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Archaea: A Gold Mine for Topoisomerase Diversity.

ABSTRACT: The control of DNA topology is a prerequisite for all the DNA transactions such as DNA replication, repair, recombination, and transcription. This global control is carried out by essential enzymes, named DNA-topoisomerases, that are mandatory for the genome stability. Since many decades, the Archaea provide a significant panel of new types of topoisomerases such as the reverse gyrase, the type IIB or the type IC. These more or less recent discoveries largely contributed to change the understanding of the role of the DNA topoisomerases in all the living world. Despite their very different life styles, Archaea share a quasi-homogeneous set of DNA-topoisomerases, except thermophilic organisms that possess at least one reverse gyrase that is considered a marker of the thermophily. Here, we discuss the effect of the life style of Archaea on DNA structure and topology and then we review the content of these essential enzymes within all the archaeal diversity based on complete sequenced genomes available. Finally, we discuss their roles, in particular in the processes involved in both the archaeal adaptation and the preservation of the genome stability.

SUBMITTER: Garnier F

PROVIDER: S-EPMC8185306 | biostudies-literature |

REPOSITORIES: biostudies-literature

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The Gene Ontology resource: enriching a GOld mine.

Project description:The Gene Ontology Consortium (GOC) provides the most comprehensive resource currently available for computable knowledge regarding the functions of genes and gene products. Here, we report the advances of the consortium over the past two years. The new GO-CAM annotation framework was notably improved, and we formalized the model with a computational schema to check and validate the rapidly increasing repository of 2838 GO-CAMs. In addition, we describe the impacts of several collaborations to refine GO and report a 10% increase in the number of GO annotations, a 25% increase in annotated gene products, and over 9,400 new scientific articles annotated. As the project matures, we continue our efforts to review older annotations in light of newer findings, and, to maintain consistency with other ontologies. As a result, 20 000 annotations derived from experimental data were reviewed, corresponding to 2.5% of experimental GO annotations. The website (http://geneontology.org) was redesigned for quick access to documentation, downloads and tools. To maintain an accurate resource and support traceability and reproducibility, we have made available a historical archive covering the past 15 years of GO data with a consistent format and file structure for both the ontology and annotations.

| S-EPMC7779012 | biostudies-literature

microbial archaea diversity

Project description:microbial archaea diversity Metagenome

| PRJNA786714 | ENA

Insertion sequence diversity in archaea.

Project description:Insertion sequences (ISs) can constitute an important component of prokaryotic (bacterial and archaeal) genomes. Over 1,500 individual ISs are included at present in the ISfinder database (www-is.biotoul.fr), and these represent only a small portion of those in the available prokaryotic genome sequences and those that are being discovered in ongoing sequencing projects. In spite of this diversity, the transposition mechanisms of only a few of these ubiquitous mobile genetic elements are known, and these are all restricted to those present in bacteria. This review presents an overview of ISs within the archaeal kingdom. We first provide a general historical summary of the known properties and behaviors of archaeal ISs. We then consider how transposition might be regulated in some cases by small antisense RNAs and by termination codon readthrough. This is followed by an extensive analysis of the IS content in the sequenced archaeal genomes present in the public databases as of June 2006, which provides an overview of their distribution among the major archaeal classes and species. We show that the diversity of archaeal ISs is very great and comparable to that of bacteria. We compare archaeal ISs to known bacterial ISs and find that most are clearly members of families first described for bacteria. Several cases of lateral gene transfer between bacteria and archaea are clearly documented, notably for methanogenic archaea. However, several archaeal ISs do not have bacterial equivalents but can be grouped into Archaea-specific groups or families. In addition to ISs, we identify and list nonautonomous IS-derived elements, such as miniature inverted-repeat transposable elements. Finally, we present a possible scenario for the evolutionary history of ISs in the Archaea.

| S-EPMC1847376 | biostudies-literature

Niacin Alternatives for Dyslipidemia: Fool's Gold or Gold Mine? Part I: Alternative Niacin Regimens.

Project description:Niacin was the first drug demonstrating lowered cholesterol prevents coronary heart disease (CHD) events, with two clinical CHD outcome studies establishing a cardioprotective niacin regimen: 1 g thrice daily with meals. Though cardioprotective, skin toxicity limits niacin's use, fostering several variations to improve tolerability. One of these, an extended-release (ER) alternative, proved immensely successful commercially, dominating clinical practice despite departing from the established regimen in several critical ways. Hence, improved tolerability may have come at the cost of diminished efficacy, posing a conundrum: Does it still help the population at risk for CHD to broaden a drug's acceptance by "watering it down"? This question is crucial at this stage now that the ER alternative failed to recapitulate the benefits of the established cardioprotective niacin regimen in two trials of the alternative approach: AIM-HIGH and HPS2-THRIVE. Part I of this review discusses how vastly the ER alternative departs from the established cardioprotective regimen, why that is important physiologically, and how it may explain the findings of AIM-HIGH and HPS2-THRIVE. Given important gaps left by statin therapy, the established cardioprotective niacin regimen remains an important evidence-based therapy for the statin intolerant or statin averse.

| S-EPMC4753247 | biostudies-literature

Niacin Alternatives for Dyslipidemia: Fool's Gold or Gold Mine? Part II: Novel Niacin Mimetics.

Project description:Two cardiovascular outcome trials established niacin 3 g daily prevents hard cardiac events. However, as detailed in part I of this series, an extended-release (ER) alternative at only 2 g nightly demonstrated no comparable benefits in two outcome trials, implying the alternative is not equivalent to the established cardioprotective regimen. Since statins leave a significant treatment gap, this presents a major opportunity for developers. Importantly, the established regimen is cardioprotective, so the pathway is likely beneficial. Moreover, though effective, the established cardioprotective regimen is cumbersome, limiting clinical use. At the same time, the ER alternative has been thoroughly discredited as a viable substitute for the established cardioprotective regimen. Therefore, by exploiting the pathway and skillfully avoiding the problems with the established cardioprotective regimen and the ER alternative, developers could validate cardioprotective variations facing little meaningful competition from their predecessors. Thus, shrewd developers could effectively tap into a gold mine at the grave of the ER alternative. The GPR109A receptor was discovered a decade ago, leading to a large body of evidence commending the niacin pathway to a lower cardiovascular risk beyond statins. While mediating niacin's most prominent adverse effects, GPR109A also seems to mediate anti-lipolytic, anti-inflammatory, and anti-atherogenic effects of niacin. Several developers are investing heavily in novel strategies to exploit niacin's therapeutic pathways. These include selective GPR109A receptor agonists, niacin prodrugs, and a niacin metabolite, with encouraging early phase human data. In part II of this review, we summarize the accumulated results of these early phase studies of emerging niacin mimetics.

| S-EPMC4773474 | biostudies-literature

Mycorrhizae and Rhizobacteria on Precambrian Rocky Gold Mine Tailings: I. Mine-Adapted Symbionts Promote White Spruce Health and Growth.

Project description:White spruce [Picea glauca (Moench) Voss] is a commercially valuable boreal tree that has been known for its ability to colonize deglaciated rock tailings. Over the last decade, there has been an increasing interest in using this species for the revegetation and successful restoration of abandoned mine spoils. Herein, we conducted a glasshouse experiment to screen mycorrhizal fungi and rhizobacteria capable of improving the health and growth of white spruce seedlings growing directly on waste rocks (WRs) or fine tailings (FTs) from the Sigma-Lamaque gold mine located in the Canadian Abitibi region. After 32 weeks, measurements of health, growth, and mycorrhizal colonization variables of seedlings were performed. Overall, symbionts isolated from roots of healthy white spruce seedlings growing on the mining site, especially Cadophora finlandia Cad. fin. MBN0213 GenBank No. KC840625 and Pseudomonas putida MBN0213 GenBank No. AY391278, were more efficient in enhancing seedling health and growth than allochthonous species and constitute promising microbial symbionts. In general, mycorrhizae promoted plant health and belowground development, while rhizobacteria enhanced aboveground plant biomass. The observed beneficial effects were substrate-, strain-, and/or strains combination-specific. Therefore, preliminary experiments in control conditions such as the one described here can be part of an efficient and integrated strategy to select ecologically well-adapted symbiotic microorganisms, critical for the success of a long-term revegetation program.

| S-EPMC6130231 | biostudies-literature

Beatrix gold mine Witwatersrand Basin South Africa

Project description:Beatrix gold mine Witwatersrand Basin South Africa Metagenome

| PRJNA1085331 | ENA

Bacterial diversity in a mine water treatment plant.

Project description:We investigated the microbial community in a pilot plant for treatment of acid mine water by biological ferrous iron oxidation using clone library analysis and calculated statistical parameters for further characterization. The microbial community in the plant was conspicuously dominated by a group of Betaproteobacteria affiliated with "Ferribacter polymyxa".

| S-EPMC2632141 | biostudies-literature

Diversity and Niche of Archaea in Bioremediation.

Project description:Bioremediation is the use of microorganisms for the degradation or removal of contaminants. Most bioremediation research has focused on processes performed by the domain Bacteria; however, Archaea are known to play important roles in many situations. In extreme conditions, such as halophilic or acidophilic environments, Archaea are well suited for bioremediation. In other conditions, Archaea collaboratively work alongside Bacteria during biodegradation. In this review, the various roles that Archaea have in bioremediation is covered, including halophilic hydrocarbon degradation, acidophilic hydrocarbon degradation, hydrocarbon degradation in nonextreme environments such as soils and oceans, metal remediation, acid mine drainage, and dehalogenation. Research needs are addressed in these areas. Beyond bioremediation, these processes are important for wastewater treatment (particularly industrial wastewater treatment) and help in the understanding of the natural microbial ecology of several Archaea genera.

| S-EPMC6140281 | biostudies-literature

Arsenic pollution in Quaternary sediments and water near a former gold mine.

Project description:Contamination of water and sediments with arsenic and heavy metals is a global issue affecting human health. Regions covered with Quaternary deposits have received little attention from the point of view of the flux of arsenic and heavy metals from sediments to surface water. This study aims to determine the flux of arsenic and other heavy metals from Quaternary sediments to surface waters in an area affected by the former Złoty Stok gold and arsenic mine. Contamination in surface waters and sediments was caused by arsenic, whereas concentrations of metals were usually within water quality standards. Arsenic contamination of surface water increased in the lower part of the basin covered by Quaternary sediments, and exceeded water quality standards by 2 orders of magnitude. Arsenic mass flux exceeded 8 kg/day near the confluence of the Trująca River with the Nysa Kłodzka, a main tributary of the Oder River. An increase in arsenic concentration in the lower part of the basin is related to mine tailings and preferential flow of groundwater through Quaternary sediments. In future, water resources scarcity may lead to an increase in arsenic contamination in surface and groundwater.

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