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Journal of Bacteriology, August 2000, p. 4628-4631, Vol. 182, No. 16
0021-9193/00/$04.00+0
Copyright © 2000, American Society for Microbiology. All rights reserved.
A Carboxy-Terminal 16-Amino-Acid Region of 
38 of
Escherichia coli Is Important for Transcription under
High-Salt Conditions and Sigma Activities In Vivo
Mio
Ohnuma,1
Nobuyuki
Fujita,2
Akira
Ishihama,2
Kan
Tanaka,1 and
Hideo
Takahashi1,*
Institute of Molecular and Cellular
Biosciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo
113-0032,1 and Department of Molecular
Genetics, National Institute of Genetics, Mishima, Shizuoka
411-8540,2 Japan
Received 11 February 2000/Accepted 15 May 2000
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ABSTRACT |
38 (or S, the rpoS gene
product) is a sigma subunit of RNA polymerase in Escherichia
coli and directs transcription from a number of stationary-phase
promoters as well as osmotically inducible promoters. In this study, we
analyzed the function of the carboxy-terminal 16-amino-acid region of
38 (residues 315 to 330), which is well conserved among
the rpoS gene products of enteric bacterial species.
Truncation of this region was shown to result in the loss of sigma
activity in vivo using promoter-lacZ fusion constructs, but
the mutant 38 retained the binding activity in vivo to
the core enzyme. The in vitro transcription analysis revealed that the
transcription activity of 38 holoenzyme under high
potassium glutamate concentrations was significantly decreased by the
truncation of the carboxy-terminal tail element.
| |
TEXT |
Sigma factor is a subunit of RNA
polymerase in eubacteria and donates to catalytic core RNA polymerase
the ability to recognize promoter sequence and to initiate specific
transcription (8). In Escherichia coli, seven
sigma subunit species are known to exist, each sigma controlling a
specific subset of genes for corresponding cellular functions. Six of
the seven sigma factors belong to the 70 family;
N does not (14).
The principal sigma factor, 70, is the most abundant and
essential sigma, responsible for transcription of most housekeeping genes. The RNA polymerase holoenzyme containing 70
(E70, where E represents the core enzyme) recognizes
so-called consensus promoters, which consist of bipartite sequences
TATAAT and TTGACA located around the 
10 and the 35 base pairs,
respectively, upstream from the transcription initiation sites
(8). E. coli cells have another primary sigma
factor, 38 (or S, the rpoS
gene product), that is structurally closely related to
70. 38 positively regulates a number of
stationary-phase specific promoters and osmotically inducible promoters
(9). The RNA polymerase holoenzyme containing
38 (E38) recognizes many consensus
promoters as well as E70 does, although the recognition
sequence preference is somehow different between the two holoenzymes
(23, 25). Both enzymes recognize similar 10 consensus
sequences, but a set of promoters are recognized only by
E38, suggesting that E38 recognizes
as-yet-unidentified unique sequence elements (4, 28).
Four conserved regions, from the amino-terminal region 1 through the
carboxy-terminal region 4, have been proposed to exist in
70 family proteins, and each region can be further
divided into subregions (14). Functions for some subregions
have been suggested or demonstrated by genetic and biochemical
analyses. In the case of 70, region 1.1 inhibits binding
of the sigma factor to DNA in the absence of the core polymerase
(3). Region 2.1 includes a binding site with the core
polymerase (13), and regions 2.4 and 4.2 are involved in the
recognition of promoter DNA sequences (19).
In this study, we focused on the function of the extreme
carboxy-terminal 16-amino-acid region of 38. This region
is located immediately downstream of region 4.2. Although contact sites
with some transcription factors were mapped in the corresponding region
of 70 (11, 15), no general function has been
assigned for this portion of sigma factors. Nevertheless, this region
is highly conserved among the rpoS gene products from
enteric bacterial species. Here we show an essential function for this
region of 38.
Structure of the carboxy-terminal region of 38.
Region 4, the carboxy-terminal region among the four conserved
sequences of the 70 family proteins, is further divided
into two parts, regions 4.1 and 4.2. Region 4.2 contains a
helix-turn-helix DNA binding motif, and in fact, the second helix has
been shown to interact directly with the promoter 35 hexamer sequence
(14). The downstream flanking sequence of region 4, which we
named here CTE for carboxy-terminal tail element, is unique for each
subunit, and a striking similarity was found among CTEs of the
rpoS gene products (38-CTE; Fig.
1) from various bacteria.
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FIG. 1.
Structure of the carboxy-terminal region of RpoS. The
thick bar represents a linear diagram of 38. N and C
indicate the amino and carboxy termini of 38,
respectively. Conserved regions 1 to 4 are indicated, and subregions
1.1, 2.1, 2.4, and 4.2, for which functions were assigned, are
indicated above the thick bar. Amino acid sequences of the
carboxy-terminal region are aligned below the thick bar. GenBank
database searches were performed by the BLAST program through homepages
of National Center for Biotechnology Information
(http://www.ncbi.nlm.nih.gov/). Amino acid sequences were aligned using
the Clustal V program with a fixed gap penalty of 10 and a floating gap
penalty of 10. Asterisks represent identical residues, and periods
represent residues having similar characteristics. The abbreviations
denote the following bacterial species: Eco, E. coli; Ecl,
Enterobacter cloacae; Eca, Erwinia carotovora;
Pae, Pseudomonas aeruginosa; Pfl, Pseudomonas
fluorescens; Ppu, Pseudomonas putida; Sente,
Salmonella enterica; Sty, S. enterica serovar
Typhimurium; Sento, Serratia entomophila; and Yen,
Yersinia enterocolitica. A bracket indicates a
helix-turn-helix DNA binding motif at region 4.2. The shaded area
indicates the carboxy-terminal 16-amino-acid region (CTE) that was
truncated in this study.
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CTE is required for promoter activation in vivo.
To analyze
the function of 38-CTE in vivo, the rpoS gene
was mutagenized so as to express a mutant 38 lacking
CTE. Using oligonucleotide I (Table 1)
and pKTF1 (a 2.3-kb KpnI fragment containing the
rpoS gene in the same direction as lacZ of vector
plasmids pTZ19R [24]), the 315th codon of the
rpoS open reading frame (ORF) was mutagenized to TAA with the MUTA-GENE In Vitro Mutagenesis Kit (Bio-Rad), and the resultant plasmid was named pKTF314. Both the wild-type and the mutant
rpoS genes were expressed under the control of the inducible
araBAD promoter. For this purpose, 1.8-kb
NcoI-PvuII fragments containing the
rpoS ORF were purified from pKTF1 and pKTF314 and were
cloned in the NcoI-SmaI site of pBAD22A
(7) to make pBF1 and pBF314, respectively.
Each of these constructs was introduced into a null
rpoS
mutant strain, MO1005EL, which was constructed based on NM522
(
16)
by P1 transduction of
rpoS::Tn
10 (
22) and
katE::
lacZ (
22).
The
corresponding gene products were detected after the arabinose
induction
(Fig.
2A), confirming that the system was
functioning
appropriately as expected. As a reporter system to detect
the
sigma activity of the
rpoS gene products, the
katE promoter that
is transcribed dependent on
rpoS (
22) was fused with
lacZ and
positioned in the
E. coli chromosome as a single copy by
using
a
phage-mediated system (
21). While the
-galactosidase activity
was increased after induction of the
wild-type
rpoS gene, no increase
of the activity was
detected after induction of the mutant sigma
factor
[
38(1-314)] (Fig.
2B). Therefore, we concluded that
the
katE promoter
transcription requires
38-CTE.
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FIG. 2.
Effect of truncation of 38-CTE on the
transcription activity of the katE promoter. MO1005EL cells
harboring pBF1 or pBF314 were grown with shaking in Luria-Bertani
medium supplemented with kanamycin (50 µg/ml), tetracycline (10 µg/ml), and ampicillin (50 µl/ml) at 37°C. RpoS proteins were
induced by the addition of arabinose at an optical density at 660 nm of
0.3. (A) The expression of 38 or
38(1-314) was monitored by Western analysis with
antiserum against 38 (25). Samples were taken
at 0 min (lanes 1 and 4), 30 min (lanes 2 and 5), and 60 min (lanes 3 and 6) after the addition of arabinose. The upper signals are an
unrelated band detected by the serum that are irrespective of the
rpoS expression. (B) The katE transcription
activity was assayed using a lacZ fusion construct. The
-galactosidase activity was assayed as previously described
(5) except that cell density was measured at 660 nm. The
solid line and dashed line correspond to results obtained with
MO1005EL/pBF1 and MO1005EL/pBF314, respectively. These results are
averages of duplicate measurements.
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|
To examine whether the CTE function is generally required for the
38 activity, expression of
lacZ fusion
constructs to other
38-dependent promoters,
fic (
26) and
bolA (
12),
were analyzed
using the same mutant
38 as in the case of
katE. Both of the tested promoters were activated
by
38 but not by
38(1-314) (data not shown).
The carboxy terminus regions of sigma
factors were shown to interact
with some
-contact transcription
factors to activate transcription
initiation (
11,
15). However,
these interactions are not
likely to explain the in vivo functional
defects of
38(1-314) because the activity was uniformly lost for
all tested
promoters which do not require additional transcription
factors
for function. In 1993, Zambrano and coworkers isolated an
rpoS mutant that has a growth advantage at the stationary
growth phase
(the GASP mutant) (
29). In this mutant, the CTE
region of
rpoS was replaced by a 46-bp duplication,
resulting in a shift of the
reading frame. The prediction that this
mutation weakened the
38 activity in vivo is consistent
with our present
observation.
CTE is not required for holoenzyme formation in vivo.
To
examine whether the loss of sigma activity by the CTE truncation is due
to impaired holoenzyme formation, either 38 or
38(1-314) was overexpressed in the null rpoS
mutant strain, MO1001FL, which was constructed based on KT1008
(22) by P1 transduction of
rpoS::kan (1) and
fic::lacZ (unpublished construct; K. Yamamoto and R. Utsumi, personal communication). In the case of 70, a glutathione S-transferase fused a
70 derivative lacking the first 72 amino acids, which
has a severe defect in open complex formation and is toxic to the cell
when overexpressed, since core enzyme is sequestered in nonproductive holoenzyme complex (27). Mutations that cause defects in
core enzyme binding relieved the toxicity (18). As shown in
Fig. 3B, overproduction of
38 severely retarded cell growth, probably because
38 competed the core enzyme with 70.
Since the overproduction of 38(1-314) caused similar
growth retardation (Fig. 3C), we concluded that the core binding was
not impaired for 38(1-314). However, the
-galactosidase activity was lost by the CTE truncation (Fig. 3B and
C, compare colony colors), indicating that the defects were involved in
later steps after the binding with the core enzyme.
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FIG. 3.
38-CTE is not required for holoenzyme
formation. pTZ19R (vector) (A), pKTF1 (38 overexpression
plasmid) (B), and pKTF314 [38(1-314) overexpression
plasmid] (C) were introduced into rpoS null mutant
MO1001FL. Effects on growth and fic-lacZ expression resulted
from 38, and 38(1-314) overexpression was
monitored using a Luria-Bertani plate containing 40 µg of X-Gal
(5-bromo-4-chloro-3-indolyl--D-galactopyranoside)/ml and
0.1 mM IPTG (isopropyl--D-thiogalactopyranoside).
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38-CTE is required for transcription activity in
vitro under high-salt conditions.
As an attempt to understand the
reason why CTE is required for the in vivo function of
38, we performed in vitro transcription experiments
using purified 38 proteins. Using oligonucleotide II
(Table 1) and pKTF18 (a 2.3-kb KpnI fragment containing the
rpoS gene in the same direction as lacZ of vector
plasmid pTZ18R), a BamHI site was introduced into the
mid-portion of the rpoS ORF without changing the amino acid sequence of the gene product, while a BamHI site in the
plasmid polylinker of the resulting plasmid pKTF18B was deleted by
partial digestion with BamHI and fill-in-ligation reactions.
From pKTFB thus constructed, a 1.5-kb
BamHI-HindIII fragment containing the 3' half
of the rpoS ORF was purified and cloned in pTZ19R to yield pRPO. To change the 315th codon of the rpoS ORF to a
nonsense TAG codon, an inverse PCR was performed using oligonucleotides III and IV as primers and pRPO as a template. The PCR-amplified product
was digested with HindIII and self-ligated to make pRPO314.
To introduce a
BamHI site into the
rpoS ORF at
the same position as pKTFB, PCRs were performed to amplify the 5' and
3' parts
of the
rpoS ORF, using pETF (
25) and two
sets of primers, oligonucleotides
V and VI and oligonucleotides VII and
VIII, respectively. Both
PCR products were purified and mixed to
perform the mega-primer
PCR (
10). The resultant fused
products were digested with
NdeI
and
SacI and
inserted into pET21b to make pETS. A 541-bp
BamHI-
HindIII
region containing the
rpoS 3' part was replaced by a 491-bp
BamHI-
HindIII
fragment of pRPO314 to yield
pETS314.
38 and
38(1-314) were overexpressed in
BL21 (DE3) pLysS (Novagen) by using pETF and pETS314, respectively, and
the protein purification
was carried out basically as previously
described (
25) except
for the protein renaturation process.
After the inclusion body
was solubilized, renaturation was performed by
dialysis against
TGED (10 mM Tris-HCl [pH 8.0]-5% glycerol-0.1 mM
EDTA-0.1 mM dithiothreitol)
buffer. The solubilized proteins were
further purified by POROS
HQ column chromatography (
6).
To examine the activity of
38 and
38(1-314), in vitro transcription experiments were
performed using the
fic promoter as a template.
Since it has
been shown by using various promoters as templates
that optimum salt
concentrations for E
38 are rather high compared with
those for E
70 (
2), we carried out in vitro
transcription reactions under
various potassium glutamate
concentrations. As shown in Fig.
4,
while
transcription activity of E
38 was increased
concomitantly with the increase in potassium glutamate
concentration at
least up to 200 mM, the optimum potassium glutamate
concentration for
E
38(1-314) was 50 mM, and the transcription activity of
E
38(1-314) was severely inhibited at 200 mM potassium
glutamate.
Therefore,
38-CTE is important for the
transcription activation by high concentrations
of potassium glutamate.
Since intracellular K
+ concentrations are kept in a range
of 0.1 to 0.5 M (
20) and
since glutamate is a natural
counterion for K
+, these results are in good agreement with
the observations shown
in Fig.
2 and
3. Thus,
38-CTE
might specifically donate salt resistance to this stationary
sigma
factor. However, underlying molecular mechanisms remain
to be analyzed.
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FIG. 4.
38-CTE is required for effective
transcription activity at high ionic strength in vitro. The core enzyme
and either 38 or 38(1-314) were mixed at
the ratio of 1:4 and incubated for 30 min at 37°C to reconstitute
holoenzymes. Single-round in vitro transcription assays were performed
essentially as previously described (17). Transcription
reactions were carried out under various ionic strengths (0, 50, 100, and 200 mM of K glutamate) with 100 nM reconstituted holoenzyme and 3 nM template DNA containing the fic promoter, i.e., the
BamHI-EcoRI fragment (776 bp) of pFL1
(26). The DNA template produced in vitro transcripts 242 nucleotides in length. Transcription activity at 50 mM K glutamate by
E38 was set at 1. Open bars represent transcription
activity of E38, and closed bars represent that of
E38(1-314). These results are averages of duplicate
experiments.
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ACKNOWLEDGMENTS |
We thank R. Utsumi and K. Yamamoto for providing unpublished
material (fic::lacZ). We also thank
K. Hayashi for technical assistance.
This work was supported by Grants-in-Aid from the Ministry of
Education, Science, and Culture of Japan, Biodesign Research Program of
RIKEN to K.T. and H.T., and CREST (Core Research for Evolutional
Science and Technology) of the Japan Science and Technology Corporation
(JST) to A.I. and K.T.
| |
FOOTNOTES |
*
Corresponding author. Mailing address: Institute of
Molecular and Cellular Biosciences, The University of Tokyo, Yayoi
1-1-1, Bunkyo-ku, Tokyo 113-0032, Japan. Phone: 81-3-5841-7825. Fax: 81-3-5841-8476. E-mail:
htakaha{at}imcbns.iam.u-tokyo.ac.jp.
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Journal of Bacteriology, August 2000, p. 4628-4631, Vol. 182, No. 16
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Copyright © 2000, American Society for Microbiology. All rights reserved.
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Gowrishankar, J., Yamamoto, K., Subbarayan, P. R., Ishihama, A.
(2003). In Vitro Properties of RpoS ({sigma}S) Mutants of Escherichia coli with Postulated N-Terminal Subregion 1.1 or C-Terminal Region 4 Deleted. J. Bacteriol.
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Cheung, K. J., Badarinarayana, V., Selinger, D. W., Janse, D., Church, G. M.
(2003). A Microarray-Based Antibiotic Screen Identifies a Regulatory Role for Supercoiling in the Osmotic Stress Response of Escherichia coli. Genome Res
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Lee, S. J., Gralla, J. D.
(2002). Promoter Use by sigma 38 (rpoS) RNA Polymerase. AMINO ACID CLUSTERS FOR DNA BINDING AND ISOMERIZATION. J. Biol. Chem.
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Jishage, M., Kvint, K., Shingler, V., Nystrom, T.
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Ruiz, R., Ramos, J. L.
(2002). Residues 137 and 153 at the N Terminus of the XylS Protein Influence the Effector Profile of This Transcriptional Regulator and the sigma Factor Used by RNA Polymerase to Stimulate Transcription from Its Cognate Promoter. J. Biol. Chem.
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Culham, D. E., Lu, A., Jishage, M., Krogfelt, K. A., Ishihama, A., Wood, J. M.
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