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Long Noncoding RNAs in Plants. 植物中的长链非编码rna。
IF 23.9 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2021-06-17 Epub Date: 2021-03-22 DOI: 10.1146/annurev-arplant-093020-035446
Andrzej T Wierzbicki, Todd Blevins, Szymon Swiezewski

Plants have an extraordinary diversity of transcription machineries, including five nuclear DNA-dependent RNA polymerases. Four of these enzymes are dedicated to the production of long noncoding RNAs (lncRNAs), which are ribonucleic acids with functions independent of their protein-coding potential. lncRNAs display a broad range of lengths and structures, but they are distinct from the small RNA guides of RNA interference (RNAi) pathways. lncRNAs frequently serve as structural, catalytic, or regulatory molecules for gene expression. They can affect all elements of genes, including promoters, untranslated regions, exons, introns, and terminators, controlling gene expression at various levels, including modifying chromatin accessibility, transcription, splicing, and translation. Certain lncRNAs protect genome integrity, while others respond to environmental cues like temperature, drought, nutrients, and pathogens. In this review, we explain the challenge of defining lncRNAs, introduce the machineries responsible for their production, and organize this knowledge by viewing the functions of lncRNAs throughout the structure of a typical plant gene.

植物具有非常多样化的转录机制,包括五种核dna依赖的RNA聚合酶。其中四种酶专门用于产生长链非编码rna (lncRNAs), lncRNAs是具有独立于其蛋白质编码潜力的功能的核糖核酸。lncRNAs显示出广泛的长度和结构,但它们不同于RNA干扰(RNAi)途径的小RNA向导。lncrna经常作为基因表达的结构、催化或调节分子。它们可以影响基因的所有元件,包括启动子、非翻译区、外显子、内含子和终止子,在不同水平上控制基因表达,包括修饰染色质可及性、转录、剪接和翻译。某些lncrna保护基因组完整性,而其他lncrna则对温度、干旱、营养和病原体等环境因素做出反应。在这篇综述中,我们解释了定义lncrna的挑战,介绍了其产生的机制,并通过观察lncrna在整个典型植物基因结构中的功能来组织这些知识。
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引用次数: 43
Tuber and Tuberous Root Development. 块茎和块根发育。
IF 23.9 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2021-06-17 Epub Date: 2021-03-31 DOI: 10.1146/annurev-arplant-080720-084456
Wolfgang Zierer, David Rüscher, Uwe Sonnewald, Sophia Sonnewald

Root and tuber crops have been an important part of human nutrition since the early days of humanity, providing us with essential carbohydrates, proteins, and vitamins. Today, they are especially important in tropical and subtropical regions of the world, where they help to feed an ever-growing population. Early induction and storage organ size are important agricultural traits, as they determine yield over time. During potato tuberization, environmental and metabolic status are sensed, ensuring proper timing of tuberization mediated by phloem-mobile signals. Coordinated cellular restructuring and expansion growth, as well as controlled storage metabolism in the tuber, are executed. This review summarizes our current understanding of potato tuber development and highlights similarities and differences to important tuberous root crop species like sweetpotato and cassava. Finally, we point out knowledge gaps that need to be filled before a complete picture of storage organ development can emerge.

自人类早期以来,块根和块茎作物一直是人类营养的重要组成部分,为我们提供必需的碳水化合物、蛋白质和维生素。今天,它们在世界热带和亚热带地区尤为重要,因为它们帮助养活了不断增长的人口。早期诱导和贮藏器官的大小是重要的农业性状,因为它们决定了长期的产量。在马铃薯形成过程中,环境和代谢状态被感知,从而通过韧皮部移动信号来确保马铃薯形成的适当时机。在块茎中进行协调的细胞重组和扩张生长,以及控制储存代谢。本文综述了目前对马铃薯块茎发育的认识,并强调了马铃薯与甘薯和木薯等重要块根作物的异同。最后,我们指出了在储存器官发育的完整图景出现之前需要填补的知识空白。
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引用次数: 56
Recent Advances in the Physiology of Ion Channels in Plants. 植物离子通道生理学研究进展。
IF 23.9 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2021-06-17 Epub Date: 2021-01-11 DOI: 10.1146/annurev-arplant-081519-035925
Omar Pantoja

Our knowledge of plant ion channels was significantly enhanced by the first application of the patch-clamp technique to isolated guard cell protoplasts over 35 years ago. Since then, research has demonstrated the importance of ion channels in the control of gas exchange in guard cells, their role in nutrient uptake in roots, and the participation of calcium-permeable cation channels in the regulation of cell signaling affected by the intracellular concentrations of this second messenger. In recent years, through the employment of reverse genetics, mutant proteins, and heterologous expression systems, research on ion channels has identified mechanisms that modify their activity through protein-protein interactions or that result in activation and/or deactivation of ion channels through posttranslational modifications. Additional and confirmatory information on ion channel functioning has been derived from the crystallization and molecular modeling of plant proteins that, together with functional analyses, have helped to increase our knowledge of the functioning of these important membrane proteins that may eventually help to improve crop yield. Here, an update on the advances obtained in plant ion channel function during the last few years is presented.

35年前,膜片钳技术首次应用于分离的保护细胞原生质体,大大提高了我们对植物离子通道的认识。从那时起,研究证明了离子通道在控制保护细胞中的气体交换中的重要性,它们在根中营养吸收中的作用,以及钙渗透阳离子通道参与调节受细胞内第二信使浓度影响的细胞信号传导。近年来,通过使用反向遗传学、突变蛋白和异种表达系统,对离子通道的研究已经确定了通过蛋白质-蛋白质相互作用改变其活性或通过翻译后修饰导致离子通道激活和/或失活的机制。通过植物蛋白的结晶和分子建模,以及功能分析,我们获得了更多关于离子通道功能的信息,这些信息有助于增加我们对这些重要膜蛋白功能的了解,最终有助于提高作物产量。本文介绍了近年来植物离子通道功能研究的最新进展。
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引用次数: 20
Perception and Signaling of Ultraviolet-B Radiation in Plants. 植物对紫外线b辐射的感知和信号转导
IF 23.9 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2021-06-17 Epub Date: 2021-02-26 DOI: 10.1146/annurev-arplant-050718-095946
Roman Podolec, Emilie Demarsy, Roman Ulm

Ultraviolet-B (UV-B) radiation is an intrinsic fraction of sunlight that plants perceive through the UVR8 photoreceptor. UVR8 is a homodimer in its ground state that monomerizes upon UV-B photon absorption via distinct tryptophan residues. Monomeric UVR8 competitively binds to the substrate binding site of COP1, thus inhibiting its E3 ubiquitin ligase activity against target proteins, which include transcriptional regulators such as HY5. The UVR8-COP1 interaction also leads to the destabilization of PIF bHLH factor family members. Additionally, UVR8 directly interacts with and inhibits the DNA binding of a different set of transcription factors. Each of these UVR8 signaling mechanisms initiates nuclear gene expression changes leading to UV-B-induced photomorphogenesis and acclimation. The two WD40-repeat proteins RUP1 and RUP2 provide negative feedback regulation and inactivate UVR8 by facilitating redimerization. Here, we review the molecular mechanisms of the UVR8 pathway from UV-B perception and signal transduction to gene expression changes and physiological UV-B responses.

紫外线b (UV-B)辐射是植物通过UVR8感光器感知的阳光的固有部分。UVR8是基态的同型二聚体,通过不同的色氨酸残基对UV-B光子吸收进行单体化。单体UVR8竞争性地与COP1的底物结合位点结合,从而抑制其E3泛素连接酶对靶蛋白的活性,靶蛋白包括转录调节因子如HY5。UVR8-COP1的相互作用也会导致PIF bHLH因子家族成员的不稳定。此外,UVR8直接与一组不同的转录因子相互作用并抑制DNA结合。这些UVR8信号机制中的每一种都启动了核基因表达的变化,从而导致uv - b诱导的光形态发生和驯化。两个WD40-repeat蛋白RUP1和RUP2提供负反馈调控,并通过促进再聚合使UVR8失活。本文综述了UVR8通路的分子机制,从UV-B感知和信号转导到基因表达变化和生理UV-B反应。
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引用次数: 39
A Comparative Overview of the Intracellular Guardians of Plants and Animals: NLRs in Innate Immunity and Beyond. 植物和动物细胞内守护者的比较综述:nlr在先天免疫和其他方面。
IF 23.9 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2021-06-17 Epub Date: 2021-03-09 DOI: 10.1146/annurev-arplant-080620-104948
Zane Duxbury, Chih-Hang Wu, Pingtao Ding

Nucleotide-binding domain leucine-rich repeat receptors (NLRs) play important roles in the innate immune systems of both plants and animals. Recent breakthroughs in NLR biochemistry and biophysics have revolutionized our understanding of how NLR proteins function in plant immunity. In this review, we summarize the latest findings in plant NLR biology and draw direct comparisons to NLRs of animals. We discuss different mechanisms by which NLRs recognize their ligands in plants and animals. The discovery of plant NLR resistosomes that assemble in a comparable way to animal inflammasomes reinforces the striking similarities between the formation of plant and animal NLR complexes. Furthermore, we discuss the mechanisms by which plant NLRs mediate immune responses and draw comparisons to similar mechanisms identified in animals. Finally, we summarize the current knowledge of the complex genetic architecture formed by NLRs in plants and animals and the roles of NLRs beyond pathogen detection.

核苷酸结合域富亮氨酸重复序列受体(NLRs)在植物和动物的先天免疫系统中都起着重要的作用。最近在NLR生物化学和生物物理学方面的突破彻底改变了我们对NLR蛋白在植物免疫中的作用的理解。本文综述了植物NLR生物学的最新研究成果,并与动物NLR进行了直接比较。我们讨论了nlr在植物和动物中识别其配体的不同机制。植物NLR抵抗体以与动物炎症小体类似的方式组装,这一发现加强了植物和动物NLR复合物形成之间惊人的相似性。此外,我们讨论了植物nlr介导免疫反应的机制,并与动物中发现的类似机制进行了比较。最后,我们总结了目前对植物和动物nlr形成的复杂遗传结构的认识,以及nlr在病原体检测之外的作用。
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引用次数: 33
Next-Generation Mass Spectrometry Metabolomics Revives the Functional Analysis of Plant Metabolic Diversity. 下一代质谱代谢组学复兴植物代谢多样性的功能分析。
IF 23.9 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2021-06-17 Epub Date: 2021-03-29 DOI: 10.1146/annurev-arplant-071720-114836
Dapeng Li, Emmanuel Gaquerel

The remarkable diversity of specialized metabolites produced by plants has inspired several decades of research and nucleated a long list of theories to guide empirical ecological studies. However, analytical constraints and the lack of untargeted processing workflows have long precluded comprehensive metabolite profiling and, consequently, the collection of the critical currencies to test theory predictions for the ecological functions of plant metabolic diversity. Developments in mass spectrometry (MS) metabolomics have revolutionized the large-scale inventory and annotation of chemicals from biospecimens. Hence, the next generation of MS metabolomics propelled by new bioinformatics developments provides a long-awaited framework to revisit metabolism-centered ecological questions, much like the advances in next-generation sequencing of the last two decades impacted all research horizons in genomics. Here, we review advances in plant (computational) metabolomics to foster hypothesis formulation from complex metabolome data. Additionally, we reflect on how next-generation metabolomics could reinvigorate the testing of long-standing theories on plant metabolic diversity.

植物产生的特殊代谢物的显著多样性激发了几十年的研究,并形成了一长串指导实证生态学研究的理论。然而,长期以来,分析限制和缺乏无目标的处理工作流程阻碍了全面的代谢物分析,因此,收集关键货币来测试植物代谢多样性生态功能的理论预测。质谱(MS)代谢组学的发展彻底改变了生物标本中化学物质的大规模库存和注释。因此,由新的生物信息学发展推动的下一代MS代谢组学为重新审视以代谢为中心的生态问题提供了一个期待已久的框架,就像过去二十年中下一代测序的进步影响了基因组学的所有研究领域一样。在这里,我们回顾了植物(计算)代谢组学的进展,以促进复杂代谢组数据的假设制定。此外,我们还思考了下一代代谢组学如何能够重振长期存在的植物代谢多样性理论的测试。
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引用次数: 46
On the Origin of Carnivory: Molecular Physiology and Evolution of Plants on an Animal Diet. 食肉动物的起源:以动物为食的植物的分子生理学和进化。
IF 23.9 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2021-06-17 Epub Date: 2021-01-12 DOI: 10.1146/annurev-arplant-080620-010429
Rainer Hedrich, Kenji Fukushima

Charles Darwin recognized that carnivorous plants thrive in nutrient-poor soil by capturing animals. Although the concept of botanical carnivory has been known for nearly 150 years, its molecular mechanisms and evolutionary origins have not been well understood until recently. In the last decade, technical advances have fueled the genome and transcriptome sequencings of active and passive hunters, leading to a better understanding of the traits associated with the carnivorous syndrome, from trap leaf development and prey digestion to nutrient absorption, exemplified, for example, by the Venus flytrap (Dionaea muscipula), pitcher plant (Cephalotus follicularis), and bladderwort (Utricularia gibba). The repurposing of defense-related genes is an important trend in the evolution of plant carnivory. In this review, using the Venus flytrap as a representative of the carnivorous plants, we summarize the molecular mechanisms underlying their ability to attract, trap, and digest prey and discuss the origins of plant carnivory in relation to their genomic evolution.

查尔斯·达尔文认识到,食肉植物通过捕捉动物在营养贫乏的土壤中茁壮成长。虽然植物食肉性的概念已经被发现了近150年,但其分子机制和进化起源直到最近才被很好地理解。在过去的十年里,技术进步推动了主动和被动猎人的基因组和转录组测序,从而更好地理解了与食肉综合征相关的特征,从捕蝇草(Dionaea muscipula)、猪笼草(Cephalotus follicularis)和狸藻(Utricularia gibba)的叶子发育和猎物消化到营养吸收。防御相关基因的再利用是植物食肉动物进化的一个重要趋势。本文以捕蝇草为代表,综述了捕蝇草吸引、诱捕和消化猎物的分子机制,并从基因组进化的角度讨论了植物食肉性的起源。
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引用次数: 26
Dissipation of Light Energy Absorbed in Excess: The Molecular Mechanisms. 过量吸收光能的耗散:分子机制。
IF 23.9 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2021-06-17 DOI: 10.1146/annurev-arplant-071720-015522
Roberto Bassi, Luca Dall'Osto

Light is essential for photosynthesis. Nevertheless, its intensity widely changes depending on time of day, weather, season, and localization of individual leaves within canopies. This variability means that light collected by the light-harvesting system is often in excess with respect to photon fluence or spectral quality in the context of the capacity of photosynthetic metabolism to use ATP and reductants produced from the light reactions. Absorption of excess light can lead to increased production of excited, highly reactive intermediates, which expose photosynthetic organisms to serious risks of oxidative damage. Prevention and management of such stress are performed by photoprotective mechanisms, which operate by cutting down light absorption, limiting the generation of redox-active molecules, or scavenging reactive oxygen species that are released despite the operation of preventive mechanisms. Here, we describe the major physiological and molecular mechanisms of photoprotection involved in the harmless removal of the excess light energy absorbed by green algae and land plants. In vivo analyses of mutants targeting photosynthetic components and the enhanced resolution of spectroscopic techniques have highlighted specific mechanisms protecting the photosynthetic apparatus from overexcitation. Recent findings unveil a network of multiple interacting elements, the reaction times of which vary from a millisecond to weeks, that continuously maintain photosynthetic organisms within the narrow safety range between efficient light harvesting and photoprotection.

光对光合作用是必不可少的。然而,其强度根据一天中的时间、天气、季节和单个树叶在冠层内的定位而广泛变化。这种可变性意味着光收集系统收集的光在光合代谢使用ATP和光反应产生的还原剂的能力的背景下,相对于光子通量或光谱质量通常是过量的。吸收过量的光会导致兴奋的高活性中间体的产生增加,这使光合生物面临严重的氧化损伤风险。这种应激的预防和管理是通过光保护机制进行的,它通过减少光吸收、限制氧化还原活性分子的产生或清除尽管有预防机制,但仍释放的活性氧来起作用。在这里,我们描述了主要的生理和分子机制的光保护涉及无害化去除多余的光能被绿藻和陆地植物吸收。针对光合成分的突变体的体内分析和光谱技术的增强分辨率强调了保护光合装置免受过度激发的特定机制。最近的研究发现揭示了一个由多种相互作用元素组成的网络,这些元素的反应时间从毫秒到几周不等,可以持续地将光合生物维持在有效的光收集和光保护之间的狭窄安全范围内。
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引用次数: 64
Reproduction Multitasking: The Male Gametophyte. 生殖多任务:雄性配子体。
IF 23.9 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2021-06-17 Epub Date: 2021-04-26 DOI: 10.1146/annurev-arplant-080620-021907
Said Hafidh, David Honys

The gametophyte represents the sexual phase in the alternation of generations in plants; the other, nonsexual phase is the sporophyte. Here, we review the evolutionary origins of the male gametophyte among land plants and, in particular, its ontogenesis in flowering plants. The highly reduced male gametophyte of angiosperm plants is a two- or three-celled pollen grain. Its task is the production of two male gametes and their transport to the female gametophyte, the embryo sac, where double fertilization takes place. We describe two phases of pollen ontogenesis-a developmental phase leading to the differentiation of the male germline and the formation of a mature pollen grain and a functional phase representing the pollen tube growth, beginning with the landing of the pollen grain on the stigma and ending with double fertilization. We highlight recent advances in the complex regulatory mechanisms involved, including posttranscriptional regulation and transcript storage, intracellular metabolic signaling, pollen cell wall structure and synthesis, protein secretion, and phased cell-cell communication within the reproductive tissues.

配子体在植物的世代交替中代表有性阶段;另一个无性生殖阶段是孢子体。本文综述了陆地植物雄性配子体的进化起源,特别是开花植物雄性配子体的个体发生。被子植物高度退化的雄性配子体是一个二细胞或三细胞的花粉粒。它的任务是产生两个雄性配子,并将它们运送到雌性配子体,即胚囊,在那里进行双受精。我们描述了花粉个体发生的两个阶段,一个是导致雄性生殖系分化和成熟花粉粒形成的发育阶段,另一个是代表花粉管生长的功能阶段,从花粉粒落在柱头上开始,到双受精结束。我们重点介绍了相关复杂调控机制的最新进展,包括转录后调控和转录物储存、细胞内代谢信号、花粉细胞壁结构和合成、蛋白质分泌以及生殖组织内的细胞-细胞相通讯。
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引用次数: 37
Plant Pan-Genomics Comes of Age. 植物泛基因组学成熟。
IF 23.9 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2021-06-17 Epub Date: 2021-04-13 DOI: 10.1146/annurev-arplant-080720-105454
Li Lei, Eugene Goltsman, David Goodstein, Guohong Albert Wu, Daniel S Rokhsar, John P Vogel

A pan-genome is the nonredundant collection of genes and/or DNA sequences in a species. Numerous studies have shown that plant pan-genomes are typically much larger than the genome of any individual and that a sizable fraction of the genes in any individual are present in only some genomes. The construction and interpretation of plant pan-genomes are challenging due to the large size and repetitive content of plant genomes. Most pan-genomes are largely focused on nontransposable element protein coding genes because they are more easily analyzed and defined than noncoding and repetitive sequences. Nevertheless, noncoding and repetitive DNA play important roles in determining the phenotype and genome evolution. Fortunately, it is now feasible to make multiple high-quality genomes that can be used to construct high-resolution pan-genomes that capture all the variation. However, assembling, displaying, and interacting with such high-resolution pan-genomes will require the development of new tools.

泛基因组是一个物种的基因和/或DNA序列的非冗余集合。大量研究表明,植物泛基因组通常比任何个体的基因组都要大得多,而且任何个体的相当一部分基因只存在于某些基因组中。由于植物基因组庞大且内容重复,植物泛基因组的构建和解释具有挑战性。大多数泛基因组主要集中在非转座元件蛋白质编码基因上,因为它们比非编码和重复序列更容易分析和定义。然而,非编码和重复DNA在决定表型和基因组进化中起着重要作用。幸运的是,现在可以制作多个高质量的基因组,这些基因组可以用来构建高分辨率的泛基因组,从而捕获所有的变异。然而,组装、展示和与这种高分辨率泛基因组相互作用将需要开发新的工具。
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引用次数: 35
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Annual review of plant biology
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