PALEOPROTEOMICS STUDIES OF ANCIENT CAPRINAE: A REVIEW

Authors

  • S.Sh. Atavliyeva М. Republican State Enterprise «National Center for Biotechnology» under the Science Committee of Ministry of Education and Science of the Republic of Kazakhstan, Kazakhstan, Nur-Sultan
  • P.V. Tarlykov М. Republican State Enterprise «National Center for Biotechnology» under the Science Committee of Ministry of Education and Science of the Republic of Kazakhstan, Kazakhstan, Nur-Sultan

DOI:

https://doi.org/10.26577/eb.2021.v89.i4.01
        129 45

Abstract

In the Neolithic era, people began to graze sheep and goats primarily due to easier access to meat, milk, and fleeces. Thus, in ancient times, Caprinae were the key animals in the development of early domestication and agriculture. The analysis of ancient proteins of Caprinae from paleontological and archeological materials reveals new data on their migration, complements research on the diet of ancient people, their culture, and habits. Here, we discuss paleoproteomics methods, such as matrix-assisted laser desorption/ionization with time-of-flight mass analyzer (MALDI-TOF MS) and liquid chromatography with tandem mass spectrometry (LC-MS / MS). We will also consider the most important discoveries in the field of the study of ancient sheep and in which direction the paleoproteomics of Caprinae will develop in the near future.  In addition, general recommendations for analyzing data from ancient proteins are considered, for example, programs and requirements for databases. We will consider the main search algorithms in proteomics, as well as identify effective ones for identifying peptides and proteins. It also describes the commonly used ancient protein targets, and the basic principles of working with ancient samples. In addition, this review describes the main research conducted on ancient Caprinae of ancient proteins such as collagen, keratin, and milk proteins.

References

Cappellini E., Prohaska A., Racimo F., et al. Ancient Biomolecules and Evolutionary Inference // Annual Review Biochem. – 2018. – Vol. 87. – P. 1029-1060.

Welker F. Palaeoproteomics for human evolution studies // Quat. Science Rev. – 2018. - Vol. 90. – P. 137-147.

Hendy J., Welker F., Demarchi B., Speller C., Warinner C., Collins M.J. A guide to ancient protein studies // Nat. Ecol. Evol. – 2018. – Vol. 2, No 5. – P.791-799.

Huq N.L., Tseng A., Chapman G.E. Partial amino acid sequence of osteocalcin from an extinct species of ratite bird // Biochem. Int. – 1990. - Vol.21, No 3. – P. 491–496.

Robbins L.L., Muyzer G., Brew K., Macromolecules from living and fossil biominerals. In: Engel, M.H., Macko, S.A. (Eds.), Organic Geochemistry: Principles and Applications. – 1993. – Vol. 11. – P. 799-816.

Solazzo C. Characterizing historical textiles and clothing with proteomics // Conserv. Patrim. – 2019. – Vol. 31. – P. 97-114.

O’Connor S., Solazzo C., Collins M. Advances in identifying archaeological traces of horn and other keratinous hard tissues // Stud. Conserv. – 2015. – Vol. 60. – P. 393-417.

Buckley M., Matthew Collins M. et al. Species identification by analysis of bone collagen using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry Michael // Rapid. Commun. Mass Spectrom. – 2009. – Vol. 23. – P. 3843–3854.

van Doorn N.L., Hollund H., Collins M.J. A novel and non-destructive approach for ZooMS analysis: Ammonium bicarbonate buffer extraction // Archaeol. Anthropol. Sci. – 2011. – Vol. 3. – P. 281-289.

Buckley M., Whitcher Kansa S., Howard S., Campbell S., Thomas-Oates J., Collins M. Distinguishing between archaeological sheep and goat bones using a single collagen peptide // J. Archaeol. Sci. – 2010. – Vol. 37. – P. 13-20.

Buckley M., Fariña R.A., Lawless C., Tambusso P.S., Varela L. et al. Collagen Sequence Analysis of the Extinct Giant Ground Sloths Lestodon and Megatherium // PLOS ONE. – 2015. – Vol. 10. e0144793.

Buckley M. Ancient collagen reveals evolutionary history of the endemic South American “ungulates.” // Proc. R. Soc. - 2015. – Vol. 282. – P. 1-9.

Salmon C.R., Giorgett A.P.O., Paes Leme A.F., Domingues R.R., Kolli T.N., Foster B.L., Nociti Jr., F.H., Microproteome of dentoalveolar tissues // Bone. - 2017. - Vol. 101. – P. 219-229.

Salmon C.R., Tomazela D.M., Ruiz K.G.S., Foster B.L., Paes Leme A.F. et al. Proteomic analysis of human dental cementum and alveolar bone // J. Proteom. - 2013. - Vol. 91. –P. 544–555.

Porto I. M., Laure H.J., Tykot R.H., de Sousa F.B., Rosa J.C., Gerlach R.F. Recovery and identification of mature enamel proteins in ancient teeth // Eur. J. Oral Sci. – 2011. – Vol. 119. – P. 83-87.

Castiblanco G.A., Rutishauser D., Ilag, L.L., Martignon S., Castellanos J.E., Mejía W. Identification of proteins from human permanent erupted enamel // Eur. J. Oral Sci. - 2015. – Vol. 123. – P. 390-395.

Stewart N. A., Gerlach R.F., Gowland R.L., Gron K.J., Montgomery J. Sex determination of human remains from peptides in tooth enamel // PNAS. - 2017. – Vol. 114. – P. 13649–13654.

Stewart N.A., Molina G.F., Issa J.P.M., Yates N.A., Sosovicka M., Vieira A.R., Line S.R.P., Montgomery J., Gerlach R.F. The identification of peptides by nanoLC-MS/MS from human surface tooth enamel following a simple acid etch extraction // RSC Adv. - 2016. – Vol. 6. –P. 61673-61679.

Jeong C., Wilkin S., Amgalantugs T. et al. Bronze Age population dynamics and the rise of dairy pastoralism on the eastern Eurasian steppe // Proc. Natl. Acad. Sci. USA. – 2018. – Vol. 115. – P. 11248-11255.

Greco E., El-Aguizy O., Ali M.F. et al. Proteomic Analyses on an Ancient Egyptian Cheese and Biomolecular Evidence of Brucellosis // Anal Chem. – 2018. – Vol. 90. – P. 9673-9676.

Presslee S., Penkman K., Fischer R. et al. Assessment of different screening methods for selecting palaeontological bone samples for peptide sequencing // Journal Proteomics. – 2021. – Vol. 230.- P. 103986.

Mackie M., Rüther P., Samodova D., et al. Palaeoproteomic Profiling of Conservation Layers on a 14th Century Italian Wall Painting. // Angew. Chemie. – Int. Ed. – 2018. – Vol. 57. - P. 7369-7374.

Welker F., Hajdinjak M., Talamo S., Jaouen K., Dannemann M., David F., Julien M., Meyer M., Kelso J., Barnes I., Brace S., Kamminga P., Fischer R., Kessler B.M., Stewart J.R., Paabo S., Collins M.J., Hublin J.-J., Palaeoproteomic evidence identifies archaic hominins associated with the Chatelperronian at the Grotte du Renne // Proc. Natl. Acad. Sci. U. S. A. – 2016. – Vol. 113. – P. 11162-11167.

Welker F., Soressi M.A., Roussel M., van Riemsdijk I., Hublin J.-J., Collins, M.J.. Variations in glutamine deamidation for a Chatelperronian bone assemblage as measured by peptide mass fingerprinting of collagen // STAR Sci. Technol. Archaeol. – 2017. – Vol. 3. – P. 15-27.

Solazzo C., Wilson J., Dyer J.M. et al. Modeling deamidation in sheep α-keratin peptides and application to archeological wool textiles // Anal. Chem. – 2014. – Vol. 86. – P. 567-575.

Warinner C. et al. Direct evidence of milk consumption from ancient human dental calculus // Sci. Rep. – 2014. – Vol. 4. –P. 7104.

Cappellini E., Jensen L.J., Szklarczyk D., Ginolhac A., da Fonseca R.A.R., et al. Proteomic analysis of a Pleistocene mammoth femur reveals more than one hundred ancient bone proteins // J. Proteome Res. -2012. – Vol. 11. – P. 917–926

Demarchi B., Hall S., Roncal-Herrero T., et al. Protein sequences bound to mineral surfaces persist into deep time // Elife – 2016. – Vol. 5.

Le Meillour L., Zirah S., Zazzo A., et al. Palaeoproteomics gives new insight into early southern African pastoralism // Sci Rep. – 2020. – Vol. 10. –P 1-14.

Tyanova et al. The MaxQuant computational platform for mass-spectrometry-based shotgun proteomics // Nature Protocols. – 2016. – Vol. 11. – P. 2301-2319.

Coutu A.N., Taurozzi A.J., Mackie M., et al. Palaeoproteomics confirm earliest domesticated sheep in southern Africa ca. 2000 BP // Sci Rep. – 2021. – Vol. 11. – P. 6631.

Zeder M.A. Domestication and early agriculture in the Mediterranean Basin: Origins, diffusion, and impact // Proc. Natl. Acad. Sci. – 2008. – Vol. 105. – P. 11597-11604.

Olivieri C., Ermini L., Rizzi E., et al. Phylogenetic position of a copper age sheep (Ovis aries) mitochondrial DNA // PLoS One. – 2012. – Vol. 7(3). –P. e33792.

Hong C., Jiang H., Lü E. et al. Identification of milk component in ancient food residue by proteomics. PLoS One. – 2012. – Vol. 7. – P. 1-7.

Azémard C., Zazzob A., Mariea A., Lepetzb S., Debaine-Francfortc C., Idrissd SZ. Animal fibre use in the Keriya valley (Xinjiang, China) during the Bronze and Iron Ages: A proteomic approach // Journal of Archaeological Science. – 2019. – Vol. 110. – P. 104996.

Prendergast M.E., Janzen A., Buckley M., Grillo K.M. Sorting the sheep from the goats in the Pastoral Neolithic: morphological and biomolecular approaches at Luxmanda, Tanzania // Archaeol. Anthropol. Sci. – 2019. – Vol. 11. – P. 3047-3062.

Buckley M., Kansa S.W. Collagen fingerprinting of archaeological bone and teeth remains from Domuztepe, South Eastern Turkey // Archaeol. Anthropol. Sci. – 2011. – Vol. 3. – P. :271-280.

Le Meillour L., Zazzo A., Lesur J., et al. Identification of degraded bone and tooth splinters from arid environments using palaeoproteomics // Palaeogeogr Palaeoclimatol Palaeoecol. – 2018. – Vol. 511. – P. 472-482.

McKittrick J., Chen P.Y., Bodde S. G., Yang W., Novitskaya E.E., Meyers M.A. The Structure, Functions, and Mechanical Properties of Keratin // JOM Journal of the Minerals, Metals and Materials Society. - 2012. – Vol. 64. – P. 449–68.

Solazzo C., Wadsley M., Dyer J.M., Clerens S., Collins M.J., Plowman J. Characterisation of novel α-keratin peptide markers for species identification in keratinous tissues using mass spectrometry // Rapid Commun Mass Spectrom. – 2013. – Vol. 27. – P. 2685-2698.

Hollemeyer K., Altmeyer W., Heinzle E., Pitra, C. Matrix- assisted Laser Desorption/Ionization Time-of-flight Mass Spectrometry Combined with Multidimensional Scaling, Binary Hierarchical Cluster Tree and Selected Diagnostic Masses Improves Species Identification of Neolithic Keratin Sequences from Furs of the Tyrolean Iceman Oetzi // Rapid Communications in Mass Spectrometry. - 2012. – Vol. 26. – P. 1735–1745.

Charlton S., Ramsoe A., Collins M. et al. New insights into Neolithic milk consumption through proteomic analysis of dental calculus// Archaeol. Anthropol. Sci. – 2019. – Vol. 11. – P. 6183-6196.

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Published

2021-12-20

How to Cite

Atavliyeva, S., & Tarlykov, P. (2021). PALEOPROTEOMICS STUDIES OF ANCIENT CAPRINAE: A REVIEW. Experimental Biology, 89(4), 4–14. https://doi.org/10.26577/eb.2021.v89.i4.01