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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
#1
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
#2
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
#3
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
#4
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
#5
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...
January 10, 2017: Extremophiles: Life Under Extreme Conditions
https://www.readbyqxmd.com/read/28072418/microbial-community-dynamics-in-inferno-crater-lake-a-thermally-fluctuating-geothermal-spring
#6
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
#7
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
#8
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
#9
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
https://www.readbyqxmd.com/read/28003359/a-single-amino-acid-mutation-converts-r-5-diphosphomevalonate-decarboxylase-into-a-kinase
#10
Kento Motoyama, Hideaki Unno, Ai Hattori, Tomohiro Takaoka, Hiroshi Ishikita, Hiroshi Kawaide, Tohru Yoshimura, Hisashi Hemmi
The biosynthesis of isopentenyl diphosphate, a fundamental precursor for isoprenoids, via the mevalonate pathway is completed by diphosphomevalonate decarboxylase. This enzyme catalyzes the formation of isopentenyl diphosphate through the ATP-dependent phosphorylation of the 3-hydroxyl group of (R)-5-diphosphomevalonate followed by decarboxylation coupled with the elimination of the 3-phosphate group. In this reaction, a conserved aspartate residue has been proposed to be involved in the phosphorylation step as the general base catalyst that abstracts a proton from the 3-hydroxyl group...
February 10, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27986854/a-type-iii-b-crispr-cas-effector-complex-mediating-massive-target-dna-destruction
#11
Wenyuan Han, Yingjun Li, Ling Deng, Mingxia Feng, Wenfang Peng, Søren Hallstrøm, Jing Zhang, Nan Peng, Yun Xiang Liang, Malcolm F White, Qunxin She
The CRISPR (clustered regularly interspaced short palindromic repeats) system protects archaea and bacteria by eliminating nucleic acid invaders in a crRNA-guided manner. The Sulfolobus islandicus type III-B Cmr-α system targets invading nucleic acid at both RNA and DNA levels and DNA targeting relies on the directional transcription of the protospacer in vivo To gain further insight into the involved mechanism, we purified a native effector complex of III-B Cmr-α from S. islandicus and characterized it in vitro Cmr-α cleaved RNAs complementary to crRNA present in the complex and its ssDNA destruction activity was activated by target RNA...
December 15, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27980065/crispr-cas-type-i-a-cascade-complex-couples-viral-infection-surveillance-to-host-transcriptional-regulation-in-the-dependence-of-csa3b
#12
Fei He, Gisle Vestergaard, Wenfang Peng, Qunxin She, Xu Peng
CRISPR-Cas (clustered regularly interspaced short palindromic repeats and the associated genes) constitute adaptive immune systems in bacteria and archaea and they provide sequence specific immunity against foreign nucleic acids. CRISPR-Cas systems are activated by viral infection. However, little is known about how CRISPR-Cas systems are activated in response to viral infection or how their expression is controlled in the absence of viral infection. Here, we demonstrate that both the transcriptional regulator Csa3b, and the type I-A interference complex Cascade, are required to transcriptionally repress the interference gene cassette in the archaeon Sulfolobus Csa3b binds to two palindromic repeat sites in the promoter region of the cassette and facilitates binding of the Cascade to the promoter region...
December 15, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27965637/genome-sequencing-of-sulfolobus-sp-a20-from-costa-rica-and-comparative-analyses-of-the-putative-pathways-of-carbon-nitrogen-and-sulfur-metabolism-in-various-sulfolobus-strains
#13
Xin Dai, Haina Wang, Zhenfeng Zhang, Kuan Li, Xiaoling Zhang, Marielos Mora-López, Chengying Jiang, Chang Liu, Li Wang, Yaxin Zhu, Walter Hernández-Ascencio, Zhiyang Dong, Li Huang
The genome of Sulfolobus sp. A20 isolated from a hot spring in Costa Rica was sequenced. This circular genome of the strain is 2,688,317 bp in size and 34.8% in G+C content, and contains 2591 open reading frames (ORFs). Strain A20 shares ~95.6% identity at the 16S rRNA gene sequence level and <30% DNA-DNA hybridization (DDH) values with the most closely related known Sulfolobus species (i.e., Sulfolobus islandicus and Sulfolobus solfataricus), suggesting that it represents a novel Sulfolobus species. Comparison of the genome of strain A20 with those of the type strains of S...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27940092/crystal-structures-of-an-archaeal-thymidylate-kinase-from-sulfolobus-tokodaii-provide-insights-into-the-role-of-a-conserved-active-site-arginine-residue
#14
Ansuman Biswas, Arpit Shukla, R S K Vijayan, Jeyaraman Jeyakanthan, Kanagaraj Sekar
Thymidylate kinase (TMK) is a key enzyme that plays an important role in DNA synthesis. Therefore, it serves as an attractive therapeutic target for the development of antibacterial, antiparasitic and anticancer drugs. Herein, we report the biochemical characterization and crystal structure determination of thymidylate kinase from a hyperthermophilic organism Sulfolobus tokodaii (StTMK) in its apo and ADP-bound forms. Our study describes the first three-dimensional structure of an archaeal TMK. StTMK is a thermostable enzyme with optimum activity at 80°C...
December 9, 2016: Journal of Structural Biology
https://www.readbyqxmd.com/read/27932585/structural-and-functional-characterization-of-the-tyw3-taw3-class-of-sam-dependent-methyltransferases
#15
Mark A Currie, Greg Brown, Andrew Wong, Takayuki Ohira, Kei Sugiyama, Tsutomu Suzuki, Alexander F Yakunin, Zongchao Jia
S-adenosylmethionine (SAM)-dependent methyltransferases regulate a wide range of biological processes through the modification of proteins, nucleic acids, polysaccharides, as well as various metabolites. TYW3/Taw3 is a SAM-dependent methyltransferase responsible for the formation of a tRNA modification known as wybutosine and its derivatives that are required for accurate decoding in protein synthesis. Here, we report the crystal structure of Taw3, a homolog of TYW3 from Sulfolobus solfataricus, which revealed a novel α/β fold...
December 8, 2016: RNA
https://www.readbyqxmd.com/read/27908245/perfect-hemihedral-twinning-in-crystals-of-the-%C3%AE-subunit-of-translation-initiation-factor-2-from-sulfolobus-solfataricus-cause-and-effect
#16
O V Kravchenko, O S Nikonov, N A Nevskaya, E A Stolboushkina, V I Arkhipova, M B Garber, S V Nikonov
The crystal structure of the γ-subunit of translation initiation factor 2 from the archaeon Sulfolobus solfataricus (SsoIF2γ) has been solved based on perfectly hemihedral twinned data. The protein was cocrystallized with the 10-fold molar excess of GTP analog (GDPCP) over protein. However, no nucleotide was found in the structure, and the model demonstrated the apo form of the protein. Two slightly different molecules in the asymmetric unit of the crystal are related by the non-crystallographic 2-fold axis and form a tightly associated dimer...
October 2016: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/27907170/complementation-of-an-aglb-mutant-of-methanococcus-maripaludis-with-heterologous-oligosaccharyltransferases
#17
Yan Ding, Helen A Vrionis, James Schneider, Alison Berezuk, Cezar M Khursigara, Ken F Jarrell
The oligosaccharyltransferase is the signature enzyme for N-linked glycosylation in all domains of life. In Archaea, this enzyme termed AglB, is responsible for transferring lipid carrier-linked glycans to select asparagine residues in a variety of target proteins including archaellins, S-layer proteins and pilins. This study investigated the ability of a variety of AglBs to compensate for the oligosaccharyltransferase activity in Methanococcus maripaludis deleted for aglB, using archaellin FlaB2 as the reporter protein since all archaellins in Mc...
2016: PloS One
https://www.readbyqxmd.com/read/27892499/recognition-of-extremophilic-archaeal-viruses-by-eukaryotic-cells-a-promising-nanoplatform-from-the-third-domain-of-life
#18
Kristine Buch Uldahl, Linping Wu, Arnaldur Hall, Pavlos Papathanasiou, Xu Peng, Seyed Moein Moghimi
Viruses from the third domain of life, Archaea, exhibit unusual features including extreme stability that allow their survival in harsh environments. In addition, these species have never been reported to integrate into human or any other eukaryotic genomes, and could thus serve for exploration of novel medical nanoplatforms. Here, we selected two archaeal viruses Sulfolobus monocaudavirus 1 (SMV1) and Sulfolobus spindle shaped virus 2 (SSV2) owing to their unique spindle shape, hyperthermostable and acid-resistant nature and studied their interaction with mammalian cells...
November 28, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27882920/repression-of-rna-polymerase-by-the-archaeo-viral-regulator-orf145-rip
#19
Carol Sheppard, Fabian Blombach, Adam Belsom, Sarah Schulz, Tina Daviter, Katherine Smollett, Emilie Mahieu, Susanne Erdmann, Philip Tinnefeld, Roger Garrett, Dina Grohmann, Juri Rappsilber, Finn Werner
Little is known about how archaeal viruses perturb the transcription machinery of their hosts. Here we provide the first example of an archaeo-viral transcription factor that directly targets the host RNA polymerase (RNAP) and efficiently represses its activity. ORF145 from the temperate Acidianus two-tailed virus (ATV) forms a high-affinity complex with RNAP by binding inside the DNA-binding channel where it locks the flexible RNAP clamp in one position. This counteracts the formation of transcription pre-initiation complexes in vitro and represses abortive and productive transcription initiation, as well as elongation...
November 24, 2016: Nature Communications
https://www.readbyqxmd.com/read/27876889/harnessing-hyperthermostable-lactonase-from-sulfolobus-solfataricus-for-biotechnological-applications
#20
Benjamin Rémy, Laure Plener, Laetitia Poirier, Mikael Elias, David Daudé, Eric Chabrière
Extremozymes have gained considerable interest as they could meet industrial requirements. Among these, SsoPox is a hyperthermostable enzyme isolated from the archaeon Sulfolobus solfataricus. This enzyme is a lactonase catalyzing the hydrolysis of acyl-homoserine lactones; these molecules are involved in Gram-negative bacterial communication referred to as quorum sensing. SsoPox exhibits promiscuous phosphotriesterase activity for the degradation of organophosphorous chemicals including insecticides and chemical warfare agents...
November 23, 2016: Scientific Reports
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