Biology subjects

Baba, A.

Publications and source records attributed to Baba, A..

3 recordsLinked to original sources

bioRxiv2026

UBL3 UBL domain exhibits distinct helix-centered dynamic control among ubiquitin-like proteins

Ubiquitin-like protein 3 (UBL3) is a post-translational modifier that sorts proteins into small extracellular vesicles and regulates the trafficking of disease-associated proteins such as -synuclein. The structural and dynamic features of the UBL domain that underlie these functions, however, remain poorly understood. Here we performed in silico structural dynamics analysis of the UBL3 UBL domain using an NMR structure ensemble combined with anisotropic network modeling (ANM) and perturbation response scanning (PRS). Principal component analysis and residue-wise fluctuation analysis consistently revealed high flexibility in the C-terminal region of UBL3. Comparative ANM analysis across 20 ubiquitin-like proteins (UBLs) further showed that C-terminal flexibility is a conserved yet variable property within the UBL family. PRS analysis demonstrated that residues forming the central -helix of the {beta}-grasp fold exert greater dynamic control over collective motions than {beta}-sheet residues. Notably, UBL3 displayed the highest helix/sheet PRS effectiveness ratio among all UBLs analyzed, highlighting the prominent dynamic contribution of helix residues in this domain. Together, these results provide a structural basis for understanding UBL3-dependent protein interactions and disease-related mechanisms, and suggest that helix-centered dynamic control in the UBL domain may represent a potential target for modulating UBL3 function.

bioinformatics↗

bioRxiv2025

A dual-domain chitinase mechanism enables marine bacteria tosense and localize sparse crystalline chitin in the ocean

Chitin is one of the most abundant biopolymers in the ocean, and its remineralisation underpins major pathways of marine carbon cycling. A central challenge for chitinolytic bacteria is to locate and remain associated with sparsely distributed crystalline chitin particles. Here, we show that the GH18 chitinase VpChi1 from Vibrio parahaemolyticus possesses a dual-domain architecture that enhances particle encounter and retention. Full-length VpChi1 displayed much higher catalytic efficiency than a CBD-truncated mutant at low chitin concentrations, whereas substrate inhibition occurred at higher concentrations. Single-molecule fluorescence imaging demonstrated that the additional C-terminal chitin-binding domain (CBD) enables selective binding to the hydrophobic surface of crystalline chitin and substantially prolongs enzyme residence time. Kinetic simulations using experimentally determined dissociation rates showed that this extended residence arises from CBD-assisted rebinding of the catalytic domain. High-speed atomic force microscopy confirmed that the CBD does not alter stepping velocity or travel distance along individual crystals, indicating that substrate inhibition likely results from CBD engagement with neighbouring particles rather than impaired motility. Screening of seawater and marine sediments across multiple depths identified Vibrio and Pseudoalteromonas species as dominant chitin degraders, many encoding GH18 chitinases with dual CBDs, whereas terrestrial bacteria generally lacked this architecture. We propose that this two-domain configuration confers an ecological advantage by increasing enzyme retention on particulate chitin and enabling sustained production of chitobiose, a potent chemotactic signal for marine bacteria. These findings reveal a mechanistic basis for how bacteria sense and exploit particulate chitin and highlight an adaptive strategy for resource acquisition in the ocean.

molecular biology↗

bioRxiv2021

Localization of planteose hydrolysis during seed germination of Orobanche minor

Root parasitic weeds of the Orobanchaceae, such as witchweeds (Striga spp.) and broomrapes (Orobanche and Phelipanche spp.), cause serious losses in agriculture worldwide. No practical method to control these parasitic weeds has been developed to date. Understanding the characteristic physiological processes in the life cycles of root parasitic weeds is particularly important to identify specific targets for growth modulators. In our previous study, planteose metabolism was revealed to be activated soon after the perception of strigolactones in germinating seeds of O. minor. Nojirimycin inhibited planteose metabolism and impeded seed germination of O. minor, indicating that planteose metabolism is a possible target for root parasitic weed control. In the present study, we investigated the distribution of planteose in dry seeds of O. minor by matrix-assisted laser desorption/ionization-mass spectrometry imaging. Planteose was detected in tissues surrounding--but not within--the embryo, supporting its suggested role as a storage carbohydrate. Biochemical assays and molecular characterization of an -galactosidase family member, OmAGAL2, indicated the enzyme is involved in planteose hydrolysis in the apoplast around the embryo after the perception of strigolactones to provide the embryo with essential hexoses for germination. These results indicated that OmAGAL2 is a potential molecular target for root parasitic weed control. HighlightPlanteose accumulated in tissues surrounding the embryo in Orobanche minor dry seeds and was indicated to be hydrolyzed in the apoplast around the embryo by -galactosidase during germination.

plant biology↗