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An Integrated Method to Reconstruct Ancient Proteins

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Environmental Microbial Evolution

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2569))

Abstract

Proteins have played a fundamental role throughout life’s history on Earth. Despite their biological importance, ancient origin, early function, and evolution of proteins are seldom able to be directly studied because few of these attributes are preserved across geologic timescales. Ancestral sequence reconstruction (ASR) provides a method to infer ancestral amino acid sequences and determine the evolutionary predecessors of modern-day proteins using phylogenetic tools. Laboratory application of ASR allows ancient sequences to be deduced from genetic information available in extant organisms and then experimentally resurrected to elucidate ancestral characteristics. In this article, we provide a generalized, stepwise protocol that considers the major elements of a well-designed ASR study and details potential sources of reconstruction bias that can reduce the relevance of historical inferences. We underscore key stages in our approach so that it may be broadly utilized to reconstruct the evolutionary histories of proteins.

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Acknowledgments

This work was supported by the National Science Foundation Emerging Frontiers Program Award No. 1724090.

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Authors and Affiliations

  1. Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA

    Amanda K. Garcia, Evrim Fer & Betul Kacar

  2. Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA

    Evrim Fer

  3. Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA, USA

    Cathryn Sephus

Authors
  1. Amanda K. Garcia
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  2. Evrim Fer
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  3. Cathryn Sephus
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  4. Betul Kacar
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Corresponding author

Correspondence to Betul Kacar .

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Editors and Affiliations

  1. School of Life Sciences, Earth and Environmental Sciences Programme, and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China

    Haiwei Luo

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Garcia, A.K., Fer, E., Sephus, C., Kacar, B. (2022). An Integrated Method to Reconstruct Ancient Proteins. In: Luo, H. (eds) Environmental Microbial Evolution. Methods in Molecular Biology, vol 2569. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2691-7_13

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  • DOI: https://doi.org/10.1007/978-1-0716-2691-7_13

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2690-0

  • Online ISBN: 978-1-0716-2691-7

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