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Annual review of plant biology最新文献

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An RNA World. RNA世界。
IF 23.9 1区 生物学
Annual review of plant biology Pub Date : 2023-05-22 DOI: 10.1146/annurev-arplant-070622-021021
David C Baulcombe
{"title":"An RNA World.","authors":"David C Baulcombe","doi":"10.1146/annurev-arplant-070622-021021","DOIUrl":"https://doi.org/10.1146/annurev-arplant-070622-021021","url":null,"abstract":"<p><p>My research career started with an ambition to work out how genes are regulated in plants. I tried out various experimental systems-artichoke tissue culture in Edinburgh; soybean root nodules in Montreal; soybean hypocotyls in Athens, Georgia; and cereal aleurones in Cambridge-but eventually I discovered plant viruses. Viral satellite RNAs were my first interest, but I then explored transgenic and natural disease resistance and was led by curiosity into topics beyond virology, including RNA silencing, epigenetics, and more recently, genome evolution. On the way, I have learned about approaches to research, finding tractable systems, and taking academic research into the real world. I have always tried to consider the broader significance of our work, and my current projects address the definition of epigenetics, the arms race concept of disease resistance, and Darwin's abominable mystery.</p>","PeriodicalId":8335,"journal":{"name":"Annual review of plant biology","volume":"74 ","pages":"1-20"},"PeriodicalIF":23.9,"publicationDate":"2023-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9505870","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: 2
Replicated Evolution in Plants. 植物的复制进化。
IF 23.9 1区 生物学
Annual review of plant biology Pub Date : 2023-05-22 DOI: 10.1146/annurev-arplant-071221-090809
Maddie E James, Tim Brodribb, Ian J Wright, Loren H Rieseberg, Daniel Ortiz-Barrientos
{"title":"Replicated Evolution in Plants.","authors":"Maddie E James,&nbsp;Tim Brodribb,&nbsp;Ian J Wright,&nbsp;Loren H Rieseberg,&nbsp;Daniel Ortiz-Barrientos","doi":"10.1146/annurev-arplant-071221-090809","DOIUrl":"https://doi.org/10.1146/annurev-arplant-071221-090809","url":null,"abstract":"<p><p>Similar traits and functions commonly evolve in nature. Here, we explore patterns of replicated evolution across the plant kingdom and discuss the processes responsible for such patterns. We begin this review by defining replicated evolution and the theoretical, genetic, and ecological concepts that help explain it. We then focus our attention on empirical cases of replicated evolution at the phenotypic and genotypic levels. We find that replication at the ecotype level is common, but evidence for repeated ecological speciation is surprisingly sparse. On the other hand, the replicated evolution of ecological strategies and physiological mechanisms across similar biomes appears to be pervasive. We conclude by highlighting where future efforts can help us bridge the understanding of replicated evolution across different levels of biological organization. Earth's landscape is diverse but also repeats itself. Organisms seem to have followed suit.</p>","PeriodicalId":8335,"journal":{"name":"Annual review of plant biology","volume":"74 ","pages":"697-725"},"PeriodicalIF":23.9,"publicationDate":"2023-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9513034","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: 8
Temperature Sensing in Plants. 植物的温度感应。
IF 23.9 1区 生物学
Annual review of plant biology Pub Date : 2023-05-22 DOI: 10.1146/annurev-arplant-102820-102235
Sandra M Kerbler, Philip A Wigge
{"title":"Temperature Sensing in Plants.","authors":"Sandra M Kerbler,&nbsp;Philip A Wigge","doi":"10.1146/annurev-arplant-102820-102235","DOIUrl":"https://doi.org/10.1146/annurev-arplant-102820-102235","url":null,"abstract":"<p><p>Temperature is a key environmental cue that influences the distribution and behavior of plants globally. Understanding how plants sense temperature and integrate this information into their development is important to determine how plants adapt to climate change and to apply this knowledge to the breeding of climate-resilient crops. The mechanisms of temperature perception in eukaryotes are only just beginning to be understood, with multiple molecular phenomena with inherent temperature dependencies, such as RNA melting, phytochrome dark reversion, and protein phase change, being exploited by nature to create thermosensory signaling networks. Here, we review recent progress in understanding how temperature sensing in four major pathways in <i>Arabidopsis thaliana</i> occurs: vernalization, cold stress, thermomorphogenesis, and heat stress. We discuss outstanding questions in the field and the importance of these mechanisms in the context of breeding climate-resilient crops.</p>","PeriodicalId":8335,"journal":{"name":"Annual review of plant biology","volume":"74 ","pages":"341-366"},"PeriodicalIF":23.9,"publicationDate":"2023-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9514863","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: 7
Salt-Tolerant Crops: Time to Deliver. 耐盐作物:交付时间。
IF 23.9 1区 生物学
Annual review of plant biology Pub Date : 2023-05-22 DOI: 10.1146/annurev-arplant-061422-104322
Vanessa Melino, Mark Tester
{"title":"Salt-Tolerant Crops: Time to Deliver.","authors":"Vanessa Melino,&nbsp;Mark Tester","doi":"10.1146/annurev-arplant-061422-104322","DOIUrl":"https://doi.org/10.1146/annurev-arplant-061422-104322","url":null,"abstract":"<p><p>Despite the numerous advances made in our understanding of the physiology and molecular genetics of salinity tolerance, there have been relatively few applications of these to improve the salt tolerance of crops. The most significant advances have historically utilized intraspecific variation, introgression of traits from close crop wild relatives, or, less frequently, introgression from more distant relatives. Advanced lines often fail due to difficulties in the introgression or tracking of traits or due to yield penalties associated with the alleles in nonsaline environments. However, the greatest limitation is that salinity is not a primary trait for breeders. We must close the gap between research and delivery, especially for farmers who have precious few alternatives. These efforts should include a reassessment of old techniques such as grafting current crops with salt-tolerant hybrid rootstocks. Alternatively, future crops can be produced via domestication of salt-tolerant wild species-an approach that is now feasible in our lifetime.</p>","PeriodicalId":8335,"journal":{"name":"Annual review of plant biology","volume":"74 ","pages":"671-696"},"PeriodicalIF":23.9,"publicationDate":"2023-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9514865","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: 13
Optogenetic Methods in Plant Biology. 植物生物学中的光遗传学方法。
IF 23.9 1区 生物学
Annual review of plant biology Pub Date : 2023-05-22 DOI: 10.1146/annurev-arplant-071122-094840
Kai R Konrad, Shiqiang Gao, Matias D Zurbriggen, Georg Nagel
{"title":"Optogenetic Methods in Plant Biology.","authors":"Kai R Konrad,&nbsp;Shiqiang Gao,&nbsp;Matias D Zurbriggen,&nbsp;Georg Nagel","doi":"10.1146/annurev-arplant-071122-094840","DOIUrl":"https://doi.org/10.1146/annurev-arplant-071122-094840","url":null,"abstract":"<p><p>Optogenetics is a technique employing natural or genetically engineered photoreceptors in transgene organisms to manipulate biological activities with light. Light can be turned on or off, and adjusting its intensity and duration allows optogenetic fine-tuning of cellular processes in a noninvasive and spatiotemporally resolved manner. Since the introduction of Channelrhodopsin-2 and phytochrome-based switches nearly 20 years ago, optogenetic tools have been applied in a variety of model organisms with enormous success, but rarely in plants. For a long time, the dependence of plant growth on light and the absence of retinal, the rhodopsin chromophore, prevented the establishment of plant optogenetics until recent progress overcame these difficulties. We summarize the recent results of work in the field to control plant growth and cellular motion via green light-gated ion channels and present successful applications to light-control gene expression with single or combined photoswitches in plants. Furthermore, we highlight the technical requirements and options for future plant optogenetic research.</p>","PeriodicalId":8335,"journal":{"name":"Annual review of plant biology","volume":"74 ","pages":"313-339"},"PeriodicalIF":23.9,"publicationDate":"2023-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9515189","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: 2
The Diversity and Functions of Plant RNA Modifications: What We Know and Where We Go from Here. 植物RNA修饰的多样性和功能:我们所知道的和我们从这里走到哪里。
IF 23.9 1区 生物学
Annual review of plant biology Pub Date : 2023-05-22 DOI: 10.1146/annurev-arplant-071122-085813
Bishwas Sharma, Wil Prall, Garima Bhatia, Brian D Gregory
{"title":"The Diversity and Functions of Plant RNA Modifications: What We Know and Where We Go from Here.","authors":"Bishwas Sharma,&nbsp;Wil Prall,&nbsp;Garima Bhatia,&nbsp;Brian D Gregory","doi":"10.1146/annurev-arplant-071122-085813","DOIUrl":"https://doi.org/10.1146/annurev-arplant-071122-085813","url":null,"abstract":"<p><p>Since the discovery of the first ribonucleic acid (RNA) modifications in transfer RNAs (tRNAs) and ribosomal RNAs (rRNAs), scientists have been on a quest to decipher the identities and functions of RNA modifications in biological systems. The last decade has seen monumental growth in the number of studies that have characterized and assessed the functionalities of RNA modifications in the field of plant biology. Owing to these studies, we now categorize RNA modifications based on their chemical nature and the RNA on which they are found, as well as the array of proteins that are involved in the processes that add, read, and remove them from an RNA molecule. Beyond their identity, another key piece of the puzzle is the functional significance of the various types of RNA modifications. Here, we shed light on recent studies that help establish our current understanding of the diversity of RNA modifications found in plant transcriptomes and the functions they play at both the molecular (e.g., RNA stability, translation, and transport) and organismal (e.g., stress response and development) levels. Finally, we consider the key research questions related to plant gene expression and biology in general and highlight developments in various technologies that are driving our insights forward in this research area.</p>","PeriodicalId":8335,"journal":{"name":"Annual review of plant biology","volume":"74 ","pages":"53-85"},"PeriodicalIF":23.9,"publicationDate":"2023-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9517940","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: 2
Decoding the Auxin Matrix: Auxin Biology Through the Eye of the Computer. 解码生长素矩阵:通过计算机之眼的生长素生物学。
IF 23.9 1区 生物学
Annual review of plant biology Pub Date : 2023-05-22 DOI: 10.1146/annurev-arplant-102720-033523
Raquel Martin-Arevalillo, Teva Vernoux
{"title":"Decoding the Auxin Matrix: Auxin Biology Through the Eye of the Computer.","authors":"Raquel Martin-Arevalillo,&nbsp;Teva Vernoux","doi":"10.1146/annurev-arplant-102720-033523","DOIUrl":"https://doi.org/10.1146/annurev-arplant-102720-033523","url":null,"abstract":"<p><p>The plant hormone auxin is certainly the most studied developmental regulator in plants. The many functions of auxin during development, from the embryo to the root and shoot construction, are mediated by an ever-growing collection of molecular regulators, with an overwhelming degree of both ubiquity and complexity that we are still far from fully understanding and that biological experiments alone cannot grasp. In this review, we discuss how bioinformatics and computational modeling approaches have helped in recent years to explore this complexity and to push the frontiers of our understanding of auxin biology. We focus on how analysis of massive amounts of genomic data and construction of computational models to simulate auxin-regulated processes at different scales have complemented wet experiments to increase the understanding of how auxin acts in the nucleus to regulate transcription and how auxin movement between cells regulates development at the tissular scale.</p>","PeriodicalId":8335,"journal":{"name":"Annual review of plant biology","volume":"74 ","pages":"387-413"},"PeriodicalIF":23.9,"publicationDate":"2023-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9505879","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: 2
Proximity Labeling in Plants. 植物中的邻近标签。
IF 23.9 1区 生物学
Annual review of plant biology Pub Date : 2023-05-22 Epub Date: 2023-02-28 DOI: 10.1146/annurev-arplant-070522-052132
Shou-Ling Xu, Ruben Shrestha, Sumudu S Karunadasa, Pei-Qiao Xie
{"title":"Proximity Labeling in Plants.","authors":"Shou-Ling Xu,&nbsp;Ruben Shrestha,&nbsp;Sumudu S Karunadasa,&nbsp;Pei-Qiao Xie","doi":"10.1146/annurev-arplant-070522-052132","DOIUrl":"10.1146/annurev-arplant-070522-052132","url":null,"abstract":"<p><p>Proteins are workhorses in the cell; they form stable and more often dynamic, transient protein-protein interactions, assemblies, and networks and have an intimate interplay with DNA and RNA. These network interactions underlie fundamental biological processes and play essential roles in cellular function. The proximity-dependent biotinylation labeling approach combined with mass spectrometry (PL-MS) has recently emerged as a powerful technique to dissect the complex cellular network at the molecular level. In PL-MS, by fusing a genetically encoded proximity-labeling (PL) enzyme to a protein or a localization signal peptide, the enzyme is targeted to a protein complex of interest or to an organelle, allowing labeling of proximity proteins within a zoom radius. These biotinylated proteins can then be captured by streptavidin beads and identified and quantified by mass spectrometry. Recently engineered PL enzymes such as TurboID have a much-improved enzymatic activity, enabling spatiotemporal mapping with a dramatically increased signal-to-noise ratio. PL-MS has revolutionized the way we perform proteomics by overcoming several hurdles imposed by traditional technology, such as biochemical fractionation and affinity purification mass spectrometry. In this review, we focus on biotin ligase-based PL-MS applications that have been, or are likely to be, adopted by the plant field. We discuss the experimental designs and review the different choices for engineered biotin ligases, enrichment, and quantification strategies. Lastly, we review the validation and discuss future perspectives.</p>","PeriodicalId":8335,"journal":{"name":"Annual review of plant biology","volume":"74 ","pages":"285-312"},"PeriodicalIF":23.9,"publicationDate":"2023-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10576617/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9514866","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: 4
BAHD Company: The Ever-Expanding Roles of the BAHD Acyltransferase Gene Family in Plants. BAHD公司:BAHD酰基转移酶基因家族在植物中的作用不断扩大。
IF 23.9 1区 生物学
Annual review of plant biology Pub Date : 2023-05-22 DOI: 10.1146/annurev-arplant-062922-050122
Gaurav Moghe, Lars H Kruse, Maike Petersen, Federico Scossa, Alisdair R Fernie, Emmanuel Gaquerel, John C D'Auria
{"title":"BAHD Company: The Ever-Expanding Roles of the BAHD Acyltransferase Gene Family in Plants.","authors":"Gaurav Moghe,&nbsp;Lars H Kruse,&nbsp;Maike Petersen,&nbsp;Federico Scossa,&nbsp;Alisdair R Fernie,&nbsp;Emmanuel Gaquerel,&nbsp;John C D'Auria","doi":"10.1146/annurev-arplant-062922-050122","DOIUrl":"https://doi.org/10.1146/annurev-arplant-062922-050122","url":null,"abstract":"<p><p>Plants' ability to chemically modify core structures of specialized metabolites is the main reason why the plant kingdom contains such a wide and rich array of diverse compounds. One of the most important types of chemical modifications of small molecules is the addition of an acyl moiety to produce esters and amides. Large-scale phylogenomics analyses have shown that the enzymes that perform acyl transfer reactions on the myriad small molecules synthesized by plants belong to only a few gene families. This review is focused on describing the biochemistry, evolutionary origins, and chemical ecology implications of one of these families-the BAHD acyltransferases. The growth of advanced metabolomic studies coupled with next-generation sequencing of diverse plant species has confirmed that the BAHD family plays critical roles in modifying nearly all known classes of specialized metabolites. The current and future outlook for research on BAHDs includes expanding their roles in synthetic biology and metabolic engineering.</p>","PeriodicalId":8335,"journal":{"name":"Annual review of plant biology","volume":"74 ","pages":"165-194"},"PeriodicalIF":23.9,"publicationDate":"2023-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9514298","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: 5
Between-Plant Signaling. 进行植物信号。
IF 23.9 1区 生物学
Annual review of plant biology Pub Date : 2023-05-22 DOI: 10.1146/annurev-arplant-070122-015430
Guojing Shen, Jingxiong Zhang, Yunting Lei, Yuxing Xu, Jianqiang Wu
{"title":"Between-Plant Signaling.","authors":"Guojing Shen,&nbsp;Jingxiong Zhang,&nbsp;Yunting Lei,&nbsp;Yuxing Xu,&nbsp;Jianqiang Wu","doi":"10.1146/annurev-arplant-070122-015430","DOIUrl":"https://doi.org/10.1146/annurev-arplant-070122-015430","url":null,"abstract":"<p><p>Parasitic plants use a special organ, the haustorium, to attach to and penetrate host tissues, forming phloem and/or xylem fusion with the host vascular systems. Across this haustorium-host interface, not only water and nutrients are extracted from the host by the parasitic plant, but also secondary metabolites, messenger RNAs, noncoding RNAs, proteins, and systemic signals are transported between the parasite and host and even among different hosts connected by a parasite. Furthermore, mycorrhizal fungi can form common mycelial networks (CMNs) that simultaneously interconnect multiple plants. Increasing lines of evidence suggest that CMNs can function as conduits, transferring stress-related systemic signals between plants. Between-plant signaling mediated by haustoria and CMNs likely has a profound impact on plant interactions with other organisms and adaptation to environmental factors. Here, we summarize the findings regarding between-plant transfer of biomolecules and systemic signals and the current understanding of the physiological and ecological implications of between-plant signaling.</p>","PeriodicalId":8335,"journal":{"name":"Annual review of plant biology","volume":"74 ","pages":"367-386"},"PeriodicalIF":23.9,"publicationDate":"2023-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9565657","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: 3
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