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Archaea: An International Microbiological Journal

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https://www.readbyqxmd.com/read/28694737/archaeal-diversity-and-co2-fixers-in-carbonate-siliciclastic-rock-groundwater-ecosystems
#1
Cassandre Sara Lazar, Wenke Stoll, Robert Lehmann, Martina Herrmann, Valérie F Schwab, Denise M Akob, Ali Nawaz, Tesfaye Wubet, François Buscot, Kai-Uwe Totsche, Kirsten Küsel
Groundwater environments provide habitats for diverse microbial communities, and although Archaea usually represent a minor fraction of communities, they are involved in key biogeochemical cycles. We analysed the archaeal diversity within a mixed carbonate-rock/siliciclastic-rock aquifer system, vertically from surface soils to subsurface groundwater including aquifer and aquitard rocks. Archaeal diversity was also characterized along a monitoring well transect that spanned surface land uses from forest/woodland to grassland and cropland...
2017: Archaea: An International Microbiological Journal
https://www.readbyqxmd.com/read/28634434/an-acidic-exopolysaccharide-from-haloarcula-hispanica-atcc33960-and-two-genes-responsible-for-its-synthesis
#2
Yang Lü, Hua Lu, Shiwei Wang, Jing Han, Hua Xiang, Cheng Jin
A 1.1 × 10(6) Da acidic exopolysaccharide (EPS) was purified from an extremely halophilic archaeon Haloarcula hispanica ATCC33960 with a production of 30 mg L(-1) when grown in AS-168 medium, which mainly composed of mannose and galactose with a small amount of glucose in a molar ratio of 55.9 : 43.2 : 0.9. Two glycosyltransferase genes (HAH_1662 and HAH_1667) were identified to be responsible for synthesis of the acidic EPS. Deletion of either HAH_1662 or HAH_1667 led to loss of the acidic EPS...
2017: Archaea: An International Microbiological Journal
https://www.readbyqxmd.com/read/28634433/the-draft-genome-of-the-non-host-associated-methanobrevibacter-arboriphilus-strain-dh1-encodes-a-large-repertoire-of-adhesin-like-proteins
#3
Anja Poehlein, Rolf Daniel, Henning Seedorf
Methanobrevibacter arboriphilus strain DH1 is an autotrophic methanogen that was isolated from the wetwood of methane-emitting trees. This species has been of considerable interest for its unusual oxygen tolerance and has been studied as a model organism for more than four decades. Strain DH1 is closely related to other host-associated Methanobrevibacter species from intestinal tracts of animals and the rumen, making this strain an interesting candidate for comparative analysis to identify factors important for colonizing intestinal environments...
2017: Archaea: An International Microbiological Journal
https://www.readbyqxmd.com/read/28536498/catalytic-intermediate-crystal-structures-of-cysteine-desulfurase-from-the-archaeon-thermococcus-onnurineus-na1
#4
Thien-Hoang Ho, Kim-Hung Huynh, Diem Quynh Nguyen, Hyunjae Park, Kyoungho Jung, Bookyo Sur, Yeh-Jin Ahn, Sun-Shin Cha, Lin-Woo Kang
Thermococcus onnurineus NA1 is an anaerobic archaeon usually found in a deep-sea hydrothermal vent area, which can use elemental sulfur (S(0)) as a terminal electron acceptor for energy. Sulfur, essential to many biomolecules such as sulfur-containing amino acids and cofactors including iron-sulfur cluster, is usually mobilized from cysteine by the pyridoxal 5'-phosphate- (PLP-) dependent enzyme of cysteine desulfurase (CDS). We determined the crystal structures of CDS from Thermococcus onnurineus NA1 (ToCDS), which include native internal aldimine (NAT), gem-diamine (GD) with alanine, internal aldimine structure with existing alanine (IAA), and internal aldimine with persulfide-bound Cys356 (PSF) structures...
2017: Archaea: An International Microbiological Journal
https://www.readbyqxmd.com/read/28348508/construction-of-expression-shuttle-vectors-for-the-haloarchaeon-natrinema-sp-j7-based-on-its-chromosomal-origins-of-replication
#5
Yuchen Wang, Beibei Chen, Linshan Sima, Mengzhuo Cao, Xiangdong Chen
Haloarchaeon Natrinema sp. J7, the first reported archaeon harboring both plasmid and chromosome-based temperate viruses, is a useful model for investigating archaeal virus-host and virus-virus interactions. However, the lack of genetic tools has limited such studies. On the basis of the automatically replicating sequences of the J7 chromosome and the pyrF marker, we constructed seven vectors, six of which were confirmed to possess replication ability in a pyrF-deletion derivative of J7 (J7-F). Among these vectors, pFJ1, pFJ4, and pFJ6 could be transformed into the host strain with relatively high efficiency (approximately 10(3) colony-forming units/μg DNA) and were present at about one copy per chromosome...
2017: Archaea: An International Microbiological Journal
https://www.readbyqxmd.com/read/28239294/transfection-studies-with-colloidal-systems-containing-highly-purified-bipolar-tetraether-lipids-from-sulfolobus-acidocaldarius
#6
Konrad H Engelhardt, Shashank Reddy Pinnapireddy, Elias Baghdan, Jarmila Jedelská, Udo Bakowsky
Lipid vectors are commonly used to facilitate the transfer of nucleic acids into mammalian cells. In this study, two fractions of tetraether lipids from the archaea Sulfolobus acidocaldarius were extracted and purified using different methods. The purified lipid fractions polar lipid fraction E (PLFE) and hydrolysed glycerol-dialkyl-nonitol tetraether (hGDNT) differ in their structures, charge, size, and miscibility from conventional lipids. Liposomes were prepared by mixing tetraether lipids with cholesterol (CH) and 1,2-dioleoyl-3-trimethylammonium-propane (DOTAP) resulting in stable vectors for gene delivery...
2017: Archaea: An International Microbiological Journal
https://www.readbyqxmd.com/read/28154498/reverse-methanogenesis-and-respiration-in-methanotrophic-archaea
#7
REVIEW
Peer H A Timmers, Cornelia U Welte, Jasper J Koehorst, Caroline M Plugge, Mike S M Jetten, Alfons J M Stams
Anaerobic oxidation of methane (AOM) is catalyzed by anaerobic methane-oxidizing archaea (ANME) via a reverse and modified methanogenesis pathway. Methanogens can also reverse the methanogenesis pathway to oxidize methane, but only during net methane production (i.e., "trace methane oxidation"). In turn, ANME can produce methane, but only during net methane oxidation (i.e., enzymatic back flux). Net AOM is exergonic when coupled to an external electron acceptor such as sulfate (ANME-1, ANME-2abc, and ANME-3), nitrate (ANME-2d), or metal (oxides)...
2017: Archaea: An International Microbiological Journal
https://www.readbyqxmd.com/read/28133437/genome-scale-metabolic-modeling-of-archaea-lends-insight-into-diversity-of-metabolic-function
#8
REVIEW
ShengShee Thor, Joseph R Peterson, Zaida Luthey-Schulten
Decades of biochemical, bioinformatic, and sequencing data are currently being systematically compiled into genome-scale metabolic reconstructions (GEMs). Such reconstructions are knowledge-bases useful for engineering, modeling, and comparative analysis. Here we review the fifteen GEMs of archaeal species that have been constructed to date. They represent primarily members of the Euryarchaeota with three-quarters comprising representative of methanogens. Unlike other reviews on GEMs, we specially focus on archaea...
2017: Archaea: An International Microbiological Journal
https://www.readbyqxmd.com/read/28096736/marine-subsurface-microbial-community-shifts-across-a-hydrothermal-gradient-in-okinawa-trough-sediments
#9
Leah D Brandt, Christopher H House
Sediments within the Okinawa back-arc basin overlay a subsurface hydrothermal network, creating intense temperature gradients with sediment depth and potential limits for microbial diversity. We investigated taxonomic changes across 45 m of recovered core with a temperature gradient of 3°C/m from the dynamic Iheya North Hydrothermal System. The interval transitions sharply from low-temperature marine mud to hydrothermally altered clay at 10 meters below seafloor (mbsf). Here, we present taxonomic results from an analysis of the 16S rRNA gene that support a conceptual model in which common marine subsurface taxa persist into the subsurface, while high temperature adapted archaeal taxa show localized peaks in abundances in the hydrothermal clay horizons...
2016: Archaea: An International Microbiological Journal
https://www.readbyqxmd.com/read/28096735/volatile-fatty-acids-production-from-codigestion-of-food-waste-and-sewage-sludge-based-on-%C3%AE-cyclodextrins-and-alkaline-treatments
#10
Xue Yang, Xiang Liu, Si Chen, Guangmin Liu, Shuyan Wu, Chunli Wan
Volatile fatty acids (VFAs) are preferred valuable resources, which can be produced from anaerobic digestion process. This study presents a novel technology using β-cyclodextrins (β-CD) pretreatment integrated alkaline method to enhance VFAs production from codigestion of food waste and sewage sludge. Experiment results showed that optimized ratio of food waste to sewage sludge was 3 : 2 because it provided adequate organic substance and seed microorganisms. Based on this optimized ratio, the integrated treatment of alkaline pH 10 and β-CD addition (0...
2016: Archaea: An International Microbiological Journal
https://www.readbyqxmd.com/read/28074084/comparative-analysis-of-methanogenic-communities-in-different-laboratory-scale-anaerobic-digesters
#11
Ayrat M Ziganshin, Elvira E Ziganshina, Sabine Kleinsteuber, Marcell Nikolausz
Comparative analysis of methanogenic archaea compositions and dynamics in 11 laboratory-scale continuous stirred tank reactors fed with different agricultural materials (chicken manure, cattle manure, maize straw, maize silage, distillers grains, and Jatropha press cake) was carried out by analysis of the methyl coenzyme-M reductase α-subunit (mcrA) gene. Various taxa within Methanomicrobiales, Methanobacteriaceae, Methanosarcinaceae, Methanosaetaceae, and Methanomassiliicoccales were detected in the biogas reactors but in different proportions depending on the substrate type utilized as well as various process parameters...
2016: Archaea: An International Microbiological Journal
https://www.readbyqxmd.com/read/28070167/the-distribution-pattern-of-sediment-archaea-community-of-the-poyang-lake-the-largest-freshwater-lake-in-china
#12
Yantian Ma, Fangpeng Liu, Zhaoyu Kong, Jianhua Yin, Wenbo Kou, Lan Wu, Gang Ge
Archaea plays an important role in the global geobiochemical circulation of various environments. However, much less is known about the ecological role of archaea in freshwater lake sediments. Thus, investigating the structure and diversity of archaea community is vital to understand the metabolic processes in freshwater lake ecosystems. In this study, sediment physicochemical properties were combined with the results from 16S rRNA clone library-sequencing to examine the sediment archaea diversity and the environmental factors driving the sediment archaea community structures...
2016: Archaea: An International Microbiological Journal
https://www.readbyqxmd.com/read/28053595/deciphering-the-translation-initiation-factor-5a-modification-pathway-in-halophilic-archaea
#13
Laurence Prunetti, Michael Graf, Ian K Blaby, Lauri Peil, Andrea M Makkay, Agata L Starosta, R Thane Papke, Tairo Oshima, Daniel N Wilson, Valérie de Crécy-Lagard
Translation initiation factor 5A (IF5A) is essential and highly conserved in Eukarya (eIF5A) and Archaea (aIF5A). The activity of IF5A requires hypusine, a posttranslational modification synthesized in Eukarya from the polyamine precursor spermidine. Intracellular polyamine analyses revealed that agmatine and cadaverine were the main polyamines produced in Haloferax volcanii in minimal medium, raising the question of how hypusine is synthesized in this halophilic Archaea. Metabolic reconstruction led to a tentative picture of polyamine metabolism and aIF5A modification in Hfx...
2016: Archaea: An International Microbiological Journal
https://www.readbyqxmd.com/read/28050162/arguments-reinforcing-the-three-domain-view-of-diversified-cellular-life
#14
REVIEW
Arshan Nasir, Kyung Mo Kim, Violette Da Cunha, Gustavo Caetano-Anollés
The archaeal ancestor scenario (AAS) for the origin of eukaryotes implies the emergence of a new kind of organism from the fusion of ancestral archaeal and bacterial cells. Equipped with this "chimeric" molecular arsenal, the resulting cell would gradually accumulate unique genes and develop the complex molecular machineries and cellular compartments that are hallmarks of modern eukaryotes. In this regard, proteins related to phagocytosis and cell movement should be present in the archaeal ancestor, thus identifying the recently described candidate archaeal phylum "Lokiarchaeota" as resembling a possible candidate ancestor of eukaryotes...
2016: Archaea: An International Microbiological Journal
https://www.readbyqxmd.com/read/27974879/unusually-high-archaeal-diversity-in-a-crystallizer-pond-pomorie-salterns-bulgaria-revealed-by-phylogenetic-analysis
#15
Margarita Kambourova, Iva Tomova, Ivanka Boyadzhieva, Nadja Radchenkova, Evgenia Vasileva-Tonkova
Recent studies on archaeal diversity in few salterns have revealed heterogeneity between sites and unique structures of separate places that hinder drawing of generalized conclusions. Investigations on the archaeal community composition in P18, the biggest crystallizer pond in Pomorie salterns (PS) (34% salinity), demonstrated unusually high number of presented taxa in hypersaline environment. Archaeal clones were grouped in 26 different operational taxonomic units (OTUs) assigned to 15 different genera from two orders, Halobacteriales and Haloferacales...
2016: Archaea: An International Microbiological Journal
https://www.readbyqxmd.com/read/27956891/nadp-dependent-aldehyde-dehydrogenase-from-archaeon-pyrobaculum-sp-1860-structural-and-functional-features
#16
Ekaterina Yu Bezsudnova, Tatiana E Petrova, Natalia V Artemova, Konstantin M Boyko, Ivan G Shabalin, Tatiana V Rakitina, Konstantin M Polyakov, Vladimir O Popov
We present the functional and structural characterization of the first archaeal thermostable NADP-dependent aldehyde dehydrogenase AlDHPyr1147. In vitro, AlDHPyr1147 catalyzes the irreversible oxidation of short aliphatic aldehydes at 60-85°С, and the affinity of AlDHPyr1147 to the NADP+ at 60°С is comparable to that for mesophilic analogues at 25°С. We determined the structures of the apo form of AlDHPyr1147 (3.04 Å resolution), three binary complexes with the coenzyme (1.90, 2.06, and 2.19 Å), and the ternary complex with the coenzyme and isobutyraldehyde as a substrate (2...
2016: Archaea: An International Microbiological Journal
https://www.readbyqxmd.com/read/27829818/archaea-in-natural-and-impacted-brazilian-environments
#17
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
#18
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
#19
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
#20
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
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