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https://www.readbyqxmd.com/read/28731479/marine-archaeal-dynamics-and-interactions-with-the-microbial-community-over-5-years-from-surface-to-seafloor
#1
Alma E Parada, Jed A Fuhrman
Marine archaea are critical contributors to global carbon and nitrogen redox cycles, but their temporal variability and microbial associations across the water column are poorly known. We evaluated seasonal variability of free living (0.2-1 μm size fraction) Thaumarchaea Marine Group I (MGI) and Euryarchaea Marine Group II (MGII) communities and their associations with the microbial community from surface to seafloor (890 m) over 5 years by 16S rRNA V4-V5 gene sequencing. MGI and MGII communities demonstrated distinct compositions at different depths, and seasonality at all depths...
July 21, 2017: ISME Journal
https://www.readbyqxmd.com/read/28731469/novel-chaperonins-are-prevalent-in-the-virioplankton-and-demonstrate-links-to-viral-biology-and-ecology
#2
Rachel L Marine, Daniel J Nasko, Jeffrey Wray, Shawn W Polson, K Eric Wommack
Chaperonins are protein-folding machinery found in all cellular life. Chaperonin genes have been documented within a few viruses, yet, surprisingly, analysis of metagenome sequence data indicated that chaperonin-carrying viruses are common and geographically widespread in marine ecosystems. Also unexpected was the discovery of viral chaperonin sequences related to thermosome proteins of archaea, indicating the presence of virioplankton populations infecting marine archaeal hosts. Virioplankton large subunit chaperonin sequences (GroELs) were divergent from bacterial sequences, indicating that viruses have carried this gene over long evolutionary time...
July 21, 2017: ISME Journal
https://www.readbyqxmd.com/read/28731467/uncultivated-microbes-in-need-of-their-own-taxonomy
#3
Konstantinos T Konstantinidis, Ramon Rosselló-Móra, Rudolf Amann
The great majority of microbial species remains uncultured, severely limiting their taxonomic characterization and thus communication among scientists. Although Candidatus was devised as a provisional category to classify uncultured taxa, it has not been widely accepted owing to technical limitations and lack of priority of Candidatus names in the official nomenclature. High-throughput sequencing provides the potential for data-rich taxonomic descriptions of uncultivated microbes, comparable in quality to those of cultured organisms...
July 21, 2017: ISME Journal
https://www.readbyqxmd.com/read/28730409/iron-oxides-alter-methanogenic-pathways-of-acetate-in-production-water-of-high-temperature-petroleum-reservoir
#4
Pan Pan, Bo Hong, Serge Maurice Mbadinga, Li-Ying Wang, Jin-Feng Liu, Shi-Zhong Yang, Ji-Dong Gu, Bo-Zhong Mu
Acetate is a key intermediate in anaerobic crude oil biodegradation and also a precursor for methanogenesis in petroleum reservoirs. The impact of iron oxides, viz. β-FeOOH (akaganéite) and magnetite (Fe3O4), on the methanogenic acetate metabolism in production water of a high-temperature petroleum reservoir was investigated. Methane production was observed in all the treatments amended with acetate. In the microcosms amended with acetate solely about 30% of the acetate utilized was converted to methane, whereas methane production was stimulated in the presence of magnetite (Fe3O4) resulting in a 48...
July 20, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28729688/improved-genome-recovery-and-integrated-cell-size-analyses-of-individual-uncultured-microbial-cells-and-viral-particles
#5
Ramunas Stepanauskas, Elizabeth A Fergusson, Joseph Brown, Nicole J Poulton, Ben Tupper, Jessica M Labonté, Eric D Becraft, Julia M Brown, Maria G Pachiadaki, Tadas Povilaitis, Brian P Thompson, Corianna J Mascena, Wendy K Bellows, Arvydas Lubys
Microbial single-cell genomics can be used to provide insights into the metabolic potential, interactions, and evolution of uncultured microorganisms. Here we present WGA-X, a method based on multiple displacement amplification of DNA that utilizes a thermostable mutant of the phi29 polymerase. WGA-X enhances genome recovery from individual microbial cells and viral particles while maintaining ease of use and scalability. The greatest improvements are observed when amplifying high G+C content templates, such as those belonging to the predominant bacteria in agricultural soils...
July 20, 2017: Nature Communications
https://www.readbyqxmd.com/read/28729513/bidirectional-eukaryotic-dna-replication-is-established-by-quasi-symmetrical-helicase-loading
#6
Gideon Coster, John F X Diffley
Bidirectional replication from eukaryotic DNA replication origins requires the loading of two ring-shaped minichromosome maintenance (MCM) helicases around DNA in opposite orientations. MCM loading is orchestrated by binding of the origin recognition complex (ORC) to DNA, but how ORC coordinates symmetrical MCM loading is unclear. We used natural budding yeast DNA replication origins and synthetic DNA sequences to show that efficient MCM loading requires binding of two ORC molecules to two ORC binding sites...
July 21, 2017: Science
https://www.readbyqxmd.com/read/28726643/reconstructed-ancestral-enzymes-reveal-that-negative-selection-drove-the-evolution-of-substrate-specificity-in-adp-dependent-kinases
#7
Víctor Castro-Fernandez, Alejandra Herrera-Morande, Ricardo Zamora, Felipe Merino, Felipe Gonzalez-Ordenes, Felipe Padilla-Salinas, Humberto M Pereira, Jose Brandão-Neto, Richard C Garratt, Victoria Guixe
One central goal in molecular evolution is to pinpoint the mechanisms and evolutionary forces that cause an enzyme to change its substrate specificity; however, these processes remain largely unexplored. Using the glycolytic ADP-dependent kinases of archaea, including the orders Thermococcales, Methanosarcinales, and Methanococcales, as a model and employing an approach involving paleoenzymology, evolutionary statistics, and protein structural analysis, we could track changes in substrate specificity during ADP-dependent kinase evolution along with the structural determinants of these changes...
July 18, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28725266/highly-efficient-methane-generation-from-untreated-microalgae-biomass
#8
Viktor Klassen, Olga Blifernez-Klassen, Daniel Wibberg, Anika Winkler, Jörn Kalinowski, Clemens Posten, Olaf Kruse
BACKGROUND: The fact that microalgae perform very efficiently photosynthetic conversion of sunlight into chemical energy has moved them into the focus of regenerative fuel research. Especially, biogas generation via anaerobic digestion is economically attractive due to the comparably simple apparative process technology and the theoretical possibility of converting the entire algal biomass to biogas/methane. In the last 60 years, intensive research on biogas production from microalgae biomass has revealed the microalgae as a rather challenging substrate for anaerobic digestion due to its high cell wall recalcitrance and unfavorable protein content, which requires additional pretreatment and co-fermentation strategies for sufficient fermentation...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/28725221/cell-surface-glycosylation-is-required-for-efficient-mating-of-haloferax-volcanii
#9
Yarden Shalev, Israela Turgeman-Grott, Adi Tamir, Jerry Eichler, Uri Gophna
Halophilic archaea use a fusion-based mating system for lateral gene transfer across cells, yet the molecular mechanisms involved remain unknown. Previous work implied that cell fusion involves cell-cell recognition since fusion occurs more efficiently between cells from the same species. Long believed to be restricted only to Eukarya, it is now known that cells of all three domains of life perform N-glycosylation, the covalent attachment of glycans to select target asparagine residues in proteins, and that this post-translational modification is common for archaeal cell surface proteins...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28724964/highly-selective-tungstate-transporter-protein-tupa-from-desulfovibrio-alaskensis-g20
#10
Ana Rita Otrelo-Cardoso, Rashmi R Nair, Márcia A S Correia, Raquel S Correia Cordeiro, Alejandro Panjkovich, Dmitri I Svergun, Teresa Santos-Silva, Maria G Rivas
Molybdenum and tungsten are taken up by bacteria and archaea as their soluble oxyanions through high affinity transport systems belonging to the ATP-binding cassette (ABC) transporters. The component A (ModA/TupA) of these transporters is the first selection gate from which the cell differentiates between MoO4(2-), WO4(2-) and other similar oxyanions. We report the biochemical characterization and the crystal structure of the apo-TupA from Desulfovibrio desulfuricans G20, at 1.4 Å resolution. Small Angle X-ray Scattering data suggests that the protein adopts a closed and more stable conformation upon ion binding...
July 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28724909/investigation-of-pyrophosphate-versus-atp-substrate-selection-in-the-entamoeba-histolytica-acetate-kinase
#11
Thanh Dang, Cheryl Ingram-Smith
Acetate kinase (ACK; E.C. 2.7.2.1), which catalyzes the interconversion of acetate and acetyl phosphate, is nearly ubiquitous in bacteria but is present only in one genus of archaea and certain eukaryotic microbes. All ACKs utilize ATP/ADP as the phosphoryl donor/acceptor in the respective directions of the reaction (acetate + ATP [Formula: see text] acetyl phosphate + ADP), with the exception of the Entamoeba histolytica ACK (EhACK) which uses pyrophosphate (PPi)/inorganic phosphate (Pi) (acetyl phosphate + Pi  [Formula: see text] acetate + PPi)...
July 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28723955/crystal-structure-and-functional-characterization-of-an-isoaspartyl-dipeptidase-cpsiada-from-colwellia-psychrerythraea-strain-34h
#12
Sun-Ha Park, Chang Woo Lee, Sung Gu Lee, Seung Chul Shin, Hak Jun Kim, Hyun Park, Jun Hyuck Lee
Isoaspartyl dipeptidase (IadA) is an enzyme that catalyzes the hydrolysis of an isoaspartyl dipeptide-like moiety, which can be inappropriately formed in proteins, between the β-carboxyl group side chain of Asp and the amino group of the following amino acid. Here, we have determined the structures of an isoaspartyl dipeptidase (CpsIadA) from Colwellia psychrerythraea, both ligand-free and that complexed with β-isoaspartyl lysine, at 1.85-Å and 2.33-Å resolution, respectively. In both structures, CpsIadA formed an octamer with two Zn ions in the active site...
2017: PloS One
https://www.readbyqxmd.com/read/28723891/the-lysosomal-potassium-channel-tmem175-adopts-a-novel-tetrameric-architecture
#13
Changkeun Lee, Jiangtao Guo, Weizhong Zeng, Sunghoon Kim, Ji She, Chunlei Cang, Dejian Ren, Youxing Jiang
TMEM175 is a lysosomal K(+) channel that is important for maintaining the membrane potential and pH stability in lysosomes. It contains two homologous copies of a six-transmembrane-helix (6-TM) domain, which has no sequence homology to the canonical tetrameric K(+) channels and lacks the TVGYG selectivity filter motif found in these channels. The prokaryotic TMEM175 channel, which is present in a subset of bacteria and archaea, contains only a single 6-TM domain and functions as a tetramer. Here, we present the crystal structure of a prokaryotic TMEM175 channel from Chamaesiphon minutus, CmTMEM175, the architecture of which represents a completely different fold from that of canonical K(+) channels...
July 19, 2017: Nature
https://www.readbyqxmd.com/read/28717594/effect-of-freshwater-mussels-on-the-vertical-distribution-of-anaerobic-ammonia-oxidizers-and-other-nitrogen-transforming-microorganisms-in-upper-mississippi-river-sediment
#14
Ellen M Black, Michael S Chimenti, Craig L Just
Targeted qPCR and non-targeted amplicon sequencing of 16S rRNA genes within sediment layers identified the anaerobic ammonium oxidation (anammox) niche and characterized microbial community changes attributable to freshwater mussels. Anammox bacteria were normally distributed (Shapiro-Wilk normality test, W-statistic =0.954, p = 0.773) between 1 and 15 cm depth and were increased by a factor of 2.2 (p < 0.001) at 3 cm below the water-sediment interface when mussels were present. Amplicon sequencing of sediment at depths relevant to mussel burrowing (3 and 5 cm) showed that mussel presence reduced observed species richness (p = 0...
2017: PeerJ
https://www.readbyqxmd.com/read/28717356/thermoplasmatales-and-methanogens-potential-association-with-the-crenarchaeol-production-in-chinese-soils
#15
Fuyan Li, Fengfeng Zheng, Yongli Wang, Weiguo Liu, Chuanlun L Zhang
Crenarchaeol is a unique isoprenoid glycerol dibiphytanyl glycerol tetraether (iGDGT) lipid, which is only identified in cultures of ammonia-oxidizing Thaumarchaeota. However, the taxonomic origins of crenarchaeol have been debated recently. The archaeal populations, other than Thaumarchaeota, may have associations with the production of crenarchaeol in ecosystems characterized by non-thaumarchaeotal microorganisms. To this end, we investigated 47 surface soils from upland and wetland soils and rice fields and another three surface sediments from river banks...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28716385/protein-lipograms
#16
Jason Laurie, Amit K Chattopadhyay, Darren R Flower
Linguistic analysis of protein sequences is an underexploited technique. Here, we capitalize on the concept of the lipogram to characterize sequences at the proteome levels. A lipogram is a literary composition which omits one or more letters. A protein lipogram likewise omits one or more types of amino acid. In this article, we establish a usable terminology for the decomposition of a sequence collection in terms of the lipogram. Next, we characterize Uniref50 using a lipogram decomposition. At the global level, protein lipograms exhibit power-law properties...
July 14, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28715975/viruses-with-circular-single-stranded-dna-genomes-are-everywhere
#17
L M Shulman, I Davidson Davidson
Circular single-stranded DNA viruses infect archaea, bacteria, and eukaryotic organisms. The relatively recent emergence of single-stranded DNA viruses, such as chicken anemia virus (CAV) and porcine circovirus 2 (PCV2), as serious pathogens of eukaryotes is due more to growing awareness than to the appearance of new pathogens or alteration of existing pathogens. In the case of the ubiquitous human circular single-stranded DNA virus family Anelloviridae, there is still no convincing direct causal relation to any specific disease...
July 17, 2017: Annual Review of Virology
https://www.readbyqxmd.com/read/28713363/geographic-distribution-of-ammonia-oxidizing-archaea-along-the-kuril-islands-in-the-western-subarctic-pacific
#18
Hongmei Jing, Shunyan Cheung, Xiaomin Xia, Koji Suzuki, Jun Nishioka, Hongbin Liu
Community composition and abundance of ammonia-oxidizing archaea (AOA) in the ocean were affected by different physicochemical conditions, but their responses to physical barriers (such as a chain of islands) were largely unknown. In our study, geographic distribution of the AOA from the surface photic zone to the deep bathypelagic waters in the western subarctic Pacific adjacent to the Kuril Islands was investigated using pyrosequencing based on the ammonia monooxygenase subunit A (amoA) gene. Genotypes of clusters A and B dominated in the upper euphotic zone and the deep waters, respectively...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28713339/concurrent-methane-production-and-oxidation-in-surface-sediment-from-aarhus-bay-denmark
#19
Ke-Qing Xiao, Felix Beulig, Kasper U Kjeldsen, Bo B Jørgensen, Nils Risgaard-Petersen
Marine surface sediments, which are replete with sulfate, are typically considered to be devoid of endogenous methanogenesis. Yet, methanogenic archaea are present in those sediments, suggesting a potential for methanogenesis. We used an isotope dilution method based on sediment bag incubation and spiking with (13)C-CH4 to quantify CH4 turnover rates in sediment from Aarhus Bay, Denmark. In two independent experiments, highest CH4 production and oxidation rates (>200 pmol cm(-3) d(-1)) were found in the top 0-2 cm, below which rates dropped below 100 pmol cm(-3) d(-1) in all other segments down to 16 cm...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28711872/cell-scientist-to-watch-kevin-corbett
#20
(no author information available yet)
Kevin Corbett graduated in biology and biochemistry from the University of Virginia. He then went to the University of California, Berkeley, to work on the structure and function of DNA topoisomerases in bacteria and archaea for his PhD with James Berger. In 2005, he moved to the laboratory of Stephen Harrison at Harvard Medical School for his postdoctoral work on kinetochore structure and function, particularly the yeast monopolin complex, which promotes proper chromosome segregation in the first meiotic division...
July 15, 2017: Journal of Cell Science
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