scholarly journals How an obscure archaeal gene inspired the discovery of selenocysteine biosynthesis in humans

IUBMB Life ◽  
2009 ◽  
Vol 61 (1) ◽  
pp. 35-39 ◽  
Author(s):  
Dan Su ◽  
Michael J. Hohn ◽  
Sotiria Palioura ◽  
R. Lynn Sherrer ◽  
Jing Yuan ◽  
...  
Keyword(s):  
Archaeal Gene

Adenylosuccinate Synthetase Genes: Molecular Cloning and Phylogenetic Analysis of a Highly Conserved Archaeal Gene

1998 ◽  
Vol 21 (4) ◽  
pp. 478-486 ◽  
Author(s):  
Isaac K.O. Cann ◽  
Satoru Kanai ◽  
Hiroyuki Toh ◽  
Yoshizumi Ishino
Keyword(s):  
Phylogenetic Analysis ◽  
Molecular Cloning ◽  
Adenylosuccinate Synthetase ◽  
Archaeal Gene

scholarly journals BAGET 2.0: an updated web tool for the effortless retrieval of prokaryotic gene context and sequence

2021 ◽  
Author(s):  
Benjamin Hepp ◽  
Violette Da Cunha ◽  
Florence Lorieux ◽  
Jacques Oberto
Keyword(s):  
Gene Sequence ◽  
Single Gene ◽  
Daily Basis ◽  
Web Tool ◽  
Web Based ◽  
Internet Explorer ◽  
Prokaryotic Genomes ◽  
Exploration Tool ◽  
Genome Browsers ◽  
Archaeal Gene

Abstract Motivation The retrieval of a single gene sequence and context from completely sequenced bacterial and archaeal genomes constitutes an intimidating task for the wet bench biologist. Existing web-based genome browsers are either too complex for routine use or only provide a subset of the available prokaryotic genomes. Results We have developed BAGET 2.0 (Bacterial and Archaeal Gene Exploration Tool), an updated web service granting access in just three mouse clicks to the sequence and synteny of any gene from completely sequenced bacteria and archaea. User-provided annotated genomes can be processed as well. BAGET 2.0 relies on a local database updated on a daily basis. Availability and implementation BAGET 2.0 befits all current browsers such as Chrome, Firefox, Edge, Opera and Safari. Internet Explorer 11 is supported. BAGET 2.0 is freely accessible at https://archaea.i2bc.paris-saclay.fr/baget/

scholarly journals Transposon Insertion Mutagenesis for Archaeal Gene Discovery

2016 ◽  
pp. 309-320 ◽  
Author(s):  
Saija Kiljunen ◽  
Maria I. Pajunen ◽  
Harri Savilahti
Keyword(s):  
Gene Discovery ◽  
Insertion Mutagenesis ◽  
Transposon Insertion ◽  
Archaeal Gene

scholarly journals Dissection of the regulatory mechanism of a heat-shock responsive promoter in Haloarchaea: a new paradigm for general transcription factor directed archaeal gene regulation

2008 ◽  
Vol 36 (9) ◽  
pp. 3031-3042 ◽  
Author(s):  
Q. Lu ◽  
J. Han ◽  
L. Zhou ◽  
J. A. Coker ◽  
P. DasSarma ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Transcription Factor ◽  
Heat Shock ◽  
Regulatory Mechanism ◽  
New Paradigm ◽  
General Transcription Factor ◽  
Archaeal Gene

scholarly journals Identification of an Alternative Nucleoside Triphosphate: 5′-Deoxyadenosylcobinamide Phosphate Nucleotidyltransferase in Methanobacterium thermoautotrophicum ΔH

2000 ◽  
Vol 182 (15) ◽  
pp. 4227-4233 ◽  
Author(s):  
Michael G. Thomas ◽  
Jorge C. Escalante-Semerena
Keyword(s):  
Kinase Activity ◽  
De Novo ◽  
Methanobacterium Thermoautotrophicum ◽  
Cell Extract ◽  
Nucleoside Triphosphate ◽  
De Novo Synthesis ◽  
Anaerobic Conditions ◽  
Gene Encoding ◽  
Reading Frame ◽  
Archaeal Gene

ABSTRACT Computer analysis of the archaeal genome databases failed to identify orthologues of all of the bacterial cobamide biosynthetic enzymes. Of particular interest was the lack of an orthologue of the bifunctional nucleoside triphosphate (NTP):5′-deoxyadenosylcobinamide kinase/GTP:adenosylcobinamide-phosphate guanylyltransferase enzyme (CobU in Salmonella enterica). This paper reports the identification of an archaeal gene encoding a new nucleotidyltransferase, which is proposed to be the nonorthologous replacement of the S. enterica cobU gene. The gene encoding this nucleotidyltransferase was identified using comparative genome analysis of the sequenced archaeal genomes. Orthologues of the gene encoding this activity are limited at present to members of the domainArchaea. The corresponding ORF open reading frame fromMethanobacterium thermoautotrophicum ΔH (MTH1152; referred to as cobY) was amplified and cloned, and the CobY protein was expressed and purified from Escherichia coli as a hexahistidine-tagged fusion protein. This enzyme had GTP:adenosylcobinamide-phosphate guanylyltransferase activity but did not have the NTP:AdoCbi kinase activity associated with the CobU enzyme of S. enterica. NTP:adenosylcobinamide kinase activity was not detected in M. thermoautotrophicum ΔH cell extract, suggesting that this organism may not have this activity. ThecobY gene complemented a cobU mutant ofS. enterica grown under anaerobic conditions where growth of the cell depended on de novo adenosylcobalamin biosynthesis.cobY, however, failed to restore adenosylcobalamin biosynthesis in cobU mutants grown under aerobic conditions where de novo synthesis of this coenzyme was blocked, and growth of the cell depended on the assimilation of exogenous cobinamide. These data strongly support the proposal that the relevant cobinamide intermediates during de novo adenosylcobalamin biosynthesis are adenosylcobinamide-phosphate and adenosylcobinamide-GDP, not adenosylcobinamide. Therefore, NTP:adenosylcobinamide kinase activity is not required for de novo cobamide biosynthesis.

Comparative 16S rRNA gene surveys of granular sludge from three upflow anaerobic bioreactors treating purified terephthalic acid (PTA) wastewater

2011 ◽  
Vol 64 (7) ◽  
pp. 1406-1412 ◽  
Author(s):  
S. D. Perkins ◽  
N. B. Scalfone ◽  
L. T. Angenent
Keyword(s):  
Terephthalic Acid ◽  
Granular Sludge ◽  
Rrna Gene ◽  
Uncultured Bacteria ◽  
Anaerobic Bioreactors ◽  
Main Degradation Product ◽  
Archaeal Gene ◽  
Hydrogenotrophic Methanogens ◽  
Main Component ◽  
Purified Terephthalic Acid

The microbial communities from three upflow anaerobic bioreactors treating purified terephthalic acid (PTA) wastewater were characterized with 16S ribosomal RNA gene sequencing surveys. Universal bacterial and archaeal primers were used to compare the bioreactor communities to each other. A total of 1,733 bacterial sequences and 383 archaeal sequences were characterized. The high number of Syntrophus spp. and Pelotomaculum spp. found within these reactors indicates efficient removal of benzoate and terephthalate. Under anaerobic conditions benzoate can be degraded through syntrophic associations between these bacteria and hydrogen-scavenging microbes, such as Desulfovibrio spp. and hydrogenotrophic methanogens, which remove H2 to force the thermodynamically unfavourable reactions to take place. The authors did not observe a relatively high percentage of hydrogenotrophic methanogens with the archaeal gene survey because of a high acetate flux (acetate is a main component in PTA wastewater and is the main degradation product of terephthalate/benzoate fermentation), and because of the presence of Desulfovibrio spp. (a sulfate reducer that scavenges hydrogen). The high acetate flux also explains the high percentage of acetoclastic methanogens from the genus Methanosaeta among the archaeal sequences. A group of uncultured bacteria (OD1) may be involved in the degradation of p-toluate (4-methyl benzoate), which is a component of PTA wastewater.

scholarly journals Patterns of Bacterial and Archaeal Gene Expression through the Lower Amazon River

2017 ◽  
Vol 4 ◽  
Author(s):  
Brandon M. Satinsky ◽  
Christa B. Smith ◽  
Shalabh Sharma ◽  
Nicholas D. Ward ◽  
Alex V. Krusche ◽  
...  
Keyword(s):  
Gene Expression ◽  
Amazon River ◽  
Archaeal Gene

An archaeal gene upstream of grpE different from eubacterial counterparts

1995 ◽  
Vol 1264 (2) ◽  
pp. 173-177 ◽  
Author(s):  
Alberto J.L. Macario ◽  
Victor H. Simon ◽  
Everly Conway de Macario
Keyword(s):  
Archaeal Gene

scholarly journals 3′ UTRs: a paradigm for archaeal gene regulation?

2016 ◽  
Vol 14 (10) ◽  
pp. 605-605
Author(s):  
Naomi Attar
Keyword(s):  
Gene Regulation ◽  
Archaeal Gene

Control regions of an archaeal gene

1991 ◽  
Vol 222 (3) ◽  
pp. 495-508 ◽  
Author(s):  
Winfried Hausner ◽  
Gerhard Frey ◽  
Michael Thomm
Keyword(s):  
Archaeal Gene ◽  
Control Regions
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