Article
Microbiology
Areum Lee, Eunji Bae, Jihee Park, Kyoung-Hwa Choi, Jaeho Cha
Summary: The study identified the genes responsible for glycogen synthesis (glgA and amyA) and degradation (glgX and gaa) in Sulfolobus acidocaldarius. It showed that the glycogen deficient strain had a higher death rate in nutrient limited conditions, suggesting that glycogen in S. acidocaldarius supports cell maintenance in harsh conditions.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biochemical Research Methods
Shohei Mine, Makoto Nakabayashi, Kazuhiko Ishikawa
Summary: Aldehyde dehydrogenase (ALDH) is widely distributed in nature and plays a crucial role in aldehyde detoxification. Thermostable ALDH from Sulfolobus tokodaii has high activity towards acetaldehyde and can be potentially used as a biosensor. However, the crystal structure of this thermostable ALDH with high activity towards acetaldehyde has not been reported. This study successfully determined the crystal structure of recombinant thermostable ALDH from S. tokodaii in complex with NADP, which provides insights for further studies on catalytic mechanisms and applications.
ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS
(2023)
Article
Ecology
Jiahao Gu, Xiaojun Wang, Xiaopan Ma, Ying Sun, Xiang Xiao, Haiwei Luo
Summary: A study found that a particular species of Thermococcus has a mutation rate much higher than other free-living prokaryotes, which is not selectively favored but driven by random genetic drift. Additionally, genome size is negatively correlated with mutation rate and positively correlated with effective population size.
Article
Biochemistry & Molecular Biology
Luca Sesta, Guido Uguzzoni, Jorge Fernandez-de-Cossio-Diaz, Andrea Pagnani
Summary: AMaLa is a new method for inferring fitness landscapes from Directed Evolution experiments sequencing data, effectively leveraging the information encoded in the entire time evolution and using a time-dependent statistical weight with two contributions to gauge possible trajectories in sequence space. This approach accurately describes Directed Evolution dynamics and infers a fitness landscape that reproduces measures of the phenotype under selection, outperforming widely used inference strategies. The reliability of AMaLa is assessed by demonstrating how the inferred statistical model can predict relevant structural properties of the wild-type sequence.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Microbiology
Maxime Tourte, Philippe Schaeffer, Vincent Grossi, Philippe M. Oger
Summary: The study investigated the influence of various factors on the lipid core composition of the hyperthermophilic neutrophilic marine archaeon Pyrococcus furiosus. It was found that factors such as temperature, pH, salinity, carbon source, and genetic background all affected the lipid core composition to some extent. Interestingly, P. furiosus appeared to rely less on the traditional responses of Archaea and instead increased the ratio of glycerol monoalkyl glycerol tetraethers (GMGT) to glycerol dialkyl glycerol tetraethers in response to changing environmental conditions, indicating a potentially common adaptive strategy in Archaea.
ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Environmental Sciences
Seong Hyuk Lee, Sunmin Lee, Sung-Mok Lee, Jaeho Cha, Hyun Sook Lee, Sung Gyun Kang
Summary: This study aims to enhance the glucose-assisted growth of Thermococcus onnurineus NA1 through adaptive evolution and investigate its potential for H-2 production using food processing waste. The glucose-adapted cells, WG-100T, showed significant improvements in cell density and glucose consumption compared to the parent strain. Genome sequencing revealed genetic changes in transcription factors and transport systems. It was demonstrated that WG-100T could produce biohydrogen from potato peel waste through simultaneous saccharification and fermentation.
WASTE AND BIOMASS VALORIZATION
(2023)
Article
Microbiology
Cornelia U. Welte, Rob de Graaf, Paula Dalcin Martins, Robert S. Jansen, Mike S. M. Jetten, Julia M. Kurth
Summary: The study found that the non-methanogenic archaeon A. fulgidus has the ability to grow on MACs, converting them to hydroxylated derivatives with CO2 as the main product and sulfate as electron acceptor. Additionally, MACs can enhance the growth of A. fulgidus in the presence of organic substrates.
ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Biology
Nils-Kare Birkeland, Boyke Bunk, Cathrin Sproeer, Hans-Peter Klenk, Peter Schoenheit
Summary: Hyperthermophiles are microorganisms that thrive in high temperature environments. A new strain of starch-degrading archaeon, Thermococcus bergensis, was isolated and characterized in this study.
Article
Biochemistry & Molecular Biology
Majida Atta Muhammad, Nasir Ahmad, Mohsina Akhter, Naeem Rashid
Summary: Genome analysis of Pyrobaculum calidifontis identified a gene called a-glucosidase (Pcal_0917), which was confirmed to have Type II alpha-glucosidase characteristics. The gene was heterologously expressed and the resulting recombinant enzyme displayed similar characteristics to Type I alpha-glucosidases. The enzyme existed as a tetramer and showed high activity at high temperature and acidic pH. It also exhibited the highest reported p-nitrophenyl alpha-D-glucopyranosidase activity and demonstrated trans-glycosylation activity. In combination with alpha-amylase, it could produce glucose syrup with a high glucose content, suggesting its potential for the starch hydrolyzing industry.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Chemistry, Multidisciplinary
Kohtaro Hirao, Immacolata Speciale, Anna Notaro, Yoshiyuki Manabe, Yoshiaki Teramoto, Takaaki Sato, Haruyuki Atomi, Antonio Molinaro, Yoshihiro Ueda, Cristina De Castro, Koichi Fukase
Summary: This study describes the isolation, structural determination, and chemical synthesis of the N-glycan from the hyperthermophilic archaeon Thermococcus kodakarensis, revealing a unique structure including myo-inositol not found in previously characterized N-glycans. The synthesis of this glycan was successfully achieved through diastereoselective phosphorylation and phosphodiester construction by S(N)2 coupling. This research is expected to provide insights into the primitive function of glycan modification at the molecular level by considering the early divergence of hyperthermophilic organisms in evolution.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Biochemistry & Molecular Biology
Paul Villain, Violette da Cunha, Etienne Villain, Patrick Forterre, Jacques Oberto, Ryan Catchpole, Tamara Basta
Summary: Research shows that expressing bacterial gyrase from Thermotoga maritima in the archaeon Thermococcus kodakarensis can induce negative supercoiling and impact gene expression and chromosomal topology. However, this artificially introduced supercoiling activity did not significantly affect the growth rate of the archaeon.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Microbiology
Yu Su, Yuta Michimori, Haruyuki Atomi
Summary: The hyperthermophilic archaeon Thermococcus kodakarensis uses amino acids as a carbon and energy source. Two Class I aminotransferases, TK0548 and TK2268, are responsible for the conversion of specific amino acids. Genetic examination reveals their importance in amino acid metabolism.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Microbiology
Ji-in Yang, Seong Hyuk Lee, Ji-Young Ryu, Hyun Sook Lee, Sung Gyun Kang
Summary: In this study, the functionality and characteristics of cytoplasmic Fdh3 in the hyperthermophilic archaeon Thermococcus onnurineus NA1 were described. Fdh3 was found to dispose of reducing equivalents by mediating electron transfer between formate and NAD(P)H or ferredoxin. Additionally, Fdh3 exhibited high NADP(+) dependent formate oxidation activity and CO2 reduction activity.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Computer Science, Information Systems
Zhiping Tan, Kangshun Li, Yi Wang
Summary: This paper proposes a differential evolution algorithm with an adaptive mutation operator based on fitness landscape (FLDE), which uses machine learning to choose the optimal mutation strategy. Experimental results show that the FLDE algorithm is highly competitive with five other DE algorithms.
INFORMATION SCIENCES
(2021)
Article
Electrochemistry
Masato Tominaga, Shino Nakao, Makoto Takafuji, Eiichiro Takamura, Shin-ichiro Suye, Takenori Satomura
Summary: By immobilizing a thermostable blue multicopper oxidase from hyperthermophilic archaeon Pyrobaculum aerophilum onto a single-walled carbon nanotube electrode, high electrochemical catalytic activity was achieved. Results from electrochemical investigation and spectroscopic measurements suggested a structural transition around 40?C.
ELECTROCHEMISTRY COMMUNICATIONS
(2021)