Metal-responsive RNA polymerase extracytoplasmic function (ECF) sigma factors

Abstract

In order to survive, bacteria must adapt to multiple fluctuations in their environment, including coping with changes in metal concentrations. Many metals are essential for viability, since they act as cofactors of indispensable enzymes. But on the other hand, they are potentially toxic because they generate reactive oxygen species or displace other metals from proteins, turning them inactive. This dual effect of metals forces cells to maintain homeostasis using a variety of systems to import and export them. These systems are usually inducible, and their expression is regulated by metal sensors and signal-transduction mechanisms, one of which is mediated by extracytoplasmic function (ECF) sigma factors. In this review, we have focused on the metal-responsive ECF sigma factors, several of which are activated by iron depletion (FecI, FpvI and PvdS), while others are activated by excess of metals such as nickel and cobalt (CnrH), copper (CarQ and CorE) or cadmium and zinc (CorE2). We focus particularly on their physiological roles, mechanisms of action and signal transduction pathways.

Figure 1

The E. coli CSS Fe³⁺‐citrate transport is regulated by the FecR/FecI system. A. In the absence of Fe³⁺‐citrate and in the presence of Fe²⁺‐Fur, the repressor binds to the region upstream of the operons fecIR and fecABCDE. Moreover, the FecR anti‐sigma factor sequesters the FecI ECF sigma factor by interaction of the N‐terminal region of the anti‐sigma factor and the σ4 domain of the ECF sigma factor, preventing transcription of these two operons. B. Signaling pathway in the presence of Fe³⁺‐citrate and under low iron availability. The Fur repressor is not bound to Fe²⁺ and cannot bind DNA. The outer membrane protein receptor FecA suffers conformational changes, interacts with TonB through the TonB box domain, and allows the transport of the substrate to the periplasm, and through FecB and the FecCDE transporter to the cytoplasm. FecA changes also allow interaction between the FecA N‐terminal region and the C‐terminal region of the anti‐sigma factor FecR, releasing the ECF sigma factor FecI. This sigma factor can now up‐regulate the transcription of fecIR and fecABCDE after recruiting the core RNAP.

Figure 2

The P. aeruginosa ferripyoverdine CSS is regulated by FpvR/FpvI/PvdS. A. In the absence of ferripyoverdine, the anti‐sigma factor FpvR sequesters the sigma factors FpvI and PvdS, preventing them from binding to the core RNAP and DNA. The expression of both ECF sigma factors is also repressed by Fur (in a similar way to that shown for FecI in Fig. 1 and not shown here). In these conditions, the target regulons for each sigma factor are not transcribed. B. When pyoverdine binds to Fe³⁺ to form ferrypioverdine, a signal is transmitted to FpvA and TonB, enabling the import of ferripyoverdine and the proteolysis of FpvR by the RseP/MucP protease, liberating FpvI and PvdS and allowing expression of the two regulons.

Figure 3

Mechanism of action of the C. metallidurans CnrH sigma factor. A. In the absence of nickel, CnrH is sequestered at the inner membrane by the protein complex CnrYX, where CnrX is an inner membrane protein that possesses a periplasmic metal sensor domain and CnrY is a transmembrane anti‐sigma factor. In this condition, CnrY wraps around CnrH and blocks the sites where the beta subunit of the RNAP binds. B. Nickel‐binding to CnrX results in a modification of the interaction between CnrX and CnrY that provokes a conformational change in CnrY, releasing CnrH to initiate transcription from the promoters cnrYp and cnrCp. Transcription from these promoters leads to synthesis of CnrH, CnrYX, the transenvelope complex CnrCBA and the exporter of cytoplasmic nickel ions CnrT.

Figure 4

Mechanism of action of the M. xanthus CarQ sigma factor. A. In the absence of light and copper, the ECF sigma factor CarQ is sequestered at the membrane by the anti‐sigma factor CarR. Genes involved in carotenogenesis (located in the gene crtIb and the operon carB) are not expressed because crtIb is regulated by CarQ and the operon carB is repressed by CarA and CarH, encoded in the carA operon. B. Light is sensed via CarF, which is activated by singlet oxygen generated by photoexcited protoporphyrin IX (PPIX). In this condition, CarF functions as an anti‐anti‐sigma factor, inactivating CarR and releasing CarQ. Copper does not require CarF to inactivate CarR. Free CarQ by any of the two stimuli can bind to two promoters, P_I, with the participation of CarD‐CarG, to express the gene crtIb, and P_QRS, in conjunction with CarD‐CarG and IhfA, to express the operon carQRS. The operon carB can now be expressed after eliminating the repression by CarA and CarH. The repressor CarA is inactivated by CarS, which is encoded in the operon carQRS. CarH is a photoreceptor that is directly inactivated by light. Although it is not known how copper inactivates CarH, most likely this metal displaces cobalt in the vitamin B12 used as a cofactor by this repressor, thus allowing transcription of carB. Once carB and crtIb are expressed, carotenoids are synthesized. Arrows indicate positive regulation and blunt‐ended lines indicate negative regulation.

Figure 5

Mechanism of action of the M. xanthus CorE sigma factor. A. In the absence of copper, CorE remains inactive. B. When copper enters the cell, CorE is activated by binding this metal in its divalent oxidation state, initiating the transcription of genes involved in the immediate response to this metal. The immediate response includes the P_1B‐type ATPases CopA and CopB, which will extrude copper to the periplasm, and the multicopper oxidase CuoB, which will oxidize Cu⁺ to Cu²⁺ in the periplasm. C. Due to the strongly reducing environment of the cytoplasm, Cu²⁺ will be quickly reduced to Cu⁺, inactivating the ECF sigma factor (presumably via a conformational change), and stopping the immediate response even when copper is still present in the medium.