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https://www.readbyqxmd.com/read/28934494/derivatives-of-bst-like-gss-polymerase-with-improved-processivity-and-inhibitor-tolerance
#1
Igor P Oscorbin, Ekaterina A Belousova, Ulyana A Boyarskikh, Aleksandr I Zakabunin, Evgeny A Khrapov, Maksim L Filipenko
At the moment, one of the actual trends in medical diagnostics is a development of methods for practical applications such as point-of-care testing, POCT or research tools, for example, whole genome amplification, WGA. All the techniques are based on using of specific DNA polymerases having strand displacement activity, high synthetic processivity, fidelity and, most significantly, tolerance to contaminants, appearing from analysed biological samples or collected under purification procedures. Here, we have designed a set of fusion enzymes based on catalytic domain of DNA polymerase I from Geobacillus sp...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28911114/coupling-transcriptional-activation-of-crispr-cas-system-and-dna-repair-genes-by-csa3a-in-sulfolobus-islandicus
#2
Tao Liu, Zhenzhen Liu, Qing Ye, Saifu Pan, Xiaodi Wang, Yingjun Li, Wenfang Peng, Yunxiang Liang, Qunxin She, Nan Peng
CRISPR-Cas system provides the adaptive immunity against invading genetic elements in prokaryotes. Recently, we demonstrated that Csa3a regulator mediates spacer acquisition in Sulfolobus islandicus by activating the expression of Type I-A adaptation cas genes. However, links between the activation of spacer adaptation and CRISPR transcription/processing, and the requirement for DNA repair genes during spacer acquisition remained poorly understood. Here, we demonstrated that de novo spacer acquisition required Csa1, Cas1, Cas2 and Cas4 proteins of the Sulfolobus Type I-A system...
September 6, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28911098/the-smap2-rna-binding-motif-in-the-3-utr-affects-mrna-stability-in-the-crenarchaeum-sulfolobus-solfataricus
#3
Birgit Märtens, Kundan Sharma, Henning Urlaub, Udo Bläsi
Sm and Sm-like proteins represent an evolutionarily conserved family with key roles in RNA metabolism in Pro- and Eukaryotes. In this study, a collection of 53 mRNAs that co-purified with Sulfolobus solfataricus (Sso) SmAP2 were surveyed for a specific RNA binding motif (RBM). SmAP2 was shown to bind with high affinity to the deduced consensus RNA binding motif (SmAP2-cRBM) in vitro. Residues in SmAP2 interacting with the SmAP2-cRBM were mapped by UV-induced crosslinking in combination with mass-spectrometry, and verified by mutational analyses...
September 6, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28891224/smv1-an-extremely-stable-thermophilic-virus-platform-for-nanoparticle-trafficking-in-the-mammalian-gi-tract
#4
Kristine B Uldahl, Seth T Walk, Stephen C Olshefsky, Mark J Young, Xu Peng
AIMS: analysis of the stability and safety of Sulfolobus monocaudavirus 1 (SMV1) during passage through the mammalian GI tract. METHODS AND RESULTS: A major challenge of using nano-vectors to target gut microbiome is their survival during passage through the extremely acidic and proteolytic environment of the mammalian GI tract. Here we investigated the thermo-acidophilic archaeal virus SMV1 as a candidate therapeutic nano-vector for the distal mammalian GI tract microbiome...
September 11, 2017: Journal of Applied Microbiology
https://www.readbyqxmd.com/read/28881299/photo-responsive-tetraether-lipids-based-vesicles-for-prophyrin-mediated-vascular-targeting-and-direct-phototherapy
#5
Gihan Mahmoud, Jarmila Jedelská, Boris Strehlow, Samia Omar, Marc Schneider, Udo Bakowsky
Tetraether lipids (TELs) derived from the thermoacidophilic archaeon Sulfolobus acidocaldarius are dominated by polyisoprenoid skeleton. The unique molecular stability of TELs is attributed to the presence of cyclopentane rings, methyl side groups and sugar residues that create extensive hydrogen bond network. In addition, the presence of ether linkages and the lacking of double bonds make them an epitome candidate for photodynamic therapy (PDT). A subtle blend of formulation design to trigger efficient photo responses of protoporphyrin IX (PpIX) exploiting TELs was developed...
August 30, 2017: Colloids and Surfaces. B, Biointerfaces
https://www.readbyqxmd.com/read/28855893/nqo-induced-dna-less-cell-formation-is-associated-with-chromatin-protein-degradation-and-dependent-on-a0a1-atpase-in-sulfolobus
#6
Wenyuan Han, Yanqun Xu, Xu Feng, Yun X Liang, Li Huang, Yulong Shen, Qunxin She
To investigate DNA damage response in the model crenarchaeon Sulfolobus islandicus, four different DNA damage agents were tested for their effects on cell death of this archaeon, including UV irradiation, methyl methanesulfonate, cisplatin, and 4-nitroquinoline 1-oxide (NQO). Cell death featured with DNA-less cell formation was revealed in DNA damage treatment with each agent. Cellular responses upon NQO treatment were characterized in details, and following sequential events were revealed, including: a modest accumulation of G1/S phase cells, membrane depolarization, proteolytic degradation of chromatin proteins, and chromosomal DNA degradation...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28846925/interaction-of-extremophilic-archaeal-viruses-with-human-and-mouse-complement-system-and-viral-biodistribution-in-mice
#7
Linping Wu, Kristine Buch Uldahl, Fangfang Chen, Halli Benasutti, Deborah Logvinski, Vivian Vu, Nirmal K Banda, Xu Peng, Dmitri Simberg, Seyed Moein Moghimi
Archaeal viruses offer exceptional biophysical properties for modification and exploration of their potential in bionanotechnology, bioengineering and nanotherapeutic developments. However, the interaction of archaeal viruses with elements of the innate immune system has not been explored, which is a necessary prerequisite if their potential for biomedical applications to be realized. Here we show complement activation through lectin (via direct binding of MBL/MASPs) and alternative pathways by two extremophilic archaeal viruses (Sulfolobus monocaudavirus 1 and Sulfolobus spindle-shaped virus 2) in human serum...
October 2017: Molecular Immunology
https://www.readbyqxmd.com/read/28794325/labeling-of-cytoskeletal-proteins-in-living-cells-using-biotin-ligase-carrying-a-fluorescent-protein
#8
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
#9
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
#10
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
#11
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-mutants
#12
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...
September 15, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28707598/protein-tagging-destruction-and-infection
#13
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
#14
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
#15
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
#16
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 post-translational modification has not been investigated. Here, we test the effect of eliminating in vivo lysine methylation on the stability of an esterase (EstA)...
September 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
#17
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...
August 21, 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
#18
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
#19
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
#20
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
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