scholarly journals Genome Evolution at the Genus Level: Comparison of Three Complete Genomes of Hyperthermophilic Archaea

2001 ◽  
Vol 11 (6) ◽  
pp. 981-993
Author(s):  
Odile Lecompte ◽  
Raymond Ripp ◽  
Valérie Puzos-Barbe ◽  
Simone Duprat ◽  
Roland Heilig ◽  
...  
Keyword(s):  
Pyrococcus Furiosus ◽  
Hyperthermophilic Archaea ◽  
Trna Genes ◽  
Distance Ratio ◽  
Genomic Plasticity ◽  
Relative Contribution ◽  
Complete Genomes ◽  
Replication Terminus ◽  
Living Organisms ◽  
High Level

We have compared three complete genomes of closely related hyperthermophilic species of Archaea belonging to thePyrococcus genus: Pyrococcus abyssi, Pyrococcus horikoshii, and Pyrococcus furiosus. At the genomic level, the comparison reveals a differential conservation among four regions of the Pyrococcus chromosomes correlated with the location of genetic elements mediating DNA reorganization. This discloses the relative contribution of the major mechanisms that promote genomic plasticity in these Archaea, namely rearrangements linked to the replication terminus, insertion sequence-mediated recombinations, and DNA integration within tRNA genes. The combination of these mechanisms leads to a high level of genomic plasticity in these hyperthermophilic Archaea, at least comparable to the plasticity observed between closely related bacteria. At the proteomic level, the comparison of the threePyrococcus species sheds light on specific selection pressures acting both on their coding capacities and evolutionary rates. Indeed, thanks to two independent methods, the “reciprocal best hits“ approach and a new distance ratio analysis, we detect the false orthology relationships within the Pyrococcus lineage. This reveals a high amount of differential gains and losses of genes since the divergence of the three closely related species. The resulting polymorphism is probably linked to an adaptation of these free-living organisms to differential environmental constraints. As a corollary, we delineate the set of orthologous genes shared by the three species, that is, the genes that may characterize the Pyrococcus genus. In this conserved core, the amino acid substitution rate is equal between P. abyssi and P. horikoshii for most of their shared proteins, even for fast-evolving ones. In contrast, strong discrepancies exist among the substitution rates observed in P. furiosus relative to the two other species, which is in disagreement with the molecular clock hypothesis.

scholarly journals Attribution of Atmospheric Sulfur Dioxide over the English Channel to Dimethylsulfide and Changing Ship Emissions

2016 ◽  
Author(s):  
Mingxi Yang ◽  
Thomas G. Bell ◽  
Frances E. Hopkins ◽  
Timothy J. Smyth
Keyword(s):  
Sulfur Dioxide ◽  
English Channel ◽  
Relative Contribution ◽  
Fold Reduction ◽  
Atmospheric Sulfur ◽  
Atmospheric Sulfur Dioxide ◽  
Carbon Dioxide Co2 ◽  
High Level ◽  
Marine Air ◽  
Sulfur Emissions

Abstract. Atmospheric sulfur dioxide (SO2) was measured continuously from the Penlee Point Atmospheric Observatory(PPAO) near Plymouth, United Kingdom between May 2014 and November 2015. This coastal site is exposed to marine air across a wide wind sector. The predominant southwesterly winds carry relatively clean background Atlantic air. In contrast, air from the southeast is heavily influenced by exhaust plumes from ships in the English Channel as well as near the Plymouth Sound. New International Maritime Organization (IMO) regulation came into force in January 2015 to reduce sulfur emissions tenfold in Sulfur Emission Control Areas such as the English Channel. Our observations suggest a three-fold reduction from 2014 to 2015 in ship-emitted SO2 from that direction. Apparent fuel sulfur content calculated from coincidental SO2 and carbon dioxide (CO2) peaks from local ship plum es show a high level of compliance to the IMO regulation (> 95 %) in both years. Dimethylsulfide (DMS) is an important source of atmospheric SO2 even in this semi-polluted region. The relative contribution of DMS oxidation to the SO2 burden over the English Channel increased from ~ 1/3 in 2014 to ~ 1/2 in 2015 due to the reduction in ship sulfur emissions. Our diel analysis suggests that SO2 is removed from the marine atmospheric boundary layer in about half a day, with dry deposition to the ocean accounting for a quarter of the total loss.

scholarly journals Production of Recombinant and Tagged Proteins in the Hyperthermophilic Archaeon Sulfolobus solfataricus

2006 ◽  
Vol 72 (1) ◽  
pp. 102-111 ◽  
Author(s):  
S.-V. Albers ◽  
M. Jonuscheit ◽  
S. Dinkelaker ◽  
T. Urich ◽  
A. Kletzin ◽  
...  
Keyword(s):  
Gene Expression ◽  
Shuttle Vector ◽  
Sulfolobus Solfataricus ◽  
Inducible Promoter ◽  
Single Step ◽  
Vector System ◽  
Hyperthermophilic Archaea ◽  
Model Organisms ◽  
Hyperthermophilic Archaeon ◽  
High Level

ABSTRACT Many systems are available for the production of recombinant proteins in bacterial and eukaryotic model organisms, which allow us to study proteins in their native hosts and to identify protein-protein interaction partners. In contrast, only a few transformation systems have been developed for archaea, and no system for high-level gene expression existed for hyperthermophilic organisms. Recently, a virus-based shuttle vector with a reporter gene was developed for the crenarchaeote Sulfolobus solfataricus, a model organism of hyperthermophilic archaea that grows optimally at 80°C (M. Jonuscheit, E. Martusewitsch, K. M. Stedman, and C. Schleper, Mol. Microbiol. 48:1241-1252, 2003). Here we have refined this system for high-level gene expression in S. solfataricus with the help of two different promoters, the heat-inducible promoter of the major chaperonin, thermophilic factor 55, and the arabinose-inducible promoter of the arabinose-binding protein AraS. Functional expression of heterologous and homologous genes was demonstrated, including production of the cytoplasmic sulfur oxygenase reductase from Acidianus ambivalens, an Fe-S protein of the ABC class from S. solfataricus, and two membrane-associated ATPases potentially involved in the secretion of proteins. Single-step purification of the proteins was obtained via fused His or Strep tags. To our knowledge, these are the first examples of the application of an expression vector system to produce large amounts of recombinant and also tagged proteins in a hyperthermophilic archaeon.

Thermostability and Thermoactivity of Citrate Synthases from the Thermophilic and Hyperthermophilic Archaea, Thermoplasma acidophilum and Pyrococcus furiosus

2000 ◽  
Vol 304 (4) ◽  
pp. 657-668 ◽  
Author(s):  
Michael A. Arnott ◽  
Rebecca A. Michael ◽  
Carl R. Thompson ◽  
David W. Hough ◽  
Michael J. Danson
Keyword(s):  
Pyrococcus Furiosus ◽  
Hyperthermophilic Archaea ◽  
Thermoplasma Acidophilum

scholarly journals The genome ofHyperthermus butylicus: a sulfur-reducing, peptide fermenting, neutrophilic Crenarchaeote growing up to 108 °C

Archaea ◽  
2007 ◽  
Vol 2 (2) ◽  
pp. 127-135 ◽  
Author(s):  
Kim Brügger ◽  
Lanming Chen ◽  
Markus Stark ◽  
Arne Zibat ◽  
Peter Redder ◽  
...  
Keyword(s):  
Genome Structure ◽  
Trna Genes ◽  
Growing Up ◽  
Circular Chromosome ◽  
Protein Coding ◽  
Electron Transfer Proteins ◽  
Good Sequence ◽  
High Level ◽  
Large Clusters ◽  
Single Circular Chromosome

Hyperthermus butylicus, a hyperthermophilic neutrophile and anaerobe, is a member of the archaeal kingdom Crenarchaeota. Its genome consists of a single circular chromosome of 1,667,163 bp with a 53.7% G+C content. A total of 1672 genes were annotated, of which 1602 are protein-coding, and up to a third are specific toH. butylicus. In contrast to some other crenarchaeal genomes, a high level of GUG and UUG start codons are predicted. Twocdc6genes are present, but neither could be linked unambiguously to an origin of replication. Many of the predicted metabolic gene products are associated with the fermentation of peptide mixtures including several peptidases with diverse specificities, and there are many encoded transporters. Most of the sulfur-reducing enzymes, hydrogenases and electron-transfer proteins were identified which are associated with energy production by reducing sulfur to H2S. Two large clusters of regularly interspaced repeats (CRISPRs) are present, one of which is associated with a crenarchaeal-typecasgene superoperon; none of the spacer sequences yielded good sequence matches with known archaeal chromosomal elements. The genome carries no detectable transposable or integrated elements, no inteins, and introns are exclusive to tRNA genes. This suggests that the genome structure is quite stable, possibly reflecting a constant, and relatively uncompetitive, natural environment.

scholarly journals Novel Type of ADP-Forming Acetyl Coenzyme A Synthetase in Hyperthermophilic Archaea: Heterologous Expression and Characterization of Isoenzymes from the Sulfate Reducer Archaeoglobus fulgidus and the Methanogen Methanococcus jannaschii

2002 ◽  
Vol 184 (3) ◽  
pp. 636-644 ◽  
Author(s):  
Meike Musfeldt ◽  
Peter Schönheit
Keyword(s):  
Coenzyme A ◽  
Pyrococcus Furiosus ◽  
Sequence Similarity ◽  
Hyperthermophilic Archaea ◽  
Archaeoglobus Fulgidus ◽  
Methanococcus Jannaschii ◽  
Acetyl Coa ◽  
Acetyl Coenzyme A ◽  
Acetyl Coenzyme ◽  
Α And Β Subunits

ABSTRACT Acetyl coenzyme A (CoA) synthetase (ADP forming) (ACD) represents a novel enzyme of acetate formation and energy conservation (acetyl-CoA + ADP + Pi ⇌ acetate + ATP + CoA) in Archaea and eukaryotic protists. The only characterized ACD in archaea, two isoenzymes from the hyperthermophile Pyrococcus furiosus, constitute 145-kDa heterotetramers (α2, β2). The coding genes for the α and β subunits are located at different sites in the P. furiosus chromosome. Based on significant sequence similarity of the P. furiosus genes, five open reading frames (ORFs) encoding putative ACD were identified in the genome of the hyperthermophilic sulfate-reducing archaeon Archaeoglobus fulgidus and one ORF was identified in the hyperthermophilic methanogen Methanococcus jannaschii. The ORFs constitute fusions of the homologous P. furiosus genes encoding the α and β subunits. Two ORFs, AF1211 and AF1938, of A. fulgidus and ORF MJ0590 of M. jannaschii were cloned and functionally overexpressed in Escherichia coli. The purified recombinant proteins were characterized as distinctive isoenzymes of ACD with different substrate specificities. In contrast to the Pyrococcus ACD, the ACDs of Archaeoglobus and Methanococcus constitute homodimers of about 140 kDa composed of two identical 70-kDa subunits, which represent fusions of the homologous P. furiosus α and β subunits in an αβ (AF1211 and MJ0590) or βα (AF1938) orientation. The data indicate that A. fulgidus and M. jannaschii contains a novel type of ADP-forming acetyl-CoA synthetase in Archaea, in which the subunit polypeptides and their coding genes are fused.

scholarly journals Draft Genome Sequence of a High-Level Colistin-Resistant Clinical Strain of the Enterobacter cloacae Complex

2017 ◽  
Vol 5 (14) ◽  
Author(s):  
Ji Lin ◽  
Feifei Zhao ◽  
Yu Feng ◽  
Zhiyong Zong
Keyword(s):  
Genome Sequence ◽  
Draft Genome ◽  
Enterobacter Cloacae ◽  
Draft Genome Sequence ◽  
Clinical Strain ◽  
Trna Genes ◽  
Coding Sequences ◽  
Content Type ◽  
High Level ◽  
Enterobacter Cloacae Complex

ABSTRACT Strain WCHECl-C4 of the Enterobacter cloacae complex, recovered from the blood of a patient with peritonitis, was high-level resistant to colistin. Here, we report its 5.1-Mb draft genome sequence, comprising 92 contigs with an average 55.74% G+C content. The genome contained 4,783 coding sequences and 68 tRNA genes.

scholarly journals Attribution of atmospheric sulfur dioxide over the English Channel to dimethyl sulfide and changing ship emissions

2016 ◽  
Vol 16 (8) ◽  
pp. 4771-4783 ◽  
Author(s):  
Mingxi Yang ◽  
Thomas G. Bell ◽  
Frances E. Hopkins ◽  
Timothy J. Smyth
Keyword(s):  
Sulfur Dioxide ◽  
Sulfur Content ◽  
Dimethyl Sulfide ◽  
English Channel ◽  
Relative Contribution ◽  
Fold Reduction ◽  
Atmospheric Sulfur ◽  
Atmospheric Sulfur Dioxide ◽  
Carbon Dioxide Co2 ◽  
High Level

Abstract. Atmospheric sulfur dioxide (SO2) was measured continuously from the Penlee Point Atmospheric Observatory (PPAO) near Plymouth, United Kingdom, between May 2014 and November 2015. This coastal site is exposed to marine air across a wide wind sector. The predominant southwesterly winds carry relatively clean background Atlantic air. In contrast, air from the southeast is heavily influenced by exhaust plumes from ships in the English Channel as well as near Plymouth Sound. A new International Maritime Organization (IMO) regulation came into force in January 2015 to reduce the maximum allowed sulfur content in ships' fuel 10-fold in sulfur emission control areas such as the English Channel. Our observations suggest a 3-fold reduction in ship-emitted SO2 from 2014 to 2015. Apparent fuel sulfur content calculated from coincidental SO2 and carbon dioxide (CO2) peaks from local ship plumes show a high level of compliance to the IMO regulation (> 95 %) in both years (∼  70 % of ships in 2014 were already emitting at levels below the 2015 cap). Dimethyl sulfide (DMS) is an important source of atmospheric SO2 even in this semi-polluted region. The relative contribution of DMS oxidation to the SO2 burden over the English Channel increased from about one-third in 2014 to about one-half in 2015 due to the reduction in ship sulfur emissions. Our diel analysis suggests that SO2 is removed from the marine atmospheric boundary layer in about half a day, with dry deposition to the ocean accounting for a quarter of the total loss.

scholarly journals Fulfilling the responsibilites of the manager of the laboratory for the selection of forage crops

2019 ◽  
Vol 2019 (1) ◽  
pp. 118-124
Author(s):  
L.H. Marinich
Keyword(s):  
Protein Content ◽  
Control Systems ◽  
Dry Matter ◽  
Dry Matter Yield ◽  
Panicle Length ◽  
Seed Productivity ◽  
Forage Crops ◽  
Relative Contribution ◽  
High Level ◽  
Selection Of

The effects of GCA samples according to the results of dialysis analysis are given. Genetic control systems of traits of each variety are reflected, in particular the relative contribution of dominant and recessive alleles. According to the analysis of the effects of general combinatorial ability, samples with high indicators were selected for most of the studied features: the number of vegetatively elongated shoots - Poltava 52; foliage - Anto; dry matter yield - Poltava 52; protein content in dry matter - Poltava 52; the number of generative shoots - Anto and Poltava 52; panicle length - Anto and Radio-mutant k-7; seed productivity - Anto. A high level of the coefficients of heredity of the studied signs in a broad sense (H2 = 0,93 – 0,99) have been established. The coefficients of heredity in the narrow sense (h2) in terms of genetic variability due to additive effects of genes were different. The highest rate was in seed productivity (0,91), the number of vegetatively elongated shoots (0,78), dry matter yield (0,70); the lowest - in the length of the panicle (0,35) and the height of the plant - (0,43). The protein content was average (0,58). Key words: unbearded hundred-spike, diallel crosses, general combination ability, heredity.

Sign in / Sign up

Export Citation Format

Share Document