当前位置： SCI文献检索 > JOURNAL OF MOLECULAR BIOLOGY期刊下所有文献 > From dusk till dawn: one-plasmid systems for light-regulated gene expression.

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 pDusk and pDawn, which employ blue-light photoreceptors to confer light-repressed or light-induced gene expression in Escherichia coli with up to 460-fold induction upon illumination. Key features of these systems are low background activity, high dynamic range, spatial control on the 20-μm scale, independence from exogenous factors, and ease of use. In optogenetic experiments, pDusk and pDawn can be used to specifically perturb individual nodes of signaling networks and interrogate their role. On the preparative scale, pDawn can induce by light the production of recombinant proteins and thus represents a cost-effective and readily automated alternative to conventional induction systems.

journal_name

J Mol Biol

journal_title

Journal of molecular biology

authors

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

doi

10.1016/j.jmb.2012.01.001

subject

Has Abstract

pub_date

2012-03-02 00:00:00

pages

534-42

issue

4

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(12)00011-3

journal_volume

416

pub_type

杂志文章

相关文献

JOURNAL OF MOLECULAR BIOLOGY文献大全
  • A novel calmodulin-like gene from the nematode Caenorhabditis elegans.

    abstract：:A novel gene from the nematode Caenorhabditis elegans was isolated by hybridization with a human calmodulin complementary DNA probe. This gene, cal-1, is present at one copy per haploid genome. In-situ hybridization of the cloned gene to metaphase chromosomes allowed us to assign it to the nematode linkage group IV. T...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(86)90002-1

    authors： Salvato M,Sulston J,Albertson D,Brenner S

    更新日期：1986-08-05 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

  • DNA combing reveals intrinsic temporal disorder in the replication of yeast chromosome VI.

    abstract：:It is generally believed that DNA replication in most eukaryotes proceeds according to a precise program in which there is a defined temporal order by which each chromosomal region is duplicated. However, the regularity of this program at the level of individual chromosomes, in terms of both the relative timing and th...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章,评审

    doi：10.1016/j.jmb.2007.10.046

    authors： Czajkowsky DM,Liu J,Hamlin JL,Shao Z

    更新日期：2008-01-04 00:00:00

  • Mechanisms of Gasdermin Family Members in Inflammasome Signaling and Cell Death.

    abstract：:The Gasdermin (GSDM) family consists of Gasdermin A (GSDMA), Gasdermin B (GSDMB), Gasdermin C (GSDMC), Gasdermin D (GSDMD), Gasdermin E (GSDME) and Pejvakin (PJVK). GSDMD is activated by inflammasome-associated inflammatory caspases. Cleavage of GSDMD by human or mouse caspase-1, human caspase-4, human caspase-5, and ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章,评审

    doi：10.1016/j.jmb.2018.07.002

    authors： Feng S,Fox D,Man SM

    更新日期：2018-09-14 00:00:00

  • The structure of an alcohol dehydrogenase from the hyperthermophilic archaeon Aeropyrum pernix.

    abstract：:The structure of the recombinant medium chain alcohol dehydrogenase (ADH) from the hyperthermophilic archaeon Aeropyrum pernix has been solved by the multiple anomalous dispersion technique using the signal from the naturally occurring zinc ions. The enzyme is a tetramer with 222 point group symmetry. The ADH monomer ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/s0022-2836(03)00857-x

    authors： Guy JE,Isupov MN,Littlechild JA

    更新日期：2003-08-29 00:00:00

  • Structure, dynamics and electrostatics of the active site of glutaredoxin 3 from Escherichia coli: comparison with functionally related proteins.

    abstract：:The chemistry of active-site cysteine residues is central to the activity of thiol-disulfide oxidoreductases of the thioredoxin superfamily. In these reactions, a nucleophilic thiolate is required, but the associated pK(a) values differ vastly in the superfamily, from less than 4 in DsbA to greater than 7 in Trx. The ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2001.4767

    authors： Foloppe N,Sagemark J,Nordstrand K,Berndt KD,Nilsson L

    更新日期：2001-07-06 00:00:00

  • Characterization and mutational analysis of the RecQ core of the bloom syndrome protein.

    abstract：:Bloom syndrome protein forms an oligomeric ring structure and belongs to a group of DNA helicases showing extensive homology to the Escherichia coli DNA helicase RecQ, a suppressor of illegitimate recombination. After over-production in E.coli, we have purified the RecQ core of BLM consisting of the DEAH, RecQ-Ct and ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/s0022-2836(03)00534-5

    authors： Janscak P,Garcia PL,Hamburger F,Makuta Y,Shiraishi K,Imai Y,Ikeda H,Bickle TA

    更新日期：2003-06-27 00:00:00

  • Design, characterization, and structure of a biologically active single-chain mutant of human IFN-gamma.

    abstract：:A mutant form of human interferon-gamma (IFN-gamma SC1) that binds one IFN-gamma receptor alpha chain (IFN-gamma R alpha) has been designed and characterized. IFN-gamma SC1 was derived by linking the two peptide chains of the IFN-gamma dimer by a seven-residue linker and changing His111 in the first chain to an aspart...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2000.3734

    authors： Landar A,Curry B,Parker MH,DiGiacomo R,Indelicato SR,Nagabhushan TL,Rizzi G,Walter MR

    更新日期：2000-05-26 00:00:00

  • Sensing Membrane Curvature in Macroautophagy.

    abstract：:In response to intracellular stress events ranging from starvation to pathogen invasion, the cell activates one or more forms of macroautophagy. The key event in these related pathways is the de novo formation of a new organelle called the autophagosome, which either surrounds and sequesters random portions of the cyt...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章,评审

    doi：10.1016/j.jmb.2017.01.006

    authors： Nguyen N,Shteyn V,Melia TJ

    更新日期：2017-02-17 00:00:00

  • The crystal structure of ZapA and its modulation of FtsZ polymerisation.

    abstract：:FtsZ is part of a mid-cell cytokinetic structure termed the Z-ring that recruits a hierarchy of fission related proteins early in the bacterial cell cycle. The widely conserved ZapA has been shown to interact with FtsZ, to drive its polymerisation and to promote FtsZ filament bundling thereby contributing to the spati...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2004.05.031

    authors： Low HH,Moncrieffe MC,Löwe J

    更新日期：2004-08-13 00:00:00

  • Catalytic metal ion rearrangements underline promiscuity and evolvability of a metalloenzyme.

    abstract：:Although largely deemed as structurally conserved, catalytic metal ion sites can rearrange, thereby contributing to enzyme evolvability. Here, we show that in paraoxonase-1, a lipo-lactonase, catalytic promiscuity and divergence into an organophosphate hydrolase are correlated with an alternative mode of the catalytic...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2013.01.009

    authors： Ben-David M,Wieczorek G,Elias M,Silman I,Sussman JL,Tawfik DS

    更新日期：2013-03-25 00:00:00

  • Prediction of transcription terminators in bacterial genomes.

    abstract：:This study describes an algorithm that finds rho-independent transcription terminators in bacterial genomes and evaluates the accuracy of its predictions. The algorithm identifies terminators by searching for a common mRNA motif: a hairpin structure followed by a short uracil-rich region. For each terminator, an energ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2000.3836

    authors： Ermolaeva MD,Khalak HG,White O,Smith HO,Salzberg SL

    更新日期：2000-08-04 00:00:00

  • Topology Prediction Improvement of α-helical Transmembrane Proteins Through Helix-tail Modeling and Multiscale Deep Learning Fusion.

    abstract：:Transmembrane proteins (TMPs) play important roles in many biological processes, such as cell recognition and communication. Their structures are crucial for revealing complex functions but are hard to obtain. A variety of computational algorithms have been proposed to fill the gap by predicting structures from primar...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2019.12.007

    authors： Feng SH,Zhang WX,Yang J,Yang Y,Shen HB

    更新日期：2020-02-14 00:00:00

  • Ribosomal protein L9: a structure determination by the combined use of X-ray crystallography and NMR spectroscopy.

    abstract：:The structure of protein L9 from the Bacillus stearothernophilus ribosome has been determined at 2.5 A resolution by refinement against single crystal X-ray diffraction data with additional constraints provided by NMR data. This highly elongated protein consists of two domains separated by a nine-turn connecting helix...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1996.0696

    authors： Hoffman DW,Cameron CS,Davies C,White SW,Ramakrishnan V

    更新日期：1996-12-20 00:00:00

  • Integrated Use of Biochemical, Native Mass Spectrometry, Computational, and Genome-Editing Methods to Elucidate the Mechanism of a Salmonella deglycase.

    abstract：:Salmonellais a foodborne pathogen that causes annually millions of cases of salmonellosis globally, yet Salmonella-specific antibacterials are not available. During inflammation, Salmonella utilizes the Amadori compound fructose-asparagine (F-Asn) as a nutrient through the successive action of three enzymes, including...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2019.08.017

    authors： Sengupta A,Wu J,Seffernick JT,Sabag-Daigle A,Thomsen N,Chen TH,Capua AD,Bell CE,Ahmer BMM,Lindert S,Wysocki VH,Gopalan V

    更新日期：2019-11-08 00:00:00

  • Exploring the regulation of tRNA distribution on the genomic scale.

    abstract：:Though up to 20% of the total RNA in bacterial cells is tRNA, the regulation of tRNA distribution on the genomic level remains unclear. tRNA distribution is governed by four processes: transcription, processing of precursor tRNA, degradation of precursor tRNA and degradation of mature tRNA. To elucidate the relationsh...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2004.01.024

    authors： Dittmar KA,Mobley EM,Radek AJ,Pan T

    更新日期：2004-03-12 00:00:00

  • Signal sequences containing multiple aromatic residues.

    abstract：:Using homopolymeric units of either phenylalanine or tryptophan to replace the natural core segment of the Escherichia coli alkaline phosphatase signal peptide, the hydrophobicity requirements for protein export and processing were further explored. The mutant signal peptide containing polyphenylalanine functioned at ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(92)90577-7

    authors： Rusch SL,Kendall DA

    更新日期：1992-03-05 00:00:00

  • Effects of surrounding sequence on the suppression of nonsense codons.

    abstract：:Using a lacI-Z fusion system, we have determined the efficiency of suppression of nonsense codons in the I gene of Escherichia coli by assaying beta-galactosidase activity. We examined the efficiency of four amber suppressors acting on 42 different amber (UAG) codons at known positions in the I gene, and the efficienc...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(83)90087-6

    authors： Miller JH,Albertini AM

    更新日期：1983-02-15 00:00:00

  • Conformational changes during the assembly of factor B from its domains by (1)H NMR spectroscopy and molecular modelling: their relevance to the regulation of factor B activity.

    abstract：:Factor B is a key component of the alternative pathway of complement and is cleaved by factor D into the Ba and Bb fragments in the presence of activated C3 (C3b or C3(H(2)O)). The Ba fragment contains three short consensus/complement repeat domains, while the Bb fragment contains a von Willebrand factor type A (vWF-A...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2000.4044

    authors： Hinshelwood J,Perkins SJ

    更新日期：2000-09-01 00:00:00

  • Alternative native flap conformation revealed by 2.3 A resolution structure of SIV proteinase.

    abstract：:A large conformational change is observed between HIV-1 proteinase in the ligand-free state and in complexes with transition-state inhibitors. Crystal structures of this enzyme have either the flaps open for the native or ligand-free enzyme or the flaps closed for peptidomimetic ligand-bound enzyme. We describe the st...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1994.1353

    authors： Wilderspin AF,Sugrue RJ

    更新日期：1994-05-27 00:00:00

  • Crystal structures of phosphotransferase system enzymes PtxB (IIB(Asc)) and PtxA (IIA(Asc)) from Streptococcus mutans.

    abstract：:Streptococcus mutans is the primary etiological agent of dental caries in man and other mammalian organisms. This bacterium metabolizes carbohydrates actively and thrives under anaerobic conditions by fermenting l-ascorbate (Asc) via the sga operon, which includes SgaT, PtxB, and PtxA. These three proteins are members...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2008.12.046

    authors： Lei J,Li LF,Su XD

    更新日期：2009-02-20 00:00:00

  • Aromatic-aromatic interactions and protein stability. Investigation by double-mutant cycles.

    abstract：:The side-chains of phenylalanine and tyrosine residues in proteins are frequently found to be involved in pairwise interactions. These occur both within repeating elements of secondary structure and in tertiary and quaternary interactions. It has been suggested that they are important in protein folding and stability,...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(91)90725-l

    authors： Serrano L,Bycroft M,Fersht AR

    更新日期：1991-03-20 00:00:00

  • TM0486 from the hyperthermophilic anaerobe Thermotoga maritima is a thiamin-binding protein involved in response of the cell to oxidative conditions.

    abstract：:The COG database was used for a comparative genome analysis with genomes from anaerobic and aerobic microorganisms with the aim of identifying proteins specific to the anaerobic way of life. A total of 33 COGs were identified, five of which correspond to proteins of unknown function. We focused our study on TM0486 fro...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2010.05.014

    authors： Dermoun Z,Foulon A,Miller MD,Harrington DJ,Deacon AM,Sebban-Kreuzer C,Roche P,Lafitte D,Bornet O,Wilson IA,Dolla A

    更新日期：2010-07-16 00:00:00

  • Tests of the single-hit DNA damage model.

    abstract：:The algebra of target theory for damage by radiation was laid out by Atwood and Norman in 1949. Their equations provide a widely embraced framework for distinguishing single-hit and multi-hit mechanisms of damage. The present work asks whether in vitro damage to DNA duplexes by different agents affects amplification b...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2009.07.012

    authors： Spangler R,Goddard NL,Spangler DN,Thaler DS

    更新日期：2009-09-18 00:00:00

  • Tetrameric structure of thermostable direct hemolysin from vibrio parahaemolyticus revealed by ultracentrifugation, small-angle X-ray scattering and electron microscopy.

    abstract：:The thermostable direct hemolysin (TDH) is a major virulence factor of Vibrio parahaemolyticus. We have characterized the conformational properties of TDH by small-angle X-ray scattering (SAXS), ultracentrifugation and transmission electron microscopy. Sedimentation equilibrium and velocity studies revealed that the p...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2006.09.070

    authors： Hamada D,Higurashi T,Mayanagi K,Miyata T,Fukui T,Iida T,Honda T,Yanagihara I

    更新日期：2007-01-05 00:00:00

  • Contributions of residue pairing to beta-sheet formation: conservation and covariation of amino acid residue pairs on antiparallel beta-strands.

    abstract：:In an effort to better understand beta-sheet assembly, we have investigated the evolutionary behavior of neighboring residues on adjacent antiparallel beta-strands. Residue pairs were classified according to solvent exposure as well as by whether their backbone NH and C==O groups are hydrogen bonded. The conservation ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2000.4364

    authors： Mandel-Gutfreund Y,Zaremba SM,Gregoret LM

    更新日期：2001-02-02 00:00:00

  • The effect of chloramphenicol in intact erythroid cells.

    abstract：:Incubation of intact reticulocytes with chloramphenicol at concentrations over 10(-3) M caused inhibition of protein synthesis and conversion of polyribosomes to single ribosomes. At 3 x 10(-3) M-chloramphenicol these effects were completely reversible, but reversibility decreased as the chloramphenicol concentration ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(66)90026-x

    authors： Godchaux W 3rd,Herbert E

    更新日期：1966-11-28 00:00:00

  • Rapid creation of a novel protein function by in vitro coevolution.

    abstract：:We have developed a simple and efficient method for creation of novel protein functions in an existing protein scaffold. The in vitro coevolution method involves design of a hypothetical pathway for the target function followed by stepwise directed evolution of the corresponding protein along the pathway. As a test ca...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2005.02.070

    authors： Chen Z,Zhao H

    更新日期：2005-05-20 00:00:00

  • Structural Basis for p53 Lys120-Acetylation-Dependent DNA-Binding Mode.

    abstract：:Normal cellular homeostasis depends on tight regulation of gene expression, which requires the modulation of transcription factors' DNA-binding specificity. That said, the mechanisms that allow transcription factors to distinguish between closely related response elements following different cellular signals are not f...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2016.06.009

    authors： Vainer R,Cohen S,Shahar A,Zarivach R,Arbely E

    更新日期：2016-07-31 00:00:00

  • Crystallization and preliminary X-ray analysis of phenylalanine hydroxylase from rat liver.

    abstract：:Phenylalanine hydroxylase from rat liver has been crystallized from polyethylene glycol 4500 with sodium formate. The crystals are tetragonal rods and belong to space group P4(1)22 or P4(3)22 with unit cell dimensions a = b = 57.6 A and c = 304.1 A. They diffract to at least 2.4 A resolution and have one molecule per ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(91)90694-2

    authors： Celikel R,Davis MD,Dai XP,Kaufman S,Xuong NH

    更新日期：1991-04-05 00:00:00