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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
#1
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
#2
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
#3
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)...
January 20, 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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
https://www.readbyqxmd.com/read/28092942/advances-in-structural-and-single-molecule-methods-for-investigating-dna-lesion-bypass-and-repair-polymerases
#14
Austin T Raper, Andrew J Reed, Varun V Gadkari, Zucai Suo
Innovative advances in X-ray crystallography and single-molecule biophysics have yielded unprecedented insight into the mechanisms of DNA lesion bypass and damage repair. Time-dependent X-ray crystallography has been successfully applied to view the bypass of 8-oxo-7,8-dihydro-2'-deoxyguanine (8-oxoG), a major oxidative DNA lesion, and the incorporation of the triphosphate form, 8-oxo-dGTP, catalyzed by human DNA polymerase β. Significant findings of these studies are highlighted here, and their contributions to the current mechanistic understanding of mutagenic translesion DNA synthesis (TLS) and base excision repair are discussed...
January 17, 2017: Chemical Research in Toxicology
https://www.readbyqxmd.com/read/28074318/boosted-large-scale-production-and-purification-of-a-thermostable-archaeal-phosphotriesterase-like-lactonase-for-organophosphate-decontamination
#15
Odile Francesca Restaino, Maria Giovanna Borzacchiello, Ilaria Scognamiglio, Elena Porzio, Giuseppe Manco, Luigi Fedele, Cinzia Donatiello, Mario De Rosa, Chiara Schiraldi
Thermostable phosphotriesterase-like lactonases (PLLs) from extremophile archaea, like SsoPox from Sulfolobus solfataricus, are attractive biotechnological tools with industrial applications as organophosphate decontaminants, but their manufacturing still remains an unresolved issue because of the high costs and the low production yields. In this paper, for the first time, an efficient biotechnological process for the production and purification of a recombinant, engineered PLL, SsoPox W263F, expressed in E...
January 11, 2017: Journal of Industrial Microbiology & Biotechnology
https://www.readbyqxmd.com/read/28074284/high-affinity-rna-binding-by-a-hyperthermophilic-single-stranded-dna-binding-protein
#16
Michael J Morten, Roland Gamsjaeger, Liza Cubeddu, Ruvini Kariawasam, Jose Peregrina, J Carlos Penedo, Malcolm F White
Single-stranded DNA-binding proteins (SSBs), including replication protein A (RPA) in eukaryotes, play a central role in DNA replication, recombination, and repair. SSBs utilise an oligonucleotide/oligosaccharide-binding (OB) fold domain to bind DNA, and typically oligomerise in solution to bring multiple OB fold domains together in the functional SSB. SSBs from hyperthermophilic crenarchaea, such as Sulfolobus solfataricus, have an unusual structure with a single OB fold coupled to a flexible C-terminal tail...
March 2017: Extremophiles: Life Under Extreme Conditions
https://www.readbyqxmd.com/read/28072418/microbial-community-dynamics-in-inferno-crater-lake-a-thermally-fluctuating-geothermal-spring
#17
Laura Ward, Michael W Taylor, Jean F Power, Bradley J Scott, Ian R McDonald, Matthew B Stott
Understanding how microbial communities respond and adjust to ecosystem perturbation is often difficult to interpret due to multiple and often simultaneous variations in observed conditions. In this research, we investigated the microbial community dynamics of Inferno Crater Lake, an acidic geothermal spring in New Zealand with a unique thermal cycle that varies between 30 and 80 °C over a period of 40-60 days. Using a combination of next-generation sequencing, geochemical analysis and quantitative PCR we found that the microbial community composition was predominantly chemolithotrophic and strongly associated with the thermal cycle...
January 10, 2017: ISME Journal
https://www.readbyqxmd.com/read/28068385/the-arginine-pairs-and-c-termini-of-the-sso7c4-from-sulfolobus-solfataricus-participate-in-binding-and-bending-dna
#18
Bo-Lin Lin, Chin-Yu Chen, Chun-Hsiang Huang, Tzu-Ping Ko, Cheng-Hung Chiang, Kuan-Fu Lin, Yuan-Chih Chang, Po-Yen Lin, Hui-Hsu Gavin Tsai, Andrew H-J Wang
The Sso7c4 from Sulfolobus solfataricus forms a dimer, which is believed to function as a chromosomal protein involved in genomic DNA compaction and gene regulation. Here, we present the crystal structure of wild-type Sso7c4 at a high resolution of 1.63 Å, showing that the two basic C-termini are disordered. Based on the fluorescence polarization (FP) binding assay, two arginine pairs, R11/R22' and R11'/R22, on the top surface participate in binding DNA. As shown in electron microscopy (EM) images, wild-type Sso7c4 compacts DNA through bridging and bending interactions, whereas the binding of C-terminally truncated proteins rigidifies and opens DNA molecules, and no compaction of the DNA occurs...
2017: PloS One
https://www.readbyqxmd.com/read/28052139/application-of-stochastic-labeling-with-random-sequence-barcodes-for-simultaneous-quantification-and-sequencing-of-environmental-16s-rrna-genes
#19
Tatsuhiko Hoshino, Fumio Inagaki
Next-generation sequencing (NGS) is a powerful tool for analyzing environmental DNA and provides the comprehensive molecular view of microbial communities. For obtaining the copy number of particular sequences in the NGS library, however, additional quantitative analysis as quantitative PCR (qPCR) or digital PCR (dPCR) is required. Furthermore, number of sequences in a sequence library does not always reflect the original copy number of a target gene because of biases caused by PCR amplification, making it difficult to convert the proportion of particular sequences in the NGS library to the copy number using the mass of input DNA...
2017: PloS One
https://www.readbyqxmd.com/read/28008327/in-situ-spectroscopy-reveals-that-microorganisms-in-different-phyla-use-different-electron-transfer-biomolecules-to-respire-aerobically-on-soluble-iron
#20
Robert C Blake Ii, Micah D Anthony, Jordan D Bates, Theresa Hudson, Kamilya M Hunter, Brionna J King, Bria L Landry, Megan L Lewis, Richard G Painter
Absorbance spectra were collected on 12 different live microorganisms, representing six phyla, as they respired aerobically on soluble iron at pH 1.5. A novel integrating cavity absorption meter was employed that permitted accurate absorbance measurements in turbid suspensions that scattered light. Illumination of each microorganism yielded a characteristic spectrum of electrochemically reduced colored prosthetic groups. A total of six different patterns of reduced-minus-oxidized difference spectra were observed...
2016: Frontiers in Microbiology
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