BMB Reports最新文献

In the last few decades, single-molecule techniques have emerged as transformative tools for exploring biological problems. By observing and analyzing individual molecules, these methods make it possible to investigate fundamental dynamics of biomolecular processes deeper. Unlike traditional ensemble methods that average the behavior of populations, single-molecule approaches provide a unique window to observe molecular heterogeneity, transient interactions, and dynamic processes that are otherwise hidden. This special issue brings together six mini-reviews that present how these cutting-edge methodologies are advancing our understanding of diverse and complex biological systems. Each review highlights unique applications, significant breakthroughs, and ongoing challenges. They collectively demonstrate the versatility and impact of single-molecule techniques. [BMB Reports 2024; 58(1): 1-1].

Base excision repair (BER) is an essential cellular mechanism that repairs small, non-helix-distorting base lesions in DNA, resulting from oxidative damage, alkylation, deamination, or hydrolysis. This review highlights recent advances in understanding the molecular mechanisms of BER enzymes through single-molecule studies. We discuss the roles of DNA glycosylases in lesion recognition and excision, with a focus on facilitated diffusion mechanisms such as sliding and hopping that enable efficient genome scanning. The dynamics of apurinic/apyrimidinic endonucleases, especially the coordination between APE1 and DNA polymerase β (Pol β), are explored to demonstrate their crucial roles in processing abasic sites. The review further explores the short-patch and long-patch BER pathways, emphasizing the activities of Pol β, XRCC1, PARP1, FEN1, and PCNA in supporting repair synthesis and ligation. Additionally, we highlight the emerging role of UV-DDB as a general damage sensor in BER, extending its recognized function beyond nucleotide excision repair. Single-molecule techniques have been instrumental in uncovering the complex interactions and mechanisms of BER proteins, offering unprecedented insights that could guide future therapeutic strategies for maintaining genomic stability. [BMB Reports 2024; 58(1): 17-23].

Prime editing is widely used in many organisms to introduce site-specific sequence modifications, such as base substitutions, insertions, and deletions, in genomic DNA without generating double-strand breaks. Despite their wide-ranging applications, prime editors (PEs) have low editing efficiency, especially in dicot plants, and are therefore barely used for genome engineering in these plant species. Here, based on the previous approaches used to improve prime editing efficiency, we generated multiple different combinations of PE components and prime editing guide RNAs (pegRNAs) and examined their prime editing efficiency in Arabidopsis thaliana protoplasts as the dicot model system. We found that v4e2, in which PE was fused to the viral nucleocapsid (NC) protein, RNase H-deleted M-MLV RT, and a dominant negative version of human mutL homolog 1 (hMLH1dn), showed the highest prime editing efficiency in Arabidopsis protoplasts when co-transfected with dual enhanced pegRNA. Overall, our results suggest that the v4e2 PE system could be used for efficient prime editing in dicot plants.

Understanding the molecular characteristics and metabolic processes of the mammalian endometrium is crucial for advancing biological research, particularly in veterinary obstetrics and pathology. This study established and analyzed organoids from the endometrial epithelial stem cells of five mammals with different placental types: cows (cotyledonary), dogs and cats (zonary), pigs (diffuse), and rats (discoid). The organoids from these five species were maintained for over 13 passages, successfully frozen-thawed, and confirmed by pathological analysis to retain the characteristics of the original tissues. Furthermore, integrative transcriptome analysis of the organoids and tissues from the five species highlighted key pathways, such as PI3K-Akt signaling and extracellular matrix-receptor interaction, which are crucial in cancer research. Despite the downregulation of genes associated with vascular smooth muscle contraction, the organoids exhibited significant activity of genes involved in hormone metabolism. In conclusion, our study achieves stable establishment of endometrial organoids from five mammals with different placental types and offers foundational data for organoid research. In the future, these organoids are suitable models for investigating uterine physiology, diseases, and assessing potential therapies.

A type of programmed cell death called ferroptosis is defined by increased iron-dependent lipid peroxidation. Mitochondria play a central role in iron metabolism. Mitochondrial defects include decreased cristae density, membrane rupture, and decreased mitochondrial membrane density, which occur as a result of ferroptosis. One of the important regulator of mitochondrial biogenesis is PGC1α. While recent studies have begun to explore the association between PGC1α and ferroptosis, the specific role of PGC1α in erastin-induced mitochondrial dysfunction during ferroptotic cell death has not been fully elucidated. In this study, we demonstrate for the first time that PGC1α is a key regulator of erastin-induced mitochondrial-dependent lipid peroxidation and dysfunction during ferroptosis in HT1080 fibrosarcoma cells. In this study, we examined PGC1α function in ferroptosis. Erastin, an inducer of ferroptosis, boosted the expression of PGC1α. Moreover, PGC1α down-regulation reduced erastin-induced ferroptosis. The most important biochemical feature of ferroptosis is the increase in iron ion (Fe2+)-dependent lipid peroxide (LOOH) concentration. Mitochondrial-dependent lipid peroxidation was abolished by PGC1α downregulation. In addition, PGC1α was induced during mitochondrial dysfunction in erastin-induced ferroptosis. Mitochondrial membrane potential loss and mitochondrial ROS production associated with erastin-induced mitochondrial dysfunction were blocked by PGC1α inhibition. In addition, erastin-induced lipid peroxidation in HT1080 fibrosarcoma cells was regulated by PGC1α inhibitor. This phenomenon was also consistent in HT1080 cells transfected with PGC1α shRNA transfected cells. Taken together, these results suggest that PGC1α is a key factor in erastin-induced mitochondrial-dependent lipid peroxidation and dysfunction during ferroptosis cell death.

Many studies on osteoblasts have suggested that Wnt5a plays a crucial role in excessive osteoblast activity, which is responsible for ectopic new bone formation, but research on osteoclasts in ankylosing spondylitis (AS) remains relatively limited. This study aimed to explore whether Wnt5a influences osteoclast-mediated bone resorption in curdlan-injected SKG mice, a model that mimics AS. Compared to the Vehicle group, the Wnt5a treatment group exhibited statistically higher clinical arthritis scores and increased hindpaw thickness values. Micro-computed tomography (microCT) analysis of hindpaws revealed a significant increase in inflamed and ectopic bone density in the Wnt5a-treated group compared to the Vehicle group. Histological examination also showed pronounced inflammation and structural bone damage in the bone marrow of ankles in the Wnt5a-treated group. Intriguingly, microCT analysis of the femur revealed that trabecular bone loss was markedly observed in the Wnt5a-treated group. Both the number of TRAP-positive osteoclasts and their activity were statistically greater in the Wnt5a-treated group compared to the Vehicle group. Serum markers of bone resorption, but not bone formation, were also significantly elevated in the Wnt5a-treated group. Notably, promotion of osteoclast differentiation by Wnt5a was inhibited following treatment with anti-Wnt5a. These findings suggest that targeting Wnt5a could be a promising strategy for mitigating pathological bone features in AS by modulating osteoclast activity.

Trichomonas vaginalis is an extracellular flagellated protozoan responsible for trichomoniasis, one of the most prevalent nonviral sexually transmitted infections. To persist in its host, T. vaginalis employs sophisticated gene regulation mechanisms to adapt to hostile environmental conditions. Although transcriptional regulation is crucial for this adaptation, the underlying molecular mechanisms remain poorly understood. Epigenetic regulation, particularly histone modifications, has emerged as a key modulator of gene expression. A previous study demonstrated that histone modifications, H3K4me3 and H3K27ac, promote active transcription. However, the complete extent of epigenetic regulation in T. vaginalis remains unclear. The present study extended these findings by exploring the repressive role of two additional histone H3 modifications, H3K9me3 and H3K27me3. Genome-wide analysis revealed that these modifications negatively correlated with gene expression, affecting protein-coding and transposable element genes (TEGs). These findings offer new insights into the dual role of histone modifications in activating and repressing gene expression and provide a more comprehensive understanding of epigenetic regulation in T. vaginalis. This expanded knowledge may inform the development of novel therapeutic strategies targeting the epigenetic machinery of T. vaginalis.

The utilization of multi-omics research has gained popularity in clinical investigations. However, effectively managing and merging extensive and diverse datasets presents a challenge due to its intricacy. This research introduces a Multi-Omics Analysis Sandbox Toolkit, an online platform designed to facilitate the exploration, integration, and visualization of datasets ranging from single-omics to multi-omics. This platform establishes connections between clinical data and omics information, allowing for versatile analysis and storage of both single and multi-omics data. Additionally, users can repeatedly utilize and exchange their findings within the platform. This toolkit offers diverse alternatives for data selection and gene set analysis. It also presents visualization outputs, potential candidates, and annotations. Furthermore, this platform empowers users to collaborate by sharing their datasets, analyses, and conclusions with others, thus enhancing its utility as a collaborative research tool. This Multi-Omics Analysis Sandbox Toolkit stands as a valuable asset in comprehensively grasping the influence of diverse factors in diseases and pinpointing potential biomarkers. [BMB Reports 2024; 57(12): 521-526].

Ring finger protein 128 (RNF128) is a transmembrane E3 ubiquitin ligase mainly localized in the endoplasmic reticulum that is involved in various processes, including T cell anergy and tumor progression. However, the biological function of RNF128 in N-glycosylation remains unexplored. To investigate the functional role of RNF128, we used the proximity-directed biotin labeling method, and identified ribophorin I (RPN1) as a novel RNF128 substrate, demonstrating that RNF128 ubiquitinated RPN1 and promoted its degradation. RPN1 is a subunit of oligosaccharyltransferase complexes that facilitate N-glycosylation by binding substrates, and presenting them to the catalytic core. RPN1 also functions as an N-glycosylation-dependent chaperone that helps export a subset of newly synthesized glycoproteins to the plasma membrane. We found that RNF128 affects the N-glycosylation of model glycoproteins, such as sex hormone- binding globulin and asialoglycoprotein receptor 1. Furthermore, RNF128 inhibits the export of the opioid receptor mu 1 (OPRM1) to the plasma membrane, while expressing ubiquitination-incompetent RPN1 mutant, rescues the defect of OPRM1 export caused by RNF128 overexpression. Additionally, RNF128 influences colorectal cancer cell migration. The RNF128-dependent degradation of RPN1 likely inhibits the cell surface expression of specific glycoproteins, thereby affecting distinct cellular functions. This study contributes to understanding of the biological and functional roles of RNF128- and RPN1-dependent N-glycosylation. [BMB Reports 2024; 57(12): 546-552].

Regulation of eukaryotic transcription is a complex process that enables precise temporal and spatial control of gene expression. Promoters, which are cis-regulatory elements (CREs) located proximal to the transcription start site (TSS), selectively integrate regulatory cues from distal CREs, or enhancers, and their associated transcriptional machinery. In this review, we discuss current knowledge regarding CRE cooperation and competition impacting gene expression, including features of enhancer-promoter, enhancer-enhancer, and promoter-promoter interplay. We also provide an overview of recent insights into the underlying molecular mechanisms that facilitate physical and functional interaction of regulatory elements, such as the involvement of enhancer RNAs and biomolecular condensates. [BMB Reports 2024; 57(12): 509-520].