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https://www.readbyqxmd.com/read/29346615/the-rna-splicing-endonuclease-from-the-euryarchaeaon-methanopyrus-kandleri-is-a-heterotetramer-with-constrained-substrate-specificity
#1
Ayano Kaneta, Kosuke Fujishima, Wataru Morikazu, Hiroyuki Hori, Akira Hirata
Four different types (α4, α'2, (αβ)2 and ε2) of RNA-splicing endonucleases (EndAs) for RNA processing are known to exist in the Archaea. Only the (αβ)2 and ε2 types can cleave non-canonical introns in precursor (pre)-tRNA. Both enzyme types possess an insert associated with a specific loop, allowing broad substrate specificity in the catalytic α units. Here, the hyperthermophilic euryarchaeon Methanopyrus kandleri (MKA) was predicted to harbor an (αβ)2-type EndA lacking the specific loop. To characterize MKA EndA enzymatic activity, we constructed a fusion protein derived from MKA α and β subunits (fMKA EndA)...
January 13, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29340843/phytoene-production-utilizing-the-isoprenoid-biosynthesis-capacity-of-thermococcus-kodakarensis
#2
Tsubasa Fuke, Takaaki Sato, Savyasachee Jha, Myra L Tansengco, Haruyuki Atomi
Phytoene (C40H64) is an isoprenoid and a precursor of various carotenoids which are of industrial value. Archaea can be considered to exhibit a relatively large capacity to produce isoprenoids, as they are components of their membrane lipids. Here, we aimed to produce isoprenoids such as phytoene in the hyperthermophilic archaeon Thermococcus kodakarensis. T. kodakarensis harbors a prenyltransferase gene involved in the biosynthesis of farnesyl pyrophosphate and geranylgeranyl pyrophosphate, which are precursors of squalene and phytoene, respectively...
January 16, 2018: Extremophiles: Life Under Extreme Conditions
https://www.readbyqxmd.com/read/29340254/response-of-methane-production-via-propionate-oxidation-to-carboxylated-multiwalled-carbon-nanotubes-in-paddy-soil-enrichments
#3
Jianchao Zhang, Xingxuan Xia, Siliang Li, Wei Ran
Carboxylated multiwalled carbon nanotubes (MWCNTs-COOH) have become a growing concern in terms of their fate and toxicity in aqueous environments. Methane (CH4) is a major product of organic matter degradation in waterlogged environments. In this study, we determined the effect of MWCNTs-COOH on the production of CH4 from propionate oxidation in paddy soil enrichments. The results showed that the methanogenesis from propionate degradation was accelerated in the presence of MWCNTs-COOH. In addition, the rates of CH4 production and propionate degradation increased with increasing concentrations of MWCNTs-COOH...
2018: PeerJ
https://www.readbyqxmd.com/read/29339602/performance-and-stability-of-an-expanded-granular-sludge-bed-reactor-modified-with-zeolite-addition-subjected-to-step-increases-of-organic-loading-rate-olr-and-to-organic-shock-load-osl
#4
T Pérez-Pérez, I Pereda-Reyes, E Pozzi, D Oliva-Merencio, M Zaiat
This paper shows the effect of organic shock loads (OSLs) on the anaerobic digestion (AD) of synthetic swine wastewater using an expanded granular sludge bed (EGSB) reactor modified with zeolite. Two reactors (R1 and R2), each with an effective volume of 3.04 L, were operated for 180 days at a controlled temperature of 30 °C and hydraulic retention time of 12 h. In the case of R2, 120 g of zeolite was added. The reactors were operated with an up-flow velocity of 6 m/h. The evolution of pH, total Kjeldahl nitrogen, chemical oxygen demand (COD) and volatile fatty acids (VFAs) was monitored during the AD process with OSL and increases in the organic loading rate (OLR)...
January 2018: Water Science and Technology: a Journal of the International Association on Water Pollution Research
https://www.readbyqxmd.com/read/29339416/exploring-the-almost-unknown-archaeal-two-component-systems
#5
Tino Krell
Two-component systems (TCS) exist in bacteria and archaea. In contrast to bacterial TCSs little information is available on their archaeal counterparts. In this issue Galperin and coworkers present a bioinformatics analysis of TCS genes from archaeal genome sequences. This study identified different aspects in which bacterial and archaeal TCS mediated signaling differ and forms a sound basis for the experimental design of studies to increase our knowledge on this poorly investigated protein family.
January 16, 2018: Journal of Bacteriology
https://www.readbyqxmd.com/read/29337314/the-reconstruction-of-2-631-draft-metagenome-assembled-genomes-from-the-global-oceans
#6
Benjamin J Tully, Elaina D Graham, John F Heidelberg
Microorganisms play a crucial role in mediating global biogeochemical cycles in the marine environment. By reconstructing the genomes of environmental organisms through metagenomics, researchers are able to study the metabolic potential of Bacteria and Archaea that are resistant to isolation in the laboratory. Utilizing the large metagenomic dataset generated from 234 samples collected during the Tara Oceans circumnavigation expedition, we were able to assemble 102 billion paired-end reads into 562 million contigs, which in turn were co-assembled and consolidated in to 7...
January 16, 2018: Scientific Data
https://www.readbyqxmd.com/read/29336668/safety-and-biodistribution-of-sulfated-archaeal-glycolipid-archaeosomes-as-vaccine-adjuvants
#7
Bassel Akache, Felicity C Stark, Umar Iqbal, Wangxue Chen, Yimei Jia, Lakshmi Krishnan, Michael J McCluskie
Archaeosomes are liposomes comprised of ether lipids derived from various archaea. Unlike conventional ester-linked liposomes, archaeosomes exhibit high pH and thermal stability. As adjuvants, archaeosomes can induce robust, long-lasting humoral and cell-mediated immune responses and enhance protection in murine models of infectious disease and cancer. Archaeosomes constituted with total polar lipids (TPL) of various archaea are relatively complex, comprising >10 different lipid compounds. Archaeosomes can be constituted with semi-synthetic glycerolipids built on ether-linked isoprenoid phytanyl cores with varied synthetic glycol- and amino-head groups...
January 16, 2018: Human Vaccines & Immunotherapeutics
https://www.readbyqxmd.com/read/29335805/effects-of-nicotine-on-the-biosynthesis-of-carotenoids-in-halophilic-archaea-class-halobacteria-an-hplc-and-raman-spectroscopy-study
#8
Aharon Oren, Joseph Hirschberg, Varda Mann, Jan Jehlička
Nicotine has a profound influence on the carotenoid metabolism in halophilic Archaea of the class Halobacteria. In a study of Halobacterium salinarum, Haloarcula marismortui and Halorubrum sodomense, using different analytical techniques to monitor the production of different carotenoids as a function of the presence of nicotine, we showed that the formation of α-bacterioruberin was inhibited in all. In Hbt. salinarum, addition of nicotine led to a significant change in the color of the culture due to the accumulation of lycopene, in addition to the formation of bisanhydrobacterioruberin which does not differ in color from α-bacterioruberin...
January 15, 2018: Extremophiles: Life Under Extreme Conditions
https://www.readbyqxmd.com/read/29335634/the-pii-signaling-protein-from-red-algae-represents-an-evolutionary-link-between-cyanobacterial-and-chloroplastida-pii-proteins
#9
Tatyana Lapina, Khaled A Selim, Karl Forchhammer, Elena Ermilova
PII superfamily consists of widespread signal transduction proteins found in all domains of life. Whereas they are well-studied in Archaea, Bacteria and Chloroplastida, no PII homolog has been analyzed in Rhodophyta (red algae), where PII is encoded by a chloroplast localized glnB gene. Here, we characterized relevant sensory properties of PII from the red alga Porphyra purpurea (PpPII) in comparison to PII proteins from different phyla of oxygenic phototrophs (cyanobacteria, Chlamydomonas and Physcomitrella) to assess evolutionary conservation versus adaptive properties...
January 15, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29335552/a-pathway-for-biological-methane-production-using-bacterial-iron-only-nitrogenase
#10
Yanning Zheng, Derek F Harris, Zheng Yu, Yanfen Fu, Saroj Poudel, Rhesa N Ledbetter, Kathryn R Fixen, Zhi-Yong Yang, Eric S Boyd, Mary E Lidstrom, Lance C Seefeldt, Caroline S Harwood
Methane (CH4) is a potent greenhouse gas that is released from fossil fuels and is also produced by microbial activity, with at least one billion tonnes of CH4 being formed and consumed by microorganisms in a single year 1 . Complex methanogenesis pathways used by archaea are the main route for bioconversion of carbon dioxide (CO2) to CH4 in nature2-4. Here, we report that wild-type iron-iron (Fe-only) nitrogenase from the bacterium Rhodopseudomonas palustris reduces CO2 simultaneously with nitrogen gas (N2) and protons to yield CH4, ammonia (NH3) and hydrogen gas (H2) in a single enzymatic step...
January 15, 2018: Nature Microbiology
https://www.readbyqxmd.com/read/29331726/impact-of-the-start-up-process-on-the-microbial-communities-in-biocathodes-for-electrosynthesis
#11
Raúl Mateos, Ana Sotres, Raúl M Alonso, Adrián Escapa, Antonio Morán
This study seeks to understand how the bacterial communities that develop on biocathodes are influenced by inocula diversity and electrode potential during start-up. Two different inocula are used: one from a highly diverse environment (river mud) and the other from a low diverse milieu (anaerobic digestion). In addition, both inocula were subjected to two different polarising voltages: oxidative (+0.2 V vs. Ag/AgCl) and reductive (-0.8 V vs. Ag/AgCl). Bacterial communities were analysed by means of high throughput sequencing...
January 7, 2018: Bioelectrochemistry
https://www.readbyqxmd.com/read/29331688/coproheme-decarboxylases-phylogenetic-prediction-versus-biochemical-experiments
#12
Vera Pfanzagl, Laurenz Holcik, Daniel Maresch, Giulia Gorgone, Hanna Michlits, Paul G Furtmüller, Stefan Hofbauer
Coproheme decarboxylases (ChdCs) are enzymes responsible for the catalysis of the terminal step in the coproporphyrin-dependent heme biosynthesis pathway. Phylogenetic analyses confirm that the gene encoding for ChdCs is widespread throughout the bacterial world. It is found in monoderm bacteria (Firmicutes, Actinobacteria), diderm bacteria (e. g. Nitrospirae) and also in Archaea. In order to test phylogenetic prediction ChdC representatives from all clades were expressed and examined for their coproheme decarboxylase activity...
January 10, 2018: Archives of Biochemistry and Biophysics
https://www.readbyqxmd.com/read/29330529/the-interaction-network-of-the-yidc-insertase-with-the-secyeg-translocon-srp-and-the-srp-receptor-ftsy
#13
Narcis-Adrian Petriman, Benjamin Jauß, Antonia Hufnagel, Lisa Franz, Ilie Sachelaru, Friedel Drepper, Bettina Warscheid, Hans-Georg Koch
YidC/Oxa1/Alb3 are essential proteins that operate independently or cooperatively with the Sec machinery during membrane protein insertion in bacteria, archaea and eukaryotic organelles. Although the interaction between the bacterial SecYEG translocon and YidC has been observed in multiple studies, it is still unknown which domains of YidC are in contact with the SecYEG translocon. By in vivo and in vitro site-directed and para-formaldehyde cross-linking we identified the auxiliary transmembrane domain 1 of E...
January 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29329319/comparative-analysis-of-uranium-bioassociation-with-halophilic-bacteria-and-archaea
#14
Miriam Bader, Katharina Müller, Harald Foerstendorf, Matthias Schmidt, Karen Simmons, Juliet S Swanson, Donald T Reed, Thorsten Stumpf, Andrea Cherkouk
Rock salt represents a potential host rock formation for the final disposal of radioactive waste. The interactions between indigenous microorganisms and radionuclides, e.g. uranium, need to be investigated to better predict the influence of microorganisms on the safety assessment of the repository. Hence, the association process of uranium with two microorganisms isolated from rock salt was comparatively studied. Brachybacterium sp. G1, which was isolated from the German salt dome Gorleben, and Halobacterium noricense DSM15987T, were selected as examples of a moderately halophilic bacterium and an extremely halophilic archaeon, respectively...
2018: PloS One
https://www.readbyqxmd.com/read/29327072/naproxen-is-transformed-via-acetogenesis-and-syntrophic-acetate-oxidation-by-a-methanogenic-wastewater-consortium
#15
Sarah J Wolfson, Abigail W Porter, Julia K Campbell, Lily Y Young
Over-the-counter pharmaceutical compounds can serve as microbial substrates in wastewater treatment processes as well as in the environment. The metabolic pathways and intermediates produced during their degradation, however, are poorly understood. In this study, we investigate an anaerobic wastewater community that metabolizes naproxen via demethylation. Enriched cultures, established from anaerobic digester inocula receiving naproxen as the sole carbon source, transformed naproxen to 6-O-desmethylnaproxen (DMN) within 22 days...
January 11, 2018: Microbial Ecology
https://www.readbyqxmd.com/read/29323202/genome-based-classification-of-micromonosporae-with-a-focus-on-their-biotechnological-and-ecological-potential
#16
Lorena Carro, Imen Nouioui, Vartul Sangal, Jan P Meier-Kolthoff, Martha E Trujillo, Maria Del Carmen Montero-Calasanz, Nevzat Sahin, Darren Lee Smith, Kristi E Kim, Paul Peluso, Shweta Deshpande, Tanja Woyke, Nicole Shapiro, Nikos C Kyrpides, Hans-Peter Klenk, Markus Göker, Michael Goodfellow
There is a need to clarify relationships within the actinobacterial genus Micromonospora, the type genus of the family Micromonosporaceae, given its biotechnological and ecological importance. Here, draft genomes of 40 Micromonospora type strains and two non-type strains are made available through the Genomic Encyclopedia of Bacteria and Archaea project and used to generate a phylogenomic tree which showed they could be assigned to well supported phyletic lines that were not evident in corresponding trees based on single and concatenated sequences of conserved genes...
January 11, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29323168/variations-in-bacterial-and-archaeal-communities-along-depth-profiles-of-alaskan-soil-cores
#17
Binu Mani Tripathi, Mincheol Kim, Yongwon Kim, Eunji Byun, Ji-Woong Yang, Jinho Ahn, Yoo Kyung Lee
Understating the microbial communities and ecological processes that influence their structure in permafrost soils is crucial for predicting the consequences of climate change. In this study we investigated the bacterial and archaeal communities along depth profiles of four soil cores collected across Alaska. The bacterial and archaeal diversity (amplicon sequencing) overall decreased along the soil depth but the depth-wise pattern of their abundances (qPCR) varied by sites. The community structure of bacteria and archaea displayed site-specific pattern, with a greater role of soil geochemical characteristics rather than soil depth...
January 11, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29322393/contribution-of-ammonia-oxidizing-archaea-and-ammonia-oxidizing-bacteria-to-ammonia-oxidation-in-two-nitrifying-reactors
#18
Papitchaya Srithep, Preeyaporn Pornkulwat, Tawan Limpiyakorn
In this study, two laboratory nitrifying reactors (NRI and NRII), which were seeded by sludge from different sources and operated under different operating conditions, were found to possess distinct dominant ammonia-oxidizing microorganisms. Ammonia-oxidizing archaeal (AOA) amoA genes outnumbered ammonia-oxidizing bacterial (AOB) amoA genes in reactor NRI, while only AOB amoA genes were detectable in reactor NRII. The AOA amoA gene sequences retrieved from NRI were characterized within the Nitrososphaera sister cluster of the group 1...
January 10, 2018: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/29315530/ecological-drivers-of-soil-microbial-diversity-and-soil-biological-networks-in-the-southern-hemisphere
#19
Manuel Delgado-Baquerizo, Frank Reith, Paul G Dennis, Kelly Hamonts, Jeff R Powell, Andrew Young, Brajesh K Singh, Andrew Bissett
The ecological drivers of soil biodiversity in the Southern Hemisphere remain underexplored. Here, in a continental survey comprising 647 sites, across 58 degrees of latitude between tropical Australia and Antarctica, we evaluated the major ecological patterns in soil biodiversity and relative abundance of ecological clusters within a co-occurrence network of soil bacteria, archaea and eukaryotes. Six major ecological clusters (modules) of co-occurring soil taxa were identified. These clusters exhibited strong shifts in their relative abundances with increasing distance from the equator...
January 9, 2018: Ecology
https://www.readbyqxmd.com/read/29315358/htt-db-new-features-and-updates
#20
Bruno Reis Dotto, Evelise Leis Carvalho, Alexandre Freitas da Silva, Filipe Zimmer Dezordi, Paulo Marcos Pinto, Tulio de Lima Campos, Antonio Mauro Rezende, Gabriel da Luz Wallau
Horizontal Transfer (HT) of genetic material between species is a common phenomenon among Bacteria and Archaea species and several databases are available for information retrieval and data mining. However, little attention has been given to this phenomenon among eukaryotic species mainly due to the lower proportion of these events. In the last years, a vertiginous amount of new HT events involving eukaryotic species was reported in the literature, highlighting the need of a common repository to keep the scientific community up to date and describe overall trends...
January 1, 2018: Database: the Journal of Biological Databases and Curation
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