Bioscience, Biotechnology, and Biochemistry最新文献

Marine ferromanganese (Fe-Mn) oxides serve as both reactive interfaces and long-term archives for oceanography and environmental changes on the Earth. These oxides are ubiquitous in the ocean and provide reactive mineral surfaces that control elemental abundances and isotope ratios in seawater. Recent synchrotron-based spectroscopy and high-precision isotope analyses have significantly improved the molecular-scale understanding of elemental partitioning and isotope fractionation, which establishes a basis for understanding the relationships between minerals and seawater. Hydrogenetic Fe-Mn crusts, which grow extremely slowly on the seafloor, archive paleoceanographic information over tens of millions of years, including ocean chemistry, water mass structure, and ocean circulation. Furthermore, ancient terrestrial Fe-Mn deposits provide constraints on the oxygenation of Earth's surface as a consequence of interactions among the atmosphere, ocean, lithosphere, and biosphere. Progress in Fe-Mn oxide research will facilitate a deeper understanding of ocean chemistry, and the evolution of marine and Earth systems.

The crystal structure of l-galactose dehydrogenase (LGDH) with l-glucose dehydrogenase activity from Luteolibacter sp. strain LG18 (Lu-LGDH) was determined in complex with l-galactose or l-glucose and NADP⁺. This structural analysis identified key residues involved in substrate binding, and alanine-substituted mutants demonstrated the roles of these residues, including Tyr56, acting as potential general base within the catalytic tetrad. Unlike plant enzymes that show a preference for NAD⁺, Lu-LGDH exhibits a marked preference for NADP⁺ as a cofactor. This preference was attributed to the interaction of the phosphate group with Arg28, Thr269, and Asn274. The binding mode of l-glucose was similar to that of l-galactose. The C4 hydroxyl group (the structural difference between these pyranoses) was not used for substrate binding, which explains the dual activity of the enzyme. Furthermore, among the substrate-binding residues that were mutated, Arg308, which is not conserved among LGDHs, was crucial for the enzymatic activity.

Restriction endonuclease DpnI is a critical tool for eliminating parental templates in site-directed mutagenesis (SDM); however, the wild-type enzyme exhibits low efficiency at low substrate concentrations. In this study, we introduced a lysine mutation into the C-terminal winged helix (wH) domain of DpnI via structure-guided design to enhance electrostatic interactions and established a rapid screening platform using rolling circle amplification (RCA) coupled with cell-free protein synthesis (CFPS). Results showed that the Q235K variant achieved a specific activity of 640,000 U/mg, four-fold higher than the wild-type, and increased the positive mutation rate in SDM from 82.7% to 92.3% while significantly reducing background plasmid residue. This study not only yielded a high-performance tool enzyme but also demonstrated the high efficiency of CFPS for rapid iteration and optimization in enzyme engineering.

The CAPRICE (CPC) transcription factor regulates root hair initiation and inhibits trichome formation in Arabidopsis thaliana. CPC transits between root epidermal cells via its N-terminal S1 motif; however, the contribution of individual amino acid residues of this motif remains unclear. We generated seven CPC variants with alanine substitutions at positions 2-4 of the S1 motif and analyzed their functions in transgenic Arabidopsis. All variants promoted root hair initiation and inhibited trichome formation with reduced GL2 expression. Confocal imaging of green fluorescent protein-tagged proteins revealed partial reduction in their cell-to-cell movement compared with that of CPC wild-type. Protein structural analysis suggested that the biochemical properties of Phe-2, Arg-3, and Ser-4 within the disordered N-terminal region may contribute to CPC transport. These findings indicate that the S1 motif fine-tunes the intercellular mobility of CPC without compromising epidermal cell differentiation in the root epidermis. (143 words).

The structural basis for dipeptides modulating PPARα remains unclear. AlphaFold2 identified Ile-His as a candidate predicted to interact with a novel alternative binding site. In HepG2 cells, Ile-His and Phe-Ala reduced cholesterol accumulation, whereas Ala-Pro had no effect. These findings support the utility of structure-based prediction as a hypothesis-generating approach for identifying dipeptides associated with PPARα-related modulation of lipid metabolism.

Sweet potatoes were cultivated in hydroponics with low nitrogen fertilization. Through 16S rRNA gene amplicon sequencing, the most abundant genera in storage roots of them were identified as Azospirillum, Sphingomonas, Burkholderia, Bradyrhizobium, and Arthrobacter, all of which have been reported as nitrogen-fixing bacteria. These results suggest that nitrogen-fixing bacteria may selectively increase to compensate for the insufficient nitrogen fertilization.

Dietary fiber may improve dysbiosis and contribute to the management of intestinal inflammation and muscle wasting. We examined whether low- and high-fermentable fibers differently influence DSS-induced colitis severity and muscle wasting. Male C57BL/6 J mice were assigned to four groups: non-fiber control (N), non-fiber with DSS (ND), cellulose with DSS (CD), and partially hydrolyzed guar-gum (PHGG) with DSS (GD), then subjected to a 27-day DSS protocol. Colitis severity was attenuated in the CD group, accompanied by increased Lactobacillus and Lactococcus lactis and decreased Clostridium innocuum group. These microbial changes were associated with maintenance of gastrocnemius muscle mass through mitochondrial biogenesis. Conversely, the GD group exhibited exacerbated colitis, associated with increased cecal succinate and expansion of Bacteroides, Blautia, and Enterococcaceae. These alterations correlated with muscle wasting accompanied by mitochondrial dysfunction. These results suggest that fiber fermentability plays a pivotal role in colitis management via gut microbiota alterations, also associated with muscle wasting.

Gibberellins (GAs) are a class of diterpenoid compounds that were originally identified as the causal toxins of rice seedling disease. GAs are phytohormones produced universally by plants, and more than 130 GAs have been isolated to date. Studies using rice and Arabidopsis have revealed the biosynthesis and inactivation pathways of GAs as well as their signaling mechanisms. However, as genome sequencing progressed, it was found that mosses, liverworts, and hornworts lacked certain genes encoding GA biosynthetic enzymes. Recent studies have revealed that partial GA biosynthetic pathways function in planta to biosynthesize bioactive substances that can be regarded as ancestral GA substances and to regulate their own growth. This review summarizes the current knowledge regarding the biosynthetic pathways of GA and ancestral GA substances.

Using a reporter assay system we screened a library of 472 compounds, and identified 1,25(OH)2D3, all-trans-retinoic acid, 9-cis-retinoic acid, 13-cis-retinoic acid, 17-allylamino-17-demethoxygeldanamycin, cantharidin and magnolol that inhibit FOXO1/3a activity. These compounds suppressed the increase in Atrogin1 gene expression induced by dexamethasone in C2C12 myoblasts. Therefore, these compounds may prevent muscle atrophy by inhibiting FOXO1/3a activity.

The gut microbiota plays a pivotal role in human health and interacts with quercetin, which undergoes extensive glucuronidation in the host organism. Microbial β-glucuronidases can deconjugate quercetin monoglucuronides, regenerating the aglycone and modulating bioavailability; however, the magnitude and drivers of inter-individual variability remain unclear. We assembled a panel of human-derived intestinal isolates and quantified the deglucuronidation of four regioisomeric quercetin monoglucuronides using intact whole cells. Deglucuronidation capacity varied by approximately an order of magnitude across taxa and depended on the conjugation site: A/C-ring glucuronides were generally more labile than B-ring forms, with some species-specific exceptions. Notably, Faecalibacterium duncaniae emerged as a high-efficiency, broad-coverage deglucuronidator, outperforming the other isolates across all substrates. Whole-community assays of cecal content and fecal pellets echoed these preferences and revealed higher activity in digesta. These findings delineate species-resolved deglucuronidation patterns underlying inter-individual differences in quercetin bioavailability and identify species microbiota-driven deconjugation into pharmacokinetic models.