Synthesis and Biophysical Characterization of RNAs Containing ( R)- and ( S)-5'- C-Aminopropyl-2'- O-methyluridines.

We designed and synthesized ( R)-5'- C-aminopropyl-2'- O-methyluridine and ( S)-5'- C-aminopropyl-2'- O-methyluridine, which are applicable to small interfering RNAs (siRNAs). We have evaluated the properties of siRNAs containing ( R)-5'- C-aminopropyl-2'- O-methyl and ( S)-5'- C-aminopropyl-2'- O-methyl modifications and have compared them to that of the 4'- C-aminopropyl-2'- O-methyl modification. Although these modifications decreased the thermal stability of double-stranded RNAs (dsRNAs) and siRNAs, the dsRNA containing the ( S)-5'- C-aminopropyl-2'- O-methyl modification showed the highest melting temperature ( Tm) among them. Silencing activity of the modified siRNAs was assessed by a dual luciferase reporter assay using HeLa cells. Incorporation of the ( R)-5'- C-aminopropyl-2'- O-methyl and ( S)-5'- C-aminopropyl-2'- O-methyl modifications on a passenger and guide strand was found to be tolerated for the silencing activity of siRNAs except for in the seed region on the guide strand. Furthermore, these modifications significantly increased the stability of single-stranded RNAs (ssRNAs) and siRNAs in a buffer containing bovine serum.

Synthesis and characterization of small interfering RNAs with haloalkyl groups at their 3'-dangling ends.

With the aim to create a small interfering RNA (siRNA) with enhanced activity and resistance to nuclease degradation, we synthesized and evaluated the properties of the following siRNAs containing haloalkyl ß-d-ribofuranosides at their 3'-dangling ends: 2,2,2-trifluoroethyl ß-d-ribofuranoside, 2,2,2-trichloroethyl ß-d-ribofuranoside and 2,2,2-tribromoethyl ß-d-ribofuranoside. The gene silencing activities of the modified siRNAs were investigated through a dual luciferase reporter assay using HeLa cells. The highest silencing activity was observed for the trichloroethyl analog modified siRNA, which was closely followed by the trifluoroethyl and tribromoethyl analogs. The modified siRNAs were found to show increased binding affinity towards the Piwi-Argonaute-Zwille (PAZ) domain protein based on computational analysis and an experimental study. Furthermore, the RNAs modified with the analogs at their 3'-ends exhibited improved resistance to hydrolysis by a 3'-exonuclease.

Synthesis of 4'-C-aminoalkyl-2'-O-methyl modified RNA and their biological properties.

In this paper, we describe the synthesis of 4'-C-aminoalkyl-2'-O-methylnucleosides and the properties of RNAs containing these analogs. Phosphoramidites of 4'-C-aminoethyl and 4'-C-aminopropyl-2'-O-methyluridines were prepared using glucose as starting material, and RNAs containing the analogs were synthesized using the phosphoramidites. Thermal denaturation studies revealed that these nucleoside analogs decreased the thermal stabilities of double-stranded RNAs (dsRNAs). Results of NMR, molecular modeling, and CD spectra measurements suggested that 4'-C-aminoalkyl-2'-O-methyluridine adopts an C2'-endo sugar puckering in dsRNA. The 4'-C-aminoalkyl modifications in the passenger strand and the guide strand outside the seed region were well tolerated for RNAi activity of siRNAs. Single-stranded RNAs (ssRNAs) and siRNAs containing the 4'-C-aminoethyl and 4'-C-aminopropyl analogs showed high stability in buffer containing bovine serum. Thus, siRNAs containing the 4'-C-aminoethyl and 4'-C-aminopropyl analogs are good candidates for the development of therapeutic siRNA molecules.

Construction of an endogenous selectable marker gene for the rice straw degrading white-rot basidiomycete Cyathus stercoreus.

Cyathus stercoreus has a superior ability to increase the cellulase saccharification yields of rice straw under biological pretreatment. As a first step to improve the biological pretreatment efficiency of C. stercoreus further, a new gene transformation system was constructed. Uracil auxotrophic mutant uv-180 was generated as host strain by ultraviolet radiation. It was transformed using plasmid pGE containing the orotate phosphoribosyltransferase (CsURA5) and enhanced green fluorescent protein (egfp). Many transformants exhibited strong fluorescence, indicating successful genetic transformation. An intron was needed for the expression of egfp. The EGFP fluorescence intensities of the three transformants did not decay even after subculturing on uracil-containing semisolid medium 5 times, suggesting that the transformed plasmids were stably retained in the absence of selective pressure.

Phylogenetic trees of closely related bacterial species and subspecies based on frequencies of short nucleotide sequences.

Bacterial phylogenetic analyses are commonly performed to explore the evolutionary relationships among various bacterial species and genera based on their 16S rRNA gene sequences; however, these results are limited by mosaicism, intragenomic heterogeneity, and difficulties in distinguishing between related species. In this study, we aimed to perform genome-wide comparisons of different bacterial species, namely Escherichia coli, Shigella, Yersinia, Klebsiella, and Neisseria spp., based on their K-mer profiles to construct phylogenetic trees. Pentanucleotide frequency analyses (512 patterns of 5 nucleotides each) were performed to distinguish between highly similar species. Moreover, Escherichia albertii strains were clearly distinguished from E. coli and Shigella, despite being closely related to enterohemorrhagic E. coli in the phylogenetic tree. In addition, our phylogenetic tree of Ipomoea species based on pentamer frequency in chloroplast genomes was correlated with previously reported morphological similarities. Furthermore, a support vector machine clearly classified E. coli and Shigella genomes based on their pentanucleotide profiles. These results suggest that phylogenetic analyses based on penta- or hexamer profiles are a useful methodology for microbial phylogenetic studies. In addition, we introduced an R application, Phy5, which generates a phylogenetic tree based on genome-wide comparisons of pentamer profiles. The online version of Phy5 can be accessed at https://phy5.shinyapps.io/Phy5R/ and its command line version Phy5cli can be downloaded at https://github.com/YoshioNakano2021/phy5.

Differential expression and function of alternative splicing variants of human liver X receptor α.

The liver X receptor α (LXRα) is a nuclear receptor that is involved in regulation of lipid metabolism, cellular proliferation and apoptosis, and immunity. In this report, we characterize three human LXRα isoforms with variation in the ligand-binding domain (LBD). While examining the expression of LXRα3, which lacks 60 amino acids within the LBD, we identified two novel transcripts that encode LXRα-LBD variants (LXRα4 and LXRα5). LXRα4 has an insertion of 64 amino acids in helix 4/5, and LXRα5 lacks the C-terminal helices 7 to 12 due to a termination codon in an additional exon that encodes an intron in the LXRα1 mRNA. LXRα3, LXRα4, and LXRα5 were expressed at lower levels compared with LXRα1 in many human tissues and cell lines. We also observed weak expression of LXRα3 and LXRα4 in several tissues of mice. LXR ligand treatment induced differential regulation of LXRα isoform mRNA expression in a cell type-dependent manner. Whereas LXRα3 had no effect, LXRα4 has weak transactivation, retinoid X receptor (RXR) heterodimerization, and coactivator recruitment activities. LXRα5 interacted with a corepressor in a ligand-independent manner and inhibited LXRα1 transactivation and target gene expression when overexpressed. Combination of LXRα5 cotransfection and LXRα antagonist treatment produced additive effects on the inhibition of ligand-dependent LXRα1 activation. We constructed structural models of the LXRα4-LBD and its complexes with ligand, RXR-LBD, and coactivator peptide. The models showed that the insertion in the LBD can be predicted to disrupt RXR heterodimerization. Regulation of LXRα pre-mRNA splicing may be involved in the pathogenesis of LXRα-related diseases.

Characterization of the Interactions between Cereal Flour and "Nata Puree" in Batter.

This study aimed to characterize the interactions between cereal flour (rice, wheat, and barley) and "nata puree" (NP), a disintegrated bacterial cellulose (BC) in the presence of a water-soluble polysaccharide, with powder-dispersion activity. Pasting properties of cereal flour with additives were analyzed using a Rapid Visco Analyzer, and disintegrated BC in water (BCW), three water-soluble polysaccharides: (1,3)(1,4)-ß-glucan, tamarind seed gum, and birchwood xylan, and the corresponding NPs were used as additives. For rice flour, additional BCW or NPs increased the initial and the peak viscosity. The addition of water-soluble polysaccharides produced the opposite trend: viscosity increased from the peak time to the end of measurements. For wheat flour, the addition of BCW or NP delayed the peak time and increased peak viscosity; the increase was maintained till the end of measurements. For barley flour, the additional BCW or NP caused a higher gelatinization rate and increased viscosity at the starch-retrogradation stage. Next, static gelatinization of a rice flour suspension in NP was successfully accomplished before placing it in a vessel; NP concentration in the gel significantly affected the firmness. Thus, the dynamic and unique interactions between various cereal flours and cell-wall polysaccharides in NPs can increase the flours' potential; static gelatinization of cereal flour with NP could expand flours' application range in both current and next-generation cooking.

Cabbage Core Powder as a New Food Material for Paste Preparation with "Nata Puree".

Cabbage core (CC) is regarded as a waste part of the vegetable, despite being edible and containing various nutritional and functional compounds. We investigated the properties of CC powder with particle sizes < 1 mm as a new food material. CC powder was more resistant to structural deformation than leaf-derived powder, particularly CC powder with particles ≥ 0.3 mm in size. To examine the application of CC powder in 3D printed foods, we investigated the effects of "nata puree," a disintegrated nata de coco made with tamarind seed gum (NPTG), on paste made with CC powder. NPTG promoted stable binding of paste made using CC powder, which was successfully extruded using a syringe to form a bar with a granular structure. Thus, CC powder possesses unique textural/structural properties for its application in next-generation foods.

Evaluation of the Enzymatic Saccharification Efficiency of an Energy Crop, Erianthus arundinaceus, Pretreated with Ca(OH)2 Using both Countercurrent Washing System and pH Adjustment by Nonpressurized CO2.

Erianthus arundinaceus (ER) is greatly appreciated among domestic energy crops in Japan for the production of fermentable sugars from lignocellulosic polysaccharides. In this study, we developed an efficient Ca(OH)2-based pretreatment of both stems and leaves of ER at ambient temperature with the addition of a washing step for enzymatic saccharification. The recoveries of glucans and xylans in the pretreated ER after four countercurrent washing cycles were 91 and 76 %, respectively, the former being considerably higher than that of rice straw (RS) (72 %). Their saccharification ratios in the washed sample under the pressure of 1 atm CO2 were 80 and 92.5 %, respectively. The application of this simple sugar production process from ER would further support the domestic bioprocess development. ER is also foreseen to provide the additional feedstock favorable for harvesting from winter to spring in Japan, preventing a risk for feedstock shortage generated by single harvesting such as RS.

"Nata Puree," a Novel Food Material for Upgrading Vegetable Powders, Made by Bacterial Cellulose Gel Disintegration in the Presence of (1,3)(1,4)-ß-Glucan.

Pulverization is a potentially powerful solution for the resource management of surplus- and non-standard agricultural products, maintaining their nutritional values for long and ensuring their homogeneity, whereas their original textures could disappear to narrow the application ranges. Therefore, new technologies should be developed for reconstructing the powders to provide them with new physical characteristics. Herein, we developed a novel food material, nata puree (NP), by nata de coco (bacterial cellulose gel) disintegration with a water-soluble polysaccharide using a household blender. The process worked well with (1,3)(1,4)-ß-glucan (BGL) as the polysaccharide, which could be substituted with barley extract. Lichenase treatment of the NP dramatically modified its physical properties, suggesting the importance of the BGL polymeric forms. NP exhibited distinct potato powder and starch binding activities, which would be attributed to its interactions with the cell wall components and a physical capture of powders by the NP network, respectively. NP supplementation into the potato paste improved its firmness and enabled its printable range shift for 3D food printing to a lower powder-concentration. NP also promoted the dispersion of powders in its suspension, and designed gelation could also be successfully performed by the laser irradiation of an NP suspension containing dispersed curdlan and turmeric powders. Therefore, NP could be applied as a powder modifier to a wide range of products in both conventional cooking, food manufacturing, and next generation processes such as 3D food printing.

Flexible ligand recognition of peroxisome proliferator-activated receptor-gamma (PPARgamma).

The peroxisome proliferator-activated receptor-gamma (PPARgamma) is a direct pharmacological target for drugs that enhance insulin sensitivity and are used clinically for the treatment of type II diabetes. Because the specificity of ligand recognition is lower for PPARgamma than for other nuclear receptors, PPARgamma can bind a larger variety of ligand types. In order to elucidate why the ligand recognition of PPARgamma is so flexible, we performed correlated fragment molecular orbital calculations for complexes of PPARgamma and each of two distinctive ligands, rosiglitazone and farglitazar. We found quite different patterns of ligand binding for these two ligands. The ligand-binding system of rosiglitazone, a drug in common clinical use, is based mainly on local electrostatic interactions around the thiazolidine ring, whereas both electrostatic interactions and van der Waals dispersion interactions with hydrophobic residues are required for the binding of farglitazar to PPARgamma. We suggest that the development of novel ligands will require adequately hydrophobic pharmacophores.

The RURAL (reciprocal upgrading for recycling of ash and lignocellulosics) process: A simple conversion of agricultural resources to strategic primary products for the rural bioeconomy.

Rice straw (RS), an agricultural resource for lignocellulosic biorefineries, can deteriorate when sun-drying is ineffective. Poultry litter ash (PLA) has been considered as a renewable phosphorus source for crops but is highly alkaline. Here, a simple process was developed for their reciprocal upgrading. RS, PLA, and water were mixed for wet storage and alkali pretreatment of the RS at 25 °C for 14 d, and solid-solid separation was performed to obtain PLA-treated RS (PT-RS) and RS-treated PLA (RT-PLA). PT-RS was susceptible to enzymatic saccharification, and 65.5-68.6% of total sugar residues in PT-RS was converted to lactic acid by its nonsterile application for simultaneous saccharification and fermentation using Bacillus coagulans. RT-PLA exhibited 1.8-points lower pH and a more sensitive response of phosphorus solubilization to acid than those of PLA. This process could thus provide a breakthrough for the rural bioeconomy by manufacturing two strategic primary products for various commercial bioproducts.

Synthesis and evaluation of (S)-5'-C-aminopropyl and (S)-5'-C-aminopropyl-2'-arabinofluoro modified DNA oligomers for novel RNase H-dependent antisense oligonucleotides.

We designed and synthesized two novel thymidine analogs: (S)-5'-C-aminopropyl-thymidine and (S)-5'-C-aminopropyl-2'-ß-fluoro-thymidine. Then, DNA oligomers containing these analogs were synthesized, and their functional properties were evaluated. Compared with the naturally occurring thymidine, it was revealed that (S)-5'-C-aminopropyl-2'-arabinofluoro-thymidine was sufficiently thermally stable, while (S)-5'-C-aminopropyl-thymidine featured thermal destabilization. The difference in thermal stability resulted from a moderate change in the secondary structure of the DNA/RNA duplexes and a molecular fluctuation in monomers derived from the (S)-5'-C-aminopropyl side chain, as well as from a variation in sugar puckering derived from the 2'-arabinofluoro modification. Meanwhile, the incorporation of these analogs significantly enhanced the nuclease resistance of the DNA oligomers. Moreover, the (S)-5'-C-aminopropyl-2'-arabinofluoro-modified DNA/RNA duplexes showed a superior ability to activate RNase H-mediated cleavage of the RNA strand compared to the (S)-5'-C-aminopropyl-modified DNA/RNA duplexes.

Supplementation of Bacillus amyloliquefaciens AS385 culture broth powder containing 1-deoxynojirimycin in a high-fat diet altered the gene expressions related to lipid metabolism and insulin signaling in mice epididymal white adipose tissue.

1-Deoxynojirimycin (DNJ) has been known for its functional properties, such as its anti-hyperglycemic and anti-obesity activities. Previously, we developed a sustainable procedure to produce culture broth powder (CBP) containing DNJ using Bacillus amyloliquefaciens AS385 and demonstrated its regulatory effect on the blood glucose and lipid parameters in C57BL/6J mice. The present study was aimed to determine the molecular mechanism underlying the physiological effects of CBP intake in different concentrations (low, medium and high) towards the development of high-fat diet (HFD)-induced metabolic disorders. Ten-week consumption of CBP-supplemented diets ameliorated HFD-induced adiposity, glucose intolerance, and reduced insulin sensitivity in C57BL/6J mice. To investigate how these physiological events could take place, we analyzed the expression of genes involved in lipid metabolism and insulin signaling in epididymal white adipose tissue and found that CBP had a regulatory effect on the expression of genes related to lipid metabolism (Pparγ, Srebf1c, Acc, Scd, Hsl, Lpl), adiponectin secretion (Foxo1 and Sirt1), and insulin signaling (Irs1 and Akt2). Next, we confirmed that DNJ acted as the main active component in CBP and detected the dose-dependent DNJ uptake in vital metabolic tissues, which may explain the dose-dependent alteration in the metabolic parameters and related gene expressions following the CBP intake in this study. Collectively, our results suggested that DNJ intake in the form of CBP prevented the progression of HFD-induced metabolic disorders through regulation of adipocyte gene expression involved in lipid metabolism and insulin signaling.

Cloning and homologous expression of novel lignin peroxidase genes in the white-rot fungus Phanerochaete sordida YK-624.

Two genes, encoding YK-LiP1 and YK-LiP2, were cloned from the white-rot fungus Phanerochaete sordida YK-624, and a homologous expression system for the gene was constructed. Two full-length cDNAs (ylpA and ylpB) were isolated by degenerate RT-PCR and RACE-PCR. The results of N-terminal amino acid sequence analysis of native YK-LiP1 and YK-LiP2 showed that ylpA and ylpB coded for YK-LiP2 and YK-LiP1 respectively. The promoter of glyceraldehyde-3-phosphate dehydrogenase cloned from P. sordida YK-624 (PsGPD) was used to drive the expression of ylpA. Expression vector pGPD-g-ylpA was transformed into a P. sordida YK-624 uracil auxotrophic mutant, UV-64. The YlpA protein was secreted in active form by the transformants after 4 d of growth in a medium containing an excessive nitrogen source, whereas endogenous YK-LiP1 and YK-LiP2 were not produced. The physical and catalytic properties of the purified YlpA protein were very similar to those of YK-LiP2. These results suggest that homologous expression of recombinant YK-LiP2 was successful.

Washing Lime-Pretreated Rice Straw with Carbonated Water Facilitates Calcium Removal and Sugar Recovery in Subsequent Enzymatic Saccharification.

Generally, Ca(OH)2 pretreatment of lignocellulosics for fermentable sugar recovery requires a subsequent washing step for calcium removal and pH control for optimized saccharification. However, washing Ca(OH)2-pretreated feedstock with water is considered problematic because of the low solubility of Ca(OH)2 and its adsorption to biomass. In this study, we estimated the availability of carbonated water for calcium removal from the slurry of Ca(OH)2-pretreated rice straw (RS). We tested two kinds of countercurrent washing sequences, four washings exclusively with water (W4) and two washings with water and subsequent two washings with carbonated water (W2C2). The ratios of calcium removal from pretreatment slurry after washing were 64.2 % for the W4 process and 92.1 % for the W2C2 process. In the W2C2 process, 49 % of the initially added calcium was recovered as CaO by calcination. In enzymatic saccharification tests under a CO2 atmosphere at 1.5 atm, in terms of recovery of both glucose and xylose, pretreated, feedstock washed through the W2C2 process surpassed that washed through the W4 process, which could be attributed to the pH difference during saccharification: 5.6 in the W2C2 process versus 6.3 in the W4 process. Additionally, under an unpressurized CO2 atmosphere at 1 atm, the feedstock washed through the W2C2 process released 78.5 % of total glucose residues and 90.0 % of total xylose residues. Thus, efficient removal of calcium from pretreatment slurry would lead to not only the recovery of added calcium but also the proposal of a new, simple saccharification system to be used under an unpressurized CO2 atmosphere condition.

Physiological Effects and Organ Distribution of Bacillus amyloliquefaciens AS385 Culture Broth Powder Containing 1-Deoxynojirimycin in C57BL/6J Mice.

1-Deoxynojirimycin (DNJ) has been known as a potent α-glucosidase inhibitor from mulberry leaves and considered beneficial in prevention of type 2 diabetes. Due to limited amount of DNJ in mulberry leaves, recent studies have focused in finding alternative source that can produce higher amount of DNJ. Previously, we produced a high DNJ-containing culture medium from Bacillus amyloliquefaciens AS385 and constructed a concentration method of bacterial culture medium using cation exchange column. However, less complicated concentration procedure is necessary to save time and cost during the large-scale production. Therefore, we developed a simpler concentration method using anion exchange resin to yield B. amyloliquefaciens AS385 culture broth powder (CBP; 1% DNJ) and evaluated the physiological effects of 5-wk dietary CBP intake in C57BL/6J mice. CBP intake tended to suppress the elevation of blood glucose level during oral glucose tolerance test. Moreover, CBP intake significantly lowered the fasting plasma glucose level and white adipose tissue mass. Next, we evaluated the absorption and distribution of DNJ in mice organs after daily CBP intake. We found detectable amount of DNJ in organs with intestine and kidney as the major targeted organs. We concluded that the DNJ content in CBP is absorbed from digestive tract, distributed and accumulated in organs, which most likely to contribute to the alteration of blood glucose regulation and adiposity in C57BL/6J mice. Our study was the first to report the physiological effects of CBP produced from B. amyloliquefaciens AS385 and the organ distribution of DNJ from CBP.

Efficient expression of laccase gene from white-rot fungus Schizophyllum commune in a transgenic tobacco plant.

Ligninolytic enzymes produced by white-rot fungi are effective degraders of recalcitrant aromatic environmental pollutants. However, gene sequences of these enzymes are rich in CpG dinucleotides, which are particularly unfavorable to efficient expression in plants. In order to develop a phytoremediation technique with a ligninolytic enzyme-producing transgenic plant, laccase cDNA (scL) from white-rot fungus Schizophyllum commune was used as a model ligninolytic enzyme, and we attempted to obtain the efficient expression of scL in a transgenic tobacco plant by decreasing the CpG-dinucleotide motif content. We constructed a mutagenized scL sequence, scL12, decreasing the CpG-dinucleotide motif content by 12%, and scL12 was introduced into the tobacco plant. Much higher laccase activity was detected in transgenic scL12 plants than in transgenic scL plants and wild-type plants. Using reverse transcriptase-PCR analysis, scL12 was translated in transgenic scL12 plants whereas mRNA of scL was not detected in the transgenic scL plants, and scL, which is the product of the scL12 gene, was produced in the transgenic scL12 plants using native-polyacrylamide gel electrophoresis analysis. Moreover, transgenic scL12 plants were able to remove trichlorophenol more effectively than transgenic scL plants and wild-type plants. These results suggest that decreasing CpG-dinucleotide motif content in fungal target genes is a useful method for efficient expression of these genes in transgenic plants.

Ab initio fragment molecular orbital study of ligand binding to human progesterone receptor ligand-binding domain.

We applied the fragment molecular orbital (FMO) method, which enables total electronic calculations of large molecules at ab initio level, to the evaluation of binding affinities between the human progesterone receptor ligand-binding domain (PR LBD) and various steroidal ligands. The FMO calculations were performed on the entire structure of the PR LBD, which is composed of approximately 4,100 atoms. Our computational binding energies of PR LBD/ligand complexes agreed well with experimental binding affinities (r=0.909). Interaction energies between each ligand and specific amino acid residues were also obtained from the FMO calculations. The principal residues involved in the interactions with these ligands were Arg766 and Asn719, with some additional contribution by Gln725. The main factor determining differences in binding affinity of the various ligands was not interactions with particular residues, but with the binding-site residues closest to the ligand. The interfragment interaction energy analysis is proving to be a useful method for gaining detailed information on ligand binding.