Department of Microbiology and Immunology, University of Texas Health Science Center, San Antonio, TX 78229-3900, USA
Correspondence
W. G. Haldenwang
Haldenwang{at}uthscsa.edu
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ABSTRACT |
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INTRODUCTION |
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RsbV and RsbW are the primary B regulators. As illustrated in Fig. 1
, RsbW is a
B-binding protein, able to sequester
B into an association that prevents it from joining RNA polymerase (Benson & Haldenwang, 1993b
; Boylan et al., 1993
). RsbV is an antagonist to the RsbW
B complex (Benson & Haldenwang, 1993b
; Dufour & Haldenwang, 1994
). RsbW forms mutually exclusive complexes with either RsbV or
B (Delumeau et al., 2002
; Dufour & Haldenwang, 1994
). The ability of RsbV to compete for RsbW is dependent on RsbV's phosphorylation state (Dufour & Haldenwang, 1994
). RsbW is both a binding protein and an RsbV-specific kinase. In unstressed B. subtilis, RsbW-dependent phosphorylation of RsbV inactivates RsbV as a potential
B release factor (Alper et al., 1996
; Dufour & Haldenwang, 1994
). The dephosphorylation and reactivation of RsbV-P are effected by two stress-activated phosphatases, RsbP and RsbU. Each of these enzymes responds to a particular class of stress: RsbP to nutritional stress and RsbU to physical stress (Kang et al., 1996
; Vijay et al., 2000
; Voelker et al., 1995a
, b
, 1996
; Yang et al., 1996
).
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The phosphatase that responds to physical stress (RsbU) requires an additional protein, RsbT, for activity (Yang et al., 1996). A current model envisions RsbT to be held inactive in unstressed B. subtilis in a complex with its binding partner RsbS. Exposure to physical stress enables RsbT to phosphorylate RsbS. This results in the release of RsbT and its activation of RsbU (Akbar et al., 1997
; Chen et al., 2003
; Voelker et al., 1995a
, b
; Yang et al., 1996
). RsbS/RsbT interactions are believed to be modulated by RsbR and a family of related proteins (Akbar et al., 1997
, 2001
; Chen et al., 2003
; Gaidenko et al., 1999
). It has been recently demonstrated that RsbR, and by inference its paralogues, can self-associate into large-molecular-mass complexes (
106 Da) that can incorporate RsbS and RsbT (Chen et al., 2003
). These complexes may represent the normal state of the RsbR, -S and -T proteins in unstressed B. subtilis. RsbR, like RsbS, can be phosphorylated by RsbT (Gaidenko et al., 1999
). In vitro, RsbR is necessary for RsbS to bind and be phosphorylated by RsbT (Chen et al., 2003
). The phosphorylation state of RsbR does not affect the binding of RsbT to RsbS in the RsbR/RsbS complex, but does influence the ability of RsbT to phosphorylate RsbS, with RsbR-P facilitating the phosphorylation reaction (Chen et al., 2003
). Inhibition of RsbT is re-established through the activity of RsbX, an RsbS-P phosphatase that reactivates RsbS and allows it to again sequester RsbT (Voelker et al., 1995a
, b
; Yang et al., 1996
).
Aside from RsbR, -S, and -T, there is evidence that a ribosome-associated process may contribute to stress activation of B.
B fails to be induced by physical stress in B. subtilis strains that are either missing ribosome protein L11 or deficient in the ribosome-associated GTP-binding protein Obg (Scott & Haldenwang, 1999
; Zhang et al., 2001
).
We previously noted that RsbR, -S and -T, as well as Obg, cofractionate with ribosomes during gel-filtration chromatography of crude B. subtilis extracts (Scott et al., 2000). Obg was subsequently shown to bind to ribosome protein L13 in an affinity blot assay (Scott et al., 2000
). Thus, Obg's cofractionation with ribosomes probably represents a direct interaction between these two entities; however, even though RsbT can interact with Obg in the yeast dihybrid assay (Scott & Haldenwang, 1999
), the significance of RsbT, as well as RsbR and RsbS, in the ribosome-containing fractions is unknown. In the present work we explore the possible associations that exist between the Rsb proteins, Obg and ribosomes in extracts of wild-type and mutant B. subtilis, and Escherichia coli engineered to express RsbR, RsbS and RsbT. The data are consistent with Obg, but not RsbR, RsbS or RsbT, being ribosome-associated. The ribosome/Obg contributions to triggering stress induction of RsbT apparently do not involve interactions that persist in crude extracts. Additionally, and unlike the inactivating complexes that form between other
B regulators (e.g. RsbW
B, RsbVRsbW) which are readily identified in crude extracts, we find no evidence for persistent associations between the RsbRRsbS complex and RsbT. Instead, RsbT appears to form Triton-sensitive aggregates in crude extracts, suggesting an inherent instability of free RsbT which may be related to its role as a stress-sensitive activator.
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METHODS |
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BSK5 rsbR2 was constructed as follows. A 502 bp EcoRI segment internal to rsbR in pRS11 (PA rsbRS; Smirnova et al., 1998
) to create pJM49. This deletion terminates the synthesis of RsbR at codon 92 of the 274 codon rsbR gene. Using a strategy similar to that described above, BSK5 was identified following transformation of wild-type B. subtilis (BSA46) with linearized pJM49, yielding KanR clones which were screened by Western blot for the absence of RsbR but normal levels of the downstream rsbS gene product.
BSJ39 (RsbS) was created using plasmid pS25. p
S25 consists of a PCR fragment that begins approximately 200 bp upstream of the sigB operon's transcriptional start site and ends at the fourth codon of RsbS, joined to a second fragment that extends from 10 codons before the rsbS carboxy terminus to the end of rsbT, cloned in pRT-2. KanR clones arising from transformation of linearized p
S25 into a wild-type B. subtilis strain (BSA46) were screened for the anticipated high
B activity (ctc : : lacZ) associated with the loss of RsbS on LB plates with X-Gal. Putative RsbS clones were then screened by Western blot for the presence of RsbR and T, and the absence of RsbS.
E. coli (TG-2) strains expressing various combinations of rsbR, -S and/or -T were constructed using pUC19-based plasmids. ECW1 carries pDRNT and expresses rsbR, -S and -T. ECW2 expresses rsbR and -S. It carries pDRS, a plasmid derived from pDRNT by cutting with NdeI and SphI to remove rsbT and recircularizing after treatment with mung bean nuclease to blunt the ends. ECW4 expresses rsbT from plasmid pKAT-1. pKAT-1 is pUK19 bearing the sigB operon's PA promoter, amplified by PCR from PY22 as a 376 bp EcoRI/BamHI fragment (315 to +60) and joined to a 450 bp BamHI/SphI fragment encoding rsbT (36 bp upstream of rsbT to 12 bp downstream of rsbT). ECW3 expresses rsbS and rsbT from pSK-X. To make pSK-X, rsbS and rsbT that had been amplified by PCR as a 715 bp HindIII/XbaI DNA fragment (23 bp upstream of rsbS to 23 bp downstream of rsbT) were cloned into pUC19. In plasmids pDNRT, pDRS and pKAT-1, the rsb genes are expressed from the sigB operon's PA promoter, which is recognized in E. coli, and in pSK-X they are expressed from Plac. Bacteria were routinely grown in LB at 37 °C.
Gel-filtration analysis.
Gel-filtration chromatography was performed as described previously (Scott et al., 2000). One litre of B. subtilis or E. coli culture (OD540, 0·4) was harvested on ice, washed with a low-salt buffer [10 mM Tris (pH 8·0), 50 µM EDTA, 1·5 mM MgCl2, 1 mM DTT, 0·03 % phenylmethyl sulfonyl fluoride (PMSF)] and resuspended in 5 ml of the same buffer. Following disruption in a French pressure cell, debris was removed by centrifugation (5 000 g for 10 min), and the resulting crude lysate loaded onto a 500 ml Sephacryl S-300 column equilibrated with the same buffer. Five millilitre fractions were collected, precipitated with 2 vols of ethanol and analysed by SDS-PAGE (13·5 % acrylamide) and Western blot. If a second round of gel filtration was to be used, the fractions containing the large-molecular-mass complexes were pooled and dialysed into buffer [10 mM Tris (pH 8·0), 50 mM KCl] containing either 10 mM magnesium acetate or no added Mg2+. The dialysed fractions were reapplied to the Sephacryl column, equilibrated with the buffer used for dialysis and fractionated/analysed as before.
Velocity-sedimentation analysis.
B. subtilis grown and harvested, as in the gel-filtration analysis, was resuspended in sedimentation buffer [20 mM Tris (pH 7·5), 10 mM Mg Cl2, 0·5 mM EDTA, 1 mM dithiotheritol, 0·1 M NH4Cl, 0·03 % PMSF], disrupted by passage through a French pressure cell, and centrifuged (8000 g, 15 min) to remove debris. Protease inhibitors were added to the following final concentrations: pepstatin, 1 µM; leupeptin, 1 µM; N--tosyl-L lysine chloromethyl ketone (TLCK), 100 µM; antitrypsin, 2 µg ml1. One hundred microlitres of extract (OD280, 200) was layered onto 9 ml 1030 % sucrose gradients prepared in the sedimentation buffer. Gradients containing identical samples were centrifuged (37 000 r.p.m. in a Sorvall TH641 swinging bucket rotor) for 1·5, 3 and 5 h. Fractions (0·5 ml) were collected from the gradients, precipitated with 2 vols of ethanol and analysed by SDS-PAGE and Western blot.
To analyse the high-molecular-mass complexes that were identified by gel filtration, 4 ml of pooled Sephacryl column fractions was precipitated with (NH4)2SO4 (0·56 g ml1), resuspended in 0·5 ml of sedimentation buffer without PMSF, and dialysed overnight against 1 l of this buffer. Two hundred microlitres of dialysed extract was layered onto sucrose gradients and analysed as above.
General methods.
Transformations of B. subtilis and E. coli were performed by standard methods (Sambrook et al., 1989; Yasbin et al., 1973
). Western blot analyses were done as previously described, using mouse monoclonal antibodies against the Rsb proteins and mouse polyclonal anti-Obg antibody (Dufour et al., 1996
; Scott et al., 2000
).
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RESULTS |
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In an alternative analysis, the high-molecular-mass fractions from the original gel-filtration column were concentrated by (NH4)2SO4 precipitation, dialysed into 10mM MgCl2 buffer and examined by velocity centrifugation. Samples of this material, as well as unfractionated whole-cell lysates, were layered in triplicate onto sucrose gradients and subjected to high-speed centrifugation. Representative gradients were removed at intervals throughout the centrifugation run and, following fractionation, analysed by SDS-PAGE and Western blot. As illustrated in Fig. 3, the velocity fractionation of both a whole-cell lysate (Fig. 3i
) and the fast-eluting gel-filtration fractions (Fig. 3ii
) resulted in the separation of the RsbR/RsbS proteins and the ribosomes during sedimentation. The RsbR/RsbS proteins sedimented more slowly than ribosomes, consistent with the sedimentation profile reported for the self-assembling RsbR/RsbS complex (Chen et al., 2003
). RsbT's sedimentation through the gradient was distinct from that of either the ribosomes or the putative RsbRRsbS complex. Additionally, RsbT's sedimentation pattern varied, depending upon whether the material analysed was pooled gel-filtration fractions or crude cell extract. The bulk of the RsbT in the whole-cell extract (Fig. 3i-c
) remains in the uppermost portions of the gradient following centrifugation, apparently unassociated with fast-sedimenting components, while in the Sephacryl-fractionated sample, a second peak of RsbT is seen, trailing the ribosomal proteins but ahead of the putative RsbR/RsbS complex (Fig. 3ii
).
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Gel-filtration profiles of Obg, RsbR, RsbS and RsbT in mutant B. subtilis
To better characterize the nature of the high-molecular-mass forms of RsbR, RsbS and RsbT that are found in B. subtilis extracts, cell lysates from B. subtilis mutants lacking RsbR, RsbS, RsbT, or RsbR and its three most homologous paralogues YkoB, YojH and YqhA (Akbar et al., 2001) were fractionated by gel filtration and analysed by Western blot (Fig. 5
ad). The abundance of RsbS in the high-molecular-mass fractions decreased only slightly, relative to its abundance in low-molecular-mass fractions, in the RsbR single mutant, but more dramatically in the mutant lacking multiple RsbR-like proteins. In contrast, the RsbT remained exclusively in the high-molecular-mass form regardless of the presence or absence of either RsbR or RsbS. These findings are consistent with the notion that RsbS, but not RsbT, is present in the high-molecular-mass fractions due to its association with RsbR, and that the RsbR paralogues can substitute for RsbR in such a complex. As would be expected from the current model, the absence of RsbT had no obvious effect on the abundance of the high-molecular-mass RsbR/RsbS complex and the loss of RsbS did not prevent the accumulation of the putative RsbR multimer. These results reinforce the notion that RsbT is not part of a stable complex with RsbR and RsbS in B. subtilis extracts. If the complex was initially present, it was unable to persist during the fractionation protocols that we employed.
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DISCUSSION |
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Recent biochemical experiments have shown that RsbR can form high-molecular-mass complexes which incorporate RsbS (Chen et al., 2003). It is thought that formation of such a complex is a prerequisite for RsbS to be able to sequester and inactivate RsbT. The high-molecular-mass RsbR/RsbS association that we observed in fractionated B. subtilis and in E. coli extracts probably represents this complex. As was seen in the biochemical experiments, RsbR is the essential element in its formation (i.e. the high-molecular-mass complex of RsbR occurs in the absence of RsbS, but the high-molecular-mass RsbS complex requires RsbR) and based on its formation when RsbR and RsbS are expressed in E. coli no additional Bacillus-specific proteins are needed. In Bacillus, in which a family of RsbR paralogues are thought to be able to substitute for RsbR (Akbar et al., 2001
), the loss of RsbR itself has only a modest effect on the presence of a high-molecular-mass complex that incorporates RsbS. Only when RsbR and several RsbR paralogues are deleted does the abundance of the RsbS-containing complex show a noticeable decline.
A curiosity in the present study is the failure of RsbT to be part of the RsbR/RsbS complex. A favoured model for the stress-activation mechanism envisions RsbT as unavailable to activate the RsbU phosphatase due to its sequestration into the complex with RsbR/RsbS. This would be similar to the inactivation of B by its sequestration in an RsbW/
B complex or the inactivation of RsbW by its binding to RsbV. Both of these complexes are readily discerned in fractionations of crude B. subtilis extracts (Dufour & Haldenwang, 1994
), yet the association of RsbT with its putative inactivating complex is not evident. This is true even in extracts prepared from a B. subtilis strain with an altered RsbS (RsbS59SA) that should not release RsbT (Kang et al., 1996
). Instead, two forms of RsbT were found in crude extracts: a low-molecular-mass form, observed when crude extracts were fractionated by velocity-gradient analysis, and a high-molecular-mass form, found following gel filtration, which, by virtue of its detergent sensitivity, probably represents aggregated RsbT.
In other stress-responsive systems, protein denaturation and chaperone-assisted protein-folding contribute to stress signalling and gene regulation (Narberhaus, 1999). It is plausible, although quite speculative, that the denaturation of RsbT, reflected in its apparent aggregation in crude extracts, could have regulatory significance. If RsbT is readily given to misfolding and aggregation, the RsbR/RsbS complex could not only serve as an inactivating RsbT-binding complex, but also play a positive role as an RsbT-chaperone complex, stabilizing and releasing a properly folded RsbT in response to a stress-generated trigger.
In an earlier analysis of the role of RsbS in B regulation, it was reported that an rsbS allele (rsbS59SD), whose product mimics phosphorylated RsbS, was more effective in allowing RsbT to activate
B than was a deletion of rsbS (Kang et al., 1996
). We have confirmed this result and, in addition, note that the rsbS59SD allele is codominant with its wild-type counterpart. We also found that the rsbS allele (rsbS59SA), whose product should sequester RsbT into stable inactive complexes (Kang et al., 1996
; Yang et al., 1996
), is recessive to the wild-type rsbS allele (A. Reeves, S. Zhang & W. Haldenwang, unpublished results). These phenotypes are unusual for an inhibitory system, where the capacity for negative control would be expected to be dominant. Although more complex models can be envisioned to explain these results, the dominance of wild-type rsbS over rsbS59SA, and rsbS59SD over the wild-type allele, could be simply explained if RsbS, when altered due to phosphorylation following stress or the rsbS59SD mutation, has a positive influence on RsbT activity. Detailed mutational analyses of rsbR, rsbS and rsbT could reveal the validity of this notion.
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ACKNOWLEDGEMENTS |
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REFERENCES |
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Received 18 June 2004;
revised 23 July 2004;
accepted 31 August 2004.
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