Biology subjects

Kurihara, M.

Publications and source records attributed to Kurihara, M..

6 recordsLinked to original sources

bioRxiv2024

NR4A3 deficiency ameliorates contact hypersensitivity and exacerbates psoriasis by regulating gene expression in dendritic cells

NR4A3 is a transcription factor that belongs to the nuclear receptor superfamily. To reveal the roles of NR4A3 in skin diseases, we constructed contact hypersensitivity (CHS)- and imiquimod-induced psoriasis models in Nr4a3-/- mice. In the CHS induced Nr4a3-/- mice, ear swelling was significantly reduced, accompanied by suppressed migration of dendritic cells (DCs), in which CCR7 expression was reduced. In contrast, ear swelling in psoriasis model Nr4a3-/- mice was enhanced. The expression levels of inflammatory cytokines in psoriasis skin lesions and in TLR7-ligand-stimulated DCs were increased by NR4A3 deficiency. Subcutaneous (s.c.) injection of hapten-treated Nr4a3+/+ DCs induced ear swelling in Nr4a3-/- mice, and s.c. injection of TLR7-ligand-stimulated Nr4a3-/- DCs caused significant ear swelling. Compared with Nr4a3+/+ DCs, Nr4a3-/- DCs expressed lower levels of CCR7 and IRF4, and higher levels of TLR7, IRF7, IFN-{beta}, and PU.1. Taken together, NR4A3 deficiency ameliorates CHS and exacerbates psoriasis by regulating the expression of CCR7, TLR7, and related transcription factors in DCs.

immunology↗

bioRxiv2023

The ABCF proteins in Escherichia coli individually alleviate nascent peptide-induced noncanonical translations.

Organisms possess a wide variety of proteins with a diverse repertoire of amino acid sequences, and their synthesis relies on the ribosome. Empirical observations have led to the misconception that ribosomes are robust protein factories, but in reality, they have several weaknesses. For instance, ribosomes stall during the translation of the proline-rich sequences, but the translation elongation factor EF-P assists in synthesizing proteins containing the poly-proline sequences. Thus, living organisms have evolved to expand the translation capability of ribosomes through the acquisition of translation elongation factors, enabling the synthesis of diverse proteins. In this study, we have revealed that Escherichia coli ATP-Binding Cassette family-F (ABCF) proteins, YheS, YbiT, EttA and Uup, individually cope with various noncanonical translations induced by nascent peptide sequences within the exit tunnel of the ribosome. The correspondence between noncanonical translations and ABCFs was YheS for the translational arrest by nascent SecM, YbiT for poly-basic sequence-dependent ribosome stalling and poly-acidic sequence-dependent intrinsic ribosome destabilization (IRD), EttA for IRD at the early stage of elongation, and Uup for poly-proline-dependent stalling. Our results suggest that the ATP hydrolysis-coupled structural rearrangement and interdomain linker sequence between the two nucleotide-binding domains play crucial roles in alleviating the noncanonical translations. Our study highlights a new aspect of ABCF proteins to reduce the potential risks that are encoded within the nascent peptide sequences. Significance statementProteins, that constitute living organisms, exhibit a diverse range of amino acid sequences. However, it has become evident that ribosomes have difficulties in synthesizing certain amino acid sequences, including the poly-basic, poly-acidic, and poly-proline sequences. The mechanisms underlying the expression of proteins with such challenging sequences remain largely elusive. In this study, we have unveiled that translation factor ABCF proteins in Escherichia coli promote various kinds of problematic amino acid sequences that inhibit efficient translation. Through the actions of translation elongation factors including the ABCF proteins, the translation system acquires robustness in synthesizing a vast repertoire of amino acid sequences.

biochemistry↗

bioRxiv2022

Proteomic profile of nuclei containing p62-positive inclusions in neuronal intranuclear inclusion disease

Neuronal intranuclear inclusion disease (NIID) is a neurodegenerative disease characterized by eosinophilic hyaline intranuclear inclusions in the neurons, glial cells, and other somatic cells. Although CGG repeat expansions in NOTCH2NLC have been identified in most East Asian patients with NIID, the pathophysiology of NIID remains unclear. Intranuclear inclusions are the pathological hallmark of NIID. Previously, immunohistochemistry has revealed that intranuclear inclusions are ubiquitin-, p62-, and SUMO-1-positive, suggesting the possible alteration of the ubiquitin-proteasomal protein degradation system in the nuclei with inclusions. However, the molecular mechanisms within these nuclei remain unclear. Herein, we analyzed the proteomic profile of nuclei with p62-positive inclusions in NIID with CGG repeat expansion in NOTCH2NLC to discover the proteins involved in the NIID pathophysiology. We used fluorescence-activated cell sorting and liquid chromatography-tandem mass spectrometry (LC-MS/MS) to quantify each protein identified in the nuclei with p62-positive inclusions. The distribution of increased proteins in the autopsy brain samples from three NIID patients was confirmed via immunofluorescence. Overall, 526 proteins were identified, of which 243 were consistently quantified using MS. A 1.4-fold increase was consistently observed for 20 proteins in nuclei with p62-positive inclusions compared to those without. Fifteen proteins identified with medium or high confidence in the LC-MS/MS analysis were further evaluated. Gene ontology enrichment analysis showed enrichment of several terms, including poly(A) RNA binding, nucleosomal DNA binding, and protein binding. Immunofluorescence studies confirmed that the fluorescent intensities of increased RNA-binding proteins identified by proteomic analysis, namely hnRNP A3, hnRNP A2/B1, and hnRNP C1/C2, were higher in the nuclei with p62-positive inclusions than those without; however, they were not confined to the intranuclear inclusions. We identified several increased proteins in nuclei with p62-positive inclusions. These data can form the basis for understanding the pathophysiology of NIID.

biochemistry↗

bioRxiv2022

Species-Specific Formation of Paraspeckles in Intestinal Epithelium Revealed by Characterization of NEAT1 in Naked Mole-rat

Paraspeckles are mammalian-specific nuclear bodies built on the long noncoding RNA NEAT1_2. The molecular mechanisms of paraspeckle formation have been mainly studied using human or mouse cells, and it is not known if the same molecular components are involved in the formation of paraspeckles in other mammalian species. We thus investigated the expression pattern of NEAT1_2 in naked mole-rats (nNEAT1_2), which exhibit extreme longevity and lower susceptibility to cancer. In the intestine, nNEAT1_2 is widely expressed along the entire intestinal epithelium, which is different from the expression of mNeat1_2, that is restricted to the cells of the distal tip in mice. Notably, the expression of FUS, a FET family RNA binding protein, essential for the formation of paraspeckles both in humans and mice, was absent in the distal part of the intestinal epithelium in naked mole-rats. Instead, mRNAs of other FET family proteins EWSR1 and TAF15 were expressed in the distal region. Exogenous expression of these proteins in Fus-deficient murine embryonic fibroblast cells rescued the formation of paraspeckles. These observations suggest that nNEAT1_2 recruits different set of RNA binding proteins in a cell type-specific manner during the formation of paraspeckles in different organisms.

molecular biology↗

bioRxiv2019

Rad51 Interaction Analysis Reveals a Functional Interplay Among Recombination Auxiliary Factors

Although Rad51 is the key protein in homologous recombination (HR), a major DNA double-strand break repair pathway, several auxiliary factors interact with Rad51 to promote productive HR. Here, we present an interdisciplinary characterization of the interaction between Rad51 and Swi5-Sfr1, a widely conserved auxiliary factor. NMR and site-specific crosslinking experiments revealed two distinct sites within the intrinsically disordered N-terminus of Sfr1 that cooperatively bind to Rad51. Although disruption of this binding severely impaired Rad51 stimulation in vitro, interaction mutants did not show any defects in DNA repair. Unexpectedly, in the absence of the Rad51 paralogs Rad55-Rad57, which constitute another auxiliary factor complex, these interaction mutants were unable to promote DNA repair. Our findings provide molecular insights into Rad51 stimulation by Swi5-Sfr1 and suggest that, rather than functioning in an independent subpathway of HR as was previously proposed, Rad55-Rad57 facilitates the recruitment of Swi5-Sfr1 to Rad51.

molecular biology↗

bioRxiv2019

Genomic profiling of PML bodies reveals transcriptional regulation by PML bodies through the DNMT3A exclusion

The promyelocytic leukaemia (PML) body is a phase-separated nuclear structure involved in various biological processes, including senescence, and tumour suppression1. PML bodies consist of various proteins, including PML proteins and several chromatin regulators2,3 and physically associate with chromatin4,5, implying their crucial roles in particular genome functions. However, their roles in transcriptional regulation are largely unknown. Here, we developed APEX-mediated chromatin labelling and purification (ALaP), to identify the genomic regions associated with PML bodies. We find that PML bodies associate with active regulatory regions across the genome and prominently with a [~]300 kb of the short arm of the Y chromosome (YS300) in mouse embryonic stem cells (mESCs). The association with YS300 is essential for the transcriptional activities of neighbouring Y-linked cluster genes. Mechanistically, we show that PML bodies play a novel role in 3D nuclear organization by providing specific nuclear spaces that the de novo DNA methyltransferase DNMT3A cannot access, which results in the robust maintenance of the hypo-methylated states at the Y-linked gene promoters. Our study underscores a new mechanism for gene regulation in the 3D-nuclear space and provides insights into the functional properties of nuclear structures for genome functions.

cell biology↗