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Journal of Bacteriology, May 2001, p. 2952-2956, Vol. 183, No. 9
0021-9193/01/$04.00+0   DOI: 10.1128/JB.183.9.2952-2956.2001
Copyright © 2001, American Society for Microbiology. All rights reserved.

Mapping of the Rsd Contact Site on the Sigma 70 Subunit of Escherichia coli RNA Polymerase

Miki Jishage,dagger Dipak Dasgupta,Dagger and Akira Ishihama*

National Institute of Genetics, Department of Molecular Genetics, Mishima, Shizuoka 411-8540, Japan

Received 21 December 2000/Accepted 20 February 2001


    ABSTRACT
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Rsd (regulator of sigma D) is an anti-sigma factor for the Escherichia coli RNA polymerase sigma 70 subunit. The contact site of Rsd on sigma 70 was analyzed after mapping of the contact-dependent cleavage sites by Rsd-tethered iron-p-bromoacetamidobenzyl EDTA and by analysis of the complex formation between Ala-substituted sigma 70 and Rsd. Results indicate that the Rsd contact site is located downstream of the promoter -35 recognition helix-turn-helix motif within region 4, overlapping with the regions involved in interaction with both core enzyme and sigma 70 contact transcription factors.


    TEXT
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The survival of bacterial cells in various environments depends on their abilities to sense the external conditions and adapt their internal metabolic systems by turning on and off the expression of specific genes (for reviews, see references 12 and 21). For quick change of the global gene expression pattern in response to sudden environmental changes, bacteria carry modulation systems for the specificity and activity of transcription apparatus. The transcription apparatus of Escherichia coli is composed of the RNA polymerase core enzyme (subunit composition, alpha 2beta beta ') with the catalytic activity of RNA polymerization and one of seven species of the sigma  subunit with the promoter recognition activity (reviewed in references 14, 15, 19, and 22). The major sigma  subunit, sigma 70, is responsible for transcription of most genes expressed during steady-state cell growth under laboratory culture conditions. The other six species of the sigma  subunit are required only during certain growth stages or under specific stress conditions. In agreement with their functional roles, the levels of these alternative sigma  subunits vary depending on the cell growth conditions (25, 26, 42), and all the sigma  subunits compete with each other for binding to a fixed amount of the core enzyme (41). In addition to the level control, the activities of at least some E. coli sigma  subunits are under a control system in which the unused sigma  subunits are stored in inactive forms by forming complexes with another set of proteins, often designated as anti-sigma factors, with the regulatory activity of sigma  functions (for reviews see references 18 and 21).

Subunit sigma F is involved in transcription of the genes needed for flagellum formation and chemotaxis. The flgM gene product is an anti-sigma F factor that acts by directly binding to sigma F and thereby preventing its interaction with the core RNA polymerase (33). Subunit sigma E is a member of the ECF family of sigma  subunits for transcription of the genes related to extracytoplasmic functions (39) as well as those required for high temperature survival or thermotolerance (9). The sigma E activity is regulated by the rseA (regulator of sigma E) gene product or anti-sigma E factor, which is associated with the inner membrane and inhibits the activity of sigma E by directly interacting with sigma E (7, 43). FecI also belongs to the ECF sigma  family and is involved in transcription activation of the ferric-citrate transport genes (fec) (1). Genetic studies revealed that FecR, an inner membrane protein, negatively regulates the activity of the FecI sigma  subunit (49). FlgM, RseA, and FecR are classified as members of anti-sigma factors for sigma F, sigma E, and sigma FecI, respectively. A heat shock protein, DnaK, can be an anti-sigma factor for the heat shock sigma H subunit (18), which is induced following heat shock and is involved in transcription of the genes encoding heat shock proteins, including DnaK, DnaJ, and GrpE (13). After returning from the transient adaptation period to heat shock to steady-state growth at high temperatures, unused sigma H becomes stored as DnaJ-DnaK-sigma H complexes (38), which are dissociated by the action of GrpE to release sigma H for reuse or for degradation by HflB (FtsH) protease (10).

Recently we discovered a novel E. coli protein, referred to as Rsd (regulator of sigma D), which forms a complex with sigma 70, the major sigma 70 subunit for growth-related gene transcription, and prevents its function (24). Purified Rsd protein formed complexes in vitro with sigma 70 but not with other sigma  subunits and inhibited transcription in vitro by the holoenzyme containing sigma 70 to various extents, depending on the promoters used (24). Since Rsd is induced in the stationary phase of cell growth, where sigma 70 is not used, we proposed that Rsd is an anti-sigma factor for the major sigma 70 subunit for storage in the stationary phase. In E. coli mutants lacking the rsd gene, the expression of sigma 70-dependent genes increases while transient overproduction of Rsd leads to a reduction in sigma 70-dependent gene expression (23). Based on these results, taken together, we proposed that Rsd is an anti-sigma factor for the sigma 70 subunit.

Cleavage sites of sigma 70 by Rsd-tethered FeBABE. Previously we estimated the contact site of Rsd on sigma 70 to be downstream from residue 500, including regions 3.2, 4.1, and 4.2, after analysis of complex formation between Rsd and sigma 70 fragments (24). For detailed mapping of the contact site of Rsd on the sigma 70 subunit, we employed the contact-dependent cleavage of target proteins by FeBABE (iron-p-bromoacetamidobenzyl EDTA)-conjugated pairing proteins (6, 20, 22). In this study, FeBABE was tethered to Rsd at all possible Lys residues by using 2-iminothiolane, which links between Lys and FeBABE (48). For detection of the cleavage sites on sigma 70, a protein kinase tag sequence was added at either its N or C terminus and the tag was phosphorylated using [gamma -32P]ATP and protein kinase A. Mixtures of a fixed amount of 32P-labeled sigma 70 and increasing amounts of FeBABE-tethered Rsd were incubated for 10 min at 37°C to form binary complexes and then were subjected to cleavage reaction by adding ascorbate and H2O2. The reaction mixtures were analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) followed by autoradiography. Fig. 1 shows a tracing of the SDS-PAGE pattern of the cleavage products. As size markers, the same 32P-labeled sigma 70 was treated with CNBr, which induces cleavage at Met residues. Although several nonspecific cleavage products were generated by the addition of H2O2 and ascorbate even in the absence of FeBABE-tethered Rsd, the specific cleavage products increased concomitantly with the increase in Rsd-FeBABE addition. At least three such bands, cleaved at sites 1a, 1b, and 2, were identified, each migrating close to the C-terminal CNBr fragment (471/475-613, 488/490-613, or 562/568-613, respectively). Thus we concluded that the FeBABE tethered on the surface of sigma 70-bound Rsd approached near the sigma 70 segment between residues 471 and 568. The cleavage sites 1a and 1b are located within sigma 70 region 3 while cleavage site 2 is within region 4 (see Fig. 3). The result, however, does not immediately indicate the location of the Rsd contact site on these regions because the spacer length between the BABE-tethered Lys and the BABE-associated Fe is about 18 Å (20, 48).


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  		FIG. 1.   Cleavage of sigma 70 by Rsd-tethered FeBABE. Purified Rsd was conjugated with FeBABE (Dojin, Kumamoto, Japan) in the presence of 2-iminothiolane according to Traviglia et al. (48), while sigma 70 with a PK tag at the C terminus was labeled in vitro with 32P with protein kinase A. Mixtures of a fixed amount of 32P-labeled sigma 70 (final concentration, 250 nM) and the indicated amounts of FeBABE-tethered Rsd were incubated for 30 min at 37°C and then were subjected to contact-dependent protein cleavage reaction by adding ascorbate and H2O2 followed by SDS-PAGE. CNBr-treated 32P-sigma 70 was run on the same gel as size markers. The gel was exposed to an imaging plate, and the plate was analyzed with the BAS 2000 Image Analyzer (Fuji, Tokyo, Japan). Migration is from left to right. The migration positions of CNBr fragments are indicated at the bottom.

The cleavage reaction by Rsd-tethered FeBABE was also performed for all six alternative subunits, sigma N, sigma S, sigma H, sigma F, sigma E, and sigma FecI, but none of them were cleaved even after the addition of excess amounts of Rsd-FeBABE (data not shown). These observations confirm our previous finding that Rsd specifically interacts only with the sigma 70 subunit and not with the other sigma  subunits (24).

Rsd-binding activity of Ala-substituted sigma 70 mutants. For detailed mapping of the contact site on sigma 70 with Rsd, we next tested the complex formation in vitro between Rsd and Ala-substituted sigma 70 subunits. The library of Ala-substituted sigma 70 was constructed and used for mapping the sigma 70 contact sites with the core enzyme (46) or with sigma 70 contact transcription factors CRP and FNR (40). The mutant sigma 70 subunits with a glutathione S-transferase (GST) tag fused at the N termini were overproduced and were purified to near homogeneity. The GST-tagged sigma 70 subunits were mixed with purified Rsd, and the complexes formed were recovered using glutathine-conjugated agarose beads. This GST pull-down assay indicated that two sigma 70 mutants with Ala substitutions at residues 595 and 598 were defective in binding to Rsd (Fig. 2A), indicating that the segment of sigma 70 including L595 and L598 is involved in molecular interaction with Rsd. The major determinant of core enzyme binding on sigma 70 is located in region 2.1 (37). L598 in region 4.2 also participates, at least in part, in binding of the core enzyme (46). The corresponding region of sigma 32 is also involved in core enzyme binding (27). In the case of core enzyme binding, multiple sites on the sigma  subunits are involved and thus a single mutation is often not so critical for overall functions of the sigma  subunits. In fact, under the assay conditions employed, the binding of L598A mutant sigma 70 with the core enzyme is stronger than that with the Rsd protein (Fig. 2A).


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  		FIG. 2.   Identification of the Rsd contact site on the sigma 70 subunit. (A) GST-sigma 70 Ala-substituted mutants were overexpressed and purified to near homogeneity. Each GST-sigma 70 mutant was mixed with an equal amount of Rsd, and after incubation for 5 min at 37°C, GST-sigma 70-Rsd complexes were isolated by the GST pull-down assay using glutathione-Sepharose beads. The bead-bound proteins were eluted with 50 mM glutathione and were analyzed by SDS-PAGE. The gel was subjected to immunoblotting against anti-Rsd, anti-sigma 70, or anti-beta beta ' antibodies. (B) Activity of the Ala-substituted mutant sigma 70 subunits. In vitro transcription was carried out under the standard reaction conditions (28) using 1 pmol each of the GST-sigma 70 mutants, 1 pmol of the core enzyme, and 1 pmol of either lacUV5 or extended -10 promoter DNA fragment (31, 32).

To analyze the role of these residues in the intrinsic sigma 70 function of promoting transcription initiation, holoenzymes were reconstituted from each of the Ala-substituted mutant sigma 70 subunits and the sigma -free core enzyme and were used for in vitro transcription. The lacUV5-directed transcription was significantly reduced for only the same two mutants, L595A and L598A, which are required for Rsd interaction (Fig. 2B). Thus, the sites required for Rsd interaction are also critical for expression of the intrinsic sigma 70 activities, presumably at the step of core enzyme binding (46). The influence of Ala substitution at residues downstream of the -35 recognition helix-turn-helix (HTH) motif of sigma 70 was also observed in RNA I promoter-directed transcription in vitro (40). The reduction of sigma 70 activity for Ala-substituted mutant sigma 70 was, however, not observed when transcription was carried out using the extended -10 promoter (Fig. 2B), which is active in directing transcription even in the absence of -35 promoter -sigma 70 region 4 interactions (2, 4, 32).

Rsd contact site on the sigma 70 subunit. FeBABE cleavage experiments indicate the close location of Rsd near the sigma 70 segment between residues 471 and 568, including regions 3.1, 3.2, and 4.1 (see Fig. 1), while the mutant studies using an Ala-substituted sigma 70 library indicate that the Rsd contact site is downstream from region 4.2 (see Fig. 2). Since the reactive Fe3+ is located 18 Å apart from the Lys residue tethered with FeBABE with the use of a 2-iminothiolane linker (20, 48), it is unlikely that the region between 471 and 568 is the direct target of Rsd binding, but instead the Rsd-binding site includes the residues L595 and L598 identified by Ala scanning. The FeEDTA moiety of the FeBABE tethered at this region may be located close to regions 3 and 4.1, where the cleavage sites were identified (see Fig. 1). Thus we conclude that the direct contact site of Rsd is located on region 4 of the sigma 70 subunit downstream of the HTH motif of region 4.2 (Fig. 3), which is involved in recognition of the promoter -35 sequence (11, 47). The -35 contact is, however, not essential for promoter complex formation when the contact of sigma 70 region 2 with the promoter -10 sequence alone is strong enough, as in the case of an extended -10 signal (3, 4, 32).


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  		FIG. 3.   The Rsd contact sites on the sigma 70 subunit. The predicted Rsd contact sites are compared with the known functional sites, including the sites involved in the molecular interaction with class II transcription factors. The HTH motif is involved in the promoter -35 recognition (11, 47). The contact sites for class II transcription factors are located upstream or downstream of this motif. For details, see the text.

The sigma 70 contact (or class II) transcription factors support the functional interaction of sigma 70 with promoters lacking the consensus -35 sequence (19). In these cases, the region upstream or downstream of the -35 contact HTH motif in sigma 70 region 4 is involved in interaction with class II factors (19, 45). Deletion mutant sigma 70 lacking region 4 is still functional with the extended -10 promoter, which alone has a high affinity to the sigma 70 region 2 but is defective in response to CRP (on class II promoters) and PhoB (31). Mutant studies indicate that the contact sites for several class II transcription factors, including lambda  cI (8, 30), PhoB (29), CRP (40), FNR (40), Ada (35, 36), AraC (17, 40), and RhaS (3) are all located upstream or downstream of the HTH promoter -35 recognition motif (Fig. 3). Transcription activation by lambda  cI becomes defective in a region 4 mutation of the sigma 70 subunit (30). At class II CRP-dependent promoters, CRP makes three different contacts, one of which, known as the activating region 3 (AR3), interacts with region 4 of the sigma 70 subunit (45). The positively charged residues K593, K597, and R599 on sigma 70 are required for this interaction. Mutations on these residues also affect the sigma 70 response to FNR (40). Most class I (or alpha  contact) factors activate transcription by stabilizing the closed complex, while class II (or sigma 70 contact) factors such as lambda  cI activate the isomerization step of transcription initiation (8).

The contact site with Rsd is located on the same surface with those of AraC, CRP, FNR, RhaS, and lambda cI (Fig. 3). Thus, the region downstream from the promoter -35 binding HTH of sigma 70 seems to be involved in binding the core enzyme, the anti-sigma factor, and a group of class II transcription factors. The anti-sigma 70 factor Rsd should compete with both the core enzyme and the class II transcription factors in binding with the sigma 70 subunit. Likewise, the contact site of FlgM, the anti-sigma F factor, has been mapped on region 4 of sigma F (34). The phage T4 AsiA protein is an anti-sigma factor against the host E. coli sigma 70 subunit to repress host cell gene transcription (5, 44). The contact site for the AsiA protein on sigma 70 is located within regions 3 and 4 (16). Thus, all the anti-sigma factors so far analyzed seem to interact with the same sigma  region near the promoter -35 recognition surface.


    ACKNOWLEDGMENTS

We thank Carol Gross for donating the expression library of Ala-substituted sigma 70 and for helpful discussion.

This work was supported by Grants-in-Aid from the Ministry of Education, Science, Culture and Sports of Japan and by the CREST fund from the Japan Science and Technology Corporation.


    FOOTNOTES

* Corresponding author. Mailing address: National Institute of Genetics, Department of Molecular Genetics, Mishima, Shizuoka 411-8540, Japan. Phone: (81) 559-81-6741. Fax: (81) 559-81-6746. E-mail: aishiham{at}lab.nig.ac.jp.

dagger Present address: Cancer Institute, Toshima-ku, Tokyo 170-8455, Japan.

Dagger On leave of absence from Biophysics Division, Saha Institute of Nuclear Physics, Calcutta-700 037, India.


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Journal of Bacteriology, May 2001, p. 2952-2956, Vol. 183, No. 9
0021-9193/01/$04.00+0   DOI: 10.1128/JB.183.9.2952-2956.2001
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