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Sugimoto, R.

Publications and source records attributed to Sugimoto, R..

2 recordsLinked to original sources

AtaA as a Self-Immobilizing Scaffold for Enzymatically Active Surfaces through Oxidative Tyrosine Coupling

Protein nanofibers are hold great promise as genetically programmable scaffolds for constructing functional material interfaces. AtaA, a giant trimeric autotransporter adhesin from Acinetobacter sp. Tol 5, forms an elongated architecture from the bacterial cell surface, enabling the cells to adhere directly to a wide variety of abiotic surfaces. However, the potential use of AtaA as a scaffold with additional biological functions remains largely unexplored. In this study, we investigated the use of AtaA as a self-immobilizing scaffold for constructing enzymatically active surfaces via horseradish peroxidase (HRP)-catalyzed tyrosine coupling. We prepared a recombinant AtaA nanofiber fragment (NhNs-AtaA) and its derivative containing two tyrosine-containing loop structures (YL-NhNs-AtaA). Both recombinant proteins retained their adhesive properties. Treatment with HRP and H2O2 generated high-molecular-weight products from both proteins, and dityrosine fluorescence emission indicated the formation of tyrosine-derived covalent cross-links. Y-Loop insertion further increased the consumption of monomeric AtaA and promoted the formation of high-molecular-weight products. The removal of arginine, which was included during purification, further increased the loss of monomeric AtaA in both constructs, indicating that intermolecular protein association influenced productive AtaA cross-linking. NhNs-AtaA and YL-NhNs-AtaA were combined with Y-tagged bacterial alkaline phosphatase (BAP-Y). HRP-mediated coupling generated high-molecular-weight products consistent with the cross-linked AtaA-BAP-Y conjugates and enabled the retention of BAP activity on AtaA-coated surfaces without prior chemical modification. Although Y-Loop insertion enhanced polymerization in solution, it reduced AtaA adhesion and consequently lowered surface-bound phosphatase activity, revealing a trade-off between cross-linking reactivity and native adhesive function. These findings establish AtaA as a self-immobilizing protein nanofiber scaffold for constructing enzymatically active surfaces, and suggest the potential extension of this strategy to other AtaA-based interfaces.

bioengineering↗

De novo virus inference and host prediction from metagenome using CRISPR spacers

Viruses are the most numerous biological entity, existing in all environments and infecting all cellular organisms. Compared with cellular life, the evolution and origin of viruses are poorly understood; viruses are enormously diverse and most lack sequence similarity to cellular genes. To uncover viral sequences without relying on either reference viral sequences from databases or marker genes known to characterize specific viral taxa, we developed an analysis pipeline for virus inference based on clustered regularly interspaced short palindromic repeats (CRISPR). CRISPR is a prokaryotic nucleic acid restriction system that stores memory of previous exposure. Our protocol can infer viral sequences targeted by CRISPR and predict their hosts using unassembled short-read metagenomic sequencing data. Analysing human gut metagenomic data, we extracted 11,391 terminally redundant CRISPR-targeted sequences which are likely complete circular genomes of viruses or plasmids. The sequences include 257 complete crAssphage family genomes, 11 genomes larger than 200 kilobases, 766 genomes of Microviridae species, 114 genomes of Inoviridae species and many entirely novel genomes of unknown taxa. We predicted the host(s) of approximately 70% of discovered genomes by linking protospacers to taxonomically assigned CRISPR direct repeats. These results support that our protocol is efficient for de novo inference of viral genomes and host prediction. In addition, we investigated the origin of the diversity-generating retroelement (DGR) locus of the crAssphage family. Phylogenetic analysis and gene locus comparisons indicate that DGR is orthologous in human gut crAssphages and shares a common ancestor with baboon-derived crAssphage; however, the locus has likely been lost in multiple lineages recently.

genomics↗