Biology subjects

Nakamura, A.

Publications and source records attributed to Nakamura, A..

42 records · Page 3Linked to original sources

bioRxiv2020

Extracellular DJ-1 induces sterile inflammation in the ischemic brain

Inflammation is implicated in the onset and progression of various diseases, including cerebral pathologies. Here we report that DJ-1, which plays a role within cells as an antioxidant protein, functions as a damage-associated molecular pattern (DAMP), and triggers inflammation if released from dead cells into the extracellular space. We first found that recombinant DJ-1 protein induces the production of various inflammatory cytokines in bone marrow-derived macrophages (BMMs). We further identified a unique peptide sequence in the G and H helices of DJ-1 that activates Toll-like receptor 2 (TLR2) and TLR4. In the ischemic brain, DJ-1 is released into the extracellular space from necrotic neurons within 24 hours after stroke onset and makes direct contact with the surfaces of infiltrating myeloid cells. Administration of an antibody against DJ-1 suppresses the expression of inflammatory cytokines in infiltrating immune cells and attenuates ischemic neuronal damage. Our results demonstrate a previously unknown function of DJ-1 as a DAMP and suggest that extracellular DJ-1 could be a therapeutic target to prevent inflammation in tissue injuries and neurodegenerative diseases. Significance statementDJ-1 has been thoroughly investigated as a cytoprotective antioxidant protein in neurons. However, here we demonstrate that extracellularly released DJ-1 triggers neurotoxic inflammation after ischemic stroke. Intracellular DJ-1 increases in response to oxidative stress in ischemic neurons, but if ischemic stresses result in necrotic cell death, DJ-1 is released extracellularly. Released DJ-1 interacts with TLR2 and TLR4 on the surface of infiltrating myeloid cells and triggers post-ischemic inflammation, leading to the exacerbated pathologies of ischemic stroke. Thus, extracellular DJ-1 is a previously unknown inflammatogenic DAMP, and may be a putative target for therapeutic intervention to prevent progression of inflammatory and neurodegenerative diseases.

immunology↗

bioRxiv2020

Intestinal progenitor P-bodies maintain stem cell identity by suppressing pro-differentiation factors.

The role of Processing bodies (P-bodies), key sites of post-transcriptional control, in adult stem cells remains poorly understood. Here, we report that adult Drosophila intestinal stem cells, but not surrounding differentiated cells such as absorptive Enterocytes (ECs), harbor P-bodies that contain Drosophila orthologs of mammalian P-body components DDX6, EDC3, EDC4 and LSM14A/B. A targeted RNAi screen in intestinal progenitor cells identified 39 previously known and 64 novel P-body regulators, including Patr-1, a gene necessary for P-body assembly. Loss of Patr-1-dependent P-bodies leads to a loss of stem cells that is associated with inappropriate translation and expression of EC-fate gene nubbin. Transcriptomic analysis of progenitor cells identifies a cadre of such weakly transcribed pro-differentiation transcripts that are elevated after P-body loss. Altogether, this study identifies a coordinated P-body dependent, translational and transcriptional repression program that maintains a defined set of in vivo stem cells in a state primed for differentiation. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=198 HEIGHT=200 SRC="FIGDIR/small/175398v2_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@d57273org.highwire.dtl.DTLVardef@14d057aorg.highwire.dtl.DTLVardef@1a2c4a5org.highwire.dtl.DTLVardef@11c5ba3_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIDrosophila intestinal progenitor cells contain constitutive and ultrastructurally organized P-bodies. C_LIO_LIA P-body regulator Patr-1 is required for intestinal progenitor cell maintenance. C_LIO_LIEnterocyte (EC) genes such as nubbin are weakly transcribed but not translated in intestinal progenitors. C_LIO_LIP-bodies repress EC gene translation to promote stem cell maintenance. C_LI

cell biology↗

bioRxiv2020

Long-lasting event-related beta synchronization and theta desynchronization of electroencephalographic activity in response to support-surface perturbations during upright stance: Novel findings from experimental and model-based results

Movement related beta band cortical oscillations, including beta rebound after execution and/or suppression of movement, have drawn attention in upper extremity motor control literature. However, fewer study focused on beta band oscillations during postural control in upright stance. Here, we examined beta rebound and other components of electroencephalogram (EEG) activity during perturbed upright stance to investigate supraspinal contributions to postural stabilization. Particularly, we aimed to clarify the timing and duration of beta rebound within a non-sustained, but long-lasting, postural recovery process that occurs more slowly compared to upper extremities. To this end, EEG signals were acquired from nine healthy young adults in response to a support-surface perturbation, together with the center of pressure (CoP) and mass (CoM) and electromyogram (EMG) activities of ankle muscles. Event-related potentials (ERPs) and event-related spectral perturbations were computed from EEG data using the perturbation-onset as a triggering event. After short-latency (< 0.3 s) ERPs, our results showed high-beta band power decrease (event-related desynchronization), which was followed by an event-related synchronization at high-beta band and theta band desynchronization. Specifically, beta synchronization (beta rebound) was sustained for as long as three seconds. EMGs of the ankle muscles and the ankle and hip joint torques remained activated in the first half period of the beta rebound. They returned to the steady-state in the remaining phase, where the CoP/CoM were in their final approach to the equilibrium. We propose possible mechanistic causes of the long-lasting beta rebound, which may be related to underlying intermittent control strategy in upright stance. New & NoteworthyBeta rebound cortical activity was identified during postural recovery from a perturbed upright stance. Contrary to upper extremities, it was initiated before the recovery of motion was completed, and sustained for as long as three seconds. Those novel characteristics of the beta rebound might be caused by slow dynamics of the upright posture and by selections of on/off switching in an intermittent feedback controller, which was shown to stabilize upright posture.

neuroscience↗

bioRxiv2020

The polyol pathway is a crucial glucose sensor in Drosophila

A major nutrient source for animals is glucose, which induces transcriptional responses that shift metabolism. Such metabolic adaptation should be appropriately scaled to the ingested glucose levels, and decoupling causes human metabolic diseases. However, the identity of the crucial sensor metabolite(s) that transmit circulating glucose levels to the transcriptional machinery remains elusive. Here we show that the polyol pathway, which converts glucose to fructose via sorbitol, is required for activation of the master metabolic regulator Mondo, the Drosophila homologue of MondoA/ChREBP. We demonstrate that under normal nutritional conditions polyol pathway metabolites promote Mondos nuclear localization and cause global changes in metabolic gene expression. Polyol pathway mutants block nuclear localization of Mondo and Mondo-mediated gene expression despite intact glycolytic and pentose phosphate pathways. Our results uncover the normal physiological function of this pathway and cast a new light on the adverse effects of high fructose diets in human health.

physiology↗

bioRxiv2019

An integrated approach unravels a crucial structural property for the function of the insect steroidogenic Halloween protein Noppera-bo

Ecdysteroids are the principal insect steroid hormones essential for insect development and physiology. In the last 18 years, several enzymes responsible for ecdysteroid biosynthesis, encoded by Halloween genes, have been identified and well characterized, both genetically and biochemically. However, none of these proteins have yet been characterized at the tertiary structure level. Here, we report an integrated in silico, in vitro, and in vivo analyses of the Halloween glutathione S-transferase (GST) protein, Noppera-bo (Nobo). We determine crystal structures of Drosophila melanogaster Nobo (DmNobo) complexed with glutathione and 17{beta}-estradiol, a DmNobo inhibitor. 17{beta}-estradiol almost fully occupied the putative ligand-binding pocket, and a prominent hydrogen bond formed between Asp113 of DmNobo and 17{beta}-estradiol. Asp113 is essential for inhibiting DmNobo enzymatic activity by 17{beta}-estradiol, as 17{beta}-estradiol does not inhibit and physically interacts less with the Asp113Ala DmNobo point mutant. Asp113 is highly conserved among Nobo proteins, but not among other GSTs, implying that Asp113 is important for endogenous Nobo function. Indeed, a homozygous nobo allele possessing the Asp113Ala point mutation exhibits embryonic lethality with undifferentiated cuticle structure, a phenocopy of complete loss-of-function nobo homozygotes. These results suggest that the nobo family of GST proteins has acquired a unique amino acid residue, which seems to be essential for binding an endogenous sterol substrate to regulate ecdysteroid biosynthesis. This is the first study to reveal the structural characteristics of insect steroidogenic Halloween proteins. This study also provides basic insight into applied entomology for developing a new type of insecticides that specifically inhibit ecdysteroid biosynthesis.\n\nSignificance StatementInsect molting and metamorphosis are drastic and dynamic biological processes and, therefore, have fascinated many scientists. Ecdysteroids represent one class of insect hormones that are indispensable for inducing molting and metamorphosis. It is well known that proteins responsible for catalyzing ecdysteroid biosynthesis reactions are encoded by \"Halloween\" genes, most of which have names of ghosts and phantoms. However, no studies have focused on the structural properties of these biosynthetic proteins. In this study, we addressed this unsolved issue and successfully unraveled a structural property that is crucial for the function of the fruit fly Halloween protein, Noppera-bo (a Japanese faceless ghost). This is the first study to reveal the structural characteristics of an insect steroidogenic Halloween protein.

biochemistry↗

bioRxiv2019

Dynamic free energy landscape of a linear motor chitinase from single-particle tracking trajectories

The mechanism of biomolecular motors has been elucidated using single-molecule experiments for visualizing motor motion. However, it remains elusive that how changes in the chemical state during the catalytic cycle of motors lead to unidirectional motions. In this study, we use singlemolecule trajectories to estimate an underlying diffusion model with chemical-state-dependent free energy profile. To consider nonequilibrium trajectories driven by the chemical energy consumed by biomolecular motors, we develop a novel framework based on a hidden Markov model, wherein switching among multiple energy profiles occurs reflecting the chemical state changes in motors. The method is tested using simulation trajectories and applied to singlemolecule trajectories of processive chitinase, a linear motor that is driven by the hydrolysis energy of a single chitin chain. The chemical-state-dependent free energy profile underlying the burnt- bridge Brownian ratchet mechanism of processive chitinase is determined. The novel framework allows us to connect the chemical state changes to the unidirectional motion of biomolecular motors.

biophysics↗