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Extremophiles: Life Under Extreme Conditions

Natsuki Takashima, Sonoko Ishino, Keisuke Oki, Mika Takafuji, Takeshi Yamagami, Ryotaro Matsuo, Kouta Mayanagi, Yoshizumi Ishino
DNA polymerase D (PolD), originally discovered in Pyrococcus furiosus, has no sequence homology with any other DNA polymerase family. Genes encoding PolD are found in most of archaea, except for those archaea in the Crenarchaeota phylum. PolD is composed of two proteins: DP1 and DP2. To date, the 3D structure of the PolD heteromeric complex is yet to be determined. In this study, we established a method that prepared highly purified PolD from Thermococcus kodakarensis, and purified DP1 and DP2 proteins formed a stable complex in solution...
November 30, 2018: Extremophiles: Life Under Extreme Conditions
Olga V Golyshina, Rafael Bargiela, Peter N Golyshin
Recently, the order Thermoplasmatales was expanded through the cultivation and description of species Cuniculiplasma divulgatum and corresponding family Cuniculiplasmataceae. Initially isolated from acidic streamers, signatures of these archaea were ubiquitously found in various low-pH settings. Eight genomes with various levels of completeness are currently available, all of which exhibit very high sequence identities and genomic conservation. Co-existence of Cuniculiplasmataceae with archaeal Richmond Mine acidophilic nanoorganisms ('ARMAN')-related archaea representing an intriguing group within the "microbial dark matter" suggests their common fundamental environmental strategy and metabolic networking...
November 29, 2018: Extremophiles: Life Under Extreme Conditions
Eskálath Morganna Silva Ferreira, Francisca Maria Pinheiro de Sousa, Luiz Henrique Rosa, Raphael Sanzio Pimenta
The interest in the diversity of yeasts in the Antarctic environment has increased in recent years, mainly because Antarctic microbiology is a recent science, and little is known about the biodiversity and genetic resources of the microorganisms that inhabit this ecosystem. This study aimed to determine the diversity of epiphytic yeasts in samples of Deschampsia antarctica, Colobanthus quitensis, and bryophytes, as well yeasts present in biofilms collected from Antarctic meltwater. Samples were collected in the summer of 2014 and 2015 during expeditions organized by the Brazilian Antarctic Program...
November 29, 2018: Extremophiles: Life Under Extreme Conditions
C Jeganathan, K Thamaraiselvi, T C Sabari Girisun
Enhanced production and growth of Halobacterium salinarum are achieved by direct supplement of essential amino acids in the modified nutrient culture medium. As arginine (R) and aspartate (D) are the main amino acid sources for producing bacteriorhodopsin efficiently from Halobacterium salinarum, both individual and combined effects of these two amino acids (in different compositions) in the basal medium were studied. The BR production is enhanced by 83% on the eighth day (saturated) for all individual and combined amino acid supplements...
November 26, 2018: Extremophiles: Life Under Extreme Conditions
A Gorlas, R Catchpole, E Marguet, P Forterre
Diverse DNA repair mechanisms are essential to all living organisms. Some of the most widespread repair systems allow recovery of genome integrity in the face of UV radiation. Here, we show that the hyperthermophilic archaeon Thermococcus nautili possesses a remarkable ability to recovery from extreme chromosomal damage. Immediately following UV irradiation, chromosomal DNA of T. nautili is fragmented beyond recognition. However, the extensive UV-induced double-stranded breaks (DSB) are repaired over the course of several hours, allowing restoration of growth...
November 22, 2018: Extremophiles: Life Under Extreme Conditions
Ana M Esteves, Gonçalo Graça, Lindsay Peyriga, Inês M Torcato, Nuno Borges, Jean-Charles Portais, Helena Santos
Pyrococcus furiosus is a remarkable archaeon able to grow at temperatures around 100 °C. To gain insight into how this model hyperthermophile copes with heat stress, we compared transcriptomic and metabolomic data of cells subjected to a temperature shift from 90 °C to 97 °C. In this study, we used RNA-sequencing to characterize the global variation in gene expression levels, while nuclear magnetic resonance (NMR) and targeted ion exchange liquid chromatography-mass spectrometry (LC-MS) were used to determine changes in metabolite levels...
November 14, 2018: Extremophiles: Life Under Extreme Conditions
Azadeh Mirfeizollahi, Bagher Yakhchali, Ali Asghar Deldar, Ali Asghar Karkhane
DNA-binding motif of bacterioopsin activator (Bat) protein is a Helix-Turn-Helix motif, which binds to bop promoter and induces bacterioopsin (Bop) expression under light and low oxygen tension. Bacterioopsin is linked to retinal to produce bacteriorhodopsin (BR), which in turn supplies energy source in Halobacterium salinarum. In this study, effect of Bat HTH motif-promoter DNA interaction on bacterioopsin (Bop) expression was investigated using in silico and experimental approaches. Molecular docking showed that the most stable DNA-protein complex was generated by Q661R/Q665R mutant...
October 22, 2018: Extremophiles: Life Under Extreme Conditions
Santina Soru, Veronica Malavasi, Pierluigi Caboni, Alessandro Concas, Giacomo Cao
The extremophile green alga Coccomyxa melkonianii SCCA 048 was investigated to evaluate its ability to grow in culture media with different pH. Specifically, Coccomyxa melkonianii was sampled in the Rio Irvi river (Sardinia, Italy) which is severely polluted by heavy metals as a result of abandoned mining activities. In this study, the strain was cultivated in growth media where the pH was kept fixed at the values of 4.0, 6.8 and 8.0, respectively. During the investigation, a significant phenotypic plasticity of this strain was observed...
October 19, 2018: Extremophiles: Life Under Extreme Conditions
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October 19, 2018: Extremophiles: Life Under Extreme Conditions
María Antonela Colonnella, Leonardo Lizarraga, Leticia Rossi, Rocío Díaz Peña, Diego Egoburo, Nancy I López, Laura J Raiger Iustman
Environments co-contaminated with heavy metals and hydrocarbons have become an important problem worldwide, especially due to the effect of metals on hydrocarbon degrading microorganisms. Pseudomonas extremaustralis, a bacterium isolated from a pristine pond in Antarctica, showed high capabilities to cope with environmental stress and a very versatile metabolism that includes alkane degradation under microaerobic conditions. In this work, we analyzed P. extremaustralis' capability to resist high copper concentrations and the effect of copper presence in diesel biodegradation...
October 17, 2018: Extremophiles: Life Under Extreme Conditions
Otakar Strunecký, Karel Kopejtka, Franz Goecke, Jürgen Tomasch, Jaromír Lukavský, Amir Neori, Silke Kahl, Dietmar H Pieper, Plamen Pilarski, David Kaftan, Michal Koblížek
Genotypic and morphological diversity of cyanobacteria in the Rupite hot spring (Bulgaria) was investigated by means of optical microscopy, cultivation, single-cell PCR, and 16S rRNA gene amplicon sequencing. Altogether, 34 sites were investigated along the 71-39 °C temperature gradient. Analysis of samples from eight representative sites shown that Illumina, optical microscopy, and Roche 454 identified 72, 45 and 19% respective occurrences of all cumulatively present taxa. Optical microscopy failed to detect species of minor occurrence; whereas, amplicon sequencing technologies suffered from failed primer annealing and the presence of species with extensive extracellular polysaccharides production...
October 4, 2018: Extremophiles: Life Under Extreme Conditions
Sonali Majumdar, Michael P Terns
Diverse CRISPR-Cas immune systems protect archaea and bacteria from viruses and other mobile genetic elements. All CRISPR-Cas systems ultimately function by sequence-specific destruction of invading complementary nucleic acids. However, each CRISPR system uses compositionally distinct crRNP [CRISPR (cr) RNA/Cas protein] immune effector complexes to recognize and destroy invasive nucleic acids by unique molecular mechanisms. Previously, we found that Type I-A (Csa) effector crRNPs from Pyrococcus furiosus function in vivo to eliminate invader DNA...
October 3, 2018: Extremophiles: Life Under Extreme Conditions
Filomena De Leo, Angelina Lo Giudice, Chiara Alaimo, Giusy De Carlo, Alessandro Ciro Rappazzo, Marco Graziano, Emilio De Domenico, Clara Urzì
The occurrence of cultivable fungi was investigated along the water column (25-2500 m depth) of four off-shore stations in the Mediterranean basin. An unexpected high abundance of fungi, accompanied by a scarce biodiversity, was observed up to 2500 m depth. The black yeast Hortaea werneckii, known to be one of the most salt tolerant eukaryotic organisms, was isolated for the first time from the Mediterranean Sea, and it was the dominant fungus present in seawater in almost all stations and depths, suggesting its ubiquitous distribution...
October 1, 2018: Extremophiles: Life Under Extreme Conditions
Juan José Marizcurrena, Wilner Martínez-López, Hongju Ma, Tilman Lamparter, Susana Castro-Sowinski
Photolyases are DNA-repairing flavoproteins that are represented in most phylogenetic taxa with the exception of placental mammals. These enzymes reduce the ultraviolet-induced DNA damage; thus, they have features that make them very attractive for dermatological or other medical uses, such as the prevention of human skin cancer and actinic keratosis. In this work, we identified a 50.8 kDa photolyase from the UVC-resistant Antarctic bacterium Hymenobacter sp. UV11. The enzyme was produced by recombinant DNA technology, purified using immobilized metal affinity chromatography and its activity was analyzed using different approaches: detection of cyclobutane pyrimidine dimers (CPDs) by immunochemistry, high-performance liquid chromatography and comet assays using Chinese Hamster Ovary (CHO) and immortalized nontumorigenic human epidermal (HaCat) cells...
September 28, 2018: Extremophiles: Life Under Extreme Conditions
Muhammad Arif, Naeem Rashid, Sumera Perveen, Qamar Bashir, Muhammad Akhtar
The gene-encoding Indole-3-glycerol phosphate synthase, a key enzyme involved in the cyclization of 1-(o-carboxyphenylamino)-1-deoxyribulose 5-phosphate, from Pyrococcus furiosus was cloned and expressed in Escherichia coli. The gene product was produced in the soluble and active form. The recombinant protein, purified to apparent homogeneity, displayed highest activity at 100 °C and pH of 5.5. The recombinant enzyme followed Michaelis-Menten kinetics exhibiting apparent Vmax and Km values of 20 ± 0...
September 27, 2018: Extremophiles: Life Under Extreme Conditions
En-Min Zhou, Wen-Dong Xian, Chrisabelle C Mefferd, Scott C Thomas, Arinola L Adegboruwa, Nathan Williams, Senthil K Murugapiran, Jeremy A Dodsworth, Rakesh Ganji, Meng-Meng Li, Yi-Ping Ding, Lan Liu, Tanja Woyke, Wen-Jun Li, Brian P Hedlund
Thermus species are widespread in natural and artificial thermal environments. Two new yellow-pigmented strains, L198T and L423, isolated from Little Hot Creek, a geothermal spring in eastern California, were identified as novel organisms belonging to the genus Thermus. Cells are Gram-negative, rod-shaped, and non-motile. Growth was observed at temperatures from 45 to 75 °C and at salinities of 0-2.0% added NaCl. Both strains grow heterotrophically or chemolithotrophically by oxidation of thiosulfate to sulfate...
November 2018: Extremophiles: Life Under Extreme Conditions
Scott Wushke, Brian Fristensky, Xiang Li Zhang, Vic Spicer, Oleg V Krokhin, David B Levin, Matthew B Stott, Richard Sparling
A metabolic, genomic and proteomic assessment of Fervidobacterium pennivorans strains was undertaken to clarify the metabolic and genetic capabilities of this Thermotogales species. The type strain Ven5 originally isolated from a hot mud spa in Italy, and a newly isolated strain (DYC) from a hot spring at Ngatamariki, New Zealand, were compared for metabolic and genomic differences. The fermentation profiles of both strains on cellobiose generated similar major end products (acetate, alanine, glutamate, H2 , and CO2 )...
November 2018: Extremophiles: Life Under Extreme Conditions
Chunli Zheng, Li Zhang, Minjie Chen, Xue Qiang Zhao, Yizhuo Duan, Ye Meng, Xuefeng Zhang, Ren Fang Shen
The glutathione synthetase system (GSS) is an important pathway of glutathione synthesis and plays a key role in heavy metal resistance. In this work, the response of Acidithiobacillus ferrooxidans to extracellular Cd2+ was investigated, and the interplay between Cd2+ resistance and the expression of GSS related-genes was analyzed by reverse-transcription quantitative PCR (RT-PCR). During growth in the presence of 5, 15 and 30 mM Cd2+ , the transcript levels of eight GSS pathway genes were affected between 0...
November 2018: Extremophiles: Life Under Extreme Conditions
Angela Casillo, Marcello Ziaco, Buko Lindner, Ermenegilda Parrilli, Dominik Schwudke, Aurora Holgado, Rudi Beyaert, Rosa Lanzetta, Maria Luisa Tutino, Maria Michela Corsaro
Psychrobacter arcticus 273-4 is a Gram-negative bacterium isolated from a 20,000-to-30,000-year-old continuously frozen permafrost in the Kolyma region in Siberia. The survival strategies adopted to live at subzero temperatures include all the outer membrane molecules. A strategic involvement in the well-known enhancement of cellular membrane fluidity is attributable to the lipopolysaccharides (LPSs). These molecules covering about the 75% of cellular surface contribute to cold adaptation through structural modifications in their portions...
November 2018: Extremophiles: Life Under Extreme Conditions
Olivier Zablocki, Leonardo van Zyl, Marla Trindade
Bacterial viruses ("phages") play important roles in the regulation and evolution of microbial communities in most ecosystems. Terrestrial hot springs typically contain thermophilic bacterial communities, but the diversity and impacts of its associated viruses ("thermophilic phages") are largely unexplored. Here, we provide a taxonomic overview of phages that have been isolated strictly from terrestrial hot springs around the world. In addition, we placed 17 thermophilic phage genomes in a global phylogenomic context to detect evolutionary patterns...
November 2018: Extremophiles: Life Under Extreme Conditions
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