{"title":"Decoding resilience: ecology, regulation, and evolution of biosynthetic gene clusters.","authors":"George Lister Cawood, Jurriaan Ton","doi":"10.1016/j.tplants.2024.09.008","DOIUrl":"https://doi.org/10.1016/j.tplants.2024.09.008","url":null,"abstract":"<p><p>Secondary metabolism is crucial for plant survival and can generate chemistry with nutritional, therapeutic, and industrial value. Biosynthetic genes of selected secondary metabolites cluster within localised chromosomal regions. The arrangement of these biosynthetic gene clusters (BGCs) challenges the long-held model of random gene order in eukaryotes, raising questions about their regulation, ecological significance, and evolution. In this review, we address these questions by exploring the contribution of BGCs to ecologically relevant plant-biotic interactions, while also evaluating the molecular-(epi)genetic mechanisms controlling their coordinated stress- and tissue-specific expression. Based on evidence that BGCs have distinct chromatin signatures and are enriched with transposable elements (TEs), we integrate emerging hypotheses into an updated evolutionary model emphasising how stress-induced epigenetic processes have shaped BGC formation.</p>","PeriodicalId":23264,"journal":{"name":"Trends in Plant Science","volume":" ","pages":""},"PeriodicalIF":17.3,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142406916","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}
Yuri G Figueiredo, Karla Gasparini, Mustafa Bulut, Alisdair R Fernie, Agustin Zsögön
{"title":"The genetic basis of prickle loss in the Solanaceae.","authors":"Yuri G Figueiredo, Karla Gasparini, Mustafa Bulut, Alisdair R Fernie, Agustin Zsögön","doi":"10.1016/j.tplants.2024.09.016","DOIUrl":"https://doi.org/10.1016/j.tplants.2024.09.016","url":null,"abstract":"<p><p>In a recent study, Satterlee et al. found that the repeated emergence of prickleless varieties in Solanaceae species is a convergent trait caused by loss of function in the cytokinin-activating enzyme LONELY GUY (LOG). New prickleless forms can be created in wild and domesticated forms using gene editing.</p>","PeriodicalId":23264,"journal":{"name":"Trends in Plant Science","volume":" ","pages":""},"PeriodicalIF":17.3,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142401424","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}
{"title":"The evolutionary advantage of artemisinin production by Artemisia annua.","authors":"Qinggang Yin, Li Xiang, Xiaoyan Han, Yujun Zhang, Ruiqing Lyn, Ling Yuan, Shilin Chen","doi":"10.1016/j.tplants.2024.09.006","DOIUrl":"https://doi.org/10.1016/j.tplants.2024.09.006","url":null,"abstract":"<p><p>Artemisinin, a potent antimalarial compound, is predominantly derived from Artemisia annua. The uniqueness of artemisinin production in A. annua lies in its complex biochemical pathways and genetic composition, distinguishing it from other plant species, even within the Asteraceae family. In this review, we investigate the potential of A. annua for artemisinin production, drawing evidence from natural populations and mutants. Leveraging high-quality whole-genome sequence analyses, we offer insights into the evolution of artemisinin biosynthesis. We also highlight current understanding of the protective functions of artemisinin in A. annua in response to both biotic and abiotic stresses. In addition, we explore the mechanisms used by A. annua to mitigate the phytotoxicity generated by artemisinin catabolism.</p>","PeriodicalId":23264,"journal":{"name":"Trends in Plant Science","volume":" ","pages":""},"PeriodicalIF":17.3,"publicationDate":"2024-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142372953","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}
Trends in Plant SciencePub Date : 2024-10-01Epub Date: 2024-05-14DOI: 10.1016/j.tplants.2024.04.011
Stefan Timm, Hu Sun, Wei Huang
{"title":"Photorespiration - emerging insights into photoprotection mechanisms.","authors":"Stefan Timm, Hu Sun, Wei Huang","doi":"10.1016/j.tplants.2024.04.011","DOIUrl":"10.1016/j.tplants.2024.04.011","url":null,"abstract":"<p><p>Two recent studies reinvestigated the phenomenon of photorespiration as a photoprotective mechanism. Smith et al. suggest alleviated negative feedback regulation of chloroplast ATP synthase as an alternative hypothesis. Von Bismarck et al. discuss how photorespiration-impaired mutants cope somewhat better with fluctuating light (FL) environments because of downregulated photosynthesis and complex metabolic re-routing.</p>","PeriodicalId":23264,"journal":{"name":"Trends in Plant Science","volume":" ","pages":"1052-1055"},"PeriodicalIF":17.3,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140945955","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}
Trends in Plant SciencePub Date : 2024-10-01Epub Date: 2024-05-26DOI: 10.1016/j.tplants.2024.04.013
Hilbert Yuen In Lam, Xing Er Ong, Marek Mutwil
{"title":"Large language models in plant biology.","authors":"Hilbert Yuen In Lam, Xing Er Ong, Marek Mutwil","doi":"10.1016/j.tplants.2024.04.013","DOIUrl":"10.1016/j.tplants.2024.04.013","url":null,"abstract":"<p><p>Large language models (LLMs), such as ChatGPT, have taken the world by storm. However, LLMs are not limited to human language and can be used to analyze sequential data, such as DNA, protein, and gene expression. The resulting foundation models can be repurposed to identify the complex patterns within the data, resulting in powerful, multipurpose prediction tools able to predict the state of cellular systems. This review outlines the different types of LLMs and showcases their recent uses in biology. Since LLMs have not yet been embraced by the plant community, we also cover how these models can be deployed for the plant kingdom.</p>","PeriodicalId":23264,"journal":{"name":"Trends in Plant Science","volume":" ","pages":"1145-1155"},"PeriodicalIF":17.3,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141155539","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}
Trends in Plant SciencePub Date : 2024-10-01Epub Date: 2024-08-08DOI: 10.1016/j.tplants.2024.07.009
David B Stern
{"title":"Revolutionizing academic hiring: a faculty cluster hire emphasizing teamwork.","authors":"David B Stern","doi":"10.1016/j.tplants.2024.07.009","DOIUrl":"10.1016/j.tplants.2024.07.009","url":null,"abstract":"<p><p>The Boyce Thompson Institute (BTI) executed a faculty cluster hiring initiative to find scientists driven by the possibilities of collaboration. Given that academic hiring rarely evaluates and rewards teamwork, BTI invented a process that would. In doing so, the Institute was able to reduce gender bias commonly found in a typical academic search.</p>","PeriodicalId":23264,"journal":{"name":"Trends in Plant Science","volume":" ","pages":"1043-1045"},"PeriodicalIF":17.3,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141914117","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}
Trends in Plant SciencePub Date : 2024-10-01Epub Date: 2024-07-06DOI: 10.1016/j.tplants.2024.05.010
Ainhoa Martínez-Medina, Arjen Biere, María J Pozo
{"title":"The imprint of microbe-induced plant resistance in plant-associated insects.","authors":"Ainhoa Martínez-Medina, Arjen Biere, María J Pozo","doi":"10.1016/j.tplants.2024.05.010","DOIUrl":"10.1016/j.tplants.2024.05.010","url":null,"abstract":"<p><p>Beneficial microbes induce resistance in plants (MIR), imposing both lethal and sublethal effects on herbivorous insects. We argue that herbivores surviving MIR carry metabolic and immunological imprints of MIR with cascading effects across food webs. We propose that incorporating such cascading effects will strongly enhance the current MIR research framework.</p>","PeriodicalId":23264,"journal":{"name":"Trends in Plant Science","volume":" ","pages":"1062-1065"},"PeriodicalIF":17.3,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141555510","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}
Trends in Plant SciencePub Date : 2024-10-01Epub Date: 2024-05-22DOI: 10.1016/j.tplants.2024.05.006
Md Atikur Rahman, Md Mahadi Hasan, Francisco J Corpas
{"title":"Enriched-Fe maize kernels to prevent dietary Fe deficiency in humans.","authors":"Md Atikur Rahman, Md Mahadi Hasan, Francisco J Corpas","doi":"10.1016/j.tplants.2024.05.006","DOIUrl":"10.1016/j.tplants.2024.05.006","url":null,"abstract":"<p><p>Iron (Fe) biofortification of edible organs without influencing crop yield is challenging, and potential solutions are largely unknown. Recently, Yan et al. identified a key regulator NAC78 (NAM/ATAF/CUC DOMAIN TRANSCRIPTION FACTOR 78) that enriches Fe in maize kernels without compromising crop yield. This may provide new crop yield management strategies for Fe acquisition and nutritional security.</p>","PeriodicalId":23264,"journal":{"name":"Trends in Plant Science","volume":" ","pages":"1049-1051"},"PeriodicalIF":17.3,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141088746","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}
Trends in Plant SciencePub Date : 2024-10-01Epub Date: 2024-05-16DOI: 10.1016/j.tplants.2024.05.003
Pengfa Li, Francisco Dini-Andreote, Jiandong Jiang
{"title":"Exploiting microbial competition to promote plant health.","authors":"Pengfa Li, Francisco Dini-Andreote, Jiandong Jiang","doi":"10.1016/j.tplants.2024.05.003","DOIUrl":"10.1016/j.tplants.2024.05.003","url":null,"abstract":"<p><p>The host-associated microbiota can promote colonization resistance against pathogens via a mechanism termed 'nutrient blocking', as highlighted in a recent article by Spragge et al. This implies that greater metabolic overlap between commensal taxa and pathogens leads to disease suppression. Here, we discuss future avenues for how this principle can be exploited in the rhizosphere microbiota to promote plant health.</p>","PeriodicalId":23264,"journal":{"name":"Trends in Plant Science","volume":" ","pages":"1056-1058"},"PeriodicalIF":17.3,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140959375","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}
Trends in Plant SciencePub Date : 2024-10-01Epub Date: 2024-05-29DOI: 10.1016/j.tplants.2024.04.006
Sara Hailemariam, Chao-Jan Liao, Tesfaye Mengiste
{"title":"Receptor-like cytoplasmic kinases: orchestrating plant cellular communication.","authors":"Sara Hailemariam, Chao-Jan Liao, Tesfaye Mengiste","doi":"10.1016/j.tplants.2024.04.006","DOIUrl":"10.1016/j.tplants.2024.04.006","url":null,"abstract":"<p><p>The receptor-like kinase (RLK) family of receptors and the associated receptor-like cytoplasmic kinases (RLCKs) have expanded in plants because of selective pressure from environmental stress and evolving pathogens. RLCKs link pathogen perception to activation of coping mechanisms. RLK-RLCK modules regulate hormone synthesis and responses, reactive oxygen species (ROS) production, Ca<sup>2+</sup> signaling, activation of mitogen-activated protein kinase (MAPK), and immune gene expression, all of which contribute to immunity. Some RLCKs integrate responses from multiple receptors recognizing distinct ligands. RLKs/RLCKs and nucleotide-binding domain, leucine-rich repeats (NLRs) were found to synergize, demonstrating the intertwined genetic network in plant immunity. Studies in arabidopsis (Arabidopsis thaliana) have provided paradigms about RLCK functions, but a lack of understanding of crop RLCKs undermines their application. In this review, we summarize current understanding of the diverse functions of RLCKs, based on model systems and observations in crop species, and the emerging role of RLCKs in pathogen and abiotic stress response signaling.</p>","PeriodicalId":23264,"journal":{"name":"Trends in Plant Science","volume":" ","pages":"1113-1130"},"PeriodicalIF":17.3,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141180780","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}