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Toward an integrated omics approach for plant biosynthetic pathway discovery in the age of AI 人工智能时代植物生物合成途径的整合组学研究
IF 11.6 1区 生物学
Trends in Biochemical Sciences Pub Date : 2025-04-01 DOI: 10.1016/j.tibs.2025.01.010
Jakob K. Reinhardt , David Craft , Jing-Ke Weng
{"title":"Toward an integrated omics approach for plant biosynthetic pathway discovery in the age of AI","authors":"Jakob K. Reinhardt ,&nbsp;David Craft ,&nbsp;Jing-Ke Weng","doi":"10.1016/j.tibs.2025.01.010","DOIUrl":"10.1016/j.tibs.2025.01.010","url":null,"abstract":"<div><div>Elucidating plant biosynthetic pathways is key to advancing a sustainable bioeconomy by enabling access to complex natural products through synthetic biology. Despite progress from genomic, transcriptomic, and metabolomic approaches, much multiomics data remain underutilized. This review highlights state-of-the-art multiomics strategies for discovering plant biosynthetic pathways, addressing challenges in data acquisition and interpretation with emerging computational tools. We propose an integrated workflow combining molecular networking, reaction pair analysis, and gene expression patterns to enhance data utilization. Additionally, artificial intelligence (AI)-driven approaches promise to revolutionize pathway discovery by streamlining data analysis and validation. Integrating multiomics data, chemical insights, and advanced algorithms can accelerate understanding of plant metabolism and bioengineering valuable natural products efficiently.</div></div>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":"50 4","pages":"Pages 311-321"},"PeriodicalIF":11.6,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143497875","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Protein N-terminal modifications: molecular machineries and biological implications 蛋白质n端修饰：分子机制和生物学意义。
IF 11.6 1区 生物学
Trends in Biochemical Sciences Pub Date : 2025-04-01 DOI: 10.1016/j.tibs.2024.12.012
Hanne Øye , Malin Lundekvam , Alessia Caiella , Monica Hellesvik , Thomas Arnesen
{"title":"Protein N-terminal modifications: molecular machineries and biological implications","authors":"Hanne Øye ,&nbsp;Malin Lundekvam ,&nbsp;Alessia Caiella ,&nbsp;Monica Hellesvik ,&nbsp;Thomas Arnesen","doi":"10.1016/j.tibs.2024.12.012","DOIUrl":"10.1016/j.tibs.2024.12.012","url":null,"abstract":"<div><div>The majority of eukaryotic proteins undergo N-terminal (Nt) modifications facilitated by various enzymes. These enzymes, which target the initial amino acid of a polypeptide in a sequence-dependent manner, encompass peptidases, transferases, cysteine oxygenases, and ligases. Nt modifications – such as acetylation, fatty acylations, methylation, arginylation, and oxidation – enhance proteome complexity and regulate protein targeting, stability, and complex formation. Modifications at protein N termini are thereby core components of a large number of biological processes, including cell signaling and motility, autophagy regulation, and plant and animal oxygen sensing. Dysregulation of Nt-modifying enzymes is implicated in several human diseases. In this feature review we provide an overview of the various protein Nt modifications occurring either co- or post-translationally, the enzymes involved, and the biological impact.</div></div>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":"50 4","pages":"Pages 290-310"},"PeriodicalIF":11.6,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142998217","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A tale of two sugars: O-GlcNAc and O-fucose orchestrate growth, development, and acclimation in plants 一个关于两种糖的故事：O- glcnac和O- focal协调植物的生长、发育和驯化。
IF 11.6 1区 生物学
Trends in Biochemical Sciences Pub Date : 2025-04-01 DOI: 10.1016/j.tibs.2025.01.003
Yalikunjiang Aizezi , Yizhong Yuan , Shou-Ling Xu , Zhi-Yong Wang
{"title":"A tale of two sugars: O-GlcNAc and O-fucose orchestrate growth, development, and acclimation in plants","authors":"Yalikunjiang Aizezi ,&nbsp;Yizhong Yuan ,&nbsp;Shou-Ling Xu ,&nbsp;Zhi-Yong Wang","doi":"10.1016/j.tibs.2025.01.003","DOIUrl":"10.1016/j.tibs.2025.01.003","url":null,"abstract":"<div><div>Post-translational modifications of nucleocytoplasmic proteins by O-linked beta-N-acetylglucosamine (O-GlcNAc) and O-linked fucose (O-fucose) are emerging as key signaling mechanisms in plants. O-fucosylation and O-GlcNAcylation are catalyzed by SPINDLY (SPY) and SECRET AGENT (SEC), respectively, which are redundantly essential for viability and growth yet function antagonistically or independently in specific developmental contexts. Proteomic studies have identified hundreds of O-GlcNAcylated and O-fucosylated nucleocytoplasmic proteins, revealing their regulatory roles and intersections with phosphorylation pathways that mediate nutrient and hormone signaling. Functional studies on O-glycosylated proteins demonstrate diverse impacts on protein activity and biological processes. Together, O-fucosylation, O-GlcNAcylation, and phosphorylation form a regulatory network that controls plant growth, development, and acclimation. This review highlights recent progress and outlines future directions in studying O-fucosylation and O-GlcNAcylation in plants.</div></div>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":"50 4","pages":"Pages 332-343"},"PeriodicalIF":11.6,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143397654","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
Advisory Board and Contents 咨询委员会及内容
IF 11.6 1区 生物学
Trends in Biochemical Sciences Pub Date : 2025-04-01 DOI: 10.1016/S0968-0004(25)00066-0
{"title":"Advisory Board and Contents","authors":"","doi":"10.1016/S0968-0004(25)00066-0","DOIUrl":"10.1016/S0968-0004(25)00066-0","url":null,"abstract":"","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":"50 4","pages":"Pages i-ii"},"PeriodicalIF":11.6,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143760370","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Maximizing grant funding: strategies for negotiating laboratory pricing 最大限度地提高资助：谈判实验室定价的策略。
IF 11.6 1区 生物学
Trends in Biochemical Sciences Pub Date : 2025-04-01 DOI: 10.1016/j.tibs.2025.01.008
Marissa Coppola , Tessa O. House , Jessica W. Tsai
{"title":"Maximizing grant funding: strategies for negotiating laboratory pricing","authors":"Marissa Coppola ,&nbsp;Tessa O. House ,&nbsp;Jessica W. Tsai","doi":"10.1016/j.tibs.2025.01.008","DOIUrl":"10.1016/j.tibs.2025.01.008","url":null,"abstract":"<div><div>For new laboratories, maintaining pricing within a budget while obtaining the necessary supplies and reagents for experiments can feel daunting. In this article, we highlight a practical guide to negotiating the best pricing for your laboratory. Using these approaches enables scientists to be fiscally responsible stewards of grant funding.</div></div>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":"50 4","pages":"Pages 281-284"},"PeriodicalIF":11.6,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143432154","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
FIGNL1 hexamer dissociates RAD51-filament: a new mechanism FIGNL1六聚体解离rad51 -丝：一个新的机制。
IF 11.6 1区 生物学
Trends in Biochemical Sciences Pub Date : 2025-04-01 DOI: 10.1016/j.tibs.2025.01.002
Rajeev Kumar
{"title":"FIGNL1 hexamer dissociates RAD51-filament: a new mechanism","authors":"Rajeev Kumar","doi":"10.1016/j.tibs.2025.01.002","DOIUrl":"10.1016/j.tibs.2025.01.002","url":null,"abstract":"<div><div>Homologous recombination (HR) is critical for maintaining genome stability, relying on RAD51 recombinase to catalyze homology-dependent accurate DNA repair. While various cellular modulators control HR, <span><span>Carver, Yu, <em>et al.</em></span><svg><path></path></svg></span> reveal a unique molecular mechanism used by FIDGETIN-LIKE-1 (FIGNL1) that dissociates RAD51 from DNA through RAD51 N terminus and FIGNL1 hexamer assembly.</div></div>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":"50 4","pages":"Pages 287-289"},"PeriodicalIF":11.6,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143073265","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
Subscription and Copyright Information 订阅及版权资料
IF 11.6 1区 生物学
Trends in Biochemical Sciences Pub Date : 2025-04-01 DOI: 10.1016/S0968-0004(25)00069-6
{"title":"Subscription and Copyright Information","authors":"","doi":"10.1016/S0968-0004(25)00069-6","DOIUrl":"10.1016/S0968-0004(25)00069-6","url":null,"abstract":"","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":"50 4","pages":"Page e1"},"PeriodicalIF":11.6,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143760350","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
Decoding ceramide function: how localization shapes cellular fate and how to study it 解码神经酰胺功能：定位如何塑造细胞命运以及如何研究它。
IF 11.6 1区 生物学
Trends in Biochemical Sciences Pub Date : 2025-04-01 DOI: 10.1016/j.tibs.2025.01.007
Shweta Chitkara , G. Ekin Atilla-Gokcumen
{"title":"Decoding ceramide function: how localization shapes cellular fate and how to study it","authors":"Shweta Chitkara ,&nbsp;G. Ekin Atilla-Gokcumen","doi":"10.1016/j.tibs.2025.01.007","DOIUrl":"10.1016/j.tibs.2025.01.007","url":null,"abstract":"<div><div>Recent studies emphasize that lipid synthesis, metabolism, and transport are crucial in modulating lipid function, underscoring the significance of lipid localization within the cell, in addition to their chemical structure. Ceramides stand out in this context because of their multifaceted roles in cellular processes. Here, we focus on the role of ceramides in apoptosis, senescence, and autophagy as these processes offer unique and contrasting perspectives on how ceramides function and can be intricately linked to their subcellular localization, providing critical insights into their complex biological interactions. Additionally, we highlight recent advancements in tools and techniques that have boosted our understanding of ceramide dynamics and different mechanisms of lipid functioning.</div></div>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":"50 4","pages":"Pages 356-367"},"PeriodicalIF":11.6,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143497868","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
Recent advances in enzymes active on lignin-derived aromatic compounds 木质素衍生芳香族化合物活性酶研究进展。
IF 11.6 1区 生物学
Trends in Biochemical Sciences Pub Date : 2025-04-01 DOI: 10.1016/j.tibs.2025.01.005
Megan E. Wolf , Lindsay D. Eltis
{"title":"Recent advances in enzymes active on lignin-derived aromatic compounds","authors":"Megan E. Wolf ,&nbsp;Lindsay D. Eltis","doi":"10.1016/j.tibs.2025.01.005","DOIUrl":"10.1016/j.tibs.2025.01.005","url":null,"abstract":"<div><div>Lignin is an attractive alternative to fossil fuels as a feedstock for the sustainable manufacture of chemicals. Emergent strategies for lignin valorization include tandem processes whereby thermochemical fractionation of the biomass yields a mixture of lignin-derived aromatic compounds (LDACs), which are then transformed into target compounds by a microbial cell factory. Identifying LDAC-degrading pathways is critical to optimize carbon yield from diverse depolymerization mixtures. Characterizing enzymes – especially those that catalyze the rate-limiting steps of <em>O</em>-demethylation, hydroxylation, and decarboxylation – informs and enables biocatalyst design. Rational, structure-based engineering of key enzymes, as well as untargeted, evolution-based approaches, further optimize biocatalysis. In this review we outline recent advances in these fields which are critical in developing biocatalysts to efficiently synthesize lignin-based bioproducts.</div></div>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":"50 4","pages":"Pages 322-331"},"PeriodicalIF":11.6,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143424687","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
Balancing act: lipid-to-protein ratios steer the aggregation fate of α-synuclein 平衡作用：脂质与蛋白质的比例控制α-突触核蛋白的聚集命运。
IF 11.6 1区 生物学
Trends in Biochemical Sciences Pub Date : 2025-04-01 DOI: 10.1016/j.tibs.2025.02.001
Christian Blum , Mireille M.A.E. Claessens
{"title":"Balancing act: lipid-to-protein ratios steer the aggregation fate of α-synuclein","authors":"Christian Blum ,&nbsp;Mireille M.A.E. Claessens","doi":"10.1016/j.tibs.2025.02.001","DOIUrl":"10.1016/j.tibs.2025.02.001","url":null,"abstract":"<div><div>A recent report by <span><span>Makasewicz <em>et al.</em></span><svg><path></path></svg></span> delineates how α-synuclein (αSyn) membrane-binding modes drive amyloid formation. Their <em>in vitro</em> data reveal a lipid-to-protein (L/P) ratio tipping point influencing fibril formation. Preliminary validation from existing literature supports that these findings are also relevant in cellular contexts, informing potential new disease-modulating strategies.</div></div>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":"50 4","pages":"Pages 285-286"},"PeriodicalIF":11.6,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143514139","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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