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。这些酶被称为碳水化合物活性酶(CAZymes)，存在于所有活着的有机体中，特别是在植物和植物相关微生物中。在植物细胞壁中发现的复杂碳水化合物是地球上最丰富、最可再生的有机物质。如果我们有高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的诱人目标。在自然界的重要影响是(I)由植物微生物病原体产生的CAZymes导致植物细胞壁破裂，导致毁灭性的作物损失(美国和加拿大每年损失50亿美元)和(Ii)动物肠道中的细菌产生数百种CAZyme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，而另一些可能对宿主产生有毒的后果。研究方法结合了基因组学和生物信息学：将绿藻的基因组测序，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，它的基因组与植物的基因组相比将显示出进化如何改变了核心碳水化合物的化学结构，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，生物能源和农业产业)，作为全球基因组学市场的一部分，到2020年，全球基因组学市场的价值预计将达到200亿美元。在这个项目过程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的应用。该项目的教育和推广目标是使学生成为研究活动的积极参与者，包括数据分析，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，包括动手技能。在第一个目标中，将开发新的生物信息学程序，以允许用预测的生化活动对CAZyme进行深入的注释。在第二个目标中，将在不同生态环境的微生物基因组和亚基因组中研究CAZymes的基因组背景。总共将开发、集成四种计算工具，并将其作为名为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在不同研究领域的研究，如基因组学、碳水化合物、生物能源、植物疾病、食品安全、人类肠道微生物组、进化和生态学。在第三个目标中，该项目将为CAZymes测序和挖掘藻类和早期植物的基因组和转录本。这包括对绿藻Zygnema arcarinata的基因组和转录组进行测序，该绿藻是所有陆地植物的直系祖先，对于了解富含碳水化合物的细胞壁的早期进化极其关键。具体的教育活动包括：(I)与北伊利诺伊大学学生参与和体验学习办公室(OSEEL)合作，将本科生，特别是未被充分代表的少数族裔学生带入CAZyMe生物信息学研究；(Ii)与北卡罗来纳大学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；以及(Iii)将Zygnema基因组注释作为新的实验室组成部分纳入BIOS308(遗传学)和BIOS441(实用生物信息学)。该项目的研究产品将在以下网址发布：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/.