Unexpected NO-dependent DNA binding by the CooA homolog from Carboxydothermus hydrogenoformans.

Abstract:

:CooA, the CO-sensing heme protein from Rhodospirillum rubrum, regulates the expression of genes that encode a CO-oxidation system, allowing R. rubrum to use CO as a sole energy source. To better understand the gas-sensing regulation mechanism used by R. rubrum CooA and its homologs in other organisms, we characterized spectroscopically and functionally the Fe(II), Fe(II)-NO, and Fe(II)-CO forms of CooA from Carboxydothermus hydrogenoformans. Surprisingly, and unlike R. rubrum CooA, C. hydrogenoformans CooA binds NO to form a six-coordinate Fe(II)-NO heme that is active for DNA binding in vitro and in vivo. In contrast, R. rubrum CooA, which is exquisitely specific for CO, forms a five-coordinate Fe(II)-NO adduct that is inactive for DNA binding. Based on analyses of protein variants and temperature studies, NO-dependent DNA binding by C. hydrogenoformans CooA is proposed to result from a greater apparent stability of the six-coordinate Fe(II)-NO adduct at room temperature. Results from the present study strengthen the proposal that CO specificity in the CooA activation mechanism is based on the requirement for a small, neutral distal ligand, which in turn affects the relative positioning of the ligand-bound heme.

authors

Clark RW,Lanz ND,Lee AJ,Kerby RL,Roberts GP,Burstyn JN

doi

10.1073/pnas.0505919103

keywords:

subject

Has Abstract

pub_date

2006-01-24 00:00:00

pages

891-6

issue

4

eissn

0027-8424

issn

1091-6490

pii

0505919103

journal_volume

103

pub_type

杂志文章
  • Inducible transcription of five globin genes in K562 human leukemia cells.

    abstract::We studied the abundance and structure of globin mRNAs present in K562 cells both before and after induction of hemoglobin synthesis by hemin. In vitro translation of poly(A)+ RNA from K562 cells generated protein products corresponding to alpha, A gamma-, G gamma-, epsilon-, and zeta-globin mRNAs. Individual globin m...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.80.18.5515

    authors: Dean A,Ley TJ,Humphries RK,Fordis M,Schechter AN

    更新日期:1983-09-01 00:00:00

  • Isolation and sequence determination of a cDNA clone for rat peroxisomal urate oxidase: liver-specific expression in the rat.

    abstract::Urate oxidase (UOxase; urate:oxygen oxidoreductase, EC 1.7.3.3), which catalyzes the oxidation of uric acid to allantoin, is present in most mammals but is absent in humans and certain primates. A cDNA clone for UOxase containing an insert of 1.3 kilobases (kb) was isolated from a lambda gt11 cDNA library prepared fro...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.85.23.9081

    authors: Reddy PG,Nemali MR,Reddy MK,Reddy MN,Yuan PM,Yuen S,Laffler TG,Shiroza T,Kuramitsu HK,Usuda N

    更新日期:1988-12-01 00:00:00

  • The spectrum of NGC 7027 (367-650 nm).

    abstract::NGC 7027 shows the richest spectrum of any known gaseous nebula. In the region of the spectrum surveyed we have measured lines of ions of H, He, C, N, O, F, Ne, Mg, Si, P, S, Cl, Ar, K, Ca, Mn, and Fe using the new Hamilton Echelle Spectrograph of Lick Observatory with a charge-coupled device (CCD) detector. Since a C...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.85.8.2417

    authors: Aller LH,Keyes CD

    更新日期:1988-04-01 00:00:00

  • Linkage mapping by simultaneous screening of multiple polymorphic loci using Alu oligonucleotide-directed PCR.

    abstract::We present the use of our recently described multiple-loci polymorphic DNA markers ("alumorphs") for linkage mapping of the human genome. By using the polymerase chain reaction (PCR) with an Alu-specific primer we could reveal, in a single experiment, up to 20 genomic polymorphisms seen as the presence or absence of a...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.89.18.8448

    authors: Zietkiewicz E,Labuda M,Sinnett D,Glorieux FH,Labuda D

    更新日期:1992-09-15 00:00:00

  • Isolation and mapping of plasmids containing the Salmonella typhimurium origin of DNA replication.

    abstract::A purified EcoRI restriction endonuclease fragment that determines resistance to kanamycin and is incapable of self-replication was used to select autonomously replicating fragments from an EcoRI digest of a Salmonella typhimurium F' plasmid containing the chromosomal region believed to include the S. typhimurium orig...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.76.7.3097

    authors: Zyskind JW,Deen LT,Smith DW

    更新日期:1979-07-01 00:00:00

  • Ribosomal RNA sequences and the diversity of symbiotic dinoflagellates (zooxanthellae).

    abstract::Zooxanthellae are unicellular algae that occur as endosymbionts in many hundreds of common marine invertebrates. The issue of zooxanthella diversity has been difficult to address. Most zooxanthellae have been placed in the dinoflagellate genus Symbiodinium as one or several species that are not easily distinguished. W...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.89.8.3639

    authors: Rowan R,Powers DA

    更新日期:1992-04-15 00:00:00

  • Four small Drosophila heat shock proteins are related to each other and to mammalian alpha-crystallin.

    abstract::The primary base sequence of the protein coding regions of the four small heat shock genes of Drosophila melanogaster present at cytological locus 67B has been determined. A single open reading frame large enough to encode a small heat shock protein is found for each gene. The molecular weights of the predicted protei...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.79.7.2360

    authors: Ingolia TD,Craig EA

    更新日期:1982-04-01 00:00:00

  • Modulation of NKG2D, NKp46, and Ly49C/I facilitates natural killer cell-mediated control of lung cancer.

    abstract::Natural killer (NK) cells play a critical role in controlling malignancies. Susceptibility or resistance to lung cancer, for example, specifically depends on NK cell function. Nevertheless, intrinsic factors that control NK cell-mediated clearance of lung cancer are unknown. Here we report that NK cells exposed to exo...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1804931115

    authors: Shi L,Li K,Guo Y,Banerjee A,Wang Q,Lorenz UM,Parlak M,Sullivan LC,Onyema OO,Arefanian S,Stelow EB,Brautigan DL,Bullock TNJ,Brown MG,Krupnick AS

    更新日期:2018-11-13 00:00:00

  • T-bet is rapidly induced by interferon-gamma in lymphoid and myeloid cells.

    abstract::Differentiation of naive CD4(+) T cells into IFN-gamma-producing T helper 1 (T(H)1) cells is pivotal for protective immune responses against intracellular pathogens. T-bet, a recently discovered member of the T-box transcription factor family, has been reported to play a critical role in this process, promoting IFN-ga...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.261570598

    authors: Lighvani AA,Frucht DM,Jankovic D,Yamane H,Aliberti J,Hissong BD,Nguyen BV,Gadina M,Sher A,Paul WE,O'Shea JJ

    更新日期:2001-12-18 00:00:00

  • Ranking essential bacterial processes by speed of mutant death.

    abstract::Mutant phenotype analysis of bacteria has been revolutionized by genome-scale screening procedures, but essential genes have been left out of such studies because mutants are missing from the libraries analyzed. Since essential genes control the most fundamental processes of bacterial life, this is a glaring deficienc...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.2001507117

    authors: Gallagher LA,Bailey J,Manoil C

    更新日期:2020-07-28 00:00:00

  • Toward a model for the molecular genetics of carcinogenesis in rats.

    abstract::Cultured rat embryo cells are resistant to neoplastic transformation by chemical carcinogens unless they are extensively subcultured or infected with a murine leukemia virus (MuLV) first. We found that, in normal cultured cells, MuLV activates expression of rat genes that are the progenitors of sarcoma virus genes, b...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.77.6.3450

    authors: Kimball PC,Simon MC,Mishra NK

    更新日期:1980-06-01 00:00:00

  • The N-terminal domain of PsaF: precise recognition site for binding and fast electron transfer from cytochrome c6 and plastocyanin to photosystem I of Chlamydomonas reinhardtii.

    abstract::The PsaF-deficient mutant 3bF of Chlamydomonas reinhardtii was used to modify PsaF by nuclear transformation and site-directed mutagenesis. Four lysine residues in the N-terminal domain of PsaF, which have been postulated to form the positively charged face of a putative amphipathic alpha-helical structure were altere...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.95.13.7339

    authors: Hippler M,Drepper F,Haehnel W,Rochaix JD

    更新日期:1998-06-23 00:00:00

  • Algorithmic design of self-assembling structures.

    abstract::We study inverse statistical mechanics: how can one design a potential function so as to produce a specified ground state? In this article, we show that unexpectedly simple potential functions suffice for certain symmetrical configurations, and we apply techniques from coding and information theory to provide mathemat...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0901636106

    authors: Cohn H,Kumar A

    更新日期:2009-06-16 00:00:00

  • Enantiomer excesses of rare and common sugar derivatives in carbonaceous meteorites.

    abstract::Biological polymers such as nucleic acids and proteins are constructed of only one-the d or l-of the two possible nonsuperimposable mirror images (enantiomers) of selected organic compounds. However, before the advent of life, it is generally assumed that chemical reactions produced 50:50 (racemic) mixtures of enantio...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1603030113

    authors: Cooper G,Rios AC

    更新日期:2016-06-14 00:00:00

  • Noninvasive functional optical spectroscopy of human breast tissue.

    abstract::Near infrared diffuse optical spectroscopy and diffuse optical imaging are promising methods that eventually may enhance or replace existing technologies for breast cancer screening and diagnosis. These techniques are based on highly sensitive, quantitative measurements of optical and functional contrast between healt...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.071511098

    authors: Shah N,Cerussi A,Eker C,Espinoza J,Butler J,Fishkin J,Hornung R,Tromberg B

    更新日期:2001-04-10 00:00:00

  • Formation of IgE-binding factors by T cells of patients infected with human immunodeficiency virus type 1.

    abstract::Peripheral blood mononuclear cells of 10 out of 26 patients with human immunodeficiency virus type 1 (HIV-1) released IgE-binding factors, as determined by two independent assays. The formation of the factors by the mononuclear cells was enhanced by incubation of the cells with homologous IgE. In the presence of IgE, ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.85.23.9214

    authors: Carini C,Margolick J,Yodoi J,Ishizaka K

    更新日期:1988-12-01 00:00:00

  • Impact of natural genetic variation on the transcriptome of autotetraploid Arabidopsis thaliana.

    abstract::Polyploidy, the presence of more than two complete sets of chromosomes in an organism, has significantly shaped the genomes of angiosperms during evolution. Two forms of polyploidy are often considered: allopolyploidy, which originates from interspecies hybrids, and autopolyploidy, which originates from intraspecies g...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1000852107

    authors: Yu Z,Haberer G,Matthes M,Rattei T,Mayer KF,Gierl A,Torres-Ruiz RA

    更新日期:2010-10-12 00:00:00

  • Binding site size limit of the 2:1 pyrrole-imidazole polyamide-DNA motif.

    abstract::Polyamides containing N-methylimidazole (Im) and N-methylpyrrole (Py) amino acids can be combined in antiparallel side-by-side dimeric complexes for sequence-specific recognition in the minor groove of DNA. Six polyamides containing three to eight rings bind DNA sites 5-10 bp in length, respectively. Quantitative DNas...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.93.14.6981

    authors: Kelly JJ,Baird EE,Dervan PB

    更新日期:1996-07-09 00:00:00

  • Recent progress in understanding hydrophobic interactions.

    abstract::We present here a brief review of direct force measurements between hydrophobic surfaces in aqueous solutions. For almost 70 years, researchers have attempted to understand the hydrophobic effect (the low solubility of hydrophobic solutes in water) and the hydrophobic interaction or force (the unusually strong attract...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0606422103

    authors: Meyer EE,Rosenberg KJ,Israelachvili J

    更新日期:2006-10-24 00:00:00

  • Characterizing long-range search behavior in Diptera using complex 3D virtual environments.

    abstract::The exemplary search capabilities of flying insects have established them as one of the most diverse taxa on Earth. However, we still lack the fundamental ability to quantify, represent, and predict trajectories under natural contexts to understand search and its applications. For example, flying insects have evolved ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1912124117

    authors: Kaushik PK,Renz M,Olsson SB

    更新日期:2020-06-02 00:00:00

  • Inactivation of maize transposon Mu suppresses a mutant phenotype by activating an outward-reading promoter near the end of Mu1.

    abstract::We described previously a mutation in maize, hcf106, caused by the insertion of a Mu1 transposon. When the Mu transposon system is in an active phase, hcf106 conditions a nonphotosynthetic, pale green phenotype. However, when the Mu system is inactive (a state correlated with hypermethylation of Mu elements), the plan...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.88.8.3502

    authors: Barkan A,Martienssen RA

    更新日期:1991-04-15 00:00:00

  • Mutations in cyclic AMP-dependent protein kinase and corticotropin (ACTH)-sensitive adenylate cyclase affect adrenal steroidogenesis.

    abstract::Two groups of mutant clones were isolated from YI adrenocortical tumor cells. One group, Y1(Kin), exhibited altered cytosolic cyclic AMP-dependent protein kinase activity; the second group, Y1(Cyc), exhibited diminished corticotropin-responsive adenylate cyclase activity. Steroidogenic responses to corticotropin and c...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.76.4.1896

    authors: Rae PA,Gutmann NS,Tsao J,Schimmer BP

    更新日期:1979-04-01 00:00:00

  • Correlated dynamics of consecutive residues reveal transient and cooperative unfolding of secondary structure in proteins.

    abstract::Nuclear spin relaxation is a powerful method for studying molecular dynamics at atomic resolution. Recent methods development in biomolecular NMR spectroscopy has enabled detailed investigations of molecular dynamics that are critical for biological function, with prominent examples addressing allostery, enzyme cataly...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0504361102

    authors: Lundström P,Mulder FA,Akke M

    更新日期:2005-11-22 00:00:00

  • Phosphorylation and dephosphorylation of spectrin from human erythrocyte ghosts under physiological conditions: autocatalysis rather than reaction with separate kinase and phosphatase.

    abstract::The mechanism of phosphosylation and dephosphorylation of spectrin from human erythrocyte membranes has been examined under closely physiological conditions. The results support the hypothesis that spectrin is an autophosphorylating and dephosphorylating system. (i) Extraction from ghosts of up to 85% of the kinase (c...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.77.6.3264

    authors: Imhof BA,Acha-Orbea HJ,Libermann TA,Reber BF,Lanz JH,Winterhalter KH,Birchmeier W

    更新日期:1980-06-01 00:00:00

  • Resolvin D1 limits 5-lipoxygenase nuclear localization and leukotriene B4 synthesis by inhibiting a calcium-activated kinase pathway.

    abstract::Imbalances between proinflammatory and proresolving mediators can lead to chronic inflammatory diseases. The balance of arachidonic acid-derived mediators in leukocytes is thought to be achieved through intracellular localization of 5-lipoxygenase (5-LOX): nuclear 5-LOX favors the biosynthesis of proinflammatory leuko...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1410851111

    authors: Fredman G,Ozcan L,Spolitu S,Hellmann J,Spite M,Backs J,Tabas I

    更新日期:2014-10-07 00:00:00

  • Anthrax pathogen evades the mammalian immune system through stealth siderophore production.

    abstract::Systemic anthrax, caused by inhalation or ingestion of Bacillus anthracis spores, is characterized by rapid microbial growth stages that require iron. Tightly bound and highly regulated in a mammalian host, iron is scarce during an infection. To scavenge iron from its environment, B. anthracis synthesizes by independe...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0607055103

    authors: Abergel RJ,Wilson MK,Arceneaux JE,Hoette TM,Strong RK,Byers BR,Raymond KN

    更新日期:2006-12-05 00:00:00

  • Identification of a new subset of lymph node stromal cells involved in regulating plasma cell homeostasis.

    abstract::Antibody-secreting plasma cells (PCs) arise rapidly during adaptive immunity to control infections. The early PCs are retained within the reactive lymphoid organ where their localization and homeostasis rely on extrinsic factors, presumably produced by local niche cells. While myeloid cells have been proposed to form ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1712628115

    authors: Huang HY,Rivas-Caicedo A,Renevey F,Cannelle H,Peranzoni E,Scarpellino L,Hardie DL,Pommier A,Schaeuble K,Favre S,Vogt TK,Arenzana-Seisdedos F,Schneider P,Buckley CD,Donnadieu E,Luther SA

    更新日期:2018-07-17 00:00:00

  • T cell leukemia I oncogene expression depends on the presence of Epstein-Barr virus in the virus-carrying Burkitt lymphoma lines.

    abstract::We used a modified subtractive suppression hybridization to identify cellular genes that show altered expression in Burkitt lymphomas (BLs) in the presence of Epstein-Barr virus (EBV). Comparison of the gene expression patterns of an EBV-negative clone of the originally EBV-positive BL line Akata, with its Neo(R)-EBV ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0730710100

    authors: Kiss C,Nishikawa J,Takada K,Trivedi P,Klein G,Szekely L

    更新日期:2003-04-15 00:00:00

  • Communication between neocortex and hippocampus during sleep in rodents.

    abstract::Both neocortical and hippocampal networks organize the firing patterns of their neurons by prominent oscillations during sleep, but the functional role of these rhythms is not well understood. Here, we show a robust correlation of neuronal discharges between the somatosensory cortex and hippocampus on both slow and fi...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0437938100

    authors: Sirota A,Csicsvari J,Buhl D,Buzsáki G

    更新日期:2003-02-18 00:00:00

  • The synthesis, discovery, and development of a highly promising class of microtubule stabilization agents: curative effects of desoxyepothilones B and F against human tumor xenografts in nude mice.

    abstract::We have evaluated two synthetic epothilone analogues lacking the 12,13-epoxide functionality, 12,13-desoxyepothilone B (dEpoB), and 12,13-desoxyepothilone F (dEpoF). The concentrations required for 50% growth inhibition (IC(50)) for a variety of anticancer agents were measured in CCRF-CEM/VBL1000 cells (2,048-fold res...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.131153098

    authors: Chou TC,O'Connor OA,Tong WP,Guan Y,Zhang ZG,Stachel SJ,Lee C,Danishefsky SJ

    更新日期:2001-07-03 00:00:00