Selectivity and proofreading both

contribute significantly to the fidelity of

RNA polymerase III transcription
1. Nazif Alic†,
2. Nayla Ayoub,
3. Emilie Landrieux‡,
4. Emmanuel Favry,
5. Peggy Baudouin-Cornu,
6. Michel Riva§, and
7. Christophe Carles

+ Author Affiliations
1. Commissariat à l'Énergie Atomique, Institut de Biologie et de
Technologies de Saclay, F-91191 Gif sur Yvette Cedex,
France
1. Communicated by E. Peter Geiduschek, University of
California at San Diego, La Jolla, CA, May 3, 2007 (received
for review December 8, 2006)

 
Next Section

Abstract
We examine here the mechanisms ensuring the fidelity of RNA synthesis
by RNA polymerase III (Pol III). Misincorporation could only be observed
by using variants of Pol III deficient in the intrinsic RNA cleavage activity.
Determination of relative rates of the reactions producing correct and
erroneous transcripts at a specific position on a tRNA gene, combined
with computational methods, demonstrated that Pol III has a highly
efficient proofreading activity increasing its transcriptional fidelity by a
factor of 103 over the error rate determined solely by selectivity (1.8 ×
10−4). We show that Pol III slows down synthesis past a misincorporation
to achieve efficient proofreading. We discuss our findings in the context
of transcriptional fidelity studies performed on RNA Pols, proposing that
the fidelity of transcription is more crucial for Pol III than Pol II.
  nucleotide selectivity

 transcriptional fidelity

Both the replication and expression of genetic material occur with

extremely high fidelity. During genome replication in Escherichia coli,
one error is created per 109nucleotides incorporated (1, 2). This high
fidelity results in part from the high accuracy of DNA synthesis by DNA-
dependent DNA polymerases (Pols). The mechanisms whereby these
enzymes ensure the fidelity of DNA synthesis are well characterized.
DNA Pols are highly selective for the correct nucleotide, using it 10 3–106
times more efficiently than an incorrect one. Furthermore, any errors
created can be immediately corrected by an intrinsic proofreading
nuclease activity (2). Importantly, different DNA Pols may have a
different level of fidelity, being optimized for the particular context in
which they perform DNA synthesis (2–4).
The expression of genetic material is also highly accurate. In E. coli cells
under standard growth conditions, the error rate of transcription is 10 −5.
Theoretical considerations argue in favor of the importance of
transcriptional fidelity for the cell (5). Several experimental approaches
have confirmed this importance in vivo and especially under conditions
favoring nucleotide triphosphate (NTP) misincorporation (6–8). However,
only a few studies have investigated the molecular mechanisms that
underlie the fidelity of RNA synthesis by DNA-dependent RNA Pols.
Presteady-state kinetic analyses of nucleotide addition by the E. coli
RNA Pol indicated that synthesis occurs through a branched kinetic
mechanism with the enzyme switching between an activated state and a
state termed “unactivated” at each template position. This unactivated
state, absent from DNA Pols, is characterized by an extremely slow
phosphotransfer reaction and can be reversed to the active state only in
the presence of the correct NTP (9, 10). Fidelity of transcription is
ensured by the selectivity of the Pol for the correct NTP and by kinetic
trapping of the ternary complexes in the unactivated state in the
absence of the correct NTP or after a misincorporation (9). Furthermore,
recent studies have demonstrated that transcriptional fidelity is
intimately linked to the mechanism of elongation, be it through the
flexibility of the F bridge domain (11), the preloading of NTPs and
dynamic error correction (12), or the association of the trigger loop with
the matched NTP in the A site, thus coupling NTP recognition and
phosphodiester bond catalysis (13).
Initially, unlike DNA Pols, RNA Pols had been thought to contain no
proofreading activity. RNA-cleavage within ternary complexes was
subsequently noted for RNA Pols from all domains of life (14–17). Unlike
DNA Pols, this activity resides in the Pol active site and for it to be
efficient the E. coli RNA Pol requires accessory proteins, GreA or GreB
(18, 19). GreA/B can improve the overall fidelity of the E. coli RNA Pol
(9). Similarly, TFS, the archeal functional equivalent of GreA/B, reduces
the steady-state error rate of the archaeal RNA Pol (20).
In eukaryotes, three similar but distinct forms of RNA Pol transcribe
each a different set of genes in the nuclear genome. Only the fidelity of
the mRNA-synthesizing Pol II has been investigated to date. The
selectivity of Pol II for the correct NTP was measured in vitro (21), and,
paralleling the situation in E. coli, the role of TFIIS, the Pol II cleavage-
stimulatory factor, in permitting efficient proofreading was determined
(21, 22). Interestingly, at least in the yeast Saccharomyces cerevisiae,
the errors committed by Pol II during the synthesis of mRNAs may be
masked by the higher error-rate of mRNA translation (23). In E. coli
during translation one error occurs per 104 residues (5).
The two other nuclear Pols, Pol I and Pol III, synthesize only untranslated
RNAs. Thus, the fidelity of their transcription may be of even greater
importance for the cell; however, their fidelity has not been examined.
Elongation complexes of Pol I appear to contain a dissociable TFIIS-like
activity (24). On the other hand, Pol III appears to be unique, because,
unlike Pol I and II, it has a high intrinsic RNA-cleavage activity that does
not require an accessory factor (16).
In this study, we examined nucleotide misincorporation by cleavage-
competent and cleavage-deficient S. cerevisiae Pol III ternary complexes
at a specific position on a tRNA gene. The results define the strategies
used by a eukaryotic RNA Pol with high intrinsic cleavage activity to
ensure the accuracy of its transcription. We used computational
methods to combine the experimental observations and predict the
steady-state error rate of Pol III and to demonstrate the equally high
contribution of proofreading and nucleotide selectivity to the overall
fidelity of Pol III.
Previous SectionNext Section

Results
Pol IIIΔ, an Incomplete Form of Pol III Lacking RNA-Cleavage
Activity, Can Quantitatively Incorporate an Incorrect
Nucleotide.
To gain an insight into the mechanisms ensuring the fidelity of Pol III
transcription, we initially examined the ability of the wild-type Pol III to
incorporate an incorrect base. Transcription by Pol III of the SUP4
template preassembled with transcription factors TFIIIC and TFIIIB was
initiated by the addition of ATP, CTP, and radiolabeled UTP. Pol III
formed stable ternary complexes containing a 17-mer RNA, due to the
absence of GTP required for synthesis at positions +18 and +19 of the
template (Fig. 1 A and B). These were purified from free NTPs and
further incubated with each of the four NTPs. As expected, the 17-mer
was correctly extended to a 19-mer in the presence of GTP (Fig. 1 B,
lane 2) whereas no synthesis was observed with the other NTPs (Fig. 1 B,
lanes 3–5). Instead, the intrinsic RNA cleavage activity of Pol III led to the
disappearance of the 17-mer generating shorter RNAs (Fig. 1 B, lanes 3–
5). In contrast to this apparent inability of Pol III to incorporate a
mispaired nucleotide, Chédin et al. (25) have reported that transcription
of SUP4 in the absence of GTP by Pol IIIΔ, an incomplete form of Pol III
lacking the C11, C37 and C53 subunits, resulted in formation of an 18-
mer transcript differing at the 3′ end from the 17-mer produced by Pol
III (25, 26). The authors suggested that Pol IIIΔ incorporated a mispaired
nucleotide at position +18, which failed to be subsequently removed
because of the lack of RNA-cleavage activity in Pol IIIΔ resulting from
the absence of the TFIIS-like C11 subunit (25). We wanted to test this
hypothesis and determine which base was misincorporated at position
+18. The SUP4 gene was transcribed in the absence of GTP by Pol IIIΔ
preincubated with the recombinant C11 subunit (rC11). The resulting
halted ternary complexes contained a 17-mer RNA and were purified to
remove rC11 and the NTPs (25, 26). Traces of the 18-mer transcript
remained, which could be attributed to a somewhat reduced cleavage
efficiency of rC11 compared with the endogenous C11, and a negligible
amount of a slippage product (27) was observed (Fig. 1 B, lane 6). The
purified complexes were assayed for their capacity to incorporate a
single nucleotide at position +18. In the presence of ATP, Pol IIIΔ
quantitatively synthesized an 18-mer (Fig. 1 B, lane 8). This 18-mer
could not have resulted from incorporation of ITP that might have
contaminated our ATP stocks, because in the presence of ITP, Pol IIIΔ
produces a 19-mer (data not shown) and a 19-mer was not observed
after 5 min (Fig. 2 B) nor after 60 min of incubation with ATP (data not
shown). Thus, the appearance of an 18-mer revealed that the enzyme
incorrectly incorporates an A instead of a G. Misincorporation of UTP
occurred less efficiently (Fig. 1 B, lane 10), whereas no incorporation of
CTP was observed (Fig. 1 B, lane 9). As for the wild-type enzyme, a 19-
mer transcript was synthesized in the presence of GTP (Fig. 1 B, lane 7).
However, on longer incubation in the presence of GTP, Pol IIIΔ also
synthesized a 20-mer transcript, indicating that it misincorporated a G
instead of a U at this position (data not shown). The results
demonstrated that Pol IIIΔ is capable of misincorporation.

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Fig. 1.
A Pol III form devoid of RNA cleavage activity incorporates a mispaired
nucleotide. (A) Template-strand sequence in the beginning of SUP4
(gray) and the sequence of the 17-mer RNA (black). (B) (Upper) Shows
the relevant sequence of SUP4 (gray) and the 3′-terminal sequence of
the 17-mer (black), with X denoting the position at which the NTP
incorporation was tested. (Lower) Purified ternary complexes containing
radiolabeled 17-mer SUP4, Pol III, or Pol IIIΔ were analyzed either
directly (lanes 1 and 6) or after a 5-min incubation with 600 μM of the
noted NTP. Arrow, residual 18-mer; asterisks, slippage product. ( C)
SUP4 was transcribed for 5 min in the presence of ATP, CTP and
radiolabeled UTP by Pol III, Pol IIIΔ alone, or Pol IIIΔ preincubated for 10
min with the indicated purified recombinant subunits.

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Fig. 2.
Pol III selectivity determined in the absence of RNA-cleavage activity. ( A)
(Upper) Shows the relevant sequence of SUP4 (gray) and the 3′-terminal
sequence of the 17-mer (black) with the newly added bases in bold.
(Lower) Time-course analysis of incorporation of GTP (0.6 μM) by
ternary complexes containing SUP4, Pol IIIΔ and the radiolabeled 17-
mer. For each reaction time, the amount of the residual 17-mer was
quantified and expressed as percentage of the initial amount ( t = 0)
after subtraction of the lowest quantity of 17-mer remaining unreacted.
Data were fitted to a single-exponential function and the apparent rate
constant (k a) calculated. (B) Same as in A, except that the ternary
complexes were incubated with ATP (600 μM) instead of GTP. The
mismatch formed is framed on the sequence representation. ( C) Same as
in A except that the ternary complexes were preincubated for 10 min
with the cleavage-incompetent rC11E92H and r(C37-C53), before being
allowed to react with either GTP (0.6 μM) (Left) or ATP (600 μM) (Right).

RNA Cleavage Activity of Pol III Is Sufficient to Prevent

Observable Misincorporations.
From the above observations, we could not conclude whether Pol IIIΔ
produced quantitatively a mispaired transcript solely because it lacked
RNA-cleavage activity or because the missing C11, C37, and/or C53
subunits were also important in preventing misincorporation. Therefore,
it remained unclear whether Pol III did not incorporate an incorrect base
to an observable degree, or whether misincorporation occurred but was
masked by the efficient subsequent cleavage of the RNA. To address this
issue, we used a Pol III form containing a complete set of subunits but
lacking the intrinsic RNA-cleavage activity. We have recently shown that
Pol IIIΔ reconstituted with rC37, rC53, and the mutant rC11 E92H subunit
displays the same transcriptional properties in all of the in vitro tests
examined (initiation, elongation rate, termination, and reinitiation
efficiency) as the wild-type enzyme except that it lacks RNA-cleavage
activity (26). When transcription of SUP4 was carried out in the absence
of GTP, Pol IIIΔ alone synthesized an 18-mer (Fig. 1 C, lane 2), whereas
Pol IIIΔ preincubated with the three wild-type recombinant subunits, and
the wild-type enzyme synthesized a 17-mer RNA (Fig. 1 C, lanes 3 and
1, respectively). However, when we used the rC11 E92H mutant subunit
instead of the wild-type rC11, an 18-mer was synthesized (Fig. 1 C,
lane 4). These observations strongly suggest that the synthesis of a 17-
mer by the wild-type Pol III reflects a steady state in which
misincorporations at position +18 occur but are rapidly corrected by the
efficient RNA cleavage activity intrinsic to Pol III.
Pol III Incorporates a Correct Base 103 Times More Efficiently
Than an Incorrect One.
The errors committed by Pol IIIΔ allowed us to characterize the
specificity of nucleotide incorporation by Pol III. We determined the
incorporation rates for the correct and an incorrect nucleotide at
position +18 of the SUP4 gene in a time-course analysis of single
nucleotide addition to a 17-mer within Pol IIIΔ ternary complexes. The
incorporation of the correct nucleotide (GTP) proceeding extremely
rapidly, the reaction was slowed by reducing the GTP concentration to
0.6 μM. Under these conditions, the reaction was virtually complete by
15 s (Fig. 2 A). Because the quantity of GTP greatly exceeds that of the
ternary complexes in the reaction, the concentration of GTP can be
considered to remain constant and the incorporation of G to occur with
pseudo-first-order kinetics. By fitting a single exponential equation to
the time-dependent loss of the 17-mer, the pseudo-rate constant ( k a)
for the incorporation of the correct nucleotide (GTP) was estimated to be
0.22 s−1 with a standard error of 0.04 s−1 (Fig. 2 A). The incorporation of
the preferred incorrect nucleotide (ATP) was much slower, taking 2.5
min for the reaction to go to completion in the presence of 600 μM ATP
(Fig. 2 B). The pseudo-rate constant for this reaction was 0.039 ± 0.004
s−1 (Fig. 2 B). When the concentration of ATP was reduced to 60 μM, the
pseudo-rate constant was equivalently reduced by an order of
magnitude [supporting information (SI) Fig. 6], indicating that ATP was
not saturating at 600 μM, and allowing us to extrapolate the rate of ATP
incorporation at 0.6 μM to 3.9 × 10−5 s−1. Hence, the correct base was
incorporated ≈6 × 103 times faster than the preferred incorrect one at
nucleotide concentrations below the effective K m for both the correct
and incorrect nucleotide.
Because our measurements were performed with Pol IIIΔ, it was
important to determine whether the selectivity observed reflected that of
the wild-type Pol III deprived only of RNA cleavage activity. We used the
rC11E92H mutant subunit, together with the r(C37-C53) complex, to
reconstitute a Pol III lacking only its intrinsic RNA cleavage activity (26).
Examination of the misincorporation rate for this enzyme form revealed
it to have the same rate of addition of the correct and incorrect
nucleotide as Pol IIIΔ (Fig. 2 C). Thus, the selectivity measured for Pol
IIIΔ also reflects the selectivity of the wild-type Pol III.
RNAs Containing a 3′-End Mismatch Are Cleaved More
Rapidly Than Those Containing a Correctly Paired End.
To clarify the importance of the RNA cleavage activity versus selectivity
in ensuring the fidelity of Pol III transcription, we sought to quantify the
rate of the former reaction. Pol III ternary complexes containing a 17-
mer were purified and allowed to cleave the RNA in transcription buffer
in the absence of NTPs (Fig. 3 A). We determined the apparent rate
constant for the cleavage of an RNA with a correctly paired 3′ end from
the time-dependent loss of the 17-mer (Fig. 3 A) to be 0.10 ± 0.01 s−1.
However, the important parameter in proofreading by Pol III is the rate
of cleavage of an RNA containing a mispaired nucleotide at its 3′-end.
This rate cannot be directly measured, because the mispaired 18-mer is
undetectable and supposedly short-lived within Pol III ternary
complexes. Therefore, purified ternary complexes containing Pol IIIΔ
and the 3′ end-mispaired 18-mer were incubated with rC11 and r(C37–
C53). We compared the rate of cleavage of the 18-mer in such
reconstituted wild-type-like ternary complexes to the rate of cleavage
of the correct 17-mer transcript in similarly obtained complexes.
Because the cleavage of the 18-mer was too rapid at 25°C, the reactions
were performed in cleavage buffer at 16°C. Despite the reconstituted
Pols cleaving only up to 40% of the RNA initially present (SI Fig. 7), we
clearly observed that the 18-mer transcript was cleaved 8 times more
rapidly than the 17-mer (Fig. 3 B). This higher rate of the 18-mer
cleavage was not due to a different sequence context (position 18
versus 17), because an 18-mer transcript ending with a 3′-OMeG was
cleaved at a rate very similar to that of the 17-mer (SI Fig. 8). Thus, the
cleavage of a 3′-end mispaired transcript by Pol III is more efficient than
the cleavage of a correctly paired one, indicating that the enzyme
discriminates between correct and incorrect bases during both synthesis
and cleavage reactions. We extrapolated from the rate of 18-mer
cleavage relative to that of the 17-mer by the reconstituted Pol III to the
wild-type Pol III, estimating the rate of cleavage of the 3′-end mispaired
18-mer transcript at 25°C by Pol III to be 0.83 s−1 (for details, see “Note
1” in SI Text).

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Fig. 3.
Time-course analysis of RNA cleavage by Pol III. (A) Time-course of RNA
cleavage in transcription buffer in the absence of NTPs by purified
ternary complexes containing SUP4, Pol III, and the radiolabeled 17-mer.
Data were analyzed as described for Fig. 2 A. (B) Purified ternary
complexes containing SUP4, PolIIIΔ and either the (radiolabeled)
correctly 3′-end-paired 17-mer or 3′-end mispaired 18-mer transcript
were preincubated for 10 min with wild-type rC11 and r(C37–C53) and
the RNA-cleavage reaction was initiated by starting incubation in
cleavage buffer (at 16°C). The data were analyzed as described for Fig. 2
A.

Misincorporation Slows the Incorporation of the Next

Nucleotide.
To appreciate the importance of the cleavage reaction in the fidelity of
Pol III, we had to determine the rate of the competing step, the addition
of the correct nucleotide after a misincorporation. In the presence of
600 μM GTP, purified Pol IIIΔ ternary complexes extended the 3′-end
mispaired 18-mer to a 19-mer that subsequently disappeared giving a
20-mer transcript (Fig. 4). Essentially all of the initially present 18-mer
was lost by 60 min (Fig. 4). The simplest explanation for the transient
appearance of a 19-mer followed by formation of a 20-mer is that the
20-mer arises from a misincorporation of GTP instead of UTP at position
+20 and that the rate-limiting step in the formation of the 20-mer is
the passage from +18 to +19, i.e., the incorporation of a correct base
after a mispaired base. The apparent rate constant for disappearance of
the 18-mer was 94 × 10−5 ± 4 × 10−5 s−1 (Fig. 4). Thus, the
incorporation of a correct base after a mispaired base is ≈105 times
slower than after a correctly paired one. Furthermore, our analyses
demonstrate that the addition of a ribonucleotide after a
misincorporation is the slowest step in the synthesis of error-containing
transcripts by Pol III. In contrast, this step is not slower than the actual
misincorporation in the case of E. coli RNA Pol and Pol II (9, 21).

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Fig. 4.
Addition of a correct nucleotide after misincorporation is extremely
inefficient. (A) (Upper) The relevant sequence of SUP4 (gray) and the 3′-
terminal sequence of the 18-mer (black) with the newly added bases in
bold and the mismatches framed. (Lower) The time-course analysis of
GTP (600 μM) incorporation by purified ternary complexes containing
SUP4, Pol IIIΔ, and the radiolabeled 3′-end mispaired 18-mer transcript.
(B) The data were analyzed as described for Fig. 2 A.

Selectivity and Proofreading Contribute Equally to the

Fidelity of Pol III Transcription.
We sought a computational approach to integrate our experimental
results and estimate the contributions of proofreading and selectivity to
the fidelity of Pol III transcription at a particular position of an RNA
chain. Our observations were consistent with the existence of two
competing pathways leading to an insertion followed by a fixation of
either a correct or an incorrect base (Fig. 5). The system of reactions we
propose to be important in determining the fidelity of Pol III is
characterized by six kinetic parameters, the first-order rate constants k
–k 6 represented in Fig. 5. A ternary complex containing a transcript of
1

n − 1 nucleotides can incorporate at the nth position either a correct

nucleotide [giving the product (n) with the first-order rate constant k 1]
or an incorrect nucleotide [product (n*), k 2]. Each product can either
undergo the cleavage reaction (k 4 and k 5, respectively), regenerating an
RNA of n − 1 nucleotides, or be extended by the incorporation of the
correct nucleotide to give the (n + 1) or (n* + 1) species, respectively (k
6 and k 3) (Fig. 5).

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Fig. 5.
Modeling the reactions determining Pol III fidelity. Diagram describing
the reactions determining the fidelity of Pol III transcription, where: ( n −
1) − RNA species of length (n − 1) within a Pol III ternary complex, (n) −
product of the correct incorporation at the template position n, (n*) −
product of misincorporation at position n, (n + 1) − product of the
extension of the correctly paired species (n), and (n* + 1) − product of
the extension of the incorrectly paired species ( n*).
Two simplifications were made in this model: (i) The cleavage of the (n)
or (n*) species will give a product of length n − x, with x ≥ 1, but
because the extension from position n − x to n − 1 (for x > 1) is rapid,
we assumed that the cleavage of the (n) or (n*) RNAs would directly
generate the (n − 1) species. (ii) We did not include the cleavage of the
(n + 1) or (n* + 1) transcripts in the model because, once a correct
nucleotide is incorporated at position n + 1, the forward synthesis rates
may be overwhelming and thus no longer have a bearing on the
misincorporation at position n. We discuss later a more complex
situation created when this second simplification is altered (see
Discussion).
One measure of transcriptional fidelity of Pol III at a particular position
in an RNA chain is the ratio of the concentrations of the correct to the
incorrect product [n + 1]/[n* + 1], which is the inverse of the error rate.
We can calculate that, after an infinite time, the [n + 1]/[n* + 1] ratio

reaches:
Assuming that the incorporations of correct ribonucleotides onto a
correctly paired 3′-end will occur with similar rates relative to the rate of
misincorporation or extension past a misincorporation, we can state that

k 1 = k 6, giving:
In essence, the fidelity of Pol III transcription is insured by two
processes: selectivity and proofreading. Selectivity is given by the ratio
of the rates of incorporation of correct to incorrect nucleotide ( k 1/k 2).
Proofreading is represented by the ratio of the rate of cleavage of an
incorrectly paired nucleotide relative to the rate of its extension ( k 5/k 3).
Indeed, visual inspection of formula (Eq. 2) and computer simulations (SI
Fig. 9), confirmed that it is not the absolute rate of cleavage that
determines fidelity of Pol III transcription but the k 5/k 3 ratio.
It is obvious from formula (Eq. 2) that if k 1 ≫ k 4 and k 5/k 3 ≫ 1, as is
the case observed for Pol III (Table 1), fidelity is given by

i.e., it is the product of “selectivity”

by “proofreading”. The rate constants measured in this study for the
incorporation of GTP and misincorporation of ATP at position +18 of
SUP4 indicate that k 1/k 2 = 5.6 × 103 at GTP and ATP concentrations
below the effective K m of the enzyme for these nucleotides.
Measurements of cleavage and extension past the misincorporation
indicate that k 5/k 3 = 0.9 × 103, at NTP = 600 μM. A reduction in [NTP]
would result in lower k 3 and higher k 5/k 3 (see SI Fig. 9). Hence, at
nonsaturating concentrations of nucleotides,

meaning that Pol III would

incorporate one error per 5 × 106 bases synthesized. Computer
simulations revealed that the limit conditions are reached rapidly (SI Fig.
9).
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Table 1.
Summary of the rate constants determined in this study
Therefore, the efficiency of proofreading by Pol III appears to be within
the order of magnitude of the selectivity ratio, indicating that both
processes have a significant contribution to Pol III fidelity.
Previous SectionNext Section

Discussion
In this study, we show that proofreading is a major determinant of the
fidelity of Pol III transcription. The measurements of relative reaction
rates combined with computer analyses demonstrate that nucleotide
selectivity and proofreading contribute equally to Pol III fidelity at the
examined position on the SUP4 gene. Further studies may reveal how
these contributions may vary in different sequence contexts or even in
vivo and whether our conclusions are generally applicable.
Mechanics of Error Avoidance and Error Correction by Pol III.
As noted in the Introduction, few studies have examined the fidelity of
RNA Pols. Still, we find it important to make some comparisons between
the functioning of different RNA Pols, although the comparisons remain
speculative, because they are based on a limited number of ternary
complexes.
The selectivity measured for Pol III (5.6 × 10 3) is similar to that reported
for the E. coli RNA Pol and Pol II (103 and >5 × 102, respectively) (9, 21),
indicating that the selectivity of RNA Pols may be in the lower end of the
range (103–106) reported for DNA Pols (2). We have measured the rate of
the most-likely misincorporation, which may have led to an
underestimate of selectivity. At the same time, maximal error rates may
have also been measured for other RNA Pols, because preloading of
NTPs may reduce their error incorporation (12).
The proportion of E. coli RNA Pol or Pol II ternary complexes able to
incorporate a correct nucleotide was higher than that capable of
misincorporation (9, 21), which Erie and coworkers interpreted as
indicating that the polymerase could assume an unproductive
conformation (i.e., become “unactivated”) at each synthesis step, thus
preventing misincorporation. Single-molecule analyses on bacterial
enzyme confirmed recently this hypothesis (28). The existence of such
an unactivated state was also inferred for Pol III from detailed analyses
of RNA chain elongation (29). We did not evidence, however, any
difference in the proportion of ternary complexes incorporating the
correct or an incorrect nucleotide. This observation reflects that the
temporal resolution of our experiments may not be fine enough to allow
detection of such a state. Alternatively, although highly speculative, one
cannot formally exclude that Pol III requires intrinsic cleavage activity to
enter an unactivated state, because unlike our study, that of Matsuzaki
and coworkers used a cleavage-competent enzyme (29).
Pol III appears to have an exceptionally high contribution of
proofreading to its fidelity; the magnitude of this contribution, as
determined in this study (103), is high even when compared with the
range reported for the proofreading activities of DNA Pols (few- to
>100-fold) (2). Interestingly, both DNA Pols and Pol III rely strongly on
kinetic partitioning between cleavage and extension reactions for
efficient proofreading despite crucial differences in the mechanism and
site of the cleavage activity.
We demonstrated that the rate of cleavage of nascent transcripts was
stimulated by a mismatched base at the 3′ end of the RNA. This may be
the extreme case of the preference to cut the nascent RNA just 5′ of an
unstable RNA-DNA base pair, demonstrated for Pol III (30). This extends
observations made on RNA-DNA “dumbbell” templates, using Pol
II+TFIIS (22). Importantly, in our study, the rates of both cleavage and
extension are measured under physiologically more relevant conditions,
within authentic ternary complexes halted on a class III gene.
C11, the protein essential for the cleavage and thus the proofreading
activity of the polymerase, is a Pol III subunit, making it very likely that
the role of proofreading in the fidelity of the Pol will be important in
different sequence contexts and in vivo. Furthermore, our calculations
may have underestimated the contribution of cleavage to Pol III fidelity.
In the model presented (Fig. 5), the assumption was made that the rate
of extension of the (n* + 1) species by a correct base is equal to the rate
of extension of (n) to (n + 1) and cancels out the effects of (n* + 1)
cleavage. However, precedents exist in DNA Pols for a reduction in the
synthesis rates several bases past the misincorporation, occurring
because of distortions in the active site (31). If we include the
extension/cleavage of the (n* + 1) species in our model, we find that
the fidelity of transcription, as measured in this case by the ( n + 2):1/m
(n + 2)/(n* + 2). (n* + 2) ratio, increases substantially if the rate of
conversion of (n* + 1) to (n* + 2) drops below ≈2 s−1 to reach 4.4 ×
109when this rate is as low as that of (n*) → (n* + 1) (SI Fig. 10 and SI
Text, “Note 2”). This increase in fidelity occurs through an increase in
proofreading. The fidelity of Pol III probably lies between these two
extremes: the rate of (n* + 1) → (n* + 2) is not as low as that of (n*) →
(n* + 1), because on addition of all four NTPs, the 3′-end mispaired 18-
mer can be extended to the complete SUP4 transcript in a time-course
similar to that in Fig. 4 without the appearance of a 19-mer (data not
shown). A further determinant of the in vivo fidelity is the local NTP
concentration, and computer simulations show that fidelity is linearely
proportional to the synthesis rates over at least two orders of magnitude
(data not shown).
RNA Cleavage Activity and in Vivo Properties of Pol III.
Even if all RNA Pols use generally similar mechanisms to achieve high
fidelity, Pol III appears to display specific properties. Why, for example,
does Pol III have a high intrinsic cleavage activity, whereas other nuclear
RNA Pols do not? This property may be due to the differences in their
mechanism of transcription, and reflect their respective biological roles.
With respect to the mechanism of transcription, the simplest
explanation would be that Pol III is less apt at avoiding transcriptional
errors than Pol II. However, the selectivity of the two polymerases
appears comparable.
Currently, the role of the Pol II cleavage factor, TFIIS, in transcriptional
fidelity is unclear. It is not a constitutive partner of Pol II (32, 33), and
there is no evidence for in vivo TFIIS-mediated Pol II proofreading under
standard growth conditions, i.e., in absence of stress (34). However,
conditions favoring transcriptional errors stimulate the association of
TFIIS with elongating Pol II (33), and the deletion the TFIIS-encoding
gene in yeast (PPR2) causes sensitivity to the same conditions (35). TFIIS
may also have other functions, such as in initiation of transcription (36)
or in elongation (37).
The in vivo nonessential or essential character of the cleavage activity is
another striking difference between the Pol II and the Pol III systems.
PPR2 is not essential for yeast viability (38). Rpb9 subunit of Pol II, a C11
paralogue recently identified as important for the in vivo fidelity of Pol II
and suggested to act in proofreading (34), is also encoded by a
nonessential gene. These findings strongly suggest that Pol II RNA
cleavage activity is not essential in vivo. In stark contrast, the point
mutations in the C11 subunit that abolish RNA cleavage activity are
lethal [double D91A E92A mutant (25); or E92H mutant, data not
shown]. Because the only known transcriptional defect of Pol III-
containing rC11E92H in vitro is the absence of cleavage activity (26), this
activity may be essential for Pol III in vivo. A simple explanation for this
difference would be that transcriptional fidelity is more crucial for Pol III
than for Pol II, because the former's untranslated RNA products are
direct players in crucial cellular processes, notably translation. The idea
that eukaryotic RNA Pols may have different accuracies depending on
the class of transcripts they produce was also proposed based on
observations made in E. coli (39). Indeed, with respect to protein-coding
genes, it appears that translation rather than Pol II transcription is the
error-prone process (23), although this may depend on the gene
examined (40).
The essential character of Pol III cleavage activity may also reflect more
profound differences in the in vivo mechanics of Pol III and II
transcription. The efficient transcription of class III genes proceeds
through facilitated reinitiation by the enzyme during which Pol III has
been suggested to remain on the template (41, 42). The movement of
the enzyme on a gene would thus be extremely reduced, making it
difficult, if at all possible, for the cell to distinguish between truly
elongating Pol III and blocked Pols, thus precluding the possibility of the
latter's degradation to save the transcription of the gene. In contrast to
Pol II, which has been observed to become ubiquitylated and degraded
under the conditions favoring elongation blocs in vivo (43), RNA
cleavage and resynthesis may be the only means for the cell to deal with
elongation-blocked Pol III.
Previous SectionNext Section

Materials and Methods

Purification of RNA Pol III, Class III Transcription Factors and
Expression and Purification of Recombinant Pol III Subunits.
Purification of Pol III and class III transcription factors was described in
ref. 44. Pol IIIwt was purified from the yMR4 strain, whereas Pol IIIΔ was
purified from either C37HA-Ct or yEL7 strain (26). Regardless of the
source, Pol IIIΔ behaved the same in all of the tests performed. Purified
recombinant (His7-C37–C53) complex, C11 and C11E92H were obtained as
described (25, 26). rC11, rC11E92H, and the r(C37–C53) complex were
purified to homogeneity (26), as monitored by Coomassie blue staining.
Promoter-Directed in Vitro Transcription, Ternary Complex
Purification, Single-Nucleotide Addition and Cleavage
Assays.
NTPs and [α-32P]UTP were from Amersham Biosciences (Little Chalfont,
U.K.). Promoter-directed in vitro transcription reactions were performed
in 50 μl of transcription buffer (20 mM Hepes KOH, pH 7.5/0.1 mM
EDTA/5 mM MgCl2/5 mM DTT/5% glycerol/90 mM KCl). pRS316-SUP4
plasmid (250 ng) was incubated in this buffer with 50 ng of each rTFIIIC,
rTBP, rTFIIIB70, and 0.4 μg of B″ fraction for 20 min at 25°C, followed by
addition of native or reconstituted Pol III (50–100 ng), and a further 20-
min incubation. Transcription was started by addition of 600 μM ATP
and CTP and 3 μM [α-32P]UTP (400 Ci/mmol) and allowed to proceed for
5 min. For add-back experiments, recombinant proteins were added to
Pol IIIΔ in PBS, or to ternary complexes, at a molar ratio shown to be
efficient in studies of termination, elongation, cleavage, and reinitiation
(25, 26) and incubated for 10 min. Unless otherwise noted, all reactions
were performed at 25°C. Ternary complexes were purified from 100 μl
of transcription reaction by gel-permeation chromatography at 4°C [1 ml
of CL2B resin (GE Healthcare Europe, Saclay, France) equilibrated in 40
mM Tris·HCl (pH 8)/90 mM KCl/0.5 mM EDTA/5% glycerol in a 1-ml
syringe]. Single-nucleotide addition and cleavage reactions were
performed on 20-μl aliquots of purified ternary complexes and initiated
by the addition of 20 μl of the reaction mix to give the final
concentration of 1× transcription or cleavage buffer with the noted
concentration of an NTP. The reactions were stopped and processed as
described in ref. 26. Transcripts were analyzed by electrophoresis on
denaturing polyacrylamide gels (15%, 20:1 acrylamide:bis-acrylamide
ratio). Gels were autoradiographed by using MR film with an intensifying
screen (Kodak, Tokyo, Japan). Quantifications were performed with
Image Quant software, Version 1.2. The lowest quantity of the 17-mer
or 18-mer observed in the reactions was subtracted from all of the
values and the data obtained were normalized so that the amount of the
oligomer at time 0 is 100%. The normalized values were fitted to a
single exponential equation (y = Ae − kx
, where A is the initial quantity of
oligomer), and the rate constant (k) was calculated by using Prism 4
software (GraphPad, San Diego, CA). R 2 values were generally >0.98 (all
were >0.94).
Computational Analyses.
Computational analyses were performed with MatLab software
(MathWorks, Natick, MA). For details, see SI Text.
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Acknowledgments
We thank Valérie Goguel for a critical reading of the manuscript, André
Sentenac for his constant support, Cécile Ducrot and Joël Acker for
providing recombinant proteins. Emilie Landrieux was supported by a
short-term grant from the Fondation pour la Recherche Médica

 Abbreviations:

Pol,
polymerase;
NTP,
nucleotide triphosphate.