keyword
MENU ▼
Read by QxMD icon Read
search

Archaea

keyword
https://www.readbyqxmd.com/read/28441577/membrane-vesicles-and-horizontal-gene-transfer-in-prokaryotes
#1
REVIEW
Sara Domingues, Kaare M Nielsen
Membrane vesicles (MVs) are released from all living cells. MVs are lumen-containing spheres of lipid-bilayers derived from the cell surface. MVs are biologically active and contain various components, including genetic material. Both chromosomal and plasmid DNA, as well as different types of RNA have been detected in MVs. Vesicle-mediated transfer of genes coding for antibiotic resistance, virulence and metabolic traits has been reported in Gram-negative and Gram-positive bacteria and in Archaea. MVs can persist over time in natural environments...
April 22, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28438890/short-ftsz-filaments-can-drive-asymmetric-cell-envelope-constriction-at-the-onset-of-bacterial-cytokinesis
#2
Qing Yao, Andrew I Jewett, Yi-Wei Chang, Catherine M Oikonomou, Morgan Beeby, Cristina V Iancu, Ariane Briegel, Debnath Ghosal, Grant J Jensen
FtsZ, the bacterial homologue of eukaryotic tubulin, plays a central role in cell division in nearly all bacteria and many archaea. It forms filaments under the cytoplasmic membrane at the division site where, together with other proteins it recruits, it drives peptidoglycan synthesis and constricts the cell. Despite extensive study, the arrangement of FtsZ filaments and their role in division continue to be debated. Here, we apply electron cryotomography to image the native structure of intact dividing cells and show that constriction in a variety of Gram-negative bacterial cells, including Proteus mirabilis and Caulobacter crescentus, initiates asymmetrically, accompanied by asymmetric peptidoglycan incorporation and short FtsZ-like filament formation...
April 24, 2017: EMBO Journal
https://www.readbyqxmd.com/read/28432991/characteristics-of-adapted-hydrogenotrophic-community-during-biomethanation
#3
Lydia Rachbauer, Reinhard Beyer, Günther Bochmann, Werner Fuchs
The results presented in this study were carried out as concomitant experiments during the start-up and operation of a biomethanation unit to evaluate the effect of process parameters on carbon conversion, product formation (methane and acetate) and community composition. For that, two different samples were withdrawn from a trickle-bed reactor with immobilized enrichment culture of hydrogenotrophic methanogens adapted from sewage sludge. One sample was taken from the recirculation liquid during start-up phase while the other was withdrawn directly from the carrier material in the reactor...
April 19, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28431358/molecular-ecological-perspective-of-methanogenic-archaeal-community-in-rice-agroecosystem
#4
REVIEW
Singh Alpana, P Vishwakarma, T K Adhya, K Inubushi, S K Dubey
Methane leads to global warming owing to its warming potential higher than carbon dioxide (CO2). Rice fields represent the major source of methane (CH4) emission as the recent estimates range from 34 to 112 Tg CH4 per year. Biogenic methane is produced by anaerobic methanogenic archaea. Advances in high-throughput sequencing technologies and isolation methodologies enabled investigators to decipher methanogens to be unexpectedly diverse in phylogeny and ecology. Exploring the link between biogeochemical methane cycling and methanogen community dynamics can, therefore, provide a more effective mechanistic understanding of CH4 emission from rice fields...
April 18, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28425930/the-peculiar-glycolytic-pathway-in-hyperthermophylic-archaea-understanding-its-whims-by-experimentation-in-silico
#5
Yanfei Zhang, Theresa Kouril, Jacky L Snoep, Bettina Siebers, Matteo Barberis, Hans V Westerhoff
Mathematical models are key to systems biology where they typically describe the topology and dynamics of biological networks, listing biochemical entities and their relationships with one another. Some (hyper)thermophilic Archaea contain an enzyme, called non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase (GAPN), which catalyzes the direct oxidation of glyceraldehyde-3-phosphate to 3-phosphoglycerate omitting adenosine 5'-triphosphate (ATP) formation by substrate-level-phosphorylation via phosphoglycerate kinase...
April 20, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28425179/resilience-of-the-prokaryotic-microbial-community-of-acropora-digitifera-to-elevated-temperature
#6
Andrian P Gajigan, Leomir A Diaz, Cecilia Conaco
The coral is a holobiont formed by the close interaction between the coral animal and a diverse community of microorganisms, including dinoflagellates, bacteria, archaea, fungi, and viruses. The prokaryotic symbionts of corals are important for host fitness but are also highly sensitive to changes in the environment. In this study, we used 16S ribosomal RNA (rRNA) sequencing to examine the response of the microbial community associated with the coral, Acropora digitifera, to elevated temperature. The A. digitifera microbial community is dominated by operational taxonomic unit (OTUs) affiliated with classes Alphaproteobacteria and Gammaproteobacteria...
April 20, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28424284/a-novel-type-of-polyhedral-viruses-infecting-hyperthermophilic-archaea
#7
Ying Liu, Sonoko Ishino, Yoshizumi Ishino, Gérard Pehau-Arnaudet, Mart Krupovic, David Prangishvili
Encapsidation of genetic material into polyhedral particles is one of the most common structural solutions employed by viruses infecting hosts in all three domains of life. Here, we describe a new virus of hyperthermophilic archaea, Sulfolobus polyhedral virus 1 (SPV1), which condenses its circular double-stranded DNA genome in a manner not previously observed for other known virus. The genome complexed with virion proteins is wound up sinusoidally into a spherical coil which is surrounded by an envelope and further encased by an outer polyhedral capsid apparently composed of the 20 kDa virion protein...
April 19, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28424282/formation-of-a-viral-replication-focus-in-sulfolobus-cells-infected-by-the-rudivirus-sirv2
#8
Laura Martínez-Alvarez, Ling Deng, Xu Peng
Viral factories are compartmentalized centres for viral replication and assembly in infected eukaryotic cells. Here, we report the formation of a replication focus by the prototypical archaeal virus SIRV2 in the model archaeon Sulfolobus. This rod-shaped virus belongs to the viral family rudiviridae, carrying linear dsDNA genomes, which are very common in geothermal environments. We demonstrate that SIRV2 DNA synthesis is confined to a focus near the periphery of infected cells. Moreover, viral and cellular replication proteins are recruited to, and concentrated in, the viral replication focus...
April 19, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28421184/the-proteasomal-atpases-use-a-slow-but-highly-processive-strategy-to-unfold-proteins
#9
Aaron Snoberger, Raymond T Anderson, David M Smith
All domains of life have ATP-dependent compartmentalized proteases that sequester their peptidase sites on their interior. ATPase complexes will often associate with these compartmentalized proteases in order to unfold and inject substrates into the protease for degradation. Significant effort has been put into understanding how ATP hydrolysis is used to apply force to proteins and cause them to unfold. The unfolding kinetics of the bacterial ATPase, ClpX, have been shown to resemble a fast motor that traps unfolded intermediates as a strategy to unfold proteins...
2017: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/28420220/the-maximal-c%C3%A2-self-complementary-trinucleotide-circular-code-x-in-genes-of-bacteria-archaea-eukaryotes-plasmids-and-viruses
#10
Christian J Michel
In 1996, a set X of 20 trinucleotides was identified in genes of both prokaryotes and eukaryotes which has on average the highest occurrence in reading frame compared to its two shifted frames. Furthermore, this set X has an interesting mathematical property as X is a maximal C 3 self-complementary trinucleotide circular code. In 2015, by quantifying the inspection approach used in 1996, the circular code X was confirmed in the genes of bacteria and eukaryotes and was also identified in the genes of plasmids and viruses...
April 18, 2017: Life
https://www.readbyqxmd.com/read/28419436/ammonia-oxidizer-populations-vary-with-nitrogen-cycling-across-a-tropical-montane-mean-annual-temperature-gradient
#11
S Pierre, I Hewson, J P Sparks, C M Litton, C Giardina, P M Groffman, T J Fahey
Functional gene approaches have been used to better understand the roles of microbes in driving forest soil nitrogen (N) cycling rates and bioavailability. Ammonia oxidation is a rate limiting step in nitrification, and is a key area for understanding environmental constraints on N availability in forests. We studied how increasing temperature affects the role of ammonia oxidizing archaea (AOA) and bacteria (AOB) in soil N cycling and availability by using a highly constrained natural mean annual temperature (MAT) elevation gradient in a tropical montane wet forest...
April 18, 2017: Ecology
https://www.readbyqxmd.com/read/28418382/structure-of-the-hexagonal-surface-layer-on-caulobacter-crescentus-cells
#12
Tanmay A M Bharat, Danguole Kureisaite-Ciziene, Gail G Hardy, Ellen W Yu, Jessica M Devant, Wim J H Hagen, Yves V Brun, John A G Briggs, Jan Löwe
Many prokaryotic cells are encapsulated by a surface layer (S-layer) consisting of repeating units of S-layer proteins. S-layer proteins are a diverse class of molecules found in Gram-positive and Gram-negative bacteria and most archaea(1-5). S-layers protect cells from the outside, provide mechanical stability and also play roles in pathogenicity. In situ structural information about this highly abundant class of proteins is scarce, so atomic details of how S-layers are arranged on the surface of cells have remained elusive...
April 18, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28416706/the-gan-exonuclease-or-the-flap-endonuclease-fen1-and-rnase-hii-are-necessary-for-viability-of-thermococcus-kodakarensis
#13
Brett W Burkhart, Lubomira Cubonova, Margaret R Heider, Zvi Kelman, John N Reeve, Thomas J Santangelo
Many aspects of and factors required for DNA replication are conserved across all three Domains of life but there are some significant differences surrounding lagging strand synthesis. In Archaea, a 5' to 3' exonuclease, related to both bacterial RecJ and eukaryotic Cdc45, that associates with the replisome specifically through interactions with GINS, was identified and designated GAN (for GINS-associated nuclease). Despite the presence of a well-characterized flap endonuclease (Fen1), it was hypothesized that GAN might participate in primer removal during Okazaki fragment maturation and, as a Cdc45 homologue, GAN might also be a structural component of an archaeal CMG (Cdc45, MCM, GINS) replication complex...
April 17, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28409190/methyl-accepting-chemotaxis-proteins-a-core-sensing-element-in-prokaryotes-and-archaea
#14
REVIEW
Abu Iftiaf Md Salah Ud-Din, Anna Roujeinikova
Chemotaxis is the directed motility by means of which microbes sense chemical cues and relocate towards more favorable environments. Methyl-accepting chemotaxis proteins (MCPs) are the most common receptors in bacteria and archaea. They are arranged as trimers of dimers that, in turn, form hexagonal arrays in the cytoplasmic membrane or in the cytoplasm. Several different classes of MCPs have been identified according to their ligand binding region and membrane topology. MCPs have been further classified based on the length and sequence conservation of their cytoplasmic domains...
April 13, 2017: Cellular and Molecular Life Sciences: CMLS
https://www.readbyqxmd.com/read/28407093/non-random-inversion-landscapes-in-prokaryotic-genomes-are-shaped-by-heterogeneous-selection-pressures
#15
Jelena Repar, Tobias Warnecke
Inversions are a major contributor to structural genome evolution in prokaryotes. Here, using a novel alignment-based method, we systematically compare 1651 bacterial and 98 archaeal genomes to show that inversion landscapes are frequently biased towards (symmetric) inversions around the origin-terminus axis. However, symmetric inversion bias is not a universal feature of prokaryotic genome evolution but varies considerably across clades. At the extremes, inversion landscapes in Bacillus-Clostridium and Actinobacteria are dominated by symmetric inversions, while there is little or no systematic bias favouring symmetric rearrangements in archaea with a single origin of replication...
April 12, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28404995/glucose-uptake-in-azotobacter-vinelandii-occurs-through-a-glup-transporter-that-is-under-the-control-of-the-cbra-cbrb-and-hfq-crc-systems
#16
Elva Quiroz-Rocha, Renata Moreno, Armando Hernández-Ortíz, Juan Carlos Fragoso-Jiménez, Luis Felipe Muriel-Millán, Josefina Guzmán, Guadalupe Espín, Fernando Rojo, Cinthia Núñez
Azotobacter vinelandii, a strict aerobic, nitrogen fixing bacterium in the Pseudomonadaceae family, exhibits a preferential use of acetate over glucose as a carbon source. In this study, we show that GluP (Avin04150), annotated as an H(+)-coupled glucose-galactose symporter, is the glucose transporter in A. vinelandii. This protein, which is widely distributed in bacteria and archaea, is uncommon in Pseudomonas species. We found that expression of gluP was under catabolite repression control thorugh the CbrA/CbrB and Crc/Hfq regulatory systems, which were functionally conserved between A...
April 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28402870/long-chain-fatty-acid-feeding-frequency-in-anaerobic-codigestion-impacts-syntrophic-community-structure-and-biokinetics
#17
Ryan M Ziels, David A C Beck, H David Stensel
This study investigated the impacts of long-chain fatty acid (LCFA) feeding frequencies on microbial community structure, bioconversion kinetics, and process stability during anaerobic codigestion. Parallel laboratory-scale anaerobic codigesters fed with dairy cattle manure were either pulse-fed every two days or continuously-fed daily, respectively, with oleate (C18:1) in incremental step increases over 200 days up to 64% of the influent chemical oxygen demand (COD). The effluent acetate concentration exceeded 3000 mg/L in the continuous-fed codigester at the highest oleate loading rate, but remained below 100 mg/L in the pulse-fed codigester at the end of its 48-hr oleate feed cycle...
March 31, 2017: Water Research
https://www.readbyqxmd.com/read/28402397/convergence-and-contrast-in-the-community-structure-of-bacteria-fungi-and-archaea-along-a-tropical-elevation-climate-gradient
#18
Kabir G Peay, Christian von Sperber, Emily Cardarelli, Hirokazu Toju, Christopher A Francis, Oliver A Chadwick, Peter M Vitousek
Changes in species richness along climatological gradients have been instrumental in developing theories about the general drivers of biodiversity. Previous studies on microbial communities along climate gradients on mountainsides have revealed positive, negative and neutral richness trends. We examined changes in richness and composition of Fungi, Bacteria and Archaea in soil along a 50-1000 m elevation, 280-3280 mm/yr precipitation gradient in Hawai'i. Soil properties and their drivers are exceptionally well understood along this gradient...
April 11, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28402213/engineering-and-expressing-circular-rnas-via-trna-splicing
#19
John J Noto, Casey A Schmidt, A Gregory Matera
Circular (circ)RNAs have recently become a subject of great biological interest. It is now clear that they represent a diverse and abundant class of RNAs with regulated expression and evolutionarily conserved functions. There are several mechanisms by which RNA circularization can occur in vivo. Here, we focus on the biogenesis of tRNA intronic circular RNAs (tricRNAs) in archaea and animals, and we detail their use as research tools for orthogonal, directed circRNA expression in vivo.
April 12, 2017: RNA Biology
https://www.readbyqxmd.com/read/28401921/distinct-soil-microbial-communities-in-habitats-of-differing-soil-water-balance-on-the-tibetan-plateau
#20
Yuntao Li, Jonathan Adams, Yu Shi, Hao Wang, Jin-Sheng He, Haiyan Chu
Global change may be a severe threat to natural and agricultural systems, partly through its effects in altering soil biota and processes, due to changes in water balance. We studied the potential influence of changing soil water balance on soil biota by comparing existing sites along a natural water balance gradient in the Qinghai-Tibetan Plateau. In this study, the community structure of bacteria, archaea and eukaryotes differed between the different soil water conditions. Soil moisture was the strongest predictor of bacterial and eukaryotic community structure, whereas C/N ratio was the key factor predicting variation in the archaeal community...
April 12, 2017: Scientific Reports
keyword
keyword
25185
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"