EAGER: Paleontological Proteomics Initiative: Developing Theory and Applications in Molecular Paleontology

EAGER：古生物学蛋白质组学计划：发展分子古生物学的理论和应用

• 批准号: 1547414
• 负责人: Ross MacPhee
• 金额: $ 28.38万
• 依托单位: American Museum Natural History
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-08-01 至 2022-01-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1547414&HistoricalAwards=false
• 关键词: EAGER; Paleontological; Proteomics; Initiative; Developing

Molecular paleontology is a new field that uses information derived from biological molecules (biomolecules) to make inferences about evolutionary relationships, in this case for extinct organisms. During life, living things produce many kinds of biomolecules encoded by their DNA, and these may be preserved for varying lengths of time after the organism's death. Proteins, for example, are composed of amino acids, and each amino acid is specified by a precise piece of genetic information that varies slightly from species to species within an evolutionary group. Thus, by working out a protein's amino acid composition, the genetic sequence that originally produced it can be worked out indirectly, even in the absence of the DNA itself. This is significant for paleontological research because structural proteins like collagen, which make up almost all of the organic fraction of a bone, are very hardy and can last a long time after an animal's death; at least 4 million years in favorable circumstances, and possibly much longer. DNA, by contrast, degrades over a few tens to a few hundreds of thousands of years, even in the best preservational contexts. In recent years, instrumentation and lab techniques for acquiring compositional information from ancient biomolecules have greatly improved, enabling the researchers and their interdisciplinary collaborators in geochemistry to undertake a focused range of experiments in molecular paleontology. This research will advance the field of paleo-proteomics by addressing two main goals. The first goal will be to explore the limits of the technique and identify what kinds of fossils and what types of fossil preservation conditions yield the best results for analyses of biomolecules of extinct taxa. The second goal will apply the newly developed technique to specific 'test cases' to highlight the feasibility of the methods and their generality for application to diverse questions in systematics. Molecular methods have already proven vitally important for improving knowledge of the history of life on Earth, and the researchers' work will lead to both theoretical and practical improvements in ancient proteomics. How far back in time can ancient collagen proteomics actually reach and yield high-quality sequence information useful for phylogenetic studies? What are the best targets for preservation and systematic interpretation? Proof-of-concept investigations designed to answer these questions will focus on two areas of interest. (1) To establish fundamental geochemical boundary conditions affecting collagen survival, experiments will be conducted with a physically stabilized protein (collagen in fossil bone) and a proteome with restricted reactants (eggshell proteome). Work will center on assessing thermal age and controlling for mineral diagenesis, with analysis conducted via state-of-the-art mass spectrometry and diagenetic modeling to estimate the kinetics of key decay parameters (racemization, hydrolysis, oxidation, deamidation). (2) To establish the practical value of collagen proteomics for solving systematic problems, taxa from various temporal intervals in North and South America, West Indies, Asia, and Antarctica will be sampled for phylogenetic studies using the same instrumental approach as in (1). In addition to providing phylogenetically useful information, these investigations will further extend assessment of taphonomic conditions that enhance fossil protein preservation. The overall aim is to create a network of collaborative systematic paleontologists and protein geochemists interested in joint research in areas of mutual interest.

分子古生物学是一个新领域，它使用源自生物分子（生物分子）的信息来推断进化关系，在这种情况下是灭绝生物的。在生命中，生物会产生由其DNA编码的多种生物分子，并且可以在生物体死后的不同时间内保存这些分子。例如，蛋白质由氨基酸组成，每种氨基酸都由精确的遗传信息指定，这些信息在进化组内因物种而异。因此，通过制定蛋白质的氨基酸组成，即使在没有DNA本身的情况下，最初产生的遗传序列也可以间接地进行。 这对于古生物学研究很重要，因为像胶原蛋白（几乎构成骨骼的所有有机分数）这样的结构蛋白非常耐用，并且在动物死亡后可以持续很长时间。在有利的情况下至少有400万年，甚至更长的时间。相比之下，DNA即使在最好的保存环境中，也会降解数十万到数十万年。近年来，从古代生物分子中获取构图信息的仪器和实验室技术已大大改善，使研究人员及其跨学科合作者在地球化学领域获得了一系列分子古生物学的实验范围。这项研究将通过解决两个主要目标来推进古蛋白质组学领域。第一个目标是探索该技术的局限性，并确定哪种化石以及哪种类型的化石保存条件为灭绝分类单元的生物分子分析带来了最佳结果。第二个目标将把新开发的技术应用于特定的“测试用例”，以突出该方法的可行性及其对系统学中各种问题的应用的一般性。分子方法已经被证明对于改善地球生活历史的知识至关重要，研究人员的工作将导致古代蛋白质组学的理论和实际改进。古老的胶原蛋白质组学可以真正到达多远，并产生高质量的序列信息，可用于系统发育研究？保存和系统解释的最佳目标是什么？旨在回答这些问题的概念证明调查将集中在两个感兴趣的领域上。 （1）为了建立影响胶原蛋白存活的基本地球化学边界条件，将使用物理稳定的蛋白质（化石骨中的胶原蛋白）和具有受限反应剂（蛋壳蛋白质组）的蛋白质组进行实验。工作将集中在评估矿物质成岩作用的热年龄和控制方面，并通过最先进的质谱和成岩成岩模型进行分析，以估计关键衰变参数的动力学（种族化，水解，氧化，脱氨酸）。 （2）为了确定胶原蛋白组学以解决系统问题的实用价值，将使用与（1）中相同的工具方法来对北美和南美各个时间间隔的分类单元，西印度群岛，亚洲和南极的各种时间间隔进行采样。除了提供系统发育有用的信息外，这些研究还将进一步扩大对化石蛋白保存的taphonomic条件的评估。总体目的是建立一个对有共同研究的联合研究感兴趣的合作系统古生物学家和蛋白质地球化学家的网络。