  Escherichia coli and Bacillus subtilis are two of the best-studied
prokaryotic model organisms. Previous analyses of their transcriptional
regulatory networks have shown that they exhibit high plasticity during
evolution and suggested that both converge to scale-free-like structures.
Nevertheless, beyond this suggestion, no analyses have been carried out to
identify the common systems-level components and principles governing these
organisms. Here we show that these two phylogenetically distant organisms
follow a set of common novel biologically consistent systems principles
revealed by the mathematically and biologically founded natural decomposition
approach. The discovered common functional architecture is a diamond-shaped,
matryoshka-like, three-layer (coordination, processing, and integration)
hierarchy exhibiting feedback, which is shaped by four systems-level
components: global transcription factors (global TFs), locally autonomous
modules, basal machinery and intermodular genes. The first mathematical
criterion to identify global TFs, the $\kappa$-value, was reassessed on B.
subtilis and confirmed its high predictive power by identifying all the
previously reported, plus three potential, master regulators and eight sigma
factors. The functional conserved cores of modules, basal cell machinery, and a
set of non-orthologous common physiological global responses were identified
via both orthologous genes and non-orthologous conserved functions. This study
reveals novel common systems principles maintained between two phylogenetically
distant organisms and provides a comparison of their lifestyle adaptations. Our
results shed new light on the systems-level principles and the fundamental
functions required by bacteria to sustain life.
