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Extremophiles: Life Under Extreme Conditions

Ravinder Kumar, Anil Kumar Pinnaka, Beena Krishnan
A moderately thermophilic Gram-negative bacterium isolated from the Polok hot spring, Sikkim, India, was identified as a strain (PL17) of Tepidimonas fonticaldi by 16S rDNA sequencing. T. fonticaldi PL17 produces a Type IIP restriction endonuclease; named TfoI. Restriction mapping, run-off sequencing of TfoI-digests of dsDNA fragments, and end compatibility of TfoI with NdeI confirmed that the enzyme recognizes and cleaves the sequence 5'-T^TAA-3', and is thus an isoschizomer of MseI. The TfoI restriction-modification genes in the T...
March 18, 2017: Extremophiles: Life Under Extreme Conditions
Saadia Basheer, Naeem Rashid, Raza Ashraf, Muhammad Sohail Akram, Masood Ahmed Siddiqui, Tadayuki Imanaka, Muhammad Akhtar
Genome search of Geobacillus thermopakistaniensis, formerly Geobacillus sp. SBS-4S, revealed the presence of an open reading frame (ESU71923) annotated as laccase. However, the gene product did not display any laccase-like activity against the substrates examined. The laccase activity was, therefore, purified from G. thermopakistaniensis cells and N-terminal amino acid residues of the enzyme were determined. These residues matched the N-terminal sequence of an open reading frame annotated as a copper oxidase (ESU72270)...
March 17, 2017: Extremophiles: Life Under Extreme Conditions
Shan Zhang, Weizhi Song, Min Yu, Xuezheng Lin
Psychrobacter has been regarded as an important genus for bacterial cold adaptation studies. However, members of this genus are highly varied in terms of both cold adaptability and genome content. To get an understanding of the diversity of members of this genus, five Psychrobacter strains (G, K5, 273-4, PAMC21119 and PRwf-1), with publicly available complete/draft genome, were selected and comprehensive comparative genomics analyses were performed among them. The closest phylogenetic relationship, highest average nucleotide identity (96...
March 17, 2017: Extremophiles: Life Under Extreme Conditions
Iram Aziz, Naeem Rashid, Raza Ashraf, Qamar Bashir, Tadayuki Imanaka, Muhammad Akhtar
Pyrobaculum calidifontis genome harbors an open reading frame Pcal_0111 annotated as fructose bisphosphate aldolase. Although the gene is annotated as fructose bisphosphate aldolase, it exhibits a high homology with previously reported fructose-1,6-bisphosphate aldolase/phosphatase from Thermoproteus neutrophilus. To examine the biochemical properties of Pcal_0111, we have cloned and expressed the gene in Escherichia coli. Purified recombinant Pcal_0111 catalyzed both phosphatase and aldolase reactions with specific activity values of 4 U and 1...
March 15, 2017: Extremophiles: Life Under Extreme Conditions
Miguel Medrano-Santillana, Elcia Margaret Souza-Brito, Robert Duran, Felix Gutierrez-Corona, Georgina Elena Reyna-López
Active volcanoes are among the most extreme environments on Earth. The extreme temperatures, presence of toxic heavy metals and low nutrient bioavailability favor the development of extremophiles. We characterized the physical-chemical parameters of and bacterial communities (T-RFLP and 16S rRNA gene libraries) inhabiting fumarole niches of the Paricutín volcano located in Michoacán (Mexico). This volcano, which surged in 1943, is one of the youngest volcanoes on Earth and the microbial diversity in this area is yet to be characterized...
March 13, 2017: Extremophiles: Life Under Extreme Conditions
Debamitra Chakravorty, Mohd Faheem Khan, Sanjukta Patra
Research on extremostable proteins has seen immense growth in the past decade owing to their industrial importance. Basic research of attributes related to extreme-stability requires further exploration. Modern mechanistic approaches to engineer such proteins in vitro will have more impact in industrial biotechnology economy. Developing a priori knowledge about the mechanism behind extreme-stability will nurture better understanding of pathways leading to protein molecular evolution and folding. This review is a vivid compilation about all classes of extremostable proteins and the attributes that lead to myriad of adaptations divulged after an extensive study of 6495 articles belonging to extremostable proteins...
March 10, 2017: Extremophiles: Life Under Extreme Conditions
Pablo Marcelo Fernández, María Martha Martorell, Mariana G Blaser, Lucas Adolfo Mauro Ruberto, Lucía Inés Castellanos de Figueroa, Walter Patricio Mac Cormack
In cold environments, biodegradation of organic pollutants and heavy metal bio-conversion requires the activity of cold-adapted or cold-tolerant microorganisms. In this work, the ability to utilize phenol, methanol and n-hexadecane as C source, the tolerance to different heavy metals and growth from 5 to 30 °C were evaluated in cold-adapted yeasts isolated from Antarctica. Fifty-nine percent of the yeasts were classified as psychrotolerant as they could grow in all the range of temperature tested, while the other 41% were classified as psychrophilic as they only grew below 25 °C...
March 7, 2017: Extremophiles: Life Under Extreme Conditions
Amrik Bhattacharya, Nidhi Goyal, Anshu Gupta
Effluents from textile industries are highly colored due to vast use of various azo dyes and color is the first visual indicator of pollution. Biological treatment of textile effluent is often hampered due to the alkaline pH and high salinity; a common characteristic of many textile industrial wastewaters. Considering this, the present study explores the potential of a newly isolated halotolerant and alkaliphilic bacterium Nesterenkonia lacusekhoensis EMLA3 for degradation of methyl red (MR) dye under alkaline condition...
March 2, 2017: Extremophiles: Life Under Extreme Conditions
Jae Kyu Lim, Hae-Chang Jung, Sung Gyun Kang, Hyun Sook Lee
Protein disulfide oxidoreductases are redox enzymes that catalyze thiol-disulfide exchange reactions. These enzymes include thioredoxins, glutaredoxins, protein disulfide isomerases, disulfide bond formation A (DsbA) proteins, and Pyrococcus furiosus protein disulfide oxidoreductase (PfPDO) homologues. In the genome of a hyperthermophilic archaeon, Thermococcus onnurineus NA1, the genes encoding one PfPDO homologue (TON_0319, Pdo) and three more thioredoxin- or glutaredoxin-like proteins (TON_0470, TON_0472, TON_0834) were identified...
March 1, 2017: Extremophiles: Life Under Extreme Conditions
Carmen Falagán, Bärbel Foesel, Barrie Johnson
Four novel strains of Acidobacteria were isolated from water samples taken from pit lakes at two abandoned metal mines in the Iberian Pyrite Belt mining district, south-west Spain. Three of the isolates belong to the genus Acidicapsa (MCF9(T), MCF10(T), and MCF14) and one of them to the genus Granulicella (MCF40(T)). All isolates are moderately acidophilic (pH growth optimum 3.8-4.1) and mesophilic (temperature growth optima 30-32 °C). Isolates MCF10(T) and MCF40(T) grew at pH lower (<3.0) than previously reported for all other acidobacteria...
February 22, 2017: Extremophiles: Life Under Extreme Conditions
Satoshi Wakai, Akihiro Abe, Sotaro Fujii, Kaoru Nakasone, Yoshihiro Sambongi
The soluble protein fraction of the extremely halophilic archaeon Haloarcula japonica exhibits substantial inorganic pyrophosphate (PPi) hydrolysis activity in the presence of 2-4 M NaCl (Wakai et al, J Biol Chem 288:29247-29251, 2013), which provides high ionic strength (2-4). In this study, much higher PPi hydrolysis activity was unexpectedly detected, even with 0 M NaCl in the presence of 100-200 mM MgSO4, providing a much lower ionic strength of 0.4-0.8, in the same protein fraction. Na(+) and Mg(2+) ions were required for activity under high and low ionic strength conditions, respectively...
February 17, 2017: Extremophiles: Life Under Extreme Conditions
Juan José Marizcurrena, María A Morel, Victoria Braña, Danilo Morales, Wilner Martinez-López, Susana Castro-Sowinski
Ultraviolet (UV) light irradiation has serious consequences for cell survival, including DNA damage by formation of cyclobutane pyrimidine dimers (CPD) and pyrimidine (6,4) pyrimidone photoproducts. In general, the Nucleotide Excision Repair pathway repairs these lesions; however, all living forms, except placental mammals and some marsupials, produce a flavoprotein known as photolyase that directly reverses these lesions. The aim of this work was the isolation and identification of Antarctic UVC-resistant bacteria, and the search for novel photolyases...
March 2017: Extremophiles: Life Under Extreme Conditions
Takumi Yamashiro, Kousaku Murata, Shigeyuki Kawai
Deinococcus radiodurans is highly resistant to ionizing radiation and UV radiation, and oxidative stress caused by such radiations. NADP(H) seems to be important for this resistance (Slade and Radman, Microbiol Mol Biol Rev 75:133-191; Slade, Radman, Microbiol Mol Biol Rev 75:133-191, 2011), but the mechanism underlying the generation of NADP(H) or NAD(H) in D. radiodurans has not fully been addressed. Intracellular concentrations of NAD(+), NADH, NADP(+), and NADPH in D. radiodurans are also not determined yet...
March 2017: Extremophiles: Life Under Extreme Conditions
Michael J Morten, Roland Gamsjaeger, Liza Cubeddu, Ruvini Kariawasam, Jose Peregrina, J Carlos Penedo, Malcolm F White
Single-stranded DNA-binding proteins (SSBs), including replication protein A (RPA) in eukaryotes, play a central role in DNA replication, recombination, and repair. SSBs utilise an oligonucleotide/oligosaccharide-binding (OB) fold domain to bind DNA, and typically oligomerise in solution to bring multiple OB fold domains together in the functional SSB. SSBs from hyperthermophilic crenarchaea, such as Sulfolobus solfataricus, have an unusual structure with a single OB fold coupled to a flexible C-terminal tail...
March 2017: Extremophiles: Life Under Extreme Conditions
Li-Jing Kang, Zi-Tong Meng, Chen Hu, Yan Zhang, Hai-Lun Guo, Qing Li, Mu Li
Organic solvent-tolerant esterases are proven to be excellent biocatalysts in chemical and pharmaceutical industries. A novel organic solvent-tolerant esterase gene, lip2, was isolated from filamentous fungi Monascus purpureus M7. The sequence analysis suggested that lip2 has a conserved "GDSL" motif near the active center. The multiple-sequence alignment and phylogenetic analysis revealed that Lip2 displayed two unique amino-acid sequence motifs that clearly separate it from any other previously described lipase family...
March 2017: Extremophiles: Life Under Extreme Conditions
Riegardt M Johnson, Jean-Baptiste Ramond, Eoin Gunnigle, Mary Seely, Don A Cowan
The central Namib Desert is hyperarid, where limited plant growth ensures that biogeochemical processes are largely driven by microbial populations. Recent research has shown that niche partitioning is critically involved in the assembly of Namib Desert edaphic communities. However, these studies have mainly focussed on the Domain Bacteria. Using microbial community fingerprinting, we compared the assembly of the bacterial, fungal and archaeal populations of microbial communities across nine soil niches from four Namib Desert soil habitats (riverbed, dune, gravel plain and salt pan)...
March 2017: Extremophiles: Life Under Extreme Conditions
Daniel Bollschweiler, Miroslava Schaffer, C Martin Lawrence, Harald Engelhardt
Most halophilic Archaea of the class Halobacteriaceae depend on the presence of several molar sodium chloride for growth and cell integrity. This poses problems for structural studies, particularly for electron microscopy, where the high salt concentration results in diminished contrast. Since cryo-electron microscopy of intact cells provides new insights into the cellular and molecular organization under close-to-live conditions, we evaluated strategies and conditions to make halophilic microbes available for investigations in situ...
March 2017: Extremophiles: Life Under Extreme Conditions
Taka-Aki Kuribayashi, Sotaro Fujii, Misa Masanari, Masaru Yamanaka, Satoshi Wakai, Yoshihiro Sambongi
Shewanella species are widely distributed in sea, brackish, and fresh water areas, growing psychrophilically or mesophilically, and piezophilically or piezo-sensitively. Here, membrane-bound 5'-nucleotidases (NTases) from deep-sea Shewanella violacea and brackish water Shewanella amazonensis were examined from the aspect of NaCl tolerance to gain an insight into protein stability against salt. Both NTases were single polypeptides with molecular masses of ~59 kDa, as determined on mass spectroscopy. They similarly required 10 mM MgCl2 for their activities, and they exhibited the same pH dependency and substrate specificity for 5'-nucleotides...
March 2017: Extremophiles: Life Under Extreme Conditions
Alexander Yu Merkel, Nikolay V Pimenov, Igor I Rusanov, Alexander I Slobodkin, Galina B Slobodkina, Ivan Yu Tarnovetckii, Evgeny N Frolov, Arseny V Dubin, Anna A Perevalova, Elizaveta A Bonch-Osmolovskaya
Microbial communities of Kamchatka Peninsula terrestrial hot springs were studied using molecular, radioisotopic and cultural approaches. Analysis of 16S rRNA gene fragments performed by means of high-throughput sequencing revealed that aerobic autotrophic sulfur-oxidizing bacteria of the genus Sulfurihydrogenibium (phylum Aquificae) dominated in a majority of streamers. Another widely distributed and abundant group was that of anaerobic bacteria of the genus Caldimicrobium (phylum Thermodesulfobacteria). Archaea of the genus Vulcanisaeta were abundant in a high-temperature, slightly acidic hot spring, where they were accompanied by numerous Nanoarchaeota, while the domination of uncultured Thermoplasmataceae A10 was characteristic for moderately thermophilic acidic habitats...
March 2017: Extremophiles: Life Under Extreme Conditions
Ivana Cavello, Agustín Albanesi, Dante Fratebianchi, Gabriela Garmedia, Silvana Vero, Sebastián Cavalitto
One hundred and three yeasts isolated from soil samples from King George Island and Tierra del Fuego province were screened in relation with their capability to produce pectinolytic enzymes. Although all the yeasts showed well-developed colonies at 20 °C, only eight showed a clear halo around the colony, indicative of pectin degradation. A secondary screening demonstrated that only four yeasts were capable to produce pectinases at low temperatures (8 °C). It could be seen that the selected yeasts were able to grow and produce high levels of polygalacturonase activity when submerged fermentations were performed using pectin-containing fruit wastes as substrates...
March 2017: Extremophiles: Life Under Extreme Conditions
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