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Archaea: An International Microbiological Journal

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https://www.readbyqxmd.com/read/27829818/archaea-in-natural-and-impacted-brazilian-environments
#1
REVIEW
Thiago Rodrigues, Aline Belmok, Elisa Catão, Cynthia Maria Kyaw
In recent years, archaeal diversity surveys have received increasing attention. Brazil is a country known for its natural diversity and variety of biomes, which makes it an interesting sampling site for such studies. However, archaeal communities in natural and impacted Brazilian environments have only recently been investigated. In this review, based on a search on the PubMed database on the last week of April 2016, we present and discuss the results obtained in the 51 studies retrieved, focusing on archaeal communities in water, sediments, and soils of different Brazilian environments...
2016: Archaea: An International Microbiological Journal
https://www.readbyqxmd.com/read/27799846/characterization-of-a-thermostable-8-oxoguanine-dna-glycosylase-specific-for-go-n-mismatches-from-the-thermoacidophilic-archaeon-thermoplasma-volcanium
#2
Miki Fujii, Chieri Hata, Munetada Ukita, Chie Fukushima, Chihiro Matsuura, Yoshie Kawashima-Ohya, Koji Tomobe, Tsuyoshi Kawashima
The oxidation of guanine (G) to 7,8-dihydro-8-oxoguanine (GO) forms one of the major DNA lesions generated by reactive oxygen species (ROS). The GO can be corrected by GO DNA glycosylases (Ogg), enzymes involved in base excision repair (BER). Unrepaired GO induces mismatched base pairing with adenine (A); as a result, the mismatch causes a point mutation, from G paired with cytosine (C) to thymine (T) paired with adenine (A), during DNA replication. Here, we report the characterization of a putative Ogg from the thermoacidophilic archaeon Thermoplasma volcanium...
2016: Archaea: An International Microbiological Journal
https://www.readbyqxmd.com/read/27774041/birth-of-archaeal-cells-molecular-phylogenetic-analyses-of-g1p-dehydrogenase-g3p-dehydrogenases-and-glycerol-kinase-suggest-derived-features-of-archaeal-membranes-having-g1p-polar-lipids
#3
Shin-Ichi Yokobori, Yoshiki Nakajima, Satoshi Akanuma, Akihiko Yamagishi
Bacteria and Eukarya have cell membranes with sn-glycerol-3-phosphate (G3P), whereas archaeal membranes contain sn-glycerol-1-phosphate (G1P). Determining the time at which cells with either G3P-lipid membranes or G1P-lipid membranes appeared is important for understanding the early evolution of terrestrial life. To clarify this issue, we reconstructed molecular phylogenetic trees of G1PDH (G1P dehydrogenase; EgsA/AraM) which is responsible for G1P synthesis and G3PDHs (G3P dehydrogenase; GpsA and GlpA/GlpD) and glycerol kinase (GlpK) which is responsible for G3P synthesis...
2016: Archaea: An International Microbiological Journal
https://www.readbyqxmd.com/read/27752237/discovering-antioxidant-molecules-in-the-archaea-domain-peroxiredoxin-bcp1-from-sulfolobus-solfataricus-protects-h9c2-cardiomyoblasts-from-oxidative-stress
#4
Carmen Sarcinelli, Gabriella Fiorentino, Elio Pizzo, Simonetta Bartolucci, Danila Limauro
Peroxiredoxins (Prxs) are ubiquitous thiol peroxidases that are involved in the reduction of peroxides. It has been reported that prokaryotic Prxs generally show greater structural robustness than their eukaryotic counterparts, making them less prone to inactivation by overoxidation. This difference has inspired the search for new antioxidants from prokaryotic sources that can be used as possible therapeutic biodrugs. Bacterioferritin comigratory proteins (Bcps) of the hyperthermophilic archaeon Sulfolobus solfataricus that belong to the Prx family have recently been characterized...
2016: Archaea: An International Microbiological Journal
https://www.readbyqxmd.com/read/27725793/archaea-and-bacteria-acclimate-to-high-total-ammonia-in-a-methanogenic-reactor-treating-swine-waste
#5
Sofia Esquivel-Elizondo, Prathap Parameswaran, Anca G Delgado, Juan Maldonado, Bruce E Rittmann, Rosa Krajmalnik-Brown
Inhibition by ammonium at concentrations above 1000 mgN/L is known to harm the methanogenesis phase of anaerobic digestion. We anaerobically digested swine waste and achieved steady state COD-removal efficiency of around 52% with no fatty-acid or H2 accumulation. As the anaerobic microbial community adapted to the gradual increase of total ammonia-N (NH3-N) from 890 ± 295 to 2040 ± 30 mg/L, the Bacterial and Archaeal communities became less diverse. Phylotypes most closely related to hydrogenotrophic Methanoculleus (36...
2016: Archaea: An International Microbiological Journal
https://www.readbyqxmd.com/read/27721668/archaeal-dna-polymerase-b-as-a-dna-template-guardian-links-between-polymerases-and-base-alternative-excision-repair-enzymes-in-handling-the-deaminated-bases-uracil-and-hypoxanthine
#6
Javier Abellón-Ruiz, Sonoko Ishino, Yoshizumi Ishino, Bernard A Connolly
In Archaea repair of uracil and hypoxanthine, which arise by deamination of cytosine and adenine, respectively, is initiated by three enzymes: Uracil-DNA-glycosylase (UDG, which recognises uracil); Endonuclease V (EndoV, which recognises hypoxanthine); and Endonuclease Q (EndoQ), (which recognises both uracil and hypoxanthine). Two archaeal DNA polymerases, Pol-B and Pol-D, are inhibited by deaminated bases in template strands, a feature unique to this domain. Thus the three repair enzymes and the two polymerases show overlapping specificity for uracil and hypoxanthine...
2016: Archaea: An International Microbiological Journal
https://www.readbyqxmd.com/read/27703410/fundamental-characteristics-of-aaa-protein-family-structure-and-function
#7
Justin M Miller, Eric J Enemark
Many complex cellular events depend on multiprotein complexes known as molecular machines to efficiently couple the energy derived from adenosine triphosphate hydrolysis to the generation of mechanical force. Members of the AAA+ ATPase superfamily (ATPases Associated with various cellular Activities) are critical components of many molecular machines. AAA+ proteins are defined by conserved modules that precisely position the active site elements of two adjacent subunits to catalyze ATP hydrolysis. In many cases, AAA+ proteins form a ring structure that translocates a polymeric substrate through the central channel using specialized loops that project into the central channel...
2016: Archaea: An International Microbiological Journal
https://www.readbyqxmd.com/read/27274708/the-proteome-and-lipidome-of-thermococcus-kodakarensis-across-the-stationary-phase
#8
Emma J Gagen, Marcos Y Yoshinaga, Franka Garcia Prado, Kai-Uwe Hinrichs, Michael Thomm
The majority of cells in nature probably exist in a stationary-phase-like state, due to nutrient limitation in most environments. Studies on bacteria and yeast reveal morphological and physiological changes throughout the stationary phase, which lead to an increased ability to survive prolonged nutrient limitation. However, there is little information on archaeal stationary phase responses. We investigated protein- and lipid-level changes in Thermococcus kodakarensis with extended time in the stationary phase...
2016: Archaea: An International Microbiological Journal
https://www.readbyqxmd.com/read/27274707/methanogen-diversity-in-indigenous-and-introduced-ruminant-species-on-the-tibetan-plateau
#9
Xiao Dan Huang, Gonzalo Martinez-Fernandez, Jagadish Padmanabha, Ruijun Long, Stuart E Denman, Christopher S McSweeney
Host factors are regarded as important in shaping the archaeal community in the rumen but few controlled studies have been performed to demonstrate this across host species under the same environmental conditions. A study was designed to investigate the structure of the methanogen community in the rumen of two indigenous (yak and Tibetan sheep) and two introduced domestic ruminant (cattle and crossbred sheep) species raised and fed under similar conditions on the high altitude Tibetan Plateau. The methylotrophic Methanomassiliicoccaceae was the predominant archaeal group in all animals even though Methanobrevibacter are usually present in greater abundance in ruminants globally...
2016: Archaea: An International Microbiological Journal
https://www.readbyqxmd.com/read/27239160/characterization-of-the-atp-dependent-lon-like-protease-in-methanobrevibacter-smithii
#10
Jihua Pei, Jianfang Yan, Yi Jiang
The Lon protease is highly evolutionarily conserved. However, little is known about Lon in the context of gut microbial communities. A gene encoding a Lon-like protease (Lon-like-Ms) was identified and characterized from Methanobrevibacter smithii, the predominant archaeon in the human gut ecosystem. Phylogenetic and sequence analyses showed that Lon-like-Ms and its homologs are newly identified members of the Lon family. A recombinant form of the enzyme was purified by affinity chromatography, and its catalytic properties were examined...
2016: Archaea: An International Microbiological Journal
https://www.readbyqxmd.com/read/27194953/discovery-and-characterization-of-iron-sulfide-and-polyphosphate-bodies-coexisting-in-archaeoglobus-fulgidus-cells
#11
Daniel B Toso, Muhammad Mohsin Javed, Elizabeth Czornyj, Robert P Gunsalus, Z Hong Zhou
Inorganic storage granules have long been recognized in bacterial and eukaryotic cells but were only recently identified in archaeal cells. Here, we report the cellular organization and chemical compositions of storage granules in the Euryarchaeon, Archaeoglobus fulgidus strain VC16, a hyperthermophilic, anaerobic, and sulfate-reducing microorganism. Dense granules were apparent in A. fulgidus cells imaged by cryo electron microscopy (cryoEM) but not so by negative stain electron microscopy. Cryo electron tomography (cryoET) revealed that each cell contains one to several dense granules located near the cell membrane...
2016: Archaea: An International Microbiological Journal
https://www.readbyqxmd.com/read/27006640/archaeal-community-changes-associated-with-cultivation-of-amazon-forest-soil-with-oil-palm
#12
Daiva Domenech Tupinambá, Maurício Egídio Cantão, Ohana Yonara Assis Costa, Jessica Carvalho Bergmann, Ricardo Henrique Kruger, Cynthia Maria Kyaw, Cristine Chaves Barreto, Betania Ferraz Quirino
This study compared soil archaeal communities of the Amazon forest with that of an adjacent area under oil palm cultivation by 16S ribosomal RNA gene pyrosequencing. Species richness and diversity were greater in native forest soil than in the oil palm-cultivated area, and 130 OTUs (13.7%) were shared between these areas. Among the classified sequences, Thaumarchaeota were predominant in the native forest, whereas Euryarchaeota were predominant in the oil palm-cultivated area. Archaeal species diversity was 1...
2016: Archaea: An International Microbiological Journal
https://www.readbyqxmd.com/read/26884723/the-vertical-distribution-of-sediment-archaeal-community-in-the-black-bloom-disturbing-zhushan-bay-of-lake-taihu
#13
Xianfang Fan, Peng Xing
Using the Illumina sequencing technology, we investigated the vertical distribution of archaeal community in the sediment of Zhushan Bay of Lake Taihu, where the black bloom frequently occurred in summer. Overall, the Miscellaneous Crenarchaeotal Group (MCG), Deep Sea Hydrothermal Vent Group 6 (DHVEG-6), and Methanobacterium dominated the archaeal community. However, we observed significant difference in composition of archaeal community among different depths of the sediment. DHVEG-6 dominated in the surface layer (0-3 cm) sediment...
2016: Archaea: An International Microbiological Journal
https://www.readbyqxmd.com/read/26880868/characterization-of-fatty-acids-in-crenarchaeota-by-gc-ms-and-nmr
#14
Timothy Hamerly, Brian Tripet, Louie Wurch, Robert L Hettich, Mircea Podar, Brian Bothner, Valérie Copié
Lipids composed of condensed isoprenyl units connected to glycerol backbones by ether linkages are a distinguishing feature of Archaea. Data suggesting that fatty acids with linear hydrocarbon chains are present in some Archaea have been available for decades. However, lack of genomic and biochemical evidence for the metabolic machinery required to synthesize and degrade fatty acids has left the field unclear on this potentially significant biochemical aspect. Because lipids are energy currency and cell signaling molecules, their presence in Archaea is significant for understanding archaeal biology...
2015: Archaea: An International Microbiological Journal
https://www.readbyqxmd.com/read/26819569/sequence-structure-and-binding-analysis-of-cyclodextrinase-tk1770-from-t-kodakarensis-kod1-using-an-in-silico-approach
#15
Ramzan Ali, Muhammad Imtiaz Shafiq
Thermostable cyclodextrinase (Tk1770 CDase) from hyperthermophilic archaeon Thermococcus kodakarensis (KOD1) hydrolyzes cyclodextrins into linear dextrins. The sequence of Tk1770 CDase retrieved from UniProt was aligned with sequences of sixteen CD hydrolyzing enzymes and a phylogenetic tree was constructed using Bayesian inference. The homology model of Tk1770 CDase was constructed and optimized with Modeller v9.14 program. The model was validated with ProSA server and PROCHECK analysis. Four conserved regions and the catalytic triad consisting of Asp411, Glu437, and Asp502 of GH13 family were identified in catalytic site...
2015: Archaea: An International Microbiological Journal
https://www.readbyqxmd.com/read/26568700/molecular-analysis-of-methanogen-richness-in-landfill-and-marshland-targeting-16s-rdna-sequences
#16
Shailendra Yadav, Sharbadeb Kundu, Sankar K Ghosh, S S Maitra
Methanogens, a key contributor in global carbon cycling, methane emission, and alternative energy production, generate methane gas via anaerobic digestion of organic matter. The methane emission potential depends upon methanogenic diversity and activity. Since they are anaerobes and difficult to isolate and culture, their diversity present in the landfill sites of Delhi and marshlands of Southern Assam, India, was analyzed using molecular techniques like 16S rDNA sequencing, DGGE, and qPCR. The sequencing results indicated the presence of methanogens belonging to the seventh order and also the order Methanomicrobiales in the Ghazipur and Bhalsawa landfill sites of Delhi...
2015: Archaea: An International Microbiological Journal
https://www.readbyqxmd.com/read/26543406/production-and-application-of-a-soluble-hydrogenase-from-pyrococcus-furiosus
#17
REVIEW
Chang-Hao Wu, Patrick M McTernan, Mary E Walter, Michael W W Adams
Hydrogen gas is a potential renewable alternative energy carrier that could be used in the future to help supplement humanity's growing energy needs. Unfortunately, current industrial methods for hydrogen production are expensive or environmentally unfriendly. In recent years research has focused on biological mechanisms for hydrogen production and specifically on hydrogenases, the enzyme responsible for catalyzing the reduction of protons to generate hydrogen. In particular, a better understanding of this enzyme might allow us to generate hydrogen that does not use expensive metals, such as platinum, as catalysts...
2015: Archaea: An International Microbiological Journal
https://www.readbyqxmd.com/read/26543405/biotechnological-uses-of-archaeal-proteins
#18
EDITORIAL
Frédéric Pecorari, Vickery L Arcus, Juergen Wiegel
No abstract text is available yet for this article.
2015: Archaea: An International Microbiological Journal
https://www.readbyqxmd.com/read/26539062/a-novel-highly-thermostable-multifunctional-beta-glycosidase-from-crenarchaeon-acidilobus-saccharovorans
#19
Vadim M Gumerov, Andrey L Rakitin, Andrey V Mardanov, Nikolai V Ravin
We expressed a putative β-galactosidase Asac_1390 from hyperthermophilic crenarchaeon Acidilobus saccharovorans in Escherichia coli and purified the recombinant enzyme. Asac_1390 is composed of 490 amino acid residues and showed high sequence similarity to family 1 glycoside hydrolases from various thermophilic Crenarchaeota. The maximum activity was observed at pH 6.0 and 93°C. The half-life of the enzyme at 90°C was about 7 hours. Asac_1390 displayed high tolerance to glucose and exhibits hydrolytic activity towards cellobiose and various aryl glucosides...
2015: Archaea: An International Microbiological Journal
https://www.readbyqxmd.com/read/26539061/archaeal-mcm-proteins-as-an-analog-for-the-eukaryotic-mcm2-7-helicase-to-reveal-essential-features-of-structure-and-function
#20
REVIEW
Justin M Miller, Eric J Enemark
In eukaryotes, the replicative helicase is the large multisubunit CMG complex consisting of the Mcm2-7 hexameric ring, Cdc45, and the tetrameric GINS complex. The Mcm2-7 ring assembles from six different, related proteins and forms the core of this complex. In archaea, a homologous MCM hexameric ring functions as the replicative helicase at the replication fork. Archaeal MCM proteins form thermostable homohexamers, facilitating their use as models of the eukaryotic Mcm2-7 helicase. Here we review archaeal MCM helicase structure and function and how the archaeal findings relate to the eukaryotic Mcm2-7 ring...
2015: Archaea: An International Microbiological Journal
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