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https://www.readbyqxmd.com/read/28431535/ion-and-water-binding-sites-inside-an-occluded-hourglass-pore-of-a-trimeric-intracellular-cation-tric-channel
#1
Xiaomin Ou, Jianli Guo, Longfei Wang, Hanting Yang, Xiuying Liu, Jianyuan Sun, Zhenfeng Liu
BACKGROUND: Trimeric intracellular cation (TRIC) channels are crucial for Ca(2+) handling in eukaryotes and are involved in K(+) uptake in prokaryotes. Recent studies on the representative members of eukaryotic and prokaryotic TRIC channels demonstrated that they form homotrimeric units with the ion-conducting pores contained within each individual monomer. RESULTS: Here we report detailed insights into the ion- and water-binding sites inside the pore of a TRIC channel from Sulfolobus solfataricus (SsTRIC)...
April 22, 2017: BMC Biology
https://www.readbyqxmd.com/read/28425930/the-peculiar-glycolytic-pathway-in-hyperthermophylic-archaea-understanding-its-whims-by-experimentation-in-silico
#2
Yanfei Zhang, Theresa Kouril, Jacky L Snoep, Bettina Siebers, Matteo Barberis, Hans V Westerhoff
Mathematical models are key to systems biology where they typically describe the topology and dynamics of biological networks, listing biochemical entities and their relationships with one another. Some (hyper)thermophilic Archaea contain an enzyme, called non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase (GAPN), which catalyzes the direct oxidation of glyceraldehyde-3-phosphate to 3-phosphoglycerate omitting adenosine 5'-triphosphate (ATP) formation by substrate-level-phosphorylation via phosphoglycerate kinase...
April 20, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28424284/a-novel-type-of-polyhedral-viruses-infecting-hyperthermophilic-archaea
#3
Ying Liu, Sonoko Ishino, Yoshizumi Ishino, Gérard Pehau-Arnaudet, Mart Krupovic, David Prangishvili
Encapsidation of genetic material into polyhedral particles is one of the most common structural solutions employed by viruses infecting hosts in all three domains of life. Here, we describe a new virus of hyperthermophilic archaea, Sulfolobus polyhedral virus 1 (SPV1), which condenses its circular double-stranded DNA genome in a manner not previously observed for other known virus. The genome complexed with virion proteins is wound up sinusoidally into a spherical coil which is surrounded by an envelope and further encased by an outer polyhedral capsid apparently composed of the 20 kDa virion protein...
April 19, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28424282/formation-of-a-viral-replication-focus-in-sulfolobus-cells-infected-by-the-rudivirus-sirv2
#4
Laura Martínez-Alvarez, Ling Deng, Xu Peng
Viral factories are compartmentalized centres for viral replication and assembly in infected eukaryotic cells. Here, we report the formation of a replication focus by the prototypical archaeal virus SIRV2 in the model archaeon Sulfolobus. This rod-shaped virus belongs to the viral family rudiviridae, carrying linear dsDNA genomes, which are very common in geothermal environments. We demonstrate that SIRV2 DNA synthesis is confined to a focus near the periphery of infected cells. Moreover, viral and cellular replication proteins are recruited to, and concentrated in, the viral replication focus...
April 19, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28409846/an-in-vitro-synthetic-biology-platform-for-the-industrial-biomanufacturing-of-myo-inositol-from-starch
#5
Chun You, Ting Shi, Yunjie Li, Pingping Han, Xigui Zhou, Yi-Heng Percival Zhang
myo-Inositol (vitamin B8) is widely used in the drug, cosmetic, and food & feed industries. Here we present an in vitro non-fermentative enzymatic pathway that converts starch to inositol in one vessel. This in vitro pathway is comprised of four enzymes that operate without ATP or NAD(+) supplementation. All enzyme BioBricks are carefully selected from hyperthermophilic microorganisms, that is, alpha-glucan phosphorylase from Thermotoga maritima, phosphoglucomutase from Thermococcus kodakarensis, inositol 1-phosphate synthase from Archaeoglobus fulgidus, and Inositol monophosphatase from T...
April 14, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28402640/mutagenic-replication-of-n-2-deoxyguanosine-benzo-a-pyrene-adducts-by-escherichia-coli-dna-polymerase-i-and-sulfolobus-solfataricus-dna-polymerase-iv
#6
A S Prakasha Gowda, Jacek Krzeminski, Shantu Amin, Zucai Suo, Thomas E Spratt
Benzo[a]pyrene, a potent human carcinogen, is metabolized in vivo to a diol epoxide that reacts with the N(2)-position of guanine to produce N(2)-BP-dG adducts. These adducts are mutagenic causing G to T transversions. These adducts block replicative polymerases but can be bypassed by the Y-family translesion synthesis polymerases. The mechanisms by which mutagenic bypass occurs is not well-known. We have evaluated base pairing structures using atomic substitution of the dNTP with two stereoisomers, 2'-deoxy-N-[(7R,8S,9R,10S)-7,8,9,10-tetrahydro-7,8,9-trihydroxybenzo[a]pyren-10-yl]guanosine and 2'-deoxy-N-[(7S,8R,9S,10R)-7,8,9,10-tetrahydro-7,8,9-trihydroxybenzo[a]pyren-10-yl]guanosine...
April 19, 2017: Chemical Research in Toxicology
https://www.readbyqxmd.com/read/28395138/formation-of-s-2-n-6-deoxyadenosinyl-ethyl-glutathione-in-dna-and-replication-past-the-adduct-by-translesion-dna-polymerases
#7
Carl A Sedgeman, Yan Su, F Peter Guengerich
1,2-Dibromoethane (DBE, ethylene dibromide) is a potent carcinogen due at least in part to its DNA cross-linking effects. DBE cross-links glutathione (GSH) to DNA, notably to sites on 2'-deoxyadenosine and 2'-deoxyguanosine ( Cmarik , J. L. , et al. ( 1991 ) J. Biol. Chem. 267 , 6672 - 6679 ). Adduction at the N6 position of 2'-deoxyadenosine (dA) had not been detected, but this is a site for the linkage of O(6)-alkylguanine DNA alkyltransferase ( Chowdhury , G. , et al. ( 2013 ) Angew. Chem. Int. Ed. 52 , 12879 - 12882 )...
April 14, 2017: Chemical Research in Toxicology
https://www.readbyqxmd.com/read/28334892/inhibition-of-homologous-phosphorolytic-ribonucleases-by-citrate-may-represent-an-evolutionarily-conserved-communicative-link-between-rna-degradation-and-central-metabolism
#8
Carlanne M Stone, Louise E Butt, Joshua C Bufton, Daniel C Lourenco, Darren M Gowers, Andrew R Pickford, Paul A Cox, Helen A Vincent, Anastasia J Callaghan
Ribonucleases play essential roles in all aspects of RNA metabolism, including the coordination of post-transcriptional gene regulation that allows organisms to respond to internal changes and environmental stimuli. However, as inherently destructive enzymes, their activity must be carefully controlled. Recent research exemplifies the repertoire of regulatory strategies employed by ribonucleases. The activity of the phosphorolytic exoribonuclease, polynucleotide phosphorylase (PNPase), has previously been shown to be modulated by the Krebs cycle metabolite citrate in Escherichia coli...
March 3, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28321616/identification-of-an-archaeal-maltooligosyltrehalose-trehalohydrolase-encoded-by-an-interrupted-gene
#9
Ye Zhou, Guiqiu Xie, Lin Chang, Yan Wang, Renjun Gao
Complete genome analysis of the thermoacidophilic Archaeon Sulfolobus tokodaii strain 7 revealed two open reading frames (ORF), namely, ST0926 and ST0927. These ORFs are interrupted by two putative insertions and encode for the N- and C-terminal fragments, respectively, of a putative Sulfolobus sp. maltooligosyltrehalose trehalohydrolase (StMTHase). Two specific deletion mutations, designed on the basis of sequence alignments of the adjacent ORFs and the published Sulfolobus sp. MTHases, allowed soluble expression in Escherichia coli of an active acidic and thermophilic enzyme...
March 21, 2017: Extremophiles: Life Under Extreme Conditions
https://www.readbyqxmd.com/read/28301812/identification-of-a-potential-proton-donor-to-the-linking-oxygen-atom-in-a-three-metal-ion-assisted-catalysis-pathway-catalyzed-by-fructose-1-6-bisphosphatase
#10
Jinhu Wang, Zhiguo Wang, Baoping Ling, Nan Cao, Wen Wang
In this paper, the dephosphorylation mechanism of FBP to F6P catalyzed by the Fructose-1, 6-bisphosphatase (St-Fbp) from Sulfolobus tokodaii was studied using quantum mechanical/molecular mechanical (QM/MM) approach. Based on the experimental results, total five possible catalytic mechanisms (path1-path4') were designed. The most possible dephosphorylation reaction follows a two-step mechanism (path2): a dephosphorylation process (with D12 being an base of W6 and residue K133 being the proton donor of the linking FBP:O4) and a proton exchange process (between K133 and the water W1)...
May 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28291751/the-hyperthermophilic-cystathionine-%C3%AE-synthase-from-the-aerobic-crenarchaeon-sulfolobus-tokodaii-expression-purification-crystallization-and-structural-insights
#11
Dan Sato, Tomoo Shiba, Sae Mizuno, Ayaka Kawamura, Shoko Hanada, Tetsuya Yamada, Mai Shinozaki, Masahiko Yanagitani, Takashi Tamura, Kenji Inagaki, Shigeharu Harada
Cystathionine γ-synthase (CGS; EC 2.5.1.48), a pyridoxal 5'-phosphate (PLP)-dependent enzyme, catalyzes the formation of cystathionine from an L-homoserine derivative and L-cysteine in the first step of the transsulfuration pathway. Recombinant CGS from the thermoacidophilic archaeon Sulfolobus tokodaii (StCGS) was overexpressed in Escherichia coli and purified to homogeneity by heat treatment followed by hydroxyapatite and gel-filtration column chromatography. The purified enzyme shows higher enzymatic activity at 353 K under basic pH conditions compared with that at 293 K...
March 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28286499/toward-time-resolved-analysis-of-rna-metabolism-in-archaea-using-4-thiouracil
#12
Robert Knüppel, Corinna Kuttenberger, Sébastien Ferreira-Cerca
Archaea are widespread organisms colonizing almost every habitat on Earth. However, the molecular biology of archaea still remains relatively uncharacterized. RNA metabolism is a central cellular process, which has been extensively analyzed in both bacteria and eukarya. In contrast, analysis of RNA metabolism dynamic in archaea has been limited to date. To facilitate analysis of the RNA metabolism dynamic at a system-wide scale in archaea, we have established non-radioactive pulse labeling of RNA, using the nucleotide analog 4-thiouracil (4TU) in two commonly used model archaea: the halophile Euryarchaeota Haloferax volcanii, and the thermo-acidophile Crenarchaeota Sulfolobus acidocaldarius...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28276174/sulfolobus-islandicus-meta-populations-in-yellowstone-national-park-hot-springs
#13
Kate M Campbell, Angela Kouris, Whitney England, Rika E Anderson, R Blaine McCleskey, D Kirk Nordstrom, Rachel J Whitaker
Abiotic and biotic forces shape the structure and evolution of microbial populations. We investigated forces that shape the spatial and temporal population structure of Sulfolobus islandicus by comparing geochemical and molecular analysis from seven hot springs in five regions sampled over three years in Yellowstone National Park. Through deep amplicon sequencing, we uncovered 148 unique alleles at two loci whose relative frequency provides clear evidence for independent populations in different hot springs...
March 9, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28267954/-decontamination-of-organophosphorus-compounds-towards-new-alternatives
#14
REVIEW
L Poirier, P Jacquet, M Elias, D Daudé, E Chabrière
Organophosphorus coumpounds (OP) are toxic chemicals mainly used for agricultural purpose such as insecticides and were also developed and used as warfare nerve agents. OP are inhibitors of acetylcholinesterase, a key enzyme involved in the regulation of the central nervous system. Chemical, physical and biological approaches have been considered to decontaminate OP. This review summarizes the current and emerging strategies that are investigated to tackle this issue with a special emphasis on enzymatic remediation methods...
March 3, 2017: Annales Pharmaceutiques Françaises
https://www.readbyqxmd.com/read/28265464/total-chemical-synthesis-of-a-thermostable-enzyme-capable-of-polymerase-chain-reaction
#15
Weiliang Xu, Wenjun Jiang, Jiaxing Wang, Linping Yu, Ji Chen, Xianyu Liu, Lei Liu, Ting F Zhu
Polymerase chain reaction (PCR) has been a defining tool in modern biology. Towards realizing mirror-image PCR, we have designed and chemically synthesized a mutant version of the 352-residue thermostable Sulfolobus solfataricus P2 DNA polymerase IV with l-amino acids and tested its PCR activity biochemically. To the best of our knowledge, this enzyme is the largest chemically synthesized protein reported to date. We show that with optimization of PCR conditions, the fully synthetic polymerase is capable of amplifying template sequences of up to 1...
2017: Cell Discovery
https://www.readbyqxmd.com/read/28251462/genetic-technologies-for-extremely-thermophilic-microorganisms-of-sulfolobus-the-only-genetically-tractable-genus-of-crenarchaea
#16
REVIEW
Nan Peng, Wenyuan Han, Yingjun Li, Yunxiang Liang, Qunxin She
Archaea represents the third domain of life, with the information-processing machineries more closely resembling those of eukaryotes than the machineries of the bacterial counterparts but sharing metabolic pathways with organisms of Bacteria, the sister prokaryotic phylum. Archaeal organisms also possess unique features as revealed by genomics and genome comparisons and by biochemical characterization of prominent enzymes. Nevertheless, diverse genetic tools are required for in vivo experiments to verify these interesting discoveries...
February 27, 2017: Science China. Life Sciences
https://www.readbyqxmd.com/read/28239294/transfection-studies-with-colloidal-systems-containing-highly-purified-bipolar-tetraether-lipids-from-sulfolobus-acidocaldarius
#17
Konrad H Engelhardt, Shashank Reddy Pinnapireddy, Elias Baghdan, Jarmila Jedelská, Udo Bakowsky
Lipid vectors are commonly used to facilitate the transfer of nucleic acids into mammalian cells. In this study, two fractions of tetraether lipids from the archaea Sulfolobus acidocaldarius were extracted and purified using different methods. The purified lipid fractions polar lipid fraction E (PLFE) and hydrolysed glycerol-dialkyl-nonitol tetraether (hGDNT) differ in their structures, charge, size, and miscibility from conventional lipids. Liposomes were prepared by mixing tetraether lipids with cholesterol (CH) and 1,2-dioleoyl-3-trimethylammonium-propane (DOTAP) resulting in stable vectors for gene delivery...
2017: Archaea: An International Microbiological Journal
https://www.readbyqxmd.com/read/28238763/structure-and-function-of-a-novel-atpase-that-interacts-with-holliday-junction-resolvase-hjc-and-promotes-branch-migration
#18
Binyuan Zhai, Kevin DuPrez, Tzanko I Doukov, Huan Li, Mengting Huang, Guijun Shang, Jinfeng Ni, Lichuan Gu, Yulong Shen, Li Fan
Holliday junction (HJ) is a hallmark intermediate in DNA recombination and must be processed by dissolution (for double HJ) or resolution to ensure genome stability. Although HJ resolvases have been identified in all domains of life, there is a long-standing effort to search in prokaryotes and eukarya for proteins promoting HJ migration. Here, we report the structural and functional characterization of a novel ATPase, Sulfolobus islandicusPilT N-terminal-domain-containing ATPase (SisPINA), encoded by the gene adjacent to the resolvase Hjc coding gene...
February 24, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28148789/extreme-mutation-tolerance-nearly-half-of-the-archaeal-fusellovirus-ssv1-genes-are-not-required-for-virus-function-including-the-minor-capsid-protein-gene-vp3
#19
Eric A Iverson, David A Goodman, Madeline E Gorchels, Kenneth M Stedman
Viruses infecting the Archaea harbor a tremendous amount of genetic diversity. This is especially true for the spindle-shaped viruses of the family Fuselloviridae, where >90% of the viral genes do not have detectable homologs in public databases. This significantly limits our ability to elucidate the role of viral proteins in the infection cycle. To address this, we have developed genetic techniques to study the well-characterized fusellovirus Sulfolobus spindle-shaped virus 1 (SSV1) which infects Sulfolobus solfataricus in volcanic hot springs at 80°C and pH 3...
February 1, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28106786/sulfolobus-acidocaldarius-udg-can-remove-du-from-the-rna-backbone-insight-into-the-specific-recognition-of-uracil-linked-with-deoxyribose
#20
Gang-Shun Yi, Wei-Wei Wang, Wei-Guo Cao, Feng-Ping Wang, Xi-Peng Liu
Sulfolobus acidocaldarius encodes family 4 and 5 uracil-DNA glycosylase (UDG). Two recombinant S. acidocaldarius UDGs (SacUDG) were prepared and biochemically characterized using oligonucleotides carrying a deaminated base. Both SacUDGs can remove deoxyuracil (dU) base from both double-stranded DNA and single-stranded DNA. Interestingly, they can remove U linked with deoxyribose from single-stranded RNA backbone, suggesting that the riboses on the backbone have less effect on the recognition of dU and hydrolysis of the C-N glycosidic bond...
January 18, 2017: Genes
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