植物蛋白互作网络图
一个国际研究小组对拟南芥细胞中上千个蛋白质之间互作进行绘图和分析，拟南芥在植物生理的研究地位如同实验小鼠在人体生理的研究地位。
Salk研究所植物学家 Joseph Ecker 称，在这项研究中，我们设法为科学家提供蛋白互作的双重数据，这些数据连同将来的蛋白互作组图谱组成一个信息库，生物学家可利用这些信息使得农业作物具有更高的抗旱性、抗病性；也使得农业作物更富有营养和对人类的益处更大。
这一研究项目为期4年，由美国国家科学基金会National Science Foundation 资助800万美元。
研究负责人Marc Vidal 称，这是一个很契合的协助，Joe 和他的同事在Salk 研究所已经对拟南芥基因组测序，并克隆出一些编码蛋白的基因，而我们在Dana Farber 研究所研究了其他生物（如酵母菌）的蛋白互作图谱。
在项目的起始阶段，技术员Mary Galli将储存的拟南芥编码蛋白的基因克隆转化成一种适合于蛋白互作测试的形式。Galli称，10000个以上的开放阅读框（ORF）被转化，它们的序列验证后用于蛋白互作检测。
基于酵母双杂交试验的蛋白质互作检测流程对这些开放阅读框进行系统的操作。在多于40万种拟南芥蛋白结合测试中，研究人员一共发现6250个蛋白互作样本，并有2774种蛋白参与其中。他们还列举出与过去蛋白互作研究的相同点，证实这些数据的真实性和可靠性。
6205种蛋白互作样本在拟南芥完整蛋白作用谱中仅占大约2%，因为，检测试验仅覆盖拟南芥完整蛋白的1/3；由于灵敏度的原因不能检测许多较弱的蛋白作用。考虑到这些因素，更大的蛋白作用图谱将会出现。
即便作为起始步骤，这一新图谱还是很有用处的。研究人员把互作蛋白分类到功能组中用于揭示协同作用蛋白的网络。Ecker 称，我们知道的信息很少，如植物中不同激素信号通路是如何交流的，但是，这项研究帮助我们发现一些通路之间的链接。
对蛋白图谱的进一步分析得到植物进化的新认识。研究人员发现，1900对互作蛋白可能是原始基因拷贝扩增的产物；拟南芥基因组数据表明植物基因的随机拷贝数比动物的多，这些基因拷贝使得植物具有适应环境变化的遗传多样性。
通过先进的基因组测年技术，研究人员能够算出单一基因拷贝扩增事件的时间跨度，并在基因拷贝扩增和结合蛋白成分更换的方面进行比较。Vidal 称，这些信息让我们能估测进化过程中这些蛋白的功能如何串并在一起，这些第一手的分析借助了拟南芥中大量的、高质量的数据集以及（自然条件下）基因拷贝的高频率扩增。
研究人员发现，拷贝扩增事件发生后，拟南芥蛋白的结合关系变化很快。随着拷贝基因参与新的生理功能后，这种结合关系的变化逐渐变慢，直至在进化压力条件下固定下来。Vidal 称，即便这些蛋白质的氨基酸序列继续保持歧化，蛋白结合关系的歧化经历初始快速变化之后大幅变慢，这是我们没有预料到的。
Ecker和他的同事希望，这项研究在认识植物生理学方面标志着快速进步时期的到来，Ecker 称，我们可以从系统的视角下观察拟南芥是如何行使生理功能的，这些认识其中一大部分也适用于其它植物物种，包括农作物和药用的植物。
20多个国立和国际实验室组成“拟南芥蛋白互作组图谱联盟”，经费由美国国家科学基金会和美国国立卫生研究院资助。（生物探索译 Pobee）
生物探索推荐英文原文
Largest-Ever Map of Plant Protein Interactions
An international team of scientists has described their mapping and early analyses of thousands of protein-to-protein interactions within the cells of Arabidopsis thaliana -- a variety of mustard plant that is to plant biology what the lab mouse is to human biology.
"With this one study we managed to double the plant protein-interaction data that are available to scientists," says Salk Institute plant biologist Joseph Ecker, a professor in the Plant Molecular and Cellular Biology Laboratory. "These data along with data from future 'interactome' mapping studies like this one should enable biologists to make agricultural plants more resistant to drought and diseases, more nutritious, and generally more useful to mankind."
The four-year project was funded by an $8 million National Science Foundation grant, and was headed by Marc Vidal, Pascal Braun, David Hill and colleagues at the Dana Farber Cancer Institute in Boston; and Ecker at the Salk Institute. "It was a natural collaboration," says Vidal, "because Joe and his colleagues at the Salk Institute had already sequenced the Arabidopsis genome and had cloned many of the protein-coding genes, whereas on our side at the Dana Farber Institute we had experience in making these protein interaction maps for other organisms such as yeast."
In the initial stages of the project, members of Ecker's lab led by research technician Mary Galli converted most of their accumulated library of Arabidopsis protein-coding gene clones into a form useful for protein-interaction tests. "For this project, over 10,000 'open reading frame' clones were converted and sequence verified in preparation for protein-interaction screening," says Galli.
Vidal, Braun, Hill and their colleagues systematically ran these open reading frames through a high quality protein-interaction screening process, based on a test known as the yeast two-hybrid screen. Out of more than forty million possible pair combinations, they found a total of 6,205 Arabidopsis protein- protein interactions, involving 2,774 individual proteins. The researchers confirmed the high quality of these data, for example by showing their overlap with protein interaction datafrom past studies.
The new map of 6,205 protein partnerings represents only about two percent of the full protein- protein "interactome" for Arabidopsis, since the screening test covered only a third of all Arabidopsis proteins, and wasn't sensitive enough to detect many weaker protein interactions. "There will be larger maps after this one," says Ecker.
Even as a preliminary step, though, the new map is clearly useful. The researchers were able to sort the protein interaction pairs they found into functional groups, revealing networks and "communities" of proteins that work together. "There had been very little information, for example, on how plant hormone signaling pathways communicate with one another," says Ecker. "But in this study we were able to find a number of intriguing links between these pathways."
A further analysis of their map provided new insight into plant evolution. Ecker and colleagues Arabidopsis genome data, reported a decade ago, had revealed that plants randomly duplicate their genes to a much greater extent than animals do. These gene duplication events apparently give plants some of the genetic versatility they need to stay adapted to shifting environments. In this study, the researchers found 1900 pairs of their mapped proteins that appeared to be the products of ancient gene-duplication events.
Using advanced genomic dating techniques, the researchers were able to gauge the span of time since each of these gene-duplication events -- the longest span being 700 million years -- and compare it with the changes in the two proteins' interaction partners. "This provides a measure of how evolution has rewired the functions of these proteins," says Vidal. "Our large, high-quality dataset and the naturally high frequency of these gene duplications in Arabidopsis allowed us to make such an analysis for the first time."
The researchers found evidence that the Arabidopsis protein partnerships tend to change quickly after the duplication event, then more slowly as the duplicated gene settles into its new function and is held there by evolutionary pressure. "Even though the divergence of these proteins' amino-acid sequences may continue, the divergence in terms of their respective partners slows drastically after a rapid initial change, which we hadn't expected to see," Vidal says.
In the July 29 issue of Science researchers from the Arabidopsis interactome mapping study reported yet another demonstration of the usefulness of their approach. Led by Jeffery L. Dangl of the University of North Carolina at Chapel Hill, they examined Arabidopsis protein interactions with the bacterium Pseudomonas syringae (Psy) and a fungus-like microbe called Hyaloperonospora arabidopsidis (Hpa). "Even though these two pathogens are separated by about a billion years of evolution, it turns out that the 'effector' proteins they use to subvert Arabidopsis cells during infection are both targeted against the same set of highly connected Arabidopsis proteins," says Ecker. "We looked at some of these targeted Arabidopsis proteins and found evidence that they serve as 'hubs' or control points for the plant immune system and related systems."
Ecker and his colleagues hope that these studies mark the start of a period of rapid advancement in understanding plant biology, and in putting that knowledge to use for human benefit. "This starts to give us a big, systems-level picture of how Arabidopsis works, and much of that systems-level picture is going to be relevant to -- and guide further research on -- other plant species, including those used in human agriculture and even pharmaceuticals,"Ecker says.
The "Arabidopsis Interactome Mapping Consortium" consists of over 20 national and international laboratories that contribute to this study with support from a number of funding agencies including the National Science Foundation and the National Institutes of Health.
