A Systems Approach to the Development and Function of C4 Photosynthesis

PI: Timothy Nelson（耶鲁大学）合作PI: Thomas Brutnell和Todd Mockler（丹佛斯植物科学中心）；刘鹏（爱荷华州立大学）；克里斯·迈尔斯、罗伯特·特金、孙琦和克拉斯·范·维克（康奈尔大学）；与水稻和小麦等c3型植物相比，玉米等c4型植物和几种有前景的生物燃料原料具有更有效的碳固定、水和氮利用以及在高温和光照强度下的表现。赋予这些C4优势的特征是：(1)两种不同的光合细胞类型（叶肉细胞和束鞘细胞）合作进行碳固定和光合作用，(2)合作细胞之间代谢物的运动增强，(3)叶片脉化密度高。这些C4性状是由已经存在于效率较低的C3植物中的遗传资源产生的，但以更有效的模式进行调节。尽管C4植物已经在不同的分类类群中独立进化了至少50次，但对更有效的C4调控系统的分子基础了解不足，无法将其优势扩展到其他作物和生物燃料原料。对玉米（C4）和水稻（C3）叶片相应发育阶段的rna、蛋白质、代谢物、解剖学和生理学的系统水平分析已经确定了产生C4性状的许多分子资源。研究还表明，需要更多的关于小调控rna、细胞类型之间的表观遗传差异、蛋白质修饰和其他一些“数据通道”的相应数据来了解这些性状的产生和调控。此外，需要更复杂的计算方法来整合产生复杂性状的RNA、蛋白质、解剖和小分子信息的许多“通道”。本项目将(1)获取C4叶片发育阶段缺失的数据通道；(2)利用新颖的计算方法整合数据通道并建立可实验验证的调控网络模型；(3)通过遗传和转基因操作测试几种C4生化细胞性状的调控基础。这一分析将确定C4性状在C3物种中引入的潜在靶点。除了对C4光合作用产生实际和深刻的理解外，该项目开发的计算工具和系统资源可应用于植物发育，生物化学，生理学和生产力的其他研究。这个项目的影响将通过小说BrachyBio！外展计划（http://bti.cornell.edu/brachybio），向高中学生介绍真实的植物遗传学研究，同时为植物研究界提供一个可访问的短尾草（Brachypodium distachyon, C3）和狗尾草（Setaria viridis, C4）的索引突变种群的网络集合。项目成果将通过项目特定的公共网站（C3-C4DB, http://c3c4.tc.cornell.edu）公布，并编入Gramene公共数据库（http://www.gramene.org）。数据也将存放在NIH NCBI和欧洲生物信息学研究所（EBI; www.ebi.ac.uk）。

PI: Timothy Nelson (Yale University)Co-PIs: Thomas Brutnell and Todd Mockler (Danforth Plant Science Center); Peng Liu (Iowa State University); Chris Myers, Robert Turgeon, Qi Sun, and Klaas van Wijk (Cornell University); and Joyce van Eck (Boyce Thompson Institute)C4-type plants such as maize and several promising biofuel feedstocks have more efficient carbon-fixation, water and nitrogen use, and performance in high temperatures and light intensities, in comparison to C3-type plants such as rice and wheat. The traits conferring these C4 advantages are (1) cooperation of two distinct photosynthetic cell types (mesophyll and bundle sheath) for carbon fixation and photosynthesis, (2) enhanced movement of metabolites between cooperating cells, and (3) high density of leaf venation. These C4 traits are produced from genetic resources already present in less-efficient C3 plants, but regulated in more efficient patterns. Although C4 plants have evolved at least 50 times independently in various taxonomic groups, the molecular basis of the more efficient C4 regulatory system is insufficiently understood to extend its advantages to other crops and biofuel feedstocks. A systems-level analysis of RNAs, proteins, metabolites, anatomy and physiology of corresponding developmental stages of maize (C4) and rice (C3) leaves has identified many of the molecular resources that produce the C4 traits. It has also revealed that additional corresponding data about small regulatory RNAs, epigenetic differences among cell types, protein modifications and several other "data channels" are needed to understand the production and regulation of these traits. In addition, more sophisticated computational approaches are needed to integrate the many "channels" of RNA, protein, anatomical and small molecule information that produce complex traits. This project will (1) obtain the missing data channels for C4 leaf developmental stages (2) utilize novel computational approaches for the integration of data channels and the modeling of regulatory networks that can be tested experimentally, and (3) test the regulatory basis for several C4 biochemical cellular traits by genetic and transgenic manipulation. This analysis will identify the regulatory points that are potential targets for the introduction of C4 traits in C3 species. Beyond producing a practical and profound understanding of C4 photosynthesis, the computational tools and systems resources developed by this project can be applied to other studies of plant development, biochemistry, physiology and productivity.The impact of this project will be broadened through the novel BrachyBio! Outreach Program (http://bti.cornell.edu/brachybio), which introduces high school students to authentic plant genetics research, while providing the plant research community with a web-accessible collection of indexed mutant stocks of Brachypodium distachyon (C3) and Setaria viridis (C4). Project outcomes will be available through a project-specific public website (C3-C4DB, http://c3c4.tc.cornell.edu), and curated into the Gramene public database (http://www.gramene.org). Data will also be deposited at the NIH NCBI and the European Bioinformatics Institute (EBI; www.ebi.ac.uk).