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https://www.readbyqxmd.com/read/27924260/molecular-mechanisms-of-substrate-specificities-of-uridinecytidine-kinase
#1
Wataru Tanaka, Mitsuo Shoji, Fumiaki Tomoike, Yuzuru Ujiie, Kyohei Hanaoka, Ryuhei Harada, Megumi Kayanuma, Katsumasa Kamiya, Toyokazu Ishida, Ryoji Masui, Seiki Kuramitsu, Yasuteru Shigeta
A uridine-cytidine kinase (UCK) catalyzes the phosphorylation of uridine (Urd) and cytidine (Cyd) and plays a significant role in the pyrimidine-nucleotide salvage pathway. Unlike ordinary ones, UCK from Thermus thermophilus HB8 (ttCK) loses catalytic activity on Urd due to lack of a substrate binding ability and possesses an unusual amino acid, i.e. tyrosine 93 (Tyr93) at the binding site, whereas histidine (His) is located in the other UCKs. Mutagenesis experiments revealed that a replacement of Tyr93 by His or glutamine (Gln) recovered catalytic activity on Urd...
2016: Biophysics and Physicobiology
https://www.readbyqxmd.com/read/27919778/a-mutation-in-the-psst-homologue-of-complex-i-nadh-ubiquinone-oxidoreductase-from-tetranychus-urticae-is-associated-with-resistance-to-meti-acaricides
#2
Sabina Bajda, Wannes Dermauw, Rafaela Panteleri, Naoya Sugimoto, Vassilis Douris, Luc Tirry, Masahiro Osakabe, John Vontas, Thomas Van Leeuwen
The acaricidal compounds pyridaben, tebufenpyrad and fenpyroximate are frequently used in the control of phytophagous mites such as Tetranychus urticae, and are referred to as Mitochondrial Electron Transport Inhibitors, acting at the quinone binding pocket of complex I (METI-I acaricides). Because of their very frequent use, resistance evolved fast more than 20 years ago, and is currently wide-spread. Increased activity of P450 monooxygenases has been often associated with resistance, but target-site based resistance mechanisms were never reported...
December 2, 2016: Insect Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/27903612/the-role-of-4u-as-an-extended-translation-termination-signal-in-bacteria
#3
Yulong Wei, Xuhua Xia
Termination efficiency of stop codons depends on the first 3' flanking (+4) base in bacteria and eukaryotes. In both Escherichia coli and Saccharomyces cerevisiae, termination read-through is reduced in the presence of +4U; however, the molecular mechanism underlying +4U function is poorly understood. Here, we perform comparative genomics analysis on 25 bacterial species (covering Actinobacteria, Bacteriodetes, Cyanobacteria, Deinococcus-Thermus, Firmicutes, Proteobacteria and Spirochaetae) with bioinformatics approaches to examine the influence of +4U in bacterial translation termination by contrasting between highly and lowly expressed genes (HEGs and LEGs)...
November 30, 2016: Genetics
https://www.readbyqxmd.com/read/27897270/trueprime-is-a-novel-method-for-whole-genome-amplification-from-single-cells-based-on-tthprimpol
#4
Ángel J Picher, Bettina Budeus, Oliver Wafzig, Carola Krüger, Sara García-Gómez, María I Martínez-Jiménez, Alberto Díaz-Talavera, Daniela Weber, Luis Blanco, Armin Schneider
Sequencing of a single-cell genome requires DNA amplification, a process prone to introducing bias and errors into the amplified genome. Here we introduce a novel multiple displacement amplification (MDA) method based on the unique DNA primase features of Thermus thermophilus (Tth) PrimPol. TthPrimPol displays a potent primase activity preferring dNTPs as substrates unlike conventional primases. A combination of TthPrimPol's unique ability to synthesize DNA primers with the highly processive Phi29 DNA polymerase (Φ29DNApol) enables near-complete whole genome amplification from single cells...
November 29, 2016: Nature Communications
https://www.readbyqxmd.com/read/27888076/proteome-wide-identification-of-lysine-succinylation-in-thermophilic-and-mesophilic-bacteria
#5
Hiroki Okanishi, Kwang Kim, Kenji Fukui, Takato Yano, Seiki Kuramitsu, Ryoji Masui
Lysine succinylation, one of post-translational acylations conserved from eukaryotes to bacteria, plays regulatory roles in various cellular processes. However, much remains unknown about the general and specific characteristics of lysine succinylation among bacteria, and about its functions different from those of other acylations. In this study, we characterized lysine succinylation, a newly discovered widespread type of lysine acylation in five bacterial species with different characteristics such as optimal growth temperature and cell wall structure...
November 23, 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27885197/a-thermostable-bilirubin-oxidizing-enzyme-from-activated-sludge-isolated-by-a-metagenomic-approach
#6
Nobutada Kimura, Yoichi Kamagata
A gene coding for a multicopper oxidase (BopA) was identified through the screening of a metagenomic library constructed from wastewater treatment activated sludge. The recombinant BopA protein produced in Escherichia coli exhibited oxidation activity toward 2,2'-azino-bis-(3-ethylbenzothiazoline-6-sulfonate) (ABTS) in the presence of copper, suggesting that BopA is laccase. A bioinformatic analysis of the bopA gene sequence indicated that it has a phylogenetically bacterial origin, possibly derived from a bacterium within the phylum Deinococcus-Thermus...
November 23, 2016: Microbes and Environments
https://www.readbyqxmd.com/read/27885192/occurrence-of-two-novel-linear-penta-amines-pyropentamine-and-homopyropentamine-in-extremely-thermophilic-thermus-composti
#7
Koei Hamana, Takemitsu Furuchi, Hidenori Hayashi, Takashi Itoh, Moriya Ohkuma, Masaru Niitsu
No abstract text is available yet for this article.
November 22, 2016: Journal of General and Applied Microbiology
https://www.readbyqxmd.com/read/27871371/effect-of-c-terminal-domain-truncation-of-thermus-thermophilus-trehalose-synthase-on-its-substrate-specificity
#8
Chang-Bae Cho, Da-Yeon Park, Soo-Bok Lee
The C-terminal domain of the three-domain-comprising trehalose synthase from Thermus thermophilus was truncated in order to study the effect on the enzyme's activity and substrate specificity. Compared with the wild-type (WT) enzyme, the two truncated enzymes (DM1 and DM2) showed lower maltose- and trehalose-converting activities and a different transglycosylation reaction mechanism. In the mutants, the glucose moiety cleaved from the maltose substrate was released from the enzyme and intercepted by external glucose oxidase, preventing the production of trehalose...
January 2017: Enzyme and Microbial Technology
https://www.readbyqxmd.com/read/27853887/identification-of-a-vapbc-toxin-antitoxin-system-in-a-thermophilic-bacterium-thermus-thermophilus-hb27
#9
Yuqi Fan, Takayuki Hoshino, Akira Nakamura
There are 12 putative toxin-antitoxin (TA) loci in the Thermus thermophilus HB27 genome, including four VapBC and three HicBA families. Expression of these seven putative toxin genes in Escherichia coli demonstrated that one putative VapC toxin TTC0125 and two putative HicA toxins, TTC1395 and TTC1705, inhibited cell growth, and co-expression with cognate antitoxin genes rescued growth, indicating that these genes function as TA loci. In vitro analysis with the purified TTC0125 and total RNA/mRNA from E. coli and T...
November 16, 2016: Extremophiles: Life Under Extreme Conditions
https://www.readbyqxmd.com/read/27831491/structure-and-function-of-an-ancestral-type-%C3%AE-decarboxylating-dehydrogenase-from-thermococcus-kodakarensis
#10
Tetsu Shimizu, Lulu Yin, Ayako Yoshida, Yuusuke Yokooji, Shin-Ichi Hachisuka, Takaaki Sato, Takeo Tomita, Hiromi Nishida, Haruyuki Atomi, Tomohisa Kuzuyama, Makoto Nishiyama
β-Decarboxylating dehydrogenases, which are involved in central metabolism, are considered to have diverged from a common ancestor with broad substrate specificity. In a molecular phylogenetic analysis of 183 β-decarboxylating dehydrogenase homologs from 84 species, TK0280 from Thermococcus kodakarensis was selected as a candidate for an ancestral-type β-decarboxylating dehydrogenase. The biochemical characterization of recombinant TK0280 revealed that the enzyme exhibited dehydrogenase activities toward homoisocitrate, isocitrate, and 3-isopropylmalate, which correspond to key reactions involved in the lysine biosynthetic pathway, tricarboxylic acid cycle, and leucine biosynthetic pathway, respectively...
November 9, 2016: Biochemical Journal
https://www.readbyqxmd.com/read/27822529/thermus-and-the-pink-discoloration-defect-in-cheese
#11
Lisa Quigley, Daniel J O'Sullivan, David Daly, Orla O'Sullivan, Zuzana Burdikova, Rostislav Vana, Tom P Beresford, R Paul Ross, Gerald F Fitzgerald, Paul L H McSweeney, Linda Giblin, Jeremiah J Sheehan, Paul D Cotter
A DNA sequencing-based strategy was applied to study the microbiology of Continental-type cheeses with a pink discoloration defect. The basis for this phenomenon has remained elusive, despite decades of research. The bacterial composition of cheese containing the defect was compared to that of control cheese using 16S rRNA gene and shotgun metagenomic sequencing as well as quantitative PCR (qPCR). Throughout, it was apparent that Thermus, a carotenoid-producing genus, was present at higher levels in defect-associated cheeses than in control cheeses...
May 2016: MSystems
https://www.readbyqxmd.com/read/27815924/the-simple-and-unique-allosteric-machinery-of-thermus-caldophilus-lactate-dehydrogenase-structure-function-relationship-in-bacterial-allosteric-ldhs
#12
Hayao Taguchi
Many bacterial L-lactate dehydrogenases (LDH) are allosteric enzymes, and usually activated by fructose 1,6-bisphosphate (FBP) and often also by substrate pyruvate. The active and inactive state structures demonstrate that Thermus caldophilus, Lactobacillus casei, and Bifidobacterium longum LDHs consistently undergo allosteric transition according to Monod-Wyman-Changeux model, where the active (R) and inactive (T) states of the enzymes coexist in an allosteric equilibrium (pre-existing equilibrium) independently of allosteric effectors...
November 5, 2016: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/27815287/microbial-and-viral-like-rhodopsins-present-in-coastal-marine-sediments-from-four-polar-and-subpolar-regions
#13
J L López, M Golemba, E Hernández, M Lozada, H M Dionisi, J Jansson, J Carroll, L Lundgren, S Sjöling, W P Mac Cormack
Rhodopsins are broadly distributed. In this work we analyzed 23 metagenomes corresponding to marine sediment samples from four regions which share cold climate conditions (Norway; Sweden; Argentina and Antarctica). In order to investigate the genes evolution of viral-rodopsins, an initial set of 6224 bacterial rhodopsins sequences according COG5524 were retrieved from the 23 metagenomes. After selection by the presence of transmembrane domains and alignment 123 viral (51) and non-viral (72) sequences (>50 aminoacids) were finally included in further analysis...
November 3, 2016: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/27799325/muts2-promotes-homologous-recombination-in-bacillus-subtilis
#14
Peter E Burby, Lyle A Simmons
: Bacterial MutS proteins are subdivided into two families, MutS1 and MutS2. MutS1 family members recognize DNA replication errors during their participation in the well-characterized mismatch repair pathway (MMR). In contrast, to the well-described function of MutS1, the function of MutS2 in bacteria has remained less clear. In Helicobacter pylori and Thermus thermophilus, MutS2 has been shown to suppress homologous recombination. The role of MutS2 is unknown in the Gram-positive bacterium Bacillus subtilis In this work, we investigated the contribution of MutS2 to maintaining genome integrity in B...
October 31, 2016: Journal of Bacteriology
https://www.readbyqxmd.com/read/27757697/novel-stand-alone-ram-domain-protein-mediated-catalytic-control-of-anthranilate-phosphoribosyltransferase-in-tryptophan-biosynthesis-in-thermus-thermophilus
#15
Tetsuo Kubota, Hajime Matsushita, Takeo Tomita, Saori Kosono, Minoru Yoshida, Tomohisa Kuzuyama, Makoto Nishiyama
Regulation of amino acid metabolism (RAM) domains are widely distributed among prokaryotes. In most cases, a RAM domain fuses with a DNA-binding domain to act as a transcriptional regulator. The extremely thermophilic bacterium, Thermus thermophilus, only carries a single gene encoding a RAM domain-containing protein on its genome. This protein is a stand-alone RAM domain protein (SraA) lacking a DNA-binding domain. Therefore, we hypothesized that SraA, which senses amino acids through its RAM domain, may interact with other proteins to modify its functions...
October 19, 2016: Extremophiles: Life Under Extreme Conditions
https://www.readbyqxmd.com/read/27754888/regulation-of-transcription-initiation-by-gfh-factors-from-deinococcus-radiodurans
#16
Aleksei Agapov, Daria Esyunina, Danil Pupov, Andrey Kulbachinskiy
The Gre-family transcription factors bind within the secondary channel of bacterial RNA polymerase (RNAP) directly modulating its catalytic activities. Universally conserved Gre factors activate RNA cleavage by RNAP, by chelating catalytic metal ions in the RNAP active site, and facilitate both promoter escape and transcription elongation. Gfh factors are Deinococcus/Thermus -specific homologues of Gre factors whose transcription functions remain poorly understood. Recently, we found that Gfh1 and Gfh2 proteins from Deinococcus radiodurans dramatically stimulate RNAP pausing during transcription elongation in the presence of Mn(2+) but not Mg(2+) ions...
October 17, 2016: Biochemical Journal
https://www.readbyqxmd.com/read/27737901/soil-phod-and-phox-alkaline-phosphatase-gene-diversity-responds-to-multiple-environmental-factors
#17
Sabine A Ragot, Michael A Kertesz, Éva Mészáros, Emmanuel Frossard, Else K Bünemann
Alkaline phosphatases such as PhoD and PhoX are important genes in organic phosphorus cycling in soil. We identified the key organisms harboring the phoD and phoX gene in soil and explored the relationships between environmental factors and the phoD- and phoX-harboring community structures across three land-uses located in arid to temperate climates on two continents using 454-sequencing. phoD was investigated using recently published primers, and new primers were designed to study phoX in soil. phoD was found in 1 archaeal, 13 bacterial and 2 fungal phyla, and phoX in 1 archaeal and 16 bacterial phyla...
October 12, 2016: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/27710943/crystallographic-study-of-the-2-thioribothymidine-synthetic-complex-ttua-ttub-from-thermus-thermophilus
#18
Minghao Chen, Shun Narai, Naoki Omura, Naoki Shigi, Sarin Chimnaronk, Yoshikazu Tanaka, Min Yao
The ubiquitin-like protein TtuB is a sulfur carrier for the biosynthesis of 2-thioribothymidine (s(2)T) at position 54 in some thermophilic bacterial tRNAs. TtuB captures a S atom at its C-terminus as a thiocarboxylate and transfers it to tRNA by the transferase activity of TtuA. TtuB also functions to suppress s(2)T formation by forming a covalent bond with TtuA. To explore how TtuB interacts with TtuA and switches between these two different functions, high-resolution structure analysis of the TtuA-TtuB complex is required...
October 1, 2016: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/27707908/arsenate-reductase-from-thermus-thermophilus-conjugated-to-polyethylene-glycol-stabilized-gold-nanospheres-allow-trace-sensing-and-speciation-of-arsenic-ions
#19
Jane Politi, Jolanda Spadavecchia, Gabriella Fiorentino, Immacolata Antonucci, Luca De Stefano
Water sources pollution by arsenic ions is a serious environmental problem all around the world. Arsenate reductase enzyme (TtArsC) from Thermus thermophilus extremophile bacterium, naturally binds arsenic ions, As(V) and As (III), in aqueous solutions. In this research, TtArsC enzyme adsorption onto hybrid polyethylene glycol-stabilized gold nanoparticles (AuNPs) was studied at different pH values as an innovative nanobiosystem for metal concentration monitoring. Characterizations were performed by UV/Vis and circular dichroism spectroscopies, TEM images and in terms of surface charge changes...
October 2016: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/27697475/understanding-the-core-of-rna-interference-the-dynamic-aspects-of-argonaute-mediated-processes
#20
Lizhe Zhu, Hanlun Jiang, Fu Kit Sheong, Xuefeng Cui, Yanli Wang, Xin Gao, Xuhui Huang
At the core of RNA interference, the Argonaute proteins (Ago) load and utilize small guide nucleic acids to silence mRNAs or cleave foreign nucleic acids in a sequence specific manner. In recent years, based on extensive structural studies of Ago and its interaction with the nucleic acids, considerable progress has been made to reveal the dynamic aspects of various Ago-mediated processes. Here we review these novel insights into the guide-strand loading, duplex unwinding, and effects of seed mismatch, with a focus on two representative Agos, the human Ago 2 (hAgo2) and the bacterial Thermus thermophilus Ago (TtAgo)...
September 30, 2016: Progress in Biophysics and Molecular Biology
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