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Abstract
Eukarya and Bacteria are the most evolutionarily distant domains of life, which is reflected by differences in their cellular structure and physiology. For example, Eukarya feature membrane-bound organelles such as nuclei and mitochondria, whereas Bacteria have none. The greater complexity of Eukarya renders them difficult to study from both an experimental and theoretical perspective. However, encouraged by a recent experimental result showing that budding yeast (a unicellular eukaryote) obeys the same proportionality between ribosomal proteome fractions and cellular growth rates as Bacteria, we derive a set of relations describing eukaryotic growth from first principles of ribosome biogenesis. We recover the observed ribosomal protein proportionality, and then continue to obtain two growth-laws for the number of RNA polymerases synthesizing ribosomal RNA per ribosome in the cell. These growth-laws, in turn, reveal two invariants of eukaryotic growth, i.e. quantities predicted to be conserved by Eukarya regardless of growth conditions. The invariants, which are the first of their kind for Eukarya, clarify the coordination of transcription and translation kinetics as required by ribosome biogenesis, and link these kinetic parameters to cellular physiology. We demonstrate application of the relations to the yeast S. cerevisiae and find the predictions to be in good agreement with currently available data. We then outline methods to quantitatively deduce several unknown kinetic and physiological parameters. The analysis is not specific to S. cerevisiae and can be extended to other lower (unicellular) Eukarya when data become available. The relations may also have relevance to certain cancer cells which, like bacteria and yeast, exhibit rapid cell proliferation and ribosome biogenesis.
Highlights
Recent advances in biological physics have led to the discovery of quantitative relations, or “laws,” describing bacterial growth [1,2,3,4,5,6], gene expression [7,8], and cell size control [9,10]; see Ref. [11] for a review and historical perspective
We recently showed that this process leads to another bound on cellular growth rates and to growth laws which were verified for the bacterium E. coli [25,26]
Our results suggest that S. cerevisiae attains the maximal growth rate permitted by bounds of ribosome production, as in E. coli, but more data are required for verification
Summary
Recent advances in biological physics have led to the discovery of quantitative relations, or “laws,” describing bacterial growth [1,2,3,4,5,6], gene expression [7,8], and cell size control [9,10]; see Ref. [11] for a review and historical perspective. There the authors demonstrated that ribosomal proteome fractions in budding yeast are proportional to cellular growth rates, as previously observed for Bacteria [19,20] Underlying this proportionality is the coupling between cell growth and ribosome biogenesis [21], i.e., that cell doubling requires a commensurate doubling of ribosomes. II, we mathematically formulate the kinetics of ribosome production in lower Eukarya These include the already known proportionality between r-protein fractions and growth rates, as well as two additional growth laws for RNAP I and RNAP III which make rRNA in eukaryotic cells. The growth laws, in turn, yield two invariants Data for the case study of S. cerevisiae, are provided in Appendices
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