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Presslee S, Penkman K, Fischer R, Richards-Slidel E, Southon J, Hospitaleche CA, Collins M, MacPhee R. Assessment of different screening methods for selecting palaeontological bone samples for peptide sequencing. J Proteomics 2020; 230:103986. [PMID: 32941991 DOI: 10.1016/j.jprot.2020.103986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 07/24/2020] [Accepted: 09/10/2020] [Indexed: 10/23/2022]
Abstract
Ancient proteomics is being applied to samples dating further and further back in time, with many palaeontological specimens providing protein sequence data for phylogenetic analysis as well as protein degradation studies. However, fossils are a precious material and proteomic analysis is destructive and costly. In this paper we consider three different techniques (ATR-FTIR, MALDI-ToF MS and chiral AA analysis) to screen fossil material for potential protein preservation, aiming to maximise the proteomic information recovered and saving costly time consuming analyses which may produce low quality results. It was found that splitting factor and C/P indices from ATR-FTIR were not a reliable indicator of protein survival as they are confounded by secondary mineralisation of the fossil material. Both MALDI-ToF MS and chiral AA analysis results were able to successfully identify samples with surviving proteins, and it is suggested that one or both of these analyses be used for screening palaeontological specimens. SIGNIFICANCE: This study has shown both chiral amino acid analysis and MALDI-ToF MS are reliable screening methods for predicting protein survival in fossils. Both these methods are quick, cheap, minimally destructive (1 mg and 15 mg respectively) and can provide crucial additional information about the endogeneity of the surviving proteins. It is hoped that the use of these screening methods will encourage the examination of a wide range of palaeontological specimens for potential proteomic analysis. This in turn will give us a better understanding of protein survival far back in time and under different environmental conditions.
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Affiliation(s)
- Samantha Presslee
- BioArCh, Department of Archaeology, University of York, York, UK; BioArCh, Department of Chemistry, University of York, York, UK.
| | - Kirsty Penkman
- BioArCh, Department of Chemistry, University of York, York, UK
| | - Roman Fischer
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Eden Richards-Slidel
- BioArCh, Department of Archaeology, University of York, York, UK; Section for Evolutionary Genomics, The Globe Institute, Faculty of Health, University of Copenhagen, Copenhagen, Denmark
| | - John Southon
- Department of Earth System Science, University of California, Irvine, USA
| | | | - Matthew Collins
- Section for Evolutionary Genomics, The Globe Institute, Faculty of Health, University of Copenhagen, Copenhagen, Denmark; McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
| | - Ross MacPhee
- Department of Mammalogy, American Museum of Natural History, New York, NY, USA
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2
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Welker F, Ramos-Madrigal J, Gutenbrunner P, Mackie M, Tiwary S, Jersie-Christensen RR, Chiva C, Dickinson MR, Kuhlwilm M, de Manuel M, Gelabert P, Martinón-Torres M, Margvelashvili A, Arsuaga JL, Carbonell E, Marques-Bonet T, Penkman K, Sabidó E, Cox J, Olsen JV, Lordkipanidze D, Racimo F, Lalueza-Fox C, de Castro JMB, Willerslev E, Cappellini E. Author Correction: The dental proteome of Homo antecessor. Nature 2020; 584:E19. [PMID: 32724207 DOI: 10.1038/s41586-020-2580-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Frido Welker
- Evolutionary Genomics Section, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
| | - Jazmín Ramos-Madrigal
- Evolutionary Genomics Section, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Petra Gutenbrunner
- Computational Systems Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Meaghan Mackie
- Evolutionary Genomics Section, Globe Institute, University of Copenhagen, Copenhagen, Denmark.,The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Shivani Tiwary
- Computational Systems Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
| | | | - Cristina Chiva
- Center for Genomic Regulation (CNAG-CRG), Barcelona Institute of Science and Technology, Barcelona, Spain.,Proteomics Unit, University Pompeu Fabra, Barcelona, Spain
| | | | - Martin Kuhlwilm
- Institute of Evolutionary Biology (UPF-CSIC), University Pompeu Fabra, Barcelona, Spain
| | - Marc de Manuel
- Institute of Evolutionary Biology (UPF-CSIC), University Pompeu Fabra, Barcelona, Spain
| | - Pere Gelabert
- Institute of Evolutionary Biology (UPF-CSIC), University Pompeu Fabra, Barcelona, Spain
| | - María Martinón-Torres
- Centro Nacional de Investigación sobre la Evolución Humana (CENIEH), Burgos, Spain.,Anthropology Department, University College London, London, UK
| | | | - Juan Luis Arsuaga
- Centro Mixto UCM-ISCIII de Evolución y Comportamiento Humanos, Madrid, Spain.,Departamento de Paleontología, Facultad de Ciencias Geológicas, Universidad Complutense de Madrid, Madrid, Spain
| | - Eudald Carbonell
- Departamento d'Història i Història de l'Art, Universidad Rovira i Virgili, Tarragona, Spain.,Institut Català de Paleoecologia Humana i Evolució Social (IPHES), Tarragona, Spain
| | - Tomas Marques-Bonet
- Center for Genomic Regulation (CNAG-CRG), Barcelona Institute of Science and Technology, Barcelona, Spain.,Institute of Evolutionary Biology (UPF-CSIC), University Pompeu Fabra, Barcelona, Spain.,Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain.,Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain
| | | | - Eduard Sabidó
- Center for Genomic Regulation (CNAG-CRG), Barcelona Institute of Science and Technology, Barcelona, Spain.,Proteomics Unit, University Pompeu Fabra, Barcelona, Spain
| | - Jürgen Cox
- Computational Systems Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Jesper V Olsen
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - David Lordkipanidze
- Georgian National Museum, Tbilisi, Georgia.,Tbilisi State University, Tbilisi, Georgia
| | - Fernando Racimo
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Carles Lalueza-Fox
- Institute of Evolutionary Biology (UPF-CSIC), University Pompeu Fabra, Barcelona, Spain
| | - José María Bermúdez de Castro
- Centro Nacional de Investigación sobre la Evolución Humana (CENIEH), Burgos, Spain. .,Anthropology Department, University College London, London, UK.
| | - Eske Willerslev
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark. .,Department of Zoology, University of Cambridge, Cambridge, UK. .,Wellcome Sanger Institute, Hinxton, UK. .,Danish Institute for Advanced Study, University of Southern Denmark, Odense, Denmark.
| | - Enrico Cappellini
- Evolutionary Genomics Section, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
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3
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Kontopoulos I, Penkman K, Mullin VE, Winkelbach L, Unterländer M, Scheu A, Kreutzer S, Hansen HB, Margaryan A, Teasdale MD, Gehlen B, Street M, Lynnerup N, Liritzis I, Sampson A, Papageorgopoulou C, Allentoft ME, Burger J, Bradley DG, Collins MJ. Screening archaeological bone for palaeogenetic and palaeoproteomic studies. PLoS One 2020; 15:e0235146. [PMID: 32584871 PMCID: PMC7316274 DOI: 10.1371/journal.pone.0235146] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 06/09/2020] [Indexed: 11/18/2022] Open
Abstract
The recovery and analysis of ancient DNA and protein from archaeological bone is time-consuming and expensive to carry out, while it involves the partial or complete destruction of valuable or rare specimens. The fields of palaeogenetic and palaeoproteomic research would benefit greatly from techniques that can assess the molecular quality prior to sampling. To be relevant, such screening methods should be effective, minimally-destructive, and rapid. This study reports results based on spectroscopic (Fourier-transform infrared spectroscopy in attenuated total reflectance [FTIR-ATR]; n = 266), palaeoproteomic (collagen content; n = 226), and palaeogenetic (endogenous DNA content; n = 88) techniques. We establish thresholds for three different FTIR indices, a) the infrared splitting factor [IRSF] that assesses relative changes in bioapatite crystals’ size and homogeneity; b) the carbonate-to-phosphate [C/P] ratio as a relative measure of carbonate content in bioapatite crystals; and c) the amide-to-phosphate ratio [Am/P] for assessing the relative organic content preserved in bone. These thresholds are both extremely reliable and easy to apply for the successful and rapid distinction between well- and poorly-preserved specimens. This is a milestone for choosing appropriate samples prior to genomic and collagen analyses, with important implications for biomolecular archaeology and palaeontology.
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Affiliation(s)
- Ioannis Kontopoulos
- Department of Archaeology, BioArCh, University of York, York, United Kingdom
- * E-mail:
| | - Kirsty Penkman
- Department of Chemistry, BioArCh, University of York, York, United Kingdom
| | - Victoria E. Mullin
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
- Department of Earth Sciences, Natural History Museum, London, United Kingdom
| | - Laura Winkelbach
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Martina Unterländer
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg-University Mainz, Mainz, Germany
- Laboratory of Physical Anthropology, Department of History and Ethnology, Democritus University of Thrace, Komotini, Greece
- German Federal Criminal Police Office, Wiesbaden, Germany
| | - Amelie Scheu
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Susanne Kreutzer
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Henrik B. Hansen
- Centre for GeoGenetics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Ashot Margaryan
- Centre for GeoGenetics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Matthew D. Teasdale
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
- Department of Archaeology, McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, United Kingdom
| | - Birgit Gehlen
- Collaborative Research Centre, project D4, Cologne University, Cologne, Germany
| | - Martin Street
- MONREPOS Archaeological Research Centre and Museum for Human Behavioural Evolution, RGZM Leibniz Research Institute for Archaeology, Neuwied, Germany
| | - Niels Lynnerup
- Unit of Forensic Anthropology, Department of Forensic Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Ioannis Liritzis
- Laboratory of Archaeometry, Department of Mediterranean Studies, University of the Aegean, Rhodes, Greece
- Center on Yellow River Civilization of Henan Province, Key Research Institute of Yellow River Civilization and Sustainable Development and Collaborative Innovation, Henan University, Kaifeng, China
| | - Adamantios Sampson
- Department of Mediterranean Studies, University of the Aegean, Rhodes, Greece
| | - Christina Papageorgopoulou
- Laboratory of Physical Anthropology, Department of History and Ethnology, Democritus University of Thrace, Komotini, Greece
| | - Morten E. Allentoft
- Centre for GeoGenetics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Joachim Burger
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Daniel G. Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Matthew J. Collins
- Department of Archaeology, McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, United Kingdom
- Centre for Evogenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
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4
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Cappellini E, Welker F, Pandolfi L, Ramos-Madrigal J, Samodova D, Rüther PL, Fotakis AK, Lyon D, Moreno-Mayar JV, Bukhsianidze M, Rakownikow Jersie-Christensen R, Mackie M, Ginolhac A, Ferring R, Tappen M, Palkopoulou E, Dickinson MR, Stafford TW, Chan YL, Götherström A, Nathan SKSS, Heintzman PD, Kapp JD, Kirillova I, Moodley Y, Agusti J, Kahlke RD, Kiladze G, Martínez-Navarro B, Liu S, Sandoval Velasco M, Sinding MHS, Kelstrup CD, Allentoft ME, Orlando L, Penkman K, Shapiro B, Rook L, Dalén L, Gilbert MTP, Olsen JV, Lordkipanidze D, Willerslev E. Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogeny. Nature 2019; 574:103-107. [PMID: 31511700 PMCID: PMC6894936 DOI: 10.1038/s41586-019-1555-y] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 08/12/2019] [Indexed: 11/10/2022]
Abstract
Ancient DNA (aDNA) sequencing has enabled reconstruction of speciation, migration, and admixture events for extinct taxa1. Outside the permafrost, however, irreversible aDNA post-mortem degradation2 has so far limited aDNA recovery to the past ~0.5 million years (Ma)3. Contrarily, tandem mass spectrometry (MS) allowed sequencing ~1.5 million year (Ma) old collagen type I (COL1)4 and suggested the presence of protein residues in Cretaceous fossil remains5, although with limited phylogenetic use6. In the absence of molecular evidence, the speciation of several Early and Middle Pleistocene extinct species remain contentious. In this study, we address the phylogenetic relationships of the Eurasian Pleistocene Rhinocerotidae7–9 using a ~1.77 Ma old dental enamel proteome of a Stephanorhinus specimen from the Dmanisi archaeological site in Georgia (South Caucasus)10. Molecular phylogenetic analyses place the Dmanisi Stephanorhinus as a sister group to the woolly (Coelodonta antiquitatis) and Merck’s rhinoceros (S. kirchbergensis) clade. We show that Coelodonta evolved from an early Stephanorhinus lineage and that the latter includes at least two distinct evolutionary lines. As such, the genus Stephanorhinus is currently paraphyletic and its systematic revision is therefore needed. We demonstrate that Early Pleistocene dental enamel proteome sequencing overcomes the limits of ancient collagen- and aDNA-based phylogenetic inference. It also provides additional information about the sex and taxonomic assignment of the specimens analysed. Dental enamel, the hardest tissue in vertebrates11, is highly abundant in the fossil record. Our findings reveal that palaeoproteomic investigation of this material can push biomolecular investigation further back into the Early Pleistocene.
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Affiliation(s)
- Enrico Cappellini
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark. .,Evolutionary Genomics Section, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
| | - Frido Welker
- Evolutionary Genomics Section, Globe Institute, University of Copenhagen, Copenhagen, Denmark.,Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Luca Pandolfi
- Dipartimento di Scienze della Terra, Università degli Studi di Firenze, Florence, Italy
| | - Jazmín Ramos-Madrigal
- Evolutionary Genomics Section, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Diana Samodova
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Patrick L Rüther
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Anna K Fotakis
- Evolutionary Genomics Section, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - David Lyon
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - J Víctor Moreno-Mayar
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Meaghan Mackie
- Evolutionary Genomics Section, Globe Institute, University of Copenhagen, Copenhagen, Denmark.,Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Aurélien Ginolhac
- Life Sciences Research Unit, University of Luxembourg, Belvaux, Luxembourg
| | - Reid Ferring
- Department of Geography and Environment, University of North Texas, Denton, TX, USA
| | - Martha Tappen
- Department of Anthropology, University of Minnesota, Minneapolis, MN, USA
| | | | | | | | - Yvonne L Chan
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Anders Götherström
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | | | - Peter D Heintzman
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA.,Tromsø University Museum, The Arctic University of Norway (UiT), Tromsø, Norway
| | - Joshua D Kapp
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Irina Kirillova
- Ice Age Museum, National Alliance of Shidlovskiy 'Ice Age', Moscow, Russia
| | - Yoshan Moodley
- Department of Zoology, University of Venda, Thohoyandou, South Africa
| | - Jordi Agusti
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.,Institut Català de Paleoecologia Humana i Evolució Social, Universitat Rovira i Virgili, Tarragona, Spain
| | | | - Gocha Kiladze
- Geology Department, Tbilisi State University, Tbilisi, Georgia
| | - Bienvenido Martínez-Navarro
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.,Institut Català de Paleoecologia Humana i Evolució Social, Universitat Rovira i Virgili, Tarragona, Spain.,Departament d'Història i Geografia, Universitat Rovira i Virgili, Tarragona, Spain
| | - Shanlin Liu
- Evolutionary Genomics Section, Globe Institute, University of Copenhagen, Copenhagen, Denmark.,BGI Shenzhen, Shenzen, China
| | | | - Mikkel-Holger S Sinding
- Evolutionary Genomics Section, Globe Institute, University of Copenhagen, Copenhagen, Denmark.,Greenland Institute of Natural Resources, Nuuk, Greenland
| | - Christian D Kelstrup
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Morten E Allentoft
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Ludovic Orlando
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.,Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, Université Paul Sabatier, Toulouse, France
| | | | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA.,Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Lorenzo Rook
- Dipartimento di Scienze della Terra, Università degli Studi di Firenze, Florence, Italy
| | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - M Thomas P Gilbert
- Evolutionary Genomics Section, Globe Institute, University of Copenhagen, Copenhagen, Denmark.,University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Jesper V Olsen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.
| | | | - Eske Willerslev
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark. .,Department of Zoology, University of Cambridge, Cambridge, UK. .,Wellcome Trust Sanger Institute, Hinxton, UK. .,Danish Institute for Advanced Study, University of Southern Denmark, Odense, Denmark.
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5
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Presslee S, Slater GJ, Pujos F, Forasiepi AM, Fischer R, Molloy K, Mackie M, Olsen JV, Kramarz A, Taglioretti M, Scaglia F, Lezcano M, Lanata JL, Southon J, Feranec R, Bloch J, Hajduk A, Martin FM, Salas Gismondi R, Reguero M, de Muizon C, Greenwood A, Chait BT, Penkman K, Collins M, MacPhee RDE. Palaeoproteomics resolves sloth relationships. Nat Ecol Evol 2019; 3:1121-1130. [PMID: 31171860 DOI: 10.1038/s41559-019-0909-z] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 04/28/2019] [Indexed: 01/16/2023]
Abstract
The living tree sloths Choloepus and Bradypus are the only remaining members of Folivora, a major xenarthran radiation that occupied a wide range of habitats in many parts of the western hemisphere during the Cenozoic, including both continents and the West Indies. Ancient DNA evidence has played only a minor role in folivoran systematics, as most sloths lived in places not conducive to genomic preservation. Here we utilize collagen sequence information, both separately and in combination with published mitochondrial DNA evidence, to assess the relationships of tree sloths and their extinct relatives. Results from phylogenetic analysis of these datasets differ substantially from morphology-based concepts: Choloepus groups with Mylodontidae, not Megalonychidae; Bradypus and Megalonyx pair together as megatherioids, while monophyletic Antillean sloths may be sister to all other folivorans. Divergence estimates are consistent with fossil evidence for mid-Cenozoic presence of sloths in the West Indies and an early Miocene radiation in South America.
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Affiliation(s)
- Samantha Presslee
- Department of Archaeology and BioArCh, University of York, Heslington, UK.,Department of Mammalogy, American Museum of Natural History, New York, NY, USA.,Paleoproteomics Group, Natural History Museum of Denmark and University of Copenhagen, Copenhagen, Denmark
| | - Graham J Slater
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL, USA
| | - François Pujos
- Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales, CCT-CONICET-Mendoza, Mendoza, Argentina
| | - Analía M Forasiepi
- Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales, CCT-CONICET-Mendoza, Mendoza, Argentina
| | - Roman Fischer
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Kelly Molloy
- Chait Laboratory and National Resource for the Mass Spectrometric Analysis of Biological Macromolecules, The Rockefeller University, New York, NY, USA
| | - Meaghan Mackie
- Paleoproteomics Group, Natural History Museum of Denmark and University of Copenhagen, Copenhagen, Denmark.,Novo Nordisk Foundation Center for Protein Research, Copenhagen, Denmark
| | - Jesper V Olsen
- Novo Nordisk Foundation Center for Protein Research, Copenhagen, Denmark
| | - Alejandro Kramarz
- Sección Paleovertebrados, Museo Argentino de Ciencias Naturales 'Bernardino Rivadavia', Buenos Aires, Argentina
| | - Matías Taglioretti
- Museo Municipal de Ciencias Naturales 'Lorenzo Scaglia', Mar del Plata, Argentina
| | - Fernando Scaglia
- Museo Municipal de Ciencias Naturales 'Lorenzo Scaglia', Mar del Plata, Argentina
| | - Maximiliano Lezcano
- Instituto de Investigaciones en Diversidad Cultural y Procesos de Cambio, CONICET and Universidad Nacional de Río Negro, Bariloche, Argentina
| | - José Luis Lanata
- Instituto de Investigaciones en Diversidad Cultural y Procesos de Cambio, CONICET and Universidad Nacional de Río Negro, Bariloche, Argentina
| | - John Southon
- Keck-CCAMS Group, Earth System Science Department, University of California, Irvine, Irvine, CA, USA
| | | | - Jonathan Bloch
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | - Adam Hajduk
- Museo de la Patagonia 'F. P. Moreno', Bariloche, Argentina
| | - Fabiana M Martin
- Centro de Estudios del Hombre Austral, Instituto de la Patagonia, Universidad de Magallanes, Punta Arenas, Chile
| | - Rodolfo Salas Gismondi
- BioGeoCiencias Lab, Facultad de Ciencias y Filosofía/CIDIS, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Marcelo Reguero
- CONICET and División Paleontología de Vertebrados, Museo de La Plata. Facultad de Ciencias Naturales, Universidad Nacional de La Plata, La Plata, Argentina
| | - Christian de Muizon
- Centre de Recherches sur la Paléobiodiversité et les Paléoenvironnements, Muséum national d'Histoire naturelle, Paris, France
| | - Alex Greenwood
- Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany.,Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Brian T Chait
- Chait Laboratory and National Resource for the Mass Spectrometric Analysis of Biological Macromolecules, The Rockefeller University, New York, NY, USA
| | - Kirsty Penkman
- Department of Chemistry, University of York, Heslington, UK
| | - Matthew Collins
- Paleoproteomics Group, Natural History Museum of Denmark and University of Copenhagen, Copenhagen, Denmark.,McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
| | - Ross D E MacPhee
- Department of Mammalogy, American Museum of Natural History, New York, NY, USA.
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6
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Wadsworth C, Procopio N, Anderung C, Carretero JM, Iriarte E, Valdiosera C, Elburg R, Penkman K, Buckley M. Comparing ancient DNA survival and proteome content in 69 archaeological cattle tooth and bone samples from multiple European sites. J Proteomics 2017; 158:1-8. [DOI: 10.1016/j.jprot.2017.01.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 12/21/2016] [Accepted: 01/06/2017] [Indexed: 12/23/2022]
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7
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Demarchi B, Hall S, Roncal-Herrero T, Freeman CL, Woolley J, Crisp MK, Wilson J, Fotakis A, Fischer R, Kessler BM, Rakownikow Jersie-Christensen R, Olsen JV, Haile J, Thomas J, Marean CW, Parkington J, Presslee S, Lee-Thorp J, Ditchfield P, Hamilton JF, Ward MW, Wang CM, Shaw MD, Harrison T, Domínguez-Rodrigo M, MacPhee RDE, Kwekason A, Ecker M, Kolska Horwitz L, Chazan M, Kröger R, Thomas-Oates J, Harding JH, Cappellini E, Penkman K, Collins MJ. Protein sequences bound to mineral surfaces persist into deep time. eLife 2016; 5. [PMID: 27668515 PMCID: PMC5039028 DOI: 10.7554/elife.17092] [Citation(s) in RCA: 136] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 08/17/2016] [Indexed: 12/14/2022] Open
Abstract
Proteins persist longer in the fossil record than DNA, but the longevity, survival mechanisms and substrates remain contested. Here, we demonstrate the role of mineral binding in preserving the protein sequence in ostrich (Struthionidae) eggshell, including from the palaeontological sites of Laetoli (3.8 Ma) and Olduvai Gorge (1.3 Ma) in Tanzania. By tracking protein diagenesis back in time we find consistent patterns of preservation, demonstrating authenticity of the surviving sequences. Molecular dynamics simulations of struthiocalcin-1 and -2, the dominant proteins within the eggshell, reveal that distinct domains bind to the mineral surface. It is the domain with the strongest calculated binding energy to the calcite surface that is selectively preserved. Thermal age calculations demonstrate that the Laetoli and Olduvai peptides are 50 times older than any previously authenticated sequence (equivalent to ~16 Ma at a constant 10°C). DOI:http://dx.doi.org/10.7554/eLife.17092.001 The pattern of chemical reactions that break down the molecules that make our bodies is still fairly mysterious. Archaeologists and geologists hope that dead organisms (or artefacts made from them) might not decay entirely, leaving behind clues to their lives. We know that some molecules are more resistant than others; for example, fats are tough and survive for a long time while DNA is degraded very rapidly. Proteins, which are made of chains of smaller molecules called amino acids, are usually sturdier than DNA. Since the amino acid sequence of a protein reflects the DNA sequence that encodes it, proteins in fossils can help researchers to reconstruct how extinct organisms are related in cases where DNA cannot be retrieved. Time, temperature, burial environment and the chemistry of the fossil all influence how quickly a protein decays. However, it is not clear what mechanisms slow down decay so that full protein sequences can be preserved and identified after millions of years. As a result, it is difficult to know where to look for these ancient sequences. In the womb of ostriches, several proteins are responsible for assembling the minerals that make up the ostrich eggshell. These proteins become trapped tightly within the mineral crystals themselves. In this situation, proteins can potentially be preserved over geological time. Demarchi et al. have now studied 3.8 million-year-old eggshells found close to the equator and, despite the extent to which the samples have degraded, discovered fully preserved protein sequences. Using a computer simulation method called molecular dynamics, Demarchi et al. calculated that the protein sequences that are able to survive the longest are stabilized by strong binding to the surface of the mineral crystals. The authenticity of these sequences was tested thoroughly using a combination of several approaches that Demarchi et al. recommend using as a standard for ancient protein studies. Overall, it appears that biominerals are an excellent source of ancient protein sequences because mineral binding ensures survival. A systematic survey of fossil biominerals from different environments is now needed to assess whether these biomolecules have the potential to act as barcodes for interpreting the evolution of organisms. DOI:http://dx.doi.org/10.7554/eLife.17092.002
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Affiliation(s)
- Beatrice Demarchi
- BioArCh, Department of Archaeology, University of York, York, United Kingdom
| | - Shaun Hall
- Department of Material Science and Engineering, University of Sheffield, Sheffield, United Kingdom
| | | | - Colin L Freeman
- Department of Material Science and Engineering, University of Sheffield, Sheffield, United Kingdom
| | - Jos Woolley
- BioArCh, Department of Archaeology, University of York, York, United Kingdom
| | - Molly K Crisp
- Department of Chemistry, University of York, York, United Kingdom
| | - Julie Wilson
- Department of Chemistry, University of York, York, United Kingdom.,Department of Mathematics, University of York, York, United Kingdom
| | - Anna Fotakis
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Roman Fischer
- Advanced Proteomics Facility, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Benedikt M Kessler
- Advanced Proteomics Facility, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | | | - Jesper V Olsen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - James Haile
- Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, United Kingdom
| | - Jessica Thomas
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Bangor, United Kingdom
| | - Curtis W Marean
- Institute of Human Origins, SHESC, Arizona State University, Tempe, United States.,Centre for Coastal Palaeoscience, Nelson Mandela Metropolitan University, Port Elizabeth, South Africa
| | - John Parkington
- Department of Archaeology, University of Cape Town, Cape Town, South Africa
| | - Samantha Presslee
- BioArCh, Department of Archaeology, University of York, York, United Kingdom
| | - Julia Lee-Thorp
- Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, United Kingdom
| | - Peter Ditchfield
- Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, United Kingdom
| | - Jacqueline F Hamilton
- Wolfson Atmospheric Chemistry Laboratories, Department of Chemistry, University of York, York, United Kingdom
| | - Martyn W Ward
- Wolfson Atmospheric Chemistry Laboratories, Department of Chemistry, University of York, York, United Kingdom
| | - Chunting Michelle Wang
- Wolfson Atmospheric Chemistry Laboratories, Department of Chemistry, University of York, York, United Kingdom
| | - Marvin D Shaw
- Wolfson Atmospheric Chemistry Laboratories, Department of Chemistry, University of York, York, United Kingdom
| | - Terry Harrison
- Center for the Study of Human Origins, Department of Anthropology, New York University, New York, United States
| | | | - Ross DE MacPhee
- Department of Mammalogy, American Museum of Natural History, New York, United States
| | | | - Michaela Ecker
- Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, United Kingdom
| | - Liora Kolska Horwitz
- National Natural History Collections, Faculty of Life Sciences, The Hebrew University, Jerusalem, Israel
| | - Michael Chazan
- Department of Anthropology, University of Toronto, Toronto, Canada.,Evolutionary Studies Institute, University of the Witwatersrand, Braamfontein, South Africa
| | - Roland Kröger
- Department of Physics, University of York, York, United Kingdom
| | - Jane Thomas-Oates
- Department of Chemistry, University of York, York, United Kingdom.,Centre of Excellence in Mass Spectrometry, University of York, New York, United States
| | - John H Harding
- Department of Material Science and Engineering, University of Sheffield, Sheffield, United Kingdom
| | - Enrico Cappellini
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Kirsty Penkman
- Department of Chemistry, University of York, York, United Kingdom
| | - Matthew J Collins
- BioArCh, Department of Archaeology, University of York, York, United Kingdom
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8
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Kim YY, Carloni JD, Demarchi B, Sparks D, Reid DG, Kunitake ME, Tang CC, Duer MJ, Freeman CL, Pokroy B, Penkman K, Harding JH, Estroff LA, Baker SP, Meldrum FC. Tuning hardness in calcite by incorporation of amino acids. Nat Mater 2016; 15:903-910. [PMID: 27135858 DOI: 10.1038/nmat4631] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 03/24/2016] [Indexed: 06/05/2023]
Abstract
Structural biominerals are inorganic/organic composites that exhibit remarkable mechanical properties. However, the structure-property relationships of even the simplest building unit-mineral single crystals containing embedded macromolecules-remain poorly understood. Here, by means of a model biomineral made from calcite single crystals containing glycine (0-7 mol%) or aspartic acid (0-4 mol%), we elucidate the origin of the superior hardness of biogenic calcite. We analysed lattice distortions in these model crystals by using X-ray diffraction and molecular dynamics simulations, and by means of solid-state nuclear magnetic resonance show that the amino acids are incorporated as individual molecules. We also demonstrate that nanoindentation hardness increased with amino acid content, reaching values equivalent to their biogenic counterparts. A dislocation pinning model reveals that the enhanced hardness is determined by the force required to cut covalent bonds in the molecules.
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Affiliation(s)
- Yi-Yeoun Kim
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK
| | - Joseph D Carloni
- Department of Materials Science and Engineering, 214 Bard Hall, Cornell University, Ithaca, New York 14853, USA
| | - Beatrice Demarchi
- BioArCh, Departments of Chemistry and Archaeology, University of York, York YO10 5DD, UK
| | - David Sparks
- Department of Materials Science and Engineering, University of Sheffield, Mappin Street, Sheffield S1 3JD, UK
| | - David G Reid
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Miki E Kunitake
- Department of Materials Science and Engineering, 214 Bard Hall, Cornell University, Ithaca, New York 14853, USA
| | - Chiu C Tang
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Melinda J Duer
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Colin L Freeman
- Department of Materials Science and Engineering, University of Sheffield, Mappin Street, Sheffield S1 3JD, UK
| | - Boaz Pokroy
- Department of Materials Science and Engineering and the Russell Berrie Nanotechnology Institute, Technion Israel Institute of Technology, Haifa 32000, Israel
| | - Kirsty Penkman
- BioArCh, Departments of Chemistry and Archaeology, University of York, York YO10 5DD, UK
| | - John H Harding
- Department of Materials Science and Engineering, University of Sheffield, Mappin Street, Sheffield S1 3JD, UK
| | - Lara A Estroff
- Department of Materials Science and Engineering, 214 Bard Hall, Cornell University, Ithaca, New York 14853, USA
- Kavli Institute at Cornell for Nanoscale Science, 420 Physical Sciences Building, Ithaca, New York 14853, USA
| | - Shefford P Baker
- Department of Materials Science and Engineering, 214 Bard Hall, Cornell University, Ithaca, New York 14853, USA
| | - Fiona C Meldrum
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK
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9
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Ieronymaki M, Androutsou ME, Pantelia A, Friligou I, Crisp M, High K, Penkman K, Gatos D, Tselios T. Use of the 2-chlorotrityl chloride resin for microwave-assisted solid phase peptide synthesis. Biopolymers 2016; 104:506-14. [PMID: 26270247 DOI: 10.1002/bip.22710] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 07/09/2015] [Accepted: 08/09/2015] [Indexed: 01/20/2023]
Abstract
A fast and efficient microwave (MW)-assisted solid-phase peptide synthesis protocol using the 2-chlorotrityl chloride resin and the Fmoc/tBu methodology, has been developed. The established protocol combines the advantages of MW irradiation and the acid labile 2-chlorotrityl chloride resin. The effect of temperature during the MW irradiation, the degree of resin substitution during the coupling of the first amino acids and the rate of racemization for each amino acid were evaluated. The suggested solid phase methodology is applicable for orthogonal peptide synthesis and for the synthesis of cyclic peptides.
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Affiliation(s)
| | - Maria Eleni Androutsou
- Department of Chemistry, University of Patras, 26504, Rion, Greece.,Eldrug S.A., Pharmaceutical Company, 26504, Platani, Greece
| | - Anna Pantelia
- Department of Chemistry, University of Patras, 26504, Rion, Greece
| | - Irene Friligou
- Department of Chemistry, University of Patras, 26504, Rion, Greece.,Eldrug S.A., Pharmaceutical Company, 26504, Platani, Greece
| | - Molly Crisp
- BioArCh, Department of Chemistry, University of York, YO10 5DD, United Kingdom
| | - Kirsty High
- BioArCh, Department of Chemistry, University of York, YO10 5DD, United Kingdom
| | - Kirsty Penkman
- BioArCh, Department of Chemistry, University of York, YO10 5DD, United Kingdom
| | - Dimitrios Gatos
- Department of Chemistry, University of Patras, 26504, Rion, Greece
| | - Theodore Tselios
- Department of Chemistry, University of Patras, 26504, Rion, Greece
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10
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Demarchi B, O'Connor S, de Lima Ponzoni A, de Almeida Rocha Ponzoni R, Sheridan A, Penkman K, Hancock Y, Wilson J. An integrated approach to the taxonomic identification of prehistoric shell ornaments. PLoS One 2014; 9:e99839. [PMID: 24936797 PMCID: PMC4061022 DOI: 10.1371/journal.pone.0099839] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 05/17/2014] [Indexed: 11/18/2022] Open
Abstract
Shell beads appear to have been one of the earliest examples of personal adornments. Marine shells identified far from the shore evidence long-distance transport and imply networks of exchange and negotiation. However, worked beads lose taxonomic clues to identification, and this may be compounded by taphonomic alteration. Consequently, the significance of this key early artefact may be underestimated. We report the use of bulk amino acid composition of the stable intra-crystalline proteins preserved in shell biominerals and the application of pattern recognition methods to a large dataset (777 samples) to demonstrate that taxonomic identification can be achieved at genus level. Amino acid analyses are fast (<2 hours per sample) and micro-destructive (sample size <2 mg). Their integration with non-destructive techniques provides a valuable and affordable tool, which can be used by archaeologists and museum curators to gain insight into early exploitation of natural resources by humans. Here we combine amino acid analyses, macro- and microstructural observations (by light microscopy and scanning electron microscopy) and Raman spectroscopy to try to identify the raw material used for beads discovered at the Early Bronze Age site of Great Cornard (UK). Our results show that at least two shell taxa were used and we hypothesise that these were sourced locally.
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Affiliation(s)
- Beatrice Demarchi
- BioArCh, Department of Archaeology, University of York, York, United Kingdom
- * E-mail: (BD); (JW)
| | - Sonia O'Connor
- School of Life Sciences, University of Bradford, Bradford, United Kingdom
| | | | | | - Alison Sheridan
- National Museums Scotland, Chambers Street, Edinburgh, United Kingdom
| | - Kirsty Penkman
- BioArCh, Department of Chemistry, University of York, York, United Kingdom
| | - Y. Hancock
- Department of Physics, University of York, York, United Kingdom
- York Centre for Complex Systems Analysis (YCCSA), University of York, York, United Kingdom
| | - Julie Wilson
- Departments of Mathematics and Chemistry, University of York, York, United Kingdom
- York Centre for Complex Systems Analysis (YCCSA), University of York, York, United Kingdom
- * E-mail: (BD); (JW)
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11
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Demarchi B, Collins M, Bergström E, Dowle A, Penkman K, Thomas-Oates J, Wilson J. New experimental evidence for in-chain amino acid racemization of serine in a model peptide. Anal Chem 2013; 85:5835-42. [PMID: 23705982 DOI: 10.1021/ac4005869] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The facile racemization of protein-bound amino acids plays an important role in the aging and pathologies of living tissues, and it can be exploited for protein geochronological studies in subfossil biominerals. However, the in-chain degradation pathways of amino acids are complex and difficult to elucidate. Serine has proven to be particularly elusive, and its ability to racemize as a peptide-bound residue (like asparagine and aspartic acid) has not been demonstrated. This study investigates the patterns of degradation of a model peptide (WNSVWAW) at elevated temperatures, quantifying the extent of racemization and peptide bond hydrolysis using reverse-phase high-performance liquid chromatography (RP-HPLC) and tracking the presence of degradation products by MALDI-MS. We provide direct evidence that, under these experimental conditions, both serine and asparagine are able to undergo racemization as internally bound residues, which shows their potential for initiating protein breakdown and provides an explanation for the presence of d-enantiomers in living mammalian tissues.
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Affiliation(s)
- Beatrice Demarchi
- BioArCh, Department of Archaeology, University of York, York YO10 5DD, United Kingdom.
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12
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Demarchi B, Williams MG, Milner N, Russell N, Bailey G, Penkman K. Amino acid racemization dating of marine shells: A mound of possibilities. Quat Int 2011; 239:114-124. [PMID: 21776187 PMCID: PMC3117143 DOI: 10.1016/j.quaint.2010.05.029] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Shell middens are one of the most important and widespread indicators for human exploitation of marine resources and occupation of coastal environments. Establishing an accurate and reliable chronology for these deposits has fundamental implications for understanding the patterns of human evolution and dispersal. This paper explores the potential application of a new methodology of amino acid racemization (AAR) dating of shell middens and describes a simple protocol to test the suitability of different molluscan species. This protocol provides a preliminary test for the presence of an intracrystalline fraction of proteins (by bleaching experiments and subsequent heating at high temperature), checking the closed system behaviour of this fraction during diagenesis. Only species which pass both tests can be considered suitable for further studies to obtain reliable age information. This amino acid geochronological technique is also applied to midden deposits at two latitudinal extremes: Northern Scotland and the Southern Red Sea. Results obtained in this study indicate that the application of this new method of AAR dating of shells has the potential to aid the geochronological investigation of shell mounds in different areas of the world.
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Affiliation(s)
- Beatrice Demarchi
- BioArCh, Department of Chemistry, University of York, Heslington, York YO10 5DD, UK
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13
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Buckley M, Walker A, Ho SYW, Yang Y, Smith C, Ashton P, Oates JT, Cappellini E, Koon H, Penkman K, Elsworth B, Ashford D, Solazzo C, Andrews P, Strahler J, Shapiro B, Ostrom P, Gandhi H, Miller W, Raney B, Zylber MI, Gilbert MTP, Prigodich RV, Ryan M, Rijsdijk KF, Janoo A, Collins MJ. Comment on "Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry". Science 2008; 319:33; author reply 33. [PMID: 18174420 DOI: 10.1126/science.1147046] [Citation(s) in RCA: 116] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
We used authentication tests developed for ancient DNA to evaluate claims by Asara et al. (Reports, 13 April 2007, p. 280) of collagen peptide sequences recovered from mastodon and Tyrannosaurus rex fossils. Although the mastodon samples pass these tests, absence of amino acid composition data, lack of evidence for peptide deamidation, and association of alpha1(I) collagen sequences with amphibians rather than birds suggest that T. rex does not.
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Affiliation(s)
- Mike Buckley
- BioArch, Departments of Biology, Archaeology, Chemistry and Technology Facility, University of York, Post Office Box 373, York YO10 5YW, UK
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