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https://www.readbyqxmd.com/read/28095753/a-functional-endonuclease-q-exists-in-the-bacterial-domain-identification-and-characterization-of-endonuclease-q-from-bacillus-pumilus
#1
Miyako Shiraishi, Sonoko Ishino, Isaac Cann, Yoshizumi Ishino
DNA base deamination occurs spontaneously under physiological conditions and is promoted by high temperature. Therefore, hyperthermophiles are expected to have efficient repair systems of the deaminated bases in their genomes. Endonuclease Q (EndoQ) was originally identified from the hyperthermophlic archaeon, Pyrococcus furiosus, as a hypoxanthine-specific endonuclease recently. Further biochemical analyses revealed that EndoQ also recognizes uracil, xanthine, and the AP site in DNA, and is probably involved in a specific repair process for damaged bases...
January 18, 2017: Bioscience, Biotechnology, and Biochemistry
https://www.readbyqxmd.com/read/28094773/methane-emissions-and-microbial-communities-as-influenced-by-dual-cropping-of-azolla-along-with-early-rice
#2
Jingna Liu, Heshui Xu, Ying Jiang, Kai Zhang, Yuegao Hu, Zhaohai Zeng
Azolla caroliniana Willd. is widely used as a green manure accompanying rice, but its ecological importance remains unclear, except for its ability to fix nitrogen in association with cyanobacteria. To investigate the impacts of Azolla cultivation on methane emissions and environmental variables in paddy fields, we performed this study on the plain of Dongting Lake, China, in 2014. The results showed that the dual cropping of Azolla significantly suppressed the methane emissions from paddies, likely due to the increase in redox potential in the root region and dissolved oxygen concentration at the soil-water interface...
January 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28089747/metabolic-engineering-of-a-diazotrophic-bacterium-improves-ammonium-release-and-biofertilization-of-plants-and-microalgae
#3
Rafael Ambrosio, Juan Cesar Federico Ortiz-Marquez, Leonardo Curatti
The biological nitrogen fixation carried out by some Bacteria and Archaea is one of the most attractive alternatives to synthetic nitrogen fertilizers. However, with the exception of the symbiotic rhizobia-legumes system, progress towards a more extensive realization of this goal has been slow. In this study we manipulated the endogenous regulation of both nitrogen fixation and assimilation in the aerobic bacterium Azotobacter vinelandii. Substituting an exogenously inducible promoter for the native promoter of glutamine synthetase produced conditional lethal mutant strains unable to grow diazotrophically in the absence of the inducer...
January 9, 2017: Metabolic Engineering
https://www.readbyqxmd.com/read/28087421/physiology-anaerobes-and-the-origin-of-mitosing-cells-50-years-on
#4
William F Martin
Endosymbiotic theory posits that some organelles or structures of eukaryotic cells stem from free-living prokaryotes that became endosymbionts within a host cell. Endosymbiosis has a long and turbulent history of controversy and debate going back over 100 years. The 1967 paper by Lynn Sagan (later Lynn Margulis) forced a reluctant field to take endosymbiotic theory seriously and to incorporate it into the fabric of evolutionary thinking. Margulis envisaged three cellular partners associating in series at eukaryotic origin: the host (an engulfing bacterium), the mitochondrion (a respiring bacterium), and the flagellum (a spirochaete), with lineages descended from that flagellated eukaryote subsequently acquiring plastids from cyanobacteria, but on multiple different occasions in her 1967 account...
January 10, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28087277/identification-of-ubact-a-ubiquitin-like-protein-along-with-other-homologous-components-of-a-conjugation-system-and-the-proteasome-in-different-gram-negative-bacteria
#5
Gilad Lehmann, Ronald G Udasin, Ido Livneh, Aaron Ciechanover
Systems analogous to the eukaryotic ubiquitin-proteasome system have been previously identified in Archaea, and Actinobacteria (gram-positive), but not in gram-negative bacteria. Here, we report the bioinformatic identification of a novel prokaryotic ubiquitin-like protein, which we name UBact. The phyletic distribution of UBact covers at least five gram-negative bacterial phyla, including Nitrospirae, Armatimonadetes, Verrucomicroba, Nitrospinae, and Planctomycetes. Additionally, it was identified in seven candidate (uncultured) phyla and one Archaeon...
January 10, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28081458/multistage-bioassociation-of-uranium-onto-an-extremely-halophilic-archaeon-revealed-by-a-unique-combination-of-spectroscopic-and-microscopic-techniques
#6
Miriam Bader, Katharina Müller, Harald Foerstendorf, Björn Drobot, Matthias Schmidt, Niculina Musat, Juliet S Swanson, Donald T Reed, Thorsten Stumpf, Andrea Cherkouk
The interactions of two extremely halophilic archaea with uranium were investigated at high ionic strength as a function of time, pH and uranium concentration. Halobacterium noricense DSM-15987 and Halobacterium sp. putatively noricense, isolated from the Waste Isolation Pilot Plant repository, were used for these investigations. The kinetics of U(VI) bioassociation with both strains showed an atypical multistage behavior, meaning that after an initial phase of U(VI) sorption, an unexpected interim period of U(VI) release was observed, followed by a slow reassociation of uranium with the cells...
December 27, 2016: Journal of Hazardous Materials
https://www.readbyqxmd.com/read/28077874/asgard-archaea-illuminate-the-origin-of-eukaryotic-cellular-complexity
#7
Katarzyna Zaremba-Niedzwiedzka, Eva F Caceres, Jimmy H Saw, Disa Bäckström, Lina Juzokaite, Emmelien Vancaester, Kiley W Seitz, Karthik Anantharaman, Piotr Starnawski, Kasper U Kjeldsen, Matthew B Stott, Takuro Nunoura, Jillian F Banfield, Andreas Schramm, Brett J Baker, Anja Spang, Thijs J G Ettema
The origin and cellular complexity of eukaryotes represent a major enigma in biology. Current data support scenarios in which an archaeal host cell and an alphaproteobacterial (mitochondrial) endosymbiont merged together, resulting in the first eukaryotic cell. The host cell is related to Lokiarchaeota, an archaeal phylum with many eukaryotic features. The emergence of the structural complexity that characterizes eukaryotic cells remains unclear. Here we describe the 'Asgard' superphylum, a group of uncultivated archaea that, as well as Lokiarchaeota, includes Thor-, Odin- and Heimdallarchaeota...
January 11, 2017: Nature
https://www.readbyqxmd.com/read/28076802/peldor-spectroscopy-reveals-two-defined-states-of-a-sialic-acid-trap-transporter-sbp-in-solution
#8
Janin Glaenzer, Martin F Peter, Gavin H Thomas, Gregor Hagelueken
The tripartite ATP-independent periplasmic (TRAP) transporters are a widespread class of membrane transporters in bacteria and archaea. Typical substrates for TRAP transporters are organic acids including the sialic acid N-acetylneuraminic acid. The substrate binding proteins (SBP) of TRAP transporters are the best studied component and are responsible for initial high-affinity substrate binding. To better understand the dynamics of the ligand binding process, pulsed electron-electron double resonance (PELDOR, also known as DEER) spectroscopy was applied to study the conformational changes in the N-acetylneuraminic acid-specific SBP VcSiaP...
January 10, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28076447/lower-methane-emissions-from-yak-compared-with-cattle-in-rusitec-fermenters
#9
Jiandui Mi, Jianwei Zhou, Xiaodan Huang, Ruijun Long
Globally methane (CH4) emissions from ruminant livestock account for 29% of total CH4 emissions. Inherited variation about CH4 emissions of different animal species might provide new opportunity for manipulating CH4 production. Six rumen-simulating fermenters (Rusitec) were set up for this study lasting for 16 d. The diet consisted of forage to concentrate ratio of 50:50 with barley straw as the forage. Treated vessels were supplied with rumen fluid from yak or cattle (3 vessels per animal species). Microbial growth was measured using 15N as a marker...
2017: PloS One
https://www.readbyqxmd.com/read/28074318/boosted-large-scale-production-and-purification-of-a-thermostable-archaeal-phosphotriesterase-like-lactonase-for-organophosphate-decontamination
#10
Odile Francesca Restaino, Maria Giovanna Borzacchiello, Ilaria Scognamiglio, Elena Porzio, Giuseppe Manco, Luigi Fedele, Cinzia Donatiello, Mario De Rosa, Chiara Schiraldi
Thermostable phosphotriesterase-like lactonases (PLLs) from extremophile archaea, like SsoPox from Sulfolobus solfataricus, are attractive biotechnological tools with industrial applications as organophosphate decontaminants, but their manufacturing still remains an unresolved issue because of the high costs and the low production yields. In this paper, for the first time, an efficient biotechnological process for the production and purification of a recombinant, engineered PLL, SsoPox W263F, expressed in E...
January 11, 2017: Journal of Industrial Microbiology & Biotechnology
https://www.readbyqxmd.com/read/28073944/a-novel-bifunctional-transcriptional-regulator-of-riboflavin-metabolism-in-archaea
#11
Irina A Rodionova, Matthew W Vetting, Xiaoqing Li, Steven C Almo, Andrei L Osterman, Dmitry A Rodionov
Riboflavin (vitamin B2) is the precursor of flavin mononucleotide (FMN) and flavin adenine dinucleotide, which are essential coenzymes in all free-living organisms. Riboflavin biosynthesis in many Bacteria but not in Archaea is controlled by FMN-responsive riboswitches. We identified a novel bifunctional riboflavin kinase/regulator (RbkR), which controls riboflavin biosynthesis and transport genes in major lineages of Crenarchaeota, Euryarchaeota and Thaumarchaeota. RbkR proteins are composed of the riboflavin kinase domain and a DNA-binding winged helix-turn-helix-like domain...
January 9, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28072454/non-neuronal-acetylcholine-involved-in-reproduction-in-mammals-and-honeybees
#12
REVIEW
Ignaz Wessler, Charles James Kirkpatrick
Bacteria and archaea synthesize acetylcholine (ACh). Thus it can be postulated that ACh was created by nature roughly 3 billion years ago. Therefore, the wide expression of ACh in nature (i.e. in bacteria, archaea, unicellular organisms, plants, fungi, non-vertebrates and vertebrates and the abundance of non-neuronal cells of mammals) is not surprising. The term non-neuronal ACh and non-neuronal cholinergic system have been introduced to describe the auto- and paracrine, i.e. local regulatory actions of cells not innervated by neuronal cholinergic fibers to communicate among themselves...
January 10, 2017: Journal of Neurochemistry
https://www.readbyqxmd.com/read/28072419/an-acid-tolerant-ammonia-oxidizing-%C3%AE-proteobacterium-from-soil
#13
Masahito Hayatsu, Kanako Tago, Ikuo Uchiyama, Atsushi Toyoda, Yong Wang, Yumi Shimomura, Takashi Okubo, Futoshi Kurisu, Yuhei Hirono, Kunihiko Nonaka, Hiroko Akiyama, Takehiko Itoh, Hideto Takami
Nitrification, the microbial oxidation of ammonia to nitrate via nitrite, occurs in a wide range of acidic soils. However, the ammonia-oxidizing bacteria (AOB) that have been isolated from soil to date are acid-sensitive. Here we report the isolation and characterization of an acid-adapted AOB from an acidic agricultural soil. The isolated AOB, strain TAO100, is classified within the Gammaproteobacteria based on phylogenetic characteristics. TAO100 can grow in the pH range of 5-7.5 and survive in highly acidic conditions until pH 2 by forming cell aggregates...
January 10, 2017: ISME Journal
https://www.readbyqxmd.com/read/28072418/microbial-community-dynamics-in-inferno-crater-lake-a-thermally-fluctuating-geothermal-spring
#14
Laura Ward, Michael W Taylor, Jean F Power, Bradley J Scott, Ian R McDonald, Matthew B Stott
Understanding how microbial communities respond and adjust to ecosystem perturbation is often difficult to interpret due to multiple and often simultaneous variations in observed conditions. In this research, we investigated the microbial community dynamics of Inferno Crater Lake, an acidic geothermal spring in New Zealand with a unique thermal cycle that varies between 30 and 80 °C over a period of 40-60 days. Using a combination of next-generation sequencing, geochemical analysis and quantitative PCR we found that the microbial community composition was predominantly chemolithotrophic and strongly associated with the thermal cycle...
January 10, 2017: ISME Journal
https://www.readbyqxmd.com/read/28071137/seasonal-variation-in-an-acid-mine-drainage-microbial-community
#15
Ryan R Auld, Nadia C S Mykytczuk, Leo G Leduc, Thomas J S Merritt
Environmental oxidation and microbial metabolism drive production of acid mine drainage (AMD). Understanding changes in the microbial community, due to geochemical and seasonal characteristics, is fundamental to AMD monitoring and remediation. Using direct sequencing of the 16S and 18S rRNA genes to identify bacterial, archaeal, and eukaryotic members of the microbial community at an AMD site in Northern Ontario, Canada, we found a dynamic community varying significantly across winter and summer sampling times...
September 27, 2016: Canadian Journal of Microbiology
https://www.readbyqxmd.com/read/28070487/unraveling-the-microbial-and-functional-diversity-of-coamo-thermal-spring-in-puerto-rico-using-metagenomic-library-generation-and-shotgun-sequencing
#16
Ricky Padilla-Del Valle, Luis R Morales-Vale, Carlos Ríos-Velázquez
In Puerto Rico, the microbial diversity of the thermal spring (ThS) in Coamo has never been studied using metagenomics. The focus of our research was to generate a metagenomic library from the ThS of Coamo, Puerto Rico and explore the microbial and functional diversity. The metagenomic library from the ThS waters was generated using direct DNA isolation. High molecular weight (40 kbp) DNA was end-repaired, electro eluted and ligated into a fosmid vector (pCCFOS1); then transduced into Escherichia coli EPI300-T1R using T1 bacteriophages...
March 2017: Genomics Data
https://www.readbyqxmd.com/read/28070216/metabolism-in-anoxic-permeable-sediments-is-dominated-by-eukaryotic-dark-fermentation
#17
Michael F Bourke, Philip J Marriott, Ronnie N Glud, Harald Hasler-Sheetal, Manoj Kamalanathan, John Beardall, Chris Greening, Perran L M Cook
Permeable sediments are common across continental shelves and are critical contributors to marine biogeochemical cycling. Organic matter in permeable sediments is dominated by microalgae, which as eukaryotes have different anaerobic metabolic pathways to prokaryotes such as bacteria and archaea. Here we present analyses of flow-through reactor experiments showing that dissolved inorganic carbon is produced predominantly as a result of anaerobic eukaryotic metabolic activity. In our experiments, anaerobic production of dissolved inorganic carbon was consistently accompanied by large dissolved H2 production rates, suggesting the presence of fermentation...
January 2017: Nature Geoscience
https://www.readbyqxmd.com/read/28065939/an-expanding-stage-for-commensal-microbes-in-host-immune-regulation
#18
REVIEW
Yan Shi, Libing Mu
Gastrointestinal commensal microbiota is a concentrated mix of microbial life forms, including bacteria, fungi, archaea and viruses. These life forms are targets of host antimicrobial defense in order to establish a homeostatic symbiosis inside the host. However, they are also instrumental in shaping the functions of our immune system via a diverse set of communication mechanisms. In the gut, T helper 17, regulatory T and B cells are continuously tuned by specific microbial strains and metabolic processes. These cells in return help to establish a mutually beneficial exchange with the gut microbial contents...
January 9, 2017: Cellular & Molecular Immunology
https://www.readbyqxmd.com/read/28063827/taxonomic-and-functional-diversity-of-a-coastal-planktonic-bacterial-community-in-a-river-influenced-marine-area
#19
Stefan Thiele, Michael Richter, Cecilia Balestra, Frank Oliver Glöckner, Raffaella Casotti
The Gulf of Naples is a dynamical area with intense exchanges between offshore oligotrophic and coastal eutrophic waters with frequent freshwater inputs. The Sarno River, one of the most polluted rivers in Europe, strongly contributes to the pollution of the area, discharging high amounts of heavy metals and organic wastes from heavily cultivated and industrial areas. This paper reports on the diversity and community structure of the marine residential Bacteria and Archaea of the Gulf of Naples in an area close to the river Sarno plume and investigates their small-scale taxonomic diversity and expression patterns as a proxy of potential metabolic activity using metagenomics and metatranscriptomics...
January 4, 2017: Marine Genomics
https://www.readbyqxmd.com/read/28063283/microbial-community-redundancy-in-anaerobic-digestion-drives-process-recovery-after-salinity-exposure
#20
Jo De Vrieze, Marlies E R Christiaens, Diego Walraedt, Arno Devooght, Umer Zeeshan Ijaz, Nico Boon
Anaerobic digestion of high-salinity wastewaters often results in process inhibition due to the susceptibility of the methanogenic archaea. The ability of the microbial community to deal with increased salinity levels is of high importance to ensure process perseverance or recovery after failure. The exact strategy of the microbial community to ensure process endurance is, however, often unknown. In this study, we investigated how the microbial community is able to recover process performance following a disturbance through the application of high-salinity molasses wastewater...
December 26, 2016: Water Research
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