Chemical modifications of the nucleosides that comprise transfer RNAs are diverse. However, the structure, location and extent of modifications have been systematically charted in very few organisms. ...Here, we describe an approach in which rapid prediction of modified sites through reverse transcription-derived signatures in high-throughput transfer RNA-sequencing (tRNA-seq) data is coupled with identification of tRNA modifications through RNA mass spectrometry. Comparative tRNA-seq enabled prediction of several Vibrio cholerae modifications that are absent from Escherichia coli and also revealed the effects of various environmental conditions on V. cholerae tRNA modification. Through RNA mass spectrometric analyses, we showed that two of the V. cholerae-specific reverse transcription signatures reflected the presence of a new modification (acetylated acp
U (acacp
U)), while the other results from C-to-Ψ RNA editing, a process not described before. These findings demonstrate the utility of this approach for rapid surveillance of tRNA modification profiles and environmental control of tRNA modification.
Non-biodegradable microplastics have become a global problem. We propose a new enzyme-embedded biodegradable plastic that can be self-biodegraded anytime and anywhere. Proteinase K from Tritirachium ...album was embedded in poly(l-lactic acid) (PLLA). The PLLA solution-cast film with embedded proteinase K showed weight loss of 78% after 96 h incubation. In addition, PLLA extruded films embedding immobilized proteinase K encapsulated in polyacrylamide were produced at 200 °C and embedded-enzyme degradation was monitored. Immobilized proteinase K embedded in the extruded film maintained its degradation activity and degraded the PLLA film from inside to make small holes and cavities, suggesting that immobilization is a powerful technique to prepare thermoforms with embedded enzymes. The rate of embedded-enzyme degradation was accelerated by dividing the film into smaller pieces, which can be regarded as a model experiment for biodegradation of microplastics. Various biodegradable plastics with specific embedded enzymes will contribute to solve global environmental problems.
The factors and mechanisms that govern tRNA stability in bacteria are not well understood. Here, we investigated the influence of posttranscriptional modification of bacterial tRNAs (tRNA ...modification) on tRNA stability. We focused on Thil-generated 4-thiouridine (s⁴U), a modification found in bacterial and archaeal tRNAs. Comprehensive quantification of Vibrio cholerae tRNAs revealed that the abundance of some tRNAs is decreased in a Δthil strain in a stationary phase-specific manner. Multiple mechanisms, including rapid degradation of a subset of hypomodified tRNAs, account for the reduced abundance of tRNAs in the absence of thil. Through transposon insertion sequencing, we identified additional tRNA modifications that promote tRNA stability and bacterial viability. Genetic analysis of suppressor mutants as well as biochemical analyses revealed that rapid degradation of hypomodified tRNA is mediated by the RNA degradosome. Elongation factor Tu seems to compete with the RNA degradosome, protecting aminoacyl tRNAs from decay. Together, our observations describe a previously unrecognized bacterial tRNA quality control system in which hypomodification sensitizes tRNAs to decay mediated by the RNA degradosome.
•Crosslinked cellulose-chitosan foam (CCLBD) was prepared using a LiBr solution.•CCLBD was stable in acidic regions in spite of a low degree of crosslinking.•CCLBD exhibited an adsorption capacity ...(qmax) of 1548.2 mg/g for Congo red (CR).•The qmax for CR was the highest value among the previously reported adsorbents.•CCLBD is an effective adsorbent for the purification of dye-polluted water.
The adsorption of Congo red (CR) was evaluated using cellulose-chitosan foam crosslinked via dialdehyde cellulose (DAC). DAC-crosslinked cellulose-chitosan foam (CCLBD) was obtained by dissolution/regeneration using a LiBr aqueous solution, followed by crosslinking between chitosan and DAC. CCLBD possessed a three-dimensional structure with 40–200 nm wide pores composed of nanofibrils with a width of 10–20 nm, resulting in a high specific surface area of 230 m2/g. CCLBD was highly stable even acidic conditions in spite of a low crosslinking degree of 10.3%, which induced a slight reduction in the amino groups that interact with CR. CCLBD showed a CR adsorption capacity of 1548.2 mg/g and the adsorption process followed the Sips isotherm and pseudo-second-order models.
In bacterial 16S rRNAs, methylated nucleosides are clustered within the decoding center, and these nucleoside modifications are thought to modulate translational fidelity. The N⁴, ...2'-O-dimethylcytidine (m⁴Cm) at position 1402 of the Escherichia coli 16S rRNA directly interacts with the P-site codon of the mRNA. The biogenesis and function of this modification remain unclear. We have identified two previously uncharacterized genes in E. coli that are required for m⁴Cm formation. mraW (renamed rsmH) and yraL (renamed rsmI) encode methyltransferases responsible for the N⁴ and 2'-O-methylations of C1402, respectively. Recombinant RsmH and RsmI proteins employed the 30S subunit (not the 16S rRNA) as a substrate to reconstitute m⁴Cm1402 in the presence of S-adenosylmethionine (Ado-Met) as the methyl donor, suggesting that m⁴Cm1402 is formed at a late step during 30S assembly in the cell. A luciferase reporter assay indicated that the lack of N⁴ methylation of C1402 increased the efficiency of non-AUG initiation and decreased the rate of UGA read-through. These results suggest that m⁴Cm1402 plays a role in fine-tuning the shape and function of the P-site, thus increasing decoding fidelity.
Surface grafting of crystalline and ultrafine cellulose nanofibrils with poly(ethylene glycol) (PEG) chains via ionic bonds was achieved by a simple ion-exchange treatment. The PEG-grafted cellulose ...nanofibrils exhibited nanodispersibility in organic solvents such as chloroform, toluene, and tetrahydrofuran. Then, the PEG-grafted cellulose nanofibril/chloroform dispersion and poly(l-lactide) (PLLA)/chloroform solution were mixed, and the PEG-grafted cellulose nanofibril/PLLA composite films with various blend ratios were prepared by casting the mixtures on a plate and drying. The tensile strength, Young’s modulus, and work of fracture of the composite films were remarkably improved, despite low cellulose addition levels (<1 wt %). The highly efficient nanocomposite effect was explained in terms of achievement of nanodispersion states of the PEG-grafted cellulose nanofibrils in the PLLA matrix. Moreover, some attractive interactions mediated by the PEG chains were likely to be formed between the cellulose nanofibrils and PLLA molecules in the composites, additionally enhancing the efficient nanocomposite effect.
Never-dried and once-dried hardwood celluloses were oxidized by a 2,2,6,6-tetramethylpiperidine-1-oxyl radical (TEMPO)-mediated system, and highly crystalline and individualized cellulose nanofibers, ...dispersed in water, were prepared by mechanical treatment of the oxidized cellulose/water slurries. When carboxylate contents formed from the primary hydroxyl groups of the celluloses reached approximately 1.5 mmol/g, the oxidized cellulose/water slurries were mostly converted to transparent and highly viscous dispersions by mechanical treatment. Transmission electron microscopic observation showed that the dispersions consisted of individualized cellulose nanofibers 3−4 nm in width and a few microns in length. No intrinsic differences between never-dried and once-dried celluloses were found for preparing the dispersion, as long as carboxylate contents in the TEMPO-oxidized celluloses reached approximately 1.5 mmol/g. Changes in viscosity of the dispersions during the mechanical treatment corresponded with those in the dispersed states of the cellulose nanofibers in water.
In bacterial tRNAs, 5-carboxymethoxyuridine (cmo
U) and its derivatives at the first position of the anticodon facilitate non-Watson-Crick base pairing with guanosine and pyrimidines at the third ...positions of codons, thereby expanding decoding capabilities. However, their biogenesis and physiological roles remained to be investigated. Using reverse genetics and comparative genomics, we identify two factors responsible for 5-hydroxyuridine (ho
U) formation, which is the first step of the cmo
U synthesis: TrhP (formerly known as YegQ), a peptidase U32 family protein, is involved in prephenate-dependent ho
U formation; and TrhO (formerly known as YceA), a rhodanese family protein, catalyzes oxygen-dependent ho
U formation and bypasses cmo
U biogenesis in a subset of tRNAs under aerobic conditions. E. coli strains lacking both trhP and trhO exhibit a temperature-sensitive phenotype, and decode codons ending in G (GCG and UCG) less efficiently than the wild-type strain. These findings confirm that tRNA hydroxylation ensures efficient decoding during protein synthesis.
Mammalian gut microbiota are integral to host health. However, how this association began remains unclear. We show that in basal chordates the gut space is radially compartmentalized into a luminal ...part where food microbes pass and an almost axenic peripheral part, defined by membranous delamination of the gut epithelium. While this membrane, framed with chitin nanofibers, structurally resembles invertebrate peritrophic membranes, proteome supports its affinity to mammalian mucus layers, where gut microbiota colonize. In ray-finned fish, intestines harbor indigenous microbes, but chitinous membranes segregate these luminal microbes from the surrounding mucus layer. These data suggest that chitin-based barrier immunity is an ancient system, the loss of which, at least in mammals, provided mucus layers as a novel niche for microbial colonization. These findings provide a missing link for intestinal immune systems in animals, revealing disparate mucosal environment in model organisms and highlighting the loss of a proven system as innovation.
Magnetic nano/microparticles offer potential benefits for environmental applications such as water purification. However, achieving functional and stable surfaces remains a critical challenge for ...magnetic particle design. Nanocellulose, a naturally occurring nanofiber, is a promising surface material candidate, owing to its ease of functionalization and chemical stability. Here, we developed a magnetically collectable nanocellulose-coated polymer microparticle synthesis method, based on Pickering emulsion templating. The average diameter of the core/shell microparticles was 2.7 μm, and they were well dispersed in water, owing to the coverage with surface-carboxylated nanocelluloses. Most magnetic Fe3O4 nanoparticles with a 30 nm diameter were encapsulated in the microparticles and enriched at the CNF/polymer interfaces. The nanocellulose shell showed high loading of cationic dye molecules. In addition, the nanocellulose-coated microparticles could be recovered even after the dye loading by exposing the aqueous dispersion to a magnetic field.
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