Biology Reference
In-Depth Information
Table 12.4 The nine mechanisms of interactions among transcript level (TL), transcription rate
(TR), and transcript degradation rate (TD).
D
TR is + when the transcription rate is increased and -
when the transcription rate is decreased.
D
TD is + when the transcript degradation rate is
increased and - when the transcript degradation rate is decreased. The numerical labels of the
Mechanisms in the fourth column are defined in Fig.
12.8
D
TL
D
TR
Relation between
D
TR and
D
TD
Mechanisms or modules
+
+
D
TR
> D
TD
2
0
D
TR
> D
TD
1
D
TR
> D
TD
8
0
+
D
TR
¼ D
TD
3
0
D
TR
¼ D
TD
9
D
TR
¼ D
TD
7
+
D
TR
< D
TD
4
0
D
TR
< D
TD
5
D
TR
< D
TD
6
in the fourth column in Table
12.4
. The third column in Table
12.4
indicates the
range of changes for
transcript degradation rates
, TD, that are inferred from the
associated changes in TL and TR.
The first three mechanisms reflect the case where the transcript level is
increasing. Mechanism 2 is activated (or realized) when TL increases due to TR
increasing more than TD. Mechanism 1 is activated when TL increases due to
decreasing TD with no change in TR. Mechanism 8 is activated when TL
increases due to TD decreasing more than TR. Similar explanations can be
provided for the remaining six cases. Please note that there is a 180
rotational
symmetry in the arrangement of the relational signs in the third column in the
table, i.e.,
>>>
¼¼¼
<<<
, which indicates that the mechanistic
explanations given in the table are logically coherent.
As evident in the second and third columns of Table
12.4
, each of the nine
possible mechanisms described entails a unique relation between the variations in
transcription rates,
D
TR, and that of the transcript degradation rates,
D
TD. Such
relations cannot arise from random interactions between these two processes, thus
leading to the following conclusion:
,
,
There exist mechanisms in living cells that control the interaction between transcription and
transcript degradation rates. (12.18)
The enzyme system catalyzing transcription is known as
transcriptosome
(Halle and Meisteerernst 1996), and that catalyzing transcript degradation is
referred to as
degradosome
in bacteriology which is here
commandeered
to
represent transcript degradation in all cell types. Thus, the second column in
Table
12.4
expresses the direction of the absolute changes in the activity of
transcriptosome while the third column indicates the relative changes in the
activities of
transcriptosome
and
degradosome
. The time-dependent patterns of
the changes in TL (i.e., the RNA trajectories or waves) that result from controlled
interactions between
transcriptosome
and
degradosome
will be referred to as
