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https://www.readbyqxmd.com/read/29149348/mechanistic-insight-into-the-assembly-of-the-hera-nura-helicase-nuclease-dna-end-resection-complex
#1
Zainab Ahdash, Andy M Lau, Robert Thomas Byrne, Katja Lammens, Alexandra Stüetzer, Henning Urlaub, Paula J Booth, Eamonn Reading, Karl-Peter Hopfner, Argyris Politis
The HerA-NurA helicase-nuclease complex cooperates with Mre11 and Rad50 to coordinate the repair of double-stranded DNA breaks. Little is known, however, about the assembly mechanism and activation of the HerA-NurA. By combining hybrid mass spectrometry with cryo-EM, computational and biochemical data, we investigate the oligomeric formation of HerA and detail the mechanism of nucleotide binding to the HerA-NurA complex from thermophilic archaea. We reveal that ATP-free HerA and HerA-DNA complexes predominantly exist in solution as a heptamer and act as a DNA loading intermediate...
November 16, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29146846/high-quality-draft-genome-sequence-of-candidatus-methanoperedens-sp-strain-blz2-a-nitrate-reducing-anaerobic-methane-oxidizing-archaeon-enriched-in-an-anoxic-bioreactor
#2
Stefanie Berger, Jeroen Frank, Paula Dalcin Martins, Mike S M Jetten, Cornelia U Welte
The high-quality draft genome of "Candidatus Methanoperedens sp." strain BLZ2, a nitrate-reducing archaeon anaerobically oxidizing methane, is presented. The genome was obtained from an enrichment culture and measures 3.74 Mb. It harbors two nitrate reductase gene clusters, an ammonium-forming nitrite reductase, and the complete reverse methanogenesis pathway. Methane that escapes to the atmosphere acts as a potent greenhouse gas. Global methane emissions are mitigated by methanotrophs, which oxidize methane to CO2 "Candidatus Methanoperedens spp...
November 16, 2017: Genome Announcements
https://www.readbyqxmd.com/read/29145643/the-merops-database-of-proteolytic-enzymes-their-substrates-and-inhibitors-in-2017-and-a-comparison-with-peptidases-in-the-panther-database
#3
Neil D Rawlings, Alan J Barrett, Paul D Thomas, Xiaosong Huang, Alex Bateman, Robert D Finn
The MEROPS database (http://www.ebi.ac.uk/merops/) is an integrated source of information about peptidases, their substrates and inhibitors. The hierarchical classification is: protein-species, family, clan, with an identifier at each level. The MEROPS website moved to the EMBL-EBI in 2017, requiring refactoring of the code-base and services provided. The interface to sequence searching has changed and the MEROPS protein sequence libraries can be searched at the EMBL-EBI with HMMER, FastA and BLASTP. Cross-references have been established between MEROPS and the PANTHER database at both the family and protein-species level, which will help to improve curation and coverage between the resources...
November 14, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29143851/phylogenetic-diversity-and-distribution-of-bacterial-and-archaeal-amoa-genes-in-the-east-china-sea-during-spring
#4
Takafumi Kataoka, Koji Suzuki, Tomohisa Irino, Masanobu Yamamoto, Seigo Higashi, Hongbin Liu
Microbial nitrification is a key process in the nitrogen cycle in the continental shelf ecosystems. The genotype compositions and abundance of the ammonia monooxygenase gene, amoA, derived from ammonia-oxidizing archaea (AOA) and bacteria (AOB) in two size fractions (2-10 and 0.2-2 µm), were investigated in the East China Sea (ECS) in May 2008 using PCR-denaturing gradient gel electrophoresis (DGGE) and quantitative PCR (qPCR). Four sites were selected across the continental shelf edge: continental shelf water (CSW), Kuroshio branch water (KBW), transition between CSW and KBW (TCSKB) and coastal KBW (CKBW)...
November 16, 2017: Archives of Microbiology
https://www.readbyqxmd.com/read/29143132/thermostable-and-highly-specific-l-aspartate-oxidase-from-thermococcus-litoralis-dsm-5473-cloning-overexpression-and-enzymological-properties
#5
Tsubasa Washio, Tadao Oikawa
We successfully expressed the L-aspartate oxidase homolog gene (accession no: OCC_06611) of Thermococcus litoralis DSM 5473 in the soluble fraction of Escherichia coli BL21 (DE3) using a pET21b vector with 6X His tag at its C-terminus. The gene product (Tl-LASPO) showed L-aspartate oxidase activity in the presence of FAD in vitro, and this report is the first that details an L-aspartate oxidase derived from a Thermococcus species. The homologs of Tl-LASPO existed mainly in archaea, especially in the genus of Thermococcus, Pyrococcus, Sulfolobus, and Halobacteria...
November 15, 2017: Extremophiles: Life Under Extreme Conditions
https://www.readbyqxmd.com/read/29140980/prokaryotic-diversity-and-biogeochemical-characteristics-of-benthic-microbial-ecosystems-at-la-brava-a-hypersaline-lake-at-salar-de-atacama-chile
#6
Maria Eugenia Farias, Maria Cecilia Rasuk, Kimberley L Gallagher, Manuel Contreras, Daniel Kurth, Ana Beatriz Fernandez, Daniel Poiré, Fernando Novoa, Pieter T Visscher
Benthic microbial ecosystems of Laguna La Brava, Salar de Atacama, a high altitude hypersaline lake, were characterized in terms of bacterial and archaeal diversity, biogeochemistry, (including O2 and sulfide depth profiles and mineralogy), and physicochemical characteristics. La Brava is one of several lakes in the Salar de Atacama where microbial communities are growing in extreme conditions, including high salinity, high solar insolation, and high levels of metals such as lithium, arsenic, magnesium, and calcium...
2017: PloS One
https://www.readbyqxmd.com/read/29139344/aeropyrum-pernix-membrane-topology-of-protein-vkor-promotes-protein-disulfide-bond-formation-in-two-subcellular-compartments
#7
Stijntje Hibender, Cristina Landeta, Mehmet Berkmen, Jon Beckwith, Dana Boyd
Disulfide bonds confer stability and activity to proteins. Bioinformatic approaches allow predictions of which organisms make protein disulfide bonds and in which subcellular compartments disulfide bond formation takes place. Such an analysis, along with biochemical and protein structural data, suggests that many of the extremophile Crenarachaea make protein disulfide bonds in both the cytoplasm and the cell envelope. We have sought to determine the oxidative folding pathways in the sequenced genomes of the Crenarchaea, by seeking homologues of the enzymes known to be involved in disulfide bond formation in bacteria...
November 15, 2017: Microbiology
https://www.readbyqxmd.com/read/29138298/first-insights-into-the-diverse-human-archaeome-specific-detection-of-archaea-in-the-gastrointestinal-tract-lung-and-nose-and-on-skin
#8
Kaisa Koskinen, Manuela R Pausan, Alexandra K Perras, Michael Beck, Corinna Bang, Maximilian Mora, Anke Schilhabel, Ruth Schmitz, Christine Moissl-Eichinger
Human-associated archaea remain understudied in the field of microbiome research, although in particular methanogenic archaea were found to be regular commensals of the human gut, where they represent keystone species in metabolic processes. Knowledge on the abundance and diversity of human-associated archaea is extremely limited, and little is known about their function(s), their overall role in human health, or their association with parts of the human body other than the gastrointestinal tract and oral cavity...
November 14, 2017: MBio
https://www.readbyqxmd.com/read/29138003/serine-threonine-protein-kinases-from-bacteria-archaea-and-eukarya-share-a-common-evolutionary-origin-deeply-rooted-in-the-tree-of-life
#9
Ivan Andreas Stancik, Martin Sebastijan Šestak, Boyang Ji, Marina Axelson-Fisk, Damjan Franjevic, Carsten Jers, Tomislav Domazet-Lošo, Ivan Mijakovic
The main family of serine/threonine/tyrosine protein kinases present in eukarya was defined and described by Hanks et al. in 1988. It was initially believed that these kinases do not exist in bacteria, but extensive genome sequencing revealed their existence in many bacteria. For historical reasons, the term "eukaryotic-type kinases" propagated in the literature to describe bacterial members of this protein family. Here, we argue that this term should be abandoned as a misnomer, and we provide several lines of evidence to support this claim...
November 11, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/29133150/structure-and-function-of-per-arnt-sim-domains-and-their-possible-role-in-the-life-cycle-biology-of-trypanosoma-cruzi
#10
REVIEW
Maura Rojas-Pirela, Daniel J Rigden, Paul A Michels, Ana J Cáceres, Juan Luis Concepción, Wilfredo Quiñones
Per-ARNT-Sim (PAS) domains of proteins play important roles as modules for signalling and cellular regulation processes in widely diverse organisms such as Archaea, Bacteria, protists, plants, yeasts, insects and vertebrates. These domains are present in many proteins where they are used as sensors of stimuli and modules for protein interactions. Characteristically, they can bind a broad spectrum of molecules. Such binding causes the domain to trigger a specific cellular response or to make the protein containing the domain susceptible to responding to additional physical or chemical signals...
November 10, 2017: Molecular and Biochemical Parasitology
https://www.readbyqxmd.com/read/29131864/comparison-of-histone-like-hu-protein-dna-binding-properties-and-hu-ihf-protein-sequence-alignment
#11
Dmitri Kamashev, Yulia Agapova, Sergey Rastorguev, Anna A Talyzina, Konstantin M Boyko, Dmitry A Korzhenevskiy, Anna Vlaskina, Raif Vasilov, Vladimir I Timofeev, Tatiana V Rakitina
BACKGROUND: The structure and function of bacterial nucleoid are controlled by histone-like proteins of HU/IHF family, omnipresent in bacteria and also founding archaea and some eukaryotes.HU protein binds dsDNA without sequence specificity and avidly binds DNA structures with propensity to be inclined such as forks, three/four-way junctions, nicks, overhangs and DNA bulges. Sequence comparison of thousands of known histone-like proteins from diverse bacteria phyla reveals relation between HU/IHF sequence, DNA-binding properties and other protein features...
2017: PloS One
https://www.readbyqxmd.com/read/29130188/quantification-of-2-o-me-residues-in-rna-using-next-generation-sequencing-illumina-ribomethseq-protocol
#12
Lilia Ayadi, Yuri Motorin, Virginie Marchand
RNA 2'-O-methylation is one of the ubiquitous nucleotide modifications found in many RNA types from bacteria, archaea, and eukarya. We and others have recently published accurate and sensitive detection of these modifications on native RNA at a single base resolution by high-throughput sequencing technologies. Relative quantification of these modifications is still under progress and would probably reduce the number of false positives due to 3D RNA structure. Therefore, here, we describe a reliable and optimized protocol for quantification of 2'-O-Methylations based on alkaline fragmentation of RNA coupled to a commonly used ligation approach followed by Illumina sequencing...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29129876/-microbial-ecology-along-the-gastrointestinal-tract
#13
Ethan T Hillman, Hang Lu, Tianming Yao, Cindy H Nakatsu
The ecosystem of the human gastrointestinal (GI) tract traverses a number of environmental, chemical, and physical conditions because it runs from the oral cavity to the anus. These differences in conditions along with food or other ingested substrates affect the composition and density of the microbiota as well as their functional roles by selecting those that are the most suitable for that environment. Previous studies have mostly focused on Bacteria, with the number of studies conducted on Archaea, Eukarya, and Viruses being limited despite their important roles in this ecosystem...
November 10, 2017: Microbes and Environments
https://www.readbyqxmd.com/read/29127454/the-distal-gut-bacterial-community-of-some-primates-and-carnivora
#14
Xiu Chen, Qin-Yuan Li, Gui-Ding Li, Fang-Ji Xu, Li Han, Yi Jiang, Xue-Shi Huang, Cheng-Lin Jiang
Huge numbers of bacteria reside in the digestive tract of host and these microorganisms play a vital role in the host health, especially in the digestion of food and the development of immune system. Host phylogeny and diet, especially long-term diet, both have great influence on the gut bacterial community. Other aspects of host, such as gender, age, and the geography and weather they lived, are also correlated to their gut bacterial community. Feces are usually used for gut bacteria study and fecal bacteria can represent the distal gut bacteria...
November 10, 2017: Current Microbiology
https://www.readbyqxmd.com/read/29126700/structure-and-function-of-haemoglobins
#15
REVIEW
David A Gell
Haemoglobin (Hb) is widely known as the iron-containing protein in blood that is essential for O2 transport in mammals. Less widely recognised is that erythrocyte Hb belongs to a large family of Hb proteins with members distributed across all three domains of life-bacteria, archaea and eukaryotes. This review, aimed chiefly at researchers new to the field, attempts a broad overview of the diversity, and common features, in Hb structure and function. Topics include structural and functional classification of Hbs; principles of O2 binding affinity and selectivity between O2/NO/CO and other small ligands; hexacoordinate (containing bis-imidazole coordinated haem) Hbs; bacterial truncated Hbs; flavohaemoglobins; enzymatic reactions of Hbs with bioactive gases, particularly NO, and protection from nitrosative stress; and, sensor Hbs...
October 31, 2017: Blood Cells, Molecules & Diseases
https://www.readbyqxmd.com/read/29126231/irrigation-management-and-phosphorus-addition-alter-the-abundance-of-carbon-dioxide-fixing-autotrophs-in-phosphorus-limited-paddy-soil
#16
Xiaohong Wu, Tida Ge, Wende Yan, Juan Zhou, Xiaomeng Wei, Liang Chen, Xiangbi Chen, Paolo Nannipieri, Jinshui Wu
In this study, we assessed the interactive effects of phosphorus (P) application and irrigation methods on the abundances of marker genes (cbbL, cbbM, accA, and aclB) of CO2-fixing autotrophs. We conducted rice-microcosm experiments using a P-limited paddy soil, with and without the addition of P fertiliser (P versus CK), and using two irrigation methods, namely alternate wetting and drying (AWD) and continuous flooding (CF). The abundances of bacterial 16S rRNA, archaeal 16S rRNA, cbbL, cbbM, accA, and aclB genes in the rhizosphere soil (RS) and bulk soil (BS) were quantified...
November 8, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/29125455/ictv-virus-taxonomy-profile-pleolipoviridae
#17
Dennis H Bamford, Maija K Pietilä, Elina Roine, Nina S Atanasova, Ana Dienstbier, Hanna M Oksanen, Ictv Report Consortium
Members of the family Pleolipoviridae (termed pleolipoviruses) are pseudo-spherical and pleomorphic archaeal viruses. The enveloped virion is a simple membrane vesicle, which encloses different types of DNA genomes of approximately 7-16 kbp (or kilonucleotides). Typically, virions contain a single type of transmembrane (spike) protein at the envelope and a single type of membrane protein, which is embedded in the envelope and located in the internal side of the membrane. All viruses infect extremely halophilic archaea in the class Halobacteria (phylum Euryarchaeota)...
November 10, 2017: Journal of General Virology
https://www.readbyqxmd.com/read/29123504/the-minimum-biological-energy-quantum
#18
REVIEW
Volker Müller, Verena Hess
Some anaerobic archaea and bacteria live on substrates that do not allow the synthesis of one mol of ATP per mol of substrate via substrate level phosphorylation (SLP). Energy conservation in these cases is only possible by a chemiosmotic mechanism that involves the generation of an electrochemical ion gradient across the cytoplasmic membrane that then drives ATP synthesis via an ATP synthase. The minimal amount of energy required for ATP synthesis is thus dependent on the magnitude of the electrochemical ion gradient, the phosphorylation potential in the cell and the ion/ATP ratio of the ATP synthase...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29123229/a-flourishing-field-going-back-to-the-roots-of-the-archaea
#19
EDITORIAL
(no author information available yet)
No abstract text is available yet for this article.
November 10, 2017: Nature Reviews. Microbiology
https://www.readbyqxmd.com/read/29123227/the-enigmatic-archaeal-virosphere
#20
REVIEW
David Prangishvili, Dennis H Bamford, Patrick Forterre, Jaime Iranzo, Eugene V Koonin, Mart Krupovic
One of the most prominent features of archaea is the extraordinary diversity of their DNA viruses. Many archaeal viruses differ substantially in morphology from bacterial and eukaryotic viruses and represent unique virus families. The distinct nature of archaeal viruses also extends to the gene composition and architectures of their genomes and the properties of the proteins that they encode. Environmental research has revealed prominent roles of archaeal viruses in influencing microbial communities in ocean ecosystems, and recent metagenomic studies have uncovered new groups of archaeal viruses that infect extremophiles and mesophiles in diverse habitats...
November 10, 2017: Nature Reviews. Microbiology
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