Preservation of the Metaproteome: Variability of Protein Preservation in Ancient Dental Calculus

Overview

Journal Sci Technol Archaeol Res

Publisher Routledge

Date 2017 Nov 4

PMID 29098079

Citations 22

Authors

Meaghan Mackie

Jessica Hendy

Abigail D Lowe

Alessandra Sperduti

Malin Holst

Matthew J Collins

Camilla F Speller

Affiliations

Soon will be listed here.

Abstract

Proteomic analysis of dental calculus is emerging as a powerful tool for disease and dietary characterisation of archaeological populations. To better understand the variability in protein results from dental calculus, we analysed 21 samples from three Roman-period populations to compare: 1) the quantity of extracted protein; 2) the number of mass spectral queries; and 3) the number of peptide spectral matches and protein identifications. We found little correlation between the quantity of calculus analysed and total protein identifications, as well as no systematic trends between site location and protein preservation. We identified a wide range of individual variability, which may be associated with the mechanisms of calculus formation and/or post-depositional contamination, in addition to taphonomic factors. Our results suggest dental calculus is indeed a stable, long-term reservoir of proteins as previously reported, but further systematic studies are needed to identify mechanisms associated with protein entrapment and survival in dental calculus.

Citing Articles

Palaeoproteomic investigation of an ancient human skeleton with abnormal deposition of dental calculus.

Uchida-Fukuhara Y, Shimamura S, Sawafuji R, Nishiuchi T, Yoneda M, Ishida H Sci Rep. 2024; 14(1):5938.

PMID: 38467689 PMC: 10928219. DOI: 10.1038/s41598-024-55779-y.

Extraction Protocol for Parallel Analysis of Proteins and DNA from Ancient Teeth and Dental Calculus.

Chocholova E, Roudnicky P, Potesil D, Fialova D, Krystofova K, Drozdova E J Proteome Res. 2023; 22(10):3311-3319.

PMID: 37699853 PMC: 10563166. DOI: 10.1021/acs.jproteome.3c00370.

Paleoproteomic evidence reveals dairying supported prehistoric occupation of the highland Tibetan Plateau.

Tang L, Wilkin S, Richter K, Bleasdale M, Fernandes R, He Y Sci Adv. 2023; 9(15):eadf0345.

PMID: 37043579 PMC: 10096579. DOI: 10.1126/sciadv.adf0345.

Permafrost preservation reveals proteomic evidence for yak milk consumption in the 13 century.

Ventresca Miller A, Wilkin S, Bayarsaikhan J, Ramsoe A, Clark J, Byambadorj B Commun Biol. 2023; 6(1):351.

PMID: 37002413 PMC: 10066276. DOI: 10.1038/s42003-023-04723-3.

Ecological flexibility and adaptation to past climate change in the Middle Nile Valley: A multiproxy investigation of dietary shifts between the Neolithic and Kerma periods at Kadruka 1 and Kadruka 21.

Le Moyne C, Roberts P, Hua Q, Bleasdale M, Desideri J, Boivin N PLoS One. 2023; 18(2):e0280347.

PMID: 36730175 PMC: 9894462. DOI: 10.1371/journal.pone.0280347.

References

Mandel A, Peyrot des Gachons C, Plank K, Alarcon S, Breslin P . Individual differences in AMY1 gene copy number, salivary α-amylase levels, and the perception of oral starch. PLoS One. 2010; 5(10):e13352. PMC: 2954178. DOI: 10.1371/journal.pone.0013352. View

Baliban R, Sakellari D, Li Z, DiMaggio P, Garcia B, Floudas C . Novel protein identification methods for biomarker discovery via a proteomic analysis of periodontally healthy and diseased gingival crevicular fluid samples. J Clin Periodontol. 2011; 39(3):203-12. PMC: 3268946. DOI: 10.1111/j.1600-051X.2011.01805.x. View

Ozga A, Nieves-Colon M, Honap T, Sankaranarayanan K, Hofman C, Milner G . Successful enrichment and recovery of whole mitochondrial genomes from ancient human dental calculus. Am J Phys Anthropol. 2016; 160(2):220-8. PMC: 4866892. DOI: 10.1002/ajpa.22960. View

Orlando L, Ginolhac A, Zhang G, Froese D, Albrechtsen A, Stiller M . Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. Nature. 2013; 499(7456):74-8. DOI: 10.1038/nature12323. View

Marsh P, Moter A, Devine D . Dental plaque biofilms: communities, conflict and control. Periodontol 2000. 2010; 55(1):16-35. DOI: 10.1111/j.1600-0757.2009.00339.x. View

Brandt L, Schmidt A, Mannering U, Sarret M, Kelstrup C, Olsen J . Species identification of archaeological skin objects from Danish bogs: comparison between mass spectrometry-based peptide sequencing and microscopy-based methods. PLoS One. 2014; 9(9):e106875. PMC: 4178020. DOI: 10.1371/journal.pone.0106875. View

Liu B, Faller L, Klitgord N, Mazumdar V, Ghodsi M, Sommer D . Deep sequencing of the oral microbiome reveals signatures of periodontal disease. PLoS One. 2012; 7(6):e37919. PMC: 3366996. DOI: 10.1371/journal.pone.0037919. View

Dewhirst F, Chen T, Izard J, Paster B, Tanner A, Yu W . The human oral microbiome. J Bacteriol. 2010; 192(19):5002-17. PMC: 2944498. DOI: 10.1128/JB.00542-10. View

Mineoka T, Awano S, Rikimaru T, Kurata H, Yoshida A, Ansai T . Site-specific development of periodontal disease is associated with increased levels of Porphyromonas gingivalis, Treponema denticola, and Tannerella forsythia in subgingival plaque. J Periodontol. 2008; 79(4):670-6. DOI: 10.1902/jop.2008.070398. View

10.

Buckley M, Melton N, Montgomery J . Proteomics analysis of ancient food vessel stitching reveals >4000-year-old milk protein. Rapid Commun Mass Spectrom. 2013; 27(4):531-8. DOI: 10.1002/rcm.6481. View

11.

Haigh B, Stewart K, Whelan J, Barnett M, Smolenski G, Wheeler T . Alterations in the salivary proteome associated with periodontitis. J Clin Periodontol. 2010; 37(3):241-7. DOI: 10.1111/j.1600-051X.2009.01525.x. View

12.

Craig R, Cortens J, Beavis R . Open source system for analyzing, validating, and storing protein identification data. J Proteome Res. 2004; 3(6):1234-42. DOI: 10.1021/pr049882h. View

13.

Colombo A, Boches S, Cotton S, Goodson J, Kent R, Haffajee A . Comparisons of subgingival microbial profiles of refractory periodontitis, severe periodontitis, and periodontal health using the human oral microbe identification microarray. J Periodontol. 2009; 80(9):1421-32. PMC: 3627366. DOI: 10.1902/jop.2009.090185. View

14.

Teles R, Gursky L, Faveri M, Rosa E, Teles F, Feres M . Relationships between subgingival microbiota and GCF biomarkers in generalized aggressive periodontitis. J Clin Periodontol. 2010; 37(4):313-23. PMC: 2910519. DOI: 10.1111/j.1600-051X.2010.01534.x. View

15.

Cappellini E, Jensen L, Szklarczyk D, Ginolhac A, da Fonseca R, Stafford T . Proteomic analysis of a pleistocene mammoth femur reveals more than one hundred ancient bone proteins. J Proteome Res. 2011; 11(2):917-26. DOI: 10.1021/pr200721u. View

16.

Rao P, Reddy A, Lu X, Dasari S, Krishnaprasad A, Biggs E . Proteomic identification of salivary biomarkers of type-2 diabetes. J Proteome Res. 2009; 8(1):239-45. DOI: 10.1021/pr8003776. View

17.

Warinner C, Speller C, Collins M . A new era in palaeomicrobiology: prospects for ancient dental calculus as a long-term record of the human oral microbiome. Philos Trans R Soc Lond B Biol Sci. 2014; 370(1660):20130376. PMC: 4275884. DOI: 10.1098/rstb.2013.0376. View

18.

Warinner C, Hendy J, Speller C, Cappellini E, Fischer R, Trachsel C . Direct evidence of milk consumption from ancient human dental calculus. Sci Rep. 2014; 4:7104. PMC: 4245811. DOI: 10.1038/srep07104. View

19.

Grant M, Creese A, Barr G, Ling M, Scott A, Matthews J . Proteomic analysis of a noninvasive human model of acute inflammation and its resolution: the twenty-one day gingivitis model. J Proteome Res. 2010; 9(9):4732-44. PMC: 2950674. DOI: 10.1021/pr100446f. View

20.

Hodge K, Have S, Hutton L, Lamond A . Cleaning up the masses: exclusion lists to reduce contamination with HPLC-MS/MS. J Proteomics. 2013; 88:92-103. PMC: 3714598. DOI: 10.1016/j.jprot.2013.02.023. View