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Four Billion Years: The Story of an Ancient Protein Family

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Theoretical Physics, Wavelets, Analysis, Genomics

Part of the book series: Applied and Numerical Harmonic Analysis ((ANHA))

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Abstract

Comparison of protein sequences has long been a very effective tool for producing biological knowledge. It was initially based on the alignment of sequences, that is to say organizing the set of sequences in columns (of a spreadsheet) of sites which have evolved from a common site of the ancestral sequence. Alignments are generally obtained by minimizing an evolution or an edition cost. Sequence comparisons are now often performed without alignments by comparing the N-mer compositions of the sequences. We present here the most popular methods used by biologists to compare sequences and place emphasis on an approach to augment the alphabet of a set of sequences in order to ease their comparison. The family of DNA topoisomerases, a set of ancient proteins whose history can be traced back 4 billion years, is used to illustrate this approach.

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Notes

  1. 1.

    Phylogeny is the study of the degree of relationship between living organisms, which enables to reconstruct their evolution. In a phylogenetic tree, the nodes represent the common ancestors. The greater the number of nodes between two taxa, the more ancient is their common ancestor and the farther they are in the tree of life—the length of the branches is approximately proportional to the time of divergence between the taxa [22, 40].

  2. 2.

    Proteins are macromolecules composed of a linear string of amino acids. They are generally made of several hundreds of the 20 different amino acids.

  3. 3.

    All the statements of this section still hold by replacing “sequence” with “set of sequences.”

  4. 4.

    The reverse gyrase exists mainly in bacteria and archaea whose growth optimum is above 80∘ C; it protects DNA from the denaturation that normally occurs at such high temperatures.

  5. 5.

    As an example, let us take the bias in the isotopic composition of carbon. Atmospheric CO2 is made up of a mixture of 12C and 13C. Since the photosynthetic organisms have a preference for the 12C-containing CO2, the biological fossil sediments will be richer in 12C than the abiotic sediments. This corresponds to the 13C depleted reduced carbon in Fig. 7.

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Acknowledgements

The authors would like to sincerely thank Marc Nadal and Jean-Loup Risler for their constructive criticism and Alessandra Riva for proofreading the article.

Author information

Authors and Affiliations

  1. IMAG, Univ Montpellier, CNRS, Montpellier, France

    Gilles Didier

  2. Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France

    Claudine Landès

  3. Université Publique Française, Evry, France

    Alain Hénaut

  4. Aix Marseille Univ, CNRS, I2M, Marseille, France

    Bruno Torrésani

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  1. Gilles Didier
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  4. Bruno Torrésani
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Correspondence to Bruno Torrésani .

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Editors and Affiliations

  1. Laboratoire de Physique, Université Lyon, ENS de Lyon, Université Claude Bernard, CNRS, Lyon, France

    Patrick Flandrin

  2. Mathematics, Université Paris Est Créteil, Créteil, France

    Stéphane Jaffard

  3. Sorbonne Université, CNRS, Université Paris Cité, Laboratoire Jacques-Louis Lions (LJLL), Paris, France

    Thierry Paul

  4. Mathematics, Université d’Aix-Marseille, Marseille, France

    Bruno Torresani

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Didier, G., Landès, C., Hénaut, A., Torrésani, B. (2023). Four Billion Years: The Story of an Ancient Protein Family. In: Flandrin, P., Jaffard, S., Paul, T., Torresani, B. (eds) Theoretical Physics, Wavelets, Analysis, Genomics. Applied and Numerical Harmonic Analysis. Birkhäuser, Cham. https://doi.org/10.1007/978-3-030-45847-8_25

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