Kinetics of transcription initiation directed by multiple cis-regulatory elements on the glnAp2 promoter
Nucleic Acids Research
Kinetics of transcription initiation directed by multiple cis-regulatory elements on the glnAp2 promoter
Yaolai Wang 1
Feng Liu 0 1
Wei Wang 0 1
0 Collaborative Innovation Center of Advanced Microstructures, Nanjing University , Nanjing 210093 , China
1 National Laboratory of Solid State Microstructures and Department of Physics, Nanjing University , Nanjing 210093 , China
Transcription initiation is orchestrated by dynamic molecular interactions, with kinetic steps difficult to detect. Utilizing a hybrid method, we aim to unravel essential kinetic steps of transcriptional regulation on the glnAp2 promoter, whose regulatory region includes two enhancers (sites I and II) and three lowaffinity sequences (sites III-V), to which the transcriptional activator NtrC binds. By structure reconstruction, we analyze all possible organization architectures of the transcription apparatus (TA). The main regulatory mode involves two NtrC hexamers: one at enhancer II transiently associates with site V such that the other at enhancer I can rapidly approach and catalyze the 54-RNA polymerase holoenzyme. We build a kinetic model characterizing essential steps of the TA operation; with the known kinetics of the holoenzyme interacting with DNA, this model enables the kinetics beyond technical detection to be determined by fitting the input-output function of the wild-type promoter. The model further quantitatively reproduces transcriptional activities of various mutated promoters. These results reveal different roles played by two enhancers and interpret why the low-affinity elements conditionally enhance or repress transcription. This work presents an integrated dynamic picture of regulated transcription initiation and suggests an evolutionarily conserved characteristic guaranteeing reliable transcriptional response to regulatory signals.
Genetic information is dynamically transcribed with the
change of cellular regulatory signals (1–4). Whereas the
structural organizations of proteins participating in
transcription have been largely determined (5–12), much less
is known about the dynamic processes of protein–DNA
and protein-protein interactions (12–17). Uncovering such
dynamics is not only fundamental to comprehending how
transcription is orchestrated, but also essential to interpret
the behaviors of gene regulatory networks – due to the
resulting complex temporal evolution of transcript numbers
(2,4,17–22). Those kinetic steps are hard to detect
experimentally, especially when unstable protein complexes and
unknown transient interactions are involved (23–26).
Recently, the steps of the holoenzyme 54-RNA polymerase
( 54RNAP) associating with promoter DNA have been
dissected (27,28). Nevertheless, how transcriptional activators
interact with the cis-regulatory elements and 54RNAP to
control transcription initiation remains unclear. Here, we
address this issue in terms of activity from the glnAp2
promoter of Escherichia coli, which is the most extensively
studied 54-depedent promoter.
glnAp2 transcription is activated by NtrC in response to
nitrogen limitation (29–33). NtrC molecules are dimeric in
their inactive state. Upon activation, NtrC dimers are
phosphorylated and bind to two enhancers centered at −140
(site I) and −108 (site II) relative to the transcription start
site (21,34–37) (Figure 1A and B). The bound dimers have
much lower mobility and nucleate free dimers to form NtrC
hexamers (38). 54RNAP binds to the −24–−12 region at
one face of the double helix (11). NtrC hexamers catalyze
54RNAP via DNA looping; the catalysis reaction takes
place at approximately −12 region and the edge of the
central pore of NtrC hexamer (10,11,29,38). Such a
regulatory mode––activators at remote enhancers direct
transcription initiation though DNA looping––is similar to that in
eukaryotes. Additionally, there are three low-affinity
binding sites for NtrC, which are separately centered at −89,
−66 and −45 (sites III-V) (21,33,39). These sites are rarely
occupied at low and intermediate concentrations of NtrC
dimers. Low-affinity sequences also widely exist in
eukaryotes, with the function largely unclear. Uncovering the
transcriptional regulation on glnAp2 is thus promising to
provide general insights.
Although the transcription apparatus (TA) on the glnAp2
promoter only involves NtrC, 54RNAP and promoter
DNA, it exhibits complicated transcriptional activities
(21,22,40). If the low-affinity sites are all substituted with
the sequences that do not bind any protein, glnAp2 is
transcribed at ∼45% of the wild-type level; but the
transcriptional level is further lowered to ∼22% if these sites are
substituted with the enhancer sequences. Moreover, the
lowaffinity sites act to repress transcription at high
concentrations of NtrC dimers. These characteristics cannot be fully
accounted for by traditional views (Figure 1C and D). The
notion that transcription initiation is activated by an NtrC
hexamer spanning the two enhancers fails to explain why
the low-affinity sites can promote transcriptional output
(35,41). Structurally, the binding of NtrC to the low-affinity
sites enhances the bending rigidity of DNA, rather than
significantly bend DNA as the integration host factor (7), and
thus prevents the hexamers at enhancers from contacting
the holoenzyme (29,36,42). An alternative postulation was
that NtrC dimers could constitute a huge octamer at the
five sites to activate transcription (22) (Figure 1D); but this
is inconsistent with the structural basis of activation––the
holoenzyme is catalyzed at the edge of the central pore of
NtrC hexamer (10,11,29,38). All these suggest that it is
necessary to revisit the role for the low-affinity sites in
transcriptional regulation and to unravel the kinetics of NtrC
interacting with the five cis-regulatory elements.
By three-dimensional structure reconstruction, we first
explore all possible architectures and conformational
transitions of the TA. Although NtrC hexamers at either
enhancer are capable of catalyzing the holoenzyme, the main
regulatory mechanism involves the II-V bridging mediated
by NtrC oligomers at enhancer II. This unstable DNA
bridging is also the structural basis for the low-affinity sites
to promote transcriptional output. We then construct a
model characterizing how the TA dynamically operates; the
model is validated by its ability to quantitatively
recapitulate transcriptional activities from various mutated
promoters. The kinetic features of key molecular interactions
are also unraveled. The proposed dynamic mechanisms for
transcriptional regulation exhibit strong robustness to
various perturbations. Since glnAp2 transcription is regulated
in a mode similar to that in eukaryotes, the unexpected
findings such as the key roles played by low-affinity sequences
may be of wide implications.
MATERIALS AND METHODS
To reveal how NtrC interacts with the five binding sites and
controls transcription initiation, the molecular surface of
NtrC hexamer and standard B-DNA double helix were
reconstructed using the software 3ds Max (Figure 1B). The
dimensions of the standard B-DNA double helix in solution
are 34 A˚ per helical turn, 24 A˚ in diameter, 22 A˚ across the
major groove and 12 A˚ across the minor groove. The NtrC
hexamer was reconstructed based on its X-ray structure
(38). Its DNA binding domains (DBDs) were not
reconstructed to the surface for accuracy since they may detach
from the main ring. The slightly raised part surrounding the
central pore was also not reconstructed for simplicity. The
X-ray structure of RNAP (PDB id: 1IW7) was used in
structural analysis. Referring to the conformations of NtrC’s
DBD interacting with DNA (29,42) and of the holoenzyme
catalyzed by NtrC at the core promoter (11,38), we
examined all possible structural organizations together with their
conformational changes. The surface structure of NtrC
hexamer changes very slightly when catalyzing the holoenzyme,
and there are no other conformational changes (38). The
spatial arrangement of NtrC hexamers on the DNA can
thus be evaluated with sufficient accuracy. Possible
conformations of DNA bridging are presented in Supplemental
Entropy theory and the Jacobson & Stockmayer function
were employed to evaluate the timescale of DNA looping
(22,43–45). The standard Gillespie method was used to fit
the experimental data and perform numerical simulations
(46,47). Details of all analytical and numerical calculations
are available in Supplemental S2 and S3. All statistical
analyses were based on sufficient sample data.
Configurations of the TA underlying transcription initiation
Based on structure reconstruction, we first analyze whether
an NtrC hexamer nucleated at any binding site can
approach and catalyze the holoenzyme. Obviously, a hexamer
at enhancer I or II can contact the holoenzyme via DNA
looping (Figure 2A and B). Nevertheless, it becomes
difficult for those enhancer-bound hexamers to approach the
holoenzyme at high NtrC concentrations, since the bending
rigidity of intervening DNA is strengthened due to the
occupancy of low-affinity sites (29,36,42). In contrast,
hexamers at any low-affinity site hardly contact the holoenzyme.
This is interpreted as follows. Given a hexamer formed at
site III, sites IV and V are also occupied at least by NtrC
dimers which block DNA bending. A hexamer at site IV is
similarly hindered from contacting the holoenzyme because
of site V. The active center of a hexamer at site V cannot
reach the -12 region because of short intervening DNA.
Together, at high concentrations hexamers at low-affinity sites
not only fail to stimulate transcription initiation but also
hinder hexamers at enhancers from contacting the
holoenzyme. If the low-affinity sites are substituted with enhancer
sequences, such a repressive effect occurs even at low
concentrations, leading to a reduction in transcriptional levels
We then probe whether any two sites can be bridged by an
NtrC oligomer (a hexamer or a tetramer that exists during
the formation of a hexamer) and whether a hexamer
spanning two sites can catalyze transcription initiation. This is
based on the consideration that two sites may be
simultaneously bound by two DBDs of an NtrC oligomer if
topologically and spatially favorable. The possible bridging manners
fall into three categories, i.e. enhancer–low-affinity site
(including I-III, I-IV, I-V, II-III, II-IV and II-V), low-affinity
site–low-affinity site (including III-IV, III-V and IV-V) and
enhancer–enhancer (I-II) bridging.
All the bridging conformations in the first two categories
are rather unstable since they involve the low-affinity sites
and unstable NtrC oligomers (38). We analyze each
possible conformation in terms of its 3D structure, stability,
dependence on NtrC concentration and potential influence
on transcriptional output (see Supplemental S1 and
Supplementary Table S1). It turns out that these conformations
rarely occur and do not significantly affect transcriptional
dynamics except the II-V bridging. The II-V bridging
exactly constrains enhancer I in the vicinity of the -12 region,
facilitating the hexamer at enhancer I to rapidly find and
catalyze the holoenzyme (Figure 2C). The II-V bridging is
the only rational architecture underlying the contribution of
low-affinity sites to elevated transcriptional output. Of note,
when the low-affinity sites are unoccupied, the II-V bridging
forms when an enhancer II-bound NtrC oligomer
encounters site V; the II-V bridging rarely forms at high
concentrations because of the occupancy of sites III and IV.
The two enhancers may be transiently bridged by an
NtrC tetramer rather than a hexamer. A previous structural
study showed that for a hexamer to span the two enhancers,
rather high energy is required to severely bend or even twist
the DNA (38) (Figure 2D; Supplementary Table S1).
Another study revealed that the putative cooperative binding
of NtrC to the two enhancers is independent of the
conformational change of DNA and lies outside the DBD (34).
Thus, the two enhancers cannot be simultaneously bound
by an NtrC hexamer. If the cooperativity exists, an eligible
speculation could be that the oligomerization domain of a
bound dimer helps recruit another free dimer that then
dissociates and binds to the other enhancer (40,48). That is,
the two enhancers may be bridged by an NtrC tetramer very
In summary, there exist three configurations of the TA
allowing for transcription initiation, i.e. an NtrC hexamer
at enhancer I or II catalyzes the holoenzyme via DNA
looping, and the II-V bridging facilitates the enhancer
Imediated transcription initiation. At low and intermediate
NtrC concentrations, NtrC oligomers (mainly hexamers as
seen later) at enhancer II are topologically and spatially
favored to engage in the II-V bridging. At high
concentrations, the occupancy of low-affinity sites represses
transcription by hindering both the formation of II-V bridging and
interplay of hexamers and the holoenzyme.
Modeling how the TA dynamically operates
The above analyses also suggest a minimal kinetic model for
how the TA operates, which comprises the essential
pathways of conformational changes (Figure 3A). In brief, an
NtrC dimer bound to DNA acts as a nucleus condensing
free dimers to form a tetramer and then a hexamer. NtrC
hexamers at either enhancer stimulate transcription
initiation when they contact the holoenzyme. NtrC oligomers at
enhancer II also tend to approach site V, bridging sites II
and V. The II-V bridging shortens the time required for a
hexamer at enhancer I to search the holoenzyme. The
occupancy of low-affinity sites hinders DNA looping. To
reveal the kinetics of essential conformational changes, we
make the following simplifications. Each binding site may
be vacant, bound by an NtrC dimer, tetramer or hexamer,
and the conversion between these states is taken into
account (Figure 3B). We need not consider whether there exist
other NtrC oligomeric structures since NtrC is recruited in
units of a dimer and only hexamers catalyze the holoenzyme
(11,38). We also ignore the rather small affinity difference
between the two enhancers and that among the three
lowaffinity sites (39,40). Additionally, at high NtrC
concentrations a very small number of free hexamers may form and
stimulate transcription without binding to DNA (40,49);
this minor effect is also neglected.
Owing to the simplicity of the TA and rather limited
reaction types (detailed reaction steps are shown in
Supplementary Figure S1 and Supplementary Table S2), the
reaction rate constants can be determined as follows.
Presumably, the kinetic data on the holoenzyme interacting with
the −24–−12 region measured at glnALG are applicable to
glnAp2 (27), since the two promoters share the same core
promoter together with the neighboring sequences. Then,
the few remaining rate constants can be estimated by fitting
the input-output function of the wild-type glnAp2 promoter
(21,22,40) (Supplemental S2 and S3). The exact fitting is
shown in Figure 4A (for the experimental data see Figure 3
in (21) and Figure 6 in (40)). As the concentration of NtrC
dimers, C, rises, the average rate of mRNA production, R,
gradually rises and drops. R changes slightly in the range of
20–50 nM, with a maximum around 30 nM. Half-maximal
production rates are separately at 2 nM and 400 nM. In the
following, we further test the validity and robustness of this
Validity and robustness of the model
With the reaction rate constants obtained above, the model
quantitatively reproduces transcriptional activities from
various types of mutated promoters (Figure 4A and B). In
Case 1, the three low-affinity sites are all substituted with
sequences without similarity to the enhancers (III- IV-
V), i.e. these sites do not associate with NtrC anymore. We
thus set the affinity of the low-affinity sites for NtrC to 0.
Consequently, at low and intermediate concentrations R is
∼45% of that in the wild-type case, quantitatively in
agreement with the experimental data (cf. Figure 5 in (22)). The
model further predicts that R nearly remains unchanged for
C ≥ 100 nM.
In Case 2, the three low-affinity sites are all substituted
with the enhancer sequences (III# IV# V#). We set the
affinity of the low-affinity sites for NtrC to that of the
enhancers. Notably, R first rises and then drops to zero quickly
with increasing C. At low concentrations, R is around ∼22%
of that in the wild-type case, also quantitatively consistent
with the data (cf. Figure 5 in (22)).
In Case 3, either one or both of sites III and IV are
mutated to sequences unable to bind any protein (III- IV+ V+
or III+ IV- V+ or III- IV- V+). The binding affinity of the
low-affinity sites for NtrC is altered accordingly. Compared
with the wild-type case, here R is the same for C ≤ 20 nM but
becomes larger for C > 20 nM; R is higher in the III- IV- V+
case than in the III+ IV- V+ case. These features agree well
with the experimental observations (21). Concretely,
Atkinson et al. obtained two groups of data at high
concentrations (cf. Table 2 in (21)). One showed that R is ∼125% in
the III- IV+ V+ or III+ IV- V+ case, while R is ∼154% in the
III- IV- V+ case. The other showed that the two values are
separately ∼224% and ∼406%. The authors speculated that
the first group was obtained at lower concentration than the
second. Our data are quantitatively consistent with those
results and reveal that the corresponding concentrations are
∼300 nM and ∼1200 nM. This consistence also indicates
that site V has a critical role in governing transcriptional
In Case 4, the promoter is mutated as in Case 1 (i.e.
IIIIV- V-), but the region comprising the three low-affinity
sites is shortened by 15 bp. The DNA double helix makes
one complete turn along its axis every ∼11.1–11.2 bp in
vivo (50,51). The orientations of the two enhancers, toward
which NtrC’s DBDs insert into the major grooves, thus
form an angle of ∼47◦ (29,36,42). The reduction of 15 bp
means that the orientations of both the enhancers are
rotated to the opposite side by an angle of ∼124◦. Of note,
according to B-DNA with 10.4 bp/turn in solution, the
two angles above are separately ∼28◦ and ∼159◦. Thus,
the central pores of hexamers at either enhancer no longer
smoothly and precisely get contact with the catalysis site of
the holoenzyme. Previous studies inferred that such an
orientation change of ∼124◦ results in a decrease of ∼80–88%
in transcriptional levels; a change of ∼159◦ leads to a
similar decrease (cf. Figure 4C in (22) and Figure 2A in (52)). In
other words, the time required for hexamers at enhancers
to find the catalysis site is increased by ∼4- to 7.3-fold on
average. Given the shortened DNA, the time is additionally
decreased by one-fifth on average (based on Equation 11 in
Supplementary Material S2). Thus, the searching time for
hexamers at enhancer I and II to find the catalysis site is
separately ∼256–427 s and 320–533 s. Consequently, R is
∼9–14% of that in the wild-type case (Figure 4B),
consistent with 12% by experiment (cf. Figure 5 in (22)).
In Case 5, sites III and IV are substituted with the
enhancer sequences, and site V is mutated unable to bind any
protein (III# IV# V-). It might be expected that R would
be greater than that in Case 2 (III# IV# V#), since the
enhanced bending rigidity of DNA due to NtrC binding is
less prominent here. Unexpectedly, R is only ∼8% of that
in the wild-type case (Figure 4B), which is quantitatively
consistent with the experimental observation on a similarly
mutated promoter (4OP, cf. Figure 5 in (22)). This result
can be explained in terms of contributions to
transcription initiation by various TA configurations. Without
incorporating transcription initiations in the presence of II-V
bridging, the rate of mRNA production in Case 5 would be
indeed higher than that in Case 2 (Supplementary Figure
S2A). The higher transcriptional output in Case 2 is due to
the II-V bridging, which seldom forms but is rather stable
once formed (Supplementary Figure S2B–D). These results
should exclusively confirm the existence of II-V bridging.
We further examine whether the operation mechanism
of the TA is robust to various perturbations (such as
fluctuations in temperature and concentrations of cellular
molecules) that affect the rates of biochemical reactions.
To this end, independent Gaussian white noise is added to
each rate constant, with the standard deviation being 20%
of its default value (see Supplementary Material S4).
Compared with the case without noise, here the average
transcription rate becomes smaller, but the relative dependence
of R on C in both the wild-type and mutation cases is almost
unchanged (Supplementary Figure S3). Further in-depth
analyses not only support such strong robustness, but also
verify the kinetic features reported above (Supplementary
Figures S4–S8). We also predict the transcriptional
activities in two cases where either of two enhancers is mutated
to a sequence that does not bind any protein – this can be
used for further testing our model (Supplementary Figure
Dynamic characteristics of molecular interactions
The above results suggest that the current model captures
the microscopic mechanisms for the TA operation. Here,
we summarize the dynamic nature of key molecular
interactions (Table 1). NtrC dynamically binds to and
dissociates from the enhancers and low-affinity sites. The average
time of its DBD in association with an enhancer and a
lowaffinity site is ∼12 min and 72 s, respectively. The
probabilities of NtrC hexamers formed at these sites gradually rise to
saturation with increasing NtrC concentration (Figure 4C).
Half the maximal occupation of an enhancer and a
lowaffinity site by hexamers appears at ∼2 nM and ∼400 nM,
respectively, and the occupation probabilities nearly remain
unchanged separately for C > 100 nM and C > 10 M.
When none of the low-affinity sites is occupied, it takes
∼64 s on average for a hexamer at enhancer I to approach
the holoenzyme within the posterior closed complex and
∼80 s for a hexamer at enhancer II (Table 1). On the other
hand, it takes only ∼16 s for a hexamer at enhancer II to
encounter site V; notably, this is also the predominant pathway
leading to the II-V bridging, compared with that mediated
by a tetramer (Supplementary Table S3). Thus, most
hexamers at enhancer II are engaged in bridging sites II and V,
rather than stimulate transcription initiation. Once formed,
the II-V bridging lasts about 55 s, during which it takes only
several seconds for a hexamer at enhancer I to contact the
holoenzyme. Most mRNA production is induced by
hexamers at enhancer I in the presence of II-V bridging (Figure
Large deviations from the optimal lifetime of II-V
bridging, either too short or too long, deteriorate effective
transcriptional regulation (Figure 5A). The existence of an
optimal lifetime suggests the importance of low affinity of site V
for NtrC and instability of NtrC hexamer. Otherwise, if the
II-V bridging existed stably, it would be required that site V
have a high affinity for NtrC and NtrC hexamer be stable.
Accordingly, at low and intermediate concentrations site V
would be bound by NtrC hexamers, inhibiting both the
formation of II-V bridging and transcription initiation. The
optimal lifetime of a hexamer is 4 min; beyond the range of
∼3–5 min, effective transcriptional modulation is also
disrupted (Figure 5B).
Although the II-V bridging effectively enhances
transcription, it is not straightforward to judge whether it plays
a role by counting transcript numbers in individual cells,
because mRNAs are produced in bursts (Supplementary
Figure S10A). Nevertheless, the dynamics of transcription
initiations via the II-V bridging present a unique signature.
When the II-V bridging is in place, transcription initiation
is faster, implying that more closely spaced polymerases get
into elongation successively and hence a sharper burst
appears. Such characteristics may be justified by using RNA
labeling technologies such as the MS2 system and
singlemolecule fluorescence in situ hybridization (FISH) (53–56).
Average lifetime of NtrC hexamer
Average time of NtrC’s DBD in association with an enhancer
Average time of NtrC’s DBD in association with a low-affinity site
Searching time for hexamers at enhancer I to encounter a holoenzyme
Searching time for hexamers at enhancer II to encounter a holoenzyme
Searching time for hexamers at enhancer II to encounter site V
Average lifetime of II-V bridging
Half the maximal occupation of an enhancer
Half the maximal occupation of a low-affinity site
Of note, measurements with high resolution are required
because of the instability of II-V bridging. On the other hand,
the distribution of transcript numbers from the wild-type
promoter over a cell population is shown in Supplementary
Figure S10B. For 10 nM ≤ C ≤ 100 nM, the distribution
does not change markedly and nearly obeys a normal
distribution. At low or high concentrations, most cells produce
fewer mRNAs. These characteristics underline the
3 s, 64 s, 128 s, 640 s and +∞ – separately corresponding to the cases where
the II-V bridging is present, none of, one of, two of and all of sites III-V
is/are bound by NtrC
80 s, 160 s, 640 s, +∞ – separately corresponding to the cases where none,
one, two and all of sites III-V is/are bound by NtrC
∼16 s, 160 s, +∞ – separately corresponding to the cases where neither,
either and both of sites III and IV is/are bound by NtrC
∼2 nM of NtrC dimers
∼400 nM of NtrC dimers
tance of transcriptional dynamics itself in determining
The kinetics of the holoenzyme 54RNAP interacting with
promoter DNA was revealed using a single-molecule
fluorescence technology called CoSMoS (27). The current work
proposes a complementary approach, which fills the gap
across studies on molecular structures, reaction kinetics and
transcriptional activities in comprehending transcriptional
dynamics. We present an integrative picture of how
transcription initiation is regulated by transcriptional activators
and cis-regulatory elements on the glnAp2 promoter. While
NtrC hexamers at either enhancer can stimulate
transcription initiation, the main regulatory mode involves their
cooperation. At low and intermediate NtrC concentrations,
it is structurally and topologically favorable for a hexamer
at enhancer II to bridge sites II and V via one of its free
DBDs. This transient bridging greatly facilitates the
interplay between NtrC hexamers at enhancer I and the
holoenzyme, underlying the contribution of low-affinity sites to
elevated transcriptional output. At high concentrations, the
three low-affinity sites are occupied, hindering DNA
looping and leading to a drop in transcriptional levels. The
unexpected implications of this work are as follows:
i) In dynamically regulating transcriptional output, the
low-affinity cis-regulatory elements can exert a marked
influence. Although the topology, torsion and
rigidity of DNA are altered transiently due to unstable
association of proteins with low-affinity sites, the
inherent nonlinear features of molecular interactions
substantially affect transcriptional output. Low-affinity
sequences also exist widely in eukaryotic genomes, but
little attention was paid to their functions. It is expected
that more functions of low-affinity sites would be found.
This work also suggests that the instability of NtrC
hexamer and II-V bridging is crucial for effective
ii) The roles played by the two enhancers are quite
different on the wild-type promoter. Whereas enhancer
I-bound hexamers catalyze the holoenzyme, enhancer
II-bound hexamers are mainly engaged in bridging the
DNA. Notably, there also exist several or more
enhancer elements in the regulatory region of higher
eukaryotic genes. Likely, the presence of multiple
enhancers is not simply for cooperatively recruiting
activators; each may also perform individual functions,
constrained by topological and structural factors such
as the orientation of major DNA grooves.
iii) A clue may be inferred as to evolution of the dynamic
mechanism of regulated transcription initiation.
Previously, a generic model for how the eukaryotic TA
operates dynamically showed that the temporal tethering
of a distant enhancer to the surrounding area of a core
promoter enables the most efficient conversion of
regulatory signals into the rate of mRNA production (4).
A more recent study reported that such tethering is
already formed before the arrival of specific cellular
signaling (57). The current study revealed the similar
feature in transcriptional regulation in prokaryotes. Thus,
such a characteristic may be a conserved evolutionary
Supplementary Data are available at NAR Online.
The authors thank Dr Jian Zhang and Dr Jun Wang for
Ministry of Science and Technology of China
[2013CB834104]; National Natural Science Foundation of
China [11175084, 31361163003, 81421091]. Funding for
open access charge: Ministry of Science and Technology of
Conflict of interest statement. None declared.
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