Journal of biochemistry最新文献

Tetrahydrobiopterin (BH4) is an essential cofactor for biosynthesis of monoamines and nitric oxide. An excess of BH4 in infiltrated macrophages was reported to cause pain, while a certain level of BH4 is essential for cell survival and proliferation. GTP cyclohydrolase I (GCH) is a rate-limiting enzyme for the de novo synthesis of BH4. Our previous study showed that GCH expression was elevated by an enhancer region containing the C/EBP and Ets binding motifs in macrophage-like RAW264.7 cells when stimulated with lipopolysaccharide (LPS). In this study, we showed that poly(I:C) and R848, Toll-like receptors ligands for RNA viruses, increased GCH expression and BH4 levels in RAW264.7 cells as well as bacterial LPS. We examined the intracellular signaling pathway for the induction of the Gch gene, and found that inhibitors for the NF-κB pathway suppressed the GCH expression by these stimuli. We for the first time identified the region required for LPS-induced GCH expression to be the 5'-untranslted region of exon 1 consisting of 149 bp using a reporter experiment. We also demonstrated that the expression of GCH with LPS was strongly suppressed by an inhibitor of NF-κB in mouse intraperitoneal macrophages in vivo.

Mitochondria contain their own DNA (mtDNA), which is essential for respiratory function. Multiple copies of mtDNA are assembled into dot-like structures called nucleoids. Nucleoids move dynamically within mitochondria, and their size and distribution are influenced by mitochondrial membrane fission and fusion. However, the molecular mechanisms and their pathophysiological significance, particularly in vivo, remain largely unknown. Here, we identify a novel role for ubiquinone, as well as natural quinones lacking electron-carrying capacity, in the organization of nucleoids and respiratory complexes, independent of their conventional roles. These quinones facilitate the association and packaging of mtDNA on the cardiolipin-enriched mitochondrial inner membrane. This quinone-dependent maintenance of nucleoids protects against mitochondrial dysfunction and heart failure induced by the anticancer drug doxorubicin. Our RNAi screen identifies a set of genes involved in mitochondrial diseases that exhibit nucleoid deformation, suggesting a novel therapeutic approach targeting mitochondrial nucleoids for various pathological conditions associated with mitochondrial dysfunction.

LRIG1, a membrane glycoprotein, has emerged as a significant stem cell marker and negative regulator of receptor tyrosine kinases (RTKs), including EGFR. Glycosylation is a major post-translational modification, which plays a crucial role in protein function and stability. In cancer biology, abnormal glycosylation can contribute to pathogenesis, which can also serve as a biomarker in clinical setting. Here, we aimed to investigate the effects of glycosylation on LRIG1 functions. Through database analysis and experimental approaches, we focused on evolutionarily conserved glycosylation sites of LRIG1, particularly N74 in humans. We found that a mutation of the N74 glycosylation site (N74Q) enhances LRIG1's binding to EGFR and promotes EGFR degradation. Furthermore, we identified a naturally occurring splice variant of LRIG1 lacking the 72-bp exon 2, which includes the N74 site, that shows similar enhanced EGFR binding and degradation. Our findings suggest that the absence of glycosylation at N74 site enhances LRIG1-EGFR binding, providing an example of glycosylation negatively regulating protein-protein interaction. This mechanism provides insights into the importance of glycosylation deficiency in cancer biology.

Ubiquitination is a central post-translational modification that regulates processes like protein degradation and signaling. This versatility is derived from ubiquitin (Ub) chains, which are formed via eight distinct linkages. Analyzing these complex functions requires the use of Ub chains with precisely defined linkage types and lengths. Although chemical synthesis allows for the preparation of these Ub chains, enzymatic reconstitution offers a more broadly accessible strategy. This review focuses on recent enzymatic advances for the in vitro synthesis of high-purity Ub chains, employing E1-E2-E3 cascades, engineered enzymes, and linkage-specific deubiquitinases (DUBs). Key discussion points include methods to control chain length, prevent unwanted cyclization, and generate complex mixed or branched topologies. Furthermore, methods for site-specific substrate ubiquitination are summarized. These robust enzymatic systems are indispensable tools, enabling the reconstruction of complex Ub modifications in vitro and advancing structural and biochemical studies of the Ub code.

In Caenorhabditis elegans, 40 insulin-like peptides (ILPs) interact with DAF-2, the sole insulin/IGF receptor, to regulate lifespan and stress responses via the FOXO transcription factor DAF-16. By examining worms deficient in the ILP member INS-7 under glucose-present and glucose-absent conditions, we uncovered a previously unrecognized DAF-2-AKT/SGK signaling output that drives reversible growth arrest specifically under glucose-present conditions, while allowing normal development in the absence of glucose, in a manner independent of DAF-16. Through genetic screening, we identified lon-1, transcriptionally downregulated by TGF-β/BMP signaling, as a potential suppressor of this arrest. The ins-7; lon-1 double mutants fully regained normal growth under glucose conditions, suggesting that LON-1 may act as a downstream effector linking insulin/IGF activity to growth regulation. We propose a model in which INS-7 antagonizes DAF-2 signaling in a glucose-dependent manner, thereby influencing LON-1-mediated developmental processes. These findings point to a DAF-16-independent branch of insulin signaling and raise the possibility of crosstalk with TGF-β/BMP pathways, offering new perspectives on hormonal regulation of nutrient-driven growth.

A growing body of evidence indicates that circadian dysregulation-caused by lifestyle factors such as short sleep, irregular sleep patterns, and shift work-constitutes an independent risk factor for insulin resistance, obesity, and diabetes. Mammalian circadian rhythms are orchestrated by a conserved transcription-translation feedback loop driven by core transcription factors, which also regulate metabolism-related genes in a tissue-specific manner. Moreover, feeding behavior and physical activity influence the circadian clock, highlighting a reciprocal relationship between the clock and metabolism. In this review, we discuss circadian regulation of key metabolic organs-including pancreatic β cells, skeletal muscle, liver, and adipose tissue-with a focus on molecular metabolisms, and we also highlight relevant human studies to explore the therapeutic potential of targeting the circadian clock. Further investigation into the interplay between the circadian clock and metabolism holds promise for uncovering novel mechanisms and identifying innovative strategies to restore or enhance metabolic homeostasis.

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.