Biology subjects

Sakamoto, R.

Publications and source records attributed to Sakamoto, R..

4 recordsLinked to original sources

bioRxiv2025

Purification and pigment analysis of diadinoxanthin-binding PSI-LHCI supercomplexes from Euglena gracilis strain Z

Euglena gracilis, a phototrophic flagellate, possesses light-harvesting complexes (LHCs) with a pigment composition distinct from that of land plants and green algae, despite notable similarities in LHC polypeptide sequences to green algae. Here, we purified photosystem I-LHCI (PSI-LHCI) supercomplexes from E. gracilis strain Z and characterized their biochemical and spectroscopic properties. The purified complex exhibited a unique pigment profile, notably including diadinoxanthin that is typically found in red-lineage organisms, setting E. gracilis apart from green-lineage organisms. The absorption spectrum displayed the Qy band of chlorophyll a at 675{square}nm, while the 77-K fluorescence-emission spectrum revealed a prominent peak at 732{square}nm, closely resembling those in land plants. These features suggest that long-wavelength chlorophylls bound to LHCI may be evolutionarily conserved. Nevertheless, the absence of neoxanthin, lutein, and violaxanthin further differentiates the Euglena LHCIs from other oxyphototrophs. Together, these results illuminate the evolutionary diversification of PSI-LHCI supercomplexes and offer insights into the unique pigment-binding features of the Euglena light-harvesting system.

plant biology↗

bioRxiv2025

Emergence of a Cell-Guided Multivalent Ligand of Enzymes on Cancer Cells Triggered by Click Reaction between Hetero Nano-Assemblies

Stimuli-responsive nanomaterials with multivalent ligands have attracted significant attention in the context of cancer chemotherapy and imaging. However, challenges remain such as non-selective stimuli response and/or existence of triggers in healthy regions in addition to the intrinsic heterogeneity of cancer that causes insufficient target recognition. In-spired by the expression of precise and diverse functions of biological machineries triggered by specific protein-protein complexation and conformational change, we report an artificial system where a bioorthogonal click reaction between hetero-nano-assemblies triggers their complexation and conformational changes, resulting in emergence of multivalent ligands for cancer-associated enzymes: carbonic anhydrase IX (CAIX). We also demonstrated that the multivalent ligands selectively inhibited the proliferation of cancer cells overexpressing CAIX under hypoxic conditions. Additionally, the click reaction between nano-assemblies in the presence of target cells provided a higher efficacy of the emerged multivalent ligands than that pre-formed in the absence of cells. Our study provides a basis for the development of multivalent ligands displaying adaptive binding interfaces for target cancer cells with high selectivity and affinity to thus potentially overcome tumor heterogeneity.

biochemistry↗

bioRxiv2023

Unique and shared functions of the Rad9-Hus1-Rad1 and Mre11-Rad50-Nbs1 complexes in ATR checkpoint activation and long-range DNA end resection in Xenopus egg extracts

Sensing and processing of DNA double-strand breaks (DSBs) are vital to genome stability. DSBs are primarily detected by the ATM checkpoint pathway, where the Mre11-Rad50-Nbs1 (MRN) complex serves as the DSB sensor. Subsequent DSB end resection promotes the transition from the ATM to the ATR checkpoint pathway, where replication protein A, MRN, and the Rad9-Hus1-Rad1 (9-1-1) checkpoint clamp serve as the DNA structure sensors. 9-1-1 and MRN recruit Topbp1, a critical checkpoint mediator that activates the ATR kinase. However, how multiple sensors contribute to regulating end resection and checkpoint activation remains ambiguous. Using DNA substrates that mimic extensively resected DSBs, we show here that MRN and 9-1-1 redundantly stimulate Dna2-dependent long-range end resection and ATR activation in Xenopus egg extracts. MRN serves as the loading platform for Dna2, ATM, and Topbp1. In contrast, 9-1-1 is dispensable for bulk Dna2 loading, and Topbp1 loading is interdependent with 9-1-1 in this pathway. ATR facilitates Mre11 phosphorylation and ATM dissociation. Our results delineate the molecular mechanism of and interplay between two redundant pathways that stimulate ATR checkpoint activation and long-range DSB end resection in vertebrates.

biochemistry↗

bioRxiv2018

Anomalous Scaling of Gene Expression in Confined Cell-Free Reactions

Cellular surface breaks the symmetry of molecular diffusion across membrane. Here, we study how steric interactions between the surface and the bulk of cell-sized emulsion droplets alters gene expression emulated by a cell-free transcription/translation (TXTL) system. The concentration of synthesized reporter proteins in droplets of radius R shows an anomalous geometric scaling of R4 different from the expected normal size-dependence of R3. Given that TXTL becomes less efficient at thin surface layer, a mathematical model explains anomalous size-dependence found in experiment. The surface of cell-sized compartment thus plays a regulatory role for cell-free gene expression.

synthetic biology↗