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The crosstalk of m6A-modified RNA with DNA damage repair. m6a修饰RNA与DNA损伤修复的串扰。
IF 11.6 1区 生物学
Trends in Biochemical Sciences Pub Date : 2025-07-21 DOI: 10.1016/j.tibs.2025.06.012
Fei Qu, Yuan Liu
{"title":"The crosstalk of m<sup>6</sup>A-modified RNA with DNA damage repair.","authors":"Fei Qu, Yuan Liu","doi":"10.1016/j.tibs.2025.06.012","DOIUrl":"https://doi.org/10.1016/j.tibs.2025.06.012","url":null,"abstract":"<p><p>N<sup>6</sup>-methyladenosine (m<sup>6</sup>A) is the most abundant epitranscriptomic mark on mRNA and plays crucial roles in gene expression, cell differentiation, stress responses, and cancer and neurodegenerative diseases. Recent studies have further revealed a new role of m<sup>6</sup>A-modified coding and noncoding RNAs in regulating DNA repair and modulating genome stability. In this review, we first discuss the roles of m<sup>6</sup>A modification in regulating RNA stability and splicing of DNA repair genes, as well as its roles in guiding DNA repair. We then discuss the crosstalk between m<sup>6</sup>A-modified RNA and DNA damage and repair, highlighting several outstanding questions.</p>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":" ","pages":""},"PeriodicalIF":11.6,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144688505","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Epic science. 史诗的科学。
IF 11.6 1区 生物学
Trends in Biochemical Sciences Pub Date : 2025-07-21 DOI: 10.1016/j.tibs.2025.06.014
Jennifer L DuBois
{"title":"Epic science.","authors":"Jennifer L DuBois","doi":"10.1016/j.tibs.2025.06.014","DOIUrl":"https://doi.org/10.1016/j.tibs.2025.06.014","url":null,"abstract":"<p><p>Science is not a list of facts in a textbook, but rather a living series of stories spanning the history of human thought and continuing to this day. Understanding how scientific consensus evolves helps mitigate distrust of research among the general public.</p>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":" ","pages":""},"PeriodicalIF":11.6,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144688504","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Mining the gut microbiota for defluorination activity. 挖掘肠道微生物群的除氟活性。
IF 11.6 1区 生物学
Trends in Biochemical Sciences Pub Date : 2025-07-18 DOI: 10.1016/j.tibs.2025.07.003
Camille V Goemans
{"title":"Mining the gut microbiota for defluorination activity.","authors":"Camille V Goemans","doi":"10.1016/j.tibs.2025.07.003","DOIUrl":"https://doi.org/10.1016/j.tibs.2025.07.003","url":null,"abstract":"<p><p>The gut microbiota harbors a vast array of enzymes, many with unknown functions. In a recent study, Probst et al. mined this ecosystem to identify potential defluorinating enzymes. Combining molecular dynamics, alanine scanning, and machine learning, they uncovered molecular features critical for defluorination enzymatic activity in human gut microbes.</p>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":" ","pages":""},"PeriodicalIF":11.6,"publicationDate":"2025-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144666758","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Molecular mimicry: ecology, evolution, and applications of doppelgänger peptides. 分子拟态：生态学、进化和doppelgänger肽的应用。
IF 11.6 1区 生物学
Trends in Biochemical Sciences Pub Date : 2025-07-16 DOI: 10.1016/j.tibs.2025.06.011
Thomas L Koch, Samuel D Robinson, Helena Safavi-Hemami
{"title":"Molecular mimicry: ecology, evolution, and applications of doppelgänger peptides.","authors":"Thomas L Koch, Samuel D Robinson, Helena Safavi-Hemami","doi":"10.1016/j.tibs.2025.06.011","DOIUrl":"https://doi.org/10.1016/j.tibs.2025.06.011","url":null,"abstract":"<p><p>Organisms engage in chemical interactions that drive cooperation, conflict, natural selection, and adaptation. Among these, doppelgänger peptides (molecular mimics of the endogenous hormones or neuropeptides of another organism) have evolved in many venomous and poisonous organisms, and some parasites and pathogens. While the discovery of these peptides has been largely anecdotal, a surge in sequence data combined with computational tools suggests they are more prevalent than previously recognized. Beyond their significance in biology, emerging techniques for studying cellular signaling and a renewed interest in peptide-based therapeutics position these molecules as candidates for translational applications. In this review, we explore the role of doppelgänger peptides in chemical ecology, molecular evolution, and medicine, and provide new perspectives to guide future research.</p>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":" ","pages":""},"PeriodicalIF":11.6,"publicationDate":"2025-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144658095","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
From transcription to export: mRNA's winding path to the cytoplasm. 从转录到输出：mRNA到细胞质的缠绕路径。
IF 11.6 1区 生物学
Trends in Biochemical Sciences Pub Date : 2025-07-15 DOI: 10.1016/j.tibs.2025.06.004
Murray Stewart
{"title":"From transcription to export: mRNA's winding path to the cytoplasm.","authors":"Murray Stewart","doi":"10.1016/j.tibs.2025.06.004","DOIUrl":"https://doi.org/10.1016/j.tibs.2025.06.004","url":null,"abstract":"<p><p>In eukaryotes, the separation of transcription from translation enables extensive mRNA processing (capping, splicing, and polyadenylation) before translation. This review focuses on recent work that provides considerable insight into how mRNAs navigate these processes in which a spectrum of RNA-binding proteins (RBPs) coordinate different processing steps and couple them to nuclear export. Although the principal components in these pathways have been identified, the precise way in which RBPs bind to mRNAs, some aspects of how their binding and release are mediated by DEAD-box ATPases, and the complete structures of some messenger ribonucleoprotein complexes (mRNPs) remain unclear. Moreover, the checkpoints that recognize both completion of mRNA processing and the generation of mature mRNPs, as well as how they are coordinated, are only partially characterized.</p>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":" ","pages":""},"PeriodicalIF":11.6,"publicationDate":"2025-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144648142","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Proteasome-derived peptides: separating the trash from the recycling. 蛋白酶体衍生多肽：从回收物中分离垃圾。
IF 11.6 1区 生物学
Trends in Biochemical Sciences Pub Date : 2025-07-12 DOI: 10.1016/j.tibs.2025.06.007
Anna Brennan, Taylor R Church, Seth S Margolis
{"title":"Proteasome-derived peptides: separating the trash from the recycling.","authors":"Anna Brennan, Taylor R Church, Seth S Margolis","doi":"10.1016/j.tibs.2025.06.007","DOIUrl":"https://doi.org/10.1016/j.tibs.2025.06.007","url":null,"abstract":"<p><p>The proteasome is an essential protein complex in all cells. Proteasomes have two main functions: protein degradation and peptide generation. While proteasome-dependent protein degradation removes proteins and is critical for cellular function, the newly generated proteasome-derived peptides, which range in size and sequence, are emerging as essential cellular effector molecules: they are expressed on MHC-I in the immune system, function as novel modulators of neuronal signaling, are involved in innate immunity and intracellular signaling, and can be metabolized further for important cellular processes. Here, we take a comprehensive look at the mechanics behind proteasome-mediated peptide generation; the function of proteasome-derived peptides in signaling and metabolism relevant to cellular biology, health, and disease; and the techniques enabling these studies.</p>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":" ","pages":""},"PeriodicalIF":11.6,"publicationDate":"2025-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144625109","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The ribosome ubiquitination code: fine-tuning translation under stress. 核糖体泛素化代码：压力下的微调翻译。
IF 11.6 1区 生物学
Trends in Biochemical Sciences Pub Date : 2025-07-10 DOI: 10.1016/j.tibs.2025.06.009
Haleigh C Wooters, Neil C Nimmagadda, Alicia M Darnell, Gustavo M Silva
{"title":"The ribosome ubiquitination code: fine-tuning translation under stress.","authors":"Haleigh C Wooters, Neil C Nimmagadda, Alicia M Darnell, Gustavo M Silva","doi":"10.1016/j.tibs.2025.06.009","DOIUrl":"https://doi.org/10.1016/j.tibs.2025.06.009","url":null,"abstract":"<p><p>It has become evident that a complex code of ribosome ubiquitination regulates protein synthesis, particularly in stress conditions. Ubiquitin is known largely for its role in protein stability; however, new high-throughput screening and advances in proteomics are underscoring its novel role as a master regulator of ribosome function. Still, much remains to be discovered about how this code acts and supports translation reprogramming in a context-specific manner. Here we discuss the nature of this code, the dynamics of site-specific ribosome ubiquitination, and the unique roles that multiple enzymes play in defining the translatome and cotranslational quality control pathways. We also provide insights on the importance of unraveling this code to understand the physiological impact of modified ribosome subpopulations in cellular stress and human disease.</p>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":" ","pages":""},"PeriodicalIF":11.6,"publicationDate":"2025-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144615699","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Conserved signaling gears that sustain circadian clock robustness. 维持生物钟稳健性的保守信号装置。
IF 11.6 1区 生物学
Trends in Biochemical Sciences Pub Date : 2025-07-10 DOI: 10.1016/j.tibs.2025.06.013
Felipe Muñoz-Guzmán, Luis F Larrondo
{"title":"Conserved signaling gears that sustain circadian clock robustness.","authors":"Felipe Muñoz-Guzmán, Luis F Larrondo","doi":"10.1016/j.tibs.2025.06.013","DOIUrl":"https://doi.org/10.1016/j.tibs.2025.06.013","url":null,"abstract":"<p><p>Circadian clocks maintain the correct period despite nutritional fluctuations, a property known as metabolic compensation (MC). In a recent report, Sárkány et al. reveal a conserved role for Ras guanine nucleotide exchange factor (RasGEF) signaling in MC from fungi to human cells. Their findings highlight how this pathway buffers circadian function under glucose deprivation, integrating metabolic cues into clock dynamic robustness.</p>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":" ","pages":""},"PeriodicalIF":11.6,"publicationDate":"2025-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144615698","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The HIF axes in cancer: angiogenesis, metabolism, and immune-modulation. 肿瘤中的HIF轴：血管生成、代谢和免疫调节。
IF 11.6 1区 生物学
Trends in Biochemical Sciences Pub Date : 2025-07-09 DOI: 10.1016/j.tibs.2025.06.005
Karen Acuña-Pilarte, Mei Yee Koh
{"title":"The HIF axes in cancer: angiogenesis, metabolism, and immune-modulation.","authors":"Karen Acuña-Pilarte, Mei Yee Koh","doi":"10.1016/j.tibs.2025.06.005","DOIUrl":"https://doi.org/10.1016/j.tibs.2025.06.005","url":null,"abstract":"<p><p>The hypoxia-inducible factors (HIFs) are central transcriptional mediators of the cellular response to hypoxia. HIF activation typically drives a physiologically beneficial adaptive response to hypoxia. However, within solid tumors, the HIF-driven adaptation to hypoxia results in alterations within major cancer cell signaling axes, including those regulating angiogenesis, metabolism, and immune modulation, which profoundly impact tumor progression. This review describes established and recent findings of the role of HIFs in the regulation of these major axes, and the impact of the 'HIF axes' on tumor progression and response to therapy. Current and emerging therapies targeting these axes will also be discussed.</p>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":" ","pages":""},"PeriodicalIF":11.6,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144607051","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Tools for illuminating the cell surface glycoRNA landscape. 用于照亮细胞表面glycoRNA景观的工具。
IF 11.6 1区 生物学
Trends in Biochemical Sciences Pub Date : 2025-07-07 DOI: 10.1016/j.tibs.2025.06.006
Xinming Zhang, Yingying Zhu, Yuan Ma
{"title":"Tools for illuminating the cell surface glycoRNA landscape.","authors":"Xinming Zhang, Yingying Zhu, Yuan Ma","doi":"10.1016/j.tibs.2025.06.006","DOIUrl":"https://doi.org/10.1016/j.tibs.2025.06.006","url":null,"abstract":"","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":" ","pages":""},"PeriodicalIF":11.6,"publicationDate":"2025-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144590148","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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