Mechanistic, Structural and Evolutionary Basis for Phenylpropanoid Metabolism

细菌和植物的苯丙类生物合成途径使人们能够研究生命系统中化学多样性出现和快速扩张背后的酶和代谢途径的进化变化。最终，这些研究将在化学水平上更好地理解控制生物多样性和生物复杂性的化学、结构和进化原理。植物和微生物等无柄生物获得并进化出被归类为次级代谢途径的专门生物合成网络，其输出是区域和立体化学复杂的小分子天然产物，包括苯丙衍生的代谢物。这些特殊代谢的化学物质在生态系统中充当化学语言，并在母体生物体上传递一种物种特有的化学“特征”。生物体获取、改进和利用各种代谢系统以产生丰富的化学复杂天然产物的手段在许多生态系统的快速扩张中起着关键作用，因此对生命多样性具有令人难以置信的适应意义。虽然看似无关紧要，但特化代谢物往往是物种内和物种间相互作用的关键媒介，导致物种形成、生存和生态稳态。在化学适应的进化约束下，与特殊代谢相关的各种分子变化通常被保存在特定物种的基因组中，并在功能和结构水平上被识别。这些通常是生态型特异性基因组是宿主生物“化学”适应特定生态位的适应度增加的直接结果。因此，这些特殊的代谢途径及其“化学输出”为我们提供了丰富的生物合成途径、天然化学物质和生物合成酶的进化记录（退化的生化特征），这些复杂的酶系统在当前具有什么适应优势（紧急功能），以及这些途径在未来可能走向的最终方向（功能可塑性）。这项研究的总体目标是绘制出在苯丙类生物合成途径中发生的适应性分子变化，因为这些酶网络在数十亿年前的初级代谢中出现并随后从其祖先根源进化而来。为了实现这些目标，这项工作涉及多学科方法，包括合成化学、蛋白质x射线晶体学、位点特异性和组合诱变、动力学分析和利用参考植物拟南芥的研究，以回答未解决的、最近发现的和意想不到的一般苯丙素生物合成途径的进化方面的问题。更广泛的影响研究活动整合了高中学生（圣地亚哥地区），教师（图森地区），本科生（加州大学圣地亚哥分校）和博士水平的科学家在最先进的多学科研究，包括结构生物学，化学，生物化学和进化生物学的培训。这项研究充分整合了这些学生的发现过程，包括共同撰写科学出版物。萨默斯将参加为期9周的亚利桑那州图森地区教师培训项目，这是他与亚利桑那大学David Gang博士合作项目的一部分。然后，这项工作将在正常学年期间扩展到课堂上，通过为高中科学课准备蛋白质结晶工具包，其中还包括选择的蛋白质样本，以潜在地解决有关蛋白质三维进化的基本问题。考虑到这一点，我们希望学生们将成为科学方法的归属，最终将导致全班共同撰写科学出版物。最后，每年至少两次，PI参加一个名为“发现的味道”的夜间公众系列研讨会。PI最近的报告侧重于植物化学生物合成的进化，为什么这项研究对陆地生命至关重要，以及人类如何利用植物和植物基化学物质来促进健康和营养。

The phenylpropanoid biosynthetic pathway of bacteria and plants allows one to study evolutionary change in enzymes and metabolic pathways underlying the emergence and rapid expansion of chemical diversity in living systems. Ultimately these studies lead to a better understanding of the chemical, structural and evolutionary tenets governing biodiversity and biocomplexity at a chemical level. Sessile organisms such as plants and microbes acquired and evolved specialized biosynthetic networks classified as secondary metabolic pathways, the output of which are regio- and stereo-chemically complex small molecule natural products including phenylpropanoid-derived metabolites. These chemicals of specialized metabolism serve as chemical languages in ecosystems and impart a species-specific chemical "signature" on the parent organism. The means by which organisms acquire, improve and exploit diverse metabolic systems to generate a rich repertoire of chemically complex natural products play key roles in the rapid expansion of many ecosystems, and therefore, hold incredible adaptive significance for the diversity of life. While seemingly insignificant, specialized metabolites often serve as key mediators of intra- and interspecies interactions resulting in speciation, survival and ecological homeostasis. Under the evolutionary restraints of chemically established adaptation, diverse molecular changes associated with specialized metabolism are often preserved genetically in a particular species' genome and are discerned at a functional and structural level. These often ecotype-specific genomes are the direct result of the increased fitness of host organisms "chemically" adapted to specific ecological niches. Therefore, these specialized metabolic pathways and their "chemical output" present us with a rich evolutionary record of where biosynthetic pathways, natural chemicals and biosynthetic enzymes have been (vestigial biochemical traits), what adaptive advantages these complex enzymatic systems hold in the present (emergent function), and ultimately where these pathways may be heading in the future (functional plasticity). The overarching goal of this research is to map the adaptive molecular changes that have occurred in the phenylpropanoid biosynthetic pathway as these enzyme networks emerged and subsequently evolved from their ancestral roots in primary metabolism billions of years ago. To accomplish these goals, the work involves a multidisciplinary approach including synthetic chemistry, protein x-ray crystallography, site-specific and combinatorial mutagenesis, kinetic assays and research using the reference plant Arabidopsis thaliana to answer unresolved, recently discovered and unexpected evolutionary aspects of the general phenylpropanoid biosynthetic pathway.Broader ImpactsThe research activities integrate the training of high school students (San Diego area), teachers (Tucson area), undergraduate students (University of California, San Diego) and PhD level scientists in state of the art multidisciplinary research including structural biology, chemistry, biochemistry and evolutionary biology. The research fully integrates these students in the discovery process that includes co-authorship on scientific publications. Summers will involve a 9-week training program for teachers in the Tucson, Arizona area as part of a collaborative program with Dr. David Gang at the University of Arizona. The work will then be extended to the classroom during the normal school year through the preparation of protein crystallization kits for high school science classes that also incorporate protein samples chosen to potentially address fundamental questions about protein evolution in three dimensions. Given this, it is hoped that the students will become vested in the scientific method that will ultimately result in the class's co-authorship on scientific publications. Finally, at least twice yearly, the PI participates in an evening seminar series for the general public called "A Taste of Discovery". The PI's most recent presentation focused on the evolution of chemical biosynthesis in plants, why this research is critical for terrestrial life and how mankind exploits plants and plant-based chemicals for health and nutrition.