Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea.

Abstract:

:Ammonia-oxidizing archaea are ubiquitous in marine and terrestrial environments and now thought to be significant contributors to carbon and nitrogen cycling. The isolation of Candidatus "Nitrosopumilus maritimus" strain SCM1 provided the opportunity for linking its chemolithotrophic physiology with a genomic inventory of the globally distributed archaea. Here we report the 1,645,259-bp closed genome of strain SCM1, revealing highly copper-dependent systems for ammonia oxidation and electron transport that are distinctly different from known ammonia-oxidizing bacteria. Consistent with in situ isotopic studies of marine archaea, the genome sequence indicates N. maritimus grows autotrophically using a variant of the 3-hydroxypropionate/4-hydroxybutryrate pathway for carbon assimilation, while maintaining limited capacity for assimilation of organic carbon. This unique instance of archaeal biosynthesis of the osmoprotectant ectoine and an unprecedented enrichment of multicopper oxidases, thioredoxin-like proteins, and transcriptional regulators points to an organism responsive to environmental cues and adapted to handling reactive copper and nitrogen species that likely derive from its distinctive biochemistry. The conservation of N. maritimus gene content and organization within marine metagenomes indicates that the unique physiology of these specialized oligophiles may play a significant role in the biogeochemical cycles of carbon and nitrogen.

authors

Walker CB,de la Torre JR,Klotz MG,Urakawa H,Pinel N,Arp DJ,Brochier-Armanet C,Chain PS,Chan PP,Gollabgir A,Hemp J,Hügler M,Karr EA,Könneke M,Shin M,Lawton TJ,Lowe T,Martens-Habbena W,Sayavedra-Soto LA,Lang D,Sieve

doi

10.1073/pnas.0913533107

subject

Has Abstract

pub_date

2010-05-11 00:00:00

pages

8818-23

issue

19

eissn

0027-8424

issn

1091-6490

pii

0913533107

journal_volume

107

pub_type

杂志文章
  • Alternative splicing generates messages encoding rat c-erbA proteins that do not bind thyroid hormone.

    abstract::The nucleotide and predicted amino acid sequences of two variant cDNAs [rat brain thyroid hormone receptor (rTR alpha) vI and vII], isolated from a rat brain cDNA library by using the Pst I fragment of v-erbA, showed virtual identity with the rat brain thyroid hormone receptor (rTR alpha) [Thompson, C. C., Weinberger,...

    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.85.16.5804

    authors: Mitsuhashi T,Tennyson GE,Nikodem VM

    更新日期:1988-08-01 00:00:00

  • Characterization of individual polynucleotide molecules using a membrane channel.

    abstract::We show that an electric field can drive single-stranded RNA and DNA molecules through a 2.6-nm diameter ion channel in a lipid bilayer membrane. Because the channel diameter can accommodate only a single strand of RNA or DNA, each polymer traverses the membrane as an extended chain that partially blocks the channel. ...

    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.93.24.13770

    authors: Kasianowicz JJ,Brandin E,Branton D,Deamer DW

    更新日期:1996-11-26 00:00:00

  • Radiolabeled somatostatin receptor antagonists are preferable to agonists for in vivo peptide receptor targeting of tumors.

    abstract::Targeting neuroendocrine tumors expressing somatostatin receptor subtypes (sst) with radiolabeled somatostatin agonists is an established diagnostic and therapeutic approach in oncology. While agonists readily internalize into tumor cells, permitting accumulation of radioactivity, radiolabeled antagonists do not, and ...

    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.0607761103

    authors: Ginj M,Zhang H,Waser B,Cescato R,Wild D,Wang X,Erchegyi J,Rivier J,Mäcke HR,Reubi JC

    更新日期:2006-10-31 00:00:00

  • Copy number alteration burden predicts prostate cancer relapse.

    abstract::Primary prostate cancer is the most common malignancy in men but has highly variable outcomes, highlighting the need for biomarkers to determine which patients can be managed conservatively. Few large prostate oncogenome resources currently exist that combine the molecular and clinical outcome data necessary to discov...

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

    pub_type: 临床试验,杂志文章

    doi:10.1073/pnas.1411446111

    authors: Hieronymus H,Schultz N,Gopalan A,Carver BS,Chang MT,Xiao Y,Heguy A,Huberman K,Bernstein M,Assel M,Murali R,Vickers A,Scardino PT,Sander C,Reuter V,Taylor BS,Sawyers CL

    更新日期:2014-07-29 00:00:00

  • Brain-blood barrier? Yes and no.

    abstract::Ventriculo-cisternal perfusion of horseradish peroxidase (HRP) in the mouse brain has demonstrated that a brain-blood barrier exists at the microvascular endothelium in brain parenchyma but not in the median eminence of the hypothalamus. The brain-blood barrier is similar to the blood-brain barrier in that: tight junc...

    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.80.23.7352

    authors: Broadwell RD,Balin BJ,Salcman M,Kaplan RS

    更新日期:1983-12-01 00:00:00

  • Optimization of rates of protein folding: the nucleation-condensation mechanism and its implications.

    abstract::Small, single-module proteins that fold in a single cooperative step may be paradigms for understanding early events in protein-folding pathways generally. Recent experimental studies of the 64-residue chymotrypsin inhibitor 2 (CI2) support a nucleation mechanism for folding, as do some computer stimulations. CI2 has ...

    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.92.24.10869

    authors: Fersht AR

    更新日期:1995-11-21 00:00:00

  • Antibodies against a synthetic peptide identify the Epstein-Barr virus-determined nuclear antigen.

    abstract::Five peptides corresponding to amino acid sequences predicted from all three reading frames of the nucleotide sequence of the third internal repeat array (IR3) of the Epstein-Barr virus (EBV) genome were synthesized chemically. All five peptides elicited antipeptide antibodies in rabbits. The antiserum raised against ...

    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.81.15.4652

    authors: Dillner J,Sternås L,Kallin B,Alexander H,Ehlin-Henriksson B,Jörnvall H,Klein G,Lerner R

    更新日期:1984-08-01 00:00:00

  • CCAAT/enhancer-binding protein δ facilitates bacterial dissemination during pneumococcal pneumonia in a platelet-activating factor receptor-dependent manner.

    abstract::CCAAT/enhancer-binding protein δ (C/EBPδ) recently emerged as an essential player in the inflammatory response to bacterial infections. C/EBPδ levels increase rapidly after a proinflammatory stimulus, and increasing C/EBPδ levels seem to be indispensable for amplification of the inflammatory response. Here we aimed to...

    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.1202641109

    authors: Duitman J,Schouten M,Groot AP,Borensztajn KS,Daalhuisen JB,Florquin S,van der Poll T,Spek CA

    更新日期:2012-06-05 00:00:00

  • The point of no return in vetoing self-initiated movements.

    abstract::In humans, spontaneous movements are often preceded by early brain signals. One such signal is the readiness potential (RP) that gradually arises within the last second preceding a movement. An important question is whether people are able to cancel movements after the elicitation of such RPs, and if so until which po...

    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.1513569112

    authors: Schultze-Kraft M,Birman D,Rusconi M,Allefeld C,Görgen K,Dähne S,Blankertz B,Haynes JD

    更新日期:2016-01-26 00:00:00

  • Variations in properties of virus released from morphologically different cell lines transformed in vitro by Friend leukemia virus.

    abstract::The properties of the virus synthesized by each of three morphologically different cell lines originating from DBA/2J fetal liver cells transformed by the anemic strain of Friend leukemia virus in vitro were analyzed. The cells of line G-1 are malignant in syngeneic DBA/2 mice, grow in suspension, and are erythroid in...

    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.77.10.5769

    authors: Tsuei D,Pogo BG,Friend C

    更新日期:1980-10-01 00:00:00

  • Phosphorylation sites required for regulation of cardiac calcium channels in the fight-or-flight response.

    abstract::L-type Ca(2+) currents conducted by CaV1.2 channels initiate excitation-contraction coupling in the heart. Their activity is increased by β-adrenergic/cAMP signaling via phosphorylation by PKA in the fight-or-flight response, but the sites of regulation are unknown. We describe the functional role of phosphorylation o...

    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.1319421110

    authors: Fu Y,Westenbroek RE,Scheuer T,Catterall WA

    更新日期:2013-11-26 00:00:00

  • Neuroimaging of cerebral activations and deactivations associated with hypercapnia and hunger for air.

    abstract::There are defined medullary, mesencephalic, hypothalamic, and thalamic functions in regulation of respiration, but knowledge of cortical control and the elements subserving the consciousness of breathlessness and air hunger is limited. In nine young adults, air hunger was produced acutely by CO(2) inhalation. Comparis...

    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.98.4.2029

    authors: Brannan S,Liotti M,Egan G,Shade R,Madden L,Robillard R,Abplanalp B,Stofer K,Denton D,Fox PT

    更新日期:2001-02-13 00:00:00

  • Processing of precursors of 21S ribosomal RNA from yeast mitochondria.

    abstract::The transcription and processing of mitochondrial 21S rRNA in a petite strain of Saccharomyces cerevisiae has been examined by electron microscopic analysis of R-loop hybrids and by hybridization of labeled mitochondrial DNA probes to RNA transferred to diazobenzyloxymethyl paper. We have shown the presence of a large...

    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.77.3.1417

    authors: Merten S,Synenki RM,Locker J,Christianson T,Rabinowitz M

    更新日期:1980-03-01 00:00:00

  • Goniometer-based femtosecond crystallography with X-ray free electron lasers.

    abstract::The emerging method of femtosecond crystallography (FX) may extend the diffraction resolution accessible from small radiation-sensitive crystals and provides a means to determine catalytically accurate structures of acutely radiation-sensitive metalloenzymes. Automated goniometer-based instrumentation developed for us...

    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.1418733111

    authors: Cohen AE,Soltis SM,González A,Aguila L,Alonso-Mori R,Barnes CO,Baxter EL,Brehmer W,Brewster AS,Brunger AT,Calero G,Chang JF,Chollet M,Ehrensberger P,Eriksson TL,Feng Y,Hattne J,Hedman B,Hollenbeck M,Holton JM,Keab

    更新日期:2014-12-02 00:00:00

  • Tropical amphibian populations experience higher disease risk in natural habitats.

    abstract::Habitat loss and disease are main drivers of global amphibian declines, yet the interaction between them remains largely unexplored. Here we show that paradoxically, habitat loss is negatively associated with occurrence, prevalence, and infection intensity of the chytrid fungus Batrachochytrium dendrobatidis (Bd) in 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.1014497108

    authors: Becker CG,Zamudio KR

    更新日期:2011-06-14 00:00:00

  • RIG-G as a key mediator of the antiproliferative activity of interferon-related pathways through enhancing p21 and p27 proteins.

    abstract::The RIG-G gene, originally isolated from an acute promyelocytic leukemia cell line NB4, codes for a 60-kDa cytoplasmic protein that is induced by all-trans retinoic acid (ATRA) treatment along with the induction of morphological differentiation of NB4 cells. Here, we provide evidence that ectopic expression of Rig-G i...

    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.0607830103

    authors: Xiao S,Li D,Zhu HQ,Song MG,Pan XR,Jia PM,Peng LL,Dou AX,Chen GQ,Chen SJ,Chen Z,Tong JH

    更新日期:2006-10-31 00:00:00

  • Tauroursodeoxycholic acid, a bile acid, is neuroprotective in a transgenic animal model of Huntington's disease.

    abstract::Huntington's disease (HD) is an untreatable neurological disorder caused by selective and progressive degeneration of the caudate nucleus and putamen of the basal ganglia. Although the etiology of HD pathology is not fully understood, the observed loss of neuronal cells is thought to occur primarily through apoptosis....

    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.162362299

    authors: Keene CD,Rodrigues CM,Eich T,Chhabra MS,Steer CJ,Low WC

    更新日期:2002-08-06 00:00:00

  • Intracellular targeting of telomeric retrotransposon Gag proteins of distantly related Drosophila species.

    abstract::The retrotransposons that maintain telomeres in Drosophila melanogaster have unique features that are shared across all Drosophila species but are not found in other retrotransposons. Comparative analysis of these features provides insight into their importance for telomere maintenance in Drosophila. Gag proteins enco...

    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.0702566104

    authors: Casacuberta E,Marín FA,Pardue ML

    更新日期:2007-05-15 00:00:00

  • Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses.

    abstract::Although the applicability of small subunit ribosomal RNA (16S rRNA) sequences for bacterial classification is now well accepted, the general use of these molecules has been hindered by the technical difficulty of obtaining their sequences. A protocol is described for rapidly generating large blocks of 16S rRNA sequen...

    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.82.20.6955

    authors: Lane DJ,Pace B,Olsen GJ,Stahl DA,Sogin ML,Pace NR

    更新日期:1985-10-01 00:00:00

  • Networks of military alliances, wars, and international trade.

    abstract::We investigate the role of networks of alliances in preventing (multilateral) interstate wars. We first show that, in the absence of international trade, no network of alliances is peaceful and stable. We then show that international trade induces peaceful and stable networks: Trade increases the density of alliances ...

    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.1520970112

    authors: Jackson MO,Nei S

    更新日期:2015-12-15 00:00:00

  • Immunoregulatory activity of the T-cell receptor alpha chain demonstrated by retroviral gene transfer.

    abstract::We have previously described an antigen-specific I-Ad-restricted T-cell hybridoma, A1.1, that constitutively releases an antigen-specific immunoregulatory activity into supernatants. Using retrovirally mediated gene transfer, we have found that transfer of the T-cell receptor alpha chain (TCR alpha) gene from A1.1 to ...

    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.88.19.8475

    authors: Green DR,Bissonnette R,Zheng HG,Onda T,Echeverri F,Mogil RJ,Steele JK,Voralia M,Fotedar A

    更新日期:1991-10-01 00:00:00

  • Strain history dependence of the nonlinear stress response of fibrin and collagen networks.

    abstract::We show that the nonlinear mechanical response of networks formed from un-cross-linked fibrin or collagen type I continually changes in response to repeated large-strain loading. We demonstrate that this dynamic evolution of the mechanical response arises from a shift of a characteristic nonlinear stress-strain relati...

    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.1222787110

    authors: Münster S,Jawerth LM,Leslie BA,Weitz JI,Fabry B,Weitz DA

    更新日期:2013-07-23 00:00:00

  • Remodeling of synaptic architecture during hippocampal "kindling".

    abstract::The "kindling" phenomenon is associated with long-lasting facilitation of synaptic transmission. A possible mechanism of such facilitation could involve changes in the number of synaptic contacts. However, previous attempts to demonstrate a synaptic morphological alteration that could account for the long-term effects...

    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.85.9.3260

    authors: Geinisman Y,Morrell F,deToledo-Morrell L

    更新日期:1988-05-01 00:00:00

  • What might we learn from climate forecasts?

    abstract::Most climate models are large dynamical systems involving a million (or more) variables on big computers. Given that they are nonlinear and not perfect, what can we expect to learn from them about the earth's climate? How can we determine which aspects of their output might be useful and which are noise? And how shoul...

    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.012580599

    authors: Smith LA

    更新日期:2002-02-19 00:00:00

  • Targeted disruption of Pax1 defines its null phenotype and proves haploinsufficiency.

    abstract::The murine paired box-containing gene Pax1 is required for normal development of the vertebral column, the sternum, and the scapula. Previous studies have shown that three natural Pax1 mouse mutants, the undulated alleles, exhibit phenotypes of different severity in these skeletal elements. Nevertheless, these analyse...

    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.95.15.8692

    authors: Wilm B,Dahl E,Peters H,Balling R,Imai K

    更新日期:1998-07-21 00:00:00

  • Complex pattern of Mycobacterium marinum gene expression during long-term granulomatous infection.

    abstract::During latent infection of humans with Mycobacterium tuberculosis, bacteria persist in the asymptomatic host within granulomas, organized collections of differentiated macrophages, and other immune cells. The mechanisms for persistence remain poorly understood, as is the metabolic and replicative state of the microbes...

    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.002024599

    authors: Chan K,Knaak T,Satkamp L,Humbert O,Falkow S,Ramakrishnan L

    更新日期:2002-03-19 00:00:00

  • Backward multiple imputation estimation of the conditional lifetime expectancy function with application to censored human longevity data.

    abstract::The conditional lifetime expectancy function (LEF) is the expected lifetime of a subject given survival past a certain time point and the values of a set of explanatory variables. This function is attractive to researchers because it summarizes the entire residual life distribution and has an easy interpretation compa...

    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.1512237112

    authors: Kong J,Klein BE,Klein R,Wahba G

    更新日期:2015-09-29 00:00:00

  • Sequence-independent upstream DNA-alphaCTD interactions strongly stimulate Escherichia coli RNA polymerase-lacUV5 promoter association.

    abstract::The C-terminal domains of the two alpha-subunits (alphaCTD) in Escherichia coli RNA polymerase (RNAP) recognize specific sequences called UP elements in some promoters. These interactions can increase transcription dramatically. Previously, effects of upstream DNA-alphaCTD interactions on transcription were quantified...

    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.0405814102

    authors: Ross W,Gourse RL

    更新日期:2005-01-11 00:00:00

  • Evolutionary EST analysis identifies rapidly evolving male reproductive proteins in Drosophila.

    abstract::Sequence comparisons of genomes or expressed sequence tags (ESTs) from related organisms provide insight into functional conservation and diversification. We compare the sequences of ESTs from the male accessory gland of Drosophila simulans to their orthologs in its close relative Drosophila melanogaster, and demonstr...

    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.131568198

    authors: Swanson WJ,Clark AG,Waldrip-Dail HM,Wolfner MF,Aquadro CF

    更新日期:2001-06-19 00:00:00

  • Modulation of type beta transforming growth factor activity in bone cultures by osteotropic hormones.

    abstract::Type beta transforming growth factor (TGF-beta) activity was found in conditioned medium harvested from fetal rat and neonatal mouse calvariae by using the anchorage-independent growth of normal rat kidney fibroblasts as an indicator system. Calvariae incubated with parathyroid hormone, 1,25-dihydroxyvitamin D3, and i...

    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.84.7.2024

    authors: Pfeilschifter J,Mundy GR

    更新日期:1987-04-01 00:00:00