Amino Acids and Proteins in Fossil Biominerals

An Introduction for Archaeologists and Palaeontologists

Beatrice Demarchi

• Publisher: Wiley-Blackwell
• Year: 2020
• Print ISBN: 9781119089445
• eBook ISBN: 9781119089513
• Edition: 1
• Topic: Physical Sciences
• Subtopic: Geology & Earth Sciences

AMINO ACIDS AND PROTEINS IN FOSSIL BIOMINERALS

An essential cross-disciplinary guide to the proteins that form biominerals and that are preserved in the fossil record

Amino Acids and Proteins in Fossil Biominerals is an authoritative guide to the patterns of survival and degradation of ancient biomolecules in the fossil record. The author brings together new research in biomineralization and ancient proteins to describe mechanisms of protein diagenesis.

The book draws on the author's experiences as well as current information from three research fields: geochemistry, archaeology and Quaternary sciences. The author examines the history of the study of ancient proteins, from the dating of Quaternary biominerals to the present advances in shotgun proteomics, and discusses their applications across archaeology, geology and evolutionary biology.

This important guide:

• Explores the main components of biominerals
• Describes the breakdown of proteins in fossils
• Reviews the applications of ancient protein studies

Written for students and researchers of biomolecular archaeology and palaeontology, Amino Acids and Proteins in Fossil Biominerals provides a cross-disciplinary guide to the proteins responsible for the formation of biominerals and to the survival of biomolecules in the archaeological and palaeontological record.

This book forms one volume of the popular New Analytical Methods in Earth and Environmental Science Series.

1
Biominerals and the Fossil Record

1.1 Why Study Old Biominerals?

Biomineralized tissues have a good chance of surviving in the fossil record and of preserving, like a geochemical time capsule, a snapshot of the environmental conditions in which the organism (or tissue) itself was formed. This has been known since the first decades of the 20th century and is the basis for reconstructing past variations in sea temperature by measuring the stable isotopic composition of fossil biominerals (e.g. shells, foraminifera; Emiliani, 1955). Studying the way in which biominerals are formed can thus reveal important information about our planet's past. At the same time, it can teach us how to build new materials with superior characteristics (so-called biomimetic and bioinspired materials).

However, fossil biominerals can also reveal the evolutionary history of life itself. Heinz Lowenstam, an intellectual giant of biomineralization, presented his famous table of biomineralized organisms (redrawn here as Table 1.1) at the ‘Biogeochemistry of Amino Acids’ meeting at Airlie House, Warrenton, Virginia, in 1978 (Lowenstam, 1980). Observing that the evolution of biomineralized organisms has its roots in deep time (~650–550 Ma ago), and that the majority of biominerals ‘appear’ during the Cambrian ‘explosion’, he suggested that: ‘extended to the fossil record of the Phanerozoic, […] the study of the organic and bioorganic fractions [in biominerals] holds promise to trace pathways of biochemical evolution.’ Lowenstam's proposal was not without substantiation: in 1978 it had already been known for a couple of decades that organic matter could be recovered from fossils (Abelson, 1954). This is due to the fact that the mineral component can protect the biological fraction (biomolecules) from degradation: after the death of an organism, a range of biological and chemical factors immediately induce the breakdown of the organic matter (soft tissues), but if these organics are somehow protected by the mineral phase, then degradation will be slow (or slower). It follows that ancient molecules (nucleic acids, proteins, lipids, carbohydrates) will be found mainly in sub-fossil (hereafter "fossil") mineralized substrates, and that we can target these for molecular palaeontology/archaeology.

Table 1.1 Types of biogenic minerals and their occurrence in extant phyla, redrawn from Lowenstam (1980).

At the time of writing, the field of palaeobiogeochemistry has expanded so much that we now use ‘fossil’ biomolecules routinely in order to recover information on the age since death of an organism (e.g. in the case of protein diagenesis/amino acid racemization dating; see Chapter 4), as well as on the physiology, phylogeny, and biogeography of extinct and extant organisms (from Neanderthals to crops), the evolution of diet, agricultural and husbandry practices, and even diseases. Indeed, we now have a whole dedicated field of ‘biomolecular archaeology’, which can be split into different subdisciplines (palaeogenomics, palaeoproteomics, palaeolipidomics, stable isotope geochemistry). Many recent reviews of the literature deal with the potential of new technologies for studying ancient biomolecules (Cappellini et al., 2018; Hendy et al., 2018; Welker, 2018).

And yet, these technological developments have not so far been able to fulfil Lowenstam's dream: in order to reconstruct evolutionary patterns in deep time, it is necessary to retrieve sequence data (DNA or proteins, bearing phylogenetic information), from really old fossils. Since DNA degrades more rapidly than proteins, the latter would be the molecules of choice. Despite repeated claims of preservation of proteins in Cretaceous (dinosaur) samples (Abelson, 1956; Miller and Wyckoff, 1968; Schweitzer et al., 1997; Asara et al., 2007; Cleland et al., 2015; Schroeter et al., 2017), which have been repeatedly dismissed (Collins et al., 2000; Buckley et al., 2008, 2017; Saitta et al., 2019), the oldest endogenous peptide sequences have been reported from Plio-Pleistocene fossils (eggshell: Demarchi et al., 2016; tooth enamel: Cappellini et al., 2019). In fact, comparatively little effort has gone into systematically assessing the survival potential of organic matrices other than those for bone, eggshell and teeth. (Incidentally, bone has been taking the lion's share of the effort, despite its being well known as a poor repository of endogenous molecules due to its porous and ‘leaky’ nature.) As a result, many scientific papers reporting protein sequence data bear two striking features: (1) the missed opportunity of linking research in ancient biomolecules with the latest theories and discoveries in the field of biomineralization; (2) the limited engagement with issues of diagenesis, which were instead at the forefront of debate at the time Lowenstam published his work.

In order to fill this gap, this book will focus on the mechanisms of degradation and survival of proteins in fossil biominerals, and look at the extent to which this affects the use of ancient proteins as a means of understanding the past. Applications for dating purposes, as well as in the newer field of ‘palaeoproteomics’, will be considered. But, before we begin, we must clarify what biominerals actually are.

1.2 What are Biominerals?

Biominerals are hybrid nanocomposite biomaterials, in which an organic fraction produces mineralized structures (skeletons) from inorganic precursor ions (Weber and Pokroy, 2015). Or, as Weiner and Dove define them, ‘where the distinctions between the chemical, biological and earth science disciplines melt away’ (Weiner and Dove, 2003). Biominerals display highly sophisticated architectures, exceptional mechanical properties and serve a variety of purposes, from protection of the soft body to scattering of light (Addadi and Weiner, 2014). Among the many studies which review research o...

Table of contents

• Cover
• Table of Contents
• Preface
• Acknowledgements
• 1 Biominerals and the Fossil Record
• 2 Mechanisms of Degradation and Survival
• 3 Proteins in Fossil Biominerals
• 4 Chiral Amino Acids: Geochronology and Other Applications
• 5 Ancient Protein Sequences
• Index
• End User License Agreement