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Extremophiles: Life Under Extreme Conditions

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https://www.readbyqxmd.com/read/29464394/functional-dissection-of-the-three-n-terminal-general-secretory-pathway-domains-and-the-walker-motifs-of-the-traffic-atpase-pilf-from-thermus-thermophilus
#1
Kerstin Kruse, Ralf Salzer, Friederike Joos, Beate Averhoff
The traffic ATPase PilF of Thermus thermophilus powers pilus assembly as well as uptake of DNA. PilF differs from other traffic ATPases by a triplicated general secretory pathway II, protein E, N-terminal domain (GSPIIABC). We investigated the in vivo and in vitro roles of the GSPII domains, the Walker A motif and a catalytic glutamate by analyzing a set of PilF deletion derivatives and pilF mutants. Here, we report that PilF variants devoid of the first two or all three GSPII domains do not form stable hexamers indicating a role of the triplicated GSPII domain in complex formation and/or stability...
February 20, 2018: Extremophiles: Life Under Extreme Conditions
https://www.readbyqxmd.com/read/29455263/halobacterium-salinarum-storage-and-rehydration-after-spray-drying-and-optimization-of-the-processes-for-preservation-of-carotenoids
#2
Sergei V Kalenov, Mariia G Gordienko, Ekaterina D Murzina, Daniil Y Poberezhniy, Dmitry V Baurin, Natalia E Suzina, Alexander N Morozov, Liubov M Yakubovich, Alexey A Belov, Victor I Panfilov, Oksana V Yarovaya, Michail M Il'in, Vladimir V Sorokin, Dmitry A Skladnev
Spray drying is appropriate for the preservation of halophilic microorganisms due to the nature of these microorganisms, as they survive in adverse environmental conditions by being encapsulated in salt crystals. Artificial neural networks were in this study used to optimize practically significant spray-drying regimes of the C50 -carotenoids producer Halobacterium salinarum. Immediately after drying, the samples contained up to 54% halobacterial biomass and less than 5% moisture, and the level of preservation of carotenoids was 95-97%...
February 17, 2018: Extremophiles: Life Under Extreme Conditions
https://www.readbyqxmd.com/read/29450709/biofilm-formation-and-potential-for-iron-cycling-in-serpentinization-influenced-groundwater-of-the-zambales-and-coast-range-ophiolites
#3
D'Arcy R Meyer-Dombard, Caitlin P Casar, Alexander G Simon, Dawn Cardace, Matthew O Schrenk, Carlo A Arcilla
Terrestrial serpentinizing systems harbor microbial subsurface life. Passive or active microbially mediated iron transformations at alkaline conditions in deep biosphere serpentinizing ecosystems are understudied. We explore these processes in the Zambales (Philippines) and Coast Range (CA, USA) ophiolites, and associated surface ecosystems by probing the relevance of samples acquired at the surface to in situ, subsurface ecosystems, and the nature of microbe-mineral associations in the subsurface. In this pilot study, we use microcosm experiments and batch culturing directed at iron redox transformations to confirm thermodynamically based predictions that iron transformations may be important in subsurface serpentinizing ecosystems...
February 15, 2018: Extremophiles: Life Under Extreme Conditions
https://www.readbyqxmd.com/read/29442249/the-vertical-distribution-of-prokaryotes-in-the-surface-sediment-of-jiaolong-cold-seep-at-the-northern-south-china-sea
#4
Yuzhi Wu, Jian-Wen Qiu, Pei-Yuan Qian, Yong Wang
In deep-sea cold seeps, microbial communities are shaped by geochemical components in seepage solutions. In the present study, we report the composition of microbial communities and potential metabolic activities in the surface sediment of Jiaolong cold seep at the northern South China Sea. Pyrosequencing of 16S rRNA gene amplicons revealed that a majority of the microbial inhabitants of the surface layers (0-6 cm) were sulfur oxidizer bacteria Sulfurimonas and archaeal methane consumer ANME-1, while sulfate reducer bacteria SEEP-SRB1, ANME-1 and ANME-2 dominated the bottom layers (8-14 cm)...
February 13, 2018: Extremophiles: Life Under Extreme Conditions
https://www.readbyqxmd.com/read/29442248/the-genes-and-enzymes-of-sucrose-metabolism-in-moderately-thermophilic-methanotroph-methylocaldum-szegediense-o12
#5
Sergey Y But, Natalia P Solntseva, Svetlana V Egorova, Ildar I Mustakhimov, Valentina N Khmelenina, Alexander Reshetnikov, Yuri A Trotsenko
Four enzymes involved in sucrose metabolism: sucrose phosphate synthase (Sps), sucrose phosphate phosphatase (Spp), sucrose synthase (Sus) and fructokinase (FruK), were obtained as his-tagged proteins from the moderately thermophilic methanotroph Methylocaldum szegediense O12. Sps, Spp, FruK and Sus demonstrated biochemical properties similar to those of other bacterial counterparts, but the translated amino acid sequences of Sps and Spp displayed high divergence from the respective microbial enzymes. The Sus of M...
February 13, 2018: Extremophiles: Life Under Extreme Conditions
https://www.readbyqxmd.com/read/29442247/thermostable-marine-microbial-proteases-for-industrial-applications-scopes-and-risks
#6
REVIEW
Noora Barzkar, Ahmad Homaei, Roohullah Hemmati, Seema Patel
Thermostable proteases are important in biotechnological and industrial sectors, due to their stability against denaturing agents and chemicals. The feature that gives them such unique applicability is their reaction at high temperatures, which affords a high concentration of substrate, and less risk of microbial contamination. Nearly 65% of industrial proteases are isolated from marine microbial source, and they can significantly resist a wide range of organic solvents at high temperatures. The most important trait of marine organisms is their adaptability, which allows them to grow optimally in harsh environments such as high salt, temperatures, and pressure-the characteristics of deep-sea hot springs and geothermal sediments...
February 13, 2018: Extremophiles: Life Under Extreme Conditions
https://www.readbyqxmd.com/read/29435649/genome-sequence-and-description-of-haloferax-massiliense-sp-nov-a-new-halophilic-archaeon-isolated-from-the-human-gut
#7
Saber Khelaifia, Aurelia Caputo, Claudia Andrieu, Frederique Cadoret, Nicholas Armstrong, Caroline Michelle, Jean-Christophe Lagier, Felix Djossou, Pierre-Edouard Fournier, Didier Raoult
By applying the culturomics concept and using culture conditions containing a high salt concentration, we herein isolated the first known halophilic archaeon colonizing the human gut. Here we described its phenotypic and biochemical characterization as well as its genome annotation. Strain Arc-HrT (= CSUR P0974 = CECT 9307) was mesophile and grew optimally at 37 °C and pH 7. Strain Arc-HrT was also extremely halophilic with an optimal growth observed at 15% NaCl. It showed gram-negative cocci, was strictly aerobic, non-motile and non-spore-forming, and exhibited catalase and oxidase activities...
February 12, 2018: Extremophiles: Life Under Extreme Conditions
https://www.readbyqxmd.com/read/29429010/shifts-of-methanogenic-communities-in-response-to-permafrost-thaw-results-in-rising-methane-emissions-and-soil-property-changes
#8
Shiping Wei, Hongpeng Cui, Youhai Zhu, Zhenquan Lu, Shouji Pang, Shuai Zhang, Hailiang Dong, Xin Su
Permafrost thaw can bring negative consequences in terms of ecosystems, resulting in permafrost collapse, waterlogging, thermokarst lake development, and species composition changes. Little is known about how permafrost thaw influences microbial community shifts and their activities. Here, we show that the dominant archaeal community shifts from Methanomicrobiales to Methanosarcinales in response to the permafrost thaw, and the increase in methane emission is found to be associated with the methanogenic archaea, which rapidly bloom with nearly tenfold increase in total number...
February 10, 2018: Extremophiles: Life Under Extreme Conditions
https://www.readbyqxmd.com/read/29380170/description-of-a-cryptic-thermophilic-pro-phage-cbp1-from-caldibacillus-debilis-strain-gb1
#9
Scott Wushke, Zimo Jin, Victor Spicer, Xiang Li Zhang, Brian Fristensky, Oleg V Krokhin, David B Levin, Richard Sparling
This study characterizes a cryptic (pro)phage-related sequence within the Caldibacillus debilis GB1 genome, designated CBP1.CBP1 is a Siphoviridae-like genome highly related to GBVS1 from Geobacillus sp. 6k51. The CBP1genome is a 37,315 bp region containing 69 putative ORFs with a GC content of 42% flanked on both sides by host DNA integrated into the main bacterial chromosome (contig 16). Bioinformatic analyses identified cassettes of genes within the CBP1 genome that were similar in function, yet distinct in sequence, from genes previously identified in GBVS1...
January 30, 2018: Extremophiles: Life Under Extreme Conditions
https://www.readbyqxmd.com/read/29353380/crystal-structure-of-the-nadp-and-tartrate-bound-complex-of-l-serine-3-dehydrogenase-from-the-hyperthermophilic-archaeon-pyrobaculum-calidifontis
#10
Kazunari Yoneda, Haruhiko Sakuraba, Tomohiro Araki, Toshihisa Ohshima
A gene encoding L-serine dehydrogenase (L-SerDH) that exhibits extremely low sequence identity to the Agrobacterium tumefaciens L-SerDH was identified in the hyperthermophilic archaeon Pyrobaculum calidifontis. The predicted amino acid sequence showed 36% identity with that of Pseudomonas aeruginosa L-SerDH, suggesting that P. calidifontis L-SerDH is a novel type of L-SerDH, like Ps. aeruginosa L-SerDH. The overexpressed enzyme appears to be the most thermostable L-SerDH described to date, and no loss of activity was observed by incubation for 30 min at temperatures up to 100 °C...
January 20, 2018: Extremophiles: Life Under Extreme Conditions
https://www.readbyqxmd.com/read/29350297/microbial-communities-and-their-predicted-metabolic-functions-in-a-desiccating-acid-salt-lake
#11
Elena Zaikova, Kathleen C Benison, Melanie R Mormile, Sarah Stewart Johnson
The waters of Lake Magic in Western Australia are among the most geochemically extreme on Earth. This ephemeral saline lake is characterized by pH as low as 1.6 salinity as high as 32% total dissolved solids, and unusually complex geochemistry, including extremely high concentrations of aluminum, silica, and iron. We examined the microbial composition and putative function in this extreme acid brine environment by analyzing lake water, groundwater, and sediment samples collected during the austral summer near peak evapoconcentration...
January 19, 2018: Extremophiles: Life Under Extreme Conditions
https://www.readbyqxmd.com/read/29340843/phytoene-production-utilizing-the-isoprenoid-biosynthesis-capacity-of-thermococcus-kodakarensis
#12
Tsubasa Fuke, Takaaki Sato, Savyasachee Jha, Myra L Tansengco, Haruyuki Atomi
Phytoene (C40H64) is an isoprenoid and a precursor of various carotenoids which are of industrial value. Archaea can be considered to exhibit a relatively large capacity to produce isoprenoids, as they are components of their membrane lipids. Here, we aimed to produce isoprenoids such as phytoene in the hyperthermophilic archaeon Thermococcus kodakarensis. T. kodakarensis harbors a prenyltransferase gene involved in the biosynthesis of farnesyl pyrophosphate and geranylgeranyl pyrophosphate, which are precursors of squalene and phytoene, respectively...
January 16, 2018: Extremophiles: Life Under Extreme Conditions
https://www.readbyqxmd.com/read/29335805/effects-of-nicotine-on-the-biosynthesis-of-carotenoids-in-halophilic-archaea-class-halobacteria-an-hplc-and-raman-spectroscopy-study
#13
Aharon Oren, Joseph Hirschberg, Varda Mann, Jan Jehlička
Nicotine has a profound influence on the carotenoid metabolism in halophilic Archaea of the class Halobacteria. In a study of Halobacterium salinarum, Haloarcula marismortui and Halorubrum sodomense, using different analytical techniques to monitor the production of different carotenoids as a function of the presence of nicotine, we showed that the formation of α-bacterioruberin was inhibited in all. In Hbt. salinarum, addition of nicotine led to a significant change in the color of the culture due to the accumulation of lycopene, in addition to the formation of bisanhydrobacterioruberin which does not differ in color from α-bacterioruberin...
January 15, 2018: Extremophiles: Life Under Extreme Conditions
https://www.readbyqxmd.com/read/29335804/identification-of-a-functional-toxin-antitoxin-system-located-in-the-genomic-island-pyg1-of-piezophilic-hyperthermophilic-archaeon-pyrococcus-yayanosii
#14
Zhen Li, Qinghao Song, Yinzhao Wang, Xiang Xiao, Jun Xu
Toxin-antitoxin (TA) system is bacterial or archaeal genetic module consisting of toxin and antitoxin gene that be organized as a bicistronic operon. TA system could elicit programmed cell death, which is supposed to play important roles for the survival of prokaryotic population under various physiological stress conditions. The phage abortive infection system (AbiE family) belongs to bacterial type IV TA system. However, no archaeal AbiE family TA system has been reported so far. In this study, a putative AbiE TA system (PygAT), which is located in a genomic island PYG1 in the chromosome of Pyrococcus yayanosii CH1, was identified and characterized...
January 15, 2018: Extremophiles: Life Under Extreme Conditions
https://www.readbyqxmd.com/read/29332142/purification-and-characterization-of-a-novel-organic-solvent-tolerant-and-cold-adapted-lipase-from-psychrobacter-sp-zy124
#15
Yue Zhang, Fangling Ji, Jingyun Wang, Zhongji Pu, Bo Jiang, Yongming Bao
By screening 25 different psychrophilic strains isolated from the Arctic habitat, we isolated a strain capable of producing lipase. We identified this strain as Psychrobacter sp. ZY124 based on the amplified 16S rDNA sequence. The lipase, named as Lipase ZC12, produced from the supernatant of Psychrobacter sp. ZY124 cultured at 15 °C was purified to homogeneity by ammonium sulfate precipitation followed by Phenyl Sepharose FF gel hydrophobic chromatography. Based on the obtained amino acid sequence, Lipase ZC12 is classified as a member of the Proteus/psychrophilic subfamily of lipase family I...
January 13, 2018: Extremophiles: Life Under Extreme Conditions
https://www.readbyqxmd.com/read/29332141/cultivable-fungi-present-in-antarctic-soils-taxonomy-phylogeny-diversity-and-bioprospecting-of-antiparasitic-and-herbicidal-metabolites
#16
Eldon C Q Gomes, Valéria M Godinho, Débora A S Silva, Maria T R de Paula, Gislaine A Vitoreli, Carlos L Zani, Tânia M A Alves, Policarpo A S Junior, Silvane M F Murta, Emerson C Barbosa, Jaquelline G Oliveira, Fabio S Oliveira, Camila R Carvalho, Mariana C Ferreira, Carlos A Rosa, Luiz H Rosa
Molecular biology techniques were used to identify 218 fungi from soil samples collected from four islands of Antarctica. These consisted of 22 taxa of 15 different genera belonging to the Zygomycota, Ascomycota, and Basidiomycota. Mortierella, Antarctomyces, Pseudogymnoascus, and Penicillium were the most frequently isolated genera and Penicillium tardochrysogenum, Penicillium verrucosus, Goffeauzyma gilvescens, and Mortierella sp. 2 the most abundant taxa. All fungal isolates were cultivated using solid-state fermentation to obtain their crude extracts...
January 13, 2018: Extremophiles: Life Under Extreme Conditions
https://www.readbyqxmd.com/read/29330650/a-cold-adapted-endoglucanase-from-camel-rumen-with-high-catalytic-activity-at-moderate-and-low-temperatures-an-anomaly-of-truly-cold-adapted-evolution-in-a-mesophilic-environment
#17
Kamran Khalili Ghadikolaei, Javad Gharechahi, Kamahldin Haghbeen, Kambiz Akbari Noghabi, Ghasem Hosseini Salekdeh, Hossein Shahbani Zahiri
Endoglucanases are important enzymes in plant biomass degradation. They have current and potential applications in various industrial sectors including human and animal food processing, textile, paper, and renewable biofuel production. It is assumed that the cold-active endoglucanases, with high catalytic rates in moderate and cold temperatures, can improve the cost-effectiveness of industrial processes by lowering the need for heating and, thus, energy consumption. In this study, the endoglucanase CelCM3 was procured from a camel rumen metagenome via gene cloning and expression in Escherichia coli BL21 (DE3)...
January 12, 2018: Extremophiles: Life Under Extreme Conditions
https://www.readbyqxmd.com/read/29330649/growth-of-leptospirillum-ferriphilum-in-sulfur-medium-in-co-culture-with-acidithiobacillus-caldus
#18
Sarah L Smith, D Barrie Johnson
Leptospirillum ferriphilum and Acidithiobacillus caldus are both thermotolerant acidophilic bacteria that frequently co-exist in natural and man-made environments, such as biomining sites. Both are aerobic chemolithotrophs; L. ferriphilum is known only to use ferrous iron as electron donor, while A. caldus can use zero-valent and reduced sulfur, and also hydrogen, as electron donors. It has recently been demonstrated that A. caldus reduces ferric iron to ferrous when grown aerobically on sulfur. Experiments were carried out which demonstrated that this allowed L...
January 12, 2018: Extremophiles: Life Under Extreme Conditions
https://www.readbyqxmd.com/read/29330648/cloning-expression-and-characterization-of-the-esterase-estut1-from-ureibacillus-thermosphaericus-which-belongs-to-a-new-lipase-family-xviii
#19
Yuliya V Samoylova, Ksenia N Sorokina, Margarita V Romanenko, Valentin N Parmon
A new esterase gene from thermophilic bacteria Ureibacillus thermosphaericus was cloned into the pET32b vector and expressed in Escherichia coli BL21(DE3). Alignment of the estUT1 amino acid sequence revealed the presence of a novel canonical pentapeptide (GVSLG) and 41-47% identity to the closest family of the bacterial lipases XIII. Thus the esterase estUT1 from U. thermosphaericus was assigned as a member of the novel family XVIII. It also showed a strong activity toward short-chain esters (C2-C8), with the highest activity for C2...
January 12, 2018: Extremophiles: Life Under Extreme Conditions
https://www.readbyqxmd.com/read/29327280/comparison-of-the-ding-protein-from-the-archaeon-sulfolobus-solfataricus-with-human-phosphate-binding-protein-and-pseudomonas-fluorescence-ding-counterparts
#20
Elena Porzio, Anna De Maio, Teresa Ricciardi, Carmela Mistretta, Giuseppe Manco, Maria Rosaria Faraone-Mennella
DING proteins represent a new group of 40 kDa-related members, ubiquitous in living organisms. The family also include the DING protein from Sulfolobus solfataricus, functionally related to poly(ADP-ribose) polymerases. Here, the archaeal protein has been compared with the human Phosphate-Binding Protein and the Pseudomonas fluorescence DING enzyme, by enzyme assays and immune cross-reactivity. Surprisingly, as the Sulfolobus enzyme, the Human and Pseudomonas proteins display poly(ADP-ribose) polymerase activity, whereas a phosphatase activity was only present in Sulfolobus and human protein, despite the conserved phosphate-binding site residues in Pseudomonas DING...
January 11, 2018: Extremophiles: Life Under Extreme Conditions
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