CAREER: Evolutionary Genomics of Enzymes for Complex Carbohydrate Metabolism

该项目旨在研究驱动碳水化合物产生和分解的核心酶。这些酶称为碳水化合物活性酶 (CAZymes)，存在于所有生物体中，特别是植物和与植物相关的微生物中。植物细胞壁中发现的复杂碳水化合物是地球上最丰富、可再生的有机材料。如果我们有有效的系统将它们转化为生物材料和生物燃料，它们将成为生物制造项目有吸引力的目标。对自然界的重要影响是 (i) 植物微生物病原体产生的 CAZymes 导致植物细胞壁破裂，导致毁灭性的农作物损失（美国和加拿大每年损失 50 亿美元），以及 (ii) 动物肠道中的细菌产生数百种 CAZymes 来消化饮食中的碳水化合物，其中一些可能对宿主产生积极的影响，而另一些则可能产生有毒的影响。研究方法结合了基因组学和生物信息学：对绿藻的基因组进行测序，然后使用生物信息学工具进行数据分析。这种绿藻是所有陆地植物的共同祖先，其基因组与植物的基因组相比将显示进化如何改变核心碳水化合物化学以应对不断变化的环境挑战。这些酶的生物工程很可能有助于美国发展更可持续和更安全的生物经济（例如生物能源和农业），作为全球基因组市场的一部分，预计到 2020 年该市场的价值将达到 200 亿美元。在该项目中接受培训的学生将成为下一代科学家，能够利用他们对比较基因组序列分析的理解来创造新的理解和新颖的应用。该项目的教育和推广目标是让学生积极参与包括数据分析在内的研究活动，并培训本科生和 K-12 科学教师了解基因组测序和比较方法的基础知识，包括实践技能。在第一个目标中，将开发新的生物信息学程序，以允许对预测的生化活性进行深入的 CAZyme 注释。在第二个目标中，将在各种生态环境的微生物基因组和宏基因组中研究 CAZymes 的基因组背景。总共将开发、集成四种计算工具，并作为名为 dbCAN2 的 CAZyme 生物信息学门户网站提供。这些免费的在线工具将促进 CAZyme 在基因组学、碳水化合物、生物能源、植物病害、食品安全、人类肠道微生物组、进化和生态学等各个研究领域的研究。在第三个目标中，该项目将对藻类和早期植物的基因组和转录组进行测序和挖掘，以用于 CAZymes。这包括对绿藻 Zygnemacircirinatum 的基因组和转录组进行测序，绿藻是所有陆地植物的直接祖先，对于了解富含碳水化合物的细胞壁的早期进化至关重要。具体教育活动包括：(i) 与北伊利诺伊大学学生参与和体验式学习办公室 (OSEEL) 合作，让本科生，特别是代表性不足的少数族裔学生参与 CAZyme 生物信息学研究； (ii) 与NIU中学科学教师教育中心合作，将DNA测序和数据分析主题纳入教师执照计划的课程以及K-12科学教师的专业发展计划； (iii) 将 Zygnema 基因组注释作为新的实验室组件纳入 BIOS308（遗传学）和 BIOS441（实用生物信息学）。该项目的研究成果将在以下网址发布：http://cys.bios.niu.edu/dbCAN2/。

This project intends to study the core enzymes that drive the production and breakdown of carbohydrates. These enzymes, called the carbohydrate active enzymes (CAZymes), are found in all living organisms and particularly in plants and plant-associated microbes. The complex carbohydrates found in plant cell walls are the most abundant, and renewable, organic material on Earth. If we had efficient systems to convert them to biomaterials and biofuels they would be attractive targets for bio-manufacturing projects. Important effects in the natural world are (i) the CAZymes produced by plant microbial pathogens cause plant cell wall breakdown leading to devastating crop loss ($5 billion in the United States and Canada each year) and (ii) bacteria in animal guts produce hundreds of CAZymes that digest the carbohydrates in the diet, some of which may have positive, and others toxic, consequences to the host. The research approach combines genomics and bioinformatics: the genome of a green algae will be sequenced and then bioinformatics tools will be used to carry out data analysis. This green algae is the common ancestor of all land plants, its genome compared to those of plants will show how evolution has modified core carbohydrate chemistry to meet changing environmental challenges. Bioengineering of these enzymes may well contribute to the development of a more sustainable and secure bioeconomy (e.g., bioenergy and agricultural industries) in the US, as part of the global Genomics market, whose value is expected to reach $20 billion by 2020. Students trained in the course of this project will be poised to become the next generation of scientists, able to exploit their understanding of comparative genome sequence analysis to create new understanding and novel applications. The educational and outreach objectives of this project are to engage students as active participants in the research activities, including data analysis, and to to train undergraduate students and K-12 Science teachers to understand the basics of genome sequencing and comparison methods, including hands-on skills. In the first Aim, new bioinformatics programs will be developed to allow in-depth CAZyme annotation with predicted biochemical activities. In the second Aim, the genomic context of CAZymes will be studied in microbial genomes and metagenomes of various ecological environments. Overall four computational tools will be developed, integrated, and delivered as a CAZyme bioinformatics web portal named dbCAN2. These free online tools will facilitate CAZyme research in various research fields such as genomics, carbohydrate, bioenergy, plant disease, food security, human gut microbiome, evolution and ecology. In the third Aim, this project will sequence and mine the genomes and transcriptomes of algae and early plants for CAZymes. This includes sequencing the genome and transcriptome of a green alga Zygnema circumcarinatum, the immediate ancestor of all land plants that is extremely critical for understanding the early evolution of carbohydrate-rich cell walls. The specific education activities include: (i) working with the Office of Student Engagement and Experiential Learning (OSEEL) of Northern Illinois University to bring undergraduate students, particularly under-represented minority students, into CAZyme bioinformatics research; (ii) collaborating with the Center for Secondary Science Teacher Education of NIU to integrate DNA sequencing and data analysis topics into the curriculum of the Teacher Licensure Program as well as the professional development programs for K-12 Science teachers; and (iii) incorporating Zygnema genome annotation as new lab components into BIOS308 (Genetics) and BIOS441 (Practical Bioinformatics). Research products of this project will be disseminated at: http://cys.bios.niu.edu/dbCAN2/.