Shin-Ichi Yokobori

Ancestral sequence reconstruction (ASR) was used to study the evolution of the translational system by inferring tRNA sequences of the Last Archaeal Common Ancestor (LACA), the Last Bacterial Common Ancestor (LBCA), and the Last Universal Common Ancestor (LUCA), referred to as “Commonote” in our previous studies. A composite phylogenetic tree inferred from the reconstructed ancestral tRNA sequences revealed a topology distinct from those of previously inferred aminoacyl-tRNA synthetase (ARS) trees. This incongruence may reflect changes in tRNA structural features or distinct evolutionary pressures on tRNAs and ARSs, suggesting a more nuanced evolutionary history of the translation system, but it may also arise from methodological differences between studies. Phylogenetic analysis identified conserved identity elements, such as the discriminator base and anticodon, across tRNAs for different amino acids, supporting their status as ancestral features. Most LUCA tRNA species retain bacterial identity elements, potentially enabling their use in modern systems such as Escherichia coli , although exceptions, including tRNA ^Gly and initiator tRNA ^Met, may present functional limitations. To evaluate the translational functionality of LUCA tRNAs and ancient codon-anticodon interactions, synthesized LUCA tRNA ^Ala and tRNA ^Ser variants with anticodons decoding ACN codons were tested in an E. coli reconstituted in vitro translation system. These reconstructed tRNAs successfully decoded ACN codons, with tRNA ^Ala variants exhibiting translation efficiencies comparable to those of native E. coli tRNA ^Thr . Notably, decoding patterns differed from Crick’s and extended wobble rules, as anticodons with various first-position bases recognized multiple third codon positions. This study offers new insights into the early evolution of the translation system and demonstrates the functional potential of ancestral tRNAs in contemporary contexts.

The hypothesis called “panspermia” proposes an interplanetary transfer of life. Experiments have exposed extremophilic organisms to outer space to test microbe survivability and the panspermia hypothesis. Microbes inside shielding material with sufficient thickness to protect them from UV-irradiation can survive in space. This process has been called “lithopanspermia,” meaning rocky panspermia. We previously proposed sub-millimeter cell pellets (aggregates) could survive in the harsh space environment based on an on-ground laboratory experiment. To test our hypothesis, we placed dried cell pellets of the radioresistant bacteria Deinococcus spp. in aluminum plate wells in exposure panels attached to the outside of the International Space Station (ISS). We exposed microbial cell pellets with different thickness to space environments. The results indicated the importance of the aggregated form of cells for surviving in harsh space environment. We also analyzed the samples exposed to space from 1 to 3 years. The experimental design enabled us to get and extrapolate the survival time course to predict the survival time of Deinococcus radiodurans. Dried deinococcal cell pellets of 500 μm thickness were alive after 3 years of space exposure and repaired DNA damage at cultivation. Thus, cell pellets 1 mm in diameter have sufficient protection from UV and are estimated to endure the space environment for 2–8 years, extrapolating the survival curve and considering the illumination efficiency of the space experiment. Comparison of the survival of different DNA repair-deficient mutants suggested that cell aggregates exposed in space for 3 years suffered DNA damage, which is most efficiently repaired by the uvrA gene and uvdE gene products, which are responsible for nucleotide excision repair and UV-damage excision repair. Collectively, these results support the possibility of microbial cell aggregates (pellets) as an ark for interplanetary transfer of microbes within several years.

The complete mitochondrial genomes of two toxic flatworm species of the genus Planocera were determined. The total length of mitochondrial DNA (mtDNA) was 15,657 bp in Planocera multitentaculata and 15,486 bp in Planocera reticulata and included 12 protein-coding genes, 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and 4 non-coding regions. The mitochondrial gene arrangement of these planocerid species was identical to that of previously described acotylean species, Hoploplana elisabelloi, and also to those of other polyclads. Maximum likelihood analysis against 14 Platyhelminthes showed that a tree was robustly constructed using 12 protein-coding genes than COI gene.

Thermophilic enzymes are generally more thermally stable but are less active at moderate temperatures than are their mesophilic counterparts. Thermophilic enzymes with improved low-temperature activity that retain their high stability would serve as useful tools for industrial processes especially when robust biocatalysts are required. Here we show an effective way to explore amino acid substitutions that enhance the low-temperature catalytic activity of a thermophilic enzyme, based on a pairwise sequence comparison of thermophilic/mesophilic enzymes. One or a combination of amino acid(s) in 3-isopropylmalate dehydrogenase from the extreme thermophile Thermus thermophilus was/were substituted by a residue(s) found in the Escherichia coli enzyme at the same position(s). The best mutant, which contained three amino acid substitutions, showed a 17-fold higher specific activity at 25 °C compared to the original wild-type enzyme while retaining high thermal stability. The kinetic and thermodynamic parameters of the mutant showed similar patterns along the reaction coordinate to those of the mesophilic enzyme. We also analyzed the residues at the substitution sites from a structural and phylogenetic point of view.

The Tanpopo mission is a multi-year passive exposure experiment for astrobiology exposure and micrometeoroid capture on board the Exposed Experiment Handrail Attachment Mechanism (ExHAM) at the Japanese Experiment Module ‘Kibo’ (JEM) Exposed Facility (EF) on the International Space Station (ISS). Temperature of space environment was measured with the mechanical thermometer using a bimetallic strip coil for the Tanpopo mission. Since its microbial exposure experiment requires recording the maximum temperature that the Tanpopo exposure panel senses, we have developed a mechanical thermometer with no electric power supplied from the ExHAM. At a given time and orbital position of the ISS, the thermometer indicator was video-imaged by the extravehicular video camera attached to the JEM-EF. With these images analyzed, we were able to derive the maximum temperature of the exposure panels on the space pointing face of the ExHAM as 29±5℃. Furthermore, the thermometer endured use more than three years and demonstrated that the durability was particularly superior.

The Tanpopo mission is an astrobiology space experiment at the Japanese Experiment Module (JEM) ‘Kibo’ on the International Space Station (ISS). One of the sub-divided themes of the Tanpopo mission is for the intact capture of organic bearing micrometeoroids in low Earth orbit using ultralow density silica aerogel (0.01 g/cm3). In order to evaluate damage to organic matter in micrometeoroids during hyper velocity impacts into the aerogel, Murchison meteorite powdered samples, analogs of organic bearing micrometeoroids, were fired into flight-grade silica aerogel (0.01 g/cm3) using a two-stage light-gas gun with velocities of 4.4 and 5.9 km/s. The recovered Murchison grains were analyzed using scanning transmission X-ray microscopy/X-ray absorption near edge structure (STXM/XANES), transmission electron microscopy (TEM) and nanoscale secondary ion mass spectrometry (NanoSIMS). TEM observation did not show significant modifications of the recovered Murchison grains. Carbon-XANES spectra, however, showed a large depletion of the organic matter after the 5.9 km/s impact, but no such effects nor any significant hydrogen isotopic fractionation were observed after the 4.4 km/s impact.

Deinococcus aerius strain TR0125 is a bacterium isolated from the high atmosphere above Japan that shows strong resistance to desiccation, UV-C, and gamma radiation. Here, we report the draft genome sequence of D. aerius (4.5 Mb), which may provide useful genetic information supporting its biochemical features.