We report a collection of amplicon sequences of putative polyethylene terephthalate (PET) hydrolases from two different composts in Japan. Employing previously designed degenerate primers, we identified 31 and 22 sequences from industrial and agricultural composts, respectively, confirming the presence of highly homologous PET hydrolase genes across different compost environments.

An extreme thermophilic bacterium, Thermus thermophilus produces more than 20 unusual polyamines, but their biosynthetic pathways, including homospermidine, are not yet fully understood. Two types of homospermidine synthases have been identified in plants and bacteria, which use spermidine and putrescine or two molecules of putrescine as substrates. However, homospermidine synthases with such substrate specificity have not been identified in T. thermophilus . Here we identified a novel agmatine homocoupling enzyme that is involved in homospermidine biosynthesis in T. thermophilus . The reaction mechanism is different from that of a previously described homospermidine synthase, and involves conjugation of two molecules of agmatine, which produces a diamidino derivative of homospermidine (caldomycin) as an immediate precursor of homospermidine. We conclude that there is a homospermidine biosynthetic pathway from agmatine via caldomycin synthase followed by ureohydrolase in T. thermophilus . Furthermore, it is shown that caldomycin is a novel compound existing in nature.

In the three domains of life, three biosynthetic pathways are known for putrescine. The first route is conversion of ornithine to putrescine by ornithine decarboxylase (ODC: SpeC), the second route is the conversion of arginine to agmatine by arginine decarboxylase (ADC: SpeA), followed by the conversion of agmatine to putrescine by agmatine ureohydrolase (AUH: SpeB), and the third route is the conversion of agmatine to N-carbamoylputrescine by agmatine deiminase (agmatine iminohydrolase, AIH), followed by the conversion of N-carbamoylputrescine to putrescine by N-carbamoylputrescine amidohydrolase (NCPAH). An extreme thermophile, Thermus thermophilus produces putrescine, although this bacterium lacks homologs for putrescine synthesizing pathways, such as ODC, AUH, AIH and NCPAH. To identify genes involved in putrescine biosynthesis in T. thermophilus, putrescine biosynthesis was examined by disruption of a predicted gene for agmatinase (agmatine ureohydrolase), or by using purified enzyme. It was found that arginase (TTHA1496) showed an agmatinase activity utilizing agmatine as a substrate. These results indicate that this bacterium can use arginase for putrescine biosynthesis. Arginase is a major contributor to putrescine biosynthesis under physiological conditions. The presence of an alternative pathway for converting agmatine into putrescine is functionally important for polyamine metabolism supporting survival at extreme environments.

In an extreme thermophile, Thermus thermophilus, sym-homospermidine is synthesized by the actions of two enzymes. The first enzyme coded by dhs gene (annotated to be deoxyhypusine synthase gene) catalyzes synthesis of an intermediate, supposed to be 1,9-bis(guanidino)-5-aza-nonane (=N1, N11-bis(amidino)-sym-homospermidine), from two molecules of agmatine in the presence of NAD. The second enzyme (aminopropylagmatinase) coded by speB gene catalyzes hydrolysis of the intermediate compound to sym-homospermidine releasing two molecules of urea.

Thermus thermophilus is reportedly polyploid and carries four to five identical genome copies per cell, based on molecular biological experiments. To directly detect polyploidy in this bacterium, we performed live cell imaging by X-ray free-electron laser (XFEL) diffraction and observed its internal structures. The use of femtosecond XFEL pulses enables snapshots of live, undamaged cells. For successful XFEL imaging, we developed a bacterial culture method using a starch- and casein-rich medium that produces a predominance of rod-shaped cells shorter than the focused XFEL beam size, which is slightly smaller than 2 µm. When cultured in the developed medium, the length of T. thermophilus cells, which is typically ~4 µm, was less than half its usual length. We placed living cells in a micro-liquid enclosure array and successively exposed each enclosure to a single XFEL pulse. A cell image was successfully obtained by the coherent diffractive imaging technique with iterative phase retrieval calculations. The reconstructed cell image revealed five peaks, which are most likely to be nucleoids, arranged in a row in the polyploid cell without gaps. This study demonstrates that XFELs offer a novel approach for visualizing the internal nanostructures of living, micrometer-sized, polyploid bacterial cells.

A Thermus thermophilus lytic phage was isolated from a Japanese hot spring by using a type IV pili-deficient strain as an indicator host, and designated as φMN1. Electron microscopic (EM) examination revealed that φMN1 had an icosahedral head and a contractile tail, suggesting that φMN1 belonged to Myoviridae. An EM analysis focused on φMN1 adsorption to the Thermus host cell showed that the receptor molecules for the phage were uniformly distributed on the outer surface of the cells. The circular double-stranded DNA of φMN1 was 76,659 base pairs in length, and the guanine and cytosine content was 61.8%. It was predicted to contain 99 open reading frames, and its putative distal tail fiber protein, which is essential for non-piliated host cell surface receptor recognition, was dissimilar in terms of sequence and length with its counterpart in the type IV pili-dependent φYS40. A phage proteomic tree revealed that φMN1 and φYS40 are in the same cluster, but many genes had low sequence similarities and some seemed to be derived from both mesophilic and thermophilic organisms. The gene organization suggested that φMN1 evolved from a non-Thermus phage through large-scale recombination events of the genes determining the host specificity, followed by gradual evolution by recombination of both the thermophilic and mesophilic DNAs assimilated by the host Thermus cells. This newly isolated phage will provide evolutionary insights into thermophilic phages.

ThermusQ is a website (https://www.thermusq.net/) that aims to gather all the molecular information on Thermus thermophilus and to provide a platform to easily access the whole view of the bacterium. ThermusQ comprises the genome sequences of 22 strains from T. thermophilus and T. oshimai strains, plus the sequences of known Thermus phages. ThermusQ also contains information and map diagrams of pathways unique to Thermus strains. The website provides tools to retrieve sequence data in different ways. By gathering the whole data of T. thermophilus strains, the strainspecific characteristics was found. This bird's-eye view of the whole data will lead the research community to identify missing important data and the integration will provide a platform to conduct future biochemical simulations of the bacterium.

AbstractThe Fukushima Daiichi Nuclear Power Plant (Tokyo Electric Power Co. Ltd.) accident caused by the Great East Japan Earthquake (11 March 2011) contaminated farmland, grassland, and grass silage in the Tohoku region of Japan with radioactive cesium. In previous studies, we have converted contaminated pasture grasses to compost by employing aerobic ultrahigh temperature fermentation and this showed below acceptable levels of radioactivity. In the present study, we verified whether the decontaminated compost could be safely applied to grassland. A 1200 m2 pastureland (average 320 Bq/kg) in Kurihara-city, Miyagi-prefecture, Japan, was divided into 6 plots, of which 4 plots were treated with 2, 5, 10, and 30 kg of grass silage compost (297 Bq/kg) per m2. In the control plot, chemical fertilizers or nonradioactive cattle manure were applied. After those plots were plowed, orchard grass (Dactylis glomerata) was sown and grown for about 2 months. No significant changes in soil radiocesium concentrations or air dose rates were observed in the pastures during and after the cultivation period. The water quality of the river in the vicinity of the pasture was also not affected. The radiocesium levels in the grass harvested from all plots, including the test plot with 30 kg per m2 of application, were below the detection limit (below 20 Bq/kg), less than one-fifth of the provisional value (100 Bq/kg) for forage. These results demonstrate that radioactive contaminated grass silage compost can be safely applied to actual pastures.

The hyperthermophilic bacterium Thermotoga maritima has an atypical peptidoglycan that contains d‐lysine alongside the usual d‐alanine and d‐glutamate. We previously identified a lysine racemase involved in d‐lysine biosynthesis, and this enzyme also possesses alanine racemase activity. However, T. maritima has neither alanine racemase nor glutamate racemase enzymes; hence, the precise biosynthetic pathways of d‐alanine and d‐glutamate remain unclear in T. maritima. In the present study, we identified and characterized a novel d‐amino acid aminotransferase (TM0831) in T. maritima. TM0831 exhibited aminotransferase activity towards 23 d‐amino acids, but did not display activity towards l‐amino acids. It displayed high specific activities towards d‐homoserine and d‐glutamine as amino donors. The most preferred acceptor was 2‐oxoglutarate, followed by glyoxylate. Additionally, TM0831 displayed racemase activity towards four amino acids including aspartate and glutamate. Catalytic efficiency (kcat/Km) for aminotransferase activity was higher than for racemase activity, and pH profiles were distinct between these two activities. To evaluate the functions of TM0831, we constructed a TTHA1643 (encoding glutamate racemase)‐deficient Thermus thermophilus strain (∆TTHA1643) and integrated the TM0831 gene into the genome of ∆TTHA1643. The growth of this TM0831‐integrated strain was promoted compared with ∆TTHA1643 and was restored to almost the same level as that of the wild‐type strain. These results suggest that TM0831 is involved in d‐glutamate production. TM0831 is a novel d‐amino acid aminotransferase with racemase activity that is involved in the production of d‐amino acids in T. maritima.

An extreme thermophile, Thermus thermophilus grows at an optimum temperature of around 70°C and produces 16 different polyamines including long-chain and branched-chain polyamines. We found that the composition of polyamines in the thermophile cells changes with culture temperature. Long-chain and branched-chain polyamines (unusual polyamines) were increased in the cells grown at high temperature such as 80°C, but they were minor components in the cells grown at relatively lower temperature such as 60°C. The effects of polyamines on cell growth were studied using T. thermophilus HB8 ΔspeA deficient in arginine decarboxylase. Cell growth of this mutant strain was significantly decreased at 70°C. This mutant strain cannot produce polyamines and grows poorly at 75°C. It was also determined whether polyamines are directly involved in protecting DNA from DNA double-strand breaks (DSBs) induced by heat. Polyamines protected DNA against double-strand breaks. Therefore, polyamines play essential roles in cell growth at extremely high temperature through maintaining a functional conformation of DNA against DSBs and depurination.

An extreme thermophile, Thermus thermophilus, produces 16 different polyamines including long-chain and branched-chain polyamines. The composition and content of polyamines in the thermophile cells change not only with growth temperature but also with pH changes. In particular, cell growth decreased greatly at alkaline medium together with significant changes in the composition and content of polyamines. The amounts of tetraamines (spermine and its homologs) markedly decreased at alkaline pH. Thus, we knocked out the speE gene, which is involved in the biosynthesis of tetraamines, and changes of composition of polyamines with pH changes in the mutant cells were studied. Cell growth in the ΔspeE strain was decreased compared with that of the wild-type strain for all pHs, suggesting that tetraamines are important for cell proliferation. Interestingly, the amount of spermidine decreased and that of putrescine increased in wild-type cells at elevated pH, although T. thermophilus lacks a putrescine synthesizing pathway. In addition, polyamines possessing a diaminobutane moiety, such as spermine, decreased greatly at high pH. We assessed whether the speB gene encoding aminopropylagmatine ureohydrolase (TtSpeB) is directly involved in the synthesis of putrescine. The catalytic assay of the purified enzyme indicated that TtSpeB accepts agmatine as its substrate and produces putrescine due to the change in substrate specificity at high pH. These results suggest that pH stress was exacerbated upon intracellular depletion of polyamines possessing a diaminobutane moiety induced by unusual changes in polyamine biosynthesis under high pH conditions.

We isolated Thermus thermophilus strain HB5018 from Mine Hot Spring in Japan, where the type strain HB8 was isolated nearly half a century ago. The complete genome sequence of HB5018 showed 99.1% average nucleotide identity with HB8, suggesting strict species conservation in the habitat over the past 50 years.

We isolated Thermus thermophilus strains HB5002 and HB5008 from Mine Hot Spring in Japan. Whole-genome sequencing revealed that they showed ∼100% average nucleotide identity to each other, ≥98.53% to the T. thermophilus strains originating from the same spot, but ≤97.64% to the T. thermophilus strains from geographically different places in Japan.

We developed micro-liquid enclosure arrays (MLEAs) for holding solution samples in coherent diffractive imaging (CDI) using x-ray free-electron lasers (XFELs). Hundreds of fully isolated micro-liquid enclosures are arranged in a single MLEA chip for efficient measurement, where each enclosure is destroyed after exposure to a single XFEL pulse. A semi-automated MLEA assembling system was also developed to enclose solution samples into MLEAs efficiently at high precision. We performed XFEL-based CDI experiments using MLEAs and imaged in-solution structures of self-assembled gold nanoparticles. The sample hit rate can be optimized by adjusting solution concentration, and we achieved a single-particle hit rate of 31%, which is not far from the theoretical upper limit of 37% derived from the Poisson statistics. MELAs allow us to perform CDI measurement under controlled solution conditions and will help reveal the nanostructures and dynamics of particles in solution.

X-ray free-electron lasers (XFELs) opened up a possibility for molecular-scale single particle imaging (SPI) without the need for crystallization. In SPI experiments, the orientation of each particle has to be determined from the measured diffraction pattern. Preparing unidirectionally-aligned particles can facilitate the determination of the sample orientation. Here, we show the design principles of a liquid cell for three-dimensional imaging of unidirectionally-aligned particles in solution with XFELs. The liquid cell was designed so that neither incident X-rays nor diffracted X-rays are blocked by the substrate of the liquid cell even at high tilt angles. As a feasibility evaluation, we performed coherent diffraction measurements using the cells with a 1 μm focused XFEL beam. We successfully measured coherent diffraction patterns of a nano-fabricated metal pattern at 70° tilt angle and obtained the reconstructed image by applying iterative phase retrieval. The liquid cell will be usefully applied to molecular-scale SPI by using more tightly focused XFELs. In particular, imaging of membrane proteins embedded in lipid membranes is expected to have an enormous impact on life science and medicine.

d-Amino acids are physiologically important components of peptidoglycan in the bacterial cell wall, maintaining cell structure and aiding adaptation to environmental changes through peptidoglycan remodelling. Therefore, the biosynthesis of d-amino acids is essential for bacteria to adapt to different environmental conditions. The peptidoglycan of the extremely thermophilic bacterium Thermus thermophilus contains d-alanine (d-Ala) and d-glutamate (d-Glu), but its d-amino acid metabolism remains poorly understood. Here, we investigated the enzyme activity and function of the product of the TTHA1643 gene, which is annotated to be a Glu racemase in the T. thermophilus HB8 genome. Among 21 amino acids tested, TTHA1643 showed highly specific activity toward Glu as the substrate. The catalytic efficiency (kcat/Km) of TTHA1643 toward d- and l-Glu was comparable; however, the kcat value was 18-fold higher for l-Glu than for d-Glu. Temperature and pH profiles showed that the racemase activity of TTHA1643 is high under physiological conditions for T. thermophilus growth. To assess physiological relevance, we constructed a TTHA1643-deficient strain (∆TTHA1643) by replacing the TTHA1643 gene with the thermostable hygromycin resistance gene. Growth of the ∆TTHA1643 strain in synthetic medium without d-Glu was clearly diminished relative to wild type, although the TTHA1643 deletion was not lethal, suggesting that alternative d-Glu biosynthetic pathways may exist. The deterioration in growth was restored by adding d-Glu to the culture medium, showing that d-Glu is required for normal growth of T. thermophilus. Collectively, our findings show that TTHA1643 is a Glu racemase and has the physiological function of d-Glu production in T. thermophilus.

Due to the Fukushima Daiichi nuclear power plant accident, a tremendous amount of organic waste (e.g., baled grass silage) contaminated with radioactivity was generated in Tohoku region, northeastern Japan. To establish a safe and efficient way to treat cesium contaminated silage, we investigated the use of aerobic, high temperature composting. Radiocesium (Cs-137 and Cs-134) contaminated silage (2000 kg, approximately 2700 Bq/kg), water (4000 kg) and matured compost soil (as inoculum, 16,000 kg) were mixed by a wheel loader, and then the mixture was piled up. Air was supplied from the bottom of a compost pile continuously, and the fermentation continued for 7 weeks. The temperature at 100 cm below the surface reached approximately 100 degrees C. The water content decreased to less than 30% after 7 weeks. The level of radioactive cesium in the final product (18,000 kg) was 265 Bq/kg, which was below the tolerance value for fertilizer (400 Bq/kg) suggested by the Japanese government. The radioactive cesium within silage remained in the final products. We cultivated tomato (fruit), soybean (seed), carrot (root), Italian ryegrass (leaf feed for livestock), Swiss chard (leaf), cosmos (flower) and field mustard (seed) in an experimental farm fertilized with the matured compost made from the radiocesium contaminated silage, for 3 months. Radiocesium levels of edible parts and non-edible parts of each crop were lower than 20 Bq/kg, which was less than one-fifth of the Japanese government value for food (100 Bq/kg). This research demonstrated that the final product can be used safely as an organic fertilizer.

Branched-chain polyamine synthase (BpsA) catalyzes sequential aminopropyl transfer from the donor, decarboxylated S-adenosylmethionine (dcSAM), to the acceptor, linear-chain polyamine, resulting in the production of a quaternary-branched polyamine via tertiary branched polyamine intermediates. Here, we analyzed the catalytic properties and X-ray crystal structure of Tth-BpsA from Thermus thermophilus and compared them with those of Tk-BpsA from Thermococcus kodakarensis, which revealed differences in acceptor substrate specificity and C-terminal structure between these two enzymes. To investigate the role of the C-terminal flexible region in acceptor recognition, a region (QDEEATTY) in Tth-BpsA was replaced with that in Tk-BpsA (YDDEESSTT) to create chimeric Tth-BpsA C9, which showed a severe reduction in catalytic efficiency toward N-4-aminopropylnorspermidine, but not toward N-4-aminopropylspermidine, mimicking Tk-BpsA substrate specificity. Tth-BpsA C9 Tyr(346) and Thr(354) contributed to discrimination between tertiary branched-chain polyamine substrates, suggesting that the C-terminal region of BpsA recognizes acceptor substrates. Liquid chromatography-tandem mass spectrometry analysis on a Tk-BpsA reaction mixture with dcSAM revealed two aminopropyl groups bound to two of five aspartate/glutamate residues (Glu(339), Asp(342), Asp(343), Glu(344), and Glu(345)) in the C-terminal flexible region. Mutating each of these five amino acid residues to asparagine/glutamine resulted in a slight decrease in activity. The quadruple mutant D342N/D343N/E344Q/E345Q exhibited a severe reduction in catalytic efficiency, suggesting that these aspartate/glutamate residues function to receive aminopropyl chains. In addition, the X-ray crystal structure of the Tk-BpsA ternary complex bound to N-4-bis(aminopropyl)spermidine revealed that Asp(126) and Glu(259) interacted with the aminopropyl moiety in N-4-aminopropylspermidine.

Depurination is accelerated by heat and reactive oxygen species under physiological conditions. We previously reported that polyamines are involved in mitigation of heat shock and oxidative stresses through stimulation of the synthesis of heat shock and antioxidant proteins. This time, we investigated whether polyamines are directly involved in protecting nucleic acids from thermal depurination induced by high temperature. The suppressing efficiencies of depurination of DNA by spermine, caldopentamine and caldohexamine in the presence of 1 mM Mg2+, were approximately 50%, 60% and 80%, respectively. Mg2+ also protected nucleic acids against depurination but to a lesser degree than polyamines. Longer unusual polyamines were more effective at protecting DNA against depurination compared to standard polyamines. The tRNA depurination suppressing efficiencies of spermine, caldopentamine and caldohexamine in the presence of 1 mM Mg2+, were approximately 60%, 70% and 80%, respectively. Standard polyamines protected tRNA and ribosomes more effectively than DNA against thermal depurination. Branched polyamines such as mitsubishine and tetrakis(3-aminopropyl)ammonium also protected RNA more effectively than DNA against depurination. These results suggest that the suppressing effect of depurination of nucleic acids (DNA and RNA) depends on the types of polyamines: i.e. to maintain functional conformation of nucleic acids at high temperature, longer and branched polyamines play important roles in protecting nucleic acids from depurination compared to standard polyamines and Mg2+.