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Sequence space and the ongoing expansion of the protein universe

Abstract

The need to maintain the structural and functional integrity of an evolving protein severely restricts the repertoire of acceptable amino-acid substitutions1,2,3,4. However, it is not known whether these restrictions impose a global limit on how far homologous protein sequences can diverge from each other. Here we explore the limits of protein evolution using sequence divergence data. We formulate a computational approach to study the rate of divergence of distant protein sequences and measure this rate for ancient proteins, those that were present in the last universal common ancestor. We show that ancient proteins are still diverging from each other, indicating an ongoing expansion of the protein sequence universe. The slow rate of this divergence is imposed by the sparseness of functional protein sequences in sequence space and the ruggedness of the protein fitness landscape: 98 per cent of sites cannot accept an amino-acid substitution at any given moment but a vast majority of all sites may eventually be permitted to evolve when other, compensatory, changes occur. Thus, 3.5 × 109 yr has not been enough to reach the limit of divergent evolution of proteins, and for most proteins the limit of sequence similarity imposed by common function may not exceed that of random sequences.

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Figure 1: Expansion of the physical and the protein universes.
Figure 2: Measuring the rate of divergence of distant protein sequences.
Figure 3: The rate of expansion of the protein sequence universe.
Figure 4: Sequence space of two nucleotide sites.
Figure 5: Divergent and convergent evolution.

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Acknowledgements

We thank E. Koonin, Y. Wolf, A. Lobkovsky, D. Petrov, D. Ivankov, J. Sharpe, B. Lehner, Y. Jaeger, P. Vlasov, M. Ptitsyn and M. Roytberg for discussions and A. Kondrashov for extensive feedback on our manuscript. We thank D. Tawfik for inspiring us to start the investigation of the functional limits in sequence space.

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Authors

Contributions

I.S.P. performed all analyses and obtained all of the data. F.A.K. conceived the study and drafted the manuscript. Both authors participated in the design of the analyses and the interpretation of the results.

Corresponding author

Correspondence to Fyodor A. Kondrashov.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Information

This file contains Supplementary Information comprising: Rationale for avoiding deep ancestral state reconstructions and Deconstructing the Nt and Na measurements, References and Supplementary Figures 1-8 with legends. (PDF 515 kb)

Supplementary Table 1

This table contains genomes that have not been used as quadruplets but were assigned to COGs that were present in LUCA. (PDF 302 kb)

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Povolotskaya, I., Kondrashov, F. Sequence space and the ongoing expansion of the protein universe. Nature 465, 922–926 (2010). https://doi.org/10.1038/nature09105

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