowicz M

    更新日期:2001-03-09 00:00:00

  • C--H...O hydrogen bond involving proline residues in alpha-helices.

    abstract::Despite proline being assumed to be a helix-breaker, a large number of alpha-helices are found to contain Pro in globular as well as membrane proteins. Proline has no free NH group and therefore cannot form the conventional intra-helical NH.O=C hydrogen bond. An analysis of known protein structures has shown that the ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1998.2199

    authors: Chakrabarti P,Chakrabarti S

    更新日期:1998-12-11 00:00:00

  • Amyloid beta (1-42) folding multiplicity and single-molecule binding behavior studied with STM.

    abstract::The fine folding and assembling characteristics of amyloid beta (Abeta) peptides are important to pharmaceutical studies of drug molecules and to the pathological analysis of neurodegenerative disorders such as Alzheimer's disease at the molecular level. Here we present observations of the multiple folding characteris...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2009.03.054

    authors: Ma X,Liu L,Mao X,Niu L,Deng K,Wu W,Li Y,Yang Y,Wang C

    更新日期:2009-05-15 00:00:00

  • High-resolution crystal structures of Drosophila melanogaster angiotensin-converting enzyme in complex with novel inhibitors and antihypertensive drugs.

    abstract::Angiotensin I-converting enzyme (ACE), one of the central components of the renin-angiotensin system, is a key therapeutic target for the treatment of hypertension and cardiovascular disorders. Human somatic ACE (sACE) has two homologous domains (N and C). The N- and C-domain catalytic sites have different activities ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2010.05.024

    authors: Akif M,Georgiadis D,Mahajan A,Dive V,Sturrock ED,Isaac RE,Acharya KR

    更新日期:2010-07-16 00:00:00

  • The rad50 signature motif: essential to ATP binding and biological function.

    abstract::The repair of double-strand breaks in DNA is an essential process in all organisms, and requires the coordinated activities of evolutionarily conserved protein assemblies. One of the most critical of these is the Mre11/Rad50 (M/R) complex, which is present in all three biological kingdoms, but is not well-understood a...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2003.11.026

    authors: Moncalian G,Lengsfeld B,Bhaskara V,Hopfner KP,Karcher A,Alden E,Tainer JA,Paull TT

    更新日期:2004-01-23 00:00:00

  • The Function of Tafazzin, a Mitochondrial Phospholipid-Lysophospholipid Acyltransferase.

    abstract::Tafazzin is a mitochondrial enzyme that exchanges fatty acids between phospholipids by phospholipid-lysophospholipid transacylation. The reaction alters the molecular species composition and, as a result, the physical properties of lipids. In vivo, the most important substrate of tafazzin is the mitochondria-specific ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.jmb.2020.03.026

    authors: Schlame M,Xu Y

    更新日期:2020-08-21 00:00:00

  • Prohead and DNA-gp3-dependent ATPase activity of the DNA packaging protein gp16 of bacteriophage phi 29.

    abstract::The ATPase activity of the DNA packaging protein gp16 (gene product 16) of bacteriophage phi 29 was studied in the completely defined in-vitro assembly system. ATP was hydrolyzed to ADP and Pi in the packaging reaction that included purified proheads, DNA-gp3 and gp16. Approximately one molecule of ATP was used in the...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(87)90121-5

    authors: Guo P,Peterson C,Anderson D

    更新日期:1987-09-20 00:00:00

  • Structural effect of complete [Rp]-phosphorothioate and phosphorodithioate substitutions in the DNA strand of a model antisense inhibitor-target RNA complex.

    abstract::Chemically modified DNA oligonucleotides have been crucial to the success of antisense therapeutics. Although such modifications are ubiquitous in the clinic, high-resolution structural studies of pharmaceutically relevant derivatives have been limited to only a few molecules. We have completed a high-resolution NMR s...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1998.2305

    authors: Furrer P,Billeci TM,Donati A,Kojima C,Karwowski B,Sierzchala A,Stec W,James TL

    更新日期:1999-01-29 00:00:00

  • Electron microscopy of decorated crystals for the determination of crystallographic rotation and translation parameters in large protein complexes.

    abstract::The lumazine synthase/riboflavin synthase complex of Bacillus subtilis consists of an icosahedral capsid of 60 beta subunits enclosing a core of 3 alpha subunits. The preparation of reconstituted hollow capsids consisting of 60 beta subunits and their crystallization in a hexagonal (space group P6(3)22) and in a monoc...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(92)90105-s

    authors: Bacher A,Weinkauf S,Bachmann L,Ritsert K,Baumeister W,Huber R,Ladenstein R

    更新日期:1992-06-20 00:00:00

  • Structures of hepatitis B virus cores presenting a model epitope and their complexes with antibodies.

    abstract::The core shell of hepatitis B virus is a potent immune stimulator, giving a strong neutralizing immune response to foreign epitopes inserted at the immunodominant region, located at the tips of spikes on the exterior of the shell. Here, we analyze structures of core shells with a model epitope inserted at two alternat...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2012.06.032

    authors: Roseman AM,Borschukova O,Berriman JA,Wynne SA,Pumpens P,Crowther RA

    更新日期:2012-10-12 00:00:00

  • ATP synthase from bovine heart mitochondria. In vitro assembly of a stalk complex in the presence of F1-ATPase and in its absence.

    abstract::Four subunits of the F1F0-ATPase from bovine heart mitochondria have been produced by heterologous over-expression in Escherichia coli. They are the oligomycin sensitivity conferral protein (OSCP), coupling factor 6 (F6) and subunits b and d. Likewise, fragments b', bI, bC, and bM (amino acid residues 79 to 214, 121 t...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1994.1591

    authors: Collinson IR,van Raaij MJ,Runswick MJ,Fearnley IM,Skehel JM,Orriss GL,Miroux B,Walker JE

    更新日期:1994-09-30 00:00:00

  • Structure of complexes between a major protein of heterogeneous nuclear ribonucleoprotein particles and polyribonucleotides.

    abstract::We have investigated the structure of complexes formed between a series of poly(A)n (n = 30 to 480) and HD40 (helix-destabilizing protein, molecular weight of 40,000), the major protein component of 30 S heterogeneous nuclear ribonucleoprotein particles (hnRNP) from the brine shrimp Artemia salina. Protein HD40 is sim...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(83)90039-6

    authors: Thomas JO,Glowacka SK,Szer W

    更新日期:1983-12-25 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

  • From dusk till dawn: one-plasmid systems for light-regulated gene expression.

    abstract::Signaling photoreceptors mediate diverse organismal adaptations in response to light. As light-gated protein switches, signaling photoreceptors provide the basis for optogenetics, a term that refers to the control of organismal physiology and behavior by light. We establish as novel optogenetic tools the plasmids pDus...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2012.01.001

    authors: Ohlendorf R,Vidavski RR,Eldar A,Moffat K,Möglich A

    更新日期:2012-03-02 00:00:00

  • Complementary DNA cloning of a protein highly homologous to mammalian sarcoplasmic reticulum Ca-ATPase from the crustacean Artemia.

    abstract::Complementary DNA clones coding for an Artemia ATPase have been isolated using an oligonucleotide probe for a region highly conserved between P-type ATPases. The nucleotide sequence of three overlapping clones, 3309 base-pairs, has been established. This sequence includes 78 nucleotides of 5' untranslated sequence, an...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(89)90106-x

    authors: Palmero I,Sastre L

    更新日期:1989-12-20 00:00:00

  • Complex of lac repressor headpiece with a 14 base-pair lac operator fragment studied by two-dimensional nuclear magnetic resonance.

    abstract::Two-dimensional nuclear Overhauser enhancement spectra are presented of the complex of lac repressor headpiece with a 14 base-pair lac operator fragment. Analysis of nuclear Overhauser enhancements observed between protein and DNA shows that the second helix of the headpiece ("the recognition helix") binds in the majo...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(87)90638-3

    authors: Boelens R,Scheek RM,van Boom JH,Kaptein R

    更新日期:1987-01-05 00:00:00

  • Crystallographic analysis of CaaX prenyltransferases complexed with substrates defines rules of protein substrate selectivity.

    abstract::Post-translational modifications are essential for the proper function of many proteins in the cell. The attachment of an isoprenoid lipid (a process termed prenylation) by protein farnesyltransferase (FTase) or geranylgeranyltransferase type I (GGTase-I) is essential for the function of many signal transduction prote...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2004.08.056

    authors: Reid TS,Terry KL,Casey PJ,Beese LS

    更新日期:2004-10-15 00:00:00

  • Temperature dependence of intramolecular dynamics of the basic leucine zipper of GCN4: implications for the entropy of association with DNA.

    abstract::The basic leucine zipper domain of the yeast transcription factor GCN4 consists of a C-terminal leucine zipper and an N-terminal basic DNA-binding region that achieves a stable structure only after association with DNA. Backbone dynamics of a peptide encompassing the basic and leucine zipper bZip domain (residues 226-...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1998.2429

    authors: Bracken C,Carr PA,Cavanagh J,Palmer AG 3rd

    更新日期:1999-02-05 00:00:00

  • Angular disorder in actin: is it consistent with general principles of protein structure?

    abstract::Harold Erickson has recently provided a useful analysis of helical structures having one class versus two classes of intersubunit bonds. His analysis is based upon an assumption that the subunits themselves are essentially unchanged upon bond formation (polymerization). He shows that such a structure having two classe...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(91)90743-p

    authors: Egelman EH,DeRosier DJ

    更新日期:1991-02-05 00:00:00

  • Capsid targeting sequence targets foreign proteins into bacteriophage T4 and permits proteolytic processing.

    abstract::A membrane-independent morphogenetic viral signal peptide is identified within bacteriophage T4 internal protein III (IPIII). Utilizing a phagederived expression-packaging-processing system, which packages foreign proteins fused with IPIII into the phage capsid, a synthetic cleavage site introduced at the C terminus o...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1996.0470

    authors: Mullaney JM,Black LW

    更新日期:1996-08-23 00:00:00

  • Sequence Specificity in the Entropy-Driven Binding of a Small Molecule and a Disordered Peptide.

    abstract::Approximately one-third of the human proteome is made up of proteins that are entirely disordered or that contain extended disordered regions. Although these disordered proteins are closely linked with many major diseases, their binding mechanisms with small molecules remain poorly understood, and a major concern is w...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2017.07.016

    authors: Heller GT,Aprile FA,Bonomi M,Camilloni C,De Simone A,Vendruscolo M

    更新日期:2017-09-01 00:00:00