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https://www.readbyqxmd.com/read/28448436/role-of-archaeal-hera-protein-in-the-biology-of-the-bacterium-thermus-thermophilus
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
https://www.readbyqxmd.com/read/28206708/physiological-metabolic-and-biotechnological-features-of-extremely-thermophilic-microorganisms
#16
REVIEW
James A Counts, Benjamin M Zeldes, Laura L Lee, Christopher T Straub, Michael W W Adams, Robert M Kelly
The current upper thermal limit for life as we know it is approximately 120°C. Microorganisms that grow optimally at temperatures of 75°C and above are usually referred to as 'extreme thermophiles' and include both bacteria and archaea. For over a century, there has been great scientific curiosity in the basic tenets that support life in thermal biotopes on earth and potentially on other solar bodies. Extreme thermophiles can be aerobes, anaerobes, autotrophs, heterotrophs, or chemolithotrophs, and are found in diverse environments including shallow marine fissures, deep sea hydrothermal vents, terrestrial hot springs-basically, anywhere there is hot water...
May 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/28197737/reactive-sites-and-course-of-reduction-in-the-rieske-protein
#17
Si Ying Li, Paul H Oyala, R David Britt, Susan T Weintraub, Laura M Hunsicker-Wang
Rieske proteins play an essential role in electron transfer in the bc 1 complex. Rieske proteins contain a [2Fe-2S] cluster with one iron ligated by two histidines and the other iron ligated by two cysteines. All Rieske proteins have pH-dependent reduction potentials with the histidines ligating the cluster deprotonating in response to increases in pH. The addition of diethylpyrocarbonate (DEPC) modifies deprotonated histidines. The previous studies on the isolated Thermus thermophilus Rieske protein have used large excesses of DEPC, and this study examines what amino acids become modified under different molar equivalents of DEPC to protein...
February 14, 2017: Journal of Biological Inorganic Chemistry: JBIC
https://www.readbyqxmd.com/read/28193326/properties-of-a-novel-thermostable-glucose-isomerase-mined-from-thermus-oshimai-and-its-application-to-preparation-of-high-fructose-corn-syrup
#18
Dong-Xu Jia, Lin Zhou, Yu-Guo Zheng
Glucose isomerase (GI) is used in vitro to convert d-glucose to d-fructose, which is capable of commercial producing high fructose corn syrup (HFCS). To manufacture HFCS at elevated temperature and reduce the cost of enriching syrups, novel refractory GIs from Thermoanaerobacterium xylanolyticum (TxGI), Thermus oshimai (ToGI), Geobacillus thermocatenulatus (GtGI) and Thermoanaerobacter siderophilus (TsGI) were screened via genome mining approach. The enzymatic characteristics research showed that ToGI had higher catalytic efficiency and superior thermostability toward d-glucose among the screened GIs...
April 2017: Enzyme and Microbial Technology
https://www.readbyqxmd.com/read/28193276/thermus-thermophilus-as-source-of-thermozymes-for-biotechnological-applications-homologous-expression-and-biochemical-characterization-of-an-%C3%AE-galactosidase
#19
Martina Aulitto, Salvatore Fusco, Gabriella Fiorentino, Danila Limauro, Emilia Pedone, Simonetta Bartolucci, Patrizia Contursi
BACKGROUND: The genus Thermus, which has been considered for a long time as a fruitful source of biotechnological relevant enzymes, has emerged more recently as suitable host to overproduce thermozymes. Among these, α-galactosidases are widely used in several industrial bioprocesses that require high working temperatures and for which thermostable variants offer considerable advantages over their thermolabile counterparts. RESULTS: Thermus thermophilus HB27 strain was used for the homologous expression of the TTP0072 gene encoding for an α-galactosidase (TtGalA)...
February 13, 2017: Microbial Cell Factories
https://www.readbyqxmd.com/read/28174620/complete-genome-sequence-of-thermus-brockianus-ge-1-reveals-key-enzymes-of-xylan-xylose-metabolism
#20
Christian Schäfers, Saskia Blank, Sigrid Wiebusch, Skander Elleuche, Garabed Antranikian
Thermus brockianus strain GE-1 is a thermophilic, Gram-negative, rod-shaped and non-motile bacterium that was isolated from the Geysir geothermal area, Iceland. Like other thermophiles, Thermus species are often used as model organisms to understand the mechanism of action of extremozymes, especially focusing on their heat-activity and thermostability. Genome-specific features of T. brockianus GE-1 and their properties further help to explain processes of the adaption of extremophiles at elevated temperatures...
2017: Standards in Genomic Sciences
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