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https://www.readbyqxmd.com/read/28340330/same-same-but-different-the-evolution-of-tbp-in-archaea-and-their-eukaryotic-offspring
#1
Fabian Blombach, Dina Grohmann
Transcription factors TBP and TF(II)B assemble with RNA polymerase at the promoter DNA forming the initiation complex. Despite a high degree of conservation, the molecular binding mechanisms of archaeal and eukaryotic TBP and TF(II)B differ significantly. Based on recent biophysical data, we speculate how the mechanisms co-evolved with transcription regulation and TBP multiplicity.
February 8, 2017: Transcription
https://www.readbyqxmd.com/read/28337468/comparative-analysis-data-of-sf1-and-sf2-helicases-from-three-domains-of-life
#2
Wafi Chaar, Hiba Ibrahim, Juliana Kozah, Hala Chamieh
SF1 and SF2 helicases are important molecular motors that use the energy of ATP to unwind nucleic acids or nucleic-acid protein complexes. They are ubiquitous enzymes and found in almost all organisms sequenced to date. This article provides a comparative analysis for SF1 and SF2 helicase families from three domains of life archaea, human, bacteria. Seven families are conserved in these three representatives and includes Upf1-like, UvrD-like, Rad3-like, DEAD-box, RecQ-like. Snf2 and Ski2-like. The data highlight conservation of the helicase core motifs for each of these families...
April 2017: Data in Brief
https://www.readbyqxmd.com/read/28335556/trm5-and-trmd-two-enzymes-from-distinct-origins-catalyze-the-identical-trna-modification-m%C3%A2-g37
#3
REVIEW
Sakurako Goto-Ito, Takuhiro Ito, Shigeyuki Yokoyama
The N¹-atom of guanosine at position 37 in transfer RNA (tRNA) is methylated by tRNA methyltransferase 5 (Trm5) in eukaryotes and archaea, and by tRNA methyltransferase D (TrmD) in bacteria. The resultant modified nucleotide m¹G37 positively regulates the aminoacylation of the tRNA, and simultaneously functions to prevent the +1 frameshift on the ribosome. Interestingly, Trm5 and TrmD have completely distinct origins, and therefore bear different tertiary folds. In this review, we describe the different strategies utilized by Trm5 and TrmD to recognize their substrate tRNAs, mainly based on their crystal structures complexed with substrate tRNAs...
March 21, 2017: Biomolecules
https://www.readbyqxmd.com/read/28334774/high-tolerance-to-self-targeting-of-the-genome-by-the-endogenous-crispr-cas-system-in-an-archaeon
#4
Aris-Edda Stachler, Israela Turgeman-Grott, Ella Shtifman-Segal, Thorsten Allers, Anita Marchfelder, Uri Gophna
CRISPR-Cas systems allow bacteria and archaea to acquire sequence-specific immunity against selfish genetic elements such as viruses and plasmids, by specific degradation of invader DNA or RNA. However, this involves the risk of autoimmunity if immune memory against host DNA is mistakenly acquired. Such autoimmunity has been shown to be highly toxic in several bacteria and is believed to be one of the major costs of maintaining these defense systems. Here we generated an experimental system in which a non-essential gene, required for pigment production and the reddish colony color, is targeted by the CRISPR-Cas I-B system of the halophilic archaeon Haloferax volcanii...
March 2, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334743/comparative-genomic-analysis-of-translation-initiation-mechanisms-for-genes-lacking-the-shine-dalgarno-sequence-in-prokaryotes
#5
So Nakagawa, Yoshihito Niimura, Takashi Gojobori
In prokaryotes, translation initiation is believed to occur through an interaction between the 3΄ tail of a 16S rRNA and a corresponding Shine-Dalgarno (SD) sequence in the 5΄ untranslated region (UTR) of an mRNA. However, some genes lack SD sequences (non-SD genes), and the fraction of non-SD genes in a genome varies depending on the prokaryotic species. To elucidate non-SD translation initiation mechanisms in prokaryotes from an evolutionary perspective, we statistically examined the nucleotide frequencies around the initiation codons in non-SD genes from 260 prokaryotes (235 bacteria and 25 archaea)...
February 21, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334283/the-microbiology-of-oil-sands-tailings-past-present-future
#6
Julia M Foght, Lisa M Gieg, Tariq Siddique
Surface mining of enormous oil sands deposits in northeastern Alberta, Canada since 1967 has contributed greatly to Canada's economy but has also received negative international attention due largely to environmental concerns and challenges. Not only have microbes profoundly affected the composition and behaviour of this petroleum resource over geological time, they currently influence the management of semi-solid tailings in oil sands tailing ponds (OSTP) and tailings reclamation. Historically, microbial impacts on OSTP were generally discounted but next-generation sequencing and biogeochemical studies have revealed unexpectedly diverse indigenous communities and expanded our fundamental understanding of anaerobic microbial functions...
March 9, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28330764/lipid-sugar-carriers-at-the-extremes-the-phosphodolichols-archaea-use-in-n-glycosylation
#7
REVIEW
Jerry Eichler, Ziqiang Guan
N-glycosylation, a post-translational modification whereby glycans are covalently linked to select Asn residues of target proteins, occurs in all three domains of life. Across evolution, the N-linked glycans are initially assembled on phosphorylated cytoplasmically-oriented polyisoprenoids, with polyprenol (mainly C55 undecaprenol) fulfilling this role in Bacteria and dolichol assuming this function in Eukarya and Archaea. The eukaryal and archaeal versions of dolichol can, however, be distinguished on the basis of their length, degree of saturation and by other traits...
March 19, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28330329/diversity-of-bacteria-and-archaea-in-the-rhizosphere-of-bioenergy-crop-jatropha-curcas
#8
Garima Dubey, Bharati Kollah, Vijay Kumar Gour, Arvind Kumar Shukla, Santosh Ranjan Mohanty
Plant-microbial interaction in rhizosphere plays vital role in shaping plant's growth and ecosystem function. Most of the rhizospheric microbial diversity studies are restricted to bacteria. In natural ecosystem, archaea also constitutes a major component of the microbial population. However, their diversity is less known compared to bacteria. Experiments were carried out to examine diversity of bacteria and archaea in the rhizosphere of bioenergy crop Jatropha curcas (J. curcas). Samples were collected from three locations varying widely in the soil physico-chemical properties...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28328021/novel-archaeal-tetraether-lipids-with-a-cyclohexyl-ring-identified-in-fayetteville-green-lake-ny-and-other-sulfidic-lacustrine-settings
#9
Xiao-Lei Liu, Ana De Santiago Torio, Tanja Bosak, Roger Everett Summons
RATIONALE: The meromictic Fayetteville Green Lake (FGL) is of significant geobiological interest because of microbial cycling of sulfur within and below the permanent chemocline and in the euxinic deep waters. Studies of glycerol dibiphytanyl glycerol tetraethers (GDGTs) may help shed light on understanding the activity of archaeal communities in these habitats. METHODS: Normal-phase and reversed-phase liquid chromatography/mass spectrometry (LC/MS) analysis on total lipid extracts of environmental samples revealed series of GDGTs with different biphytane structures...
May 30, 2016: Rapid Communications in Mass Spectrometry: RCM
https://www.readbyqxmd.com/read/28326066/beneficial-microorganisms-for-corals-bmc-proposed-mechanisms-for-coral-health-and-resilience
#10
REVIEW
Raquel S Peixoto, Phillipe M Rosado, Deborah Catharine de Assis Leite, Alexandre S Rosado, David G Bourne
The symbiotic association between the coral animal and its endosymbiotic dinoflagellate partner Symbiodinium is central to the success of corals. However, an array of other microorganisms associated with coral (i.e., Bacteria, Archaea, Fungi, and viruses) have a complex and intricate role in maintaining homeostasis between corals and Symbiodinium. Corals are sensitive to shifts in the surrounding environmental conditions. One of the most widely reported responses of coral to stressful environmental conditions is bleaching...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28324256/legacy-effects-of-simulated-short-term-climate-change-on-ammonia-oxidisers-denitrifiers-and-nitrous-oxide-emissions-in-an-acid-soil
#11
Xiaoya Xu, Xiaorui Liu, Yong Li, Yu Ran, Yapeng Liu, Qichun Zhang, Zheng Li, Yan He, Jianming Xu, Hongjie Di
Although the effect of simulated climate change on nitrous oxide (N2O) emissions and on associated microbial communities has been reported, it is not well understood if these effects are short-lived or long-lasting. Here, we conducted a field study to determine the interactive effects of simulated warmer and drier conditions on nitrifier and denitrifier communities and N2O emissions in an acidic soil and the longevity of the effects. A warmer (+2.3 °C) and drier climate (-7.4% soil moisture content) was created with greenhouses...
March 21, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28321126/genomic-reconstruction-of-multiple-lineages-of-uncultured-benthic-archaea-suggests-distinct-biogeochemical-roles-and-ecological-niches
#12
Cassandre S Lazar, Brett J Baker, Kiley W Seitz, Andreas P Teske
No abstract text is available yet for this article.
April 2017: ISME Journal
https://www.readbyqxmd.com/read/28321009/energy-metabolism-during-anaerobic-methane-oxidation-in-anme-archaea
#13
Shawn E McGlynn
Anaerobic methane oxidation in archaea is often presented to operate via a pathway of "reverse methanogenesis". However, if the cumulative reactions of a methanogen are run in reverse there is no apparent way to conserve energy. Recent findings suggest that chemiosmotic coupling enzymes known from their use in methylotrophic and acetoclastic methanogens-in addition to unique terminal reductases-biochemically facilitate energy conservation during complete CH4 oxidation to CO2. The apparent enzyme modularity of these organisms highlights how microbes can arrange their energy metabolisms to accommodate diverse chemical potentials in various ecological niches, even in the extreme case of utilizing "reverse" thermodynamic potentials...
March 17, 2017: Microbes and Environments
https://www.readbyqxmd.com/read/28317562/normal-oral-flora-and-the-oral-ecosystem
#14
REVIEW
Lakshman Samaranayake, Victor H Matsubara
The oral ecosystem comprises the oral flora, so-called oral microbiome, the different anatomic microniches of the oral cavity, and its bathing fluid, saliva. The oral microbiome comprises a group of organisms and includes bacteria, archaea, fungi, protozoa, and viruses. The oral microbiome exists suspended in saliva as planktonic phase organisms or attached to oral surfaces as a plaque biofilm. Homeostasis of the plaque biofilm and its symbiotic relationship with the host is critical for oral health. Disequilibrium or dysbiosis within the plaque biofilms is the initiating event that leads to major oral diseases, such as caries and periodontal disease...
April 2017: Dental Clinics of North America
https://www.readbyqxmd.com/read/28303666/is-the-methanogenic-community-reflecting-the-methane-emissions-of-river-sediments-comparison-of-two-study-sites
#15
Prem Prashant Chaudhary, Martin Rulík, Martin Blaser
Studies on methanogenesis from freshwater sediments have so far primarily focused on lake sediments. To expand our knowledge on the community composition of methanogenic archaea in river sediments, we studied the abundance and diversity of methanogenic archaea at two localities along a vertical profile (top 50 cm) obtained from sediment samples from Sitka stream (the Czech Republic). In this study, we compare two sites which previously have been shown to have a 10-fold different methane emission. Archaeal and methanogen abundance were analyzed by real-time PCR and T-RFLP...
March 16, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28302716/the-recj2-protein-in-the-thermophilic-archaeon-thermoplasma-acidophilum-is-a-3-5-exonuclease-and-associates-with-a-dna-replication-complex
#16
Hiromi Ogino, Sonoko Ishino, Daisuke Kohda, Yoshizumi Ishino
RecJ/cell division cycle 45 (Cdc45) proteins are widely conserved in the three domains of life, i.e., in Bacteria, Eukarya and Archaea. Bacterial RecJ is a 5' 3' exonuclease and functions in DNA repair pathways, while using its 5' 3' exonuclease activity. Eukaryotic Cdc45 has no identified enzymatic activity, but participates in the CMG complex so named because it is composed of Cdc45, minichromosome maintenance protein complex (MCM) proteins 2-7, and GINS complex proteins (Sld5, Psf11 to 3). Eukaryotic Cdc45 and bacterial/archaeal RecJ share similar amino acid sequences and are considered functional counterparts...
March 16, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28299854/induction-of-a-transient-acidosis-in-the-rumen-simulation-technique
#17
M Eger, S Riede, G Breves
Feeding high concentrate diets to cattle results in an enhanced production of short-chain fatty acids by the micro-organisms in the rumen. Excessive fermentation might result in subclinical or clinical rumen acidosis, characterized by low pH, alterations in the microbial community and lactate production. Here, we provide an in vitro model of a severe rumen acidosis. A transient acidosis was induced in the rumen simulation technique by lowering bicarbonate, dihydrogen phosphate and hydrogen phosphate concentrations in the artificial saliva while providing a concentrate-to-forage ratio of 70:30...
March 16, 2017: Journal of Animal Physiology and Animal Nutrition
https://www.readbyqxmd.com/read/28299451/pcal_0111-a-highly-thermostable-bifunctional-fructose-1-6-bisphosphate-aldolase-phosphatase-from-pyrobaculum-calidifontis
#18
Iram Aziz, Naeem Rashid, Raza Ashraf, Qamar Bashir, Tadayuki Imanaka, Muhammad Akhtar
Pyrobaculum calidifontis genome harbors an open reading frame Pcal_0111 annotated as fructose bisphosphate aldolase. Although the gene is annotated as fructose bisphosphate aldolase, it exhibits a high homology with previously reported fructose-1,6-bisphosphate aldolase/phosphatase from Thermoproteus neutrophilus. To examine the biochemical properties of Pcal_0111, we have cloned and expressed the gene in Escherichia coli. Purified recombinant Pcal_0111 catalyzed both phosphatase and aldolase reactions with specific activity values of 4 U and 1...
March 15, 2017: Extremophiles: Life Under Extreme Conditions
https://www.readbyqxmd.com/read/28298445/the-structure-and-function-of-mycobacterium-tuberculosis-mazf-mt6-provides-insights-into-conserved-features-of-mazf-endonucleases
#19
Eric D Hoffer, Stacey J Miles, Christine M Dunham
Toxin-antitoxin systems are ubiquitous in prokaryotic and archaea genomes and regulate growth in response to stress. E. coli contains at least 36 putative toxin-antitoxin gene pairs, and some pathogens such as Mycobacterium tuberculosis (Mtb) have over 90 toxin-antitoxin operons. E. coli MazF cleaves free mRNA after encountering stress and nine Mtb MazF family members cleave mRNA, tRNA, or rRNA. Moreover, Mtb MazF-mt6 cleaves 23S rRNA Helix 70 to inhibit protein synthesis. The overall tertiary folds of these MazFs are predicted to be similar, therefore it is unclear how they recognize structurally distinct RNAs...
March 15, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28294213/towards-artificial-methanogenesis-biosynthesis-of-the-fe-hydrogenase-cofactor-and-characterization-of-the-semi-synthetic-hydrogenase
#20
Liping Bai, Takashi Fujishiro, Gangfeng Huang, Jürgen Koch, Atsushi Takabayashi, Makio Yokono, Ayumi Tanaka, Tao Xu, Xile Hu, Ulrich Ermler, Seigo Shima
The greenhouse gas and energy carrier methane is produced on Earth mainly by methanogenic archaea. In the hydrogenotrophic methanogenic pathway the reduction of one CO2 to one methane molecule requires four molecules of H2 containing eight electrons. Four of the electrons from two H2 are supplied for reduction of an electron carrier F420, which is catalyzed by F420-reducing [NiFe]-hydrogenase under nickel-sufficient conditions. The same reaction is catalysed under nickel-limiting conditions by [Fe]-hydrogenase coupled with a reaction catalyzed by F420-dependent methylene tetrahydromethanopterin dehydrogenase...
March 15, 2017: Faraday Discussions
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