CorE from Myxococcus xanthus Is a Copper-Dependent RNA Polymerase Sigma Factor

CorE from Myxococcus xanthus Is a Copper-Dependent RNA Polymerase Sigma Factor Nuria Go ´mez-Santos, Juana Pe ´rez, Marı ´a Celestina Sa ´nchez-Sutil, Aurelio Moraleda-Mun ˜oz, Jose ´Mun ˜ozDorado* Departamento de Microbiologı ´a, Facultad de Ciencias, Universidad de Granada, Granada, Spain Abstract The dual toxicity/essentiality of copper forces cells to maintain a tightly regulated homeostasis for this metal in all living organisms, from bacteria to humans. Consequently, many genes have previously been reported to participate in copper detoxification in bacteria. Myxococcus xanthus, a prokaryote, encodes many proteins involved in copper homeostasis that are differentially regulated by this metal. A sfactor of the ECF (extracytoplasmic function) family, CorE, has been found to regulate the expression of the multicopper oxidase cuoB, the P1B-type ATPases copA and copB, and a gene encoding a protein with a heavy-metal-associated domain. Characterization of CorE has revealed that it requires copper to bind DNA in vitro. Genes regulated by CorE exhibit a characteristic expression profile, with a peak at 2 h after copper addition. Expression rapidly decreases thereafter to basal levels, although the metal is still present in the medium, indicating that the activity of CorE is modulated by a process of activation and inactivation. The use of monovalent and divalent metals to mimic Cu(I) and Cu(II), respectively, and of additives that favor the formation of the two redox states of this metal, has revealed that CorE is activated by Cu(II) and inactivated by Cu(I). The activation/inactivation properties of CorE reside in a Cys-rich domain located at the C terminus of the protein. Point mutations at these residues have allowed the identification of several Cys involved in the activation and inactivation of CorE. Based on these data, along with comparative genomic studies, a new group of ECF sfactors is proposed, which not only clearly differs mechanistically from the other sfactors so far characterized, but also from other metal regulators. Citation: Go ´mez-Santos N, Pe ´rez J, Sa ´nchez-Sutil MC, Moraleda-Mun ˜oz A, Mun ˜oz-Dorado J (2011) CorE from Myxococcus xanthus Is a Copper-Dependent RNA Polymerase Sigma Factor. PLoS Genet 7(6): e1002106. doi:10.1371/journal.pgen.1002106 Editor: Josep Casadesu ´s, Universidad de Sevilla, Spain Received January 19, 2011; Accepted April 11, 2011; Published June 2, 2011 Copyright: ß2011 Go ´mez-Santos et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: This work has been supported by grants from ‘‘Ministerio de Ciencia e Innovacio ´n,’’ Spain (BFU2006-00972/BMC, 70% funded by FEDER; and the program CONSOLIDER-INGENIO 2010, ref. CSD2009-00006) and Junta de Andalucı ´a (CVI-1377). AM-M has been funded by a postdoctoral fellowship from the ‘‘Plan Propio de la Universidad de Granada.’’ The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: [email protected] Introduction Myxococcus xanthus is a soil-dwelling d-proteobacterium of the group of myxobacteria used as a model to study multicellular behavior and differentiation, because it exhibits a complex developmental cycle triggered by starvation [1]. However, M. xanthus cells not only have to adapt their metabolism and behavior to changing nutritional concentrations, but also to other parameters, such as metals. Copper is a transition metal that functions as an ideal biological cofactor due to its ability to alternate between the redox states Cu(I) and Cu(II). However, copper also generates reactive oxygen species that cause cell damage [2]. This duality forces organisms to maintain a strict homeostasis for this metal. The most representative examples of the effect of disturbances in copper homeostasis are two inherited human disorders, Wilson disease and Menkes syndrome, which are directly linked to overload and deficiency of this metal, respectively [3]. Copper is required by prokaryotes in trace amounts because it is used as a cofactor by a few proteins. Hence, most bacterial homeostatic mechanisms are devoted to conferring resistance to this metal. The most common mechanisms are copper-transporting P1B-type ATPases, copper chaperones, multicopper oxidases (MCOs), and Cus systems [4]. In bacteria such as Escherichia coli, one of each of these elements is encoded in the genome [4]. In other bacteria, the homeostatic mechanism is even simpler, consisting of two P1B-type ATPases and one chaperone (Synechocystis PCC6803, Enterococcus hirae, and Lactococcus lactis), or one ATPase and one chaperone (Bacillus subtilis) [4,5]. In contrast, the large M. xanthus genome encodes a large number of paralogous genes to confer copper tolerance: three MCOs, at least two Cus systems, and three P1B-type ATPases, as well as the genes required for the biosynthesis of carotenoids [6–9]. This gene redundancy indicates that copper homeostasis in this myxobacterium is more complex than in other prokaryotes. All of these genes have been shown to be differentially regulated [6–9], suggesting that this sophisticated network must be finely regulated by specific metal sensors. One of the signal transduction mechanisms used by bacteria to direct gene expression at the transcriptional level in response to stress signalsisrepresentedbyalternativesfactors [10]. The largest group of alternative sfactors is the ECF (extracytoplasmic function) family, which corresponds to group 4 of the s 70 proteins [11]. ECF sfactors are small proteins, quite divergent in sequence, that contain only two regions (s 2 and s 4 ) required for interaction with the RNA polymerase core enzyme and recognition of the promoter [12]. Their ability to promote transcription relies on a protein that is PLoS Genetics | www.plosgenetics.org 1 June 2011 | Volume 7 | Issue 6 | e1002106 normally cotranscribed with the sfactor, named anti-sfactor. In the absence of external signals, ECF sfactors are sequestered by their cognate anti-s. After detecting the specific stimulus, the anti-sfactor releases the ssubunit, which can then promote gene expression after recruitment of the core RNA polymerase [13–16]. In this report, we identify a novel metal sensor involved in copper homeostasis in M. xanthus named CorE (for copperregulated ECF sfactor). We demonstrate that CorE requires copper in order to bind to DNA and that its activity is modulated by the redox state of this metal. According to these data, we propose a new group of ECF sfactors, defined by a Cys-rich domain (CRD) located at the C terminus of the protein, which is essential for activation and inactivation of the protein. Results/Discussion CorE is an ECF sfactor involved in copper homeostasis Most M. xanthus genes involved in copper homeostasis are located in the genome in two clusters [8]. In copper region 2, and next to the MCO cuoB, a gene encoding a protein with high similarity to ECF sfactors was found (MXAN_3426), suggesting that it could regulate the expression of genes involved in conferring copper resistance. This sfactor has been designated as CorE. The analysis of the CorE sequence has revealed a domain architecture with the conserved regions s 2 (sigma70_r2, PF04542; E-value of 3.2e-14) and s 4 (sigma70_r4_2, PF08281; E-value of 4.3e-06) typical of this type of sfactors [11,12]. To determine the role of CorE in copper homeostasis, a strain harboring a corE-lacZ fusion was constructed, and the analysis of this strain revealed that corE was up-regulated by copper (Figure 1A). Additionally, an in-frame deletion mutant (DcorE) was also generated, and the phenotypic analysis of this strain confirmed that this regulator conferred copper tolerance (Figure 1B). Genes regulated by CorE To identify genes regulated by CorE, plasmids containing fusions between the genes that have so far been involved in copper and/or other metal homeostasis in M. xanthus and lacZ were electroporated into the DcorE mutant. When the expression profiles of these genes in the mutant were compared with those exhibited in the wild-type (WT) strain, it was observed that only the MCO cuoB and the P1B-type ATPase copB remained undetectable in the DcorE background in the presence of copper (Figure 2A and Figure S1), indicating that they are regulated by this sfactor. Interestingly, these two M. xanthus genes exhibit a characteristic expression profile, with a peak at 2 h after the addition of exogenous copper. As ECF sfactors are usually autoregulated, corE expression was analyzed in the DcorE mutant. The results obtained showed that this sfactor is only partially responsible for its own up-regulation by copper, especially in the early stages after metal addition. However, some up-regulation by the metal still remains in the mutant (Figure 1A, red lines), indicating that although cuoB and corE are very close in the genome (Figure S2), their regulation exhibits some differences. The comparison and analysis of the upstream regions of cuoB and copB has allowed the identification of two similar sequences that could function as the promoter elements recognized by CorE (Figure S3), one located upstream of copB, and the other upstream of a third gene genetically linked to cuoB and corE which encodes an outer membrane efflux protein (MXAN_3424). A manual search for homologous sequences to this putative CorE-binding site in the M. xanthus copper regions 1 and 2 [8] revealed the presence of two other matches, one upstream of the gene for the P1B-type ATPase CopA and the other upstream of the gene identifier MXAN_3427, which encodes a protein with a heavymetal-associated domain (PF00403, with an E-value of 4.7e-14). To corroborate that these two genes are regulated by CorE, plasmids harboring fusions between these two genes and lacZ were introduced into the WT and DcorE backgrounds and b–gal specific activity was determined in these strains. The results obtained revealed that the gene for the heavy-metal-associated protein exhibits an expression profile in the WT strain very similar to those of cuoB and copB after copper supplementation (compare Figure 2A and 2B). Up-regulation by copper was completely eliminated in the DcorE mutant, demonstrating that this gene is also part of the CorE regulon. In the case of copA the result was less clear. The expression profile of copA in the WT strain clearly differs from those exhibited by the CorE-regulated genes (compare panel C with panels A and B in Figure 2), and instead of a peak at 2 h, a plateau is reached 24 h after copper addition. Accordingly, the expression profile of copA in the DcorE mutant is quite similar to that of the WT strain (Figure 2C). However, when the expression level of copA in these two strains was analyzed with greater precision at short intervals (Figure 2D), it could be observed that the rapid induction of this gene obtained in the WT strain was no longer observed in the mutant. This result suggests that copA is subject to double regulation by CorE and another unidentified copper-dependent regulator. Nevertheless, further work will be required to unambiguously demonstrate that copA is regulated by CorE. Finally, using the consensus sequence of the promoters for these four genes, we tried to determine which other genes could also be under control of CorE. By using the approach described in Materials and Methods, another 13 similar sequences were identified in the M. xanthus genome (Figure S3). However, the fact that only two of them contain the seven invariable residues found in the other promoters, and that none of the proteins encoded by the genes located downstream of these sequences exhibit similarities to other proteins known to be involved in copper handling and trafficking, preventing us from drawing the conclusion that they are indeed regulated by CorE. Author Summary Copper exerts a dual effect on living organisms. It is essential for life, but an excess provokes cell damage, forcing cells to maintain a regulated homeostasis for this metal. These two antagonistic biological effects of copper are clearly illustrated by two human genetic disorders, Menkes syndrome and Wilson disease, caused by deficiency or accumulation of this metal, respectively. Myxococcus xanthus, a soil-dwelling bacterium, also has to cope with changes in copper concentration in its environment. The large genome of this myxobacterium encodes many genes involved in copper homeostasis, all of which are differentially regulated, indicating that many regulators participate in copper homeostasis in this prokaryote. Here, we identify one of these regulators (CorE), which belongs to the family of the extracytoplasmic function (ECF) sfactors. We demonstrate that CorE represents a novel group of ECF sfactors and of metal regulators, because its activity is modulated by the redox state of copper. This ability resides in a Cys-rich domain, which has also been found in other sfactors of different bacterial phyla. Therefore, we propose that CorE is the first member of a mechanistically new group of ECF sfactors. A Copper-Dependent Sigma Factor PLoS Genetics | www.plosgenetics.org 2 June 2011 | Volume 7 | Issue 6 | e1002106 Figure 1. CorE is involved in copper homeostasis. (A) Copper up-regulation of corE.b-gal specific activity was determined in cell extracts of the WT (blue lines) and DcorE (red lines) strains (harboring the fusion corE-lacZ) from CTT agar plates containing no copper (open symbols) or 0.6 mM (closed symbols) copper sulfate. (B) Effect of copper on M. xanthus growth. WT (blue line) and DcorE (red line) strains were grown in the absence of the metal and diluted to an OD 600 of 0.05 into fresh CTT liquid media containing the indicated copper concentrations. The OD 600 was then monitored after 24 h of incubation. Error bars indicate standard deviations. doi:10.1371/journal.pgen.1002106.g001 Figure 2. CorE-dependent genes. (A) Regulation of cuoB and copB by CorE. Plasmids containing cuoB-lacZ (blue lines) and copB-lacZ (red lines) fusions were introduced into the WT (solid symbols) or the DcorE (open symbols) backgrounds, and incubated on CTT agar plates containing 0.6 mM CuSO 4 .b-gal specific activity was determined in cell extracts harvested at the indicated times. The same approach reported above was followed to study the regulation of MXAN_3427 (B) and copA (C and D) by CorE, although 0.3 mM CuSO 4 was used to get an optimal difference in the copA expression levels between the WT and the DcorE strains at early times (panels C and D). The dashed arrow from panel C to D indicates that in panel D only the indicated part of panel C is shown. Please note the difference in the scale in each panel, and the different time course of panel D. Error bars indicate standard deviations. doi:10.1371/journal.pgen.1002106.g002 A Copper-Dependent Sigma Factor PLoS Genetics | www.plosgenetics.org 3 June 2011 | Volume 7 | Issue 6 | e1002106 As the activation of CorE by copper could be caused either by the general oxidative stress induced by this metal or by the direct binding of the protein to copper in either of its two redox states, cuoB expression in the WT strain was tested in the presence of several concentrations of the oxidants hydrogen peroxide and diamide, and the Cu(II) mimetic divalent metals Cd 2+ ,Ni 2+ , and Zn 2+ . Similarly, Ag + was used to mimic Cu(I). The results obtained revealed that only Cd 2+ and Zn 2+ could induce cuoB expression (Figure 3A and Figure S4). The fact that Ni 2+ does not up-regulate cuoB is not surprising, because the same metals cannot always mimic the copper effect. As an example, the M. xanthus P1B-type ATPase copA has been reported to be induced by copper, Ni 2+ and Co 2+ , but not by Zn 2+ [9]. It is notable that the expression levels obtained with Cd 2+ and Zn 2+ were not only much lower than with copper, but also that the expression profiles were different. In the case of Cd 2+ , no peak was observed at 2 h; instead, a plateau was reached 24 h after metal supplementation (Figure 3B). Although Zn 2+ also yielded a rapid cuoB induction, the peak at 2 h was not as evident as in the case of copper (Figure 3C). cuoB up-regulation by Cd 2+ and Zn 2+ is also dependent on CorE (Figure 3B and 3C). These data indicate that Cu(II) is the redox state of copper that activates CorE. It should be noted that the Cd 2+ and Zn 2+ concentrations needed to observe a clear cuoB induction are close to the maxima that M. xanthus cells can tolerate [7], while 0.3 mM copper has almost no effect on myxobacterial growth (Figure 1B). It should also be noted that the addition of metals to the media not only alters the growth rates of the cultures, but also inhibits cell motility, explaining why the morphology of the cell spots is not the same in all of the media tested. Searching for the CorE cognate anti-sfactor Many ECF sfactors function with a cognate anti-swhich is genetically linked to the ssubunit [11–16]. Analyses of the genes located in the proximity of corE revealed that they encode either proteins located in the periplasmic space or in the outer membrane, or that they exhibit striking similarities to wellcharacterized proteins involved in specific functions, suggesting that no anti-sfactor is cotranscribed with corE. However, the possibility remained that it could be encoded in some other region of the M. xanthus genome. To test for the existence of an anti-s factor, a strategy was designed consisting of the over-expression of corE [17]. If CorE were present in higher quantities than an unidentified anti-sfactor, it would be released from the antagonistic effect of the anti-s, and cuoB should be expressed even in the absence of any stimulus. To follow this approach, corE was cloned under control of the oar promoter and introduced into the DcorE mutant harboring cuoB-lacZ to facilitate the analysis of cuoB expression. The oar promoter allows genes to be expressed constitutively at high levels [18]. As a control, a corE’ cuoB-lacZ strain was also constructed, in which the corE gene was under control of its own promoter (Figure S2 displays the cuoB-lacZ fusions used in this study). Quantitative analyses of cuoB expression in both strains reported no expression of this gene in the absence of copper (Figure 4A), indicating that an excess of CorE was not Figure 3. cuoB is only up-regulated by copper and other divalent metals. (A) The WT strain harboring the cuoB-lacZ fusion was spotted onto CTT agar plates containing metals or oxidants at the concentrations indicated above each picture. Plates also contained 5-bromo-4-chloro-3-indolylb-D-galacto-pyranoside to qualitatively monitor b-gal activity (blue color development). Pictures were taken after 48 h of incubation. (B) Upregulation of cuoB by Cd 2+ . The WT (continuous line) and the DcorE strains (dashed line) harboring the cuoB-lacZ fusion were incubated on CTT agar plates containing 0.1 mM Cd(NO 3 ) 2 .b-gal specific activity was determined in cell extracts harvested at the indicated times. (C) Up-regulation of cuoB by Zn 2+ . The approach followed was the same as the one reported in panel B. The concentration of metal used was 0.4 mM Zn(NO 3 ) 2 . Error bars indicate standard deviations. doi:10.1371/journal.pgen.1002106.g003 A Copper-Dependent Sigma Factor PLoS Genetics | www.plosgenetics.org 4 June 2011 | Volume 7 | Issue 6 | e1002106 sufficient to activate the transcription of cuoB. To corroborate that CorE expressed under the oar promoter was functional, copper was added to the media. In this case, up-regulation of cuoB was observed in both strains and with similar expression profiles (Figure 4B). Finally, to confirm that corE was over-expressed when cloned under the oar promoter, we constructed the same two strains described above but introducing a His tag at the N terminus of CorE (hCorE’). Western blot analyses using antibodies against the His tag confirmed that corE was indeed expressed at very high levels in the absence as well as in the presence of copper (Figure 4C and 4D). CorE migrates as a double band, which must correspond to different forms of the protein. Activity of the hCorE’ protein was further tested by following cuoB expression. The results obtained indicated that the proteins holding the His tag could promote cuoB transcription in the same manner as the native ones (Figure S5). Although it cannot be completely ruled out that a cognate anti-sfactor for CorE is encoded in the M. xanthus genome, all of these results indicate that CorE functions in a different manner from the one reported for the other characterized ECF sfactors. CorE needs copper to bind DNA The fact that the over-expression of corE did not lead to the induction of cuoB unless copper was added to the medium suggested that CorE might require the binding of copper to promote transcription. Hence, the ability of CorE to bind DNA in vitro was tested by using electrophoretic mobility shift assays. CorE was expressed in E. coli with an N-terminal His tag and purified by affinity chromatography. Additionally, a 265-bp fragment containing the copB promoter was amplified and labeled with 32 Ptobe used as a probe. As shown in Figure 5, an electrophoretic mobility shift was only observed in the reaction mixture containing copper and bathocuproine disulfonic acid (BCS), a specific chelating agent for Cu(I) [19,20]. These results not only confirm that CorE uses copper as a cofactor, but also suggest that Cu(I) prevents CorE from binding to DNA, and hence, that CorE-Cu(II) is the active form of this sfactor. This is also supported by the fact that only divalent metals can mimic the effect of copper on cuoB upregulation. No other sfactor has so far been reported to require any metal to bind DNA. The redox state of copper directs the activation/ inactivation of CorE The expression profiles of the CorE-regulated genes exhibit a peak around 2 h after copper addition (Figure 2A and 2B), in spite of the fact that corE expression is maintained for 48 h (Figure 1A). This observation could be explained by proteolysis of the sfactor. Figure 4. Searching for the CorE anti-sfactor. (A and B) Quantification of b-gal activity (cuoB expression) in strains where corE was cloned under the control of the oar promoter (red lines) or its own promoter (blue lines). Activities were determined in the absence of metal (A) or in the presence of 0.3 mM copper (B). Note the difference in the scales of the two panels. Error bars indicate standard deviations. (C and D) Western blot analyses to confirm the over-production of CorE in the absence (C) or in the presence (D) of 0.3 mM copper in the strains harboring the gene corE cloned under the oar promoter (lane 1) or its own promoter (lane 2). Proteins were collected at 2 h after copper addition. The band of equal intensity in all the lanes corresponds to an unidentified M. xanthus protein that reacts with the anti-His tag antibody used in the assay. The intensity of this band, which does not change in the conditions tested, has been used to standardize the amount of protein loaded in each lane. doi:10.1371/journal.pgen.1002106.g004 Figure 5. CorE needs copper and BCS to bind DNA. Electrophoretic mobility shift assay with purified hCorE and a radiolabeled DNA fragment containing the copB promoter was carried out with the additives indicated in each lane. Details are given in Materials and Methods. doi:10.1371/journal.pgen.1002106.g005 A Copper-Dependent Sigma Factor PLoS Genetics | www.plosgenetics.org 5 June 2011 | Volume 7 | Issue 6 | e1002106 To investigate this option, Western blot analyses were carried out using the hcorE’ cuoB-lacZ strain. The data shown in Figure 6A demonstrate that CorE was stable for 24 h after copper addition. Another explanation could be that CorE underwent a cycle of activation/inactivation, whereby the regulator would only be in the active form for a limited period of time. As shown in Figure 5, to obtain binding of CorE to DNA, the reaction mixture must include not only copper, but also a chelating agent for Cu(I). Moreover, only other divalent metals can mimic the copper effect on cuoB up-regulation (Figure 3 and Figure S4). These data suggest that the redox state of copper could be the key in this process. To investigate this possibility, the expression of cuoB was assayed in vivo in conditions that favor the formation of Cu(I) and Cu(II). As shown in Figure 6B and 6C, cuoB up-regulation could only be observed when copper was added to the medium. However, the maximum expression levels were diminished when the reducing agent ascorbate was also included in the medium to favor the formation of Cu(I) (Figure 6C, brown line). Similarly, the addition of Ag + , which mimics Cu(I), also yielded expression levels lower than those obtained with only copper (Figure 6C, green line). In contrast, when copper was added with the Cu(I) chelators BCS or bicinchoninic acid (BCA) [19,20], cuoB expression was around three times that of the control (Figure 6C, blue versus red and black lines). Moreover, the addition of copper with tetrathiomolybdate (TTM), a chelator of Cu(I) and Cu(II) [21], decreased the up-regulation mediated by this metal to a very basal level (Figure 6C, orange line). In contrast, when these three chelators were tested with Zn 2+ as the inducer, the expression levels of cuoB were diminished as the concentrations of all the chelators increased (Figure S6), due to the fact they can also chelate Zn 2+ , although to a much lesser extent than copper. According to all these data, CorE requires copper for activation, and it only acquires an active conformation in the presence of Cu(II), while the reduced state of the metal leads to an inactive conformation. This notion agrees well with the lack of a peak when up-regulation of cuoB is achieved by Zn 2+ and Cd 2+ , which are metals with only one redox state (Figure 3B and 3C). To confirm the results obtained in vivo, the DNA-binding assay was carried out again including Ag + or TTM in the reaction mixtures. As shown in Figure 7, these two additives overrode the electrophoretic mobility shift achieved by the addition of copper and BCS. It should be reminded that Ag + mimics Cu(I) and that TTM chelates Cu(II). All of the data presented in this section demonstrate that CorE activity is modulated by the redox state of copper. This mechanism of action implies that Cu(II) must be available in the cytosol during the next 2 h after copper supplementation. Although it is assumed that all the copper in the reducing environment of the cytoplasm is present as Cu(I) under normal circumstances [2,22], it is also expected that the cytoplasm will become more oxidizing in the presence of agents such as copper [23], favoring the formation of Cu(II) until the reducing conditions are restored by the participation of the elements involved in copper detoxification. Furthermore, as free copper in the cells is estimated to be less than one atom per cell [24], it is plausible to speculate that CorE functions with an unidentified Cu(II)-specific metallochaperone, which would ferry the cupric form through the cytoplasm to activate this sfactor. Such an activator working upstream of CorE would explain why the expression levels of cuoB do not increase when corE is over-expressed (Figure 4). However, Figure 6. Activation and inactivation of CorE. (A) CorE is not degraded. M. xanthus cells harboring the hCorE protein were harvested at the times (h) indicated above each lane after the addition of 0.3 mM copper sulfate and analyzed by Western blot using an anti-His tag antibody. (B) cuoB is not up-regulated by any of the additives indicated in the panel. (C) CorE is activated and inactivated by the redox state of copper. cuoB expression was analyzed in the presence of different additives that modify the redox state of copper, that mimic Cu(I), or that chelate copper in any of its two redox states. For panel B and C, M. xanthus cells harboring the fusion cuoB-lacZ were incubated on CTT agar plates containing the additives indicated. Samples were harvested at different times and b-gal specific activity was determined. Error bars indicate standard deviations. doi:10.1371/journal.pgen.1002106.g006 A Copper-Dependent Sigma Factor PLoS Genetics | www.plosgenetics.org 6 June 2011 | Volume 7 | Issue 6 | e1002106 another possible explanation for this observation could be that CorE aggregates when produced in large amounts. One paradox is the fact that CorE is activated by Cu(II) and inactivated by Cu(I), while genes under its control encode proteins, such as CopA, CopB, and CuoB, that utilize Cu(I) as a substrate [7,9]. Nevertheless, this contradiction can be explained by considering two facts: i) Out of the two redox states of copper, Cu(I) is the most toxic form [2]. As CorE-regulated genes represent the first protective barrier against the deleterious effect of copper (please note that these genes are rapidly up-regulated after copper addition, as shown in Figure 2 and Figure S1) and this protein is activated by Cu(II), it is plausible to speculate that copper will initially get into the cytoplasm in the form of Cu(II), activating CorE, and preparing the cells to act on Cu(I) as soon as it appears. At this point, the CorE regulon will be inactivated by the presence of Cu(I) in the cytoplasm. ii) If the presence of copper persists in the environment, M. xanthus cells will obtain protection against the metal by means of at least two other mechanisms (first, by the P1B-type ATPase CopA and the MCO CuoA, and later, by the Cus2 and Cus3 systems), which are sequentially induced after copper addition [7–9] (see also Figure 2 and Figure S1). Although many bacterial transcriptional regulators need metal to bind DNA [25,26], none of them have been reported to be modulated by the redox state of the metal. Moreover, those that function with copper show selectivity for Cu(I) [24,27]. Hence, CorE represents a novel type of bacterial copper sensor. CRD controls the activity of CorE CorE contains a short C-terminal extension after the s 4 domain consisting of 38 residues named CRD. Six of these residues are Cys. As different arrangements of Cys have been proved to be key elements in several metal-binding proteins [22,27,28], we tried to determine whether CRD was involved in the activation/ inactivation of CorE mediated by copper. An M. xanthus in-frame deletion mutant was constructed in which most of the CRD region was deleted. This strain, designated as DcorE CRD , encoded a protein containing the two domains s 2 and s 4 of CorE, but none of the six Cys of CRD. To analyze the activity of CorE CRD , the two fusions cuoB-lacZ and copB-lacZ were introduced in this mutant and b-gal activity was assayed in the absence and in the presence of copper. The data obtained revealed that neither cuoB or copB were up-regulated by copper (data not shown), a result identical to that shown in Figure 2A, when the entire corE gene was deleted. These data demonstrate that CRD is essential for the copperdependent transcription of the genes controlled by CorE. To determine which Cys are involved in CorE activity, each residue was individually mutated to an Ala by site-directed mutagenesis. The six mutated genes were introduced into the DcorE strain harboring the fusion cuoB-lacZ. The effect of the mutations was evaluated by analyzing the expression of cuoB in the absence and in the presence of copper. The results obtained showed different patterns. Mutations C181A and C206A exhibited transcription profiles very similar to those of the WT (Figure 8A), although some small differences regarding the maximum expression levels and timing were observed, indicating that these residues play a minor role in CorE activity. More severe effects were obtained with the mutations C192A and C194A. In these mutants, the expression levels of cuoB in the absence of copper were higher than in the WT (Figure 8B, dashed lines), suggesting that both Cys play some role in CorE inactivation. Moreover, although cuoB expression was up-regulated by copper in both mutants, the rapid induction and the peak exhibited by the WT at 2 h were not replicated (Figure 8B, continuous lines). The effect of the mutation C189A was even more drastic, because no expression was observed in the absence of copper and the up-regulation by the metal was almost completely non-existent (Figure 8C and 8D). Accordingly, it can be concluded that these three residues are important in the CorE activation process. Cys184 was clearly required for CorE inactivation, because mutation C184A yielded a constitutive expression in the absence of copper (Figure 8E) and the addition of copper provoked a rapid up-regulation of cuoB. Interestingly, the expression level did not peak at 2 h, but kept increasing until it reached a plateau at 24 h (Figure 8F). The effect of each point mutation in cuoB expression was also analyzed in cells grown on media containing copper plus BCS or silver (Figure S7). Mutations C181A and C206, which in the presence of copper yielded expression profiles similar to that of the WT (Figure 8A), also exhibited higher expression levels in the presence of copper plus BCS, and lower levels with copper plus Ag + (Figure S7). In the case of substitutions C189A, C192A, and Figure 7. Silver and TTM prevent CorE from binding to DNA. An electrophoretic mobility shift assay was carried out as described in Figure 5, with the additives indicated in each lane. doi:10.1371/journal.pgen.1002106.g007 A Copper-Dependent Sigma Factor PLoS Genetics | www.plosgenetics.org 7 June 2011 | Volume 7 | Issue 6 | e1002106 C194A, BCS and Ag + barely affected the expression levels obtained with only copper (Figure S7). However, it should be reminded that these three residues are important for activation, and that cuoB up-regulation by copper was impaired in these mutants (Figure 8B and 8D), suggesting that these three proteins might only have a limited affinity for the metal. Surprisingly, however, the protein with the mutation C184A (the most important residue in CorE inactivation as shown in Figure 8E and 8F), can still be modulated by the two redox states of copper (Figure S7). This result indicates that some other residues must also be involved in the inactivation of CorE. As mentioned above, two of them could be Cys192 and Cys194, because mutations Figure 8. Expression of cuoB in strains harboring point mutations in the CRD region of CorE. The mutated Cys are indicated in each panel. Cells were incubated on CTT agar plates containing 0.3 mM copper (continuous lines) or without metal (dashed lines), and samples were harvested at different times to determine b-gal specific activity. Note that the scale in panel F is different from that used in the other panels. Error bars indicate standard deviations. doi:10.1371/journal.pgen.1002106.g008 A Copper-Dependent Sigma Factor PLoS Genetics | www.plosgenetics.org 8 June 2011 | Volume 7 | Issue 6 | e1002106 C192A and C194A yield constitutive expression of cuoB. However, it is expected that other residue(s) of CRD might also be required for the proper functioning of the protein (see below). Taken as a whole, the results demonstrate that at least four of the Cys of CRD form a coordination environment for copper. This domain is able to recognize copper and sense its redox state, allowing the binding of CorE to DNA to activate transcription in those conditions that favor the formation of Cu(II), and inactivating the sfactor in those that favor the formation of Cu(I). However, how exactly CorE distinguishes between Cu(I) and Cu(II) is not easy to predict, because all of the residues identified so far that modulate the activity of CorE are Cys. Although Cys are able to coordinate Cu(I) and Cu(II), they require the presence of other amino acids, such as His, Asp, Glu, or Met to exert this function [22,29]. Accordingly, it is expected that other residues also participate in the coordination of copper in either of the two redox states. Moreover, thiols are known to allow different types of modifications in an oxidative environment [30]. The exact modification of each individual Cys might also be crucial in the CorE activation/inactivation process. Further genetic, biochemical, and structural studies will be required to elucidate this intriguing question. The role of CRD in CorE resembles the function of the anti-s domain present in many anti-sfactors [31]. Anti-sdomains require Zn 2+ binding to sequester their cognate sfactor. However, the anti-sdomain and CRD differ in many aspects: i) CRD is an extra portion of the sfactor; ii) elimination of CRD does not activate the sfactor; and iii) CRD senses the redox state of copper to activate or inactivate the sfactor. ECF sfactors with CRD in other bacteria BLASTP analyses have allowed the identification of 21 ECF s factors with CRD, which are distributed in only four phyla. Fourteen belong to Proteobacteria (9 aand 5 d), four to Acidobacteria, two to Verrucomicrobia, and one to Nitrospira (Figure 9). As in the case of CorE, anti-sfactors are not linked to any of these sfactors. The alignments of these CRDs have revealed that only 4 Cys (corresponding to residues 181, 184, 192, and 194 in CorE) are absolutely conserved among these sfactors (Figure 9A). Surprisingly, Cys181, whose mutation causes a minor effect on CorE activity, is conserved in all these regulators. In contrast, Cys189, which is the main residue in CorE activation by copper, is only present in 11 sfactors. Interestingly, however, several of the strains with sfactors that conserve this Cys exhibit some synteny in the regions where they are encoded. The surrounding genes encode proteins with high similarities to others known to be implicated in copper handling and trafficking (Figure 9B). Due to the diversity of the ECF sfactors, Staron ´et al. [13] have proposed a classification of this family of regulatory proteins into 44 groups based on sequence similarities and domain architectures. However, CorE did not fit into any of the groups they defined and it was excluded from this classification. The data presented in this report support the notion that a new group should be added to the list, which will include the 21 ECF s factors that contain CRD. So far, seven families of metal de-repressors, metal corepressors, and metal activators are known [25,26,32], all of which clearly differ mechanistically from CorE. Hence, elucidation of the exact mode of action of CorE will offer new insights into our current knowledge of metal sensors. Moreover, identification of the factor(s) working upstream of CorE will also help to elucidate how this type of sfactors works and how the trafficking of metals in the bacterial cytoplasm occurs. Finally, characterization of CorE-like proteins identified in other bacteria will also contribute to understanding the role, mechanism of action, and distribution of this novel type of regulators. Materials and Methods Plasmids, bacterial strains, and growth conditions Genotypes of the bacterial strains and plasmids used in this study are listed in Table S1 and Table S2, respectively. M. xanthus was grown in CTT medium at 30uC, supplemented with the additives indicated in each figure, as previously described [6]. E. coli was grown on Luria-Bertani (LB) medium at 37uC [33]. Construction of in-frame deletion mutants and strains harboring lacZ fusions The methodologies used for obtaining the in-frame deletion mutants and the transcriptional lacZ fusion strains used in this study are the same as previously reported [7]. To generate the corresponding plasmids (listed in Table S2), the desired fragments were amplified by polymerase chain reaction (PCR), using WT chromosomal DNA as a template, the oligonucleotides listed in Table S3 as primers, and the high-fidelity polymerase PrimeSTAR HS (Takara) [33]. PCR products were ligated to vectors pBJ113 and pKY481 [34,35] to generate in-frame deletion mutants and lacZ fusions, respectively. Plasmids were always introduced into M. xanthus strains by electroporation to obtain integration into the chromosome by homologous recombination. Southern blot analyses were carried out to confirm the proper recombination events. b-gal specific activity in cell extracts obtained by sonication of the strains harboring lacZ fusions was determined as previously described [7], and it is expressed as nmol of o-nitrophenol produced per min and mg of protein. Measurements shown are the averages of data from triplicate experiments. Over-expression of corE in M. xanthus using the oar promoter Appropriate oligonucleotide pairs (Table S3) were used to amplify by PCR an 817-bp fragment upstream of the oar gene (MXAN_1450) using M. xanthus chromosomal DNA as a template [33]. Simultaneously, corE was also amplified by PCR. A BamHI site was introduced at the start codon of oar in frame with another BamHI site introduced at the start codon of corE. Both PCR products were cloned in a vector derived from pUC19 in which the ampicillin-resistance gene was substituted by one that encodes resistance to tetracycline (Tet r ). The resulting plasmid, pNG06, was introduced by electroporation into an M. xanthus strain with the genotype DcorE cuoB-lacZ, and several kanamycin-resistant (Km r ) and Tet r colonies were analyzed by Southern blot to confirm the proper recombination event. b-gal specific activity was determined to quantify cuoB expression. As a control, the plasmid pNG00 was constructed, in which corE was cloned under control of its own promoter. This plasmid was also electroporated into the DcorE cuoB-lacZ to restore corE at its original genomic location (see Table S1 and Figure S2). To corroborate that CorE was being over-produced under the constitutive oar promoter, we constructed the same strains described above, but introducing an N-6His tag upstream of CorE, to obtain the strains hcorE’ cuoB-lacZ and oarhcorE’ cuoB-lacZ (Table S1). Briefly, the corE gene with an N-6His tag was amplified with appropriate oligonucleotide pairs (Table S3) using pETTOPOCorE plasmid (see below) as a template. The PCR product obtained was cloned under control of the oar promoter and its own promoter as above, obtaining plasmids pNG08 and pNG05, respectively. Plasmids were introduced into the DcorE cuoB-lacZ strain, and Km r Tet r colonies were also analyzed by Southern blot hybridization. A Copper-Dependent Sigma Factor PLoS Genetics | www.plosgenetics.org 9 June 2011 | Volume 7 | Issue 6 | e1002106