Pub Date : 2024-07-30DOI: 10.1038/s41477-024-01741-9
Bayley R. McDonald, Colette L. Picard, Ian M. Brabb, Marina I. Savenkova, Robert J. Schmitz, Steven E. Jacobsen, Sascha H. Duttke
Unstable transcripts have emerged as markers of active enhancers in vertebrates and shown to be involved in many cellular processes and medical disorders. However, their prevalence and role in plants is largely unexplored. Here, we comprehensively captured all actively initiating (nascent) transcripts across diverse crops and other plants using capped small (cs)RNA sequencing. We discovered that unstable transcripts are rare in plants, unlike in vertebrates, and when present, often originate from promoters. In addition, many ‘distal’ elements in plants initiate tissue-specific stable transcripts and are likely bona fide promoters of as-yet-unannotated genes or non-coding RNAs, cautioning against using reference genome annotations to infer putative enhancer sites. To investigate enhancer function, we integrated data from self-transcribing active regulatory region (STARR) sequencing. We found that annotated promoters and other regions that initiate stable transcripts, but not those marked by unstable or bidirectional unstable transcripts, showed stronger enhancer activity in this assay. Our findings underscore the blurred line between promoters and enhancers and suggest that cis-regulatory elements can encompass diverse structures and mechanisms in eukaryotes, including humans. Unstable transcripts like enhancer RNAs are common in vertebrates. McDonald et al. show that such unstable transcripts are rare in plants and that promoters can function as potent enhancers, suggesting diverse cis-regulatory mechanisms in eukaryotes.
{"title":"Enhancers associated with unstable RNAs are rare in plants","authors":"Bayley R. McDonald, Colette L. Picard, Ian M. Brabb, Marina I. Savenkova, Robert J. Schmitz, Steven E. Jacobsen, Sascha H. Duttke","doi":"10.1038/s41477-024-01741-9","DOIUrl":"10.1038/s41477-024-01741-9","url":null,"abstract":"Unstable transcripts have emerged as markers of active enhancers in vertebrates and shown to be involved in many cellular processes and medical disorders. However, their prevalence and role in plants is largely unexplored. Here, we comprehensively captured all actively initiating (nascent) transcripts across diverse crops and other plants using capped small (cs)RNA sequencing. We discovered that unstable transcripts are rare in plants, unlike in vertebrates, and when present, often originate from promoters. In addition, many ‘distal’ elements in plants initiate tissue-specific stable transcripts and are likely bona fide promoters of as-yet-unannotated genes or non-coding RNAs, cautioning against using reference genome annotations to infer putative enhancer sites. To investigate enhancer function, we integrated data from self-transcribing active regulatory region (STARR) sequencing. We found that annotated promoters and other regions that initiate stable transcripts, but not those marked by unstable or bidirectional unstable transcripts, showed stronger enhancer activity in this assay. Our findings underscore the blurred line between promoters and enhancers and suggest that cis-regulatory elements can encompass diverse structures and mechanisms in eukaryotes, including humans. Unstable transcripts like enhancer RNAs are common in vertebrates. McDonald et al. show that such unstable transcripts are rare in plants and that promoters can function as potent enhancers, suggesting diverse cis-regulatory mechanisms in eukaryotes.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":null,"pages":null},"PeriodicalIF":15.8,"publicationDate":"2024-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41477-024-01741-9.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141794606","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}
Pub Date : 2024-07-26DOI: 10.1038/s41477-024-01747-3
Sergi Munné-Bosch, Jessyca Adelle Silva Santos
Plant invasions are becomingly increasingly common with global climate change. As a significant threat to biodiversity, appropriate management of invasive species is critical for the protection of native flora. However, many of the management strategies aimed at combating the impacts of invasive species only end up exacerbating them.
{"title":"The dramatic effects of well-intentioned but ill-designed management strategies in plant biological invasions","authors":"Sergi Munné-Bosch, Jessyca Adelle Silva Santos","doi":"10.1038/s41477-024-01747-3","DOIUrl":"10.1038/s41477-024-01747-3","url":null,"abstract":"Plant invasions are becomingly increasingly common with global climate change. As a significant threat to biodiversity, appropriate management of invasive species is critical for the protection of native flora. However, many of the management strategies aimed at combating the impacts of invasive species only end up exacerbating them.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":null,"pages":null},"PeriodicalIF":15.8,"publicationDate":"2024-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141764282","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}
Pub Date : 2024-07-26DOI: 10.1038/s41477-024-01760-6
Duy-Chi Trinh, Isaty Melogno, Marjolaine Martin, Christophe Trehin, Richard S. Smith, Olivier Hamant
In most plant species, sepals—the outermost floral organs—provide a protective shield for reproductive organs. How the floral bud becomes sealed is unknown. In Arabidopsis, we identified a small region at the sepal tip that is markedly curved inward early on and remains curved even after anthesis. Through modelling and quantitative growth analysis, we find that this hook emerges from growth arrest at the tip at a stage when cortical microtubules align with growth-derived tensile stress. Depolymerizing microtubules specifically at young sepal tips hindered hook formation and resulted in open floral buds. Mutants with defective growth pattern at the tip failed to curve inwards, whereas mutants with enhanced alignment of cortical microtubules at the tip exhibited a stronger hook. We propose that floral buds are locked due to a stress-derived growth arrest event curving the sepal tip and forming a rigid hook early on during flower development. Floral buds are closed structures that protect reproductive organs. Here the authors find that differential growth prescribes transverse tensile stress and growth arrest at the sepal tip, which in turn curve it and form a rigid hook to seal the floral bud.
{"title":"Arabidopsis floral buds are locked through stress-induced sepal tip curving","authors":"Duy-Chi Trinh, Isaty Melogno, Marjolaine Martin, Christophe Trehin, Richard S. Smith, Olivier Hamant","doi":"10.1038/s41477-024-01760-6","DOIUrl":"10.1038/s41477-024-01760-6","url":null,"abstract":"In most plant species, sepals—the outermost floral organs—provide a protective shield for reproductive organs. How the floral bud becomes sealed is unknown. In Arabidopsis, we identified a small region at the sepal tip that is markedly curved inward early on and remains curved even after anthesis. Through modelling and quantitative growth analysis, we find that this hook emerges from growth arrest at the tip at a stage when cortical microtubules align with growth-derived tensile stress. Depolymerizing microtubules specifically at young sepal tips hindered hook formation and resulted in open floral buds. Mutants with defective growth pattern at the tip failed to curve inwards, whereas mutants with enhanced alignment of cortical microtubules at the tip exhibited a stronger hook. We propose that floral buds are locked due to a stress-derived growth arrest event curving the sepal tip and forming a rigid hook early on during flower development. Floral buds are closed structures that protect reproductive organs. Here the authors find that differential growth prescribes transverse tensile stress and growth arrest at the sepal tip, which in turn curve it and form a rigid hook to seal the floral bud.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":null,"pages":null},"PeriodicalIF":15.8,"publicationDate":"2024-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141764313","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}
Pub Date : 2024-07-25DOI: 10.1038/s41477-024-01757-1
Dustin Wolkis, Cecily Eltringham, Jeremie Fant, Jeremy Foster, Tiffany Knight, Abby Meyer, Hugo Romero-Saltos, Seana K Walsh, Alina Wood, Kayri Havens
{"title":"Pollen banking is a critical need for conserving plant diversity.","authors":"Dustin Wolkis, Cecily Eltringham, Jeremie Fant, Jeremy Foster, Tiffany Knight, Abby Meyer, Hugo Romero-Saltos, Seana K Walsh, Alina Wood, Kayri Havens","doi":"10.1038/s41477-024-01757-1","DOIUrl":"https://doi.org/10.1038/s41477-024-01757-1","url":null,"abstract":"","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":null,"pages":null},"PeriodicalIF":15.8,"publicationDate":"2024-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141759880","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}
Pub Date : 2024-07-24DOI: 10.1038/s41477-024-01749-1
Hongwei Liu, Jiayu Li, Brajesh K. Singh
Streptomyces is a drought-tolerant bacterial genus in soils, which forms close associations with plants to provide host resilience to drought stress. Here we synthesize the emerging research that illuminates the multifaceted interactions of Streptomyces spp. in both plant and soil environments. It also explores the potential co-evolutionary relationship between plants and Streptomyces spp. to forge mutualistic relationships, providing drought tolerance to plants. We propose that further advancement in fundamental knowledge of eco-evolutionary interactions between plants and Streptomyces spp. is crucial and holds substantial promise for developing effective strategies to combat drought stress, ensuring sustainable agriculture and environmental sustainability in the face of climate change. A growing body of evidence suggests that plant interactions with Streptomyces species confer resilience to drought. In this Perspective, Liu et al. discuss this potential co-evolutionary relationship and how it can be exploited to achieve sustainable agriculture in a hotter and drier world.
{"title":"Harnessing co-evolutionary interactions between plants and Streptomyces to combat drought stress","authors":"Hongwei Liu, Jiayu Li, Brajesh K. Singh","doi":"10.1038/s41477-024-01749-1","DOIUrl":"10.1038/s41477-024-01749-1","url":null,"abstract":"Streptomyces is a drought-tolerant bacterial genus in soils, which forms close associations with plants to provide host resilience to drought stress. Here we synthesize the emerging research that illuminates the multifaceted interactions of Streptomyces spp. in both plant and soil environments. It also explores the potential co-evolutionary relationship between plants and Streptomyces spp. to forge mutualistic relationships, providing drought tolerance to plants. We propose that further advancement in fundamental knowledge of eco-evolutionary interactions between plants and Streptomyces spp. is crucial and holds substantial promise for developing effective strategies to combat drought stress, ensuring sustainable agriculture and environmental sustainability in the face of climate change. A growing body of evidence suggests that plant interactions with Streptomyces species confer resilience to drought. In this Perspective, Liu et al. discuss this potential co-evolutionary relationship and how it can be exploited to achieve sustainable agriculture in a hotter and drier world.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":null,"pages":null},"PeriodicalIF":15.8,"publicationDate":"2024-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141755091","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}
Pub Date : 2024-07-23DOI: 10.1038/s41477-024-01762-4
The variety of species and systems available to scientists fascinated by plants is remarkably rich and deserves to be celebrated.
对植物着迷的科学家可利用的物种和系统非常丰富，值得赞美。
{"title":"Spice of life","authors":"","doi":"10.1038/s41477-024-01762-4","DOIUrl":"10.1038/s41477-024-01762-4","url":null,"abstract":"The variety of species and systems available to scientists fascinated by plants is remarkably rich and deserves to be celebrated.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":null,"pages":null},"PeriodicalIF":15.8,"publicationDate":"2024-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41477-024-01762-4.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141752149","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}
Pub Date : 2024-07-23DOI: 10.1038/s41477-024-01765-1
Sébastjen Schoenaers, Hyun Kyung Lee, Martine Gonneau, Elvina Faucher, Thomas Levasseur, Elodie Akary, Naomi Claeijs, Steven Moussu, Caroline Broyart, Daria Balcerowicz, Hamada AbdElgawad, Andrea Bassi, Daniel Santa Cruz Damineli, Alex Costa, José A. Feijó, Celine Moreau, Estelle Bonnin, Bernard Cathala, Julia Santiago, Herman Höfte, Kris Vissenberg
{"title":"Author Correction: Rapid alkalinization factor 22 has a structural and signalling role in root hair cell wall assembly","authors":"Sébastjen Schoenaers, Hyun Kyung Lee, Martine Gonneau, Elvina Faucher, Thomas Levasseur, Elodie Akary, Naomi Claeijs, Steven Moussu, Caroline Broyart, Daria Balcerowicz, Hamada AbdElgawad, Andrea Bassi, Daniel Santa Cruz Damineli, Alex Costa, José A. Feijó, Celine Moreau, Estelle Bonnin, Bernard Cathala, Julia Santiago, Herman Höfte, Kris Vissenberg","doi":"10.1038/s41477-024-01765-1","DOIUrl":"10.1038/s41477-024-01765-1","url":null,"abstract":"","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":null,"pages":null},"PeriodicalIF":15.8,"publicationDate":"2024-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41477-024-01765-1.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141752148","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}
Pub Date : 2024-07-16DOI: 10.1038/s41477-024-01748-2
We present a comprehensive quantitative analysis of the proteome across 14 major rice tissues, which reveals that N6-methyladenosine (m6A) is negatively correlated with protein abundance. This finding provides insight into the longstanding discrepancy observed between RNA and protein levels in plants.
{"title":"Generation and analysis of the rice proteome reveals a role for m6A in posttranscriptional regulation","authors":"","doi":"10.1038/s41477-024-01748-2","DOIUrl":"10.1038/s41477-024-01748-2","url":null,"abstract":"We present a comprehensive quantitative analysis of the proteome across 14 major rice tissues, which reveals that N6-methyladenosine (m6A) is negatively correlated with protein abundance. This finding provides insight into the longstanding discrepancy observed between RNA and protein levels in plants.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":null,"pages":null},"PeriodicalIF":15.8,"publicationDate":"2024-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141625093","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}
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