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https://www.readbyqxmd.com/read/28206708/physiological-metabolic-and-biotechnological-features-of-extremely-thermophilic-microorganisms
#1
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...
February 16, 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/28197737/reactive-sites-and-course-of-reduction-in-the-rieske-protein
#2
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
#3
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
#4
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
#5
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
https://www.readbyqxmd.com/read/28161633/insight-into-the-transition-between-the-open-and-closed-conformations-of-thermus-thermophilus-carboxypeptidase
#6
Masahiko Okai, Akihiro Yamamura, Kou Hayakawa, Shiho Tsutsui, Ken-Ichi Miyazono, Woo-Cheol Lee, Koji Nagata, Yumiko Inoue, Masaru Tanokura
Carboxypeptidase cleaves the C-terminal amino acid residue from proteins and peptides. Here, we report the functional and structural characterizations of carboxypeptidase belonging to the M32 family from the thermophilic bacterium Thermus thermophilus HB8 (TthCP). TthCP exhibits a relatively broad specificity for both hydrophilic (neutral and basic) and hydrophobic (aliphatic and aromatic) residues at the C-terminus and shows optimal activity in the temperature range of 75-80 °C and in the pH range of 6.8-7...
February 2, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28160372/design-and-discovery-of-new-combinations-of-mutant-dna-polymerases-and-modified-dna-substrates
#7
Sydney L Rosenblum, Aurora G Weiden, Eliza L Lewis, Alexie L Ogonowsky, Hannah E Chia, Susanna E Barrett, Mira D Liu, Aaron Morgan Leconte
Chemical modifications can enhance the properties of DNA by imparting nuclease resistance or generating more diverse physical structures. However, native DNA polymerases genearlly cannot synthesize any length of DNA with modified nucleotide triphosphates. Previous efforts have identified a mutant of DNA polymerase I from Thermus aquaticus DNA (SFM19) as capable of synthesizing a range of short, 2' modified DNAs; however, it is limited by the length of the products that it can synthesize. Here, we have rationally designed and characterized ten mutants of SFM19...
February 3, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28153912/complete-genome-sequence-of-thermus-thermophilus-tmy-isolated-from-a-geothermal-power-plant
#8
Yasuhiro Fujino, Yuko Nagayoshi, Toshihisa Ohshima, Seiya Ogata, Katsumi Doi
Thermus thermophilus TMY (JCM 10668) was isolated from silica scale formed at a geothermal power plant in Japan. Here, we report the complete genome sequence for this strain, which contains a chromosomal DNA of 2,121,526 bp with 2,500 predicted genes and a pTMY plasmid of 19,139 bp, with 28 predicted genes.
February 2, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28115258/cryo-em-analysis-of-a-domain-antibody-bound-rotary-atpase-complex
#9
Roberta B Davies, Callum Smits, Andrew Sw Wong, Daniela Stock, Mary Christie, Sara Sandin, Alastair G Stewart
The bacterial A/V-type ATPase/synthase rotary motor couples ATP hydrolysis/synthesis with proton translocation across biological membranes. The A/V-type ATPase/synthase from Thermus thermophilus has been extensively studied both structurally and functionally for many years. Here we provide an 8.7 Å resolution cryo-electron microscopy 3D reconstruction of this complex bound to single-domain antibody fragments, small monomeric antibodies containing just the variable heavy domain. Docking of known structures into the density revealed the molecular orientation of the domain antibodies, suggesting that structure determination of co-domain antibody:protein complexes could be a useful avenue for unstable or smaller proteins...
January 20, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28114398/rna-and-dna-targeting-by-a-reconstituted-thermus-thermophilus-type-iii-a-crispr-cas-system
#10
Tina Y Liu, Anthony T Iavarone, Jennifer A Doudna
CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated) systems are RNA-guided adaptive immunity pathways used by bacteria and archaea to defend against phages and plasmids. Type III-A systems use a multisubunit interference complex called Csm, containing Cas proteins and a CRISPR RNA (crRNA) to target cognate nucleic acids. The Csm complex is intriguing in that it mediates RNA-guided targeting of both RNA and transcriptionally active DNA, but the mechanism is not well understood...
2017: PloS One
https://www.readbyqxmd.com/read/28097217/amylose-recognition-and-ring-size-determination-of-amylomaltase
#11
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
#12
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
#13
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
#14
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 24, 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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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