Biology subjects

Arakawa, M.

Publications and source records attributed to Arakawa, M..

6 recordsLinked to original sources

bioRxiv2026

Secretion is a second fate for p62 and is coupled to KEAP1/NRF2 signaling

Cells degrade the autophagy receptor p62/sequestosome 1 (SQSTM1) in lysosomes. By knocking the HiBiT peptide into the endogenous SQSTM1 locus, we show that export is a second, quantitatively comparable fate. Specifically, p62 leaves cells continuously inside membrane-enclosed carriers at a rate similar to that of LC3B. Blocking lysosomal degradation amplifies release through an ATG5- and FIP200-dependent route, whereas a basal route persists in autophagy-deficient cells. Thus, p62 exits by at least two parallel pathways. Export requires PB1-mediated self-oligomerization but not LC3 binding, Kelch-like ECH-associated protein 1 (KEAP1) binding, or an intact ubiquitin-associated domain. Hence, oligomerization is the sorting determinant. KEAP1 is also released, and dominant-negative RAB27A retains both proteins inside cells and lowers nuclear factor erythroid 2-related factor 2 transcriptional output. Secretion is therefore a second outlet for the p62-KEAP1 module, and its interruption co-varies with a dampened oxidative stress response.

cell biology↗

bioRxiv2026

High-resolution temporal profiling reveals synchronized dynamics of the mouse gut microbiome

The gut microbiome is a highly dynamic ecosystem, yet its temporal organization remains poorly understood because microbiome sampling is typically limited to sparse time points. To overcome this challenge, we developed an automated device to enable continuous fecal sampling from individual mice at minute-to hour-scale resolution. Combining full-length 16S rRNA amplicon sequencing with a limited set of long-read metagenomic references, we economically reconstructed genome- and function-level trajectories at high temporal resolution. Automated hourly sampling over 14 consecutive days enabled phase analysis, revealing collective synchronization of taxa partitioned by carbohydrate utilization strategies between day and night, with microbial taxa and functional genes showing reproducible temporal succession across mice. Perturbations such as cage transfer or antibiotic treatment transiently disrupted this functional synchronization, followed by recovery toward a coherent dynamical state. This system and analytic frameworks will enable us to explore rapid microbiome dynamics in health and disease.

microbiology↗

bioRxiv2025

Phosphorylation-Coupled Autoregulation Maintains Functional ER Exit Sites

Secretory proteins are synthesized in the endoplasmic reticulum (ER) and begin their transport from specialized domains on the ER called ER exit sites (ERES). We previously demonstrated that the interaction between TANGO1 and Sec16 is critical for ERES formation. In this study, we reveal that the phosphorylation of TANGO1 and Sec16 is regulated by a FAM83A/CK1-mediated negative feedback loop. Conversely, their dephosphorylation is regulated in a spatially distinct manner by different phosphatase complexes: PPP6R3/PPP6C for Sec16 and PPP1R15B/PPP1C for TANGO1. Excessive phosphorylation of either TANGO1 or Sec16 leads to ERES disassembly, while excessive dephosphorylation impairs secretion. Our findings demonstrate that maintaining a balanced phosphorylation state of TANGO1 and Sec16 through autoregulation by FAM83A/CK1 and the phosphatases PP1 and PP6 is essential for sustaining proper secretory activity at the ERES.

cell biology↗

bioRxiv2025

Amyloid-β fibrils accumulated in preeclamptic placentas suppress syncytialization of cytotrophoblasts

Cerebral deposition of fibrillar amyloid-{beta} (A{beta}) is a pathological hallmark of Alzheimers disease. While A{beta} is present in human placentas and accumulates in preeclamptic placentas characterized by poor placentation, the production and role of A{beta} in the human placenta remain unclear. Because hypoxia in mid-to-late pregnancy is a risk for preeclampsia, we found that levels of hypoxia-inducible factor 1- and {beta}-secretase (BACE-1) increased concurrently with placental A{beta} deposition in late stage preeclamptic placentas. We also found that a human cytotrophoblast (CTB) model, BeWo cells, actually produced A{beta} species, and that hypoxia increased A{beta} production and BACE-1 protein levels. A{beta}42 fibrils inhibited CTB syncytialization, a critical step in maintaining pregnancy, by inducing loss of membrane localization of cell-cell adhesion molecules. Primary human CTBs confirmed these observations. Taken together, our results suggest that increased A{beta} production in CTBs by hypoxia may lead to the formation of A{beta} fibrils, which inhibit syncytiotrophoblast formation and are detrimental to pregnancy. Thus, our results reveal the novel role of A{beta} fibrils in the pathogenesis of preeclampsia.

biochemistry↗

bioRxiv2024

A Novel Method to Visualize Active Small GTPases Unveils Distinct Sites of Sar1 Activation During Collagen Secretion.

Small GTPases are essential in various cellular signaling pathways, and detecting their activation within living cells is crucial for understanding cellular processes. Fluorescence resonance energy transfer is widely used to study the interaction between activated small GTPases and their effectors, but it is limited to those with well-defined effectors, excluding Sar1. Here, we present a novel method, SAIYAN (Small GTPase ActIvitY ANalyzing), for detecting the activation of endogenous small GTPases via fluorescent signals utilizing a split mNeonGreen system. We demonstrated Sar1 activation at the endoplasmic reticulum (ER) exit site and successfully detected its activation state in various cellular conditions. Utilizing the SAIYAN system in collagen-secreting cells, we discovered activated Sar1 localized both at ER exit sites and ER-Golgi intermediate compartment (ERGIC) regions. Additionally, impaired collagen secretion led to the confinement of activated Sar1 at the ER exit sites, underscoring the significance of Sar1 activation through the ERGIC in collagen secretion.

cell biology↗

bioRxiv2021

Deceleration of cell cycle underpins a switch from proliferative- to terminal division in plant stomatal lineage

Differentiation of specialized cell types from self-renewing progenitors requires precise cell cycle control. Plant stomata are generated through asymmetric divisions of a stem-cell-like precursor meristemoid followed by the single symmetric division that creates an adjustable pore surrounded by paired guard cells. The stomatal-lineage-specific transcription factor MUTE terminates the asymmetric divisions and triggers differentiation. However, the role of cell cycle machinery in this transition remains unknown. Through time-lapse imaging, we discover that the symmetric division is slower than the asymmetric division. We identify a plant-specific cyclin-dependent kinase inhibitor, SIAMESE-RELATED4 (SMR4), as a molecular brake that decelerates cell cycle during this transition. SMR4 is directly induced by MUTE and transiently accumulates in differentiating meristemoids. SMR4 physically and functionally associates with CYCD3;1 and extends G1-phase of asymmetric divisions. By contrast, SMR4 fails to interact with CYCD5;1, a MUTE-induced G1 cyclin, and permits the symmetric division. Our work unravels a molecular framework of the proliferation-to-differentiation switch within the stomatal lineage and suggests that a timely proliferative cell cycle is critical for the stomatal fate specification.

plant biology↗