A5084487892- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- Genomics and Phylogenetic Studies
- Origins and Evolution of Life
- Astro and Planetary Science
- RNA Research and Splicing
- Protein Structure and Dynamics
- Enzyme Structure and Function
- Machine Learning in Bioinformatics
- Bacteriophages and microbial interactions
- CRISPR and Genetic Engineering
- Methane Hydrates and Related Phenomena
- Isotope Analysis in Ecology
- Planetary Science and Exploration
- RNA Interference and Gene Delivery
- Biochemical and Molecular Research
- Microbial Community Ecology and Physiology
- Amino Acid Enzymes and Metabolism
- Spacecraft and Cryogenic Technologies
- Mass Spectrometry Techniques and Applications
- Monoclonal and Polyclonal Antibodies Research
- Metalloenzymes and iron-sulfur proteins
- Advanced biosensing and bioanalysis techniques
- Photosynthetic Processes and Mechanisms
- Cancer Research and Treatments
Keio University Shonan Fujisawa
2009-2025
Life Science Institute
2016-2025
Institute of Science Tokyo
2024-2025
Shanghai Institute for Science of Science
2025
Tokyo Institute of Technology
2016-2024
Keio University
2007-2024
Fukushima Medical University
2024
Southern Tohoku General Hospital
2023
Earth-Life Science Institute
2019-2022
Japan Agency for Marine-Earth Science and Technology
2019-2020
Whereas modern proteins rely on a quasi-universal repertoire of 20 canonical amino acids (AAs), numerous lines evidence suggest that ancient relied limited alphabet 10 "early" AAs and the "late" were products biosynthetic pathways. However, many nonproteinogenic also prebiotically available, which begs two fundamental questions: Why do we have current acid would be able to fold into globular structures as well if different comprised genetic code? Here, experimentally evaluate solubility...
Samples from the carbonaceous asteroid (162173) Ryugu provide information on chemical evolution of organic molecules in early solar system. Here we show element partitioning major component ions by sequential extractions salts, carbonates, and phyllosilicate-bearing fractions to reveal primordial brine composition primitive asteroid. Sodium is dominant electrolyte salt fraction extract. Anions NH4+ are more abundant than carbonate phyllosilicate fractions, with molar concentrations order...
Polycyclic aromatic hydrocarbons (PAHs) contain ≲20% of the carbon in interstellar medium. They are potentially produced circumstellar environments (at temperatures ≳1000 kelvin), by reactions within cold (~10 kelvin) clouds, or processing carbon-rich dust grains. We report isotopic properties PAHs extracted from samples asteroid Ryugu and meteorite Murchison. The doubly-13C substituted compositions (Δ2×13C values) naphthalene, fluoranthene, pyrene 9 to 51‰ higher than values expected for a...
Transfer RNA (tRNA) is essential for decoding the genome sequence into proteins. In Archaea, previous studies have revealed unique multiple intron-containing tRNAs and that are encoded on 2 separate genes, so-called split tRNAs. Here, we discovered 10 fragmented tRNA genes in complete of hyperthermoacidophilic Archaeon Caldivirga maquilingensis individually transcribed further trans -spliced to generate all missing encoding glycine, alanine, glutamate. Notably, 3 mature Gly 's with...
RNA-peptide/protein interactions have been of utmost importance to life since its earliest forms, reaching even before the last universal common ancestor (LUCA). However, ancient molecular mechanisms behind this key biological interaction remain enigmatic because extant RNA-protein rely heavily on positively charged and aromatic amino acids that were absent (or under-represented) in early pre-LUCA evolutionary period. Here, an RNA-binding variant ribosomal uL11 C-terminal domain was selected...
Abstract We report primordial aqueous alteration signatures in water-soluble organic molecules from the carbonaceous asteroid (162173) Ryugu by Hayabusa2 spacecraft of JAXA. Newly identified low-molecular-weight hydroxy acids (HO-R-COOH) and dicarboxylic (HOOC-R-COOH), such as glycolic acid, lactic glyceric oxalic succinic are predominant samples two touchdown locations at Ryugu. The quantitative qualitative profiles for hydrophilic between sampling shows similar trends within order ppb...
The analysis of archaeal tRNA genes is becoming more important to evaluate the origin and evolution molecule. Even with recent accumulation complete genomes numerous species, several are still required for a full complement codon table. We conducted comprehensive screening from 47 by using combination different types prediction programs extracted total 2,143 reliable gene candidates including 437 intron-containing genes, which covered than 99.9% tables in Archaea. Previously, content Archaea...
Abstract The Martian regolith is known to contain a maximum of 0.5% (w/v) perchlorate (ClO 4 − ) that toxic for most living organisms. With such high concentrations perchlorates on Mars, there any possibility life? Here, in order search and identify potential organisms Earth, which could survive the levels we have isolated four resistant, halophilic/halotolerant bacterial species from Big Soda Lake (BSL) Nevada, USA. 16S ribosomal RNA sequences revealed these halophiles belong genera...
Tubulins are critical for the internal organization of eukaryotic cells, and understanding their emergence is an important question in eukaryogenesis. Asgard archaea closest known prokaryotic relatives to eukaryotes. Here, we elucidated apo nucleotide-bound x-ray structures tubulin from hydrothermal living Odinarchaeota (OdinTubulin). The guanosine 5'-triphosphate (GTP)-bound structure resembles a microtubule protofilament, with GTP bound between subunits, coordinating "+" end subunit...
The earliest proteins had to rely on amino acids available early Earth before the biosynthetic pathways for more complex evolved. In extant proteins, a significant fraction of ‘late’ (such as Arg, Lys, His, Cys, Trp and Tyr) belong essential catalytic structure-stabilizing residues. How (or if) could sustain an biosphere has been major puzzle. Here, we analysed two combinatorial protein libraries representing proxies sequence space at different evolutionary stages. first is composed entire...
The reductive tricarboxylic acid (rTCA) cycle is among the most plausible candidates for first autotrophic metabolism in earliest life. Extant enzymes fixing CO2 this contain cofactors at catalytic centers, but it unlikely that protein/cofactor system emerged once a prebiotic process. Here, we discuss feasibility of non-enzymatic cofactor-assisted drive rTCA reactions primitive Earth environments, particularly focusing on acetyl-CoA conversion to pyruvate. Based energetic and mechanistic...
DNA is an attractive candidate for integration into nanoelectronics as a biological nanowire due to its linear geometry, definable base sequence, easy, inexpensive and non-toxic replication self-assembling properties. Recently we discovered that by intercalating Ag+ in polycytosine-mismatch oligonucleotides, the resulting C-Ag+-C duplexes are able conduct charge efficiently. To map functionality biostability of this system, built characterized internally-functionalized nanowires through...
Reconstituted cell-free protein synthesis systems (e.g., the PURE system) allow expression of toxic proteins, hetero-oligomeric subunits, and proteins with noncanonical amino acids high levels homogeneity. In these systems, an artificial ATP/GTP regeneration system is required to drive synthesis, which accomplished using three kinases phosphocreatine. Here, we demonstrate replacement one bifunctional Cytophaga hutchinsonii polyphosphate kinase that phosphorylates nucleosides in exchange...
The discovery of separate 5' and 3' halves transfer RNA (tRNA) molecules-so-called split tRNA-in the archaeal parasite Nanoarchaeum equitans made us wonder whether ancestral tRNA was encoded on 1 or 2 genes. We performed a comprehensive phylogenetic analysis tRNAs in 45 species to explore relationship between three types (nonintronic, intronic split). classified 1953 mature sequences into 22 clusters. All have shown relationships with other possessing same anticodon. also mimicked by...
Abstract Background In many eukaryotes, microRNAs (miRNAs) bind to complementary sites in the 3'-untranslated regions (3'-UTRs) of target messenger RNAs (mRNAs) and regulate their expression at stage translation. Recent studies have revealed that miRNAs are evolutionarily conserved; however, evolution genes has yet be systematically characterized. We sought elucidate a set conserved miRNA/target-gene pairs analyse mechanism underlying miRNA-mediated gene regulation early bilaterian...
MicroRNAs have been identified and analyzed in various model species, but an investigation of miRNAs nonmodel species is required for a more complete understanding miRNA evolution. In this study, we investigated the Triops cancriformis (tadpole shrimp), “living fossil,” whose morphological form has not changed almost 200 million years. Dramatic ontogenetic changes occur during its development. To clarify evolution miRNAs, comparatively components RNAi machinery. We used deep sequencing to...
Chemical evolution is an abiotic reaction process in which complex organic molecules arise from a combination of simple inorganic and chemical compounds. To assess the possible ongoing subsurface ocean Saturn's icy satellite Enceladus, we explored water–rock aqueous reactions peptide formation capability under hydrothermal environment similar to that on Enceladus. It has been suggested core Enceladus not experienced high temperatures time present. The major components are assumed be...
tRNA splicing endonucleases, essential enzymes found in Archaea and Eukaryotes, are involved the processing of pre-tRNA molecules. In Archaea, three types endonuclease [homotetrameric: α 4 , homodimeric: 2 heterotetrameric: (αβ) ] have been identified, each representing different substrate specificity during intron cleavage. Here, we discovered a fourth type archaeal (ε ) genome acidophilic archaeon Candidatus Micrarchaeum acidiphilum, referred to as ARMAN-2 its closely related species,...
Fe-S clusters are essential cofactors mediating electron transfer in respiratory and metabolic networks. However, obtaining active [4Fe-4S] proteins with heterologous expression is challenging due to (i) the requirements for cluster assembly, (ii) O2 lability of clusters, (iii) copurification undesired (e.g., ferredoxins). Here, we established a facile efficient protocol express mature PURE system under aerobic conditions. An enzyme aconitase thermophilic ferredoxin were selected as model...
Recent advances in synthetic biology have enabled the vitro operation of central dogma reconstituted cell-free protein synthesis system (i.e., PURE system), which represents a convenient platform to address molecular-level biochemical questions and robust workhorse for biomanufacturing noncanonical peptides, polyketides, enzymes that are difficult express vivo. However, unlike living cells regenerating their building blocks from substrates, systems require an extra supply 20 amino acids...