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Pairing omics to decode the diversity of plant specialized metabolism 配对 omics，解码植物特化代谢的多样性。
IF 8.3 2区 生物学
Current opinion in plant biology Pub Date : 2024-11-10 DOI: 10.1016/j.pbi.2024.102657
Felicia C. Wolters , Elena Del Pup , Kumar Saurabh Singh , Klaas Bouwmeester , M. Eric Schranz , Justin J.J. van der Hooft , Marnix H. Medema
{"title":"Pairing omics to decode the diversity of plant specialized metabolism","authors":"Felicia C. Wolters ,&nbsp;Elena Del Pup ,&nbsp;Kumar Saurabh Singh ,&nbsp;Klaas Bouwmeester ,&nbsp;M. Eric Schranz ,&nbsp;Justin J.J. van der Hooft ,&nbsp;Marnix H. Medema","doi":"10.1016/j.pbi.2024.102657","DOIUrl":"10.1016/j.pbi.2024.102657","url":null,"abstract":"<div><div>Plants have evolved complex bouquets of specialized natural products that are utilized in medicine, agriculture, and industry. Untargeted natural product discovery has benefitted from growing plant omics data resources. Yet, plant genome complexity limits the identification and curation of biosynthetic pathways via single omics. Pairing multi-omics types within experiments provides multiple layers of evidence for biosynthetic pathway mining. The extraction of paired biological information facilitates connecting genes to transcripts and metabolites, especially when captured across time points, conditions and chemotypes. Experimental design requires specific adaptations to enable effective paired-omics analysis. Ultimately, metadata standards are required to support the integration of paired and unpaired public datasets and to accelerate collaborative efforts for natural product discovery in the plant research community.</div></div>","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"82 ","pages":"Article 102657"},"PeriodicalIF":8.3,"publicationDate":"2024-11-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142616343","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Advancements and challenges in gene editing for improvement of vegetatively propagated crops 基因编辑改良无性繁殖作物的进展与挑战。
IF 8.3 2区 生物学
Current opinion in plant biology Pub Date : 2024-11-08 DOI: 10.1016/j.pbi.2024.102653
Jaindra Nath Tripathi, Samwel Muiruri, Leena Tripathi
{"title":"Advancements and challenges in gene editing for improvement of vegetatively propagated crops","authors":"Jaindra Nath Tripathi,&nbsp;Samwel Muiruri,&nbsp;Leena Tripathi","doi":"10.1016/j.pbi.2024.102653","DOIUrl":"10.1016/j.pbi.2024.102653","url":null,"abstract":"<div><div>Gene editing technologies, particularly CRISPR-Cas9, have revolutionized agriculture by offering precise and efficient tools to enhance crop production. The vegetatively propagated crops, crucial for global food security, face challenges such as climate change, pests, and limited genetic diversity. CRISPR-Cas9 enables targeted modifications to improve traits like disease resistance, drought tolerance, and nutritional content, thereby boosting productivity and sustainability. Despite its transformative potential, the adoption of gene editing in vegetatively propagated crops is hampered by technical complexities and regulatory frameworks. This review explores recent advancements, challenges, and prospects of gene editing in vegetatively propagated crops, emphasizing strategies to overcome technical barriers and regulatory constraints. Addressing these issues is essential for realizing the full agricultural potential of gene editing and ensuring food security in a changing global climate.</div></div>","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"82 ","pages":"Article 102653"},"PeriodicalIF":8.3,"publicationDate":"2024-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142616439","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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 molecular coordination of tuberization: Current status and future directions 块茎化的分子协调：现状与未来方向。
IF 8.3 2区 生物学
Current opinion in plant biology Pub Date : 2024-11-08 DOI: 10.1016/j.pbi.2024.102655
Sarah R. Mathura , Fedora Sutton , Judy Rouse-Miller , Valerie Bowrin
{"title":"The molecular coordination of tuberization: Current status and future directions","authors":"Sarah R. Mathura ,&nbsp;Fedora Sutton ,&nbsp;Judy Rouse-Miller ,&nbsp;Valerie Bowrin","doi":"10.1016/j.pbi.2024.102655","DOIUrl":"10.1016/j.pbi.2024.102655","url":null,"abstract":"<div><div>The integration of bulk transcriptomic, proteomic, and genomic data generated from numerous systems biology studies of tuberizing plants has resulted in a better understanding of the molecular and morphological aspects of tuberization. The identified conserved integrated hormonal, transcriptional, and metabolic pathways of tuberization in crops from various plant lineages support the hypothesis of a fundamental tuberization process. However, further studies are required to specify the additional processes defined by the genomics and phylogeny of the particular plant lineages, which control the morphological diversity of tubers. This review summarizes the latest molecular and morphological discoveries on the tuberization process in stem tubers and tuberous roots and discusses future trajectories of the field.</div></div>","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"82 ","pages":"Article 102655"},"PeriodicalIF":8.3,"publicationDate":"2024-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142616344","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Enjoy the silence: Canonical and non-canonical RNA silencing activity during plant sexual reproduction 享受沉默植物有性生殖过程中的规范和非规范 RNA 沉默活动
IF 8.3 2区 生物学
Current opinion in plant biology Pub Date : 2024-11-04 DOI: 10.1016/j.pbi.2024.102654
Jinping Cheng, German Martinez
{"title":"Enjoy the silence: Canonical and non-canonical RNA silencing activity during plant sexual reproduction","authors":"Jinping Cheng,&nbsp;German Martinez","doi":"10.1016/j.pbi.2024.102654","DOIUrl":"10.1016/j.pbi.2024.102654","url":null,"abstract":"<div><div>Plants produce small RNAs that accomplish a surprisingly versatile number of functions. The heterogeneity of functions of plant small RNAs is evident at the tissue-specific level. In particular, in the last years, the study of their activity in reproductive tissues has unmasked an unexpected diversity in their biogenesis and roles. Here, we review recent findings about the biogenesis pathways and roles of small RNAs during plant sexual reproduction.</div></div>","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"82 ","pages":"Article 102654"},"PeriodicalIF":8.3,"publicationDate":"2024-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142579049","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
The m6A-YTH regulatory system in plants: A status 植物中的 m6A-YTH 调节系统：现状。
IF 8.3 2区 生物学
Current opinion in plant biology Pub Date : 2024-11-01 DOI: 10.1016/j.pbi.2024.102650
Peter Brodersen , Laura Arribas-Hernández
{"title":"The m6A-YTH regulatory system in plants: A status","authors":"Peter Brodersen ,&nbsp;Laura Arribas-Hernández","doi":"10.1016/j.pbi.2024.102650","DOIUrl":"10.1016/j.pbi.2024.102650","url":null,"abstract":"<div><div>Plants use mRNA methylation to regulate gene expression. As in other eukaryotes, the only abundant methylated nucleotide in plant mRNA bodies is <em>N6</em>-methyladenosine (m<sup>6</sup>A). The conserved core components of m<sup>6</sup>A-based genetic control are a multi-subunit nuclear methyltransferase, and a set of nuclear and cytoplasmic RNA-binding proteins consisting of an m<sup>6</sup>A recognition module, the YT521-B homology (YTH) domain, and long intrinsically disordered regions (IDRs). In plants, this system is essential for growth during embryonic and post-embryonic development, but emerging evidence also points to key functions in plant-virus interactions and stimulus-dependent gene regulation. Cytoplasmic YTH-domain proteins are particularly important for these functions, and recent progress has identified two elements of the underlying molecular mechanisms: IDR-mediated phase separation and conserved short linear motifs mediating interactions with other key mRNA-binding proteins.</div></div>","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"82 ","pages":"Article 102650"},"PeriodicalIF":8.3,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142564159","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Unlocking diversity from wild relatives of perennial fruit crops in the pan-genomics era 在泛基因组学时代发掘多年生水果作物野生近缘植物的多样性。
IF 8.3 2区 生物学
Current opinion in plant biology Pub Date : 2024-10-30 DOI: 10.1016/j.pbi.2024.102652
Jean Sabety, Anze Svara, Richard Tegtmeier, Hana Feulner, Patrick Cho, Aafreen Sakina, David Hickok, Awais Khan
{"title":"Unlocking diversity from wild relatives of perennial fruit crops in the pan-genomics era","authors":"Jean Sabety,&nbsp;Anze Svara,&nbsp;Richard Tegtmeier,&nbsp;Hana Feulner,&nbsp;Patrick Cho,&nbsp;Aafreen Sakina,&nbsp;David Hickok,&nbsp;Awais Khan","doi":"10.1016/j.pbi.2024.102652","DOIUrl":"10.1016/j.pbi.2024.102652","url":null,"abstract":"<div><div>Crop wild relatives of perennial fruit crops have a wealth of untapped genetic diversity that can be utilized for cultivar development. However, barriers such as linkage drag, long juvenility, and high heterozygosity have hindered their utilization. Advancements in genome sequencing technologies and assembly methods, combined with the integration of chromosome conformation capture have made it possible to construct high-quality reference genomes. These genome assemblies can be combined into pan-genomes, capturing inter- and intraspecific variations across coding and non-coding regions. Pan-genomes of perennial fruit crops are being developed to identify the genetic basis of traits. This will help overcome breeding challenges, enabling faster and more targeted development of new cultivars with novel traits through breeding and biotechnology.</div></div>","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"82 ","pages":"Article 102652"},"PeriodicalIF":8.3,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142544293","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Current status of MSI research in Japan to measure the localization of natural products in plants 日本测量植物中天然产品定位的 MSI 研究现状。
IF 8.3 2区 生物学
Current opinion in plant biology Pub Date : 2024-10-19 DOI: 10.1016/j.pbi.2024.102651
Kotaro Yamamoto , Mai Uzaki , Katsutoshi Takahashi , Tetsuro Mimura
{"title":"Current status of MSI research in Japan to measure the localization of natural products in plants","authors":"Kotaro Yamamoto ,&nbsp;Mai Uzaki ,&nbsp;Katsutoshi Takahashi ,&nbsp;Tetsuro Mimura","doi":"10.1016/j.pbi.2024.102651","DOIUrl":"10.1016/j.pbi.2024.102651","url":null,"abstract":"<div><div>To understand biological functions in organisms, it is important to investigate what is happening in different locations in cells and tissues. The conventional approach is to extract compounds from whole tissue, and then to measure their concentrations or other characteristics using equipment tailored to the different molecules. Recent advances in mass spectrometry have made it possible to measure trace amounts of compounds. Mass spectrometry imaging (MSI), which uses positional information and mass spectrometry data to show where and how much of each compound is present in tissues, has been in the spotlight. Improvements in MSI over the past few decades have enabled its use for visualizing the localization of small molecules including drugs, lipids, and many other compounds in a range of organisms. MSI has also been used to clarify the localization of natural products in plant tissues.</div><div>This review summarizes the recent research related to MSI technology in Japan.</div></div>","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"82 ","pages":"Article 102651"},"PeriodicalIF":8.3,"publicationDate":"2024-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142460095","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Biosynthesis of oxindole alkaloids: Recent advances and challenges 吲哚生物碱的生物合成：最新进展与挑战。
IF 8.3 2区 生物学
Current opinion in plant biology Pub Date : 2024-10-03 DOI: 10.1016/j.pbi.2024.102648
Ana C. Ramos-Valdivia , Carlos M. Cerda-García-Rojas
{"title":"Biosynthesis of oxindole alkaloids: Recent advances and challenges","authors":"Ana C. Ramos-Valdivia ,&nbsp;Carlos M. Cerda-García-Rojas","doi":"10.1016/j.pbi.2024.102648","DOIUrl":"10.1016/j.pbi.2024.102648","url":null,"abstract":"<div><div>The monoterpenoid oxindole alkaloids (MOA) are specialized plant metabolites of pharmacological importance, whose biosynthesis is linked to a unique oxidative process of monoterpenoid indole alkaloids (MIA). These transformations arise from complex biosynthetic pathways defined by species, organs, tissues, and growth stages. Initial studies of their biosynthesis using labeled precursors date back more than five decades ago. This review shows the advances in this topic within the years 2022–2023, which highlight the research by integrative omics strategies, validating previously stated hypotheses. The MOA biosynthesis pathway is beginning to be elucidated, especially in the early and intermediate stages starting from MIA. Also, progress in the characterization of enzymes that regulate the process has been made. The discovery of a key enzyme in the formation of the spirooxindole scaffold represents a starting point for an enormous amount of work that remains to be done to clarify and understand the formation mechanisms of MOA.</div></div>","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"82 ","pages":"Article 102648"},"PeriodicalIF":8.3,"publicationDate":"2024-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142375280","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Diversity and development of domatia: Symbiotic plant structures to host mutualistic ants or mites 蚁巢的多样性和发展：寄生蚂蚁或螨虫的共生植物结构
IF 8.3 2区 生物学
Current opinion in plant biology Pub Date : 2024-09-30 DOI: 10.1016/j.pbi.2024.102647
Guillaume Chomicki , Nathanael Walker–Hale , J. Peter Etchells , Eleanore J. Ritter , Marjorie G. Weber
{"title":"Diversity and development of domatia: Symbiotic plant structures to host mutualistic ants or mites","authors":"Guillaume Chomicki ,&nbsp;Nathanael Walker–Hale ,&nbsp;J. Peter Etchells ,&nbsp;Eleanore J. Ritter ,&nbsp;Marjorie G. Weber","doi":"10.1016/j.pbi.2024.102647","DOIUrl":"10.1016/j.pbi.2024.102647","url":null,"abstract":"<div><div>Across the tree of life, specialized structures that offer nesting sites to ants or mites – known as domatia – have evolved independently hundreds of times, facilitating ecologically important defence and/or nutritional mutualisms. Domatia show remarkable diversity in morphology and developmental origin. Here we review the morpho-anatomical diversity of domatia, aiming to unveil the primary mechanisms governing their development. We propose hypotheses to explain the formation of these structures, based on anatomical studies of domatia and developmental genetic analyses in model species. While genes involved in domatium formation are so far unknown, domatia appear to originate via spatiotemporal shifts in the expression of common developmental genetic pathways. Our review paves the way to the genetic dissection of domatium development.</div></div>","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"82 ","pages":"Article 102647"},"PeriodicalIF":8.3,"publicationDate":"2024-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142357884","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Emerging trends in plant natural products biosynthesis: a chemical perspective 植物天然产物生物合成的新趋势：化学视角
IF 8.3 2区 生物学
Current opinion in plant biology Pub Date : 2024-09-30 DOI: 10.1016/j.pbi.2024.102649
Sarah Szwarc, Pierre Le Pogam, Mehdi A. Beniddir
{"title":"Emerging trends in plant natural products biosynthesis: a chemical perspective","authors":"Sarah Szwarc,&nbsp;Pierre Le Pogam,&nbsp;Mehdi A. Beniddir","doi":"10.1016/j.pbi.2024.102649","DOIUrl":"10.1016/j.pbi.2024.102649","url":null,"abstract":"<div><div>Biosynthetic pathways are multistep processes transforming simple substrates into more complex structures. Over the past two decades, our understanding of these pathways, especially for specialized plant metabolites, has significantly increased. This surge is due to numerous scientific advancements such as next-generation sequencing, improved analytical platforms, and metabolite-transcript networks. The uprising of data sharing through public databases has also fostered collaboration and knowledge dissemination. Growing concerns about the supply of therapeutic natural products and their environmental impact have led to exploring sustainable alternatives like heterologous expression, which requires extensive knowledge of these pathways. Herein, we review emerging approaches in biosynthetic pathway elucidations and their prospects for their efficient integration.</div></div>","PeriodicalId":11003,"journal":{"name":"Current opinion in plant biology","volume":"82 ","pages":"Article 102649"},"PeriodicalIF":8.3,"publicationDate":"2024-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142357883","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
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