TY - UNPB
T1 - Transcription-translation machinery
T2 - an autocatalytic network coupling all cellular cycles and generating a plethora of growth laws
AU - Roy, Anjan
AU - Goberman, Dotan
AU - Pugatch, Rami
PY - 2021
Y1 - 2021
N2 - Recently discovered simple quantitative relations, known as bacterial
growth laws, hint on the existence of simple underlying principles at
the heart of bacterial growth. In this work, we provide a unifying
picture on how these known relations, as well as new relations that we
derive, stems from a universal autocatalytic network common to all
bacteria, facilitating balanced exponential growth of individual cells.
We show that the core of the cellular autocatalytic network is the
transcription -- translation machinery -- in itself an autocatalytic
network comprising several coupled autocatalytic cycles, including the
ribosome, RNA polymerase, and tRNA charging cycles. We derive two types
of growth laws per autocatalytic cycle, one relating growth rate to the
relative fraction of the catalyst and its catalysis rate, and the other
relating growth rate to all the time scales in the cycle. The structure
of the autocatalytic network generates numerous regimes in state space,
determined by the limiting components, while the number of growth laws
can be much smaller. We also derive a growth law that accounts for the
RNA polymerase autocatalytic cycle, which we use to explain how growth
rate depends on the inducible expression of the rpoB and rpoC genes,
which code for the RpoB and C protein subunits of RNA polymerase, and
how the concentration of rifampicin, which targets RNA polymerase,
affects growth rate without changing the RNA-to-protein ratio. We derive
growth laws for tRNA synthesis and charging, and predict how growth rate
depends on temperature, perturbation to ribosome assembly, and membrane
synthesis.
AB - Recently discovered simple quantitative relations, known as bacterial
growth laws, hint on the existence of simple underlying principles at
the heart of bacterial growth. In this work, we provide a unifying
picture on how these known relations, as well as new relations that we
derive, stems from a universal autocatalytic network common to all
bacteria, facilitating balanced exponential growth of individual cells.
We show that the core of the cellular autocatalytic network is the
transcription -- translation machinery -- in itself an autocatalytic
network comprising several coupled autocatalytic cycles, including the
ribosome, RNA polymerase, and tRNA charging cycles. We derive two types
of growth laws per autocatalytic cycle, one relating growth rate to the
relative fraction of the catalyst and its catalysis rate, and the other
relating growth rate to all the time scales in the cycle. The structure
of the autocatalytic network generates numerous regimes in state space,
determined by the limiting components, while the number of growth laws
can be much smaller. We also derive a growth law that accounts for the
RNA polymerase autocatalytic cycle, which we use to explain how growth
rate depends on the inducible expression of the rpoB and rpoC genes,
which code for the RpoB and C protein subunits of RNA polymerase, and
how the concentration of rifampicin, which targets RNA polymerase,
affects growth rate without changing the RNA-to-protein ratio. We derive
growth laws for tRNA synthesis and charging, and predict how growth rate
depends on temperature, perturbation to ribosome assembly, and membrane
synthesis.
KW - Quantitative Biology - Molecular Networks
KW - Physics - Biological Physics
M3 - ???researchoutput.researchoutputtypes.workingpaper.preprint???
T3 - arXiv preprint
BT - Transcription-translation machinery
ER -