Journal of biochemistry最新文献

Type 2 diabetes, which is closely linked to obesity, results from complex genetic and environmental interactions. Despite high heritability estimates, genome-wide association studies have not fully explained the heritability, suggesting the involvement of epigenetic mechanisms. This review highlights two distinct genome-independent pathways for intergenerational transmission of diabetic risk: (1) epigenetic transmission via gametes, whereby parental exposures induce heritable epigenetic changes in germ cells, and (2) developmental programming, in which prenatal or early postnatal environments shape the metabolism of offspring. Both processes are increasingly understood to involve epigenetic modifications, including DNA methylation, histone modifications, and non-coding RNAs. These epigenetic modifications have been suggested to contribute to intergenerational disease transmission in both animal and human studies. Understanding these mechanisms is essential for developing preventive strategies targeting the intergenerational risk of metabolic diseases.

Pancreatic β cells maintain glucose homeostasis through insulin production, and their loss underlies both type 1 and type 2 diabetes. Among the signaling systems that govern β-cell biology, insulin and insulin-like growth factor (IGF) receptor pathways have long attracted attention as intrinsic modulators of β-cell growth, survival, and secretory competence. However, the physiological and pathological relevance of these receptors in β cells remains uncertain, reflecting model-specific discrepancies and the complex interplay between local autocrine and systemic endocrine effects. Recent analyses have expanded this view, revealing the coexistence of insulin receptor-dependent and insulin receptor-independent regulatory modules that govern β-cell adaptation to metabolic stress. Furthermore, molecular regulators, including inceptor and IGF2R, reshape our understanding of insulin/IGF receptor signaling as a flexible, adaptive network. Together, these insights suggest that precise modulation of receptor networks may hold the key to unlocking endogenous β-cell regenerative capacity.

Liquid-liquid phase separation (LLPS) is a fundamental organizing principle in biology, driving the formation of membraneless compartments and thereby orchestrating a vast array of biochemical reactions in a spatiotemporal manner. LLPS is mediated by weak, multivalent interactions between biomolecules. While intrinsically disordered regions (IDRs) are widely recognized as major drivers of LLPS, coiled-coils, one of the most ubiquitous protein motifs, are emerging as functionally distinct, versatile contributors. This review systematically explores the multifaceted roles of coiled-coils in LLPS, highlighting their capabilities that contrast with those of IDRs. A key feature distinguishing coiled-coils is their ability to span an exceptionally broad range of interaction affinities, from picomolar to millimolar levels. This vast dynamic range allows them to operate across a continuous functional spectrum-from serving as high-affinity oligomerization platforms to acting as modules that mediate weak, transient interactions-a functional duality not recapitulated by IDRs. Through this inherent tunability, coiled-coils can play a pivotal role in modulating both the propensity for phase separation and the material properties of the resultant condensates.

Peroxisomes are dynamic organelles found in almost all eukaryotic cells and play a central role in intracellular metabolism. The number of peroxisomes is maintained through the balance of peroxisome biogenesis and degradation. Peroxisomes multiply by growth and division from preexisting peroxisomes but have also been shown to be synthesized de novo under experimental conditions. During de novo synthesis, pre-peroxisome vesicles mature in a stepwise process into functional peroxisomes. While the growth and division cycle is well studied, de novo synthesis, including whether it physiologically occurs, remains poorly understood. Although studies using several models have been proposed, the origin of the membranes required for peroxisome assembly remain controversial. This review provides an overview of the studies on de novo synthesis of peroxisomes in multiple organisms and discusses the evolutionary insights and biological meanings of peroxisome de novo synthesis.

The T1r family of receptors is essential for the detection of sweet and umami tastants, which are categorized as class C G protein-coupled receptors (GPCRs). Although these receptors share structural characteristics with other class C GPCRs, such as metabotropic glutamate receptors, they are uniquely characterized by a significantly shorter C-terminal intracellular domain, consisting of approximately 30-40 amino acid residues. Yoshida et al. recently demonstrated that the C-terminal region of mouse T1rs directly binds to calmodulin in a Ca2+-dependent manner. This interaction highlights a previously unrecognized aspect of the intracellular signalling mechanism of T1rs and indicates that the C-terminal region contributes to taste signal regulation, particularly through Ca2+-dependent feedback mechanisms.

Proteasomal degradation of ubiquitinated proteins involves various accessory factors, including p97 and shuttle factors, but their requirements and relationship with substrate structural properties are not fully understood, especially in human cells. Here, we demonstrate that substrate structure dictates the dependency on p97 and RAD23A/B for proteasomal degradation in human cells, using two ubiquitin-fusion model substrates, Ub-GFP (well-folded) and Ub-GFP-tail (with an unstructured tail). Both substrates exhibited similar ubiquitin chain composition, primarily mediated by the UBR4-KCMF1 E3 ligase. Interactome analyses revealed that Ub-GFP preferentially interacts with p97 and RAD23B, while Ub-GFP-tail binds more strongly with the proteasome. The degradation of Ub-GFP depends on p97 and RAD23A/B, whereas that of Ub-GFP-tail bypasses these accessory factors. RAD23A/B knockdown resulted in a reduction in the apparent lengths of ubiquitin chains on both substrates, yet it only affected Ub-GFP degradation, suggesting that even a lower level of ubiquitination is sufficient to support proteasomal degradation of substrates with an unstructured tail. Overall, our findings highlight substrate structure as a key determinant of accessory factor requirement, offering valuable insights for the development of targeted protein degradation.

(Pro)renin receptor [(P)RR], encoded by Atp6ap2, is a transmembrane protein found in many organs. It functions in lysosomes as part of the vacuolar-ATPase complex, facilitating autophagy and degradation. Mutations in ATP6AP2 are linked to neurological conditions, including X-linked parkinsonism with spasticity. However, our understanding of the role of (P)RR in whole brain development remains incomplete. Here, we generated mice with neural stem cell (NSC)-specific (P)RR deficiency (CKO). CKO mice exhibited significant brain atrophy during mid-gestation, leading to perinatal lethality. Foetal CKO brains showed lateral ventricular enlargement with malformation of neocortex and ganglionic eminence from mid-gestation. CKO brains showed massive apoptosis in multiple regions along with microglial activation at E15. On the contrary, CKO NSCs showed normal self-renewal ability, suggesting that (P)RR is critical for survival of differentiated cells. In line with this, the mechanistic study using RNA-seq of primary NSCs revealed downregulation of genes related to neurodevelopment and myelination. We also found p62 and LC3-II protein accumulation, hallmarks of deregulated autophagic pathways, in CKO foetal brains and NSCs. These findings demonstrate that (P)RR is crucial for guiding NSC differentiation and ensuring the coordinated construction of brain architecture during development.

REV1 is a eukaryotic error-prone DNA polymerase belonging to the Y-family, with a central role in translesion DNA synthesis (TLS) to continue DNA replication even in the presence of DNA damage in the template strand. TLS is stimulated by monoubiquitination of proliferating cell nuclear antigen (PCNA), a toroidal-shaped protein functioning as a scaffold for DNA polymerases and repair enzymes. Mammals possess four types of Y-family DNA polymerases: Pol η, Pol κ, Pol ι and REV1. Among those, Pol η, Pol κ and Pol ι interact with PCNA through PCNA-binding motifs, low-affinity variants of PCNA-interacting protein box (PIP-box). To date, several studies have reported that REV1 interacts with PCNA, but identified PCNA-binding regions are inconsistent; therefore, a structural basis for interaction between REV1 and PCNA also remains unclear. Here, we identified a signature sequence conserved within vertebrates REV1 responsible for PCNA-binding. Furthermore, we unveiled a mechanism underlying the physical interaction between the PCNA-binding motif of human REV1 and PCNA by X-ray crystallography, thus revealing that REV1 binds to PCNA through a PIP-box variant located in the C-terminal side of the little finger domain. Our study provides a convincing answer for a long-standing controversy regarding the physical interaction between REV1 and PCNA.

Phospholipase C (PLC) plays crucial roles in phospholipid metabolism by generating second messengers regulating diverse cellular processes. PLCs are classified into phosphatidylinositol-specific PLCs (PI-PLCs) and nonspecific PLCs. Among them, PI-PLCs are highly conserved across mammals, plants and bacteria, with distinct structural organizations and regulatory mechanisms. Mammalian PI-PLCs participate in intracellular signalling and modulate various pathways, such as the G protein-coupled receptor- and receptor tyrosine kinase-mediated cascades, whereas plant PI-PLCs regulate the growth and stress responses via phosphatidic acid and inositol phosphate signalling. Bacterial PI-PLCs contribute to virulence by targeting the host cell membranes and glycosylphosphatidylinositol-anchored proteins. Despite structural variations, PI-PLCs share conserved catalytic mechanisms integral to cellular physiology across different organisms. This review article highlights the structural diversity and functional significance of PI-PLCs in mammals, plants and bacteria.

Human serum albumin (HSA) has three major binding sites for drugs: Site I, Site II, and FA1 site. Dansyl amino acids (Dans-AAs) have long been used as convenient markers to judge whether a low molecular weight molecule of interest (ligand) binds to Sites I or II. However, crystal structures of HSA-Dans-AA complexes have revealed that Dans-AAs with strict site specificity are also bound to non-marker sites. To characterize the multiple binding of Dans-AAs in detail, the average number of the bound ligands per HSA molecule were obtained in a free ligand concentration of 1-400 μM for dansylate (DA) and 17 Dans-AAs using microbore frontal gel filtration chromatography. Analysis of the binding curves indicated that there are three specific binding sites for Dans-AAs. Four Dans-AAs with hydrophobic sidechain bind to all the sites with identical affinity, whereas DA and four Dans-AAs bind equally to two of them. Nine Dans-AAs bind to one of the three sites with the maximum occupancy ranging from 72 to 94%. The UV-vis absorption spectrum of HSA-ligand complex was obtained for DA and 10 Dans-AAs, revealing that the dansyl moiety is in hydrophobic environment and conformational changes in the binding site residues are induced.