当前位置： SCI文献检索 > JOURNAL OF MOLECULAR BIOLOGY期刊下所有文献 > Bacterial comparative genomic hybridization: a method for directly identifying lateral gene transfer.

Bacterial comparative genomic hybridization: a method for directly identifying lateral gene transfer.

Abstract：

:Horizontally transferred DNA is largely responsible for the dissemination of virulence traits amongst bacteria. Rapid identification of acquired DNA remains difficult as whole-genome sequencing of outbreak strains is impractical, and microarray-based approaches, while powerful, are limited to genes present only in the reference strains. Here we present a novel bacterial comparative genomic hybridization method that directly compares the genomes of related strains at sub-kilobase resolution in order to identify acquired DNA. Bacterial comparative genomic hybridization utilizes the concept of metaphase chromosome comparative genomic hybridization, and exploits the resolving power of two-dimensional DNA electrophoresis. Comparison of isogenic variants of the pathogen Pseudomonas aeruginosa detected a single-copy gene insertion responsible for gentamicin resistance.

journal_name

J Mol Biol

journal_title

Journal of molecular biology

authors

Malloff CA,Fernandez RC,Lam WL

doi

10.1006/jmbi.2001.4925

keywords:

subject

Has Abstract

pub_date

2001-09-07 00:00:00

pages

1-5

issue

1

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(01)94925-3

journal_volume

312

pub_type

杂志文章

相关文献

JOURNAL OF MOLECULAR BIOLOGY文献大全
  • Noncoding RNAs: Regulators of the Mammalian Transcription Machinery.

    abstract：:Transcription by RNA polymerase II (Pol II) is required to produce mRNAs and some noncoding RNAs (ncRNAs) within mammalian cells. This coordinated process is precisely regulated by multiple factors, including many recently discovered ncRNAs. In this perspective, we will discuss newly identified ncRNAs that facilitate ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章,评审

    doi：10.1016/j.jmb.2016.02.019

    authors： Eidem TM,Kugel JF,Goodrich JA

    更新日期：2016-06-19 00:00:00

  • Identification of a GUAAY Pentaloop Sequence Involved in a Novel RNA Loop-Helix Interaction.

    abstract：:Large RNAs often utilize GNRA tetraloops as structural elements to stabilize the overall tertiary fold. These tetraloop-receptor (TR) interactions have a conserved geometry in which the tetraloop docks into the receptor at an angle of ~15° from the helix containing the receptor. Here, we show that the conserved GUAAY ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2016.10.015

    authors： Chan RT,Keating KS,Go MC,Toor N

    更新日期：2016-12-04 00:00:00

  • Target Residence Time-Guided Optimization on TTK Kinase Results in Inhibitors with Potent Anti-Proliferative Activity.

    abstract：:The protein kinase threonine tyrosine kinase (TTK; also known as Mps1) is a critical component of the spindle assembly checkpoint and a promising drug target for the treatment of aggressive cancers, such as triple negative breast cancer. While the first TTK inhibitors have entered clinical trials, little is known abou...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2017.05.014

    authors： Uitdehaag JCM,de Man J,Willemsen-Seegers N,Prinsen MBW,Libouban MAA,Sterrenburg JG,de Wit JJP,de Vetter JRF,de Roos JADM,Buijsman RC,Zaman GJR

    更新日期：2017-07-07 00:00:00

  • Serpin acceleration of amyloid fibril formation: a role for accessory proteins.

    abstract：:Protein aggregation underlies an increasing number of human diseases. Recent experiments have shown that the aggregation reaction is exquisitely specific involving particular interactions between non-native proteins. However, aggregation of certain proteins, for example beta-amyloid, in vivo leads to the recruitment o...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2006.11.062

    authors： Powers GA,Pham CL,Pearce MC,Howlett GJ,Bottomley SP

    更新日期：2007-02-16 00:00:00

  • Autonomous and reversible folding of a soluble amino-terminally truncated segment of the mouse prion protein.

    abstract：:Prion diseases are assumed to be caused by the infectious isoform, PrPsc, of a single cellular surface protein, PrPc. PrPsc is an insoluble form of PrPc and is believed to possess a different three-dimensional fold. It may propagate by causing PrPc to adopt its own infectious conformation by an unknown mechanism. Stud...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1996.0487

    authors： Hornemann S,Glockshuber R

    更新日期：1996-09-06 00:00:00

  • Folding amphipathic helices into membranes: amphiphilicity trumps hydrophobicity.

    abstract：:High amphiphilicity is a hallmark of interfacial helices in membrane proteins and membrane-active peptides, such as toxins and antimicrobial peptides. Although there is general agreement that amphiphilicity is important for membrane-interface binding, an unanswered question is its importance relative to simple hydroph...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2007.05.016

    authors： Fernández-Vidal M,Jayasinghe S,Ladokhin AS,White SH

    更新日期：2007-07-13 00:00:00

  • Crystal structure of Thermoactinomyces vulgaris R-47 alpha-amylase II (TVAII) hydrolyzing cyclodextrins and pullulan at 2.6 A resolution.

    abstract：:The crystal structure of Thermoactinomyces vulgaris R-47 alpha-Amylase II (TVAII) has been determined by multiple isomorphous replacement at 2.6 A resolution. TVAII was crystallized in an orthorhombic system with the space group P212121 and the cell dimensions a=118.5 A, b=119.5 A, c=114.5 A. There are two molecules i...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1999.2647

    authors： Kamitori S,Kondo S,Okuyama K,Yokota T,Shimura Y,Tonozuka T,Sakano Y

    更新日期：1999-04-16 00:00:00

  • The protein synthesis inhibitors, oxazolidinones and chloramphenicol, cause extensive translational inaccuracy in vivo.

    abstract：:The oxazolidinone family is a new class of synthetic antibiotics that bind to the bacterial 50S ribosomal subunit. Two members of the family, linezolid and XA043, were examined for their effects on translational fidelity using a lacZ reporter gene in vivo. Both promoted highly significant frameshifting and nonsense su...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/s0022-2836(02)00784-2

    authors： Thompson J,O'Connor M,Mills JA,Dahlberg AE

    更新日期：2002-09-13 00:00:00

  • The structure of Xis reveals the basis for filament formation and insight into DNA bending within a mycobacteriophage intasome.

    abstract：:The recombination directionality factor, Xis, is a DNA bending protein that determines the outcome of integrase-mediated site-specific recombination by redesign of higher-order protein-DNA architectures. Although the attachment site DNA of mycobacteriophage Pukovnik is likely to contain four sites for Xis binding, Xis...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2013.10.002

    authors： Singh S,Plaks JG,Homa NJ,Amrich CG,Héroux A,Hatfull GF,VanDemark AP

    更新日期：2014-01-23 00:00:00

  • Insights from atomic-resolution X-ray structures of chemically synthesized HIV-1 protease in complex with inhibitors.

    abstract：:The human immunodeficiency virus 1 (HIV-1) protease (PR) is an aspartyl protease essential for HIV-1 viral infectivity. HIV-1 PR has one catalytic site formed by the homodimeric enzyme. We chemically synthesized fully active HIV-1 PR using modern ligation methods. When complexed with the classic substrate-derived inhi...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2007.07.054

    authors： Johnson EC,Malito E,Shen Y,Pentelute B,Rich D,Florián J,Tang WJ,Kent SB

    更新日期：2007-10-26 00:00:00

  • Ion-coupling determinants of Na+-driven and H+-driven flagellar motors.

    abstract：:The bacterial flagellar motor is a tiny molecular machine that uses a transmembrane flux of H(+) or Na(+) ions to drive flagellar rotation. In proton-driven motors, the membrane proteins MotA and MotB interact via their transmembrane regions to form a proton channel. The sodium-driven motors that power the polar flage...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/s0022-2836(03)00096-2

    authors： Asai Y,Yakushi T,Kawagishi I,Homma M

    更新日期：2003-03-21 00:00:00

  • Molecular size and symmetry of Pseudomonas aeruginosa catabolic ornithine carbamoyltransferase. An X-ray crystallography analysis.

    abstract：:The catabolic ornithine carbamoyltransferase (EC 2.1.3.3) from Pseudomonas aeruginosa, that shows allosteric behaviour, and a mutant version of this enzyme has been crystallized in several different crystal forms. All of these have been characterized by X-ray diffraction methods. A 4.5 A resolution data set has been c...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(91)90375-g

    authors： Marcq S,Diaz-Ruano A,Charlier P,Dideberg O,Tricot C,Piérard A,Stalon V

    更新日期：1991-07-05 00:00:00

  • A neutral molecule in a cation-binding site: specific binding of a PEG-SH to acetylcholinesterase from Torpedo californica.

    abstract：:The crystal structure of acetylcholinesterase from Torpedo californica complexed with the uncharged inhibitor, PEG-SH-350 (containing mainly heptameric polyethylene glycol with a terminal thiol group) is determined at 2.3 A resolution. This is an untypical acetylcholinesterase inhibitor, since it lacks the cationic mo...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/s0022-2836(02)00475-8

    authors： Koellner G,Steiner T,Millard CB,Silman I,Sussman JL

    更新日期：2002-07-19 00:00:00

  • New Views of Functionally Dynamic Proteins by Solution NMR Spectroscopy.

    abstract：:In the past several decades solution NMR spectroscopy has emerged as a powerful technique for the study of the structure and dynamics of proteins, providing detailed insights into biomolecular function. Herein, I provide a summary of two important areas of application, focusing on NMR studies of (i) supramolecular sys...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章,评审

    doi：10.1016/j.jmb.2015.11.028

    authors： Kay LE

    更新日期：2016-01-29 00:00:00

  • Crystal structure and putative mechanism of 3-methylitaconate-delta-isomerase from Eubacterium barkeri.

    abstract：:3-Methylitaconate-Delta-isomerase (Mii) participates in the nicotinate fermentation pathway of the anaerobic soil bacterium Eubacterium barkeri (order Clostridiales) by catalyzing the reversible conversion of (R)-3-methylitaconate (2-methylene-3-methylsuccinate) to 2,3-dimethylmaleate. The enzyme is also able to catal...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2009.06.052

    authors： Velarde M,Macieira S,Hilberg M,Bröker G,Tu SM,Golding BT,Pierik AJ,Buckel W,Messerschmidt A

    更新日期：2009-08-21 00:00:00

  • Oct-1 POU and octamer DNA co-operate to recognise the Bob-1 transcription co-activator via induced folding.

    abstract：:The expression of immunoglobulin genes is controlled in part by the DNA-binding protein Oct-1 and the B cell-specific transcription co-activator, Bob1 (also known as OCA-B or OBF-1) that together form a complex on the Igkappa promoter. We have characterised the assembly of the ternary complex using biophysical methods...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1999.2711

    authors： Chang JF,Phillips K,Lundbäck T,Gstaiger M,Ladbury JE,Luisi B

    更新日期：1999-05-21 00:00:00

  • Structure-based design of a protein immunogen that displays an HIV-1 gp41 neutralizing epitope.

    abstract：:Antibody Z13e1 is a relatively broadly neutralizing anti-human immunodeficiency virus type 1 antibody that recognizes the membrane-proximal external region (MPER) of the human immunodeficiency virus type 1 envelope glycoprotein gp41. Based on the crystal structure of an MPER epitope peptide in complex with Z13e1 Fab, ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2011.10.014

    authors： Stanfield RL,Julien JP,Pejchal R,Gach JS,Zwick MB,Wilson IA

    更新日期：2011-12-02 00:00:00

  • Thioredoxin fusions increase folding of single chain Fv antibodies in the cytoplasm of Escherichia coli: evidence that chaperone activity is the prime effect of thioredoxin.

    abstract：:In this study we investigate the effect of thioredoxin (Trx1) protein fusions in the production, oxidation, and folding of single chain Fv (scFv) antibodies in the cytoplasm of Escherichia coli. We analyze the expression levels, solubility, disulfide-bond formation, and antigen-binding properties of Trx1-scFv fusions ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2005.12.058

    authors： Jurado P,de Lorenzo V,Fernández LA

    更新日期：2006-03-17 00:00:00

  • An algorithm for the prediction of proteasomal cleavages.

    abstract：:Proteasomes, major proteolytic sites in eukaryotic cells, play an important part in major histocompatibility class I (MHC I) ligand generation and thus in the regulation of specific immune responses. Their cleavage specificity is of outstanding interest for this process. In order to generalize previously determined cl...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2000.3683

    authors： Kuttler C,Nussbaum AK,Dick TP,Rammensee HG,Schild H,Hadeler KP

    更新日期：2000-05-05 00:00:00

  • Mutation spectrum following transfection of ultraviolet-irradiated single-stranded or double-stranded shuttle vector DNA into monkey cells.

    abstract：:We designed a shuttle vector system that allowed a comparison of the mutation spectrum on the supF target gene after transfection of single-stranded or double-stranded DNA into monkey cells. Single-strand-derived plasmids exhibited a spontaneous mutation frequency tenfold higher than double-strand-derived ones. These ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(91)90252-2

    authors： Madzak C,Sarasin A

    更新日期：1991-04-20 00:00:00

  • Protein Interaction Energy Landscapes are Shaped by Functional and also Non-functional Partners.

    abstract：:In the crowded cell, a strong selective pressure operates on the proteome to limit the competition between functional and non-functional protein-protein interactions. We developed an original theoretical framework in order to interrogate how this competition constrains the behavior of proteins with respect to their pa...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2019.12.047

    authors： Schweke H,Mucchielli MH,Sacquin-Mora S,Bei W,Lopes A

    更新日期：2020-02-14 00:00:00

  • Electrostatic properties of two porin channels from Escherichia coli.

    abstract：:The electrostatic interactions in the channels of OmpF and PhoE porins from Escherichia coli were analysed on the basis of a macroscopic multi-dielectric model of the protein-membrane complex derived from the respective porin X-ray structures. The membrane was represented as layers of distinct dielectric constants cor...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1994.1451

    authors： Karshikoff A,Spassov V,Cowan SW,Ladenstein R,Schirmer T

    更新日期：1994-07-22 00:00:00

  • Structural and functional analyses of beta-glucosidase 3B from Thermotoga neapolitana: a thermostable three-domain representative of glycoside hydrolase 3.

    abstract：:Based on sequence and phylogenetic analyses, glycoside hydrolase (GH) family 3 can be divided into several clusters that differ in the length of their primary sequences. However, structural data on representatives of GH3 are still scarce, since only three of their structures are known and only one of them has been tho...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2010.01.072

    authors： Pozzo T,Pasten JL,Karlsson EN,Logan DT

    更新日期：2010-04-02 00:00:00

  • Towards the molecular architecture of the asymmetric unit membrane of the mammalian urinary bladder epithelium: a closed "twisted ribbon" structure.

    abstract：:The asymmetric unit membrane (AUM) forms numerous plaques covering the apical surface of mammalian urinary bladder epithelium. These plaques contain four major integral membrane proteins called uroplakins Ia, Ib, II and III, which form particles arranged in a well-ordered hexagonal lattice with p6 symmetry and a latti...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1995.0269

    authors： Walz T,Häner M,Wu XR,Henn C,Engel A,Sun TT,Aebi U

    更新日期：1995-05-19 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

  • Functional interactions of Mycobacterium leprae RuvA with Escherichia coli RuvB and RuvC on holliday junctions.

    abstract：:The Mycobacterium leprae RuvA homologue (MlRuvA) was over-expressed in Escherichia coli and purified to homogeneity. The DNA-binding specificity and the functional interactions of MlRuvA with E. coli RuvB and RuvC (EcRuvB and EcRuvC) were examined using synthetic Holliday junctions. MlRuvA bound specifically to Hollid...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2000.4009

    authors： Arenas-Licea J,van Gool AJ,Keeley AJ,Davies A,West SC,Tsaneva IR

    更新日期：2000-08-25 00:00:00

  • Conserved structural features are found upstream from the three co-ordinately regulated discoidin I genes of Dictyostelium discoideum.

    abstract：:The discoidin I genes of Dictyostelium form a small, co-ordinately regulated multigene family. We have sequenced and compared the upstream regions of the DiscI-alpha, -beta and -gamma genes. For the most part the upstream regions of the three genes are non-homologous. The upstream sequences of the beta and gamma genes...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/s0022-2836(84)80038-8

    authors： Poole SJ,Firtel RA

    更新日期：1984-01-15 00:00:00

  • Folding of RNA involves parallel pathways.

    abstract：:Folding kinetics of large RNAs are just beginning to be investigated. We show that the Tetrahymena self-splicing RNA partitions into a population that rapidly reaches the native state, and a slowly folding population that is trapped in metastable misfolded structures. Transitions from the misfolded structures to the n...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1997.1311

    authors： Pan J,Thirumalai D,Woodson SA

    更新日期：1997-10-17 00:00:00

  • Thermal expansion of hen egg-white lysozyme. Comparison of the 1.9 A resolution structures of the tetragonal form of the enzyme at 100 K and 298 K.

    abstract：:The average structural and dynamic properties of tetragonal hen egg-white lysozyme have been compared, in structures refined at 1.9 A resolution, using data collected at 100 K and 298 K. The molecule expands by 1.8% over this temperature range with the expansion occurring primarily in its small sub-atomic-sized spaces...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/s0022-2836(05)80034-8

    authors： Young AC,Tilton RF,Dewan JC

    更新日期：1994-01-07 00:00:00

  • Decay of rplN and lacZ mRNA in Escherichia coli.

    abstract：:To examine the previously proposed retroregulation model of spc mRNA degradation, two strains of Escherichia coli B/r were used; one has wild-type spc and lac operons and the other has a lac operon deletion, a wild-type spc operon, and a Pspc-rplN-lacZ fusion operon lacking the normal control sites of the spc operon (...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1999.2710

    authors： Liang ST,Ehrenberg M,Dennis P,Bremer H

    更新日期：1999-05-14 00:00:00