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https://www.readbyqxmd.com/read/28544464/structural-and-biochemical-insights-into-the-2-o-methylation-of-pyrimidines-34-in-trna
#1
Panjiao Pang, Xiangyu Deng, Zhong Wang, Wei Xie
tRNA molecules undergo extensive modifications during their maturation process 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 behaviors 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
#2
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
#3
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
#4
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...
May 12, 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
#5
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
https://www.readbyqxmd.com/read/28448436/role-of-archaeal-hera-protein-in-the-biology-of-the-bacterium-thermus-thermophilus
#6
Alba Blesa, Nieves G Quintans, Ignacio Baquedano, Carlos P Mata, José R Castón, José Berenguer
Intense gene flux between prokaryotes result in high percentage of archaeal genes in the genome of the thermophilic bacteria Thermus spp. Among these archaeal genes a homolog to the Sulfolobus spp. HerA protein appears in all of the Thermus spp. strains so far sequenced (HepA). The role of HepA in Thermus thermophilus HB27 has been analyzed using deletion mutants, and its structure resolved at low resolution by electron microscopy. Recombinant HepA shows DNA-dependent ATPase activity and its structure revealed a double ring, conically-shaped hexamer with an upper diameter of 150 Å and a bottom module of 95 Å...
April 27, 2017: Genes
https://www.readbyqxmd.com/read/28397787/correlated-mutation-in-the-evolution-of-catalysis-in-uracil-dna-glycosylase-superfamily
#7
Bo Xia, Yinling Liu, Jose Guevara, Jing Li, Celeste Jilich, Ye Yang, Liangjiang Wang, Brian N Dominy, Weiguo Cao
Enzymes in Uracil DNA glycosylase (UDG) superfamily are essential for the removal of uracil. Family 4 UDGa is a robust uracil DNA glycosylase that only acts on double-stranded and single-stranded uracil-containing DNA. Based on mutational, kinetic and modeling analyses, a catalytic mechanism involving leaving group stabilization by H155 in motif 2 and water coordination by N89 in motif 3 is proposed. Mutual Information analysis identifies a complexed correlated mutation network including a strong correlation in the EG doublet in motif 1 of family 4 UDGa and in the QD doublet in motif 1 of family 1 UNG...
April 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28384323/correction-rna-and-dna-targeting-by-a-reconstituted-thermus-thermophilus-type-iii-a-crispr-cas-system
#8
Tina Y Liu, Anthony T Iavarone, Jennifer A Doudna
[This corrects the article DOI: 10.1371/journal.pone.0170552.].
2017: PloS One
https://www.readbyqxmd.com/read/28317434/dynamics-of-the-active-site-loops-in-catalyzing-aminoacylation-reaction-in-seryl-and-histidyl-trna-synthetases
#9
Saheb Dutta, Soumya Kundu, Amrita Saha, Nilashis Nandi
Aminoacylation reaction is the first step of protein biosynthesis. The catalytic reorganization at the active site of aminoacyl tRNA synthetases (aaRSs) is driven by the loop motions. There remain lacunae of understanding concerning the catalytic loop dynamics in aaRSs. We analyzed the functional loop dynamics in seryl tRNA synthetase from Methanopyrus kandleri ((mk)SerRS) and histidyl tRNA synthetases from Thermus thermophilus ((tt)HisRS), respectively, using molecular dynamics. Results confirm that the motif 2 loop and other active site loops are flexible spots within the catalytic domain...
March 20, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28303404/phylogenetic-analysis-of-proteins-involved-in-the-stringent-response-in-plant-cells
#10
Doshun Ito, Yuta Ihara, Hidenori Nishihara, Shinji Masuda
The nucleotide (p)ppGpp is a second messenger that controls the stringent response in bacteria. The stringent response modifies expression of a large number of genes and metabolic processes and allows bacteria to survive under fluctuating environmental conditions. Recent genome sequencing analyses have revealed that genes responsible for the stringent response are also found in plants. These include (p)ppGpp synthases and hydrolases, RelA/SpoT homologs (RSHs), and the pppGpp-specific phosphatase GppA/Ppx. However, phylogenetic relationship between enzymes involved in bacterial and plant stringent responses is as yet generally unclear...
March 16, 2017: Journal of Plant Research
https://www.readbyqxmd.com/read/28282376/the-transjugation-machinery-of-thermus-thermophilus-identification-of-tdta-an-atpase-involved-in-dna-donation
#11
Alba Blesa, Ignacio Baquedano, Nieves G Quintáns, Carlos P Mata, José R Castón, José Berenguer
In addition to natural competence, some Thermus thermophilus strains show a high rate of DNA transfer via direct cell-to-cell contact. The process is bidirectional and follows a two-step model where the donor cell actively pushes out DNA and the recipient cell employs the natural competence system to take up the DNA, in a hybrid transformation-dependent conjugation process (transjugation). While the DNA uptake machinery is well known as in other bacterial species that undergo transformation, the pushing step of transjugation remains to be characterized...
March 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28262506/autonomous-generation-and-loading-of-dna-guides-by-bacterial-argonaute
#12
Daan C Swarts, Malwina Szczepaniak, Gang Sheng, Stanley D Chandradoss, Yifan Zhu, Elizabeth M Timmers, Yong Zhang, Hongtu Zhao, Jizhong Lou, Yanli Wang, Chirlmin Joo, John van der Oost
Several prokaryotic Argonaute proteins (pAgos) utilize small DNA guides to mediate host defense by targeting invading DNA complementary to the DNA guide. It is unknown how these DNA guides are being generated and loaded onto pAgo. Here, we demonstrate that guide-free Argonaute from Thermus thermophilus (TtAgo) can degrade double-stranded DNA (dsDNA), thereby generating small dsDNA fragments that subsequently are loaded onto TtAgo. Combining single-molecule fluorescence, molecular dynamic simulations, and structural studies, we show that TtAgo loads dsDNA molecules with a preference toward a deoxyguanosine on the passenger strand at the position opposite to the 5' end of the guide strand...
March 16, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28256579/proline-dehydrogenase-from-thermus-thermophilus-does-not-discriminate-between-fad-and-fmn-as-cofactor
#13
Mieke M E Huijbers, Marta Martínez-Júlvez, Adrie H Westphal, Estela Delgado-Arciniega, Milagros Medina, Willem J H van Berkel
Flavoenzymes are versatile biocatalysts containing either FAD or FMN as cofactor. FAD often binds to a Rossmann fold, while FMN prefers a TIM-barrel or flavodoxin-like fold. Proline dehydrogenase is denoted as an exception: it possesses a TIM barrel-like fold while binding FAD. Using a riboflavin auxotrophic Escherichia coli strain and maltose-binding protein as solubility tag, we produced the apoprotein of Thermus thermophilus ProDH (MBP-TtProDH). Remarkably, reconstitution with FAD or FMN revealed that MBP-TtProDH has no preference for either of the two prosthetic groups...
March 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28256317/anoxic-biodegradation-of-btex-in-a-biotrickling-filter
#14
Ilker Akmirza, Celia Pascual, Andrea Carvajal, Rebeca Pérez, Raúl Muñoz, Raquel Lebrero
Emissions of BTEX (benzene, toluene, ethylbenzene and xylene) from the petrochemical industry are characterized by a low pollutants concentration and the absence of oxygen. Biodegradation of these pollutants using nitrate as the electron acceptor is of key interest to reuse the residual gas for inertization purposes. However, the biological mineralization of BTEX is often limited by their recalcitrant nature and the toxicity of the secondary metabolites produced. The potential of an anoxic biotrickling filter for the treatment of a model O2-free BTEX-laden emission at inlet individual concentrations of ~700mgm(-3) was here evaluated...
February 27, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28242762/conserved-functions-of-the-trigger-loop-and-gre-factors-in-rna-cleavage-by-bacterial-rna-polymerases
#15
Nataliya Miropolskaya, Daria Esyunina, Andrey Kulbachinskiy
RNA cleavage by RNA polymerase (RNAP) is the central step in co-transcriptional RNA proofreading. Bacterial RNAPs were proposed to rely on the same mobile element of the active site, the trigger loop (TL), for both nucleotide addition and RNA cleavage. RNA cleavage can also be stimulated by universal Gre factors, which should replace the TL to get access to the RNAP active site. The contributions of the TL and Gre factors to RNA cleavage reportedly vary between RNAPs from different bacterial species and, probably, different types of transcription complexes...
April 21, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28236191/production-of-whole-cell-lipase-from-streptomyces-clavuligerus-in-a-bench-scale-bioreactor-and-its-first-evaluation-as-biocatalyst-for-synthesis-in-organic-medium
#16
Jéssica Bravin Carmello Dos Santos, Rosineide Gomes da Silva Cruz, Paulo Waldir Tardioli
This work evaluated a wild-type Streptomyces clavuligerus strain as a whole-cell lipase (Sc-WCL) producer by submerged fermentation. In an orbital shaker, lipase hydrolytic activity of 3000 U L(-1), measured at pH 9.0 and 37 °C by using p-nitrophenyl palmitate as substrate, was achieved after 36 h fermentation using glycerol-free production medium in a baffled Erlenmeyer flask at 28 °C and pH 6.8. Maximum productivity of 52.5 U L(-1) h(-1) was achieved after 24 h in bioreactor using glycerol-free production medium at pH 6...
February 24, 2017: Applied Biochemistry and Biotechnology
https://www.readbyqxmd.com/read/28235746/exploring-the-binding-sites-of-staphylococcus-aureus-phenylalanine-trna-synthetase-a-homology-model-approach
#17
Samar S Elbaramawi, Samy M Ibrahim, El-Sayed M Lashine, Mohamed E El-Sadek, Efi Mantzourani, Claire Simons
Increased resistance of MRSA (multidrug resistance Staphylococcus aureus) to anti-infective drugs is a threat to global health necessitating the development of anti-infectives with novel mechanisms of action. Phenylalanine tRNA synthetase (PheRS) is a unique enzyme of the aminoacyl-tRNA synthetases (aaRSs), which are essential enzymes for protein biosynthesis. PheRS is an (αb)2 tetrameric enzyme composed of two alpha subunits (PheS) and two larger beta subunits (PheT). Our potential target in the drug development for the treatment of MRSA infections is the phenylalanine tRNA synthetase alpha subunit that contains the binding site for the natural substrate...
May 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28223966/geological-and-geochemical-controls-on-subsurface-microbial-life-in-the-samail-ophiolite-oman
#18
Kaitlin R Rempfert, Hannah M Miller, Nicolas Bompard, Daniel Nothaft, Juerg M Matter, Peter Kelemen, Noah Fierer, Alexis S Templeton
Microbial abundance and diversity in deep subsurface environments is dependent upon the availability of energy and carbon. However, supplies of oxidants and reductants capable of sustaining life within mafic and ultramafic continental aquifers undergoing low-temperature water-rock reaction are relatively unknown. We conducted an extensive analysis of the geochemistry and microbial communities recovered from fluids sampled from boreholes hosted in peridotite and gabbro in the Tayin block of the Samail Ophiolite in the Sultanate of Oman...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28219522/molecular-assessment-of-the-bacterial-community-associated-with-cassava-manihot-esculenta-crantz-cultivation-in-cameroon
#19
Papa Saliou Sarr, Akifumi Sugiyama, Aime Didier Boyogueno Begoude, Kazufumi Yazaki, Shigeru Araki, Eiji Nawata
Bacterial communities play an important role in nutrient cycles and plant development. Their distribution and activity may depend on location and environmental heterogeneity. This study characterized soil bacterial communities in cassava fields of Eastern (Andom) and Southern (Bityili) Cameroon using molecular tools. In both sites, two improved varieties (TMS-96/1414; TMS-92/0326) and a local variety (Local) were grown in a randomized block design. Composite bulk soils were collected at 10months after planting from cassava plots...
April 2017: Microbiological Research
https://www.readbyqxmd.com/read/28218714/hciv-1-and-other-tailless-icosahedral-internal-membrane-containing-viruses-of-the-family-sphaerolipoviridae
#20
REVIEW
Tatiana A Demina, Maija K Pietilä, Julija Svirskaitė, Janne J Ravantti, Nina S Atanasova, Dennis H Bamford, Hanna M Oksanen
Members of the virus family Sphaerolipoviridae include both archaeal viruses and bacteriophages that possess a tailless icosahedral capsid with an internal membrane. The genera Alpha- and Betasphaerolipovirus comprise viruses that infect halophilic euryarchaea, whereas viruses of thermophilic Thermus bacteria belong to the genus Gammasphaerolipovirus. Both sequence-based and structural clustering of the major capsid proteins and ATPases of sphaerolipoviruses yield three distinct clades corresponding to these three genera...
February 18, 2017: Viruses
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