Multicellular Systems - Molecular Theory of the Living Cell - page 514

15.2 The Role of DNA, RNA, and Protein Gradients
in Drosophila Embryogenesis
At the syncytial blastodermal stage of Drosophila embryo (see K3 in Fig. 15.1 ), we
can recognize three kinds of macromolecular gradients:
1. The DNA gradients high in the periphery of the embryo and low in its interior
(as can be inferred from the RNA Images A2, B4, E4, and K4 in Fig. 15.1 ),
2. The RNA gradients along the anterior-posterior axes (see Images A4, C2, D3,
F2, G2, H2, H4, J3, and K4), the dorsal-ventral axes (see Images A1, A2, and
B4), and other directions (see Images E4, G2, H1, H3, I3, and K4), and
3. The protein gradients that can be inferred from RNA gradients since no RNA
would be synthesized or degraded without the associated catalytic proteins or
enzymes. Protein gradients must also be present to act as molecular transporters
or motors (Chap. 8 ) responsible for generating DNA and/or RNA gradients.
A macromolecular gradient has two fundamental properties - (1) the property
intrinsic to the macromolecule (hence to be referred to as the intrinsic or single-
molecule property ) and (2) the property arising from its being a part of a gradient (to
be referred to as the extrinsic or collective property ). Of course, any gradient can
be of two distinct kinds - (1) the spatial gradient (more here than there ) such as those
asymmetric RNA localization images given in Fig. 15.1 , and (2) the temporal
gradient (more now than before ) such as the RNA trajectories shown in Figs. 12.1
and 12.2a . The shape (i.e., the cooperative property of a macromolecule) of a
gradient may be compared to an audio music and the intrinsic property of a
macromolecule to a sheet music . In this analogy, the cellular genome is a master
sheet music and the RNA and protein gradients are the audio music in two different
media or channels having different effective ranges or fields of activity (see Row 3 in
Table 15.1 ). Another way to characterize the roles of DNA, RNA, and protein
gradients in an embryo is in terms of the concept of molecular computing or a system
of molecular computers that are communicating with one another (to accomplish a
common task) using the cell language (Sect. 6.1.2 ) mediated by intercellular protein
messengers (see Row 5 in Table 15.1 ). Viewed in this manner, the RNA localization
(or gradient) images such as displayed in Fig. 15.1 can be considered to represent an
instantaneous computing activity (observed through the lens of RNA) that is being
carried out by the Drosophila embryo as it develops toward an adult fruit fly.
15.3 The Triadic Control Principle (TCP)
The analysis of the genome-wide variations of the RNA levels in budding yeast
undergoing glucose-galactose shift (see Sect. 12.3 ) strongly indicates that the
intracellular concentration of RNA molecules is constantly controlled by the cell