keyword
MENU ▼
Read by QxMD icon Read
search

Sulfolobus

keyword
https://www.readbyqxmd.com/read/28794325/labeling-of-cytoskeletal-proteins-in-living-cells-using-biotin-ligase-carrying-a-fluorescent-protein
#1
Sairi Nishi, Chihiro Yamamoto, Sawako Yoneda, Shinji Sueda
Labeling with fluorescent proteins is now widely exploited for elucidating the functions and roles of target proteins in living cells. Previously, we developed a protein labeling method by combining a fluorescent protein with a biotinylation reaction from archaeon Sulfolobus tokodaii. Biotinylation from S. tokodaii has a unique property that biotin protein ligase (BPL) forms a stable complex with its biotinylated substrate protein (BCCP). By taking advantage of this unique property, a target protein carrying BCCP in living cells can be labeled through biotinylation with BPL carrying a fluorescent protein...
2017: Analytical Sciences: the International Journal of the Japan Society for Analytical Chemistry
https://www.readbyqxmd.com/read/28765217/rip-seq-suggests-translational-regulation-by-l7ae-in-archaea
#2
Michael Daume, Michael Uhl, Rolf Backofen, Lennart Randau
L7Ae is a universal archaeal protein that recognizes and stabilizes kink-turn (k-turn) motifs in RNA substrates. These structural motifs are widespread in nature and are found in many functional RNA species, including ribosomal RNAs. Synthetic biology approaches utilize L7Ae/k-turn interactions to control gene expression in eukaryotes. Here, we present results of comprehensive RNA immunoprecipitation sequencing (RIP-Seq) analysis of genomically tagged L7Ae from the hyperthermophilic archaeon Sulfolobus acidocaldarius A large set of interacting noncoding RNAs was identified...
August 1, 2017: MBio
https://www.readbyqxmd.com/read/28718834/dna-interacting-characteristics-of-the-archaeal-rudiviral-protein-sirv2_gp1
#3
Eveline Peeters, Maarten Boon, Clare Rollie, Ronnie G Willaert, Marleen Voet, Malcolm F White, David Prangishvili, Rob Lavigne, Tessa E F Quax
Whereas the infection cycles of many bacterial and eukaryotic viruses have been characterized in detail, those of archaeal viruses remain largely unexplored. Recently, studies on a few model archaeal viruses such as SIRV2 (Sulfolobus islandicus rod-shaped virus) have revealed an unusual lysis mechanism that involves the formation of pyramidal egress structures on the host cell surface. To expand understanding of the infection cycle of SIRV2, we aimed to functionally characterize gp1, which is a SIRV2 gene with unknown function...
July 18, 2017: Viruses
https://www.readbyqxmd.com/read/28710489/kinetic-insights-into-the-temperature-dependence-of-dna-strand-cleavage-and-religation-by-topoisomerase-iii-from-the-hyperthermophile-sulfolobus-solfataricus
#4
Junhua Zhang, Bailong Pan, Zhimeng Li, Xin Sheng Zhao, Li Huang
All cellular organisms encode type IA topoisomerases which catalyze DNA topological changes essential for DNA transactions. However, the kinetics of the reaction catalyzed by these enzymes remains poorly characterized. Here we measured the rapid kinetics of template binding, cleavage and religation by Sso topo III, a type IA topoisomerase from the hyperthermophilic archaeon Sulfolobus solfataricus, by using a novel FRET/PIFE-based method in a stopped-flow spectrometer. We show that Sso topo III bound the template rapidly, and the rate of binding was 2-3 orders of magnitudes higher than that of template cleavage at 25 °C...
July 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28710267/increased-processivity-misincorporation-and-nucleotide-incorporation-efficiency-in-sulfolobus-solfataricus-dpo4-thumb-domain-mutations
#5
Li Wang, Chenchen Liang, Jing Wu, Liming Liu, Keith E J Tyo
The present study aimed to increase the processivity of Sulfolobus solfataricus DNA polymerase Dpo4. Protein engineering and bioinformatics were used to compile a library of potential Dpo4 mutation sites. Ten potential mutants were identified and constructed. A primer extension assay was used to evaluate the processivity of Dpo4 mutants. Thumb (A181D) and finger (E63K) domain mutants showed a processivity of 20 and 19 nucleotides (nt), respectively. A little finger domain mutant (I248Y) exhibited a processivity of 17 nt, only 1 nt more than wild-type Dpo4...
July 14, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28707598/protein-tagging-destruction-and-infection
#6
Chetana Bhaskarla, Manoj Bhosale, Pip Banerjee, Nagasuma Chandra, Dipankar Nandi
Cells possess protein quality control mechanisms to maintain proper cellular homeostasis. In eukaryotes, the roles of the ubiquitination and proteasome-mediated degradation of cellular proteins is well established. Recent studies have elucidated protein tagging mechanisms in prokaryotes, involving transfer messenger RNA (tmRNA) and pupylation. In this review, newer insights and bioinformatics analysis of two distinct bacterial protein tagging machineries are discussed. The machinery for tmRNA-mediated tagging is present in several eubacterial representatives, e...
July 13, 2017: Current Protein & Peptide Science
https://www.readbyqxmd.com/read/28692669/systems-biology-of-the-modified-branched-entner-doudoroff-pathway-in-sulfolobus-solfataricus
#7
Ana Sofia Figueiredo, Theresa Kouril, Dominik Esser, Patrick Haferkamp, Patricia Wieloch, Dietmar Schomburg, Peter Ruoff, Bettina Siebers, Jörg Schaber
Sulfolobus solfataricus is a thermoacidophilic Archaeon that thrives in terrestrial hot springs (solfatares) with optimal growth at 80°C and pH 2-4. It catabolizes specific carbon sources, such as D-glucose, to pyruvate via the modified Entner-Doudoroff (ED) pathway. This pathway has two parallel branches, the semi-phosphorylative and the non-phosphorylative. However, the strategy of S.solfataricus to endure in such an extreme environment in terms of robustness and adaptation is not yet completely understood...
2017: PloS One
https://www.readbyqxmd.com/read/28689401/hole-hopping-through-tryptophan-in-cytochrome-p450
#8
Maraia E Ener, Harry B Gray, Jay R Winkler
Electron-transfer kinetics have been measured in four conjugates of cytochrome P450 with surface-bound Ru-photosensitizers. The conjugates are constructed with enzymes from Bacillus megaterium (CYP102A1) and Sulfolobus acidocaldarius (CYP119). A W96 residue lies in the path between Ru and the heme in CYP102A1, whereas H76 is present at the analogous location in CYP119. Two additional conjugates have been prepared with (CYP102A1)W96H and (CYP119)H76W mutant enzymes. Heme oxidation by photochemically generated Ru(3+) leads to P450 compound II formation when a tryptophan residue is in the path between Ru and the heme; no heme oxidation is observed when histidine occupies this position...
July 18, 2017: Biochemistry
https://www.readbyqxmd.com/read/28681456/the-extraordinary-thermal-stability-of-esta-from-s-islandicus-is-independent-of-post-translational-modifications
#9
Daniel Stiefler-Jensen, Troels Schwarz-Linnet, Casper de Lichtenberg, Tam T T N Nguyen, Kasper D Rand, Li Huang, Qunxin She, Kaare Teilum
Enzymes from thermophilic and hyper-thermophilic organisms have an intrinsic high stability. Understanding the mechanisms behind their high stability will be important knowledge for the engineering of novel enzymes with high stability. Lysine methylation of proteins is prevalent in Sulfolobus, a genus of hyperthermophilic and acidophilic archaea. Both unspecific and temperature dependent lysine methylations are seen, but the significance of this posttranslational modification has not been investigated. Here we test the effect of eliminating in vivo lysine methylation on the stability of an esterase (EstA)...
July 6, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28655184/characterization-of-a-coupled-dna-replication-and-translesion-synthesis-polymerase-supraholoenzyme-from-archaea
#10
Matthew T Cranford, Aurea M Chu, Joshua K Baguley, Robert J Bauer, Michael A Trakselis
The ability of the replisome to seamlessly coordinate both high fidelity and translesion DNA synthesis requires a means to regulate recruitment and binding of enzymes from solution. Co-occupancy of multiple DNA polymerases within the replisome has been observed primarily in bacteria and is regulated by posttranslational modifications in eukaryotes, and both cases are coordinated by the processivity clamp. Because of the heterotrimeric nature of the PCNA clamp in some archaea, there is potential to occupy and regulate specific polymerases at defined subunits...
June 26, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28647366/crystal-structure-of-the-crenarchaeal-exoiii-ap-endonuclease-sisexoiii-reveals-a-conserved-disulfide-bond-endowing-the-protein-with-thermostability
#11
Zhou Yan, Zenglin Yuan, Jinfeng Ni, Lichuan Gu, Yulong Shen
AP endonuclease recognizes and cleaves apurinic/apyrimidinic (AP) sites and plays a critical role in base excision repair. Many ExoIII and EndoIV family AP endonucleases have been characterized both biochemically and structurally in Eukaryote and Bacteria. However, relatively fewer have been studied in Euryarchaeota and there is no such report on an AP endonuclease from Crenarchaeota. Here we report, for the first time, the crystal structure of a crenarchaeal ExoIII AP endonuclease, SisExoIII, from Sulfolobus islandicus REY15A...
August 26, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28640207/reverse-gyrase-functions-in-genome-integrity-maintenance-by-protecting-dna-breaks-in-vivo
#12
Wenyuan Han, Xu Feng, Qunxin She
Reverse gyrase introduces positive supercoils to circular DNA and is implicated in genome stability maintenance in thermophiles. The extremely thermophilic crenarchaeon Sulfolobus encodes two reverse gyrase proteins, TopR1 (topoisomerase reverse gyrase 1) and TopR2, whose functions in thermophilic life remain to be demonstrated. Here, we investigated the roles of TopR1 in genome stability maintenance in S. islandicus in response to the treatment of methyl methanesulfonate (MMS), a DNA alkylation agent. Lethal MMS treatment induced two successive events: massive chromosomal DNA backbone breakage and subsequent DNA degradation...
June 22, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28636911/direct-conversion-of-an-enzyme-from-native-like-to-amyloid-like-aggregates-within-inclusion-bodies
#13
Francesco Elia, Francesca Cantini, Fabrizio Chiti, Christopher Martin Dobson, Francesco Bemporad
The acylphosphatase from Sulfolobus solfataricus (Sso AcP) is a globular protein able to aggregate in vitro from a native-like conformational ensemble without the need for a transition across the major unfolding energy barrier. This process leads to the formation of assemblies in which the protein retains its native-like structure, which subsequently convert into amyloid-like aggregates. Here, we investigate the mechanism by which Sso AcP aggregates in vivo to form bacterial inclusion bodies after expression in E...
June 20, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28633403/structured-populations-of-sulfolobus-acidocaldarius-with-susceptibility-to-mobile-genetic-elements
#14
Rika E Anderson, Angela Kouris, Christopher H Seward, Kate M Campbell, Rachel J Whitaker
The impact of a structured environment on genome evolution can be determined through comparative population genomics of species that live in the same habitat. Recent work comparing three genome sequences of Sulfolobus acidocaldarius suggested that highly structured, extreme, hot spring environments do not limit dispersal of this thermoacidophile, in contrast to other co-occurring Sulfolobus species. Instead, a high level of conservation among these three S. acidocaldarius genomes was hypothesized to result from rapid, global-scale dispersal promoted by low susceptibility to viruses that sets S...
June 14, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28630130/how-a-genetically-stable-extremophile-evolves-modes-of-genome-diversification-in-the-archaeon-sulfolobus-acidocaldarius
#15
Dominic Mao, Dennis W Grogan
In order to analyze in molecular terms how Sulfolobus genomes diverge, damage-induced mutations and natural polymorphisms (PMs) were identified in laboratory constructs and wild-type isolates, respectively, of Sulfolobus acidocaldarius Among wild-type isolates drawn from one local population, pairwise nucleotide divergence averaged 4 × 10(-6), which is about 0.15% of the corresponding divergence reported for Sulfolobus islandicus The most variable features of wild-type S. acidocaldarius genomes were homopolymer (mononucleotide) tracts and longer tandem repeats, consistent with the spontaneous mutations that occur under laboratory conditions...
September 1, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28628237/wing-phosphorylation-is-a-major-functional-determinant-of-the-lrs14-type-biofilm-and-motility-regulator-abfr1-in-sulfolobus-acidocaldarius
#16
Lingling Li, Ankan Banerjee, Lisa Franziska Bischof, Hassan Ramadan Maklad, Lena Hoffmann, Anna-Lena Henche, Fabian Veliz, Wolfgang Bildl, Uwe Schulte, Alvaro Orell, Lars-Oliver Essen, Eveline Peeters, Sonja-Verena Albers
In response to a variety of environmental cues, prokaryotes can switch between a motile and a sessile, biofilm-forming mode of growth. The regulatory mechanisms and signaling pathways underlying this switch are largely unknown in archaea but involve small winged helix-turn-helix DNA-binding proteins of the archaea-specific Lrs14 family. Here, we study the Lrs14 member AbfR1 of Sulfolobus acidocaldarius. Small-angle X-ray scattering data are presented, which are consistent with a model of dimeric AbfR1 in which dimerization occurs via an antiparallel coiled coil as suggested by homology modeling...
June 19, 2017: Molecular Microbiology
https://www.readbyqxmd.com/read/28625421/insights-into-the-anticancer-properties-of-the-first-antimicrobial-peptide-from-archaea
#17
Rosa Gaglione, Luciano Pirone, Biancamaria Farina, Salvatore Fusco, Giovanni Smaldone, Martina Aulitto, Eliana Dell'Olmo, Emanuela Roscetto, Annarita Del Gatto, Roberto Fattorusso, Eugenio Notomista, Laura Zaccaro, Angela Arciello, Emilia Pedone, Patrizia Contursi
BACKGROUND: The peptide VLL-28, identified in the sequence of an archaeal protein, the transcription factor Stf76 from Sulfolobus islandicus, was previously identified and characterized as an antimicrobial peptide, possessing a broad-spectrum antibacterial activity. METHODS: Through a combined approach of NMR and Circular Dichroism spectroscopy, Dynamic Light Scattering, confocal microscopy and cell viability assays, the interaction of VLL-28 with the membranes of both parental and malignant cell lines has been characterized and peptide mechanism of action has been studied...
September 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28604696/a-front-face-sni-synthase-engineered-from-a-retaining-double-sn2-hydrolase
#18
Javier Iglesias-Fernández, Susan M Hancock, Seung Seo Lee, Maola Khan, Jo Kirkpatrick, Neil J Oldham, Katherine McAuley, Anthony Fordham-Skelton, Carme Rovira, Benjamin G Davis
SNi-like mechanisms, which involve front-face leaving group departure and nucleophile approach, have been observed experimentally and computationally in chemical and enzymatic substitution at α-glycosyl electrophiles. Since SNi-like, SN1 and SN2 substitution pathways can be energetically comparable, engineered switching could be feasible. Here, engineering of Sulfolobus solfataricus β-glycosidase, which originally catalyzed double SN2 substitution, changed its mode to SNi-like. Destruction of the first SN2 nucleophile through E387Y mutation created a β-stereoselective catalyst for glycoside synthesis from activated substrates, despite lacking a nucleophile...
June 12, 2017: Nature Chemical Biology
https://www.readbyqxmd.com/read/28557139/functional-assignment-of-multiple-escrt-iii-homologs-in-cell-division-and-budding-in-sulfolobus-islandicus
#19
Junfeng Liu, Renxia Gao, Chengtao Li, Jinfeng Ni, Zhaojie Yang, Qi Zhang, Haining Chen, Yulong Shen
The archaea Sulfolobus utilizes the ESCRT-III-based machinery for cell division. This machinery comprises three proteins: CdvA, Eukaryotic-like ESCRT-III and Vps4. In addition to ESCRT-III, Sulfolobus cells also encode three other ESCRT-III homologs termed ESCRT-III-1, -2 and -3. Herein, we show that ESCRT-III-1 and -2 in S. islandicus REY15A are localized at midcell between segregating chromosomes, indicating that both are involved in cell division. Genetic analysis reveals that escrt-III-2 is indispensable for cell viability and cells with reduced overall level of ESCRT-III-1 exhibit growth retardation and cytokinesis defect with chain-like cell morphology...
May 29, 2017: Molecular Microbiology
https://www.readbyqxmd.com/read/28534836/differentiation-and-structure-in-sulfolobus-islandicus-rod-shaped-virus-populations
#20
Maria A Bautista, Jesse A Black, Nicholas D Youngblut, Rachel J Whitaker
In the past decade, molecular surveys of viral diversity have revealed that viruses are the most diverse and abundant biological entities on Earth. In culture, however, most viral isolates that infect microbes are represented by a few variants isolated on type strains, limiting our ability to study how natural variation affects virus-host interactions in the laboratory. We screened a set of 137 hot spring samples for viruses that infect a geographically diverse panel of the hyperthemophilic crenarchaeon Sulfolobus islandicus...
May 19, 2017: Viruses
keyword
keyword
25184
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"