14 P. Doerner
Much progress has recently been made in the identification of transcripts
that vary periodically according to cell cycle phase in plants and to iden-
tify the entire set of genes regulated in this fashion. However, much less is
known about the transcription factors that mediate cell cycle regulated gene
expression in plants than about the key components involved in phosphory-
lation – the cyclin-dependent kinase (CDK) complexes. This has two reasons.
First, the transcription factors responsible for cell cycle phase-specific expres-
sion of cell cycle regulatory genes are poorly conserved. Second, this is also
due to a now dated view of cell cycle regulation as a hierarchy of processes or-
chestrated by a succession of cyclin–CDK complexes that “drive” the cell cycle
forward by enslaving dependent processes such as protein degradation and
temporally regulated gene expression.
Recent studies of the budding and fission yeast cell cycle (Bähler 2005) and
of factors that contribute to robustness of the cell cycle (Li et al. 2004; Jensen
et al. 2006; Braunewell and Bornholdt 2007), lead me to propose a different
view of the relation between the distinct regulatory mechanisms that in con-
cert mediate cell cycle control. Such studies reveal that these mechanisms are
coupled by regulatory interactions, for example: cell cycle phase-specific ex-
pression of individual cyclins conditions high-level CDK activity at specific
times, which in turn controls the activity of the proteasome that regulates the
stability of cell cycle transcription factors. In other words, each of the major
oscillating processes (protein phosphorylation, degradation and temporally
regulated gene expression) comprises a complete and self-regulating cycle that
is interlocked and intersects with other oscillating mechanisms for enhanced
stability. Such coupled oscillators are more robust, and inherently less prone to
interference by inevitable stochastic noise caused by fluctuations in abundance
of individual proteins and their activity (Raser and O’Shea 2004; Braunewell
and Bornholdt 2007); interconnected oscillators are also more easily regulated,
in a coordinate manner, as they continually entrain each other.
In contrast to the highly conserved cyclin–CDK modules, and the core
components of the cellular proteolysis machinery, the key transcriptional
regulators that mediate cell cycle phase-specific gene expression programs
are poorly conserved between different eukaryotic model systems. This has
made it substantially more difficult to identify the components of the tran-
scriptional networks involved in plant cell cycle control as reverse genetic
approaches are not likely to succeed. A recent study of the evolution of cell
cycle regulatory mechanisms has revealed that the regulated subunits (i.e.
those that change their abundance or activity) of different regulatory com-
plexes vary between organisms (Jensen et al. 2006). However, the same study
found that these regulated subunits were likely to be regulated both transcrip-
tionally and post-transcriptionally. This striking convergence of different
regulatory mechanisms involved in cell cycle control onto shared targets is ex-
pected to increase the overall robustness of cell cycle regulation (Braunewell
and Bornholdt 2007), and provides further support to the notion that the