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Annual review of plant biology最新文献

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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
Plant Hormone Transport and Localization: Signaling Molecules on the Move. 植物激素运输和定位:运动中的信号分子。
IF 23.9 1区 生物学
Annual review of plant biology Pub Date : 2023-05-22 DOI: 10.1146/annurev-arplant-070722-015329
Yuqin Zhang, Amichai Berman, Eilon Shani
{"title":"Plant Hormone Transport and Localization: Signaling Molecules on the Move.","authors":"Yuqin Zhang,&nbsp;Amichai Berman,&nbsp;Eilon Shani","doi":"10.1146/annurev-arplant-070722-015329","DOIUrl":"https://doi.org/10.1146/annurev-arplant-070722-015329","url":null,"abstract":"<p><p>Plant hormones are a group of small signaling molecules produced by plants at very low concentrations that have the ability to move and function at distal sites. Hormone homeostasis is critical to balance plant growth and development and is regulated at multiple levels, including hormone biosynthesis, catabolism, perception, and transduction. In addition, plants move hormones over short and long distances to regulate various developmental processes and responses to environmental factors. Transporters coordinate these movements, resulting in hormone maxima, gradients, and cellular and subcellular sinks. Here, we summarize the current knowledge of most of the characterized plant hormone transporters with respect to biochemical, physiological, and developmental activities. We further discuss the subcellular localizations of transporters, their substrate specificities, and the need for multiple transporters for the same hormone in the context of plant growth and development.</p>","PeriodicalId":8335,"journal":{"name":"Annual review of plant biology","volume":"74 ","pages":"453-479"},"PeriodicalIF":23.9,"publicationDate":"2023-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9884313","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
Where, When, and Why Do Plant Volatiles Mediate Ecological Signaling? The Answer Is Blowing in the Wind. 植物挥发物在何时、何地以及为何介导生态信号?答案在风中飘荡。
IF 23.9 1区 生物学
Annual review of plant biology Pub Date : 2023-05-22 DOI: 10.1146/annurev-arplant-040121-114908
Meredith C Schuman
{"title":"Where, When, and Why Do Plant Volatiles Mediate Ecological Signaling? The Answer Is Blowing in the Wind.","authors":"Meredith C Schuman","doi":"10.1146/annurev-arplant-040121-114908","DOIUrl":"https://doi.org/10.1146/annurev-arplant-040121-114908","url":null,"abstract":"<p><p>Plant volatiles comprise thousands of molecules from multiple metabolic pathways, distinguished by sufficient vapor pressure to evaporate into the headspace under normal environmental conditions. Many are implicated as ecological signals, but what is the evidence-and how do they work? Volatiles diffuse, are carried by wind, and may be taken up by other organisms or degrade with exposure to atmospheric ozone, radicals, and UV light; visual signals such as color are not subject to these complications (but require a line of sight). Distantly related plants-and nonplants-produce many of the same volatiles, yet specific compounds and blends may be distinct. Here, I present a quantitative review of the literature on plant volatiles as ecological signals, illustrating a field that has focused on developing ideas as much as reporting primary data. I discuss advantages and constraints, review recent advances, and propose considerations for primary studies to elucidate particular functions of plant volatiles.</p>","PeriodicalId":8335,"journal":{"name":"Annual review of plant biology","volume":"74 ","pages":"609-633"},"PeriodicalIF":23.9,"publicationDate":"2023-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9513585","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
Chloroplast Proteostasis: Import, Sorting, Ubiquitination, and Proteolysis. 叶绿体蛋白质静止:输入、分选、泛素化和蛋白质水解。
IF 23.9 1区 生物学
Annual review of plant biology Pub Date : 2023-05-22 DOI: 10.1146/annurev-arplant-070122-032532
Yi Sun, R Paul Jarvis
{"title":"Chloroplast Proteostasis: Import, Sorting, Ubiquitination, and Proteolysis.","authors":"Yi Sun,&nbsp;R Paul Jarvis","doi":"10.1146/annurev-arplant-070122-032532","DOIUrl":"https://doi.org/10.1146/annurev-arplant-070122-032532","url":null,"abstract":"<p><p>Chloroplasts are the defining plant organelles with responsibility for photosynthesis and other vital functions. To deliver these functions, they possess a complex proteome comprising thousands of largely nucleus-encoded proteins. Composition of the proteome is controlled by diverse processes affecting protein translocation and degradation-our focus here. Most chloroplast proteins are imported from the cytosol via multiprotein translocons in the outer and inner envelope membranes (the TOC and TIC complexes, respectively), or via one of several noncanonical pathways, and then sorted by different systems to organellar subcompartments. Chloroplast proteolysis is equally complex, involving the concerted action of internal proteases of prokaryotic origin and the nucleocytosolic ubiquitin-proteasome system (UPS). The UPS degrades unimported proteins in the cytosol and chloroplast-resident proteins via chloroplast-associated protein degradation (CHLORAD). The latter targets the TOC apparatus to regulate protein import, as well as numerous internal proteins directly, to reconfigure chloroplast functions in response to developmental and environmental signals.</p>","PeriodicalId":8335,"journal":{"name":"Annual review of plant biology","volume":"74 ","pages":"259-283"},"PeriodicalIF":23.9,"publicationDate":"2023-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9514861","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
Epigenetic Regulation During Plant Development and the Capacity for Epigenetic Memory. 植物发育过程中的表观遗传调控与表观遗传记忆能力。
IF 23.9 1区 生物学
Annual review of plant biology Pub Date : 2023-05-22 DOI: 10.1146/annurev-arplant-070122-025047
Elizabeth A Hemenway, Mary Gehring
{"title":"Epigenetic Regulation During Plant Development and the Capacity for Epigenetic Memory.","authors":"Elizabeth A Hemenway,&nbsp;Mary Gehring","doi":"10.1146/annurev-arplant-070122-025047","DOIUrl":"https://doi.org/10.1146/annurev-arplant-070122-025047","url":null,"abstract":"<p><p>The establishment, maintenance, and removal of epigenetic modifications provide an additional layer of regulation, beyond genetically encoded factors, by which plants can control developmental processes and adapt to the environment. Epigenetic inheritance, while historically referring to information not encoded in the DNA sequence that is inherited between generations, can also refer to epigenetic modifications that are maintained within an individual but are reset between generations. Both types of epigenetic inheritance occur in plants, and the functions and mechanisms distinguishing the two are of great interest to the field. Here, we discuss examples of epigenetic dynamics and maintenance during selected stages of growth and development and their functional consequences. Epigenetic states are also dynamic in response to stress, with consequences for transposable element regulation. How epigenetic resetting between generations occurs during normal development and in response to stress is an emerging area of research.</p>","PeriodicalId":8335,"journal":{"name":"Annual review of plant biology","volume":"74 ","pages":"87-109"},"PeriodicalIF":23.9,"publicationDate":"2023-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10280588/pdf/nihms-1907770.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9719952","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: 2
Why Are Invasive Plants Successful? 入侵植物为什么会成功?
IF 23.9 1区 生物学
Annual review of plant biology Pub Date : 2023-05-22 DOI: 10.1146/annurev-arplant-070522-071021
Margherita Gioria, Philip E Hulme, David M Richardson, Petr Pyšek
{"title":"Why Are Invasive Plants Successful?","authors":"Margherita Gioria,&nbsp;Philip E Hulme,&nbsp;David M Richardson,&nbsp;Petr Pyšek","doi":"10.1146/annurev-arplant-070522-071021","DOIUrl":"https://doi.org/10.1146/annurev-arplant-070522-071021","url":null,"abstract":"<p><p>Plant invasions, a byproduct of globalization, are increasing worldwide. Because of their ecological and economic impacts, considerable efforts have been made to understand and predict the success of non-native plants. Numerous frameworks, hypotheses, and theories have been advanced to conceptualize the interactions of multiple drivers and context dependence of invasion success with the aim of achieving robust explanations with predictive power. We review these efforts from a community-level perspective rather than a biogeographical one, focusing on terrestrial systems, and explore the roles of intrinsic plant properties in determining species invasiveness, as well as the effects of biotic and abiotic conditions in mediating ecosystem invasibility (or resistance) and ecological and evolutionary processes. We also consider the fundamental influences of human-induced changes at scales ranging from local to global in triggering, promoting, and sustaining plant invasions and discuss how these changes could alter future invasion trajectories.</p>","PeriodicalId":8335,"journal":{"name":"Annual review of plant biology","volume":"74 ","pages":"635-670"},"PeriodicalIF":23.9,"publicationDate":"2023-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9514814","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
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