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https://www.readbyqxmd.com/read/28720495/crystal-structure-of-lysk-an-enzyme-catalyzing-the-last-step-of-lysine-biosynthesis-in-thermus-thermophilus-in-complex-with-lysine-insight-into-the-mechanism-for-recognition-of-the-amino-group-carrier-protein-lysw
#1
Satomi Fujita, Su-Hee Cho, Ayako Yoshida, Fumihito Hasebe, Takeo Tomita, Tomohisa Kuzuyama, Makoto Nishiyama
LysK is an M20 peptidase family enzyme that hydrolyzes the isopeptide bond between the carrier protein LysW and lysine in order to release lysine, which is the last step of lysine biosynthesis in Thermus thermophilus. In the present study, we determined the crystal structure of LysK in complex with lysine at a resolution of 2.4 Å. The α-amino group of the bound lysine was oriented toward the catalytic center, which was composed of the residues coordinating divalent metal ions for the hydrolysis of the isopeptide bond...
July 15, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28716925/symmetry-related-proton-transfer-pathways-in-respiratory-complex-i
#2
Andrea Di Luca, Ana P Gamiz-Hernandez, Ville R I Kaila
Complex I functions as the initial electron acceptor in aerobic respiratory chains of most organisms. This gigantic redox-driven enzyme employs the energy from quinone reduction to pump protons across its complete approximately 200-Å membrane domain, thermodynamically driving synthesis of ATP. Despite recently resolved structures from several species, the molecular mechanism by which complex I catalyzes this long-range proton-coupled electron transfer process, however, still remains unclear. We perform here large-scale classical and quantum molecular simulations to study the function of the proton pump in complex I from Thermus thermophilus The simulations suggest that proton channels are established at symmetry-related locations in four subunits of the membrane domain...
July 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28710637/stabilization-of-enzymes-by-using-thermophiles
#3
Ana Luisa Ribeiro, Mercedes Sánchez, Aurelio Hidalgo, José Berenguer
Manufactured steroid compounds have many applications in the pharmaceutical industry. Due to the chemical complexity and chirality of steroids, there is an increasing demand for enzyme-based bioconversion processes to replace those based on chemical synthesis. In this context, thermostability of the involved enzymes is a highly desirable property as both the increased half-life of the enzyme and the enhanced solubility of substrates and products will improve the yield of the reactions. Metagenomic libraries from thermal environments are potential sources of thermostable enzymes of prokaryotic origin, but the number of expected hits could be quite low for enzymes handling substrates such as steroids, rarely found in prokaryotes...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28699116/high-taxonomic-diversity-of-cultivation-recalcitrant-endophytic-bacteria-in-grapevine-field-shoots-their-in-vitro-introduction-and-unsuspected-persistence
#4
Pious Thomas, Aparna C Sekhar, Sadiq Pasha Shaik
Molecular and microscopic analyses reveal enormous non-cultivable endophytic bacteria in grapevine field shoots with functional significance. Diverse bacteria enter tissue cultures through surface-sterilized tissues and survive surreptitiously with varying taxonomic realignments. The study was envisaged to assess the extent of endophytic bacterial association with field shoot tissues of grapevine and the likelihood of introduction of such internally colonizing bacteria in vitro adopting molecular techniques targeting the non-cultivable bacterial community...
July 11, 2017: Planta
https://www.readbyqxmd.com/read/28696001/an-arsr-smtb-family-member-regulates-arsenic-resistance-genes-unusually-arranged-in-thermus-thermophilus-hb27
#5
Immacolata Antonucci, Giovanni Gallo, Danila Limauro, Patrizia Contursi, Ana Luisa Ribeiro, Alba Blesa, José Berenguer, Simonetta Bartolucci, Gabriella Fiorentino
Arsenic resistance is commonly clustered in ars operons in bacteria; main ars operon components encode an arsenate reductase, a membrane extrusion protein, and an As-sensitive transcription factor. In the As-resistant thermophile Thermus thermophilus HB27, genes encoding homologues of these proteins are interspersed in the chromosome. In this article, we show that two adjacent genes, TtsmtB, encoding an ArsR/SmtB transcriptional repressor and, TTC0354, encoding a Zn(2+) /Cd(2+) -dependent membrane ATPase are involved in As resistance; differently from characterized ars operons, the two genes are transcribed from dedicated promoters upstream of their respective genes, whose expression is differentially regulated at transcriptional level...
July 11, 2017: Microbial Biotechnology
https://www.readbyqxmd.com/read/28680127/the-discovery-of-novel-heat-stable-keratinases-from-meiothermus-taiwanensis-wr-220-and-other-extremophiles
#6
Wan-Ling Wu, Mei-Yi Chen, I-Fan Tu, Yu-Ching Lin, Nadendla EswarKumar, Ming-Yi Chen, Meng-Chiao Ho, Shih-Hsiung Wu
Billions of tons of keratin bio-wastes are generated by poultry industry annually but discarded that result in serious environmental pollution. Keratinase is a broad spectrum protease with the unique ability to degrade keratin, providing an eco-friendly way to convert keratin wastes to valuable amino acids. In this report, a feather-degrading thermophilic bacterium, Meiothermus taiwanensis WR-220, was investigated due to its ability to apparently complete feather decay at 65 °C in two days. By genomics, proteomics, and biochemical approaches, the extracellular heat-stable keratinase (MtaKer) from M...
July 5, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28674417/serial-femtosecond-crystallography-structure-of-cytochrome-c-oxidase-at-room-temperature
#7
Rebecka Andersson, Cecilia Safari, Robert Dods, Eriko Nango, Rie Tanaka, Ayumi Yamashita, Takanori Nakane, Kensuke Tono, Yasumasa Joti, Petra Båth, Elin Dunevall, Robert Bosman, Osamu Nureki, So Iwata, Richard Neutze, Gisela Brändén
Cytochrome c oxidase catalyses the reduction of molecular oxygen to water while the energy released in this process is used to pump protons across a biological membrane. Although an extremely well-studied biological system, the molecular mechanism of proton pumping by cytochrome c oxidase is still not understood. Here we report a method to produce large quantities of highly diffracting microcrystals of ba 3-type cytochrome c oxidase from Thermus thermophilus suitable for serial femtosecond crystallography. The room-temperature structure of cytochrome c oxidase is solved to 2...
July 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28653911/bacterial-communities-in-soil-samples-from-the-mingyong-glacier-of-southwestern-china
#8
Haoyu Li, Muhammad Kamran Taj, Xiuling Ji, Qi Zhang, Liangbing Lin, Zhimei Zhou, Yunlin Wei
The present study was an effort to determine the bacterial diversity of soils in Mingyong Glacier located at the Meili Snow Mountains of southwestern China. Mingyong Glacier has different climatic zones within a very narrow area, and bacterial community diversity in this low temperature area remains largely unknown. In this study, soil samples were collected from four different climatic zones: M11A (dry warm valley), M14 (forest), M15 (grass land), and M16 (glacier zones). Phylogenetic analysis based on 16S rRNA gene V6 hypervariable region showed high bacterial abundance in the glacier...
May 2017: Pakistan Journal of Pharmaceutical Sciences
https://www.readbyqxmd.com/read/28652344/x-ray-crystal-structure-of-a-reiterative-transcription-complex-reveals-an-atypical-rna-extension-pathway
#9
Katsuhiko S Murakami, Yeonoh Shin, Charles L Turnbough, Vadim Molodtsov
Reiterative transcription is a noncanonical form of RNA synthesis in which a nucleotide specified by a single base in the DNA template is repetitively added to the nascent transcript. Here we determined the crystal structure of an RNA polymerase, the bacterial enzyme from Thermus thermophilus, engaged in reiterative transcription during transcription initiation at a promoter resembling the pyrG promoter of Bacillus subtilis The structure reveals that the reiterative transcript detours from the dedicated RNA exit channel and extends toward the main channel of the enzyme, thereby allowing RNA extension without displacement of the promoter recognition σ-factor...
June 26, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28651873/improving-trehalose-synthase-activity-by-adding-the-c-terminal-domain-of-trehalose-synthase-from-thermus-thermophilus
#10
Yan Li, Ziwei Wang, Yue Feng, Qipeng Yuan
The aim of this work was to study the activities of four other TreS enzymes from different sources linked with or without TtTreS-C. The results showed that a flexible linker peptide between TreS enzymes and TtTreS-C is essential for their activity enhancement. Moreover, the specific activities of the four enzymes were also improved by linking to the TtTreS-C fragment. Together, our study provides novel insights into the functions of the C-terminal domain of TtTreS, and would facilitate its future application in enzyme engineering...
June 8, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28648609/critical-role-of-water-molecules-in-proton-translocation-by-the-membrane-bound-transhydrogenase
#11
Pius S Padayatti, Josephine H Leung, Paween Mahinthichaichan, Emad Tajkhorshid, Andrii Ishchenko, Vadim Cherezov, S Michael Soltis, J Baz Jackson, C David Stout, Robert B Gennis, Qinghai Zhang
The nicotinamide nucleotide transhydrogenase (TH) is an integral membrane enzyme that uses the proton-motive force to drive hydride transfer from NADH to NADP(+) in bacteria and eukaryotes. Here we solved a 2.2-Å crystal structure of the TH transmembrane domain (Thermus thermophilus) at pH 6.5. This structure exhibits conformational changes of helix positions from a previous structure solved at pH 8.5, and reveals internal water molecules interacting with residues implicated in proton translocation. Together with molecular dynamics simulations, we show that transient water flows across a narrow pore and a hydrophobic "dry" region in the middle of the membrane channel, with key residues His42(α2) (chain A) being protonated and Thr214(β) (chain B) displaying a conformational change, respectively, to gate the channel access to both cytoplasmic and periplasmic chambers...
July 5, 2017: Structure
https://www.readbyqxmd.com/read/28630929/splitting-of-the-o-o-bond-at-the-heme-copper-catalytic-site-of-respiratory-oxidases
#12
Federica Poiana, Christoph von Ballmoos, Nathalie Gonska, Margareta R A Blomberg, Pia Ädelroth, Peter Brzezinski
Heme-copper oxidases catalyze the four-electron reduction of O2 to H2O at a catalytic site that is composed of a heme group, a copper ion (CuB), and a tyrosine residue. Results from earlier experimental studies have shown that the O-O bond is cleaved simultaneously with electron transfer from a low-spin heme (heme a/b), forming a ferryl state (PR ; Fe(4+)=O(2-), CuB(2+)-OH(-)). We show that with the Thermus thermophilus ba3 oxidase, at low temperature (10°C, pH 7), electron transfer from the low-spin heme b to the catalytic site is faster by a factor of ~10 (τ ≅ 11 μs) than the formation of the PR ferryl (τ ≅110 μs), which indicates that O2 is reduced before the splitting of the O-O bond...
June 2017: Science Advances
https://www.readbyqxmd.com/read/28630126/a-key-enzyme-of-the-nad-salvage-pathway-in-thermus-thermophilus-characterization-of-nicotinamidase-and-the-impact-of-its-gene-deletion-at-high-temperatures
#13
Hironori Taniguchi, Sathidaphorn Sungwallek, Phatcharin Chotchuang, Kenji Okano, Kohsuke Honda
Nicotinamide adenine dinucleotide (NAD(+)) is a cofactor related to many cellular processes. This cofactor is known to be unstable, especially at high temperatures, where it chemically decomposes to nicotinamide and ADP-ribose. Bacteria, yeast, and higher organisms possess the salvage pathway for reconstructing NAD(+) from these decomposition products; however, the importance of the salvage pathway for survival is not well elucidated, except for in pathogens lacking the NAD(+)de novo synthesis pathway. Herein, we report the importance of the NAD(+) salvage pathway in the thermophilic bacterium Thermus thermophilus HB8 at high temperatures...
June 19, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28624535/atp-free-biosynthesis-of-a-high-energy-phosphate-metabolite-fructose-1-6-diphosphate-by-in-vitro-metabolic-engineering
#14
Wei Wang, Meixia Liu, Chun You, Zhimin Li, Yi-Heng Percival Zhang
Fructose 1,6-diphosphate (FDP) is a widely used medicine and is also a precursor of two important three-carbon phosphates - glyceraldehyde 3-phosphate (GA3P) and dihydroxyacetone phosphate (DHAP) for the biosynthesis of numerous fine chemicals. An in vitro synthetic cofactor-free enzymatic pathway comprised of four hyperthermophilic enzymes was designed to produce FDP from starch and pyrophosphate. All of four hyperthermophilic enzymes (i.e., alpha-glucan phosphorylase from Thermotaga maritima, phosphoglucomutase from Thermococcus kodakarensis, glucose 6-phosphate isomerase from Thermus thermophilus, and pyrophosphate phosphofructokinase from T...
July 2017: Metabolic Engineering
https://www.readbyqxmd.com/read/28580926/crystal-structure-of-recombinant-phosphoribosylpyrophosphate-synthetase-2-from-thermus-thermophilus-hb27-complexed-with-adp-and-sulfate-ions
#15
Vladimir I Timofeev, Ekaterina V Sinitsyna, Maria A Kostromina, Tatiana I Muravieva, Dmitry A Makarov, Olga O Mikheeva, Inna P Kuranova, Roman S Esipov
Phosphoribosylpyrophosphate synthetase (PRPPS) from the thermophilic bacterial strain Thermus thermophilus HB27 catalyzes the synthesis of phosphoribosylpyrophosphate from ribose 5-phosphate and ATP, and belongs to the class I PRPPSs. The three-dimensional structure of the recombinant enzyme was solved at 2.2 Å resolution using crystals grown in microgravity from protein solution containing ATP, magnesium and sulfate ions. An ADP molecule was located in the active site of each subunit of the hexameric enzyme molecule and sulfate ions were located in both the active and allosteric sites...
June 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28544464/structural-and-biochemical-insights-into-the-2-o-methylation-of-pyrimidines-34-in-trna
#16
Panjiao Pang, Xiangyu Deng, Zhong Wang, Wei Xie
tRNA molecules undergo extensive modifications during their maturation and these modifications play important cellular roles. TrmL is a tRNA-modification enzyme that catalyzes the transfer of a methyl group to the 2'-hydroxyl group of the pyrimidines at the wobble position 34 in two tRNA(L)(eu) isoacceptors, but the mechanism remains elusive. In this study, we determined the crystal structure of TrmL from Thermus thermophilus (TtTrmL) to 1.7 Å. The enzyme contains only the conserved minimal SPOUT fold, but displays distinct biochemical behavior from its Escherichia coli counterpart, EcTrmL...
May 25, 2017: FEBS Journal
https://www.readbyqxmd.com/read/28544195/long-and-branched-polyamines-are-required-for-maintenance-of-the-ribosome-trna-his-and-trna-tyr-in-thermus-thermophilus-cells-at-high-temperatures
#17
Misa Nakashima, Ryota Yamagami, Chie Tomikawa, Yuki Ochi, Toshiyuki Moriya, Haruichi Asahara, Dominique Fourmy, Satoko Yoshizawa, Tairo Oshima, Hiroyuki Hori
Thermus thermophilus is an extremely thermophilic eubacterium that produces various polyamines. Aminopropylagmatine ureohydrolase (SpeB) and SAM decarboxylase-like protein 1 (SpeD1) are involved in the biosynthesis of spermidine from arginine. Because long and branched polyamines in T. thermophilus are synthesized from spermidine, the speB and speD1 gene-deleted strains (ΔspeB and ΔspeD1, respectively) cannot synthesize long and branched polyamines. Although neither strain grew at high temperatures (>75°C) in minimal medium, both strains survived at 80°C when they were cultured at 70°C until the mid-log phase and then shifted to 80°C...
May 24, 2017: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
https://www.readbyqxmd.com/read/28506931/in-vitro-affinity-of-deinococcus-radiodurans-muts-towards-mismatched-dna-exceeds-that-of-its-orthologues-from-escherichia-coli-and-thermus-thermophilus
#18
Michał Banasik, Anna Stanisławska-Sachadyn, Ewa Hildebrandt, Paweł Sachadyn
The mismatch binding protein MutS is responsible for the recognition of mispaired and unpaired bases, which is the initial step in DNA repair. Among the MutS proteins most extensively studied in vitro are those derived from Thermus thermophilus, Thermus aquaticus and Escherichia coli. Here, we present the first report on the in vitro examination of DNA mismatch binding activity of MutS protein from Deinococcus radiodurans and confront this with the properties of those from E. coli and T. thermophilus. The analyses which included mobility gel-shift assay, colorimetric and qPCR estimation of MutS-bound DNA clearly showed that D...
May 12, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28500387/thermal-adaptation-strategies-of-the-extremophile-bacterium-thermus-filiformis-based-on-multi-omics-analysis
#19
F Mandelli, M B Couger, D A A Paixão, C B Machado, C M Carnielli, J A Aricetti, I Polikarpov, R Prade, C Caldana, A F Paes Leme, A Z Mercadante, D M Riaño-Pachón, Fabio Marcio Squina
Thermus filiformis is an aerobic thermophilic bacterium isolated from a hot spring in New Zealand. The experimental study of the mechanisms of thermal adaptation is important to unveil response strategies of the microorganism to stress. In this study, the main pathways involved on T. filiformis thermoadaptation, as well as, thermozymes with potential biotechnological applications were revealed based on omics approaches. The strategy adopted in this study disclosed that pathways related to the carbohydrate metabolism were affected in response to thermoadaptation...
July 2017: Extremophiles: Life Under Extreme Conditions
https://www.readbyqxmd.com/read/28494027/no-evidence-of-genome-editing-activity-from-natronobacterium-gregoryi-argonaute-ngago-in-human-cells
#20
Parisa Javidi-Parsijani, Guoguang Niu, Meghan Davis, Pin Lu, Anthony Atala, Baisong Lu
The argonaute protein from the thermophilic bacterium Thermus thermophilus shows DNA-guided DNA interfering activity at high temperatures, complicating its application in mammalian cells. A recent work reported that the argonaute protein from Natronobacterium gregoryi (NgAgo) had DNA-guided genome editing activity in mammalian cells. We compared the genome editing activities of NgAgo and Staphylococcus aureus Cas9 (SaCas9) in human HEK293T cells side by side. EGFP reporter assays and DNA sequencing consistently revealed high genome editing activity from SaCas9...
2017: PloS One
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