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Oxygen content of transmembrane proteins over macroevolutionary time scales

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Abstract

We observe that the time of appearance of cellular compartmentalization correlates with atmospheric oxygen concentration. To explore this correlation, we predict and characterize the topology of all transmembrane proteins in 19 taxa and correlate differences in topology with historical atmospheric oxygen concentrations. Here we show that transmembrane proteins, individually and as a group, were probably selectively excluding oxygen in ancient ancestral taxa, and that this constraint decreased over time when atmospheric oxygen levels rose. As this constraint decreased, the size and number of communication-related transmembrane proteins increased. We suggest the hypothesis that atmospheric oxygen concentrations affected the timing of the evolution of cellular compartmentalization by constraining the size of domains necessary for communication across membranes.

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Figure 1: Oxygen content density functions on full proteome, transmembrane and non-transmembrane protein sets.
Figure 2: Ternary diagrams of compositional data for transmembrane, extracellular and intracellular domains for the entire predicted transmembrane protein set.
Figure 3: Mean domain length versus time of appearance of class.
Figure 4: Inside, outside and transmembrane domain oxygen content versus time of appearance of class.
Figure 5: Mean proteome oxygen content.

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  • 31 January 2008

    The institute in address 2 should have been listed as 'Institute of Molecular Biology and Bioinformatics' and not 'Institute of Molecular Biology and Biochemistry'. This was corrected in the HTML on 31 January 2008.

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Acknowledgements

The authors would like to thank J. Anderson for help with the estimates of the time of appearance of the organisms used for this study, and D. Schomburg, R. Wünschiers, D. Bauer, A. Scialpi, M. Koornneef, H. Hillebrand, A. M. Tarchi, P. Bruni, T. Wiehe, B. Haubold and T. Rothery for valuable discussions. Author Contributions C.A. initiated and devised the project; C.A., S.C. and J.K. analysed the data; and S.C. and C.A. wrote the manuscript.

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Correspondence to Claudia Acquisti.

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This file contains Supplementary Table showing organisms names and data sets sample sizes and Supplementary Figures 1- 7 with legends. (PDF 2115 kb)

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Acquisti, C., Kleffe, J. & Collins, S. Oxygen content of transmembrane proteins over macroevolutionary time scales. Nature 445, 47–52 (2007). https://doi.org/10.1038/nature05450

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