Relevant bibliographies by topics / Archaeon

Academic literature on the topic 'Archaeon'

Author: Grafiati
Published: 4 June 2021
Last updated: 20 February 2023

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Journal articles on the topic "Archaeon"

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Imachi, Hiroyuki, Masaru K. Nobu, Nozomi Nakahara, Yuki Morono, Miyuki Ogawara, Yoshihiro Takaki, Yoshinori Takano, et al. "Isolation of an archaeon at the prokaryote–eukaryote interface." Nature 577, no. 7791 (January 15, 2020): 519–25. http://dx.doi.org/10.1038/s41586-019-1916-6.

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Abstract The origin of eukaryotes remains unclear1–4. Current data suggest that eukaryotes may have emerged from an archaeal lineage known as ‘Asgard’ archaea5,6. Despite the eukaryote-like genomic features that are found in these archaea, the evolutionary transition from archaea to eukaryotes remains unclear, owing to the lack of cultured representatives and corresponding physiological insights. Here we report the decade-long isolation of an Asgard archaeon related to Lokiarchaeota from deep marine sediment. The archaeon—‘Candidatus Prometheoarchaeum syntrophicum’ strain MK-D1—is an anaerobic, extremely slow-growing, small coccus (around 550 nm in diameter) that degrades amino acids through syntrophy. Although eukaryote-like intracellular complexes have been proposed for Asgard archaea6, the isolate has no visible organelle-like structure. Instead, Ca. P. syntrophicum is morphologically complex and has unique protrusions that are long and often branching. On the basis of the available data obtained from cultivation and genomics, and reasoned interpretations of the existing literature, we propose a hypothetical model for eukaryogenesis, termed the entangle–engulf–endogenize (also known as E3) model.
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Denis, Antonia, Mario Alberto Martínez-Núñez, Silvia Tenorio-Salgado, and Ernesto Perez-Rueda. "Dissecting the Repertoire of DNA-Binding Transcription Factors of the Archaeon Pyrococcus furiosus DSM 3638." Life 8, no. 4 (September 21, 2018): 40. http://dx.doi.org/10.3390/life8040040.

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In recent years, there has been a large increase in the amount of experimental evidence for diverse archaeal organisms, and these findings allow for a comprehensive analysis of archaeal genetic organization. However, studies about regulatory mechanisms in this cellular domain are still limited. In this context, we identified a repertoire of 86 DNA-binding transcription factors (TFs) in the archaeon Pyrococcus furiosus DSM 3638, that are clustered into 32 evolutionary families. In structural terms, 45% of these proteins are composed of one structural domain, 41% have two domains, and 14% have three structural domains. The most abundant DNA-binding domain corresponds to the winged helix-turn-helix domain; with few alternative DNA-binding domains. We also identified seven regulons, which represent 13.5% (279 genes) of the total genes in this archaeon. These analyses increase our knowledge about gene regulation in P. furiosus DSM 3638 and provide additional clues for comprehensive modeling of transcriptional regulatory networks in the Archaea cellular domain.
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Jansson, B. P. Mattias, Laurence Malandrin, and Hans E. Johansson. "Cell Cycle Arrest in Archaea by the Hypusination Inhibitor N1-Guanyl-1,7-Diaminoheptane." Journal of Bacteriology 182, no. 4 (February 15, 2000): 1158–61. http://dx.doi.org/10.1128/jb.182.4.1158-1161.2000.

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ABSTRACT Hypusination is an essential posttranslational modification unique to archaeal and eukaryotic protein synthesis initiation factor 5A (aIF5A and eIF5A, respectively). We have investigated the effect of the efficient hypusination inhibitorN 1-guanyl-1,7-diaminoheptane (GC7) on four archaeal and one bacterial species. We found that (i) archaea are sensitive to GC7, whereas the bacteriumEscherichia coli is not, (ii) GC7 causes rapid and reversible arrest of growth of the archaeon Sulfolobus acidocaldarius, and (iii) the growth arrest is accompanied by a specific reversible arrest of the cell cycle prior to cell division. Our findings establish a link between hypusination and sustained growth of archaea and thereby provide the framework to study molecular details of archaeal cell cycle in connection with in vivo functions of hypusine and of aIF5A and eIF5A.
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Ishibashi, Yumi, Natsumi Matsushima, Tomokazu Ito, and Hisashi Hemmi. "Isopentenyl diphosphate/dimethylallyl diphosphate-specific Nudix hydrolase from the methanogenic archaeon Methanosarcina mazei." Bioscience, Biotechnology, and Biochemistry 86, no. 2 (December 1, 2021): 246–53. http://dx.doi.org/10.1093/bbb/zbab205.

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ABSTRACT Nudix hydrolases typically catalyze the hydrolysis of nucleoside diphosphate linked to moiety X and yield nucleoside monophosphate and X-phosphate, while some of them hydrolyze a terminal diphosphate group of non-nucleosidic compounds and convert it into a phosphate group. Although the number of Nudix hydrolases is usually limited in archaea comparing with those in bacteria and eukaryotes, the physiological functions of most archaeal Nudix hydrolases remain unknown. In this study, a Nudix hydrolase family protein, MM_2582, from the methanogenic archaeon Methanosarcina mazei was recombinantly expressed in Escherichia coli, purified, and characterized. This recombinant protein shows higher hydrolase activity toward isopentenyl diphosphate and short-chain prenyl diphosphates than that toward nucleosidic compounds. Kinetic studies demonstrated that the archaeal enzyme prefers isopentenyl diphosphate and dimethylallyl diphosphate, which suggests its role in the biosynthesis of prenylated flavin mononucleotide, a recently discovered coenzyme that is required, for example, in the archaea-specific modified mevalonate pathway.
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Meyer, Benjamin H., and Sonja-Verena Albers. "Hot and sweet: protein glycosylation in Crenarchaeota." Biochemical Society Transactions 41, no. 1 (January 29, 2013): 384–92. http://dx.doi.org/10.1042/bst20120296.

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Every living cell is covered with a dense and complex array of covalently attached sugars or sugar chains. The majority of these glycans are linked to proteins via the so-called glycosylation process. Protein glycosylation is found in all three domains of life: Eukarya, Bacteria and Archaea. However, on the basis of the limit in analytic tools for glycobiology and genetics in Archaea, only in the last few years has research on archaeal glycosylation pathways started mainly in the Euryarchaeota Haloferax volcanii, Methanocaldococcus maripaludis and Methanococcus voltae. Recently, major steps of the crenarchaeal glycosylation process of the thermoacidophilic archaeon Sulfolobus acidocaldarius have been described. The present review summarizes the proposed N-glycosylation pathway of S. acidocaldarius, describing the phenotypes of the mutants disrupted in N-glycan biosynthesis as well as giving insights into the archaeal O-linked and glycosylphosphatidylinositol anchor glycosylation process.
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Elshafey, Naglaa, Samy Selim, Asmaa H. Mohammed, Nashwa Hagagy, Mennatalla Samy, Ehab M. Mostafa, Fatmah A. Safhi, et al. "Mapping Archaeal Diversity in Soda Lakes by Coupling 16S rRNA PCR-DGGE Analysis with Remote Sensing and GIS Technology." Fermentation 8, no. 8 (July 30, 2022): 365. http://dx.doi.org/10.3390/fermentation8080365.

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The haloarchaeal diversity of four hypersaline alkaline lakes from the Wadi El-Natrun depression (Northern Egypt) was investigated using culture-independent polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) of 16S rRNA gene phylotypes, which was combined with remote sensing and geographic information system (GIS) data to highlight the distribution pattern of the microbial diversity in water and sediment samples. The majority of archaeal sequences identified in all four lakes belonged to the phyla Euryarchaeota and Crenarchaeota. Sediment samples from Beida Lake and water samples from El-Hamra Lake showed the highest levels of archaeal diversity. Sequence similarities ≥ 95% were found between six of the acquired clones and uncultured Halorhabdus, Euryarchaeota, and archaeon clones. In addition, two clones shared a high level of sequence similarity (97%) with unclassified archaea, while other nine clones exhibited 96% to 99% sequence similarity with uncultured archaeon clones, and only one clone showed 97% identity with an uncultured Crenarchaeota. Likewise, 7 DGGE bands presented a sequence similarity of 90 to 98% to Halogranum sp., Halalkalicoccus tibetensis, Halalkalicoccus jeotgali, uncultured Halorubrum, Halobacteriaceae sp., or uncultured haloarchaeon. In conclusion, while the variety of alkaliphilic haloarchaea in the examined soda lakes was restricted, the possibility of uncovering novel species for biotechnological applications from these extreme habitats remains promising.
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Shiraishi, Miyako, Michihi Hidaka, and Shigenori Iwai. "Endonuclease V from the archaeon Thermococcus kodakarensis is an inosine-specific ribonuclease." Bioscience, Biotechnology, and Biochemistry 86, no. 3 (December 20, 2021): 313–20. http://dx.doi.org/10.1093/bbb/zbab219.

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ABSTRACT Endonuclease V (EndoV) is an inosine-specific endonuclease which is highly conserved in all domains of life: Bacteria, Archaea, and Eukarya; and, therefore, may play an important role in nucleic acid processes. It is currently thought that bacterial EndoVs are involved in DNA repair, while eukaryotic EndoVs are involved in RNA editing based on the differences in substrate preferences. However, the role of EndoV proteins, particularly in the archaeal domain, is still poorly understood. Here, we explored the biochemical properties of EndoV from the hyperthermophilic archaeon Thermococcus kodakarensis (TkoEndoV). We show that TkoEndoV has a strong preference for RNA over DNA. Further, we synthesized 1-methylinosine-containing RNA that is a simple TΨC loop mimic of archaeal tRNA and found that TkoEndoV discriminates between 1-methylinosine and inosine, and selectively acts on inosine. Our findings suggest a potential role of archaeal EndoV in the regulation of inosine-containing RNA.
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Walters, Alison D., and James P. J. Chong. "Methanococcus maripaludis: an archaeon with multiple functional MCM proteins?" Biochemical Society Transactions 37, no. 1 (January 20, 2009): 1–6. http://dx.doi.org/10.1042/bst0370001.

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There are a large number of proteins involved in the control of eukaryotic DNA replication, which act together to ensure DNA is replicated only once every cell cycle. Key proteins involved in the initiation and elongation phases of DNA replication include the MCM (minchromosome maintenance) proteins, MCM2–MCM7, a family of six related proteins believed to act as the replicative helicase. Genome sequencing has revealed that the archaea possess a simplified set of eukaryotic replication homologues. The complexity of the DNA replication machinery in eukaryotes has led to a number of archaeal species being adapted as model organisms for the study of the DNA replication process. Most archaea sequenced to date possess a single MCM homologue that forms a hexameric complex. Recombinant MCMs from several archaea have been used in the biochemical characterization of the protein, revealing that the MCM complex has ATPase, DNA-binding and -unwinding activities. Unusually, the genome of the methanogenic archaeon Methanococcus maripaludis contains four MCM homologues, all of which contain the conserved motifs required for function. The availability of a wide range of genetic tools for the manipulation of M. maripaludis and the relative ease of growth of this organism in the laboratory makes it a good potential model for studying the role of multiple MCMs in DNA replication.
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Liu, Yuchen, David J. Vinyard, Megan E. Reesbeck, Tateki Suzuki, Kasidet Manakongtreecheep, Patrick L. Holland, Gary W. Brudvig, and Dieter Söll. "A [3Fe-4S] cluster is required for tRNA thiolation in archaea and eukaryotes." Proceedings of the National Academy of Sciences 113, no. 45 (October 24, 2016): 12703–8. http://dx.doi.org/10.1073/pnas.1615732113.

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The sulfur-containing nucleosides in transfer RNA (tRNAs) are present in all three domains of life; they have critical functions for accurate and efficient translation, such as tRNA structure stabilization and proper codon recognition. The tRNA modification enzymes ThiI (in bacteria and archaea) and Ncs6 (in archaea and eukaryotic cytosols) catalyze the formation of 4-thiouridine (s4U) and 2-thiouridine (s2U), respectively. The ThiI homologs were proposed to transfer sulfur via cysteine persulfide enzyme adducts, whereas the reaction mechanism of Ncs6 remains unknown. Here we show that ThiI from the archaeon Methanococcus maripaludis contains a [3Fe-4S] cluster that is essential for its tRNA thiolation activity. Furthermore, the archaeal and eukaryotic Ncs6 homologs as well as phosphoseryl-tRNA (Sep-tRNA):Cys-tRNA synthase (SepCysS), which catalyzes the Sep-tRNA to Cys-tRNA conversion in methanogens, also possess a [3Fe-4S] cluster similar to the methanogenic archaeal ThiI. These results suggest that the diverse tRNA thiolation processes in archaea and eukaryotic cytosols share a common mechanism dependent on a [3Fe-4S] cluster for sulfur transfer.
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Woodson, Jesse D., Carmen L. Zayas, and Jorge C. Escalante-Semerena. "A New Pathway for Salvaging the CoenzymeB12 Precursor Cobinamide in Archaea RequiresCobinamide-Phosphate Synthase (CbiB) EnzymeActivity." Journal of Bacteriology 185, no. 24 (December 15, 2003): 7193–201. http://dx.doi.org/10.1128/jb.185.24.7193-7201.2003.

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ABSTRACT The ability of archaea to salvage cobinamide has been under question because archaeal genomes lack orthologs to the bacterial nucleoside triphosphate:5′-deoxycobinamide kinase enzyme (cobU in Salmonella enterica). The latter activity is required for cobinamide salvaging in bacteria. This paper reports evidence that archaea salvage cobinamide from the environment by using a pathway different from the one used by bacteria. These studies demanded the functional characterization of two genes whose putative function had been annotated based solely on their homology to the bacterial genes encoding adenosylcobyric acid and adenosylcobinamide-phosphate synthases (cbiP and cbiB, respectively) of S. enterica. A cbiP mutant strain of the archaeon Halobacterium sp. strain NRC-1 was auxotrophic for adenosylcobyric acid, a known intermediate of the de novo cobamide biosynthesis pathway, but efficiently salvaged cobinamide from the environment, suggesting the existence of a salvaging pathway in this archaeon. A cbiB mutant strain of Halobacterium was auxotrophic for adenosylcobinamide-GDP, a known de novo intermediate, and did not salvage cobinamide. The results of the nutritional analyses of the cbiP and cbiB mutants suggested that the entry point for cobinamide salvaging is adenosylcobyric acid. The data are consistent with a salvaging pathway for cobinamide in which an amidohydrolase enzyme cleaves off the aminopropanol moiety of adenosylcobinamide to yield adenosylcobyric acid, which is converted by the adenosylcobinamide-phosphate synthase enzyme to adenosylcobinamide-phosphate, a known intermediate of the de novo biosynthetic pathway. The existence of an adenosylcobinamide amidohydrolase enzyme would explain the lack of an adenosylcobinamide kinase in archaea.
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Dissertations / Theses on the topic "Archaeon"

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Berger, Stefanie [Verfasser]. "Energy conservation in aceticlastic methanogenic archaea and the human gut archaeon Methanomassiliicoccus luminyensis / Stefanie Berger." Bonn : Universitäts- und Landesbibliothek Bonn, 2015. http://d-nb.info/1077290292/34.

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Lower, Brian Howard. "Protein O-Kinases in the Archaeon Sulfolobus solfataricus." Diss., Virginia Tech, 2001. http://hdl.handle.net/10919/28471.

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For many years, it has been understood that protein phosphorylation-dephosphorylation constitutes one of the most ubiquitous mechanisms for controlling the functional properties of proteins. Although originally believed to be a eukaryotic phenomenon, protein phosphorylation is now known to occur in all three domains of life Eukarya, Bacteria, and Archaea. Very little is known, however, concerning the origins and evolution of protein phosphorylation-dephosphorylation. Knowledge of the structure and properties of the protein kinases resident in the members of the Archaea represents a key piece of this puzzle. The extreme acidothermophilic archaeon, Sulfolobus solfataricus, exhibits a membrane-associated protein kinase activity. Solubilization of the kinase activity requires the presence of detergent such as Triton X-100 or octyl glucoside, indicating its activity reside in an integral membrane protein. This protein kinase utilizes purine nucleotides as phosphoryl donors in vitro with a requirement for a divalent metal ion cofactor, favoring Mn⁺². A preference for NTPs over NDPs and for adenyl nucleotides over the analogous guanyl nucleotides was observed. The enzyme appears to be a glycoprotein that displays catalytic activity on SDS-PAGE corresponding to a molecular mass of ≈67 kDa, as well as an apparent molecular mass of –125 kDa on a gel filtration column. Challenged with several exogenous substrates revealed the protein kinase to be relatively selective. Only casein, reduced carboxyamidomethylated and maleylated lysozyme (RCM lysozyme), histone H4 proved, and a peptide modeled after myosin light chains (KKRAARATSNVFA) were phosphorylated to appreciable levels in vitro. All of the aforementioned substrates were phosphorylated on threonine, while histone H4 was phosphorylated on serine as well. When the phosphoacceptor threonine in the MLC peptide was substituted with serine an appreciable decrease in phosphorylation was noted. The protein kinase underwent autophosphorylation on threonine and was relatively insensitive to several known "eukaryotic" protein kinase inhibitors. Primary sequence motifs based on known conserved subdomains of eukaryotic protein kinases were used to search the genome of S. solfataricus for eukaryotic-like protein kinase sequences. Six hypothetical proteins were identified from S. solfataricus whose primary sequence exhibited noticeable similarities to eukaryotic protein kinases. The hypothetical protein encoded by ORF sso0197 contained 7 putative subdomains, ORFs sso0433, sso2291, sso2387, and sso3207 contained 8 putative subdomains, and ORF sso3182, contained 9 putative subdomains of the 12 characteristically conserved subdomains found within eukaryotic protein kinases. ORF sso2387 was cloned and expressed in Escherichia coli. The expressed protein, SsPK2, was solubilized from inclusion bodies using 5 M urea. SsPK2 was able to phosphorylate casein, BSA, RCM lysozyme, and mixed histones in vitro. Phosphoamino acid analysis of casein, BSA, and mixed histones revealed that they were all phosphorylated on serine. SsPK2 underwent autophosphorylation on serine at elevated temperature using both purine nucleotide triphosphates as phosphoryl donors in vitro, but exhibited a noticeable preference for ATP. Autophosphorylate of SsPK2 also occurred at elevated temperature using a variety of divalent metals cofactors in order of Mn⁺² > Mg⁺² >> Ca²⁺ ≈ Zn⁺². Polycations such as polyLys stimulated the phosphorylation of exogenous substrates while polyanions such as poly(Glu:Tyr) were shown to inhibit the phosphorylation of exogenous substrates. Of the "eukaryotic" protein kinases inhibitors tested, only tamoxifen had any noticeable effect of the catalytic activity of SsPK2 towards itself and exogenous substrates. A truncated form of SsPK2 containing the perceived catalytic domain also exhibited protein kinase activity towards itself and exogenous substrates. The observed protein kinase activity for SsPK2trunk was similar to that observed for SsPK2. Proteins from the membrane fraction of S. solfataricus subject to phosphorylation in vitro on serine or threonine residues were identified using MALDI-MS / peptide fingerprinting techniques. Nine phosphoproteins were assigned a tentative identification using the ProFound protein search engine from Rockefeller University. The identity of two of nine phosphoproteins, a translational endoplasmic reticulum ATPase and an ≈ 42 kDa hypothetical protein, were determined with a relatively high degree of confidence. Collectively the results suggested MALDI-MS peptide mapping coupled with [³²P] labeling in vivo will have a tremendous potential for mapping out a major portion of the phosphoproteome of S. solfataricus.
Ph. D.
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Cong, Xinyu. "Genetic stability in the hyperthermophilic archaeon Sulfolobus acidocaldarius." University of Cincinnati / OhioLINK, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1439309763.

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Maddocks, Deborah G. "Citrate synthase from the halophilic archaeon Haloferax volcanii." Thesis, University of Bath, 1999. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.301966.

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Muir, Jacqueline M. "Citrate synthase from the hyperthermophilic archaeon, Pyrococcus furiosus." Thesis, University of Bath, 1995. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.260247.

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Heyer, Narinder Isabel. "Glucose dehydrogenase from the hyperthermophilic archaeon Sulfolobus solfataricus." Thesis, University of Bath, 1999. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.301967.

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Daifuku, Takashi. "Genomic analysis of the marine hyperthermophilic archaeon Aeropyrum." Kyoto University, 2015. http://hdl.handle.net/2433/199358.

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Kyoto University (京都大学)
0048
新制・課程博士
博士(農学)
甲第19034号
農博第2112号
新制||農||1031(附属図書館)
学位論文||H27||N4916(農学部図書室)
31985
京都大学大学院農学研究科応用生物科学専攻
(主査)教授 左子 芳彦, 教授 澤山 茂樹, 准教授 吉田 天士
学位規則第4条第1項該当
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Kessler, Peter S. "Nitrogen fixation in the mesophilic marine archaeon Methanococcus maripaludis /." Thesis, Connect to this title online; UW restricted, 1998. http://hdl.handle.net/1773/11520.

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Kydd, Catriona L. "A novel aldolase from the hyperthermophilic archaeon Sulfolobus solfataricus." Thesis, University of Bath, 1999. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.311181.

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Qu, Qiuhao. "Sugar metabolism and regulation in the hyperthermophilic archaeon Thermococcus litoralis." Konstanz, 2004. http://www.ub.uni-konstanz.de/kops/volltexte/2004/1409/index.html.

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Books on the topic "Archaeon"

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Barker, David. Archaea: Salt-lovers, methane-makers, thermophiles, and other archaeans. New York: Crabtree Pub., 2010.

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Barker, David. Archaea: Salt-lovers, methane-makers, thermophiles, and other archaeans. New York, N.Y: Crabtree Pub. Co., 2010.

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Diethnes Symposio Archaiou Hellēnikou Dramatos (5th 1998 Drousa, Cyprus). To archaio hellēniko drama: Synchrones hermēneutikes prosengiseis : E' Diethnes Symposio Archaiou Hellēnikou Dramatos. Leukōsia: Kypriako Kentro tou D.I.Th., 1999.

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Solon. Solōn: Archaion Hellēnikon dikaion. Athēna: Peleia, 1988.

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Cavicchioli, Ricardo, ed. Archaea. Washington, DC, USA: ASM Press, 2007. http://dx.doi.org/10.1128/9781555815516.

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Ferreira-Cerca, Sébastien, ed. Archaea. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2445-6.

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Garrett, Roger A., and Hans-Peter Klenk, eds. Archaea. Malden, MA, USA: Blackwell Publishing Ltd, 2006. http://dx.doi.org/10.1002/9780470750865.

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Archaeo-anthropology of Chhattīsgaṛh. New Delhi: Sundeep Prakashan, 2000.

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Diethnes Symposio Archaiou Hellēnikou Dramatos (6th [2000 Paphos, Cyprus]). Hekto Diethnes Symposio Archaiou Hellēnikou Dramatos: Hyvris kai typhlōsis sto archaio Hellēniko drama : synchrones skēnikes prosengiseis. Leukōsia: [Kypriako Kentro tou D. I. Th.], 2002.

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G, Giannelos, Kroustalē Eleutheria, and Ekdoseis Milētos (Firm), eds. Archaioi topoi. Athēna]: Ekdoseis Milētos, 2009.

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Book chapters on the topic "Archaeon"

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Costa, Mariana Inés, and María Inés Giménez. "Metal nanoparticles Biosynthesis Using the Halophilic Archaeon Haloferax volcanii." In Archaea, 345–50. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2445-6_22.

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Gelsinger, Diego Rivera, and Jocelyne DiRuggiero. "Small RNA-Sequencing Library Preparation for the Halophilic Archaeon Haloferax volcanii." In Archaea, 243–54. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2445-6_15.

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Kern, Michael, and Sébastien Ferreira-Cerca. "Differential Translation Activity Analysis Using Bioorthogonal Noncanonical Amino Acid Tagging (BONCAT) in Archaea." In Ribosome Biogenesis, 229–46. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2501-9_14.

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AbstractThe study of protein production and degradation in a quantitative and time-dependent manner is a major challenge to better understand cellular physiological response. Among available technologies bioorthogonal noncanonical amino acid tagging (BONCAT) is an efficient approach allowing for time-dependent labeling of proteins through the incorporation of chemically reactive noncanonical amino acids like l-azidohomoalanine (L-AHA). The azide-containing amino-acid derivative enables a highly efficient and specific reaction termed click chemistry, whereby the azide group of the L-AHA reacts with a reactive alkyne derivate, like dibenzocyclooctyne (DBCO) derivatives, using strain-promoted alkyne–azide cycloaddition (SPAAC). Moreover, available DBCO containing reagents are versatile and can be coupled to fluorophore (e.g., Cy7) or affinity tag (e.g., biotin) derivatives, for easy visualization and affinity purification, respectively.Here, we describe a step-by-step BONCAT protocol optimized for the model archaeon Haloferax volcanii, but which is also suitable to harness other biological systems. Finally, we also describe examples of downstream visualization, affinity purification of L-AHA-labeled proteins and differential expression analysis.In conclusion, the following BONCAT protocol expands the available toolkit to explore proteostasis using time-resolved semiquantitative proteomic analysis in archaea.
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Angelov, Angel, and Wolfgang Liebl. "Erratum to: Heterologous Gene Expression in the Hyperthermophilic Archaeon Sulfolobus solfataricus." In Methods in Molecular Biology, E1. Totowa, NJ: Humana Press, 2010. http://dx.doi.org/10.1007/978-1-60761-823-2_24.

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Angelov, Angel, and Wolfgang Liebl. "Retracted Chapter: Heterologous Gene Expression in the Hyperthermophilic Archaeon Sulfolobus solfataricus." In Methods in Molecular Biology, 109–16. Totowa, NJ: Humana Press, 2010. http://dx.doi.org/10.1007/978-1-60761-823-2_7.

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Santangelo, Thomas J., and John N. Reeve. "Genetic Tools and Manipulations of the Hyperthermophilic Heterotrophic Archaeon Thermococcus kodakarensis." In Extremophiles Handbook, 567–82. Tokyo: Springer Japan, 2011. http://dx.doi.org/10.1007/978-4-431-53898-1_26.

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Splechtna, Barbara, Inge Petzelbauer, Bernhard Kuhn, Klaus D. Kulbe, and Bernd Nidetzky. "Hydrolysis of Lactose by ß-Glycosidase CelB from Hyperthermophilic Archaeon Pyrococcus Furiosus." In Biotechnology for Fuels and Chemicals, 473–88. Totowa, NJ: Humana Press, 2002. http://dx.doi.org/10.1007/978-1-4612-0119-9_39.

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Kimura, Makoto, and Yoshimitsu Kakuta. "Structural Biology of the Ribonuclease P in the Hyperthermophilic Archaeon Pyrococcus horikoshii OT3." In Microorganisms in Sustainable Agriculture and Biotechnology, 487–508. Dordrecht: Springer Netherlands, 2011. http://dx.doi.org/10.1007/978-94-007-2214-9_23.

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Moracci, Marco, Maria Ciaramella, Laurence H. Pearl, and Mosé Rossi. "Structure and Reaction Mechanism of the β-Glycosidase from the Archaeon Sulfolobus Solfataricus." In New Developments in Marine Biotechnology, 209–12. Boston, MA: Springer US, 1998. http://dx.doi.org/10.1007/978-1-4757-5983-9_44.

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Chavez C., P., Y. Sako, and A. Uchida. "A Super Heat-Stable Extracellular Proteinase from the Hyperthermophilic Archaeon Aeropyrum pernix K1." In New Developments in Marine Biotechnology, 269–72. Boston, MA: Springer US, 1998. http://dx.doi.org/10.1007/978-1-4757-5983-9_57.

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Conference papers on the topic "Archaeon"

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Tremberger, Jr., George, Victor Gallardo, Carola Espinoza, Todd Holden, N. Gadura, E. Cheung, P. Schneider, D. Lieberman, and T. Cheung. "Archaeon and archaeal virus diversity classification via sequence entropy and fractal dimension." In SPIE Optical Engineering + Applications, edited by Richard B. Hoover, Gilbert V. Levin, Alexei Y. Rozanov, and Paul C. W. Davies. SPIE, 2010. http://dx.doi.org/10.1117/12.860097.

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Zhuo, Z., C. Zhang, P. Liu, L. Fu, R. Laso-Pérez, G. Wegener, M. Li, and L. Cheng. "A SINGLE ARCHAEON COUPLES HYDROCARBON DEGRADATION TO METHANOGENESIS." In 30th International Meeting on Organic Geochemistry (IMOG 2021). European Association of Geoscientists & Engineers, 2021. http://dx.doi.org/10.3997/2214-4609.202134161.

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Welander, Paula V., Zhirui Zeng, Xiaolei Liu, Jeremy H. Wei, and Roger E. Summons. "BIOSYNTHESIS OF TETRAETHER MEMBRANE LIPIDS IN THE ARCHAEON SULFOLOBUS ACIDOCALDARIUS." In GSA Annual Meeting in Indianapolis, Indiana, USA - 2018. Geological Society of America, 2018. http://dx.doi.org/10.1130/abs/2018am-323962.

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Melnichuk, T. N., A. Yu Egovtseva, S. F. Abdurashitov, E. R. Abdurashytova, E. N. Turin, V. V. Gorelova, and A. A. Zubochenko. "Microbiocenosis of southern chernozem under the influence of no-till." In CURRENT STATE, PROBLEMS AND PROSPECTS OF THE DEVELOPMENT OF AGRARIAN SCIENCE. Federal State Budget Scientific Institution “Research Institute of Agriculture of Crimea”, 2020. http://dx.doi.org/10.33952/2542-0720-2020-5-9-10-114.

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The purpose of the research was to assess microbocenosis of the southern chernozem under the influence of no-till and microbial preparations. A metagenomic analysis of the southern chernozem revealed 12 phyla, including 11 bacteria and 1 archaeon. The number of cellulolytic microorganisms increased under the influence of farming systems compared to virgin soil. The use of microbial preparations contributed to an increase in the number of microorganisms of ecological-trophic groups and the representation of the majority of phyla, which also depended on the farming system.
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Tourte, M., P. Schaeffer, V. Grossi, and P. Oger. "Uncommon Glycerol Monoalkyl Glycerol Tetraethers (GMGT) Support Membrane Adaption in the Archaeon Pyrococcus Furiosus." In 30th International Meeting on Organic Geochemistry (IMOG 2021). European Association of Geoscientists & Engineers, 2021. http://dx.doi.org/10.3997/2214-4609.202134189.

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Wang, Fei, Bo Liu, and Tanming Liu. "Characterization of an exo-a#946;-D-glucosaminidase from the hyperthermophilic archaeon Pyrococcus furiosus." In 2015 2nd International Conference on Machinery, Materials Engineering, Chemical Engineering and Biotechnology. Paris, France: Atlantis Press, 2016. http://dx.doi.org/10.2991/mmeceb-15.2016.52.

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Drochioiu, Gabi. "THE ROLE OF BACTERIORHODOPSIN IN LIGHT HARVESTING AND ATP PRODUCTION BY HALOBACTERIUM SALINARUM CELLS." In 22nd SGEM International Multidisciplinary Scientific GeoConference 2022. STEF92 Technology, 2022. http://dx.doi.org/10.5593/sgem2022/6.1/s25.17.

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Halobacterium salinarum is an extremely halophilic marine Gram-negative obligate aerobic archaeon. Despite its name, this is not a bacterium, but rather a member of the domain Archaea, which lives in hypersaline lakes. Bacteriorhodopsin (BRh) is the red retinal-containing protein found in the cell membranes of H. salinarum and is considered a light-activated proton pump that transports protons across the plasma membrane. Bacteriorhodopsin photointermediates have been defined in kinetic and spectroscopic terms as BR568, K590, L550, M412, N560, and O640. We have previously shown, using the Forster cycle for BRh that its acidity increases greatly on illumination. Therefore, protons released upon illumination of the L550 intermediate with 412 nm light may not play an essential role in ATP production. Instead, the light-induced excitation energy, which represents the energy difference between the L550 and M412 states, can be used to extract an ATP molecule attached to ATP synthase. Thus, we have shown that this amount of energy corresponds to a near-infrared vibration, which is sufficient for ATP production and provides the most feasible molecular mechanism for this phenomenon. Here, we provide new evidence that protons are released due to BRh excitation, unrelated to ATP synthesis, being only a secondary phenomenon. In addition, once released from H. salinarum cells, protons should return back into the cells via ATP-synthase molecules to produce ATP. This is not possible at pH > 7.0, such as pH 9.5. However, the stability of M intermediates and ATP formation appear to be increased at higher pH values. Indeed, a spectral shift of 138 nm may be associated with an energy amount of about 17 kcal mol-1, which is enough energy to release a mole of ATP from ATP-synthase. In general, light excitation of fluorescent molecules is a phenomenon that induces a strong increase in their acidity. Recent data suggest that the chemiosmotic hypothesis put forward by Peter Mitchell to explain ATP formation in living cells is not correct, at least in terms of explaining light-induced ATP production in H. salinarum cells.
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Popinako, Anna V., Mikhail Yu Antonov, Ekaterina Yu Bezsudnova, Georgiy A. Prokopiev, and Vladimir O. Popov. "Molecular dynamics study of the structural and dynamic characteristics of the polyextremophilic short-chain dehydrogenase from the Thermococcus sibiricus archaeon and its homologues." In PROCEEDINGS OF THE 3RD INTERNATIONAL CONFERENCE ON CONSTRUCTION AND BUILDING ENGINEERING (ICONBUILD) 2017: Smart Construction Towards Global Challenges. Author(s), 2017. http://dx.doi.org/10.1063/1.5012651.

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Astafieva, Marina M., Richard B. Hoover, Alexei Yu Rozanov, and Alexander B. Vrevskiy. "Fossil microorganisms in the Archaean." In SPIE Optics + Photonics, edited by Richard B. Hoover, Gilbert V. Levin, and Alexei Y. Rozanov. SPIE, 2006. http://dx.doi.org/10.1117/12.681660.

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Oshurkova, Viktoriia, Olga Troshina, Vladimir Trubitsyn, Yana Ryzhmanova, Olga Bochkareva, and Viktoria Shcherbakova. "Characterization of <em>Methanosarcina mazei</em> JL01 isolated from Holocene Arctic Permafrost and study of the archaeon cooperation with bacterium <em>Sphaerochaeta associata</em> GLS2<sup>T</sup>." In 1st International Electronic Conference on Microbiology. Basel, Switzerland: MDPI, 2020. http://dx.doi.org/10.3390/ecm2020-07116.

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Reports on the topic "Archaeon"

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Peak, M. J., J. G. Peak, F. J. Stevens, J. Blamey, X. Mai, Z. H. Zhou, and M. W. W. Adams. Characterization of the glycolytic enzyme enolase which is abundant in the hyperthermophilic archaeon, Pyrococcus furiosus. Office of Scientific and Technical Information (OSTI), December 1993. http://dx.doi.org/10.2172/10124321.

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Kim, Ung-Jin, and Melvin I. Simon. Final Report: Complete Sequencing of the 2.3Mbp Genome of the Hyperthermophilic Archaeon Pyrbaculum Aerophilum, January 1, 1998 - December 31, 1998. Office of Scientific and Technical Information (OSTI), December 1998. http://dx.doi.org/10.2172/765662.

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Trent, J. D., H. K. Kagawa, Takuro Yaoi, E. Olle, and N. J. Zaluzec. Chaperonin filaments: The archael cytoskeleton. Office of Scientific and Technical Information (OSTI), August 1997. http://dx.doi.org/10.2172/510354.

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Ernenwein, Eileen, Michael L. Hargrave, Jackson Cothren, and George Avery. Streamlined Archaeo-geophysical Data Processing and Integration for DoD Field Use. Fort Belvoir, VA: Defense Technical Information Center, April 2012. http://dx.doi.org/10.21236/ada571820.

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Trent, J. D., H. K. Kagawa, and N. J. Zaluzec. Chaperonin polymers in archaea: The cytoskeleton of prokaryotes? Office of Scientific and Technical Information (OSTI), July 1997. http://dx.doi.org/10.2172/505321.

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Elkins, James G., Victor Kunin, Iain Anderson, Kerrie Barry, Eugene Goltsman, Alla Lapidus, Brian Hedlund, et al. The Korarchaeota: Archaeal orphans representing an ancestral lineage of life. Office of Scientific and Technical Information (OSTI), May 2007. http://dx.doi.org/10.2172/960397.

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Charles J. Daniels. The Role of Multiple Transcription Factors In Archaeal Gene Expression. Office of Scientific and Technical Information (OSTI), September 2008. http://dx.doi.org/10.2172/937513.

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Kelley, John. Expanding Metabolic Diversity of Two Archaeal Phyla: Nanoarchaeota and Korarchaeota. Portland State University Library, January 2000. http://dx.doi.org/10.15760/etd.5729.

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Kelly, R. M. Bioenergetic and physiological studies of hyperthermophilic archaea. Final report. Office of Scientific and Technical Information (OSTI), March 1999. http://dx.doi.org/10.2172/325744.

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El-Sayed, Najib M. A. High Throughput Technologies for Functional Analysis of Archael Genomics. Office of Scientific and Technical Information (OSTI), September 1998. http://dx.doi.org/10.2172/899965.

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