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

分子古生物学是一个新领域，它利用从生物分子（生物分子）中获得的信息来推断进化关系，在本例中是针对灭绝的生物体。在生命过程中，生物体会产生多种由 DNA 编码的生物分子，这些生物分子在生物体死亡后可能会保存不同长短的时间。例如，蛋白质是由氨基酸组成的，每个氨基酸都是由一条精确的遗传信息指定的，这些遗传信息在进化群体中的物种之间略有不同。因此，通过计算出蛋白质的氨基酸组成，即使在DNA本身不存在的情况下，也可以间接计算出最初产生该蛋白质的基因序列。 这对于古生物学研究具有重要意义，因为胶原蛋白等结构蛋白几乎构成了骨骼的所有有机部分，它们非常坚固，在动物死亡后可以保存很长时间；在有利的情况下，至少需要 400 万年，甚至可能更长。相比之下，即使在最好的保存环境下，DNA 也会在几十到几十万年的时间内降解。近年来，从古代生物分子中获取成分信息的仪器和实验室技术有了很大改进，使地球化学领域的研究人员及其跨学科合作者能够在分子古生物学领域进行一系列集中的实验。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，并确定哪种类型的化石以及哪种类型的化石保存条件可以为灭绝类群的生物分子分析提供最佳结果。第二个目标是将新开发的技术应用于特定的“测试用例”，以突出这些方法的可行性及其应用于系统学中不同问题的通用性。分子方法已被证明对于提高对地球生命历史的了解至关重要，研究人员的工作将导致古代蛋白质组学的理论和实践改进。古代胶原蛋白质组学可以追溯到多久以前，能够真正获得并产生对系统发育研究有用的高质量序列信息？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验证调查将集中在两个感兴趣的领域。 (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）和具有限制反应物的蛋白质组（蛋壳蛋白质组）进行实验。工作将集中在评估热年龄和控制矿物成岩作用，通过最先进的质谱和成岩模型进行分析，以估计关键衰变参数（外消旋、水解、氧化、脱酰胺）的动力学。 (2) 为了确定胶原蛋白质组学对于解决系统问题的实用价值，将使用与 (1) 中相同的仪器方法对来自北美和南美、西印度群岛、亚洲和南极洲不同时间间隔的类群进行采样，进行系统发育研究。除了提供系统发育上有用的信息外，这些研究还将进一步扩展对增强化石蛋白质保存的埋藏条件的评估。总体目标是建立一个由系统古生物学家和蛋白质地球化学家组成的协作网络，对共同感兴趣的领域进行联合研究。

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.