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Histone Variants in the Specialization of Plant Chromatin. 植物染色质特化过程中的组蛋白变异
IF 21.3 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2022-05-20 Epub Date: 2022-02-15 DOI: 10.1146/annurev-arplant-070221-050044
Maryam Foroozani, Dylan H Holder, Roger B Deal

The basic unit of chromatin, the nucleosome, is an octamer of four core histone proteins (H2A, H2B, H3, and H4) and serves as a fundamental regulatory unit in all DNA-templated processes. The majority of nucleosome assembly occurs during DNA replication when these core histones are produced en masse to accommodate the nascent genome. In addition, there are a number of nonallelic sequence variants of H2A and H3 in particular, known as histone variants, that can be incorporated into nucleosomes in a targeted and replication-independent manner. By virtue of their sequence divergence from the replication-coupled histones, these histone variants can impart unique properties onto the nucleosomes they occupy and thereby influence transcription and epigenetic states, DNA repair, chromosome segregation, and other nuclear processes in ways that profoundly affect plant biology. In this review, we discuss the evolutionary origins of these variants in plants, their known roles in chromatin, and their impacts on plant development and stress responses. We focus on the individual and combined roles of histone variants in transcriptional regulation within euchromatic and heterochromatic genome regions. Finally, we highlight gaps in our understanding of plant variants at the molecular, cellular, and organismal levels, and we propose new directions for study in the field of plant histone variants.

染色质的基本单位--核小体是由四种核心组蛋白(H2A、H2B、H3 和 H4)组成的八聚体,是所有 DNA 触发过程的基本调控单位。核小体的组装大多发生在 DNA 复制过程中,此时这些核心组蛋白会大量产生,以适应新生基因组。此外,特别是 H2A 和 H3 的一些非等位序列变体(称为组蛋白变体),可以以定向和不依赖复制的方式结合到核小体中。由于它们的序列与复制偶联组蛋白不同,这些组蛋白变体可以赋予它们所占据的核小体独特的性质,从而影响转录和表观遗传状态、DNA 修复、染色体分离和其他核过程,对植物生物学产生深远影响。在本综述中,我们将讨论这些变体在植物中的进化起源、它们在染色质中的已知作用以及它们对植物发育和胁迫响应的影响。我们将重点关注组蛋白变体在同源染色体和异源染色体基因组区域内转录调控中的单独作用和综合作用。最后,我们强调了在分子、细胞和生物体水平上我们对植物变体认识的差距,并提出了植物组蛋白变体领域研究的新方向。
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引用次数: 0
Plant GATA Factors: Their Biology, Phylogeny, and Phylogenomics. 植物GATA因子:生物学、系统发育和系统基因组学。
IF 23.9 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2022-05-20 Epub Date: 2022-02-07 DOI: 10.1146/annurev-arplant-072221-092913
Claus Schwechheimer, Peter Michael Schröder, Crysten E Blaby-Haas

GATA factors are evolutionarily conserved transcription factors that are found in animals, fungi, and plants. Compared to that of animals, the size of the plant GATA family is increased. In angiosperms, four main GATA classes and seven structural subfamilies can be defined. In recent years, knowledge about the biological role and regulation of plant GATAs has substantially improved. Individual family members have been implicated in the regulation of photomorphogenic growth, chlorophyll biosynthesis, chloroplast development, photosynthesis, and stomata formation, as well as root, leaf, and flower development. In this review, we summarize the current knowledge of plant GATA factors. Using phylogenomic analysis, we trace the evolutionary origin of the GATA classes in the green lineage and examine their relationship to animal and fungal GATAs. Finally, we speculate about a possible conservation of GATA-regulated functions across the animal, fungal, and plant kingdoms.

GATA因子是进化上保守的转录因子,存在于动物、真菌和植物中。与动物相比,植物GATA家族的规模增加了。在被子植物中,可以定义四个主要的GATA类和七个结构亚科。近年来,对植物GATAs的生物学作用和调控的认识有了很大的提高。单个家族成员参与光形态形成生长、叶绿素生物合成、叶绿体发育、光合作用和气孔形成以及根、叶和花的发育。本文就植物GATA因子的研究现状进行综述。利用系统基因组学分析,我们追踪了绿色谱系中GATA类的进化起源,并研究了它们与动物和真菌GATA的关系。最后,我们推测gata调控的功能在动物、真菌和植物界可能是守恒的。
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引用次数: 19
Phosphorus Acquisition and Utilization in Plants. 植物磷的获取与利用。
IF 23.9 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2022-05-20 Epub Date: 2021-12-15 DOI: 10.1146/annurev-arplant-102720-125738
Hans Lambers

Tremendous progress has been made on molecular aspects of plant phosphorus (P) nutrition, often without heeding information provided by soil scientists, ecophysiologists, and crop physiologists. This review suggests ways to integrate information from different disciplines. When soil P availability is very low, P-mobilizing strategies are more effective than mycorrhizal strategies. Soil parameters largely determine how much P roots can acquire from P-impoverished soil, and kinetic properties of P transporters are less important. Changes in the expression of P transporters avoid P toxicity. Plants vary widely in photosynthetic P-use efficiency, photosynthesis per unit leaf P. The challenge is to discover what the trade-offs are of different patterns of investment in P fractions. Less investment may save P, but are costs incurred? Are these costs acceptable for crops? These questions can be resolved only by the concerted action of scientists working at both molecular and physiological levels, rather than pursuing these problems independently.

在植物磷营养的分子方面取得了巨大进展,但往往没有听取土壤科学家、生态生理学家和作物生理学家提供的信息。这篇综述提出了整合不同学科信息的方法。土壤磷有效度较低时,磷动员策略比菌根策略更有效。土壤参数在很大程度上决定了磷根能从缺磷土壤中获得多少磷,而磷转运体的动力学性质则不太重要。磷转运蛋白表达的改变避免了磷毒性。植物在光合作用P的利用效率,单位叶片P的光合作用方面差异很大。挑战在于发现不同模式的P部分投资的权衡是什么。较少的投资可以节省P,但是会产生成本吗?这些成本对于农作物来说是可以接受的吗?这些问题只能通过在分子和生理水平上工作的科学家的协调行动来解决,而不是独立地追求这些问题。
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引用次数: 140
Long-Distance Transported RNAs: From Identity to Function. 远距离转运rna:从身份到功能。
IF 23.9 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2022-05-20 Epub Date: 2021-12-15 DOI: 10.1146/annurev-arplant-070121-033601
Julia Kehr, Richard J Morris, Friedrich Kragler

There is now a wealth of data, from different plants and labs and spanning more than two decades, which unequivocally demonstrates that RNAs can be transported over long distances, from the cell where they are transcribed to distal cells in other tissues. Different types of RNA molecules are transported, including micro- and messenger RNAs. Whether these RNAs are selected for transport and, if so, how they are selected and transported remain, in general, open questions. This aspect is likely not independent of the biological function and relevance of the transported RNAs, which are in most cases still unclear. In this review, we summarize the experimental data supporting selectivity or nonselectivity of RNA translocation and review the evidence for biological functions. After discussing potential issues regarding the comparability between experiments, we propose criteria that need to be critically evaluated to identify important signaling RNAs.

现在有大量的数据,来自不同的植物和实验室,跨越二十多年,明确表明rna可以远距离运输,从它们转录的细胞到其他组织中的远端细胞。不同类型的RNA分子被运输,包括微RNA和信使RNA。总的来说,这些rna是否被选择进行转运,如果是这样,它们是如何被选择和转运的,仍然是一个悬而未决的问题。这方面可能不是独立于转运rna的生物学功能和相关性,这在大多数情况下仍不清楚。本文综述了支持RNA易位选择性或非选择性的实验数据,并对其生物学功能的证据进行了综述。在讨论了关于实验之间可比性的潜在问题之后,我们提出了需要严格评估的标准,以识别重要的信号rna。
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引用次数: 11
Plant Proteome Dynamics. 植物蛋白质组动力学。
IF 23.9 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2022-05-20 Epub Date: 2022-02-09 DOI: 10.1146/annurev-arplant-102620-031308
Julia Mergner, Bernhard Kuster

Proteins are intimately involved in executing and controlling virtually all cellular processes. To understand the molecular mechanisms that underlie plant phenotypes, it is essential to investigate protein expression, interactions, and modifications, to name a few. The proteome is highly dynamic in time and space, and a plethora of protein modifications, protein interactions, and network constellations are at play under specific conditions and developmental stages. Analysis of proteomes aims to characterize the entire protein complement of a particular cell type, tissue, or organism-a challenging task, given the dynamic nature of the proteome. Modern mass spectrometry-based proteomics technology can be used to address this complexity at a system-wide scale by the global identification and quantification of thousands of proteins. In this review, we present current methods and technologies employed in mass spectrometry-based proteomics and provide examples of dynamic changes in the plant proteome elucidated by proteomic approaches.

蛋白质密切参与执行和控制几乎所有的细胞过程。为了了解植物表型的分子机制,有必要研究蛋白质表达、相互作用和修饰等。蛋白质组在时间和空间上是高度动态的,在特定的条件和发育阶段,大量的蛋白质修饰、蛋白质相互作用和网络星座在起作用。蛋白质组学分析的目的是表征特定细胞类型、组织或生物体的整个蛋白质补体——鉴于蛋白质组学的动态特性,这是一项具有挑战性的任务。现代基于质谱的蛋白质组学技术可以通过对数千种蛋白质的全球鉴定和定量,在全系统范围内解决这种复杂性。在这篇综述中,我们介绍了目前基于质谱的蛋白质组学的方法和技术,并提供了用蛋白质组学方法阐明植物蛋白质组的动态变化的例子。
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引用次数: 14
Engineering Apomixis: Clonal Seeds Approaching the Fields. 工程无杂交:无性系种子接近田间。
IF 23.9 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2022-05-20 Epub Date: 2022-02-09 DOI: 10.1146/annurev-arplant-102720-013958
Charles J Underwood, Raphael Mercier

Apomixis is a form of reproduction leading to clonal seeds and offspring that are genetically identical to the maternal plant. While apomixis naturally occurs in hundreds of plant species distributed across diverse plant families, it is absent in major crop species. Apomixis has a revolutionary potential in plant breeding, as it could allow the instant fixation and propagation though seeds of any plant genotype, most notably F1 hybrids. Mastering and implementing apomixis would reduce the cost of hybrid seed production, facilitate new types of hybrid breeding, and make it possible to harness hybrid vigor in crops that are not presently cultivated as hybrids. Synthetic apomixis can be engineered by combining modifications of meiosis and fertilization. Here, we review the current knowledge and recent major achievements toward the development of efficient apomictic systems usable in agriculture.

无融合生殖是一种生殖形式,导致克隆种子和后代在遗传上与母株相同。虽然无融合性自然存在于分布在不同植物科的数百种植物中,但在主要作物物种中却不存在。无融合在植物育种中具有革命性的潜力,因为它可以通过任何植物基因型的种子进行即时固定和繁殖,尤其是F1杂交种。掌握和实施无融合生殖将降低杂交种子生产的成本,促进新型杂交育种,并使利用目前未作为杂交作物的杂交活力成为可能。合成无融合可以通过减数分裂和受精的结合来实现。在这里,我们回顾了目前的知识和最近的主要成就,朝着发展高效的无杂交系统可用于农业。
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引用次数: 15
Phloem Loading and Unloading of Sucrose: What a Long, Strange Trip from Source to Sink. 蔗糖韧皮部的装载和卸载:从源头到汇的漫长而奇怪的旅程。
IF 23.9 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2022-05-20 Epub Date: 2022-02-16 DOI: 10.1146/annurev-arplant-070721-083240
David M Braun

Sucrose is transported from sources (mature leaves) to sinks (importing tissues such as roots, stems, fruits, and seeds) through the phloem tissues in veins. In many herbaceous crop species, sucrose must first be effluxed to the cell wall by a sugar transporter of the SWEET family prior to being taken up into phloem companion cells or sieve elements by a different sugar transporter, called SUT or SUC. The import of sucrose into these cells is termed apoplasmic phloem loading. In sinks, sucrose can similarly exit the phloem apoplasmically or, alternatively, symplasmically through plasmodesmata into connecting parenchyma storage cells. Recent advances describing the regulation and manipulation of sugar transporter expression and activities provide stimulating new insights into sucrose phloem loading in sources and unloading processes in sink tissues. Additionally, new breakthroughs have revealed distinct subpopulations of cells in leaves with different functions pertaining to phloem loading. These and other discoveries in sucrose transport are discussed.

蔗糖通过静脉的韧皮部组织从来源(成熟的叶子)运输到汇(进口组织,如根、茎、果实和种子)。在许多草本作物物种中,蔗糖必须首先由SWEET家族的糖转运蛋白外排到细胞壁,然后再由另一种称为SUT或SUC的糖转运蛋白进入韧皮部伴细胞或筛元。蔗糖进入这些细胞的过程称为胞浆韧皮部负荷。在汇中,蔗糖同样可以从韧皮部胞浆排出,或者通过胞间连丝进入连接薄壁储存细胞的共浆排出。最近的研究进展描述了糖转运蛋白表达和活性的调控和操纵,为糖源组织韧皮部的负荷和卸载过程提供了新的见解。此外,新的突破揭示了叶片中具有不同功能的细胞亚群与韧皮部负荷有关。本文讨论了蔗糖转运中的这些发现和其他发现。
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引用次数: 35
Spatial Features and Functional Implications of Plant 3D Genome Organization. 植物三维基因组组织的空间特征及其功能意义
IF 23.9 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2022-05-20 Epub Date: 2022-02-07 DOI: 10.1146/annurev-arplant-102720-022810
Katherine Domb, Nan Wang, Guillaume Hummel, Chang Liu

The advent of high-throughput sequencing-based methods for chromatin conformation, accessibility, and immunoprecipitation assays has been a turning point in 3D genomics. Altogether, these new tools have been pushing upward the interpretation of pioneer cytogenetic evidence for a higher order in chromatin packing. Here, we review the latest development in our understanding of plant spatial genome structures and different levels of organization and discuss their functional implications. Then, we spotlight the complexity of organellar (i.e., mitochondria and plastids) genomes and discuss their 3D packing into nucleoids. Finally, we propose unaddressed research axes to investigate functional links between chromatin-like dynamics and transcriptional regulation within organellar nucleoids.

基于高通量测序的染色质构象、可及性和免疫沉淀测定方法的出现是3D基因组学的一个转折点。总的来说,这些新工具已经推动了对染色质包装更高阶的先驱细胞遗传学证据的解释。本文综述了植物空间基因组结构和不同层次组织的最新进展,并讨论了它们的功能意义。然后,我们聚焦细胞器(即线粒体和质体)基因组的复杂性,并讨论它们的三维包装成类核。最后,我们提出了未解决的研究轴,以研究细胞器类核内染色质样动力学和转录调控之间的功能联系。
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引用次数: 7
Adventures in Life and Science, from Light to Rhythms. 生命与科学的冒险,从光到节奏。
IF 23.9 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2022-05-20 Epub Date: 2022-02-07 DOI: 10.1146/annurev-arplant-090921-091346
Elaine Tobin

The author describes her life's pathway from her beginnings at a time when women were not well represented in the sciences. Her grandparents were immigrants to the United States. Although her parents were not able to go to college because of the Great Depression, they supported her education and other adventures. In addition to her interest in science, she describes her interest and involvement in politics. Her education at Oberlin, Stanford, and Harvard prepared her for her independent career at the University of California, Los Angeles, where she was an affirmative action appointment. Her research initially centered on the plant photoreceptor phytochrome, but later in her career she investigated circadian rhythms in plants, discovering and characterizing one of the members of the central oscillator.

作者描述了她的人生之路,从她开始的时候,女性在科学中没有很好的代表。她的祖父母是移民到美国的。虽然由于大萧条,她的父母没能上大学,但他们支持她的教育和其他冒险。除了对科学的兴趣,她还描述了自己对政治的兴趣和参与。她在奥伯林大学、斯坦福大学和哈佛大学所受的教育为她在加州大学洛杉矶分校的独立职业生涯做好了准备,在那里她获得了平权法案的任命。她的研究最初集中在植物光感受器光敏色素上,但后来在她的职业生涯中,她研究了植物的昼夜节律,发现并描述了中央振荡器的一个成员。
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引用次数: 1
VIGS Goes Viral: How VIGS Transforms Our Understanding of Plant Science. VIGS病毒:VIGS如何改变我们对植物科学的理解。
IF 23.9 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2022-05-20 Epub Date: 2022-02-09 DOI: 10.1146/annurev-arplant-102820-020542
Clemens Rössner, Dominik Lotz, Annette Becker

Virus-induced gene silencing (VIGS) has developed into an indispensable approach to gene function analysis in a wide array of species, many of which are not amenable to stable genetic transformation. VIGS utilizes the posttranscriptional gene silencing (PTGS) machinery of plants to restrain viral infections systemically and is used to downregulate the plant's endogenous genes. Here, we review the molecular mechanisms of DNA- and RNA-virus-based VIGS, its inherent connection to PTGS, and what is known about the systemic spread of silencing. Recently, VIGS-based technologies have been expanded to enable not only gene silencing but also overexpression [virus-induced overexpression (VOX)], genome editing [virus-induced genome editing (VIGE)], and host-induced gene silencing (HIGS). These techniques expand the genetic toolbox for nonmodel organisms even more. Further, we illustrate the versatility of VIGS and the methods derived from it in elucidating molecular mechanisms, using tomato fruit ripening and programmed cell death as examples. Finally, we discuss challenges of and future perspectives on the use of VIGS to advance gene function analysis in nonmodel plants in the postgenomic era.

病毒诱导的基因沉默(VIGS)已经发展成为一种不可缺少的基因功能分析方法,用于广泛的物种,其中许多物种不适合稳定的遗传转化。VIGS利用植物的转录后基因沉默(PTGS)机制来系统性地抑制病毒感染,并用于下调植物的内源基因。在这里,我们回顾了基于DNA和rna病毒的VIGS的分子机制,它与PTGS的内在联系,以及已知的沉默的系统性传播。最近,基于vigs的技术已经扩展到不仅可以实现基因沉默,还可以实现过表达[病毒诱导的过表达(VOX)]、基因组编辑[病毒诱导的基因组编辑(VIGE)]和宿主诱导的基因沉默(HIGS)。这些技术进一步扩展了非模式生物的基因工具箱。此外,我们以番茄果实成熟和程序性细胞死亡为例,说明了VIGS的多功能性及其在阐明分子机制方面的衍生方法。最后,我们讨论了利用VIGS在后基因组时代推进非模式植物基因功能分析的挑战和未来前景。
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引用次数: 20
期刊
Annual review of plant biology
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