keyword
MENU ▼
Read by QxMD icon Read
search

Thermus

keyword
https://www.readbyqxmd.com/read/28097217/amylose-recognition-and-ring-size-determination-of-amylomaltase
#1
Christian Roth, Nicole Weizenmann, Nicola Bexten, Wolfram Saenger, Wolfgang Zimmermann, Timm Maier, Norbert Sträter
Starch is a major carbon and energy source throughout all kingdoms of life. It consists of two carbohydrate polymers, branched amylopectin and linear amylose, which are sparingly soluble in water. Hence, the enzymatic breakdown by glycoside hydrolases (GHs) is of great biological and societal importance. Amylomaltases (AMs) are GHs specialized in the hydrolysis of α-1,4-linked sugar chains such as amylose. They are able to catalyze an intramolecular transglycosylation of a bound sugar chain yielding polymeric sugar rings, the cycloamyloses (CAs), consisting of 20 to 100 glucose units...
January 2017: Science Advances
https://www.readbyqxmd.com/read/28077870/the-role-of-interfacial-lipids-in-stabilizing-membrane-protein-oligomers
#2
Kallol Gupta, Joseph A C Donlan, Jonathan T S Hopper, Povilas Uzdavinys, Michael Landreh, Weston B Struwe, David Drew, Andrew J Baldwin, Phillip J Stansfeld, Carol V Robinson
Oligomerization of membrane proteins in response to lipid binding has a critical role in many cell-signalling pathways but is often difficult to define or predict. Here we report the development of a mass spectrometry platform to determine simultaneously the presence of interfacial lipids and oligomeric stability and to uncover how lipids act as key regulators of membrane-protein association. Evaluation of oligomeric strength for a dataset of 125 α-helical oligomeric membrane proteins reveals an absence of interfacial lipids in the mass spectra of 12 membrane proteins with high oligomeric stability...
January 19, 2017: Nature
https://www.readbyqxmd.com/read/28071645/integrating-mass-spectrometry-with-md-simulations-reveals-the-role-of-lipids-in-na-h-antiporters
#3
Michael Landreh, Erik G Marklund, Povilas Uzdavinys, Matteo T Degiacomi, Mathieu Coincon, Joseph Gault, Kallol Gupta, Idlir Liko, Justin L P Benesch, David Drew, Carol V Robinson
Na(+)/H(+) antiporters are found in all kingdoms of life and exhibit catalysis rates that are among the fastest of all known secondary-active transporters. Here we combine ion mobility mass spectrometry and molecular dynamics simulations to study the conformational stability and lipid-binding properties of the Na(+)/H(+) exchanger NapA from Thermus thermophilus and compare this to the prototypical antiporter NhaA from Escherichia coli and the human homologue NHA2. We find that NapA and NHA2, but not NhaA, form stable dimers and do not selectively retain membrane lipids...
January 10, 2017: Nature Communications
https://www.readbyqxmd.com/read/28069938/crystal-structure-and-mechanistic-basis-of-a-functional-homolog-of-the-antigen-transporter-tap
#4
Anne Nöll, Christoph Thomas, Valentina Herbring, Tina Zollmann, Katja Barth, Ahmad Reza Mehdipour, Thomas M Tomasiak, Stefan Brüchert, Benesh Joseph, Rupert Abele, Vincent Oliéric, Meitian Wang, Kay Diederichs, Gerhard Hummer, Robert M Stroud, Klaas M Pos, Robert Tampé
ABC transporters form one of the largest protein superfamilies in all domains of life, catalyzing the movement of diverse substrates across membranes. In this key position, ABC transporters can mediate multidrug resistance in cancer therapy and their dysfunction is linked to various diseases. Here, we describe the 2.7-Å X-ray structure of heterodimeric Thermus thermophilus multidrug resistance proteins A and B (TmrAB), which not only shares structural homology with the antigen translocation complex TAP, but is also able to restore antigen processing in human TAP-deficient cells...
January 9, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28052466/effect-of-postharvest-practices-including-degreening-on-citrus-carpoplane-microbial-biomes
#5
A Gomba, L Chidamba, L Korsten
AIMS: To investigate the effect of commercial citrus packhouse processing steps on the fruit surface microbiome of Clementines and Palmer navel oranges. METHODS AND RESULTS: Viable bacteria, yeasts and fungi counts, and pyrosequencing analysis of the 16S rRNA and ITS were used to evaluate the community structure and population dynamics of phylloepiphytic bacteria and fungi associated with commercial postharvest processing. Drenching significantly reduced microbial counts in all cases except for yeasts on navels, while the extend of degreening effects varied between the citrus varieties...
January 4, 2017: Journal of Applied Microbiology
https://www.readbyqxmd.com/read/28050858/thermophilic-bacteria-are-potential-sources-of-novel-rieske-non-heme-iron-oxygenases
#6
Joydeep Chakraborty, Chiho Suzuki-Minakuchi, Kazunori Okada, Hideaki Nojiri
Rieske non-heme iron oxygenases, which have a Rieske-type [2Fe-2S] cluster and a non-heme catalytic iron center, are an important family of oxidoreductases involved mainly in regio- and stereoselective transformation of a wide array of aromatic hydrocarbons. Though present in all domains of life, the most widely studied Rieske non-heme iron oxygenases are found in mesophilic bacteria. The present study explores the potential for isolating novel Rieske non-heme iron oxygenases from thermophilic sources. Browsing the entire bacterial genome database led to the identification of 45 homologs from thermophilic bacteria distributed mainly among Chloroflexi, Deinococcus-Thermus and Firmicutes...
December 2017: AMB Express
https://www.readbyqxmd.com/read/28050269/a-cascade-of-thermophilic-enzymes-as-an-approach-to-the-synthesis-of-modified-nucleotides
#7
R S Esipov, Yu A Abramchik, I V Fateev, I D Konstantinova, M A Kostromina, T I Muravyova, K G Artemova, A I Miroshnikov
We propose a new approach for the synthesis of biologically important nucleotides which includes a multi-enzymatic cascade conversion of D-pentoses into purine nucleotides. The approach exploits nucleic acid exchange enzymes from thermophilic microorganisms: ribokinase, phosphoribosylpyrophosphate synthetase, and adenine phosphoribosyltransferase. We cloned the ribokinase gene from Thermus sp. 2.9, as well as two different genes of phosphoribosylpyrophosphate synthetase (PRPP-synthetase) and the adenine phosphoribosyltransferase (APR-transferase) gene from Thermus thermophilus HB27 into the expression vectors, generated high-yield E...
October 2016: Acta Naturae
https://www.readbyqxmd.com/read/28026953/role-of-the-conserved-valine-236-in-access-of-ligands-to-the-active-site-of-thermus-thermophilus-ba3-cytochrome-oxidase
#8
Chie Funatogawa, Yang Li, Ying Chen, William McDonald, Istvan Szundi, James A Fee, C David Stout, Ólöf Einarsdóttir
Knowledge of the role of conserved residues in the ligand channel of heme-copper oxidases is critical for understanding how the protein scaffold modulates the function of these enzymes. In this study, we investigated the role of the conserved valine 236 in the ligand channel of ba3 cytochrome c oxidase from Thermus thermophilus by mutating the residue to a more polar (V236T), smaller (V236A), or larger (V236I, V236N, V236L, V236M, and V236F) residue. The crystal structures of the mutants were determined, and the effects of the mutations on the rates of CO, O2, and NO binding were investigated...
December 27, 2016: Biochemistry
https://www.readbyqxmd.com/read/27977164/a-single-point-mutation-in-mitochondrial-hsp70-cochaperone-mge1-gains-thermal-stability-and-resistance
#9
Adinarayana Marada, Srinivasu Karri, Swati Singh, Praveen Kumar Allu, Yerranna Boggula, Thanuja Krishnamoorthy, Lalitha Guruprasad, Naresh Babu V Sepuri
Mge1, a yeast homologue of Escherichia coli GrpE, is an evolutionarily conserved homodimeric nucleotide exchange factor of mitochondrial Hsp70. Temperature-dependent reversible structural alteration from a dimeric to a monomeric form is critical for Mge1 to act as a thermosensor. However, very limited information about the structural component or amino acid residue(s) that contributes to thermal sensing of Mge1/GrpE is available. In this report, we have identified a single point mutation, His167 to Leu (H167L), within the hinge region of Mge1 that confers thermal resistance to yeast...
December 27, 2016: Biochemistry
https://www.readbyqxmd.com/read/27957494/the-gut-microbial-community-of-antarctic-fish-detected-by-16s-rrna-gene-sequence-analysis
#10
Wei Song, Lingzhi Li, Hongliang Huang, Keji Jiang, Fengying Zhang, Xuezhong Chen, Ming Zhao, Lingbo Ma
Intestinal bacterial communities are highly relevant to the digestion, nutrition, growth, reproduction, and a range of fitness in fish, but little is known about the gut microbial community in Antarctic fish. In this study, the composition of intestinal microbial community in four species of Antarctic fish was detected based on 16S rRNA gene sequencing. As a result, 1 004 639 sequences were obtained from 13 samples identified into 36 phyla and 804 genera, in which Proteobacteria, Actinobacteria, Firmicutes, Thermi, and Bacteroidetes were the dominant phyla, and Rhodococcus, Thermus, Acinetobacter, Propionibacterium, Streptococcus, and Mycoplasma were the dominant genera...
2016: BioMed Research International
https://www.readbyqxmd.com/read/27933038/computing-and-applying-atomic-regulons-to-understand-gene-expression-and-regulation
#11
José P Faria, James J Davis, Janaka N Edirisinghe, Ronald C Taylor, Pamela Weisenhorn, Robert D Olson, Rick L Stevens, Miguel Rocha, Isabel Rocha, Aaron A Best, Matthew DeJongh, Nathan L Tintle, Bruce Parrello, Ross Overbeek, Christopher S Henry
Understanding gene function and regulation is essential for the interpretation, prediction, and ultimate design of cell responses to changes in the environment. An important step toward meeting the challenge of understanding gene function and regulation is the identification of sets of genes that are always co-expressed. These gene sets, Atomic Regulons (ARs), represent fundamental units of function within a cell and could be used to associate genes of unknown function with cellular processes and to enable rational genetic engineering of cellular systems...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27929414/pb-2-effects-on-growth-lipids-and-protein-and-dna-profiles-of-the-thermophilic-bacterium-thermus-thermophilus
#12
Barbara Nicolaus, Annarita Poli, Paola Di Donato, Ida Romano, Giusi Laezza, Alessia Gioiello, Sergio Ulgiati, Florinda Fratianni, Filomena Nazzaro, Pierangelo Orlando, Stefano Dumontet
Extremophiles are organisms able to thrive in extreme environmental conditions and some of them show the ability to survive high doses of heavy metals thanks to defensive mechanisms provided by primary and secondary metabolic products, i.e., extremolytes, lipids, and extremozymes. This is why there is a growing scientific and industrial interest in the use of thermophilic bacteria in a host of tasks, from the environmental detoxification of heavy metal to industrial activities, such as bio-machining and bio-metallurgy...
December 6, 2016: Microorganisms
https://www.readbyqxmd.com/read/27928680/proteome-wide-identification-of-lysine-propionylation-in-thermophilic-and-mesophilic-bacteria-geobacillus-kaustophilus-thermus-thermophilus-escherichia-coli-bacillus-subtilis-and-rhodothermus-marinus
#13
Hiroki Okanishi, Kwang Kim, Ryoji Masui, Seiki Kuramitsu
Recent studies have revealed the physiological significance of post-translational lysine acylations such as acetylation in the regulation of various cellular processes. Here, we characterized lysine propionylation, a recently discovered post-translational acylation, in five representative bacteria: Geobacillus kaustophilus, Thermus thermophilus, Escherichia coli, Bacillus subtilis, and Rhodothermus marinus. Using antibody-based propionyl peptide enrichment followed by identification with nano-liquid chromatography tandem mass spectrometry, we showed that proteins were subject to lysine propionylation in all five bacterial species analyzed...
December 7, 2016: Extremophiles: Life Under Extreme Conditions
https://www.readbyqxmd.com/read/27928679/development-of-a-pyre-based-selective-system-for-thermotoga-sp-strain-rq7
#14
Dongmei Han, Zhaohui Xu
To fully unlock the biotechnological potentials of Thermotoga species, this study aimed to expand the genetic toolbox of Thermotoga by developing a new selective system. The developed system was composed of two components: a recipient strain bearing a deletion in its orotate phosphoribosyltransferase gene pyrE and a shuttle vector expressing a heterologous pyrE as the selectable marker. A spontaneous uracil auxotroph, T. sp. strain RQ7-15, was isolated at 70 °C with 2 mg/ml 5-fluoroorotic acid. The mutant carried a 112 bp deletion in pyrE and was a suitable recipient strain...
December 7, 2016: Extremophiles: Life Under Extreme Conditions
https://www.readbyqxmd.com/read/27924260/molecular-mechanisms-of-substrate-specificities-of-uridinecytidine-kinase
#15
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
#16
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...
January 2017: Insect Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/27903612/the-role-of-4u-as-an-extended-translation-termination-signal-in-bacteria
#17
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
#18
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
#19
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...
February 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27885197/a-thermostable-bilirubin-oxidizing-enzyme-from-activated-sludge-isolated-by-a-metagenomic-approach
#20
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...
December 23, 2016: Microbes and Environments
keyword
keyword
45583
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"