Biology subjects

Yamamoto, S.

Publications and source records attributed to Yamamoto, S..

6 recordsLinked to original sources

bioRxiv2018

A theory of centriole duplication based on self-organized spatial pattern formation

In each cell cycle, centrioles are duplicated to produce a single copy of each pre-existing centriole. At the onset of centriole duplication, the master regulator Polo-like kinase 4 (Plk4) undergoes a dynamic change in its spatial pattern on the periphery of the pre-existing centriole, forming a single duplication site. However, the significance and mechanisms of this pattern transition remain largely unknown. Using super-resolution imaging, we found that centriolar Plk4 exhibits periodic discrete patterns resembling pearl necklaces, frequently with single prominent foci. We constructed mathematical models that simulated the pattern formation of Plk4 to gain insight into the discrete ring patterns. The simulations incorporating the self-organization properties of Plk4 successfully generated the experimentally observed patterns. We therefore propose that the self-patterning of Plk4 is crucial for the regulation of centriole duplication. These results, defining the mechanisms of self-organized regulation, provide a fundamental principle for understanding centriole duplication.

cell biology↗

bioRxiv2018

Loss-of-function in IRF2BPL is associated with neurological phenotypes

The Interferon Regulatory Factor 2 Binding Protein Like (IRF2BPL) gene encodes a member of the IRF2BP family of transcriptional regulators. Currently the biological function of this gene is obscure, and the gene has not been associated with a Mendelian disease. Here we describe seven individuals affected with neurological symptoms who carry damaging heterozygous variants in IRF2BPL. Five cases carrying nonsense variants in IRF2BPL resulting in a premature stop codon display severe neurodevelopmental regression, hypotonia, progressive ataxia, seizures, and a lack of coordination. Two additional individuals, both with missense variants, display global developmental delay and seizures and a relatively milder phenotype than those with nonsense alleles. The bioinformatics signature for IRF2BPL based on population genomics is consistent with a gene that is intolerant to variation. We show that the IRF2BPL ortholog in the fruit fly, called pits (protein interacting with Ttk69 and Sin3A), is broadly expressed including the nervous system. Complete loss of pits is lethal early in development, whereas partial knock-down with RNA interference in neurons leads to neurodegeneration, revealing requirement for this gene in proper neuronal function and maintenance. The nonsense variants in IRF2BPL identified in patients behave as severe loss-of-function alleles in this model organism, while ectopic expression of the missense variants leads to a range of phenotypes. Taken together, IRF2BPL and pits are required in the nervous system in humans and flies, and their loss leads to a range of neurological phenotypes in both species.

genetics↗

bioRxiv2018

Self-organization of Plk4 regulates symmetry breaking in centriole duplication.

During centriole duplication, a single daughter centriole is formed near the mother centriole. The mechanism that determines a single duplication site is unknown. Here, we demonstrate that intrinsic self-organization of Plk4 underlies symmetry breaking in centriole duplication. We show that in its nonphosphorylated state, Plk4 preferentially self-assembles via a disordered linker and that this self-assembly is prevented by autophosphorylation. Consistently, the dissociation dynamics of centriolar Plk4 are controlled by autophosphorylation. We further found that autophophorylated Plk4 is localized as a single focus around the mother centriole before procentriole formation, and is subsequently targeted for STIL-HsSAS6 loading. Perturbing Plk4 self-organization affects the asymmetry of centriolar Plk4 distribution and centriole duplication. We propose that the spatial patterning of Plk4 directs a single duplication site per mother centriole.

cell biology↗

bioRxiv2018

Structural diversity across arbuscular mycorrhizal, ectomycorrhizal, and endophytic plant-fungus networks

BackgroundBelow-ground linkage between plant and fungal communities is one of the major drivers of terrestrial ecosystem dynamics. However, we still have limited knowledge of how such plant-fungus associations vary in their community-scale properties depending on fungal functional groups and geographic locations.\n\nMethodsBased on high-throughput sequencing of root-associated fungi in eight forests along the Japanese Archipelago, we performed a comparative analysis of arbuscular mycorrhizal, ectomycorrhizal, and saprotrophic/endophytic associations across a latitudinal gradient from cool-temperate to subtropical regions.\n\nResultsIn most of the plant-fungus networks analyzed, host-symbiont associations were significantly specialized but lacked \"nested\" architecture, which has been commonly reported in plant-pollinator and plant-seed disperser networks. Meanwhile, the structure of arbuscular mycorrhizal networks was differentiated from that of ectomycorrhizal and saprotrophic/endophytic networks, characterized by high connectance. Our data also suggested that geographic factors affected the organization of plant-fungus network structure. For example, the southernmost subtropical site analyzed in this study displayed lower network-level specificity of host-symbiont associations and higher (but still low) nestedness than northern localities.\n\nConclusionsOur comparative analyses suggest that arbuscular mycorrhizal, ectomycorrhizal, and saprotrophic/endophytic plant-fungus associations often lack nested network architecture, while those associations can vary, to some extent, in their community-scale properties along a latitudinal gradient. Overall, this study provides a basis for future studies that will examine how different types of plant-fungus associations collectively structure terrestrial ecosystems.

microbiology↗

bioRxiv2017

Plant-soil feedbacks between arbuscular- and ecto-mycorrhizal communities

Soil microbiomes of adult trees exert species-specific effects on the survival and growth of seedlings1-6, yet empirical evidence that such plant-soil microbiome interaction drives seedling community assembly remains scarce. Here we show that mycorrhizal fungal communities determine seedling community assembly by controlling how resident plant communities alter the growth of newly established seedlings. We reciprocally introduced seedling communities of arbuscular-and ecto-mycorrhizal plant species to replicated mesocosms to follow the effects of mycorrhizal type match/mismatch with resident plant communities on seedling growth rates. The growth rates of recruited seedlings were generally higher under resident trees of the same mycorrhizal types than under those of different mycorrhizal types, generating positive plant-soil feedbacks through mycorrhizal-type matching. Such positive effects of matching were linked with seedlings greater acquisition rates of mycorrhizal symbionts from matched resident plants than from mismatched plants, and such linkage was pronounced for ecto-mycorrhizal plant species. In contrast, under the condition of mycorrhizal-type matching between resident plants and seedlings (i.e., within-mycorrhizal-type comparison), plant-soil feedback effects varied considerably in their sign and strength among resident-seedling species combinations. Consequently, the assembly of a temperate tree seedling community is driven by a combination of species-specific plant-soil feedbacks and the match/mismatch of mycorrhizal type between resident plants and seedlings.

ecology↗

bioRxiv2017

A systems approach to the characterization and classification of T-cell responses

Types of T-cell responses are categorized on the basis of a limited number of molecular markers selected using a priori knowledge about T-cell immunobiology. We sought to develop a novel systems-based approach for the creation of an unbiased framework enabling assessment of antigenic-peptide specific T-cell responses in vitro. A meta-analysis of transcriptome data from PBMCs stimulated with a wide range of peptides identified patterns of gene regulation that provided an unbiased classification of types of antigen-specific responses. Further analysis yielded new insight about the molecular processes engaged following antigenic stimulation. This led for instance to the identification of transcription factors not previously studied in the context of T-cell differentiation. Taken together this profiling approach can serve as a basis for the unbiased characterization of antigen-specific responses and as a foundation for the development of novel systems-based immune profiling assays.

genomics↗