Update on Legume Transcription Factors Legume Transcription Factor Genes : What Makes Legumes-猫眼课题宝

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2009

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作者：

Marc Libault;T. Joshi;V. Benedito;Dong Xu;M. Udvardi;G. Stacey

所有真核生物都具有多种转录因子 (TF) 基因家族，编码调节基因表达的关键蛋白质。 TF 家族在真核生物（尤其是植物）中高度保守。这些 TF 基因中的每一个的特定功能都令人感兴趣，因为它们在控制植物发育过程和对环境条件的反应中发挥作用，包括对农艺性能至关重要的功能。在这篇综述中，我们重点关注 TF 基因在豆科植物中的作用。该综述还提供了几种真核生物中 TF 基因的鉴定和分类的最新信息，包括三个部分或完全测序的豆科植物基因组（大豆 [Glycine max]、Medicago truncatula 和 Lotus japonicus）。基于 TF 基因分布和从大量豆科植物 TF 基因获得的直接实验数据的综合比较，在进化背景下讨论了 TF 基因在豆科植物中的作用。 TF 基因存在于所有真核生物门中。它们编码与基因组 DNA 启动子和增强子序列相互作用的调节蛋白。这些相互作用促进近端基因的转录激活或抑制，并使细胞能够对其环境的变化（例如生物和非生物胁迫）做出反应，调节细胞周期，并且在最复杂的生物体的情况下，控制细胞命运。正如 Carroll (2001) 所提到的，调节蛋白数量和相互作用的扩展，以及它们的空间和时间表达的变化，是导致生物体日益复杂的进化过程的一部分。因此，确定基因组中 TF 基因的组成、其表达调控及其生化特性（即 DNA 和蛋白质结合亲和力）对于理解 TF 调控网络和生物体进化非常重要。与动物相比，植物的不动性是一个主要缺点，动物可以逃避许多环境攻击。面对环境挑战的能力意味着植物必须拥有复杂的调节系统才能做出适当的反应。这有时涉及改变发育程序，这是由植物维持活跃的干细胞（称为分生组织）这一事实所促进的，分生组织可以根据环境和内源线索分化并发育成各种器官。作为转录调节因子，转录因子在帮助植物应对和应对环境挑战方面发挥着重要作用。因此，植物比动物拥有更多的 TF 基因也就不足为奇了（Riechmann et al., 2000；本研究）。大多数现有的植物TF基因知识都是从植物生物学中主要遗传模型拟南芥（Arabidopsis thaliana）的研究中获得的。然而，虽然拟南芥是所有高等植物共有的许多发育和其他过程的有用模型，但它缺乏某些对农业具有巨大价值的性状，例如与根瘤菌形成固氮共生体以及与菌根真菌形成土壤养分清除共生体的能力。另一方面，豆类能够建立这种有益的共生关系，因此数千年来一直是可持续农业的支柱。豆科植物包括重要的食用植物，如菜豆 (Phaseolus vulgaris)、大豆和豌豆 (Pisum sativum)，以及重要的饲料物种，如苜蓿 (Medicago sativa) 和三叶草 (Trifolium spp.)。人们对使用豆类作为生物燃料生产的生物质来源也越来越感兴趣。尽管菌根共生在植物科中广泛存在，约占所有物种的 90%，但共生固氮 (SNF) 仅限于豆科植物和少数非豆科植物。这使得豆类变得特殊，但 SNF 是如何在豆类中进化的仍然很大程度上未知。这个问题的答案可能来自豆类和非豆类基因组的比较分析。三种豆科植物（L. japonicus (http://www.kazusa.or.jp/lotus)、大豆 (http://www.phytozome.net/soybean) 和 M. truncatula (http://www.medicago.org/genome)）的基因组测序已接近完成，并且几种豆科植物的基因组测序已接近完成。非豆科植物，包括拟南芥（Arabidopsis Ge1）这项工作得到了美国国家科学基金会植物基因组计划（授权号 DBI-0421620）的支持。*通讯作者；电子邮件 staceyg@missouri.edu。根据作者须知 (www.plantphyol.org) 中描述的政策，负责分发本文研究结果的材料的作者是：加里·史黛西（staceyg@missouri.edu）。 [W] 本文的在线版本包含仅限网络的数据。 www.plantphyol.org/cgi/doi/10.1104/pp.109.144105

All eukaryotic organisms have a diversity of transcription factor (TF) gene families, encoding key proteins regulating gene expression. TF families are strongly conserved across eukaryotic organisms, especially plants. The specific function of each of these TF genes is of interest due to their role in controlling plant developmental processes and responses to environmental conditions, including functions of key importance to agronomic performance. In this review, we focus on the role of TF genes in legume species. The review also provides an update on the identification and categorization of TF genes in several eukaryotes, including three partially or completely sequenced legume genomes (soybean [Glycine max], Medicago truncatula, and Lotus japonicus). The role of TF genes in legumes is discussed in an evolutionary context based upon a comprehensive comparison of TF gene distribution and direct experimental data obtained for a significant number of legume TF genes. TF genes are present in all eukaryotic phyla. They encode regulatory proteins that interact with genomic DNA promoter and enhancer sequences. These interactions facilitate the transcriptional activation or repression of proximal genes and enable cells to respond to changes in their environment (e.g. biotic and abiotic stresses), to regulate the cell cycle, and, in the case of the most complex organisms, to control cell fate. As mentioned by Carroll (2001), the expansion of regulatory protein numbers and interactions, as well as changes to their spatial and temporal expression, is part of the evolutionary process leading to increasingly complex organisms. Therefore, determining the repertoire of TF genes in genomes, the regulation of their expression, and their biochemical properties (i.e. DNAand protein-binding affinities) is important to the understanding of TF regulatory networks and organism evolution. The immobile nature of plants represents a major disadvantage compared with animals, which can flee many environmental assaults. The ability to face environmental challenges implies that plants must possess complex regulatory systems to respond appropriately. This sometimes involves changing developmental programs, which is facilitated by the fact that plants maintain active stem cells, called meristems, which can differentiate and develop into various organs depending on environmental and endogenous cues. As regulators of transcription, TFs play important roles in helping plants meet and master environmental challenges. Therefore, it is not surprising that plants have more TF genes than animals (Riechmann et al., 2000; this study). Most of the extant knowledge of plant TF genes was obtained from studies of the major genetic model in plant biology, Arabidopsis (Arabidopsis thaliana). However, while Arabidopsis is a useful model for many developmental and other processes common to all higher plants, it lacks certain traits that are of immense value to agriculture, such as the ability to form nitrogen-fixing symbioses with rhizobia and soil nutrient-scavenging symbioses with mycorrhizal fungi. Legumes, on the other hand, are able to establish such beneficial symbioses and, as a result, have been mainstays for sustainable agriculture for thousands of years. The legume family includes important food plants such as common bean (Phaseolus vulgaris), soybean, and pea (Pisum sativum) and important forage species such as alfalfa (Medicago sativa) and clover (Trifolium spp.). There is also growing interest in the use of legumes as a source of biomass for biofuel production. Although mycorrhizal symbioses are widespread among plant families, occurring in approximately 90% of all species, symbiotic nitrogen fixation (SNF) is restricted to legumes and a few nonlegume families. This makes legumes special, but just how SNF evolved in legumes remains largely unknown. Answers to this question may emerge from comparative analysis of the genomes of legumes and nonlegumes. Genome sequencing of three legume species, L. japonicus (http://www.kazusa.or.jp/lotus), soybean (http://www.phytozome.net/soybean), and M. truncatula (http://www.medicago.org/genome), is nearing completion, and the genome sequences of several nonlegumes, including Arabidopsis (Arabidopsis Ge1 This work was supported by the National Science Foundation Plant Genome Program (grant no. DBI–0421620). * Corresponding author; e-mail staceyg@missouri.edu. The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantphysiol.org) is: Gary Stacey (staceyg@missouri.edu). [W] The online version of this article contains Web-only data. www.plantphysiol.org/cgi/doi/10.1104/pp.109.144105

Update on Legume Transcription Factors Legume Transcription Factor Genes : What Makes Legumes

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