Journal of biochemistry最新文献

Whole blood transcriptomics promises a practical readout of human physiology. However, several key gaps have limited its utility. Systematic analyses in healthy participants within prospective cohorts remain scarce. In addition, there is uncertainty about how age and sex shape whole-blood expression profiles, and no methodological consensus exists on whether globin mRNAs should be removed before analysis. Against this backdrop, Aoki and colleagues conducted a large-scale study using whole-blood RNA sequencing (RNA-seq) from 576 participants in the Tohoku Medical Megabank Project, aiming to generate foundational data for the Japanese population. By retaining globin transcripts and then applying in silico removal, they detected rare Hereditary Persistence of Fetal Hemoglobin (HPFH) cases, showed that immune-cell composition-particularly the neutrophil-to-lymphocyte ratio-drives major variance, and uncovered extensive age- and sex-dependent signatures, including pregnancy-associated NRF2 activation. Together, these results move the field toward establishing a Japanese whole-blood gene-expression reference by providing standardized, stratified baseline profiles and practical guidance on globin handling. This commentary explains why these choices matter and how the dataset will inform population-aware blood transcriptomics.

Macroautophagy is an evolutionarily conserved degradation pathway in eukaryotes that mediates the turnover of cytoplasmic components. The formation of autophagosomes, a hallmark of autophagy, involves autophagy-related (Atg) proteins, including two ubiquitin-like conjugation systems, Atg12 system and Atg8 system. In most species, Atg12 covalently binds Atg5, forming the Atg12-Atg5-Atg16 complex that functions as an E3-like enzyme to promote Atg8 conjugation with phosphatidylethanolamine (PE), a step essential for autophagosomal maturation. By contrast, certain species such as yeast Komagataella phaffii lack Atg10 and/or the C-terminal glycine of Atg12, relying instead on a non-covalent Atg12-Atg5 complex. However, the physiological significance of this reductively evolved non-covalent system and its divergence in molecular mechanisms from species harboring the canonical covalent Atg12 system remain undiscussed. In this study, we demonstrate that under nitrogen starvation, KpAtg12 is phosphorylated, and lipidation of KpAtg8 is enhanced. Our results with a phosphorylation-deficient mutant of KpAtg12 suggest that KpAtg12 phosphorylation modulates the activity of nitrogen starvation-induced macroautophagy through KpAtg8 lipidation reaction.

Phage research has played a pioneering role in the transition from genetics to molecular biology, primarily by advancing our understanding of the "3Rs": Replication, Recombination, and Repair. Historically, discoveries arising from the evolutionary arms race between phages and their hosts have provided essential molecular tools, such as restriction enzymes and polymerases, and more recently, have led to genome engineering technologies like CRISPR/Cas9. This commentary outlines the multifaced function of T7 endonuclease I, another important enzyme derived from 3R research, based on new findings by Matsubara et al. (1)).

The extension of the human lifespan has increased the incidence of age-related metabolic disorders, such as type 2 diabetes and sarcopenia, which markedly impair quality of life and reduce life expectancy in older adults. Aging and insulin resistance synergistically compromise the functional integrity of the adipose and skeletal muscles. During aging, the adipose tissue exhibits impaired progenitor differentiation, chronic inflammation, fibrotic remodeling, and loss of thermogenic capacity. Skeletal muscles also exhibit changes, including satellite cell decline, mitochondrial dysfunction, defective protein turnover, and progressive sarcopenia. These changes diminish tissue plasticity and endocrine function and exacerbate insulin resistance through disrupted intracellular signaling and accumulation of metabolic burden. Notably, the deterioration of adipose and muscle tissue functions is interconnected, further exacerbating systemic metabolic dysfunction. Recent studies have contributed to elucidating the physiopathological causes and mechanisms of age-dependent cellular and molecular alterations in adipose and muscle tissues. This review summarizes the current insights into the cellular and molecular mechanisms underlying age-related alterations in adipose and muscle tissues and discusses emerging therapeutic strategies, including lifestyle interventions, pharmacological agents, approaches targeting senescent cells, and inter-organ communication that aim to preserve metabolic health in aging populations.

Cellular senescence is a stress-induced, stable growth arrest accompanied by marked metabolic alterations and acquisition of the senescence-associated secretory phenotype (SASP). While enhanced glycolysis, mitochondrial dysfunction, and lysosomal abnormalities are well-established features, emerging evidence identifies progressive intracellular acidification as an important yet underappreciated regulator of cellular senescence. Acidification results from suppressed NHE1-mediated proton efflux, elevated glycolytic proton production, and lysosomal membrane permeabilization. This lowered pH alters redox balance, inhibits HDAC activity, and promotes transcription of senescence-associated genes. Recent work by Kawakami et al. demonstrates that acidification activates a glycolysis-linked inflammatory circuit through accumulation of glucose-6-phosphate and induction of the MondoA targets TXNIP and ARRDC4, which correlate with SASP induction and define a highly secretory subset of senescent cells. These findings suggest that intracellular pH functions as a key metabolic cue linking altered glycolysis to inflammatory output, offering a conceptual framework that may guide future efforts to modulate age-associated chronic inflammation.

LAMP2 is one of the major lysosomal membrane proteins. It contains a large luminal domain, a single transmembrane (TM) domain, and an unusually short cytoplasmic tail composed of only 11 amino acids. Three splicing variants-LAMP-2A, LAMP-2B, and LAMP-2C-share an identical luminal domain but differ in their TM and cytoplasmic tail sequences, resulting in distinct trafficking pathways and functions. Yamaguchi et al. demonstrated that the ultimate target compartments of these isoforms diverge according to the binding affinities of their cytoplasmic tails for μ-subunits of adaptor protein (AP) complexes AP-1, AP-2, AP-3, and AP-4. Intriguingly, each isoform contributes to specific lysosomal functions. It is remarkable that such short cytoplasmic tails not only determine subcellular localization but also underlie the functional diversity of LAMP-2 isoforms.

Mitochondrial quality control plays a critical role in maintaining cellular homeostasis by eliminating dysfunctional mitochondria. The PINK1/Parkin-dependent mitophagy mediates the selective clearance of damaged mitochondria. Dysfunction of PINK1 and Parkin is closely linked to Parkinson's disease. Upon mitochondrial depolarization, PINK1 accumulates on the outer membrane and phosphorylates both ubiquitin and the UBL domain of Parkin to initiate a positive feedback loop of ubiquitination. Parkin catalyzes the assembly of heterogeneous ubiquitin chains on outer mitochondrial membrane proteins, which serve as signals for autophagy adaptors. These adaptors are regulated by kinases such as TANK-binding kinase (TBK1). Deubiquitinating enzymes such as USP30 act as negative regulators. Recent structural and biochemical studies have advanced our understanding of the PINK1/Parkin-dependent mitophagy. Nonetheless, important questions remain regarding the regulatory mechanisms of PINK1, the catalytic mechanism of ubiquitin chain formation by Parkin, and the recognition of ubiquitin chains by autophagy adaptors. Here, we review the current understanding and outstanding questions on the molecular mechanisms underlying the PINK1/Parkin-dependent mitophagy with a focus on ubiquitin signaling.

Ubiquitin modifications are a central hub for numerous biomolecular reactions, finely tuning essential processes such as protein degradation and cellular signal transduction. The architecture of ubiquitin chains-linkage types, branching patterns, and lengths-encodes a rich layer of information, referred to as the ubiquitin code. This intricate code orchestrates diverse biological outcomes. Notably, earlier studies have revealed that branched ubiquitin chains accelerate proteasomal degradation. Yet, the delicate molecular choreography that drives this enhancement remains a mystery, waiting to be fully unraveled. Recent structural, biochemical, and chemical biology approaches have provided new insights into the molecular mechanisms underlying the encoding and decoding of branched ubiquitin chain. In this review, we focus on the proteolytic codes of K11/K48-, K29/K48-, and K48/K63-branched ubiquitin chains, offering an overview of recent research and discussing future challenges and prospects.

Macromolecular crowding is a fundamental property of the intracellular environment that influences protein folding, enzymatic activity, and phase behavior. Disruptions to the homeostasis of macromolecular crowding can drive pathological processes, such as aberrant liquid-liquid phase separation and protein aggregation, which are central features of several neurodegenerative diseases. However, tools for quantifying crowding and aggregation remain limited. Here, we describe moxCRONOS, a Förster resonance energy transfer (FRET)-based biosensor that enables the quantitative measurement of macromolecular crowding and protein condensation. moxCRONOS retains the optical properties of the original CRONOS sensor but offers enhanced stability in oxidative environments, such as within the endoplasmic reticulum or under sodium arsenite treatment, allowing for direct comparison of crowding levels across organelles regardless of redox conditions. Moreover, when fused to dipeptide repeat proteins associated with C9ORF72-linked neurodegeneration, moxCRONOS detects aggregation-prone states-especially in cells expressing glycine-alanine (GA) repeats. Using fluorescence-activated cell sorting, we achieved sensitive and quantitative detection of heterogeneous high-FRET cell populations containing GA aggregates. FRET signal intensity increased upon treatment with a molecular crowding agent or a proteasome inhibitor. These findings establish moxCRONOS as a versatile biosensor for investigating both physiological macromolecular crowding and pathological protein aggregation, with significant potential for disease modeling and therapeutic screening.

Human aldehyde dehydrogenase IV (hALDH4) role in the metabolism of aldehydic compounds is apodictic. Fisetin, a bioactive flavonoid, having myriad of pharmacological activities with inexhaustible therapeutic potentials. Howbeit, the interactive mechanism and inhibitory potential of fisetin on hALDH4 still remain unclear and untold. Here, multi-spectroscopic technique, molecular modelling and dynamic simulations were comprehensively explored to elucidate this. Fisetin quenched the intrinsic fluorescence of the hALDH4 and showed a significant inhibitory effect on the enzyme (IC50 = 17.45 μM) with kinetic inhibition constant, KI, of 25.97 μM. It reversibly inhibited the enzyme in a mixed competitive manner. The interaction, though predominantly electrostatic interaction, perturbed the intrinsic hALDH4 conformation by compromising the predominant α-helix structure. hALDH4 has one ligand competent site for fisetin with a binding constant (Ka) of 3.80 × 104 L·mol-1 at 25°C. The molecular docking and atomistic simulations demonstrated affinity of fisetin for hALDH4 causing the protein structural strain, resulting in unusual but stable conformations. These findings provided important insight into the kinetics and thermodynamics of fisetin and hALDH4 interaction; thus. shedding light on the potential treatment of hALDH-implicated pathological conditions.