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Schweitzer MH, Schroeter ER, Cleland TP, Zheng W. Paleoproteomics of Mesozoic Dinosaurs and Other Mesozoic Fossils. Proteomics 2019; 19:e1800251. [PMID: 31172628 DOI: 10.1002/pmic.201800251] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 05/07/2019] [Indexed: 12/20/2022]
Abstract
Molecular studies have contributed greatly to our understanding of evolutionary processes that act upon virtually every aspect of living organisms. However, these studies are limited with regard to extinct organisms, particularly those from the Mesozoic because fossils pose unique challenges to molecular workflows, and because prevailing wisdom suggests no endogenous molecular components can persist into deep time. Here, the power and potential of a molecular approach to Mesozoic fossils is discussed. Molecular methods that have been applied to Mesozoic fossils-including iconic, non-avian dinosaurs- and the challenges inherent in such analyses, are compared and evaluated. Taphonomic processes resulting in the transition of living organisms from the biosphere into the fossil record are reviewed, and the possible effects of taphonomic alteration on downstream analyses that can be problematic for very old material (e.g., molecular modifications, limitations of on comparative databases) are addressed. Molecular studies applied to ancient remains are placed in historical context, and past and current studies are evaluated with respect to producing phylogenetically and/or evolutionarily significant data. Finally, some criteria for assessing the presence of endogenous biomolecules in very ancient fossil remains are suggested as a starting framework for such studies.
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Affiliation(s)
- Mary Higby Schweitzer
- Department of Biological Sciences, North Carolina State University, Raleigh, 27695, NC.,North Carolina Museum of Natural Sciences, Raleigh, NC.,Museum of the Rockies, Montana State University, Bozeman, MT.,Department of Geology, Lund University, Sölvegatan 12, SE-223 62, Lund, Sweden
| | - Elena R Schroeter
- Department of Biological Sciences, North Carolina State University, Raleigh, 27695, NC
| | - Timothy P Cleland
- Museum Conservation Institute, Smithsonian Institution, Suitland, 20746, MD
| | - Wenxia Zheng
- Department of Biological Sciences, North Carolina State University, Raleigh, 27695, NC
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Hendy J, Welker F, Demarchi B, Speller C, Warinner C, Collins MJ. A guide to ancient protein studies. Nat Ecol Evol 2018; 2:791-799. [PMID: 29581591 DOI: 10.1038/s41559-018-0510-x] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 02/19/2018] [Indexed: 12/24/2022]
Abstract
Palaeoproteomics is an emerging neologism used to describe the application of mass spectrometry-based approaches to the study of ancient proteomes. As with palaeogenomics (the study of ancient DNA), it intersects evolutionary biology, archaeology and anthropology, with applications ranging from the phylogenetic reconstruction of extinct species to the investigation of past human diets and ancient diseases. However, there is no explicit consensus at present regarding standards for data reporting, data validation measures or the use of suitable contamination controls in ancient protein studies. Additionally, in contrast to the ancient DNA community, no consolidated guidelines have been proposed by which researchers, reviewers and editors can evaluate palaeoproteomics data, in part due to the novelty of the field. Here we present a series of precautions and standards for ancient protein research that can be implemented at each stage of analysis, from sample selection to data interpretation. These guidelines are not intended to impose a narrow or rigid list of authentication criteria, but rather to support good practices in the field and to ensure the generation of robust, reproducible results. As the field grows and methodologies change, so too will best practices. It is therefore essential that researchers continue to provide necessary details on how data were generated and authenticated so that the results can be independently and effectively evaluated. We hope that these proposed standards of practice will help to provide a firm foundation for the establishment of palaeoproteomics as a viable and powerful tool for archaeologists, anthropologists and evolutionary biologists.
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Affiliation(s)
- Jessica Hendy
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany.
| | - Frido Welker
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. .,Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
| | - Beatrice Demarchi
- Department of Life Science and Systems Biology, University of Turin, Turin, Italy.,BioArCh, Department of Archaeology, University of York, York, UK
| | - Camilla Speller
- BioArCh, Department of Archaeology, University of York, York, UK
| | - Christina Warinner
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany.,Department of Anthropology, University of Oklahoma, Norman, OK, USA.,Institute for Evolutionary Medicine, University of Zürich, Zürich, Switzerland
| | - Matthew J Collins
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,BioArCh, Department of Archaeology, University of York, York, UK
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Cleland TP, Schroeter ER. A Comparison of Common Mass Spectrometry Approaches for Paleoproteomics. J Proteome Res 2018; 17:936-945. [PMID: 29384680 DOI: 10.1021/acs.jproteome.7b00703] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The last two decades have seen a broad diversity of methods used to identify and/or characterize proteins in the archeological and paleontological record. Of these, mass spectrometry has opened an unprecedented window into the proteomes of the past, providing protein sequence data from long extinct animals as well as historical and prehistorical artifacts. Thus, application of mass spectrometry to fossil remains has become an attractive source for ancient molecular sequences with which to conduct evolutionary studies, particularly in specimens older than the proposed limit of amplifiable DNA detection. However, "mass spectrometry" covers a range of mass-based proteomic approaches, each of which utilize different technology and physical principles to generate unique types of data, with their own strengths and challenges. Here, we discuss a variety of mass spectrometry techniques that have or may be used to detect and characterize archeological and paleontological proteins, with a particular focus on MALDI-MS, LC-MS/MS, TOF-SIMS, and MSi. The main differences in their functionality, the types of data they produce, and the potential effects of diagenesis on their results are considered.
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Affiliation(s)
- Timothy P Cleland
- Museum Conservation Institute, Smithsonian Institution , Suitland, Maryland 20746, United States
| | - Elena R Schroeter
- Department of Biological Sciences, North Carolina State University , Raleigh, North Carolina 27695, United States
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Dallongeville S, Garnier N, Rolando C, Tokarski C. Proteins in Art, Archaeology, and Paleontology: From Detection to Identification. Chem Rev 2015; 116:2-79. [PMID: 26709533 DOI: 10.1021/acs.chemrev.5b00037] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Sophie Dallongeville
- Miniaturisation pour la Synthèse, l'Analyse & la Protéomique (MSAP), USR CNRS 3290, Université de Lille 1 Sciences et Technologies , 59655 Villeneuve d'Ascq Cedex, France
| | - Nicolas Garnier
- SARL Laboratoire Nicolas Garnier , 63270 Vic le Comte, France
| | - Christian Rolando
- Miniaturisation pour la Synthèse, l'Analyse & la Protéomique (MSAP), USR CNRS 3290, Université de Lille 1 Sciences et Technologies , 59655 Villeneuve d'Ascq Cedex, France
| | - Caroline Tokarski
- Miniaturisation pour la Synthèse, l'Analyse & la Protéomique (MSAP), USR CNRS 3290, Université de Lille 1 Sciences et Technologies , 59655 Villeneuve d'Ascq Cedex, France
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Hill RC, Wither MJ, Nemkov T, Barrett A, D'Alessandro A, Dzieciatkowska M, Hansen KC. Preserved Proteins from Extinct Bison latifrons Identified by Tandem Mass Spectrometry; Hydroxylysine Glycosides are a Common Feature of Ancient Collagen. Mol Cell Proteomics 2015; 14:1946-58. [PMID: 25948757 DOI: 10.1074/mcp.m114.047787] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Indexed: 11/06/2022] Open
Abstract
Bone samples from several vertebrates were collected from the Ziegler Reservoir fossil site, in Snowmass Village, Colorado, and processed for proteomics analysis. The specimens come from Pleistocene megafauna Bison latifrons, dating back ∼ 120,000 years. Proteomics analysis using a simplified sample preparation procedure and tandem mass spectrometry (MS/MS) was applied to obtain protein identifications. Several bioinformatics resources were used to obtain peptide identifications based on sequence homology to extant species with annotated genomes. With the exception of soil sample controls, all samples resulted in confident peptide identifications that mapped to type I collagen. In addition, we analyzed a specimen from the extinct B. latifrons that yielded peptide identifications mapping to over 33 bovine proteins. Our analysis resulted in extensive fibrillar collagen sequence coverage, including the identification of posttranslational modifications. Hydroxylysine glucosylgalactosylation, a modification thought to be involved in collagen fiber formation and bone mineralization, was identified for the first time in an ancient protein dataset. Meta-analysis of data from other studies indicates that this modification may be common in well-preserved prehistoric samples. Additional peptide sequences from extracellular matrix (ECM) and non-ECM proteins have also been identified for the first time in ancient tissue samples. These data provide a framework for analyzing ancient protein signatures in well-preserved fossil specimens, while also contributing novel insights into the molecular basis of organic matter preservation. As such, this analysis has unearthed common posttranslational modifications of collagen that may assist in its preservation over time. The data are available via ProteomeXchange with identifier PXD001827.
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Affiliation(s)
- Ryan C Hill
- From the ‡Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado 80045, USA
| | - Matthew J Wither
- From the ‡Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado 80045, USA
| | - Travis Nemkov
- From the ‡Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado 80045, USA
| | - Alexander Barrett
- From the ‡Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado 80045, USA
| | - Angelo D'Alessandro
- From the ‡Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado 80045, USA
| | - Monika Dzieciatkowska
- From the ‡Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado 80045, USA
| | - Kirk C Hansen
- From the ‡Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado 80045, USA
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Caputo I, Lepretti M, Scarabino C, Esposito C, Proto A. An acetic acid-based extraction method to obtain high quality collagen from archeological bone remains. Anal Biochem 2012; 421:92-6. [DOI: 10.1016/j.ab.2011.10.024] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Revised: 09/29/2011] [Accepted: 10/14/2011] [Indexed: 10/16/2022]
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Affiliation(s)
- A R Doberenz
- DEPARTMENT OF PHYSICS, UNIVERSITY OF ARIZONA, TUCSON
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Abstract
Selected fossil vertebrates and the enclosing sediments dating from 1300 years B.C. to approximately 400 million years ago were subjected to amino acid assay. The amino acid analyses revealed little evidence of intact collagen in fossils of Tertiary, Mesozoic or Palaeozoic age. There was, however, evidence of contemporary proteinaceous material which may have been derived from bacteria. In Palaeozoic material the analyses detected a general background of amino acids common to both fossils and sediments. The degree of racemization was routinely determined as a means of measuring modern contamination of geologically older samples. An electron microscope study of Quaternary (Pleistocene) collagen revealed a significant reduction of the 64 nm banding to about 50 nm. The same Pleistocene material gave amino acid compositional profiles typical of collagen. However, when this material was subjected to digestion by the proteolytic enzymes collagenase, pronase and subtilisin, the resulting peptide fingerprints showed small but significant differences from those obtained from modern collagen digests, indicating the possibility of changes having occurred during fossilization affecting susceptible cleavage sites in the molecule.
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Barraco RA. Preservation of proteins in mummified tissues. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 1978; 48:487-91. [PMID: 655269 DOI: 10.1002/ajpa.1330480407] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Protein material was extracted from the dessicated tissues of several Egyptian mummies and a frozen Eskimo. The distribution and degree of preservation of high molecular weight protein was analyzed by gel filtration, protein assays, amino acid analysis, and polyacrylamide gel electrophoresis. The protein has undergone considerable degradation although some high molecular weight protein (C. 130,000 daltons) remains intact. Amino acid analysis of the extracted protein indicates the basic amino acids have undergone a chemical modification and may represent a point of preferential breakdown in the polypeptide chain. Atomic absorption spectrophotometry of tissue cations suggests a correlation between degree of preservation of mummified tissue and levels of sodium salts (natron) in the tissue.
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Williams KM, Smith GG. A critical evaluation of the application of amino acid racemization to geochronology and geothermometry. ORIGINS OF LIFE 1977; 8:91-144. [PMID: 335314 DOI: 10.1007/bf00927978] [Citation(s) in RCA: 111] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In this review we have critically evaluated the application of the diagenetic racemization of amino acids to geochronology and geothermometry. Although there has been enthusiastic support given to this new method, it is our opinion that recent developments suggest a more cautious approach. We have discussed the pitfalls and inhereent complications, while outlining the advances which have been accomplished. We conclude that this is an innovative approach which will add valuable information to the scientific literature. However, since our fundamental understanding of diagnetic racemization is still limited, many of the age and paleotemperature estimates which have been assigned to fossil specimens may be unreliable.
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Heller W. [Paleobiochemical aspects of evolution]. THE SCIENCE OF NATURE - NATURWISSENSCHAFTEN 1973; 60:460-8. [PMID: 4594016 DOI: 10.1007/bf00592855] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Abstract
Lipids and fatty acids were extracted from eight specimens of fossil teeth that were reliably estimated to be 100,000 to 230,000,000 years old. The kinds and relative amounts of individual fatty acids present in the extract were estimated by gas-liquid chromatography. These ancient teeth were found to be similar to modern animal teeth in lipid and fatty acid content. It is noteworthy that unsaturated fatty acids (ie, oleic and linoleic acids) survived storage in teeth for millions of years.
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