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

分子古生物学是一个新的领域，它使用来自生物分子(生物分子)的信息来推断进化关系，在这种情况下，是针对灭绝的生物。在生命过程中，生物会产生多种由DNA编码的生物分子，这些分子可能会在生物体死亡后保存不同的时间长度。例如，蛋白质是由氨基酸组成的，每个氨基酸都由一段精确的遗传信息指定，该信息在进化群体中因物种而略有不同。因此，通过计算蛋白质的氨基酸组成，即使在没有DNA本身的情况下，也可以间接地计算出最初产生蛋白质的基因序列。这对古生物学研究意义重大，因为像胶原蛋白这样的结构蛋白几乎构成了骨骼的所有有机部分，非常耐寒，可以在动物死亡后持续很长时间；在有利的环境下，至少是400万年，甚至可能更长。相比之下，DNA会在几十年到数十万年的时间里降解，即使在最好的保存环境中也是如此。近年来，从古代生物分子中获取组成信息的仪器和实验室技术有了很大的进步，使研究人员和他们在地球化学领域的跨学科合作者能够在分子古生物学方面进行一系列有针对性的实验。这项研究将通过解决两个主要目标来推动古蛋白质组学领域的发展。第一个目标将是探索这项技术的局限性，并确定哪些类型的化石和哪些类型的化石保存条件对分析已灭绝类群的生物分子产生最好的结果。第二个目标是将新开发的技术应用于具体的“测试用例”，以突出这些方法的可行性及其应用于系统学中各种问题的普遍性。分子方法已经被证明对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方面的改进。在多长时间以前，古代胶原蛋白蛋白质组实际上可以达到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(化石骨骼中的胶原)和具有限制性反应物的蛋白质组(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，通过最先进的质谱学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)为了确定胶原蛋白组学在解决系统问题中的实用价值，将从北美和南美洲、西印度群岛、亚洲和南极洲的不同时间段采集分类群，采用与(1)相同的工具方法进行系统发育研究。除了提供系统发育方面的有用信息外，这些调查还将进一步扩大对加强化石蛋白质保存的挖掘条件的评估。总的目标是建立一个合作的系统古生物学家和蛋白质地球化学家的网络，他们对共同感兴趣的领域的联合研究感兴趣。

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.